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Natalie D. Fedorova
Researcher at J. Craig Venter Institute
Publications - 43
Citations - 14165
Natalie D. Fedorova is an academic researcher from J. Craig Venter Institute. The author has contributed to research in topics: Aspergillus fumigatus & Genome. The author has an hindex of 30, co-authored 43 publications receiving 13137 citations. Previous affiliations of Natalie D. Fedorova include Baylor College of Medicine & National Institutes of Health.
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Journal ArticleDOI
The COG database: an updated version includes eukaryotes
Roman L. Tatusov,Natalie D. Fedorova,John D. Jackson,Aviva R. Jacobs,Boris Kiryutin,Eugene V. Koonin,Dmitri M. Krylov,Raja Mazumder,Sergei L. Mekhedov,Anastasia N. Nikolskaya,B Sridhar Rao,Sergei Smirnov,Alexander V. Sverdlov,Sona Vasudevan,Yuri I. Wolf,Jodie J. Yin,Darren A. Natale +16 more
TL;DR: A major update of the previously developed system for delineation of Clusters of Orthologous Groups of proteins (COGs) from the sequenced genomes of prokaryotes and unicellular eukaryotes is described and is expected to be a useful platform for functional annotation of newlysequenced genomes, including those of complex eukARYotes, and genome-wide evolutionary studies.
Journal ArticleDOI
The COG database: new developments in phylogenetic classification of proteins from complete genomes
Roman L. Tatusov,Darren A. Natale,Igor Garkavtsev,Tatiana Tatusova,Uma Shankavaram,Bachoti S. Rao,Boris Kiryutin,Michael Y. Galperin,Natalie D. Fedorova,Eugene V. Koonin +9 more
TL;DR: The new features added to the COG database include information pages with structural and functional details on each COG and literature references, improvements of the COGNITOR program that is used to fit new proteins into the COGs, and classification of genomes and COGs constructed by using principal component analysis.
Journal ArticleDOI
Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus
William C. Nierman,William C. Nierman,Arnab Pain,Michael J. Anderson,Jennifer R. Wortman,Jennifer R. Wortman,H. Stanley Kim,H. Stanley Kim,Javier Arroyo,Matthew Berriman,Keietsu Abe,David B. Archer,Clara Bermejo,Joan W. Bennett,Paul Bowyer,Dan Chen,Dan Chen,Matthew Collins,Richard Coulsen,Robert L. Davies,Paul S. Dyer,Mark L. Farman,Nadia Fedorova,Nadia Fedorova,Natalie D. Fedorova,Natalie D. Fedorova,T. Feldblyum,T. Feldblyum,Reinhard Fischer,Nigel Fosker,Audrey Fraser,José Luis García,María Josefa Marcos García,Ariette Goble,Gustavo H. Goldman,Katsuya Gomi,Sam Griffith-Jones,R. Gwilliam,Brian J. Haas,Brian J. Haas,Hubertus Haas,David Harris,H. Horiuchi,Jiaqi Huang,Jiaqi Huang,Sean Humphray,Javier Jiménez,Nancy P. Keller,H. Khouri,H. Khouri,Katsuhiko Kitamoto,Tetsuo Kobayashi,Sven Konzack,Resham Kulkarni,Resham Kulkarni,Toshitaka Kumagai,Anne Lafton,Jean-Paul Latgé,Weixi Li,Angela Lord,Charles Lu,Charles Lu,William H. Majoros,William H. Majoros,Gregory S. May,Bruce L. Miller,Yasmin Ali Mohamoud,Yasmin Ali Mohamoud,María Molina,Michel Monod,Isabelle Mouyna,Stephanie Mulligan,Stephanie Mulligan,Lee Murphy,Susan O'Neil,Ian T. Paulsen,Ian T. Paulsen,Miguel A. Peñalva,Mihaela Pertea,Mihaela Pertea,Claire Price,Bethan L. Pritchard,Michael A. Quail,Ester Rabbinowitsch,Neil Rawlins,Marie Adele Rajandream,Utz Reichard,Hubert Renauld,Geoffrey D. Robson,Santiago Rodríguez de Córdoba,José Manuel Rodríguez-Peña,Catherine M. Ronning,Catherine M. Ronning,Simon Rutter,Steven L. Salzberg,Steven L. Salzberg,Miguel del Nogal Sánchez,Juan C. Sánchez-Ferrero,David L. Saunders,Kathy Seeger,Rob Squares,S. Squares,Michio Takeuchi,Fredj Tekaia,Geoffrey Turner,Carlos R. Vázquez de Aldana,J. Weidman,J. Weidman,Owen White,Owen White,John Woodward,Jae-Hyuk Yu,Claire M. Fraser,Claire M. Fraser,James E. Galagan,Kiyoshi Asai,Masayuki Machida,Neil Hall,Neil Hall,Bart Barrell,David W. Denning +120 more
TL;DR: The Af293 genome sequence provides an unparalleled resource for the future understanding of this remarkable fungus and revealed temperature-dependent expression of distinct sets of genes, as well as 700 A. fumigatus genes not present or significantly diverged in the closely related sexual species Neosartorya fischeri, many of which may have roles in the pathogenicity phenotype.
Journal ArticleDOI
Genome sequencing and analysis of Aspergillus oryzae
Masayuki Machida,Kiyoshi Asai,Motoaki Sano,Toshihiro Tanaka,Toshitaka Kumagai,Goro Terai,Goro Terai,Ken Ichi Kusumoto,Toshihide Arima,Osamu Akita,Yutaka Kashiwagi,Keietsu Abe,Katsuya Gomi,Hiroyuki Horiuchi,Katsuhiko Kitamoto,Tetsuo Kobayashi,Michio Takeuchi,David W. Denning,James E. Galagan,William C. Nierman,Jiujiang Yu,David B. Archer,Joan W. Bennett,Deepak Bhatnagar,Thomas E. Cleveland,Natalie D. Fedorova,Osamu Gotoh,Hiroshi Horikawa,Akira Hosoyama,Masayuki Ichinomiya,Rie Igarashi,Kazuhiro Iwashita,Praveen R. Juvvadi,Masashi Kato,Yumiko Kato,Taishin Kin,Akira Kokubun,Hiroshi Maeda,Noriko Maeyama,Jun-ichi Maruyama,Hideki Nagasaki,Tasuku Nakajima,Ken Oda,Kinya Okada,Ian T. Paulsen,Kazutoshi Sakamoto,Toshihiko Sawano,Mikio Takahashi,Kumiko Takase,Yasunobu Terabayashi,Jennifer R. Wortman,Osamu Yamada,Youhei Yamagata,Hideharu Anazawa,Yoji Hata,Yoshinao Koide,Takashi Komori,Yasuji Koyama,Toshitaka Minetoki,Sivasundaram Suharnan,Akimitsu Tanaka,Katsumi Isono,Satoru Kuhara,Naotake Ogasawara,Hisashi Kikuchi +64 more
TL;DR: Specific expansion of genes for secretory hydrolytic enzymes, amino acid metabolism and amino acid/sugar uptake transporters supports the idea that A. oryzae is an ideal microorganism for fermentation.
Journal ArticleDOI
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes
Eugene V. Koonin,Natalie D. Fedorova,John D. Jackson,Aviva R. Jacobs,Dmitri M. Krylov,Kira S. Makarova,Raja Mazumder,Raja Mazumder,Sergei L. Mekhedov,Anastasia N. Nikolskaya,B Sridhar Rao,Igor B. Rogozin,Sergei Smirnov,Alexander V. Sorokin,Alexander V. Sverdlov,Sona Vasudevan,Yuri I. Wolf,Jodie J. Yin,Darren A. Natale,Darren A. Natale +19 more
TL;DR: Functional and evolutionary patterns in the recently constructed set of 5,873 clusters of predicted orthologs (eukaryotic orthologous groups or KOGs) from seven eukaryosis genomes are examined, revealing a conserved core of largely essential eukARYotic genes as well as major diversification and innovation associated with evolution of eUKaryotic genomes.