Publications

Preprints

Model-X knockoffs reveal data-dependent limits on regulatory network identification.
Kernfeld EM, Keener RM, Cahan P#, Battle A#
bioRxiv 2023 Mar 24.
bioRxiv
Signaling and transcriptional networks governing late synovial joint development.
Bian Q, Cheng YH,Su EY, Kim DW, Yoo S, Blackshaw S, Cahan P
bioRxiv 2021 Aug 27.
bioRxiv
Quantitative comparison of in vitro and in vivo embryogenesis at a single cell resolution.
Tan Y, Spangler A, Farid M, Peng D, Cahan P
bioRxiv 2021 May 8.
bioRxiv

Peer reviewed

Platform-agnostic CellNet enables cross-study analysis of cell fate engineering protocols.
Lo EKW, Velazquez J, Peng D, Kwon C, Ebrahimkhani MR, Cahan P
Stem Cell Reports 2023 July 20.
j.stemcr.2023.06.008
RANK+TLR2+ myeloid subpopulation converts autoimmune to joint destruction in rheumatoid arthritis.
Zhang W#, Noller K#, Crane J, Wan M, Wu X, Cahan P, Cao X.
Elife. 2023 May 19;12:e85553.
PMID: 37204303
Sympathetic Innervation Regulates Osteocyte-Mediated Cortical Bone Resorption during Lactation.
Guo Q, Chen N, Qian C, Qi C, Noller K, Wan M, Liu X, Zhang W, Cahan P, Cao X.
Advanced Science 2023 Apr 26:e2207602
PMID: 37186379
Gene regulation network inference using k-nearest neighbor-based mutual information estimation: revisiting an old DREAM.
Shachaf LI, Roberts E, Cahan P, Xiao J.
BMC Bioinformatics. 2023 Mar 6;24(1):84.
PMID: 36879188
Immune Checkpoint Molecule TIGIT Regulates Kidney T Cell Functions and Contributes to AKI.
Noel S, Lee K, Gharaie S, Kurzhagen JT, Pierorazio PM, Arend LJ, Kuchroo VK, Cahan P, Rabb H.
J Am Soc Nephrol. 2023 Jan 13.
PMID: 36747315
A conversation with ChatGPT on the role of computational systems biology in stem cell research
Cahan P#, Treutlein B#
Stem Cell Reports. 22023 Jan 10;18(1):1-2
PMID: 36630899
Single-Cell Transcriptomic Census of Endothelial Changes Induced by Matrix Stiffness and the Association with Atherosclerosis.
Zamani M*, Cheng YH*,Charbonier F, Kumar V, Mayer AT, Trevino AE, Quertermous T, Chaudhuri O, Cahan P#, Huang NF#
Advanced Functional Materials. 2022 Nov 17;32(47):2203069
PMID: 36816792
Engineering Skeletal Muscle Grafts with PAX7::GFP-Sorted Human Pluripotent Stem Cell-Derived Myogenic Progenitors on Fibrin Microfiber Bundles for Tissue Regeneration
Somers SM, Gilbert-Honick J, Choi IY, Lo EKW, Lim H, Dias S, Wagner KR, Mao HQ, Cahan P, Lee G, Grayson WL
Bioengineering (Basel). 2022 Nov 15;9(11):693.
PMID: 36421094
Reconstruction of dynamic regulatory networks reveals signaling-induced topology changes associated with germ layer specification.
Su EY*, Spangler A*,Bian Q, Kasamoto JY, Cahan P
Stem Cell Reports. 2022 Jan 10
PMID: 35090587
Spatial transcriptomics reveals a role for sensory nerves in preserving cranial suture patency through modulation of BMP/TGF-β signaling.
Tower RJ, Li Z, Cheng YH, Wang XW, Rajbhandari L, Zhang Q, Negri S, Uytingco CR, Venkatesan A, Zhou FQ, Cahan P, James AW, Clemens TL.
Proc Natl Acad Sci U S A. 2021 Oct 19;118(42)
PMID: 34663698
Computational reconstruction of the signalling networks surrounding implanted biomaterials from single-cell transcriptomics.
Cherry C, Maestas DR, Han J, Andorko JI, Cahan P, Fertig EJ, Garmire LX, Elisseeff JH.
Nature Biomedical Engineering 2021 Aug 2.
PMID: 34341534
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.
PMID: 33926541
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
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
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
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
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
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
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
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
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
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
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
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
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
Cell Fate Engineering Tools for iPSC Disease Modeling.
Lo EKW, Cahan P.
Methods Mol Biol. 2019;1975:427-454.
PMID: 31062321
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
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
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
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
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
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
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
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
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
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
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
Enabling direct fate conversion with network biology
Cahan P
Nature Genetics. 2016 Feb 24;48(3):226-7.
PMID: 26906680
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
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

Papers below published prior to joining Johns Hopkins

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Integrated genomics of susceptibility to alkylator-induced leukemia in mice

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

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

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

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

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

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

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

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

Systems pharmacogenomics in yeast

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

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

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

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

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)