Advisory Board and Editors Bioinformatics
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.
Luiz Gadelha
Luiz Gadelha works in the German Human Genome-Phenome Archive (GHGA) at the German Cancer Research Center (DKFZ) in Germany and the National Laboratory for Scientific Computing (LNCC) in Brazil. He received his D.Sc. degree in Computer and Systems Engineering from the Federal University of Rio de Janeiro, Brazil. He has been involved in the research and development of parallel and distributed scientific workflow management systems and scientific databases. He has participated in research projects in the bioinformatics and biodiversity application areas. His main research interests are scientific data management, computational reproducibility, and high performance computing.
Aleksandra A Galitsyna
Aleksandra is a PostDoc at IMES Massachusetts Institute of Technology (MIT), specializing in chromatin architecture analysis using Hi-C, Micro-C, and imaging data. Notable for contributing to Open2C software with the Open Chromosome Collective. Currently, Aleksandra explores polymer simulations of chromatin in early embryogenesis of vertebrates. Her focus centers on understanding the biological implications of various 3D genome structures and their connection to cell fate decisions.
Jianye Ge
Dr. Jianye Ge is the Associate Director of the Center for Human Identification and an Associate Professor in the Department of Microbiology, Immunology & Genetics at the University of North Texas Health Science Center. His research relates primarily to forensic genetics, bioinformatics, and data mining. The software programs he developed have been used by the Federal and State government agencies to assist in solving criminal cases.
Mikhail S Gelfand
Vice-Director for Science at the Kharkevich Institute for Information Transmission Problems. Professor of the Lomonosov Moscow State University, Skolkovo Institute of Science and Technology, and Higher School of Economics. Member of Academia Europaea. Recipient of the 2007 Baev Prize of the Russian Academy of Sciences. Member of Editorial Boards of PeerJ and Biology Direct.
Sandra Gesing
Scientific Outreach and DEI Lead at the Discovery Partner Institute, University of Illinois Chicago
Before: Associate Research Professor (Dep. of Computer Science and Engineering and Center for Research Computing) at the University of Notre Dame, USA
Research associate in the Data-Intensive Research Group at the University of Edinburgh, UK; Research Associate in the Applied Bioinformatics Group at the University of Tübingen, Germany.
Perennial experience in industry as head of a system programmer group, project manager, system developer.
Noushin Ghaffari
Dr. Noushin Ghaffari is a senior member of the bioinformatics team at Texas A&M AgriLife Genomics and Bioinformatics (TxGen), where she is involved in various projects from planning experiments to data analysis. She is also focused on method development and application projects that will impact scientific community. Her research activities have encompassed various areas of computational biology and have enabled her to study and learn more about the characteristics of multiple species. Furthermore, she intensely pursues her theoretical interests focusing on applications of mathematics in solving biological problems. Dr. Ghaffari has led numerous genome and transcriptome assembly projects for novel species such as cattle tick, gene discovery research though RNA-Seq studies, studying microbiome communities via metagenomics research and etc. Dr. Ghaffari has vast teaching experiences and continues to educate Texas A&M faculty/students/researcher on high performance computing, data analysis and bioinformatics.