National Institute for Basic Biology
| Organizers | Ikuo Uchiyama (NIBB) Christophe Dessimoz (UNIL) Toni Gabaldón Estevan (CRG) Erik Sonnhammer (SU) Paul D. Thomas (USC) Wataru Iwasaki (UTokyo) Shigehiro Kuraku (RIKEN BDR) Shuji Shigenobu (NIBB) |
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| Venue | Okazaki Conference Center, Okazaki, Japan |
| Date | Jul. 31-Aug. 2, 2019 |
| Link | Official Website （http://www.nibb.ac.jp/conf67/） |
| Poster |
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The 67th NIBB conference “Quest for Orthologs” was held with a focus on orthology analysis as a fundamental technology in the field of comparative genomics, which is becoming more important as genomic technology is applied to a broader range of organisms. This meeting originated from the international consortium of the same name “Quest for Orthologs,” which was established in 2009 by developers of orthology inference methods. Since then, the consortium has held a meeting biennially to discuss common subjects in the development of orthology inference methods such as benchmark tests for evaluating methods, a reference sequence set commonly used as input, and a common data format to represent orthology relationships, in addition to presenting the latest results from this field. This meeting, which marked the tenth anniversary of these events being conducted, was held in Japan. This made it the first time that it had been held outside of Europe and United States, and about a half of the participants were from local institutions. As a part of the NIBB conference series, application of orthology inference methods to gene function predictions and/or evolutionary studies with application to biological studies using various organisms in mind were also featured in this meeting,.
| Program | |
| July 31 (Wed) at the Okazaki Conference Center (OCC) | |
| Optional Session | |
| 10:00 - 12:00 | QfO Consortium Session I: Working Group Update |
| 12:00 - 13:00 | Registration |
| Opening Remarks | |
| 13:00 - 13:05 | Naoto Ueno (Vice-Director General, National Institute for Basic Biology, Japan) |
| 13:05 - 13:10 | Ikuo Uchiyama (National Institute for Basic Biology, Japan) |
| Session 1 | |
| 13:10 - 13:35 | "Quest for Orthologs at 10 years" |
| Christophe Dessimoz (University of Lausanne, Switzerland) | |
| 13:35 - 14:00 | "InParanoid improvements and spin-offs" |
| Erik Sonnhammer (Stockholm University, Sweden) | |
| 14:00 - 14:25 | "Ortholog Finder: A Tool for Constructing an Ortholog Data Set for phylogenetic analysis" |
| Tokumasa Horiike (Shizuoka University, Japan) | |
| 14:25 - 14:40 | "A genetic algorithm for refining orthology determinations" |
| Madison Hansen (American Museum of Natural History, USA) | |
| 14:40 - 15:10 | Coffee Break |
| 15:10 - 15:45 | "OrthoFinder: phylogenetic orthology inference for comparative genomics" |
| Steven Kelly (University of Oxford, UK) | |
| 15:45 - 16:10 | "Orthology predictions at scale in Ensembl" |
| Mateus Patricio (EMBL-EBI, UK) | |
| 16:10 - 16:35 | "Orthology Relationships among Pan-Genomes: the Microbial Genome Database (MBGD) for Exploring Microbial Diversity" |
| Ikuo Uchiyama (National Institute for Basic Biology, Japan) | |
| 16:35 - 16:50 | "OrthoDB Recent Developments" |
| Evgenia Kriventseva (University of Geneva Medical School, Switzerland) | |
| 16:50 - 17:00 | "Investigating evolutionary histories with OrthoInspector 3.0" |
| Yannis Nevers (ICUBE/University of Strasbourg, France) | |
| 17:00 - 17:10 | Short Break |
| Poster Session | |
| 17:10 - 17:50 | Poster Flash Talk |
| 17:50 - 18:50 | Poster Session |
| August 1 (Thu) at the Okazaki Conference Center (OCC) | |
| Session 2 | |
| 09:00 - 09:35 | "From KEGG Orthology to Modules and Human Diseases" |
| Minoru Kanehisa (Kyoto University, Japan) | |
| 09:35 - 10:00 | "Towards accessible functional discovery in any fully sequenced genome" |
| Damian Szklarczyk (University of Zurich, Switzerland) | |
| 10:00 - 10:25 |
"Targeted and feature-aware searches in the quest for functionally equivalent—and diverged—orthologs in large taxon collections" |
| Ingo Ebersberger (Goethe University Frankfurt, Germany) | |
| 10:25 - 10:50 | Coffee Break |
| 10:50 - 11:15 |
"Uncovering Strategies and Evolution of Microbes by Comparative Genomics, Comparative Metagenomics, and Metaepigenomics" |
| Wataru Iwasaki (The University of Tokyo, Japan) | |
| 11:15 - 11:40 | "Multi-level phylogenetic profiling with BLUR" |
| Odile Lecompte (ICUBE/University of Strasbourg, France) | |
| 11:40 - 11:50 | "Computationally Efficient Phylogenetic Profiling using Orthology Datasets" |
| David Moi (UNIL, Switzerland) | |
| 11:50 - 12:00 | "Unraveling the Microbial Gene Repertoire by Sub-gene Level Orthologous Clustering" |
| Hirokazu Chiba (Research Organization of Information and Systems, Japan) | |
| 12:00 - 12:10 | Group Photo |
| 12:10 - 13:00 | Lunch |
| Session 3 | |
| 13:00 - 13:35 | "Evolutionary Plasticity of Multidomain Proteins has Surprising Consequences for Orthology" |
| Dannie Durand (Carnegie Mellon University, USA) | |
| 13:35 - 14:00 | "Evolution of gene clustering in eukaryotes" |
| Toni Gabaldón (Institute for Research in Biomedicine and Barcelona Supercomputing Center, Spain) | |
| 14:00 - 14:25 | "Ortholog Analyses Reveal Genomic Basis of Evolutionary Novelty - Lessons from Insect Genomes" |
| Shuji Shigenobu (National Institute for Basic Biology, Japan) | |
| 14:25 - 14:55 | Coffee Break |
| 14:55 - 15:20 | "Orthology and ancestral genome reconstruction" |
| Paul D. Thomas (University of Southern California, USA) | |
| 15:20 - 15:45 | "Reshaping the Polyploidized Vertebrate Genomes: Case Studies on Developmental Regulators" |
| Shigehiro Kuraku (RIKEN Center for Biosystems Dynamics Research, Japan) | |
| 15:45 - 16:10 | "Disparity of genomic fields may affect the fate of genes" |
| Yuichiro Hara (Nagoya University, Japan) | |
| 16:10 - 16:20 | "Fitting Evolutionary Distances to Hierarchical Orthologous Groups" |
| Alex Warwick Vesztrocy (University College London, UK) | |
| 16:20 - 16:30 | Short Break |
| 16:30 - 17:30 | Round Table Discussion |
| 17:30 - 19:30 | Banquet along with Poster Session |
| August 2 (Fri) at the Okazaki Conference Center (OCC) | |
| Session 4 | |
| 09:00 - 09:35 |
"Accounting for alternative splicing for the reconstruction of gene and transcript evolution" |
| Aida Ouangraoua (Université de Sherbrooke, Canada) | |
| 09:35 - 10:00 | "Improving Protein Sequence Quality – Shrinking the Gaps" |
| William R. Pearson (University of Virginia, USA) | |
| 10:00 - 10:25 | "Improving gene Classification with Phylo-kmers" |
| Benjamin Linard (LIRMM, France) | |
| 10:25 - 10:50 | Coffee Break |
| 10:50 - 11:15 | "OpenEBench. The ELIXIR Platform For Benchmarking" |
| Salvador Capella-Gutierrez (Barcelona Supercomputing Center, Spain) | |
| 11:15 - 11:30 | "Orthology Benchmarking in the Quest for Orthologs Community" |
| Adrian Altenhoff (ETH Zurich / Swiss Institute of Bioinformatics, Switzerland) | |
| 11:30 - 11:55 |
"Assigning Standardized Gene Nomenclature To Vertebrate Orthologs: Updates From The Vertebrate Gene Nomenclature Committee" |
| Tamsin Jones (EMBL-EBI, UK) | |
| 11:55 - 12:10 | "Querying Explicit and Implicit Homology Relations with ORTHology Ontology" |
| Tarcisio M. de Farias (University of Lausanne, Switzerland) | |
| Closing Remarks | |
| 12:10 - 12:15 | Christophe Dessimoz (University of Lausanne, Switzerland) |
| 12:15 - 13:15 | Lunch |
| Optional Session | |
| 13:15 - 15:00 |
QfO Consortium Session II: Future Planning |
