Genomes and Genes
Roderick V Jensen
Affiliation: Virginia Polytechnic Institute and State University
- Differentially expressed alternatively spliced genes in malignant pleural mesothelioma identified using massively parallel transcriptome sequencingLingsheng Dong
The Thoracic Surgery Oncology Laboratory and Division of Thoracic Surgery, Brigham and Women s Hospital, Harvard Medical School, Boston, MA, USA
BMC Med Genet 10:149. 2009..We hypothesized that alternative splicing profiles might be detected in the sequencing data for the expressed genes in these samples...
- Gene expression and isoform variation analysis using Affymetrix Exon ArraysAmandine Bemmo
Universite de Montreal, Montreal, QC, Canada
BMC Genomics 9:529. 2008..Here, we use the well studied Microarray Quality Control (MAQC) dataset to benchmark the Affymetrix Exon Array, and compare it to two other popular platforms: Illumina, and Affymetrix U133...
- The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studiesLeming Shi
National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
BMC Bioinformatics 9:S10. 2008..The resultant variety of existing and emerging methods exacerbates confusion and continuing debate in the microarray community on the appropriate choice of methods for identifying reliable DEG lists...
- Transcriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencingShrinivasrao P Mane
Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
BMC Genomics 10:264. 2009..As a preliminary evaluation of these promising technologies, we performed deep sequencing of cDNA synthesized from the Microarray Quality Control (MAQC) reference RNA samples using Roche's 454 Genome Sequencer FLX...
- The genome of woodland strawberry (Fragaria vesca)Vladimir Shulaev
Department of Biological Sciences, University of North Texas, Denton, Texas, USA
Nat Genet 43:109-16. 2011..New phylogenetic analysis of 154 protein-coding genes suggests that assignment of Populus to Malvidae, rather than Fabidae, is warranted...
- Rescuing chemotaxis of the anticancer agent Salmonella enterica serovar Typhimurium VNP20009Katherine M Broadway
Department of Biological Sciences, Life Sciences I, Virginia Polytechnic Institute and State University, Blacksburg, VA 24, 061, USA
J Biotechnol 211:117-20. 2015..Potential reasons for the lack of complete restoration and implications for bacterial tumor colonization will be discussed. ..
- Analyzing the Transcriptomes of Two Quorum-Sensing Controlled Transcription Factors, RcsA and LrhA, Important for Pantoea stewartii VirulenceAlison Kernell Burke
Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, United States of America
PLoS ONE 10:e0145358. 2015..These efforts further define the hierarchy of the QS-regulated network controlling plant virulence in P. stewartii. ..
- Complete genome sequence of Salmonella enterica serovar Typhimurium VNP20009, a strain engineered for tumor targetingKatherine M Broadway
Department of Biological Sciences, Life Sciences I, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
J Biotechnol 192:177-8. 2014..6-kbp inversion leading to the disruption of purM, a 108-kbp Suwwan deletion resulting in the loss of 128 genes, and 50 non-synonymous SNPs. ..
- OpaR controls a network of downstream transcription factors in Vibrio parahaemolyticus BB22OPAlison Kernell Burke
Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States of America
PLoS ONE 10:e0121863. 2015..Identification of the direct and indirect targets of OpaR, including small RNAs, will enable the construction of a network map of regulatory interactions important for the switch between the nonpathogenic and pathogenic states. ..
- Genomic comparison between a virulent type A1 strain of Francisella tularensis and its attenuated O-antigen mutantThero Modise
Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
J Bacteriol 194:2775-6. 2012..Compared to the wild type, the mutant strain had 45 point mutations and a 75.9-kb duplicated region that had not been previously observed in Francisella species...
- Identification of new genes in Sinorhizobium meliloti using the Genome Sequencer FLX systemChunhong Mao
Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
BMC Microbiol 8:72. 2008..meliloti, and search for new bacterial genes missed in the previous genome annotation. This is the first report of sequencing a bacterial transcriptome using the pyrosequencing technology...