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Author Details

Xianghong Jasmine Zhou
David Geffen School of Medicine, University of California at Los Angeles
2004
69
32
Gloria M Sheynkman (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
35908246HCC EV ECG score: An extracellular vesicle-based protein assay for detection of early-stage hepatocellular carcinoma.Hepatology2023
37580627Evaluating the role of the nuclear microenvironment in gene function by population-based modeling.Nat Struct Mol Biol2023
37399400Comprehensive tissue deconvolution of cell-free DNA by deep learning for disease diagnosis and monitoring.Proc Natl Acad Sci U S A2023
36849599cfSNV: a software tool for the sensitive detection of somatic mutations from cell-free DNA.Nat Protoc2023
35149536cfTrack: A Method of Exome-Wide Mutation Analysis of Cell-free DNA to Simultaneously Monitor the Full Spectrum of Cancer Treatment Outcomes Including MRD, Recurrence, and Evolution.Clin Cancer Res2022
35671506Computational Analysis of High-Dimensional DNA Methylation Data for Cancer Prognosis.J Comput Biol2022
35817938Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations.Nat Methods2022
36175411Cost-effective methylome sequencing of cell-free DNA for accurately detecting and locating cancer.Nat Commun2022
33045922Cell-free DNA Methylation and Transcriptomic Signature Prediction of Pregnancies with Adverse Outcomes.Epigenetics2021
34377977ARG-SHINE: improve antibiotic resistance class prediction by integrating sequence homology, functional information and deep convolutional neural network.NAR Genom Bioinform2021
34234141Sensitive detection of tumor mutations from blood and its application to immunotherapy prognosis.Nat Commun2021
32732909Methylation extends the reach of liquid biopsy in cancer detection.Nat Rev Clin Oncol2020
31906978Rapid diagnosis and comprehensive bacteria profiling of sepsis based on cell-free DNA.J Transl Med2020
32637655Somatic copy number profiling from hepatocellular carcinoma circulating tumor cells.NPJ Precis Oncol2020
30668638CMEP: a database for circulating microRNA expression profiling.Bioinformatics2019
31598384The size of cell-free mitochondrial DNA in blood is inversely correlated with tumor burden in cancer patients.Precis Clin Med2019
30338927Detecting early-warning signals of influenza outbreak based on dynamic network marker.J Cell Mol Med2019
29622804Producing genome structure populations with the dynamic and automated PGS software.Nat Protoc2018
29897492CancerDetector: ultrasensitive and non-invasive cancer detection at the resolution of individual reads using cell-free DNA methylation sequencing data.Nucleic Acids Res2018
28760140The three-dimensional genome organization of Drosophila melanogaster through data integration.Genome Biol2017
28335812CancerLocator: non-invasive cancer diagnosis and tissue-of-origin prediction using methylation profiles of cell-free DNA.Genome Biol2017
26238263Pushing the annotation of cellular activities to a higher resolution: Predicting functions at the isoform level.Methods2016
26602695Cancer RNA-Seq Nexus: a database of phenotype-specific transcriptome profiling in cancer cells.Nucleic Acids Res2016
27240697Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities.Nat Commun2016
26704975TopDom: an efficient and deterministic method for identifying topological domains in genomes.Nucleic Acids Res2016
26951677Population-based 3D genome structure analysis reveals driving forces in spatial genome organization.Proc Natl Acad Sci U S A2016
26871637Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing.Cell2016
25391400Hi-Corrector: a fast, scalable and memory-efficient package for normalizing large-scale Hi-C data.Bioinformatics2015
25684200Finding genetic overlaps among diseases based on ranked gene lists.J Comput Biol2015
25708095Network tuned multiple rank aggregation and applications to gene ranking.BMC Bioinformatics2015
25707505IIIDB: a database for isoform-isoform interactions and isoform network modules.BMC Genomics2015
25799503Comparative 3D genome structure analysis of the fission and the budding yeast.PLoS One2015
25567984DNA binding by FOXP3 domain-swapped dimer suggests mechanisms of long-range chromosomal interactions.Nucleic Acids Res2015
24369432High-resolution functional annotation of human transcriptome: predicting isoform functions by a novel multiple instance-based label propagation method.Nucleic Acids Res2014
25030932Matrix factorization methods for integrative cancer genomics.Methods Mol Biol2014
24895436DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections.Nucleic Acids Res2014
24583115Integrative analysis of many RNA-seq datasets to study alternative splicing.Methods2014
23408854Functional DNA demethylation is accompanied by chromatin accessibility.Nucleic Acids Res2013
23637628SNF5 is an essential executor of epigenetic regulation during differentiation.PLoS Genet2013
22923582Dense chromatin activates Polycomb repressive complex 2 to regulate H3 lysine 27 methylation.Science2012
23018997Zooming in on genome organization.Nat Methods2012
23046974Integrating many co-splicing networks to reconstruct splicing regulatory modules.BMC Syst Biol2012
22697243Algorithm to identify frequent coupled modules from two-layered network series: application to study transcription and splicing coupling.J Comput Biol2012
22863767Identifying multi-layer gene regulatory modules from multi-dimensional genomic data.Bioinformatics2012
22879375Discovery of multi-dimensional modules by integrative analysis of cancer genomic data.Nucleic Acids Res2012
21270055Smad1 and its target gene Wif1 coordinate BMP and Wnt signaling activities to regulate fetal lung development.Development2011
22153073Polycomb-repressed genes have permissive enhancers that initiate reprogramming.Cell2011
21685098A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules.Bioinformatics2011
21698123Integrative analysis of many weighted co-expression networks using tensor computation.PLoS Comput Biol2011
20083231Unraveling complex temporal associations in cellular systems across multiple time-series microarray datasets.J Biomed Inform2010
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Collaborators

Wenyuan Li
Harvard Medical School
Co-authored papers 29
Frank Alber
University of California los angeles
Co-authored papers 13
Michael S Waterman
Biocomplexity Institute and Initiative
Co-authored papers 8
Yonggang Zhou
David Geffen School of Medicine, University of California at Los Angeles
Co-authored papers 8
Steven M Dubinett
David Geffen School of Medicine at university of california los angeles
Co-authored papers 5
Vatche G Agopian
David Geffen School of Medicine , University of California los angeles
Co-authored papers 5
Michael R Mehan
University of Southern California
Co-authored papers 5
Wing Hung Wong
Stanford University
Co-authored papers 5
Edward B Garon
David Geffen School of Medicine, University of California Los Angeles
Co-authored papers 4
Haiyan Huang
Washington State University
Co-authored papers 4
Hsian-Rong Tseng
Jonsson Comprehensive Cancer Center, University of California los angeles
Co-authored papers 3
Xiaohui Ni
EarlyDiagnostics Inc.
Co-authored papers 3
Steven-Huy B Han
David Geffen School of Medicine , University of California los angeles
Co-authored papers 3
Zorawar S Noor
David Geffen School of Medicine at university of california los angeles
Co-authored papers 3
Kurinji Pandiyan
Keck School of Medicine, University of Southern California
Co-authored papers 2
Preeti Ahuja
David Geffen School of Medicine, University of California at Los Angeles
Co-authored papers 2
Kostyantyn Krysan
David Geffen School of Medicine at University of California at Los Angeles
Co-authored papers 2
Jiawei Han
University of Illinois at Urbana-Champaign
Co-authored papers 2
Daniel D De Carvalho
Princess Margaret Cancer Centre, University Health Network
Co-authored papers 2
Clara E Magyar
David Geffen School of Medicine, University of California at Los Angeles
Co-authored papers 2
Matteo Pellegrini
Co-authored papers 2
Samuel W French
David Geffen School of Medicine, University of California at Los Angeles
Co-authored papers 2
Yi Shi
Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai
Co-authored papers 2
Denise R Aberle
David Geffen School of Medicine at university of california los angeles
Co-authored papers 2
Matthew E Johnson
Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia
Co-authored papers 1
Brenda J Andrews
University of Toronto
Co-authored papers 1
Arjan Gower
David Geffen School of Medicine at University of California at Los Angeles
Co-authored papers 1
David S K Lu
University of California, Los Angeles David Geffen School of Medicine
Co-authored papers 1
Michael Costanzo
Co-authored papers 1
Andrew D Wells
Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia
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Release 1.2