2
2023
Murphy D, Salataj E, Campigli Di Giammartino D, Rodriguez-Hernaez J, Kloetgen A, Garg V, Char E, M. Uyehara C, Ee L, Lee U, Stadtfeld S, Hadjantonakis AK, Tsirigos A, Polyzos A, Apostolou E. Systematic mapping and modeling of 3D enhancer-promoter interactions in early mouse embryonic lineages reveal regulatory principles that determine the levels and cell-type specificity of gene expression. Nat Struct Mol Biol. 2023 Dec 5. doi: 10.1038/s41594-023-01130-4. Online ahead of print.PMID: 38053013
2022
Garipler G, Lu C, Morrissey A, Lopez-Zepeda LS, Pei Y, Vidal SE, Zen Petisco Fiore AP, Aydin B, Stadtfeld M, Ohler U, Mahony S, Sanjana NE, Mazzoni EO. The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by repressing pro-differentiation genes. Cell Rep. 2022 Mar 15;38(11):110524.
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2021
Aronson BE, Scourzic L, Shah V, Swanzey E, Kloetgen A, Polyzos A, Sinha A, Azziz A, Caspi I, Li J, Pelham-Webb B, Glenn RA, Vierbuchen T, Wichterle H, Tsirigos A, Dawlaty MM, Stadtfeld M*, Apostolou E*. A bipartite element with allele-specific functions safeguards DNA methylation imprints at the Dlk1-Dio3 locus. Dev Cell. 2021 Nov 22;56(22):3052-3065.
* corresponding author
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Barton LJ, Sanny J, Dawson EP, Nouzova M, Noriega FG, Stadtfeld M, Lehmann R. Juvenile hormones direct primordial germ cell migration to the embryonic gonad. bioRxiv 2021.09.30.462471; doi: https://doi.org/10.1101/2021.09.30.462471
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2020
Vidal SE, Polyzos A, Chatterjee K, Ee LS, Swanzey E, Morales-Valencia J, Wang H, Parikh CN, Amlani B, Tu S, Gong Y, Snetkova V, Skok JA, Tsirigos A, Kim S, Apostolou E, Stadtfeld M. Context-Dependent Requirement of Euchromatic Histone Methyltransferase Activity during Reprogramming to Pluripotency. Stem Cell Reports. 2020 Sep 7:S2213-6711(20)30342-8.
Swanzey E, McNamara TF, Apostolou E, Tahiliani M and Stadtfeld M. A susceptibility locus on chromosome 13 profoundly impacts the stability of genomic imprinting in mouse pluripotent stem cells. Cell Rep. 2020 Mar 17;30(11):3597-3604.
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2019
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Lhoumaud P, Sethia G, Izzo F, Sakellaropoulos T, Snetkova V, Vidal S, Badri S, Cornwell M, Di Giammartino DC, Kim KT, Apostolou E, Stadtfeld M, Landau DA, Skok J. EpiMethylTag: simultaneous detection of ATAC-seq or ChIP-seq signals with DNA methylation. Genome Biol. 2019 Nov 21;20(1):248.
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Di Giammartino DC, Kloetgen A, Polyzos A, Liu Y, Kim D, Murphy D, Abuhashem A, Cavaliere P, Aronson B, Shah V, Dephoure N, Stadtfeld M, Tsirigos A, Apostolou E. KLF4 is involved in the organization and regulation of pluripotency-associated three-dimensional enhancer networks. Nat Cell Biol. 2019 Oct;21(10):1179-1190.
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2018
Amlani B, Liu Y, Chen T, Ee LS, Lopez P, Heguy A, Apostolou E, Kim SY, Stadtfeld M. Nascent Induced Pluripotent Stem Cells Efficiently Generate Entirely iPSC-Derived Mice while Expressing Differentiation-Associated Genes. Cell Reports Jan 23;22(4):876-884
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2017
Donato V, Bonora M, Simoneschi D, Sartini D, Kudo Y, Saraf A, Florens L, Washburn MP, Stadtfeld M, Pinton P, Pagano M. The TDH-GCN5L1-Fbxo15-KBP axis limits mitochondrial biogenesis in mouse embryonic stem cells. Nat Cell Biol. 2017 Mar 20.
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2016
Liu LL, Brumbaugh J, Bar-Nur O, Smith Z, Stadtfeld M, Meissner A, Hochedlinger K, Michor F. Probabilistic Modeling of Reprogramming to Induced Pluripotent Stem Cells. Cell Rep. 2016 Dec 20;17(12):3395-3406.
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Swanzey E, Stadtfeld M. A reporter model to visualize imprinting stability at the Dlk1 locus during mouse development and in pluripotent cells. Development 2016 Nov 15;143(22):4161-4166
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Strikoudis A, Lazaris C, Trimarchi T, Galvao Neto AL, Yang Y, Ntziachristos P, Rothbart S, Buckley S, Dolgalev I, Stadtfeld M, Strahl BD, Dynlacht BD, Tsirigos A, Aifantis I. Regulation of transcriptional elongation in pluripotency and cell differentiation by the PHD-finger protein Phf5a. Nat Cell Biol. 2016 Oct 17.
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Tu S, Narendra V, Yamaji M, Vidal SE, Rojas LA, Wang X, Kim SY, Garcia BA, Tuschl T, Stadtfeld M, Reinberg D. Co-repressor CBFA2T2 regulates pluripotency and germline development.Nature. 2016 Jun 8;534(7607):387-90.
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2015
Cheloufi S, Elling U, Hopfgartner B, Jung YL, Murn J, Ninova M, Hubmann M, Badeaux AI, Euong Ang C, Tenen D, Wesche DJ, Abazova N, Hogue M, Tasdemir N, Brumbaugh J, Rathert P, Jude J, Ferrari F, Blanco A, Fellner M, Wenzel D, Zinner M, Vidal SE, Bell O, Stadtfeld M, Chang HY, Almouzni G, Lowe SW, Rinn J, Wernig M, Aravin A, Shi Y, Park PJ, Penninger JM, Zuber J, Hochedlinger K. The histone chaperone CAF-1 safeguards somatic cell identity. Nature. 2015 Dec 10;528(7581):218-24.
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2014
Vidal SE, Amlani B, Chen T, Tsirigos A, Stadtfeld M. Combinatorial modulation of signaling pathways reveals cell-type-specific requirements for highly efficient and synchronous iPSC reprogramming. Stem Cell Reports. Oct 14;3(4):574-84
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Wu T, Liu Y, Wen D, Tseng Z, Tahmasian M, Zhong M, Rafii S, Stadtfeld M, Hochedlinger K, Xiao A. Histone variant H2A.X deposition pattern serves as a functional epigenetic mark for distinguishing the developmental potentials of iPSCs. Cell Stem Cell. 2014 Sep 4;15(3):281-294.
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2013
Apostolou E, Ferrari F, Walsh RM, Bar-Nur O, Stadtfeld M, Cheloufi S, Stuart HT, Polo JM, Ohsumi TK, Borowsky ML, Kharchenko PV, Park PJ, Hochedlinger K. Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogramming. Cell Stem Cell. 2013 Jun 6;12(6):699-712
González F, Georgieva D, Vanoli F, Shi ZD, Stadtfeld M, Ludwig T, Jasin M, Huangfu D. Homologous recombination DNA repair genes play a critical role in reprogramming to a pluripotent state. Cell Reports. 2013 Mar 28;3(3):651-60
2012
Polo JM, Anderssen E, Walsh RM, Schwarz BA, Nefzger CM, Lim SM, Borkent M, Apostolou E, Alaei S, Cloutier J, Bar-Nur O, Cheloufi S, Stadtfeld M, Figueroa ME, Robinton D, Natesan S, Melnick A, Zhu J, Ramaswamy S, Hochedlinger K. A molecular roadmap of reprogramming somatic cells into iPS cells. Cell. 2012 Dec 21;151(7):1617-32
Buckley SM, Aranda-Orgilles B, Strikoudis A, Apostolou E, Loizou E, Moran-Crusio K, Farnsworth CL, Koller AA, Dasgupta R, Silva JC, Stadtfeld M, Hochedlinger K, Chen EI, Aifantis I. Regulation of pluripotency and cellular reprogramming by the ubiquitin-proteasome system. Cell Stem Cell. 2012 Dec 7;11(6):783-98
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Stadtfeld M, Apostolou E, Ferrari F, Choi J, Walsh RM, Chen T, Ooi SS, Kim SY, Bestor TH, Shioda T, Park PJ, Hochedlinger K. Ascorbic acid prevents loss of Dlk1-Dio3 imprinting and facilitates generation of all-iPS cell mice from terminally differentiated B cells. Nature Genetics. 2012 Mar 4;44(4):398-405
before 2012 (most relevant)
Stadtfeld M, Apostolou E, Akutsu H, Fukuda A, Follett P, Natesan S, Kono T, Shioda T, Hochedlinger K. Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells. Nature. 2010 May 13;465(7295):175-81
Stadtfeld M, Maherali N, Borkent M, Hochedlinger K. A reprogrammable mouse strain from gene-targeted embryonic stem cells. Nature Methods. 2010 Jan;7(1):53-5
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Stadtfeld M, Nagaya M, Utikal J, Weir G, Hochedlinger K. Induced pluripotent stem cells generated without viral integration. Science. Nov 7;322(5903):945-9
Stadtfeld M, Brennand K, Hochedlinger K. Reprogramming of pancreatic beta cells into induced pluripotent stem cells. Current Biology. 2008 Jun 24;18(12):890-4.
Stadtfeld M, Maherali N, Breault DT, Hochedlinger K. Defining molecular cornerstones during fibroblast to iPS cell reprogramming in mouse. Cell Stem Cell. 2008 Mar 6;2(3):230-40
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Stadtfeld M, Ye M, Graf T. Identification of interventricular septum precursor cells in the mouse embryo. Developmental Biology. 2007 Feb 1;302(1):195-207
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Stadtfeld M, Graf T. Assessing the role of hematopoietic plasticity for endothelial and hepatocyte development by non-invasive lineage tracing. Development. 2005 Jan;132(1):203-13