Publications - Jean-Pierre A. Kocher, Ph.D.

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1. 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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2. 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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3. 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; 10(1):15-20.
4. 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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5. 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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6. 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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7. 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 9.
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8. 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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9. 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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10. 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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11. 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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12. 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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13. 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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14. 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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15. 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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16. 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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17. 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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18. 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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19. 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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20. 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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21. 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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22. 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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23. 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.
24. 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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25. 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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26. 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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27. 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.
28. 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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29. 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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30. 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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31. 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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32. 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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