T
Timothy L. Bailey
Researcher at University of Nevada, Reno
Publications - 165
Citations - 42616
Timothy L. Bailey is an academic researcher from University of Nevada, Reno. The author has contributed to research in topics: Sequence motif & Internal medicine. The author has an hindex of 59, co-authored 147 publications receiving 35797 citations. Previous affiliations of Timothy L. Bailey include University of Washington & University of California, San Diego.
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Journal ArticleDOI
MEME Suite: tools for motif discovery and searching
Timothy L. Bailey,Mikael Bodén,Fabian A. Buske,Martin C. Frith,Charles E. Grant,Luca Clementi,Jingyuan Ren,Wilfred W. Li,William Stafford Noble +8 more
TL;DR: The popular MEME motif discovery algorithm is now complemented by the GLAM2 algorithm which allows discovery of motifs containing gaps, and all of the motif-based tools are now implemented as web services via Opal.
Proceedings Article
Fitting a mixture model by expectation maximization to discover motifs in biopolymers.
Timothy L. Bailey,Charles Elkan +1 more
TL;DR: The algorithm described in this paper discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences.
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
FIMO: scanning for occurrences of a given motif.
TL;DR: Find Individual Motif Occurrences (FIMO), a software tool for scanning DNA or protein sequences with motifs described as position-specific scoring matrices, and provides output in a variety of formats, including HTML, XML and several Santa Cruz Genome Browser formats.
Journal ArticleDOI
MEME: discovering and analyzing DNA and protein sequence motifs
TL;DR: The freely accessible web server and its architecture are described, and ways to use MEME effectively to find new sequence patterns in biological sequences and analyze their significance are discussed.