Software Development and Informatics
Clinical and translational use of genomic data
The Software Development and Informatics team both develops and makes use of novel methods and applications to analyze genomic and clinical datasets to support the interpretation of genomic data. A major interest is in using these tools and methods to provide definitive diagnoses in the case of Mendelian disease. We provide informatics and software support for HudsonAlpha Institute for Biotechnology as required and tools for Clinical Genomics applications such as those used at Smith Family Clinic for Genomic Medicine.
In addition to clinical application for rare disease, we are also involved in the application of whole genome sequencing in a research setting to identify causative mutations in individuals with a variety of presumed single gene or complex disorders. We have a number of ongoing internal and external collaborations aimed at analyzing data from individuals, families or cohorts to uncover the presumed disease associated molecular changes. Goals are to not only identify causal variants, but also to identify molecular relationships that assist in the selection of new or repurposed treatments.
The team supports analysis of genomic sequencing data from the sequencer to the final clinical report converting raw sequencing data into clinically actionable information. Currently supported analyses include: DNA sequencing data alignment and variant calling, ChIP analysis, methylation analysis and RNA-seq analysis, as well as development and application of various methods for data QC, integration and visualization.
Liz Worthey, PhD, has degrees in immunology, genomics, and genetics and has studied at leading universities including Glasgow, Birmingham, Oxford, and Stanford Universities, Imperial College London and the University of Washington. She has more than 20 years of experience in the development and application of tools, methods and algorithms to extract knowledge from large genomics and other research and clinical datasets. Worthey performed the first analyses that successfully used genomic data to change medical treatment and together with colleagues built the first genomic medicine program in the world. She has been invited to give talks around the world on this topic. At HudsonAlpha, she is the head of the Software Development and Informatics (SDI) Group.
The SDI group has three distinct missions: 1) to support the institutional informatics needs within HudsonAlpha by developing software for analysis of genomics datasets and through application of these tools to turn big data into generalizable research knowledge, 2) to support the clinical informatics needs of the various HudsonAlpha clinical entities to turn genomic data into knowledge with clinical utility and 3) to undertake novel research into the genetic underpinnings of rare and more common disease including cancer in order to provide research findings and clinically useful data for human diseases.
Julie Anderson is a software developer with HudsonAlpha’s software development and informatics team. Julie has a BS in electrical engineering from Grove City College and a MS in computer science and engineering from Pennsylvania State University. Her past work experience includes working with Wyle CAS Group, Applied Data Trends and Scientific Research Corporation on a variety of air and missile defense projects. Currently, Julie is a member of the Codicem software development team. She has improved many software development build processes during her time at HudsonAlpha and has a passion for developing innovative visualization approaches to elegantly present complex data.
Camille Birch is a University of Arizona graduate with a PhD in biomedical engineering. Camille works as a clinical analyst within the software development and informatics group. Her interests include biophysics, genetically linked cardiovascular disease, biomaterials, and systems engineering. Camille was the recipient of a biomedical cardiovascular training grant from the NIH. She currently works towards providing answers for undiagnosed patients.
Donna Brown joined HudsonAlpha as a clinical analyst following a biotech career that includes everything from building genomic infrastructure, QTL mapping, and lab management at Massachusetts General Hospital to marketing, product management, and heading the genomics lab at Research Genetics. As a member of the software development and informatics team, Donna works toward providing answers for previously undiagnosed patients.
Mana Gajapathy is postdoctoral researcher in Liz Worthey’s software development and informatics group. Mana recently completed his PhD in biotechnology science and engineering at the University of Alabama in Huntsville. Mana has a strong research background in bioinformatics, crystallography, biochemistry and molecular biology. Mana is working towards developing cutting edge computational biology techniques to have maximum impact on human health.
Lori Handley is the project manager for Liz Worthey’s software development and informatics team. She is a University of Alabama in Huntsville graduate with a BS in biology and chemistry. She has worked with HudsonAlpha since 2008 and joined Liz’s group in 2015. Lori began her time at HudsonAlpha as a sequencing group leader and computational biologist. Her previous professional experience includes time with Operon Biotechnologies, Qualitest Pharmaceuticals, and Research Genetics.
Jeremy Harris is an expert in molecular biology and computer programming. His primary focus is developing algorithms pertaining to computational biology. He specializes in computer high/medium throughput automation pipelines made to handle ‘big’ data. Jeremy received his MS in health care informatics from the University of Wisconsin and has a BS in bioinformatics from BYU. He came to HudsonAlpha as a software developer in 2015 from the Medical College of Wisconsin.
Matt Holt recently obtained his PhD in computer science from the University of North Carolina. He completed his undergraduate and graduate studies at Auburn University, studying computer science and wireless engineering. Matt joined SDI August 2016 as a postdoctoral researcher. He has experience developing a variety of web-based tools for accessing and visualizing sequencing data.
Jacob Kelly is an Auburn University graduate with a BS in computer science. His professional background includes working with Intergraph Corporation, Applied Data Trends and Wyle CAS Group in Huntsville. He has over ten years experience in the software engineering industry and currently works as a software developer on Liz Worthey’s software development and informatics team. Jacob is the technical lead for the reporting module for Codicem, a software application developed at HudsonAlpha that assists in the analysis of patient sequence data.
Jessica Merritt joined the software development and informatics team in late 2015 as Liz Worthey’s business coordinator. She is a University of South Alabama graduate with a BS in business administration and a concentration in marketing. Prior to joining the HudsonAlpha team, Jessica specialized in sales and marketing in the healthcare industry, working with a variety of physician groups, hospitals and facilities in the Huntsville area.
Scott Newberry is an Auburn University graduate with a BS in software engineering and a BS in applied mathematics. He began working at HudsonAlpha in 2010. Scott is currently a software architect within the software development and informatics group. He is responsible for designing the software infrastructure and analytics platform used to support the research and clinical mission at HudsonAlpha. Prior to his work with HudsonAlpha, Scott worked as a software engineer at Lockheed Martin.
Fariba Shater-Ferdosian has a BA in information technology and is currently in the process of obtaining her MS in computer science. She currently works as a software developer for Liz Worthey’s team. Fariba previously worked with IBM Canada as an application developer, as well a teaching assistant at the University of Alabama in Huntsville before joining HudsonAlpha in 2014.
Angelina Uno-Antonison is a software developer in Dr. Liz Worthey’s group. She is a University of Alabama in Huntsville graduate with a BS in computer science and a BA in music. Prior to joining the software development and informatics team at HudsonAlpha, Angelina worked with Wyle and CDL Systems in the Huntsville area. She is an accomplished software developer with experience developing UI and visualization tools. She spends her spare time serving as a mentor for the Columbia High School robotics team and enjoys teaching programming to high school students and establishing STEM outreach initiatives.
Arthur Weborg is a Milwaukee School of Engineering graduate with a degree in software engineering. He has worked on a large handful of projects ranging from software bots to embedded systems that transcribe sheet music from sound. Arthur has spent several years under Liz Worthey’s direction developing software for genomics and genomic medicine, touching topics in every aspect of software development.
Collin White is a University of Alabama graduate with a BS in computer science. Collin is a software developer on Liz Worthey’s software development and informatics team. He is responsible for developing and managing new data analysis pipelines for clinical and research uses. Collin coordinates with end-users and helps to design and implement new tools.
Brandon Wilk is a graduate of the Milwaukee School of Engineering with dual degrees in biomedical engineering and computer engineering. He is currently a doctoral candidate in medical informatics at the University of Wisconsin-Milwaukee. Brandon works as a software developer on Liz Worthey’s team. He is involved in the design and development of new clinical analysis systems for the genomic medicine clinic at HudsonAlpha. He is well versed in informatics application design and informatics in the biological sciences, specifically in the areas of genetics and genomics.
Melissa Wilk is a postdoctoral researcher at HudsonAlpha who splits her time working in the Jacob and Worthey labs. Wilk earned her PhD from the Medical College of Wisconsin. Her research interests include exploring the genetics of eye disease, modifiers in genotype-phenotype relationships and pharmacogenomics.