Publications From The Santos Lab
The deubiquitinase Usp9x regulates PRC2-mediated chromatin reprogramming during mouse development
Authors: Macrae TA, Ramalho-Santos M.
Reference: Nature Communications. 2021 Mar 25;12(1):1865.
PMID: 33767158
Tet2 Rescues Age-Related Regenerative Decline and Enhances Cognitive Function in the Adult Mouse Brain.
Authors: Gontier G, Iyer M, Shea JM, Bieri G, Wheatley EG, Ramalho-Santos M, Villeda SA.
Reference: Cell Rep. 2018 Feb 20;22(8):1974-1981. doi: 10.1016/j.celrep.2018.02.001.
PMID: 29466726
CHD1 loss sensitizes prostate cancer to DNA damaging therapy by promoting error-prone double-strand break repair
Authors: Shenoy TR, Boysen G, Wang MY, Xu QZ, Guo W, Koh FM, Wang C, Zhang LZ, Wang Y, Gil V, Aziz S, Christova R, Rodrigues DN, Crespo M, Rescigno P, Tunariu N, Riisnaes R, Zafeiriou Z, Flohr P, Yuan W, Knight E, Swain A, Ramalho-Santos M, Xu DY, de Bono J, Wu H.
Reference: Ann Oncol. 2017 Jul 1;28(7):1495-1507. doi: 10.1093/annonc/mdx165.
PMID: 28383660
Unwind and transcribe: chromatin reprogramming in the early mammalian embryo.
Authors: Biechele S, Lin CJ, Rinaudo PF, Ramalho-Santos M.
Reference: Curr Opin Genet Dev. 2015 Oct;34:17-23. doi: 10.1016/j.gde.2015.06.003. Epub 2015 Jul 13. Review.
PMID: 26183187
HiTSelect: a comprehensive tool for high-complexity-pooled screen analysis.
Authors: Diaz AA, Qin H, Ramalho-Santos M, Song JS.
Reference: Nucleic Acids Res. 2015 Feb 18;43(3):e16. doi: 10.1093/nar/gku1197. Epub 2014 Nov 26.
PMID: 25428347
A comparative encyclopedia of DNA elements in the mouse genome.
Authors: Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B; Mouse ENCODE Consortium.
Reference: Nature. 2014 Nov 20;515(7527):355-64. doi: 10.1038/nature13992.
PMID: 25409824
Systematic identification of barriers to human iPSC generation.
Authors: Qin H, Diaz A, Blouin L, Lebbink RJ, Patena W, Tanbun P, LeProust EM, McManus MT, Song JS, Ramalho-Santos M.
Reference: Cell. 2014 Jul 17;158(2):449-461. doi: 10.1016/j.cell.2014.05.040.
PMID: 25036638
Somatic cells regulate maternal mRNA translation and developmental competence of mouse oocytes.
Authors: Chen J, Torcia S, Xie F, Lin CJ, Cakmak H, Franciosi F, Horner K, Onodera C, Song JS, Cedars MI, Ramalho-Santos M, Conti M.
Reference: Nat Cell Biol. 2013 Dec;15(12):1415-23. doi: 10.1038/ncb2873. Epub 2013 Nov 24.
PMID: 24270888
Histone variant H3.3 maintains a decondensed chromatin state essential for mouse preimplantation development.
Authors: Lin CJ, Conti M, Ramalho-Santos M.
Reference: Development. 2013 Sep;140(17):3624-34. doi: 10.1242/dev.095513. Epub 2013 Jul 31.
PMID: 23903189
Smad2 is essential for maintenance of the human and mouse primed pluripotent stem cell state.
Authors: Sakaki-Yumoto M, Liu J, Ramalho-Santos M, Yoshida N, Derynck R.
Reference: J Biol Chem. 2013 Jun 21;288(25):18546-60. doi: 10.1074/jbc.M112.446591. Epub 2013 May 6.
PMID: 23649632
Transcriptional analysis of pluripotency reveals the Hippo pathway as a barrier to reprogramming.
Authors: Qin H, Blaschke K, Wei G, Ohi Y, Blouin L, Qi Z, Yu J, Yeh RF, Hebrok M, Ramalho-Santos M.
Reference: Hum Mol Genet. 2012 May 1;21(9):2054-67. doi: 10.1093/hmg/dds023. Epub 2012 Jan 27.
PMID: 22286172
Polycomb-like 3 promotes polycomb repressive complex 2 binding to CpG islands and embryonic stem cell self-renewal.
Authors: Hunkapiller J, Shen Y, Diaz A, Cagney G, McCleary D, Ramalho-Santos M, Krogan N, Ren B, Song JS, Reiter JF.
Reference: PLoS Genet. 2012;8(3):e1002576. doi: 10.1371/journal.pgen.1002576. Epub 2012 Mar 15.
PMID: 22438827
Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells.
Authors: Ohi Y, Qin H, Hong C, Blouin L, Polo JM, Guo T, Qi Z, Downey SL, Manos PD, Rossi DJ, Yu J, Hebrok M, Hochedlinger K, Costello JF, Song JS, Ramalho-Santos M.
Reference: Nat Cell Biol. 2011 May;13(5):541-9. doi: 10.1038/ncb2239. Epub 2011 Apr 17.
PMID: 21499256
Parallel gateways to pluripotency: open chromatin in stem cells and development.
Authors: Koh FM, Sachs M, Guzman-Ayala M, Ramalho-Santos M.
Reference: Curr Opin Genet Dev. 2010 Oct;20(5):492-9. doi: 10.1016/j.gde.2010.06.002. Epub 2010 Jul 2. Review.
PMID: 20598875
iPS cells: insights into basic biology.
Authors: Ramalho-Santos M.
Reference: Cell. 2009 Aug 21;138(4):616-8. doi: 10.1016/j.cell.2009.08.012.
PMID: 19703387
CompMoby: comparative MobyDick for detection of cis-regulatory motifs.
Authors: Chaivorapol C, Melton C, Wei G, Yeh RF, Ramalho-Santos M, Blelloch R, Li H.
Reference: BMC Bioinformatics. 2008 Oct 27;9:455. doi: 10.1186/1471-2105-9-455.
PMID: 18950538
The pluripotent transcriptome.
Authros: Grskovic M, Ramalho-Santos M.
Reference: StemBook [Internet]. Cambridge (MA): Harvard Stem Cell Institute; 2008-. 2008 Oct 10.
PMID: 20614622
High-efficiency stem cell fusion-mediated assay reveals Sall4 as an enhancer of reprogramming.
Authors: Wong CC, Gaspar-Maia A, Ramalho-Santos M, Reijo Pera RA.
Reference: PLoS One. 2008 Apr 16;3(4):e1955. doi: 10.1371/journal.pone.0001955.
PMID: 18414659
Generation of induced pluripotent stem cells in the absence of drug selection.
Authors: Blelloch R, Venere M, Yen J, Ramalho-Santos M.
Reference: Cell Stem Cell. 2007 Sep 13;1(3):245-7. doi: 10.1016/j.stem.2007.08.008. Epub 2007 Sep 6. No abstract available.
PMID: 18371358
Systematic identification of cis-regulatory sequences active in mouse and human embryonic stem cells.
Authors: Grskovic M, Chaivorapol C, Gaspar-Maia A, Li H, Ramalho-Santos M.
Reference: PLoS Genet. 2007 Aug;3(8):e145.
PMID: 17784790