Building pan-African Bioinformatics Capacity
University of Illinois Urbana-Champaign
Member Node
University of Illinois Urbana-Champaign
Member Node
Chris is the Associate Director for HPCBio. His focus is developing infrastructure within the HPCBio group for genomic analyses; this includes high-throughput analysis workflows for whole genome data processing and analysis, implementing and deploying self-contained pipelines such as MAKER and Interproscan, and developing custom solutions based on a project's particular needs. Chris coordinates with the IGB Computer Network Resource Group for server-side scalability and cluster job submission. Chris is also actively involved with bioinformatics open-source development, as a core developer for the BioPerl project an active contributor to the Generic Genome Browser (GBrowse), and more recently as a contributor to the Toil workflow system. He actively collaborates with various bioinformaticists from other open-source projects, specifically other projects from the Open Bioinformatics Foundation (such as Biopython, BioRuby, BioJava, and EMBOSS), and resources in the Generic Model Organism Database (GMOD) consortium of projects. Chris is also acts as the Secretary of the Board of the Open Bioinformatics Foundation (OBF) Chris earned his undergraduate degree in biology from Baylor University and the University of North Texas, followed by a Ph.D. in molecular microbiology at the University of North Texas in 2002, the latter primarily in a wet-lab research environment. He always had a strong interest in computational biology, and during his second postdoctoral appointment switched to focus completely on computational biology, joining the Carl R. Woese Institute for Genomic Biology as an IGB Postdoctoral Fellow. His experience and background as a BioPerl core developer has led to a number of diverse collaborations over the last several years, including work that led to the standardization for the ubiquitous FASTQ format. Chris's role as BioPerl developer has also led to mentoring opportunities in the Google Summer of Code for NESCent and four more with the Open Bioinformatics Foundation.
Dr Christopher Fields - Director
Chris is the Associate Director for HPCBio at the University of Illinois Urbana-Champaign. His focus is developing infrastructure within the HPCBio group for genomic analyses; this includes high-throughput analysis workflows for whole genome data processing and analysis, implementing and deploying self-contained pipelines such as MAKER and Interproscan, and developing custom solutions based on a project's particular needs.
BioinformaticsComputer ScienceData Submission, Annotation and Curation Data VisualizationGenomicsMachine Learning ChIP-SeqComparative Genomics Computational BiologyGenetic VariationEpigeneticsRNA-Seq Sequence AnalysisSequence AssemblyTranscriptomicsMolecular Biology EpigenomicsPlant Biology Evolutionary BiologyFunctional Genomics Gene ExpressionGene StructureGenotyping ExperimentMedical Biotechnology MetagenomicsMicrobiologyEvolutionary BiologySimulation Experiment Whole Genome SequencingWorkflows
Prof C Victor Jongeneel - Senior Research Scientist (Retired)
Victor Jongeneel is a consultant to the H3ABioNet network, having retired from the University of Illinois in 2018. He received his PhD from the University of North Carolina at Chapel Hill and was a post-doctoral fellow at the University of California, San Francisco and at the Swiss Institute for Experimental Cancer Research. Dr Jongeneel's career spans multiple domains of science. He was trained as a biochemist at the University of Lausanne (Switzerland), worked on mechanisms of viral DNA replication and transcription as a graduate student and a post-doctoral fellow, participated in the testing of the first antiviral drug (acyclovir) by the pharmaceutical company Burroughs-Wellcome, then became interested in the structure, genetics and regulation of the tumor necrosis factor loci when he became a group leader at the Ludwig Institute for Cancer Research in Lausanne (Switzerland). In parallel to his experimental work, Dr Jongeneel has had a life-long interest in the application of computational techniques to biological research. In 1997 he became a full-time computational biologist, taking responsibility for the Swiss node of the EMBnet bioinformatics network, and then for worldwide support for the research activities of the Ludwig Institute including a number of international genomics projects. He was one of the founders and the first director of the Swiss Institute of Bioinformatics (SIB), where he is a lifetime member of the Board of Trustees. He was the founding director of the Vital-IT high-performance computing center of the SIB, a collaborative venture between the Universities of Lausanne and Geneva, the Swiss Federal Institute of Technology, Intel and Hewlett-Packard. From 2007 to 2009 Dr Jongeneel was the Vice-President for Research of the Cyprus Institute in Nicosia, Cyprus, and from 2010 to 2018 he was a Senior Research Scientist at the National Center for Supercomputing Applications and the Institute for Genomic Biology at the University of Illinois, Urbana-Champaign. He has published over 120 peer-reviewed articles.
BioinformaticsComputer ScienceGenomicsComputational Biology Biomedical ScienceGenetic VariationHuman GeneticsImmunology Whole Genome Sequencing
Dr Lindsay Clark - Research Specialist
Dr. Clark is a Research Specialist with HPCBio, performing data analysis and training for a wide variety of bioinformatics applications. She earned a Ph.D. in Genetics from the University of California at Davis in 2011, and specialized in plant genetics until joining HPCBio in 2019. She is an expert in genetic marker analysis, including population genetics and genome-wide association studies. She is the author of two R packages for genetic analysis of polyploid organisms: polysat, for population genetics using microsatellite markers, and polyRAD, for genotype calling from sequence read depth. She has a decade of experience in R programming and has taught R in classroom and workshop settings.
BioinformaticsGenomicsAgricultural Science Genetic VariationGWAS Sequence AnalysisGenotyping Experiment Population GeneticsPlant Biology Population Genomics 
Liqian Ma - Research Assistant
Liqian Ma is a fourth year Ph.D. student in the Department of Molecular and Integrative Physiology at the University of Illinois Urbana-Champaign. She is specialized in tumor immuno-oncology and her thesis research focuses on investigating the mechanism by which a cholesterol metabolite, 27-hydroxycholesterol, promotes breast cancer metastasis. Her expertise lies in immunology, molecular biology, cell biology, nuclear receptor pharmacology, and genomics. She works with H3ABioNet on applying machine learning methods to omics data to help with disease classification and prediction. She has a strong interest to further contribute to therapeutic discovery and development by integrating immuno-oncology with omics studies. In her free time, she loves traveling, hiking, exploring palatable food and cooking tasty food.
BioinformaticsGenomicsMedicine Biomedical ScienceGWAS Sequence AnalysisGene Expression Human GeneticsData Visualisation Drug DiscoveryGenotype and PhenotypeImmunologyInfectious Disease Machine LearningOncologyRNA-SeqTranscriptomicsTranslational Medicine 
Gloria Rendon - Bioinformatics Specialist
Gloria Rendon is a bioformatics specialist and a member of the HPCBio group (https://hpcbio.illinois.edu/) housed at the IGB, Institute for Genomic Biology, at the University of Illinois at Urbana-Champaign, USA. The group provides bioinformatics support and training for researchers in Computational Biology on and off campus. She has participated in a wide range of projects in genomics. In recent years her interests have focused in the area of scientific replication with workflows and have actively participated in the development, testing and deployment of bioinformatics workflows. Some salient examples include: dada pipeline for microbiome analysis, human paleogenomics pipeline, chopchop-based CRISPR design pipeline, Cut-and-Run chromatin profiling pipeline, ViRema-based viral-DIP-analysis, deepSNV-based viral variant calling pipeline.
BioinformaticsGenomicsWorkflows 
Yuan Tian - Junior Statistical Analysis/Graduate Student
Yuan Tian is a junior statistical analyst in High Performance Computing in Biology (HPCBio) of the Roy J. Carver Biotechnology Center and a doctoral candidate in the department of cell and developmental biology at University of Illinois at Urbana-Champaign. Her thesis study focuses on the mechanisms that chromatin regulators control tissue regeneration in Drosophila melanogaster. Regeneration is an amazing ability that some organisms have to recognize, repair and replace missing tissues. Her work identified the important roles the Polycomb and Trithorax group genes play in this precisely regulated process. Specifically, the two SWI/SNF chromatin-remodeling complexes play separate roles in regenerative growth and proper patterning. She is interested in identifying the underlying mechanisms through statistical and bioinformatics analysis of gene expression and genomics data. Her goal is to combine genetic, bioinformatics and molecular biology strategies to study human diseases and promote human health.
BioinformaticsChIP-SeqStatistics and Probability EpigeneticsGene ExpressionRNA-Seq 
Kim Walden - Research Specialist
Kim Walden is a Research Specialist in Life Sciences with the HPCBio group at the University of Illinois at Urbana-Champaign. Her area of expertise is assembling high-throughput sequencing data for genomes and transcriptomes. She works with current assembly software packages for Illumina, PacBio, and Oxford Nanopore sequencing. Kim also has extensive experience working with NCBI and their data submission requirements, coordinating the deposition of over 500 datasets from genome, transcriptome, and phylogenomic projects. Kim received her B.S in Biology at Millikin University in Decatur, Illinois and her M.S. in Entomology from the University of Illinois at Urbana-Champaign. Her Master's Degree work focused on mariner transposable elements in a group of stingless bees and the debunking of ancient DNA claims from amber-entombed insects. Prior to joining the HPCBio group in January 2017, she worked for 20 years in the Department of Entomology at the University of Illinois at Urbana-Champaign as a Research Specialist in Life Sciences managing the laboratory of Dr. Hugh Robertson. Kim has worked on a multitude of projects mostly focused on insect olfaction and gustation using a wide range of molecular biology techniques. For the last 15 years, she has been involved with over 15 genome assembly projects including those for the apple maggot fly, Rhagoletis pomonella, the Western corn rootworm beetle, Diabrotica virgifera, and the European honey bee, Apis mellifera.
BioinformaticsData Submission, Annotation and CurationMolecular Biology GenomicsSequence AnalysisSequence AssemblyTranscriptomics Whole Genome Sequencing 
