Bioinformatics and Computational Biosciences Branch

Darrell Hurt, Ph.D., Branch Chief

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. Major Areas of Research: computational biology collaboration and training, bioinformatics software development, and biocomputing resources.

Abstract 3D Rendering of a Network

Program Overview

The BCBB drives innovation in biomedical informatics at NIAID for global health clinicians and researchers by fostering a pipeline of products, platforms, and solutions. 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. While BCBB services and resources are tailored to meet the needs of the NIAID intramural and extramural research communities, the branch regularly engages in formal collaborations with other NIH Institutes. The BCBB staff consists 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 and design specialists. Each BCBB project is completed with input from a specialized team that contributes interdisciplinary expertise. 

Additionally, 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

Bioinformatics and Computational Biosciences Branch Group Members

Publications

Manuscripts

​Anuradha, R., Munisankar, S., Bhootra, Y., Jagannathan, J., Dolla, C., Kumaran, P., Shen, K., Nutman, T.B., & Babu, S. (2015). Systemic cytokine profiles in Strongyloides stercoralis infection and alterations following treatment. Infection and Immunity, 84, 2, 425–31.

​​Banadyga, L., Dolan, M.A., & Ebihara, H. (2016). Rodent-adapted filoviruses and the molecular basis of pathogenesis. Journal of Molecular Biology, 428, 17, 3449–66.

Coakley, M., Hurt, D.E. (2016). 3D printing in the laboratory: Maximize time and funds with customized and open-source labware​. Journal of Laboratory Automation, 21, 4, 489–95.​

Falcone, E.L., Abusleme, L., Swamydas, M., Lionakis, M.S., Ding, L., Hsu, A.P., Zelazny, A.M., Moutsopoulos, N.M., Kuhns, D.B., Deming, C., Quiñones,. M, Segre, J.A., Bryant, C.E., & Holland, S.M. (2016). Colitis susceptibility in p47phox−/− mice is mediated by the microbiome​.  Microbiome, 4, 13.

Fonseca, D.M., Hand, T.W., Han, S.J., Gerner, M.Y., Glatman Zaretsky, A., Byrd, A.L., Harrison, O.J,, Ortiz, A.M., Quinones, M., Trinchieri, G., Brenchley, J.M., Brodsky, I.E., Germain, R.N., Randolph, G.J., & Belkaid, Y. (2015). Microbiota-dependent sequelae of acute infection compromise tissue-specific immunity​. Cell, 163, 2, 354–366.

​George, P.J., Kumar, N.P., Jaganathan, J., Dolla, C., Kumaran, P., Nair, D., Banurekha, V.V., Shen, K., Nutman, T.B., & Babu, S. (2015) Modulation of pro- and anti-inflammatory cytokines in active and latent tuberculosis by coexistent Strongyloides stercoralis infection. Tuberculosis, 95, 6, 822–8.

​Hoenen, T., Groseth, A., Rosenke, K., Fischer, R.J., Hoenen, A., Judson, S.D., Martellaro, C., Falzarano, D., Marzi, A., Squires, R.B., Wollenberg, K.R., de Wit, E., Prescott, J., Safronetz, D., van Doremalen, N., Bushmaker, T., Feldmann, F., McNally, K., Bolay, F.K., Fields, B., Sealy, T., Rayfield, M., Nichol, S.T., Zoon, K.C., Massaquoi, M., Munster, V.J,, & Feldmann, H. (2016). Nanopore sequencing as a rapidly deployable ebola outbreak tool. Emerg Infect Diseases, 22, 2, 331–4.

​Hurt, D.E., Suzuki, S., Mayama, T., & Charmandari, E. (2016). Structural analysis on the pathologic mutant glucocorticoid receptor ligand-binding domains. Molecular Endocrinology, 30, 2, 173–188.

​Kirshenbaum, A.S., Cruse, G., Desai, A., Bandara, G., Leerkes, M., Lee, C.C., Fischer, E.R., O'Brien, K.J., Gochuico, B.R., Stone, K., Gahl, W.A., & Metcalfe, D.D. (2016). Immunophenotypic and ultrastructural analysis of mast cells in Hermansky-Pudlak Syndrome  type-1: A possible connection to pulmonary fibrosis. PLoS One, 11, 7.

​Larson, C.L., Martinez, E., Beare, P.A., Jeffrey, B., Heinzen, R.A., & Bonazzi, M. (2016). Right on Q: Genetics begin to unravel Coxiella burnetii host cell interactions. Future Microbiology, 11, 7, 919–939.

​Lensink, M.F., Velankar, S., Kryshtafovych, A., Huang, S.Y., Schneidman-Duhovny, D., Sali, A., Segura, J., Fernandez-Fuentes, N., Viswanath, S., Elber, R., Grudinin, S., Popov, P., Neveu, E., Lee, H., Baek, M., Park, S., Heo, L, Rie Lee, G., Seok, C., Qin, S., Zhou, H.X,, Ritchie, D.W., Maigret, B., Devignes, M.D,, Ghoorah, A., Torchala, M., Chaleil, R.A., Bates, P.A., Ben-Zeev, E., Eisenstein, M., Negi, S.S., Weng, Z., Vreven, T., Pierce, B.G., Borrman, T.M., Yu, J., Ochsenbein, F., Guerois, R., Vangone, A., Rodrigues, J.P., van Zundert, G., Nellen, M., Xue, L., Karaca, E., Melquiond, A.S., Visscher, K., Kastritis, P.L., Bonvin, A.M., Xu, X., Qiu, L., Yan, C., Li, J., Ma, Z., Cheng, J., Zou, X., Shen, Y., Peterson, L.X., Kim, H.R., Roy, A., Han, X., Esquivel-Rodriguez, J., Kihara, D., Yu, X., Bruce, N.J., Fuller, J.C., Wade, R.C., Anishchenko, I., Kundrotas, P.J., Vakser, I.A., Imai, K., Yamada, K., Oda, T., Nakamura, T., Tomii, K., Pallara, C., Romero-Durana, M., Jiménez-García, B., Moal, I.H., Férnandez-Recio, J., Joung, J.Y., Kim, J.Y., Joo, K., Lee, J., Kozakov, D., Vajda, S., Mottarella, S., Hall, D.R,, Beglov, D., Mamonov, A., Xia, B., Bohnuud, T., Del Carpio, C.A., Ichiishi, E., Marze, N., Kuroda, D., Roy Burman, S.S., Gray, J.J., Chermak, E., Cavallo, L., Oliva, R., Tovchigrechko, A., & Wodak, S.J. (2016). Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment. Proteins, doi: 10.1002/prot.25007.

Li, J., Cai, B., Qi, Y., Zhao, W., Liu, J., Xu, R., Pang, Q., Tao, Z., Hong, L., Liu, S., Leerkes, M., Quiñones, & M., Su, X.Z. (2016). UTR introns, antisense RNA and differentially spliced transcripts between Plasmodium yoelii subspecies. Malaria Journal, 15, 30.

Morozov, G.I., Zhao, H., Mage, M.G., Boyd, L.F., Jiang, J., Dolan, M.A., Venna, R., Norcross, M.A., McMurtrey, C.P., Hildebrand, W., Schuck, P., Natarajan, K., & Margulies, D.H. (2016). Interaction of TAPBPR, a tapasin homolog, with MHC-I molecules promotes peptide editing. Proc Natl Acad Sci USA, 113, 8, E1006–15.

Morozov, G.I., Zhao, H., Mage, M.G., Boyd, L.F., Jiang, J., Dolan, M.A., Venna, R., Norcross, M.A., McMurtrey, C.P., Hildebrand, W., Schuck, P., Natarajan, K., & Margulies, D.H. (2016). Interaction of TAPBPR, a tapasin homolog, with MHC-I molecules promotes peptide editing. Proc Natl Acad Sci USA, 113, 8, E1006–15.

Moyer, E., Hagenauer, M., Lesko, M., Francis, F., Rodriguez, O., Nagarajan, V., Huser, V., & Busby, B. (2016). MetaNetVar: Pipeline for applying network analysis tools for genomic variants analysis​. F1000 Research, 5, 674.

Pirtskhalava, M., Gabrielian, A., Cruz, P., Griggs, H.L., Squires, R.B., Hurt, D.E., Grigolava, M., Chubinidze, M., Gogoladze, M., Vishnepolsky, B., Alekseev, V., Rosenthal, A. & Tartakovsky, M. (2016). DBAASP v.2: an enhanced database of structure and antimicrobial/cytotoxic activity of natural and synthetic peptides. Nucleic Acids Research, 44, D1, D1104–D1112.

Sergeev, R., Kavaliou, I., Gabrielian, A., Rosenthal, A., & Tuzikov, A. (2016). ​Methods for genome-wide analysis of MDR and XDR tuberculosis from Belarus. Proceedings of the 2016 International Symposium on Bioinformatics Research and Applications​, 9683, 258–268.

Roy, A., Hua, D. P., & Post, C. B. (2015). Analysis of multi-domain protein dynamics. Journal of Chemical Theory and Computation, 12, 1, 274–280.

Posters

​Cruz, P., Squires, R., Griggs, H., Gabrielian, A., & Hurt, D. (2016, October). Similarity-ordered heat maps: A new tool for analyzing molecular dynamics simulations. Poster session presented at 2016 NIH Research Festival, Bethesda, Maryland.

​​Gabrielian, A., Engle, E., & Juarez-Espinosa, O. (2016, October). Comparative study for classification of radiology images for Tuberculosis patients​. Poster session presented at 2016 NIH Research Festival, Bethesda, Maryland.

​Howe, M.K., Dowdell, K., Roy, A., Niemela, J.E., Wilson, W., McElwee, J.J., Hughes, J.D., & Cohen, J.I. (2016, July). A missense mutation impairs ITK function in a patient with severe Epstein-Barr virus disease​. Poster session presented at the 41st Annual International Herpesvirus Workshop, Madison, Wisconsin.

Juarez-Espinosa, O.H., Engle, E., & Gabrielian, A. (2016, July). Exploring new interactions for querying a tuberculosis database. Poster session presented at Worldcomp ‘16, Las Vegas, Nevada.

Misner, I., Dommer, J., Ezeji, S., Kim, L., Liou, D., MacMenamin, P., Noble, K., Oler, A., Quiñones, M., Shyu, C., Weber, N., & Hurt, D. (2016, April). Nephele: a cloud-based scientific computing platform for improved efficiency, standardization, and collaboration in microbiome data analysis​. Poster session presented at 2016 BioIT World, Boston, Massachusetts.

​Misner, I., Dommer, J., Ezeji, S., Kim, L., Liou, D., MacMenamin, P., Noble, K., Oler, A., Quiñones, M., Shyu, C., Weber, N., & Hurt, D. (2016). Nephele: A cloud-based scientific computing platform for improved efficiency, standardization, and collaboration in microbiome data analysis​. F1000 Research 2016, 5: 908 (poster) (doi: 10.7490/f1000research.1111899.1​)

Quiñones, M., Dommer, J., Ezeji, S., Kim, L., Liou, D., MacMenamin, P., Misner, I., Noble, K., Oler, A., Shyu, C., Weber, N., & Hurt, D. (2016, March). Nephele: Microbiome analysis without boundaries. Poster session presented at 2016 NIH Pi Day, Bethesda, Maryland.

​Quiñones, M., Kim, L., Liou, D., Misner, I., Shyu, C., Weber, N., & Hurt, D. (2016, October). A conceptual framework to address challenges in applying standards to metadata collected in microbiome studies​. Poster session presented at 2016 NIH Research Festival, Bethesda, Maryland.

​​Quiñones, M., Liou, D., Kim, L., Shyu, C., Misner, I., Weber, N., & Hurt, D. (2016, August). METAGENOTE: A microbiome annotation system. Poster session presented at the Standards for Microbiome Measurements Workshop, Gaithersburg, Maryland.

Roy, A., Hua, D.P., & Post, C.B. (2016, July). Analysis of multidomain protein dynamics. Poster session presented at the 2016 Protein Society Symposium, Baltimore, Maryland.

Schmeisser, H., Balinsky, C., Singh, K., Sreedhara, K., Dolan, M., Garboczi, D., & Zoon, K. (2015, October). Characterization of the antiviral properties of IFIT3. Poster session presented at Cytokines 2015, Bamberg, Germany.

​Wollenberg, K., Desjardins, C., Zalutskaya, A., Slodovnikova, V., Quiñones, M., Oler, A., Abeel, T., Tartakovsky, M., Gabrielian, A., Hoffner, S., Rosenthal, A., Skrahin, A., Birren, B., Earl, A., & Skrahina, A. (2016, September). Molecular epidemiology, genomics and evolution of Mycobacterium tuberculosis antibiotic resistance in Belarus, 2010-2013​. Poster session presented at 2016 NIH Research Festival, Bethesda, Maryland.

Presentations

​Misner, I., Dommer, J., Ezeji, S., Kim, L., Liou, D., MacMenamin, P., Noble, K., Oler, A., Quiñones, M., Shyu, C., Weber, N., & Hurt, D. (2016, April 7). Nephele: A cloud-based scientific computing platform for improved efficiency, standardization, and collaboriation in microbiome data analysis​. Presented at BioIT World 2016, Boston, Massachusetts.

Resources / Software

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

Sample videos and explore examples of our Web and Desktop applications:

YouTube Channel

Explore videos at:

Web Applications

Twitter

Downloadable Desktop Applications

Content last reviewed on December 27, 2016