Advisory Board and Editors Bioinformatics
Jason Ernst
Jason joined the faculty at UCLA in the Department of Biological Chemistry, the Computer Science Department, and the Bioinformatics Program in 2012. Prior to that, he was a postdoctoral fellow in Manolis Kellis' Computational Biology Group in the Computer Science and Artificial Intelligence Laboratory at MIT and affiliated with the Broad Institute. In 2008, Jason completed a PhD advised by Ziv Bar-Joseph where he was part of the Systems Biology Group, Machine Learning Department, and School of Computer Science at Carnegie Mellon University. Jason also earned BS degrees in Computer Science and Mathematics from the University of Maryland College Park. He is a member of the editorial board at Genome Research and has been a program co-chair for the ISMB Regulatory Genomics Special Interest Group (RegGenSIG) meeting. He is a recipient of a Sloan Fellowship, NSF Career Award, NSF Postdoctoral Fellowship, a Siebel Scholarship, and a Goldwater Scholarship.
Marcial Escudero
Assistant Professor of Plant Biology and Ecology, University of Seville (Spain). Past postdoctoral researcher at Doñana Biological Station (CSIC, Seville, Spain), at the Field Museum of Natural History of Chicago (Illionois, USA) and at The Morton Arboretum (Lisle, Illinois, USA). Past PhD student at University Pablo de Olavide (Seville, Spain).
Rudi H. Ettrich
Rudi received his prediploma in chemistry (Vordiplom) from Eberhard-Karls-University, Tuebingen, Germany, in 1993, his Master of sciences (Mgr.) in physical and macromolecular chemistry from Charles University, Prague, in 1998 and his PhD. in physical chemistry from Charles University, Prague, in 2002.
Since 2013 he is a full Professor (Prof.) in biophysics and currently acts as the President/CEO of Larkin University, Miami, FL and holds a faculty appointment at the College of Biomedical Sciences. He also holds community-based adjunct faculty positions at the Wertheim College of Medicine, Florida International University, Miami, FL, and the Department of Mathematics and Physics, Charles University, Czechia.
Prior to joining Larkin University Rudi was affiliated with the Czech Academy of Sciences, where he acted as director, group leader and senior researcher at the Center for Nanobiology and Structural Biology of the Institute of Microbiology in Nové Hrady, Academy of Sciences of the Czech Republic
Rudi's research is focused on the relationship between structure and function of proteins, dynamic changes related to functional processes on the level of proteins and the mutual interaction of cofactors and subunits in protein complexes. The research approach is very complex using various methods of protein research with a synthesis of theoretical and experimental methods.
Kjiersten Fagnan
Kjiersten Fagnan joined the JGI in 2012 after completing a petascale postdoctoral fellowship at NERSC and CRD. In 2014 Fagnan became the JGI-NERSC Engagement Lead with a focus on adapting JGI workloads to run on supercomputing hardware. She is also working to understand the data-intensive nature of JGI workloads. Fagnan earned her PhD in Applied Mathematics at the University of Washington in 2010 and her BA from UC Berkeley in 2002.
Brant C Faircloth
Associate Professor of Biological Sciences at Louisiana State University and Research Associate as the LSU Museum of Natural Sciences. Research interests include population and evolutionary genomics of non-model organisms; community genomics; genotype-phenotype interactions; (immuno-)genetic basis of mate choice; mating behavior; social behavior; and natural history.
Noemi Fernandes
Assistant Professor of Bioinformatics and other disciplines at the Federal University of Itajuba, Brazil. She conducts research in the field of diversity and evolution of unicellular eukaryotes, with a special focus on the phylum Ciliophora. She is experienced in DNA metabarcoding analysis, molecular clock and protist phylogenomics.
Carlos Fernandez-Lozano
Dr. Carlos Fernandez-Lozano is an Associate Professor at the University of A Coruña (UDC). He is a biomedical data scientist with a deep interest in discovering the complex relationships between different biological levels. His research track is multidisciplinary as he is trained in computer science, machine learning, bioinformatics, and biostatistics. His research line is focused on how biological interactions are manifested at the disease level through the use, development, and application of kernel-based computational approaches that integrate different levels of biological data on the microorganism, gene, protein, and medical imaging axis.
Pedro G Ferreira
Pedro G. Ferreira graduated in Systems and Informatics Engineering from the University of Minho in 2002 and obtained his Ph. D. in Artificial Intelligence from the same University in 2007. From 2008 to 2012, he was a Postdoctoral Researcher at the Bioinformatics and Genomics Laboratory, Centre for Genomic Regulation, Barcelona. From 2012 to 2014, he was a Postdoctoral Fellow the Functional Population Genomics and Genetics of Complex Traits group, School of Medicine, University of Geneva. He has been involved in several large international consortia including: ICGC-CLL, ENCODE, GEUVADIS, SYSCOL and GTEx. He published several papers in high impact journals, including the multidisciplinary journals: Nature, Science, Nature Communications, Scientific Reports, PNAS and eLife. Other papers have been published in high impact specialized journals including Genome Biology, Genome Research, American Journal of Human Genetics, Nature Cell Biology, RNA or Leukemia. He is the author of 3 book chapters and 2 books. He has an h-index of 31, with a total > 32 000 citations. In 2015, he was awarded an FCT Investigator Starting grant and he joined Ipatimup/i3s. He was awrded the Research Award 2015 and 2019 from Portuguese Society of Human Genetics - SPGH and the Microsoft Azure Research Award for Data Science 2017. He is a partner in a bioinformatics data analysis company with national and international clients, including hospitals, diagnostic clinics and research centres. From 2015 to 2018, he was an invited assistant professor at the Department of Informatics at the University of Minho, where he taught bioinformatics and data analysis at master's level. He has been involved in the final supervision of 1 postdoctoral fellow, 2 PhD students, 22 Masters students and 3 research assistants, and in the ongoing (main and co-) supervision of 5 PhD students and 5 Masters students. He was the director of the Masters and Specialisation in Bioinformatics and Computational Biology (2020-2023). He has experience in the genomics start-up environment, where he developed information systems for personal genomics data interpretation. He is currently an Assistant Professor (since 02/2019) with Habilitation (since 10/2022) at Department of Computer Science, Faculty of Sciences of the University of Porto and a Senior Researcher at the Artificial Intelligence and Decision Support Group at INESCTEC. He is currently the Director of the Bachelor in Bioinformatics and Adjunct Director of the Bachelor in Artificial Intelligence and Data Science. His main research focus is on developing methods for a variety of problems in genomic data science. In particular, he is interested in unravelling the role of genomics in human health and disease. To achieve this goal, he applies and develops data analysis models using machine learning and probabilistic methods to analyse and interpret diverse, complex and large-scale genomic datasets.
Daniel Fischer
I studied Statistics and Computer Sciences at the Technical University of Dortmund, Germany. During that time, my interest was particularly in mathematical statistics with a focus on high-dimensional extensions of the univariate median. After graduating, I moved to Tampere, Finland and completed my PhD in at the University of Tampere in Biostatistics with minor Bioinformatics.
While still being enrolled as PhD student at the University I started to work as a researcher in Bioinformatics at the MTT, Jokioinen, Finland. Since 2015 I am working at the Natural Resources Institute Finland (Luke) where I finalized my PhD.
My published articles in peer-reviewed journals cover a wide range of applications as well as statistical theory. My areas of expertise are target gene detection, biomarker identification and novel gene detection with a special focus on long non-coding RNAs. Further, I have experiences in the development of statistical methods for DE testing as well as deriving novel non-parametrical tests for (e)QTL analyses. I published and maintain currently six R-packages, i.e. for (e)QTL testing, cross-species ortholog detection and dimension reduction methods.
M. Pilar Francino
M. P. Francino studied Biology at the National University of Mexico and obtained her Ph.D. at the University of Rochester (New York), working on analyses of rates and patterns of DNA sequence evolution in bacteria and primates. She conducted postdoctoral research in bacterial genetics as an EMBO Fellow at the University of Paris. After that, she served as a Research Scientist at the DOE Joint Genome Institute (JGI) for five years, and was Head of the JGI Evolutionary Genomics Program from 2007 to 2009. Since 2009, she is a Senior Scientist at the Genomics and Health Department of FISABIO-Public Health in Valencia, and has been Head of the Department since 2012. Her current research focuses on the metagenomic analysis of human microbiome communities, in particular on understanding the development of the gut microbiota in infants. Work in her group analyzes the taxonomic composition, coding capabilities and gene expression patterns of the gut microbial community at different stages during infancy, as well as the relationships of these features with infant health. In addition, she is also interested in understanding the forces that shape the structure, organization and evolution of genomes. In previous and current work, she has addressed genome and molecular evolution subjects at different scales, ranging from the impact of mutational biases during DNA sequence evolution, to the evolution of new genes and their regulatory regions and the coevolution of different genomic traits.
Simon DW Frost
Reader in Pathogen Dynamics at the University of Cambridge; formerly Adjunct Associate Professor in the Dept. of Pathology, University of California San Diego (UCSD). Graduated with a BA in Natural Sciences (1st class), Trinity College, Cambridge (1992), DPhil in Mathematical Biology, Merton College, Oxford (1996). Postdoctoral positions at Princeton University, Oxford University, University of Edinburgh and UCSD. Awards include: NATO Postdoctoral Fellowship (1996), MRC Nonclinical Training Fellowship (1997-2000), a Royal Society Wolfson Research Merit Award (2008-2013), and Thomson-Reuters Highly Cited Researcher awards in 2014, 2015, and 2016.
Atsushi Fukushima
I am a professor at Kyoto Prefectural University. My current research interests focus on characterization of metabolic regulatory networks and integrated analysis of multi-omics data in plants. I am a member of the editorial board for BMC Genomics, Plant Methods, Frontiers in Plant Science, Plants, BioTech, and PeerJ.