Jean-Pierre A. Kocher

Publication Activity (10 Years)

Years Active: 2008-2024
Publications (10 Years): 22

Top Topics

Medical Literature

Top Venues

Briefings Bioinform.

Nucleic Acids Res.

Publications

Zachary Stephens, Jean-Pierre A. Kocher
Characterization of telomere variant repeats using long reads enables allele-specific telomere length estimation. BMC Bioinform. 25 (1) (2024)
Zachary Stephens, Alejandro Ferrer, Lisa Boardman, Ravishankar K. Iyer, Jean-Pierre A. Kocher
Telogator: a method for reporting chromosome-specific telomere lengths from long reads. Bioinform. 38 (7) (2022)
Ting Wei, Jinfu J. Nie, Nicholas B. Larson, Zhenqing Ye, Jeanette E. Eckel-Passow, Keith D. Robertson, Jean-Pierre A. Kocher, Liguo Wang
CpGtools: a python package for DNA methylation analysis. Bioinform. 37 (11) (2021)
Nicholas B. Larson, Melissa C. Larson, Jie Na, Carlos P. Sosa, Chen Wang, Jean-Pierre A. Kocher, Ross A. Rowsey
Coverage Profile Correction of Shallow-Depth Circulating Cell-Free DNA Sequencing via Multi-Distance Learning. PSB (2020)
Nicholas B. Larson, Chen Wang, Jie Na, Ross A. Rowsey, William Edward Highsmith, Nicole L. Hoppman, Jean-Pierre A. Kocher, Eric W. Klee
Improving Single-Nucleotide Polymorphism-Based Fetal Fraction Estimation of Maternal Plasma Circulating Cell-Free DNA Using Bayesian Hierarchical Models. J. Comput. Biol. 25 (9) (2018)
Zachary Stephens, Chen Wang, Ravishankar K. Iyer, Jean-Pierre A. Kocher
Detection and visualization of complex structural variants from long reads. BMC Bioinform. (20) (2018)
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
HGT-ID: an efficient and sensitive workflow to detect human-viral insertion sites using next-generation sequencing data. BMC Bioinform. 19 (1) (2018)
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, Jean-Pierre A. Kocher, Pak Chung Sham, Junwen Wang
mTCTScan: a comprehensive platform for annotation and prioritization of mutations affecting drug sensitivity in cancers. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
Zachary D. Stephens, Ravishankar K. Iyer, Chen Wang, Jean-Pierre A. Kocher
Unraveling complex local genomic rearrangements from long-read data. BIBM (2017)
Zhenqing Ye, Tao Ma, Michael Kalmbach, Surendra Dasari, Jean-Pierre A. Kocher, Liguo Wang
CircularLogo: A lightweight web application to visualize intra-motif dependencies. BMC Bioinform. 18 (1) (2017)
Zhifu Sun, Aditya Bhagwate, Naresh Prodduturi, Ping Yang, Jean-Pierre A. Kocher
Indel detection from RNA-seq data: tool evaluation and strategies for accurate detection of actionable mutations. Briefings Bioinform. 18 (6) (2017)
Steven N. Hart, Patrick H. Duffy, Daniel J. Quest, Asif Hossain, Michael A. Meiners, Jean-Pierre A. Kocher
VCF-Miner: GUI-based application for mining variants and annotations stored in VCF files. Briefings Bioinform. 17 (2) (2016)
Liguo Wang, 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, Manish Kohli, Jean-Pierre A. Kocher
Measure transcript integrity using RNA-seq data. BMC Bioinform. 17 (2016)
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
GWASdb v2: an update database for human genetic variants identified by genome-wide association studies. Nucleic Acids Res. 44 (Database-Issue) (2016)
Jun Chen, Allan C. Just, Joel Schwartz, Lifang Hou, Nadereh Jafari, Zhifu Sun, Jean-Pierre A. Kocher, Andrea A. Baccarelli, Xihong Lin
CpGFilter: model-based CpG probe filtering with replicates for epigenome-wide association studies. Bioinform. 32 (3) (2016)
Ravikumar Komandur Elayavilli, Kavishwar B. Wagholikar, Dingcheng Li, Jean-Pierre A. Kocher, Hongfang Liu
Erratum to: Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature. BMC Bioinform. 17 (2016)
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, Junwen Wang
Predicting regulatory variants with composite statistic. Bioinform. 32 (18) (2016)
Li Chen, Han Liu, Jean-Pierre A. Kocher, Hongzhe Li, Jun Chen
glmgraph: an R package for variable selection and predictive modeling of structured genomic data. Bioinform. 31 (24) (2015)
Ravikumar Komandur Elayavilli, Kavishwar B. Wagholikar, Dingcheng Li, Jean-Pierre A. Kocher, Hongfang Liu
Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature. BMC Bioinform. 16 (2015)
Xing Li, Saranya Wyles, Sybil C. Hrstka, Jean-Pierre A. Kocher, Andre Terzic, Timothy Olson, Timothy J. Nelson
Time course transcriptome data analysis for in vitro modeling of dilated cardiomyopathy using patient-derived induced pluripotent stem cells. BMC Bioinform. 16 (S15) (2015)
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, Yuan-Xiao Zhu, K. Martin Kortüm, Tamas Ordog, Zhiguo Zhang, Richard W. Joseph, A. Keith Stewart, Jean-Pierre A. Kocher, Eric Jonasch, Keith D. Robertson, Raoul Tibes, Thai H. Ho
Bioinformatics Strategies for Identifying Regions of Epigenetic Deregulation Associated with Aberrant Transcript Splicing and RNA-editing. BIOINFORMATICS (2015)
Liguo Wang, Jinfu J. Nie, Jean-Pierre A. Kocher
PVAAS: identify variants associated with aberrant splicing from RNA-seq. Bioinform. 31 (10) (2015)
Hao Zhao, Zhifu Sun, Jing Wang, Haojie Huang, Jean-Pierre A. Kocher, Liguo Wang
CrossMap: a versatile tool for coordinate conversion between genome assemblies. Bioinform. 30 (7) (2014)
Huihuang Yan, Jared Evans, Mike Kalmbach, Raymond M. Moore, Sumit Middha, Stanislav Luban, Liguo Wang, Aditya Bhagwate, Ying Li, Zhifu Sun, Xianfeng Chen, Jean-Pierre A. Kocher
HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data. BMC Bioinform. 15 (2014)
Chen Wang, 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, Anne J. Novak, Susan L. Slager, James R. Cerhan, Yan W. Asmann
PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data. Bioinform. 30 (18) (2014)
Xing Li, Almudena Martinez-Fernandez, Jeanne Theis, Jean-Pierre A. Kocher, Andre Terzic, Timothy Olson, Timothy J. Nelson
Prioritizing disease-related genes and pathways by integrating patient-specific iPSC-derived RNA-seq and whole genome sequencing in hypoplastic left heart syndrome. BMC Bioinform. 15 (S-10) (2014)
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, E. Aubrey Thompson, Yan W. Asmann, Jean-Pierre A. Kocher
MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing. BMC Bioinform. 15 (2014)
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
The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation. Bioinform. 30 (13) (2014)
Chen Wang, 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
RVboost: RNA-seq variants prioritization using a boosting method. Bioinform. 30 (23) (2014)
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
A new statistic for identifying batch effects in high-throughput genomic data that uses guided principal component analysis. Bioinform. 29 (22) (2013)
Jean-Pierre A. Kocher
Biomedical Informatics and the Future of Medicine. BDI (2013)
Steven N. Hart, Terry M. Therneau, Yuji Zhang, Gregory A. Poland, Jean-Pierre A. Kocher
Calculating Sample Size Estimates for RNA Sequencing Data. J. Comput. Biol. 20 (12) (2013)
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, Eric W. Klee, Krishna R. Kalari, Jean-Pierre A. Kocher
TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data. Bioinform. 28 (2) (2012)
Zhifu Sun, Saurabh Baheti, Sumit Middha, Rahul Kanwar, Yuji Zhang, Xing Li, Andreas S. Beutler, Eric W. Klee, Yan W. Asmann, E. Aubrey Thompson, Jean-Pierre A. Kocher
SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing. Bioinform. 28 (16) (2012)
Andrew P. Norgan, Paul K. Coffman, Jean-Pierre A. Kocher, David J. Katzmann, Carlos P. Sosa
Multilevel Parallelization of AutoDock 4.2. J. Cheminformatics 3 (2011)
Hugues Sicotte, David N. Rider, Gregory A. Poland, Neelam Dhiman, Jean-Pierre A. Kocher
SNPPicker: High quality tag SNP selection across multiple populations. BMC Bioinform. 12 (2011)
Sunghwan Sohn, Jean-Pierre A. Kocher, Christopher G. Chute, Guergana K. Savova
Drug side effect extraction from clinical narratives of psychiatry and psychology patients. J. Am. Medical Informatics Assoc. 18 (Supplement) (2011)
High-Seng Chai, Terry M. Therneau, Kent R. Bailey, Jean-Pierre A. Kocher
Spatial normalization improves the quality of genotype calling for Affymetrix SNP 6.0 arrays. BMC Bioinform. 11 (2010)
High-Seng Chai, Hugues Sicotte, Kent R. Bailey, Stephen T. Turner, Yan W. Asmann, Jean-Pierre A. Kocher
GLOSSI: a method to assess the association of genetic loci-sets with complex diseases. BMC Bioinform. 10 (2009)
TaeHyun Hwang, Hugues Sicotte, Ze Tian, Baolin Wu, Jean-Pierre A. Kocher, Dennis A. Wigle, Vipin Kumar, Rui Kuang
Robust and efficient identification of biomarkers by classifying features on graphs. Bioinform. 24 (18) (2008)
TaeHyun Hwang, Ze Tian, Rui Kuang, Jean-Pierre A. Kocher
Learning on Weighted Hypergraphs to Integrate Protein Interactions and Gene Expressions for Cancer Outcome Prediction. ICDM (2008)