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：Sunjin Moon (1) (12) (2)
Tae-Hun Kim (3)
Kyung-Tai Lee (3)
Woori Kwak (4) (5)
Taeheon Lee (1)
Si-Woo Lee (3)
Myung-Jick Kim (6)
Kyuho Cho (7)
Namshin Kim (8)
Won-Hyong Chung (8)
Samsun Sung (5)
Taesung Park (9)
Seoae Cho (5)
Martien AM Groenen (10)
Rasmus Nielsen (11)
Yuseob Kim (2)
Heebal Kim (1) (4) (5)

1. Department of Agricultural biotechnology ; Seoul National University ; Seoul ; 151-921 ; Republic of Korea
12. Current address ; Department of Genome Sciences ; University of Washington ; Seattle ; WA ; USA
2. Department of Life Science and Division of EcoScience ; Ewha Womans University ; Seoul ; 120-750 ; Republic of Korea
3. Animal Genomics and Bioinformatics Division ; National Institute of Animal Science ; Rural Development Administration ; Suwon ; 441-706 ; Republic of Korea
4. Interdisciplinary Program in Bioinformatics ; Seoul National University ; Seoul ; 151-747 ; Republic of Korea
5. C&K Genomics ; Seoul National University Research Park ; Seoul ; 151-919 ; Republic of Korea
6. Animal Genetic Resources Station ; National Institute of Animal Science ; Rural Development Administration ; Suwon ; 441-706 ; Republic of Korea
7. Swine Science Division ; National Institute of Animal Science ; Rural Development Administration ; Suwon ; 441-706 ; Republic of Korea
8. Korean Bioinformation Center ; Korea Research Institute of Bioscience and Biotechnology ; Daejeon ; 305-806 ; Republic of Korea
9. Department of Statistics ; Seoul National University ; Seoul ; Republic of Korea
10. Animal Breeding and Genomics Centre ; Wageningen University ; De Elst 1 ; 6708 WD ; Wageningen ; The Netherlands
11. Department of Integrative Biology and Department of Statistics ; University of California Berkeley ; Berkeley ; CA ; 94820 ; USA

关键词：Pig ; Domestication ; Selective sweep ; Directional selection ; Quantitative traits

刊名：BMC Genomics

出版年：2015

作者：Sungho Won (1) (2) (3)
Wonji Kim (2)
Sungyoung Lee (2)
Young Lee (4)
Joohon Sung (1) (3)
Taesung Park (2) (5)

1. Department of Public Health Science ; Seoul National University ; Seoul ; Korea
2. Interdisciplinary Program of Bioinformatics ; Seoul National University ; Seoul ; Korea
3. Institute of Health and Environment ; Seoul National University ; Seoul ; Korea
4. The Center for Genome Science ; Korea National Institute of Health ; KCDC ; Osong ; Korea
5. Department of Statistics ; Seoul National University ; Seoul ; Korea

关键词：Family ; based association analysis ; Multiple variants ; Multiple phenotypes

刊名：BMC Bioinformatics

出版年：2015

作者：Bie Verbist (1)
Lieven Clement (2)
Joke Reumers (3)
Kim Thys (3)
Alexander Vapirev (3) (4)
Willem Talloen (3)
Yves Wetzels (3)
Joris Meys (1)
Jeroen Aerssens (3)
Luc Bijnens (3)
Olivier Thas (1) (5)

1. Department of Mathematical Modeling ; Statistics and Bioinformatics ; Ghent University ; Coupure Links 653 ; Gent ; 9000 ; Belgium
2. Department of Applied Mathematics ; Informatics and Statistics ; Ghent University ; Krijgslaan 281 S9 ; Gent ; 9000 ; Belgium
3. Janssen R&D ; Janssen Pharmaceutical Companies of J&J ; Turnhoutseweg 30 ; Beerse ; 2340 ; Belgium
4. ExaScience Life Lab ; Kapeldreef 75 ; Leuven ; 3001 ; Belgium
5. University of Wollongong ; National Institute for Applied Statistics Research Australia (NIASRA) ; School of Mathematics and Applied Statistics ; NSW ; 2522 ; Australia

关键词：Illumina sequencing ; Codon ; Second best base call ; Model ; based clustering ; Viral quasispecies

刊名：BMC Bioinformatics

出版年：2015

作者：Sebastian Kurscheid (1) (16) (2) (3)
Pierre Bady (1) (2) (3) (4)
Davide Sciuscio (1) (2)
Ivana Samarzija (1) (2)
Tal Shay (5)
Irene Vassallo (1) (2)
Wim V Criekinge (6)
Roy T Daniel (1)
Martin J van den Bent (7)
Christine Marosi (8)
Michael Weller (10) (9)
Warren P Mason (11)
Eytan Domany (12)
Roger Stupp (1) (13)
Mauro Delorenzi (14) (15) (3)
Monika E Hegi (1) (2)

1. Neurosurgery ; Lausanne University Hospital ; Lausanne ; 1011 ; Switzerland
16. Present address ; The John Curtin School of Medical Research ; The Australian National University ; Canberra ; ACT 2601 ; Australia
2. Neuroscience Research Center ; Lausanne University Hospital ; Lausanne ; 1011 ; Switzerland
3. Bioinformatics Core Facility ; Swiss Institute for Bioinformatics ; Lausanne ; 1005 ; Switzerland
4. Department of Education and Research ; University of Lausanne ; Lausanne ; 1011 ; Switzerland
5. Ben-Gurion University of the Negev ; Beersheba ; Israel
6. Department of Mathematical Modelling ; Statistics and Bioinformatics ; Ghent University ; Ghent ; Belgium
7. Department of Neurology/Neurooncology ; Erasmus MC Cancer Center ; Rotterdam ; The Netherlands
8. Department of Medicine ; Medical University Vienna ; Vienna ; Austria
10. Department of Neurology ; University Hospital Zurich ; Zurich ; Switzerland
9. Department of Neurology ; University of T眉bingen ; T眉bingen ; Germany
11. Princess Margaret Hospital ; University of Toronto ; Toronto ; Canada
12. Department of Physics of Complex Systems ; Weizmann Institute of Science ; Rehovot ; Israel
13. Department of Oncology ; University Hospital Zurich ; Zurich ; 8091 ; Switzerland
14. Ludwig Center for Cancer Research ; University of Lausanne ; Lausanne ; 1011 ; Switzerland
15. Department of Oncology ; University of Lausanne ; Lausanne ; 1011 ; Switzerland

刊名：Genome Biology

出版年：2015

作者：Xiaowei Wu (1)
Ming-an Sun (2)
Hongxiao Zhu (1)
Hehuang Xie (2) (3)

1. Department of Statistics ; Virginia Tech ; 250 Drillfield Drive ; Blacksburg ; 24061 ; VA ; USA
2. Virginia Bioinformatics Institute ; Virginia Tech ; 1015 Life Science Circle ; Blacksburg ; 24061 ; VA ; USA
3. Department of Biological Sciences ; Virginia Tech ; 1405 Perry Street ; Blacksburg ; 24061 ; VA ; USA

关键词：DNA methylation ; Epigenetics ; Nonparametric Bayesian

刊名：BMC Bioinformatics

出版年：2015

作者：Federico Comoglio (1)
Cem Sievers (1) (2) (3)
Renato Paro (1) (4)

1. Department of Biosystems Science and Engineering ; Swiss Federal Institute of Technology Zurich ; Mattenstrasse 26 ; Basel ; 4058 ; Switzerland
2. Department of Pathology and Center for Cancer Research ; Massachusetts General Hospital and Harvard Medical School ; Boston ; USA
3. Broad Institute of MIT and Harvard ; Cambridge ; USA
4. Faculty of Science ; University of Basel ; Klingelbergstrasse 504056 ; Basel ; Switzerland

关键词：PAR ; CLIP ; RNA ; RNA binding proteins ; Bayesian statistics

刊名：BMC Bioinformatics

出版年：2015

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：Steve Hoffmann (1) (2) (3)
Peter F Stadler (2) (3) (4) (5) (6) (7) (8)
Korbinian Strimmer (10) (9)

1. Junior Research Group Transcriptome Bioinformatics ; University Leipzig ; H盲rtelstra脽e 16-18 ; Leipzig ; Germany
2. Interdisciplinary Center for Bioinformatics and Bioinformatics Group ; University Leipzig ; H盲rtelstra脽e 16-18 ; Leipzig ; Germany
3. LIFE Research Center for Civilization Diseases ; University Leipzig ; H盲rtelstra脽e 16-18 ; Leipzig ; Germany
4. Department of Theoretical Chemistry ; University Vienna ; W盲hringer Stra脽e 17 ; Vienna ; Austria
5. RNomics Group ; Fraunhofer Institute for Cell Therapy and Immunology 鈥?IZI ; Perlickstra脽e 1 ; Leipzig ; Germany
6. Max-Planck-Institute for Mathematics in the Sciences ; Inselstra脽e 22 ; Leipzig ; Germany
7. Center for non-coding RNA in Technology and Health ; University of Copenhagen ; Gr酶nneg氓rdsvej 3 ; Frederiksberg ; Denmark
8. Santa Fe Institute ; 1399 Hyde Park Road ; Santa Fe ; USA
10. Department of Epidemiology and Biostatistics ; Imperial College London ; Norfolk Place ; London W2 1PG ; UK
9. Institute for Medical Informatics ; Statistics and Epidemiology ; University of Leipzig ; H盲rtelstra脽e 16鈥?8 ; Leipzig ; D-04107 ; Germany

刊名：Algorithms for Molecular Biology

出版年：2015

作者：Daniela Ferreira Domingos (1)
Andreia Fonseca de Faria (2)
Renan de Souza Galaverna (3)
Marcos Nogueira Eberlin (3)
Paul Greenfield (4)
Tiago Domingues Zucchi (5)
Itamar Soares Melo (5)
Nai Tran-Dinh (6)
David Midgley (6)
Val茅ria Maia de Oliveira (1)

1. Microbial Resources Division ; Research Center for Chemistry ; Biology and Agriculture (CPQBA) ; University of Campinas (UNICAMP) ; Av. Alexandre Cazelatto ; 999 ; Campinas ; SP ; 13148-218 ; Brazil
2. Department of Chemical and Environmental Engineering ; Yale University ; New Haven ; CT ; 06520-8286 ; USA
3. ThoMSon Mass Spectrometry Laboratory ; Institute of Chemistry ; University of Campinas (UNICAMP) ; Campinas ; SP ; Brazil
4. CSIRO Mathematics ; Informatics and Statistics ; North Ryde ; NSW ; Australia ; 2113
5. Laboratory of Environmental Microbiology ; EMBRAPA Environment ; Jaguari煤na ; S茫o Paulo ; Brazil
6. CSIRO Animal ; Food and Health Sciences ; North Ryde ; NSW ; 2113 ; Australia

关键词：Pumilacidin ; Metabolic pathway ; Chemical characterization ; Surfactant ; Bacillus

刊名：Applied Microbiology and Biotechnology

出版年：2015