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Function COSI Track Presentations

Welcome, Day 1
Date: Monday, July 24
Time: 10:00 AM - 10:10 AM
Room: Panorama
  • Function SIG organizers
The landscape of microbial phenotypic traits and associated genes
Date: Monday, July 24
Time: 10:10 AM - 10:30 AM
Room: Panorama
  • Maria Brbic, IRB, Croatia
  • Fran Supek, IRB, Spain
fusionDB: assessing microbial diversity and environmental preference via functional similarity networks
Date: Monday, July 24
Time: 10:30 AM - 10:50 AM
Room: Panorama
  • Chengsheng Zhu, Rutgers University, United States
  • Yannick Mahlich, TUM Munich, Germany
  • Maximilian Miller, TUM Munich, Germany
  • Yana Bromberg, Rutgers University, United States
Region-specific Function Prediction: automatically inferring function labels for protein regions
Date: Monday, July 24
Time: 10:50 AM - 11:10 AM
Room: Panorama
  • Da Chen Emily Koo, New York University, United States
  • Noah Youngs, NYU & Simons Foundation, United States
  • Richard Bonneau, NYU , United States
Investigation of Multi-task Deep Neural Networks in Automated Protein Function Prediction
Date: Monday, July 24
Time: 11:10 AM - 11:30 AM
Room: Panorama
  • Ahmet Süreyya Rifaioğlu, Middle East Technical University, Turkey
  • Maria Martin, EMBL-EBI, United Kingdom
  • Rengul Cetin-Atalay, Informatics Institute, Middle East Technical University, Turkey
  • Volkan Atalay, Middle East Technical University, Turkey
  • Tunca Dogan, EMBL-EBI, United Kingdom
Determining Rewiring Functional Effects of Alternative Splicing Variants on Protein-Protein Interactions
Date: Monday, July 24
Time: 11:40 AM - 12:00 PM
Room: Panorama
  • Nathan Johnson, Worcester Polytechnic Institute (WPI), United States
  • Oleksandr Narykov, Worcester Polytechnic Institute (WPI), United States
  • Dmitry Korkin, Worcester Polytechnic Institute (WPI), United States
Keynote: Community Driven Critical Assessment: how well does it work, what have we learned, and what next?
Date: Monday, July 24
Time: 12:00 PM - 12:30 PM
Room: Panorama
  • John Moult, University of Maryland
Reasoning on Gene Ontology Networks Predicts Novel Protein Annotations
Date: Monday, July 24
Time: 02:00 PM - 02:20 PM
Room: Panorama
  • Ilya Novikov, Baylor College of Medicine, United States
  • Angela Wilkins, Baylor College of Medicine, United States
  • Olivier Lichtarge, Baylor College of Medicine, United States
Predicting Protein Function Directly from STRING Network Topology using Deep Learning Techniques
Date: Monday, July 24
Time: 02:20 PM - 02:40 PM
Room: Panorama
  • Cen Wan, University College London, United Kingdom
  • Domenico Cozzetto, University College London, United Kingdom
  • Rui Fa, University College London, United Kingdom
  • David Jones, University College London, United Kingdom
Proceedings: Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference
Date: Monday, July 24
Time: 02:40 PM - 03:00 PM
Room: Panorama
  • Clement Train, University of Lausanne, Switzerland
  • Natasha Glover, University of Lausanne, Switzerland
  • Gaston Gonnet, ETH Zurich, Switzerland
  • Adrian Altenhoff, University of Lausanne, Switzerland
  • Christophe Dessimoz, University of Lausanne, Switzerland
All-to-all spectra comparisons within minutes for peptides identification in tandem mass spectrometry
Date: Monday, July 24
Time: 03:10 PM - 03:30 PM
Room: Panorama
  • Matthieu David, University of Nantes, France
  • Guillaume Fertin, University of Nantes, France
  • Hélène Rogniaux, INRA, France
  • Dominique Tessier, INRA, France
Comparing residue-coevolution networks across protein families
Date: Monday, July 24
Time: 03:30 PM - 03:50 PM
Room: Panorama
  • Franco Simonetti, Fundación Instituto Leloir, Argentina
  • Cristina Marino Buslje, Fundación Instituto Leloir, Argentina
Automatic Generation of Functional Annotation Rules Using Inferred GO-Domain Associations
Date: Monday, July 24
Time: 04:30 PM - 04:50 PM
Room: Panorama
  • Seyed Ziaeddin Alborzi, INRIA Nancy Grand-Est, France
  • Sabeur Aridhi, University of Lorraine, France
  • Marie-Dominique Devignes, LORIA-CNRS, France
  • Rabie Saidi, EMBL-EBI, United Kingdom
  • Alexandre Renaux, EMBL-EBI, United Kingdom
  • Maria J. Matrin, EMBL-EBI, United Kingdom
  • David W. Ritchie, INRIA , France
Protein Function Prediction by COFACTOR in CAFA3
Date: Monday, July 24
Time: 04:50 PM - 05:10 PM
Room: Panorama
  • Chengxin Zhang, University of Michigan, United States
  • Peter Freddolino, University of Michigan, United States
  • Yang Zhang, University of Michigan, United States
A Domain-Based Machine Learning Approach for Function Prediction using CATH FunFams
Date: Monday, July 24
Time: 05:10 PM - 05:15 PM
Room: Panorama
  • Jonathan G. Lees, UCL, United Kingdom
  • Sayoni Das, UCL, United Kingdom
  • Christine A. Orengo, UCL, United Kingdom
Computational Functional Annotation: The Predictive Power of Different Data Sources
Date: Monday, July 24
Time: 05:15 PM - 05:20 PM
Room: Panorama
  • Itamar Borukhov, Compugen Ltd., Israel
  • Yossef Klinger, Compugen Ltd., Israel
Predicting protein functions from sequence using a neuro-symbolic deep learning model
Date: Monday, July 24
Time: 05:20 PM - 05:25 PM
Room: Panorama
  • Maxat Kulmanov, King Abdullah University of Science and Technology, Saudi Arabia
  • Mohammed Asif Khan, King Abdullah University of Science and Technology, Saudi Arabia
  • Robert Hoehndorf, King Abdullah University of Science and Technology, Saudi Arabia
Crowdsourcing Protein Family Database Curation
Date: Monday, July 24
Time: 05:25 PM - 05:30 PM
Room: Panorama
  • Matt Jeffryes, European Bioinformatics Institute
Proteome-wide chemical-genetic interaction map in human cells reveals drug mechanisms and novel gene functions
Date: Monday, July 24
Time: 05:40 PM - 06:00 PM
Room: Panorama
  • Jasmin Coulombe-Huntington, Universite de Montreal, Canada
  • Thierry Bertomeu, Universite de Montreal, Canada
  • Corinne St-Denis, Universite de Montreal, Canada
  • Michael Tyers, Universite de Montreal, Canada
Welcome, Day 2
Date: Tuesday, July 25
Time: 08:30 AM - 08:40 AM
Room: Panorama
  • Function SIG organizers
KEYNOTE: Tell Us where You are Going: Pondering Literature, Locations, Life and Proteins.
Date: Tuesday, July 25
Time: 08:40 AM - 09:10 AM
Room: Panorama
  • Hagit Shatkay, University of Delaware
Proceedings: DextMP: Deep dive into Text for predicting Moonlighting Proteins
Date: Tuesday, July 25
Time: 09:10 AM - 09:30 AM
Room: Panorama
  • Ishita Khan, Purdue University, United States
  • Mansurul Bhuiyan, IUPUI, United States
  • Daisuke Kihara, Purdue University, United States
The third Critical Assessment of Function Annotation: Lessons Learned and Preliminary Results
Date: Tuesday, July 25
Time: 10:00 AM - 11:00 AM
Room: Panorama
  • Naihui Zhou, Iowa State Uninversity, United States
  • Iddo Friedberg, Iowa State Uninversity, United States
CAFA Predictor 1
Date: Tuesday, July 25
Time: 11:00 AM - 11:20:00
Room: Panorama
  • TBD TBD
CAFA Predictor 2
Date: Tuesday, July 25
Time: 11:30 AM - 11:50 AM
Room: Panorama
  • TBD TBD
Phylogenetic- based gene function prediction in the Gene Ontology Consortium
Date: Tuesday, July 25
Time: 11:50 AM - 12:10 PM
Room: Panorama
  • Huaiyu Mi, University of Southern California, United States
  • Pascale Gaudet, Swiss Institute of Bioinformatics, Swaziland
  • Marc Feuermann, Swiss Institute of Bioinformatics, Switzerland
  • Anushya Muruganujan, University of Southern California, United States
  • Suzanna E. Lewis, Lawrence Berkeley National Laboratory, United States
  • Paul D. Thomas, University of Southern California, United States
A Self-training Approach for Functional Annotation of UniProtKB Proteins
Date: Tuesday, July 25
Time: 12:10 PM - 12:15 PM
Room: Panorama
  • Maryam Abdollahyan, Queen Mary University of London, United Kingdom
  • Rabie Saidi, European Molecular Biology Laboratory, European Bioinformatics Institute, United Kingdom
  • Fabrizio Smeraldi, Queen Mary University of London, United Kingdom
  • Maria-Jesus Martin, European Molecular Biology Laboratory, European Bioinformatics Institute, United Kingdom
BAR 3.0: going beyond protein function annotation
Date: Tuesday, July 25
Time: 12:15 PM - 12:20 PM
Room: Panorama
  • Giuseppe Profiti, Università di Bologna, Italy
  • Pier Luigi Martelli, University of Bologna, Italy
  • Rita Casadio, UNIBO, Italy
PANNZER 2: Annotate a complete proteome in minutes!
Date: Tuesday, July 25
Time: 12:20 PM - 12:25 PM
Room: Panorama
  • Alan Medlar, University of Helsinki, Finland
  • Petri Törönen, University of Helsinki, Finland
  • Liisa Holm, University of Helsinki, Finland
  • Elaine Zosa, University of Helsinki, Finland
Thinking outside the informatics box: Computed chemical properties for protein function annotation
Date: Tuesday, July 25
Time: 12:25 PM - 12:30 PM
Room: Panorama
  • Caitlyn Mills, Northeastern University, United States
  • Mary Jo Ondrechen, Northeastern University, United States
Artificial Dilution Series: A General Framework for Benchmarking Classifier Evaluation Metrics
Date: Tuesday, July 25
Time: 02:00 PM - 02:20 PM
Room: Panorama
  • Petri Törönen, University of Helsinki, Finland
Elucidating the Function Space of Proteins Defined by Ontologies
Date: Tuesday, July 25
Time: 02:20 PM - 02:40 PM
Room: Panorama
  • Yuxiang Jiang, Indiana University, United States
Label-Space Dimensionality Reduction and a Similarity-Based Representation for Protein Function Prediction
Date: Tuesday, July 25
Time: 02:40 PM - 03:00 PM
Room: Panorama
  • Stavros Makrodimitris, Delft University of Technology
Predicting Novel Abnormal Circadian Phenotypes in Mouse
Date: Tuesday, July 25
Time: 03:00 PM - 03:20 PM
Room: Panorama
  • John Williams, MRC Harwell Institute, United Kingdom
  • Siddharth Sethi, MRC Harwell Institute, United Kingdom
  • Kenneth Condon, MRC Harwell Institute, United Kingdom
  • Patrick Nolan, MRC Harwell Institute, United Kingdom
  • Michelle Simon, MRC Harwell Institute, United Kingdom
  • Georgios Gkoutos, University of Birmingham, United Kingdom
  • Ann-Marie Mallon, MRC Harwell Institute, United Kingdom
Structure-based prediction of protein-peptide binding regions using Random Forest
Date: Tuesday, July 25
Time: 03:30 PM - 03:50 PM
Room: Panorama
  • Ghazaleh Taherzadeh, Griffith University, Australia
  • Yaoqi Zhou, Griffith University, Australia
  • Alan Wee-Chung Liew, Griffith University, Australia
  • Yuedong Yang, Griffith University, Australia
Automating Genomic Context Analysis with a Probabilistic Model of Protein Function and Relatedness
Date: Tuesday, July 25
Time: 03:50 PM - 04:00 PM
Room: Panorama
  • Jeffrey Yunes, University of California, San Francisco, United States
  • Patricia Babbit, University of California, San Francisco, United States
Awards and Close
Date: Tuesday, July 25
Time: 04:00 PM - 04:20 PM
Room: Panorama
  • TBD TBD