Publications

  1. Evaluating the transcriptional fidelity of cancer models.

    Peng D*, Gleyzer R*, Tai WH, Kumar P, Bian Q, Isaacs B, Rocha EL, Cai S, DiNapoli K, Huang FW, Cahan P
    Genome Medicine 2021 Apr 13;73. Paper

  2. Challenges for Computational Stem Cell Biology: A Discussion for the Field.

    Rackham O, Cahan P, Mah N, Morris S, Ouyang JF, Plant AL, Tanaka Y, Wells CA.
    Stem Cell Reports 2021 Jan 12;16(1):3-9. PMID: 33440181

  3. Computational Stem Cell Biology: Open Questions and Guiding Principles.

    Cahan P, Cacchiarelli D, Dunn SJ, Hemberg M, de Sousa Lopes SMC, Morris SA, Rackham OJL, Del Sol A, Wells CA.
    Cell Stem Cell 2021 Jan 7;28(1):20-32. PMID: 33417869

  4. Gene Regulatory Network Analysis and Engineered Directs Development and Vascularization of Multilineage Human Liver Organoids.

    Velazquez JJ, LeGraw R, Moghadam F, Tan Y, Kilbourne J, Maggiore JC, Hislop J, Liu S, Cats D, Chuva de Sousa Lopes SM, Plaisier C, Cahan P, Kiani S, Ebrahimkhani MR.
    Cell Systems 2020 Nov 30:S2405-4712(20)30420-8. PMID: 33290741

  5. Hepatocyte-like cells derived from human induced pluripotent stem cells using small molecules: implications of a transcriptomic study.

    Gao X, Li R, Cahan P, Zhao Y, Yourick JJ, Sprando RL.
    Stem Cell Res Ther. 2020 Sep 11;11(1):393. PMID: 32917265

  6. A single cell transcriptional atlas of early synovial joint development.

    Bian Q, Cheng YH, Wilson JP, Su EY, Kim DQ, Yoo S, Blackshaw S, Cahan P
    Development. 2020 June 20;147(14):dev185777 PMID: 32580935

  7. Evaluation of Bunina et al.: Synthesizing Multi-omics Data to Delineate Neuronal Differentiation.

    Lo EKW, Su EY, Cahan P
    Cell Systems. 2020 Jun 24;10(6):459-460. PMID: 32585153

  8. Small-Molecule PAPD5 Inhibitors Restore Telomerase Activity in Patient Stem Cells.

    Nagpal N, Wang J, Zeng J, Lo E, Moon DH, Luk K, Braun RO, Burroughs LM, Keel SB, Reilly C, Lindsley RC, Wolfe SA, Tai AK, Cahan P, Bauer DE, Fong YW, Agarwal S.
    Cell Stem Cell. 2020 Apr 17:S1934-5909(20)30138-7 PMID: 32320679

  9. Transcriptome Dynamics of Hematopoietic Stem Cell Formation Revealed Using a Combinatorial Runx1 and Ly6a Reporter System.

    Chen MJ, Lummertz da Rocha E, Cahan P, Kubaczka C, Hunter P, Sousa P, Mullin NK, Fujiwara Y, Nguyen M, Tan Y, Landry S, Han A, Yang S, Lu YF, Jha DK, Vo LT, Zhou Y, North TE, Zon LI, Daley GQ, Schlaeger TM.
    Stem Cell Reports.2020 Apr 9S2213-6711(20)30110-7. PMID: 32302558

  10. Multi-scale cellular engineering: From molecules to organ-on-a-chip.

    Huang NF, Chaudhuri O, Cahan P, Wang A, Engler AJ, Wang Y, Kumar S, Khademhosseini A, Li S.
    APL Bioengineering.2020 Mar 3;4(1). PMID: 32161833

  11. Interleukin-36γ-producing macrophages drive IL-17-mediated fibrosis.

    Sommerfeld SD, Cherry C, Schwab RM, Chung L, Maestas DR Jr, Laffont P, Stein JE, Tam A, Ganguly S, Housseau F, Taube JM, Pardoll DM, Cahan P, Elisseeff JH.
    Science Immunology. 2019 Oct 11;4(40). PMID: 31604843

  12. SingleCellNet: A Computational Tool to Classify Single Cell RNA-Seq Data Across Platforms and Across Species.

    Tan Y and Cahan P
    Cell Systems. 2019 Jul 17. pii: S2405-4712(19)30199-1. PMID: 31377170

  13. A systems biology pipeline identifies regulatory networks for stem cell engineering.

    Kinney MA, Vo LT, Frame JM, Barragan J, Conway AJ, Li S, Wong KK, Collins JJ, Cahan P, North TE, Lauffenburger DA, Daley GQ
    Nature Biotechnology. 2019 Jul;37(7):810-818 PMID: 31267104

  14. A Public BCR Present in a Unique Dual-Receptor-Expressing Lymphocyte from Type 1 Diabetes Patients Encodes a Potent T Cell Autoantigen

    Ahmed R, Omidian Z, Giwa A, Cornwell B, Majety N, Bell DR, Lee S, Zhang H, Michels A, Desiderio S, Sadegh-Nasseri S, Rabb H, Gritsch S, Suva ML, Cahan P, Zhou R, Jie C, Donner T, Hamad ARA
    Cell. 2019 May 30;177(6):1583-1599 PMID: 31150624

  15. Cell Fate Engineering Tools for iPSC Disease Modeling.

    Lo EKW, Cahan P.
    Methods Mol Biol. 2019;1975:427-454. PMID: 31062321

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

    Spangler, A, Su, E, Craft, AM, Cahan P
    Stem Cell Research. 2018 Aug;31:201-215. PMID: 30118958


  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. 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

  24. 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

  25. 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

  26. 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


  27. Enabling direct fate conversion with network biology

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

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  33. Back-to-Back CellNet Papers
  34. 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

  35. 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


  36. 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

  37. 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

  38. 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


  39. 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

  40. 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

  41. 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

  42. 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

  43. 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

  44. 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

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

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

  46. 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

  47. 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

  48. 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


  49. 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

  50. 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

  51. 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

  52. 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

  53. Systems pharmacogenomics in yeast

    Cahan P, Marsh S, McLeod HL
    Pharmacogenomics.2006 Mar;7(2):255-9. PMID: 16515406

  54. 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

  55. 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

  56. 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

  57. 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)