Our Experts

Brian is the finance analyst for Research Computing, which includes the Minnesota Supercomputing Institute, U of M Informatics Institute, and U-Spatial. He is the point of contact for all accounting and budgetary functions for DeptIDs 11062, 12165, 12221.

Monalisa is a Data Manager for various MIDB projects. She handles the research projects' data management needs. Over the years she has worked intensively in data acquisition, statistical analysis, data curation, data storage, and data usage needs. Prior to joining MSI she worked in a pulmonary imaging lab and also has knowledge of image analysis.

Nick manages the user-facing software library and profiles user behavior on MSI systems. During his graduate studies, he extended methods for thermodynamic accuracy and transferability of coarse-grained molecular dynamics models. These methods allow for the simulation of accurate bottom-up coarse-grained models at state points away from their parameterization. He also studied the aggregation behavior of model asphaltene compounds by molecular dynamics simulation.

Ham started working at MSI as an undergraduate before moving on to the UMN graduate school to pursue a PhD degree in Scientific Computation. Coming back to MSI, he joined the LM&P bioinformatics group as an analyst working on clinical pipelines development. Ham joined the SCS group in early 2020 as a scientific computing consultant and has been actively working on Machine Learning and Deep Learning projects. His current interests are in neural network , deep learning architecture, and distributed training methodology.  

Jeff is an ecologist and evolutionary biologist, with a specific background in phylogenetics, biogeography, macroevolution, and models of trait evolution and speciation/extinction -- primarily in bats, but he has broader experience in other vertebrate clades. He has expertise in data/workflow management, data visualization, and statistical methods testing/development. Currently, he consults on a variety of cyberinfrastructure and biomedical research projects as MSI's Project Lead for the Masonic Institute for the Developing Brain - Informatics Core. He also teaches programming and scripting workshops through MSI and Software Carpentry, and occasionally teaches evolutionary biology courses in the College of Biological Sciences.

Tracey is the editor for the Minnesota Supercomputing Institute. She creates website and social-media content, develops marketing and public-relations materials, and writes and edits internal and external communications for the Institute. She also organizes events such as MSI's annual Research Exhibition and coordinates outreach activities. She has worked at MSI since early 2002. Prior to that, she served in the US Air Force and was the Administrative Manager for a small engineering consulting company.

At MSI

Adam started as the Department of Surgery Bioinformatics Analyst in June 2022. He previously worked as a core RIS Informatics Analyst starting in 2018. While his current projects focus primarily on human, mouse, and non-human primates, his previous collaborations spanned the tree of life (and viruses!). In addition to broad 'omics experience detailed below, he has worked on analysis pipeline development, genomics database maintenance, as well as basic image analysis in Fiji.

Previous

While working on a Botany degree at Northern Michigan University, Adam's interest in genetics began during a summer internship in Arabidopsis developmental genetics at the Carnegie Institute of Plant Biology. This led to a PhD in the genetics of plant mating system evolution at McGill University followed by a post-doc at University of Minnesota working on population genomics in plants (Asteraceae sunflowers) and animals (Astyanax cave and surface fish).

Todd is a bioinformatics analyst and molecular biology researcher in the Research Informatics Solutions (RIS) division of MSI. He supports research projects and custom clinical genomics pipelines for the Department of Laboratory Medicine and Pathology (LMP) and the Molecular Diagnostics Laboratory (MDL). He has experience analyzing high-throughput datasets for gene expression analysis, microbial detection and genome assembly, and variant detection. Todd's graduate training focused on the genetic mechanisms of breast cancer, where he investigated how activated growth factor signaling pathways regulate post-translational modifications of the progesterone receptor, causing altered gene expression programming and tumor progression. As a postdoc in the UMN Veterinary Diagnostic Laboratory, he transitioned to microbial genomics, where he developed pipelines for analyzing metagenomic shotgun sequencing data for the discovery of novel viral and bacterial pathogens. At MSI, he enjoys working with new collaborators and facilitating computational biology projects. 

• Public scripts on GitHub page
  • Projects on the UMN GitHub instance (requires X.500 to view)

Rebecca is a bioinformatics analyst in the Research Informatics Solutions (RIS) division of MSI. She supports research projects for the Department of Laboratory Medicine and Pathology (LM&P) and designs and supports custom clinical bioinformatics pipelines for the Molecular Diagnostics Laboratory (MDL). Rebecca’s graduate training focused on the comparative molecular biology of host-pathogen interactions. During her post-doc training, Rebecca focused on the functional genomics of cancer biology where she developed computational skills to analyze different types of NGS data.

Sarah has extensive experience and expertise in bioinformatics and biostatistical analysis, with a focus on RNA-Seq and microarray gene expression analysis. She has supported a variety of research projects during her time at MSI in several disciplines, including cancer biology, immunology, and epidemiology. Sarah also develops and maintains clinical analysis pipelines for germline and exome DNA sequencing assays. Prior to joining MSI Sarah was a staff scientist at the National Institute of Standards and Technology (NIST). At NIST she developed RNA controls and analysis methods to provide confidence in gene expression experiments. Her software package, the erccdashboard, is a widely used tool for QC analysis of gene expression experiments.

Christine is a bioinformatics analyst in the Research Informatics Solutions (RIS) division of MSI. She supports research projects and custom clinical genomics pipelines for the Department of Laboratory Medicine and Pathology and the Molecular Diagnostics Laboratory. Her graduate training focused on understanding the genetic basis of complex traits using experimental evolution, gene expression data and next-generation sequencing data. As a postdoc she worked on a number of different projects that all focused on better understanding genome content variation in a maize diversity panel using next-generation sequencing data.

Yinjie is a bioinformatics analyst in the Research Informatics (RI) division of MSI. He supports research projects for the Department of Agronomy and Plant Genetics (APG). Yinjie's graduate training focused on the molecular biology, plant transcriptomics, and comparative genomics. During his post-doc training, Yinjie focused on structural variation, transpoable element, and pan-genomics. He developed computational skills to analyze different types of NGS data, PacBio long reads data, and single cell genomics. 

Kevin has spent decades performing large-scale bioinformatics analyses involving cutting-edge high-throughput data from bacteria, fungi, plants, mammals and complex communities. He has performed detailed investigations of plant-microbe systems in continued research since 2001. Additionally, in 2010-2012, he led an effort to identify mutations in clinical patients with Fairview Hospital which has been expanded in partnership with MSI and continues to be used today. The knowledge gained from handling protected patient data has been brought over to design of the GEMS Agroinformatics platform to protect farmer and corporate data.

Jeff is a high-performance computing geospatial analyst in the Research Informatics Solutions (RIS) group at the Minnesota Supercomputing Institute (MSI). He has more than fifteen year’s experience working with remote sensing, climate, and geospatial data. His specialty is applying remotely sensed image time-series to phenological studies, and he is particularly interested in improving our understanding of the interactions between vegetation and climate dynamics. Having worked on projects in agriculture, mining, resource management and environmental issues, his geospatial experience is wide ranging.

Publications and Presentations

Tom spent 28 years developing software at Hewlett-Packard Company, 3M, and Medtronic before joining the Minnesota Supercomputing Institute in 2012. As part of his software engineering experience, he is very familiar with industry best practices maintaining quality systems and managing software lifecycles.

After graduating with a dual-major in physics & mathematics and a brief role in a University of Minnesota cosmology laboratory, Reid began his software development career in a variety of fields. He first worked as a DevOps engineer for an order-to-cash enterprise system before pivoting to firmware and robotics, and then finally settling into his current position at MSI. Here he maintains the MSI Galaxy website, develops Galaxy wrappers for metaproteomics tools, and is a principal contributor to the CloudForest phylogenomics application.

Publications and Presentations

Trevor has extensive experience in the programming languages Clojure and Ruby, with ongoing full-time programming experience since 2004. In addition he has experience in constructing large multi-component service oriented architectures and is skilled in the creation and usage of multiple database systems such as SQL, Datomic / Datalog, and SPARQL / RDF. He has been a contributing member of the GalaxyP project team where he contributed to core code development ensuring full compatibility with the Galaxy Central repository.

Publications and Presentations

Nick has been a Linux and Windows system administrator since 2002. He is passionate about introducing automation wherever possible to maximize productivity and minimize downtime. He is currently focusing on migrating MSI's internal infrastructure to a new configuration management system that will provide quicker time to deploy and improved reporting and monitoring.

Luke has had a varied career within IT including working in; systems administration, supporting large corporations, and data center. He is currently focusing on migrating servers and services to new infrastructure.

Yectli is a UNIX administrator of HPC systems.

Matt has eight years of professional experience in Linux and networking adminstrations. He is primarily passionate about automation and understanding system internals. His current main focus is maintaining HPC resources and networks at MSI.

Publications and Presentations

Edward began his career as a system administrator at the New Mexico Bureau of Geology and Mineral Resources. In 2013 he moved to Minnesota and started working at the University of Minnesota. During his career he has managed many Linux and Windows servers, set up databases, converted physical servers to virtual, performed security audits, and has kept things running.

Publications and Presentations