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Author Details

Patrick Cahan
Johns Hopkins University
2005
69
30
PMIDPaper TitleJournal TitlePublished Year
36630899A conversation with ChatGPT on the role of computational systems biology in stem cell research.Stem Cell Reports2023
38017015Single cell and spatial transcriptomics analysis of kidney double negative T lymphocytes in normal and ischemic mouse kidneys.Sci Rep2023
37478860Platform-agnostic CellNet enables cross-study analysis of cell fate engineering protocols.Stem Cell Reports2023
37577640A systematic comparison of computational methods for expression forecasting.bioRxiv2023
38091407Analysis of the human kidney transcriptome and plasma proteome identifies markers of proximal tubule maladaptation to injury.Sci Transl Med2023
37186379Sympathetic Innervation Regulates Osteocyte-Mediated Cortical Bone Resorption during Lactation.Adv Sci (Weinh)2023
37204303RANK<sup>+</sup>TLR2<sup>+</sup> myeloid subpopulation converts autoimmune to joint destruction in rheumatoid arthritis.Elife2023
36879188Gene regulation network inference using k-nearest neighbor-based mutual information estimation: revisiting an old DREAM.BMC Bioinformatics2023
36747315Immune Checkpoint Molecule TIGIT Regulates Kidney T Cell Functions and Contributes to AKI.J Am Soc Nephrol2023
35090587Reconstruction of dynamic regulatory networks reveals signaling-induced topology changes associated with germ layer specification.Stem Cell Reports2022
36816792Single-Cell Transcriptomic Census of Endothelial Changes Induced by Matrix Stiffness and the Association with Atherosclerosis.Adv Funct Mater2022
36421094Engineering Skeletal Muscle Grafts with PAX7::GFP-Sorted Human Pluripotent Stem Cell-Derived Myogenic Progenitors on Fibrin Microfiber Bundles for Tissue Regeneration.Bioengineering (Basel)2022
33290741Gene Regulatory Network Analysis and Engineering Directs Development and Vascularization of Multilineage Human Liver Organoids.Cell Syst2021
33926541Evaluating the transcriptional fidelity of cancer models.Genome Med2021
34663698Spatial 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 A2021
34341534Computational reconstruction of the signalling networks surrounding implanted biomaterials from single-cell transcriptomics.Nat Biomed Eng2021
33417869Computational Stem Cell Biology: Open Questions and Guiding Principles.Cell Stem Cell2021
33440181Challenges for Computational Stem Cell Biology: A Discussion for the Field.Stem Cell Reports2021
32161833Multi-scale cellular engineering: From molecules to organ-on-a-chip.APL Bioeng2020
32580935A single cell transcriptional atlas of early synovial joint development.Development2020
32917265Hepatocyte-like cells derived from human induced pluripotent stem cells using small molecules: implications of a transcriptomic study.Stem Cell Res Ther2020
32585153Evaluation of Bunina et al.: Synthesizing Multi-omics Data to Delineate Neuronal Differentiation.Cell Syst2020
32302558Transcriptome Dynamics of Hematopoietic Stem Cell Formation Revealed Using a Combinatorial Runx1 and Ly6a Reporter System.Stem Cell Reports2020
31062321Cell Fate Engineering Tools for iPSC Disease Modeling.Methods Mol Biol2019
31267104A systems biology pipeline identifies regulatory networks for stem cell engineering.Nat Biotechnol2019
31377170SingleCellNet: A Computational Tool to Classify Single Cell RNA-Seq Data Across Platforms and Across Species.Cell Syst2019
31604843Interleukin-36γ-producing macrophages drive IL-17-mediated fibrosis.Sci Immunol2019
31312048Author Correction: A systems biology pipeline identifies regulatory networks for stem cell engineering.Nat Biotechnol2019
31150624A Public BCR Present in a Unique Dual-Receptor-Expressing Lymphocyte from Type 1 Diabetes Patients Encodes a Potent T Cell Autoantigen.Cell2019
29229492Programming Morphogenesis through Systems and Synthetic Biology.Trends Biotechnol2018
30118958A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo.Stem Cell Res2018
29625070A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development.Cell Stem Cell2018
28049689Understanding development and stem cells using single cell-based analyses of gene expression.Development2017
28448485Assessment of engineered cells using CellNet and RNA-seq.Nat Protoc2017
26906680Enabling direct fate conversion with network biology.Nat Genet2016
28009288Engineered Murine HSCs Reconstitute Multi-lineage Hematopoiesis and Adaptive Immunity.Cell Rep2016
27777239TGF-β inhibitors stimulate red blood cell production by enhancing self-renewal of BFU-E erythroid progenitors.Blood2016
27482890Posttranscriptional manipulation of TERC reverses molecular hallmarks of telomere disease.J Clin Invest2016
27383785Multiple mechanisms disrupt the let-7 microRNA family in neuroblastoma.Nature2016
27320042LIN28 Regulates Stem Cell Metabolism and Conversion to Primed Pluripotency.Cell Stem Cell2016
27318512Computational Tools for Stem Cell Biology.Trends Biotechnol2016
26586429Transcriptional Landscape of Cardiomyocyte Maturation.Cell Rep2015
26482878Poly(A)-specific ribonuclease (PARN) mediates 3'-end maturation of the telomerase RNA component.Nat Genet2015
24906150Hippo pathway activity influences liver cell fate.Cell2014
25471879Deconstructing transcriptional heterogeneity in pluripotent stem cells.Nature2014
25485572Defining cellular identity through network biology.Cell Cycle2014
25324523A nontranscriptional role for Oct4 in the regulation of mitotic entry.Proc Natl Acad Sci U S A2014
25126793CellNet: network biology applied to stem cell engineering.Cell2014
25126792Dissecting engineered cell types and enhancing cell fate conversion via CellNet.Cell2014
23673969Origins and implications of pluripotent stem cell variability and heterogeneity.Nat Rev Mol Cell Biol2013
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Collaborators

George Q Daley
Boston Children's Hospital, Harvard Medical School
Co-authored papers 20
Hu Li
Co-authored papers 7
Timothy A Graubert
Massachusetts General Hospital
Co-authored papers 7
Timothy J Ley
Washington University School of Medicine
Co-authored papers 4
Mohammad R Ebrahimkhani
Co-authored papers 3
Howard L McLeod
Center for Precision Medicine and Functional Genomics, Utah Tech University
Co-authored papers 3
Jeremy J Velazquez
Co-authored papers 3
Douglas A Lauffenburger
Massachusetts Institute of Technology
Co-authored papers 2
Owen J L Rackham
Duke-National University of Singapore
Co-authored papers 2
Todd A Richmond
Co-authored papers 2
Christine A Wells
The University of Melbourne
Co-authored papers 2
Yuin-Han Loh
Co-authored papers 2
Stuart H Orkin
Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School
Co-authored papers 2
Jacqueline E Payton
Washington University School of Medicine.
Co-authored papers 2
Jingjing Cao
Co-authored papers 1
Michael H Guo
Co-authored papers 1
Amit U Sinha
Memorial Sloan Kettering Cancer Center
Co-authored papers 1
Nan Zhu
Shanghai General Hospital, Shanghai Jiaotong University
Co-authored papers 1
Sherry G Mansour
Yale School of Medicine
Co-authored papers 1
Frank Berthold
Co-authored papers 1
Christine E Seidman
Brigham and Women's Hospital (Y.K.
Co-authored papers 1
Xian Fan
Rice University
Co-authored papers 1
William T Pu
Boston Children's Hospital, Harvard Medical School
Co-authored papers 1
Song Li
Co-authored papers 1
Thomas C Ferrante
Wyss Institute for Biologically Inspired Engineering, Harvard University
Co-authored papers 1
Joel N Hirschhorn
Broad Institute of MIT and Harvard
Co-authored papers 1
Matthew J Walter
Washington University School of Medicine in St. Louis
Co-authored papers 1
Rahul Satija
Center for Genomics and Systems Biology, New York University
Co-authored papers 1
Tarjei S Mikkelsen
Harvard University, USA Broad Institute, USA Harvard Stem Cell Institute
Co-authored papers 1
Tamara L Lamprecht
St. Jude Children's Research Hospital
Co-authored papers 1
Release 1.2