Learning on Weighted Hypergraphs to Integrate Protein Interactions and Gene Expressions for Cancer Outcome Prediction. - TaeHyun Hwang; Ze Tian; Rui Kuang; Jean-Pierre A. Kocher (ICDM, 2008)

Robust and efficient identification of biomarkers by classifying features on graphs. - TaeHyun Hwang; Hugues Sicotte; Ze Tian; Baolin Wu; Jean-Pierre A. Kocher; Dennis A. Wigle; Vipin Kumar 001; Rui Kuang (Bioinform., 2008)

GLOSSI: a method to assess the association of genetic loci-sets with complex diseases. - High-Seng Chai; Hugues Sicotte; Kent R. Bailey; Stephen T. Turner; Yan W. Asmann; Jean-Pierre A. Kocher (BMC Bioinform., 2009)

Spatial normalization improves the quality of genotype calling for Affymetrix SNP 6.0 arrays. - High-Seng Chai; Terry M. Therneau; Kent R. Bailey; Jean-Pierre A. Kocher (BMC Bioinform., 2010)

SNPPicker: High quality tag SNP selection across multiple populations. - Hugues Sicotte; David N. Rider; Gregory A. Poland; Neelam Dhiman; Jean-Pierre A. Kocher (BMC Bioinform., 2011)

Drug side effect extraction from clinical narratives of psychiatry and psychology patients. - Sunghwan Sohn; Jean-Pierre A. Kocher; Christopher G. Chute; Guergana K. Savova (J. Am. Medical Informatics Assoc., 2011)

Multilevel Parallelization of AutoDock 4.2. - Andrew P. Norgan; Paul K. Coffman; Jean-Pierre A. Kocher; David J. Katzmann; Carlos P. Sosa (J. Cheminformatics, 2011)

TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data. - Yan W. Asmann; Sumit Middha; Asif Hossain; Saurabh Baheti; Ying Li; High-Seng Chai; Zhifu Sun; Patrick H. Duffy; Ahmed A. Hadad; Asha A. Nair; Xiaoyu Liu; Yuji Zhang 001; et al. (Bioinform., 2012)

SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing. - Zhifu Sun; Saurabh Baheti; Sumit Middha; Rahul Kanwar; Yuji Zhang 001; Xing Li; Andreas S. Beutler; Eric W. Klee; Yan W. Asmann; E. Aubrey Thompson; Jean-Pierre A. Kocher (Bioinform., 2012)

Biomedical Informatics and the Future of Medicine. - Jean-Pierre A. Kocher (BDI, 2013)

A new statistic for identifying batch effects in high-throughput genomic data that uses guided principal component analysis. - Sarah E. Reese; Kellie J. Archer; Terry M. Therneau; Elizabeth J. Atkinson; Celine M. Vachon; Mariza de Andrade; Jean-Pierre A. Kocher; Jeanette E. Eckel-Passow (Bioinform., 2013)

Calculating Sample Size Estimates for RNA Sequencing Data. - Steven N. Hart; Terry M. Therneau; Yuji Zhang 001; Gregory A. Poland; Jean-Pierre A. Kocher (J. Comput. Biol., 2013)

The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation. - Jean-Pierre A. Kocher; Daniel J. Quest; Patrick H. Duffy; Michael A. Meiners; Raymond M. Moore; David N. Rider; Asif Hossain; Steven N. Hart; Valentin Dinu (Bioinform., 2014)

RVboost: RNA-seq variants prioritization using a boosting method. - Chen Wang 001; Jaime I. Dávila; Saurabh Baheti; Aditya Bhagwate; Xue Wang; Jean-Pierre A. Kocher; Susan L. Slager; Andrew L. Feldman; Anne J. Novak; James R. Cerhan; E. Aubrey Thompson; Yan W. Asmann (Bioinform., 2014)

PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data. - Chen Wang 001; Jared Evans; Aditya Bhagwate; Naresh Prodduturi; Vivekananda Sarangi; Mridu Middha; Hugues Sicotte; Peter T. Vedell; Steven N. Hart; Gavin R. Oliver; Jean-Pierre A. Kocher; Matthew J. Maurer; et al. (Bioinform., 2014)

CrossMap: a versatile tool for coordinate conversion between genome assemblies. - Hao Zhao; Zhifu Sun; Jing Wang; Haojie Huang; Jean-Pierre A. Kocher; Liguo Wang 002 (Bioinform., 2014)

MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing. - Krishna R. Kalari; Asha A. Nair; Jaysheel D. Bhavsar; Daniel R. O'Brien; Jaime I. Dávila; Matthew A. Bockol; Jinfu J. Nie; Xiaojia Tang; Saurabh Baheti; Jay B. Doughty; Sumit Middha; Hugues Sicotte; et al. (BMC Bioinform., 2014)

Prioritizing disease-related genes and pathways by integrating patient-specific iPSC-derived RNA-seq and whole genome sequencing in hypoplastic left heart syndrome. - Xing Li; Almudena Martinez-Fernandez; Jeanne Theis; Jean-Pierre A. Kocher; Andre Terzic; Timothy Olson; Timothy J. Nelson (BMC Bioinform., 2014)

HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data. - Huihuang Yan; Jared Evans; Mike Kalmbach; Raymond M. Moore; Sumit Middha; Stanislav Luban; Liguo Wang 002; Aditya Bhagwate; Ying Li; Zhifu Sun; Xianfeng Chen; Jean-Pierre A. Kocher (BMC Bioinform., 2014)

Bioinformatics Strategies for Identifying Regions of Epigenetic Deregulation Associated with Aberrant Transcript Splicing and RNA-editing. - Mia D. Champion; Ryan A. Hlady; Huihuang Yan; Jared Evans; Jeff Nie; Jeong-Heon Lee; James M. Bogenberger; Kannabiran Nandakumar; Jaime I. Dávila; Raymond M. Moore; Asha A. Nair; Daniel R. O'Brien; et al. (BIOINFORMATICS, 2015)

glmgraph: an R package for variable selection and predictive modeling of structured genomic data. - Li Chen 029; Han Liu 001; Jean-Pierre A. Kocher; Hongzhe Li; Jun Chen (Bioinform., 2015)

PVAAS: identify variants associated with aberrant splicing from RNA-seq. - Liguo Wang 002; Jinfu J. Nie; Jean-Pierre A. Kocher (Bioinform., 2015)

Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature. - Ravikumar Komandur Elayavilli; Kavishwar B. Wagholikar; Dingcheng Li; Jean-Pierre A. Kocher; Hongfang Liu (BMC Bioinform., 2015)

Time course transcriptome data analysis for in vitro modeling of dilated cardiomyopathy using patient-derived induced pluripotent stem cells. - Xing Li; Saranya Wyles; Sybil C. Hrstka; Jean-Pierre A. Kocher; Andre Terzic; Timothy Olson; Timothy J. Nelson (BMC Bioinform., 2015)

VCF-Miner: GUI-based application for mining variants and annotations stored in VCF files. - Steven N. Hart; Patrick H. Duffy; Daniel J. Quest; Asif Hossain; Michael A. Meiners; Jean-Pierre A. Kocher (Briefings Bioinform., 2016)

CpGFilter: model-based CpG probe filtering with replicates for epigenome-wide association studies. - Jun Chen; Allan C. Just; Joel Schwartz; Lifang Hou; Nadereh Jafari; Zhifu Sun; Jean-Pierre A. Kocher; Andrea A. Baccarelli; Xihong Lin (Bioinform., 2016)

Predicting regulatory variants with composite statistic. - Mulin Jun Li; Zhicheng Pan; Zipeng Liu; Jiexing Wu; Panwen Wang; Yun Zhu; Feng Xu; Zhengyuan Xia; Pak Chung Sham; Jean-Pierre A. Kocher; Miao-Xin Li; Jun S. Liu; et al. (Bioinform., 2016)

Erratum to: Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature. - Ravikumar Komandur Elayavilli; Kavishwar B. Wagholikar; Dingcheng Li; Jean-Pierre A. Kocher; Hongfang Liu (BMC Bioinform., 2016)

Measure transcript integrity using RNA-seq data. - Liguo Wang 002; Jinfu J. Nie; Hugues Sicotte; Ying Li; Jeanette E. Eckel-Passow; Surendra Dasari; Peter T. Vedell; Poulami Barman; Liewei Wang; Richard Weinshiboum; Jin Jen; Haojie Huang; et al. (BMC Bioinform., 2016)

GWASdb v2: an update database for human genetic variants identified by genome-wide association studies. - Mulin Jun Li; Zipeng Liu; Panwen Wang; Maria P. Wong; Matthew R. Nelson; Jean-Pierre A. Kocher; Meredith Yeager; Pak Chung Sham; Stephen J. Chanock; Zhengyuan Xia; Junwen Wang (Nucleic Acids Res., 2016)

Unraveling complex local genomic rearrangements from long-read data. - Zachary D. Stephens; Ravishankar K. Iyer; Chen Wang 001; Jean-Pierre A. Kocher (BIBM, 2017)

Indel detection from RNA-seq data: tool evaluation and strategies for accurate detection of actionable mutations. - Zhifu Sun; Aditya Bhagwate; Naresh Prodduturi; Ping Yang; Jean-Pierre A. Kocher (Briefings Bioinform., 2017)

CircularLogo: A lightweight web application to visualize intra-motif dependencies. - Zhenqing Ye; Tao Ma; Michael Kalmbach; Surendra Dasari; Jean-Pierre A. Kocher; Liguo Wang 002 (BMC Bioinform., 2017)

mTCTScan: a comprehensive platform for annotation and prioritization of mutations affecting drug sensitivity in cancers. - Mulin Jun Li; Hongcheng Yao; Dandan Huang; Huanhuan Liu; Zipeng Liu; Hang Xu; Yiming Qin; Jeanette Prinz; Weiyi Xia; Panwen Wang; Bin Yan; Nhan L. Tran; et al. (Nucleic Acids Res., 2017)

HGT-ID: an efficient and sensitive workflow to detect human-viral insertion sites using next-generation sequencing data. - Saurabh Baheti; Xiaojia Tang; Daniel R. O'Brien; Nicholas Chia; Lewis R. Roberts; Heidi Nelson; Judy C. Boughey; Liewei Wang; Matthew P. Goetz; Jean-Pierre A. Kocher; Krishna R. Kalari (BMC Bioinform., 2018)

Detection and visualization of complex structural variants from long reads. - Zachary Stephens; Chen Wang 001; Ravishankar K. Iyer; Jean-Pierre A. Kocher (BMC Bioinform., 2018)

Improving Single-Nucleotide Polymorphism-Based Fetal Fraction Estimation of Maternal Plasma Circulating Cell-Free DNA Using Bayesian Hierarchical Models. - Nicholas B. Larson; Chen Wang 001; Jie Na; Ross A. Rowsey; William Edward Highsmith; Nicole L. Hoppman; Jean-Pierre A. Kocher; Eric W. Klee (J. Comput. Biol., 2018)

Coverage Profile Correction of Shallow-Depth Circulating Cell-Free DNA Sequencing via Multi-Distance Learning. - Nicholas B. Larson; Melissa C. Larson; Jie Na; Carlos P. Sosa; Chen Wang 001; Jean-Pierre A. Kocher; Ross A. Rowsey (PSB, 2020)

CpGtools: a python package for DNA methylation analysis. - Ting Wei; Jinfu J. Nie; Nicholas B. Larson; Zhenqing Ye; Jeanette E. Eckel-Passow; Keith D. Robertson; Jean-Pierre A. Kocher; Liguo Wang 002 (Bioinform., 2021)

Telogator: a method for reporting chromosome-specific telomere lengths from long reads. - Zachary Stephens; Alejandro Ferrer; Lisa Boardman; Ravishankar K. Iyer; Jean-Pierre A. Kocher (Bioinform., 2022)

Characterization of telomere variant repeats using long reads enables allele-specific telomere length estimation. - Zachary Stephens; Jean-Pierre A. Kocher (BMC Bioinform., 2024)