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2021

Triana, S., Vonficht, D., Jopp-Saile, L., Raffel, S., Lutz, R., Leonce, D., Antes, M., Hernández-Malmierca, P., Ordoñez-Rueda, D., Ramasz, B., Boch, T., Jann, J. C., Nowak, D., Hofmann, W. K., Müller-Tidow, C., Hübschmann, D., Alexandrov, T., Benes, V., Trumpp, A., Paulsen, M., Velten, L. and Haas, S. (2021). Single-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell statesNature Immunology, 10.1038/s41590-021-01059-0. doi: 10.1038/s41590-021-01059-0.

Song, R., Tikoo, S., Jain, R., Pinello, N., Au, A. Y., Nagarajah, R., Porse, B., Rasko, J., and Wong, J. J. (2021). Dynamic intron retention modulates gene expression in the monocytic differentiation pathwayImmunology, 10.1111/imm.13435. doi: 10.1111/imm.13435.

Malani, D., Kumar, A., Bruck, O., Kontro, M., Yadav, B., Hellesoy, M., Kuusanmaki, H., Dufva, O., Kankainen, M., Eldfors, S., Potdar, S., Saarela, J., Turunen, L., Parsons, A., Vastrik, I., Kivinen, K., Saarela, J., Raty, R., Lehto, M., Wolf, M., Gjertsen, B. T., Mustjoki, S., Aittokallio, T., Wennerberg, K., Heckman, C. A., Kallioniemi, O. and Porkka, K. (2021). Implementing a functional precision medicine tumor board for acute myeloid leukemiaCancer Discovery, candisc.0410.2021. doi: 10.1158/2159-8290.CD-21-0410.

Lopez-Beltran, A., Blanca, A., Cimadamore, A., Gogna, R., Montironi, R., and Cheng, L. (2021). Molecular Classification of Bladder Urothelial Carcinoma Using NanoString-Based Gene Expression AnalysisCancers13(21), 5500. doi: 10.3390/cancers13215500.

Handin, N., Mickols, E., Ölander, M., Rudfeldt, J., Blom, K., Nyberg, F., Senkowski, W., Urdzik, J., Maturi, V., Fryknäs, M., and Artursson, P. (2021). Conditions for maintenance of hepatocyte differentiation and function in 3D culturesiScience24(11), 103235. doi: 10.1016/j.isci.2021.103235.

Husby, S., Favero, F., Rodriguez-Gonzalez, F. G., Sutton, L. A., Haastrup, E. K., Ørskov, A. D., Hansen, J. W., Arboe, B., Aslan, D., Clasen-Linde, E., Rahbek Gjerdrum, L. M., Gørlev, J. S., Brown, P., Fischer-Nielsen, A., Rosenquist, R., Weischenfeldt, J., and Grønbæk, K. (2021). Mutations known from B-cell lymphoid malignancies are not found in CD34+ stem cells from patients with lymphomaLeukemia & Lymphoma62(11), 2808–2811. doi: 10.1080/10428194.2021.1933473.

Jaiswal, A., Gautam, P., Pietilä, E. A., Timonen, S., Nordström, N., Akimov, Y., Sipari, N., Tanoli, Z., Fleischer, T., Lehti, K., Wennerberg, K., and Aittokallio, T. (2021). Multi-modal meta-analysis of cancer cell line omics profiles identifies ECHDC1 as a novel breast tumor suppressorMolecular Systems Biology17(3), e9526. doi: 10.15252/msb.20209526.

Yekelchyk, M., Madan, E., Wilhelm, J., Short, K. R., Palma, A. M., Liao, L., Camacho, D., Nkadori, E., Winters, M. T., Rice, E. S., Rolim, I., Cruz-Duarte, R., Pelham, C. J., Nagane, M., Gupta, K., Chaudhary, S., Braun, T., Pillappa, R., Parker, M. S., Menter, T., Matter, M., Haslbauer, J. D., Tolnay, M., Galior, K. D., Matkwoskyj, K. A., McGregor, S. M., Muller, L. K., Rakha, E. A., Lopez-Beltran, A., Drapkin, R., Ackermann, M., Fisher, P. B., Grossman, S. R. Godwin, A. K., Kulasinghe, A., Martinez, I., Marsh, C. B., Tang, B., Wicha, M. S., Won, K. J., Tzankov, A., Eduardo, M. and Gogna, R. (2021). Flower lose, a cell fitness marker, predicts COVID-19 prognosis. EMBO Molecular Medicine, e13714. doi: 10.15252/emmm.202013714.

Wang, X., Rosikiewicz, W., Sedkov, Y., Martinez, T., Hansen, B. S., Schreiner, P., Christensen, J., Xu, B., Pruett-Miller, S. M., Helin, K., and Herz, H. M. (2021). PROSER1 mediates TET2 O-GlcNAcylation to regulate DNA demethylation on UTX-dependent enhancers and CpG islands. Life Science Alliance5(1), e202101228. doi: 10.26508/lsa.202101228.

Tulstrup, M., Soerensen, M., Hansen, J. W., Gillberg, L., Needhamsen, M., Kaastrup, K., Helin, K., Christensen, K., Weischenfeldt, J., and Grønbæk, K. (2021). TET2 mutations are associated with hypermethylation at key regulatory enhancers in normal and malignant hematopoiesisNature Communications12(1), 6061. doi: 10.1038/s41467-021-26093-2.

Tsujita, K., Satow, R., Asada, S., Nakamura, Y., Arnes, L., Sako, K., Fujita, Y., Fukami, K., and Itoh, T. (2021). Homeostatic membrane tension constrains cancer cell dissemination by counteracting BAR protein assemblyNature Communications12(1), 5930. doi: 10.1038/s41467-021-26156-4.

Heilmann, S., Semb, H., and Nyeng, P. (2021). Quantifying spatial position in a branched structure in immunostained mouse tissue sections. STAR Protocols2(4), 100806. doi: 10.1016/j.xpro.2021.100806.

Guiu, J., and Jensen, K. B. (2021). Counter Piece to Organoid vs Mouse Models: Which is a Better Research Tool…. Cellular and Molecular Gastroenterology and Hepatology, S2352-345X(21)00199-5. doi: 10.1016/j.jcmgh.2021.09.011.

Nguyen, T. M., and Aragona, M. (2021). Stress-responsive transcription factors train stem cells to rememberCell Stem Cell28(10), 1679–1680. doi:10.1016/j.stem.2021.09.005.

Sanjiv, K., Calderón-Montaño, J. M., Pham, T. M., Erkers, T., Tsuber, V., Almlöf, I., Höglund, A., Heshmati, Y., Seashore-Ludlow, B., Nagesh Danda, A., Gad, H., Wiita, E., Göktürk, C., Rasti, A., Friedrich, S., Centio, A., Estruch, M., Våtsveen, T. K., Struyf, N., Visnes, T., Scobie, M., Koolmeister, T., Henriksson, M., Wallner, O., Sandvall, T., Lehmann, S., Theilgaard-Mönch, K., Garnett, M. J., Östling, P., Walfridsson, J., Helleday, T., and Warpman Berglund, U. (2021). MTH1 inhibitor TH1579 induces oxidative DNA damage and mitotic arrest in acute myeloid leukemiaCancer Research, canres.0061.2021.  doi:10.1158/0008-5472.CAN-21-0061.

Guiu, J., and Jensen, K. B. (2021). In vivo studies should take priority when defining mechanisms of intestinal crypt morphogenesisCellular and Molecular Gastroenterology and Hepatology, S2352-345X(21)00201-0. doi: 10.1016/j.jcmgh.2021.06.028.

Gu, W., Wang, H., Huang, X., Kraiczy, J., Singh, P., Ng, C., Dagdeviren, S., Houghton, S., Pellon-Cardenas, O., Lan, Y., Nie, Y., Zhang, J., Banerjee, K. K., Onufer, E. J., Warner, B. W., Spence, J., Scherl, E., Rafii, S., Lee, R. T., Verzi, M. P., Redmon, D., Longman, R., Helin, K., Shivdasani, R. A.,  and Zhou, Q. (2021). SATB2 preserves colon stem cell identity and mediates ileum-colon conversion via enhancer remodelingCell Stem Cell, S1934-5909(21)00380-5. doi: 10.1016/j.stem.2021.09.004.

Ghezelayagh, Z., Zabihi, M., Zarkesh, I., Gonçalves, C., Larsen, M., Hagh-Parast, N., Pakzad, M., Vosough, M., Arjmand, B., Baharvand, H., Larijani, B., Grapin-Botton, A., Aghayan, H. R., and Tahamtani, Y. (2021). Improved Differentiation of hESC-Derived Pancreatic Progenitors by Using Human Fetal Pancreatic Mesenchymal Cells in a Micro-scalable Three-Dimensional Co-culture SystemStem Cell Reviews and Reports, 10.1007/s12015-021-10266-z. doi: 10.1007/s12015-021-10266-z.

Nguyen, T. M., and Aragona, M. (2021). Regulation of tissue architecture and stem cell dynamics to sustain homeostasis and repair in the skin epidermisSeminars in Cell and Developmental Biology, S1084-9521(21)00243-3. doi: 10.1016/j.semcdb.2021.09.008.

Wedge, E., Hansen, J. W., Dybedal, I., Creignou, M., Ejerblad, E., Lorenz, F., Werlenius, O., Ungerstedt, J., Holm, M. S., Nilsson, L., Kittang, A. O., Antunovic, P., Rohon, P., Andersen, M. K., Papaemmanuil, E., Bernard, E., Jädersten, M., Hellström-Lindberg, E., Grønbæk, K., Ljungman, P., and Friis, L. S. (2021). Allogeneic hematopoietic stem cell transplantation for chronic myelomonocytic leukemia: Clinical and molecular genetic prognostic factors in a Nordic populationTransplantation and Cellular Therapy, S2666-6367(21)01219-7. doi:10.1016/j.jtct.2021.08.028.

Lien, Y. C., Lu, X. M., Won, K. J., Wang, P. Z., Osei-Bonsu, W., and Simmons, R. A. (2021). The Transcriptome and Epigenome Reveal Novel Changes in Transcription Regulation During Pancreatic Rat Islet MaturationEndocrinology, bqab181. doi:  10.1210/endocr/bqab181.

Talwelkar, S. S., Mäyränpää, M. I., Søraas, L., Potdar, S., Bao, J., Hemmes, A., Linnavirta, N., Lømo, J., Räsänen, J., Knuuttila, A., Wennerberg, K., and Verschuren, E. W. (2021). Functional diagnostics using fresh uncultured lung tumor cells to guide personalized treatmentsCell Reports Medicine2(8), 100373. doi: 10.1016/j.xcrm.2021.100373.

Rønnov-Jessen, L., Kim, J., Goldhammer, N., Klitgaard, M. C., Smicius, M., Bechmann, M. B., Villadsen, R., and Petersen, O. W. (2021). Desensitization of human breast progenitors by a transient exposure to pregnancy levels of estrogenScientific Reports11(1), 17232. doi: 10.1038/s41598-021-96785-8.

Mariani, L., Guo, X., Menezes, N. A., Drozd, A. M., Çakal, S. D., Wang, Q., and Ferretti, E. (2021). A TALE/HOX code unlocks WNT signalling response towards paraxial mesodermNature Communications12(1), 5136. doi: 10.1038/s41467-021-25370-4.

Parker, T. M., Gupta, K., Palma, A. M., Yekelchyk, M., Fisher, P. B., Grossman, S. R., Won, K. J., Madan, E., Moreno, E., and Gogna, R. (2021). Cell competition in intratumoral and tumor microenvironment interactions. The EMBO Journal. doi: 10.15252/embj.2020107271.

Succony, L., Gómez-López, S., Pennycuick, A., Alhendi, A. S. N., Davies, D., Clarke, S. E., Gowers, K. H. C., Wright, N. A., Jensen, K. B. and Janes, S. M. (2021) Lrig1 expression identifies airway basal cells with high proliferative capacity and restricts lung squamous cell carcinoma growth. European Respiratory Journal. doi: 10.1183/13993003.00816-2020.

Skov‐Jeppesen, K., Hepp, N., Oeke, J., Hansen, M. S., Jafari, A., Svane, M. S., Balenga, N., Olson, J. A. Jr, Frost, M., Kassem, M., Madsbad, S., Beck Jensen J. E., Holst, J. J., Rosenkilde, M. M., and Hartmann, B. (2021). The Antiresorptive Effect of GIP, But Not GLP‐2, Is Preserved in Patients With Hypoparathyroidism—A Randomized Crossover Study. Journal of Bone and Mineral Research, 36(8), 1448-1458. doi: 10.1002/jbmr.4308.

He, L., Bulanova, D., Oikkonen, J., Häkkinen, A., Zhang, K., Zheng, S., Wang, W., Erkan, E. P., Carpén, O., Joutsiniemi, T., Hietanen, S., Hynninen, J., Huhtinen, K., Hautaniemi, S., Vähärautio, A., Tang, J., Wennerberg, K. and Aittokallio, T. (2021). Network-guided identification of cancer-selective combinatorial therapies in ovarian cancer. Briefings in Bioinformatics. doi: 10.1093/bib/bbab272.

Cordero-Espinoza, L., Dowbaj, A. M., Kohler, T. N., Strauss, B., Sarlidou, O., Belenguer, G., Pacini, C., Martins, N. P., Dobie, R., Wilson-Kanamori, J. R., Butler, R., Prior, N., Serup, P., Jug, F., Henderson, N. C., Hollfelder, F., and Huch, M. (2021). Dynamic cell contacts between periportal mesenchyme and ductal epithelium act as a rheostat for liver cell proliferation. Cell Stem Cell. doi: 10.1016/j.stem.2021.07.002.

Schreiber, V., Mercier, R., Jímenez, S., Ye, T., García-Sánchez, E., Klein, A., Meunier, A., Ghimire, S., Birck, C., Jost, B., Honnens de Lichtenberg, K., Honoré, C., Serup, P., and Gradwohl, G. (2021). Extensive NEUROG3 occupancy in the human pancreatic endocrine gene regulatory network. Molecular Metabolism. doi: 10.1016/j.molmet.2021.101313.

Messling, J. E., Agger, K., Andersen, K. L., Kromer, K., Kuepper, H. M., Lund, A. H. and Helin, K. (2021) Targeting RIOK2 ATPase activity leads to decreased protein synthesis and cell death in acute myeloid leukemia. Blood. doi: 10.1182/blood.2021012629.

Lokhande, L., Kuci Emruli, V., Eskelund, C. W., Kolstad, A., Hutchings, M., Räty, R., Niemann, C. U., Grønbæk, K., Jerkeman, M. and Ek, S. (2021). Serum proteome modulations upon treatment provides biological insight on response to treatment in relapsed mantle cell lymphomaCancer Reports, e1524. doi: 10.1002/cnr2.1524.

White, B. S., Khan, S. A., Mason, M. J., Potdar, S., Malani, D., Kuusanmäki, H., Druker, B. J., Heckman, C., Kallioniemi, O., Kurtz, S. E., Porkka, K., Tognon, C. E., Tyner, J. W., Aittokallio, T., Wennerberg, K. and Guinney, J. (2021). Bayesian multi-source regression and monocyte-associated gene expression predict BCL-2 inhibitor resistance in acute myeloid leukemianpj Precision Oncology5(1), 1-11. doi: 10.1038/s41698-021-00209-9.

Kaastrup, K., and Grønbæk, K. (2021). The Impact of Sedentary Lifestyle, High-fat Diet, Tobacco Smoke, and Alcohol Intake on the Hematopoietic Stem Cell NichesHemaSphere5(8). doi: 10.1097/HS9.0000000000000615.

Dahl, M., Husby, S., Eskelund, C. W., Besenbacher, S., Fjelstrup, S., Côme, C., Ek, S., Kolstad, A., Räty, R., Jerkeman, M., Geisler, C. H., Kjems, J., Kristensen, L. S., and Grønbæk, K. (2021) Expression patterns and prognostic potential of circular RNAs in mantle cell lymphoma: a study of younger patients from the MCL2 and MCL3 clinical trials. Leukemia. doi: 10.1038/s41375-021-01311-4.

 Nyeng, P., Cruz, G. V. D., and Semb, H. (2021). Flow cytometry detection of surface and intracellular antigens in pancreas from a single mouse embryo. STAR Protocols2(3). doi: 10.1016/j.xpro.2021.100636.

Husby, S., Favero, F., Rodriguez-Gonzalez, F. G., Sutton, L. A., Haastrup, E. K., Ørskov, A. D., Hansen, J. W., Arboe, B., Aslan, D., Clasen-Linde, E., Rahbek Gjerdrum, L. M., Gørlev, J. S., Brown, P., Fischer-Nielsen, A., Rosenquist, R., Weischenfeldt, J., and Grønbæk, K. (2021) Mutations known from B-cell lymphoid malignancies are not found in CD34+ stem cells from patients with lymphoma. Leukemia & Lymphoma, 1-4. doi: 10.1080/10428194.2021.1933473.

Damhofer, H., Radzisheuskaya, A., and Helin, K. (2021). Generation of locus-specific degradable tag knock-ins in mouse and human cell lines. STAR Protocols2(2). doi: 10.1016/j.xpro.2021.100575.

Thijssen, M. S., Bintz, J., and Arnes, L. (2021). In Vitro Silencing of lncRNA Expression Using siRNAsMethods in Molecular Biology2348, 141–156. doi: 10.1007/978-1-0716-1581-2_9.

Lauritsen, T. B., Nørgaard, J. M., Grønbæk, K., Vallentin, A. P., Ahmad, S. A., Hannig, L. H., Severinsen, M. T., Adelborg, K., and Østgård, L. S. G. (2021). The Danish Myelodysplastic Syndromes Database: Patient Characteristics and Validity of Data Records. Clinical Epidemiology13, 439-451. doi: 10.2147/CLEP.S306857.

Ye, X., Tian, C., Liu, L., Feng, G., Jin, K., Wang, H., Chen, J., and Liu, L. (2021). Oncostatin M Maintains Naïve Pluripotency of mESCs by Tetraploid Embryo Complementation (TEC) AssayFrontiers in cell and developmental biology9, 1341. doi: 10.3389/fcell.2021.675411.

Schoof, E. M., Furtwängler, B., Üresin, N., Rapin, N., Savickas, S., Gentil, C., Lechman, E., Keller, U. A. D., Dick, J. E., and Porse, B. T. (2021). Quantitative single-cell proteomics as a tool to characterize cellular hierarchies. Nature Communications12(1), 1-15. doi: 10.1038/s41467-021-23667-y.

Ellman, D. G., Slaiman, I. M., Mathiesen, S. B., Andersen, K. S., Hofmeister, W., Ober, E. A., and Andersen, D.C. (2021) Apex Resection in Zebrafish (Danio rerio) as a Model of Heart Regeneration: A Video-Assisted GuideInternational Journal of Molecular Sciences22. doi: 10.3390/ijms22115865.

Montes, M., and Arnes, L. (2021). lncRNAs: potential therapeutic targets and biomarkers for pancreatic cancer? Expert Opinion on Therapeutic Target. doi: 10.1080/14728222.2021.1938541.

Larsen, H. L., and Jensen, K. B. (2021). Reprogramming cellular identity during intestinal regeneration. Current Opinion in Genetics & Development, 70, 40-47. doi: 10.1016/j.gde.2021.05.005.

Müller, I., Moroni, A. S., Shlyueva, D., Sahadevan, S., Schoof, E. M., Radzisheuskaya, A., Højfeldt, J. W., Tatar, T., Koche, R.P., Huang, C. and Helin K. (2021) MPP8 is essential for sustaining self-renewal of ground-state pluripotent stem cells. Nature Communications, 12(1), 1-17. doi: 10.1038/s41467-021-23308-4.

Gonçalves, C. A, Larsen, M., Jung, S., Stratmann, J., Nakamura, A., Leuschner, M., Hersemann, L., Keshara, R., Perlman, S., Lundvall, L., Langhoff Thuesen, L., Hare, K. J., Amit, I., Jørgensen, A., Kim, Y. H., del Sol A. and Grapin-Botton, A. (2021) A 3D system to model human pancreas development and its reference single cell transcriptome atlas identify signaling pathways required for progenitor expansion. Nature Communications, 12(1), 1-17. doi: 10.1038/s41467-021-23295-6.

Rasmussen, K. D., and Helin, K. (2021). ChIP-Sequencing of TET ProteinsMethods in molecular biology, 2272, 251–262. doi: 10.1007/978-1-0716-1294-1_15.

Venning, F. A., Zornhagen, K. W., Wullkopf, L., Sjölund, J., Rodriguez-Cupello, C., Kjellman, P., Morsing, M., Hajkarim, M. C., Won, K. J., Erler, J. T., and Madsen, C. D. (2021). Deciphering the temporal heterogeneity of cancer-associated fibroblast subpopulations in breast cancer. Journal of Experimental & Clinical Cancer Research40(1), 175. doi: 10.1186/s13046-021-01944-4.

Weng, G., Kim, J., and Won, K. J. (2021). VeTra: a new trajectory inference tool based on RNA velocity. Bioinformatics. doi: 10.1093/bioinformatics/btab364.

McGinn, J., Hallou, A., Han, S., Krizic, K., Ulyanchenko, S., Iglesias-Bartolome, R., England, F. J., Verstreken, C., Chalut, K. J., Jensen, K. B., Simons, B. J., and Alcolea, M. P. (2021). A biomechanical switch regulates the transition towards homeostasis in oesophageal epithelium. Nature Cell Biology, 1-15. doi: 10.1038/s41556-021-00679-w.

Kowal, J. M., Möller, S., Ali, D., Figeac, F., Barington, T., Schmal, H., and Kassem, M. (2021). Identification of a clinical signature predictive of differentiation fate of human bone marrow stromal cells. Stem Cell Research & Therapy12(1), 1-15. doi: 10.1186/s13287-021-02338-1.

Palmerini, V., Monzani, S., Laurichesse, Q., Loudhaief, R., Mari, S., Cecatiello, V., Olieric, V., Pasqualato, S., Colombani, J., Andersen, D. S. and Mapelli, M. (2021) Drosophila TNFRs Grindelwald and Wengen bind Eiger with different affinities and promote distinct cellular functions. Nature Communications, 12(1), 1-12. doi: 10.1038/s41467-021-22080-9.

Mikkelsen, S. U., Gillberg, L., Lykkesfeldt, J., and Grønbæk, K. (2021). The role of vitamin C in epigenetic cancer therapy. Free Radical Biology & Medicine, S0891-5849. doi: 10.1016/j.freeradbiomed.2021.03.017.

Parri, E., Kuusanmäki, H., Bulanova, D., Mustjoki, S., and Wennerberg, K. (2021). Selective drug combination vulnerabilities in STAT3-and TP53-mutant malignant NK cells. Blood Advances5(7), 1862-1875. doi: 10.1182/bloodadvances.2020003300.

Narita, T., Ito, S., Higashijima, Y., Chu, W. K., Neumann, K., Walter, J., Satpathy, S., Liebner, T., Hamilton, W.B., Maskey, E., Prus, G., Shibata, M., Iesmantavicius, V., Brickman, J.M., Anastassiadis, K., Koseki, H and Choudhary, C. (2021). Enhancers are activated by p300/CBP activity-dependent PIC assembly, RNAPII recruitment, and pause release. Molecular Cell, 81(10), 2166-2182. doi: 10.1016/j.molcel.2021.03.008.

Jaiswal, A., Gautam, P., Pietilä, E. A., Timonen, S., Nordström, N., Akimov, Y., Sipari, N., Tanoli, Z., Fleischer, T., Lehti, K., Wennerberg, K., and Aittokallio, T. (2021). Multi‐modal meta‐analysis of cancer cell line omics profiles identifies ECHDC1 as a novel breast tumor suppressor. Molecular Systems Biology17(3). doi: 10.15252/msb.20209526.

Radzisheuskaya, A., Shliaha, P. V., Grinev, V. V., Shlyueva, D., Damhofer, H., Koche, R., Gorshkov, V., Kovalchuk, S., Zhan, Y., Rodriguez, K. L., Johnstone, A. L., Keogh, M. C., Hendrickson, R. C., Jensen, O. N. and Helin, K. (2021) Complex-dependent histone acetyltransferase activity of KAT8 determines its role in transcription and cellular homeostasis. Molecular Cell, 81(8), 1749-1765. doi: 10.1016/j.molcel.2021.02.012.

Ianevski, A., Lahtela, J., Javarappa, K. K., Sergeev, P., Ghimire, B. R., Gautam, P., Vähä-Koskela, M., Turunen, L., Linnavirta, N., Kuusanmäki, H., Kontro, M., Porkka, K., Heckman, C. A., Mattila, P., Wennerberg, K., Giri, A. K. and Aittokallio, T. (2021). Patient-tailored design for selective co-inhibition of leukemic cell subpopulationsScience Advances7(8). doi: 10.1126/sciadv.abe4038.

Tjalsma, S. J. D., Hori, M., Sato, Y., Bousard, A., Ohi, A., Raposo, A. C., Roensch, J., Le Saux, A., Nogami, J., Maehara, K., Kujirai, T., Handa, T., Bagés-Arnal, S., Ohkawa, Y., Kurumizaka, H., da Rocha, S. T., Żylicz, J. J., Kimura, H., and Heard, E. (2021). H4K20me1 and H3K27me3 are concurrently loaded onto the inactive X chromosome but dispensable for inducing gene silencing. EMBO Reports, 22(3). doi: 10.15252/embr.202051989.

AlMuraikhi, N., Alaskar, H., Binhamdan, S., Alotaibi, A., Kassem, M., and Alfayez, M. (2021). JAK2 Inhibition by Fedratinib Reduces Osteoblast Differentiation and Mineralisation of Human Mesenchymal Stem Cells. Molecules26, 606. doi: 10.3390/molecules26030606.

Reuten, R., Zendehroud, S., Nicolau, M., Fleischhauer, L., Laitala, A., Kiderlen, S., Nikodemus, D., Wullkopf, L., Nielsen, S. R., McNeill, S., Prein, C., Rafaeva, M., Schoof, E. M., Furtwängler, B., Porse, B. T., Kim, H., Won, K. J., Sudhop, S., Zornhagen, K. W., Suhr, F., Maniati, E., Pearce, O. M. T., Koch, M., Oddershede, L. B., Agtmael, T. V., Madsen, C. D., Mayorca-Guiliani, A. E., Bloch, W., Netz, R. R., Clausen-Schaumann, H., and Erler, J. T. (2021). Basement membrane stiffness determines metastases formationNature Materials, 1-12. doi: 10.1038/s41563-020-00894-0.

de Maturana, E. L., Rodríguez, J. A., Alonso, L., Lao, O., Molina-Montes, E., Martín-Antoniano, I. A., ... Arnes, L., … and Malats, N. (2021). A multilayered post-GWAS assessment on genetic susceptibility to pancreatic cancer. Genome Medicine13(1), 1-18. doi: 10.1186/s13073-020-00816-4.

Sever, D., Hershko-Moshe, A., Srivastava, R., Eldor, R., Hibsher, D., Keren-Shaul, H., Amit, I., Bertuzzi, F., Krogvold, L., Dahl-Jørgensen, K., Ben-Dov, I. Z., Landsman, L. and Melloul, D. (2021) NF-κB activity during pancreas development regulates adult β-cell mass by modulating neonatal β-cell proliferation and apoptosis. Cell Death Discovery7, 1-16. doi: 10.1038/s41420-020-00386-9.

2020

Sakamoto, T., Matsuura, T. R., Wan, S., Ryba, D. M., Kim, J. U., Won, K. J., Lai, L., Petucci, C., Petrenko, N., Musunuru, K., Vega, R. B. and Kelly, D. P. (2020) A Critical Role for Estrogen-Related Receptor Signaling in Cardiac MaturationCirculation Research126(12), 1685-1702. doi: 10.1161/CIRCRESAHA.119.316100.

Flasse, L., Schewin, C., and Grapin-Botton, A. (2020). Pancreas morphogenesis: Branching in and then out. Current Topics in Developmental Biology143, 75-110. doi: 10.1016/bs.ctdb.2020.10.006.

Husby, S., Hjermind Justesen, E., and Grønbæk, K. (2020). Protein phosphatase, Mg2+/Mn2+‐dependent 1D (PPM1D) mutations in haematological cancer. British Journal of Haematology, 192 (4), 697-705. doi: 10.1111/bjh.17120.

Zwiggelaar, R., Lindholm, H., Fosslie, M., Pedersen, M. T., Ohta, Y., Díez-Sánchez, A., Martín-Alonso, M., Ostrop, J., Matano, M., Parmar, N., Kvaløy, E., Spanjers, R. R., Nazmi, K., Rye, M., Drabløs, F., Arrowsmith, C., Dahl, J. A., Jensen, K. B., Sato, T., and Oudhoff, M. J. (2020). LSD1 represses a neonatal/reparative gene program in adult intestinal epithelium. Science Advances, 6(37). doi: 10.1126/sciadv.abc0367.

Krogh, N., Asmar, F., Côme, C., Munch-Petersen, H. F., Grønbæk, K. and Nielsen, H. (2020) Profiling of ribose methylations in ribosomal RNA from diffuse large B-cell lymphoma patients for evaluation of ribosomes as drug targetsNAR Cancer, 2(4). doi: 10.1093/narcan/zcaa035.

Bechmann, M. B., Brydholm, A. V., Codony, V. L., Kim, J., and Villadsen, R. (2020). Heterogeneity of CEACAM5 in breast cancer. Oncotarget11 (43), 3886-3899. doi: 10.18632/oncotarget.27778.

Eskelund, C. W., Dimopoulos, K., Kolstad, A., Glimelius, I., Räty, R., Gjerdrum, L. M. R., Sonnevi, K., Josefsson, P., Nilsson-Ehle, H., Bentzen, H. H. N., Fagerli, U. M., Kuittinen, O., Haaber, J., Niemann, C. U., Pedersen, L. B., Larsen, M. T., Geisler, C. H.,  Hutchings, M., Jerkeman, M. and Grønbæk, K. (2020). Detailed Long-Term Follow-Up of Patients Who Relapsed After the Nordic Mantle Cell Lymphoma Trials: MCL2 and MCL3. HemaSphere5(1), e510. doi: 10.1097/HS9.0000000000000510.

Panda, A., Zylicz, J. J., and Pasque, V. (2020). New Insights into X-Chromosome Reactivation during Reprogramming to PluripotencyCells9(12), 2706. doi: 10.3390/cells9122706.

Kriegbaum, M. C., and Wennerberg, K. (2020). Mitochondria in Their Prime Drive Venetoclax Response in Acute Myeloid Leukemia. Cancer Cell38(6), 776-778. doi: 10.1016/j.ccell.2020.10.018.

Kim, H., Muñoz, S., Osuna, P., and Gershenson, C. (2020). Antifragility Predicts the Robustness and Evolvability of Biological Networks through Multi-class Classification with a Convolutional Neural Network. Entropy, 22(9), 986. doi:10.3390/e22090986.

Yu, Y. S., Shin, H. R., Kim, D., Baek, S. A., Choi, S. A., Ahn, H., K. J. Shamim, A., Kim, J., Kim, I. S., Kim, K. K., Won, K. J. and Baek, S. H. (2020). Pontin arginine methylation by CARM1 is crucial for epigenetic regulation of autophagy. Nature Communications11(1), 1-18. doi: 10.1038/s41467-020-20080-9.

Estruch, M., Reckzeh, K., Vittori, C., Centio, A., Ali, M., Engelhard, S., Zhao, L., Won, K. J., Liu, P., Porse, B. T., and Theilgaard-Mönch, K. (2020). Targeted inhibition of cooperative mutation- and therapy-induced AKT activation in AML effectively enhances response to chemotherapy. Leukemia, 1-13. doi: 10.1038/s41375-020-01094-0.

Antfolk, M., and Jensen, K. B. (2020) A bioengineering perspective on modelling the intestinal epithelial physiology in vitro. Nature Communications, 11(1), 1-11. doi: 10.1038/s41467-020-20052-z.

Bornholdt, J., Broholm, C., Chen, Y., Rago, A., Sloth, S., Hendel, J., Melsæther, C., Müller, C. V., Nielsen, M. J., Strickertsson, J., Engelholm, L., Vitting-Seerup, K., Jensen, K. B., Baker, A., and Sandelin, A. (2020). Personalized B cell response to the Lactobacillus rhamnosus GG probiotic in healthy human subjects: a randomized trial. Gut Microbes12, 1-14. doi: 10.1080/19490976.2020.1854639.

Lewis, A., Keshara, R., Kim, Y. H., and Grapin-Botton, A. (2020). Self-organization of organoids from endoderm-derived cellsJournal of Molecular Medicine, 1-14. doi: 10.1007/s00109-020-02010-w.

Fairfield, H., Dudakovic, A., Khatib, C. M., Farrell, M., Costa, S., Falank, C., Hinge, M., Murphy, C. S., DeMambro, V., Pettitt, J. A., Lary, C. W., Driscoll, H. E., McDonald, M. M., Kassem, M., Rosen, C., Andersen, T. L., van Wijnen, A. J., Jafari, A., and Reagan, M. R. (2020). Myeloma-modified adipocytes exhibit metabolic dysfunction and a senescence-associated secretory phenotype (SASP). Cancer Research, 81(3), 634-647. doi: 10.1158/0008-5472.CAN-20-1088.

Saini, S. K., Ørskov, A. D., Bjerregaard, A. M., Unnikrishnan, A., Holmberg-Thydén, S., Borch, A., Jensen, K. V., Anande, G., Bentzen, A. K., Marquard, A. M., Tamhane, T., Treppendahl, M. B, Gang, A. O., Dufva, I. H., Szallasi, Z., Ternette, N., Pedersen, A. G., Eklund, A. C., Pimanda, J., Grønbæk, K. and Hadrup, S. R. (2020). Human endogenous retroviruses form a reservoir of T cell targets in hematological cancers. Nature Communications, 11, 1-14. doi: 10.1038/s41467-020-19464-8.

Mikkelsen, S. U., Safavi, S., Dimopoulos, K., O’Rourke, C. J., Andersen, M. K., Holm, M. S., Marcher, C. W., Andersen, J. B., Hansen, J. W. and Grønbæk, K. (2020). Structural aberrations are associated with poor survival in patients with clonal cytopenia of undetermined significance. Haematologica. doi: 10.3324/haematol.2020.263319.

Kim, J., T Jakobsen, S., Natarajan, K. N., and Won, K. J. (2020). TENET: gene network reconstruction using transfer entropy reveals key regulatory factors from single cell transcriptomic data. Nucleic Acids Research, 49(1),e1. doi: 10.1093/nar/gkaa1014.

Feehan, J., Kassem, M., Pignolo, R. J., and Duque, G. (2020). Bone from blood: Characteristics and clinical implications of circulating osteogenic progenitor (COP) cells. Journal of Bone and Mineral Research, 36(1), 12-23. doi: 10.1002/jbmr.4204.

Lien, Y. C., Won, K. J., and Simmons, R. A. (2020). Transcriptomic and Quantitative Proteomic Profiling Reveals Signaling Pathways Critical for Pancreatic Islet Maturation. Endocrinology ,161(12), bqaa187. doi: 10.1210/endocr/bqaa187.

Engelsen, A. S., Wnuk-Lipinska, K., Bougnaud, S., Vatter, F. A. P., Tiron, C., Villadsen, R., Miyano, M., Lotsberg, M. L., Madeleine, N., Panahandeh, P., Dhakal, S., Tan, T Z., Peters, S. D., Grøndal, S., Aziz, S. M., Nord, S., Herfindal, L., Stampfer, M. R., Sørlie, T., Brekken, R. A., Straume, O., Halberg, N., Gausdal, G., Thiery, J. P., Akslen, L. A., Petersen, O. W., LaBarge, M. A., and Lorens, J. B. (2020). AXL is a driver of stemness in normal mammary gland and breast cancer. iScience23. doi: 10.1016/j.isci.2020.101649.

Almasoud, N., Binhamdan, S., Younis, G., Alaskar, H., Alotaibi, A., Manikandan, M., Alfayez, M., Kassem, M., and AlMuraikhi, N. (2020). Tankyrase inhibitor XAV-939 enhances osteoblastogenesis and mineralization of human skeletal (mesenchymal) stem cells. Scientific Reports11(1), 4559. doi: 10.1038/s41598-020-73439-9.

Okla, M., and Kassem, M. (2020). Thermogenic Potentials of Bone Marrow AdipocytesBone, 143, 115658. doi: 10.1016/j.bone.2020.115658.

Morsing, M., Kim, J., Villadsen, R., Goldhammer, N., Jafari, A., Kassem, M., Petersen, O. W. and Rønnov-Jessen, L. (2020). Fibroblasts direct differentiation of human breast epithelial progenitors. Breast Cancer Research22, 1-16. doi: 10.1186/s13058-020-01344-0.

Kellermann, L., Jensen, K. B., Bergenheim, F., Gubatan, J., Chou, N. D., Moss, A., and Nielsen, O. H. (2020). Mucosal vitamin D signaling in inflammatory bowel disease. Autoimmunity Reviews, 19(11), 102672. doi: 10.1016/j.autrev.2020.102672.

Vishnubalaji, R., Elango, R., Manikandan, M., Siyal, A. A., Ali, D., Al-Rikabi, A., Hamam, D., Hamam, R., Benabdelkamel, H., Masood, A., Alanazi, I. O., Alfadda, A. A., Alfayez, M., Aldahmash, A., Kassem, M. and Alajez, N. M. (2020). MicroRNA-3148 acts as molecular switch promoting malignant transformation and adipocytic differentiation of immortalized human bone marrow stromal cells via direct targeting of the SMAD2/TGFβ pathway. Cell Death Discovery6(1), 1-16. doi: 10.1038/s41420-020-00312-z.

Chen, L., Shi, K., Qiu, W., Aagaard, L., and Kassem, M. (2020). Generation of Inducible CRISPRi and CRISPRa Human Stromal/Stem Cell Lines for Controlled Target Gene Transcription during Lineage Differentiation. Stem Cells International, 2020. doi: 10.1155/2020/8857344.

Katsumoto, K., and Grapin-Botton, A. (2020). Nutrients men-TOR β-Cells to AdulthoodDevelopmental Cell54, 140-141. doi: 10.1016/j.devcel.2020.06.028.

Riveiro, A. R., and Brickman, J. M. (2020). From pluripotency to totipotency: an experimentalist's guide to cellular potency. Development147(16). doi: 10.1242/dev.189845.

Kolovos, P., Nishimura, K., Sankar, A., Sidoli, S., Cloos, P. A., Helin, K., and Christensen, J. (2020). PR-DUB maintains the expression of critical genes through FOXK1/2-and ASXL1/2/3-dependent recruitment to chromatin and H2AK119ub1 deubiquitination. Genome Research30, 1119-1130. doi: 10.1101/gr.261016.120.

Burns, J. S., and Kassem, M. (2020) Less is more: Corroborating a genomic biomarker identifying human bone marrow multipotent stromal cells with high scalability. Stem Cells38(11), E5-E6. doi: 10.1002/stem.3265.

Rodrigues, J. M., Hassan, M., Freiburghaus, C., Eskelund, C. W., Geisler, C., Räty, R., Kolstad, A., Sundström, C., Glimelius, I., Grønbæk, K., Kwiecinska, A., Porwit, A., Jerkeman, M., and Ek, S. (2020) p53 is associated with high‐risk and pinpoints TP53 missense mutations in mantle cell lymphoma. British Journal of Haematology ,191(5), 796-805. doi: 10.1111/bjh.17023.

Sever, D., and Grapin-Botton, A. (2020). Regeneration of the pancreas: proliferation and cellular conversion of surviving cells. Current Opinion in Genetics & Development64, 84-93. doi: 10.1016/j.gde.2020.06.005. 

Malani, D., Yadav, B., Kumar, A., Potdar, S., Kontro, M., Kankainen, M., Javarappa, K. K., Porkka, K., Wolf, M., Aittokallio, T., Wennerberg, K., Heckman, C. A., Murumägi, A., and Kallioniemi, O. (2020). KIT pathway upregulation predicts dasatinib efficacy in acute myeloid leukemia. Leukemia34(10), 2780-2784. doi: 10.1038/s41375-020-0978-7.

Jaberi, E., Tresse, E., Grønbæk, K., Weischenfeldt, J., and Issazadeh-Navikas, S. (2020). Identification of unique and shared mitochondrial DNA mutations in neurodegeneration and cancer by single-cell mitochondrial DNA structural variation sequencing (MitoSV-seq). EBioMedicine57. doi: 10.1016/j.ebiom.2020.102868.

Bassatne, A., Jafari, A., Kassem, M., Mantzoros, C., Rahme, M., and Fuleihan, G. E. (2020). Delta-like 1 (DLK1) is a possible mediator of vitamin D effects on bone and energy metabolism. Bone, 138, 115510. doi: 10.1016/j.bone.2020.115510.

Weis-Banke, S. E., Lerdrup, M., Kleine-Kohlbrecher, D., Mohammad, F., Sidoli, S., Jensen, O. N., Yanase, T., Nakamura, T., Iwase, A., Stylianou, A., Abu-Rustum, N. R., Aghajanian, C., Soslow, R., Da Cruz Paula, A., Koche, R. P., Weigelt, B., Christensen, J., Helin, K., and Cloos, P. A. C. (2020). Mutant FOXL2C134W highjacks SMAD4 and SMAD2/3 to drive adult granulosa cell tumors. Cancer Research, 80(17), 3466-3479. doi: 10.1158/0008-5472.CAN-20-0259.

Tambe, M., Karjalainen, E., Vähä-Koskela, M., Bulanova, D., Gjertsen, B. T., Kontro, M., Porkka, K., Heckman, C. A., and Wennerberg, K. (2020). Pan-RAF inhibition induces apoptosis in acute myeloid leukemia cells and synergizes with BCL2 inhibition. Leukemia34, 3186-3196. doi: 10.1038/s41375-020-0972-0.

Kim, J., and Villadsen, R. (2020). The Expression Pattern of Epidermal Differentiation Marker Keratin 10 in the Normal Human Breast and Breast Cancer CellsJournal of Histochemistry & Cytochemistry, 68(8), 561-570. doi: 10.1369/0022155420940220.

Rubert, J., Schweiger, P. J., Mattivi, F., Tuohy, K., Jensen, K. B., and Lunardi, A. (2020) Intestinal Organoids: A Tool for Modelling Diet–Microbiome–Host InteractionsTrends in Endocrinology & Metabolism, 31(11), 848-858. doi: 10.1016/j.tem.2020.02.004.

Wan, S., Kim, J., and Won, K. J. (2020). SHARP: hyperfast and accurate processing of single-cell RNA-seq data via ensemble random projectionGenome Research, 30, 205-213. doi: 10.1101/gr.254557.119.

Teves, J. M., and Won, K. J. (2020). Mapping Cellular Coordinates through Advances in Spatial Transcriptomics Technology. Molecules and Cells, 43(7), 591-599. doi: 10.14348/molcells.2020.0020.

Liu, D., Kousa, A. I., O'Neill, K. E., Rouse, P., Popis, M., Farley, A. M., Tomlinson, S. R., Ulyanchenko, S., Guillemot, F., Seymour, P. A., Jørgensen, M. C., Serup, P., Koch, U., Radtke, and F., Blackburn, C. (2020). Canonical Notch signaling controls the early thymic epithelial progenitor cell state and emergence of the medullary epithelial lineage in fetal thymus developmentDevelopment, 147(12), dev178582. doi: 10.1242/dev.178582.

Flasse, L., Yennek, S., Cortijo, C., Barandiaran, I. S., Kraus, M. R. C., and Grapin-Botton, A. (2020). Apical restriction of the planar cell polarity component VANGL in pancreatic ducts is required to maintain epithelial integrity. Cell Reports31(8). doi: 10.1016/j.celrep.2020.107677.

Rifes, P., Isaksson, M., Rathore, G.S., Aldrin-Kirk, P., Møller, O.K., Barzaghi, G., Lee, J., Egerod, K.L., Rausch, D.M., Parmar, M., Pers, T.H., Laurell, T., and Kirkeby, A. (2020) Modeling neural tube development by differentiation of human embryonic stem cells in a microfluidic WNT gradientNew Biotechnology, 38(11), 1265-1273. doi: 10.1038/s41587-020-0525-0.

Tiklová, K., Nolbrant, S., Fiorenzano, A., Björklund, Å. K., Sharma, Y., Heuer, A., Gillberg, L., Hoban, D. B., Cardoso, T., Adler, A. F., Birtele, M., Lundén-Miguel, H., Volakakis, N., Kirkeby, A., Perlmann, T., and Parmar, M. (2020). Single cell transcriptomics identifies stem cell-derived graft composition in a model of Parkinson’s diseaseNature Communications, 11(1), 1-11. doi: 10.1038/s41467-020-16225-5.

Knudsen, T. E., and Brickman, J. M. (2020). Can a Cell Put Its Arms around a Memory?. Cell Stem Cell, 26(5), 609-610. doi: j.stem.2020.04.013.

Bagger, F. O., Kinalis, S., and Rapin, N. (2019). BloodSpot: a database of healthy and malignant haematopoiesis updated with purified and single cell mRNA sequencing profiles. Nucleic Acids Research, 47, D881-D885. doi: 10.1093/nar/gky1076.

Singer, R. A., Arnes, L., Cui, Y., Wang, J., Gao, Y., Guney, M. A., Burnum-Johnson, K. E., Rabadan, R., Ansong, C., Orr, G and Sussel, L. (2019). The Long Noncoding RNA Paupar Modulates PAX6 Regulatory Activities to Promote Alpha Cell Development and Function. Cell metabolism30, 1091-1106. doi: 10.1016/j.cmet.2019.09.013.

Ianevski, A., Giri, A. K., Gautam, P., Kononov, A., Potdar, S., Saarela, J., Wennerberg, K., and Aittokallio, T. (2019). Prediction of drug combination effects with a minimal set of experimentsNature Machine Intelligence1, 568-577. doi: 10.1038/s42256-019-0122-4.

Colombani, J., and Andersen, D. S. (2020). The Drosophila gut: A gatekeeper and coordinator of organism fitness and physiology. Wiley Interdisciplinary Reviews: Developmental Biology, 9(6), e378. doi: 10.1002/wdev.378.

Caviglia, S., Flores-Benitez, D., Lattner, J., Luschnig, S., and Brankatschk, M. (2019). Rabs on the fly: functions of Rab GTPases during developmentSmall GTPases10, 89-98. doi: 10.1080/21541248.2017.1279725.

Ohtani, H., Ørskov, A. D., Helbo, A. S., Gillberg, L., Liu, M., Zhou, W., Ungerstedt, J., Hellström-Lindberg, E., Sun, W., Liang, G., Jones, P. A., and Grønbæk, K. (2020) Activation of a Subset of Evolutionarily Young Transposable Elements and Innate Immunity are Linked to Clinical Responses to 5-Azacytidine. Cancer Research80(12), 2441-2450. doi: 10.1158/0008-5472.CAN-19-1696.

Prabha, R. D., Ding, M., Bollen, P., Ditzel, N., Varma, H. K., Nair, P. D., and Kassem, M. (2020). Strontium ion reinforced bioceramic scaffold for load bearing bone regeneration. Materials Science and Engineering C, 109, 110427. doi: 10.1016/j.msec.2019.110427.

Parri, E., Kuusanmäki, H., van Adrichem, A. J., Kaustio, M., and Wennerberg, K. (2020) Identification of novel regulators of STAT3 activity. PLoS One, 15(3), e0230819. doi:10.1371/journal.pone.0230819.

Sankar, A., Lerdrup, M., Manaf, A., Johansen, J.V., Gonzalez, J.M., Borup, R., Blanshard, R., Klungland, A., Hansen, K., Andersen, C.Y., Dahl, J.A., Helin, K., and Hoffmann, E.R. (2020). KDM4A regulates the maternal-to-zygotic transition by protecting broad H3K4me3 domains from H3K9me3 invasion in oocytes. Nature Cell Biology, 30, 380-388. doi: 10.1038/s41556-020-0494-z.

Akimov, Y., Bulanova, D., Timonen, S., Wennerberg, K., and Aittokallio, T. (2020). Improved detection of differentially represented DNA barcodes for high‐throughput clonal phenomics. Molecular Systems Biology16. doi: 10.15252/msb.20199195.

Côme, C., Balhuizen, A., Bonnet, D., and Porse, B. T. (2020) Myelodysplastic syndrome patient-derived xenografts: from no options to many. Haematologica, 105, 864-869.  doi: 10.3324/haematol.2019.233320.

Eskelund, C. W., Husby, S., Favero, F., Klausen, T. W., Rodriguez-Gonzalez, F. G., Kolstad, A., Pedersen, L. B., Räty, R. K., Geisler, C. H., Jerkeman, M., Weischenfeldt, J., and Grønbæk, K. (2020). Clonal hematopoiesis evolves from pre-treatment clones and stabilizes after end of chemotherapy in patients with MCLBlood, 135, 2000 - 2004. doi: 10.1182/blood.2019003539.

Husby, S., Favero, F., Nielsen, C., Sørensen, B. S., Bæch, J., Grell, K., Hansen, J. W., Rodriguez-Gonzalez, F. G., Haastrup, E., Fischer-Nielsen, A., Andersen, P., Arboe, B., Sækmose, S. G., Hansen, P. B., Christiansen, I., Clasen-Linde, E., Meldgaard, L., Ebbesen, L. H., Segel, E. K., Josefsson, P., Thorsgaard, M., El-Galaly, T. C., Brown, P., Weischenfeldt, J., Larsen, T. S., and Grønbæk, K. (2020). Clinical impact of clonal hematopoiesis in patients with lymphoma undergoing ASCT: a national population-based cohort studyLeukemia34(12), 3256-3268. doi: 10.1038/s41375-020-0795-z.

Wedge, E., Sengeløv, H., Hansen, J. W., Andersen, N. S., Schjoedt, I., Petersen, S. L., Kornblit, B., Grønbæk, K., and Friis, L. S. (2020). Improved outcomes after allogenic hematopoietic stem cell transplantation with Fludarabine/Treosulfan for patients with myelodysplastic syndromes. Biology of Blood and Marrow Transplantation, 26(6), 1091-1098. doi: 10.1016/j.bbmt.2020.02.010.

Juul Belling, H., Hofmeister, W., and Andersen, D. C. (2020). A Systematic Exposition of Methods used for Quantification of Heart Regeneration after Apex Resection in ZebrafishCells, 9(3), 548. doi: 10.3390/cells9030548

Wilhelmson, A. S., and Porse, B. T. (2020). CCAAT enhancer binding protein alpha (CEBPA) biallelic acute myeloid leukaemia: cooperating lesions, molecular mechanisms and clinical relevance. British Journal of Haematology, 190(4), 495-507. doi: 10.1111/bjh.16534.

Seymour, P. A., Collin, C. A., Egeskov-Madsen, A. la R., Jørgensen, M. C., Shimojo, H., Imayoshi, I., de Lichtenberg, K. H., Kopan, R., Kageyama, R., and Serup, P. (2020). Jag1 Modulates an Oscillatory Dll1-Notch-Hes1 Signaling Module to Coordinate Growth and Fate of Pancreatic Progenitors. Developmental Cell, 52(6), 731-747. doi: 10.1016/j.devcel.2020.01.015.

Ali, D., Chen, L., Kowal, J. M., Okla, M., Manikandan, M., AlShehri, M., AlMana, Y., AlObaidan, R., AlOtaibi, N., Hamam, R., Alajez, N. M., Aldahmash, A., Kassem, M., and Alfayez, M (2020). Resveratrol inhibits adipocyte differentiation and cellular senescence of human bone marrow stromal stem cells. Bone, 133. doi: 10.1016/j.bone.2020.115252.

Gupta, A., Gautam, P., Wennerberg, K., and Aittokallio, T. (2020). A normalized drug response metric improves accuracy and consistency of anticancer drug sensitivity quantification in cell-based screening. Communications Biology3(1), 1-12. doi: 10.1038/s42003-020-0765-z.

Kim, S.H., Da Cruz Paula, A., Basili, T., Dopeso, H., Bi, R., Pareja, F., da Silva, E. M., Gularte-Mérida, R., Sun, Z., Fujisawa, S., Smith, C. G., Ferrando, L., Martins Sebastião, A. P., Bykov, Y., Li, A., Silveira, C., Ashley, C. W., Stylianou, A., Selenica, P., Samore, W. R., Jungbluth, A. A., Zamarin, D., Abu-Rustum, N. R., Helin, K., Soslow, R. A., Reis-Filho, J. S., Oliva, E., and Weigelt, B. (2020) Identification of recurrent FHL2-GLI2 oncogenic fusion in sclerosing stromal tumors of the ovary. Nature Communication, 11, 1 - 16. doi:10.1038/s41467-019-13806-x.

2019

Waibel, D. J. E., Tiemann, U., Lupperger, V., Semb, H., and Marr, C. (2019). In-Silico Staining from Bright-Field and Fluorescent Images Using Deep Learning. In International Conference on Artificial Neural Networks (pp. 184-186). Springer, Cham. doi: 10.1007/978-3-030-30508-6_15.

Barrio-Hernandez, I., Jafari, A., Rigbolt, K. T., Hallenborg, P., Sanchez-Quiles, V., Skovrind, I., Akimov, V., Kratchmarova, I., Dengjel, J., Kassem, M., and Blagoev, B. (2019). Phosphoproteomic profiling reveals a defined genetic program for osteoblastic lineage commitment of human bone marrow–derived stromal stem cells. Genome Research. doi: 10.1101/gr.248286.119.

AlMuraikhi, N., Almasoud, N., Binhamdan, S., Younis, G., Ali, D., Manikandan, M., Vishnubalaji, R., Atteya, M., Siyal, A., Alfayez, M., Aldahmash, A., Kassem, M., and Alajez, N. M. (2019). Hedgehog Signaling Inhibition by Smoothened Antagonist BMS-833923 Reduces Osteoblast Differentiation and Ectopic Bone Formation of Human Skeletal (Mesenchymal) Stem CellsStem Cells International. doi: 10.1155/2019/3435901.

Goldhammer, N., Kim, J., Timmermans-Wielenga, V., and Petersen, O.W. (2019). Characterization of organoid cultured human breast cancerBreast Cancer Research, 21, 1-8. doi: 10.1186/s13058-019-1233-x.

Gerdur Ísberg, Ó., Kim, J., Fridriksdottir, A.J., Morsing, M., Timmermans-Wielenga, V., Rønnov-Jessen, L., Petersen, O.W., and Villadsen R. (2019). A CD146 FACS Protocol Enriches for Luminal Keratin 14/19 Double Positive Human Breast Progenitors. Scientific Reports, 9, 1-11. doi: 10.1038/s41598-019-50903-9.

Berest, I., Arnold, C., Reyes-Palomares, A., Palla, G., Rasmussen, K. D., Giles, H., Bruch, P. M., Huber, W., Dietrich, S., Helin, K., and Zaugg, J. B. (2019). Quantification of differential transcription factor activity and multiomics-based classification into activators and repressors: diffTFCell Reports, 29, 3147-3159. doi: 10.1016/j.celrep.2019.10.106.

Pozzi, S., Bowling, S., Apps, J., Brickman, J. M., Rodriguez, T. A., and Martinez-Barbera, J. P. (2019). Genetic Deletion of Hesx1 Promotes Exit from the Pluripotent State and Impairs Developmental DiapauseStem Cell Reports, 13, 970-979. doi: 10.1016/j.stemcr.2019.10.014.

Tencerova, M., Okla, M. and Kassem, M. (2019) Insulin Signaling in Bone Marrow AdipocytesCurrent Osteoporosis Report. 1 – 9. doi: 10.1007/s11914-019-00552-8.

Tencerova, M., Rendina-Ruedy, E., Neess, D., Færgeman, N., Figeac, F., Ali, D., Danielsen, M., Haakonsson, A., Rosen, C. J., and Kassem, M. (2019). Metabolic programming determines the lineage-differentiation fate of murine bone marrow stromal progenitor cells. Bone Research7(1), 1-14. doi: 10.1038/s41413-019-0076-5.

Kowal, J. M., Schmal, H., Halekoh, U., Hjelmborg, J. B., and Kassem, M. (2019). Single‐cell high content imaging parameters predict functional phenotype of cultured human bone marrow stromal stem cells. Stem Cells Translational Medicine. doi: 10.1002/sctm.19-0171.

Søndergaard, E., Rauch, A., Michaut, M., Rapin, N., Rehn, M., Wilhelmson, A. S., Camponeschi, A., Hasemann, M. S., Bagger, F. O., Jendholm, J., Knudsen, K. J., Mandrup, S., Mårtensson, I., and Porse, B. T. (2019) ERG Controls B Cell Development by Promoting Igh V-to-DJ RecombinationCell Reports, 29, 2756 – 2769. doi: 10.1016/j.celrep.2019.10.098.

Thestrup, M.I., Caviglia, S., Cayuso, J., Heyne, R. L. S., Ahmad, R., Hofmeister, W., Satriano, L., Wilkinson, D. G., Andersen, J. B., and Ober, E. A. (2019) A morphogenetic EphB/EphrinB code controls hepatopancreatic duct formation. Nature Communications, 10, 1-15. doi: 10.1038/s41467-019-13149-7.

Linneberg-Agerholm, M., Wong, Y. F., Herrera, J. A. R., Monteiro, R. S., Anderson, K. G. V., and Brickman, J. M. (2019) Naïve human pluripotent stem cells respond to Wnt, Nodal, and LIF signalling to produce expandable naïve extra-embryonic endodermDevelopment, 146doi: 10.1242/dev.180620.

Garland, W., Comet, I., Wu, M., Radzisheuskaya, A., Rib, L., Vitting-Seerup, K., Lloret-Llinares, M., Sandelin, A., Helin, K., and Jensen, T. H. (2019). A Functional Link between Nuclear RNA Decay and Transcriptional Control Mediated by the Polycomb Repressive Complex 2Cell Reports, 29, 1800-1811. doi: 10.1016/j.celrep.2019.10.011.

Poeta, L., Padula, A., Attianese, B., Valentino, M., Verrillo, L., Filosa, S., Shoubridge, C., Barra, A., Schwartz, C., Christensen, J., van Bokhoven, H., Helin, K., Lioi, M. B., Collombat, P., Gecz, J., Altucci, L., Di Schiavi, E., and Miano M. G. (2019). Histone demethylase KDM5C is a SAHA-sensitive central hub at the crossroads of transcriptional axes involved in multiple neurodevelopmental disorders. Human molecular genetics. Human Molecular Genetics, doi: 10.1093/hmg/ddz254.

Hansen, J. W., Pedersen, D. A., Larsen, L. A., Husby, S., Clemmensen, S. B., Hjelmborg, J., Favero, F., Weischenfeldt, J., Christensen, K., and Grønbæk, K. (2019). Clonal hematopoiesis in elderly twins: concordance, discordance and mortality. Blood. doi: 10.1182/blood.2019001793.

Hamilton, W.B., Mosesson, Y., Monteiro, R.S., Emdal, K.B., Knudsen, T.E., Francavilla, C., Barkai, N., Olsen, J.V. and Brickman, J.M. (2019). Dynamic lineage priming is driven via direct enhancer regulation by ERK. Nature, 575, 355-360. doi: 10.1038/s41586-019-1732-z.

Gillberg, L., Ørskov, A. D., Nasif, A., Ohtani, H., Madaj, Z., Hansen, J. W., Rapin, N., Mogensen, J. B., Liu, M., Dufva, I. H., Lykkesfeldt, J., Hajkova, P., Jones, P. A. and Grønbæk, K. (2019). Oral vitamin C supplementation to patients with myeloid cancer on azacitidine treatment: Normalization of plasma vitamin C induces epigenetic changesClinical Epigenetics, 11, 1-11. doi: 10.1186/s13148-019-0739-5.

Johnson, J. L., Stoica, L., Liu, Y., Zhu, P. J., Bhattacharya, A., Buffington, S., Huq, R., Eissa, N. T., Larsson, O., Porse, B. T., Domingo, D., Nawaz, U., Carroll, R., Jolly, L., Scerri, T. S., Kim, G. G., Brignell, A., Coleman, M. J., Braden, R., Kini, U., Jackson, V., Baxter, A., Bahlo, M., Scheffer, I. E., Amor, D. J., Hildebrand, M. S., Bonnen, P. E., Beeton, C., Gecz, J., Morgan, A. T., and Costa-Mattioli, M. (2019). Inhibition of Upf2-Dependent Nonsense-Mediated Decay Leads to Behavioral and Neurophysiological Abnormalities by Activating the Immune Response. Neuron, 104, 665-679. doi: 10.1016/j.neuron.2019.08.027.

Falster, C., Poulsen, S. S., Storaas, A. M., Schroeder, H. M., Vinther, J. H., Kassem, M. and Joergensen, U. (2019). Mesenchymal stem cells isolated from both distal femurs of patients with unilateral trauma or osteoarthritis of the knee exhibit similar in-vitro ability of bone formationJournal of Orthopaedic Science, 24, 918-924. doi: 10.1016/j.jos.2019.01.008.

Laing, A. F., Tirumala, V., Hegarty, E., Mondal, S., Zhao, P., Hamilton, W. B., Brickman, J. M., and Ben-Yakar, A. (2019). An automated microfluidic device for time-lapse imaging of mouse embryonic stem cells. Biomicrofluidics13. doi: 10.1063/1.5124057.

Nielsen, O. H., Hansen, T. I., Gubatan, J. M., Jensen, K. B., and Rejnmark, L. (2019). Managing vitamin D deficiency in inflammatory bowel diseaseFrontline Gastroenterology10, 394-400. doi: 10.1136/flgastro-2018-101055.

Manda-Handzlik, A., Bystrzycka, W., Cieloch, A., Glodkowska-Mrowka, E., Jankowska-Steifer, E., Heropolitanska-Pliszka, E., Skrobot, A., Muchowicz, A., Olga Ciepiela, O., Wachowska, M. and Demkow, U. (2019). Nitric oxide and peroxynitrite trigger and enhance release of neutrophil extracellular traps. Cellular and Molecular Life Sciences, 1-17. doi: 10.1007/s00018-019-03331-x.

Cossarizza, A., Chang, H., Radbruch, A., Acs, A. … (Dela Cruz, G. V.,)… and Zychlinsky, A. (2019), Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition). European Journal of Immunology, 49, 1457-1973. doi: 10.1002/eji.201970107.

Radzisheuskaya, A., Shliaha, P.V., Grinev, V., Lorenzini, E, Kovalchuk, S., Shlyueva, D., Gorshkov, V., Hendrickson, R.C., Jensen, O.N., and Helin, K. (2019) PRMT5 methylome profiling uncovers a direct link to splicing regulation in acute myeloid leukemia. Nature Structural & Molecular Biology, 26, 999-1012. doi: 10.1038/s41594-019-0313-z.

Filimonow, K., Saizz, N., Suwiska, A., Wyszomirski, T., Grabarek, J.B., Ferretti, E., Piliszek, A., Plusa, B., and Maleszewski, M. (2019). No evidence of involvement of E-cadherin in cell fate specification or the segregation of Epi and PrE in mouse blastocysts. PLoS One 14:e0212109. doi: 10.1371/journal.pone.0212109.

Ferretti, E. and Hadjantonakis, A.-K. (2019). Mesoderm specification and diversification: from single cells to emergent tissuesCurrent Opinions in Cell Biology, 61, 110-116. doi: 10.1016/j.ceb.2019.07.012.

Agger, K., Nishimura, K., Miyagi, S., Messling, J.E., Rasmussen, K.D. and Helin, K. (2019). The KDM4/JMJD2 histone demethylases are required for hematopoietic stem cell maintenance. Blood, 134, 1154-1158. doi: 10.1182/blood.2019000855.

Andersen, M.S., Hannezo, E., Ulyanchenko, S., Estrach, S., Antoku, Y., Pisano, S., Boonekamp, K.E., Sendrup, S., Maimets, M., Pedersen M.T., Johansen, J.V., Clement, D.L., Feral, C.C., Simons, B.D., and Jensen, K.B. (2019). Tracing the cellular dynamics of sebaceous gland development in normal and perturbed states. Nature Cell Biology, 21, 924-932. doi: 10.1038/s41556-019-0362-x.

Ahn, B., Wan, S., Jaiswal, N., Vega, R.B., Ayer, D.E., Titchenell, P.M., Han, X., Won, K.J., and Kelly, D.P. (2019). MondoA drives muscle lipid accumulation and insulin resistanceJCI Insight, 4, e129119. doi: 10.1172/jci.insight.129119.

Drissen, R., Thongjuea, S., Theilgaard-Mönch, K., and Nerlov, C. (2019). Identification of two distinct pathways of human myelopoiesis. Science Immunology, 4, eaau7148. doi: 10.1126/sciimmunol.aau7148.

D'Altri, T., Schuster, M.B., Wenzel, A., and Porse, B.T. (2019). Heterozygous loss of Srp72 in mice is not associated with major hematological phenotypes. European Journal of Haematology, 103, 319-328. doi: 10.1111/ejh.13286.

Jakobsen, J.S., Laursen, L.G., Schuster, M.B., Pundhir, S., Schoof, E., Ge, Y., d’Altri, T., Vitting-Seerup, K., Rapin, N., Gentil, C., Jendholm, J., Theilgaard-Mönch, K., Reckzeh, K., Bullinger, L., Döhner, K., Hokland, P., Fitzgibbon, J., and Porse, B.T. (2019) Mutant CEBPA directly drives the expression of the targetable tumor-promoting factor CD73 in AML. Science Advances, 5, eaaw4304. doi: 10.1126/sciadv.aaw4304.

Miyagi, S., Sroczynska, P., Kato, Y., Nakajima-Takagi, Y., Oshima, M., Rizq, O., Takayama, N., Saraya, A., Mizuno, S., Sugiyama, F., Takahashi, S., Matsuzaki, Y., Christensen, J., Helin, K., and Iwama, A. (2019). The chromatin-binding protein Phf6 restricts the self-renewal of hematopoietic stem cells. Blood, 133, 2495-2506. doi: 10.1182/blood.2019000468.

Vishnubalaji, R., Elango, R., Al-Toub, M., Manikandan, M., Al-Rikabi, A., Harkness, L., Ditzel N., Atteya M., Hamam, R., Alfayez, M., Aldahmash, A., Kassem, M., and Alajez, N.M. (2019). Neoplastic Transformation of Human Mesenchymal Stromal Cells Mediated via LIN28B. Scientific Reports, 9, 8101. doi: 10.1038/s41598-019-44536-1.

Clevers, H., Conder, R.K., Li, V.S.W., Lutolf, M.P., Vallier, L., Chan, S., Grikscheit, T.C., Jensen, K.B., and De Coppi, P. (2019) Tissue-Engineering the intestine: The Trials before the Trials. Cell Stem Cell, 24, 855-859. doi: 10.1016/j.stem.2019.04.018.

Boulan, L., Andersen, D.S., Colombani, J., Boone, E., and Léopold, P. (2019). Inter-Organ Growth Coordination Is Mediated by the Xrp1-Dilp8 Axis in Drosophila. Developmental Cell, 49, 811-818. doi: 10.1016/j.devcel.2019.03.016.

Guiu, J., Hannezo, E., Yui, S., Demharter, S., Ulyanchenko, S., Maimets, M., Jørgensen, A., Perlman, S., Lundvall, L., Mamsen, L.S., Larsen, A., Olesen, R.H., Andersen, C.Y., Thuesen, L.L., Hare, K.J., Pers, T.H., Khodosevich, K., Simons, B.D., and Jensen, K.B. (2019). Tracing the origin of adult intestinal stem cells. Nature, 570, 107-111doi: 10.1038/s41586-019-1212-5.

Gautam, P., Jaiswal, A., Aittokallio, T., Al-Ali, H., and Wennerberg, K. (2019) Phenotypic Screening Combined with Machine Learning for Efficient Identification of Breast Cancer-Selective Therapeutic Targets. Cell Chemical Biology, 26, 970-979.e4. doi: 10.1016/j.chembiol.2019.03.011.

Nehlin, J.O., Jafari, A., Tencerova, M., and Kassem, M. (2019). Aging and lineage allocation changes of bone marrow skeletal (stromal) stem cellsBone, 123, 265-273. doi: 10.1016/j.bone.2019.03.041.

Al-Toub, M., Almohawes, M., Vishnubalaji, R., Alfayez, M., Aldahmash, A., Kassem, M., and Alajez N.M. (2019). CXCR7 signaling promotes breast cancer survival in response to mesenchymal stromal stem cell-derived factors. Cell Death Discovery, 5, 87. doi: 10.1038/s41420-019-0169-3.

Dimopoulos, K., and Grønbæk, K. (2019). Epigenetic therapy in hematological cancersAPMIS, 127, 316-328. doi: 10.1111/apm.12906.

Kirkeby, A., and Barker, R.A. (2019). Parkinson disease and growth factors - is GDNF good enough? Nature Reviews Neurology, 15, 312-314. doi: 10.1038/s41582-019-0180-6.

Laugesen, A., Westergaard-Højfeldt, J., and Helin, K. (2019). Molecular Mechanisms Directing PRC2 Recruitment and H3K27 Methylation. Molecular Cell, 74, 8-18. doi: 10.1016/j.molcel.2019.03.011.

Nyeng, P., Heilmann, S., Löf-Öhlin, Z.M., Pettersson, N.F., Hermann, F.M., Reynolds, A.B., and Semb, H. (2019). p120ctn-Mediated Organ Patterning Precedes and Determines Pancreatic Progenitor Fate. Developmental Cell, 49, 1-17. doi: 10.1016/j.devcel.2019.02.005.

Rasmussen, K.D., Berest, I., Kessler, S., Nishimura, K., Simon-Carrasco, L., Vassiliou, G.S., Pedersen, M.T., Christensen, J., Zaugg, J., and Helin, K. (2019). TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells. Genome Research, 29, 564-575. doi: 10.1101/gr.239277.118.

Selleri, L., Zappavigna, V., and Ferretti, E. (2019). 'Building a perfect body': control of vertebrate organogenesis by PBX-dependent regulatory networksGenes & Development, 33, 258-275. doi: 10.1101/gad.318774.118.

Abdallah, B.M., Alzahrani, A.M., Abdel-Moneim, A.M., Ditzel, N., and Kassem, M. (2019). A simple and reliable protocol for long-term culture of murine bone marrow stromal (mesenchymal) stem cells that retained their in vitro and in vivo stemness in long-term culture. Biological Procedures Online, 21, 3. doi: 10.1186/s12575-019-0091-3.

Chen, L., Shi, K., Andersen, T.L., Qiu, W., and Kassem, M. (2019). KIAA1199 is a secreted molecule that enhances osteoblastic stem cell migration and recruitment. Cell Death & Disease, 10, 126. doi: 10.1038/s41419-018-1202-9.

Agrawal Singh, S., Lerdrup, M., Gomes, A.R., van de Werken, H.J., Vilstrup Johansen, J., Andersson, R., Sandelin, A., Helin, K., and Hansen, K. (2019). PLZF targets developmental enhancers for activation during osteogenic differentiation of human mesenchymal stem cells. Elife 8, e40364. doi: 10.7554/eLife.40364.

Huijbregts, L., Kjær Petersen, M.B., Berthault, C., Hansson, M., Aiello, V., Rachdi, L., Grapin-Botton, A., Honore, C., and Scharfmann, R. (2019). Bromodomain and Extra Terminal Proteins Inhibitors Promote Pancreatic Endocrine Cell Fate. Diabetes, 68, 761-773. doi: 10.2337/db18-0224.

Chen, X., Cai, G., Liu, C., Zhao, J., Gu, C., Wu, L., Hamilton, T.A., Zhang, C.J., Ko, J., Zhu, L., Qin, J., Vidimos, A., Koyfman, S., Gastman, B.R., Jensen, K.B., and Li, X. (2019). IL-17R-EGFR axis links wound healing to tumorigenesis in Lrig1+ stem cellsJournal of Experimental Medicine, 216, 195-214. doi: 10.1084/jem.20171849.

Morgan, M., Kabayama, Y., Much, C., Ivanova, I., Di Giacomo, M., Auchynnikava, T., Monahan, J.M., Vitsios, D.M., Vasiliauskaitė, L., Comazzetto, S., Rappsilber, J., Allshire, R.C., Porse, B.T., Enright, A.J., and O'Carroll, D. (2019). A programmed wave of uridylation-primed mRNA degradation is essential for meiotic progression and mammalian spermatogenesisCell Research, 29, 221-232. doi: 10.1038/s41422-018-0128-1.

Ge, Y., Schuster, M.B., Pundhir, S., Rapin, N., Bagger, F.O., Sidiropoulos, N., Hashem, N., and Porse, B.T. (2019). The splicing factor RBM25 controls MYC activity in acute myeloid leukemia. Nature Communications 10, 172. doi: 10.1038/s41467-018-08076-y.

Backe, M.B., Jin, C., Andreone, L., Sankar, A., Agger, K., Helin, K., Madsen, A.N., Poulsen, S.S., Bysani, M., Bacos, K., Ling, C., Perone, M.J., Holst, B., and Mandrup-Poulsen, T. (2019) The Lysine Demethylase KDM5B Regulates Islet Function and Glucose Homeostasis. Journal of Diabetes Research, 2019, 5451038. doi: 10.1155/2019/5451038.

Højfeldt, J.W., Hedehus, L., Laugesen, A., Tatar, T., Wiehle, L., and Helin, K. (2019). Non-core Subunits of the PRC2 Complex Are Collectively Required for Its Target-Site Specificity. Molecular Cell, 76, 1-14. doi: 10.1016/j.molcel.2019.07.031.

Paroni, G., Bolis, M., Zanetti, A., Ubezio, P., Helin, K. Staller, P., Gerlach, L.O., Fratelli, M., Neve, R.M., Terao, M., and Garattini, E. (2019). HER2-positive breast-cancer cell lines are sensitive to KDM5 inhibition: definition of a gene-expression model for the selection of sensitive cases. Oncogene, 38, 2675-2689. doi: 10.1038/s41388-018-0620-6.

Hajkarim, M.C., and Won, K.J. (2019). Single Cell RNA-sequencing for the Study of AtherosclerosisJournal of Lipid and Atherosclerosis, 8, 152-161. doi: 10.12997/jla.2019.8.2.152.

Bergenheim, F., Seidelin, J.B., Pedersen, M.T., Mead, B.E., Jensen, K.B., Karp, J.M., and Nielsen, O.H.  (2019). Fluorescence-based tracing of transplanted intestinal epithelial cells using confocal laser endomicroscopy. Stem Cell Research & Therapy, 10, 148. doi: 10.1186/s13287-019-1246-5.

Muthu, V., Rohacek, A.M., Yao, Y., Rakowiecki, S.M., Brown, A.S., Zhao, Y.T., Meyers, J., Won, K.J., Ramdas, S., Brown, C.D., Peterson, K.A., and Epstein, D.J. (2019). Genomic architecture of Shh-dependent cochlear morphogenesis. Development, 146. doi: 10.1242/dev.181339.

Bosnjak, T., Solberg, R., Hemati, P.D., Jafari, A., Kassem, M., and Johansen, H.T. (2019). Lansoprazole inhibits the cysteine protease legumain by binding to the active site. Basic & Clinical Pharmacology & Toxicology, 125, 89-99. doi: 10.1111/bcpt.13230.

Tencerova, M., Frost, M., Figeac, F., Nielsen, T.K., Ali, D., Lauterlein, J.L., Andersen, T.L., Haakonsson, A.K., Rauch, A., Madsen, J.S., Ejersted, C., Højlund, K., and Kassem, M. (2019) Obesity-Associated Hypermetabolism and Accelerated Senescence of Bone Marrow Stromal Stem Cells Suggest a Potential Mechanism for Bone Fragility. Cell Reports, 27, 2050-2062.e6. doi: 10.1016/j.celrep.2019.04.066.

Walker, J.V., Zhuang, H., Singer, D., Illsley, C.S., Kok, W.L., Sivaraj, K.K., Gao, Y., Bolton, C., Liu, Y., Zhao, M., Grayson, P.R.C., Wang, S., Karbanová, J., Lee, T., Ardu, S., Lai, Q., Liu, J., Kassem, M. Chen, S., Yang, K., Bai, Y., Tredwin, C., Zambon, A.C., Corbeil, D., Adams, R., Abdallah, B.M., and Hu, B. (2019). Transit amplifying cells coordinate mouse incisor mesenchymal stem cell activation. Nature communications, 10, 1 - 18. doi: 10.1038/s41467-019-11611-0.

AlMuraikhi, N., Ali, D., Vishnubalaji, R., Manikandan, M., Atteya, M., Siyal, A., Alfayez, M., Aldahmash, A., Kassem, M., and Alajez, N.M. (2019). Notch Signaling Inhibition by LY411575 Attenuates Osteoblast Differentiation and Decreased Ectopic Bone Formation Capacity of Human Skeletal (Mesenchymal) Stem Cells. Stem Cells International, 2019, 3041262. doi: 10.1155/2019/3041262.

Dimopoulos, K. Hansen, O.K., Sjö, L.D., Saft, L., Schjødt, I.M., Werner Hansen, J., and Grønbæk, K. (2019). The diagnostic and prognostic role of flow cytometry in idiopathic and clonal cytopenia of undetermined significance (ICUS/CCUS): A single-center analysis of 79 patients. Cytometry Part B: Clinical Cyrometry. doi: 10.1002/cyto.b.21842.

2018

Abbot, S., Agbanyo, F., Ahlfors, J.E., Baghbaderani, B.A., Bartido, S., Bharti, K., Burke, C., Carlsson, B., Cavagnaro, J., Creasey, A., DiGiusto, D., Francissen, K., Gaffney, A., Goldring, C., Gorba, T., Griffiths, E., Hanatani, T., Hayakawa, T., Heki, T., Hoogendoorn, K., Kawamata, S., Kimura, H., Kirkeby, A., Knezevic, I., Lebkowski, J., Lin, S., Lin-Gibson, S., Lubiniecki, A., O'Shea, O., Pera, M., Petricciani, J., Pigeau, G., Ratcliffe, A., Sato, Y., Schumann, G.G., Shingleton, W., Stacey, G., Sullivan, S., Svendsen, C.N., Trouvin, J.H., Vandeputte, J., Yuan, B.Z., and Zoon, K. (2018). Report of the international conference on manufacturing and testing of pluripotent stem cells. Biologicals, 56, 67–83. doi:10.1016/j.biologicals.2018.08.004 Meeting report.

Abdallah, B.M., Alzahrani, A.M., and Kassem, M. (2018). Secreted Clusterin protein inhibits osteoblast differentiation of bone marrow mesenchymal stem cells by suppressing ERK1/2 signaling pathway. Bone, 110, 221–229. doi:10.1016/j.bone.2018.02.018.

Ali, D., Chalisserry, E.P, Manikandan, M., Hamam, R., Alfayez, M., Kassem, M., Aldahmash, A., and Alajez, N.M. (2018). Romidepsin Promotes Osteogenic and Adipocytic Differentiation of Human Mesenchymal Stem Cells through Inhibition of Histondeacetylase Activity. Stem Cells International, 2018, 2379456. doi: 10.1155/2018/2379546.

AlMuraikhi, N., Ali, D., Alshanwani, A., Vishnubalaji, R., Manikandan, M., Atteya, M., Siyal, A., Alfayez, M., Aldahmash, A., Kassem, M., and Alajez, N.M. (2018). Stem cell library screen identified ruxolitinib as regulator of osteoblastic differentiation of human skeletal stem cells. Stem Cell Research and Therapy, 9, 319. doi: 10.1186/s13287-018-1068-x.

Bagger, S.O., Hopkinson, B.M., Pandey, D.P., Bak, M., Brydholm, A.V., Villadsen, R., Helin, K., Rønnov-Jessen, L., Petersen, O.W., and Kim, J. (2018). Aggressiveness of non-EMT breast cancer cells relies on FBXO11 activity. Molecular Cancer, 17, 171. doi: 10.1186/s12943-018-0918-6.

Boyd, M., Thodberg, M., Vitezic, M., Bornholdt, J., Vitting-Seerup, K., Chen, Y., Coskun, M., Li, Y., Lo, B.Z.S., Klausen, P., Jan Schweiger, P., Pedersen, A.G., Rapin, N., Skovgaard, K., Dahlgaard, K., Andersson, R., Terkelsen, T.B., Lilje, B., Troelsen, J.T., Petersen, A.M., Jensen, K.B., Gogenur, I., Thielsen, P., Seidelin, J.B., Nielsen, O.H., Bjerrum, J.T., and Sandelin, A. (2018). Characterization of the enhancer and promoter landscape of inflammatory bowel disease from human colon biopsies. Nature Communications, 9, 1661. doi:10.1038/s41467-018-03766-z.

Cardoso, T., Adler, A.F., Mattsson, B., Hoban, D.B., Nolbrant, S., Wahlestedt, J.N., Kirkeby, A., Grealish, S., Bjorklund, A., and Parmar, M. (2018). Target‐specific forebrain projections and appropriate synaptic inputs of hESC‐derived dopamine neurons grafted to the midbrain of parkinsonian rats. Journal of Comparative Neurology, 526, 2133–2146. doi:10.1002/cne.24500.

Caviglia, S., and Ober, E.A. (2018). Non-conventional protrusions: The diversity of cell interactions at short and long distance. Current Opinion in Cell Biology, 54, 106–113. doi:10.1016/j.ceb.2018.05.013.

Chang, C., Venø, M.Y., Chen, L., Ditzel, N., Le, D.Q.S, Dillschneider, P., Kassem, M., and Kjems, J. (2018). Global microRNA profiling in human bone marrow skeletal—Stromal or mesenchymal–stem cells identified candidates for bone regeneration. Molecular Therapy, 26, 593–605. doi:10.1016/j.ymthe.2017.11.018.

Chen, L., Hu, H., Qiu, W., Shi, K., and Kassem, M. (2018). Actin depolymerization enhances adipogenic differentiation in human stromal stem cells. Stem Cell Research, 29, 76–83. doi:10.1016/j.scr.2018.03.010.

Dahl-Jensen, S.B., Yennek, S., Flasse, L., Larsen, H.L., Sever, S., Karemore, Gopal, Novak, I., Sneppen K., and Grapin-Botton, A. (2018). Deconstructing the principles of ductal network formation in the pancreas. PLoS Biology, 16, e2002842. doi:10.1371/journal.pbio.2002842.

Figeac, F., Andersen, D.C., Nipper Nielsen, C.A., Ditzel, N., Sheikh, S.P., Skjødt, K., Kassem, M., Jensen, C.H., and Abdallah, B.M. (2018). Antibody-based inhibition of circulating DLK1 protects from estrogen deficiency-induced bone loss in mice. Bone, 110, 312–320. doi:10.1016/j.bone.2018.02.030.

Gauvrit, S., Villasenor, A., Strilic, B., Kitchen, P., Collins, M.M., Marin-Juez, R., Guenther, S., Maischein, H.M., Fukuda, N., Canham, M.A., Brickman, J.M., Bogue, C.W., Jayaraman, P.S., and Stainier, D.Y.R. (2018). HHEX is a transcriptional regulator of the VEGFC/FLT4/PROX1 signaling axis during vascular development. Nature Communications, 9, 2704. doi:10.1038/s41467-018-05039-1.

Gu, X., Ebrahem, Q., Mahfouz, R.Z., Hasipek, M., Enane, F., Radivoyevitch, T., Rapin, N., Przychodzen, B., Hu, Z., Balusu, R., Cotta, C.V., Wald, D., Argueta, C., Landesman, Y., Martelli, M.P., Falini, B., Carraway, H., Porse, B.T., Maciejewski, J., Jha, B.K., and Saunthararajah, Y. (2018). Leukemogenic nucleophosmin mutation disrupts the transcription factor hub that regulates granulomonocytic fates. The Journal of Clinical Investigation, 128, 4260–4279. doi:10.1172/jci97117.

Højfeldt, J.W., Laugesen, A., Willumsen, B.M., Damhofer, H., Hedehus, L., Tvardovskiy, A., Mohammad, F., Jensen , O.N, and Helin, K. (2018). Accurate H3K27 methylation can be established de novo by SUZ12-directed PRC2. Nature Structural and Molecular Biology, 25, 225–232. doi:10.1038/s41594-018-0036-6.

Jafari, A., Isa, A., Chen, L., Ditzel, N., Zaher, W., Harkness, L., Johnsen, H.E., Abdallah, B.M., Clausen, C., Kassem, M. (2018). TAFA2 induces skeletal (stromal) stem cell migration through activation of Rac1-p38 signaling. Stem Cells, 37, 407-416. doi: 10.1002/stem.2955.

Jorgensen, M.C., de Lichtenberg, K.H., Collin, C.A., Klinck, R., Ekberg, J.H., Engelstoft, M.S., Lickert, H., and Serup, P. (2018). Neurog3-dependent pancreas dysgenesis causes ectopic pancreas in Hes1 mutant mice. Development, 145, dev163568. doi:10.1242/dev.163568.

Lauridsen, F.K.B., Jensen, T.L., Rapin, N., Aslan, D., Wilhelmson, A.S., Pundhir, S., Rehn, M., Paul, F., Giladi, A., Hasemann, M.S., Serup, P., Amit, I., and Porse, B.T. (2018). Differences in cell cycle status underlie transcriptional heterogeneity in the HSC compartment. Cell Reports, 24, 766–780. doi:10.1016/j.celrep.2018.06.057.

Li, Y., Soendergaard, C., Bergenheim, F.H., Aronoff, D.M., Milne, G., Riis, L.B., Seidelin, J.B., Jensen, K.B., and Nielsen, O.H. (2018). COX-2–PGE2 signaling impairs intestinal epithelial regeneration and associates with tnf inhibitor responsiveness in ulcerative colitisEbioMedicine, 36, 497–507. doi: 10.1016/j.ebiom.2018.08.040.

Liu, K.C., Leuckx, G., Sakano, D., Seymour, P.A., Mattsson, C.L., Rautio, L., Staels, W., Verdonck, Y., Serup, P., Kume, S., Heimberg, H., and Andersson, O. (2018). Inhibition of Cdk5 promotes beta-cell differentiation from ductal progenitors. Diabetes, 67, 58–70. doi:10.2337/db16-1587.

Losa, M., Risolino, M., Li, B., Hart, J., Quintana, L., Grishina, I., Yang, H., Choi, I.F., Lewicki, P., Khan, S., Aho, R., Feenstra, J., Vincent, C.T., Brown, A.M.C., Ferretti, E., Williams, T., and Selleri, L. (2018). Face morphogenesis is promoted by Pbx-dependent EMT via regulation of Snail1 during frontonasal prominence fusion. Development, 145, dev157628. doi:10.1242/dev.157628.

Mamidi, A., Prawiro, C., Seymour, P.A., de Lichtenberg, K.H., Jackson, A., Serup, P., and Semb, H. (2018). Mechanosignalling via integrins directs fate decisions of pancreatic progenitors. Nature, 564, 114-118. doi: 10.1038/s41586-018-0762-2.

Martin Gonzalez, J., Baudet, A., Abelechian, S., Bonderup, K., d'Altri, T., Porse, B., Brakebusch, C., Juliusson, G., and Cammenga, J. (2018). A new genetic tool to improve immune-compromised mouse models: Derivation and CRISPR/Cas9-mediated targeting of NRG embryonic stem cell lines. Genesis, 56, e23238. doi:10.1002/dvg.23238.

Moestrup, K.S., Chen, Y., Schepeler, T., Schweiger, P.J., and Jensen, K.B. (2018). Dietary control of skin lipid composition and microbiome. Journal of Investigational Dermatology, 138, 1225–1228. doi:10.1016/j.jid.2017.12.005.

Mohammad, F., and Helin, K. (2018). Oncohistones: Drivers of pediatric cancers. Genes & Development, 31, 2313–2324. doi:10.1101/gad.309013.117.

Mondal, T., Juvvuna, P.K., Kirkeby, A., Mitra, S., Kosalai, S.T., Traxler, L., Hertwig, F., Wernig-Zorc, S., Miranda, C., Deland, L., Volland, R., Bartenhagen, C., Bartsch, D., Bandaru, S., Engesser, A., Subhash, S., Martinsson, T., Caren, H., Akyurek, L.M., Kurian, L., Kanduri, M., Huarte, M., Kogner, P., Fischer, M., and Kanduri, C. (2018). Sense-antisense lncRNA pair encoded by locus 6p22.3 determines neuroblastoma susceptibility via the USP36-CHD7-SOX9 regulatory axis. Cancer Cell, 33, 417–434.e417. doi:10.1016/j.ccell.2018.01.020.

Ober, E.A., and Lemaigre, F.P. (2018). Development of the liver: Insights into organ and tissue morphogenesis. Journal of Hepatology, 68, 1049–1062. doi:10.1016/j.jhep.2018.01.005.

Petersen, M.B.K., Gonçalves,C.A.C., Kim, Y.H., and Grapin-Botton, A. (2018) Recapitulating and deciphering human pancreas development from human pluripotent stem cells in a dish. Current Topics in Developmental Biology, 129, 143–190. doi:10.1016/bs.ctdb.2018.02.009.

Petersen, N., Frimurer, T.M., Pedersen, M.T., Egerod, K.L., Wewer Albrechtsen, N.J., Holst, J.J., Grapin-Botton, A., Jensen, K.B., Schwartz, T.W. (2018) Inhibiting RHOA signaling in mice increases glucose tolerance and numbers of enteroendocrine and other secretory cells in the intestine. Gastroenterology, 155(4), 1164–1176.e2. doi:10.1053/j.gastro.2018.06.039.

Porrello, E.R., and Kirkeby, A. (2018). A symphony of stem cells in Vienna – looking to the future. Development, 145, dev163501. doi:10.1242/dev.163501 Meeting report.

Pundhir, S., Bratt Lauridsen, F.K., Schuster, M.B., Jakobsen, J.S., Ge, Y., Schoof, E.M., Rapin, N., Waage, J., Hasemann, M.S., and Porse, B.T. (2018). Enhancer and transcription factor dynamics during myeloid differentiation reveal an early differentiation block in Cebpa null progenitors. Cell Reports, 23, 2744–2757. doi:10.1016/j.celrep.2018.05.012.

Ramond, C., Beydag-Tasöz, B.S., Azad, A., van de Bunt, M., Petersen, M.K.B., Beer, , N.L., Glaser, N., Berthault, C., Gloyn, A.L., Hansson, M., McCarthy, M.I., Honoré, C., Grapin-Botton, A., and Scharfmann, R. (2018). Understanding human fetal pancreas development using subpopulation sorting, RNA sequencing and single-cell profiling. Development, 145, dev.165480. doi:10.1242/dev.165480.

Reckzeh, K., Kizilkaya, H., Helbo, A.S., Alrich, M.E., Deslauriers, A.G., Grover, A., Rapin, N., Asmar, F., Gronbæk, K., Porse, B., Borregaard, N., Vestweber, D., Nerlov, C., and Theilgaard-Monch, K. (2018). Human adult HSCs can be discriminated from lineage-committed HPCs by the expression of endomucin. Blood advances, 2, 1628–1632. doi:10.1182/bloodadvances.2018015743.

Schweiger, P.J., Clement, D.L., Page, M.E., Schepeler, T., Zou, X., Sirokmány, G., Watt, F.M., and Jensen K.B. (2018). Lrig1 marks a population of gastric epithelial cells capable of long-term tissue maintenance and growth in vitro. Scientific Reports, 8, 15255. doi: 10.1038/s41598-018-33578-6.

Seymour, P.A., and Serup, P. (2018). Mesodermal induction of pancreatic fate commitment. Seminars in Cell and Developmental Biology, 92, 77-88. doi:10.1016/j.semcdb.2018.08.008.

Tencerova, M., Figeac, F., Ditzel, N., Taipaleenmäki, H., Nielsen, T.K., and Kassem, M. (2018). High-fat diet-induced obesity promotes expansion of bone marrow adipose tissue and Impairs skeletal stem cell functions in mice. Journal of Bone and Mineral Research, 33, 1154–1165. doi:10.1002/jbmr.3408.

Tencerova, M., Figeac, F., Ditzel, N., Taipaleenmäki, H., Nielsen, T.K., and Kassem M. (2018). Induction of quiescence (G0) in bone marrow stromal stem cells enhances their stem cell characteristics. Stem Cell Research, 30, 69–80. doi:10.1016/j.scr.2018.05.010.

Tsonkova, V.G., Sand, F.W., Wolf, X.A., Grunnet, L.G., Kirstine Ringgaard, A., Ingvorsen, C., Winkel, L., Kalisz, M., Dalgaard, K., Bruun, C., Fels, J.J., Helgstrand, C., Hastrup, S., Öberg, F.K., Vernet, E., Sandrini, M.P.B., Shaw, A.C., Jessen, C., Grønborg, M., Hald, J., Willenbrock, H., Madsen, D., Wernersson, R., Hansson, L., Jensen, J.N., Plesner, A., Alanentalo, T., Petersen, M.B.K., Grapin-Botton, A., Honoré, C., Ahnfelt-Rønne, J., Hecksher-Sørensen, J., Ravassard, P., Madsen, O.D., Rescan, C., and Frogne, T. (2018). The EndoC-βH1 cell line is a valid model of human beta cells and applicable for screenings to identify novel drug target candidates. Molecular Metabolism, 8, 144–157. doi:10.1016/j.molmet.2017.12.007.

Tu, F., Sedzinski, J., Ma, Y., Marcotte, E.M., and Wallingford, J.B. (2018). Protein localization screening in vivo reveals novel regulators of multiciliated cell development and function. Journal of Cell Science, 131, jcs206565. doi:10.1242/jcs.206565.

Vishnubalaji, R., Manikandan, M., Fahad, M., Hamam, R., Alfayez, M., Kassem, M., Aldahmash, A., and Alajez, N.M. (2018). Molecular profiling of ALDH1+ colorectal cancer stem cells reveals preferential activation of MAPK, FAK, and oxidative stress pro-survival signalling pathways. Oncotarget, 9, 13551–13564. doi:10.18632/oncotarget.24420.

Weinert, B.T., Narita, T., Satpathy, S., Srinivasan, B., Hansen, B.K., Scholz, C., Hamilton, W.B., Zucconi, B.E., Wang, W.W., Liu, W.R., Brickman, J.M., Kesicki, E.A., Lai, A., Bromberg, K.D., Cole, P.A., and Choudhary, C. (2018). Time-resolved analysis reveals rapid dynamics and broad scope of the CBP/p300 acetylome. Cell, 174, 231–244.e212. doi:10.1016/j.cell.2018.04.033.

Weissmann, S., Cloos, P.A., Sidoli, S., Jensen, O.N., Pollard, S., and Helin, K. (2018). The tumor suppressor CIC directly regulates MAPK pathway genes via histone deacetylation. Cancer Research, 78, 4114-4125. doi: 10.1158/0008-5472.CAN-18-0342.

Welsh, I.C., Hart, J., Brown, J.M., Hansen, K., Marques, M.R., Aho, R.J., Grishina, I., Hurtado, R., Herzlinger, D., Ferretti, E., Garcia‐Garcia, M.J., and Selleri, L. (2018). Pbx loss in cranial neural crest, unlike in epithelium, results in cleft palate only and a broader midface. Journal of Anatomy, 233, 222–242. doi:10.1111/joa.12821.

Wilhelmson, A.S., Lantero Rodriguez, M., Stubelius, A., Fogelstrand, P., Johansson, I., Buechler, M.B., Lianoglou, S., Kapoor, V.N., Johansson, M.E., Fagman, J.B., Duhlin, A., Tripathi, P., Camponeschi, A., Porse, B.T., Rolink, A.G., Nissbrandt, H., Turley, S.J., Carlsten, H., Martensson, I.L., Karlsson, M.C.I., and Tivesten, A. (2018). Testosterone is an endogenous regulator of BAFF and splenic B cell number. Nature Communications, 9, 2067. doi:10.1038/s41467-018-04408-0.

Yui, S., Azzolin, L., Maimets, M., Pedersen, M.T., Fordham, R.P., Hansen, S.L., Larsen, H.L., Guiu, J., Alves, M.R.P., Rundsten, C.F., Johansen, J.V., Li, Y., Madsen, C.D., Nakamura, T., Watanabe, M., Nielsen, O.H., Schweiger, P.J., Piccolo, S., and Jensen, K.B. (2018). YAP/TAZ-dependent reprogramming of colonic epithelium links ECM remodeling to tissue regeneration. Cell Stem Cell, 22, 35–49.e7. doi:10.1016/j.stem.2017.11.001.

2017

Ameri, J., Borup, R., Prawiro, C., Ramond, C., Schachter, K.A., Scharfmann, R., and Semb, H. (2017). Efficient generation of glucose-responsive beta cells from isolated GP2+ human pancreatic progenitors. Cell Reports, 19, 36–49. doi:10.1016/j.celrep.2017.03.032.

Anderson, K.G.V., Hamilton, W.B., Roske, F.V., Azad, A., Knudsen, T.E., Canham, M.A., Forrester, L.M., and Brickman, J.M. (2017). Insulin fine-tunes self-renewal pathways governing naive pluripotency and extra-embryonic endoderm. Nature Cell Biology, 19, 1164–1177. doi:10.1038/ncb3617.

Ben-Othman, N., Vieira, A., Courtney, M., Record, F., Gjernes, E., Avolio, F., Hadzic, B., Druelle, N., Napolitano, T., Navarro-Sanz, S., Silvano, S., Al-Hasani, K., Pfeifer, A., Lacas-Gervais, S., Leuckx, G., Marroquí, L., Thévenet, J., Madsen, O.D., Eizirik, D.L., Heimberg, H., Kerr-Conte, J., Pattou, F., Mansouri, A., and Collombat, P. (2017). Long-term GABA administration induces alpha cell-mediated beta-like cell neogenesis. Cell, 168, 73–85. doi:10.1016/j.cell.2016.11.002.

Brickman, J.M., and Serup, P. (2017). Properties of embryoid bodies. Wiley Interdiscip Reviews in Developmental Biology, 6:e259. doi:10.1002/wdev.259.

Burnsa, J.S., Harknessa, L., Aldahmasha, A., Gautiere, L., and Kassem, M. (2017). Chromosome copy number variation in telomerized human bone marrow stromal cells; insights for monitoring safe ex-vivo expansion of adult stem cells. Stem Cell Research, 25, 6–17. doi:10.1016/j.scr.2017.09.006.

Dahl-Jensen, S., and Grapin-Botton, A. (2017). The physics of organoids: A biophysical approach to understanding organogenesis. Development, 144, 946–951. doi:10.1242/dev.143693.

Dombernowsky, S.L., Schwarz, J., Samsoe-Petersen, J., Albrechtsen, R., Jensen, K.B., Thomas, G., and Kveiborg, M. (2017). Loss of PACS-2 delays regeneration in DSS-induced colitis but does not affect the Apc(Min) model of colorectal cancer. Oncotarget, 8, 108303–108315. doi:10.18632/oncotarget.22661.

Dong, X., Landford, W.N., Hart, J., Risolino, M., Kaymakcalan, O., Jin, J., Toyoda, Y., Ferretti, E., Selleri, L., and Spector, J.A. (2017). Towards microsurgical correction of cleft lip ex utero via restoration of craniofacial developmental programs. Plastic and Reconstructive Surgery, 144, 75–85. doi:10.1097/PRS.0000000000003417.

Fridriksdottir, A.J., Villadsen, R., Morsing, M., Klitgaard, M.C., Kim, J., Petersen, O.W., and Rønnov-Jessen, L. (2017). Proof of region-specific multipotent progenitors in human breast epithelia. Proceedings of the National Academy of Sciences of the United States of America, 21, E10102-E10111. doi:10.1073/pnas.1714063114.

Grapin-Botton, A., and Serup, P. (2017). Parsing the pancreas. New England Journal of Medicine, 376, 886–888. doi:10.1056/NEJMcibr1616217.

Hamilton, W.B., and Brickman, J.M. (2017). Surveillance for secure differentiation. Cell Stem Cell, 20, 3–5. doi:10.1016/j.stem.2016.12.011.

Helin, K., and Minucci, S., (2017). The role of chromatin-associated proteins in cancer. Annual Reviews Cancer Biology. 1, 355–77. doi: 10.1146/annurev-cancerbio-050216-034422.

Holmberg, F.E.O., Pedersen, J., Jorgensen, P., Soendergaard, C., Jensen, K.B., and Nielsen, O.H. (2017). Intestinal barrier integrity and inflammatory bowel disease: Stem cell-based approaches to regenerate the barrier. Journal of Tissue Engineering & Regenerative Medicine 12, 923–935. doi:10.1002/term.2506.

Hopkinson, B.M., Klitgaard, M.C., Petersen, O.W., Villadsen, R., Rønnov-Jessen, L., and Kim, J. (2017).Establishment of a normal-derived estrogen receptor-positive cell line comparable to the prevailing human breast cancer subtype. Oncotarget, 8, 10580–10593. doi:10.18632/oncotarget.14554.

Jafari, A., Qanie, D., Andersen, T.L., Zhang, Y., Chen, L., Postert, B., Parsons, S., Ditzel, N., Khosla, S., Johansen, H.T., Kjærsgaard-Andersen, P., Delaisse, J., Abdallah, B.M., Hesselson, D., Solberg, R., and Kassem, M. (2017). Legumain regulates differentiation fate of human bone marrow stromal cells and is altered in postmenopausal osteoporosis. Stem Cell Reports, 8, 373–386. doi:10.1016/j.stemcr.2017.01.003.

Larsen, H.L., and Grapin-Botton, A. (2017). The molecular and morphogenetic basis of pancreas organogenesis. Seminars in Cell and Developmental Biology, 66, 51–68. doi:10.1016/j.semcdb.2017.01.005.

Larsen, H.L., Martín-Coll, L., Nielsen, A.V., Wright, C.V.E., Trusina, A., Kim, Y.H.*,Grapin-Botton, A.* (2017). Stochastic priming and spatial cues orchestrate heterogeneous clonal contribution to mouse pancreas organogenesis. Nature Communications 8, 605. doi:10.1038/s41467-017-00258-4 (*shared last authorship).

Lehnen, D., Barral, S., Cardoso, T., Grealish, S., Heuer, A., Smiyakin, A., Kirkeby, A., Kollet, J., Cremer, H., Parmar, M., Bosio, A., and Knöbel, S. (2017). IAP-based cell sorting results in homogeneous transplantable dopaminergic precursor cells derived from human pluripotent stem cells. Stem Cell Reports. 9, 1207–1220. doi:10.1016/j.stemcr.2017.08.016.

Lonowski, L.A., Narimatsu, Y., Riaz, A., Delay, C.E., Yang, Z., Niola, F., Duda, K., Ober, E.A., Clausen, H., Wandall, H., Hansen, S.H., Bennett, E.P., and Frödin, M. (2017). Genome editing using FACS enrichment of nuclease-expressing cells and indel detection by amplicon analysis. Nature Protocols, 12, 581–603. doi:10.1038/nprot.2016.165.

Martin, D., and Grapin-Botton, A. (2017). The importance of REST for development and function of beta cells. Frontiers in Cell and Developmental Biology, 5,12. doi:10.3389/fcell.2017.00012.

Migueles, R.P., Shaw, L., Rodrigues, N.P., May, G., Henseleit, K., Anderson, K.G., Goker, H., Jones, C.M., de Bruijn, M.F., Brickman, J.M., and Enver, T. (2017). Transcriptional regulation of Hhex in hematopoiesis and hematopoietic stem cell ontogeny. Developmental Biology, 424, 236–245. doi:10.1016/j.ydbio.2016.12.021.

Mohammad, F., Weissmann, S., Leblanc, B., Pandey, D.P., Hojfeldt, J.W., Comet, I., Zheng, C., Johansen, J.V., Rapin, N., Porse, B.T., Tvardovskiy, A., Jensen, O.N., Olaciregui, N.G., Lavarino, C., Sunol, M., de Torres, C., Mora, J., Carcaboso, A.M., and Helin, K. (2017). EZH2 is a potential therapeutic target for H3K27M-mutant pediatric gliomas. Nature Medicine, 23, 483–492. doi:10.1038/nm.4293.

Moraghebi, R., Kirkeby, A., Chaves, P., Ronn, R.E., Sitnicka, E., Parmar, M., Larsson, M., Herbst, A., and Woods, N.B. (2017). Term amniotic fluid: an unexploited reserve of mesenchymal stromal cells for reprogramming and potential cell therapy applications. Stem Cell Research and Therapy, 8, 190. doi:10.1186/s13287-017-0582-6.

Nielsen, H.M., Andersen, C.L., Westman, M., Kristensen, L.S., Asmar, F., Kruse, T.A., Thomassen, M., Larsen, T.S., Skov, V., Hansen, L.L., Bjerrum, O.W., Hasselbalch, H.C., Punj, V., and Grønbæk, K. (2017). Epigenetic changes in myelofibrosis: Distinct methylation changes in the myeloid compartments and in cases with ASXL1 mutations. Scientific Reports, 7, 6774. doi: 10.1038/s41598-017-07057-3.

Nissen, S.B., Perera, M., Gonzalez, J.M., Morgani, S.M., Jensen, M.H., Sneppen, K., Brickman, J.M.*, and Trusina, A.* (2017). Four simple rules that are sufficient to generate the mammalian blastocyst. PLoS Biology, 15, e2000737. doi:10.1371/journal.pbio.2000737 (*joint senior author).

Nolbrant, S., Heuer, A., Parmar, M., and Kirkeby, A. (2017). Generation of high-purity human ventral midbrain dopaminergic progenitors for in vitro maturation and intracerebral transplantation. Nature Protocols, 12, 1962–1979. doi:10.1038/nprot.2017.078.

Öhlin, Z.L., Nyeng, P., Bechard, M., Hess, K., Bankaitis, E., Greiner, T.U., Ameri, J., Wright, C.V., and Semb, H. (2017). Context-specific regulation of apicobasal polarity by EGFR orchestrates epithelial morphogenesis and cellular fate. Nature Cell Biology, 19, 1313-1325. doi: 10.1038/ncb3628.

Perea, D., Guiu, J., Hudry, B., Konstantinidou, C., Milona, A., Hadjieconomou, D., Carroll, T., Hoyer, N., Natarajan, D., Kallijärvi, J., Walker, J.A., Soba, P., Thapar, N., Burns, A.J., Jensen, K.B., and Miguel-Aliaga, I. (2017). Ret receptor tyrosine kinase sustains proliferation and tissue maturation in intestinal epithelia. The EMBO Journal, 36, 2925–3095. doi:10.15252/embj.201696247.

Petersen, M.B.K., Azad, A., Ingvorsen, C., Hess, K., Hansson, M., Grapin-Botton, A.*, Honoré, C.* (2017). Single-cell gene expression analysis of a human ESC model of pancreatic endocrine development reveals different paths to β-cell differentiation. Stem Cell Reports, 9, 1246–1261. doi:10.1016/j.stemcr.2017.08.009 (*shared last authorship).

Ramond, C., Glaser, N., Berthault, C., Ameri, J., Kirkegaard, J.S., Hansson, M., Honoré, C., Semb, H., and Scharfmann, R. (2017). Reconstructing human pancreatic differentiation by mapping specific cell populations during development. eLife 6, e27564. doi:10.7554/eLife.27564.

Sankar, A., Kooistra, S.M., Gonzalez, J.M., Ohlsson, C., Poutanen, M., and Helin, K. (2017). Maternal expression of the JMJD2A/KDM4A histone demethylase is critical for pre-implantation development. Development 144, 3264–3277. doi: 10.1242/dev.155473.

Sørensen, K.M.J., Meldgaard, T., Melchjorsen, C.J., Fridriksdottir, A.J., Pedersen, H., Petersen, O.W., and Kristensen, P. (2017). Upregulation of Mrps18a in breast cancer identified by selecting phage antibody libraries on breast tissue sections. BMC Cancer, 17, 1–11. doi:10.1186/s12885-016-2987-5.

Turner, D.A., Girgin, M., Alonso-Crisostomo, L., Trivedi, V., Baillie-Johnson, P., Glodowski, C.R., Hayward, P.C., Collignon, J., Gustavsen, C., Serup, P., Steventon, B., Lutoff., M.P., and Martinez-Arias, A. (2017). Anteroposterior polarity and elongation in the absence of extra-embryonic tissues and of spatially localised signalling in gastruloids: mammalian embryonic organoids. Development, 144, 3894–3906. doi:10.1242/dev.150391.

Wang, S., Miller, S.R., Ober, E.A., and Sadler, K.C. (2017). Making it new again: Insight into liver development, regeneration, and disease from zebrafish research. Current Topics in Developmental Biology, 124, 161–195. doi:10.1016/bs.ctdb.2016.11.012.

2016

Abdallah, B.M., Figeac, F., Larsen, K.H., Ditzel, N., Keshari, P., Isa, A., Jafari, A., Andersen, T.L., Delaisse, J., Goshima, Y., Ohshima, T., and Kassem, M. (2016). CRMP4 Inhibits Bone Formation by Negatively Regulating BMP and RhoA Signaling. Journal of Bone Mineral Research, 32(5), 913–926. doi:10.1002/jbmr.3069.

Agger, K., Miyagi, S., Pedersen, M.T., Kooistra, S.M., Johansen, J.V., and Helin, K. (2016). Jmjd2/Kdm4 demethylases are required for expression of Il3ra and survival of acute myeloid leukemia cells. Genes & Development, 30, 1278–1288. doi:10.1101/gad.280495.116.

Aggerholm-Pedersen, N., Demuth, C., Safwat, A., Meldgaard, P., Kassem, M., and Sorensen, B.S. (2016). Dasatinib and doxorubicin treatment of sarcoma initiating cells: a possible new treatment strategy. Stem Cells International, 9607493. doi:10.1155/2016/9601493.

Arregi, I., Climent, M., Iliev, D., Strasser, J., Gouignard, N., Johansson, J.K., Singh, T., Mazur, M., Semb, H., Artner, I., Minichiello, L., and Pera, E.M. (2016). Retinol dehydrogenase-10 regulates pancreas organogenesis and endocrine cell differentiation via paracrine retinoic acid signaling. Endocrinology, 157, 4615–4631. doi:10.1210/en.2016-1745.

Bagger, F.O., Sasivarevic, D., Sohi, S.H., Laursen, L.G., Pundhir, S., Sonderby, C.K., Winther, O., Rapin, N., and Porse, B.T. (2016). BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis. Nucleic Acids Research, 44, D917–924. doi:10.1093/nar/gkv1101.

Bao, J., Vitting-Seerup, K., Waage, J., Tang, C., Ge, Y., Porse, B.T., and Yan, W. (2016). UPF2-dependent nonsense-mediated mRNA decay pathway is essential for spermatogenesis by selectively eliminating longer 3'UTR transcripts. PLoS Genetics, 12, e1005863. doi:10.1371/journal.pgen.1005863.

Berclaz, C., Schmidt-Christensen, A., Szlag, D., Extermann, J., Hansen, L., Bouwens, A., Villiger, M., Goulley, J., Schuit, F., Grapin-Botton, A., Lasser, T., and Holmberg, D. (2016). Longitudinal three-dimensional visualisation of autoimmune diabetes by functional optical coherence imaging. Diabetologia, 59, 550–559. doi:10.1007/s00125-015-3819-x.

Berclaz, C., Szlag, D., Nguyen, D., Extermann, J., Bouwens, A., Marchand, P.J., Nilsson, J., Schmidt-Christensen, A., Holmberg, D., Grapin-Botton, A., and Lasser, T. (2016). Label-free fast 3D coherent imaging reveals pancreatic islet micro-vascularization and dynamic blood flow. Biomedical Optics Express, 7, 4569–4580. doi: 10.1364/BOE.7.004569.

Cayuso, J., Dzementsei, A., Fischer, J.C., Karemore, G., Caviglia, S., Bartholdson, J., Wright, G.J., and Ober E.A. (2016). EphrinB1/EphB3b coordinate bidirectional epithelial-mesenchymal interactions controlling liver morphogenesis and laterality. Developmental Cell, 39, 316–328. doi:10.1016/j.devcel.2016.10.009 (Recommended by the Faculty of 1000).

Comet, I., Riising, E.M., Leblanc, B., and Helin, K. (2016). Maintaining cell identity: PRC2-mediated regulation of transcription and cancer. Nature Reviews Cancer, 16, 803–810. doi:10.1038/nrc.2016.83.

Cooper, S, Grijzenhout, A., Underwood, E., Ancelin, K., Zhang, T., Nesterova, T.B., Anil-Kirmizitas, B., Bassett, A., Kooistra, S.M., Agger, K., Helin, K., Heard, E., and Brockdorff, N. (2016). Jarid2 binds mono-ubiquitylated H2A lysine 119 to mediate crosstalk between Polycomb complexes PRC1 and PRC2. Nature Communications, 7, 13661. doi:10.1038/ncomms13661.

Dahl-Jensen, S.B., Figueiredo -Larsen, M., Grapin-Botton, A*, and Sneppen, K.* (2016). Short-range growth inhibitory signals from the epithelium can drive non-stereotypic branching in the pancreas. Physical Biology, 13, 016007. doi:10.1088/1478-3975/13/1/016007 (*shared last authorship).

Di Stefano, B., Collombet, S., Jakobsen, J.S., Wierer, M., Sardina, J.L., Lackner, A., Stadhouders, R., Segura-Morales, C., Francesconi, M., Limone, F., Mann, M., Porse, B.T., Thieffry, D., and Graf, T. (2016). C/EBPalpha creates elite cells for iPSC reprogramming by upregulating Klf4 and increasing the levels of Lsd1 and Brd4. Nature Cell Biology, 18, 371–381. doi:10.1038/ncb3326.

Grapin-Botton, A. (2016) Three-dimensional pancreas organogenesis models. Diabetes Obesity and Metabolism, Suppl 1, 33–40. doi:10.1111/dom.12720.

Grassilli, E., Pisano, F., Cialdella, A., Bonomo, S., Missaglia, C., Cerrito, M.G., Masiero, L., Ianzano, L., Giordano, F., Cicirelli, V.,Narloch, R., D'Amato, F., Noli, B., Ferri, G.L., Leone, B.E., Stanta, G., Bonin, S., Helin, K., Giovannoni, R., and Lavitrano, M. (2016). A novel oncogenic BTK isoform is overexpressed in colon cancers and required for RAS-mediated transformation. Oncogene, 35, 4368–4378. doi:10.1038/onc.2015.504.

Harkness, L., Zaher, W., Ditzel, N., Isa, A. and Kassem, M. (2016). CD146/MCAM defines functionality of human bone marrow stromal stem cell populations. Stem Cell Research & Therapy, 7, 4. doi:10.1186/s13287-015-0266-z.

Højfeldt, J.W., and Helin, K. (2016). Regional tumour glutamine supply affects chromatin and cell identity. Nature Cell Biology, 18, 1027–1029. doi:10.1038/ncb3414.

Illingworth, R.S., Hölzenspies, J.J., Roske, F.V., Bickmore, W.A., and Brickman, J.M. (2016). Polycomb enables primitive endoderm lineage priming in embryonic stem cells. eLife, 5:e14926.  doi:10.7554/eLife.14926.

Larsen, S.A., Meldgaard, T., Fridriksdottir, A.J., Lykkemark, S., Poulsen, P.C., Overgaard, L.F., Petersen, H.B., Petersen, O.W., and Kristensen, P. (2016). Raising an Antibody Specific to Breast Cancer Subpopulations Using Phage Display on Tissue Sections. Cancer Genomics Proteomics, 13(1), 21–30.

Laugesen, A., Højfeldt, J.W., and Helin, K. (2016). Role of the Polycomb repressive complex 2 (prc2) in transcriptional regulation and cancer. Cold Spring Harbor Perspectives in Medicine, 6, a026575. doi:10.1101/cshperspect.a026575.

Martin Gonzalez, J., Morgani, S.M., Bone, R.A., Bonderup, K., Abelchian, S., Brakebusch, C., and Brickman, J.M. (2016). Embryonic stem cell culture conditions support distinct states associated with different developmental stages and potency. Stem Cell Reports, 7, 177–191. doi:10.1016/j.stemcr.2016.07.009.

Morsing, M., Klitgaard, M.C., Jafari, A., Villadsen, R., Kassem, M., Petersen, O.W., and Rønnov-Jessen, L. (2016). Evidence of two distinct functionally specialized fibroblast lineages in breast stroma. Breast Cancer Research, 18, 108. doi:10.1186/s13058-016-0769-2.

O'Connor, C., Lohan, F., Campos, J., Ohlsson, E., Salome, M., Forde, C., Artschwager, R., Liskamp, R.M., Cahill, M.R., Kiely, P.A., Porse, B.T., and Keeshan, K. (2016). The presence of C/EBPalpha and its degradation are both required for TRIB2-mediated leukaemia. Oncogene, 35, 5272–5281. doi:10.1038/onc.2016.66.

Ohlsson, E., Schuster, M.B., Hasemann, M., and Porse, B.T. (2016). The multifaceted functions of C/EBPalpha in normal and malignant haematopoiesis. Leukemia, 30, 767–775. doi:10.1038/leu.2015.324.

Pedersen, M.T., Kooistra, S.M., Radzisheuskaya, A., Laugesen, A., Johansen, J.V., Hayward, D.G., Nilsson, J., Agger, K., and Helin, K. (2016). Continual removal of H3K9 promoter methylation by Jmjd2 demethylases is vital for ESC self-renewal and early development. The EMBO Journal, 35, 1550–1564. doi:10.15252/embj.201593317.

Pundhir, S., Bagger, F.O., Lauridsen, F.B., Rapin, N., and Porse, B.T. (2016). Peak-valley-peak pattern of histone modifications delineates active regulatory elements and their directionality. Nucleic Acids Research, 44, 4037–4051. doi:10.1093/nar/gkw250.

Radzisheuskaya, A., Shlyueva, D., Müller, I., and Helin, K. (2016). Optimizing sgRNA position markedly improves the efficiency of CRISPR/dCas9-mediated transcriptional repression. Nucleic Acids Research, 44, e141. doi: 10.1093/nar/gkw583.

Rasmussen, K.D., and Helin, K. (2016). Role of TET enzymes in DNA methylation, development, and cancer. Genes and Development 30, 733–750. doi:10.1101/gad.276568.115.

Riso, V., Cammisa, M., Kukreja, H., Anvar, Z., Verde, G., Sparago, A., Acurzio, B., Lad, S., Lonardo, E., Sankar, A., Helin, K., Feil, R., Fico, A., Angelini, C., Grimaldi, G., and Riccio, A. (2016). ZFP57 maintains the parent-of-origin-specific expression of the imprinted genes and differentially affects non-imprinted targets in mouse embryonic stem cells. Nucleic Acids Research, 44, 8165–8178. doi: 10.1093/nar/gkw505.

Rothova, M., Holzenspies, J.J., Livigni, A., Villegas, S.N., and Brickman, J.M. (2016). Differentiation of mouse embryonic stem cells into ventral foregut precursors. Current Protocols in Stem Cell Biology, 36, 1g.3.1–12. doi:10.1002/9780470151808.sc01g03s36.

Schwämmle, V., Sidoli, S., Ruminowicz, C., Wu, X., Lee, C., Helin, K., and Jensen, O.N. (2016). Systems level analysis of histone H3 post-translational modifications reveals features of PTM crosstalk in chromatin regulation. Molecular & Cellular Proteomics, 15, 2715–2729. doi:10.1074/mcp.M115.054460.

Scourzic, L., Couronne, L., Pedersen, M.T., Valle, V.D., Diop, M., Mylonas, E., Calvo, J., Mouly, E., Lopez, C.K., Martin, N., Fontenay, M., Bender, A., Guibert, S, Dubreuil, P., Dessen, P., Droin, N., Pflumio, F., Weber, M., Gaulard, P., Helin, K., Mercher, Y., and Bernard, O.A. (2016). DNMT3AR882H mutant and Tet2 inactivation cooperate in the deregulation of DNA methylation control to induce lymphoid malignancies in mice. Leukemia, 30, 1388–1398. doi:10.1038/leu.2016.29.

Stunnenberg, H.G. [international epigenome consortium (incl.  Helin, K., and Porse, B.T.)] and Hirst, M. (2016). The International Human Epigenome Consortium: A blueprint for scientific collaboration and discovery. Cell, 167, 1145–1149. doi:10.1016/j.cell.2016.11.007.

Vishnubalaji, R., Hamam, R., Yue, S., Al-Obeed, O., Kassem, M., Liu, F., Aldahmash, A., and Alajez, N.M. (2016). MicroRNA-320 suppresses colorectal cancer by targeting SOX4, FOXM1, and FOXQ1. Oncotarget, 7, 35789–35802. doi:10.18632/oncotarget.8937.

2015

Abdallah, B.M., Ditzel, N., Laborda, J., Karsenty, G., and Kassem, M. (2015). DLK1 regulates whole body glucose metabolism: A negative feedback regulation of the osteocalcin-insulin loop. Diabetes, 64, 3069-3080. doi: 10.2337/db14-1642.

Abdallah, B.M., Jafari, A., Zaher, W., Qiu, W., and Kassem, M. (2015). Skeletal (stromal) stem cells: An update on intracellular signaling pathways controlling osteoblast differentiation. Bone, 70, 28–36. doi:10.1016/j.bone.2014.07.028.

Al-Toub, M., Vishnubalaji, R., Hamam, R., Kassem, M., Aldahmash A., and Alajez, N.M. (2015). CDH1 and IL1-beta expression dictates FAK and MAPKK-dependent cross-talk between cancer cells and human mesenchymal stem cells. Stem Cell Research and Therapy, 6, 135. doi:10.1186/s13287-015-0123-0.

Andersen, R.K., Zaher, W., Larsen, K.H., Ditzel, N., Drews, K., Wruck, W., Adjaye, J., Abdallah, B.M., and Kassem, M. (2015). Association between in vivo bone formation and ex vivo migratory capacity of human bone marrow stromal cells. Stem Cell Research and Therapy, 6, 196. doi:10.1186/s13287-015-0188-9.

Bao, J., Tang, C., Yuan, S., Porse, B.T., and Yan, W. (2015). UPF2, a nonsense-mediated mRNA decay factor, is required for prepubertal Sertoli cell development and male fertility by ensuring fidelity of the transcriptome. Development, 142, 352–362. doi:10.1242/dev.115642.

Berclaz, C., Pache, C., Bouwens, A., Szlag, D., Lopez, A., Joosten, L., Ekim, S., Brom, M., Gotthardt, M., Grapin-Botton, A., and Lasser, T. (2015). Combined optical coherence and fluorescence microscopy to assess dynamics and specificity of pancreatic beta-cell tracers. Scientific Reports, 5, 10385. doi:10.1038/srep10385.

Chen, L., Shi, K., Frary, C.E., Ditzel, N., Hu, H., Qiu, W., and Kassem, M. (2015). Inhibiting actin depolymerization enhances osteoblast differentiation and bone formation in human stromal stem cells. Stem Cell Reserch, 15(2), 281–289. doi:10.1016/j.scr.2015.06.009.

Cruickshank, V.A., Sroczynska, P., Sankar, A., Miyagi, S., Rundsten, C.F., Johansen, J.V., and Helin, K. (2015). SWI/SNF subunits SMARCA4, SMARCD2 and DPF2 collaborate in MLL-rearranged leukaemia maintenance. PLoS One, 10, e0142806. doi:10.1371/journal.pone.0142806.

Fork, C., Gu, L., Hitzel, J., Josipovic, I., Hu, J., Wong, M.S., Ponomareva, Y., Albert, M., Schmitz, S.U., Uchida, S., Fleming, I., Helin, K., Steinhilber, D., Leisegang, M.S., and Brandes, R.P. (2015). Epigenetic Regulation of Angiogenesis by JARID1B-Induced Repression of HOXA5. Arteriosclerosis Thrombosis and Vascular Biology, 35, 1645-1652. doi:10.1161/atvbaha.115.305561.

Fridriksdottir, A.J., Kim, J., Villadsen, R., Klitgaard, M.C., Hopkinson, B.M., Petersen, O.W., and Ronnov-Jessen, L. (2015). Propagation of oestrogen receptor-positive and oestrogen-responsive normal human breast cells in culture. Nature Communications, 6, 8786. doi:10.1038/ncomms9786.

Funa, N.S., Schachter, K.A., Lerdrup, M., Ekberg, J., Hess, K., Dietrich, N., Honore, C., Hansen, K., and Semb, H. (2015). ß-catenin regulates primitive streak induction through collaborative interactions with SMAD2/SMAD3 and OCT4. Cell Stem Cell, 16, 639–652. doi:10.1016/j.stem.2015.03.008.

Galán-Díez, M., Isa, A., Ponzetti, M., Nielsen, M.F., Kassem, M., and Kousteni, S. (2015). Normal hematopoiesis and lack of β-catenin activation in osteoblasts of patients and mice harboring Lrp5 gain-of-function mutations. Biochimica et Biophysica Acta - Molecular Cell Research, 1863, 490-498. doi:10.1016/j.bbamcr.2015.11.037.

Golonzhka, O., Nord, A., Tang, P.L.F., Lindtner, S., Ypsilanti, A.R., Ferretti, E., Visel, A., Selleri, L., and Rubenstein, J.L.R. (2015). Pbx regulates patterning of the cerebral cortex in progenitors and postmitotic neurons. Neuron, 88, 1192–1207. doi:10.1016/j.neuron.2015.10.045.

Grapin-Botton, A., Seymour, P.A., and Gradwohl, G. (2015). Pairing-up SOX to kick-start beta cell genesis. Diabetologia, 58, 859–861. doi: 10.1007/s00125-015-3539-2.

Greggio, C., De Franceschi, F. and Grapin-Botton, A. (2015). Concise reviews: In Vitro-Produced pancreas organogenesis models in three dimensions: Self-organization from few stem cells or progenitors. Stem Cells, 33, 8–14. doi:10.1002/stem.1828.

Helbo, A.S., Treppendahl, M., Aslan, D., Dimopoulos, K., Nandrup-Bus, C., Holm, M.S., Andersen, M.K., Liang, G., Kristensen, L.S., and Grønbæk, K. (2015). Hypermethylation of the VTRNA1-3 promoter is associated with poor outcome in lower risk myelodysplastic syndrome patients. Genes, 6, 977–990. doi:10.3390/genes6040977.

Holzenspies, J., Cruz, G.D., and Brickman, J.M. (2015). Resolving heterogeneity: fluorescence-activated cell sorting of dynamic cell populations from feeder-free mouse embryonic stem cell culture. Methods in Molecular Biology, 1341, 25–40. doi:10.1007/7651_2015_254.

Horn, S., Kirkegaard, J.S., Hoelper, S.H., Seymour, P.A., Rescan, C., Nielsen, J.H., Madsen, O.D., Jensen, J.N., Krüger, M., Grønborg, M., and Ahnfelt-Rønne, J. (2015). Research resource: A dual proteomic approach identifies regulated islet proteins during beta cell mass expansion in vivo. Molecular Endocrinology, 30(1), 133–143. doi:10.1210/me.2015-1208.

Jafari, A., Siersbaek, M.S., Chen, L., Qanie, D., Zaher, W., Abdallah, B.M., and Kassem, M. (2015). Pharmacological inhibition of PRKG1 enhances bone formation by human skeletal stem cells through activation of RhoA-Akt signaling. Stem Cells, 33, 2219–2231. doi:10.1002/stem.2013.

Jakobsen, J.S., Bagger, F.O., Hasemann, M.S., Schuster, M.B., Frank, A.K., Waage, J., Vitting-Seerup, K., and Porse, B.T. (2015). Amplification of pico-scale DNA mediated by bacterial carrier DNA for small-cell-number transcription factor ChIP-seq. BMC Genomics, 16, 46. doi:10.1186/s12864-014-1195-4.

Kassem, M., and Bianco, P. (2015). Skeletal stem cells in space and time. Cell, 160, 17–19. doi: 10.1016/j.cell.2014.12.034.

Kim, Y. H., List Larsen, H., Rué, P., Lemaire, L.A., Ferrer, J., and Grapin-Botton, A. (2015). Cell cycle-dependent differentiation dynamics balances growth and endocrine differentiation in the pancreas. PLoS Biology, 13:e1002111. doi:10.1371/journal.pbio.1002111.

Knudsen, K.J., Rehn, M., Hasemann, M.S., Rapin, N., Bagger, F.O., Ohlsson, E., Willer, A., Frank, A.K., Sondergaard, E., Jendholm, J., Thoren, L., Lee, J., Rak, J., Theilgaard-Monch, K., and Porse, B.T. (2015). ERG promotes the maintenance of hematopoietic stem cells by restricting their differentiation. Genes and development, 29, 1915–1929. doi:10.1101/gad.268409.115.

Koltowska, K., Lagendijk, A.K., Pichol-Thievend, C., Fischer, J.C., Francois, M., Ober, E.A., Yap, A.S., and Hogan, B.M. (2015). Vegfc regulates bipotential precursor division and Prox1 expression to promote lymphatic identity in zebrafish. Cell Reports, 13, 1828–1841. doi:10.1016/j.celrep.2015.10.055.

Laing, A.F., Lowell, S., and Brickman, J.M. (2015). Gro/TLE enables embryonic stem cell differentiation by repressing pluripotent gene expression. Developmental Biology, 397, 56–66. doi:10.1016/j.ydbio.2014.10.007.

Larsen, S.A., Meldgaard, T., Fridriksdottir, A.J., Lykkemark, S., Poulsen, P.C., Overgaard, L.F., Petersen, H.B., Petersen, O.W., and Kristensen, P. (2015). Selection of a breast cancer subpopulation-specific antibody using phage display on tissue sections. Immunologic Research, 62, 263-272. doi:10.1007/s12026-015-8657-x.

Lemaire, L.A, Goulley, J., Kim, Y.H., Carat, S., Jacquemin, P., Rougemont, J., Constam, D. and Grapin-Botton, A. (2015). Bicaudal C1 promotes pancreatic NEUROG3+ endocrine progenitor differentiation and ductal homeostasis. Development, 142, 858–870. doi:10.1242/dev.114611.

Martin, D., Kim, Y.H., Sever, D., Mao, C.A., Haefliger, J.A., and Grapin-Botton, A. (2015). REST represses a subset of the pancreatic endocrine differentiation program. Developmental Biology, 405, 316–327. doi: 10.1016/j.ydbio.2015.07.002.

Mora-Jensen, H., Jendholm, J., Rapin, N., Andersen, M.K., Roug, A.S., Bagger, F.O., Bullinger, L., Winther, O., Borregaard, N., Porse, B.T., and Theilgaard-Monch, K. (2015). Cellular origin of prognostic chromosomal aberrations in AML patients. Leukemia, 29, 1785–1789. doi:10.1038/leu.2015.30.

Morgani, S.M., and Brickman, J.M. (2015). LIF supports primitive endoderm expansion during pre-implantation development. Development, 142, 3488–3499. doi:10.1242/dev.125021.

Ober, E.A., and Grapin-Botton, A. (2015). At new heights - endodermal lineages in development and disease. Development, 142, 1912–1917. doi: 10.1242/dev.121095.

Paul, F., Arkin, Y., Giladi, A., Jaitin, D.A., Kenigsberg, E., Keren-Shaul, H., Winter, D., Lara-Astiaso, D., Gury, M., Weiner, A., David, E., Cohen, N., Lauridsen, F.K.B., Haas, S., Schlitzer, A., Mildner, A., Ginhoux, F., Jung, S., Trumpp, A., Porse, B.T., Tanay, A., and Amit, I. (2015). Transcriptional heterogeneity and lineage commitment in myeloid progenitors. Cell, 163, 1663–1677. doi:10.1016/j.cell.2015.12.046.

Ptaschinski, C., Mukherjee, S., Moore, M.L., Albert, M., Helin, K., Kunkel, S.L., and Lukacs, N.W. (2015). RSV-induced H3K4 demethylase KDM5B leads to regulation of dendritic cell-derived innate cytokines and exacerbates pathogenesis in vivo. PLoS Pathology, 11, e1004978. doi:10.1371/journal.ppat.1004978

Rasmussen, K.D., and Helin, K. (2015). TET1: an epigenetic guardian of lymphomagenesis. Nature Immunology, 16, 592–594. doi:10.1038/ni.3176.

Rasmussen, K.D., Jia, G., Johansen, J.V., Pedersen, M.T., Rapin, N., Bagger, F.O., Porse, B.T., Bernard, O.A., Christensen, J., and Helin, K. (2015). Loss of TET2 in hematopoietic cells leads to DNA hypermethylation of active enhancers and induction of leukemogenesis. Genes and Development, 29, 910–922. doi:10.1101/gad.260174.115.

Rumman, M., Dhawan, J., and Kassem, M. (2015). Quiescence in adult stem cells: biological significance and relevance to tissue regeneration. Stem Cells, 33, 2903–2912. doi:10.1002/stem.2056.

Shih, H.P., Seymour, P.A., Patel, N.A, Xie, R., Wang, A., Liu, P.P., Yeo, G.W., Magnuson, M.A., and Sander, M. (2015). A gene regulatory network cooperatively controlled by Pdx1 and Sox9 governs lineage allocation of foregut progenitor cells. Cell Reports, 13, 326-336. doi: 10.1016/j.celrep.2015.08.082.

Stasiulewicz, M., Gray, S.D., Mastromina, I., Silva, J.C., Bjorklund, M., Seymour, P.A., Booth, D., Thompson, C., Green, R.J., Hall, E.A., Serup, P., and Dale, J.K. (2015). A conserved role for Notch signaling in priming the cellular response to Shh through ciliary localisation of the key Shh transducer Smo. Development, 142, 2291–2303. doi:10.1242/dev.125237.

Tawana, K., Wang, J., Renneville, A., Bodor, C., Hills, R., Loveday, C., Savic, A., Van Delft, F.W., Treleaven, J., Georgiades, P., Uglow, E., Asou, N., Uike, N., Debeljak, M., Jazbec, J., Ancliff, P., Gale, R., Thomas, X., Mialou, V., Dohner, K., Bullinger, L., Mueller, B., Pabst, T., Stelljes, M., Schlegelberger, B., Wozniak, E., Iqbal, S., Okosun, J., Araf, S., Frank, A.K., Lauridsen, F.B., Porse, B., Nerlov, C., Owen, C., Dokal, I., Gribben, J., Smith, M., Preudhomme, C., Chelala, C., Cavenagh, J., and Fitzgibbon, J. (2015). Disease evolution and outcomes in familial AML with germline CEBPA mutations. Blood, 126, 1214–1223. doi:10.1182/blood-2015-05-647172.

Ueda, T., Nagamachi, A., Takubo, K., Yamasaki, N., Matsui, H., Kanai, A., Nakata, Y., Ikeda, K., Konuma, T., Oda, H., Wolff, L., Honda, Z., Wu, X., Helin, K., Iwama, A., Suda, T., Inaba, T., and Honda, H. (2015). Fbxl10 overexpression in murine hematopoietic stem cells induces leukemia involving metabolic activation and upregulation of Nsg2. Blood, 125, 3437–3446. doi:10.1182/blood-2014-03-562694.

Vandamme, J., Sidoli, S., Mariani, L., Friis, C., Christensen, J., Helin, K., Jensen, O.N., and Salcini, A.E. (2015). H3K23me2 is a new heterochromatic mark in Caenorhabditis elegans. Nucleic Acids Research, 43, 9694-9710. doi:10.1093/nar/gkv1063.

Vishnubalaji, R., Hamam, R., Abdulla, M.H., Mohammed, M.A., Kassem, M., Al-Obeed, O., Aldahmash, A., and Alajez, N.M. (2015). Genome-wide mRNA and miRNA expression profiling reveal multiple regulatory networks in colorectal cancer. Cell Death Disease, 6, e1614. doi: 10.1038/cddis.2014.556.

Wu, X., Bekker-Jensen, I.H., Christensen, J., Rasmussen, K.D., Sidoli, S., Qi, Y., Kong, Y., Wang, X, Cui, Y., Xiao, Z., Xu, G., Williams, K., Rappsilber, J., Sonderby, C.K., Winther, O., Jensen, O.N., and Helin, K. (2015). Tumor suppressor ASXL1 is essential for the activation of INK4B expression in response to oncogene activity and anti-proliferative signals. Cell Research, 25, 1205-1218. doi:10.1038/cr.2015.121.

Xu, M.J., Feng, D., Wu, H., Wang, H., Chan, Y., Kolls, J., Borregaard, N., Porse, B., Berger, T., Mak, T.W., Cowland, J.B., Kong, X., and Gao, B. (2015). Liver is the major source of elevated serum lipocalin-2 levels after bacterial infection or partial hepatectomy: A critical role for IL-6/STAT3. Hepatology, 61, 692–702. doi:10.1002/hep.27447.

2014

Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M., Chen, Y., Zhao, X., Schmidl, C., Suzuki, T., Ntini, E., Arner, E., Valen, E., Li, K., Schwarzfischer, L., Glatz, D., Raithel, J., Lilje, B., Rapin, N., Bagger, F.O., Jørgensen, M., Andersen, P.R., Bertin, N., Rackham, O., Burroughs, A.M., Baillie, J.K., Ishizu, Y., Shimizu, Y., Furuhata, E., Maeda, S., Negishi, Y., Mungall, C.J., Meehan, T., Lassmann, T., Itoh, M., Kawaji, H., Kondo, N., Kawai, J., Lennartsson, A., Daub, C.O., Heutink, P., Hume, D.A., Jensen, T.H., Suzuki, H., Hayashizaki, Y., Müller, F., Forrest, A.R.R., Carninci, P., Rehli, M., and Sandelin, A. (2014). An atlas of active enhancers across human cell types and tissues. Nature, 507, 455–461. doi:10.1038/nature12787.

Balk-Møller, E., Kim, J., Hopkinson, B., Timmermans-Wielenga, V., Petersen, O.W., and Villadsen, R. (2014). A marker of endocrine receptor-positive cells, CEACAM6, is shared by two major classes of breast cancer luminal and HER2-enriched. American Journal of Pathology, 184, 1198–1208. doi:10.1016/j.ajpath.2013.12.013.

Chen, L., Holmstrøm, K., Qiu, W., Ditzel, N., Shi, K., Hokland, L., and Kassem, M. (2014) MicroRNA-34a inhibits osteoblast differentiation and in vivo bone formation of human stromal stem cells. Stem Cells, 32, 902–912. doi:10.1002/stem.1615.

Comet, I., and Helin, K. (2014). Revolution in the Polycomb hierarchy. Nature Structural & Molecular Biology, 21, 573–575. doi:10.1038/nsmb.2848.

da Rocha, S.T., Boeva, V., Escamilla-Del-Arenal, M., Ancelin, K., Granier, C., Matias, N.R., Sanulli, S., Chow, J., Schulz, E., Picard, C., Kaneko, S., Helin, K., Reinberg, D., Stewart, A.F., Wutz, A., Margueron, R., and Heard, E. (2014). Jarid2 is implicated in the initial Xist-induced targeting of PRC2 to the inactive X chromosome. Molecular Cell, 53, 301–316. doi:10.1016/j.molcel.2014.01.002.

Dawson, J.I., Kanczler, J., Tare, R., Kassem, M., and Oreffo, R.O.C. (2014). Concise review: Bridging the gap: Bone regeneration using skeletal stem cell-based strategies—Where are we now? Stem Cells, 32, 35–44. doi:10.1002/stem.1559.

De Raedt, T., Beert, E., Pasmant, E., Luscan, A., Brems, H., Ortonne, N., Helin, K., Hornick, J.L., Mautner, V., Kehrer-Sawatzki, H., Clapp, W., Bradner, J., Vidaud, M., Upadhyaya, M., Legius, E., and Cichowski, K. (2014). PRC2 loss amplifies Ras-driven transcription and confers sensitivity to BRD4-based therapies. Nature, 514, 247–251. doi:10.1038/nature13561.

Dunworth, W.P., Cardona-Costa, J., Bozkulak, E.C., Kim, J.-D., Meadows, S., Fischer, J.C., Wang, Y., Cleaver, O., Qyang, Y., Ober, E.A., and Jin, S.-W. (2014). Bone morphogenetic protein 2 signaling negatively modulates lymphatic development in vertebrate embryos. Circulation Research, 114, 56–66. doi:10.1161/circresaha.114.302452.

Frankenberg, S.R., Frank, D., Harland, R., Johnson, A.D., Nichols, J., Niwa, H., Scholer, H.R., Tanaka, E., Wylie, C., and Brickman, J.M. (2014). The POU-er of gene nomenclature. Development, 141, 2921–2923. doi:10.1242/dev.108407.

Ge, Y., and Porse, B.T. (2014). The functional consequences of intron retention: alternative splicing coupled to NMD as a regulator of gene expression. Bioessays, 36, 236–243. doi:10.1002/bies.201300156.

Gingold, H., Tehler, D., Christoffersen, N.R., Nielsen, M.M., Asmar, F., Kooistra, S.M., Christophersen, N.S., Christensen, L.L., Borre, M., Sørensen, K.D., Andersen, L.D., Andersen, C.L., Hulleman, E., Wurdinger, T., Ralfkiær, E., Helin, K., Grønbæk, K., Omtoft, T., Waszak, S.M., Dahan, O., Pedersen, J.S., Lund, A.H., and Pilpel, Y. (2014). A dual program for translation regulation in cellular proliferation and differentiation. Cell, 158, 1281–1292. doi:10.1016/j.cell.2014.08.011.

Greggio, C., De Franceschi, F., Figueiredo-Larsen, M., and Grapin-Botton, A. (2014). In vitro pancreas organogenesis from dispersed mouse embryonic progenitors. Journal of Visual Expression, 89. doi: 10.3791/51725.

Hamilton, W.B., and Brickman, J.M. (2014). Erk signaling suppresses embryonic stem cell self-renewal to specify endoderm. Cell Reports, 9, 2056–2070. doi:10.1016/j.celrep.2014.11.032.

Hanotel, J., Bessodes, N., Thélie, A., Hedderich, M., Parain, K., Van Driessche, B., Brandão Kde O., Kricha, S., Jorgensen, M.C., Grapin-Botton, A., Serup, P., Van Lint, C., Perron, M., Pieler, T., Henningfeld, K.A., and Bellefroid, E.J. (2014). The Prdm13 histone methyltransferase encoding gene is a Ptf1a-Rbpj downstream target that suppresses glutamatergic and promotes GABAergic neuronal fate in the dorsal neural tube. Developmental Biology, 386, 340–357. doi: 10.1016/j.ydbio.2013.12.024.

Hasemann, M.S., Lauridsen, F.K., Waage, J., Jakobsen, J.S., Frank, A.K., Schuster, M.B., Rapin, N., Bagger, F.O., Hoppe, P.S., Schroeder, T., and Porse, B.T. (2014). C/EBPalpha is required for long-term self-renewal and lineage priming of hematopoietic stem cells and for the maintenance of epigenetic configurations in multipotent progenitors. PLoS Genetics, 10, e1004079. doi:10.1371/journal.pgen.1004079.

Heinemann, B., Nielsen, J.M., Hudlebusch, H.R., Lees, M.J., Larsen, D.V., Boesen, T., Labelle, M., Gerlach, L., Birk, P., and Helin, K. (2014). Inhibition of demethylases by GSK-J1/J4. Nature, 514(7520), E1–E2. doi:10.1038/nature13688.

Kesavan, G., Lieven, O., Mamidi, A., Öhlin, Z.L., Johansson, J.K., Li, W.-C., Lommel, S., Greiner, T.U., and Semb, H. (2014). Cdc42/N-WASP signaling links actin dynamics to pancreatic beta cell delamination and differentiation. Development, 141, 685–696. doi:10.1242/dev.100297 Link to Press Release.

Klein, H.U., Schafer, M., Porse, B.T., Hasemann, M.S., Ickstadt, K., and Dugas, M. (2014). Integrative analysis of histone ChIP-seq and transcription data using Bayesian mixture models. Bioinformatics, 30, 1154–1162. doi:10.1093/bioinformatics/btu003.

Kooistra, S.M., Nørgaard, L.C.R., Lees, M.J., Steinhauer, C., Johansen, J.V., and Helin, K. (2014). A screen identifies the oncogenic micro-RNA miR-378a-5p as a negative regulator of oncogene-induced senescence. PLoS One, 9(3), e91034. doi:10.1371/journal.pone.0091034.

Langlois, T., Monte-Mor, B.C.R., Lenglet, G., Droin, N., Marty, C., Couedic, J.L., Almire, C., Auger, N., Mercher, T., Delhommeau, F., Christensen, J., Helin, K., Debili, N., Fuks, F., Bernard, O.A., Solary, E., Vainchenker, W., and Isabelle Plo, I. (2014). TET2 deficiency inhibits mesoderm and hematopoietic differentiation in human embryonic stem cells. Stem Cells, 32(8), 2084–2097. doi:10.1002/stem.1718.

Laugesen, A., and Helin, K. (2014). Chromatin repressive complexes in stem cells, development, and cancer. Cell Stem Cell, 14(6), 735–751. doi:10.1016/j.stem.2014.05.006.

Li, H., Ghazanfari, R., Zacharaki, D., Ditzel, N., Isern, J., Ekblom, M., Mendez-Ferrer, S., Kassem, M., and Scheding, S. (2014). Low/Negative expression of PDGFR-alpha identifies the candidate primary mesenchymal stromal cells in adult human bone marrow. Stem Cell Reports, 3(6), 965–974. doi:10.1016/j.stemcr.2014.09.018.

Lieven, O., Dronka, J., Burmuhl, S., and Rüther, U. (2014). Differential binding of Lef1 and Msx1/2 transcription factors to Dkk1 CNEs correlates with reporter gene expression in vivo. PLoS One, 9, 23, e115442. doi:10.1371/journal.pone.0115442.

Liu, Y., Carlsson, R., Comabella, M., Wang, J., Kosicki, M., Carrion, B., Hasan, M., Wu, X., Montalban, X., Dziegiel, M.H., Sellebjerg, F., Sørensen, P.S., Helin, K., and Issazadeh-Navikas, S. (2014). FoxA1 directs the lineage and immunosuppressive properties of a novel regulatory T cell population in EAE and MS. Nature Medicine, 20(3), 272–282. doi:10.1038/nm.3485.

Markmiller, S., Cloonan, N., Lardelli, R.M., Doggett, K., Keightley, M.C., Boglev, Y., Trotter, A.J., Ng, A.Y., Wilkins, S.J., Verkade, H., Ober, E.A., Field, H.A., Grimmond, S.M., Lieschke, G.J., Stainier, D.Y., and Heath, J.K. (2014). Minor class splicing shapes the zebrafish transcriptome during development. Proceedings of the National Academy of Sciences of the United States of America, 111, 3062–3067. doi:10.1073/pnas.1305536111.

Martin, J., Morgani, S., Bonderup, K., Abelechian, S., Brakebusch, C., and Brickman, J. (2014). 100 % Coat-coloured chimaera generation by single es cell injection. Transgenic Research, 23(5), 848–848.

Morgani, S.M., and Brickman, J.M. (2014). The molecular underpinnings of totipotency. Philosophical Transactions of the Royal Society London B Biological Science, 369, 20130549. doi:10.1098/rstb.2013.0549.

Norrie, I.C., Ohlsson, E., Nielsen, O., Hasemann, M.S., and Porse, B.T. (2014). C/EBPalpha is dispensable for the ontogeny of PD-1+ CD4+ memory T cells but restricts their expansion in an age-dependent manner. PLoS One, 9, e84728. doi:10.1371/journal.pone.0084728.

Ohlsson, E., Hasemann, M.S., Willer, A., Lauridsen, F.K., Rapin, N., Jendholm, J., and Porse, B.T. (2014). Initiation of MLL-rearranged AML is dependent on C/EBPalpha. The Journal of Experimental Medicine, 211, 5–13. doi:10.1084/jem.20130932.

Piunti, A., Rossi, A., Cerutti, A., Albert, M., Jammula, S., Scelfo, A., Cedrone, L., Fragola, G., Olsson, L., Koseki, H., Testa, G., Casola, S., Helin, K., di Fagagna, F.D., and Pasini, D. (2014). Polycomb proteins control proliferation and transformation independently of cell cycle checkpoints by regulating DNA replication. Nature Communications, 5, 3649. doi:10.1038/ncomms4649.

Rapin, N., and Porse, B.T. (2014). Oncogenic fusion proteins expressed in immature hematopoietic cells fail to recapitulate the transcriptional changes observed in human AML. Oncogenesis, 3, e106. doi:10.1038/oncsis.2014.22.

Rapin, N., Bagger, F.O., Jendholm, J., Mora-Jensen, H., Krogh, A., Kohlmann, A., Thiede, C., Borregaard, N., Bullinger, L., Winther, O., Theilgaard-Monch, K., and Porse, B.T. (2014). Comparing cancer vs normal gene expression profiles identifies new disease entities and common transcriptional programs in AML patients. Blood, 123, 894–904. doi:10.1182/blood-2013-02-485771.

Riising, E.M., Comet, I., Leblanc, B., Wu, X., Johansen, J.V., and Helin, K. (2014). Gene silencing triggers Polycomb repressive complex 2 recruitment to CpG islands genome wide. Molecular Cell, 55, 347–360. doi:10.1016/j.molcel.2014.06.005.

Rishi, L., Hannon, M., Salome, M., Hasemann, M., Frank, A.K., Campos, J., Timoney, J., O'Connor, C., Cahill, M.R., Porse, B., and Keeshan, K. (2014). Regulation of Trib2 by an E2F1-C/EBPalpha feedback loop in AML cell proliferation. Blood, 123, 2389–2400. doi:10.1182/blood-2013-07-511683.

Rué, P., Kim, Y.H., List Larsen, H., Grapin-Botton, A., and Martinez-Arias, A. (2014). A framework for the analysis of symmetric and asymmetric divisions in developmental processes. biorXiv/2014/010835. doi:10.1101/010835 (nonreviewed).

Seymour, P.A. (2014). Sox9: a master regulator of the pancreatic program. The Review of Diabetic Studies, 11, 51–83. doi:10.1900/rds.2014.11.51.

Sroczynska, P., Cruickshank, V.A., Bukowski, J.P., Miyagi, S., Bagger, F.O., Walfridsson, J., Schuster, M.B., Porse, B., and Helin, K. (2014). shRNA screening identifies JMJD1C as being required for leukemia maintenance. Blood, 123, 1870–1882. doi:10.1182/blood-2013-08-522094.

Terndrup, M., Agger, K., Laugesen, A., Johansen, J.V., Cloos, P.A.C., Christensen, J., and Helin, K. (2014). The demethylase JMJD2C localizes to H3K4me3-positive transcription start sites and is dispensable for embryonic development. Molecular and Cellular Biology, 34, 1031–1045. doi:10.1128/mcb.00864-13.

Twine, N.A., Chen, L., Pang, C.N., Wilkins, M.R., and Kassem, M. (2014). Identification of differentiation-stage specific markers that define the ex vivo osteoblastic phenotype. Bone, 67, 23–32. doi:10.1016/j.bone.2014.06.027.

van Impel, A., Zhao, Z., Hermkens, D.M., Roukens, M.G., Fischer, J.C., Peterson-Maduro, J., Duckers, H., Ober, E.A., Ingham, P.W., and Schulte-Merker, S. (2014). Divergence of zebrafish and mouse lymphatic cell fate specification pathways. Development, 141, 1228–U1101. doi:10.1242/dev.105031.

Vitting-Seerup, K., Porse, B.T., Sandelin, A., and Waage, J. (2014). spliceR: An R package for classification of alternative splicing and prediction of coding potential from RNA-seq data. BMC Bioinformatics, 15, 81. doi:10.1186/1471-2105-15-81.

Weimin, Q., and Kassem, M. (2014). miR-141-3p inhibits human stromal (mesenchymal) stem cell proliferation and differentiation. Biochimica Et Biophysica Acta-Molecular Cell Research, 1843, 2114–2121. doi:10.1016/j.bbamcr.2014.06.004.

Willer, A., Jakobsen, J.S., Ohlsson, E., Rapin, N., Waage, J., Billing, M., Bullinger, L., Karlsson, S., and Porse, B.T. (2014). TGIF1 is a negative regulator of MLL-rearranged acute myeloid leukemia. Leukemia, 29, 1018–1031. doi:10.1038/leu.2014.307.

Willet, S.G., Hale, M.A., Grapin-Botton, A., Magnuson, M.A., MacDonald, R.J., and Wright, C.V. (2014). Dominant and context-specific control of endodermal organ allocation by Ptf1a. Development, 141, 4385–4394. doi: 10.1242/dev.114165.

Williams, K., Christensen, J., Rappsilber, J., Nielsen, A.L., Johansen, J.V., and Helin, K. (2014). The Histone Lysine Demethylase JMJD3/KDM6B Is Recruited to p53 Bound Promoters and Enhancer Elements in a p53 Dependent Manner. PLoS One, 9(5), e96545. doi:10.1371/journal.pone.0096545.

Wong, Y., Micklem, C.N., Taguchi, M., Itonaga, H., Sawayama, Y., Imanishi, D., Nishikawa, S., Miyazaki, Y., and Jakt, L.M. (2014). Longitudinal analysis of DNA methylation in CD34+hematopoietic progenitors in myelodysplastic syndrome. Stem Cells Translational Medicine, 3(10), 1188–1198. doi:10.5966/sctm.2014-0035.

Zaher, W., Harkness, L., Jafari, A., and Kassem, M. (2014). An update of human mesenchymal stem cell biology and their clinical uses. Archives of Toxicology, 88(5), 1069–1082. doi:10.1007/s00204-014-1232-8.

2013

Albert, M., Schmitz, S.U., Kooistra, S.M., Malatesta, M., Torres, C.M., Rekling, J.C., Johansen, J.V., Abarrategui, I., and Helin, K. (2013). The Histone Demethylase Jarid1b Ensures Faithful Mouse Development by Protecting Developmental Genes from Aberrant H3K4me3. Plos Genetics, 9, e1003461. doi:10.1371/journal.pgen.1003461.

Arteaga, M.F., Mikesch, J., Qiu, J., Christensen, J., Helin, K., Kogan, S.C., Dong, S., and So, C.W.E., (2013). The histone demethylase PHF8 governs retinoic acid response in acute promyelocytic leukemia. Cancer Cell, 23, 376–389. doi:10.1016/j.ccr.2013.02.014.

Asmar, F.l., Punj, V., Christensen, J., Pedersen, M.T., Pedersen, A., Nielsen, A.B., Hother, C., Ralfkiær, U., Brown, P., Ralfkiær, E., Helin, K., and Grønbæk, K. (2013). Genome-wide profiling identifies a DNA methylation signature that associates with TET2 mutations in diffuse large B-cell lymphoma. Haematologica, 98, 1912–1920. doi:10.3324/haematol.2013.088740.

Bagger, F.O., Rapin, N., Theilgaard-Mönch, K., Kaczkowski, B., Thoren, L.A., Jendholm, J., Winther, O., and Porse, B.T. (2013). HemaExplorer: a database of mRNA expression profiles in normal and malignant haematopoiesis. Nucleic Acids Research, 41, D1034–1039. doi:10.1093/nar/gks1021.

Ballabeni, A., Zamponi, R., Moore, J.K., Helin, K., and Kirschner, M.W. (2013). Geminin deploys multiple mechanisms to regulate Cdt1 before cell division thus ensuring the proper execution of DNA replication. Proceedings of the National Academy of Sciences of the United States of America, 110, E2848–E2853. doi:10.1073/pnas.1310677110.

Bender, S., Tang, Y., Lindroth, A.M., Hovestadt, V., Jones, D.T., Kool, M., Zapatka, M., Northcott, P.A., Sturm, D., Wang, W., Radlwimmer, B., Højfeldt, J.W., Truffaux, N., Castel, D., Schubert, S., Ryzhova, M., Seker-Cin, H., Gronych, J., Johann, P.D., Stark, S., Meyer, J., Milde, T., Schuhmann, M., Ebinger, M., Monoranu, C.M., Ponnuswami, A., Chen, S., Jones, C., Witt, O., Collins, V.P., von Deimling, A., Jabado, N., Puget, S., Grill, J., Helin, K., Korshunov, A., Lichter, P., Monje, M., Plass, C., Cho, Y.J., Pfister, S.M. (2013). Reduced H3K27me3 and DNA Hypomethylation Are Major Drivers of Gene Expression in K27M Mutant Pediatric High-Grade Gliomas. Cancer Cell, 24, 660–672. doi:10.1016/j.ccr.2013.10.006.

Colak, D., Ji, S.J., Porse, B.T., and Jaffrey, S.R. (2013). Regulation of axon guidance by compartmentalized nonsense-mediated mRNA decay. Cell, 153, 1252–1265. doi:10.1016/j.cell.2013.04.056.

de la Rica, L., Rodriguez-Ubreva, J., Garcia, M., Islam, A.B., Urquiza, J.M., Hernando, H., Christensen, J., Helin, K., Gomez-Vaquero, C., and Ballestar, E. (2013). PU.1 target genes undergo Tet2-coupled demethylation and DNMT3b-mediated methylation in monocyte-to-osteoclast differentiation. Genome Biology 14, R99. doi:10.1186/gb-2013-14-9-r99.

Di Croce, L., and Helin, K. (2013). Transcriptional regulation by Polycomb group proteins. Nature Structural and Molecular Biology, 20, 1147–1155. doi:10.1038/nsmb.2669.

Egan, C.M., Nyman, U., Skotte, J., Streubel, G., Turner, S., O'Connell, D.J., Rraklli, V., Dolan, M.J., Chadderton, N., Hansen, K., Farrar, G.J., Helin, K., Holmberg, J., and Bracken, A.P. (2013). CHD5 is required for neurogenesis and has a dual role in facilitating gene expression and polycomb gene repression. Developmental Cell, 26, 223–236. doi:10.1016/j.devcel.2013.07.008.

Grassilli, E., Narloch, R., Federzoni, E., Ianzano, L., Pisano, F., Giovannoni, R., Romano, G., Masiero, L., Leone, B.E., Bonin, S., Donada, M., Stanta, G., Helin, K., and Lavitrano, M. (2013). Inhibition of GSK3B bypass drug resistance of p53-null colon carcinomas by enabling necroptosis in response to chemotherapy. Clinical Cancer Research, 19, 3820–3831. doi:10.1158/1078-0432.ccr-12-3289.

Greggio, C., De Franceschi, F., Figueiredo-Larsen, M., Gobaa, S., Ranga, A., Semb, H., Lutolf, M. and Grapin-Botton, A. (2013). Artificial three-dimensional niches deconstruct pancreas development in vitro. Development, 140, 4452–4462. doi:10.1242/dev.096628. Link to Press Release.

Hattori, N., Niwa, T., Kimura, K., Helin, K., and Ushijima, T. (2013). Visualization of multivalent histone modification in a single cell reveals highly concerted epigenetic changes on differentiation of embryonic stem cells. Nucleic Acids Research, 41, 7231–7239. doi:10.1093/nar/gkt528.

Helin, K., and Dhanak, D., (2013). Chromatin proteins and modifications as drug targets. Nature, 502, 480–488. doi:10.1038/nature12751.

Hernebring, M., Fredriksson, A., Liljevald, M., Cvijovic, M., Norrman, K., Wiseman, J., Semb, H., and Nyström, T. (2013). Removal of damaged proteins during ES cell fate specification requires the proteasome activator PA28. Scientific Reports, 3, 1381. doi:10.1038/srep01381.

Hojfeldt, J. W., Agger, K., and Helin, K. (2013). Histone lysine demethylases as targets for anticancer therapy. Nature Reviews Drug Discovery, 12, 917-930. doi:10.1038/nrd4154.

Jakobsen, J.S., Waage, J., Rapin, N., Bisgaard, H.C., Larsen, F.S., and Porse, B.T. (2013). Temporal mapping of CEBPA and CEBPB binding during liver regeneration reveals dynamic occupancy and specific regulatory codes for homeostatic and cell cycle gene batteries. Genome Research, 23, 592–603. doi:10.1101/gr.146399.112.

Jung, H.R., Sidoli, S., Haldbo, S., Sprenger, R.R., Schwammle, V., Pasini, D., Helin, K., and Jensen, O.N. (2013). Precision Mapping of Coexisting Modifications in Histone H3 Tails from Embryonic Stem Cells by ETD-MS/MS. Analytical Chemistry, 85, 8232–8239. doi:10.1021/ac401299w.

Kartikasari, A.E., Zhou, J.X., Kanji, M.S., Chan, D.N., Sinha, A., Grapin-Botton, A., Magnuson, M.A., Lowry, W.E., and Bhushan, A. (2013). The histone demethylase Jmjd3 sequentially associates with the transcription factors Tbx3 and Eomes to drive endoderm differentiation. The EMBO Journal, 32, 1393–1408. doi:10.1038/emboj.2013.78.

Katsumoto, K., and Kume, S. (2013). The role of CXCL12-CXCR4 signaling pathway in pancreatic development. Theranostics, 3, 11–17. doi:10.7150/thno.4806.

Klauke, K., Radulovic, V., Broekhuis, M., Weersing, E., Zwart, E., Olthof, S., Ritsema, M., Bruggeman, S., Wu, X., Helin, K., Bystrykh, L., and Haan, G.D. (2013). Polycomb Cbx family members mediate the balance between haematopoietic stem cell self-renewal and differentiation. Nature Cell Biology, 15, 353–362. doi:10.1038/ncb2701.

Leucci, E., Patella, F., Waage, J., Holmstrom, K., Lindow, M., Porse, B., Kauppinen, S., and Lund, A.H. (2013). microRNA-9 targets the long non-coding RNA MALAT1 for degradation in the nucleus. Scientific Reports, 3, 2535. doi:10.1038/srep02535.

Livigni, A., and Brickman, J.M. (2013). Oct4: the final frontier, differentiation defining pluripotency. Developmental Cell, 25, 547–548. doi:10.1016/j.devcel.2013.06.002.

Livigni, A., Peradziryi, H., Sharov, A.A., Chia, G., Hammachi, F., Migueles, R.P., Sukparangsi, W., Pernagallo, S., Bradley, M., Nichols, J., Ko, M.S.H., and Brickman, J.M. (2013). A conserved Oct4/POUV-dependent network links adhesion and migration to progenitor maintenance. Current Biology, 23, 2233–2244. doi:10.1016/j.cub.2013.09.048. Link to Press Release.

Malatesta, M., Steinhauer, C., Mohammad, F., Pandey, D.P., Squatrito, M., and Helin, K. (2013). Histone acetyltransferase PCAF is required for Hedgehog-Gli-dependent transcription and cancer cell proliferation. Cancer Research, 73, 6323–6333. doi:10.1158/0008-5472.can-12-4660.

Morgani, S.M., and Brickman, J.M. (2013). Survival of the fattest. Elife, 2, e01760. doi:10.7554/eLife.01760.

Morgani, S.M., Canham, M.A., Nichols, J., Sharov, A.A., Migueles, R.P., Ko, M.S., and Brickman, J.M. (2013). Totipotent embryonic stem cells arise in ground-state culture conditions. Cell Reports, 3, 1945–1957. doi:10.1016/j.celrep.2013.04.034. Link to press release.

Musacchio, A., and Helin, K. (2013). Cell cycle, differentiation and disease. Current Opinion in Cell Biology, 25, 673–675. doi:10.1016/j.ceb.2013.09.003.

Norrman, K., Strömbeck, A., Semb, H., and Ståhlberg, A. (2013). Distinct gene expression signatures in human embryonic stem cells differentiated towards definitive endoderm at single-cell level. Methods, 59, 59–70. doi:10.1016/j.ymeth.2012.03.030.

Qu, X., Afelik, S., Jensen, J.N., Bukys, M.A., Kobberup, S., Schmerr, M., Xiao, F., Nyeng, P., Albertoni, M.V., Grapin-Botton, A., and Jensen, J. (2013). Notch-mediated post-translational control of Ngn3 protein stability regulates pancreatic patterning and cell fate commitment. Developmental Biology, 376, 1–12. doi:10.1016/j.ydbio.2013.01.021.

Schuster, M.B., Frank, A.K., Bagger, F.O., Rapin, N., Vikesaa, J., and Porse, B.T. (2013). Lack of the p42 form of C/EBPalpha leads to spontaneous immortalization and lineage infidelity of committed myeloid progenitors. Experimental Hematology, 41, 882–893.e16. doi:10.1016/j.exphem.2013.06.003.

Seymour, P.A., and Serup, P. (2013). Bulking up on beta cells. New England Journal of Medicine, 369, 777–779. doi:10.1056/NEJMcibr1307038.

Thoren, L.A., Fog, C.K., Jensen, K.T., Buza-Vidas, N., Come, C., Lund, A.H., and Porse, B.T. (2013). PRDM11 is dispensable for the maintenance and function of hematopoietic stem and progenitor cells. Stem Cell Research, 11, 1129–1136. doi:10.1016/j.scr.2013.07.009.

Torres, C.M., Laugesen, A., and Helin, K. (2013). Utx is required for proper induction of ectoderm and mesoderm during differentiation of embryonic stem cells. PLoS One, 8, e60020. doi:10.1371/journal.pone.0060020.

Vella, P., Scelfo, A., Jammula, S., Chiacchiera, F., Williams, K., Cuomo, A., Roberto, A., Christensen, J., Bonaldi, T., Helin, K., and Pasini, D. (2013). Tet proteins connect the O-linked N-acetylglucosamine transferase Ogt to chromatin in embryonic stem cells. Molecular Cell, 49, 645–656. doi:10.1016/j.molcel.2012.12.019.

Villegas, S.N., Rothova, M., Barrios-Llerena, M.E., Pulina, M., Hadjantonakis, A.K., Le Bihan, T., Astrof, S., and Brickman, J.M. (2013). PI3K/Akt1 signalling specifies foregut precursors by generating regionalized extra-cellular matrix. eLife, 2, e00806. doi:10.7554/eLife.00806.

Wu, X., Johansen, J.V., and Helin, K. (2013). Fbxl10/kdm2b recruits Polycomb repressive complex 1 to CpG islands and regulates H2A ubiquitylation. Molecular Cell, 49, 1134–1146. doi: 10.1016/j.molcel.2013.01.016.

2012

Bagger, F.O., Rapin, N., Theilgaard-Monch, K., Kaczkowski, B., Jendholm, J., Winther, O., and Porse, B. (2012). HemaExplorer: A Web server for easy and fast visualization of gene expression in normal and malignant hematopoiesis. Blood, 119, 6394–6395. doi:10.1182/blood-2012-05-427310

Choi, E., Kraus, M.R.C., Lemaire L.A., Yoshimoto, M., Vemula, S, Potter, L.A., Manduchi, E., Stoeckert, C.J., Grapin-Botton, A., and Magnuson, M.A. (2012). Dual lineage-specific expression of Sox17 during mouse embryogenesis. Stem Cells, 30, 2297–2308. doi:10.1002/stem.1192.

Cortijo, C., Gouzi, M., Tissir, F., and Grapin-Botton, A. (2012). Planar cell polarity controls pancreatic beta cell differentiation and glucose homeostasis. Cell Reports, 2, 1593–1606. doi:10.1016/j.celrep.2012.10.016 Link to press release

Garbe, J.C.,Pepin, F., Pelissier, F.A., Sputova, K., Fridriksdottir, A.J., Guo, D.E., Villadsen, R., Park, M., Petersen, O.W., Borowsky, A.D., Stampfer, M.R., and LaBarge, M.A. (2012). Accumulation of multipotent progenitors with a basal differentiation bias during aging of human mammary epithelia. Cancer Research, 72, 3687–370. doi:10.1158/0008-5472.can-12-0157.

Hammachi, F., Morrison, G.M., Sharov, A.A., Livigni, A., Narayan, S., Papapetrou, E.P., O'Malley, J., Kaji, K., Ko, M.S., Ptashne, M., and Brickman, J.M. (2012). Transcriptional activation by Oct4 is sufficient for the maintenance and induction of pluripotency. Cell Reports, 1, 99–109. doi:10.1016/j.celrep.2011.12.002. Link to press release.

Hasemann, M.S., Schuster, M.B., Frank, A.K., Theilgaard-Monch, K., Pedersen, T.A., Nerlov, C., and Porse, B.T. (2012). Phosphorylation of serine 248 of C/EBPalpha is dispensable for myelopoiesis but its disruption leads to a low penetrant myeloid disorder with long latency. PLoS One, 7, e38841. doi:10.1371/journal.pone.0038841.

Horn, S., Kobberup, S., Jorgensen, M.C., Kalisz, M., Klein, T., Kageyama, R., Gegg, M., Lickert, H., Lindner, J., Magnuson, M.A., Kong, Y.Y., Serup, P., Ahnfelt-Ronne, J., and Jensen, J.N. (2012). Mind bomb 1 is required for pancreatic beta-cell formation. Proceedings of the National Academy of Sciences of the United States of America, 109, 7356–7361. doi:10.1073/pnas.1203605109. Link to press release.

Johannesson, M., Semb, H., Serup, P., and Hansson, M. (2012). A functional assay for putative mouse and human definitive endoderm using chick whole-embryo cultures. Stem Cell Research and Therapy, 2,128. doi:10.4172/2157-7633.1000128.

Kim, J., Villadsen, R., Sørlie, T., Fogh, L., Grønlund, S.Z., Fridriksdottir, A.J., Kuhn, I., Rank, F., Wielenga, V.T., Solvang, H., Edwards, P.A.W., Børresen-Dale, A., Rønnov-Jessen, L., Bissell, M.J., and Petersen, O.W. (2012). Tumor initiating but differentiated luminal-like breast cancer cells are highly invasive in the absence of basal-like activity. Proceedings of the National Academy of Sciences of the United States of America, 109, 6124–6129. doi:10.1073/pnas.1203203109.

Kraus, M.R. and Grapin-Botton, A. (2012). Patterning and shaping the endoderm in vivo and in culture. Current Opinions in Genetics and Development, 22, 347–353. doi:10.1016/j.gde.2012.05.002.

Leth-Larsen, R., Terp, M.G., Christensen, A.G., Elias, D., Kuhlwein, T., Jensen, O.N., Petersen, O.W., and Ditzel, H.J. (2012). Functional heterogeneity within the CD44 high human breast cancer stem cell-like compartment reveals a gene signature predictive of distant metastasis. Molecular Medicine 18, 1109–1121. doi:10.2119/molmed.2012.00091.

Serup, P. (2012). Signaling pathways regulating murine pancreatic development. Seminars in Cell and Developmental Biology, 23, 663–672. doi:10.1016/j.semcdb.2012.06.004.

Serup, P., Gustavsen, C., Klein, T., Potter, L.A., Lin, R., Mullapudi, N., Wandzioch, E., Hines, A., Davis, A., Bruun, C., Engberg, N., Petersen, D.R., Peterslund, J.M., Macdonald, R.J., Grapin-Botton, A., Magnuson, M.A., and Zaret, K.S. (2012). Partial promoter substitutions generating transcriptional sentinels of diverse signaling pathways in embryonic stem cells and mice. Disease Models and Mechanisms, 5, 956–966. doi:10.1242/dmm.009696.

Shih, H.P., Kopp, J.L., Sandhu, M., Dubois, C.L., Seymour, P.A., Grapin-Botton, A., and Sander, M. (2012). A Notch-dependent molecular circuitry initiates pancreatic endocrine and ductal cell differentiation. Development 139, 2488–2499. doi:10.1242/dev.078634.

Thompson, N., Gésina, E., Scheinert, P., Bucher, P. and Grapin-Botton, A. (2012). RNA profiling and chromatin immunoprecipitation-sequencing reveal that PTF1a stabilizes pancreas progenitor identity via the control of MNX1/HLXB9 and a network of other transcription factors. Molecular Cell Biology 32, 118–1199. doi:10.1128/MCB.06318-11.

Vaapil, M., Helczynska, K., Villadsen, R., Petersen, O.W., Johansson, E., Beckman, S., Larsson, C., Pahlman, S., and Jogi, A. (2012). Hypoxic conditions induce a cancer-like phenotype in human breast epithelial cells. Plos One, 7, e46543. doi:10.1371/journal.pone.0046543.

2011

Fridriksdottir, A.J.R., Petersen, O.W., and Ronnov-Jessen, L. (2011). Mammary gland stem cells: Current status and future challenges. International Journal of Developmental Biology, 55, 719–729. doi:10.1387/ijdb.113373af.

Sigurdsson, V., Hilmarsdottir, B., Sigmundsdottir, H., Fridriksdottir, A.J.R., Ringner, M., Villadsen, R., Borg, A., Agnarsson, B.A., Petersen, O.W., Magnusson, M.K., and Gudjonsson, T. (2011). Endothelial induced EMT in breast epithelial cells with stem cell properties. PLoS One, 6(9), e23833. doi:10.1371/journal.pone.0023833.