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

• PI: Faye D. Schilkey

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

• B. Wheaton, J. Sena, A. Sundararajan, P. Umale, F. Schilkey and R. Miller.
  Identification of regenerative processes in neonatal spinal cord injury in the opossum (Monodelphis domestica): A transcriptomic study
  J Comp Neurol, 529(5), 969--986, 2021
  INBRE 
• T. Lowe, R. Reiss, P. Illescas, C. Davis, M. Connick and J. Sena.
  Effect of surface grain boundary density on preosteoblast proliferation on titanium
  Mater Res Lett, 8(6), 239--246, 2020
  INBRE 
• K. Arora, M. Belcaid, M. Lantz, R. Taketa and R. Nichols.
  Transcriptome Profile of Nicotinic Receptor-Linked Sensitization of Beta Amyloid Neurotoxicity
  Sci Rep, 10(1), 5696, 2020
  INBRE 
• V. Troselj, D. Pathak and D. Wall.
  Conditional requirement of SglT for type IV pili function and S-motility in Myxococcus xanthus
  Microbiology (Reading), 166(4), 349--358, 2020
  INBRE 
• C. Yuan, X. Zhao, Z. Wang, T. Borg, T. Ye, Z. Khalpey, R. Runyan, Y. Shao and B. Gao.
  Study of the Expression Transition of Cardiac Myosin Using Polarization-Dependent SHG Microscopy
  Biophys J, 118(5), 1058--1066, 2020
  INBRE 
• S. Buddenborg, B. Kamel, B. Hanelt, L. Bu, S. Zhang, G. Mkoji and E. Loker.
  The in vivo transcriptome of Schistosoma mansoni in the prominent vector species Biomphalaria pfeifferi with supporting observations from Biomphalaria glabrata
  PLoS Negl Trop Dis, 13(9), e0007013, 2019
  INBRE 
• 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, 189(4), 1107--1120, 2019, DOI 10.1007/s00442-019-04371-7
  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, 13(8), e0201969, 2018, DOI 10.1371/journal.pone.0201969
  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, 38(19), 2018, DOI 10.1128/mcb.00084-18
  INBRE 
• H. Castillo, X. Li, F. Schilkey and G. Smith.
  Transcriptome analysis reveals a stress response of Shewanella oneidensis deprived of background levels of ionizing radiation
  PloS one, 13(5), e0196472, 2018, DOI 10.1371/journal.pone.0196472
  INBRE 
• H. Tsujimoto, K. Hanley, A. Sundararajan, N. Devitt, F. Schilkey and I. Hansen.
  Correction: Dengue virus serotype 2 infection alters midgut and carcass gene expression in the Asian tiger mosquito, Aedes albopictus
  PLOS ONE, 13(1), e0192128, 2018, DOI 10.1371/journal.pone.0192128
  INBRE 
• S. Buddenborg, L. Bu, S. Zhang, F. Schilkey, G. Mkoji and E. Loker.
  Transcriptomic responses of Biomphalaria pfeifferi to Schistosoma mansoni: Investigation of a neglected African snail that supports more S. mansoni transmission than any other snail species
  PLOS Neglected Tropical Diseases, 11(10), e0005984, 2017, DOI 10.1371/journal.pntd.0005984
  INBRE 
• D. Neupane, B. Jacquez, A. Sundararajan, T. Ramaraj, F. Schilkey and E. Yukl.
  Zinc-Dependent Transcriptional Regulation in Paracoccus denitrificans
  Frontiers in Microbiology, 8, 2017, DOI 10.3389/fmicb.2017.00569
  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, 12(2), e0171345, 2017, DOI 10.1371/journal.pone.0171345
  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, 17(2), 161--171, 2016, DOI 10.1111/1755-0998.12555
  INBRE 
• J. He, A. Sundararajan, N. Devitt, F. Schilkey, T. Ramaraj and C. Melançon.
  Complete Genome Sequence of Streptomyces venezuelae ATCC 15439, Producer of the Methymycin/Pikromycin Family of Macrolide Antibiotics, Using PacBio Technology
  Genome Announcements, 4(3), 2016, DOI 10.1128/genomea.00337-16
  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, 2(2), 108--114, 2015, DOI 10.15436/2376-0949.15.031
  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, 8(1), 2015, DOI 10.1186/s13104-015-1485-1
  INBRE 
• Y. Ogasawara, N. Torrez-Martinez, A. Aragon, B. Yackley, J. Weber, A. Sundararajan, T. Ramaraj, J. Edwards and C. Melançon.
  High-Quality Draft Genome Sequence of Actinobacterium Kibdelosporangium sp. MJ126-NF4, Producer of Type II Polyketide Azicemicins, Using Illumina and PacBio Technologies
  Genome Announcements, 3(2), 2015, DOI 10.1128/genomea.00114-15
  INBRE 
• E. Schirtzinger, C. Andrade, N. Devitt, T. Ramaraj, J. Jacobi, F. Schilkey and K. Hanley.
  Repertoire of virus-derived small RNAs produced by mosquito and mammalian cells in response to dengue virus infection
  Virology, 476, 54--60, 2015, DOI 10.1016/j.virol.2014.11.019
  INBRE 
• T. Ramaraj, S. Matyi, A. Sundararajan, I. Lindquist, N. Devitt, F. Schilkey, R. Lamichhane-Khadka, P. Hoyt, J. Mudge and J. Gustafson.
  Draft Genome Sequences of Vancomycin-Susceptible Staphylococcus aureus Related to Heterogeneous Vancomycin-Intermediate S. aureus
  Genome Announcements, 2(5), 2014, DOI 10.1128/genomea.01033-14
  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, 2(4), 2014, DOI 10.1128/genomea.00688-14
  INBRE 
• M. Mukherjee, P. Kakarla, S. Kumar, E. Gonzalez, J. Floyd, M. Inupakutika, A. Devireddy, S. Tirrell, M. Bruns, G. He, I. Lindquist, A. Sundararajan, F. Schilkey, J. Mudge and M. Varela.
  Comparative genome analysis of non-toxigenic non-O1 versus toxigenic O1 Vibrio cholerae
  Genomics Discovery, 2(1), 1, 2014, DOI 10.7243/2052-7993-2-1
  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, 1(1), 2013, DOI 10.1128/genomea.00227-12
  INBRE 
• V. Pravosudov, T. Roth, M. Forister, L. Ladage, R. Kramer, F. Schilkey and A. Van.
  Differential hippocampal gene expression is associated with climate-related natural variation in memory and the hippocampus in food-caching chickadees
  Molecular ecology, 22(2), 397--408, 2013, DOI 10.1111/mec.12146
  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, 21(12), 2991--3005, 2012, DOI 10.1111/j.1365-294x.2012.05513.x
  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, 7(8), e44583, 2012, DOI 10.1371/journal.pone.0044583
  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, 3(65), 65ra4, 2011, DOI 10.1126/scitranslmed.3001756
  INBRE 
• S. Baranzini, J. Mudge, J. Velkinburgh, P. Khankhanian, I. Khrebtukova, N. Miller, L. Zhang, A. Farmer, C. Bell, R. Kim, G. May, J. Woodward, S. Caillier, J. McElroy, R. Gomez, M. Pando, L. Clendenen, E. Ganusova, F. Schilkey, T. Ramaraj, O. Khan, J. Huntley, S. Luo, P. Kwok, T. Wu, G. Schroth, J. Oksenberg, S. Hauser and S. Kingsmore.
  Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis
  Nature, 464(7293), 1351--1356, 2010, DOI 10.1038/nature08990
  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, 4(10), e856, 2010, DOI 10.1371/journal.pntd.0000856
  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, 460(7258), 1011--1015, 2009, DOI 10.1038/nature08211
  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, 1, 132, 2008
  INBRE