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Bioinformatics and Computational Biosciences Branch

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 National Institutes of Health (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.; Alex Levitsky, Ph.D.; Ramandeep Kaur; Meghan Coakley; Andrew Oler, Ph.D.; Kui Shen; Ning Hua; Wongyu (Lewis) Kim; Michael Dolan, Ph.D; Arthur Luarsabov; ​Jennifer Dommer; Richard (Burke) Squires, Ph.D.; Lindsay Tonon; Vijayaraj Nagarajan, Ph.D.; Qiang (Charlie) Sun; Lingwen Zhang; Kurt Wollenberg, Ph.D.; David Liou; Sergey Karimov; Maarten Leerkes, Ph.D.; Mariam Quiñones, Ph.D.; Matt Reardon; Yongjie (Fan) Fan; Octavio Juarez-Espinosa; Jenny Peterson; Jin Chen​; Phil Cruz, Ph.D.

Not Pictured: Xiaoming Wang

Publications

Published Manuscripts

Zhu J, Jankovic D, Oler AJ, Wei G, Sharma S, Hu G, Guo L, Yagi R, Yamane H, Punkosdy G, Feigenbaum L, Zhao K, Paul WE (2012). The transcription factor T-bet is induced by multiple pathways and prevents an endogenous Th2 cell program during Th1 cell responses. Immunity, 10.1016/j.immuni.2012.09.007.

Moyer B, Whalen C, Hoopengardner L, Huyen Y, Watkins K, Holdsworth M, Sun J, Newell K, Vogel S, Das R, Rosenthal A, Tartakovsky M. (2012). Satisfying clinical research guidance and regulations for mHealth technologies. Journal of Mobile Technology in Medicine, 1:4S, 33.

Klatt NR, Canary LA, Sun X, Vinton CL, Funderburg NT, Morcock DR, Quiñones M, Deming CB, Perkins M, Hazuda DJ, Miller MD, Lederman MM, Segre JA, Lifson JD, Haddad EK, Estes JD, Brenchley JM. (2013). Probiotic/prebiotic supplementation of antiretrovirals improves gastrointestinal immunity in SIV-infected macaques. J Clin Invest, 123, 2, 903-7.

Mage MG, Dolan MA, Wang R, Boyd LF, Revilleza MJ, Robinson H, Natarajan K, Myers NB, Hansen TB, Margulies DH. (2013). A structural and molecular dynamics approach to understanding the peptide-receptive transition state of MHC-I molecules. Molecular Immunology, 55, 2, 123–5.

Houzet L, Klase Z, Yeung ML, Wu A, Le SY, Quiñones M, Jeang KT. (2012). The extent of sequence complementarity correlates with the potency of cellular miRNA-mediated restriction of HIV-1. Nucleic Acids Res, 40, 22, 11684–96.

Mine KL, Shulzhenko N, Yambartsev A, Rochman M, Sanson GF, Lando M, Varma S, Skinner J, Volfovsky N, Deng T, Brenna SM, Carvalho CR, Ribalta JC, Bustin M, Matzinger P, Silva ID, Lyng H, Gerbase-Delima M, Morgun A. (2013). Gene network reconstruction reveals cell cycle and antiviral genes as major drivers of cervical cancer. Nature Communications, 4, 1806.

Escaffre O, Le Nouën C, Amelot M, Ambroggio X, Ogden KM, Guionie O, Toquin D, Müller H, Islam MR, Eterradossi N. (2013). Both genome segments contribute to the pathogenicity of very virulent infectious bursal disease virus. Journal of Virology, 87, 5, 2767–80.

Van Doorslaer, K., Tan, Q., Xirasagar, S., Bandaru, S., Gopalan, V., Mohamoud, Y., Huyen, Y., & McBride, A.A. (2013). The Papillomavirus Episteme: A central resource for papillomavirus sequence data analysis. Nucleic Acids Research, 41, D571–8.

Ambroggio X, Jiang L, Aebig J, Obiakor H, Lukszo J, Narum DL. (2013). The epitope of monoclonal antibodies blocking erythrocyte invasion by Plasmodium falciparum map to the dimerization and receptor glycan binding sites of EBA-175. PLoS One, 8, 2, e56326.

Zhu J, Ofek G, Yang Y, Zhang B, Louder MK, Lu G, McKee K, Pancera M, Skinner J, Zhang Z, Parks R, Eudailey J, Lloyd KE, Blinn J, Alam SM, Haynes BF., Simek M, Burton DR, Koff WC., NISC Comparative Sequencing Program, Mulliken JC, Mascola JR, Shapiro L, Kwong PD. (2013). Mining the antibodyome for HIV-1-neutralizing antibodies with next-generation sequencing and phylogenetic pairing of heavy/light chains. PNAS, 110, 16, 6470–5.

Roberts ML, Kino T, Nicolaides NC, Hurt DE, Katsantoni E, Sertedaki A, Komianou F, Kassiou K, Chrousos GP, Charmandari E. (2013). A novel point mutation in the DNA-binding domain (DBD) of the human glucocorticoid receptor causes primary generalized glucocorticoid resistance by disrupting the hydrophobic structure of its DBD. The Journal of Clinical Endocrinology & Metabolism, 98(4), E790.

Sharma P, Wollenberg K, Sellers M, Zainabadi K, Galinsky K, Moss E, Nguitragool W, Neafsey D, Desai SA. (2013). An epigenetic antimalarial resistance mechanism involving parasite genes linked to nutrient uptake. Journal of Biological Chemistry, 27, 19429-40.

Ambroggio XI, Dommer J, Gopalan V, Dunham EJ, Taubenberger JK, Hur DE. (2013). HASP Server: A database and structural visualization platform for comparative models of influenza A hemagglutinin proteins. BMC Bioinformatics, 14, 197.

Martin C, Buckler-White A, Wollenberg K, Kozak CA. (2013). The avian XPR1 gammaretrovirus receptor is under positive selection and is disabled in bird species in contact with virus-infected wild mice. Journal of Virology, 87, 18, 10094-104.

Zhou T, Zhu J, Wu X, Moquin S, Zhang B, Acharya P, Georgiev IS, Altae-Tran HR, Chuang GY, Joyce MG, Do Kwon Y, Longo NS, Louder MK, Luongo T, McKee K, Schramm CA, Skinner J, Yang Y, Yang Z, Zhang Z, Zheng A, Bonsignori M, Haynes BF, Scheid JF, Nussenzweig MC, Simek M, Burton DR, Koff WC, NISC Comparative Sequencing Program, Mullikin JC, Connors M, Shapiro L, Nabel GJ, Mascola JR, Kwong PD. (2013). Multidonor analysis reveals structural elements, genetic determinants, and maturation pathway for HIV-1 neutralization by VRC01-class antibodies. Immunity, 39, 2, 245-58.

Molloy MJ, Grainger JR, Bouladoux N, Hand TW, Koo LY, Naik S, Quinones M, Dzutse AK, Gao JL, Trinchieri G, Murphy PM, Belkaid Y. (2013). Intraluminal containment of commensal outgrowth in the gut during infection-induced dysbiosis. Cell Host Microbe, 14, 3, 318–28.

Coakley MF, Leerkes MR, Barnett J, Gabrielian AE, Noble K, Weber MN, Huyen Y. (2013). Unlocking the power of big data at the National Institutes of Health. Big Data, 1, 3, 183–186.

Selected Paper and Poster Presentations

Oler, A.J. & Quiñones, M. (2013, January 9). RNA-seq analysis. Presented at the NIH-University of Pennsylvania Bioinformatics Mini-Course, Bethesda, Maryland.

Oler, A. J. & Quiñones, M. (2013, March 13). Mapping and de novo assembly of next-generation sequencing reads. Presented at ISCB Africa ASBCB Conference on Bioinformatics 2013, Casablanca, Morocco.

Oler, A.J. (2013, August 23). Overview of ENCODE. Presented at the Division of Cancer Epidemiology and Genetics (DCEG) Fellows’ Colloquium, National Cancer Institute, Rockville, Maryland.

Margulies, D.H., Hong, M., Wang, R., Mulualem, T., Dolan, M.A., Boyd, L.F., Revilleza, M.J.R., Mans, J., Mage, M., Carey, R., Robinson, H., Jiang, J., Xiao, T.S., & Natarajan, K. (2013, September 18). Structural evolution of NKG2D ligands and cytomegalovirus immunoevasins. Presented at NK2013, Heidelberg, Germany.

Bekisz, J., Eichberg, D., Dolan, M., Zhao, T., & Zoon, K. (2013, September 29). Characterization of human interferon-alpha subtypes and mutants. Presented at Cytokines 2013, San Francisco, California.

Hurt, D.E., Faucette, L.J., Bernardo, M., Hufton, J., Ragland, D., & Avila, N.A. (2012, November). MR guided histopathology in infectious disease. Poster session presented at the 98th Scientific Assembly and Annual Meeting of the Radiological Society of North America, Chicago, Illinois.

Skinner, J., Li, Q.Q., Liou, D.T., Bennett, J.E., & Huyen, Y. (2012, October). Identifying stable reference genes for RT qPCR with hkgFinder. Poster session presented at the 2012 NIH Research Festival, Bethesda, Maryland.

Yu, C., Barnett, J., Huyen, Y., & Shinko, G.S. (2012, October). NIAID FreeStuff: A Web-based forum to promote resource sharing and reuse. Poster session presented at the 2012 NIH Research Festival, Bethesda, Maryland.

Bamunusinghe, D., Liu, Q., Lu, X., Oler, A., & Kozak, C.A. (2012, October). Wild mouse origins of the laboratory mouse gammaretroviruses and their restrictive XPR1 receptor. Poster session presented at the 24th Workshop on Retroviral Pathogenesis, College of Physicians, Philadelphia, Pennsylvania.

Henderson, R.M., Hurt, D.E., Nagarajan, V., Quiñones, M., Lawson, J., Peck, B., Singh, R., Hunsberger, J., Chibane, F., Elkahoun, A., McMahon, F., Munson, P., Demirkale, Y., Alda, M., Chuang, D., Hultner, M., & Huyen, Y. (2012, October). An agent-based software simulation suite for modeling gene regulatory networks. Poster session presented at the 2012 NIH Research Festival, Bethesda, Maryland.

Weber, N., Gopalan, V., Li, J., Levitsky, A., Dommer, J., Kaur, R., Liang, W., Sun, Q., Bandaru, S., Noble, K., Barnett, J., Quiñones, M., Nagarajan, V., Oler, A., Wollenberg, K., Ambroggio, X., Lumpkin, J., Hurt, D., & Huyen, Y. (2013, March). HPC Web: Democratizing high performance computing at the National Institute of Allergy and Infectious Diseases. Poster session presented at the 2013 International Society for Computational Biology (ISCB) and African Society for Bioinformatics and Computational Biology (ASBCB) Conference on Bioinformatics, Casablanca, Morocco.

Oler, A. J., Gopalan, V., Narayanan, M., Hurt, D. & Huyen, Y. (2012, October). A configurable pipeline for RNA-seq data analysis. Poster session presented at the 2012 NIH Research Festival 2012, Bethesda, Maryland.

Oler, A. J., Gopalan, V., Narayanan, M., Hurt, D. & Huyen, Y. (2013, March). A configurable pipeline for RNA-seq data analysis. Poster session presented at the X-Gen Congress & Expo 2013, San Diego, California.

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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Resources

YouTube Channel

 

 

Last Updated March 04, 2013