Peilin Jia

Peilin Jia

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Peilin Jia

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TSEA-DB: a trait-tissue association map for human complex traits and diseases.

Nucleic Acids Res 2019 Nov 4. Epub 2019 Nov 4.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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http://dx.doi.org/10.1093/nar/gkz957DOI Listing
November 2019

deTS: tissue-specific enrichment analysis to decode tissue specificity.

Bioinformatics 2019 Oct;35(19):3842-3845

School of Biomedical Informatics, Center for Precision Health, The University of Texas Health Science Center at Houston, Houston, TX, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6761978PMC
October 2019

Critical microRNAs and regulatory motifs in cleft palate identified by a conserved miRNA-TF-gene network approach in humans and mice.

Brief Bioinform 2019 Oct 7. Epub 2019 Oct 7.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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http://dx.doi.org/10.1093/bib/bbz082DOI Listing
October 2019

VISDB: a manually curated database of viral integration sites in the human genome.

Nucleic Acids Res 2019 Oct 10. Epub 2019 Oct 10.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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http://dx.doi.org/10.1093/nar/gkz867DOI Listing
October 2019

Decoding regulatory structures and features from epigenomics profiles: A Roadmap-ENCODE Variational Auto-Encoder (RE-VAE) model.

Methods 2019 Oct 28. Epub 2019 Oct 28.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2019.10.012DOI Listing
October 2019

Distinct telomere length and molecular signatures in seminoma and non-seminoma of testicular germ cell tumor.

Brief Bioinform 2019 07;20(4):1502-1512

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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http://dx.doi.org/10.1093/bib/bby020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6781582PMC
July 2019

MicroRNA-655-3p and microRNA-497-5p inhibit cell proliferation in cultured human lip cells through the regulation of genes related to human cleft lip.

BMC Med Genomics 2019 05 23;12(1):70. Epub 2019 May 23.

Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, USA.

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http://dx.doi.org/10.1186/s12920-019-0535-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6533741PMC
May 2019

CNet: A Multi-omics Approach to Detecting Clinically Associated, Combinatory Genomic Signatures.

Bioinformatics 2019 May 28. Epub 2019 May 28.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz441DOI Listing
May 2019

Mega-analysis of Odds Ratio: A Convergent Method for a Deep Understanding of the Genetic Evidence in Schizophrenia.

Schizophr Bull 2019 04;45(3):698-708

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX.

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http://dx.doi.org/10.1093/schbul/sby085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6483587PMC
April 2019

A Convergent Study of Genetic Variants Associated With Crohn's Disease: Evidence From GWAS, Gene Expression, Methylation, eQTL and TWAS.

Front Genet 2019 9;10:318. Epub 2019 Apr 9.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States.

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http://dx.doi.org/10.3389/fgene.2019.00318DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6467075PMC
April 2019

TET2 stabilization by 14-3-3 binding to the phosphorylated Serine 99 is deregulated by mutations in cancer.

Cell Res 2019 Mar 3;29(3):248-250. Epub 2019 Jan 3.

Laboratory of Epigenetics, Liver Cancer Institute, Zhongshan Hospital, and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.

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http://www.nature.com/articles/s41422-018-0132-5
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http://dx.doi.org/10.1038/s41422-018-0132-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6460428PMC
March 2019

Investigation of multi-trait associations using pathway-based analysis of GWAS summary statistics.

BMC Genomics 2019 Feb 4;20(Suppl 1):79. Epub 2019 Feb 4.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 820, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1186/s12864-018-5373-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6360716PMC
February 2019

Gene2vec: distributed representation of genes based on co-expression.

BMC Genomics 2019 Feb 4;20(Suppl 1):82. Epub 2019 Feb 4.

The University of Texas School of Biomedical Informatics, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1186/s12864-018-5370-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6360648PMC
February 2019

Characterization of Tumor-Suppressor Gene Inactivation Events in 33 Cancer Types.

Cell Rep 2019 01;26(2):496-506.e3

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.12.066DOI Listing
January 2019

Network-based identification of critical regulators as putative drivers of human cleft lip.

BMC Med Genomics 2019 Jan 31;12(Suppl 1):16. Epub 2019 Jan 31.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St., Suite 820, Houston, TX, 77030, USA.

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https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s1
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http://dx.doi.org/10.1186/s12920-018-0458-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357351PMC
January 2019

Multiple transcription factors contribute to inter-chromosomal interaction in yeast.

BMC Syst Biol 2018 12 21;12(Suppl 8):140. Epub 2018 Dec 21.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 820, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1186/s12918-018-0643-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6302461PMC
December 2018

Kinase impact assessment in the landscape of fusion genes that retain kinase domains: a pan-cancer study.

Brief Bioinform 2018 05;19(3):450-460

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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http://dx.doi.org/10.1093/bib/bbw127DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5952959PMC
May 2018

Convergent roles of de novo mutations and common variants in schizophrenia in tissue-specific and spatiotemporal co-expression network.

Transl Psychiatry 2018 05 24;8(1):105. Epub 2018 May 24.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA.

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http://dx.doi.org/10.1038/s41398-018-0154-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5967316PMC
May 2018

Genes and microRNAs associated with mouse cleft palate: A systematic review and bioinformatics analysis.

Mech Dev 2018 04 21;150:21-27. Epub 2018 Feb 21.

Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, USA; Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, USA; MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA. Electronic address:

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http://dx.doi.org/10.1016/j.mod.2018.02.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5906164PMC
April 2018

Weak sharing of genetic association signals in three lung cancer subtypes: evidence at the SNP, gene, regulation, and pathway levels.

Genome Med 2018 02 27;10(1):16. Epub 2018 Feb 27.

Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA.

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http://dx.doi.org/10.1186/s13073-018-0522-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5828003PMC
February 2018

TissGDB: tissue-specific gene database in cancer.

Nucleic Acids Res 2018 01;46(D1):D1031-D1038

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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http://dx.doi.org/10.1093/nar/gkx850DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753286PMC
January 2018

Splicing QTL of human adipose-related traits.

Sci Rep 2018 01 10;8(1):318. Epub 2018 Jan 10.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA.

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http://dx.doi.org/10.1038/s41598-017-18767-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5762880PMC
January 2018

An integrative functional genomics framework for effective identification of novel regulatory variants in genome-phenome studies.

Genome Med 2018 01 29;10(1). Epub 2018 Jan 29.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 820, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1186/s13073-018-0513-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5789733PMC
January 2018

ANCO-GeneDB: annotations and comprehensive analysis of candidate genes for alcohol, nicotine, cocaine and opioid dependence.

Database (Oxford) 2018 01 1;2018. Epub 2018 Jan 1.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA.

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https://academic.oup.com/database/article/doi/10.1093/databa
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http://dx.doi.org/10.1093/database/bay121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6310508PMC
January 2018

scRNASeqDB: A Database for RNA-Seq Based Gene Expression Profiles in Human Single Cells.

Genes (Basel) 2017 Dec 5;8(12). Epub 2017 Dec 5.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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http://dx.doi.org/10.3390/genes8120368DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5748686PMC
December 2017

Unique protein expression signatures of survival time in kidney renal clear cell carcinoma through a pan-cancer screening.

BMC Genomics 2017 Oct 3;18(Suppl 6):678. Epub 2017 Oct 3.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St., Suite 820, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1186/s12864-017-4026-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5629613PMC
October 2017

SZGR 2.0: a one-stop shop of schizophrenia candidate genes.

Nucleic Acids Res 2017 01 12;45(D1):D915-D924. Epub 2016 Oct 12.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA

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http://dx.doi.org/10.1093/nar/gkw902DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210619PMC
January 2017

Targeted activation of CREB in reactive astrocytes is neuroprotective in focal acute cortical injury.

Glia 2016 May 16;64(5):853-74. Epub 2016 Feb 16.

Institut De Neurociències and Unitat De Bioquímica, Facultat De Medicina, Universitat Autònoma De Barcelona, Bellaterra, Barcelona, 08193, Spain.

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http://dx.doi.org/10.1002/glia.22969DOI Listing
May 2016

MSEA: detection and quantification of mutation hotspots through mutation set enrichment analysis.

Genome Biol 2014 ;15(10):489

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, USA.

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http://dx.doi.org/10.1186/s13059-014-0489-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4226881PMC
October 2015

A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3,000 Cancer Genomes across 9 Cancer Types.

PLoS Comput Biol 2015 Sep 9;11(9):e1004497. Epub 2015 Sep 9.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004497DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4564226PMC
September 2015

EW_dmGWAS: edge-weighted dense module search for genome-wide association studies and gene expression profiles.

Bioinformatics 2015 Aug 24;31(15):2591-4. Epub 2015 Mar 24.

Department of Biomedical Informatics, Center for Quantitative Sciences.

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http://dx.doi.org/10.1093/bioinformatics/btv150DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4514922PMC
August 2015

Inconsistency and features of single nucleotide variants detected in whole exome sequencing versus transcriptome sequencing: A case study in lung cancer.

Methods 2015 Jul 23;83:118-27. Epub 2015 Apr 23.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, United States; Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN 37232, United States; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, United States. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2015.04.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4509831PMC
July 2015

Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action.

PLoS Comput Biol 2015 Jun 17;11(6):e1004202. Epub 2015 Jun 17.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America; Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4470683PMC
June 2015

Network and pathway analysis of cancer susceptibility (a).

Cancer Inform 2014 12;13(Suppl 5):125-7. Epub 2014 Mar 12.

Director of Bioinformatics and Biostatistics, Associate Professor, Department of Internal Medicine and Biochemistry, Rush University Medical Center, Chicago, IL, USA.

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http://dx.doi.org/10.4137/CIN.S24095DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4364546PMC
April 2015

Consensus rules in variant detection from next-generation sequencing data.

PLoS One 2012 8;7(6):e38470. Epub 2012 Jun 8.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0038470PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3371040PMC
February 2015

Heterogeneous DNA methylation contributes to tumorigenesis through inducing the loss of coexpression connectivity in colorectal cancer.

Genes Chromosomes Cancer 2015 Feb 19;54(2):110-21. Epub 2014 Nov 19.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN.

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http://dx.doi.org/10.1002/gcc.22224DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4785867PMC
February 2015

Optimizing the sequence of anti-EGFR-targeted therapy in EGFR-mutant lung cancer.

Mol Cancer Ther 2015 Feb 4;14(2):542-52. Epub 2014 Dec 4.

Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee. Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee. Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee.

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http://dx.doi.org/10.1158/1535-7163.MCT-14-0723DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4338015PMC
February 2015

VERSE: a novel approach to detect virus integration in host genomes through reference genome customization.

Genome Med 2015 20;7(1). Epub 2015 Jan 20.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203 USA ; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232 USA ; Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN 37232 USA ; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232 USA.

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http://dx.doi.org/10.1186/s13073-015-0126-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4333248PMC
February 2015

Key regulators in prostate cancer identified by co-expression module analysis.

BMC Genomics 2014 Nov 24;15:1015. Epub 2014 Nov 24.

Center for Systems Biology, Soochow University, Jiangsu, China.

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http://dx.doi.org/10.1186/1471-2164-15-1015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4258300PMC
November 2014

Multi-dimensional prioritization of dental caries candidate genes and its enriched dense network modules.

PLoS One 2013 11;8(10):e76666. Epub 2013 Oct 11.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0076666PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3795720PMC
August 2014

Studying tumorigenesis through network evolution and somatic mutational perturbations in the cancer interactome.

Mol Biol Evol 2014 Aug 31;31(8):2156-69. Epub 2014 May 31.

Department of Biomedical Informatics, Vanderbilt University School of MedicineDepartment of Cancer Biology, Vanderbilt University School of MedicineDepartment of Psychiatry, Vanderbilt University School of MedicineCenter for Quantitative Sciences, Vanderbilt University Medical Center

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http://dx.doi.org/10.1093/molbev/msu167DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4104318PMC
August 2014

Top associated SNPs in prostate cancer are significantly enriched in cis-expression quantitative trait loci and at transcription factor binding sites.

Oncotarget 2014 Aug;5(15):6168-77

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA; Center for Quantitative Sciences, Vanderbilt University, Nashville, TN, USA; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4171620PMC
http://dx.doi.org/10.18632/oncotarget.2179DOI Listing
August 2014

A meta-analysis of somatic mutations from next generation sequencing of 241 melanomas: a road map for the study of genes with potential clinical relevance.

Mol Cancer Ther 2014 Jul 22;13(7):1918-28. Epub 2014 Apr 22.

Authors' Affiliations: Department of Biomedical Informatics; Center for Quantitative Sciences; Department of Cancer Biology; Vanderbilt-Ingram Cancer Center; and

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http://dx.doi.org/10.1158/1535-7163.MCT-13-0804DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4090262PMC
July 2014

Quantitative network mapping of the human kinome interactome reveals new clues for rational kinase inhibitor discovery and individualized cancer therapy.

Oncotarget 2014 06;5(11):3697-710

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4116514PMC
http://dx.doi.org/10.18632/oncotarget.1984DOI Listing
June 2014

Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers.

Genome Med 2013 11;5(10):91. Epub 2013 Oct 11.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA ; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA ; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA ; Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN, USA.

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http://dx.doi.org/10.1186/gm495DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3971343PMC
May 2014

Acquired resistance of EGFR-mutant lung adenocarcinomas to afatinib plus cetuximab is associated with activation of mTORC1.

Cell Rep 2014 May 9;7(4):999-1008. Epub 2014 May 9.

Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Medicine (Medical Oncology), Yale University School of Medicine, New Haven, CT 06510, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2014.04.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4074596PMC
May 2014

Association signals unveiled by a comprehensive gene set enrichment analysis of dental caries genome-wide association studies.

PLoS One 2013 14;8(8):e72653. Epub 2013 Aug 14.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0072653PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3743773PMC
March 2014

VarWalker: personalized mutation network analysis of putative cancer genes from next-generation sequencing data.

PLoS Comput Biol 2014 Feb 6;10(2):e1003460. Epub 2014 Feb 6.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America ; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America ; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America ; Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1003460DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3916227PMC
February 2014

Patterns and processes of somatic mutations in nine major cancers.

BMC Med Genomics 2014 Feb 19;7:11. Epub 2014 Feb 19.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, USA.

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http://dx.doi.org/10.1186/1755-8794-7-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3942057PMC
February 2014

Protein-protein interaction and pathway analyses of top schizophrenia genes reveal schizophrenia susceptibility genes converge on common molecular networks and enrichment of nucleosome (chromatin) assembly genes in schizophrenia susceptibility loci.

Schizophr Bull 2014 Jan 12;40(1):39-49. Epub 2013 May 12.

*To whom correspondence should be addressed; Flaum Eye Institute and Department of Ophthalmology, 601 Elmwood Avenue, Box 659, University of Rochester, Rochester, NY 14642, US; tel: 585-880-8814, fax: 585-276-2432, e-mail:

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http://dx.doi.org/10.1093/schbul/sbt066DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3885298PMC
January 2014

Deciphering the unique microRNA signature in human esophageal adenocarcinoma.

PLoS One 2013 28;8(5):e64463. Epub 2013 May 28.

Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0064463PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3665888PMC
January 2014

VirusFinder: software for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data.

PLoS One 2013 24;8(5):e64465. Epub 2013 May 24.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0064465PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3663743PMC
November 2013

Integrative pathway analysis of genome-wide association studies and gene expression data in prostate cancer.

BMC Syst Biol 2012 17;6 Suppl 3:S13. Epub 2012 Dec 17.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA.

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http://dx.doi.org/10.1186/1752-0509-6-S3-S13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3524313PMC
June 2013

Gastric adenocarcinoma has a unique microRNA signature not present in esophageal adenocarcinoma.

Cancer 2013 Jun 1;119(11):1985-93. Epub 2013 Mar 1.

Department of Surgery, Vanderbilt University Medical Center, Nashville, TN 37232, USA.

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http://dx.doi.org/10.1002/cncr.28002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3731210PMC
June 2013

Searching joint association signals in CATIE schizophrenia genome-wide association studies through a refined integrative network approach.

BMC Genomics 2012 26;13 Suppl 6:S15. Epub 2012 Oct 26.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA.

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http://dx.doi.org/10.1186/1471-2164-13-S6-S15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3481439PMC
April 2013

Network-assisted investigation of combined causal signals from genome-wide association studies in schizophrenia.

PLoS Comput Biol 2012 5;8(7):e1002587. Epub 2012 Jul 5.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1002587DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390381PMC
January 2013

Enriched pathways for major depressive disorder identified from a genome-wide association study.

Int J Neuropsychopharmacol 2012 Nov 16;15(10):1401-11. Epub 2012 Jan 16.

Department of Public Health and Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan.

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http://ijnp.oxfordjournals.org/cgi/doi/10.1017/S146114571100
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http://dx.doi.org/10.1017/S1461145711001891DOI Listing
November 2012

A comprehensive network and pathway analysis of candidate genes in major depressive disorder.

BMC Syst Biol 2011 23;5 Suppl 3:S12. Epub 2011 Dec 23.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA.

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http://link.springer.com/content/pdf/10.1186%2F1752-0509-5-S
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http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287567PMC
November 2012

Personalized pathway enrichment map of putative cancer genes from next generation sequencing data.

PLoS One 2012 18;7(5):e37595. Epub 2012 May 18.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3356304PMC
September 2012

NGS catalog: A database of next generation sequencing studies in humans.

Hum Mutat 2012 Jun 19;33(6):E2341-55. Epub 2012 Apr 19.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, USA.

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http://dx.doi.org/10.1002/humu.22096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4431973PMC
June 2012

Two non-synonymous markers in PTPN21, identified by genome-wide association study data-mining and replication, are associated with schizophrenia.

Schizophr Res 2011 Sep 14;131(1-3):43-51. Epub 2011 Jul 14.

Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Suite 390, 800 E. Leigh Street, Richmond, VA 23298, USA.

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http://dx.doi.org/10.1016/j.schres.2011.06.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4117700PMC
September 2011

Histone H2B ubiquitylation and H3 lysine 4 methylation prevent ectopic silencing of euchromatic loci important for the cellular response to heat.

Mol Biol Cell 2011 Aug 16;22(15):2741-53. Epub 2011 Jun 16.

Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.

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http://dx.doi.org/10.1091/mbc.E11-05-0426DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3145549PMC
August 2011

Gene set analysis of genome-wide association studies: methodological issues and perspectives.

Genomics 2011 Jul 30;98(1):1-8. Epub 2011 Apr 30.

Department of Biostatistics, Vanderbilt University, Nashville, TN 37232, USA.

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http://dx.doi.org/10.1016/j.ygeno.2011.04.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3852939PMC
July 2011

Do cancer proteins really interact strongly in the human protein-protein interaction network?

Comput Biol Chem 2011 Jun;35(3):121-5

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.

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http://dx.doi.org/10.1016/j.compbiolchem.2011.04.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3111062PMC
June 2011

Pathway-based analysis of GWAS datasets: effective but caution required.

Int J Neuropsychopharmacol 2011 May 16;14(4):567-72. Epub 2010 Dec 16.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA.

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May 2011

Assessing gene length biases in gene set analysis of Genome-Wide Association Studies.

Int J Comput Biol Drug Des 2010 4;3(4):297-310. Epub 2011 Feb 4.

Departments of Biomedical Informatics and Psychiatry, Vanderbilt University Medical Centre, Nashville, Tennessee 37232, USA.

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http://dx.doi.org/10.1504/IJCBDD.2010.038394DOI Listing
May 2011

An efficient hierarchical generalized linear mixed model for pathway analysis of genome-wide association studies.

Bioinformatics 2011 Mar 25;27(5):686-92. Epub 2011 Jan 25.

Department of Biostatistics, Vanderbilt University, Nashville, TN 37232, USA.

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http://dx.doi.org/10.1093/bioinformatics/btq728DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3042187PMC
March 2011

Prioritization of epilepsy associated candidate genes by convergent analysis.

PLoS One 2011 Feb 24;6(2):e17162. Epub 2011 Feb 24.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3044734PMC
February 2011

dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks.

Bioinformatics 2011 Jan 2;27(1):95-102. Epub 2010 Nov 2.

Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37232, USA.

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http://dx.doi.org/10.1093/bioinformatics/btq615DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3008643PMC
January 2011

Network-assisted Causal Gene Detection in Genome-wide Association Studies: An Improved Module Search Algorithm.

IEEE Int Workshop Genomic Signal Process Stat 2011 :131-134

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.

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http://dx.doi.org/10.1109/GENSiPS.2011.6169462DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418601PMC
January 2011

Common variants conferring risk of schizophrenia: a pathway analysis of GWAS data.

Schizophr Res 2010 Sep 24;122(1-3):38-42. Epub 2010 Jul 24.

Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.

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http://dx.doi.org/10.1016/j.schres.2010.07.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2933424PMC
September 2010