A customized Web portal for the genome of the ctenophore Mnemiopsis leidyi

[1]  T. Wolfsberg,et al.  A customized Web portal for the genome of the ctenophore Mnemiopsis leidyi , 2014, BMC Genomics.

[2]  Robert Buels,et al.  JBrowse: A Next-Generation Genome Browser , 2014 .

[3]  Nicholas H. Putnam,et al.  The Genome of the Ctenophore Mnemiopsis leidyi and Its Implications for Cell Type Evolution , 2013, Science.

[4]  Morgan Park,et al.  Genomic organization, evolution, and expression of photoprotein and opsin genes in Mnemiopsis leidyi: a new view of ctenophore photocytes , 2012, BMC Biology.

[5]  A. Baxevanis,et al.  MicroRNAs and essential components of the microRNA processing machinery are not encoded in the genome of the ctenophore Mnemiopsis leidyi , 2012, BMC Genomics.

[6]  Paolo Fontana,et al.  Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms , 2012, BMC Bioinformatics.

[7]  A. Baxevanis,et al.  The Diversification of the LIM Superclass at the Base of the Metazoa Increased Subcellular Complexity and Promoted Multicellular Specialization , 2012, PloS one.

[8]  B. Liebeskind.  Evolution of sodium channels and the new view of early nervous system evolution , 2011, Communicative & integrative biology.

[9]  M. Martindale,et al.  Evolution of the TGF-β Signaling Pathway and Its Potential Role in the Ctenophore, Mnemiopsis leidyi , 2011, PloS one.

[10]  J. Mullikin,et al.  Extreme mitochondrial evolution in the ctenophore Mnemiopsis leidyi: Insight from mtDNA and the nuclear genome , 2011, Mitochondrial DNA.

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

[12]  Robert D. Finn,et al.  HMMER web server: interactive sequence similarity searching , 2011, Nucleic Acids Res..

[13]  T. Tatusova,et al.  Entrez Gene: gene-centered information at NCBI , 2010, Nucleic Acids Res..

[14]  J. Mullikin,et al.  Nuclear receptors from the ctenophore Mnemiopsis leidyi lack a zinc-finger DNA-binding domain: lineage-specific loss or ancestral condition in the emergence of the nuclear receptor superfamily? , 2011, EvoDevo.

[15]  J. Mullikin,et al.  Genomic insights into Wnt signaling in an early diverging metazoan, the ctenophore Mnemiopsis leidyi , 2010, EvoDevo.

[16]  J. Mullikin,et al.  The homeodomain complement of the ctenophore Mnemiopsis leidyi suggests that Ctenophora and Porifera diverged prior to the ParaHoxozoa , 2010, EvoDevo.

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

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

[19]  Nicholas H. Putnam,et al.  The Trichoplax genome and the nature of placozoans , 2008, Nature.

[20]  Jules J Berman,et al.  Perl: The Programming Language , 2008 .

[21]  Jonathan E. Allen,et al.  Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments , 2007, Genome Biology.

[22]  David C. Nickle,et al.  ViroBLAST: a stand-alone BLAST web server for flexible queries of multiple databases and user's datasets , 2007, Bioinform..

[23]  Guido van Rossum,et al.  Python Programming Language , 2007, USENIX Annual Technical Conference.

[24]  Joseph F. Ryan,et al.  StellaBase: The Nematostella vectensis Genomics Database , 2005, Nucleic Acids Res..

[25]  Juan Miguel García-Gómez,et al.  Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research , 2005, Bioinform..

[26]  Robert D. Finn,et al.  The Pfam protein families database , 2004, Nucleic Acids Res..

[27]  Eric M. Just,et al.  dictyBase: a new Dictyostelium discoideum genome database , 2004, Nucleic Acids Res..

[28]  Douglas A. Hosack,et al.  Identifying biological themes within lists of genes with EASE , 2003, Genome Biology.

[29]  J. Finnerty,et al.  The Radiata and the evolutionary origins of the bilaterian body plan. , 2002, Molecular phylogenetics and evolution.

[30]  J. Stoye,et al.  REPuter: the manifold applications of repeat analysis on a genomic scale. , 2001, Nucleic acids research.

[31]  M. Martindale,et al.  Regulation and regeneration in the ctenophore Mnemiopsis leidyi. , 2000, Developmental biology.

[32]  G. Reynolds,et al.  The development of bioluminescence in the ctenophore Mnemiopsis leidyi. , 1973, Developmental biology.