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HPCBIO PEOPLE

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Matthew Hudson, Director

  Matthew Hudson is a Professor in the Department of Crop Sciences at the University of Illinois, and a faculty affiliate with the Carl R. Woese Institute for Genomic Biology (IGB) and Department of Entomology. He also serves as Associate Chief Scientist of the National Center for Supercomputer Applications (NCSA), and is the Director of the High-Performance Biological Computing (HPCBio) group at the IGB, NCSA, and the Roy J. Carver Biotechnology Center.

  Dr. Hudson was trained in Natural Sciences at the University of Cambridge and received his PhD in Biology from the University of Leicester in England. He completed a postdoctoral fellowship on signal transduction and the control of gene expression in plants at the University of California, Berkeley, where he began to work with the analysis of genome sequence and microarray expression data in the model plant Arabidopsis. He then worked at the Torrey Mesa Research Institute and at Diversa corporation in San Diego, CA as a Bioinformatics Scientist on plant, human and microbial projects before moving to the University of Illinois as a faculty member.

  Since moving to the University Dr. Hudson has pursued research that applies computational methods to biological problems across a wide range of organisms. His research interests center on the use of high-performance computational techniques to pursue questions in genomic biology. His research program focuses on identifying the genomic variants that control trait variation in plants, nonhuman animals and human populations, funded by grants from the NSF, DOE, and USDA as well as private companies, foundations, and commodity boards. Past and current major research collaborations include the Energy Biosciences Institute and the Center for Computational Biotechnology and Genomic Medicine. He also teaches award-winning classes at Illinois on the interface between biology and computing.

Christopher J. Fields

I am the Associate Director for HPCBio.  My focus is architecting and developing infrastructure within the HPCBio group for genomic analyses; this includes implementations of such web-based tools as GBrowse,and Galaxy, high-throughput analysis pipelines for whole genome annotation such as MAKER and Interproscan, and custom solutions based on a project’s particular needs. I coordinate with the IGB Computer Network Resource Groups and the Galaxy project on code optimizations for server-side scalability and cluster job submission, with the final end-goal being a working Galaxy instance at the University of Illinois. 

     I am also a core developer for the BioPerl project, am an active contributor to the Generic Genome Browser (GBrowse). Furthermore, I am actively collaborating 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.  I am currently a member of the board of the Open Bioinformatics Foundation (OBF).

     I earned my undergraduate degree in biology from Baylor University, followed by my Ph.D. in molecular microbiology at the University of North Texas in 2002, the latter primarily in a wet-lab research environment. However, I have always had a strong interest in computational biology, and over the course of my second postdoctoral appointment decided that I wanted to focus completely on computational biology, joining the Carl R. Woese Institute for Genomic Biology as an IGB Postdoctoral Fellow. As previously alluded to, I also became one of the lead developers of the BioPerl open-source bioinformatics toolkit during my post-graduate research, in 2007. My 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.  My 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.

Jenny Drnevich

Jenny Drnevich is a Functional Genomics Bioinformatics Specialist with the High-Performance Biological Computing (HPCBio) group and the Roy J. Carver Biotechnology Center. Her areas of expertise are statistical analyses of gene expression data from microarrays and RNA-Seq, post-analysis data mining and bioinformatics instruction.  

Jenny received a B.S. in 1996 from Purdue University in Ecology, Evolution and Population Biology and then a Ph.D. in 2001 from Arizona State University studying Evolution and Behavioral Ecology in insects. During her undergraduate and graduate studies, she did field work in Australia, Venezuela, Costa Rica, Panama and Thailand, and also spent a semester at the University of Sheffield, England. Jenny then switched her research focus to quantitative genetics and genomics, moving to the University of Illinois in 2001 to do post-doctoral work studying mating success and longevity in Drosophila melanogaster. She started her first microarray experiment in 2002 and was the first user of the Affymetrix microarray system at the Carver Biotechnology Center at the University of Illinois.

In 2005 she joined the Carver Biotechnology Center's Bioinformatics Unit in her present job title to provide microarray analysis services to researchers at the University and elsewhere. In 2012, the Bioinformatics Unit joined with groups from the Carl R. Woese Institute for Genomic Biology and the National Center for Supercomputing Applications to form the HPCBio group, and her services expanded to include other sequencing data, particularly RNA-Seq. To date, she has analyzed over 250 expression experiments from 80+ research groups across the world. She also has taught or co-taught dozens of different workshops for undergraduates, graduates, postdoc and faculty members covering gene expression analysis, metagenomics analysis, basic R programming, data management, Linux and using large computer clusters, reaching over 450 participants from within and outside the University of Illinois.

Jessica (Kirkpatrick) Holmes

Jessica (Kirkpatrick) Holmes is a Research and Instructional Specialist in Life Sciences with the HPCBio group. Her areas of expertise are bioinformatics instruction, RNA-Seq analysis, microbiome analysis with QIIME, perl scripting, and plant genomics.

She received her Bachelor’s degree in 2010 from Iowa State University in Bioinformatics & Computational Biology where she collaboratively worked on a Gbrowse-based database of zinc finger nuclease sites. She then received her Master’s degree in 2013 from the University of Illinois at Urbana-Champaign in Bioinformatics, where she was supported by the Jonathan Baldwin Turner Fellowship. As a graduate student in Dr. Stephen Moose’s lab, she analyzed the highly polyploid and complex bioenergy crop, Miscanthus. Specifically, she performed several alignment, assembly, and variant-calling methods on a variety of Miscanthus species’ exomes and transcriptomes in order to disentangle their unique complexities resulting from whole genome duplication and chromosomal fusion/deletion events.

In January of 2015, she joined HPCBio. She works on a diverse set of organisms and projects including RNA-Seq and 16S microbiome analysis, pipeline development, and perl scripting for file formatting and data extraction. She organizes and teaches workshops catering to undergraduates, graduates, post-docs, and research faculty over introductory bioinformatics, Linux, high performance computing, R programming, RNA-Seq analysis, QIIME analysis, data management (project organization and git basics), and genome browsers. In addition, she is Program Coordinator for an R25 program/partnership between KnowEng, Mayo Clinic, and Fisk University. Her role is to coordinate remote access to Bioinformatics seminar courses at UIUC, to organize Fisk faculty attendance at UIUC Bioinformatics workshops, and to develop and manage a Summer research experience aimed at sophomore Fisk students, during which she also instructs and advises the students.

George Lixin Gong

George Gong is a Research Programmer with HPCBio and has been with the group since its formation in March 2012. George’s core responsibilities are supporting the DNA Sequencing Facility’s data processing needs in data acquisition from instrument to customer; supporting the Keck Center’s database management including the consolidation of its LIMS infrastructure;  participating in HPCBio bioinformatics analysis efforts by ensuring that datasets, both internally generated and publically available, are stored, updated, and backed up in a consistent manner; engaging in the planning and implementation of data analysis workflows for HPCBio bioinformatics projects and conducting individual data analysis projects within the HPCBio group as needed. 

     Prior to joining HPCBio, George was a Research Programmer at the University of Illinois’s Biotechnology Center’s Bioinformatics Unit for 12 years, where he worked as Database Administrator of Oracle, DB2, and Mysql database servers. He was also actively involved in technical research and development to enable continuing innovation within the unit’s computing infrastructure, participated in designing and developing numerous software applications for data analysis and sequence annotations using Java, C, and Perl, and performed sequencing analyses for bioinformatics projects. Before joining the University of Illinois, George was Senior Software Engineer at ERES consultants Inc., where he designed and developed interstate highway and airport pavement management systems.

     George has a MS in Computer Science from Cleveland State University and a MS in Zoology from Ohio State University.

Liudmila Sergeevna Mainzer

Liudmila Sergeevna Mainzer is a Senior Research Scientist at NCSA and the HPCBio group. 

    She received her bachelor's in Physics in 1999 from Belarus State University, where she focused on designing vector quantization algorithms to train artificial neural networks for pattern recognition. Luda then received her PhD in 2006 from the University of Illinois at Urbana-Champaign, specializing in Biophysics and Computational Biology. In graduate school she studied physiology and experimental neurophysiology of invertebrates, created mathematical models of intracellular signaling processes, and computer simulations of neural networks that engage in behavioral decision making. She also pursued part-time her lifelong passion for neuromorphic engineering.

    Dr. Mainzer subsequently undertook two postdoctoral research projects. First, with Dr. Caetano-Anolles, studying evolution of life and the persistence strategies of organisms from diverse environments. During this time she also taught for two semesters an introductory course in neuromorphic engineering. Then, in 2011-2012, she worked in the group of Dr. Matthew Hudson to perform a transcriptomics analysis of mycorrhizal symbioses. Having joined HPCBio in 2013, Luda is focusing on the R&D mission of the group.

Ravi Kiran Donthu

Ravi Kiran Donthu is a Research Specialist in Life Sciences with the High-Performance Biological Computing (HPCBio) group. He received his Ph.D. from University of Illinois at Urbana-Champaign.

     Kiran received his bachelor's degree in Pharmacy from Shadan College of Pharmacy affiliated with Jawaharlal Nehru Technological University, Hyderabad. He received a research master's degree in Bioinformatics from University of Leeds, UK. As a graduate student at Leeds he created a database, web interface and visualization tool for protein-ligand interactions. During his graduate studies at University of Illinois with Dr. Harris Lewin, he developed a tool to define homologous synteny blocks and studied a QTL region on cattle chromosome 3 to understand genomic basis of quantitative traits. 

     He joined the Bioinformatics unit of W.M. Keck Center in 2009 and became part of HPCBio in 2012. He has been involved in wide variety of data analysis projects.

 

Gloria Rendon

Gloria Rendon works jointly with HPCBio and NCSA on HPC (high-performance/high-throughput computing). 

     She has experience in several different areas of biology that involve analysis of big data: genomic human variant calling, epistasis analysis of genome-wide association studies (GWAS), proteomic studies of membrane proteins, microbial evolution, novel drug design with antimicrobials based on antisense RNA and delivered via nanoparticles. Her experience also includes developing software applications  and data-processing pipelines, running and benchmarking MPI/GPU/CPU applications on different computing platforms (everything ranging from smaller local clusters to petascale systems like Blue Waters). She has participated in collaborative projects in the private sector as well as in academia, including with the Mayo Clinic, University of New Mexico, San Diego State University, Universidad de Antioquia. Her teaching experience includes computer science courses at UIUC and Illinois State U, as well as bioinformatics workshops in the summer programs of Supercomputing Education.

     Her educational background is in Computer Science, specifically in Software Engineering, Database Systems, and Artificial Intelligence. She recieved her M.S. in Applied Computer Science from Illinois State University, and her Ph.D. (ABD) in Computer Science from the University of Illinois  at Urbana-Champaign.

 

 

Affiliates -

Biotech Center's DNA Services Unit

 

Biotech Center's Functional Genomics Unit

 

IGB's CNRG group