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The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
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The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Zhou, Naihui ; Jiang, Yuxiang ; Lee, Alexandra J ; Kacsoh, Balint Z ; Crocker, Alex W ; Georghiou, George ; Nguyen, Huy N ; Hamid, Md Nafiz ; Davis, Larry ; Atalay, Volkan ; Rifaioglu, Ahmet S ; Dalkıran, Alperen ; Cetin Atalay, Rengul ; Zhang, Chengxin ; Hurto, Rebecca L ; Freddolino, Peter L ; Supek, Fran ; Fernández, José M ; Gemovic, Branislava ; Sumonja, Neven ; Veljkovic, Nevena ; Asgari, Ehsaneddin ; Mofrad, Mohammad R K ; Savojardo, Castrense ; Martelli, Pier Luigi ; Casadio, Rita ; Boecker, Florian ; Schoof, Heiko ; Thurlby, Natalie ; McHardy, Alice C ; Renaux, Alexandre ; Saidi, Rabie ; Gough, Julian ; Freitas, Alex A ; Antczak, Magdalena ; Fabris, Fabio ; Wass, Mark N ; Hou, Jie ; Wang, Zheng ; Romero, Alfonso E ; Paccanaro, Alberto ; Yang, Haixuan ; Goldberg, Tatyana ; Zhao, Chenguang ; Holm, Liisa ; Tseng, Wei-Cheng ; Linial, Michal ; Rose, Peter W ; Dessimoz, Christophe ; Dzeroski, Saso ; Sillitoe, Ian ; Das, Sayoni ; Wan, Cen ; Fa, Rui ; Notaro, Marco ; Grossi, Giuliano ; Valentini, Giorgio ; Mesiti, Marco ; Ritchie, David W ; Aridhi, Sabeur ; Bonneau, Richard ; Gligorijević, Vladimir ; Fang, Hai ; Toppo, Stefano ; Falda, Marco ; Berselli, Michele ; Mao, Qizhong ; Black, Gage S ; Suh, Erica ; Dayton, Jonathan B ; Larsen, Dallas J ; Omdahl, Ashton R ; McGuffin, Liam J ; Brackenridge, Danielle A ; Babbitt, Patricia C ; Yunes, Jeffrey M ; Fontana, Paolo ; Zhang, Feng ; Zhu, Shanfeng ; Dai, Suyang ; Yao, Shuwei ; Cao, Renzhi ; Amezola, Miguel ; Johnson, Devon ; Liu, Yi-Wei ; Frank, Yotam ; Hoehndorf, Robert ; Kulmanov, Maxat ; Björne, Jari ; Tolvanen, Martti E E ; Salakoski, Tapio ; Altenhoff, Adrian ; Ben-Hur, Asa ; Rost, Burkhard ; Orengo, Christine A ; Bosco, Giovanni ; Martin, Maria J ; Mooney, Sean D ; Greene, Casey S ; Radivojac, Predrag

Genome Biology, 2019-11, Vol.20 (1), p.244-244, Article 244 [Periódico revisado por pares]

England: BioMed Central

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2
A beginner's guide to eukaryotic genome annotation
A beginner's guide to eukaryotic genome annotation
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A beginner's guide to eukaryotic genome annotation

YANDELL, Mark ; ENCE, Daniel

Nature reviews. Genetics, 2012-05, Vol.13 (5), p.329-342 [Periódico revisado por pares]

London: Nature Publishing Group

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3
The status of the human gene catalogue
The status of the human gene catalogue
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The status of the human gene catalogue

Amaral, Paulo ; Carbonell-Sala, Silvia ; De La Vega, Francisco M ; Faial, Tiago ; Frankish, Adam ; Gingeras, Thomas ; Guigo, Roderic ; Harrow, Jennifer L ; Hatzigeorgiou, Artemis G ; Johnson, Rory ; Murphy, Terence D ; Pertea, Mihaela ; Pruitt, Kim D ; Pujar, Shashikant ; Takahashi, Hazuki ; Ulitsky, Igor ; Varabyou, Ales ; Wells, Christine A ; Yandell, Mark ; Carninci, Piero ; Salzberg, Steven L

Nature (London), 2023-10, Vol.622 (7981), p.41-47 [Periódico revisado por pares]

England: Nature Publishing Group

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4
Progress, Challenges, and Surprises in Annotating the Human Genome
Progress, Challenges, and Surprises in Annotating the Human Genome
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Progress, Challenges, and Surprises in Annotating the Human Genome

Zerbino, Daniel R ; Frankish, Adam ; Flicek, Paul

Annual review of genomics and human genetics, 2020-08, Vol.21 (1), p.55-79 [Periódico revisado por pares]

United States: Annual Reviews

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5
Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow
Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow
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Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow

Wright, James C ; Mudge, Jonathan ; Weisser, Hendrik ; Barzine, Mitra P ; Gonzalez, Jose M ; Brazma, Alvis ; Choudhary, Jyoti S ; Harrow, Jennifer

Nature communications, 2016-06, Vol.7 (1), p.11778-11778, Article 11778 [Periódico revisado por pares]

England: Nature Publishing Group

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6
Evaluation of chloroplast genome annotation tools and application to analysis of the evolution of coffee species
Evaluation of chloroplast genome annotation tools and application to analysis of the evolution of coffee species
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Evaluation of chloroplast genome annotation tools and application to analysis of the evolution of coffee species

Guyeux, Christophe ; Charr, Jean-Claude ; Tran, Hue T M ; Furtado, Agnelo ; Henry, Robert J ; Crouzillat, Dominique ; Guyot, Romain ; Hamon, Perla Chiang, Tzen-Yuh

PloS one, 2019-06, Vol.14 (6), p.e0216347-e0216347 [Periódico revisado por pares]

United States: Public Library of Science

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7
Accurate Transposable Element Annotation Is Vital When Analyzing New Genome Assemblies
Accurate Transposable Element Annotation Is Vital When Analyzing New Genome Assemblies
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Accurate Transposable Element Annotation Is Vital When Analyzing New Genome Assemblies

Platt, 2nd, Roy N ; Blanco-Berdugo, Laura ; Ray, David A

Genome biology and evolution, 2016-02, Vol.8 (2), p.403-410

England: Oxford University Press

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8
Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus
Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus
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Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus

Athanasouli, Marina ; Witte, Hanh ; Weiler, Christian ; Loschko, Tobias ; Eberhardt, Gabi ; Sommer, Ralf J ; Rödelsperger, Christian

BMC genomics, 2020-10, Vol.21 (1), p.708-708, Article 708 [Periódico revisado por pares]

England: BioMed Central Ltd

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9
Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis
Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis
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Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis

Zhu, Yafeng ; Engström, Pär G ; Tellgren-Roth, Christian ; Baudo, Charles D ; Kennell, John C ; Sun, Sheng ; Billmyre, R Blake ; Schröder, Markus S ; Andersson, Anna ; Holm, Tina ; Sigurgeirsson, Benjamin ; Wu, Guangxi ; Sankaranarayanan, Sundar Ram ; Siddharthan, Rahul ; Sanyal, Kaustuv ; Lundeberg, Joakim ; Nystedt, Björn ; Boekhout, Teun ; Dawson, Jr, Thomas L ; Heitman, Joseph ; Scheynius, Annika ; Lehtiö, Janne

Nucleic acids research, 2017-03, Vol.45 (5), p.2629-2643 [Periódico revisado por pares]

England: Oxford University Press

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10
Automated Update, Revision, and Quality Control of the Maize Genome Annotations Using MAKER-P Improves the B73 RefGen_v3 Gene Models and Identifies New Genes
Automated Update, Revision, and Quality Control of the Maize Genome Annotations Using MAKER-P Improves the B73 RefGen_v3 Gene Models and Identifies New Genes
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Automated Update, Revision, and Quality Control of the Maize Genome Annotations Using MAKER-P Improves the B73 RefGen_v3 Gene Models and Identifies New Genes

Law, MeiYee ; Childs, Kevin L. ; Campbell, Michael S. ; Stein, Joshua C. ; Olson, Andrew J. ; Holt, Carson ; Panchy, Nicholas ; Lei, Jikai ; Jiao, Dian ; Andorf, Carson M. ; Lawrence, Carolyn J. ; Ware, Doreen ; Shiu, Shin-Han ; Sun, Yanni ; Jiang, Ning ; Yandell, Mark

Plant physiology (Bethesda), 2015-01, Vol.167 (1), p.25-39 [Periódico revisado por pares]

United States: American Society of Plant Biologists

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