Team - National Microbiome Data Collaborative

NMDC Team Members

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.

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.

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.

Bea Meluch (PNNL)

Bea is a graduate student intern at Pacific Northwest National Laboratory. She works on identifying and preparing relevant datasets produced at DOE user facilities for upload to the NMDC portal. She is completing her Master’s degree in Bioinformatics and Genomics through the University of Oregon.

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.

Brynn Zalmanek (PNNL)

Brynn is a Data Architect at the Pacific Northwest National Laboratory. She studied biochemistry at the University of Colorado and has a master’s degree in library and information science from the University of Washington. Her work involves developing metadata schemas to improve the findability, accessibility, interoperability, and reusability of scientific research resources.

Cameron Giberson (PNNL)

Cameron Giberson is a software engineer at PNNL. He joined PNNL in 2016, and primarily develops software for ion mobility and mass spectrometry systems in addition to pipeline development.

Camilo Posso (PNNL)

Camilo is a post masters intern at PNNL. For the last two years, he has worked on data analysis of proteomic data, as well as tool development in Python and R. As part of the NMDC, he is working on a tool to produce a metagenome for use in existing proteomic pipelines.

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.

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.

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.

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.

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.

Eric Cavanna (LBNL)

Eric is a software engineer in the Environmental Genomics & Systems Bioimaging group at Berkeley Lab (LBNL). He holds a BS in Computer Engineering. Before joining LBNL in 2023, he worked at UC Davis and in the private sector.

Francie Rodriguez (LANL)

Francie Rodriguez is a Technical Project Manager at Los Alamos National Laboratory supporting the Mass Spectrometry Center for Integrated 'Omics. She received a Bachelor's degree in Ecology and Evolutionary Biology from the University of Utah, and an M.S. in Botany from the University of Hawaii. Francie supports the NMDC's outreach efforts by creating new training materials and expanding our workshop capabilities.

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.

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, creates new communications materials, and serves as the primary social media contact.

@ingrid_rocket

James Tessmer (PNNL)

James has been a Software Engineer at PNNL for 3 years working the high performance computing/machine learning group. He's interested in bioinformatics and computational biology related work and have participated in a few projects relating to those at the lab, mostly focused on helping to build the pipelines and tools needed to ensure correct and smooth processing of data.

Jeff Baumes

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.

Julia Kelliher (LANL)

Julia Kelliher is the Engagement Team Lead for the NMDC and is a Research Technologist in the Genomics & Bioanalytics Group at the Los Alamos National Laboratory (LANL). Her background is in Neuroscience and Biotechnology, and since joining LANL in 2017, she has worked on a variety of projects focused on the gut microbiome, the soil microbiome, bacterial-fungal interactions, as well as infectious disease and biothreat mitigation

Kaitlyn Li (LANL)

Kaitlyn is a bioinformatics graduate student intern at the Los Alamos National Laboratory. She is involved in workflow development and testing for NMDC EDGE. She is completing her Master's in the Bioinformatics and Genomics Track of the Knight Campus Graduate Internship Program at the University of Oregon.

Katherine Heal (PNNL)

Katherine is a computational scientist at PNNL, starting in 2023. She received her Ph.D. and did postdoctoral research in Oceanography at the University of Washington, focusing on the marine microbial ecology using advanced mass spectrometry techniques. Katherine has previously worked as data analyst in environmental consultant and has applied and developed workflows for the analysis and interpretation of high-resolution metabolomics and lipidomics data.

Kevin Fox (PNNL)

Kevin Fox is an information technology engineer in the Advanced Scientific Computing team in PNNL’s Environmental Molecular Sciences Division and the Environmental Molecular Sciences Laboratory (EMSL) user program. He is a system administrator and software developer who maintains multiple Kubernetes clusters, as well as workloads that run within it.

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.

Leah Johnson (LANL)

Leah graduated from Michigan State University in 2022 with a Ph.D. in Cell and Molecular Biology and Molecular Plant Sciences. She joined LANL in 2023 and will be using multi-omics approaches to characterize bacterial-fungal interactions and their role in soil ecosystem functioning. Her work with the NMDC engagement team focuses on user research and usability testing.

Lee Ann McCue (PNNL)

Lee Ann is a senior computational scientist at the Pacific Northwest National Laboratory. Her research experience spans comparative genomics, microbiome science computational biology, high performance computing, scientific software development for data analysis and visualization, project management and strategic planning.

@LeennMcCue1

Marcel Huntemann (LBNL)

Marcel is a Computer Systems Engineer at the DOE Joint Genome Institute and has over 15 years of experience in developing tools to help analyze microbial datasets. He joined the JGI in 2007 and is currently the head of the IMG Pipelines group. He holds a M.S. degree in Computer Science from the University of Bremen, Germany and worked as a Scientific Programmer at the Max Planck Institute for Marine Microbiology prior to coming to the JGI.

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.

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.

Mary Salvi (Kitware)

Mary is a R&D Engineer at Kitware Inc. on the Data and Analytics team. She has experience with several web based technologies and is focused on usability and accessibility.

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.

Michael Thorton (LBNL)

Michael is a data scientist who has designed and built user-facing bioinfo / biotech applications for large biotechnology companies. He has worked for a number of biotech startups and co-founded Incyte Pharmaceuticals in 1991. He attended Stanford, studying Biological Sciences, with a focus on ecology and systems biology.

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.

Mike Nagler

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.

Montana Smith (PNNL)

Montana is a data scientist at PNNL in the Environmental Molecular Sciences Division (EMSD). Her background has been in soil systems studying microbial ecology and the effects of environmental perturbations on carbon and nitrogen cycling. Now, Montana uses her research experience in the field and laboratory to improve and develop metadata standards and collaborate with researchers to adhere to FAIR data practices

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.

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.

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.

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.

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.

Samuel Purvine (PNNL)

Sam Purvine has worked in shotgun-style 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.

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.

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.

Shalki Shrivastava (LBNL)

Shalki is a Computer Systems Engineer in Integrated Data Systems Group in the Scientific Data Division group at Berkeley Lab. She is interested in designing efficient and effective techniques integrating data from diverse sources and unlocking their inherent value. She has experience developing software tools and services for various research projects for findable, accessible, and interoperable data.

Shreyas Cholia (LBNL)

Shreyas leads the Integrated Data 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.

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.

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.

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.

Yan Xu (LANL)

Yan Xu is a software developer at Los Alamos National Laboratory. She has 18 years of experience in software development, database design, system testing and end user support. Yan develops customized software and web-based applications for use in bioscience related projects.

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.