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Items: 50

1.

Maternal vitamin C regulates reprogramming of DNA methylation and germline development.

DiTroia SP, Percharde M, Guerquin MJ, Wall E, Collignon E, Ebata KT, Mesh K, Mahesula S, Agathocleous M, Laird DJ, Livera G, Ramalho-Santos M.

Nature. 2019 Sep;573(7773):271-275. doi: 10.1038/s41586-019-1536-1. Epub 2019 Sep 4.

PMID:
31485074
2.

Paying PIs from grants blocks talent and diversity.

Bernstein E, Meissner A, Ramalho-Santos M.

Nature. 2018 Nov;563(7731):325. doi: 10.1038/d41586-018-07382-1. No abstract available.

PMID:
30429558
3.

A LINE1-Nucleolin Partnership Regulates Early Development and ESC Identity.

Percharde M, Lin CJ, Yin Y, Guan J, Peixoto GA, Bulut-Karslioglu A, Biechele S, Huang B, Shen X, Ramalho-Santos M.

Cell. 2018 Jul 12;174(2):391-405.e19. doi: 10.1016/j.cell.2018.05.043. Epub 2018 Jun 21.

4.

The Transcriptionally Permissive Chromatin State of Embryonic Stem Cells Is Acutely Tuned to Translational Output.

Bulut-Karslioglu A, Macrae TA, Oses-Prieto JA, Covarrubias S, Percharde M, Ku G, Diaz A, McManus MT, Burlingame AL, Ramalho-Santos M.

Cell Stem Cell. 2018 Mar 1;22(3):369-383.e8. doi: 10.1016/j.stem.2018.02.004.

5.

Tet2 Rescues Age-Related Regenerative Decline and Enhances Cognitive Function in the Adult Mouse Brain.

Gontier G, Iyer M, Shea JM, Bieri G, Wheatley EG, Ramalho-Santos M, Villeda SA.

Cell Rep. 2018 Feb 20;22(8):1974-1981. doi: 10.1016/j.celrep.2018.02.001.

6.

Vitamin C induces specific demethylation of H3K9me2 in mouse embryonic stem cells via Kdm3a/b.

Ebata KT, Mesh K, Liu S, Bilenky M, Fekete A, Acker MG, Hirst M, Garcia BA, Ramalho-Santos M.

Epigenetics Chromatin. 2017 Jul 12;10:36. doi: 10.1186/s13072-017-0143-3. eCollection 2017.

7.

Global Hypertranscription in the Mouse Embryonic Germline.

Percharde M, Wong P, Ramalho-Santos M.

Cell Rep. 2017 Jun 6;19(10):1987-1996. doi: 10.1016/j.celrep.2017.05.036.

8.

CHD1 loss sensitizes prostate cancer to DNA damaging therapy by promoting error-prone double-strand break repair.

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.

Ann Oncol. 2017 Jul 1;28(7):1495-1507. doi: 10.1093/annonc/mdx165.

9.

Hypertranscription in Development, Stem Cells, and Regeneration.

Percharde M, Bulut-Karslioglu A, Ramalho-Santos M.

Dev Cell. 2017 Jan 9;40(1):9-21. doi: 10.1016/j.devcel.2016.11.010. Epub 2016 Dec 15. Review.

10.

Inhibition of mTOR induces a paused pluripotent state.

Bulut-Karslioglu A, Biechele S, Jin H, Macrae TA, Hejna M, Gertsenstein M, Song JS, Ramalho-Santos M.

Nature. 2016 Dec 1;540(7631):119-123. doi: 10.1038/nature20578. Epub 2016 Nov 23.

11.

YAP Induces Human Naive Pluripotency.

Qin H, Hejna M, Liu Y, Percharde M, Wossidlo M, Blouin L, Durruthy-Durruthy J, Wong P, Qi Z, Yu J, Qi LS, Sebastiano V, Song JS, Ramalho-Santos M.

Cell Rep. 2016 Mar 15;14(10):2301-12. doi: 10.1016/j.celrep.2016.02.036. Epub 2016 Mar 3.

12.

Unwind and transcribe: chromatin reprogramming in the early mammalian embryo.

Biechele S, Lin CJ, Rinaudo PF, Ramalho-Santos M.

Curr Opin Genet Dev. 2015 Oct;34:17-23. doi: 10.1016/j.gde.2015.06.003. Epub 2015 Jul 13. Review.

13.

Emergence of hematopoietic stem and progenitor cells involves a Chd1-dependent increase in total nascent transcription.

Koh FM, Lizama CO, Wong P, Hawkins JS, Zovein AC, Ramalho-Santos M.

Proc Natl Acad Sci U S A. 2015 Apr 7;112(14):E1734-43. doi: 10.1073/pnas.1424850112. Epub 2015 Mar 23.

14.

Chd1 is essential for the high transcriptional output and rapid growth of the mouse epiblast.

Guzman-Ayala M, Sachs M, Koh FM, Onodera C, Bulut-Karslioglu A, Lin CJ, Wong P, Nitta R, Song JS, Ramalho-Santos M.

Development. 2015 Jan 1;142(1):118-27. doi: 10.1242/dev.114843. Epub 2014 Dec 5.

15.

HiTSelect: a comprehensive tool for high-complexity-pooled screen analysis.

Diaz AA, Qin H, Ramalho-Santos M, Song JS.

Nucleic Acids Res. 2015 Feb 18;43(3):e16. doi: 10.1093/nar/gku1197. Epub 2014 Nov 26.

16.

A comparative encyclopedia of DNA elements in the mouse genome.

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.

Nature. 2014 Nov 20;515(7527):355-64. doi: 10.1038/nature13992.

17.

Hira-mediated H3.3 incorporation is required for DNA replication and ribosomal RNA transcription in the mouse zygote.

Lin CJ, Koh FM, Wong P, Conti M, Ramalho-Santos M.

Dev Cell. 2014 Aug 11;30(3):268-79. doi: 10.1016/j.devcel.2014.06.022. Epub 2014 Jul 31.

18.

Systematic identification of barriers to human iPSC generation.

Qin H, Diaz A, Blouin L, Lebbink RJ, Patena W, Tanbun P, LeProust EM, McManus MT, Song JS, Ramalho-Santos M.

Cell. 2014 Jul 17;158(2):449-461. doi: 10.1016/j.cell.2014.05.040.

19.

Somatic cells regulate maternal mRNA translation and developmental competence of mouse oocytes.

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.

Nat Cell Biol. 2013 Dec;15(12):1415-23. doi: 10.1038/ncb2873. Epub 2013 Nov 24.

20.

Histone variant H3.3 maintains a decondensed chromatin state essential for mouse preimplantation development.

Lin CJ, Conti M, Ramalho-Santos M.

Development. 2013 Sep;140(17):3624-34. doi: 10.1242/dev.095513. Epub 2013 Jul 31.

21.

Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells.

Blaschke K, Ebata KT, Karimi MM, Zepeda-Martínez JA, Goyal P, Mahapatra S, Tam A, Laird DJ, Hirst M, Rao A, Lorincz MC, Ramalho-Santos M.

Nature. 2013 Aug 8;500(7461):222-6. doi: 10.1038/nature12362. Epub 2013 Jun 30.

22.

Bivalent chromatin marks developmental regulatory genes in the mouse embryonic germline in vivo.

Sachs M, Onodera C, Blaschke K, Ebata KT, Song JS, Ramalho-Santos M.

Cell Rep. 2013 Jun 27;3(6):1777-84. doi: 10.1016/j.celrep.2013.04.032. Epub 2013 May 30.

23.

Smad2 is essential for maintenance of the human and mouse primed pluripotent stem cell state.

Sakaki-Yumoto M, Liu J, Ramalho-Santos M, Yoshida N, Derynck R.

J Biol Chem. 2013 Jun 21;288(25):18546-60. doi: 10.1074/jbc.M112.446591. Epub 2013 May 6.

24.

Polycomb-like 3 promotes polycomb repressive complex 2 binding to CpG islands and embryonic stem cell self-renewal.

Hunkapiller J, Shen Y, Diaz A, Cagney G, McCleary D, Ramalho-Santos M, Krogan N, Ren B, Song JS, Reiter JF.

PLoS Genet. 2012;8(3):e1002576. doi: 10.1371/journal.pgen.1002576. Epub 2012 Mar 15.

25.

Transcriptional analysis of pluripotency reveals the Hippo pathway as a barrier to reprogramming.

Qin H, Blaschke K, Wei G, Ohi Y, Blouin L, Qi Z, Yu J, Yeh RF, Hebrok M, Ramalho-Santos M.

Hum Mol Genet. 2012 May 1;21(9):2054-67. doi: 10.1093/hmg/dds023. Epub 2012 Jan 27.

26.

Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells.

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.

Nat Cell Biol. 2011 May;13(5):541-9. doi: 10.1038/ncb2239. Epub 2011 Apr 17.

27.

Open chromatin in pluripotency and reprogramming.

Gaspar-Maia A, Alajem A, Meshorer E, Ramalho-Santos M.

Nat Rev Mol Cell Biol. 2011 Jan;12(1):36-47. doi: 10.1038/nrm3036. Review. Erratum in: Nat Rev Mol Cell Biol. 2011 Apr;12(4):273.

28.

The pluripotent transcriptome.

Grskovic M, Ramalho-Santos M.

StemBook [Internet]. Cambridge (MA): Harvard Stem Cell Institute; 2008-.
2008 Oct 10.

29.

Parallel gateways to pluripotency: open chromatin in stem cells and development.

Koh FM, Sachs M, Guzman-Ayala M, Ramalho-Santos M.

Curr Opin Genet Dev. 2010 Oct;20(5):492-9. doi: 10.1016/j.gde.2010.06.002. Epub 2010 Jul 2. Review.

30.

iPS cells: insights into basic biology.

Ramalho-Santos M.

Cell. 2009 Aug 21;138(4):616-8. doi: 10.1016/j.cell.2009.08.012.

31.

Chd1 regulates open chromatin and pluripotency of embryonic stem cells.

Gaspar-Maia A, Alajem A, Polesso F, Sridharan R, Mason MJ, Heidersbach A, Ramalho-Santos J, McManus MT, Plath K, Meshorer E, Ramalho-Santos M.

Nature. 2009 Aug 13;460(7257):863-8. doi: 10.1038/nature08212. Epub 2009 Jul 8.

32.

CompMoby: comparative MobyDick for detection of cis-regulatory motifs.

Chaivorapol C, Melton C, Wei G, Yeh RF, Ramalho-Santos M, Blelloch R, Li H.

BMC Bioinformatics. 2008 Oct 27;9:455. doi: 10.1186/1471-2105-9-455.

33.

High-efficiency stem cell fusion-mediated assay reveals Sall4 as an enhancer of reprogramming.

Wong CC, Gaspar-Maia A, Ramalho-Santos M, Reijo Pera RA.

PLoS One. 2008 Apr 16;3(4):e1955. doi: 10.1371/journal.pone.0001955.

34.

Generation of induced pluripotent stem cells in the absence of drug selection.

Blelloch R, Venere M, Yen J, Ramalho-Santos M.

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.

35.

On the origin of the term "stem cell".

Ramalho-Santos M, Willenbring H.

Cell Stem Cell. 2007 Jun 7;1(1):35-8. doi: 10.1016/j.stem.2007.05.013.

36.

Systematic identification of cis-regulatory sequences active in mouse and human embryonic stem cells.

Grskovic M, Chaivorapol C, Gaspar-Maia A, Li H, Ramalho-Santos M.

PLoS Genet. 2007 Aug;3(8):e145.

37.

RNA interference in embryonic stem cells and the prospects for future therapies.

Heidersbach A, Gaspar-Maia A, McManus MT, Ramalho-Santos M.

Gene Ther. 2006 Mar;13(6):478-86. Review.

PMID:
16520820
38.

Stem cells as probabilistic self-producing entities.

Ramalho-Santos M.

Bioessays. 2004 Sep;26(9):1013-6.

39.

"Stemness": transcriptional profiling of embryonic and adult stem cells.

Ramalho-Santos M, Yoon S, Matsuzaki Y, Mulligan RC, Melton DA.

Science. 2002 Oct 18;298(5593):597-600. Epub 2002 Sep 12.

40.
41.
42.

Hedgehog signals regulate multiple aspects of gastrointestinal development.

Ramalho-Santos M, Melton DA, McMahon AP.

Development. 2000 Jun;127(12):2763-72.

43.

Will cell alliance breed bureaucracy and leave contributors out?

Haggarty SJ, Ramalho-Santos M.

Nature. 2000 Feb 10;403(6770):591. No abstract available.

PMID:
10688171
44.

Cloning and characterization of cDNA encoding cardosin A, an RGD-containing plant aspartic proteinase.

Faro C, Ramalho-Santos M, Vieira M, Mendes A, Simões I, Andrade R, Veríssimo P, Lin X, Tang J, Pires E.

J Biol Chem. 1999 Oct 1;274(40):28724-9.

45.

Identification and proteolytic processing of procardosin A.

Ramalho-Santos M, Veríssimo P, Cortes L, Samyn B, Van Beeumen J, Pires E, Faro C.

Eur J Biochem. 1998 Jul 1;255(1):133-8.

46.

Structural and functional aspects of cardosins.

Faro C, Ramalho-Santos M, Veríssimo P, Pissarra J, Frazão C, Costa J, Lin XL, Tang J, Pires E.

Adv Exp Med Biol. 1998;436:423-33. Review. No abstract available.

PMID:
9580379
47.

A comparative study on the aspartic proteinases from different species of Cynara.

Veríssimo P, Ramalho-Santos M, Faro C, Pires E.

Adv Exp Med Biol. 1998;436:459-63. Review. No abstract available.

PMID:
9561253
48.

Cardosinogen A. The precursor form of the major aspartic proteinase from cardoon.

Ramalho-Santos M, Pissarra J, Pires E, Faro C.

Adv Exp Med Biol. 1998;436:253-8. No abstract available.

PMID:
9561227
49.

Cardosin A, an abundant aspartic proteinase, accumulates in protein storage vacuoles in the stigmatic papillae of Cynara cardunculus L.

Ramalho-Santos M, Pissarra J, Veríssimo P, Pereira S, Salema R, Pires E, Faro CJ.

Planta. 1997 Oct;203(2):204-12.

PMID:
9362566
50.

Action on bovine alpha s1-casein of cardosins A and B, aspartic proteinases from the flowers of the cardoon Cynara cardunculus L.

Ramalho-Santos M, Veríssimo P, Faro C, Pires E.

Biochim Biophys Acta. 1996 Sep 13;1297(1):83-9.

PMID:
8841384

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