The vision of the Bioinformatics Core is to facilitate, amplify, and accelerate biological research and discovery through application of bioinformatics. It will do so by delivering high quality analysis in a timely and economical manner. It will be responsive to customer needs and evolve with advances in the field. It will actively engage in and seek out opportunities to advance the educational mission of the University.
Submissions from 2014
Draft Genome Sequence of Acetobacter aceti Strain 1023, a Vinegar Factory Isolate, John Hung, Christopher Mill, Sandra Clifton, Vincent Magrini, Ketaki Bhide, Julie Francois, Aaron Ransome, Lucinda Fulton, Jyothi Thimmapuram, Richard Wilson, and T. Joseph Kappock
MED18 interaction with distinct transcription factors regulates multiple plant functions., Z Lai, C Schluttenhofer, Ketaki Bhide, J Schreve, Jyothi Thimmapuram, S Y. Lee, D J. Yum, and T Mengiste
Genetic Determinants for Enzymatic Digestion of Lignocellulosic Biomass Are Independent of Those for Lignin Abundance in a Maize Recombinant Inbred Population, Bryan W. Penning, Robert W. Sykes, Nicholas C. Babcock, Christopher K Dugard, Michael A. Held, John F. Klimek, Jacob T Shreve, Matthew Fowler, Angela Ziebell, Mark F. Davis, Stephen R. Decker, Geoffrey B. Turner, Nathan S. Mosier, Nathan M. Springer, Jyothi Thimmapuram, Clifford F. Weil, Maureen C. McCann, and Nicholas C. Carpita
Transcriptomic and proteomic dynamics in the metabolism of a diazotrophic cyanobacterium, Cyanothece sp. PCC 7822 during a diurnal light–dark cycle, David G. Welkie, Xiaohui Zhang, Meng Lye Markillie, Ronald Taylor, Galya Orr, Jon Jacob, Ketaki Bhide, Jyothi Thimmapuram, Marina Gritsenko, Richard D. Smith, and Louis A. Sherman
CYCLIN-DEPENDENT KINASE8 Differentially Regulates Plant Immunity to Fungal Pathogens through Kinase-Dependent and -Independent Functions in ArabidopsisC, Yingfang Zhu, Craig Schluttenhofer, Pengcheng Wang, Fuyou Fu, Jyothi Thimmapuram, Jian-Kang Zhu, Sang Yeol Lee, Dae-Jin Yun, and Tesfaye Mengiste
Submissions from 2012
Auxin and ABA act as central regulators of developmental networks associated with paradormancy in Canada thistle (Cirsium arvense)., JV Anderson, M Dogramaci, DP Horvath, ME Foley, WS Chao, JC Suttle, Jyothi Thimmapuram, AG Hernandez, S Ali, and MA Mikel
Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle Supporting Information, Denis M. Larkin, Hans D. Daetwyler, Alvaro G. Hernandez, Chris L. Wright, Lorie A. Hetrick, Lisa Boucek, Sharon Bachman, and Jyothi Thimmapuram
Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle., DM Larkin, HD Daetwyler, AG Hernandez, CL Wright, LA Hetrick, L Boucek, SL Bachman, MR Brand, TV Akraiko, M Cohen-Zinder, Jyothi Thimmapuram, IM Macleod, TT Harkin, JE McCaque, ME Goddard, BJ Hayes, and HA Lewin
Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle., DM Larkin, HD Daetwyler, AG Hernandez, CL Wright, LA Hetrick, L Boucek, SL Bachman, MR Brand, TV Akraiko, M Cohen-Zinder, Jyothi Thimmapuram, IM Macleod, TT Harkin, JE McCaque, BJ Hayes, and HA Lewin
The bench scientist's guide to statistical analysis of RNA-Seq data, Craig R. Yendrek, Elizabeth A. Ainsworth, and Jyothi Thimmapuram
Submissions from 2011
Orchardgrass (Dactylis glomerata L.) EST and SSR marker development, annotation, and transferability., B.S. Bushman, S.R. Larson, M Tuna, M.S. West, A.G. Hernandez, D Vullaganti, G Gong, J.G. Robbins, K. B. Jensen, and Jyothi Thimmapuram
Identification and analysis of common bean (Phaseolus vulgaris L.) transcriptomes by massively parallel pyrosequencing, Venu Kalavacharla, Zhanji Liu, Blake C. Meyers, Jyothi Thimmapuram, and Kalpalatha Melmaiee
Transcriptome Sequencing of the Blind Subterranean Mole Rat, Spalax galili: Utility and Potential for the Discovery of Novel Evolutionary Patterns, Assaf Malik, Abraham Korol, Sariel Hubner, Aaron Avivi, Alvaro Hernandez, Jyothi Thimmapuram, Shahjahan Ali, Mark Bond, Fabian Glaser, and Arnon Paz
Mitochondrial Small RNAs that are Up-Regulated in Hippocampus during Olfactory Discrimination Training in Mice, Neil R. Smalheiser, Giovanni Lugli, Jyothi Thimmapuram, Edwin H. Cook, and John Larson
Submissions from 2010
Endogenous siRNAs and noncoding RNA-derived small RNAs are expressed in adult mouse hippocampus and are up-regulated in olfactory discrimination training., Neil Smalheiser, G Lugli, Jyothi Thimmapuram, E.H. Cook, and J Larson
Submissions from 2009
Diversity and Strain Specificity of Plant Cell Wall Degrading Enzymes Revealed by the Draft Genome of Ruminococcus flavefaciens FD-1, Margret E. Berg Miller, Dionysios A. Antonopoulos, Mark Brand, Albert Bari, Alvaro Hernandez, Jyothi Thimmapuram, Bryan A. White, Marco Rincon, Harry J. Flint, Bernard Henrissat, and Pedro M. Coutinho
Transcriptome pathways unique to dehydration tolerant relatives of modern wheat., N Z. Ergen, Jyothi Thimmapuram, H J. Bohnert, and H Budak
Submissions from 2008
Development and annotation of perennial Triticeae ESTs and SSR markers., B.S. Bushman, S R Larson, I W Mott, P F Cliften, R R Wang, N J Chatterton, A G Hernandez, S Ali, R W Kim, Jyothi Thimmapuram, G Gong, L Liu, and M A Mikel
Transcriptome analysis identifies novel responses and potential regulatory genes involved in seasonal dormancy transitions of leafy spurge (Euphorbia esula L.), David P. Horvath, Wun S. Chao, Jeffrey C. Suttle, Jyothi Thimmapuram, and James V. Anderson
Genes controlling plant growth habit in Leymus (Triticeae): maize barren stalk1 (ba1), rice lax panicle, and wheat tiller inhibition (tin3) genes as possible candidates., Paraminder Kaur, Steven R. Larson, B.S. Bushman, Richard R. Wang, Ivan W. Mott, Jyothi Thimmapuram, George Gong, and Lei Liu
The draft genome of the transgenic tropical fruit tree papaya ( Carica papaya Linnaeus), Ray Ming, Shaobin Hou, Yun Feng, Qinguyi Yu, and Jyothi Thimmapuram
Gene expression in developing watermelon fruit, Pat Wechter, Amnon Levi, Karen Harris, Angela Davis, Zhangjun Fei, Nurit Katzir, James Giovannoni, Ayelet Salman-Minkov, Alvaro Hernandez, Jyothi Thimmapuram, Yaakov Tadmore, Vitaly Portnoy, and Tova Trebitsh
Submissions from 2004
Bicistronic and fused monocistronic transcripts are derived from adjacent loci in the Arabidopsis genome, Jyothi Thimmapuram, Hui Duan, Lei Liu, and Mary A. Schuler