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Jean-Pierre A. Kocher

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affiliation: Mayo Clinic College of Medicine, Rochester, USA

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2022
[j35]
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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): 1788-1793 (2022)
2021
[j34]
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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): 1598-1599 (2021)
2018
[j33]
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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): 271:1-271:11 (2018)
[j32]
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Zachary Stephens, Chen Wang, Ravishankar K. Iyer, Jean-Pierre A. Kocher:
Detection and visualization of complex structural variants from long reads. BMC Bioinform. 19-S(20): 67-77 (2018)
[j31]
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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): 1040-1049 (2018)
2017
[j30]
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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): 973-983 (2017)
[j29]
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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): 269:1-269:8 (2017)
[j28]
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  - journals/nar/LiYHLLXQPXWYTKS17
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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): W215-W221 (2017)
2016
[j27]
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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): 346-351 (2016)
[j26]
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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): 469-471 (2016)
[j25]
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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): 2729-2736 (2016)
[j24]
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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: 58 (2016)
[j23]
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  - journals/bmcbi/ElayavilliWLKL16
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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: 162 (2016)
[j22]
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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): 869-876 (2016)
2015
[j21]
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Liguo Wang, Jinfu J. Nie, Jean-Pierre A. Kocher:
PVAAS: identify variants associated with aberrant splicing from RNA-seq. Bioinform. 31(10): 1668-1670 (2015)
[j20]
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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): 3991-3993 (2015)
[j19]
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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: 185:1-185:15 (2015)
[j18]
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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): P8 (2015)
2014
[j17]
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  - journals/bioinformatics/ZhaoSWHKW14
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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): 1006-1007 (2014)
[j16]
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  - journals/bioinformatics/KocherQDMMRHHD14
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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): 1920-1922 (2014)
[j15]
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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): 2678-2680 (2014)
[j14]
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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): 3414-3416 (2014)
[j13]
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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: 224 (2014)
[j12]
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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: 280 (2014)
[j11]
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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): P7 (2014)
2013
[j10]
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  - journals/bioinformatics/ReeseATAVAKE13
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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): 2877-2883 (2013)
[j9]
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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): 970-978 (2013)
2012
[j8]
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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): 277-278 (2012)
[j7]
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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): 2180-2181 (2012)
2011
[j6]
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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: 129 (2011)
[j5]
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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): 144-149 (2011)
[j4]
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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: 12 (2011)
2010
[j3]
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  - journals/bmcbi/ChaiTBK10
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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: 356 (2010)
2009
[j2]
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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)
2008
[j1]
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  - journals/bioinformatics/HwangSTWKWKK08
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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): 2023-2029 (2008)

Conference and Workshop Papers

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2020
[c5]
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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: 599-610
2017
[c4]
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Zachary D. Stephens, Ravishankar K. Iyer, Chen Wang, Jean-Pierre A. Kocher:
Unraveling complex local genomic rearrangements from long-read data. BIBM 2017: 181-187
2015
[c3]
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  - conf/biostec/ChampionHYENLBN15
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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: 163-170
2013
[c2]
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Jean-Pierre A. Kocher:
Biomedical Informatics and the Future of Medicine. BDI 2013: 3
2008
[c1]
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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: 293-302

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