The aquatic animals’ transcriptome resource for comparative functional analysis

[1]  Evan Bolton,et al.  Database resources of the National Center for Biotechnology Information , 2017, Nucleic Acids Res..

[2]  Saurabh Chaudhary,et al.  Optimization of De Novo Short Read Assembly of Seabuckthorn (Hippophae rhamnoides L.) Transcriptome , 2013, PloS one.

[3]  M. Miya,et al.  MitoFish and MitoAnnotator: A Mitochondrial Genome Database of Fish with an Accurate and Automatic Annotation Pipeline , 2013, Molecular biology and evolution.

[4]  J. Postlethwait,et al.  Evolution of the Eye Transcriptome under Constant Darkness in Sinocyclocheilus Cavefish , 2013, Molecular biology and evolution.

[5]  D. Hartline,et al.  In silico characterization of the insect diapause-associated protein couch potato (CPO) in Calanus finmarchicus (Crustacea: Copepoda). , 2013, Comparative biochemistry and physiology. Part D, Genomics & proteomics.

[6]  Joshua B. Gross,et al.  An Integrated Transcriptome-Wide Analysis of Cave and Surface Dwelling Astyanax mexicanus , 2013, PloS one.

[7]  Xin-Jiang Lu,et al.  Sequencing of the first ayu (Plecoglossus altivelis) macrophage transcriptome and microarray development for investigation the effect of LECT2 on macrophages. , 2013, Fish & shellfish immunology.

[8]  Jiale Li,et al.  Comparative Analysis of the Transcriptome in Tissues Secreting Purple and White Nacre in the Pearl Mussel Hyriopsis cumingii , 2013, PloS one.

[9]  Jean Thierry-Mieg,et al.  The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics , 2012, Nucleic Acids Res..

[10]  Narmada Thanki,et al.  CDD: conserved domains and protein three-dimensional structure , 2012, Nucleic Acids Res..

[11]  Stephen A. Smith,et al.  Optimizing de novo assembly of short-read RNA-seq data for phylogenomics , 2013, BMC Genomics.

[12]  Jian Wang,et al.  SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler , 2012, GigaScience.

[13]  Victor Zeng,et al.  ASGARD: an open-access database of annotated transcriptomes for emerging model arthropod species , 2012, Database J. Biol. Databases Curation.

[14]  Joanna L. Kelley,et al.  Genomic resources for a model in adaptation and speciation research: characterization of the Poecilia mexicana transcriptome , 2012, BMC Genomics.

[15]  J. Lee,et al.  Development of Microsatellite Markers for the Korean Mussel, Mytilus coruscus (Mytilidae) Using Next-Generation Sequencing , 2012, International journal of molecular sciences.

[16]  M. Yandell,et al.  Elucidation of the molecular envenomation strategy of the cone snail Conus geographus through transcriptome sequencing of its venom duct , 2012, BMC Genomics.

[17]  Christiaan V. Henkel,et al.  Genomics in Eels — Towards Aquaculture and Biology , 2012, Marine Biotechnology.

[18]  Guiming Liu,et al.  Characterization of Common Carp Transcriptome: Sequencing, De Novo Assembly, Annotation and Comparative Genomics , 2012, PloS one.

[19]  L. Seeb,et al.  Development of Genomic Resources for Pacific Herring through Targeted Transcriptome Pyrosequencing , 2012, PloS one.

[20]  Martin Vingron,et al.  Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels , 2012, Bioinform..

[21]  Rasko Leinonen,et al.  The sequence read archive: explosive growth of sequencing data , 2011, Nucleic Acids Res..

[22]  Andrew Whitehead,et al.  RNA-Seq reveals complex genetic response to deepwater horizon oil release in Fundulus grandis , 2012, BMC Genomics.

[23]  Jeffrey Heer,et al.  SpanningAspectRatioBank Easing FunctionS ArrayIn ColorIn Date Interpolator MatrixInterpola NumObjecPointI Rectang ISchedu Parallel Pause Scheduler Sequen Transition Transitioner Transiti Tween Co DelimGraphMLCon IData JSONCon DataField DataSc Dat DataSource Data DataUtil DirtySprite LineS RectSprite , 2011 .

[24]  K. Wada,et al.  Expression Profiling without Genome Sequence Information in a Non-Model Species, Pandalid Shrimp (Pandalus latirostris), by Next-Generation Sequencing , 2011, PloS one.

[25]  Zhong Wang,et al.  Next-generation transcriptome assembly , 2011, Nature Reviews Genetics.

[26]  Colin N. Dewey,et al.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.

[27]  N. Friedman,et al.  Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.

[28]  Mukesh Jain,et al.  Gene Discovery and Tissue-Specific Transcriptome Analysis in Chickpea with Massively Parallel Pyrosequencing and Web Resource Development1[W][OA] , 2011, Plant Physiology.

[29]  Jeffrey Heer,et al.  D³ Data-Driven Documents , 2011, IEEE Transactions on Visualization and Computer Graphics.

[30]  J. Montoya-Burgos,et al.  Optimization of de novo transcriptome assembly from next-generation sequencing data. , 2010, Genome research.

[31]  Thomas Werner,et al.  Next generation sequencing in functional genomics , 2010, Briefings Bioinform..

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

[33]  L. Holm,et al.  The Pfam protein families database , 2005, Nucleic Acids Res..

[34]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[35]  Mark Johnston,et al.  Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics. , 2009, Molecular biology and evolution.

[36]  M. Gerstein,et al.  RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.

[37]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

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

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

[40]  Yuki Moriya,et al.  KAAS: an automatic genome annotation and pathway reconstruction server , 2007, Nucleic Acids Res..

[41]  F. Cabello,et al.  Heavy use of prophylactic antibiotics in aquaculture: a growing problem for human and animal health and for the environment. , 2006, Environmental microbiology.

[42]  Adam Godzik,et al.  Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..

[43]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[44]  Susumu Goto,et al.  The KEGG resource for deciphering the genome , 2004, Nucleic Acids Res..

[45]  C. Stoeckert,et al.  OrthoMCL: identification of ortholog groups for eukaryotic genomes. , 2003, Genome research.

[46]  Robert Costanza,et al.  Economic Reasons for Conserving Wild Nature , 2002, Science.

[47]  M. Vidal,et al.  Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs". , 2001, Genome research.

[48]  H. Mooney,et al.  Effect of aquaculture on world fish supplies , 2000, Nature.

[49]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[50]  G. Schwartsmann Marine organisms and other novel natural sources of new cancer drugs. , 2000, Annals of oncology : official journal of the European Society for Medical Oncology.

[51]  X. Huang,et al.  CAP3: A DNA sequence assembly program. , 1999, Genome research.

[52]  D. Lipman,et al.  A genomic perspective on protein families. , 1997, Science.