Jacob Kocher - Publications

Affiliations: 
2009-2014 Department of Biomedical Sciences and Pathobiology Virgina Tech 

77 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2017 Li MJ, Li M, Liu Z, Yan B, Pan Z, Huang D, Liang Q, Ying D, Xu F, Yao H, Wang P, Kocher JA, Xia Z, Sham PC, Liu JS, et al. cepip: context-dependent epigenomic weighting for prioritization of regulatory variants and disease-associated genes. Genome Biology. 18: 52. PMID 28302177 DOI: 10.1186/s13059-017-1177-3  0.4
2016 Lei S, Ramesh A, Twitchell E, Wen K, Bui T, Weiss M, Yang X, Kocher J, Li G, Giri-Rachman E, Trang NV, Jiang X, Ryan EP, Yuan L. High Protective Efficacy of Probiotics and Rice Bran against Human Norovirus Infection and Diarrhea in Gnotobiotic Pigs. Frontiers in Microbiology. 7: 1699. PMID 27853451 DOI: 10.3389/fmicb.2016.01699  0.48
2016 Nair AA, Niu N, Tang X, Thompson KJ, Wang L, Kocher JP, Subramanian S, Kalari KR. Circular RNAs and their associations with breast cancer subtypes. Oncotarget. PMID 27829232 DOI: 10.18632/oncotarget.13134  0.72
2016 Sun Z, Bhagwate A, Prodduturi N, Yang P, Kocher JA. Indel detection from RNA-seq data: tool evaluation and strategies for accurate detection of actionable mutations. Briefings in Bioinformatics. PMID 27473065 DOI: 10.1093/bib/bbw069  0.4
2016 Wang H, Gao K, Wen K, Allen IC, Li G, Zhang W, Kocher J, Yang X, Giri-Rachman E, Li GH, Clark-Deener S, Yuan L. Lactobacillus rhamnosus GG modulates innate signaling pathway and cytokine responses to rotavirus vaccine in intestinal mononuclear cells of gnotobiotic pigs transplanted with human gut microbiota. Bmc Microbiology. 16: 109. PMID 27301272 DOI: 10.1186/s12866-016-0727-2  0.32
2016 Li MJ, Pan Z, Liu Z, Wu J, Wang P, Zhu Y, Xu F, Xia Z, Sham PC, Kocher JA, Li M, Liu JS, Wang J. Predicting regulatory variants with composite statistic. Bioinformatics (Oxford, England). PMID 27273672 DOI: 10.1093/bioinformatics/btw288  0.36
2016 Baheti S, Kanwar R, Goelzenleuchter M, Kocher JP, Beutler AS, Sun Z. Targeted alignment and end repair elimination increase alignment and methylation measure accuracy for reduced representation bisulfite sequencing data. Bmc Genomics. 17: 149. PMID 26922377 DOI: 10.1186/s12864-016-2494-8  0.36
2016 Wang L, Nie J, Sicotte H, Li Y, Eckel-Passow JE, Dasari S, Vedell PT, Barman P, Wang L, Weinshiboum R, Jen J, Huang H, Kohli M, Kocher JP. Measure transcript integrity using RNA-seq data. Bmc Bioinformatics. 17: 58. PMID 26842848 DOI: 10.1186/s12859-016-0922-z  0.36
2016 Wen K, Bui T, Weiss M, Li G, Kocher J, Yang X, Jobst PM, Vaught T, Ramsoondar J, Ball S, Clark-Deener S, Ayares D, Yuan L. B-Cell-Deficient and CD8 T-Cell-Depleted Gnotobiotic Pigs for the Study of Human Rotavirus Vaccine-Induced Protective Immune Responses. Viral Immunology. PMID 26824402 DOI: 10.1089/vim.2015.0105  0.32
2015 Li MJ, Liu Z, Wang P, Wong MP, Nelson MR, Kocher JA, Yeager M, Sham PC, Chanock SJ, Xia Z, Wang J. GWASdb v2: an update database for human genetic variants identified by genome-wide association studies. Nucleic Acids Research. PMID 26615194 DOI: 10.1093/nar/gkv1317  0.36
2015 Kocher J, Yuan L. Norovirus vaccines and potential antinorovirus drugs: recent advances and future perspectives. Future Virology. 10: 899-913. PMID 26568768 DOI: 10.2217/fvl.15.57  0.48
2015 Yang X, Twitchell E, Li G, Wen K, Weiss M, Kocher J, Lei S, Ramesh A, Ryan EP, Yuan L. High protective efficacy of rice bran against human rotavirus diarrhea via enhancing probiotic growth, gut barrier function, and innate immunity. Scientific Reports. 5: 15004. PMID 26459937 DOI: 10.1038/srep15004  0.32
2015 Chen J, Just AC, Schwartz J, Hou L, Jafari N, Sun Z, Kocher JA, Baccarelli A, Lin X. CpGFilter: model-based CpG probe filtering with replicates for epigenome-wide association studies. Bioinformatics (Oxford, England). PMID 26449931 DOI: 10.1093/bioinformatics/btv577  0.36
2015 Sun Z, Cunningham J, Slager S, Kocher JP. Base resolution methylome profiling: considerations in platform selection, data preprocessing and analysis. Epigenomics. PMID 26366945 DOI: 10.2217/epi.15.21  0.4
2015 Hart SN, Duffy P, Quest DJ, Hossain A, Meiners MA, Kocher JP. VCF-Miner: GUI-based application for mining variants and annotations stored in VCF files. Briefings in Bioinformatics. PMID 26210358 DOI: 10.1093/bib/bbv051  0.36
2015 Sun Z, Prodduturi N, Sun SY, Thompson EA, Kocher JA. Chromosome X genomic and epigenomic aberrations and clinical implications in breast cancer by base resolution profiling. Epigenomics. 1-12. PMID 26039248 DOI: 10.2217/epi.15.43  0.36
2015 Chien J, Sicotte H, Fan JB, Humphray S, Cunningham JM, Kalli KR, Oberg AL, Hart SN, Li Y, Davila JI, Baheti S, Wang C, Dietmann S, Atkinson EJ, Asmann YW, ... ... Kocher JP, et al. TP53 mutations, tetraploidy and homologous recombination repair defects in early stage high-grade serous ovarian cancer. Nucleic Acids Research. PMID 25916844 DOI: 10.1093/nar/gkv111  0.36
2015 Wang Y, Cao Y, Yamada S, Thirunavukkarasu M, Nin V, Joshi M, Rishi MT, Bhattacharya S, Camacho-Pereira J, Sharma AK, Shameer K, Kocher JP, Sanchez JA, Wang E, Hoeppner LH, et al. Cardiomyopathy and Worsened Ischemic Heart Failure in SM22-α Cre-Mediated Neuropilin-1 Null Mice: Dysregulation of PGC1α and Mitochondrial Homeostasis. Arteriosclerosis, Thrombosis, and Vascular Biology. 35: 1401-12. PMID 25882068 DOI: 10.1161/ATVBAHA.115.305566  0.36
2015 Du J, Aleff RA, Soragni E, Kalari K, Nie J, Tang X, Davila J, Kocher JP, Patel SV, Gottesfeld JM, Baratz KH, Wieben ED. RNA toxicity and missplicing in the common eye disease fuchs endothelial corneal dystrophy. The Journal of Biological Chemistry. 290: 5979-90. PMID 25593321 DOI: 10.1074/jbc.M114.621607  0.36
2015 Wang L, Nie JJ, Kocher JP. PVAAS: identify variants associated with aberrant splicing from RNA-seq. Bioinformatics (Oxford, England). 31: 1668-70. PMID 25573917 DOI: 10.1093/bioinformatics/btv001  0.72
2015 Wen K, Liu F, Li G, Bai M, Kocher J, Yang X, Wang H, Clark-Deener S, Yuan L. Lactobacillus rhamnosus GG Dosage Affects the Adjuvanticity and Protection Against Rotavirus Diarrhea in Gnotobiotic Pigs. Journal of Pediatric Gastroenterology and Nutrition. 60: 834-43. PMID 25564808 DOI: 10.1097/MPG.0000000000000694  0.32
2015 Wang L, Huang H, Dougherty G, Zhao Y, Hossain A, Kocher JP. Epidaurus: aggregation and integration analysis of prostate cancer epigenome. Nucleic Acids Research. 43: e7. PMID 25378314 DOI: 10.1093/nar/gku1079  0.72
2014 Yang X, Li G, Wen K, Bui T, Liu F, Kocher J, Jortner BS, Vonck M, Pelzer K, Deng J, Zhu R, Li Y, Qian Y, Yuan L. A neonatal gnotobiotic pig model of human enterovirus 71 infection and associated immune responses. Emerging Microbes & Infections. 3: e35. PMID 26038741 DOI: 10.1038/emi.2014.35  0.32
2014 Jeraldo P, Kalari K, Chen X, Bhavsar J, Mangalam A, White B, Nelson H, Kocher JP, Chia N. IM-TORNADO: a tool for comparison of 16S reads from paired-end libraries. Plos One. 9: e114804. PMID 25506826 DOI: 10.1371/journal.pone.0114804  0.36
2014 Tang X, Baheti S, Shameer K, Thompson KJ, Wills Q, Niu N, Holcomb IN, Boutet SC, Ramakrishnan R, Kachergus JM, Kocher JP, Weinshilboum RM, Wang L, Thompson EA, Kalari KR. The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data. Nucleic Acids Research. 42: e172. PMID 25352556 DOI: 10.1093/nar/gku1005  0.36
2014 Zhang H, Wang H, Shepherd M, Wen K, Li G, Yang X, Kocher J, Giri-Rachman E, Dickerman A, Settlage R, Yuan L. Probiotics and virulent human rotavirus modulate the transplanted human gut microbiota in gnotobiotic pigs. Gut Pathogens. 6: 39. PMID 25349634 DOI: 10.1186/s13099-014-0039-8  0.48
2014 Wang L, Chen J, Wang C, Uusküla-Reimand L, Chen K, Medina-Rivera A, Young EJ, Zimmermann MT, Yan H, Sun Z, Zhang Y, Wu ST, Huang H, Wilson MD, Kocher JP, et al. MACE: model based analysis of ChIP-exo. Nucleic Acids Research. 42: e156. PMID 25249628 DOI: 10.1093/nar/gku846  0.36
2014 Wang C, Davila JI, Baheti S, Bhagwate AV, Wang X, Kocher JP, Slager SL, Feldman AL, Novak AJ, Cerhan JR, Thompson EA, Asmann YW. RVboost: RNA-seq variants prioritization using a boosting method. Bioinformatics (Oxford, England). 30: 3414-6. PMID 25170027 DOI: 10.1093/bioinformatics/btu577  0.36
2014 Wieben ED, Aleff RA, Eckloff BW, Atkinson EJ, Baheti S, Middha S, Brown WL, Patel SV, Kocher JP, Baratz KH. Comprehensive assessment of genetic variants within TCF4 in Fuchs' endothelial corneal dystrophy. Investigative Ophthalmology & Visual Science. 55: 6101-7. PMID 25168903 DOI: 10.1167/iovs.14-14958  0.36
2014 Yan H, Evans J, Kalmbach M, Moore R, Middha S, Luban S, Wang L, Bhagwate A, Li Y, Sun Z, Chen X, Kocher JP. HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data. Bmc Bioinformatics. 15: 280. PMID 25128017 DOI: 10.1186/1471-2105-15-280  0.36
2014 Yang X, Wen K, Tin C, Li G, Wang H, Kocher J, Pelzer K, Ryan E, Yuan L. Dietary rice bran protects against rotavirus diarrhea and promotes Th1-type immune responses to human rotavirus vaccine in gnotobiotic pigs. Clinical and Vaccine Immunology : Cvi. 21: 1396-403. PMID 25080551 DOI: 10.1128/CVI.00210-14  0.48
2014 Sun Z, Wu Y, Ordog T, Baheti S, Nie J, Duan X, Hojo K, Kocher JP, Dyck PJ, Klein CJ. Aberrant signature methylome by DNMT1 hot spot mutation in hereditary sensory and autonomic neuropathy 1E. Epigenetics : Official Journal of the Dna Methylation Society. 9: 1184-93. PMID 25033457 DOI: 10.4161/epi.29676  0.36
2014 Kalari KR, Nair AA, Bhavsar JD, O'Brien DR, Davila JI, Bockol MA, Nie J, Tang X, Baheti S, Doughty JB, Middha S, Sicotte H, Thompson AE, Asmann YW, Kocher JP. MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing. Bmc Bioinformatics. 15: 224. PMID 24972667 DOI: 10.1186/1471-2105-15-224  0.36
2014 Kocher J, Bui T, Giri-Rachman E, Wen K, Li G, Yang X, Liu F, Tan M, Xia M, Zhong W, Jiang X, Yuan L. Intranasal P particle vaccine provided partial cross-variant protection against human GII.4 norovirus diarrhea in gnotobiotic pigs. Journal of Virology. 88: 9728-43. PMID 24920797 DOI: 10.1128/JVI.01249-14  0.32
2014 Sun Z, Evans J, Bhagwate A, Middha S, Bockol M, Yan H, Kocher JP. CAP-miRSeq: a comprehensive analysis pipeline for microRNA sequencing data. Bmc Genomics. 15: 423. PMID 24894665 DOI: 10.1186/1471-2164-15-423  0.36
2014 Wang C, Evans JM, Bhagwate AV, Prodduturi N, Sarangi V, Middha M, Sicotte H, Vedell PT, Hart SN, Oliver GR, Kocher JP, Maurer MJ, Novak AJ, Slager SL, Cerhan JR, et al. PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data. Bioinformatics (Oxford, England). 30: 2678-80. PMID 24876377 DOI: 10.1093/bioinformatics/btu363  0.36
2014 Giri K, Shameer K, Zimmermann MT, Saha S, Chakraborty PK, Sharma A, Arvizo RR, Madden BJ, Mccormick DJ, Kocher JP, Bhattacharya R, Mukherjee P. Understanding protein-nanoparticle interaction: a new gateway to disease therapeutics. Bioconjugate Chemistry. 25: 1078-90. PMID 24831101 DOI: 10.1021/bc500084f  0.36
2014 Li X, Martinez-Fernandez A, Hartjes KA, Kocher JPA, Olson TM, Terzic A, Nelson TJ. Transcriptional atlas of cardiogenesis maps congenital heart disease interactome Physiological Genomics. 46: 482-495. PMID 24803680 DOI: 10.1152/physiolgenomics.00015.2014  0.36
2014 Wen K, Tin C, Wang H, Yang X, Li G, Giri-Rachman E, Kocher J, Bui T, Clark-Deener S, Yuan L. Probiotic Lactobacillus rhamnosus GG enhanced Th1 cellular immunity but did not affect antibody responses in a human gut microbiota transplanted neonatal gnotobiotic pig model. Plos One. 9: e94504. PMID 24722168 DOI: 10.1371/journal.pone.0094504  0.32
2014 Dasari S, Theis JD, Vrana JA, Zenka RM, Zimmermann MT, Kocher JP, Highsmith WE, Kurtin PJ, Dogan A. Clinical proteome informatics workbench detects pathogenic mutations in hereditary amyloidoses. Journal of Proteome Research. 13: 2352-8. PMID 24650283 DOI: 10.1021/pr4011475  0.36
2014 Kocher JP, Quest DJ, Duffy P, Meiners MA, Moore RM, Rider D, Hossain A, Hart SN, Dinu V. The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation. Bioinformatics (Oxford, England). 30: 1920-2. PMID 24618464 DOI: 10.1093/bioinformatics/btu137  0.36
2014 Borad MJ, Champion MD, Egan JB, Liang WS, Fonseca R, Bryce AH, McCullough AE, Barrett MT, Hunt K, Patel MD, Young SW, Collins JM, Silva AC, Condjella RM, Block M, ... ... Kocher JP, et al. Integrated genomic characterization reveals novel, therapeutically relevant drug targets in FGFR and EGFR pathways in sporadic intrahepatic cholangiocarcinoma. Plos Genetics. 10: e1004135. PMID 24550739 DOI: 10.1371/journal.pgen.1004135  0.36
2014 Ansell SM, Hodge LS, Secreto FJ, Manske M, Braggio E, Price-Troska T, Ziesmer S, Li Y, Johnson SH, Hart SN, Kocher JP, Vasmatzis G, Chanan-Kahn A, Gertz M, Fonseca R, et al. Activation of TAK1 by MYD88 L265P drives malignant B-cell Growth in non-Hodgkin lymphoma. Blood Cancer Journal. 4: e183. PMID 24531446 DOI: 10.1038/bcj.2014.4  0.36
2014 Middha S, Baheti S, Hart SN, Kocher JP. From days to hours: reporting clinically actionable variants from whole genome sequencing. Plos One. 9: e86803. PMID 24505267 DOI: 10.1371/journal.pone.0086803  0.36
2014 Sakuma T, Davila JI, Malcolm JA, Kocher JP, Tonne JM, Ikeda Y. Murine leukemia virus uses NXF1 for nuclear export of spliced and unspliced viral transcripts. Journal of Virology. 88: 4069-82. PMID 24478440 DOI: 10.1128/JVI.03584-13  0.36
2014 Zhao H, Sun Z, Wang J, Huang H, Kocher JP, Wang L. CrossMap: a versatile tool for coordinate conversion between genome assemblies. Bioinformatics (Oxford, England). 30: 1006-7. PMID 24351709 DOI: 10.1093/bioinformatics/btt730  0.72
2014 Liu F, Wen K, Li G, Yang X, Kocher J, Bui T, Jones D, Pelzer K, Clark-Deener S, Yuan L. Dual functions of Lactobacillus acidophilus NCFM as protection against rotavirus diarrhea. Journal of Pediatric Gastroenterology and Nutrition. 58: 169-76. PMID 24126832 DOI: 10.1097/MPG.0000000000000197  0.48
2013 Liu F, Li G, Wen K, Wu S, Zhang Y, Bui T, Yang X, Kocher J, Sun J, Jortner B, Yuan L. Lactobacillus rhamnosus GG on rotavirus-induced injury of ileal epithelium in gnotobiotic pigs. Journal of Pediatric Gastroenterology and Nutrition. 57: 750-8. PMID 24280990 DOI: 10.1097/MPG.0b013e3182a356e1  0.48
2013 Sun Z, Asmann YW, Nair A, Zhang Y, Wang L, Kalari KR, Bhagwate AV, Baker TR, Carr JM, Kocher JP, Perez EA, Thompson EA. Impact of library preparation on downstream analysis and interpretation of RNA-Seq data: comparison between Illumina PolyA and NuGEN Ovation protocol. Plos One. 8: e71745. PMID 23977132 DOI: 10.1371/journal.pone.0071745  0.36
2013 Reese SE, Archer KJ, Therneau TM, Atkinson EJ, Vachon CM, de Andrade M, Kocher JP, Eckel-Passow JE. A new statistic for identifying batch effects in high-throughput genomic data that uses guided principal component analysis. Bioinformatics (Oxford, England). 29: 2877-83. PMID 23958724 DOI: 10.1093/bioinformatics/btt480  0.36
2013 Wu S, Yuan L, Zhang Y, Liu F, Li G, Wen K, Kocher J, Yang X, Sun J. Probiotic Lactobacillus rhamnosus GG mono-association suppresses human rotavirus-induced autophagy in the gnotobiotic piglet intestine. Gut Pathogens. 5: 22. PMID 23924832 DOI: 10.1186/1757-4749-5-22  0.48
2013 Bui T, Kocher J, Li Y, Wen K, Li G, Liu F, Yang X, LeRoith T, Tan M, Xia M, Zhong W, Jiang X, Yuan L. Median infectious dose of human norovirus GII.4 in gnotobiotic pigs is decreased by simvastatin treatment and increased by age. The Journal of General Virology. 94: 2005-16. PMID 23804568 DOI: 10.1099/vir.0.054080-0  0.48
2013 Klein CJ, Wu Y, Duan X, Middha S, Dawson BD, Kocher JP, Dyck PJ. Novel SOD1 mutation discovered in atypical ALS by whole exome sequencing. Journal of Neurology, Neurosurgery, and Psychiatry. 84: 943-4. PMID 23744890 DOI: 10.1136/jnnp-2013-305400  0.36
2013 Patowary A, Purkanti R, Singh M, Chauhan R, Singh AR, Swarnkar M, Singh N, Pandey V, Torroja C, Clark MD, Kocher JP, Clark KJ, Stemple DL, Klee EW, Ekker SC, et al. A sequence-based variation map of zebrafish. Zebrafish. 10: 15-20. PMID 23590399 DOI: 10.1089/zeb.2012.0848  0.36
2013 Mahoney DW, Therneau TM, Anderson SK, Jen J, Kocher JP, Reinholz MM, Perez EA, Eckel-Passow JE. Quality assessment metrics for whole genome gene expression profiling of paraffin embedded samples. Bmc Research Notes. 6: 33. PMID 23360712 DOI: 10.1186/1756-0500-6-33  0.36
2013 Wang L, Park HJ, Dasari S, Wang S, Kocher JP, Li W. CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model. Nucleic Acids Research. 41: e74. PMID 23335781 DOI: 10.1093/nar/gkt006  0.36
2012 Wen K, Li G, Yang X, Bui T, Bai M, Liu F, Kocher J, Yuan L. CD4+ CD25- FoxP3+ regulatory cells are the predominant responding regulatory T cells after human rotavirus infection or vaccination in gnotobiotic pigs. Immunology. 137: 160-71. PMID 22716916 DOI: 10.1111/j.1365-2567.2012.03617.x  0.48
2012 Sun Z, Baheti S, Middha S, Kanwar R, Zhang Y, Li X, Beutler AS, Klee E, Asmann YW, Thompson EA, Kocher JP. SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing. Bioinformatics (Oxford, England). 28: 2180-1. PMID 22689387 DOI: 10.1093/bioinformatics/bts337  0.36
2012 Kalari KR, Rossell D, Necela BM, Asmann YW, Nair A, Baheti S, Kachergus JM, Younkin CS, Baker T, Carr JM, Tang X, Walsh MP, Chai HS, Sun Z, Hart SN, ... ... Kocher JP, et al. Deep Sequence Analysis of Non-Small Cell Lung Cancer: Integrated Analysis of Gene Expression, Alternative Splicing, and Single Nucleotide Variations in Lung Adenocarcinomas with and without Oncogenic KRAS Mutations. Frontiers in Oncology. 2: 12. PMID 22655260 DOI: 10.3389/fonc.2012.00012  0.36
2012 Arvizo RR, Giri K, Moyano D, Miranda OR, Madden B, McCormick DJ, Bhattacharya R, Rotello VM, Kocher JP, Mukherjee P. Identifying new therapeutic targets via modulation of protein corona formation by engineered nanoparticles. Plos One. 7: e33650. PMID 22442705 DOI: 10.1371/journal.pone.0033650  0.36
2012 Dutta T, Chai HS, Ward LE, Ghosh A, Persson XM, Ford GC, Kudva YC, Sun Z, Asmann YW, Kocher JP, Nair KS. Concordance of changes in metabolic pathways based on plasma metabolomics and skeletal muscle transcriptomics in type 1 diabetes. Diabetes. 61: 1004-16. PMID 22415876 DOI: 10.2337/db11-0874  0.36
2012 Wen K, Bui T, Li G, Liu F, Li Y, Kocher J, Yuan L. Characterization of immune modulating functions of γδ T cell subsets in a gnotobiotic pig model of human rotavirus infection. Comparative Immunology, Microbiology and Infectious Diseases. 35: 289-301. PMID 22333156 DOI: 10.1016/j.cimid.2012.01.010  0.48
2012 Wen K, Li G, Bui T, Liu F, Li Y, Kocher J, Lin L, Yang X, Yuan L. High dose and low dose Lactobacillus acidophilus exerted differential immune modulating effects on T cell immune responses induced by an oral human rotavirus vaccine in gnotobiotic pigs. Vaccine. 30: 1198-207. PMID 22178726 DOI: 10.1016/j.vaccine.2011.11.107  0.48
2012 Asmann YW, Middha S, Hossain A, Baheti S, Li Y, Chai HS, Sun Z, Duffy PH, Hadad AA, Nair A, Liu X, Zhang Y, Klee EW, Kalari KR, Kocher JP. TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data. Bioinformatics (Oxford, England). 28: 277-8. PMID 22088845 DOI: 10.1093/bioinformatics/btr612  0.36
2011 Sun Z, Chai HS, Wu Y, White WM, Donkena KV, Klein CJ, Garovic VD, Therneau TM, Kocher JP. Batch effect correction for genome-wide methylation data with Illumina Infinium platform. Bmc Medical Genomics. 4: 84. PMID 22171553 DOI: 10.1186/1755-8794-4-84  0.36
2011 Sohn S, Kocher JP, Chute CG, Savova GK. Drug side effect extraction from clinical narratives of psychiatry and psychology patients. Journal of the American Medical Informatics Association : Jamia. 18: i144-9. PMID 21946242 DOI: 10.1136/amiajnl-2011-000351  0.36
2011 Bielinski SJ, Chai HS, Pathak J, Talwalkar JA, Limburg PJ, Gullerud RE, Sicotte H, Klee EW, Ross JL, Kocher JP, Kullo IJ, Heit JA, Petersen GM, de Andrade M, Chute CG. Mayo Genome Consortia: a genotype-phenotype resource for genome-wide association studies with an application to the analysis of circulating bilirubin levels. Mayo Clinic Proceedings. 86: 606-14. PMID 21646302 DOI: 10.4065/mcp.2011.0178  0.36
2011 Asmann YW, Hossain A, Necela BM, Middha S, Kalari KR, Sun Z, Chai HS, Williamson DW, Radisky D, Schroth GP, Kocher JP, Perez EA, Thompson EA. A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines. Nucleic Acids Research. 39: e100. PMID 21622959 DOI: 10.1093/nar/gkr362  0.36
2011 Sicotte H, Rider DN, Poland GA, Dhiman N, Kocher JP. SNPPicker: high quality tag SNP selection across multiple populations. Bmc Bioinformatics. 12: 129. PMID 21535878 DOI: 10.1186/1471-2105-12-129  0.36
2011 Norgan AP, Coffman PK, Kocher JP, Katzmann DJ, Sosa CP. Multilevel Parallelization of AutoDock 4.2. Journal of Cheminformatics. 3: 12. PMID 21527034 DOI: 10.1186/1758-2946-3-12  0.36
2010 Chai HS, Therneau TM, Bailey KR, Kocher JP. Spatial normalization improves the quality of genotype calling for Affymetrix SNP 6.0 arrays. Bmc Bioinformatics. 11: 356. PMID 20587065 DOI: 10.1186/1471-2105-11-356  0.36
2010 Kalari KR, Hebbring SJ, Chai HS, Li L, Kocher JP, Wang L, Weinshilboum RM. Copy number variation and cytidine analogue cytotoxicity: a genome-wide association approach. Bmc Genomics. 11: 357. PMID 20525348 DOI: 10.1186/1471-2164-11-357  0.36
2009 Asmann YW, Klee EW, Thompson EA, Perez EA, Middha S, Oberg AL, Therneau TM, Smith DI, Poland GA, Wieben ED, Kocher JP. 3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer. Bmc Genomics. 10: 531. PMID 19917133 DOI: 10.1186/1471-2164-10-531  0.36
2009 Chai HS, Sicotte H, Bailey KR, Turner ST, Asmann YW, Kocher JP. GLOSSI: a method to assess the association of genetic loci-sets with complex diseases. Bmc Bioinformatics. 10: 102. PMID 19344520 DOI: 10.1186/1471-2105-10-102  0.36
2008 Hwang T, Sicotte H, Tian Z, Wu B, Kocher JP, Wigle DA, Kumar V, Kuang R. Robust and efficient identification of biomarkers by classifying features on graphs. Bioinformatics (Oxford, England). 24: 2023-9. PMID 18653521 DOI: 10.1093/bioinformatics/btn383  0.36
2008 Turner ST, Bailey KR, Fridley BL, Chapman AB, Schwartz GL, Chai HS, Sicotte H, Kocher JP, Rodin AS, Boerwinkle E. Genomic association analysis suggests chromosome 12 locus influencing antihypertensive response to thiazide diuretic. Hypertension. 52: 359-65. PMID 18591461 DOI: 10.1161/HYPERTENSIONAHA.107.104273  0.36
1992 Pattou D, Bach LH, Kocher JP, Maigret B. MOL3D--a modular and interactive program for molecular modeling and conformational analysis: II. Extended modules. Journal of Molecular Graphics. 10: 241-6. PMID 1476998 DOI: 10.1016/0263-7855(92)80076-P  0.36
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