John Martin,  McDonnell Genome Institute

Publications

title citation publication date
Genomic introgression mapping of field-derived multiple-anthelmintic resistance in Teladorsagia circumcincta PLoS Genet. 2017 Jun 23;13(6):e1006857. doi: 10.1371/journal.pgen.1006857. eCollection 2017 Jun. 1970-08-22
Genome Sequence of Christensenella minuta DSM 22607T Genome Announc. 2017 Jan 12;5(2). pii: e01451-16. doi: 10.1128/genomeA.01451-16. 2016-08-22
Environmental Enteric Dysfunction and the Fecal Microbiota in Malawian Children. Am J Trop Med Hyg. 2016 Dec 12. pii: 16-0617. [Epub ahead of print] 2016-12-12
Genomic diversity in Onchocerca volvulus and its Wolbachia endosymbiont. Nat Microbiol. 2016 Nov 21;2:16207. doi: 10.1038/nmicrobiol.2016.207. 2016-11-21
Dictyocaulus viviparus genome, variome and transcriptome elucidate lungworm biology and support future intervention. Sci Rep. 2016 Feb 9;6:20316. doi: 10.1038/srep20316. 2016-02-09
mBLAST: Keeping up with the sequencing explosion for (meta)genome analysis. J Data Mining Genomics Proteomics. 2015 Aug;4(3). pii: 135. Epub 2013 Jul 31. 2013-01-01
The effect of dietary resistant starch type 2 on the microbiota and markers of gut inflammation in rural Malawi children. Microbiome. 2015 Sep 3;3:37. doi: 10.1186/s40168-015-0102-9. 2015-09-03
Cracking the nodule worm code advances knowledge of parasite biology and biotechnology to tackle major diseases of livestock. Biotechnol Adv. 2015 May 27. pii: S0734-9750(15)30003-3. doi: 10.1016/j.biotechadv.2015.05.004. [Epub ahead of print] 2015-05-27
Dynamic changes in the subgingival microbiome and their potential for diagnosis and prognosis of periodontitis. MBio. 2015 Feb 17;6(1):e01926-14. doi: 10.1128/mBio.01926-14. 2015-02-17
Helminth.net: expansions to Nematode.net and an introduction to Trematode.net. Nucleic Acids Res. 2014 Nov 11. pii: gku1128. [Epub ahead of print] 2014-11-11
Endosymbiont DNA in endobacteria-free filarial nematodes indicates ancient horizontal genetic transfer PLoS One. 2010 Jun 9;5(6):e11029. doi: 10.1371/journal.pone.0011029. 2010-06-09
A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics. Cell. 2014 Sep 11;158(6):1402-14. doi: 10.1016/j.cell.2014.08.032. 2014-09-11
Exploration of bacterial community classes in major human habitats. Genome Biol. 2014 May 7;15(5):R66. [Epub ahead of print] 2014-05-07
Genome of the human hookworm Necator americanus. Nat Genet. 2014 Jan 19. doi: 10.1038/ng.2875. [Epub ahead of print] 2014-01-19
An expressed sequence tag analysis of the life-cycle of the parasitic nematode Strongyloides ratti. Mol Biochem Parasitol. 2005 Jul;142(1):32-46. Epub 2005 Apr 18. 2005-07-01
Systematic analysis of insertions and deletions specific to nematode proteins and their proposed functional and evolutionary relevance. BMC Evol Biol. 2009 Jan 28;9:23. doi: 10.1186/1471-2148-9-23. 2009-01-28
NemaPath: online exploration of KEGG-based metabolic pathways for nematodes. BMC Genomics. 2008 Nov 4;9:525. doi: 10.1186/1471-2164-9-525. 2008-11-04
Nematode.net update 2008: improvements enabling more efficient data mining and comparative nematode genomics. Nucleic Acids Res. 2009 Jan;37(Database issue):D571-8. doi: 10.1093/nar/gkn744. Epub 2008 Oct 21. 2009-01-01
Intestinal transcriptomes of nematodes: comparison of the parasites Ascaris suum and Haemonchus contortus with the free-living Caenorhabditis elegans. PLoS Negl Trop Dis. 2008 Aug 6;2(8):e269. doi: 10.1371/journal.pntd.0000269. 2008-08-01
Gene expression analysis distinguishes tissue-specific and gender-related functions among adult Ascaris suum tissues. Mol Genet Genomics. 2013 Apr 10. [Epub ahead of print] 2013-04-10
Using existing drugs as leads for broad spectrum anthelmintics targeting protein kinases. PLoS Pathog. 2013 Feb;9(2):e1003149. doi: 10.1371/journal.ppat.1003149. Epub 2013 Feb 14. 2013-02-14
Widespread Colonization of the Lung by Tropheryma whipplei in HIV Infection. Am J Respir Crit Care Med. 2013 Feb 7. [Epub ahead of print] 2013-02-07
Genomic variation landscape of the human gut microbiome. Nature. 2012 Dec 5. doi: 10.1038/nature11711. [Epub ahead of print] 2012-12-05
Exploring metazoan evolution through dynamic and holistic changes in protein families and domains. BMC Evol Biol. 2012 Aug 3;12(1):138. [Epub ahead of print] 2012-08-03
Optimizing read mapping to reference genomes to determine composition and species prevalence in microbial communities. PLoS One. 2012;7(6):e36427. Epub 2012 Jun 13. 2012-06-13
A framework for human microbiome research. Nature. 2012 Jun 13;486(7402):215-21. doi: 10.1038/nature11209. 2012-06-13
Structure, function and diversity of the healthy human microbiome. Nature. 2012 Jun 13;486(7402):207-14. doi: 10.1038/nature11234. 2012-06-13
Nematode.net update 2011: addition of data sets and tools featuring next-generation sequencing data. Nucleic Acids Res. 2011 Dec 1. [Epub ahead of print] 2011-12-01
HelmCoP: an online resource for helminth functional genomics and drug and vaccine targets prioritiza PLoS One. 2011;6(7):e21832. Epub 2011 Jul 8. 2011-07-08
The transcriptomes of the cattle parasitic nematode Ostertagia ostartagi. Vet Parasitol. 2009 May 26;162(1-2):89-99. Epub 2009 Feb 27. 2009-05-26
Targeting protein-protein interactions for parasite control. PLoS One. 2011 Apr 27;6(4):e18381. 2011-04-27
A vertebrate case study of the quality of assemblies derived from next-generation sequences. Genome Biol. 2011 Mar 31;12(3):R31. [Epub ahead of print] 2011-03-31
The draft genome of the parasitic nematode Trichinella spiralis Nat Genet. 2011 Mar;43(3):228-35. Epub 2011 Feb 20. 2011-02-20
Identification of hookworm DAF-16/FOXO response elements and direct gene targets. PLoS One. 2010 Aug 19;5(8):e12289. 2010-08-19
Characterizing Ancylostoma caninum transcriptome and exploring nematode parasitic adaptation. BMC Genomics. 2010 May 14;11:307. 2010-05-14
Comparative Analysis and Functional Annotation of a Large Expressed Sequence Tag Collection of Apple. The Plant Genome. 2009 March:2:23-38. 2009-03-01
Molecular determinants archetypical to the phylum Nematoda. BMC Genomics. 2009 Mar 18;10:114. 2009-03-18
Sequence mining and transcript profiling to explore cyst nematode parasitism. BMC Genomics. 2009 Jan 30;10:58. 2009-01-30
The canine hookworm genome: analysis and classification of Ancylostoma caninum survey sequences. Mol Biochem Parasitol. 2008 Feb;157(2):187-92. Epub 2007 Nov 9. 2008-02-15
Divergent evolution of arrested development in the dauer stage of Caenorhabditis elegans and the infective stage of Heterodera glycine. Genome Biol. 2007 Oct 5;8(10):R211 [Epub ahead of print] 2007-10-05
Investigating hookworm genomes by comparative analysis of two Ancylostoma species. BMC Genomics. 2005 Apr 26;6(1):58. 2005-04-26
Identification and analysis of genes expressed in the adult filarial parasitic nematode Dirofilaria immitis. Int J Parasitol. 2006 Jun;36(7):829-39. Epub 2006 Mar 31. 2006-03-15
Gene discovery in the apicomplexa as revealed by EST sequencing and assembly of a comparative gene database. Genome Res. 2003 Mar;13(3):443-54. 2003-03-01
Analysis and functional classification of transcripts from the nematode Meloidogyne incognita. Genome Biol. 2003;4(4):R26. Epub 2003 Mar 31. 2003-03-31
Comparative genomics of gene expression in the parasitic and free-living nematodes Strongyloides stercoralis and Caenorhabditis elegans. Genome Res. 2004 Feb;14(2):209-20. 2004-02-01
Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes. Nucleic Acids Res. 2004 Jan 1;32 Database issue:D423-6. 2004-01-01
Genome sequence of the nematode C. elegans: a platform for investigating biology. The C. elegans Sequencing Consortium. Science. 1998 Dec 11;282(5396):2012-8. Review. Erratum in: Science 1999 Jan 1;283(5398):35. Science 1999 Mar 26;283(5410):2103. Science 1999 Sep 3;285(5433):1493. 1998-12-10
An encyclopedia of mouse genes. Nat Genet. 1999 Feb;21(2):191-4. 1999-02-01
A transcriptomic analysis of the phylum Nematoda Nat Genet. 2004 Dec;36(12):1259-67. Epub 2004 Dec. 2004-11-14
Gene discovery in the adenophorean nematode Trichinella spiralis: an analysis of transcription from three life cycle stages. Mol Biochem Parasitol. 2004 Oct;137(2):277-91. 2004-10-25
A survey of the Leishmania major Friedlin strain V1 genome by shotgun sequencing: a resource for DNA microarrays and expression profiling. Mol Biochem Parasitol. 2001 Apr 6;113(2):337-40. 2001-04-06
A compilation of soybean ESTs: generation and analysis. Genome. 2002 Apr;45(2):329-38. 2002-03-31