J
Jonathan E. Allen
Researcher at Lawrence Livermore National Laboratory
Publications - 80
Citations - 15880
Jonathan E. Allen is an academic researcher from Lawrence Livermore National Laboratory. The author has contributed to research in topics: Computer science & Biology. The author has an hindex of 26, co-authored 65 publications receiving 13584 citations. Previous affiliations of Jonathan E. Allen include University of Maryland, College Park & J. Craig Venter Institute.
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Journal ArticleDOI
Genome sequence of the human malaria parasite Plasmodium falciparum
Malcolm J. Gardner,Neil Hall,Eula Fung,Owen White,Matthew Berriman,Richard W. Hyman,Jane M. Carlton,Arnab Pain,Karen E. Nelson,Sharen Bowman,Ian T. Paulsen,Keith D. James,Jonathan A. Eisen,Kim Rutherford,Steven L. Salzberg,Alister Craig,Sue Kyes,Man Suen Chan,Vishvanath Nene,Shamira J. Shallom,Bernard B. Suh,Jeremy Peterson,Samuel V. Angiuoli,Mihaela Pertea,Jonathan E. Allen,Jeremy D. Selengut,Daniel H. Haft,Michael W. Mather,Akhil B. Vaidya,David M. A. Martin,Alan H. Fairlamb,Martin Fraunholz,David S. Roos,Stuart A. Ralph,Geoffrey I. McFadden,Leda M. Cummings,G. Mani Subramanian,Christopher J. Mungall,J. Craig Venter,Daniel J. Carucci,Stephen L. Hoffman,Chris I. Newbold,Ronald W. Davis,Claire M. Fraser,Bart Barrell +44 more
TL;DR: The genome sequence of P. falciparum clone 3D7 is reported, which is the most (A + T)-rich genome sequenced to date and is being exploited in the search for new drugs and vaccines to fight malaria.
Journal ArticleDOI
The Transcriptional Landscape of the Mammalian Genome
Piero Carninci,Takeya Kasukawa,Shintaro Katayama,Julian Gough,Martin C. Frith,N. Maeda,Rieko Oyama,Timothy Ravasi,Boris Lenhard,Christine A. Wells,Christine A. Wells,Rimantas Kodzius,Kazuro Shimokawa,Vladimir B. Bajic,Steven E. Brenner,Serge Batalov,Alistair R. R. Forrest,Mihaela Zavolan,Melissa J. Davis,Laurens G. Wilming,Vassilis Aidinis,Jonathan E. Allen,Alberto Ambesi-Impiombato,Rolf Apweiler,Rajith N. Aturaliya,Timothy L. Bailey,Mukesh Bansal,Laura L. Baxter,Kirk W. Beisel,T. Bersano,Hidemasa Bono,Alistair M. Chalk,Kuo Ping Chiu,V. Choudhary,Alan Christoffels,D. R. Clutterbuck,Mark L. Crowe,Emiliano Dalla,Brian P. Dalrymple,Bernard de Bono,G. Della Gatta,Diego di Bernardo,Thomas A. Down,Pär G. Engström,Michela Fagiolini,Geoffrey J. Faulkner,Colin F. Fletcher,T. Fukushima,Masaaki Furuno,Sugiko Futaki,Manuela Gariboldi,P. Georgii-Hemming,Thomas R. Gingeras,Takashi Gojobori,Richard E. Green,Stefano Gustincich,Matthias Harbers,Yoshitaka Hayashi,Takao K. Hensch,Nobutaka Hirokawa,David E. Hill,Lukasz Huminiecki,M. Iacono,Kazuho Ikeo,Atsushi Iwama,T. Ishikawa,M. Jakt,Alexander Kanapin,Masaru Katoh,Yuka Imamura Kawasawa,Janet Kelso,Hiroshi Kitamura,Hiroaki Kitano,George Kollias,S. P. T. Krishnan,Adele Kruger,Sarah K. Kummerfeld,Igor V. Kurochkin,Liana F. Lareau,Dejan Lazarevic,Leonard Lipovich,Jinfeng Liu,Sabino Liuni,Sean McWilliam,M. Madan Babu,Martin Madera,Luigi Marchionni,Hideo Matsuda,Shu-ichi Matsuzawa,Harukata Miki,Flavio Mignone,Sou Miyake,Ken A. Morris,Salim Mottagui-Tabar,Salim Mottagui-Tabar,Nicola Mulder,Naoko Nakano,Hiromitsu Nakauchi,P. Ng,Roland Nilsson,S. Nishiguchi,Seishi Nishikawa,Franco Nori,Osamu Ohara,Yasushi Okazaki,Valerio Orlando,Ken C Pang,William J. Pavan,Giulio Pavesi,Graziano Pesole,Nikolai Petrovsky,Silvano Piazza,Jonathan C. Reed,James F. Reid,Brian Z. Ring,M. Ringwald,Burkhard Rost,Yijun Ruan,Steven L. Salzberg,Albin Sandelin,Claudio Schneider,Christian Schönbach,K. Sekiguchi,Colin A. Semple,Shigeto Seno,Luca Sessa,Y. Sheng,Y. Shibata,Hiroshi Shimada,Kiyo Shimada,D. Silva,B. Sinclair,Silke Sperling,Elia Stupka,Koji Sugiura,Razvan Sultana,Yoichi Takenaka,Kohei Taki,K. Tammoja,Sin Lam Tan,S. Tang,Martin S. Taylor,Jesper Tegnér,Sarah A. Teichmann,Hiroki R. Ueda,Erik van Nimwegen,Roberto Verardo,Chia-Lin Wei,Ken Yagi,H. Yamanishi,E. Zabarovsky,S. Zhu,Andreas Zimmer,Winston Hide,Carol J. Bult,Sean M. Grimmond,Rohan D. Teasdale,Edison T. Liu,Vladimir Brusic,John Quackenbush,Claes Wahlestedt,Claes Wahlestedt,John S. Mattick,David A. Hume,C. Kai,D. Sasaki,Yasuhiro Tomaru,S. Fukuda,Mutsumi Kanamori-Katayama,M. Suzuki,Junken Aoki,Taku Arakawa,J. Iida,Kengo Imamura,Masayoshi Itoh,T. Kato,Hideya Kawaji,N. Kawagashira,Tsugumi Kawashima,M. Kojima,S. Kondo,Hideaki Konno,K. Nakano,Noriko Ninomiya,T. Nishio,M. Okada,Charles Plessy,K. Shibata,Toshiyuki Shiraki,S. Suzuki,Michihira Tagami,Kazunori Waki,Akira Watahiki,Yuko Okamura-Oho,Harukazu Suzuki,Jun Kawai,Yoshihide Hayashizaki,Yoshihide Hayashizaki +197 more
TL;DR: Detailed polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.
Journal ArticleDOI
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
Brian J. Haas,Brian J. Haas,Steven L. Salzberg,Wei Zhu,Mihaela Pertea,Jonathan E. Allen,Jonathan E. Allen,Joshua Orvis,Joshua Orvis,Owen White,Owen White,C. Robin Buell,C. Robin Buell,Jennifer R. Wortman,Jennifer R. Wortman +14 more
TL;DR: In this article, an automated eukaryotic gene structure annotation tool, EVM, is presented as a weighted consensus of all available evidence, combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein coding genes and alternatively spliced isoforms.
Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments
Brian J. Haas,Steven L. Salzberg,Wei Zhu,Mihaela Pertea,Jonathan E. Allen,Joshua Orvis,Owen White,C R Buell,Jennifer R. Wortman +8 more
TL;DR: The experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.
Journal ArticleDOI
Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii
Jane M. Carlton,Samuel V. Angiuoli,Bernard B. Suh,Taco W. A. Kooij,Mihaela Pertea,Joana C. Silva,Maria D. Ermolaeva,Jonathan E. Allen,Jeremy D. Selengut,Hean L. Koo,Jeremy Peterson,Mihai Pop,Daniel S. Kosack,Martin Shumway,Shelby L. Bidwell,Shamira J. Shallom,Susan Van Aken,Steven B. Riedmuller,Tamara Feldblyum,Jennifer Cho,John Quackenbush,Martha Sedegah,Azadeh Shoaibi,Leda M. Cummings,Laurence Florens,John R. Yates,J. Dale Raine,Robert E. Sinden,Michael Harris,Deirdre A. Cunningham,Peter R. Preiser,Lawrence W. Bergman,Akhil B. Vaidya,Leo H.M. van Lin,Chris J. Janse,Andrew P. Waters,Hamilton O. Smith,Owen White,Steven L. Salzberg,J. Craig Venter,Claire M. Fraser,Stephen L. Hoffman,Malcolm J. Gardner,Daniel J. Carucci +43 more
TL;DR: This is the first genome sequence of a model eukaryotic parasite, and it provides insight into the use of such systems in the modelling of Plasmodium biology and disease.