NCGR Research Faculty

 

 

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Callum J. Bell, Ph.D., President

In addition to leading the organization, Dr. Bell has two main research interests. He provides technical leadership to a collaboration with Washington State University funded by the National Science Foundation to understand the genome of red alder and its symbiosis with the nitrogen-fixing bacterium, Frankia alni. This project aims to understand the complex interactions among tree genes, bacterial strains, soil types, and microbial communities, and how these influence growth of this important tree crop, which is used for many timber applications and as a biofuel. Another project, funded by the Gordon and Betty Moore Foundation, aims to develop technology to enable transcriptome studies of individual plant cells. Plant cell walls present challenges to single cell studies that are not encountered in animal investigations. This project aims to bring the benefits of single cell biology to plant researchers. Dr. Bell received his Ph.D. From the University of Edinburgh where he carried out pioneering work on the gravitational biology of Arabidopsis thaliana.   

 

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Andrew Farmer, Bioinformatics Fellow

Mr. Farmer's work focuses on the use of bioinformatics to address questions in plant biology, with an emphasis on enabling crop improvement efforts though the development of clade-oriented information resources utilizing phylogenetic and comparative genomic analyses. He leads NCGR participation in the USDA-funded  Legume Information System (http://legumeinfo.org) as a collaborative effort with partners at Iowa State University and USDA-ARS. He also serves as co-PI on an NSF-funded grant to develop a federation of independently developed and separately maintained web-based genomic data resources in the legume family, the Legume Federation (http://legumefederation.org). His current research interests are focused on how plant species have adapted to a wide range of environments through diversification mechanisms associated with large scale genome duplications, while at the same time maintaining core functions. He participates in a variety  of open source  software development  projects and in other efforts to facilitate data sharing and improving adherence to standards among groups involved in information resource management in plant biology.   

 

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Joann Mudge, Ph.D., Senior Research Scientist

Dr. Joann Mudge works on structural genomics, studying how genomes are organized and how genome structure affects gene expression, phenotypes, and genomic plasticity. Her main area of focus is in plant genetics, especially of nitrogen-fixing species in the bean and pea family (legumes). Her current projects include de novo sequencing, assembly and analysis of multiple genomes in Medicago truncatula and its relative, alfalfa. She also has a project on pangenomics algorithm development and is applying these algorithms to gain biological insights in multi-genome datasets, including Medicago truncatula. In addition, she works in the area of plant microbiomes, especially looking at plant/fungal interactions that buffer plant growth against abiotic stressors and implications for climate change. Dr. Mudge has also worked in human genomics, playing a major role in the sequencing of the 6th ever human genome (of a Korean individual) and of female monozygotic twins discordant for multiple sclerosis. Dr. Mudge is also dedicated to outreach and helping the upcoming generation to develop an interest in science. An NIH-supported project allows her to work with elementary and secondary education teachers to teach them about genomics and bioinformatics and to help them develop computer-based case studies for their classrooms. She also has an innovative high school intern program in which she works with high school students, teaching them about DNA sequencing and bioinformatics and helping them to develop case studies. She regularly visits schools and science fairs to teach and promote science.   

 

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Thiru Ramaraj, Ph.D., Bioinformatics Research Scientist

Dr. Thiruvarangan (Thiru) Ramaraj’s background and training is in Computer Science. His research focus is mainly on Bioinformatics and Computational Biology. At NCGR, Dr. Ramaraj and his team primarily focus on developing workflows for large-scale biological sequence data analysis such as complex plant de novo genome/transcriptome assemblies. His current NSF funded projects include, (i) Investigation of genome-wide structural re-arrangements of diploid and polyploid cotton genomes, (ii) Resequencing several accessions of cotton to address fundamental biological questions of polyploidy genomes and the genetic diversity of cotton, and (iii) Investigating graph data structures to effectively represent pan-genomes and associated algorithms for analyzing pan-genomes. Dr. Ramaraj is the PI on a new NSF systems-biology proposal on biofilms that is expected to start in August 2017. He is also an Adjunct Assistant Professor in the Department of Biology at the University of New Mexico, Albuquerque. He supervises summer interns and participates in outreach activities at NCGR.   

 

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Anitha Sundararajan, Ph.D., Research Scientist

Dr. Anitha Sundararajan is an environmental microbiologist/microbial physiologist with training and expertise in microbial biofilm physiology.  At NCGR, she has been involved in a variety of projects and her research interests are diverse.  As a post-doc, she was involved in an NSF project that focused on maize recombination.  She is also working on the NIH-funded INBRE project where she contributes bioinformatics analyses, organization of an annual conference as well as organizing NCGR's summer internship program.  Additionally, she works closely with Dr. Mudge on outreach activities.  She also has expertise in sequencing protocols and is a long time contributor to the NCGR sequencing center.  Her interests are primarily in the field of microbial physiology, and she is working towards independent funding in this area in collaboration with colleagues at Montana State University.   

 

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Stephanie Guida, Ph.D., Senior Bioinformatics Analyst

Dr. Guida-English’s main research interest is identifying the role of epigenetic mechanisms in human disease. She is currently working with collaborators at the University of Wyoming to study how the obese maternal environment in the model species of ovine influences the regulation of biological pathways in the fetus. The group is also interested in establishing how epigenetic mechanisms are involved in stabilizing the pathways altered in the fetus in response to the maternally obese environment, predisposing offspring and possibly future generations to disease later in life through heritable epigenetic marks, such as DNA methylation. She has been involved with the Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP), a large effort funded by the Gordon and Betty Moore Foundation to sequence, assemble, and annotate nearly 700 diverse marine microbial eukaryote transcriptomes. Through a collaboration with Northwest Advanced Renewables Alliance (NARA), she has also assisted in the development of a Douglas Fir SNP chip to aid in forestry breeding programs.   

 

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Diego Fajardo, Ph.D., Bioinformatics Analyst

Dr. Fajardo earned his Ph.D. in Plant Breeding and Plant Genetics from the University of Wisconsin - Madison. Prior to joining NCGR, he was a Research Assistant at USDA-ARS and the University of Wisconsin - Madison in the department of horticulture. His research interests focuses mostly on plant genomics, from genome assembly and annotation, to variant discovery and differential expression analyses, as well as single molecule sequencing using modern technologies. As a self-educated bioinformatician with life sciences background, one of his goals is to educate and share his knowledge with other scientists with little or no experience on bioinformatics.   


 

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Sam Hokin, Ph.D., Sr. Computational Scientist

Sam is a physicist turned computational biologist who works at NCGR on database and Web applications to make genetic and genomic data from diverse plant species readily available to plant biologists and agricultural breeders. He focuses on Java programming, and currently specializes in the data warehouse application InterMine. Sam also has an appointment at the Carnegie Institution for Science Department of Plant Biology at Stanford, where he analyses and models DNA and mRNA sequence data from Arabidopsis and maize experiments. He is particularly interested in modeling experiments in which a transcription factor, a protein which drives or suppresses expression from target genes, is rapidly introduced into the cell nucleus in order to study the gene regulatory networks governing leaf growth.   

 

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Sudhansu Dash, Ph.D., Senior Researcher

Dr. Sudhansu Dash has a background in Agriculture and Plant Genetics with his Ph.D. research in transposon genetics in maize at Iowa State University. His current focus is on developing genomics information resources for the plant science research community. He has served as the curator and managed the plant gene expression database PLEXdb (plexdb.org) for several years. He is working with PeanutBase (peanutbase.org) and LIS (legumeinfo.org) as curator and developer and as a co-PI for the PeanutBase project. His research interests are in the areas of functional annotation and clade-based presentation of curated expression data, upstream regulatory elements, gene network and pollen genomics.   

 

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Joel Berendzen, Ph.D., Sr. Computational Biologist

Dr. Berendzen is a Senior Computational Scientist at NCGR, where he architects and implements software that uses biological theory to put sequences in evolutionary and ecological context.  Applications in which he is expert include: (i) Rapid, scalable Big-Data phylogenomic methods that work across the whole Tree of Life, (ii) Characterization of host/biota interactions, including lower eukaryotes and virusesMolecular etiology of complex diseases by integrating host-transcriptome, microbiome, (iii) and other information, and (iv) Pandiagnostics for infectious diseases. His other interests include protein structural, protein dynamics, the behavior of water at protein surfaces, and figure skating.  He has over 10,000 citations to his papers in these fields.   

 

 

 


 NCGR Adjunct Faculty


GregMayGreg D. May, Ph.D.,  Research Fellow

Dr. May’s interests are in the understanding of the recruitment of genes to serve new biological functions and in the biology of the genome.  When novel organs or biological functions such as vision evolve, genes are often recruited to serve new purposes. Lens proteins in the eye, for example, were recruited from metabolic enzymes and in some instances still retain metabolic activity. Plant genome duplication or increased ploidy facilitates genome plasticity and the opportunity for genes to be recruited to serve novel functional roles. The effect of these duplication events on the biology of the genome, in particular, the molecular mechanisms, such as DNA methylation and histone modification employed to compensate for changes in genome content are also of interest.





 

SK

Stephen Kingsmore, MB, ChB, BAO, DSc, FRCPathResearch Fellow

Dr. Stephen F. Kingsmore was appointed Director of the Children's Mercy Center for Pediatric Genomic Medicine in January 2011. He was named one of the best physicians of 2012 by Medscape. Previously, Dr. Kingsmore was variously the President, CEO and Chief Scientific Officer of the National Center for Genome Resources, Santa Fe, New Mexico. Prior to this, Dr. Kingsmore was Chief Operating Officer of Molecular Staging Inc., Vice President of Research of CuraGen Corp. and Assistant Professor at the University of Florida. Dr. Kingsmore received a B.Sc. in medical microbiology, degrees in medicine (M.B., Ch.B., B.A.O.) and D.Sc. in molecular genetics from the Queen's University Belfast in Northern Ireland. He completed residency in Internal Medicine and fellowship in Rheumatology at Duke. Dr. Kingsmore is a Fellow of the Royal College of Pathologists (UK) and a member of the DHHS Secretary's Advisory Committee on Heritable Disorders in Newborns and Children Carrier Screening Workgroup. His research interests are genome analysis, systems surveys and individualized medicine.





Lewis

Norman G. Lewis, Ph.D., Research Fellow

Dr. Lewis was initially trained in chemistry (natural product/organic chemistry/biochemistry specializations) receiving B.Sc. and Ph.D. degrees from the University of Strathclyde (Glasgow) and University of British Columbia, where he received ICI and NATO/SRC scholarships to support his studies. He next worked with Professor (Sir) Alan R. Battersby on Vitamin B12 biosynthesis at the University of Cambridge through NRC (Canada) post-doctoral support, prior to taking up a NRC (Canada) Research Associate position. Dr. Lewis has also previously held positions as Group Leader at PAPRICAN (Pulp and Paper Research Institute of Canada), and as Associate Professor at Virginia Tech.His research has largely been supported by the U.S. Department of Energy, National Aeronautics and Space Administration, National Institutes of Health, National Science Foundation, U.S. Department of Agriculture, as well as from Thomas G. and Anita Hargrove Foundation, and the Arthur M. and Katie Eisig-Tode Foundation. Dr. Lewis has also received support from NSERC (Canada), Tembec (Canada), ICI, McMillan Bloedel (Canada), NATO/SRC, Philip Morris Tobacco Company and many other funding entities. 









Craig BCraig Beattie, Ph.D., Program Leader

Dr. Beattie works on the structural and functional genomics of pathogen entry into eukaryotic cells, the genetics of disease susceptibility in multiple mammalian species, and structural and comparative genomics. The subjects of his research include commercial animal species where his group’s efforts led to the first comprehensive genomic and sequence maps for livestock as well as the discovery of unique, clinically active agents for use in human and veterinary medicine. His current research is focused on applying RNA-seq to identify structural differences in differentially expressed gene clusters and potential allelic imbalances relevant to host susceptibility to disease and the etiology of infection, and computational modeling of pathogen entry and neutralization to improve vaccine development. 









FieldsMatthew Fields, Ph.D.  Research Fellow

Dr. Matthew Fields is an associate professor in the Department of Microbiology at Montana State University.  His lab is in the Center for Biofilm Engineering, and he is also associated with the Thermal Biology Institute and the Energy Research Institute at Montana State University.  His laboratory uses molecular ecology to study microbial communities associated with different environments in the field that include subsurface sediments, groundwater, coal, and industrial environments. Laboratory work includes sulfate-reducing bacteria, methanogens, and lipid-producing algae, and these types of organisms are important to bioremediation, metal corrosion, and biofuel production, respectively.  Ultimately, a driving question is to understand the relationships between structure and function at different scales of biology and how ecological and physiological responses help shape the structure and function relationships. An improved understanding of structure/function relationships will allow predictive modeling and design for a variety of natural and engineered systems. 

 

 

Matt-BellgardMatthew Bellgard, Ph.D., Research Fellow

Professor Bellgard is Murdoch University’s Bioinformatics Chair and Director of the Western Australian State Government Centre of Excellence, the Centre for Comparative Genomics. His scientific work has resulted in developments in both the areas of pairwise sequence alignment and artificial intelligence, bacterial bioformatics, whole genome comparative analysis and annotation for a range of species, as well as advances in the development of web-based integrated systems utilizing high performance computing. Major discoveries include vaccine candidates in bacteria and cattle tick, evolutionary mechanisms in bacterial genomes, molecular plant breeding, new computational bioinformatics tools and the development of integrated web-based systems for human health and agricultural applications. Current research interests are human rare diseases, food security (biosecurity, crop improvement, host/pathogen interaction and weed research) and cattle tick genomics.