作者：Josep Basha Gutierrez (20)
Martin Frith (21)
Kenta Nakai (22)

20. Department of Medical Bioinformatics ; Graduate School of Frontier Sciences ; The University of Tokyo ; 5-1-5 Kashiwanoha ; Kashiwa-shi ; Chiba-ken ; 277-8561 ; Japan
21. Computational Biology Research Center ; AIST Tokyo Waterfront Bio-IT Research Building ; 2-4-7 Aomi ; Koto-ku ; Tokyo ; 135-0064 ; Japan
22. Human Genome Center ; The Institute of Medical Science ; The University of Tokyo ; 4-6-1 Shirokane-dai ; Minato-ku ; Tokyo ; 108-8639 ; Japan

关键词：Motif finding ; Genetic Algorithm ; Transcription Factor Binding Site ; Statistical significance

刊名：Lecture Notes in Computer Science

出版年：2015

作者：Koki Tsuyuzaki (1) (5)
Gota Morota (2) (3)
Manabu Ishii (5)
Takeru Nakazato (4)
Satoru Miyazaki (1)
Itoshi Nikaido (5)

1. Department of Medical and Life Science ; Faculty of Pharmaceutical Science ; Tokyo University of Science ; 2641 Yamazaki ; Noda ; 278-8510 ; Chiba ; Japan
5. Bioinformatics Research Unit ; Advanced Center for Computing and Communication ; RIKEN ; 2-1 Hirosawa ; Wako ; 351-0198 ; Saitama ; Japan
2. Department of Animal Science ; University of Nebraska-Lincoln ; Lincoln ; NE ; USA
3. Department of Animal Sciences ; University of Wisconsin-Madison ; Madison ; WI ; USA
4. Database Center for Life Science (DBCLS) ; Research Organization of Information and Systems (ROIS) ; Faculty of Engineering Building 12 ; The University of Tokyo ; 2-11-16 Yayoi ; Bunkyo-ku ; 113-0032 ; Tokyo ; Japan

关键词：MeSH ; Over ; representation analysis ; Enrichment analysis ; Annotation

刊名：BMC Bioinformatics

出版年：2015

作者：Takanori Hasegawa (1)
Tomoya Mori (1)
Rui Yamaguchi (2)
Teppei Shimamura (3)
Satoru Miyano (2)
Seiya Imoto (2)
Tatsuya Akutsu (1)

1. Bioinformatics Center ; Institute for Chemical Research ; Kyoto University ; Gokasho ; Kyoto ; 611-0011 Uji ; Japan
2. Human Genome Center ; The Institute of Medical Science ; The University of Tokyo ; 4-6-1 Shirokanedai ; Tokyo ; 108-8639 Minato-ku ; Japan
3. Division of Systems Biology ; Nagoya University Graduate School of Medicine ; 65 Tsurumai-cho ; Nagoya ; 466-8550 Showa-ku ; Japan

关键词：Gene regulatory networks ; Time series analysis ; Systems biology ; Data assimilation ; Monte Carlo

刊名：BMC Systems Biology

出版年：2015

作者：Yu-Cheng T Yang (1)
Chao Di (1)
Boqin Hu (1)
Meifeng Zhou (1)
Yifang Liu (1)
Nanxi Song (1)
Yang Li (1)
Jumpei Umetsu (1) (2)
Zhi John Lu (1)

1. MOE Key Laboratory of Bioinformatics ; Center for Synthetic and Systems Biology and Center for Plant Biology ; School of Life Sciences ; Tsinghua University ; Beijing ; 100084 ; China
2. Department of Biological Information ; Tokyo Institute of Technology ; Tokyo ; 152-8850 ; Japan

关键词：CLIP ; seq ; RNA ; binding protein ; RNA ; Regulatory networks ; Data integration

刊名：BMC Genomics

出版年：2015

作者：Erich D Jarvis (1)
Siavash Mirarab (2)
Andre J Aberer (3)
Bo Li (4) (5) (6)
Peter Houde (7)
Cai Li (4) (6)
Simon Y W Ho (8)
Brant C Faircloth (10) (9)
Benoit Nabholz (11)
Jason T Howard (1)
Alexander Suh (12)
Claudia C Weber (12)
Rute R da Fonseca (6)
Alonzo Alfaro-N煤帽ez (6)
Nitish Narula (13) (7)
Liang Liu (14)
Dave Burt (15)
Hans Ellegren (12)
Scott V Edwards (16)
Alexandros Stamatakis (17) (3)
David P Mindell (18)
Joel Cracraft (19)
Edward L Braun (20)
Tandy Warnow (2)
Wang Jun (21) (22) (23) (24) (4)
M Thomas Pius Gilbert (25) (6)
Guojie Zhang (26) (4)
The Avian Phylogenomics Consortium

1. Department of Neurobiology ; Howard Hughes Medical Institute and Duke University Medical Center ; Durham ; NC ; 27710 ; USA
2. Department of Computer Science ; The University of Texas at Austin ; Austin ; TX ; 78712 ; USA
3. Scientific Computing Group ; Heidelberg Institute for Theoretical Studies ; Heidelberg ; Germany
4. China National GeneBank ; BGI-Shenzhen ; Shenzhen ; 518083 ; China
5. College of Medicine and Forensics ; Xi鈥檃n Jiaotong University ; Xi鈥檃n ; 710061 ; China
6. Centre for GeoGenetics ; Natural History Museum of Denmark ; University of Copenhagen ; 脴ster Voldgade 5-7 ; 1350 ; Copenhagen ; Denmark
7. Department of Biology ; New Mexico State University ; Las Cruces ; NM ; 88003 ; USA
8. School of Biological Sciences ; University of Sydney ; Sydney ; NSW ; 2006 ; Australia
10. Department of Biological Sciences ; Louisiana State University ; Baton Rouge ; LA ; 70803 ; USA
9. Department of Ecology and Evolutionary Biology ; University of California Los Angeles ; Los Angeles ; CA ; 90095 ; USA
11. CNRS UMR 5554 ; Institut des Sciences de l鈥橢volution de Montpellier ; Universit茅 Montpellier II ; Montpellier ; France
12. Department of Evolutionary Biology ; Uppsala University ; SE-752 36 ; Uppsala ; Sweden
13. Biodiversity and Biocomplexity Unit ; Okinawa Institute of Science and Technology Onna-son ; Okinawa ; 904-0495 ; Japan
14. Department of Statistics and Institute of Bioinformatics ; University of Georgia ; Athens ; 30602 ; USA
15. Department of Genomics and Genetics ; The Roslin Institute and Royal (Dick) School of Veterinary Studies ; University of Edinburgh ; Easter Bush Campus ; Midlothian ; EH25 9RG ; UK
16. Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology ; Harvard University ; Cambridge ; MA ; USA
17. Institute of Theoretical Informatics ; Department of Informatics ; Karlsruhe Institute of Technology ; D- 76131 ; Karlsruhe ; Germany
18. Department of Biochemistry & Biophysics ; University of California ; San Francisco ; CA ; 94158 ; USA
19. Department of Ornithology ; American Museum of Natural History ; New York ; NY ; 10024 ; USA
20. Department of Biology and Genetics Institute ; University of Florida ; Gainesville ; FL ; 32611 ; USA
21. Department of Biology ; University of Copenhagen ; Ole Maal酶es Vej 5 ; 2200 ; Copenhagen ; Denmark
22. Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders ; King Abdulaziz University ; Jeddah ; 21589 ; Saudi Arabia
23. Macau University of Science and Technology ; Avenida Wai long ; Taipa ; Macau ; 999078 ; China
24. Department of Medicine ; University of Hong Kong ; Hong Kong ; Hong Kong
25. Trace and Environmental DNA Laboratory Department of Environment and Agriculture ; Curtin University ; Perth ; WA ; 6102 ; Australia
26. Centre for Social Evolution ; Department of Biology ; Universitetsparken 15 ; University of Copenhagen ; DK-2100 ; Copenhagen ; Denmark

关键词：Avian genomes ; Phylogenomics ; Sequence alignments ; Species tree ; Gene trees ; Indels ; Transposable elements

刊名：GigaScience

出版年：2015

作者：Marie JJ Huysman (1) (2) (3) (4)
Atsuko Tanaka (4) (5)
Chris Bowler (4)
Wim Vyverman (3)
Lieven De Veylder (1) (2)

1. Department of Plant Systems Biology ; Flanders Institute for Biotechnology (VIB) ; 9052 ; Ghent ; Belgium
2. Department of Plant Systems Biology ; VIB ; and Bioinformatics ; Ghent University ; 9052 ; Ghent ; Belgium
3. Protistology and Aquatic Ecology ; Department of Biology ; Ghent University ; 9000 ; Ghent ; Belgium
4. Environmental and Evolutionary Genomics Section ; Institut de Biologie de l鈥橢cole Normale Sup茅rieure ; Centre National de la Recherche Scientifique ; Unit茅 Mixte de Recherche 8186 ; Institut National de la Sant茅 et de la Recherche M茅dicale U1024 ; Ecole Normale Sup茅rieure ; 75230 ; Paris ; Cedex 05 ; France
5. Current address ; Muroran Marine Station ; Field Science Center for Northern Biosphere ; Hokkaido University ; Muroran ; Hokkaido ; 051-0013 ; Japan

关键词：Cyclin ; dependent kinase ; CDKA2 ; Cell cycle ; Cell division ; Cytokinesis ; Diatom ; Mitosis ; Phaeodactylum tricornutum

刊名：BMC Plant Biology

出版年：2015

作者：Timo Lassmann (1) (2)

1. RIKEN Center for Life Science Technologies (CLST) ; RIKEN Yokohama Institute ; 1-7-22 Suehiro-cho ; Tsurumi-ku ; Yokohama ; 230-0045 ; Kanagawa ; Japan
2. Telethon Kids Institute ; The University of Western Australia ; 100 Roberts Road ; Subiaco ; Subiaco ; 6008 ; Western Australia ; Australia

关键词：Next generation sequencing ; TagDust

刊名：BMC Bioinformatics

出版年：2015

作者：Keisuke Ueno (1)
Akihiro Ishii (2)
Kimihito Ito (1)

1. Division of Bioinformatics ; Research Center for Zoonosis Control ; Hokkaido University ; Sapporo ; Hokkaido ; 001-0020 ; Japan
2. Hokudai Center for Zoonosis Control in Zambia ; Research Center for Zoonosis Control ; Hokkaido University ; Sapporo ; Hokkaido ; 001-0020 ; Japan

关键词：Next generation sequencing ; Virus discovery ; Diagnostic virology ; Virome ; Taxonomic identification

刊名：BMC Bioinformatics

出版年：2014

作者：Jun-ichi Satoh (13)
Nobutaka Motohashi (14)
Yoshihiro Kino (13)
Tsuyoshi Ishida (15)
Saburo Yagishita (16)
Kenji Jinnai (17)
Nobutaka Arai (18)
Kiyotaka Nakamagoe (19)
Akira Tamaoka (19)
Yuko Saito (20)
Kunimasa Arima (21)

13. Department of Bioinformatics and Molecular Neuropathology ; Meiji Pharmaceutical University ; Tokyo ; Japan
14. Department of Psychiatry ; University of Yamanashi ; Faculty of Medicine ; Yamanashi ; Japan
15. Department of Pathology and Laboratory Medicine ; Kohnodai Hospital ; National Center for Global Health and Medicine ; Chiba ; Japan
16. Department of Pathology ; Kanagawa Rehabilitation Center ; Kanagawa ; Japan
17. Department of Neurology ; NHO Hyogo-Chuo Hospital ; Hyogo ; Japan
18. Brain Pathology Research Center ; Tokyo Metropolitan Institute of Medical Science ; Tokyo ; Japan
19. Department of Neurology ; Institute of Clinical Medicine ; University of Tsukuba ; Ibaraki ; Japan
20. Department of Laboratory Medicine ; National Center Hospital ; NCNP ; Tokyo ; Japan
21. Department of Psychiatry ; National Center Hospital ; NCNP ; Tokyo ; Japan

关键词：Autophagy ; LC3 ; Leukoencephalopathy ; Nasu ; Hakola disease ; Oligodendrocytes

刊名：Orphanet Journal of Rare Diseases

出版年：2014

作者：Masaki Suzuki (1)
Hiroshi Nagamochi (1)
Tatsuya Akutsu (2)

1. Department of Applied Mathematics and Physics ; Graduate School of Informatics ; Kyoto University Yoshida ; 606-8501 ; Kyoto ; Japan
2. Bioinformatics Center ; Institute for Chemical Research ; Kyoto University ; Gokasho ; Uji ; 611-0011 ; Kyoto ; Japan

关键词：Chemical graphs ; Enumeration ; Monocyclic structure ; Feature vector

刊名：Journal of Cheminformatics

出版年：2014