Contributors

Gary D. Bader, PhD  is a Professor at The Donnelly Centre at the University of Toronto, Toronto, Canada, and a leader in the field of Network Biology. Gary completed his postdoctoral work in Chris Sander's group in the Computational Biology Center (cBio) at Memorial Sloan-Kettering Cancer Center in New York. Gary completed his PhD in the laboratory of Christopher Hogue in the Department of Biochemistry at the University of Toronto and a BSc in Biochemistry at McGill University in Montreal. Dr. Bader uses molecular interaction, pathway, and -omics data to gain a “causal” mechanistic understanding of normal and disease phenotypes. His laboratory develops novel computational approaches that combine molecular interaction and pathway information with -omics data to develop clinically predictive models and identify therapeutically targetable pathways. He also helps lead the Cytoscape, GeneMANIA, and Pathway Commons pathway and network analysis projects.

Geoffrey J. Barton, PhD  is Professor of Bioinformatics and Head of the Division of Computational Biology at the University of Dundee School of Life Sciences, Dundee, UK. Before moving to Dundee in 2001, he was Head of the Protein Data Bank in Europe and the leader of the Research and Development Team at the EMBL European Bioinformatics Institute (EBI). Prior to joining EMBL-EBI, he was Head of Genome Informatics at the Wellcome Trust Centre for Human Genetics, University of Oxford, a position he held concurrently with a Royal Society University Research Fellowship in the Department of Biochemistry. Geoff's longest running research interest is using computational methods to study the relationship between a protein's sequence, its structure, and its function. His group has contributed many tools and techniques in the field of protein sequence and structure analysis and structure prediction. Two of the best known are the Jalview multiple alignment visualization and analysis workbench, which is in use by over 70 000 groups for research and teaching, and the JPred multi-neural net protein secondary structure prediction algorithm, which performs predictions on up to 500 000 proteins/month for users worldwide. In addition to his work related to protein sequence and structure, Geoff has collaborated on many projects that probe biological processes using proteomic and high-throughput sequencing approaches. Geoff's group has deep expertise in RNA-seq methods and has recently published a two-condition 48-replicate RNA-seq study that is now a key reference work for users of this technology.

Andreas D. Baxevanis, PhD  is the Director of Computational Biology for the National Institutes of Health's (NIH) Intramural Research Program. He is also a Senior Scientist leading the Computational Genomics Unit at the NIH's National Human Genome Research Institute, Bethesda, MD, USA. His research program is centered on probing the interface between genomics and developmental biology, focusing on the sequencing and analysis of invertebrate genomes that can yield insights of relevance to human health, particularly in the areas of regeneration, allorecognition, and stem cell biology. His accomplishments have been recognized by the Bodossaki Foundation's Academic Prize in Medicine and Biology in 2000, Greece's highest award for young scientists of Greek heritage. In 2014, he was elected to the Johns Hopkins Society of Scholars, recognizing alumni who have achieved marked distinction in their field of study. He was the recipient of the NIH's Ruth L. Kirschstein Mentoring Award in 2015, in recognition of his commitment to scientific training, education, and mentoring. In 2016, Dr. Baxevanis was elected as a Senior Member of the International Society for Computational Biology for his sustained contributions to the field and, in 2018, he was elected as a Fellow of the American Association for the Advancement of Science for his distinguished contributions to the field of comparative genomics.

Robert G. Beiko, PhD  is a Professor and Associate Dean for Research in the Faculty of Computer Science at Dalhousie University, Halifax, Nova Scotia, Canada. He is a former Tier II Canada Research Chair in Bioinformatics (2007–2017), an Associate Editor at mSystems and BMC Bioinformatics, and a founding organizer of the Canadian Bioinformatics Workshops in Metagenomics and Genomic Epidemiology. He is also the lead editor of the recently published book Microbiome Analysis in the Methods in Molecular Biology series. His research focuses on microbial genomics, evolution, and ecology, with concentrations in the area of lateral gene transfer and microbial community analysis.

Fiona S.L. Brinkman, PhD, FRSC  is a Professor in Bioinformatics and Genomics in the Department of Molecular Biology and Biochemistry at Simon Fraser University, Vancouver, British Columbia, Canada, with cross-appointments in Computing Science and the Faculty of Health Sciences. She is most known for her research and development of widely used computer software that aids both microbe (PSORTb, IslandViewer) and human genomic (InnateDB) evolutionary/genomics analyses, along with her insights into pathogen evolution. She is currently co-leading a national effort – the Integrated Rapid Infectious Disease Analysis Project – the goal of which is to use microbial genomes as a fingerprint to better track and understand the spread and evolution of infectious diseases. She has also been leading development into an approach to integrate very diverse data for the Canadian CHILD Study birth cohort, including microbiome, genomic, epigenetic, environmental, and social data. She coordinates community-based genome annotation and database development for resources such as the Pseudomonas Genome Database. She also has a strong interest in bioinformatics education, including developing the first undergraduate curricula used as the basis for the first White Paper on Canadian Bioinformatics Training in 2002. She is on several committees and advisory boards, including the Board of Directors for Genome Canada; she chairs the Scientific Advisory Board for the European Nucleotide Archive (EMBL-EBI). She has received a number of awards, including a TR100 award from MIT, and, most recently, was named as a Fellow of the Royal Society of Canada.

Andrew Emili, PhD  is a Professor in the Departments of Biochemistry (Medical School) and Biology (Arts and Sciences) at Boston University (BU), Boston, MA, USA, and the inaugural Director of the BU Center for Network Systems Biology (CNSB). Prior to Boston, Dr. Emili was a founding member and Principal Investigator for 18 years at the Donnelly Center for Cellular and Biomolecular Research at the University of Toronto, one of the premier research centers in integrative molecular biology. Dr. Emili is an internationally recognized leader in functional proteomics, systems biology, and precision mass spectrometry. His group develops and applies innovative technologies to systematically map protein interaction networks and macromolecular complexes of cells and tissues on a global scale, publishing “interactome” maps of unprecedented quality, scope, and resolution.

Tatyana Goldberg, PhD  is a postdoctoral scientist at the Technical University of Munich, Germany. She obtained her PhD in Bioinformatics under the supervision of Dr. Burkhard Rost. Her research focuses on developing models that can predict the localization of proteins within cells. The results of her study contribute to a variety of applications, including the development of pharmaceuticals for the treatment of Alzheimer disease and cancer.

Emma J. Griffiths, PhD  is a research associate in the Department of Pathology and Laboratory Medicine at the University of British Columbia in Vancouver, Canada, working with Dr. William Hsiao. Dr. Griffiths received her PhD from the Department of Biochemistry and Biomedical Sciences at McMaster University in Hamilton, Canada, with her doctoral work focusing on the evolutionary relationships between different groups of bacteria. She has since pursued postdoctoral training in the fields of chemical and fungal genetics and microbial genomics with Dr. Fiona Brinkman in the Department of Biochemistry and Molecular Biology at Simon Fraser University in Vancouver, Canada. Her current work focuses on the development of ontology-driven applications designed to improve pathogen genomics contextual data (“metadata”) exchange during public health investigations.

Desmond G. Higgins, PhD  is Professor of Bioinformatics in University College Dublin, Ireland, where his laboratory works on genomic data analysis and sequence alignment algorithms. He earned his doctoral degree in zoology from Trinity College Dublin, Ireland, and has worked in the field of bioinformatics since 1985. His group maintains and develops the Clustal package for multiple sequence alignment in collaboration with groups in France, Germany, and the United Kingdom. Dr. Higgins wrote the first version of Clustal in Dublin in 1988. He then moved to the EMBL Data Library group located in Heidelberg in 1990 and later to EMBL-EBI in Hinxton. This coincided with the release of ClustalW and, later, ClustalX, which has been extremely widely used and cited. Currently, he has run out of version letters so is working on Clustal Omega, specifically designed for making extremely large protein alignments.

Lynn B. Jorde, PhD  has been on the faculty of the University of Utah School...