Publications by authors named "Peilin Jia"

100Publications

A developmental stage specific network approach for studying dynamic transcription factor-microRNA co-regulation during craniofacial development.

Development 2020 Nov 24. Epub 2020 Nov 24.

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1242/dev.192948DOI Listing
November 2020

CSEA-DB: an omnibus for human complex trait and cell type associations.

Nucleic Acids Res 2020 Nov 19. Epub 2020 Nov 19.

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkaa1064DOI Listing
November 2020

Editorial: Advanced Interpretable Machine Learning Methods for Clinical NGS Big Data of Complex Hereditary Diseases.

Front Genet 2020 23;11:600902. Epub 2020 Oct 23.

University of Texas Health Science Center at Houston, Houston, TX, United States.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3389/fgene.2020.600902DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7644923PMC
October 2020

Differential Expression of Viral Transcripts From Single-Cell RNA Sequencing of Moderate and Severe COVID-19 Patients and Its Implications for Case Severity.

Front Microbiol 2020 16;11:603509. Epub 2020 Oct 16.

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2020.603509DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7596306PMC
October 2020

KinaseMD: kinase mutations and drug response database.

Nucleic Acids Res 2020 Nov 2. Epub 2020 Nov 2.

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkaa945DOI Listing
November 2020

Molecular signatures identified by integrating gene expression and methylation in non-seminoma and seminoma of testicular germ cell tumours.

Epigenetics 2020 Jul 13:1-15. Epub 2020 Jul 13.

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1080/15592294.2020.1790108DOI Listing
July 2020

H19, a Long Non-coding RNA, Mediates Transcription Factors and Target Genes through Interference of MicroRNAs in Pan-Cancer.

Mol Ther Nucleic Acids 2020 Sep 27;21:180-191. Epub 2020 May 27.

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.omtn.2020.05.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7321791PMC
September 2020

Deep4mC: systematic assessment and computational prediction for DNA N4-methylcytosine sites by deep learning.

Brief Bioinform 2020 Jun 24. Epub 2020 Jun 24.

Center for Precision Health, School of Biomedical Informatics.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bib/bbaa099DOI Listing
June 2020

Decoding whole-genome mutational signatures in 37 human pan-cancers by denoising sparse autoencoder neural network.

Oncogene 2020 07 11;39(27):5031-5041. Epub 2020 Jun 11.

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41388-020-1343-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7334101PMC
July 2020

An integrative, genomic, transcriptomic and network-assisted study to identify genes associated with human cleft lip with or without cleft palate.

BMC Med Genomics 2020 04 3;13(Suppl 5):39. Epub 2020 Apr 3.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 600, Houston, TX, 77030, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12920-020-0675-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7118807PMC
April 2020

Dense module searching for gene networks associated with multiple sclerosis.

BMC Med Genomics 2020 04 3;13(Suppl 5):48. Epub 2020 Apr 3.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 600, Houston, TX, 77030, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12920-020-0674-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7118851PMC
April 2020

T cell exhaustion is associated with antigen abundance and promotes transplant acceptance.

Am J Transplant 2020 09 17;20(9):2540-2550. Epub 2020 Apr 17.

Immunobiology and Transplant Science Center, Department of Surgery, Houston Methodist Research Institute and Institute for Academic Medicine, Houston Methodist Hospital, Houston, Texas, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/ajt.15870DOI Listing
September 2020

Diverse types of genomic evidence converge on alcohol use disorder risk genes.

J Med Genet 2020 Nov 13;57(11):733-743. Epub 2020 Mar 13.

School of Biomedical Science, University of Texas Health Science Center at Houston, Houston, Texas, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1136/jmedgenet-2019-106490DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7487038PMC
November 2020

6mA-Finder: a novel online tool for predicting DNA N6-methyladenine sites in genomes.

Bioinformatics 2020 05;36(10):3257-3259

School of Biomedical Informatics, Center for Precision Health.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btaa113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7214014PMC
May 2020

MicroRNA and transcription factor co-regulatory networks and subtype classification of seminoma and non-seminoma in testicular germ cell tumors.

Sci Rep 2020 01 21;10(1):852. Epub 2020 Jan 21.

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-020-57834-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6972857PMC
January 2020

Multi-level transcriptome sequencing identifies COL1A1 as a candidate marker in human heart failure progression.

BMC Med 2020 01 6;18(1). Epub 2020 Jan 6.

Department of Cardiac Surgery, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167A Beilishi Road, Xi Cheng District, Beijing, 10037, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12916-019-1469-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6943904PMC
January 2020

MicroRNA-124-3p suppresses mouse lip mesenchymal cell proliferation through the regulation of genes associated with cleft lip in the mouse.

BMC Genomics 2019 Nov 14;20(1):852. Epub 2019 Nov 14.

Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, 1941 East Road, BBS 4208, Houston, TX, 77054, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-019-6238-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6854646PMC
November 2019

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

Nucleic Acids Res 2020 01;48(D1):D1022-D1030

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkz957DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145616PMC
January 2020

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:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ymeth.2019.10.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7431277PMC
October 2019

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

Nucleic Acids Res 2020 01;48(D1):D633-D641

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkz867DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6943068PMC
January 2020

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

Brief Bioinform 2020 07;21(4):1465-1478

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bib/bbz082DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7412957PMC
July 2020

CNet: a multi-omics approach to detecting clinically associated, combinatory genomic signatures.

Bioinformatics 2019 12;35(24):5207-5215

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btz441DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6954662PMC
December 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.

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

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

Bioinformatics 2019 10;35(19):3842-3845

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

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

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

BMC Med Genomics 2019 01 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.

View Article

Download full-text PDF

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.celrep.2018.12.066DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7375892PMC
January 2019

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

Cell Res 2019 03 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.

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

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.

View Article

Download full-text PDF

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

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.

View Article

Download full-text PDF

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

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.

View Article

Download full-text PDF

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

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.

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

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.

View Article

Download full-text PDF

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

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.

View Article

Download full-text PDF

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

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.

View Article

Download full-text PDF

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

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

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

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

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.

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

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.

View Article

Download full-text PDF

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

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.

View Article

Download full-text PDF

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

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.

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

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.

View Article

Download full-text PDF

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

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.

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

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

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:

View Article

Download full-text PDF

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

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.

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

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.

View Article

Download full-text PDF

Source
http://link.springer.com/content/pdf/10.1186%2F1752-0509-5-S
Web Search
http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0
Publisher Site
http://dx.doi.org/10.1186/1752-0509-5-S3-S12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287567PMC
November 2012