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Bioinformatics and Computational Biosciences Branch

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Abstract 3D rendering of a network.

Yentram Huyen, Ph.D., Chief

Major Areas of Research

  • Computational biology collaboration and training
  • Bioinformatics software development
  • Biocomputing resources
 

Program Description

The Bioinformatics and Computational Biosciences Branch (BCBB) supports the NIAID research mission by leveraging the latest computational technologies to accelerate discovery and remain at the forefront of today's rapid scientific pace. The BCBB partners with clients in the research process by applying bioinformatics and computational biology methods to generate new hypotheses and data, analyze existing data, and ultimately elevate the use of these methods and resources throughout the NIH. The branch is organized into three sections based on expertise: Office of the Chief, Computational Biology Section, and Bioinformatics Development Section. Staff consist of an integrated team of computational biology specialists, bioinformatics software developers, and operations support staff, which includes project managers, business and infrastructure analysts, and communications specialists. The following services are offered:

  • Molecular modeling, simulation, and analysis
    • Model building
    • Drug design
    • Molecular interfaces
    • Visualization
  • Phylogenetics and evolutionary analysis
    • Alignments
    • Trees
    • Selection analysis
  • Next-generation sequencing and microarray genomic analysis
    • Assembly and mapping of high-throughput sequencing data
    • RNA-Seq, CHiP-Seq, variant analysis, and metagenomics
    • Genome browsers and annotations
    • Differential expression, CHiP-Chip, and re-sequencing arrays
  • Sequence design and analysis
    • Primer design
    • Function prediction
    • Molecular cloning
    • Data mining
  • Biostatistics and experimental design
    • Curve fitting and regression
    • Tests and ANOVA
    • PCA and factor analysis
    • Design of experiments
  • Custom scientific software
    • Web-based and stand-alone apps
    • Plug-in development
  • Database and web portal development
    • Electronic notebooks and collaborative work
    • Shared lab resources and calendars
    • Custom databases and queries with web access
  • Automation and acceleration of routine analyses
    • Pipelines and workflows
    • High-performance computing

Group Members

Photo of staff members

From L to R, top to bottom: Yentram (Tram) Huyen, Ph.D.; Darrell Hurt, Ph.D.; Nick Weber; Sandhya Xirasagar, Ph.D.; Ross Henderson, Ph.D.; Andrei Gabrielian, Ph.D.; Shahzad Majeed; Jason Barnett; Karlynn Noble; Jianchang (Jeff) Ning, Ph.D.; Arthur Luarsabov; Ramandeep Kaur; Meghan Coakley; Andrew Oler, Ph.D.; Kui Shen; Ning Hua; Wongyu (Lewis) Kim; Michael Dolan, Ph.D; Alex Levitsky, Ph.D.; Richard (Burke) Squires, Ph.D.; Jennifer Dommer; Kurt Wollenberg, Ph.D.; Vijayaraj Nagarajan, Ph.D.; Mariam Quiñones, Ph.D.; Lingwen Zhang; Qiang (Charlie) Sun; Wei Liang; David Liou; Sergey Karimov; Maarten Leerkes, Ph.D.

Not Pictured: Xiaoming Wang & Lindsay Tonon

Publications

Published Manuscripts

Komarow HD, Skinner J, Young M, Gaskins D, Nelson C, Gergen PJ, Metcalfe DD. A study of the use of impulse oscillometry in the evaluation of children with asthma: analysis of lung parameters, order effect, and utility compared with spirometry. Pediatr Pulmonol. 2012 Jan;47(1):18-26.

Sheng ZM, Chertow DS, Ambroggio X, McCall S, Przygodzki RM, Cunningham RE, Maximova OA, Kash JC, Morens DM, Taubenberger JK. Autopsy series of 68 cases dying before and during the 1918 influenza pandemic peak. Proc Natl Acad Sci U S A. 2011 Sep 27;108(39):16416–21.

Vázquez N, Schmeisser H, Dolan MA, Bekisz J, Zoon KC, Wahl SM. Structural variants of IFN alpha preferentially promote antiviral functions. Blood. 2011 Sep 1;118(9):2567–77.

Srinivasan P, Beatty WL, Diouf A, Herrera R, Ambroggio X, Moch JK, Tyler JS, Narum DL, Pierce SK, Boothroyd JC, Haynes JD, Miller LH. Binding of Plasmodium merozoite proteins RON2 and AMA1 triggers commitment to invasion. Proc Natl Acad Sci U S A. 2011 Aug 9;108(32):13275–80.

Kolar SL, Nagarajan V, Oszmiana A, Rivera FE, Miller HK, Davenport JE, Riordan JT, Potempa J, Barber DS, Koziel J, Elasri MO, Shaw LN. NsaRS is a cell-envelope-stress-sensing two-component system of Staphylococcus aureus. Microbiology. 2011 Aug;157(Pt 8):2206–19.

Riordan JT, Dupre JM, Cantore-Matyi SA, Kumar-Singh A, Song Y, Zaman S, Horan S, Helal NS, Nagarajan V, Elasri MO, Wilkinson BJ, Gustafson JE. Alterations in the transcriptome and antibiotic susceptibility of Staphylococcus aureus grown in the presence of diclofenac. Ann Clin Microbiol Antimicrob. 2011 Jul 21;10:30.

Skinner J, Kotliarov Y, Varma S, Mine KL, Yambartsev A, Simon R, Huyen Y, Morgun A. Construct and compare gene coexpression networks with DAPfinder and DAPview. BMC Bioinformatics. 2011 Jul 14;12:286.

Adler A, Park Y, Larsen P, Nagarajan V, Wollenberg K, Qiu J, Myers TG, Williamson PR. A novel specificity protein 1 (SP1)-like gene, regulating protein kinase C-1 (Pkc1)-dependent cell wall integrity and virulence factors in Cryptococcus neoformans. J Biol Chem. 2011 Jun 10;286(23):20977–90.

Ashktorab H, Varma S, Brim H. Epigenetic instability via genomic-wide DNA methylation and histone modification profile predicts colorectal adenoma and cancer. Gastroenterology. 2011 May;140(5):S–191.

Ramanathan R, Varma S, Ribeiro JM, Myers TG, Nolan TJ, Abraham D, Lok JB, Nutman TB. Microarray-based analysis of differential gene expression between infective and noninfective larvae of Strongyloides stercoralis. PLoS Negl Trop Dis. 2011 May 3;5(5):e1039.

Gaiser T, Camps J, Meinhardt S, Wangsa D, Nguyen QT, Varma S, Dittfield C, Kunz-Schughart LA, Kemmerling R, Becker MR, Heselmeyer-Haddad K, Ried T. Genome and transcriptome profiles of CD133-positive colorectal cancer cells. Am J Pathol. 2011 Apr;178(4):1478–88.

Musselwhite LW, Sheikh V, Norton TD, Rupert A, Porter BO, Penzak SR, Skinner J, Mican JM, Hadigan C, Sereti I. Markers of endothelial dysfunction, coagulation, and tissue fibrosis independently predict venous thromboembolism in HIV. AIDS. 2011 Mar 27;25(6):787–95.

Gupta A, Schulze T, Nagarajan V, Akula N, Corona W, Jiang X, Hunter N, McMahon FJ, Detera-Wadleigh SD. Interaction networks of lithium and valproate molecular targets reveal a striking enrichment of apoptosis functional clusters and neurotrophin signaling. Pharmacogenomics J. 2011 Mar 8. Epub ahead of print.

López-Barragán MJ, 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.

Fabozzi G, Nabel CS, Dolan MA, Sullivan NJ. Ebolavirus proteins suppress the effects of small interfering RNA by direct interaction with the mammalian RNA interference pathway. J Virol. 2011 Mar;85(6):2512-23.

Roederer M, Nozzi JL, Nason MC. SPICE: exploration and analysis of post-cytometric complex multivariate datasets. Cytometry A. 2011 Feb;79(2):167–74.

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.

Jiang H, Li N, Gopalan V, Zilversmit MM, Varma S, Nagarajan V, Li J, Mu J, Hayton K, Henschen B, Yi M, Stephens R, McVean G, Awadalla P, Wellems TE, Su XZ. High recombination rates and hotspots in a Plasmodium falciparum genetic cross. Genome Biol. 2011;12(4):R33.

Price DP, Nagarajan V, Chourbanov A, Houde P, Milligan B, Drake LL, Gustafson JE, Hansen IA. The fat body transcriptomes of the yellow fever mosquito Aedes aegypti, pre- and post- blood meal. PLoS One. 2011;6(7):e22573.

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.

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.

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.

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. Computer Technology and Development (ICCTD), 2010 2nd International Conference Proceedings. 2010:70–74.

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):17880–7.

Uchime O, Plassmeyer ML, Herrera R, Reiter K, Kotova S, Shimp RL Jr, 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. Am J Trop Med Hyg. 2010;83(5):41.

Selected Paper and Poster Presentations

Ogden K, Dolan MA, Patton J. Roles of the priming loop in of rotavirus RNA polymerase VP1 in RNA synthesis. Poster session presented at: Viruses and Cells Gordon Research Conference; 2011 Aug; Lucca, Italy.

Gladue DP, Holinka LG, Fernandez-Sainz IJ, Baker-Branstetter R, O’Donnell V, Lu Z, Ambroggio X, Risatti GR, Borca MV. Novel host protein interaction partners for the viral P7 protein in classical swine fever virus. Poster session presented at: the American Society for Virology 30th Annual Meeting; 2011 Jul; Minneapolis, MN.

Parra GI, Bok K, Sosnovtsev SV, Dolan MA, Cottingham B, Green KY. Evidence for shared ABH histo-blood group antigen blocking epitopes between norovirus genogroups II and IV. Poster session presented at: the American Society for Virology 30th Annual Meeting; 2011 Jul; Minneapolis, MN.

Adler A, Park Y, Larsen P, Nagarajan V, Wollenberg K, Qui J, Myers TG, Williamson PR. (2011, April 12). A novel specificity protein (SP1)-like gene, regulating protein kinase C-1 (Pkc1)-dependent cell wall integrity and virulence factors in Cryptococcus neoformans. Paper presented at: the Israel Society for Microbiology Annual Meeting; 2011 Apr 12; Ramat-Gan, Israel.

Huyen Y. Modeling complex biological systems: an agent-based approach. Paper presented at: the 2011 ISCB Africa ASBCB Conference on Bioinformatics; 2011 Mar 9; Cape Town, South Africa.

Musselwhite L, Sheikh V, Norton T, Rupert A, Porter B, Penzak S, Skinner J, Mican J, Hadigan C, Sereti I. Circulating markers of endothelial dysfunction, coagulation, and tissue gibrosis prior to incident venous thromboembolism in patients with HIV infection. Poster session presented at: the 2011 Conference on Retroviruses and Opportunistic Infections (CROI); 2011 Feb; Boston, MA. 

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: the IEEE International Conference on Computer Technology and Development, ICCTD 2010; 2010 Nov 2; Cairo, Egypt.

Detera-Wadleigh SD, Schulze TG, Gupta A, Akula N, Nagarajan V, Jiang X, Corona W, Hunter N, McMahon F. Molecular networks for lithium and valproate regulated genes highlight a marked enrichment of apoptosis functional clusters. Paper presented at: the American Society of Human Genetics Annual Meeting; 2010 Nov 2; Washington, DC.

Shulzehnko N, Ribalta J, Yambartsev A, Sanson G, Silva I, Brenna S, Carvalho C, Varma S, Skinner J, Gerbase-DeLima M, Mine K, Morgun A. Integration of transcriptome and genome networks reveals the missing link between antiviral response and progression of cervical cancer. Paper presented at: the International Conference on Systems Biology; 2010 Oct 11; Edinburgh, Scotland.

Software

BCBB creates applications prepared by NIAID researchers and collaborators to share with the broader research community.

Examples of Web applications include the following:

The following are examples of downloadable desktop applications:

Additionally, BCBB is developing a new Web application called Nexplorer:

Evolutionary and comparative analyses are important tools used for the annotation of genomes. These analyses are hampered by the diverse file formats used in computational evolutionary analysis and the inability of analysis tools to sync with one another. Visualization and data management applications that can overcome these limitations are valuable for NIAID researchers performing these analyses. Comparative Data Analysis Ontology (CDAO), a data model developed and supported by the phylogenetic community, represents all the sets of concepts in an evolutionary analysis and the relationships among those concepts. BCBB is developing a Web application, Nexplorer3, using a semantic Web framework for visually manipulating comparative data in CDAO format and extracting biologically significant results based on reasoning. In addition, the ontology-based framework allows representation of data in different formats and improves interoperability of applications.

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Last Updated March 04, 2013