{ "lab": "Cahan Lab", "institution": "Johns Hopkins University", "lastUpdated": "2026-03-19", "publications": [ { "number": 82, "title": "TGF-β-induced fibrotic scar formation limits recovery of spinal cord injury", "journal": "Bone Research", "authors": ["Pan D", "Wu P", "Noller K", "Cahan P", "Cao X"], "date": "Feb 2026", "pmid": "41741406", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/41741406/", "summary": "TGF-beta-driven fibrotic scarring by macrophages and pericytes impedes spinal cord repair; neutralizing TGF-beta improves functional recovery in mice." }, { "number": 81, "title": "Protocol to investigate the effects of localized gene expression disruption on mouse limb development via direct siRNA injection and explant culture", "journal": "STAR Protocols", "authors": ["Yea JH", "Onggo SES", "Dewagan S", "Chen K", "Young KK", "Cahan P"], "date": "Feb 2026", "pmid": "41764661", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/41764661/", "summary": "Step-by-step protocol for localized siRNA knockdown in embryonic mouse hindlimb explants with a morphology scoring system." }, { "number": 80, "title": "Mapping somatosensory afferent circuitry to bone identifies neurotrophic signals required for fracture healing", "journal": "Science", "authors": ["Xu M", "Li Z", "Thottappillil N", "Cherief M", "Zhu M", "Xing X", "Gomez-Salazar M", "Rao C", "Ramesh S", "Mwirigi JM", "Sankaranarayanan I", "Tavares-Ferreira D", "Zhang C", "Wang XW", "Archer M", "Guan Y", "Tower RJ", "Cahan P", "Price TJ", "Clemens TL", "James AW"], "date": "Jan 2026", "pmid": "41505527", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/41505527/", "summary": "Single-cell profiling of bone-innervating sensory neurons identifies FGF9 as a key neurotrophic signal promoting fracture repair." }, { "number": 79, "title": "A comparison of computational methods for expression forecasting", "journal": "Genome Biology", "authors": ["Kernfeld E*", "Yang Y", "Weinstock JS", "Battle A#", "Cahan P#"], "date": "Nov 2025", "pmid": "41250104", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/41250104/", "summary": "Benchmarking expression forecasting methods across 11 perturbation datasets reveals most fail to outperform simple baselines." }, { "number": 78, "title": "CrebA regulation of secretory capacity: Genome-wide transcription profiling coupled with in vivo DNA binding studies", "journal": "Genetics", "authors": ["Jackson DJ*", "Peng D*", "Shinde SA", "Holenarasipura A", "Ajay V", "Cahan P#", "Andrew DJ#"], "date": "Oct 2025", "pmid": "41052780", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/41052780/", "summary": "scRNA-seq of CrebA-null Drosophila embryos reveals CrebA directly activates secretory pathway genes via proximal promoter binding." }, { "number": 77, "title": "Polyamine Depletion by D,L-alpha-difluoromethylornithine Inhibits Ewing Sarcoma Metastasis by Inducing Ferroptosis", "journal": "Clinical Cancer Research", "authors": ["Offenbacher R", "Jackson KW", "Hayashi M", "Zhang J", "Peng D", "Tan Y", "Stewart TM", "Ciero P", "Foley J", "Casero RA", "Cahan P", "Loeb DM"], "date": "Jul 2025", "pmid": "40705089", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/40705089/", "summary": "DFMO prevents Ewing sarcoma metastasis by inducing ferroptosis, providing preclinical rationale for clinical testing." }, { "number": 76, "title": "DNA methylation memory of pancreatic acinar-ductal metaplasia transition state altering Kras-downstream PI3K and Rho GTPase signaling in the absence of Kras mutation", "journal": "Genome Medicine", "authors": ["Lo EKW", "Idrizi A", "Tryggvadottir R", "Zhou W", "Wenpin Hou", "Ji H", "Cahan P#", "Feinberg AP#"], "date": "Mar 2025", "pmid": "39553977", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/39553977/", "summary": "Pancreatic cells retain DNA methylation marks from ADM transition at Kras-downstream pathway genes even after expression normalizes." }, { "number": 75, "title": "Inhibition of DKK-1 by WAY262611 Inhibits Osteosarcoma Metastasis", "journal": "Molecular Cancer Therapeutics", "authors": ["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"], "date": "2025", "pmid": "39781890", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/39781890/", "summary": "Small-molecule DKK-1 inhibitor activates Wnt signaling, induces osteoblast differentiation, and prevents osteosarcoma metastasis in vivo." }, { "number": 74, "title": "OneSC: A computational platform for recapitulating cell state transitions", "journal": "Bioinformatics", "authors": ["Peng D", "Cahan P"], "date": "2024", "pmid": "39570626", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/39570626/", "summary": "OneSC simulates cell state transitions via stochastic differential equations on core TF networks, accurately predicting perturbation outcomes." }, { "number": 73, "title": "Cell cycle expression heterogeneity predicts degree of differentiation", "journal": "Briefings in Bioinformatics", "authors": ["Noller K", "Cahan P"], "date": "Sep 2024", "pmid": "39446193", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/39446193/", "summary": "stemFinder predicts differentiation state from cell cycle gene expression heterogeneity, outperforming existing methods with better scalability." }, { "number": 72, "title": "Transcriptome data are insufficient to control false discoveries in regulatory network inference", "journal": "Cell Systems", "authors": ["Kernfeld EM", "Keener RM", "Cahan P#", "Battle A#"], "date": "Aug 2024", "pmid": "39173585", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/39173585/", "summary": "Unmeasured confounding variables are a major driver of false discoveries in transcriptional regulatory network inference from expression data." }, { "number": 71, "title": "Direct comparison of mass cytometry and single-cell RNA sequencing of human peripheral blood mononuclear cells", "journal": "Scientific Data", "authors": ["Su EY*", "Fread K", "Goggin S", "Zunder ER#", "Cahan P#"], "date": "May 2024", "pmid": "38816402", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/38816402/", "summary": "Split-sample CyTOF vs scRNA-seq comparison reveals cell-type-specific concordance between protein and mRNA measurements." }, { "number": 70, "title": "Organogenetic transcriptomes of the Drosophila embryo at single cell resolution", "journal": "Development", "authors": ["Peng D", "Jackson D", "Palicha B", "Kernfeld EM", "Laughner N", "Shoemaker A", "Celniker SE", "Loganathan R", "Cahan P#", "Andrew DJ#"], "date": "Jan 2024", "pmid": "38174902", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/38174902/", "summary": "Single-cell atlas of Drosophila organogenesis reveals tissue-specific transcription programs and matrisome cell origins." }, { "number": 69, "title": "Analysis of the human kidney transcriptome and plasma proteome identifies markers of proximal tubule maladaptation to injury.", "journal": "Science Translational Medicine", "authors": ["Wen Y", "Su E", "Xu L", "Menez S", "Moledina DG", "Obeid W", "Palevsky PM", "Mansour SG", "Devarajan P", "Cantley LG", "Cahan P", "Parikh CR"], "date": "Dec 2023", "pmid": "38091407", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/38091407/", "summary": "Multi-omics analysis identifies plasma protein markers of maladaptive proximal tubule repair predicting adverse outcomes after AKI." }, { "number": 68, "title": "Single cell and spatial transcriptomics analysis of kidney double negative T lymphocytes in normal and ischemic mouse kidneys.", "journal": "Scientific Reports", "authors": ["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"], "date": "Nov 2023", "pmid": "38017015", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/38017015/", "summary": "Combined scRNA-seq and spatial transcriptomics characterize kidney double-negative T cells and their localization during AKI." }, { "number": 67, "title": "Platform-agnostic CellNet enables cross-study analysis of cell fate engineering protocols.", "journal": "Stem Cell Reports", "authors": ["Lo EKW", "Velazquez J", "Peng D", "Kwon C", "Ebrahimkhani MR", "Cahan P"], "date": "Aug 2023", "pmid": "37478860", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/37478860/", "summary": "PACNet enables cross-platform, cross-study comparison of cell engineering protocols by scoring transcriptional fidelity against natural cell types." }, { "number": 66, "title": "RANK+TLR2+ myeloid subpopulation converts autoimmune to joint destruction in rheumatoid arthritis.", "journal": "Elife", "authors": ["Zhang W#", "Noller K#", "Crane J", "Wan M", "Wu X", "Cahan P", "Cao X"], "date": "May 2023", "pmid": "37204303", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/37204303/", "summary": "A RANK+TLR2+ myeloid subset drives the transition from autoimmunity to osteoclast-mediated joint destruction in rheumatoid arthritis." }, { "number": 65, "title": "Sympathetic Innervation Regulates Osteocyte-Mediated Cortical Bone Resorption during Lactation.", "journal": "Advanced Science", "authors": ["Guo Q", "Chen N", "Qian C", "Qi C", "Noller K", "Wan M", "Liu X", "Zhang W", "Cahan P", "Cao X"], "date": "Apr 2023", "pmid": "37186379", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/37186379/", "summary": "Sympathetic nerves promote osteocyte-driven cortical bone resorption during lactation through beta-adrenergic signaling and extracellular vesicle secretion." }, { "number": 64, "title": "Gene regulation network inference using k-nearest neighbor-based mutual information estimation: revisiting an old DREAM.", "journal": "BMC Bioinformatics", "authors": ["Shachaf LI", "Roberts E", "Cahan P", "Xiao J"], "date": "Mar 2023", "pmid": "36879188", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/36879188/", "summary": "A kNN mutual information estimator combined with a new inference algorithm improves gene regulatory network reconstruction by 20-35%." }, { "number": 63, "title": "Immune Checkpoint Molecule TIGIT Regulates Kidney T Cell Functions and Contributes to AKI.", "journal": "J Am Soc Nephrol", "authors": ["Noel S", "Lee K", "Gharaie S", "Kurzhagen JT", "Pierorazio PM", "Arend LJ", "Kuchroo VK", "Cahan P", "Rabb H"], "date": "Jan 2023", "pmid": "36747315", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/36747315/", "summary": "TIGIT is upregulated on kidney T cells after acute kidney injury, and its deletion protects mice from ischemic and nephrotoxic damage." }, { "number": 62, "title": "A conversation with ChatGPT on the role of computational systems biology in stem cell research", "journal": "Stem Cell Reports", "authors": ["Cahan P#", "Treutlein B#"], "date": "Jan 2023", "pmid": "36630899", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/36630899/", "summary": "Commentary: Explores the potential roles and limitations of large language models like ChatGPT in computational stem cell biology." }, { "number": 61, "title": "Single-Cell Transcriptomic Census of Endothelial Changes Induced by Matrix Stiffness and the Association with Atherosclerosis.", "journal": "Advanced Functional Materials", "authors": ["Zamani M*", "Cheng YH*", "Charbonier F", "Kumar V", "Mayer AT", "Trevino AE", "Quertermous T", "Chaudhuri O", "Cahan P#", "Huang NF#"], "date": "Nov 2022", "pmid": "36816792", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/36816792/", "summary": "Pathological matrix stiffness promotes endothelial-to-mesenchymal transition, enriching transcriptional signatures associated with atherosclerosis." }, { "number": 60, "title": "Engineering Skeletal Muscle Grafts with PAX7::GFP-Sorted Human Pluripotent Stem Cell-Derived Myogenic Progenitors on Fibrin Microfiber Bundles for Tissue Regeneration", "journal": "Bioengineering (Basel)", "authors": ["Somers SM", "Gilbert-Honick J", "Choi IY", "Lo EKW", "Lim H", "Dias S", "Wagner KR", "Mao HQ", "Cahan P", "Lee G", "Grayson WL"], "date": "Nov 2022", "pmid": "36421094", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/36421094/", "summary": "PAX7-sorted human PSC-derived myogenic progenitors on fibrin microfiber bundles form skeletal muscle grafts that promote regeneration in vivo." }, { "number": 59, "title": "Reconstruction of dynamic regulatory networks reveals signaling-induced topology changes associated with germ layer specification.", "journal": "Stem Cell Reports", "authors": ["Su EY*", "Spangler A*", "Bian Q", "Kasamoto JY", "Cahan P"], "date": "Jan 2022", "pmid": null, "pubmedUrl": null, "summary": "A computational method reconstructs time-varying gene regulatory networks to reveal signaling-induced topology changes during germ layer specification." }, { "number": 58, "title": "Spatial transcriptomics reveals a role for sensory nerves in preserving cranial suture patency through modulation of BMP/TGF-β signaling.", "journal": "Proc Natl Acad Sci U S A", "authors": ["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"], "date": "Oct 2021", "pmid": "34663698", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/34663698/", "summary": "Sensory nerve-derived signals maintain cranial suture patency by promoting progenitor proliferation and inhibiting premature ossification." }, { "number": 57, "title": "Computational reconstruction of the signalling networks surrounding implanted biomaterials from single-cell transcriptomics.", "journal": "Nature Biomedical Engineering", "authors": ["Cherry C", "Maestas DR", "Han J", "Andorko JI", "Cahan P", "Fertig EJ", "Garmire LX", "Elisseeff JH"], "date": "Aug 2021", "pmid": "34341534", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/34341534/", "summary": "Single-cell transcriptomics of implanted biomaterials reveals modular intercellular signaling networks characterizing material-specific immune responses." }, { "number": 56, "title": "Evaluating the transcriptional fidelity of cancer models.", "journal": "Genome Medicine", "authors": ["Peng D*", "Gleyzer R*", "Tai WH", "Kumar P", "Bian Q", "Isaacs B", "Rocha EL", "Cai S", "DiNapoli K", "Huang FW", "Cahan P"], "date": "Apr 2021", "pmid": "33926541", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/33926541/", "summary": "CancerCellNet scores how faithfully cancer cell lines, xenografts, and tumoroids recapitulate the transcriptional identity of natural tumors." }, { "number": 55, "title": "Challenges for Computational Stem Cell Biology: A Discussion for the Field.", "journal": "Stem Cell Reports", "authors": ["Rackham O", "Cahan P", "Mah N", "Morris S", "Ouyang JF", "Plant AL", "Tanaka Y", "Wells CA"], "date": "Jan 2021", "pmid": "33440181", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/33440181/", "summary": "Perspective: Identifies key opportunities and barriers facing computational stem cell research requiring coordinated action across the field." }, { "number": 54, "title": "Computational Stem Cell Biology: Open Questions and Guiding Principles.", "journal": "Cell Stem Cell", "authors": ["Cahan P", "Cacchiarelli D", "Dunn SJ", "Hemberg M", "de Sousa Lopes SMC", "Morris SA", "Rackham OJL", "Del Sol A", "Wells CA"], "date": "Jan 2021", "pmid": "33417869", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/33417869/", "summary": "Review: Articulates guiding principles for computational stem cell biology across cell typing, trajectory inference, and network analysis." }, { "number": 53, "title": "Gene Regulatory Network Analysis and Engineered Directs Development and Vascularization of Multilineage Human Liver Organoids.", "journal": "Cell Systems", "authors": ["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"], "date": "Nov 2020", "pmid": "33290741", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/33290741/", "summary": "Engineering gene regulatory networks via PROX1, ATF5, and CYP3A4 activation directs maturation and vascularization of human liver organoids." }, { "number": 52, "title": "Hepatocyte-like cells derived from human induced pluripotent stem cells using small molecules: implications of a transcriptomic study.", "journal": "Stem Cell Res Ther", "authors": ["Gao X", "Li R", "Cahan P", "Zhao Y", "Yourick JJ", "Sprando RL"], "date": "Sep 2020", "pmid": "32917265", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/32917265/", "summary": "Small molecule-driven iPSC differentiation produces hepatocyte-like cells with a mixed fetal-adult phenotype; transcriptomics suggests pathways for further maturation." }, { "number": 51, "title": "A single cell transcriptional atlas of early synovial joint development.", "journal": "Development", "authors": ["Bian Q", "Cheng YH", "Wilson JP", "Su EY", "Kim DQ", "Yoo S", "Blackshaw S", "Cahan P"], "date": "Jun 2020", "pmid": "32580935", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/32580935/", "summary": "A scRNA-seq atlas of the developing murine knee joint reveals transcriptional programs governing synovial joint progenitor fate diversification." }, { "number": 50, "title": "Evaluation of Bunina et al.: Synthesizing Multi-omics Data to Delineate Neuronal Differentiation.", "journal": "Cell Systems", "authors": ["Lo EKW", "Su EY", "Cahan P"], "date": "Jun 2020", "pmid": "32585153", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/32585153/", "summary": "Commentary: Evaluates how multi-omics data integration delineates SOX2 chromatin interaction network rewiring during neuronal differentiation." }, { "number": 49, "title": "Small-Molecule PAPD5 Inhibitors Restore Telomerase Activity in Patient Stem Cells.", "journal": "Cell Stem Cell", "authors": ["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"], "date": "Apr 2020", "pmid": "32320679", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/32320679", "summary": "Small-molecule PAPD5 inhibitors restore telomerase RNA maturation and telomere length in dyskeratosis congenita patient stem cells." }, { "number": 48, "title": "Transcriptome Dynamics of Hematopoietic Stem Cell Formation Revealed Using a Combinatorial Runx1 and Ly6a Reporter System.", "journal": "Stem Cell Reports", "authors": ["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"], "date": "Apr 2020", "pmid": "32302558", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/32302558", "summary": "A dual reporter mouse and scRNA-seq reveal that maturing pre-HSCs acquire interferon signatures and quiescence as they transition to fetal liver HSCs." }, { "number": 47, "title": "Multi-scale cellular engineering: From molecules to organ-on-a-chip.", "journal": "APL Bioengineering", "authors": ["Huang NF", "Chaudhuri O", "Cahan P", "Wang A", "Engler AJ", "Wang Y", "Kumar S", "Khademhosseini A", "Li S"], "date": "Mar 2020", "pmid": "32161833", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/32161833", "summary": "Review: Summarizes advances in molecular, cellular, and organ-on-a-chip engineering for designing complex living systems." }, { "number": 46, "title": "Interleukin-36γ-producing macrophages drive IL-17-mediated fibrosis.", "journal": "Science Immunology", "authors": ["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"], "date": "Oct 2019", "pmid": "31604843", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/31604843", "summary": "scRNA-seq identifies a CD9+IL-36gamma+ macrophage subset at biomaterial implant sites that drives IL-17-mediated fibrosis." }, { "number": 45, "title": "SingleCellNet: A Computational Tool to Classify Single Cell RNA-Seq Data Across Platforms and Across Species.", "journal": "Cell Systems", "authors": ["Tan Y", "Cahan P"], "date": "Jul 2019", "pmid": "31377170", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/31377170", "summary": "SingleCellNet classifies scRNA-seq data by cell type across platforms and species, enabling quantitative identity assessment of engineered cells." }, { "number": 44, "title": "A systems biology pipeline identifies regulatory networks for stem cell engineering.", "journal": "Nature Biotechnology", "authors": ["Kinney MA", "Vo LT", "Frame JM", "Barragan J", "Conway AJ", "Li S", "Wong KK", "Collins JJ", "Cahan P", "North TE", "Lauffenburger DA", "Daley GQ"], "date": "Jul 2019", "pmid": "31267104", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/31267104", "summary": "A computational pipeline identifies ErbB4 as a regulator that improves erythroid differentiation from pluripotent stem cells." }, { "number": 43, "title": "A Public BCR Present in a Unique Dual-Receptor-Expressing Lymphocyte from Type 1 Diabetes Patients Encodes a Potent T Cell Autoantigen", "journal": "Cell", "authors": ["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"], "date": "May 2019", "pmid": "31150624", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/31150624", "summary": "A novel dual TCR/BCR-expressing lymphocyte in type 1 diabetes patients carries a public clonotype encoding a potent CD4 T cell autoantigen." }, { "number": 42, "title": "Cell Fate Engineering Tools for iPSC Disease Modeling.", "journal": "Methods Mol Biol", "authors": ["Lo EKW", "Cahan P"], "date": "2019", "pmid": "31062321", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/31062321", "summary": "A methods chapter demonstrating how to use CellNet with RNA-seq to assess and improve iPSC-derived cell populations for disease modeling." }, { "number": 41, "title": "A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo", "journal": "Stem Cell Research", "authors": ["Spangler A", "Su E", "Craft AM", "Cahan P"], "date": "Aug 2018", "pmid": "30118958", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/30118958", "summary": "scRNA-seq of embryoid bodies reveals distinct pluripotent, neuroectodermal, and mesendodermal populations and their differentiation trajectories." }, { "number": 40, "title": "A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development", "journal": "Cell Stem Cell", "authors": ["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"], "date": "Apr 2018", "pmid": "29625070", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/29625070", "summary": "A CLK3-HMGA2 alternative splicing axis enables human HSCs to maintain HMGA2 function by evading let-7 miRNA silencing across development." }, { "number": 39, "title": "Programming Morphogenesis through Systems and Synthetic Biology", "journal": "Trends in Biotechnology", "authors": ["Velazquez JJ*", "Su E*", "Cahan P^", "Ebrahimkhani MR^"], "date": "Dec 2017", "pmid": "29229492", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/29229492", "summary": "Review: Proposes that synthetic biology, single-cell genomics, and multiscale modeling can be combined to program tissue morphogenesis." }, { "number": 38, "title": "Assessment of engineered cells using CellNet and RNA-seq", "journal": "Nature Protocols", "authors": ["Radley AH", "Schwab RM", "Tan Y", "Kim J", "Lo EKW", "Cahan P"], "date": "Apr 2017", "pmid": "28448485", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/28448485", "summary": "A protocol for using CellNet with RNA-seq to evaluate how well engineered cells establish cell-type-specific gene regulatory networks." }, { "number": 37, "title": "Understanding development and stem cells using single cell-based analyses of gene expression", "journal": "Development", "authors": ["Kumar P", "Tan Y", "Cahan P"], "date": "2017", "pmid": "28049689", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/28049689", "summary": "Review: Examines how scRNA-seq reveals mammalian developmental dynamics and stem cell biology through specialized analytical approaches." }, { "number": 36, "title": "Engineered Murine HSCs Reconstitute Multi-lineage Hematopoiesis and Adaptive Immunity.", "journal": "Cell Rep", "authors": ["Lu YF", "Cahan P", "Ross S", "Sahalie J", "Sousa PM", "Hadland BK", "Cai W", "Serrao E", "Engelman AN", "Bernstein ID", "Daley GQ"], "date": "Dec 2016", "pmid": "28009288", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/28009288", "summary": "Notch ligand exposure of HoxB4-expressing ESC-derived HSCs enables multi-lineage hematopoietic reconstitution and adaptive immunity in mice." }, { "number": 35, "title": "TGF-β inhibitors stimulate red blood cell production by enhancing self-renewal of BFU-E erythroid progenitors.", "journal": "Blood", "authors": ["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"], "date": "Oct 2016", "pmid": "27777239", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/27777239", "summary": "TGF-beta receptor III marks early erythroid progenitors; blocking TGF-beta signaling increases their self-renewal and red blood cell output." }, { "number": 34, "title": "Posttranscriptional manipulation of TERC reverses molecular hallmarks of telomere disease", "journal": "Journal of Clinical Investigation", "authors": ["Boyraz B", "Moon DH", "Segal M", "Muosieyiri MZ", "Aykanat A", "Tai AK", "Cahan P", "Agarwal S"], "date": "Aug 2016", "pmid": "27482890", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/27482890", "summary": "Inhibiting PAPD5 poly(A) polymerase restores telomerase RNA levels, telomerase activity, and telomere length in PARN-mutant patient cells." }, { "number": 33, "title": "Multiple mechanisms disrupt the let-7 microRNA family in neuroblastoma", "journal": "Nature", "authors": ["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"], "date": "Jul 2016", "pmid": "27383785", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/27383785", "summary": "Let-7 miRNA disruption via LIN28B, MYCN sponging, or genetic loss is a unifying oncogenic mechanism in neuroblastoma." }, { "number": 32, "title": "LIN28 Regulates Stem Cell Metabolism and Conversion to Primed Pluripotency", "journal": "Cell Stem Cell", "authors": ["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"], "date": "Jun 2016", "pmid": "27320042", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/27320042", "summary": "LIN28A and LIN28B cooperatively regulate reprogramming, naive-to-primed pluripotency conversion, and mitochondrial metabolism in stem cells." }, { "number": 31, "title": "Computational Tools for Stem Cell Biology", "journal": "Trends in Biotechnology", "authors": ["Bian Q", "Cahan P"], "date": "Jun 2016", "pmid": null, "pubmedUrl": null, "summary": "Review: Surveys computational tools and approaches for analyzing and engineering stem cell identity and fate decisions." }, { "number": 30, "title": "Enabling direct fate conversion with network biology", "journal": "Nature Genetics", "authors": ["Cahan P"], "date": "Feb 2016", "pmid": "26906680", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/26906680", "summary": "Perspective: Describes Mogrify, a network biology framework that predicts transcription factor combinations needed for direct conversion between human cell types." }, { "number": 29, "title": "Transcriptional Landscape of Cardiomyocyte Maturation", "journal": "Cell Reports", "authors": ["Uosaki H", "Cahan P", "Lee DI", "Wang S", "Miyamoto M", "Fernandez L", "Kass DA", "Kwon C"], "date": "Nov 2015", "pmid": "26586429", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/26586429", "summary": "An atlas of gene regulatory networks across cardiomyocyte maturation reveals stem-cell-derived cardiomyocytes arrest at the late embryonic stage." }, { "number": 28, "title": "Poly(A)-specific ribonuclease (PARN) mediates 3′-end maturation of the telomerase RNA component", "journal": "Nature Genetics", "authors": ["Moon DH", "Segal M", "Boyraz B", "Guinan E", "Hofmann I", "Cahan P", "Tai AK", "Agarwal S"], "date": "Oct 2015", "pmid": "26482878", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/26482878", "summary": "PARN removes oligo(A) tails from telomerase RNA; its mutation causes TERC degradation leading to telomere disease." }, { "number": 27, "title": "Defining cellular identity through network biology", "journal": "Cell Cycle", "authors": ["Cahan P", "Morris SA", "Collins JJ", "Daley GQ"], "date": "Nov 2014", "pmid": "25485572", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/25485572", "summary": "Perspective: Discusses how network biology approaches, including CellNet, can quantify and guide cellular identity in engineered cells." }, { "number": 26, "title": "Deconstructing transcriptional heterogeneity in pluripotent stem cells", "journal": "Nature", "authors": ["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"], "date": "Dec 2014", "pmid": "25471879", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/25471879", "summary": "MicroRNA removal or signaling inhibition drives pluripotent stem cells into a low-noise ground state via the Myc/Lin28/let-7 axis." }, { "number": 25, "title": "A non-transcriptional role for Oct4 in the regulation of mitotic entry", "journal": "Proceedings of the National Academy of Sciences", "authors": ["Zhao R*", "Deiblerb RW*", "Lerou PH", "Ballabeni A", "Heffner GC", "Cahan P", "Unternaehrer JJ", "Kirschner MW", "Daley GQ"], "date": "Nov 2014", "pmid": "25324523", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/25324523", "summary": "Oct4 directly inhibits Cdk1 activation to prevent premature mitotic entry in embryonic stem cells, independent of its transcriptional activity." }, { "number": 24, "title": "CellNet: Network Biology Applied to Stem Cell Engineering", "journal": "Cell", "authors": ["Cahan P*", "Li H*", "Morris SA*", "Lummertz da Rocha E", "Daley GQ", "Collins JJ"], "date": "Aug 2014", "pmid": "25126793", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/25126793", "summary": "CellNet uses gene regulatory networks to assess how faithfully engineered cells recapitulate target cell types and suggests improvements." }, { "number": 23, "title": "Dissecting Engineered Cell Types and Enhancing Cell Fate Conversion via CellNet", "journal": "Cell", "authors": ["Morris SA*", "Cahan P*", "Li H*", "Zhao AM", "San Roman AK", "Shivdasani RA", "Collins JJ", "Daley GQ"], "date": "Aug 2014", "pmid": "25126792", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/25126792", "summary": "CellNet diagnoses aberrant gene networks in engineered cells and reveals that induced hepatocytes harbor an intestinal program." }, { "number": 22, "title": "Hippo pathway activity influences liver cell fate", "journal": "Cell", "authors": ["Yimlamai D", "Christodoulou C", "Galli GG", "Yanger K", "Pepe-Mooney B", "Gurung B", "Shrestha K", "Cahan P", "Stanger BZ", "Camargo FD"], "date": "Jun 2014", "pmid": "24906150", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/24906150", "summary": "Inactivation of Hippo signaling in vivo dedifferentiates mature hepatocytes into self-renewing progenitor-like cells via Notch activation." }, { "number": 21, "title": "Origins and implications of pluripotent stem cell variability and heterogeneity", "journal": "Nature Reviews Molecular Cell Biology", "authors": ["Cahan P", "Daley GQ"], "date": "Jun 2013", "pmid": "23673969", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/23673969", "summary": "Review: Examines how genetic and epigenetic variation drives functional variability between pluripotent stem cell lines and heterogeneity within clones." }, { "number": 20, "title": "The transcriptional landscape of hematopoietic stem cell ontogeny", "journal": "Cell Stem Cell", "authors": ["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"], "date": "Nov 2012", "pmid": "23122293", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/23122293", "summary": "Transcriptome profiling of embryonic HSCs reveals distinct developmental stages and validates novel regulators of HSC specification." }, { "number": 19, "title": "Chromatin-modifying enzymes as modulators of reprogramming", "journal": "Nature", "authors": ["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"], "date": "Mar 2012", "pmid": "22388813", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/22388813", "summary": "Inhibition of H3K79 methyltransferase DOT1L enhances iPSC reprogramming and can substitute for KLF4 and c-Myc." }, { "number": 18, "title": "Polycomb repressive complex 2 regulates normal development of the mouse heart", "journal": "Circulation Research", "authors": ["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"], "date": "Feb 2012", "pmid": "22158708", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/22158708", "summary": "Cardiac-specific loss of EZH2 disrupts cardiomyocyte proliferation and gene silencing, causing lethal congenital heart malformations." }, { "number": 17, "title": "Investigating monogenic and complex diseases with pluripotent stem cells", "journal": "Nature Reviews Genetics", "authors": ["Zhu H", "Lensch MW", "Cahan P", "Daley GQ"], "date": "Apr 2011", "pmid": "21386866", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/21386866", "summary": "Review: Surveys the use of pluripotent stem cells combined with genome-wide analyses to study monogenic and complex genetic diseases." }, { "number": 16, "title": "Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells", "journal": "Nature Biotechnology", "authors": ["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"], "date": "Nov 2011", "pmid": "22119740", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/22119740", "summary": "Human iPSCs retain residual DNA methylation signatures of their donor tissue, creating an epigenetic memory that biases differentiation." }, { "number": 15, "title": "Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression", "journal": "Journal of Clinical Investigation", "authors": ["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"], "date": "Apr 2011", "pmid": "21436584", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/21436584", "summary": "Whole-genome sequencing of a mouse APL identified a recurrent Jak1 mutation and Kdm6a deletion relevant to human leukemia." }, { "number": 14, "title": "Structural variation of the mouse natural killer gene complex", "journal": "Genes and Immunity", "authors": ["Higuchi DA", "Cahan P", "Gao J", "Ferris ST", "Poursine-Laurent J", "Graubert TA", "Yokoyama WM"], "date": "Dec 2010", "pmid": "20861859", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/20861859", "summary": "Array CGH across 21 mouse strains reveals structural copy number variation in the natural killer gene complex predicting strain phenotypes." }, { "number": 13, "title": "Integrated genomics of susceptibility to alkylator-induced leukemia in mice", "journal": "BMC Genomics", "authors": ["Cahan P", "Graubert TA"], "date": "Nov 2010", "pmid": "21080971", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/21080971", "summary": "Integrated genomic networks identify cell cycle and DNA repair pathways as key contributors to therapy-related AML susceptibility in mice." }, { "number": 12, "title": "Epigenetic memory in induced pluripotent stem cells", "journal": "Nature", "authors": ["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"], "date": "Sep 2010", "pmid": "20644535", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/20644535", "summary": "iPSCs retain donor-tissue DNA methylation patterns that bias differentiation; nuclear transfer more completely resets the epigenome." }, { "number": 11, "title": "POU4F1 is associated with t(8;21) acute myeloid leukemia and contributes directly to its unique transcriptional signature", "journal": "Leukemia", "authors": ["Fortier JM", "Payton JE", "Cahan P", "Ley TJ", "Walter MJ", "Graubert TA"], "date": "May 2010", "pmid": "20376082", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/20376082", "summary": "POU4F1 is overexpressed in t(8;21) AML and directly contributes to its unique transcriptional signature independently of AML1/ETO." }, { "number": 10, "title": "The impact of copy number variation on local gene expression in mouse hematopoietic stem and progenitor cells", "journal": "Nature Genetics", "authors": ["Cahan P", "Li Y", "Izumi M", "Graubert TA"], "date": "Apr 2009", "pmid": "19270704", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/19270704", "summary": "Germline DNA copy number variants account for up to 28% of strain-dependent gene expression variation in mouse HSCs." }, { "number": 9, "title": "wuHMM: a robust algorithm to detect DNA copy number variation using long oligonucleotide microarray data", "journal": "Nucleic Acids Research", "authors": ["Cahan P", "Godfrey LE", "Eis PS", "Richmond TA", "Selzer RR", "Brent M", "McLeod HL", "Ley TJ", "Graubert TA"], "date": "Apr 2008", "pmid": "19270704", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/19270704", "summary": "Presents wuHMM, a hidden Markov model algorithm for detecting DNA copy number variants from array CGH data." }, { "number": 8, "title": "Meta-analysis of microarray results: challenges, opportunities, and recommendations for standardization", "journal": "Gene", "authors": ["Cahan P", "Rovegno F", "Mooney D", "Newman JC", "St Laurent G 3rd", "McCaffrey TA"], "date": "Oct 2007", "pmid": "19270704", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/19270704", "summary": "Describes a meta-analysis approach for integrating microarray results across studies to identify reproducible gene expression signatures." }, { "number": 7, "title": "A high-resolution map of segmental DNA copy number variation in the mouse genome", "journal": "PLoS Genetics", "authors": ["Graubert TA", "Cahan P*", "Edwin D*", "Selzer RR", "Richmond TA", "Eis PS", "Shannon WD", "Li X", "McLeod HL", "Cheverud JM", "Ley TJ"], "date": "Jan 2007", "pmid": "17206864", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/17206864", "summary": "High-resolution CGH identifies over 1,300 copy number variant regions across 21 inbred mouse strains, spanning 3.2% of the genome." }, { "number": 6, "title": "Involvement of HTLV-I Tax and CREB in aneuploidy: a bioinformatics approach", "journal": "Retrovirology", "authors": ["de la Fuente C", "Gupta MV", "Klase Z", "Strouss K", "Cahan P", "McCaffery T", "Galante A", "Soteropoulos P", "Pumfery A", "Fujii M", "Kashanchi F"], "date": "Jul 2006", "pmid": "16822311", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/16822311", "summary": "Tax-mediated CREB transactivation alters kinetochore assembly gene expression, contributing to aneuploidy in HTLV-I-infected cells." }, { "number": 5, "title": "Systems pharmacogenomics in yeast", "journal": "Pharmacogenomics", "authors": ["Cahan P", "Marsh S", "McLeod HL"], "date": "Mar 2006", "pmid": "16515406", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/16515406", "summary": "Review: Surveys genome-wide deletion screens in yeast revealing genes required for resistance to 12 DNA-damaging anticancer agents." }, { "number": 4, "title": "List of lists-annotated (LOLA): a database for annotation and comparison of published microarray gene lists", "journal": "Gene", "authors": ["Cahan P", "Ahmad AM", "Burke H", "Fu S", "Lai Y", "Florea L", "Dharker N", "Kobrinski T", "Kale P", "McCaffrey TA"], "date": "Oct 2005", "pmid": "16140476", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/16140476", "summary": "LOLA is a database for storing, reannotating, and comparing gene lists from microarray studies across platforms and species." }, { "number": 3, "title": "Genomic profiling of acquired resistance to apoptosis in cells derived from human atherosclerotic lesions: potential role of STATs, cyclinD1, BAD, and Bcl-XL", "journal": "Journal of Molecular and Cellular Cardiology", "authors": ["Gagarin D", "Yang Z", "Butler J", "Wimmer M", "Du B", "Cahan P", "McCaffrey TA"], "date": "Sep 2005", "pmid": "16005468", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/16005468", "summary": "Transcript profiling of atherosclerotic lesion cells identifies STATs, cyclin D1, and Bcl-xL as mediators of acquired apoptosis resistance." }, { "number": 2, "title": "Identification and distribution of sequences having similarity to mitochondrial plasmids in mitochondrial genomes of filamentous fungi", "journal": "Molecular Genetics and Genomics", "authors": ["Cahan P", "Kennell JC"], "date": "Jul 2005", "pmid": "15891911", "pubmedUrl": "http://www.ncbi.nlm.nih.gov/pubmed/15891911", "summary": "Mitochondrial plasmid sequences have invaded fungal mitochondrial genomes, comprising over 2% of Neurospora crassa mitochondrial DNA." }, { "number": 1, "title": "Ranking Retrieval Systems without Relevance Judgments", "journal": "Proceedings of the 24th Annual International Conference on Research and Development in Information Retrieval", "authors": [], "date": "2001", "pmid": null, "pubmedUrl": "http://dl.acm.org/citation.cfm?id=383961", "summary": "Proposes a method for evaluating information retrieval system performance without requiring manual relevance judgments." }, { "number": "P2", "type": "preprint", "title": "The Hippo-YAP/TAZ-TEAD axis promotes multipotency in bone marrow stromal cells", "journal": "bioRxiv", "authors": ["Cheng YH", "Chan CHR", "Bian Q", "Merling RK", "Kuznetsov SA", "Robey PG", "Cahan P"], "date": "May 2024", "pmid": "38798468", "pubmedUrl": "https://pubmed.ncbi.nlm.nih.gov/38798468/", "summary": "TEAD transcription factors, regulated by Hippo signaling, maintain bone marrow stromal cell multipotency and inhibit differentiation." } ] }