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Bioinformatics and Systems Biology

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Selected Publications—Authored

López-Barragán MG, Quiñones M, Cui K, Lemieux J, Zhao K, Su XZ. Effect of PCR extension temperature on high-throughput sequencing. Mol Biochem Parasitol. 2011 Mar;176(1):64-7.

Madala SK, Dolan MA, Sharma D, Ramalingam TR, Wilson MS, Mentink-Kane MM, Masison DC, Wynn TA. Mapping mouse IL-13 binding regions using structure modeling, molecular docking, and high-density peptide microarray analysis. Proteins. 2011 Jan;79(1):282-93.

Teferedegne B, Murata H, Quiñones M, Peden K, Lewis AM. Patterns of microRNA expression in non-human primate cells correlate with neoplastic development in vitro. PLoS One. 2010 Dec 22;5(12):e14416.

Yan Y, Liu Q, Wollenberg K, Martin C, Buckler-White A, Kozak CA. Evolution of functional and sequence variants of the mammalian XPR1 receptor for mouse xenotropic gammaretroviruses and the human-derived XMRV. J Virol. 2010 Nov;84(22):11970-80.

Das SR, Puigbò P, Hensley SE, Hurt DE, Bennink JR, Yewdell JW. Glycosylation focuses sequence variation in the influenza A virus H1 hemagglutinin globular domain. PLoS Pathog. 2010 Nov 24;6(11):e1001211.

Ofek G, Guenaga FJ, Schief WR, Skinner J, Baker D, Wyatt R, Kwong PD. Elicitation of structure-specific antibodies by epitope scaffolds. Proc Natl Acad Sci U S A. 2010 Oct 19;107(42):17859-60.

Kong L, Huang CC, Coales SJ, Molnar KS, Skinner J, Hamuro Y, Kwong PD. Local conformational stability of HIV-1 gp120 in unliganded and CD4-bound states as defined by amide hydrogen/deuterium exchange. J Virol. 2010 Oct;84(19):10311-21.

Wang HY, Gopalan V, Aksentijevich I, Yeager M, Ma CA, Mohamoud YA, Quiñones M, Matthews C, Boland J, Niemela JE, Torgerson TR, Giliani S, Uzel G, Orange JS, Shapiro R, Notarangelo L, Ochs GD, Fleisher T, Kastner D, Chanock SJ, Jain A. A custom 148 gene-based resequencing chip and the SNP explorer software: new tools to study antibody deficiency. Hum Mutat. 2010 Sep;31(9):1080-8.

Sanville B, Dolan MA, Wollenberg K, Yan Y, Martin C, Yeung ML, Strebel K, Buckler-White A, Kozak CA. Adaptive evolution of Mus Apobec3 includes retroviral insertion and positive selection at two clusters of residues flanking the substrate groove. PLoS Pathog.2010 Jul 1;6:e1000974.

Fleming JM, Miller TC, Quiñones M, Xiao Z, Xu X, Meyer MJ, Ginsburg E, Veenstra TD,  Vonderhaar BK. The normal breast microenvironment of premenopausal women differentially influences the behavior of breast cancer cells in vitro and in vivo. BMC Med. 2010 May 21;8:27.

Nader N, Bachrach BE, Hurt DE, Gajula S, Pittman A, Lescher R, Kino T. A novel point mutation in Helix 10 of the human glucocorticoid receptor causes generalized glucocorticoid resistance by disrupting the structure of the ligand-binding domain. J Clin Endocrinol Metabol. 2010 May;95(5):2281-5.

Lopez JE, Schrumpf ME, Nagarajan V, Raffel SJ, McCoy BN, Schwan TG. A novel surface antigen of relapsing fever spirochetes can discriminate between relapsing fever and Lyme borreliosis. Clin Vaccine Immunol. 2010 Apr;17(4):564-71.

Ofek G, McKee K, Yang Y, Yang ZY, Skinner J, Guenaga FJ, Wyatt R, Zwick MB, Nabel GJ, Mascola JR, Kwong PD. Relationship between antibody 2F5 neutralization of HIV-1 and hydrophobicity of its heavy chain third complementarity-determining loop. J Virol. 2010 Mar;84(6):2955-62.

Kino T, Hurt DE, Ichijo T, Nader N, Chrousos GP. Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor. Sci Signal. 2010 Feb 2;3(107):ra8.

Pancera M, Majeed S, Ban YE, Chen L, Huang CC, Kong L, Kwon YD, Stuckey J, Zhou T, Robinson JE, Schief WR, Sodroski J, Wyatt R, Kwong PD. Structure of HIV-1 gp120 with gp41-interactive region reveals layered envelope architecture and basis of conformational mobility. Proc Natl Acad Sci U S A. 2010 Jan 19;107(3):1166-71.

Oramasionwu CU, Skinner J, Ryan L, Frei CR. Disparities in antiretroviral prescribing for blacks and whites in the United States. J Natl Med Assoc. 2009 Nov;101(11):1140-4.

Selected Publications—Acknowledged

Rai G, Ray S, Milton J, Yang J, Ren P, Lempicki R, Mage RG. Gene expression profiles in a rabbit model of systemic lupus erythematosus autoantibody production. J Immunol. 2010 Oct 1;185(7):4446-56.

Engel AR, Rumyantsev AA, Maximova OA, Speicher JM, Heiss B, Murphy BR, Pletnev AG. The neurovirulence and neuroinvasiveness of chimeric tick-borne encephalitis/dengue virus can be attenuated by introducing defined mutations into the envelope and NS5 protein genes and the 3′ non-coding region of the genome. Virology. 2010 Sep 15;405(1):243-52.

Pancera M, McLellan JS, Wu X, Zhu J, Changela A, Schmidt SD, Yang Y, Zhou T, Phogat S, Mascola JR, Kwong PD. Crystal structure of PG16 and chimeric dissection with somatically related PG9: structure-function analysis of two quaternary-specific antibodies that effectively neutralize HIV-1. J Virol. 2010 Aug;84(16):8098-110.

Ventura CL, Malachowa N, Hammer CH, Nardone GA, Robinson MA, Kobayashi SD, DeLeo FR. Identification of a novel Staphylococcus aureus two-component leukotoxin using cell surface proteomics. PLoS One. 2010 Jul 16;5(7):e11634.

Yang Z, Bruno DP, Martens CA, Porcella SF, Moss B. Simultaneous high-resolution analysis of vaccinia virus and host cell transcriptomes by deep RNA sequencing. Proc Natl Acad Sci U S A. 2010 Jun 22;107(25):11513-8.

Hensley LE, Mulangu S, Asiedu C, Johnson J, Honko AN, Stanley D, Fabozzi G, Nichol ST, Ksiazek TG, Rollin PE, Wahl-Jensen V, Bailey M, Jahrling PB, Roederer M, Koup RA, Sullivan NJ. Demonstration of cross-protective vaccine immunity against an emerging pathogenic Ebolavirus species. PLoS Pathog. 2010 May 20;6(5):e1000904.

Chen GL, Lamirande EW, Jin H, Kemble G, Subbarao K. Safety, immunogenicity, and efficacy of a cold-adapted A/Ann Arbor/6/60 (H2N2) vaccine in mice and ferrets. Virology. 2010 Mar 1;398(1):109-14.

Yang J, Pospisil R, Ray S, Milton J, Mage RG. Investigations of a rabbit (Oryctolagus cuniculus) model of systemic lupus erythematosus (SLE), BAFF and its receptors. PLoS One. 2009 Dec 30;4(12):e8494.

Liang Y, Vogel JL, Narayanan A, Peng H, Kristie TM. Inhibition of the histone demethylase LSD1 blocks α-herpesvirus lytic replication and reactivation from latency. Nat Med. 2009 Nov;15(11):1312-7.

Bok K, Abente EJ, Realpe-Quintero M, Mitra T, Sosnovtsev SV, Kapikian AZ, Green KY. Evolutionary dynamics of GII.4 noroviruses over a 34-year period. J Virol. 2009 Nov;83(22):11890-901.

Sá JM, Twu O, Hayton K, Reyes S, Fay MP, Ringwald P, Wellems TE. Geographic patterns of Plasmodium falciparum drug resistance distinguished by differential responses to amodiaquine and chloroquine. Proc Natl Acad Sci U S A. 2009 Nov 10;106(45):18883-9.

Selected Paper and Poster Presentations

Uchime O, Plassmeyer ML, Herrera R, Reiter K, Kotova S, Shimp RL, Lebowitz J, Hurt DE, Jin AJ, Miller LH, Narum DL. A recombinant Plasmodium falciparum merozoite-specific thrombospondin-related anonymous protein (MTRAP) is a highly extended flexible rod-like protein that binds human erythrocytes. Paper presented at: American Society of Tropical Medicine and Hygiene 59th Annual Meeting; 2010 Nov 3-7; Atlanta, GA.

Nagarajan V, Varma S, Hurt D, Guo Y, Huyen Y. Microarray Meta-Miner (MMM): an integrated method and a Web tool to identify genes with similar expression profile. Paper presented at: IEEE 2nd International Conference on Computer Technology and Development 2010; 2010 Nov 2-4; Cairo, Egypt.

Barnett J, Weber N, Lumpkin J, Huyen Y. Evaluation of Microsoft OneNote integrated with an electronic records and documents management system: a potential Electronic Laboratory Notebook? Poster session presented at: 2010 NIH Research Festival; 2010 Oct 6; Bethesda, MD.

Skinner J, Gopalan V, Huyen Y.  HDX_NAME: a Web tool for analysis of hydrogen exchange. Poster session presented at: 2010 NIH Research Festival; 2010 Oct 5; Bethesda, MD.

Weber N, Gopalan V, Bandaru S, Phillips K, Barnett J, Quiñones M, Hurt D, Lumpkin J, Huyen Y. HPC Web: democratizing high-performance computing at the NIAID. Poster session presented at: 2010 NIH Research Festival; 2010 Oct 5; Bethesda, MD.

Nagarajan V, Varma S, Hurt D, Huyen Y. Prediction of proteins that are functionally related to RB1 using human Microarray Meta-Miner. Poster session presented at: 2010 NIH Research Festival; 2010 Oct 5; Bethesda, MD.

Gillet J, Varma S, Gottesman MM. Characterization of ABCB5 transcript variants using NextGen sequencing. Poster session presented at: 2010 NIH Research Festival; 2010 Oct 5; Bethesda, MD.

Backus K, Dolan MA, Barry CE 3rd. Putative membrane binding interface of TB antigen 85 determined by molecular dynamics. Poster session presented at: 2010 NIH Research Festival; 2010 Oct 5; Bethesda, MD.

Makiya M, Dolan MA, Chen Z. Antibody binding to anthrax edema factor (EF) determined by RosettaDock using flexible loop modeling. Poster session presented at: 2010 NIH Research Festival; 2010 Oct 5; Bethesda, MD.

Gopalan V, Tan Q, Mohamoud Y, Stoltzfus A, Huyen Y. CDAO and Nexplorer3: an example of ontology-driven application development. Poster session presented at: 2010 NIH Research Festival; 2010 Oct 5; Bethesda, MD.

Jin A, Kotova S, Reiter K, Smith P, Lebowitz J, Hurt D, Narum D. Biological atomic force microscopy and bioanalysis of malaria vaccine candidates. Poster session presented at: 2010 NIH Research Festival; 2010 Oct 5; Bethesda, MD. 

Makiya M, Dolan MA, Chen Z. Antibody binding to anthrax edema factor (EF) determined by RosettaDock using flexible loop modeling. Poster session presented at: RosettaCon2010; 2010 Aug 2; Leavenworth, WA.

Nader N, Bachrach BE, Hurt DE, Gajula S, Pittman A, Lescher R, Kino T. A novel point mutation in the Helix 10 of the human glucocorticoid receptor causes generalized glucocorticoid resistance by disrupting the structure of the ligand-binding domain. Poster session presented at: ENDO 2010, the 92nd Annual Meeting & Expo; 2010 Jun 19; San Diego, CA.

Gopalan V, Tan Q, Mohamoud Y, Stoltzfus A, Huyen Y. CDAO and Nexplorer3: an example of ontology-driven application development.  Poster session presented at: Bioinformatics Tools and Techniques for Allergy and Infectious Disease Research; Joint NIAID-ISTC Conference; 2010 Jun 7; Moscow, Russian Federation.

Hurt DE, Taylor L, Swanson KA, Nagarajan V, Caldwell HD, Huyen Y. Comprehensive bioinformatics and computational biology assault on the functional mysteries of Chlamydia trachomatis polymorphic membrane protein D. Poster session presented at: Bioinformatics Tools and Techniques for Allergy and Infectious Disease Research; Joint NIAID-ISTC Conference; 2010 Jun 7; Moscow, Russian Federation.

Backus K, Dolan MA, Barry CE 3rd. Putative membrane binding interface of TB antigen 85 determined by molecular dynamics. Poster session presented at: Research Opportunities in TB Drug Discovery and Diagnostics Workshop; 2010 May 24; Moscow, Russian Federation.

Barnett J, Barrick B, Weber N, Lumpkin J, Huyen Y. Use of a collaborative Web portal to facilitate transparency and manage communications among research groups in the NIAID Integrated Research Facility. Poster session presented at: Bio-IT World Conference and Expo 2010; 2010 Apr 21; Boston, MA.

Weber N, Gopalan V, Quiñones M, Hernandez H, Reed R, Kassing K, Huyen Y, Tartakovsky M. A centralized and scalable infrastructure approach to support next-generation sequencing at the National Institute of Allergy and Infectious Diseases. Poster session presented at: Bio-IT World Conference and Expo 2010; 2010 Apr 21; Boston, MA.

Mine KL, Shulzhenko N, Yambartsev A, Sanson G, Silva ID, Brenna S, Carvalho C, Ribalta J, Varma S, Skinner J, Gerbase-DeLima M, Morgun A. Meta-analysis integrates transcriptome and genome networks in cervical cancer revealing major regulators and potential therapeutic targets. Poster session presented at: Translational Genomics: Looking Back and Moving Forward; 2010 Mar 5; Bethesda, MD.

Rivera JM, Pando J, Cuaron JA, Song Y, Singh AK, Nagarajan V, Dupre J, Wilkinson BJ, Gustafson JE. Characterization of ethanol-adapted Staphylococcus aureus mutants. Poster session presented at: 110th American Society for Microbiology General Meeting; 2010 Jan 12; San Diego, CA.

Cuaron JA, Dulal S, Rivera J, Nagarajan V, Yang S, Singh AK, Jayaswal RK, Wilkinson BJ, Gustafson JE. The Staphylococcus aureus tea tree oil stimulon. Poster session presented at: 110th American Society for Microbiology General Meeting; 2010 Jan 6; San Diego, CA.

Nagarajan V, Varma S, Hurt D, Huyen Y. Prediction of proteins that are functionally related to RB1 using human Microarray Meta-Miner. Poster session presented at: First International Rb Meeting; 2009 Nov 20; Toronto, Canada.

Jiang H, Gopalan V, Varma S, Nagarajan V, Hayton K, Henschen B, Yi M, Stephens R, Wellems T, Su X. A high-resolution linkage map and estimation of recombination hotspots for Plasmodium falciparum. Poster session presented at: ASTMH 58th Annual Meeting; 2009 Nov 19; Washington, DC.

Fabozzi G, Nabel C, Dolan M, Nabel GJ, Sullivan NJ. Ebola VP30 and VP35 revert siRNA effects by direct interaction with RNAi pathway. Poster session presented at: 47th Annual Meeting of the Infectious Diseases Society of America; 2009 Oct 29; Philadelphia, PA.

Skinner J, Varma S, Yambartsev A, Kotliarov Y, Huyen Y, Morgun A. Novel tool for identification and comparison of gene-gene association networks. Poster session presented at: 2009 NIH Research Festival; 2009 Oct 6; Bethesda, MD.

Li J, Tan Q, Nagarajan V, Quiñones M, Mohamoud Y, Huyen Y. NetCirChro: a novel cytoscape plug-in for network visualization on circular chromosomes. Poster session presented at: 2009 NIH Research Festival; 2009 Oct 6; Bethesda, MD.

Last Updated April 19, 2011

Last Reviewed April 13, 2011