IDeA Network for Biomedical Research Excellence (INBRE) Sequencing and Bioinformatics Core (SBC)

The SBC is a collaborative resource that supports hypothesis and discovery-driven genomic studies in five thematic areas: Structure & Function of Biomolecules, Cell and Organism, Pathogens, and Community-Based Participatory Research (CBPR). The SBC’s objectives are to:
o Advance cutting-edge knowledge discovery through innovative bioinformatics analysis techniques, resources, and tools.
o Engage the network in education and training through outreach, mentorships, internships, and symposia.
o Build and maintain research-enabling IT Infrastructure and mechanisms for communication within the network and to the public.

Publications

  • M. Chadiarakou, A. Sundararajan, I. Lindquist, G. DeFrancesca, M. Kwicklis, D. Lighthall, N. Farmer, M. Shuster and J. Mudge.
    MRSA in the NICU: Outbreak or Coincidence?
    National Center for Case Study Teaching in Science, http://sciencecases.lib.buffalo.edu/cs/collection/detail.asp?case_id=1002&id=1002, 2018
    INBRE  Science Tools in the Classroom 
  • S. Scroggs, N. Grubaugh, J. Sena, A. Sundararajan, F. Schilkey, D. Smith, G. Ebel and K. Hanley.
    Endless Forms: Within-Host Variation in the Structure of the West Nile Virus RNA Genome during Serial Passage in Bird Hosts
    mSphere, 4(3), 2019
    INBRE 
  • K. Whitney, J. Mudge, D. Natvig, A. Sundararajan, W. Pockman, J. Bell, S. Collins and J. Rudgers.
    Experimental drought reduces genetic diversity in the grassland foundation species Bouteloua eriopoda
    Oecologia (PMID: 30850884), 189(4), 1107--1120, 2019
    INBRE 
  • A. Sundararajan, H. Rane, T. Ramaraj, J. Sena, A. Howell, S. Bernardo, F. Schilkey and S. Lee.
    Cranberry-derived proanthocyanidins induce a differential transcriptomic response within Candida albicans urinary biofilms
    PLOS ONE (PMID: 30089157), 13(8), e0201969, 2018
    INBRE 
  • S. DeVore, C. Young, G. Li, A. Sundararajan, T. Ramaraj, J. Mudge, F. Schilkey, A. Muth, P. Thompson and B. Cherrington.
    Histone Citrullination Represses MicroRNA Expression, Resulting in Increased Oncogene mRNAs in Somatolactotrope Cells
    Molecular and Cellular Biology (PMID: 29987187), 38(19), 2018
    INBRE 
  • H. Tsujimoto, K. Hanley, A. Sundararajan, N. Devitt, F. Schilkey and I. Hansen.
    Dengue virus serotype 2 infection alters midgut and carcass gene expression in the Asian tiger mosquito, Aedes albopictus
    PLOS ONE (PMID: 28152011), 12(2), e0171345, 2017
    INBRE 
  • R. Horn, T. Ramaraj, N. Devitt, F. Schilkey and D. Cowley.
    De novo assembly of a tadpole shrimp (Triops newberryi) transcriptome and preliminary differential gene expression analysis
    Molecular Ecology Resources (PMID: 27292122), 17(2), 161--171, 2016
    INBRE 
  • V. Shah, . , S. Lambeth, T. Carson, J. Lowe, T. Ramaraj, J. Leff, L. Luo and C. Bell.
    Composition Diversity and Abundance of Gut Microbiome in Prediabetes and Type 2 Diabetes
    Journal of Diabetes and Obesity (PMID: 26756039), 2(2), 108--114, 2015
    INBRE 
  • D. Ramírez-Gordillo, T. Powers, J. Velkinburgh, C. Trujillo-Provencio, F. Schilkey and E. Serrano.
    RNA-Seq and microarray analysis of the Xenopus inner ear transcriptome discloses orthologous OMIM® genes for hereditary disorders of hearing and balance
    BMC Research Notes (PMID: 26582541), 8(1), 2015
    INBRE 
  • S. Matyi, T. Ramaraj, A. Sundararajan, I. Lindquist, N. Devitt, F. Schilkey, R. Lamichhane-Khadka, P. Hoyt, J. Mudge and J. Gustafson.
    Draft Genomes of Heterogeneous Vancomycin-Intermediate Staphylococcus aureus Strain MM66 and MM66 Derivatives with Altered Vancomycin Resistance Levels
    Genome Announcements (PMID: 25013145), 2(4), 2014
    INBRE 
  • S. Kumar, I. Lindquist, A. Sundararajan, C. Rajanna, J. Floyd, K. Smith, J. Andersen, G. He, R. Ayers, J. Johnson, J. Werdann, A. Sandoval, N. Mojica, F. Schilkey, J. Mudge and M. Varela.
    Genome Sequence of Non-O1 Vibrio cholerae PS15
    Genome Announcements (PMID: 23409261), 1(1), 2013
    INBRE 
  • T. PARCHMAN, Z. GOMPERT, J. MUDGE, F. SCHILKEY, C. BENKMAN and C. BUERKLE.
    Genome-wide association genetics of an adaptive trait in lodgepole pine
    Molecular Ecology (PMID: 22404645), 21(12), 2991--3005, 2012
    INBRE 
  • L. Nfonsam, C. Cano, J. Mudge, F. Schilkey and J. Curtiss.
    Analysis of the transcriptomes downstream of Eyeless and the Hedgehog, Decapentaplegic and Notch signaling pathways in Drosophila melanogaster
    PLoS One (PMID: 22952997), 7(8), e44583, 2012
    INBRE 
  • C. Bell, D. Dinwiddie, N. Miller, S. Hateley, E. Ganusova, J. Mudge, R. Langley, L. Zhang, C. Lee, F. Schilkey, V. Sheth, J. Woodward, H. Peckham, G. Schroth, R. Kim and S. Kingsmore.
    Carrier testing for severe childhood recessive diseases by next-generation sequencing
    Sci Transl Med (PMID: 21228398), 3(65), 65ra4, 2011
    INBRE 
  • D. Brackney, J. Scott, F. Sagawa, J. Woodward, N. Miller, F. Schilkey, J. Mudge, J. Wilusz, K. Olson, C. Blair and []. others.
    C6/36 Aedes albopictus cells have a dysfunctional antiviral RNA interference response
    PLoS neglected tropical diseases (PMID: 21049065), 4(10), e856, 2010
    INBRE 
  • J. Kim, Y. Ju, H. Park, S. Kim, S. Lee, J. Yi, J. Mudge, N. Miller, D. Hong, C. Bell, H. Kim, I. Chung, W. Lee, J. Lee, S. Seo, J. Yun, H. Woo, H. Lee, D. Suh, S. Lee, H. Kim, M. Yavartanoo, M. Kwak, Y. Zheng, M. Lee, H. Park, J. Kim, O. Gokcumen, R. Mills, A. Zaranek, J. Thakuria, X. Wu, R. Kim, J. Huntley, S. Luo, G. Schroth, T. Wu, H. Kim, K. Yang, W. Park, H. Kim, G. Church, C. Lee, S. Kingsmore and J. Seo.
    A highly annotated whole-genome sequence of a Korean individual
    Nature (PMID: 19587683), 460(7258), 1011--1015, 2009
    INBRE 
  • N. Miller, S. Kingsmore, A. Farmer, R. Langley, J. Mudge, J. Crow, A. Gonzalez, F. Schilkey, R. Kim, J. Van and []. others.
    Management of high-throughput DNA sequencing projects: Alpheus
    Journal of computer science and systems biology (PMID: 20151039), 1, 132, 2008
    INBRE 

About NCGR

The National Center for Genome Resources is a not-for-profit research institute that innovates, collaborates, and educates in the field of genomic data science. As leaders in DNA sequence analysis, we partner with government, industry, and academia to drive biological discovery in all kingdoms of life. We deliver value through expertise in experimental design, software, computation, data integration and training a skilled workforce.

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