Advisory Board and Editors Bioinformatics
Shujiro Okuda
Associate Professor of Niigata University, Graduate School of Medical and Dental Sciences
Research Professor of Institute for Research Promotion, Niigata University
Brenda Oppert
EDUCATION
University of Texas at El Paso (9/75-8/78), B.S. in Biology, 1978
University of Texas at El Paso (1/83-12/86), M.S. in Biology, 1986
Kansas State University (8/86-5/91), Ph.D. in Biochemistry, 1991
PROFESSIONAL
• Research Molecular Biologist (GS-15), CGAHR, Manhattan, KS (4/91-present)
• Adjunct Professor, Department of Entomology, Kansas State University (1/99-present)
Krishna Dev Oruganty
I can best describe myself as a simulation biologist. I am interested in simulating life processes at multiple scales. From the atomic scale to understand protein function to cellular or systems scale to understand physiological processes. My main tool is the computer which I use to analyze, understand and predict biology. Secondary tools are in vitro biochemistry and biophysics experiments that I use to validate my predictions.
Vera Pancaldi
I was trained as a physicist at Imperial College London and soon found my way in systems and computational biology. Since 2018 I lead a computational biology team at the Cancer Research Center of Toulouse (CRCT) working on modelling cancer and its interactions with the immune system.
I have worked on various projects on stress response in fission yeast and prediction of protein interactions (in the group of Jurg Bahler at Sanger Institute/University College London), epigenomics and hybrid vigour in plants (with David Baulcombe at Cambridge University) and integrative epigenomics in cancer (with Alfonso Valencia at CNIO, Madrid and Barcelona Supercomputing Center). My main current focus is understanding the relationship between genome architecture and heterogeneity at various levels and relating heterogeneity of tumour infiltrating immune cells to patient's prognoses in different cancers. I also co-founded Cambridge Networks Network in 2011, an online forum for scientists interested in networks in Cambridge in beyond.
Anna Panchenko
National Center for Biotechnology Information, National Institutes of Health. Editor, Journal of Molecular Biology
Thiago Parente
Scientist in Public Health at the Laboratory of Functional Genomics and Bioinformatics at the Oswaldo Cruz Institute (IOC, Fiocruz), Rio de Janeiro, Brazil. Scientific coordinator of the Institutional Bioinformatics Platform. CNPq Level 2 Research Productivity Scholar (Genetics). Permanent professor at the Graduate program on Systems and Computational Biology IOC, Fiocruz. Graduated in Biological Sciences - Genetics major - from the Federal University of Rio de Janeiro (2006), with a Master's degree in Cell and Molecular Biology from the IOC (2008) and PhD in Biophysics from UFRJ (2012). Through high performance technologies for DNA sequencing and computational data analysis, I investigate the effects of pollution on fauna, using fish as model organisms, and their responses and genetic adaptations to pollutants, especially those involved in the xenobiotic biotransformation system.
Helen E Parkinson
Dr Helen Parkinson head of Molecular Archival Resources at EMBL-EBI and leads the Samples, Phenotypes and Ontologies team, delivering databases, data integration tools and ontologies for biomedicine. She is also Interim Team Leader for the Variation Archive team. Trained as a geneticist, Helen's research focused on Drosophila biology, behaviour, molecular biology and medical genetics. Helen's passion is semantic data integration and providing users with useful data. Her team participates extensively in external collaborations ranging from data analysis and generation projects to infrastructural integration projects such as the ELIXIR initiatives BioMedBridges, CORBEL and EXELERATE. In collaboration with partners in the KOMP2 project and the International Mouse Phenotyping Consortium, Helen's SPOT team manages, analyses, and distributes complex phenotypic data from knockout mouse lines and promotes mouse data integration internationally.They also develop open-source software tools for managing data, developing and integrating ontologies and data, and integrating semantic web technologies.
Prior to joining EMBL-EBI in 2000, Helen was a post-doctoral researcher at the University of Leicester, where she worked on the genetic basis of Primary Pulmonary Hypertension, Hyphophatasia and synteny at human chromosomes 7 and 12. Her PhD thesis examined the temperature compensation of circadian rhythms in Drosophila with Professor Bambos Kyriacou.
Donovan H Parks
Donovan Parks holds a PhD in computer science and has developed a number of bioinformatic programs used by the research community including CheckM, STAMP, and GenGIS. He has expertise in bioinformatics relating to microbial ecology, phylogenetics, and metagenome-assembled genomes. He is currently working as a bioinformatic consultant with the Australian Centre for Ecogenomics where he is working on an initiative to resolve long-standing issues within bacterial and archaeal nomenclature and developing new tools for reconstructing and validating genomes obtained directly from environmental samples.
Santosh K Patnaik
After completing my training as a physician, I enrolled in a Ph.D. program to become a biomedical researcher. My doctoral training, in the broad field of biochemistry, and cell and molecular biology, focused on mechanisms of glycosylation, which is altered in diseases such as cancer and neuromuscular dystrophy. My current primary research focus is on RNA editing, and on microRNAs.
Yonghong Peng
Dr. Peng is a Professor of Data Science at the University of Sunderland. He is a Principal Investigator in Bioinformatics and Systems Biology and Medicine, and Principal Data Scientist working on Big Data Integration, Data Mining and Computational Intelligence. Dr. Peng's Data Science and BioMedical informatics (DS & BMI) research group focuses on development of innovative data analytics approaches to enable systematical analysis of biological data, medical images, and healthcare data and to gain new knowledge and insights from the integrative analytics of diverse data sources.
Tomas Perez-Acle
Biologist, PhD in Biotechnology. Director of the Centro BASAL Ciencia & Vida. Head Researcher of the Computational Biology Lab (dLab) at Fundacion Ciencia & Vida, Santiago, Chile. Research Professor at Facultad de Ingeniería y Tecnología, Universidad San Sebastián.
Brett S Phinney
I am currently the director of the UC Davis Genome Center Proteomics Core and I am on the Executive board of the Association of Biomolecular Resource Facilities (www.abrf.org). I obtained my Ph D. in Biology studying viral protein structure using mass spectrometry and did a Post-doc with the noted Mass Spectrometrist Jack Watson at Michigan State University before founding the Proteomics Core there and becoming the co-director of the Michigan State Proteome Consortium