Decoding the Ascaris suum Genome using Massively Parallel Sequencing and Advanced Bioinformatic Methods - Unprecedented Prospects for Fundamental and Applied Research

[1]  A. Jex,et al.  Monoaminergic signaling as a target for anthelmintic drug discovery: receptor conservation among the free-living and parasitic nematodes. , 2012, Molecular and biochemical parasitology.

[2]  G. Samson-Himmelstjerna Anthelmintic resistance in equine parasites – detection, potential clinical relevance and implications for control , 2012 .

[3]  C. Reinemeyer Anthelmintic resistance in non-strongylid parasites of horses. , 2012, Veterinary parasitology.

[4]  Peer Bork,et al.  OGEE: an online gene essentiality database , 2011, Nucleic Acids Res..

[5]  Paul W. Sternberg,et al.  Ascaris suum draft genome , 2011, Nature.

[6]  S. G. Monteiro,et al.  Meta-analysis of the effects of endoparasites on pig performance. , 2011, Veterinary parasitology.

[7]  Lior Pachter,et al.  Identification of novel transcripts in annotated genomes using RNA-Seq , 2011, Bioinform..

[8]  C. Holland,et al.  Ascaris and ascariasis. , 2011, Microbes and infection.

[9]  R. Gasser,et al.  Norcantharidin analogues with nematocidal activity in Haemonchus contortus. , 2011, Bioorganic & medicinal chemistry letters.

[10]  P. Sternberg,et al.  Atypical (RIO) protein kinases from Haemonchus contortus--promise as new targets for nematocidal drugs. , 2011, Biotechnology advances.

[11]  Elaine R. Mardis,et al.  The draft genome of the parasitic nematode Trichinella spiralis , 2011, Nature Genetics.

[12]  Zi-Guo Yuan,et al.  Ascaris suum: RNAi mediated silencing of enolase gene expression in infective larvae. , 2011, Experimental parasitology.

[13]  P. Hotez,et al.  Soil-transmitted helminths of humans in Southeast Asia--towards integrated control. , 2011, Advances in parasitology.

[14]  A. Hofmann,et al.  Serine/threonine phosphatases in socioeconomically important parasitic nematodes--prospects as novel drug targets? , 2011, Biotechnology advances.

[15]  P. Smooker,et al.  Cathepsin B proteases of flukes: the key to facilitating parasite control? , 2010, Trends in parasitology.

[16]  M. Xu,et al.  RNAi-mediated silencing of a novel Ascaris suum gene expression in infective larvae , 2010, Parasitology Research.

[17]  Ross S Hall,et al.  A practical, bioinformatic workflow system for large data sets generated by next-generation sequencing , 2010, Nucleic acids research.

[18]  S. Koren,et al.  Assembly algorithms for next-generation sequencing data. , 2010, Genomics.

[19]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[20]  Dawei Li,et al.  The sequence and de novo assembly of the giant panda genome , 2010, Nature.

[21]  Neil D. Rawlings,et al.  MEROPS: the peptidase database , 2009, Nucleic Acids Res..

[22]  J. McCarthy,et al.  Unresolved issues in anthelmintic pharmacology for helminthiases of humans. , 2010, International journal for parasitology.

[23]  J. Utzinger,et al.  The drugs we have and the drugs we need against major helminth infections. , 2010, Advances in parasitology.

[24]  M. Metzker Sequencing technologies — the next generation , 2010, Nature Reviews Genetics.

[25]  R. Maizels,et al.  Helminth immunoregulation: The role of parasite secreted proteins in modulating host immunity , 2009, Molecular and biochemical parasitology.

[26]  John P. Overington,et al.  The genome of the blood fluke Schistosoma mansoni , 2009, Nature.

[27]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[28]  Peter J Hotez,et al.  Rescuing the bottom billion through control of neglected tropical diseases , 2009, The Lancet.

[29]  E. Liu,et al.  Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. , 2009, Genome research.

[30]  T. Veenstra,et al.  Brugia malayi Excreted/Secreted Proteins at the Host/Parasite Interface: Stage- and Gender-Specific Proteomic Profiling , 2009, PLoS neglected tropical diseases.

[31]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[32]  Nansheng Chen,et al.  Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences , 2009, Current protocols in bioinformatics.

[33]  Sheila Donnelly,et al.  Helminth pathogen cathepsin proteases: it's a family affair. , 2008, Trends in biochemical sciences.

[34]  R. Durbin,et al.  Mapping Quality Scores Mapping Short Dna Sequencing Reads and Calling Variants Using P

, 2022 .

[35]  Christoph Dieterich,et al.  The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism , 2008, Nature Genetics.

[36]  P. Abad,et al.  Direct Identification of the Meloidogyne incognita Secretome Reveals Proteins with Host Cell Reprogramming Potential , 2008, PLoS pathogens.

[37]  Varghese P. Thomas,et al.  Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism , 2008, Proceedings of the National Academy of Sciences.

[38]  R. Martin,et al.  Levamisole resistance resolved at the single‐channel level in Caenorhabditis elegans , 2008, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[39]  R. Maizels,et al.  The secretome of the filarial parasite, Brugia malayi: proteomic profile of adult excretory-secretory products. , 2008, Molecular and biochemical parasitology.

[40]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[41]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[42]  A. Sluder,et al.  A new class of anthelmintics effective against drug-resistant nematodes , 2008, Nature.

[43]  A. Fraser,et al.  A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans , 2008, Nature Genetics.

[44]  Shivashankar H. Nagaraj,et al.  Gender-enriched transcripts in Haemonchus contortus--predicted functions and genetic interactions based on comparative analyses with Caenorhabditis elegans. , 2008, International journal for parasitology.

[45]  J. Yates,et al.  Proteomic analysis of Schistosoma mansoni egg secretions. , 2007, Molecular and biochemical parasitology.

[46]  Jonathan E. Allen,et al.  Draft Genome of the Filarial Nematode Parasite Brugia malayi , 2007, Science.

[47]  P. Hotez,et al.  Control of neglected tropical diseases. , 2007, The New England journal of medicine.

[48]  M. Brent How does eukaryotic gene prediction work? , 2007, Nature Biotechnology.

[49]  Liqiang Chen,et al.  Recent development of IMP dehydrogenase inhibitors for the treatment of cancer. , 2007, Current opinion in drug discovery & development.

[50]  Zhao Xu,et al.  LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons , 2007, Nucleic Acids Res..

[51]  Erik L. L. Sonnhammer,et al.  Advantages of combined transmembrane topology and signal peptide prediction—the Phobius web server , 2007, Nucleic Acids Res..

[52]  R. Gasser,et al.  Single-strand conformation polymorphism (SSCP) for the analysis of genetic variation , 2006, Nature Protocols.

[53]  Adam R Renslo,et al.  Drug discovery and development for neglected parasitic diseases , 2006, Nature chemical biology.

[54]  Cori Bargmann Chemosensation in C. elegans. , 2006, WormBook : the online review of C. elegans biology.

[55]  R. Gasser,et al.  Recent insights into the epidemiology and genetics of Ascaris in China using molecular tools , 2006, Parasitology.

[56]  G. Saunders,et al.  RNA interference in parasitic helminths: current situation, potential pitfalls and future prospects , 2006, Parasitology.

[57]  Weiwei Zhong,et al.  Genome-Wide Prediction of C. elegans Genetic Interactions , 2006, Science.

[58]  J. Matthews,et al.  An immunogenic cathepsin F secreted by the parasitic stages of Teladorsagia circumcincta. , 2006, International journal for parasitology.

[59]  P. Loke,et al.  Proteases in parasitic diseases. , 2006, Annual review of pathology.

[60]  Cathy H. Wu,et al.  The Universal Protein Resource (UniProt): an expanding universe of protein information , 2005, Nucleic Acids Res..

[61]  C. Cameron,et al.  Mechanisms of action of ribavirin against distinct viruses , 2005, Reviews in medical virology.

[62]  Rolf Apweiler,et al.  InterProScan: protein domains identifier , 2005, Nucleic Acids Res..

[63]  R. Haque,et al.  Ascariasis Is a Zoonosis in Denmark , 2005, Journal of Clinical Microbiology.

[64]  Yong Zhang,et al.  SPD—a web-based secreted protein database , 2004, Nucleic Acids Res..

[65]  Un Millennium,et al.  Investing in development : a practical plan to achieve the Millennium Development Goals , 2005 .

[66]  Eugene W. Myers,et al.  PILER : identification and classification of genomic repeats , 2005 .

[67]  Pavel A. Pevzner,et al.  De novo identification of repeat families in large genomes , 2005, ISMB.

[68]  Thet Thet Zin,et al.  Soil‐transmitted helminthiasis in Myanmar and approximate costs for countrywide control , 2004, Tropical medicine & international health : TM & IH.

[69]  B Marshall,et al.  Gene Ontology Consortium: The Gene Ontology (GO) database and informatics resource , 2004, Nucleic Acids Res..

[70]  L. Holden-Dye,et al.  Cyclooctadepsipeptides--an anthelmintically active class of compounds exhibiting a novel mode of action. , 2003, International journal of antimicrobial agents.

[71]  Rick M. Maizels,et al.  Immune Regulation by helminth parasites: cellular and molecular mechanisms , 2003, Nature Reviews Immunology.

[72]  H. Frankish Initiative launched to develop drugs of neglected diseases , 2003, The Lancet.

[73]  A. Loukas,et al.  Helminth vaccines: from mining genomic information for vaccine targets to systems used for protein expression. , 2003, International journal for parasitology.

[74]  Maria Jesus Martin,et al.  The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 , 2003, Nucleic Acids Res..

[75]  Colin N. Dewey,et al.  Initial sequencing and comparative analysis of the mouse genome. , 2002 .

[76]  P. Cohen Protein kinases — the major drug targets of the twenty-first century? , 2002, Nature reviews. Drug discovery.

[77]  M. Sajid,et al.  Cysteine proteases of parasitic organisms. , 2002, Molecular and biochemical parasitology.

[78]  M. Borodovsky,et al.  GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. , 2001, Nucleic acids research.

[79]  T. Anderson,et al.  The dangers of using single locus markers in parasite epidemiology: Ascaris as a case study. , 2001, Trends in parasitology.

[80]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[81]  V. Reinke,et al.  Genome-wide analysis of developmental and sex-regulated gene expression profiles in Caenorhabditis elegans. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[82]  D. Crompton Ascaris and ascariasis. , 2001, Advances in parasitology.

[83]  J. Boes,et al.  Animal models of intestinal nematode infections of humans , 2000, Parasitology.

[84]  F. Müller,et al.  Chromatin diminution in the parasitic nematodes ascaris suum and parascaris univalens. , 2000, International journal for parasitology.

[85]  Stephen M. Mount,et al.  The genome sequence of Drosophila melanogaster. , 2000, Science.

[86]  P. Geenen,et al.  The morphogenesis of Ascaris suum to the infective third-stage larvae within the egg. , 1999, The Journal of parasitology.

[87]  G. Benson,et al.  Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.

[88]  Andrew Smith Genome sequence of the nematode C-elegans: A platform for investigating biology , 1998 .

[89]  Frank McCormick,et al.  The GTPase superfamily: conserved structure and molecular mechanism , 1991, Nature.

[90]  E. Lander,et al.  Genomic mapping by fingerprinting random clones: a mathematical analysis. , 1988, Genomics.

[91]  A. Spicher,et al.  Structure and genomic organization of proretrovirus‐like elements partially eliminated from the somatic genome of Ascaris lumbricoides. , 1986, The EMBO journal.

[92]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[93]  W. Campbell,et al.  Ivermectin: a potent new antiparasitic agent. , 1983, Science.