Gearing up to handle the mosaic nature of life in the quest for orthologs-Reference-Cited by-同舟云学术

Gearing up to handle the mosaic nature of life in the quest for orthologs

Published:2017-08-30 Issue:2 Volume:34 Page:323-329
ISSN:1367-4803
Container-title:Bioinformatics
language:en
Short-container-title:

Author:

Forslund Kristoffer¹^ORCID,Pereira Cecile²³⁴,Capella-Gutierrez Salvador⁵^ORCID,da Silva Alan Sousa⁶,Altenhoff Adrian⁷⁸,Huerta-Cepas Jaime¹,Muffato Matthieu⁶,Patricio Mateus⁶,Vandepoele Klaas⁹,Ebersberger Ingo¹⁰¹¹,Blake Judith¹²,Fernández Breis Jesualdo Tomás¹³,Boeckmann Brigitte¹⁴,Gabaldón Toni¹⁵¹⁶¹⁷,Sonnhammer Erik¹⁸,Dessimoz Christophe¹⁹²⁰²¹²²²³,Lewis Suzanna²⁴,Altenhoff Adrian,Bello Carla,Blake Judith,Boeckmann Brigitte,Briois Sébastien,Capella-Gutierrez Salvador,Chalstrey Edward,Chiba Hirokazu,Conchillo-Solé Oscar,Daubin Vincent,DeLuca Todd,Dessimoz Christophe,Dufayard Jean-Francois,Durand Dannie,Ebersberger Ingo,Fernández-Breis Jesualdo Tomás,Forslund Kristoffer,Glover Natasha,Hauser Alexander,Heller Davide,Huerta-Cepas Jaime,Kaduk Mateusz,Koch Jan,Koonin Eugene V,Kriventseva Evgenia,Kuraku Shigehiro,Lecompte Odile,Lespinet Olivier,Levy Jeremy,Lewis Suzanna,Liebeskind Benjamin,Linard Benjamin,Marcet-Houben Marina,Martin Maria,McWhite Claire,Mekhedov Sergei,Moretti Sebastien,Muffato Matthieu,Müller Steven,Nadia El-Mabrouk,Notredame Cédric,Patricio Mateus,Penel Simon,Pereira Cécile,Pilizota Ivana,Redestig Henning,Robinson-Rechavi Marc,Schreiber Fabian,Sjölander Kimmen,Škunca Nives,Sonnhammer Erik,da Silva Alan Sousa,Steinegger Martin,Szklarczyk Damian,Thomas Paul,Thuer Ernst,Train Clément,Uchiyama Ikuo,Vandepoele Klaas,Wittwer Lucas,Xenarios Ioannis,Yates Bethan,Zdobnov Evgeny,Waterhouse Robert M, ,

Affiliation:

1. Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany

2. Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida at Gainesville, Gainesville, FL, USA

3. Laboratoire de Recherche en Informatique (LRI)

4. Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette cedex, France

5. Spanish National Bioinformatics Institute (INB), Spanish National Cancer Research Centre, Madrid, Spain

6. European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK

7. Department of Computer Science, ETH Zurich, Zurich, Switzerland

8. Computational Biochemistry Research Group, Swiss Institute of Bioinformatics (SIB), Zurich, Switzerland

9. VIB & Department of Plant Biotechnology and Bioinformatics, Center for Plant Systems Biology, Ghent University, Ghent, Belgium

10. Applied Bioinformatics, Goethe-Universitet Frankfurt, Frankfurt, Germany

11. Senckenberg Climate and Research Center Frankfurt (BIK-F), Frankfurt, Germany

12. Jackson Laboratory, Bar Harbor, ME, USA

13. Faculty of Computer Science, University of Murcia, IMIB-Arrixaca, Murcia, Spain

14. Swiss-Prot Group, Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland

15. Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain

16. Universitat Pompeu Fabra (UPF), Barcelona, Spain

17. Institució Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Spain

18. Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm Bioinformatics Center, Stockholm University, Solna, Sweden

19. Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland

20. Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland

21. Department of Genetics, Evolution, and Environment, University College London, London, UK

22. Department Computer Science, University College London, London, UK

23. Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland

24. Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA

Funder

European Research Council

National Institutes of Health

NIH

Swiss National Science Foundation

Wellcome Trust

Publisher

Oxford University Press (OUP)

Subject

Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability

Link

http://academic.oup.com/bioinformatics/article-pdf/34/2/323/25170769/btx542.pdf

Reference28 articles.

1. The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements;Altenhoff;Nucleic Acids Res,2014

2. Standardized benchmarking in the quest for orthologs;Altenhoff;Nat. Methods,2016

3. Quest for orthologs entails quest for tree of life: in search of the gene stream;Boeckmann;Genome Biol. Evol,2015

4. TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction;Chang;Nucleic Acids Res,2015

5. The NCBI Taxonomy database;Federhen;Nucleic Acids Res,2011

Cited by 28 articles. 订阅此论文施引文献订阅此论文施引文献，注册后可以免费订阅5篇论文的施引文献，订阅后可以查看论文全部施引文献

1. The interkingdom horizontal gene transfer in 44 early diverging fungi boosted their metabolic, adaptive, and immune capabilities;Evolution Letters;2024-03-05

2. NeMu: A Comprehensive Pipeline for Accurate Reconstruction of Neutral Mutation Spectra from Evolutionary Data;2023-12-14

3. Real or fake? Measuring the impact of protein annotation errors on estimates of domain gain and loss events;Frontiers in Bioinformatics;2023-04-20

4. The Quest for Orthologs orthology benchmark service in 2022;Nucleic Acids Research;2022-05-12

5. Chromosome‐level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long‐reads, linked‐reads and Hi‐C;Molecular Ecology Resources;2022-01-11