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：Dirk Helbing (1) (2)
Dirk Brockmann (3) (4)
Thomas Chadefaux (1)
Karsten Donnay (1)
Ulf Blanke (5)
Olivia Woolley-Meza (1)
Mehdi Moussaid (6)
Anders Johansson (7) (8)
Jens Krause (9)
Sebastian Schutte (10)
Matja啪 Perc (11)

1. ETH Zurich ; Swiss Federal Institute of Technology ; 8092 ; Zurich ; Switzerland
2. Risk Center ; ETH Zurich ; Swiss Federal Institute of Technology ; 8092聽 ; Zurich ; Switzerland
3. Robert Koch-Institute ; 13353聽 ; Berlin ; Germany
4. Institute for Theoretical Biology ; Humboldt-University ; 10115聽 ; Berlin ; Germany
5. Wearable Computing Laboratory ; ETH Zurich ; Swiss Federal Institute of Technology ; 8092 ; Zurich ; Switzerland
6. Center for Adaptive Rationality (ARC) ; Max Planck Institute for Human Development ; 14195 ; Berlin ; Germany
7. Centre for Advanced Spatial Analysis ; University College London ; London ; W1T 4TJ ; UK
8. Systems Centre ; Department of Civil Engineering ; University of Bristol ; Bristol ; BS8 1UB ; UK
9. Department of Biology and Ecology of Fishes ; Leibniz-Institute of Freshwater Ecology and Inland Fisheries ; 12587 ; Berlin ; Germany
10. Center for Comparative and International Studies ; ETH Zurich ; Swiss Federal Institute of Technology ; 8092 ; Zurich ; Switzerland
11. Faculty of Natural Sciences and Mathematics ; University of Maribor ; 2000 ; Maribor ; Slovenia

关键词：Crowd disasters ; Crime ; Terrorism ; War ; Disease spreading ; Complexity science

刊名：Journal of Statistical Physics

出版年：2015

作者：Girolamo Fiorentino (1)
Juan Pedro Ferrio (2)
Amy Bogaard (3)
Jos茅 Luis Araus (4)
Simone Riehl (5)

1. Laboratory of Archaeobotany and Palaeoecology ; University of Salento ; Lecce ; Italy
2. Department of Crop and Forest Science-AGROTECNIO Center ; University of Lleida ; Lleida ; Spain
3. School of Archaeology ; University of Oxford ; Oxford ; Great Britain
4. Department of Plant Biology ; University of Barcelona ; Barcelona ; Spain
5. Institute for Archaeological Science and Senckenberg Research Center for Human Evolution and Palaeoecology ; University of T眉bingen ; Tubingen ; Germany

关键词：Stable isotopes ; Archaeobotany ; Seeds ; Charcoal

刊名：Vegetation History and Archaeobotany

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：Fabian Amman (30) (31)
Michael T Wolfinger (31) (32) (33)
Ronny Lorenz (31)
Ivo L Hofacker (31) (34) (38)
Peter F Stadler (30) (31) (34) (35) (36) (37)
Sven Findei脽 (31) (38)

30. Bioinformatics Group ; Department of Computer Science and the Interdisciplinary Center for Bioinformatic ; University of Leipzig ; H盲rtelstra脽e 16鈥?8 ; 04107 ; Leipzig ; Germany
31. Institute for Theoretical Chemistry ; University of Vienna ; W盲hringerstra脽e 17 ; 1090 ; Vienna ; Austria
32. Center for Integrative Bioinformatics Vienna (CIBIV) ; Max F. Perutz Laboratories ; University of Vienna ; Medical University of Vienna ; Dr. Bohr-Gasse 9 ; 1030 ; Vienna ; Austria
33. Department of Biochemistry and Molecular Cell Biology ; Max F. Perutz Laboratories ; University of Vienna ; Dr. Bohr-Gasse 9 ; 1030 ; Vienna ; Austria
34. Center for RNA in Technology and Health ; University of Copenhagen ; Gr酶nneg氓rdsvej 3 ; Frederiksberg C ; Denmark
38. Research group Bioinformatics and Computational Biology ; Faculty of Computer Science ; University of Vienna ; W盲hringerstra脽e 29 ; 1090 ; Vienna ; Austria
35. Max Planck Institute for Mathematics in the Sciences ; Inselstra脽e 22 ; D-04103 ; Leipzig ; Germany
36. Fraunhofer Institute for Cell Therapy and Immunology ; Perlickstra脽e 1 ; D-04103 ; Leipzig ; Germany
37. Santa Fe Institute ; 1399 Hyde Park Road ; Santa Fe NM ; 87501 ; USA

关键词：Differential RNA sequencing ; dRNA ; seq ; TSS ; Transcription start site annotation ; Transcriptome ; RESTful Web service ; Next generation sequencing

刊名：BMC Bioinformatics

出版年：2014

作者：Nils Rosjat (1)
Svitlana Popovych (1)
Silvia Daun-Gruhn (1)

1. Heisenberg Research Group of Computational Biology ; Department of Animal Physiology ; Institute of Zoology ; University of Cologne ; Z眉lpicher Str. 47b ; 50674 ; Cologne ; Germany

关键词：Mathematical modeling ; Phase oscillators ; EEG ; Synchronization

刊名：Theoretical Biology and Medical Modelling

出版年：2014

作者：Philipp Erdrich (1)
Henning Knoop (2)
Ralf Steuer (2)
Steffen Klamt (1)

1. Max Planck Institute for Dynamics of Complex Technical Systems ; Sandtorstra脽e 1 ; Magdeburg ; 39106 ; Germany
2. Humboldt-University of Berlin ; Institute for Theoretical Biology ; Invalidenstra脽e 43 ; Berlin ; 10115 ; Germany

关键词：Biofuels ; Metabolic engineering ; Cyanobacteria ; Minimal cut sets ; Photosynthesis ; Synechocystis sp. PCC 6803

刊名：Microbial Cell Factories

出版年：2014

作者：Robert Lanfear (10) (9)
Brett Calcott (7)
David Kainer (9)
Christoph Mayer (8)
Alexandros Stamatakis (10) (9)

10. Karlsruhe Institute of Technology ; Institute for Theoretical Informatics ; Postfach 6980 ; 76128 ; Karlsruhe ; Germany
9. The Exelixis Lab ; Scientific Computing Group ; Heidelberg Institute for Theoretical Studies ; Heidelberg ; Germany
7. Philosophy Program ; Research School of Social Sciences ; Australian National University ; Canberra ; ACT ; Australia
8. Zoologisches Forschungsmuseum Alexander Koenig ; Bonn ; Germany

关键词：Model selection ; Partitioning ; Partitionfinder ; BIC ; AICc ; AIC ; Phylogenetics ; Phylogenomics ; Clustering ; Hierarchical clustering

刊名：BMC Evolutionary Biology

出版年：2014

作者：Rosario M Piro (1) (2) (6)
Stefan Wiesberg (3)
Gunnar Schramm (1) (2)
Nico Rebel (3)
Marcus Oswald (1) (4) (5)
Roland Eils (1) (2)
Gerhard Reinelt (3)
Rainer K枚nig (1) (4) (5)

1. Division of Theoretical Bioinformatics ; German Cancer Research Center (Deutsches Krebsforschungszentrum ; DKFZ) ; Heidelberg ; Germany
2. Department of Bioinformatics and Functional Genomics ; Institute of Pharmacy and Molecular Biotechnology ; BioQuant ; University of Heidelberg ; Heidelberg ; Germany
6. German Consortium for Translational Cancer Research (DKTK) and Division of Molecular Genetics ; German Cancer Research Center (Deutsches Krebsforschungszentrum ; DKFZ) ; Heidelberg ; Germany
3. Institute of Computer Science and Interdisciplinary Center for Scientific Computing ; University of Heidelberg ; Heidelberg ; Germany
4. Center for Sepsis Control and Care ; University Hospital Jena ; Jena ; Germany
5. Hans-Kn枚ll-Institute (HKI) ; Jena ; Germany

关键词：Pathway analysis ; Network topology ; Pathway networks ; Gene expression

刊名：BMC Systems Biology

出版年：2014

作者：Sibylle Schirm (1) (2)
Christoph Engel (1)
Markus Loeffler (1)
Markus Scholz (1) (2)

1. Institute for Medical Informatics ; Statistics and Epidemiology ; University of Leipzig ; Leipzig ; Germany
2. LIFE Research Center of Civilization Diseases ; University of Leipzig ; Leipzig ; Germany

关键词：Leucopenia ; Anaemia ; G ; CSF ; EPO ; Filgrastim ; Pegfilgrastim ; Darbepoetin

刊名：Theoretical Biology and Medical Modelling

出版年：2014