Publications by Year

2020

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. 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. 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 Cells. 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. p53 is associated with high‐risk and pinpoints TP53 missense mutations in mantle cell lymphoma. British Journal of Haematology. doi: 10.1111/bjh.17023

Manda-Handzlik, A., Bystrzycka, W., Cieloch, A., Glodkowska-Mrowka, E., Jankowska-Steifer, E., Heropolitanska-Pliszka, E., Skrobot, A., Muchowicz, A., 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.

Sever, D., and Grapin-Botton, A. (2020). Regeneration of the pancreas: proliferation and cellular conversion of surviving cells. Current Opinion in Genetics & Development, 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. Leukemia, 1-5. 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. 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. 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. Leukemia, 1-11. 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. 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 Interactions. Trends in Endocrinology & Metabolism. doi: 10.1016/j.tem.2020.02.004

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

Teves, J. M., & Won, K. J. (2020). Mapping Cellular Coordinates through Advances in Spatial Transcriptomics Technology. Molecules and Cells. 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. 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 gradient. Nature Biotechnology, 1-9. 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, 1-11. doi: 10.1038/s41467-020-16225-5

Knudsen, T. E., & 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., & 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 metabolism, 30, 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., & Andersen, D. S. (2020). The Drosophila gut: A gatekeeper and coordinator of organism fitness and physiology. Wiley Interdisciplinary Reviews: Developmental Biology. doi: 10.1002/wdev.378

Caviglia, S., Flores-Benitez, D., Lattner, J., Luschnig, S., & 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 Research. 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. 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. 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.*, 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.
* joint corresponding authors

Akimov, Y., Bulanova, D., Timonen, S., Wennerberg, K., & 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., & 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 studyLeukemia, 1-13. 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. doi: 10.1016/j.bbmt.2020.02.010

Juul Belling, H., Hofmeister, W., & Andersen, D. C. (2020). A Systematic Exposition of Methods used for Quantification of Heart Regeneration after Apex Resection in ZebrafishCells, 9. 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. 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. doi: 10.1016/j.devcel.2020.01.015

Korshunova, I., Rhein, S., García-González, D., Stölting, I., Pfisterer, U., Barta, A., Dmytriyeva, O., Kirkeby, A., Schwaninger, M., and Khodosevich, K. (2020). Genetic modification increases the survival and the neuroregenerative properties of transplanted neural stem cellsJCI insight. doi: 10.1172/jci.insight.126268

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, doi: 10.1016/j.bone.2020.115252

Gupta, A., Gautam, P., Wennerberg, K., & 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

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

Lavitrano, M., Ianzano, L., Bonomo, S., Cialdella, A., Cerrito, M.G., Pisano, F., Missaglia C., Giovannoni, R., Romano, G., McLean, C.M., Voest, E.E., D'Amato, F., Noli, B., Ferri, G.L., Agostini, M., Pucciarelli, S., Helin, K., Leone, B.E., Canzonieri, V., and Grassilli, E. (2019). BTK inhibitors synergize with 5-FU to treat drug-resistant TP53-null colon cancers. Journal of Pathology, doi: 10.1002/path.5347

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

Majumder, M.M., Leppä, A.M., Hellesøy, M., Dowling, P., Malyutina, A., Kopperud, R., Bazou, D., Andersson, E., Parsons, A., Tang, J., Kallioniemi, O., Mustjoki, S., O'Gorman, P., Wennerberg, K., Porkka, K., Gjertsen, B.T., and Heckman, C.A. (2019). Multi-parametric single cell evaluation defines distinct drug responses in healthy hematological cells that are retained in corresponding malignant cell types. Haematologica, haematol.2019.217414. doi: 10.3324/haematol.2019.217414

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*, 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., 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