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Author Details

Stefan Bekiranov
University of Virginia
2000
81
32
Andrej Sali (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36864611Interpretable meta-learning of multi-omics data for survival analysis and pathway enrichment.Bioinformatics2023
37546819Genome-scale chromatin interaction dynamic measurements for key components of the RNA Pol II general transcription machinery.bioRxiv2023
37540223ProtoCell4P: an explainable prototype-based neural network for patient classification using single-cell RNA-seq.Bioinformatics2023
36538614A Step Toward Personalized Surgical Decision Making: Machine Learning Predicts 1 Versus Numerous Melanoma Lymph Node Metastases Using RNA-sequencing.Ann Surg2023
36358927Generalization Performance of Quantum Metric Learning Classifiers.Biomolecules2022
35369706Inhibition of DYRK1a Enhances Cardiomyocyte Cycling After Myocardial Infarction.Circ Res2022
32682541Upregulation of human endogenous retrovirus-K (HML-2) mRNAs in hepatoblastoma: Identification of potential new immunotherapeutic targets and biomarkers.J Pediatr Surg2021
33580203Genomic and evolutionary portraits of disease relapse in acute myeloid leukemia.Leukemia2021
34454518Associations of immune cell homing gene signatures and infiltrates of lymphocyte subsets in human melanomas: discordance with CD163<sup>+</sup> myeloid cell infiltrates.J Transl Med2021
34031486IGF1R and Src inhibition induce synergistic cytotoxicity in HNSCC through inhibition of FAK.Sci Rep2021
31433065Antitumor effect of insulin-like growth factor-1 receptor inhibition in head and neck squamous cell carcinoma.Laryngoscope2020
32029477Pausing sites of RNA polymerase II on actively transcribed genes are enriched in DNA double-stranded breaks.J Biol Chem2020
33271747A Machine Learning Model Utilizing a Novel SNP Shows Enhanced Prediction of Coronary Artery Disease Severity.Genes (Basel)2020
32637500Human endogenous retrovirus-K mRNA expression and genomic alignment data in hepatoblastoma.Data Brief2020
32879908Implementation of a Hamming distance-like genomic quantum classifier using inner products on ibmqx2 and ibmq_16_melbourne.Quantum Mach Intell2020
32674599Stem Cell Pluripotency Genes Klf4 and Oct4 Regulate Complex SMC Phenotypic Changes Critical in Late-Stage Atherosclerotic Lesion Pathogenesis.Circulation2020
32894181COCOA: coordinate covariation analysis of epigenetic heterogeneity.Genome Biol2020
30673605Neurons with Complex Karyotypes Are Rare in Aged Human Neocortex.Cell Rep2019
31842941HIV-1 Rev interacts with HERV-K RcREs present in the human genome and promotes export of unspliced HERV-K proviral RNA.Retrovirology2019
31741768Systems analysis of barrier molecule and ARNT-related gene expression regulation in melanoma.Oncoimmunology2019
30098338Temporal and Spatial Epigenome Editing Allows Precise Gene Regulation in Mammalian Cells.J Mol Biol2019
31461456A Sir2-regulated locus control region in the recombination enhancer of Saccharomyces cerevisiae specifies chromosome III structure.PLoS Genet2019
30885209NF-κB upregulates glutamine-fructose-6-phosphate transaminase 2 to promote migration in non-small cell lung cancer.Cell Commun Signal2019
30597148High-content phenotypic assay for proliferation of human iPSC-derived cardiomyocytes identifies L-type calcium channels as targets.J Mol Cell Cardiol2019
29682595An Improved Method for Measuring Chromatin-binding Dynamics Using Time-dependent Formaldehyde Crosslinking.Bio Protoc2018
30001206Alternative DNA secondary structure formation affects RNA polymerase II promoter-proximal pausing in human.Genome Biol2018
30420518Histone H3 lysine 4 methylation signature associated with human undernutrition.Proc Natl Acad Sci U S A2018
28051102RNA synthesis is associated with multiple TBP-chromatin binding events.Sci Rep2017
29034364Microenvironmental agonists generate <i>de novo</i> phenotypic resistance to combined ibrutinib plus venetoclax in CLL and MCL.Blood Adv2017
28972159Second-generation method for analysis of chromatin binding with formaldehyde-cross-linking kinetics.J Biol Chem2017
28665995Transcriptomes of six mutants in the Sen1 pathway reveal combinatorial control of transcription termination across the Saccharomyces cerevisiae genome.PLoS Genet2017
27047702A pan-cancer analysis of prognostic genes.PeerJ2016
26673621Combinatorial drug screening and molecular profiling reveal diverse mechanisms of intrinsic and adaptive resistance to BRAF inhibition in V600E BRAF mutant melanomas.Oncotarget2016
27226635The Modifier of Transcription 1 (Mot1) ATPase and Spt16 Histone Chaperone Co-regulate Transcription through Preinitiation Complex Assembly and Nucleosome Organization.J Biol Chem2016
27183216Activation of the pluripotency factor OCT4 in smooth muscle cells is atheroprotective.Nat Med2016
25432175Activin upregulation by NF-κB is required to maintain mesenchymal features of cancer stem-like cells in non-small cell lung cancer.Cancer Res2015
26405815Systems Analysis of Adaptive Responses to MAP Kinase Pathway Blockade in BRAF Mutant Melanoma.PLoS One2015
26617673Genome-wide predictors of NF-κB recruitment and transcriptional activity.BioData Min2015
25769345Functional genomic analysis reveals overlapping and distinct features of chronologically long-lived yeast populations.Aging (Albany NY)2015
24472558Combinatorial epigenetic patterns as quantitative predictors of chromatin biology.BMC Genomics2014
25448301Analysis of chromatin binding dynamics using the crosslinking kinetics (CLK) method.Methods2014
24503860Tolerogenic properties of lymphatic endothelial cells are controlled by the lymph node microenvironment.PLoS One2014
23210685Sexual differentiation in the developing mouse brain: contributions of sex chromosome genes.Genes Brain Behav2013
24349163The network architecture of the Saccharomyces cerevisiae genome.PLoS One2013
24091704Measuring chromatin interaction dynamics on the second time scale at single-copy genes.Science2013
23861383Bubble-seq analysis of the human genome reveals distinct chromatin-mediated mechanisms for regulating early- and late-firing origins.Genome Res2013
23935876NF-κB regulates mesenchymal transition for the induction of non-small cell lung cancer initiating cells.PLoS One2013
24004852Epigenetic coordination of signaling pathways during the epithelial-mesenchymal transition.Epigenetics Chromatin2013
23710766Genome-wide analysis of functional sirtuin chromatin targets in yeast.Genome Biol2013
23236151Reelin is a target of polyglutamine expanded ataxin-7 in human spinocerebellar ataxia type 7 (SCA7) astrocytes.Proc Natl Acad Sci U S A2012
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Collaborators

David T Auble
University of Virginia
Co-authored papers 12
Thomas R Gingeras
Stanley Institute for Cognitive Genomics
Co-authored papers 8
Emanuel F Petricoin
Center for Applied Proteomics and Molecular Medicine, George Mason University
Co-authored papers 6
Philipp Kapranov
Co-authored papers 5
Jorg Drenkow
Co-authored papers 5
Terry Gaasterland
Scripps Institution of Oceanography, University of California San Diego
Co-authored papers 4
Craig L Slingluff
University of Virginia
Co-authored papers 4
Anindya Dutta
Co-authored papers 4
Marcin Cieslik
Co-authored papers 4
Aakrosh Ratan
Center for Public Health Genomics, University of Virginia
Co-authored papers 3
Simon Cawley
Clinical Sequencing Division
Co-authored papers 3
Gregg A Helt
Lawrence Berkeley National Laboratory
Co-authored papers 3
Jae K Lee
Co-authored papers 3
Jill Cheng
Co-authored papers 3
Hari Tammana
Co-authored papers 3
Brian J Capaldo
Center for Cancer Research, National Cancer Institute
Co-authored papers 3
Sandeep Patel
Co-authored papers 2
Neerja Karnani
Co-authored papers 2
Alexander Sczyrba
Center for Biotechnology (CeBiTec), Bielefeld University, Universitatsstrasse 27
Co-authored papers 2
Aaron J Mackey
HemoShear Therapeutics LLC
Co-authored papers 2
Aidong Zhang (CM4AI)
University of Virginia
Co-authored papers 2
Margaret E Wierman
Co-authored papers 2
Taesung Park
Co-authored papers 2
Jeffrey J Saucerman
University of Virginia
Co-authored papers 2
Jef D Boeke
Institute for Systems Genetics, NYU School of Medicine
Co-authored papers 2
Victor H Engelhard
University of Virginia School of Medicine
Co-authored papers 2
Francine E Garrett-Bakelman
University of Virginia
Co-authored papers 2
Srinka Ghosh
Co-authored papers 2
Larry D Mesner
Center for Public Health Genomics, University of Virginia
Co-authored papers 2
Stuart L Schreiber
Broad Institute
Co-authored papers 1
Release 1.2