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Items: 40

1.

A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo.

Spangler A, Su EY, Craft AM, Cahan P.

Stem Cell Res. 2018 Aug;31:201-215. doi: 10.1016/j.scr.2018.07.022. Epub 2018 Jul 29.

2.

A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development.

Cesana M, Guo MH, Cacchiarelli D, Wahlster L, Barragan J, Doulatov S, Vo LT, Salvatori B, Trapnell C, Clement K, Cahan P, Tsanov KM, Sousa PM, Tazon-Vega B, Bolondi A, Giorgi FM, Califano A, Rinn JL, Meissner A, Hirschhorn JN, Daley GQ.

Cell Stem Cell. 2018 Apr 5;22(4):575-588.e7. doi: 10.1016/j.stem.2018.03.012.

PMID:
29625070
3.

Programming Morphogenesis through Systems and Synthetic Biology.

Velazquez JJ, Su E, Cahan P, Ebrahimkhani MR.

Trends Biotechnol. 2018 Apr;36(4):415-429. doi: 10.1016/j.tibtech.2017.11.003. Epub 2017 Dec 8. Review.

PMID:
29229492
4.

Assessment of engineered cells using CellNet and RNA-seq.

Radley AH, Schwab RM, Tan Y, Kim J, Lo EKW, Cahan P.

Nat Protoc. 2017 May;12(5):1089-1102. doi: 10.1038/nprot.2017.022. Epub 2017 Apr 27.

5.

Understanding development and stem cells using single cell-based analyses of gene expression.

Kumar P, Tan Y, Cahan P.

Development. 2017 Jan 1;144(1):17-32. doi: 10.1242/dev.133058. Review.

6.

Engineered Murine HSCs Reconstitute Multi-lineage Hematopoiesis and Adaptive Immunity.

Lu YF, Cahan P, Ross S, Sahalie J, Sousa PM, Hadland BK, Cai W, Serrao E, Engelman AN, Bernstein ID, Daley GQ.

Cell Rep. 2016 Dec 20;17(12):3178-3192. doi: 10.1016/j.celrep.2016.11.077.

7.

TGF-β inhibitors stimulate red blood cell production by enhancing self-renewal of BFU-E erythroid progenitors.

Gao X, Lee HY, da Rocha EL, Zhang C, Lu YF, Li D, Feng Y, Ezike J, Elmes RR, Barrasa MI, Cahan P, Li H, Daley GQ, Lodish HF.

Blood. 2016 Dec 8;128(23):2637-2641. Epub 2016 Oct 24.

8.

Posttranscriptional manipulation of TERC reverses molecular hallmarks of telomere disease.

Boyraz B, Moon DH, Segal M, Muosieyiri MZ, Aykanat A, Tai AK, Cahan P, Agarwal S.

J Clin Invest. 2016 Sep 1;126(9):3377-82. doi: 10.1172/JCI87547. Epub 2016 Aug 2.

9.

Multiple mechanisms disrupt the let-7 microRNA family in neuroblastoma.

Powers JT, Tsanov KM, Pearson DS, Roels F, Spina CS, Ebright R, Seligson M, de Soysa Y, Cahan P, Theißen J, Tu HC, Han A, Kurek KC, LaPier GS, Osborne JK, Ross SJ, Cesana M, Collins JJ, Berthold F, Daley GQ.

Nature. 2016 Jul 14;535(7611):246-51. doi: 10.1038/nature18632. Epub 2016 Jul 6.

10.

LIN28 Regulates Stem Cell Metabolism and Conversion to Primed Pluripotency.

Zhang J, Ratanasirintrawoot S, Chandrasekaran S, Wu Z, Ficarro SB, Yu C, Ross CA, Cacchiarelli D, Xia Q, Seligson M, Shinoda G, Xie W, Cahan P, Wang L, Ng SC, Tintara S, Trapnell C, Onder T, Loh YH, Mikkelsen T, Sliz P, Teitell MA, Asara JM, Marto JA, Li H, Collins JJ, Daley GQ.

Cell Stem Cell. 2016 Jul 7;19(1):66-80. doi: 10.1016/j.stem.2016.05.009. Epub 2016 Jun 16.

11.

Computational Tools for Stem Cell Biology.

Bian Q, Cahan P.

Trends Biotechnol. 2016 Dec;34(12):993-1009. doi: 10.1016/j.tibtech.2016.05.010. Epub 2016 Jun 15. Review.

12.

Enabling direct fate conversion with network biology.

Cahan P.

Nat Genet. 2016 Mar;48(3):226-7. doi: 10.1038/ng.3516.

PMID:
26906680
13.

Transcriptional Landscape of Cardiomyocyte Maturation.

Uosaki H, Cahan P, Lee DI, Wang S, Miyamoto M, Fernandez L, Kass DA, Kwon C.

Cell Rep. 2015 Nov 24;13(8):1705-16. doi: 10.1016/j.celrep.2015.10.032. Epub 2015 Nov 12.

14.

Poly(A)-specific ribonuclease (PARN) mediates 3'-end maturation of the telomerase RNA component.

Moon DH, Segal M, Boyraz B, Guinan E, Hofmann I, Cahan P, Tai AK, Agarwal S.

Nat Genet. 2015 Dec;47(12):1482-8. doi: 10.1038/ng.3423. Epub 2015 Oct 19.

15.

Defining cellular identity through network biology.

Cahan P, Morris SA, Collins JJ, Daley GQ.

Cell Cycle. 2014;13(21):3313-4. doi: 10.4161/15384101.2014.972918. No abstract available.

16.

Deconstructing transcriptional heterogeneity in pluripotent stem cells.

Kumar RM, Cahan P, Shalek AK, Satija R, DaleyKeyser A, Li H, Zhang J, Pardee K, Gennert D, Trombetta JJ, Ferrante TC, Regev A, Daley GQ, Collins JJ.

Nature. 2014 Dec 4;516(7529):56-61. doi: 10.1038/nature13920.

17.

A nontranscriptional role for Oct4 in the regulation of mitotic entry.

Zhao R, Deibler RW, Lerou PH, Ballabeni A, Heffner GC, Cahan P, Unternaehrer JJ, Kirschner MW, Daley GQ.

Proc Natl Acad Sci U S A. 2014 Nov 4;111(44):15768-73. doi: 10.1073/pnas.1417518111. Epub 2014 Oct 16.

18.

CellNet: network biology applied to stem cell engineering.

Cahan P, Li H, Morris SA, Lummertz da Rocha E, Daley GQ, Collins JJ.

Cell. 2014 Aug 14;158(4):903-915. doi: 10.1016/j.cell.2014.07.020.

19.

Dissecting engineered cell types and enhancing cell fate conversion via CellNet.

Morris SA, Cahan P, Li H, Zhao AM, San Roman AK, Shivdasani RA, Collins JJ, Daley GQ.

Cell. 2014 Aug 14;158(4):889-902. doi: 10.1016/j.cell.2014.07.021.

20.

Hippo pathway activity influences liver cell fate.

Yimlamai D, Christodoulou C, Galli GG, Yanger K, Pepe-Mooney B, Gurung B, Shrestha K, Cahan P, Stanger BZ, Camargo FD.

Cell. 2014 Jun 5;157(6):1324-38. doi: 10.1016/j.cell.2014.03.060.

21.

Origins and implications of pluripotent stem cell variability and heterogeneity.

Cahan P, Daley GQ.

Nat Rev Mol Cell Biol. 2013 Jun;14(6):357-68. doi: 10.1038/nrm3584. Epub 2013 May 15. Review.

22.

The transcriptional landscape of hematopoietic stem cell ontogeny.

McKinney-Freeman S, Cahan P, Li H, Lacadie SA, Huang HT, Curran M, Loewer S, Naveiras O, Kathrein KL, Konantz M, Langdon EM, Lengerke C, Zon LI, Collins JJ, Daley GQ.

Cell Stem Cell. 2012 Nov 2;11(5):701-14. doi: 10.1016/j.stem.2012.07.018.

23.

Chromatin-modifying enzymes as modulators of reprogramming.

Onder TT, Kara N, Cherry A, Sinha AU, Zhu N, Bernt KM, Cahan P, Marcarci BO, Unternaehrer J, Gupta PB, Lander ES, Armstrong SA, Daley GQ.

Nature. 2012 Mar 4;483(7391):598-602. doi: 10.1038/nature10953.

24.

Polycomb repressive complex 2 regulates normal development of the mouse heart.

He A, Ma Q, Cao J, von Gise A, Zhou P, Xie H, Zhang B, Hsing M, Christodoulou DC, Cahan P, Daley GQ, Kong SW, Orkin SH, Seidman CE, Seidman JG, Pu WT.

Circ Res. 2012 Feb 3;110(3):406-15. doi: 10.1161/CIRCRESAHA.111.252205. Epub 2011 Dec 8.

25.

Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells.

Kim K, Zhao R, Doi A, Ng K, Unternaehrer J, Cahan P, Huo H, Loh YH, Aryee MJ, Lensch MW, Li H, Collins JJ, Feinberg AP, Daley GQ.

Nat Biotechnol. 2011 Nov 27;29(12):1117-9. doi: 10.1038/nbt.2052. Erratum in: Nat Biotechnol. 2012 Jan;30(1):112.

26.

Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression.

Wartman LD, Larson DE, Xiang Z, Ding L, Chen K, Lin L, Cahan P, Klco JM, Welch JS, Li C, Payton JE, Uy GL, Varghese N, Ries RE, Hoock M, Koboldt DC, McLellan MD, Schmidt H, Fulton RS, Abbott RM, Cook L, McGrath SD, Fan X, Dukes AF, Vickery T, Kalicki J, Lamprecht TL, Graubert TA, Tomasson MH, Mardis ER, Wilson RK, Ley TJ.

J Clin Invest. 2011 Apr;121(4):1445-55. doi: 10.1172/JCI45284. Epub 2011 Mar 23.

27.

Investigating monogenic and complex diseases with pluripotent stem cells.

Zhu H, Lensch MW, Cahan P, Daley GQ.

Nat Rev Genet. 2011 Apr;12(4):266-75. doi: 10.1038/nrg2951. Epub 2011 Mar 9. Review.

PMID:
21386866
28.

Integrated genomics of susceptibility to alkylator-induced leukemia in mice.

Cahan P, Graubert TA.

BMC Genomics. 2010 Nov 17;11:638. doi: 10.1186/1471-2164-11-638.

29.

Structural variation of the mouse natural killer gene complex.

Higuchi DA, Cahan P, Gao J, Ferris ST, Poursine-Laurent J, Graubert TA, Yokoyama WM.

Genes Immun. 2010 Dec;11(8):637-48. doi: 10.1038/gene.2010.48. Epub 2010 Sep 23.

30.

Epigenetic memory in induced pluripotent stem cells.

Kim K, Doi A, Wen B, Ng K, Zhao R, Cahan P, Kim J, Aryee MJ, Ji H, Ehrlich LI, Yabuuchi A, Takeuchi A, Cunniff KC, Hongguang H, McKinney-Freeman S, Naveiras O, Yoon TJ, Irizarry RA, Jung N, Seita J, Hanna J, Murakami P, Jaenisch R, Weissleder R, Orkin SH, Weissman IL, Feinberg AP, Daley GQ.

Nature. 2010 Sep 16;467(7313):285-90. doi: 10.1038/nature09342.

31.

POU4F1 is associated with t(8;21) acute myeloid leukemia and contributes directly to its unique transcriptional signature.

Fortier JM, Payton JE, Cahan P, Ley TJ, Walter MJ, Graubert TA.

Leukemia. 2010 May;24(5):950-7. doi: 10.1038/leu.2010.61. Epub 2010 Apr 8.

32.

The impact of copy number variation on local gene expression in mouse hematopoietic stem and progenitor cells.

Cahan P, Li Y, Izumi M, Graubert TA.

Nat Genet. 2009 Apr;41(4):430-7. doi: 10.1038/ng.350. Epub 2009 Mar 8.

33.

wuHMM: a robust algorithm to detect DNA copy number variation using long oligonucleotide microarray data.

Cahan P, Godfrey LE, Eis PS, Richmond TA, Selzer RR, Brent M, McLeod HL, Ley TJ, Graubert TA.

Nucleic Acids Res. 2008 Apr;36(7):e41. doi: 10.1093/nar/gkn110. Epub 2008 Mar 11.

34.

Meta-analysis of microarray results: challenges, opportunities, and recommendations for standardization.

Cahan P, Rovegno F, Mooney D, Newman JC, St Laurent G 3rd, McCaffrey TA.

Gene. 2007 Oct 15;401(1-2):12-8. Epub 2007 Jul 3. Review.

35.

A high-resolution map of segmental DNA copy number variation in the mouse genome.

Graubert TA, Cahan P, Edwin D, Selzer RR, Richmond TA, Eis PS, Shannon WD, Li X, McLeod HL, Cheverud JM, Ley TJ.

PLoS Genet. 2007 Jan 5;3(1):e3. Epub 2006 Nov 22.

36.

Involvement of HTLV-I Tax and CREB in aneuploidy: a bioinformatics approach.

de la Fuente C, Gupta MV, Klase Z, Strouss K, Cahan P, McCaffery T, Galante A, Soteropoulos P, Pumfery A, Fujii M, Kashanchi F.

Retrovirology. 2006 Jul 5;3:43.

37.

Systems pharmacogenomics in yeast.

Cahan P, Marsh S, McLeod HL.

Pharmacogenomics. 2006 Mar;7(2):255-9.

PMID:
16515406
38.

List of lists-annotated (LOLA): a database for annotation and comparison of published microarray gene lists.

Cahan P, Ahmad AM, Burke H, Fu S, Lai Y, Florea L, Dharker N, Kobrinski T, Kale P, McCaffrey TA.

Gene. 2005 Oct 24;360(1):78-82. Epub 2005 Sep 2. Review.

PMID:
16140476
39.

Genomic profiling of acquired resistance to apoptosis in cells derived from human atherosclerotic lesions: potential role of STATs, cyclinD1, BAD, and Bcl-XL.

Gagarin D, Yang Z, Butler J, Wimmer M, Du B, Cahan P, McCaffrey TA.

J Mol Cell Cardiol. 2005 Sep;39(3):453-65.

PMID:
16005468
40.

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