Cahan Lab | at JHMI
Publications
CrebA regulation of secretory capacity: Genome-wide transcription profiling coupled with in vivo DNA binding studies
Genetics
Jackson DJ*, Peng D*, Shinde SA, Holenarasipura A, Ajay V, Cahan P#, Andrew DJ#
Polyamine Depletion by D,L-alpha-difluoromethylornithine Inhibits Ewing Sarcoma Metastasis by Inducing Ferroptosis
Clinical Cancer Research
Offenbacher R, Jackson KW, Hayashi M, Zhang J, Peng D, Tan Y, Stewart TM, Ciero P, Foley J, Casero RA, Cahan P, Loeb DM.
DNA methylation memory of pancreatic acinar-ductal metaplasia transition state altering Kras-downstream PI3K and Rho GTPase signaling in the absence of Kras mutation
Genome Medicine
Lo EKW, Idrizi A, Tryggvadottir R, Zhou W, Wenpin Hou, Ji H, Cahan P#, Feinberg AP#
Inhibition of DKK-1 by WAY262611 Inhibits Osteosarcoma Metastasis
Molecular Cancer Therapeutics
Tal A, Gunawardana-Zeigler S, Peng D, Tan Y, Munoz Perez N, Offenbacher R, Kastner L, Ciero P, Randolph ME, Gong Y, Deng HW, Cahan P, Loeb DM.
OneSC: A computational platform for recapitulating cell state transitions
Bioinformatics
Peng D and Cahan P
Cell cycle expression heterogeneity predicts degree of differentiation
Briefings in Bioinformatics
Noller K and Cahan P
Transcriptome data are insufficient to control false discoveries in regulatory network inference
Cell Systems
Kernfeld EM, Keener RM, Cahan P#, Battle A#
Direct comparison of mass cytometry and single-cell RNA sequencing of human peripheral blood mononuclear cells
Scientific Data
Su EY*, Fread K*, Goggin S, Zunder ER#, Cahan P#
Organogenetic transcriptomes of the Drosophila embryo at single cell resolution
Development
Peng D, Jackson D, Palicha B, Kernfeld EM, Laughner N, Shoemaker A, Celniker SE, Loganathan R, Cahan P#, Andrew DJ#
Analysis of the human kidney transcriptome and plasma proteome identifies markers of proximal tubule maladaptation to injury.
Science Translational Medicine
Wen Y, Su E, Xu L, Menez S, Moledina DG, Obeid W, Palevsky PM, Mansour SG, Devarajan P, Cantley LG, Cahan P, Parikh CR; Kidney Precision Medicine Project; Translational Investigation of Biomarker Endpoint of Acute Kidney Injury.
Single cell and spatial transcriptomics analysis of kidney double negative T lymphocytes in normal and ischemic mouse kidneys.
Scientific Reports
Gharaie S, Lee K, Noller K, Lo EK, Miller B, Jung HJ, Newman-Rivera AM, Kurzhagen JT, Singla N, Welling PA, Fan J, Cahan P, Noel S, Rabb H.
Platform-agnostic CellNet enables cross-study analysis of cell fate engineering protocols.
Stem Cell Reports
Lo EKW, Velazquez J, Peng D, Kwon C, Ebrahimkhani MR, Cahan P
RANK+TLR2+ myeloid subpopulation converts autoimmune to joint destruction in rheumatoid arthritis.
Elife.
Zhang W#, Noller K#, Crane J, Wan M, Wu X, Cahan P, Cao X.
Sympathetic Innervation Regulates Osteocyte-Mediated Cortical Bone Resorption during Lactation.
Advanced Science
Guo Q, Chen N, Qian C, Qi C, Noller K, Wan M, Liu X, Zhang W, Cahan P, Cao X.
Gene regulation network inference using k-nearest neighbor-based mutual information estimation: revisiting an old DREAM.
BMC Bioinformatics.
Shachaf LI, Roberts E, Cahan P, Xiao J.
Immune Checkpoint Molecule TIGIT Regulates Kidney T Cell Functions and Contributes to AKI.
J Am Soc Nephrol.
Noel S, Lee K, Gharaie S, Kurzhagen JT, Pierorazio PM, Arend LJ, Kuchroo VK, Cahan P, Rabb H.
A conversation with ChatGPT on the role of computational systems biology in stem cell research
Stem Cell Reports.
Cahan P#, Treutlein B#
Single-Cell Transcriptomic Census of Endothelial Changes Induced by Matrix Stiffness and the Association with Atherosclerosis.
Advanced Functional Materials.
Zamani M*, Cheng YH*,Charbonier F, Kumar V, Mayer AT, Trevino AE, Quertermous T, Chaudhuri O, Cahan P#, Huang NF#
Engineering Skeletal Muscle Grafts with PAX7::GFP-Sorted Human Pluripotent Stem Cell-Derived Myogenic Progenitors on Fibrin Microfiber Bundles for Tissue Regeneration
Bioengineering (Basel).
Somers SM, Gilbert-Honick J, Choi IY, Lo EKW, Lim H, Dias S, Wagner KR, Mao HQ, Cahan P, Lee G, Grayson WL
Reconstruction of dynamic regulatory networks reveals signaling-induced topology changes associated with germ layer specification.
Stem Cell Reports.
Su EY*, Spangler A*,Bian Q, Kasamoto JY, Cahan P
Spatial transcriptomics reveals a role for sensory nerves in preserving cranial suture patency through modulation of BMP/TGF-β signaling.
Proc Natl Acad Sci U S A.
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.
Computational reconstruction of the signalling networks surrounding implanted biomaterials from single-cell transcriptomics.
Nature Biomedical Engineering
Cherry C, Maestas DR, Han J, Andorko JI, Cahan P, Fertig EJ, Garmire LX, Elisseeff JH.
Evaluating the transcriptional fidelity of cancer models.
Genome Medicine
Peng D*, Gleyzer R*, Tai WH, Kumar P, Bian Q, Isaacs B, Rocha EL, Cai S, DiNapoli K, Huang FW, Cahan P
Challenges for Computational Stem Cell Biology: A Discussion for the Field.
Stem Cell Reports
Rackham O, Cahan P, Mah N, Morris S, Ouyang JF, Plant AL, Tanaka Y, Wells CA.
Computational Stem Cell Biology: Open Questions and Guiding Principles.
Cell Stem Cell
Cahan P, Cacchiarelli D, Dunn SJ, Hemberg M, de Sousa Lopes SMC, Morris SA, Rackham OJL, Del Sol A, Wells CA.
Gene Regulatory Network Analysis and Engineered Directs Development and Vascularization of Multilineage Human Liver Organoids.
Cell Systems
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
Hepatocyte-like cells derived from human induced pluripotent stem cells using small molecules: implications of a transcriptomic study.
Stem Cell Res Ther.
Gao X, Li R, Cahan P, Zhao Y, Yourick JJ, Sprando RL
A single cell transcriptional atlas of early synovial joint development.
Development.
Bian Q, Cheng YH, Wilson JP, Su EY, Kim DQ, Yoo S, Blackshaw S, Cahan P
Evaluation of Bunina et al.: Synthesizing Multi-omics Data to Delineate Neuronal Differentiation.
Cell Systems.
Lo EKW, Su EY, Cahan P
Small-Molecule PAPD5 Inhibitors Restore Telomerase Activity in Patient Stem Cells.
Cell Stem Cell.
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.
Transcriptome Dynamics of Hematopoietic Stem Cell Formation Revealed Using a Combinatorial Runx1 and Ly6a Reporter System.
Stem Cell Reports.
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.
Multi-scale cellular engineering: From molecules to organ-on-a-chip.
APL Bioengineering.
Huang NF, Chaudhuri O, Cahan P, Wang A, Engler AJ, Wang Y, Kumar S, Khademhosseini A, Li S.
Interleukin-36γ-producing macrophages drive IL-17-mediated fibrosis.
Science Immunology.
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.
SingleCellNet: A Computational Tool to Classify Single Cell RNA-Seq Data Across Platforms and Across Species.
Cell Systems.
Tan Y and Cahan P
A systems biology pipeline identifies regulatory networks for stem cell engineering.
Nature Biotechnology.
Kinney MA, Vo LT, Frame JM, Barragan J, Conway AJ, Li S, Wong KK, Collins JJ, Cahan P, North TE, Lauffenburger DA, Daley GQ
A Public BCR Present in a Unique Dual-Receptor-Expressing Lymphocyte from Type 1 Diabetes Patients Encodes a Potent T Cell Autoantigen
Cell.
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 Fate Engineering Tools for iPSC Disease Modeling.
Methods Mol Biol.
Lo EKW, Cahan P.
A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo
Stem Cell Research.
Spangler, A, Su, E, Craft, AM, Cahan P
A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development
Cell Stem Cell.
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
Programming Morphogenesis through Systems and Synthetic Biology
Trends in Biotechnology.
Velazquez JJ*, Su E*, Cahan P^, Ebrahimkhani MR^
Assessment of engineered cells using CellNet and RNA-seq
Nature Protocols.
Radley AH, Schwab RM, Tan Y, Kim J, Lo EKW, Cahan P
Understanding development and stem cells using single cell-based analyses of gene expression
Development.
Kumar P, Tan Y, Cahan P
Engineered Murine HSCs Reconstitute Multi-lineage Hematopoiesis and Adaptive Immunity.
Cell Rep.
Lu YF, Cahan P, Ross S, Sahalie J, Sousa PM, Hadland BK, Cai W, Serrao E, Engelman AN, Bernstein ID, Daley GQ.
TGF-β inhibitors stimulate red blood cell production by enhancing self-renewal of BFU-E erythroid progenitors.
Blood.
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.
Posttranscriptional manipulation of TERC reverses molecular hallmarks of telomere disease
Journal of Clinical Investigation.
Boyraz B, Moon DH, Segal M, Muosieyiri MZ, Aykanat A, Tai AK, Cahan P, Agarwal S.
Multiple mechanisms disrupt the let-7 microRNA family in neuroblastoma
Nature.
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
LIN28 Regulates Stem Cell Metabolism and Conversion to Primed Pluripotency
Cell Stem Cell.
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
Computational Tools for Stem Cell Biology
Trends in Biotechnology.
Bian Q and Cahan P
Enabling direct fate conversion with network biology
Nature Genetics.
Cahan P
Transcriptional Landscape of Cardiomyocyte Maturation
Cell Reports.
Uosaki H, Cahan P, Lee DI, Wang S, Miyamoto M, Fernandez L, Kass DA, Kwon C
Poly(A)-specific ribonuclease (PARN) mediates 3′-end maturation of the telomerase RNA component
Nature Genetics.
Moon DH, Segal M, Boyraz B, Guinan E, Hofmann I, Cahan P, Tai AK, Agarwal S
Preprints
The Hippo-YAP/TAZ-TEAD axis promotes multipotency in bone marrow stromal cells
bioRxiv
Cheng YH, Chan CHR , Bian Q, Merling RK, Kuznetsov SA, Robey PG, Cahan P
A systematic comparison of computational methods for expression forecasting
bioRxiv
Kernfeld EM, Yang Y, Weinstock JS, Battle A#, Cahan P#
Published prior to joining Johns Hopkins
Defining cellular identity through network biology
Cell Cycle.
Cahan P, Morris SA, Collins JJ, Daley GQ
Deconstructing transcriptional heterogeneity in pluripotent stem cells
Nature.
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
A non-transcriptional role for Oct4 in the regulation of mitotic entry
Proceedings of the National Academy of Sciences.
Zhao R*, Deiblerb RW*, Lerou PH, Ballabeni A, Heffner GC, Cahan P, Unternaehrer JJ, Kirschner MW, and Daley GQ
CellNet: Network Biology Applied to Stem Cell Engineering
Cell.
Cahan P*, Li H*, Morris SA*, Lummertz da Rocha E, Daley GQ, Collins JJ
Dissecting Engineered Cell Types and Enhancing Cell Fate Conversion via CellNet
Cell.
Morris SA*, Cahan P*, Li H*, Zhao AM, San Roman AK, Shivdasani RA, Collins JJ, Daley GQ
Hippo pathway activity influences liver cell fate
Cell.
Yimlamai D, Christodoulou C, Galli GG, Yanger K, Pepe-Mooney B, Gurung B, Shrestha K, Cahan P, Stanger BZ, Camargo FD
Origins and implications of pluripotent stem cell variability and heterogeneity
Nature Reviews Molecular Cell Biology.
Cahan P, Daley GQ
The transcriptional landscape of hematopoietic stem cell ontogeny
Cell Stem Cell.
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
Chromatin-modifying enzymes as modulators of reprogramming
Nature.
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
Polycomb repressive complex 2 regulates normal development of the mouse heart
Circulation Research.
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
Investigating monogenic and complex diseases with pluripotent stem cells
Nature Reviews Genetics.
Zhu H, Lensch MW, Cahan P, Daley GQ
Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells
Nature Biotechnology.
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
Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression
Journal of Clinical Investigation.
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.
Structural variation of the mouse natural killer gene complex
Genes and Immunity.
Higuchi DA, Cahan P, Gao J, Ferris ST, Poursine-Laurent J, Graubert TA, Yokoyama WM.
Integrated genomics of susceptibility to alkylator-induced leukemia in mice
BMC Genomics.
Cahan P, Graubert TA
Epigenetic memory in induced pluripotent stem cells
Nature.
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.
POU4F1 is associated with t(8;21) acute myeloid leukemia and contributes directly to its unique transcriptional signature
Leukemia.
Fortier JM, Payton JE, Cahan P, Ley TJ, Walter MJ, Graubert TA.
The impact of copy number variation on local gene expression in mouse hematopoietic stem and progenitor cells
Nature Genetics.
Cahan P, Li Y, Izumi M, Graubert TA
wuHMM: a robust algorithm to detect DNA copy number variation using long oligonucleotide microarray data
Nucleic Acids Research.
Cahan P, Godfrey LE, Eis PS, Richmond TA, Selzer RR, Brent M, McLeod HL, Ley TJ, Graubert TA.
Meta-analysis of microarray results: challenges, opportunities, and recommendations for standardization
Gene.
Cahan P, Rovegno F, Mooney D, Newman JC, St Laurent G 3rd, McCaffrey TA
A high-resolution map of segmental DNA copy number variation in the mouse genome
PLoS Genetics.
Graubert TA, Cahan P*, Edwin D*, Selzer RR, Richmond TA, Eis PS, Shannon WD, Li X, McLeod HL, Cheverud JM, Ley TJ
Involvement of HTLV-I Tax and CREB in aneuploidy: a bioinformatics approach
Retrovirology.
de la Fuente C, Gupta MV, Klase Z, Strouss K, Cahan P, McCaffery T, Galante A, Soteropoulos P, Pumfery A, Fujii M, Kashanchi F
Systems pharmacogenomics in yeast
Pharmacogenomics.
Cahan P, Marsh S, McLeod HL
List of lists-annotated (LOLA): a database for annotation and comparison of published microarray gene lists
Gene.
Cahan P, Ahmad AM, Burke H, Fu S, Lai Y, Florea L, Dharker N, Kobrinski T, Kale P, McCaffrey TA
Genomic profiling of acquired resistance to apoptosis in cells derived from human atherosclerotic lesions: potential role of STATs, cyclinD1, BAD, and Bcl-XL
Journal of Molecular and Cellular Cardiology.
Gagarin D, Yang Z, Butler J, Wimmer M, Du B, Cahan P, McCaffrey TA
Identification and distribution of sequences having similarity to mitochondrial plasmids in mitochondrial genomes of filamentous fungi
Molecular Genetics and Genomics.
Cahan P, Kennell JC
Ranking Retrieval Systems without Relevance Judgments