Research articles, presentations, and other scholarship

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  • Comparing time series transcriptome data between plants using a network module finding algorithm 

    Lee, Jiyoung; Heath, Lenwood S.; Grene, Ruth; Li, Song (2019-06-01)
    Abstract Background Comparative transcriptome analysis is the comparison of expression patterns between homologous genes in different species. Since most molecular mechanistic ...
  • Rapidly evolving changes and gene loss associated with host switching in Corynebacterium pseudotuberculosis 

    Canario Viana, Marcus Vinicius; Sahm, Arne; Goes Neto, Aristoteles; Pereira Figueiredo, Henrique Cesar; Wattam, Alice Rebecca; Azevedo, Vasco (PLOS, 2018-11-12)
    Phylogenomics and genome scale positive selection analyses were performed on 29 Corynebacterium pseudotuberculosis genomes that were isolated from different hosts, including representatives of the Ovis and Equi biovars. A ...
  • Genomic characterization of NDM-1 and 5, and OXA-1 81 carbapenemases in uropathogenic Escherichia coli isolates from Riyadh, Saudi Arabia 

    Abd El Ghany, Moataz; Sharaf, Hazem; Al-agamy, Mohamed H.; Shibi, Atef; Hill-Cawthorne, Grant A.; Hong, Pei-Ying (PLOS, 2018-08-15)
    Urinary tract infections (UTIs) associated with Escherichia coli are a growing threat with an increase in the prevalence of multidrug resistant (MDR) strains, particularly beta-lactamase producers, occurring globally. We ...
  • Comparative Genomics of Early-Diverging Brucella Strains Reveals a Novel Lipopolysaccharide Biosynthesis Pathway 

    Wattam, Alice R.; Inzana, Thomas J.; Williams, Kelly P.; Mane, Shrinivasrao P.; Shukla, Maulik; Almeida, Nalvo F.; Dickerman, Allan W.; Mason, Steven; Moriyon, Ignacio; O'Callaghan, David; Whatmore, Adrian M.; Sobral, Bruno W.; Tiller, Rebekah V.; Hoffmaster, Alex R.; Frace, Michael A.; De Castro, Cristina; Molinaro, Antonio; Boyle, Stephen M.; De, Barun K.; Setubal, Joao C. (American Society for Microbiology, 2012-11)
    Brucella species are Gram-negative bacteria that infect mammals. Recently, two unusual strains (Brucella inopinata BO1T and B. inopinata-like BO2) have been isolated from human patients, and their similarity to some atypical ...
  • Systems Modeling of the Role of Interleukin-21 in the Maintenance of Effector CD4(+) T Cell Responses during Chronic Helicobacter pylori Infection 

    Carbo, Adria; Olivares-Villagomez, Danyvid; Hontecillas, Raquel; Bassaganya-Riera, Josep; Chaturvedi, Rupesh; Piazuelo, M. Blanca; Delgado, Alberto; Washington, M. Kay; Wilson, Keith T.; Algood, Holly M. Scott (American Society for Microbiology, 2014-07)
    The development of gastritis during Helicobacter pylori infection is dependent on an activated adaptive immune response orchestrated by T helper (Th) cells. However, the relative contributions of the Th1 and Th17 subsets ...
  • Origin, Evolution, and Genotyping of Emergent Porcine Epidemic Diarrhea Virus Strains in the United States 

    Huang, Yao-Wei; Dickerman, Allan W.; Pineyro, Pablo; Li, Long; Fang, Li; Kiehne, Ross; Opriessnig, Tanja; Meng, Xiang-Jin (American Society for Microbiology, 2013-09)
    Coronaviruses are known to infect humans and other animals and cause respiratory and gastrointestinal diseases. Here we report the emergence of porcine epidemic diarrhea virus (PEDV) in the United States and determination ...
  • The Complete Genome Sequence of the Emerging Pathogen Mycobacterium haemophilum Explains Its Unique Culture Requirements 

    Tufariello, JoAnn M.; Kerantzas, Christopher A.; Vilcheze, Catherine; Calder, R. Brent; Nordberg, Eric K.; Fischer, Jack A.; Hartman, Travis E.; Yang, Eva; Driscoll, Timothy; Cole, Laura E.; Sebra, Robert; Maqbool, Shahina B.; Wattam, Alice R.; Jacobs, William R., Jr. (American Society for Microbiology, 2015-11)
    Mycobacterium haemophilum is an emerging pathogen associated with a variety of clinical syndromes, most commonly skin infections in immunocompromised individuals. M. haemophilum exhibits a unique requirement for iron ...
  • A Burkholderia pseudomallei Colony Variant Necessary for Gastric Colonization 

    Austin, C. R.; Goodyear, A. W.; Bartek, I. L.; Stewart, A.; Sutherland, M. D.; Silva, E. B.; Zweifel, A.; Vitko, N. P.; Tuanyok, A.; Highnam, G.; Mittelman, D.; Keim, P.; Schweizer, H. P.; Vazquez-Torres, A.; Dow, S. W. C.; Voskuil, M. I. (American Society for Microbiology, 2015-01)
    Diverse colony morphologies are a hallmark of Burkholderia pseudomallei recovered from infected patients. We observed that stresses that inhibit aerobic respiration shifted populations of B. pseudomallei from the canonical ...
  • Mapping the Regulatory Network for Salmonella enterica Serovar Typhimurium Invasion 

    Smith, Carol; Stringer, Anne M.; Mao, Chunhong; Palumbo, Michael J.; Wade, Joseph T. (American Society for Microbiology, 2016-09)
    Salmonella enterica pathogenicity island 1 (SPI-1) encodes proteins required for invasion of gut epithelial cells. The timing of invasion is tightly controlled by a complex regulatory network. The transcription factor (TF) ...
  • Metabolomics as a hypothesis-generating functional genomics tool for the annotation of Arabidopsis thaliana genes of "unknown function" 

    Quanbeck, Stephanie M.; Brachova, Libuse; Campbell, Alexis A.; Guan, Xin; Perera, Ann; He, Kun; Rhee, Seung Y.; Bais, Preeti; Dickerson, Julie A.; Dixon, Philip; Wohlgemuth, Gert; Fiehn, Oliver; Barkan, Lenore; Lange, Iris; Lange, B. Markus; Lee, Insuk; Cortes, Diego; Salazar, Carolina; Shuman, Joel; Shulaev, Vladimir; Huhman, David V.; Sumner, Lloyd W.; Roth, Mary R.; Welti, Ruth; Ilarslan, Hilal; Wurtele, Eve S.; Nikolau, Basil J. (Frontiers, 2012)
    Metabolomics is the methodology that identifies and measures global pools of small molecules (of less than about 1,000 Da) of a biological sample, which are collectively called the metabolome. Metabolomics can therefore ...
  • Mining and visualization of microarray and metabolomic data reveal extensive cell wall remodeling during winter hardening in Sitka spruce (Picea sitchensis) 

    Grene, Ruth; Klumas, Curtis; Suren, Haktan; Yang, Kuan; Collakova, Eva; Myers, Elijah; Heath, Lenwood S.; Holliday, Jason A. (Frontiers, 2012)
    Microarray gene expression profiling is a powerful technique to understand complex developmental processes, but making biologically meaningful inferences from such studies has always been challenging. We previously reported ...
  • Diverse Evolutionary Trajectories for Small RNA Biogenesis Genes in the Oomycete Genus Phytophthora 

    Bollmann, Stephanie R.; Fang, Yufeng; Press, Caroline M.; Tyler, Brett M.; Gruenwald, Niklaus J. (Frontiers, 2016-03-15)
    Gene regulation by small RNA pathways is ubiquitous among eukaryotes, but little is known about small RNA pathways in the Stramenopile kingdom. Phytophthora a genus of filamentous oomycetes, contains many devastating plant ...
  • RECoN: Rice Environment Coexpression Network for Systems Level Analysis of Abiotic-Stress Response 

    Krishnan, Arjun; Gupta, Chirag; Ambavaram, Madana M. R.; Pereira, Andy (2017-09-20)
    Transcriptional profiling is a prevalent and powerful approach for capturing the response of crop plants to environmental stresses, e.g., response of rice to drought. However, functionally interpreting the resulting ...
  • Reproducibility, bioinformatic analysis and power of the SAGE method to evaluate changes in transcriptome 

    Dinel, S; Bolduc, C; Belleau, P; Boivin, A; Yoshioka, M; Calvo, E; Piedboeuf, B; Snyder, EE; Labrie, F; St-Amand, J (2005-01-01)
    The serial analysis of gene expression (SAGE) method is used to study global gene expression in cells or tissues in various experimental conditions. However, its reproducibility has not yet been definitively assessed. In ...
  • Tomato Expression Database (TED): a suite of data presentation and analysis tools 

    Fei, Zhangjun; Tang, Xuemei; Alba, Rob; Giovannoni, James (2006-01-01)
    The Tomato Expression Database (TED) includes three integrated components. The Tomato Microarray Data Warehouse serves as a central repository for raw gene expression data derived from the public tomato cDNA microarray. ...
  • VMD: a community annotation database for oomycetes and microbial genomes 

    Tripathy, Sucheta; Pandey, Varun N.; Fang, Bing; Salas, Fidel; Tyler, Brett M. (2006-01-01)
    The VBI Microbial Database (VMD) is a database system designed to host a range of microbial genome sequences. At present, the database contains genome sequence and annotation data of two plant pathogens Phytophthora sojae ...
  • Unprecedented bacterial community richness in soybean nodules vary with cultivar and water status 

    Sharaf, Hazem; Rodrigues, Richard R; Moon, Jinyoung; Zhang, Bo; Mills, Kerri; Williams, Mark A (2019-04-16)
    Abstract Background Soybean (Glycine max) and other legumes are key crops grown around the world, providing protein and nutrients to a growing population, in a way that is ...
  • A versatile computational pipeline for bacterial genome annotation improvement and comparative analysis, with Brucella as a use case 

    Yu, G. X.; Snyder, E. E.; Boyle, S. M.; Crasta, O. R.; Czar, M.; Mane, S. P.; Purkayastha, A.; Sobral, B.; Setubal, J. C. (2007-06)
    We present a bacterial genome computational analysis pipeline, called GenVar. The pipeline, based on the program GeneWise, is designed to analyze an annotated genome and automatically identify missed gene calls and sequence ...
  • PATRIC: The VBI PathoSystems Resource Integration Center 

    Snyder, E. E.; Kampanya, N.; Lu, J.; Nordberg, E. K.; Karur, H. R.; Shukla, M.; Soneja, J.; Tian, Y.; Xue, T.; Yoo, H.; Zhang, F.; Dharmanolla, C.; Dongre, N. V.; Gillespie, J. J.; Hamelius, J.; Hance, M.; Huntington, K. I.; Jukneliene, D.; Koziski, J.; Mackasmiel, L.; Mane, S. P.; Nguyen, V.; Purkayastha, A.; Shallom, J.; Yu, G.; Guo, Y.; Gabbard, J.; Hix, D.; Azad, A. F.; Baker, S. C.; Boyle, S. M.; Khudyakov, Y.; Meng, X. J.; Rupprecht, C.; Vinje, J.; Crasta, O. R.; Czar, M. J.; Dickerman, A.; Eckart, J. D.; Kenyon, R.; Will, R.; Setubal, J. C.; Sobral, B. W. S. (2007-01)
    The PathoSystems Resource Integration Center (PATRIC) is one of eight Bioinformatics Resource Centers (BRCs) funded by the National Institute of Allergy and Infection Diseases (NIAID) to create a data and analysis resource ...
  • GeneTrees: a phylogenomics resource for prokaryotes 

    Tian, Yuying; Dickerman, Allan W. (2007-01)
    The GeneTrees phylogenomics system pursues comparative genomic analyses from the perspective of gene phylogenies for individual genes. The GeneTrees project has the goal of providing detailed evolutionary models for all ...

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