NMDC Team Members
Michal Babinski (LANL)
Michal is a bioinformatics graduate student intern at LANL. He is involved in workflow testing and checking to make sure reproducibility is achieved within and between environments. On the NMDC team he ensures consistency is accounted for in workflow processing and output, an essential part of setting the reproducibility standards for NMDC. He is a Master's student in Bioinformatics and Genomics at the University of Oregon.
Jeff is the Director of Data and Analytics at Kitware Inc. The Data and Analytics team creates production-ready web services and interfaces for data-oriented discovery, with a focus on open source and open science solutions.
Antonio Camargo (LBNL)
Antonio Camargo is a scientist at the Joint Genome Institute, where he integrates the Microbiome Data Science group. His current work involves the development of computational methods to allow large-scale analysis of the ecology and diversity of mobile genetic elements.
Shane Canon (LBNL)
Shane is a Senior Engineer at KBase and Berkeley Lab’s Supercomputing Facility. For over 20 years, he has helped scientists conduct breakthrough science using some of the fastest computers in the world.
Patrick Chain (LANL)
Patrick is a Los Alamos National Laboratory Research Fellow, and is the head of Bioscience Division's Bioinformatics and Genome Analytics group, and a senior scientist within the Biosecurity and Public Health Group.
Shreyas Cholia (LBNL)
Shreyas leads the Usable Software Systems Group in the Scientific Data Division at Berkeley Lab. He has extensive experience as a technical leader and software engineer across a diverse range of interdisciplinary teams, including ESS-DIVE, Materials Project, and the NERSC Jupyter projects.
Alicia Clum (LBNL)
Alicia is NMDC’s Microbiome QA/QC Manager. Alicia has 16 years of experience at Berkeley Lab and previously served as the group lead for the Genome Assembly and Analysis team at the Joint Genome Institute. In her role as the Microbiome QA/QC Manager, she will be responsible for overseeing NMDC's portable workflows and corresponding documentation, assuring data generated by NMDC workflows meet quality standards, and increasing the utility of NMDC's Data Portal.
Yuri Corilo (PNNL)
Yuri is a computational scientist in the Environmental Molecular Sciences Laboratory (EMSL) at PNNL. He joined PNNL in 2019 after six years as a Research Scientist and four years serving as the director of computational science for the Ion Cyclotron Resonance (ICR) program at the National High Magnetic Field Laboratory (NHMFL). He received his Ph.D. in Organic Chemistry from the University of Campinas and has over ten years of experience in the development of scientific software applied to complex mixtures characterization by high-resolution mass spectrometry.
Matt Covalt (Kitware, Inc.)
Matt Covalt is a Senior R&D Engineer at Kitware, Inc. He writes web services and visualizations that enable scientists to make discoveries.
Emiley Eloe-Fadrosh (LBNL)
Emiley joined the Joint Genome Institute at Berkeley Lab in 2014 to pursue microbial ecology and metagenomics research. She is Head of the Metagenome Program and leads the Environmental Genomics Group.
Kjiersten Fagnan (LBNL)
Kjiersten is Chief Informatics Officer and Data Science and Informatics Department Head at the Joint Genome Institute, Berkeley Lab. She has over 10 years of experience in scientific computing and experimental data analysis.
Mark Flynn (LANL)
Mark is a software developer at Los Alamos National Laboratory (LANL). He received his Ph.D. in Neurobiology from the University of Delaware in 2001 and M.S. in Computer science from the University of New Mexico in 2011. He has worked in both industry and academia, using HPC and cloud systems, in a variety of roles including as a developer, architect and as a devops engineer.
Grant Fujimoto (PNNL)
Grant Fujimoto is a full stack software engineer in the National Security Directorate. He focuses on developing reliable, maintainable, and scalable solutions for a variety of government sponsors. He has experience developing applications in the cloud, high performance algorithms, desktop applications, SQL and document databases, and UI work as well.
Bin Hu (LANL)
Bin Hu is a staff scientist at Los Alamos National Laboratory. His current research interests are on computational inference of phenotype using genotype information, antibody dynamics, bioinformatics software algorithm, and software development.
Patrick Kalita (LBNL)
Patrick is a software developer in the Environmental Genomics and Systems Biology (EGSB) Division at LBNL. He has extensive experience in both frontend and backend web development for scientific applications and biological and environmental databases.
Julia Kelliher (LANL)
Julia Kelliher is a post-Masters student in the Biosecurity and Public Health Group at the Los Alamos National Laboratory (LANL). She received a Bachelor’s degree in Neuroscience from Skidmore College and an M.S. in Biotechnology from Johns Hopkins University. Since joining LANL in 2017, she has worked on a variety of projects focused on the gut microbiome, the soil microbiome and bacterial-fungal interactions, as well as infectious disease and biothreat detection and treatment.
Po-E “Paul” Li (LANL)
Po-E (Paul) Li is a senior level bioinformatician with formal education in computer science and MS in bioinformatics, and 10+ years of professional experience in designing and implementing pipelines and algorithms for analyzing genomic and sequencing data. As a research technologist at Los Alamos National Laboratory, he has had a focus on assay design, signature identification, microbiome analysis, taxonomic profiling and transforming results to visualization.
Chien-Chi Lo (LANL)
Chien-Chi Lo is a research technologist at Los Alamos National Laboratory (LANL). He has more than 10 years of work experience on developing bioinformatics workflows, analytical software, and genomic data analysis. He holds two M.S. degrees: in Bioinformatics from the National Yang-Ming University, Taipei, Taiwan; and in Computer Science from the University of New Mexico.
Wendi Lynch (LBNL)
Wendi Lynch has been with Lawrence Berkeley National Laboratory since 2015, starting as an Administrator in the Lab's Directorate, supporting the ALD/COO and Advisor to the ALD/COO. Moving to the JGI in 2016, she was Administrator to the Lab's Director before joining the NMDC in 2022 and taking on the team's administrative support needs.
Douglas Mans (PNNL)
Douglas oversees the entire EMSL user program and serves as the primary interface with BER, PNNL and the user community for science, management, and operations of EMSL. He is responsible for establishing a scientific vision to attract outstanding staff scientists and users to EMSL facilities and programs, promoting innovative research, and fostering the creation of robust scientific teams and communities.
Lee Ann McCue (PNNL)
With over 20 years in comparative genomics and high-throughput data analyses, Lee Ann is a senior computational scientist at the Pacific Northwest National Laboratory.
Mark Miller (LBNL)
Mark has held laboratory and computational roles at workplaces including the University of Pennsylvania’s dental and medical schools and Merck Vaccine Basic Research. Mark holds an MS in bioinformatics from the University of the Sciences in Philadelphia and identifies as an ontologist.
Nigel Mouncey (LBNL)
In 2017, Nigel became the Director of the Joint Genome Institute at Berkeley Lab after nearly 19 years leading Industry research and development teams. He also leads the Secondary Metabolites Group.
Chris Mungall (LBNL)
Chris is head of Molecular Ecosystems Biology in Environmental Genomics and Systems Biology at Berkeley Lab. His group builds integrated databases, algorithms, and ontologies for various bioscience applications.
Mike Nagler is an R&D Engineer at Kitware, Inc. He has experience with a variety of software development technologies and strives to create applications that are a joy to use.
Ingrid Ockert (LBNL)
Ingrid is a Communications and Outreach Specialist. She holds a PhD in the History of Science and has worked in communications for over a decade. Ingrid supports the NMDC's outreach efforts, create new communications materials, and serves as the primary social media contact.
Sujay Patil (LBNL)
Sujay Patil is a Bioinformatics Software Engineer and contributes to the metadata standards activities. Sujay has computational expertise and works on developing software tools for faster, reproducible research.
Paul Piehowski (PNNL)
Paul is a staff scientist and Team Lead for proteomics in EMSL. He joined PNNL 10 years ago as a post-doctoral researcher and has over 15 years experience applying mass spectrometry to biological research, primarily in the fields of proteomics and metabolomics.
Elais Player (LANL)
Elais Player is an application developer at Los Alamos National Laboratory (LANL). He has more than ten years of work experience in both academia and industry writing software for use science, finance, and supply-chain management. His current interests include reproducible software deployment for high-performance computing and smart visualization of genomics data and analysis.
Anastasiya Prymolenna (PNNL)
Anastasiya is a data scientist at PNNL in the Environmental Molecular Sciences Division (EMSD). Her primary focus is on developing data processing workflows, database curation, and API development for multiomics related data.
Samuel Purvine (PNNL)
Sam Purvine has worked in bottom-up mass spectrometric proteomics since 1998, with deep knowledge of all aspects of the art. He serves as final data product liaison for EMSL Users who wish to use the mass spec proteomics capability.
Francie Rodriguez (LANL)
Francie is a member of the NMDC's Engagement Team. She joined Los Alamos National Laboratory in 2022 as a Technical Project Manager, supporting the Bioscience Division. As a member of the Engagement Team, Francie will support the NMDC's outreach efforts by creating new training materials, and expanding our workshop capabilities.
Simon Roux (LBNL)
Dr. Roux joined the JGI in 2017 to lead viral genomics research as part of the Metagenome Program. His responsibilities include the development of novel computational tools to identify and characterize virus sequences, the design of new experimental approaches to link viruses to their host(s), collaboration with JGI users for analyzing viral datasets, and the organization of community-building efforts in the field of viral ecogenomics.
Setareh Sarrafan (LBNL)
Setareh joined Berkeley Lab in February 2021. She previously worked at both UC Berkeley and UC San Francisco as a Scrum Master, Product Owner, Project Manager and Informatics Implementation Manager.
Migun Shakya (LANL)
Migun Shakya is a staff scientist at Los Alamos National Laboratory (LANL). He received his Ph.D in Genome Science from the University of Tennessee at Knoxville in 2013. His current research interests include terrestrial viruses and their effect on ecosystems, large scale comparative metagenomics using k-mers, and development of workflows to analyze whole genome and transcriptomic datasets.
Montana Smith (PNNL)
Montana is an earth scientist at PNNL in the Environmental Molecular Sciences Division (EMSD). She works primarily on soil systems studying microbial ecology and the effects of environmental perturbations on carbon and nitrogen cycling.
Donny Winston (Polyneme, LLC)
Donny studied electrical engineering and computer science (EECS) at the University of California at Berkeley and completed his master’s and PhD degrees in the EECS department at MIT. Donny was the principal web developer (full-stack) and data/systems engineer for the Materials Project at LBNL. He now runs a software and data consulting practice, with expertise in helping researchers do data-intensive science together.
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