Our Team

Scientific Staff

Callum 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.
Joel Berendzen, Ph.D

Senior 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.
Connor Cameron

Bioinformatics Analyst

Connor has been with NCGR since 2010 after graduating from the New Mexico Institute of Mining and Technology. His primary focus is on bioinformatic assembly and analysis pipelines utilizing hybrid and multi-generational datasets. He also develops RESTful web applications for accessing and organizing information as part of the Legume Federation and Legume Information System, and believes in FAIR data standards and open source technology. He has recently been tussling with how to represent the pangenome and various pseudo-chromosome assembly finishing efforts.
Alan Cleary, Ph.D

Computational Research Scientist

Alan joined NCGR in 2013 as an intern and then stayed on part time while earning his Ph.D in Computer Science at Montana State University. During this time he worked on the Legume Information System as a computational research scientist and software engineer. This work primarily involved developing and implementing real-time algorithms for computing synteny between closely related legume species housed in a variety of geographically distributed data stores maintained by independently funded groups. Alan continues to work on the Legume Information System but is now also involved in projects related to the topic of his dissertation: computational pangenomics. Specifically, Alan works on pangenome representation, construction, and analysis, including annotation, read mapping, variant calling, gene clustering, and (multiple) alignment. Alan's own research is concerned with the development of new methods for graphical pangenome analysis. This includes the development of parallel algorithms to enable pangenome analysis at scale in high-performance computing environments as well as the application of machine learning to make associations between complex graphical structure and phenotypic traits.
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 and gene network.
Stephanie English, Ph.D.

Senior Bioinformatics Analyst

Stephanie received her Ph.D. from the University of Delaware, during which she spent two research seasons in Antarctica and studied the role of epigenetics in environmental adaptations. She joined NCGR in 2012 and has worked on a variety of projects ranging from the development of a SNP chip to support Douglas Fir breeding programs to the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) which provided a valuable genomic resource to the marine microbial community. Today, her work is mostly focused on variant discovery and marker-trait associations in agricultural species. Stephanie’s other current research includes studying the epigenetic mechanisms involved in fetal programming in the over- and under-nourished maternal environment.
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.
Sam Hokin, Ph.D.

Senior Computational Scientist

A physicist at heart, Sam is particularly interested in systematic approaches to biological function and disease diagnosis. He believes that while biological processes are complex and often redundant, important effects may be described by simplified models which take into account the key inputs and outputs. Sam also enjoys the field of genomics, especially coming up with new approaches to analyzing biological activity. As a longtime computer programmer, Sam enjoys writing analysis software and user interfaces, particularly in the Java programming language. In this capacity he has learned a great deal about curation of biological data and is a regular contributor to the InterMine data warehouse application. Although to date his work in bioinformatics has been focused on plants, Sam has become interested in medical applications of his expertise. In that regard, he is interested in the use of new genomic techniques for complex disease classification of human pan-genomes. Complex diseases, which have many associated DNA variants, have been a difficult nut to crack in precision medicine, and Sam hopes that we can make an impact in that area with entirely new methods.
Evan Lavelle, M.S.

Bioinformatics Analyst

Evan received a M.S. in Bioinformatics and Computational Biology and a graduate minor in Molecular Biology from New Mexico State University. His research during this program focused on differential expression analysis between host phenotypes upon parasite exposure. He joined NCGR in 2019 and assists with workshops as well as projects.
Karen Moll

Bioinformatics Pre Doctoral Fellow

Karen has been working as an analyst at NCGR while completing her Ph.D. in Microbiology. As part of her doctorate work, Karen worked on the assembly, annotation and characterization of a novel, extremophilic, high lipid-producing diatom for algal biofuels applications. She has experience in gene, pathway and ontology annotation. Stemming from her doctorate work, Karen has an interest in the algae-bacteria interactions within the phycosphere. Currently, Karen focuses much of her time analyzing variant-calling and introgression projects.
Joann Mudge, Ph.D

Senior Research Scientist

Dr. Joann Mudge works on structural genomics and plant microbe interactions. Her main area of focus is in plant genetics, especially of nitrogen-fixing species in the bean and pea family (legumes). She studies genome plasticity and organization and how genome structure and flexibility affects phenotypes. She currently works with pangenomic algorithm development and application. Taking a pangenomic approach allows for the comparison of genome structure between different individuals with the same species and identifying differences that drive phenotypic divergence and adaptation in a species. 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, through early intervention and teacher training. She 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 and present case studies. She regularly visits schools and science fairs to teach and promote science and serves on the Santa Fe Public Schools Science Advisory Board.
Faye Schilkey

Director, Strategic Projects

Faye's interest in computers created a career that spanned programming automotive assembly line controllers, to real-time missile autopilot and guidance systems, to IT, databases and developing bioinformatics software. She has worked at the National Center for Genome Resources since 1996 holding various technical, project leadership and business development posts. As the Director of Strategic Projects and the Director of the New Mexico IDeA Network for Biomedical Research Excellence (NIH NIGMS 2P20GM103451) Sequencing and Bioinformatics Core, she specializes in next generation sequencing and bioinformatics technologies. With an interest in integrative omics, she leads multidisciplinary teams in productive research collaborations with academic and commercial partners. Ms. Schilkey received a BS in Computer Engineering and presently is pursuing her PhD in Biotechnology at the New Mexico Institute of Mining and Technology. As part of her research program, she is developing analytics to study mobile DNA elements.
Kelly Schilling, M.S.

Bioinformatics Analyst

Kelly received her M.S. in Pharmacology and Toxicology from the University of California, Davis in 2004. She worked for eight years as an environmental toxicologist before joining NCGR as a bioinformatics analyst in 2012. Kelly performs bioinformatics analyses and develops custom bioinformatics pipelines to meet clients’ project needs. Examples include variant discovery, trait association studies, generation of transcriptome assemblies, and structural and functional annotation. Kelly works mainly with agricultural crops, but has participated in a variety of projects, including the Marine Microbial Eukaryote Transcriptome Sequencing project funded by the Gordon and Betty Moore Foundation.
Johnny Sena, Ph.D

Bioinformatics Research Associate & Lab Coordinator

Johnny received a PhD in molecular biology from the University of Colorado Anschutz Medical Campus in 2014, where he studied epigenetics, transcription and alternative splicing of hypoxia regulated genes and their roles in cancer. He joined NCGR in 2014. As a molecular biologist, he is fascinated by the molecular mechanism underlying human and plant health and disease. Currently, he is interested in developing Next Generation Sequencing (NGS) library preparation and sequencing protocols for various organism including viruses, bacteria, plants and animals. In particular, he is developing high throughput NGS and bioinformatics methods to study uptake and biodistribution of human extracellular vesicles in model organisms. In collaboration with Dr. Joann Mudge at NCGR, Johnny is working to understand how extracellular vesicles might be important for establishing and or maintaining symbiosis of soybean with the nitrogen-fixing bacterium, Bradyrhizobium japonicum.

Administration and Technical Staff

Tyler Exe

Accounting Assistant

Tyler joined NCGR in 2019 after participating in an internship program co-sponsored by Santa Fe Community College. As Accounting Assistant Tyler processes accounts receivable, accounts payable and provides overall support for the office.
Doreen Landau, Controller

Controller

Doreen joined NCGR in February 2006 and brings many years of financial management experience to the position. Leading the Finance team, her responsibilities include audit supervision, financial reporting, budgeting, cash flow management and compliance. Doreen also manages Human Resources for the organization.
Kathy Myers, B.S.

Director of Information Technology

As an Animal Science major (Biology+, UC Davis) turned Information Technologist, Kathy brought a rare mix of computer with biological science skills when she joined NCGR in 2005. Pioneering a number of Silicon Valley startups along with stints at NASA, Lawrence Livermore National Labs, Apple, Oracle and Nickelodeon earned her a deep wealth of knowledge in research-grade IT systems. She has served as a six-term president of the New Mexico Oracle User’s Group, and is currently on the Santa Fe Community College Information Systems and Computer Science Advisory Committee. In 2010 she and her horse "Blue" completed the Tevis Cup 100-mile endurance race.
Ethan Price

Project Assistant

Ethan joined NCGR in 2019 and provides administrative, marketing and project management support to the NCGR and NM-INBRE teams. He plans and organizes bioinformatics workshops and our annual NMBIST symposium, and also supports our Pilot Award program.
Pete Wargo

Senior Systems Administrator

Pete provides three decades of varied IT experience to NCGR. He has managed systems and IT groups at several organizations and industries, including Sun Microsystems, UBS, and Rensselaer Polytechnic Institute. Previously part of the NCGR team from 1996-2000, he returned in 2018 to help extend and support our IT infrastructure. His specialities include high-performance computing, infrastructure design, datacenter management, and Unix/Linux administration. He is also the co-author of US Patent number tar 6,950,773 "Detecting thermal anomalies in computer systems based on correlations between instrumentation signals."

About NCGR

The National Center for Genome Resources is a not-for-profit research institute that innovates, collaborates, and educates in the field of genomic data science. As leaders in DNA sequence analysis, we partner with government, industry, and academia to drive biological discovery in all kingdoms of life. We deliver value through expertise in experimental design, software, computation, data integration and training a skilled workforce.

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