Staff of GAS

Our staff and consultants consist of world-leading experts in all types of genome analytics who publish regularly in top life-science journals.

  • 2014 Science: Green RE, et al. (Lyons E, McCarthy F). Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science 346.6215: 1254449
  • 2014 Science: Zhang G, et al. (Lyons E, McCarthy F as part of the Avian Genome Consortium). Comparative genomics reveals insights into avian genome evolution and adaptation. Science 346.6215: 1311-1320
  • 2014 Science: Chalhoub B, Denoeud France, Liu S, et al. (Lyons E). Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science  2014: 345 (6199), 950-953
  • 2014 Science: Amborella Genome Project.   (Lyons E). The Amborella genome and the Evolution of Flowering Plants.  Science 342:6165 
  • 2013 Nature: Ibarra-Laclette E, Lyons E, Hernández-Guzmán G, Pérez-Torres CA, Carretero-Paulet L, Chang T-H, Lan T, Welch AJ, Juárez MJA, Simpson J, Fernández-Cortés A, Arteaga-Vázquez M, Góngora-Castillo E, Acevedo-Hernández G, Schuster SC, Himmelbauer H, Minoche AE, Xu S, Lynch M, Oropeza-Aburto A, et al. Architecture and evolution of a minute plant genome. Nature doi:10.1038/nature12132
  • 2012 Nature: D’Hont A, et al. (Lyons E).  The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature doi:10.1038/nature11241
  • 2015 Genome Biol: Tang H, Zhang X, Miao C, Zhang J, Ming R, Schnable J, Schnable P, Lyons E, Lu J. ALLMAPS: robust scaffold ordering based on multiple maps. Genome Biol. 16(1):3
  • 2014 Plant Cell:Jiao Y, Li J, Tang H, Paterson AH. Integrated Syntenic and Phylogenomic Analyses Reveal an Ancient Genome Duplication in Monocots. Plant Cell. pii: tpc.114.127597
  • 2013 PNAS: Tang H, Cuevas HE, Das S, Sezen UU, Zhou C, et al. Seed shattering in a wild sorghum is conferred by a locus unrelated to domestication. Proc Natl Acad Sci U S A, 110, 15824-15829.
  • 2012 Nature:  Paterson AH, Wendel JF, Gundlach H, Guo H, Jenkins J, Jin D, Llewellyn D, Showmaker KC, Shu S, Udall J, Yoo MJ, Byers R, Chen W, Doron-Faigenboim A, Duke MV, Gong L, Grimwood J, Grover C, Grupp K, Hu G, Lee TH, Li J, Lin L, Liu T, Marler BS, Page JT, Roberts AW, Romanel E, Sanders WS, Szadkowski E, Tan X, Tang H, Xu C, Wang J, Wang Z, et al. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature, 492(7429):423-427.
  • 2012 Nature: Tomato Genome Consortium (Tang H)  The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485: 635-641.
  • 2014 PLoS One: Fox SE, Geniza M, Hanumappa M, Naithani S, Sullivan C, Preece J, Tiwari VK, Elser J, Leonard JM, Sage A, Gresham C, Kerhornou A, Bolser D, McCarthy F, Kersey P, Lazo GR, Jaiswal P. De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum. 2014 May 12;9(5):e96855. doi: 10.1371/journal.pone.0096855. eCollection 2014.
  • 2013 PLoS One: Das PJ, McCarthy F, Vishnoi M, Paria N, Gresham C, Li G, Kachroo P, Sudderth AK, Teague S, Love CC, Varner DD, Chowdhary BP, Raudsepp T,Stallion sperm transcriptome comprises functionally coherent coding and regulatory RNAs as revealed by microarray analysis and RNA-seq, 2013;8(2):e56535. doi: 10.1371/journal.pone.0056535. Epub 2013 Feb 11.
  • 2012 PLoS One: Chouvarine P, Cooksey AM, McCarthy FM, Ray DA, Baldwin BS, Burgess SC, Peterson DG,Transcriptome-based differentiation of closely-related Miscanthus lines,2012;7(1):e29850. doi: 10.1371/journal.pone.0029850. Epub 2012 Jan 10.
  • 2011 Immunogenetics:Xianyao Li, Christina L. Swaggerty, Michael H. Kogut, Hsin-I Chiang, Ying Wang, Kenneth J. Genovese, Haiqi He, Fiona M. McCarthy, Shane C. Burgess, Igal Y. Pevzner, et.al.,Systemic response to Campylobacter jejuni infection by profiling gene transcription in the spleens of two genetic lines of chickens,January 2012, Volume 64, Issue 1, pp 59-69
  • 2010 PLoS One: van den Berg BH, McCarthy FM, Lamont SJ, Burgess SC,Re-annotation is an essential step in systems biology modeling of functional genomics data. 2010 May 14;5(5):e10642. doi: 10.1371/journal.pone.0010642.
  • 2010 BMC Genomics: Higgins SE, Ellestad LE, Trakooljul N, McCarthy F, Saliba J, Cogburn LA, Porter TE, Transcriptional and pathway analysis in the hypothalamus of newly hatched chicks during fasting and delayed feeding, 2010 Mar 9;11:162. doi: 10.1186/1471-2164-11-162.
  • 2009 Trends in Microbiology: : Fiona M. McCarthy,Timothy J. Mahony, Mark S. Parcells, Shane C. Burgess, Understanding animal viruses using the Gene Ontology, Volume 17, Issue 7, July 2009, Pages 328–335.
  • 2015 Genetics: Krishna R Veeramah, August E Woerner, Laurel Johnstone, et.al. Examining Phylogenetic Relationships Among Gibbon Genera Using Whole Genome Sequence Data Using an Approximate Bayesian Computation ApproachGenetics 03/2015; DOI:10.1534/genetics.115.174425
  • 2014 Nature: Lucia Carbone, R. Alan Harris, Sante Gnerre, Krishna R Veeramah, Belén Lorente-Galdos, et. al (Laurel Johnstone) Gibbon genome and the fast karyotype evolution of small apes. Nature 09/2014; 513(7517):195-201. DOI: 10.1038/nature13679
  • 2013 Gut Pathogens: Kirk E Anderson, Andreas Johansson, Tim H Sheehan, Brendon M Mott, Vanessa Corby-Harris, Laurel Johnstone, Ryan Sprissler, William Fitz. Draft genome sequences of two Bifidobacterium sp. from the honey bee (Apis mellifera). DOI:10.1186/1757-4749-5-42.
  • 2013 Epilepsia: Krishna R Veeramah, Laurel Johnstone, Tatiana M Karafet, et. al. Exome sequencing reveals new causal mutations in children with epileptic encephalopathies. Epilepsia 05/2013; DOI:10.1111/epi.12201
  • 2014 BMC medical genomics: V Shanmugam, RK Ramanathan, NA Lavender, S Sinari, M Chadha, et.al. Whole genome sequencing reveals potential targets for therapy in patients with refractory KRAS mutated metastatic colorectal cancer. BMC medical genomics 2014, 7:36 doi:10.1186/1755-8794-7-36
  • 2013 Mol Cancer Ther: DW Craig, JA O'Shaughnessy, JA Kiefer, J Aldrich, S Sinari, TM Moses, et.al. Genome and Transcriptome Sequencing in Prospective Metastatic Triple-Negative Breast Cancer Uncovers Therapeutic Vulnerabilities. Molecular cancer therapeutics 12 (1), 104-116
  • 2012 Blood: Jan B. Egan, Chang-Xin Shi, Waibhav Tembe, Alexis Christoforides, Ahmet Kurdoglu, Shripad Sinari, et. al. Whole-genome sequencing of multiple myeloma from diagnosis to plasma cell leukemia reveals genomic initiating events, evolution, and clonal tides. Blood 8/2012 Vol 120 Issue 5 1060-1066.
  • 2012 Electrophoresis: Barry Merriman, Ion Torrent R&D Team (S. Sinari), Jonathan M. Rothberg. Progress in Ion Torrent semiconductor chip based sequencing. Electrophoresis 12/2012 Vol. 33 Issue 23, 3397-3417
  • 2012 Applied and Environmental Microbiology: Xiuli Hao, Pin Xie, Laurel Johnstone, Susan Miller, Christopher Rensing, Gehong Wei. Genome sequence and mutational analysis of plant-growth-promoting bacterium Agrobacterium tumefaciens CCNWGS0286 Isolated from a zinc-lead mine tailing. Applied and Environmental Microbiology 05/2012; 78(15):5384-94 DOI: 10.1128/AEM.01200-12
  • 2011 Journal of bacteriology: Yanbin Lin, Xiuli Hao, Laurel Johnstone, Susan Miller, David Baltrus, Christopher Rensing, Gehong Wei. Draft Genome of Streptomyces zinciresistens K42, a Novel Metal-Resistant Species Isolated from Copper-Zinc Mine Tailings, Journal of bacteriology 11/2011; 193(22):6408-9. DOI: 10.1128/JB.06165-11
  • 2010 BMC Microbiology: Minyan He, Xiangyang Li, Liang Guo, Susan J Miller, Christopher Rensing and Gejiao Wang. Characterization and genomic analysis of chromate resistant and reducing Bacillus cereus strain SJ1. BMC Microbiology10:221 doi:10.1186/1471-2180-10-221
  • 2006 Journal of Biomolecular Techinques: Paul A. Haynes, Susan Miller,Tim Radabaugh, Michael Galligan, Linda Breci, James Rohrbough, Fatimah Hickman, and Nirav Merchant. The Wildcat Toolbox: A Set of Perl Script Utilities for Use in Peptide Mass Spectral Database Searching and Proteomics Experiments. J Biomol Tech. 2006 Apr; 17(2): 97–102.
  • 2012 PNAS:  Maiti A, Noon MS, MacKerell AD Jr, Pozharski E, Drohat AC, Lesion processing by a repair enzyme is severely curtailed by residues needed to prevent aberrant activity on undamaged DNA,2012 May 22;109(21):8091-6. doi: 10.1073/pnas.1201010109. Epub 2012 May 9.