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Method: Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes
- Paras Verma,
- Deeksha Thakur,
- Deepanshi Awasthi,
- and Shashi Bhushan Pandit
Genome Res. June 2025 35: 1440-1455; Published in Advance May 7, 2025, doi:10.1101/gr.279878.124
...remains limited owing to dearth of subsequent proteogenomic consequences. To coalesce the genomic information embedded in exons with isoform sequences, we present an innovative framework, “Exon Nomenclature And Classification of Transcripts” (ENACT). This centralizes exonic loci such that protein sequence...
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Research: Profiling the RNA editomes of wild-type C. elegans and ADAR mutants
- Han-Qing Zhao,
- Pan Zhang,
- Hua Gao,
- Xiandong He,
- Yanmei Dou,
- August Y. Huang,
- Xi-Ming Liu,
- Adam Y. Ye,
- Meng-Qiu Dong,
- and Liping Wei
Genome Res. January 2015 25: 66-75; Published in Advance November 4, 2014, doi:10.1101/gr.176107.114
..., Aruscavage PJ, Bass BL. 2002. RNA hairpins in noncoding regions of human brain and Caenorhabditis elegans mRNA are edited by Zhao et al. 74 Genome Research www..org adenosine deaminases that act on RNA. Proc Natl Acad Sci 99: 7906– 7911. Neeman Y, Levanon EY, Jantsch MF, Eisenberg E. 2006. RNA editing level...
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LETTER: Systematic Identification of Novel Protein Domain Families Associated with Nuclear Functions
- Tobias Doerks,
- Richard R. Copley,
- Jörg Schultz,
- Chris P. Ponting,
- and Peer Bork
Genome Res. January 1, 2002 12: 47-56; doi:10.1101/gr.203201
..., C.P Richard R, Copley 10.1101/gr.203201 1549-5469 genome;12/1/47 1088-9051 Systematic Identification of Novel Protein Domain Families Associated with Nuclear Functions Systematic Identification of Novel Protein Domain Families Associated with Nuclear Functions Tobias Doerks 1 , 2 , 4 , 5 , Richard...
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Research: Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth
- Christina A. Cuomo,
- Christopher A. Desjardins,
- Malina A. Bakowski,
- Jonathan Goldberg,
- Amy T. Ma,
- James J. Becnel,
- Elizabeth S. Didier,
- Lin Fan,
- David I. Heiman,
- Joshua Z. Levin,
- Sarah Young,
- Qiandong Zeng,
- and Emily R. Troemel
Genome Res. December 2012 22: 2478-2488; Published in Advance July 18, 2012, doi:10.1101/gr.142802.112
...address questions about microsporidia biology and evolution. We sequenced three microsporidian genomes from two species, Nematocida parisii and Nematocida sp1, which are natural pathogens of Caenorhabditis nematodes and provide model systems for studying microsporidian pathogenesis. We performed...
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ARTICLE: The Family of Caenorhabditis elegans Tyrosine Kinase Receptors: Similarities and Differences with Mammalian Receptors
- Cornel Popovici,
- Régine Roubin,
- François Coulier,
- Pierre Pontarotti,
- and Daniel Birnbaum
Genome Res. November 1, 1999 9: 1026-1039; doi:10.1101/gr.9.11.1026
...Régine Birnbaum, D Birnbaum, Daniel Daniel C Popovici Popovici 1549-5469 10.1101/gr.9.11.1026 1088-9051 genome;9/11/1026 The Family of Caenorhabditis elegans Tyrosine Kinase Receptors: Similarities and Differences with Mammalian Receptors The Family of Caenorhabditis elegans Tyrosine Kinase Receptors...
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LETTER: The amphioxus genome illuminates vertebrate origins and cephalochordate biology
- Linda Z. Holland,
- Ricard Albalat,
- Kaoru Azumi,
- Èlia Benito-Gutiérrez,
- Matthew J. Blow,
- Marianne Bronner-Fraser,
- Frederic Brunet,
- Thomas Butts,
- Simona Candiani,
- Larry J. Dishaw,
- David E.K. Ferrier,
- Jordi Garcia-Fernàndez,
- Jeremy J. Gibson-Brown,
- Carmela Gissi,
- Adam Godzik,
- Finn Hallböök,
- Dan Hirose,
- Kazuyoshi Hosomichi,
- Tetsuro Ikuta,
- Hidetoshi Inoko,
- Masanori Kasahara,
- Jun Kasamatsu,
- Takeshi Kawashima,
- Ayuko Kimura,
- Masaaki Kobayashi,
- Zbynek Kozmik,
- Kaoru Kubokawa,
- Vincent Laudet,
- Gary W. Litman,
- Alice C. McHardy,
- Daniel Meulemans,
- Masaru Nonaka,
- Robert P. Olinski,
- Zeev Pancer,
- Len A. Pennacchio,
- Mario Pestarino,
- Jonathan P. Rast,
- Isidore Rigoutsos,
- Marc Robinson-Rechavi,
- Graeme Roch,
- Hidetoshi Saiga,
- Yasunori Sasakura,
- Masanobu Satake,
- Yutaka Satou,
- Michael Schubert,
- Nancy Sherwood,
- Takashi Shiina,
- Naohito Takatori,
- Javier Tello,
- Pavel Vopalensky,
- Shuichi Wada,
- Anlong Xu,
- Yuzhen Ye,
- Keita Yoshida,
- Fumiko Yoshizaki,
- Jr-Kai Yu,
- Qing Zhang,
- Christian M. Zmasek,
- Pieter J. de Jong,
- Kazutoyo Osoegawa,
- Nicholas H. Putnam,
- Daniel S. Rokhsar,
- Noriyuki Satoh,
- and Peter W.H. Holland
Genome Res. July 2008 18: 1100-1111; Published in Advance June 18, 2008, doi:10.1101/gr.073676.107
...families, and conserved noncoding elements in the sequenced genome of the cephalochordate Branchiostoma floridae , commonly called amphioxus or lancelets. Special attention was given to homeobox genes, opsin genes, genes involved in neural crest development, nuclear receptor genes, genes encoding...
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RESOURCE: Neuropeptides and Neuropeptide Receptors in the Drosophila melanogaster Genome
- Randall S. Hewes and
- Paul H. Taghert
Genome Res. June 1, 2001 11: 1126-1142; doi:10.1101/gr.169901
...receptors (NMURs), growth hormone secretagogue receptors (GHSRs), neurotensin receptors (NTRs), thyrotropin releasing hormone receptors (TRFRs), and a large family of related orphan receptors from Caenorhabditis elegans . The C. elegans orphan receptors included here belong to one of three clades (classes A...
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ARTICLE: Functional Classification of cNMP-binding Proteins and Nucleotide Cyclases with Implications for Novel Regulatory Pathways in Mycobacterium tuberculosis
- Lee Ann McCue,
- Kathleen A. McDonough,
- and Charles E. Lawrence
Genome Res. February 1, 2000 10: 204-219; doi:10.1101/gr.10.2.204
...for Laboratories and Research, New York State Department of Health, Albany, New York 12201-0509 USA Abstract We have analyzed the cyclic nucleotide (cNMP)-binding protein and nucleotide cyclase superfamilies using Bayesian computational methods of protein family identification and classification...
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Letter: Evolution of gene function and regulatory control after whole-genome duplication: Comparative analyses in vertebrates
- Karin S. Kassahn,
- Vinh T. Dang,
- Simon J. Wilkins,
- Andrew C. Perkins,
- and Mark A. Ragan
Genome Res. August 2009 19: 1404-1418; Published in Advance May 13, 2009, doi:10.1101/gr.086827.108
...invertebrate chordates; the insects Aedes aegypti, Anopheles gambiae, or Drosophila melanogaster; the worm Caenorhabditis elegans; or the yeast Saccharomyces cerevisiae. Protein families that contained a WGD-duplicate were more likely to also contain invertebrate chordate, insect, worm, or yeast sequences than...
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ARTICLE: Tandem Clusters of Membrane Proteins in Complete Genome Sequences
- Daisuke Kihara and
- Minoru Kanehisa
Genome Res. June 1, 2000 10: 731-743; doi:10.1101/gr.10.6.731
...was investigated in 16 complete genomes: 4 archaea, 11 bacteria, and 1 eukaryote. Membrane proteins were identified by our new method of predicting transmembrane segments ( Kihara et al. 1998 ) after the removal of amino-terminal signal peptides. Interestingly, about half of the membrane protein genes in each...

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