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Author Details

Venkat S Malladi
UT Southwestern Medical Center
2008
54
27
PMIDPaper TitleJournal TitlePublished Year
36283570Enhancer and super-enhancer landscape in polycystic kidney disease.Kidney Int2023
37503119The ENCODE Uniform Analysis Pipelines.Res Sq2023
37066421The ENCODE Uniform Analysis Pipelines.bioRxiv2023
37092555Tumor loss-of-function mutations in STK11/LKB1 induce cachexia.JCI Insight2023
36899011Novel long non-coding RNAs associated with inflammation and macrophage activation in human.Sci Rep2023
34019633Improving Renal Tumor Biopsy Prognostication With BAP1 Analyses.Arch Pathol Lab Med2022
35561311Epigenetic Repression of STING by MYC Promotes Immune Evasion and Resistance to Immune Checkpoint Inhibitors in Triple-Negative Breast Cancer.Cancer Immunol Res2022
35881485Targeting ESR1 mutation-induced transcriptional addiction in breast cancer with BET inhibition.JCI Insight2022
35250265Decoding Human Genome Regulatory Features That Influence HIV-1 Proviral Expression and Fate Through an Integrated Genomics Approach.Bioinform Biol Insights2022
34995509Glucose starvation induces a switch in the histone acetylome for activation of gluconeogenic and fat metabolism genes.Mol Cell2022
35134110SeqWho: reliable, rapid determination of sequence file identity using k-mer frequencies in Random Forest classifiers.Bioinformatics2022
34538873Germline and sporadic mTOR pathway mutations in low-grade oncocytic tumor of the kidney.Mod Pathol2022
34173975Single-cell analysis of mouse and human prostate reveals novel fibroblasts with specialized distribution and microenvironment interactions.J Pathol2021
33761354IRF1 governs the differential interferon-stimulated gene responses in human monocytes and macrophages by regulating chromatin accessibility.Cell Rep2021
34739872A multi-omic single-cell landscape of human gynecologic malignancies.Mol Cell2021
34158394PARP-1 Regulates Estrogen-Dependent Gene Expression in Estrogen Receptor α-Positive Breast Cancer Cells.Mol Cancer Res2021
32220301Loss of CHD1 Promotes Heterogeneous Mechanisms of Resistance to AR-Targeted Therapy via Chromatin Dysregulation.Cancer Cell2020
33139957Perivascular mesenchymal cells control adipose-tissue macrophage accrual in obesity.Nat Metab2020
33139246Acute interstitial nephritis, a potential predictor of response to immune checkpoint inhibitors in renal cell carcinoma.J Immunother Cancer2020
32497356Urethral luminal epithelia are castration-insensitive cells of the proximal prostate.Prostate2020
30612451High-Phosphate Diet Induces Exercise Intolerance and Impairs Fatty Acid Metabolism in Mice.Circulation2019
31351877Activation of PARP-1 by snoRNAs Controls Ribosome Biogenesis and Cell Growth via the RNA Helicase DDX21.Mol Cell2019
31233491Open collaborative writing with Manubot.PLoS Comput Biol2019
30975722Twist2 amplification in rhabdomyosarcoma represses myogenesis and promotes oncogenesis by redirecting MyoD DNA binding.Genes Dev2019
30728077Suppression of Myeloid Cell Arginase Activity leads to Therapeutic Response in a NSCLC Mouse Model by Activating Anti-Tumor Immunity.J Immunother Cancer2019
31080136Cardiac Reprogramming Factors Synergistically Activate Genome-wide Cardiogenic Stage-Specific Enhancers.Cell Stem Cell2019
31134894Human pancreatic cancer cell exosomes, but not human normal cell exosomes, act as an initiator in cell transformation.Elife2019
30564890Identification and characterization of an alternative cancer-derived PD-L1 splice variant.Cancer Immunol Immunother2019
29273624Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis.Genome Res2018
30127033Identification of a multipotent Twist2-expressing cell population in the adult heart.Proc Natl Acad Sci U S A2018
30566875A Cellular Anatomy of the Normal Adult Human Prostate and Prostatic Urethra.Cell Rep2018
29458327Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes.BMC Genomics2018
27662874Computational Approaches for Mining GRO-Seq Data to Identify and Characterize Active Enhancers.Methods Mol Biol2017
28403240SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata.PLoS One2017
29174978Transcription pausing regulates mouse embryonic stem cell differentiation.Stem Cell Res2017
28868519Dynamic Change of Transcription Pausing through Modulating NELF Protein Stability Regulates Granulocytic Differentiation.Blood Adv2017
26980513Principles of metadata organization at the ENCODE data coordination center.Database (Oxford)2016
26527727ENCODE data at the ENCODE portal.Nucleic Acids Res2016
25776021Ontology application and use at the ENCODE DCC.Database (Oxford)2015
25409824A comparative encyclopedia of DNA elements in the mouse genome.Nature2014
23155063The UCSC Genome Browser database: extensions and updates 2013.Nucleic Acids Res2013
23193274ENCODE data in the UCSC Genome Browser: year 5 update.Nucleic Acids Res2013
22075998ENCODE whole-genome data in the UCSC Genome Browser: update 2012.Nucleic Acids Res2012
22889292An encyclopedia of mouse DNA elements (Mouse ENCODE).Genome Biol2012
22086951The UCSC Genome Browser database: extensions and updates 2011.Nucleic Acids Res2012
21207104The effect of SNP discovery method and sample size on estimation of population genetic data for Chinese and Indian rhesus macaques (Macaca mulatta).Primates2011
21433046Association between hybrid status and reproductive success of captive male and female rhesus macaques (Macaca mulatta) at the California National Primate Research Center (CNPRC).Am J Primatol2011
21037257ENCODE whole-genome data in the UCSC genome browser (2011 update).Nucleic Acids Res2011
20618591Detecting signatures of inter-regional and inter-specific hybridization among the Chinese rhesus macaque specific pathogen-free (SPF) population using single nucleotide polymorphic (SNP) markers.J Med Primatol2010
18715266Development of a Chinese-Indian hybrid (Chindian) rhesus macaque colony at the California National Primate Research Center by introgression.J Med Primatol2009
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Collaborators

Brian T Lee
Genomics Institute, University of California Santa Cruz
Co-authored papers 8
William James Kent
Co-authored papers 7
Kate R Rosenbloom
Co-authored papers 7
Katrina Learned
Co-authored papers 7
Jean M Davidson
Stanford University School of Medicine
Co-authored papers 6
Benjamin C Hitz
Stanford University School of Medicine
Co-authored papers 6
Melissa S Cline
Genomics Institute, University of California Santa Cruz
Co-authored papers 6
Eurie L Hong
Stanford University School of Medicine
Co-authored papers 6
J Michael Cherry
Stanford University
Co-authored papers 6
Ann S Zweig
Co-authored papers 5
Galt P Barber
Genomics Institute, University of California Santa Cruz
Co-authored papers 5
David Haussler
Genomics Institute, University of California Santa Cruz
Co-authored papers 5
Idan Gabdank
Co-authored papers 5
Robert M Kuhn
Genomics Institute, University of California Santa Cruz
Co-authored papers 5
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Co-authored papers 5
J Seth Strattan
Co-authored papers 4
Rachel A Harte
Co-authored papers 4
Mark Diekhans
Genomics Institute, University of California Santa Cruz
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Barbara J Wold
Merkin Institute for Translational Research, California Institute of Technology
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Douglas W Strand
University of Texas Southwestern Medical Center
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Richard Sandstrom
Altius Institute for Biomedical Sciences
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Angie S Hinrichs
Co-authored papers 4
Stuart R Miyasato
Stanford University
Co-authored papers 4
Ali Mortazavi
Co-authored papers 4
Diane Trout
Co-authored papers 4
Thomas R Gingeras
Stanley Institute for Cognitive Genomics
Co-authored papers 4
Alexander Dobin
Co-authored papers 4
Brooke Rhead
Co-authored papers 4
Hiram Clawson
Co-authored papers 4
Gervaise H Henry
UT Southwestern Medical Center
Co-authored papers 4
Release 1.2