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Peer Reviewed Papers, Books, Chapters

Year Title Citation Authors
1. 2011 SNPPicker: High quality tag SNP selection across multiple populations. BMC Bioinformatics. 2011; 12:129. Epub 2011 May 2 PMID:21535878. DOI:10.1186/1471-2105-12-129
2. 2011 Multilevel Parallelizaton of AutoDock 4. Journal of Cheminformatics. 2011; 3(12). DOI:10.1186/1758-2946-3-12.
3. 2011 A Novel Bioinformatics Pipeline for Identification and Characterization of Fusion Transcripts in 31 Breast Cancer and Normal Cell Lines. Nucleic Acids Research
4. 2010 Classification of medication status change in clinical narratives. AMIA Annu Symp Proc. 2010; 2010:762-6. Epub 2010 Nov 13. PMID:21347081. PMCID:3041444.
5. 2010 Spatial normalization improves the quality of genotype calling for Affymetrix SNP 6.0 arrays. BMC Bioinformatics. 2010; 11:356. Epub 2010 Jun 29. PMID:20587065. PMCID:2910027. DOI:10.1186/1471-2105-11-356
6. 2010 Copy number variation and cytidine analogue cytotoxicity: a genome-wide association approach. BMC Genomics. 2010; 11:357. Epub 2010 Jun 04. PMID:20525348. PMCID:2894803. DOI:10.1186/1471-2164-11-357
7. 2009 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. PMID:19917133. PMCID:2781828. DOI:10.1186/1471-2164-10-531.
8. 2009 GLOSSI: a method to assess the association of genetic loci-sets with complex diseases. BMC Bioinformatics. 2009; 10:102. Epub 2009 Apr 03. PMID:19344520. PMCID:2678095. DOI:10.1186/1471-2105-10-102.
9. 2008 Learning on Weighted Hypergraphs to Integrate Protein Interactions and Gene Expressions for Cancer Outcome Predication. Proceedings of the. 2008 Eighth International Conference on Data Mining; IEEE Computer Society. 2008:293-302.
10. 2008 Robust and efficient identification of biomarkers by classifying features on graphs. Bioinformatics. 2008 Sep 15; 24(18):2023-9. Epub 2008 Jul 24. PMID:18653521. DOI:10.1093/bioinformatics/btn383.
11. 2008 Genomic association analysis suggests chromosome 12 locus influencing antihypertensive response to thiazide diuretic. Hypertension. 2008 Aug; 52(2):359-65. Epub 2008 Jun 30. PMID:18591461. PMCID:2692710. NIHMS:98838. DOI:10.1161/HYPERTENSIONAHA.107.104273
12. 2004 Models for cytochrome P450-mediated metabolism. In: Pharmaceutical profiling in drug discovery for lead selection. AAPS Pharmaceutica Press. Prous Science Publishers; p. 69-80.
13. 2001 Cavities of alpha(1)-antitrypsin that play structural and functional roles. Protein Sci ; 10(7):1446-53. PMID:11420446. PMCID:2374102. DOI:10.1110/ps.840101.
14. 1999 Structural characterization by computer experiments of the lipid-free LDL-receptor-binding domain of apolipoprotein E. Protein Eng ; 12(6):475-83. PMID:10388844.
15. 1996 Properties of the protein matrix revealed by the free energy of cavity formation. Structure ; 4(12):1517-29. PMID:8994976
16. 1996 Free energy of cavity formation in liquid water and hexane J Phys Chem ; 100:2738-43
17. 1995 Effective potentials derived from known protein structures and their use in predicting 3D structure from sequence. In: Sanz F, Giraldo J, and Manaut F. QSAR and molecular modelling: concepts. Computational tools and biological applications Prous Science Publishers; p. 206-14.
18. 1994 Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J Mol Biol ; 235(5):1598-613. PMID:8107094.
19. 1993 Prediction of regions with well defined conformational preferences in proteins, and their relevance to protein folding. In: Doyama M, Kihara J, Tanaka M, and Yamamoto R. Computer aided innovation of new materials II. Elsevier Science Publishers; p. 1129-235
20. 1992 MOL3D--a modular and interactive program for molecular modeling and conformational analysis: II. Extended modules J Mol Graph; 10(4):241-6. PMID:1476998.
21. 1992 Extracting information on folding from the amino acid sequence: accurate predictions for protein regions with preferred conformation in the absence of tertiary interactions. 31(42):10226-38. PMID:1420144.
22. 1991 Prediction of protein backbone conformation based on seven structure assignments. Influence of local interactions J Mol Biol ; 221(3):961-79. PMID:1942039.
23. 1991 Conformational properties of apolipoproteins studied by computer graphics Adv Exp Med Biol; 285:141-5. PMID:1907079.


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