Items where Author is "Martin, John"

Article

Martin, John and Sykes, Sean and Young, Sarah and Kota, Karthik and Sanka, Ravi and Sheth, Nihar and Orvis, Joshua and Sodergren, Erica and Weinstock, George M and Mitreva, Makedonka and Wang, Zhengyuan (2012) Optimizing read mapping to reference genomes to determine composition and species prevalence in microbial communities. PLoS One, 7 (6). e36427.

Wang, Zhengyuan and Zarlenga, Dante S. and Martin, John and Abubucker, Sahar and Mitreva, Makedonka (2012) Exploring metazoan evolution through dynamic and holistic changes in protein families and domains. BMC Evolutionary Biology. pp. 2-17.

Abubucker, Sahar and Martin, John and Taylor, Christina M. and Mitreva, Makedonka (2011) HelmCoP: An Online Resource for Helminth Functional Genomics and Drug and Vaccine Targets Prioritization. PLoS One, 6 (7). e21832.

Taylor, Christina M. and Abubucker, Sahar and Fischer, Kerstin and Wang, Zhengyuan and Martin, John and Jiang, Dao-Jun and Rosso, Marie and Li, Ben-Wen and Fischer, Peter U. and Mitreva, Makedonka (2011) Targeting Protein-Protein Interactions for Parasite Control. Plos One, 6 (4). pp. 1-12.

Ye, Liang and Hillier, LaDeana W and Minx, Patrick and Thane, Nay and Locke, Devin P. and Martin, John and Chen, Lei and Mitreva, Makedonka and Miller, Jason R and Haub, Kevin V and Dooling, David J and Mardis, Elaine and Wilson, Richard K. and Weinstock, George M and Warren, Wesley (2011) A vertebrate case study of the quality of assemblies derived from next-generation sequences. Genome Biology, 12 (3). pp. 1-7.

McNulty, Samantha N. and Foster, Jeremy M. and Mitreva, Makedonka and Dunning Hotopp, Julie C. and Martin, John and Fischer, Kerstin and Wu, Bo and Davis, Paul J. and Kumar, Sanjay and Brattig, Norbert W. and Slatko, Barton E. and Weil, Gary J. and Fischer, Peter U. (2010) Endosymbiont DNA in Endobacteria-Free Filarial Nematodes Indicates Ancient Horizontal Genetic Transfer. HGT in Filarial Nematodes, 5 (6). pp. 1-9.

Wang, Zhengyuan and Abubucker, Sahar and Martin, John and Wilson, Richard K. and Hawdon, John and Mitreva, Makedonka (2010) Characterizing Ancylostoma caninum transcriptome and exploring nematode parasitic adaptation. BMC Genomics - Plos Neglected tropical diseases (www.plosntds.org ) - Open Acecess. pp. 1-19.

Martin, John and Abubucker, Sahar and Heizer, Esley and Taylor, Christina M. and Mitreva, Makedonka (2010) Nematode.net update 2011: addition of data sets and tools featuring next-generation sequencing data. Nucleic Acids Research, 40. D720-D728.

Gao, Xin and Wang, Zhengyuan and Martin, John and Abubucker, Sahar and Zhang, Ziping and Mitreva, Makedonka and Hawdon, John (2010) Identification of hookworm DAF-16/FOXO response elements and direct gene targets. PLoS One, 5 (8). e12289.

Sahar, Abubuckar and Zarlenga, Dante S. and Martin, John and Yin, Yong and Wang, Zhengyuan and McCarter, James P. and Gasparree, Louis and Wilson, Richard K. and Mitreva, Makedonka (2009) The transcriptomes of the cattle parasitic nematode Ostertagia ostartagi. Veterinary Parasitology, 162 (1-2). pp. 89-99.

Yin, Yong and Martin, John and Abubucker, Sahar and Wang, Zhengyuan and Wyrwicz, Lucijan and Rychlewski, Leszek and McCarter, James P. and Wilson, Richard K. and Mitreva, Makedonka (2009) Molecular determinants archetypical to the phylum Nematoda. BMC Genomics. pp. 1-14.

Elling, Axel A. and Mitreva, Makedonka and Gai, Xiaowu and Martin, John and Recknor, Justin and Hussey, Richard S and Nettleton, Dan and McCarter, James P. and Baum, Thomas J. (2009) Sequence mining and transcript profiling to explore cyst nematode parasitism. Directory of Open Access Journals. pp. 1-17.

Martin, John and Abubucker, Sahar and Wylie, Todd and Yin, Yong and Wang, Zhengyuan and Mitreva, Makedonka (2009) Nematode.net update 2008: improvements enabling more efficient data mining and comparative nematode genomics . Nucleic Acids Research, 37. D571-D578.

Wang, Zhengyuan and Martin, John and Abubucker, Sahar and Yin, Yong and Gasser, Robin B. and Mitreva, Makedonka (2009) Systematic analysis of insertions and deletions specific to nematode proteins and their proposed functional and evolutionary relevance. BMC Evolutionary Biology, 9 (23). pp. 1-14.

Yin, Yong and Martin, John and Abubucker, Sahar and Scott, Alan L. and McCarter, James P. and Wilson, Richard K. and Jasmer, Douglas P. and Mitreva, Makedonka (2008) Intestinal Transcriptomes of Nematodes: Comparison of the Parasites Ascarissuum and Haemonchuscontortus with the Free-living Caenorhabditiselegans. Plos Neglected tropical diseases (www.plosntds.org ) - Open Access, 2 (8). pp. 1-12.

Abubucker, Sahar and Martin, John and Yin, Yong and Fulton, Lucinda and Yang, Shiaw-Pyng and Hallsworth-Pepin, Kym and Johnston, J. Spencer and Hawdon, John and McCarter, James P. and Wilson, Richard K. and Mitreva, Makedonka (2008) The canine hookworm genome: analysis and classification of Ancylostoma caninum survey sequences. Mol Biochem Parasitol, 157 (2). pp. 187-192.

Wylie, Todd and Martin, John and Abubucker, Sahar and Yin, Yong and Messina, David and Wang, Zhengyuan and McCarter, James P. and Mitreva, Makedonka (2008) NemaPath: online exploration of KEGG-based metabolic pathways for nematodes. BMC Genomics, 9 (525). pp. 1-10.

Mitreva, Makedonka and Wendl, Michael C and Martin, John and Wylie, Todd and Yin, Yong and Larson, Allan and Parkinson, John and Waterston, Robert H. and McCarter, James P. (2006) Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species. Genome Biology, 7.

Yin, Yong and Martin, John and McCarter, James P. and Clifton, Sandra W. and Wilson, Richard K. and Mitreva, Makedonka (2006) Identification and analysis of genes expressed in the adult filarial parasitic nematode Dirofilaria immitis. International Journal for Parasitology, 36 (7). pp. 829-839.

Mitreva, Makedonka and McCarter, James P. and Arasu, Prema and Hawdon, John and Martin, John and Dante, Mike (2005) Investigating hookworm genomes by comparative analysis of two Ancylostoma species. BMC Genomics. pp. 1-19.

Mitreva, Makedonka and McCarter, James P. and Martin, John (2004) Comparative genomics of gene expression in the parasitic and free-living nematodes Strongyloides stercoralis and Caenorhabditis elegans. Genome Research. pp. 209-220.

Mitreva, Makedonka and Jasmer, Douglas P. and Appleton, Judith and Martin, John and Dante, Mike and Wylie, Todd and Clifton, Sandra W. and Waterston, Robert H. and McCarter, James P. (2004) Gene discovery in the adenophorean nematode Trichinella spiralis: an analysis of transcription from three life cycle stages. Molecular and Biochemical Parasitology, 137 (2). pp. 277-291.

Wylie, Todd and Martin, John and Dante, Michael and Mitreva, Makedonka and Clifton, Sandra W. and Chinwalla, Asif and Waterston, Robert H. and Wilson, Richard K. and McCarter, James P. (2004) Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes. Nucleic Acids Research, 32. D423-D426.

McCarter, James P. and Mitreva, Makedonka and Martin, John and Dante, Mike and Wylie, Todd and Rao, Uma and Pape, Deana and Bowers, Yvette and Theising, Brenda and Murphy, Claire V and Kloek, Andrew P and Chiapelli, Brandi J and Clifton, Sandra W. and Bird, David M. and Waterston, Robert H. (2003) Analysis and functional classification of transcripts from the nematode Meloidogyne incognita. Genome Biology, 4 (4). R26.1-R26.19.

Book Section

Thompson, Fiona J. and Mitreva, Makedonka and Barker, Gary L.A. and Martin, John and Waterston, Robert H. and McCarter, James P. and Viney, Mark E. (2005) An expressed sequence tag analysis of the life-cycle of the parasitic nematode Strongyloides ratti. In: Molecular and Biochemical Parasitology. Elsever, pp. 32-46.