Читать книгу Bioinformatics - Группа авторов - Страница 11

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 of Medicine, Salt Lake City, UT, USA, since 1979 and holds the Mark and Kathie Miller Presidential Endowed Chair in Human Genetics. He was appointed Chair of the Department of Human Genetics in September 2009. Dr. Jorde's laboratory has published scientific articles on human genetic variation, high-altitude adaptation, the genetic basis of human limb malformations, and the genetics of common diseases such as hypertension, juvenile idiopathic arthritis, and inflammatory bowel disease. Dr. Jorde is the lead author of Medical Genetics, a textbook that is now in its fifth edition and translated into multiple foreign languages. He is the co-recipient of the 2008 Award for Excellence in Education from the American Society of Human Genetics (ASHG). He served two 3-year terms on the Board of Directors of ASHG and, in 2011, he was elected as president of ASHG. In 2012, he was elected as a Fellow of the American Association for the Advancement of Science.

Marieke L. Kuijjer, PhD is a Group Leader at the Centre for Molecular Medicine Norway (NCMM, a Nordic EMBL partner), University of Oslo, Norway, where she runs the Computational Biology and Systems Medicine group. She obtained her doctorate in the laboratory of Dr. Pancras Hogendoorn in the Department of Pathology at the Leiden University Medical Center in the Netherlands. After this, she continued her scientific training as a postdoctoral researcher in the laboratory of Dr. John Quackenbush at the Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, during which she won a career development award and a postdoctoral fellowship. Dr. Kuijjer's research focuses on solving fundamental biological questions through the development of new methods in computational and systems biology and on implementing these techniques to better understand gene regulation in cancer. Dr. Kuijjer serves on the editorial board of Cancer Research.

David H. Mathews, MD, PhD is a professor of Biochemistry and Biophysics and also of Biostatistics and Computational Biology at the University of Rochester Medical Center, Rochester, NY, USA. He also serves as the Associate Director of the University of Rochester's Center for RNA Biology. His involvement in education includes directing the Biophysics PhD program and teaching a course in Python programming and algorithms for doctoral students without a programming background. His group studies RNA biology and develops methods for RNA secondary structure prediction and molecular modeling of three-dimensional structure. His group developed and maintains RNAstructure, a widely used software package for RNA structure prediction and analysis.

Sean D. Mooney, PhD has spent his career as a researcher and group leader in biomedical informatics. He now leads Research IT for UW Medicine and is leading efforts to support and build clinical research informatic platforms as its first Chief Research Information Officer (CRIO) and as a Professor in the Department of Biomedical Informatics and Medical Education at the University of Washington, Seattle, WA, USA. Previous to being appointed as CRIO, he was an Associate Professor and Director of Bioinformatics at the Buck Institute for Research on Aging. As an Assistant Professor, he was appointed in Medical and Molecular Genetics at Indiana University School of Medicine and was the founding Director of the Indiana University School of Medicine Bioinformatics Core. In 1997, he received his BS with Distinction in Biochemistry and Molecular Biology from the University of Wisconsin at Madison. He received his PhD from the University of California in San Francisco in 2001, then pursued his postdoctoral studies under an American Cancer Society John Peter Hoffman Fellowship at Stanford University.

Stephen J. Mooney, PhD is an Acting Assistant Professor in the Department of Epidemiology at the University of Washington, Seattle, WA, USA. He developed the CANVAS system for collecting data from Google Street View imagery as a graduate student, and his research focuses on contextual influences on physical activity and transport-related injury. He's a methods geek at heart.

Hunter N.B. Moseley, PhD is an Associate Professor in the Department of Molecular and Cellular Biochemistry at the University of Kentucky, Lexington, KY, USA. He is also the Informatics Core Director within the Resource Center for Stable Isotope Resolved Metabolomics, Associate Director for the Institute for Biomedical Informatics, and a member of the Markey Cancer Center. His research interests include developing computational methods, tools, and models for analyzing and interpreting many types of biological and biophysical data that enable new understanding of biological systems and related disease processes. His formal education spans multiple disciplines including chemistry, mathematics, computer science, and biochemistry, with expertise in algorithm development, mathematical modeling, structural bioinformatics, and systems biochemistry, particularly in the development of automated analyses of nuclear magnetic resonance and mass spectrometry data as well as knowledge–data integration.

Yanay Ofran, PhD is a Professor and head of the Laboratory of Functional Genomics and Systems Biology at Bar Ilan University in Tel Aviv, Israel. His research focuses on biomolecular recognition and its role in health and disease. Professor Ofran is also the founder of Biolojic Design, a biopharmaceutical company that uses artificial intelligence approaches to design epitope-specific antibodies. He is also the co-founder of Ukko, a biotechnology company that uses computational tools to design safe proteins for the food and agriculture sectors.

Joseph N. Paulson, PhD is a Statistical Scientist within Genentech's Department of Biostatistics, San Francisco, CA, USA, working on designing clinical trials and biomarker discovery. Previously, he was a Research Fellow in the Department of Biostatistics and Computational Biology at the Dana-Farber Cancer Institute and Department of Biostatistics at the Harvard T.H. Chan School of Public Health. He graduated with a PhD in Applied Mathematics, Statistics, and Scientific Computation from the University of Maryland, College Park where he was a National Science Foundation Graduate Fellow. As a statistician and computational biologist, his interests include clinical trial design, biomarker discovery, development of computational methods for the analysis of high-throughput sequencing data while accounting for technical artifacts, and the microbiome.

Sadhna Phanse, MSc is a Bioinformatics Analyst at the Donnelly Centre for Cellular and Biomolecular Research at the University of Toronto, Toronto, Canada. She has been active in the field of proteomics since 2006 as a member of the Emili research group. Her current work involves the use of bioinformatics methods to investigate biological systems and molecular association networks in human cells and model organisms.

John Quackenbush, PhD is Professor of Computational Biology and Bioinformatics and Chair of the Department of Biostatistics at the Harvard T.H. Chan School of Public Health, Boston, MA, USA. He also holds appointments in the Channing Division of Network Medicine of Brigham and Women's Hospital and at the Dana-Farber Cancer Institute. He is a recognized expert in computational and systems biology and its applications to the study of a wide range of human diseases and the factors that drive those diseases and their responses to therapy. Dr. Quackenbush has long been an advocate for open science and reproducible research. As a founding member and past president of the Functional Genomics Data Society (FGED), he was a developer of the Minimal Information About a Microarray Experiment (MIAME) and other data-reporting standards. Dr. Quackenbush was honored by President Barack Obama in 2013 as a White House Open Science Champion of Change.

Jonas Reeb, MSc is a PhD student in the laboratory of Burkhard Rost at the Technical University of Munich, Germany (TUM). During his studies at TUM, he has worked on predictive methods for the analysis and evaluation of transmembrane proteins; he has also worked on the NYCOMPS structural genomics pipeline. His doctoral thesis focuses on the effect of sequence variants and their prediction.

Burkhard Rost, PhD is a professor and Alexander von Humboldt Award recipient at the Technical University of Munich, Germany (TUM). He was the first to combine machine learning with evolutionary information, using this combination to accurately predict secondary structure. Since that time, his group has repeated this success in developing many other tools that are actively used to predict and understand aspects of protein structure and function. All tools developed by his research group are available through the first internet server in the field of protein structure prediction (PredictProtein), a resource that has been online for over 25 years. Over the last several years, his research group has been shifting its focus to the development of methods that predict and annotate the effect of sequence variation and their implications for precision medicine and personalized health.

Fabian Sievers, PhD is currently a postdoctoral research fellow in the laboratory of Des Higgins at University College Dublin, Ireland. He works on multiple sequence alignment algorithms and, in particular, on the development of Clustal Omega. He received his PhD in mathematics from Trinity College, Dublin and has worked in industry in the fields of algorithm development and high-performance computing.

Michael F. Sloma, PhD is a data scientist at Xometry, Gaithersburg, MD, USA. He received his BA degree in Chemistry from Wells College. He earned his doctoral degree in Biochemistry in the laboratory of David Mathews at the University of Rochester, where his research focused on computational methods to predict RNA structure from sequence.

W. Scott Watkins, MS is a researcher and laboratory manager in the Department of Human Genetics at the University of Utah, Salt Lake City, UT, USA. He has a long-standing interest in human population genetics and evolution. His current interests include the development and application of high-throughput computational methods to mobile element biology, congenital heart disease, and personalized medicine.

David S. Wishart, PhD is a Distinguished University Professor in the Departments of Biological Sciences and Computing Science at the University of Alberta, Edmonton, Alberta, Canada. Dr. Wishart has been developing bioinformatics programs and databases since the early 1980s and has made bioinformatics an integral part of his research program for nearly four decades. His interest in bioinformatics led to the development of a number of widely used bioinformatics tools for structural biology, bacterial genomics, pharmaceutical research, and metabolomics. Some of Dr. Wishart's most widely known bioinformatics contributions include the Chemical Shift Index (CSI) for protein secondary structure identification by nuclear magnetic resonance spectroscopy, PHAST for bacterial genome annotation, the DrugBank database for drug research, and MetaboAnalyst for metabolomic data analysis. Over the course of his academic career, Dr. Wishart has published more than 400 research papers, with many being in the field of bioinformatics. In addition to his long-standing interest in bioinformatics research, Dr. Wishart has been a passionate advocate for bioinformatics education and outreach. He is one of the founding members of the Canadian Bioinformatics Workshops (CBW) – a national bioinformatics training program that has taught more than 3000 students over the past two decades. In 2002 he established Canada's first undergraduate bioinformatics degree program at the University of Alberta and has personally mentored nearly 130 undergraduate and graduate students, many of whom have gone on to establish successful careers in bioinformatics.

Tyra G. Wolfsberg, PhD is the Associate Director of the Bioinformatics and Scientific Programming Core at the National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, MD, USA. Her research program focuses on developing methodologies to integrate sequence, annotation, and experimentally generated data so that bench biologists can quickly and easily obtain results for their large-scale experiments. She maintains a long-standing commitment to bioinformatics education and outreach. She has authored a chapter on genomic databases for previous editions of this textbook, as well as a chapter on the NCBI MapViewer for Current Protocols in Bioinformatics and Current Protocols in Human Genetics. She serves as the co-chair of the NIH lecture series Current Topics in Genome Analysis; these lectures are archived online and have been viewed over 1 million times to date. In addition to teaching bioinformatics courses at NHGRI, she served for 13 years as a faculty member in bioinformatics at the annual AACR Workshop on Molecular Biology in Clinical Oncology.

Michael Zuker, PhD retired as a Professor of Mathematical Sciences at Rensselaer Polytechnic Institute, Troy, NY, USA, in 2016. He was an Adjunct Professor in the RNA Institute at the University of Albany and remains affiliated with the RNA Institute. He works on the development of algorithms to predict folding, hybridization, and melting profiles in nucleic acids. His nucleic acid folding and hybridization web servers have been running at the University of Albany since 2010. His educational activities include developing and teaching his own bioinformatics course at Rensselaer and participating in both a Chautauqua short course in bioinformatics for college teachers and an intensive bioinformatics course at the University of Michigan. He currently serves on the Scientific Advisory Board of Expansion Therapeutics, Inc. at the Scripps Research Institute in Jupiter, Florida.