Keynote Speakers

Cathy Wu

Cathy Wu

Director of the Center for Bioinformatics & Computational Biology, University of Delaware

Dr. Cathy Wu is the Edward G. Jefferson Chair and Director of the Center for Bioinformatics & Computational Biology, and Founding Director of the Bioinformatics Master’s, PhD and Graduate Certificate programs at University of Delaware. She is also Director of the Protein Information Resource (PIR) and Professor at Georgetown University. She has conducted bioinformatics and computational biology research for 25 years. She leads or co-leads several multi-institutional Consortium projects, including the international UniProt Consortium, Protein Ontology Consortium, and BioCreative Consortium, and also a funded member of the NIH Big Data to Knowledge network. Dr. Wu serves on many advisory boards, including the Board of Directors of ACM SIGBio (Association for Computing Machinery) and USHUPO (Human Proteome Organization) and the NIH National Advisory General Medical Sciences Council, as well as service on several journal editorial boards and over 60 international conference organizing committees. Recognized as a “Highly Cited Researcher” (top 1%), she has published more than 250 peer-reviewed papers with over 26,000 citations, along with 14 books, conference proceedings and journal special issues. Dr. Wu’s research encompasses genomic and protein annotation, biomedical text mining and ontology, systems biology, and big data analytics in precision medicine. 


Steven E. Brenner

Steven E. Brenner

Professor at the University of California, Berkeley

Dr. Brenner’s undergraduate research was in the first genome laboratory, mentored by Walter Gilbert at Harvard. He received his M.Phil. from the Department of Biochemistry at Cambridge University, and earned a Ph.D. from the University of Cambridge and the MRC Laboratory of Molecular Biology where he studied with Cyrus Chothia. After graduation, Brenner had a brief fellowship at the Japan National Institute of Bioscience, followed by postdoctoral research supervised by Michael Levitt at Stanford University School of Medicine.
Dr. Brenner’s research is primarily in the area of computational genomics, covering topics in individual genome interpretation, protein structure, RNA regulation, and function prediction. Brenner has a commitment to supporting open science and development of the scientific community. He is also currently a director of the Human Genome Variation Society and is a founding editor of PLoS Computational Biology. He was founding chair of the Computational Biology graduate program at Berkeley. He has served two terms as a director of the International Society for Computational Biology, was founding chair of the Global Alliance for Genomics and Health’s Data Working Group Variant Annotation Task Team and was a founding director of the Open Bioinformatics Foundation. His recognitions including being a Miller Professor, a Sloan Research Fellow, a Searle Scholar, an AAAS Fellow, an ISCB Fellow, and the recipient of ISCB’s Overton Prize.


Li JIN

Li JIN

Vice President of Fudan University

Professor Jin received his doctoral degree in genetics from the University of Texas and is an academician of the Chinese Academy of Sciences. He worked as a faculty at University of Texas and University of Cincinnati College of Medicine. He is also an external member of Max-Planck Society and served as a board member of Human Genome Organization (HUGO). He is one of the founders of CAS-MPG Partner Institute of Computational Biology, National Center of Human Genome at Shanghai, and Fudan Taizhou Institute of Health Sciences. Professor Jin assumed his current position of Vice President in 2007. He is Director of the Collaborative Innovation Centre of Genetics and Development. Professor Jin holds a Haoqing-Fudan Professorship and has been awarded the Ho Leung Ho Lee Foundation Award for Science and Technology Achievement, Second Prize for National Natural Science Award (twice) among others. He serves as co-editor-in-chief of NPJ: Molecular Phenomics and an editorial board member for nine international academic journals, is Vice President of the Chinese Anthropological Society and Genetics Society of China. His research interests lie in medical genetics and genetic epidemiology, computational biology, human population genetics and genomics. Professor Jin has published over 500 articles, in journals including Nature, Science, Cell, New England Journal of Medicine, PNAS, JCI and JAMA.


Martin Romacker

Martin Romacker

Principal Scientist at Roche Innovation Center Basel, Switzerland

Martin is a Data and Information Architect in Technical Solution Delivery and Architecture (Pharma Research and Early Development Informatics) at F. Hoffmann-LaRoche in Basel Switzerland. His main areas of activities are terminology management, semantic engineering, scientific data curation, text mining and semantic search. Martin has been active in the design and deployment of Data Standards within Research and Early Development but also cross-functional aligning data with Clinical Development, Marketing and Diagnostics. As a part of the data integration efforts Martin has also been teaming up with external partners: as a part of Roche’s precompetitive engagements he has been contributing to projects of the Pistoia Alliance and the European Innovative Medicine Initiative. More recently he has entered into a collaboration with the Swiss Institute of Bioinformatics on cell line curation.

Before joining Roche Martin worked at the Novartis Institutes of Biomedical Research as a Senior Knowledge Engineering Consultant leading various ontology development and text mining projects such as the implementation of a set of BioAssay Ontologies. Martin was also the Managing Director of a Start-Up company in Freiburg (Germany) where he focused on R&D activities for NLP. He holds a PhD in Computation Linguistics from the University of Freiburg on Semantic Interpretation of technical and medical texts.

Invited Speakers

Zhiyong Lu, PhD

Zhiyong Lu, PhD

http://www.ncbi.nlm.nih.gov/research/bionlp
Deputy Director for Literature Search/Senior Investigator
National Center of Biotechnology Information (NCBI)/National Library of Medicine (NLM)/National Institutes of Health (NIH)

Dr. Lu is the NCBI Deputy Director for Literature Search at the National Institutes of Health (NIH), leading its overall efforts (in both research and engineering) to improve search quality and usability in NCBI production resources such as PubMed & PubMed Labs. He was the first NIH Earl Stadtman Investigator in bioinformatics and computational biology and is now a Senior Investigator (with tenure) directing NCBI’s Text Mining Research Program. Over the years, his research group has developed a number of widely used software tools (e.g. PubTator and DNorm) for mining the scientific literature and electronic medical records. Dr. Lu is an Associate Editor for BMC Bioinformatics, Journal of Health Informatics Research, and serves on the editorial board for the Journal Database. He is an organizer of the international BioCreative text-mining challenge and has authored over 140 publications since 2004.


Henning Hermjakob

Henning Hermjakob

European Bioinformatics Institute (EMBL-EBI)

Henning Hermjakob leads the Molecular Systems Cluster at the European Bioinformatics Institute, and since August 2015 has a joint appointment as Director of Bioinformatics at the National Center for Protein Sciences, Beijing. His team provides a broad portfolio of resources for systems biology, ranging from molecular interactions (IntAct)[1] and curated pathways (Reactome)[2-3] to systems biology models (BioModels)[4] at the highest level of abstraction. Supporting the domain-specific resources, his team develops broad-scope data infrastructure resources identifiers.org [5] and the Omics Discovery Index [6]. As founding member and co-chair of the HUPO Proteomics Standards Initiative, and SAB member in systems and translational molecular biology projects, he contributes to the international standardization of data representation in molecular biology, and the implementation of community standards in high availability, stable public resources [7,8].

  • Orchard S, et al. The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res. 2014 Jan;42(Database issue):D358-63.
  • Sidiropoulos K, et al. Reactome enhanced pathway visualization. Bioinformatics 2017 Jul; btx441.
  • Fabregat A, et al. The Reactome pathway Knowledgebase. Nucleic Acids Res. 2016 Jan 4;44(D1):D481-7.
  • Chelliah V, et al. BioModels: ten-year anniversary. Nucleic Acids Res. 2015 Jan;43 (Database issue):D542-8.
  • Sarala Wimalaratne, et al. Uniform Resolution of Compact Identifiers for Biomedical Data. bioRxiv 101279.
  • Perez-Riverol Y, et al. Discovering and linking public omics data sets using the Omics Discovery Index. Nat Biotechnol. 2017 May 9;35(5):406-409.
  • Orchard S, et al. Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat Methods. 2012 Mar 27;9(4):345-350.
  • Vizcaíno JA, et al. ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat Biotechnol. 2014 Mar 10;32(3):223-6.

Vladimir Bajic, D.Eng.Sc

Vladimir Bajic, D.Eng.Sc

Professor, Director of the Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Saudi Arabia.

Vladimir Bajic is the director of the Computational Bioscience Research Center (CBRC) and a professor in the Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division at King Abdullah University of Science and Technology (KAUST), Saudi Arabia. He was professor of bioinformatics and acting and deputy director of the South African National Bioinformatics Institute (SANBI) at the University of the Western Cape. He worked in industry and several academic and research institutions in Yugoslavia, South Africa, Singapore and Saudi Arabia, including Vinca Nuclear Science Institute in Serbia and the Institute for Infocomm Research in Singapore, where he was head of the Knowledge Extraction Laboratory. Dr. Bajic published across various fields. His work in modeling and artificial intelligence has resulted in several bioinformatic tools and a knowledge discovery platform that found commercial applications. Prof. Bajic was awarded the first South African National Research (Tier 1) Chair in Bioinformatics and Human Health. More than 60 master and doctoral students have graduated under his supervision. He serves on the editorial boards of Briefings in Bioinformatics and several other journals. Dr. Bajic earned graduate and master’s degrees in electrical engineering sciences from the University of Belgrade in Serbia, followed by a doctorate of engineering sciences in electrical engineering from the University of Zagreb in Croatia. 


Jing-Dong Jackie Han

Jing-Dong Jackie Han

director of the CAS-MPG Partner Institute for Computational Biology.

Dr Jing-Dong Jackie Han obtained Ph.D. degree from Albert Einstein College of Medicine. She had her postdoctoral training at The Rockefeller University and Dana-Farber Cancer Institute. In 2004, she became an investigator/professor at the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences. She is currently a director of the CAS-MPG Partner Institute for Computational Biology. Her research focuses on the topology, dynamics and structure inference of molecular networks. She was awarded the Chinese Academy Sciences Hundred Talent Plan and NSFC Outstanding Young Scientist Award in 2006, and the Hundred Talent Plan Outstanding Achievement Award in 2009, and selected as Max Planck Follow in 2011, MaxNetAging Fellow in 2014, Shanghai Science Leader in 2015, National Talent with Outstanding Contribution in 2015, core investigator in the Chinese Academy of Sciences Center for Excellence in Molecular Cell Science in 2015, and Faculty 1000 in Developmental Biology in 2016.


HuiLv

Hui Lu,Shanghai Jiaotong University

Data Driven Biomedical Discovery

Dr. Hui Lu is a Distinguished Professor and Head of the Department of Bioinformatics and Biostatistics, Shanghai Jiaotong University, the co-director of SJTU-Yale Joint Center for Biostatistics, and an adjunct professor of biostatistics of Yale University. He is also the Director of Center for Biomedical Informatics in Shanghai Children’s Hospital. He got Bachelor’s degree from Peking University and PhD from University of Illinois at Urbana-Champaign. After that, he joined University of Illinois at Chicago as a faculty in Bioinformatics and got tenure in 2008. His research areas include big data analysis in biomedical research, bioinformatics, biostatistics, molecular network modeling, systems biology, and drug design. His current research interests are in translational medicine: integrating multi-omics data and disease phenotypes, constructing disease network, investigating self-adapting methods for clinical trial, set up high speed genomics data processing pipeline, large scale patient record analysis, building a phenotype-genotype based diagnosis system.