Publications by Year


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


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/

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

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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


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/

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


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

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