Publications

  1. Klein CJ, Middha S, Duan X, Wu Y, Litchy WJ, Gu W, Dyck PJ, Gavrilova RH, Smith DI, Kocher JP, Dyck PJ. Application of whole exome sequencing in undiagnosed inherited polyneuropathies. J Neurol Neurosurg Psychiatry. 2014 Nov; 85(11):1265-72. Epub 2014 Mar 06.
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  2. Wang L, Chen J, Wang C, Uuskula-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, Li W. MACE: model based analysis of ChIP-exo. Nucleic Acids Res. 2014 Sep 23.
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  3. 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, Asmann YW. PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data. Bioinformatics. 2014 Sep 15; 30(18):2678-80. Epub 2014 May 29.
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  4. Eric WD, 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. Invest Ophthalmol Vis Sci. 2014 Aug 28. [Epub ahead of print]
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  5. 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. 2014 Aug 27.
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  6. 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. 2014 Jul 7; 9(8). [Epub ahead of print]
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  7. Li X, Martinez-Fernandez A, Hartjes KA, Kocher JP, Olson TM, Terzic A, Nelson TJ. Transcriptional atlas of cardiogenesis maps congenital heart disease interactome. Physiol Genomics. 2014 Jul 1; 46(13):482-95. Epub 2014 May 06.
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  8. 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. 2014 Jul 1; 30(13):1920-2. Epub 2014 Mar 10.
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  9. 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. Bioconjug Chem. 2014 Jun 18; 25(6):1078-90. Epub 2014 May 22.
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  10. Zhao H, Sun Z, Wang J, Huang H, Kocher JP, Wang L. CrossMap: a versatile tool for coordinate conversion between genome assemblies. Bioinformatics. 2014 Apr 1; 30(7):1006-7. Epub 2013 Dec 18.
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  11. 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. J Virol. 2014 Apr; 88(8):4069-82. Epub 2014 Jan 29.
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  12. 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, McWilliams RR, Lazaridis KN, Klee EW, Bible KC, Harris P, Oliver GR, Bhavsar JD, Nair AA, Integrated genomic characterization reveals novel, therapeutically relevant drug targets in FGFR and EGFR pathways in sporadic intrahepatic cholangiocarcinoma. PLoS Genet. 2014 Feb; 10(2):e1004135. Epub 2014 Feb 13.
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  13. Ruan X, Liu H, Boardman L, Kocher JP. Genome-Wide Analysis of Loss of Heterozygosity in Breast Infiltrating Ductal Carcinoma Distant Normal Tissue Highlights Arm Specific Enrichment and Expansion across Tumor Stages. PLoS One. 2014; 9(4):e95783. Epub 2014 Apr 18.
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  14. Li X, Martinez-Fernandez A, Therneau T, Kocher JP, Nelson TJ. Rcircle: an R package for Integrating and Visualizing multiple “–omics” data for Knowledge Discovery BMC Bioinformatics 2014. BMC Bioinformatics. 2014.
  15. Dasari S, Theis JD, Vrana JA, Zenka RM, Zimmermann MT, Kocher JP, Highsmith WE Jr, Kurtin PJ, Dogan A. Clinical Proteome Informatics Workbench Detects Pathogenic Mutations in Hereditary Amyloidoses. J Proteome Res. 2014; 13(5). Epub 2014 Apr 3
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  16. Middha S, Baheti S, Hart SN, Kocher JP. From days to hours: reporting clinically actionable variants from whole genome sequencing. PLoS One. 2014; 9(2):e86803. Epub 2014 Feb 05.
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  17. 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. 2014; 15:423. Epub 2014 Jun 03.
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  18. 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. 2014; 15:224. Epub 2014 Jun 27.
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  19. 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. 2014; 15(1):280. Epub 2014 Aug 15.
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  20. Hart SN, Therneau TM, Zhang Y, Poland GA, Kocher JP. Calculating sample size estimates for RNA sequencing data. J Comput Biol. 2013 Dec; 20(12):970-8. Epub 2013 Aug 20.
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  21. 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. 2013 Nov 15; 29(22):2877-83. Epub 2013 Aug 19.
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  22. 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 Res. 2013 Apr 1; 41(6):e74. Epub 2013 Jan 17.
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  23. 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, Scaria V, Sivasubbu S. A sequence-based variation map of zebrafish. Zebrafish. 2013 Mar; 10(1):15-20.
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  24. Hart SN, Sarangi V, Moore R, Baheti S, Bhavsar JD, Couch FJ, Kocher JP. SoftSearch: integration of multiple sequence features to identify breakpoints of structural variations. PLoS One. 2013; 8(12):e83356. Epub 2013 Dec 16.
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  25. 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 Res Notes. 2013; 6:33. Epub 2013 Jan 30.
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  26. 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. 2013; 8(8):e71745. Epub 2013 Aug 19.
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  27. 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. 2012 Aug 15; 28(16):2180-1. Epub 2012 Jun 10.
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  28. 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. 2012 May; 61(5):1004-16. Epub 2012 Mar 13.
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  29. 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. 2012 Jan 15; 28(2):277-8. Epub 2011 Nov 15.
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  30. 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, Leontovich AA, Hossain A, Kocher JP, Perez EA, Reisman DN, Fields AP, Thompson EA. 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. Front Oncol. 2012; 2:12. Epub 2012 Feb 10.
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  31. 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. 2012; 7(3):e33650. Epub 2012 Mar 19.
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  32. Ruan X, Kocher JP, Pommier Y, Liu H, Reinhold WC. Mass homozygotes accumulation in the NCI-60 cancer cell lines as compared to HapMap Trios, and relation to fragile site location. PLoS One. 2012; 7(2):e31628. Epub 2012 Feb 09.
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  33. Sohn S, Kocher JP, Chute CG, Savova GK. Drug side effect extraction from clinical narratives of psychiatry and psychology patients. J Am Med Inform Assoc. 2011 Dec; 18 Suppl 1:i144-9. Epub 2011 Sep 21.
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  34. 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 Res. 2011 Aug; 39(15):e100. Epub 2011 May 27.
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  35. 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 Clin Proc. 2011 Jul; 86(7):606-14. Epub 2011 Jun 06.
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  36. Norgan AP, Coffman PK, Kocher JP, Katzmann DJ, Sosa CP. Multilevel Parallelization of AutoDock 4.2. J Cheminform. 2011; 3(1):12. Epub 2011 Apr 28.
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  37. Sicotte H, Rider DN, Poland GA, Dhiman N, Kocher JP. SNPPicker: high quality tag SNP selection across multiple populations. BMC Bioinformatics. 2011; 12:129. Epub 2011 May 02.
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  38. 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 Med Genomics. 2011; 4:84. Epub 2011 Dec 16.
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  39. Chai HS, Therneau TM, Bailey KR, Kocher JP. Spatial normalization improves the quality of genotype calling for Affymetrix SNP 6.0 arrays. BMC Bioinformatics. 2010; 11:356. Epub 2010 Jun 29.
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  40. 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. 2010; 11:357. Epub 2010 Jun 04.
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  41. Sohn S, Murphy SP, Masanz JJ, Kocher JP, Savova GK. Classification of medication status change in clinical narratives. AMIA Annu Symp Proc. 2010; 2010:762-6. Epub 2010 Nov 13.
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  42. 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. 2009; 10:102. Epub 2009 Apr 03.
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  43. 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. 2009; 10:531. Epub 2009 Nov 16.
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  44. 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. 2008 Sep 15; 24(18):2023-9. Epub 2008 Jul 24.
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  45. 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. 2008 Aug; 52(2):359-65. Epub 2008 Jun 30.
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  46. Hwang T, Tian Z, Kuang R, Kocher JP. Learning on Weighted Hypergraphs to Integrate Protein Interactions and Gene Expressions for Cancer Outcome Predication. in Proceedings of the. 2008 Eighth International Conference on Data Mining; IEEE Computer Society. 2008:293-302.
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  47. Lee C, Maeng JS, Kocher JP, Lee B, Yu MH. Cavities of alpha(1)-antitrypsin that play structural and functional roles. Protein Sci. 2001 Jul; 10(7):1446-53.
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  48. Prevost M, Kocher JP. Structural characterization by computer experiments of the lipid-free LDL-receptor-binding domain of apolipoprotein E. Protein Eng. 1999 Jun; 12(6):475-83.
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  49. Kocher JP, Prevost M, Wodak SJ, Lee B. Properties of the protein matrix revealed by the free energy of cavity formation. Structure. 1996 Dec 15; 4(12):1517-29.
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  50. Prévost M, Oliveira I, Kocher JP, Wodak SJ. Free energy of cavity formation in liquid water and hexane. J Phys Chem. 1996; 100:2738-43.
  51. Kocher JP, Rooman MJ, Wodak SJ. Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J Mol Biol. 1994 Feb 4; 235(5):1598-613.
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  52. Pattou D, Bach LH, Kocher JP, Maigret B. MOL3D--a modular and interactive program for molecular modeling and conformational analysis: II. Extended modules. J Mol Graph. 1992 Dec; 10(4):241-6.
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  53. Rooman MJ, Kocher JP, Wodak SJ. Extracting information on folding from the amino acid sequence: accurate predictions for protein regions with preferred conformation in the absence of tertiary interactions. Biochemistry. 1992 Oct 27; 31(42):10226-38.
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  54. Rooman MJ, Kocher JP, Wodak SJ. Prediction of protein backbone conformation based on seven structure assignments. Influence of local interactions. J Mol Biol. 1991 Oct 5; 221(3):961-79.
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  55. De Coen JL, Kocher JP, Delcroix C, Lontie JF, Malmendier CL. Conformational properties of apolipoproteins studied by computer graphics. Adv Exp Med Biol. 1991; 285:141-5.
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