Publications

  1. 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 PMID: 29625070

  2. Programming Morphogenesis through Systems and Synthetic Biology

    Velazquez JJ*, Su E*, Cahan P^, Ebrahimkhani MR^
    Trends in Biotechnology. 2017 Dec 08 pii: S0167-7799(17)30301-3 PMID: 29229492

  3. Assessment of engineered cells using CellNet and RNA-seq

    Radley AH, Schwab RM, Tan Y, Kim J, Lo EKW, Cahan P
    Nature Protocols. 2017 Apr 27;12:1089-1102 PMID: 28448485

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

    Kumar P, Tan Y, Cahan P
    Development. 2017 144: 17-32; PMID: 28049689

  5. 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. PMID: 28009288

  6. 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 Oct 24. pii: blood-2016-05-718320. PMID: 27777239

  7. 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.
    Journal of Clinical Investigation. 2016 Aug 2; pii: 87547. PMID: 27482890

  8. 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 July 6; doi:10.1038/nature18632. PMID: 27383785

  9. 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 Jun 15. pii: S1934-5909(16)30093-5. PMID: 27320042

  10. Computational Tools for Stem Cell Biology

    Bian Q and Cahan P
    Trends in Biotechnology. 2016 Jun 15;34(12):993–1009. DOI: 10.1016/j.tibtech.2016.05.010


  11. Enabling direct fate conversion with network biology

    Cahan P
    Nature Genetics. 2016 Feb 24;48(3):226-7. PMID: 26906680

  12. Transcriptional Landscape of Cardiomyocyte Maturation

    Uosaki H, Cahan P, Lee DI, Wang S, Miyamoto M, Fernandez L, Kass DA, Kwon C
    Cell Reports. 2015 Nov 24;13(8):1705-1716. Epub 2015 Nov 12. PMID:26586429

  13. 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
    Nature Genetics. 2015 Oct 19. PMID: 26482878

  14. Defining cellular identity through network biology

    Cahan P, Morris SA, Collins JJ, Daley GQ
    Cell Cycle. 2014 Nov 1;13(21):3313-3314. PMID: 25485572

  15. Deconstructing transcriptional heterogeneity in pluripotent stem cells

    Kumar RM*, Cahan P*, Shalek A, Satija R, DaleyKeyser A, Li H, ZhangJ, Pardee K, Gennert D, Trombetta JJ, FerranteTC, Regev A, Daley GQ, Collins JJ
    Nature. 2014 Dec 4;516(7529):56-61. PMID: 25471879

  16. A non-transcriptional role for Oct4 in the regulation of mitotic entry

    Zhao R*, Deiblerb RW*, Lerou PH, Ballabeni A, Heffner GC, Cahan P, Unternaehrer JJ, Kirschner MW, and Daley GQ
    Proceedings of the National Academy of Sciences. 2014 Nov 4;111(44):15768-73. PMID: 25324523

  17. Back-to-Back CellNet Papers
  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):903-15. PMID: 25126793

  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. PMID: 25126792

  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. PMID: 24906150

  21. Origins and implications of pluripotent stem cell variability and heterogeneity

    Cahan P, Daley GQ
    Nature Reviews Molecular Cell Biology. 2013 Jun;14:357-68. PMID: 23673969


  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. PMID: 23122293


  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. PMID: 22388813

  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
    Circulation Research. 2012 Feb 3;110(3):406-15. PMID: 22158708

  25. Investigating monogenic and complex diseases with pluripotent stem cells

    Zhu H, Lensch MW, Cahan P, Daley GQ
    Nature Reviews Genetics. 2011 Apr;12(4):266-75. PMID: 21386866

  26. 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
    Nature Biotechnology. 2011 Nov 27;29(12):1117-9. PMID: 22119740

  27. 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.
    Journal of Clinical Investigation. 2011 Apr;121(4):1445-55. PMID: 21436584

  28. 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 and Immunity. 2010 Dec;11(8):637-48. PMID:20861859

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

    Cahan P, Graubert TA
    BMC Genomics. 2010 Nov 17;11:638. PMID: 21080971

  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. PMID: 20644535

  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. PMID: 20376082


  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
    Nature Genetics. 2009 Apr;41(4):430-7. PMID: 19270704


  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 Research. 2008 Apr;36(7):e41. PMID: 18334530

  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. PMID: 17651921

  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 Genetics. 2007 Jan 5;3(1):e3. PMID: 17206864

  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. PMID: 16822311

  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. 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
    Journal of Molecular and Cellular Cardiology. 2005 Sep;39(3):453-65. PMID: 16005468

  40. Identification and distribution of sequences having similarity to mitochondrial plasmids in mitochondrial genomes of filamentous fungi

    Cahan P, Kennell JC
    Molecular Genetics and Genomics. 2005 Jul;273(6):462-73. PMID:15891911

  41. Ranking Retrieval Systems without Relevance Judgments

    Soboroff I, Nicholas C and Cahan P
    Proceedings of the 24th Annual International Conference on Research and Development in Information Retrieval. (2001)