Sheri Sanders, PhD
Bioinformatics | Research Software Engineering
Professional Summary
Over the last decade, I have built nationally recognized research support programs that combine software development, scalable computational workflows, and collaborative scientific consulting. My work has focused on developing accessable workflows and scalable infrastructure that enable scientists to extract meaningful insights from complex, noisy, and novel genomic data. I have supported research in neurodevelopmental disease, cancer modeling, bioaccoustics, and evolutionary theory.
Selected Achievements
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Built national bioinformatics infrastructure supporting over 3,000 researchers.
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Developed software and workflows supporting 39 presentations, 18 manuscripts, 5 PR articles.
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Designed numerous educational offerings, including a workshop with a full textbook.
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Managed 300+ scientific software packages with ~3 million annual uses.
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Increased sequencing core bioinformatics revenue by 300%.
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Trained 1,200+ researchers through national cloud-based workshops.
Relevant Work Experience
Kallista Consulting
April 2022 - current
University of Notre Dame
January 2023 - April 2025
Indiana University
May 2016 - April 2022
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Provide contract-based bioinformatics consulting, research software engineering, and statistical analysis for academic collaborators.
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Continue development, documentation, tutorials, and deployment of dockerized comparative genomics platform for emerging model systems.
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Provide statistical analysis for complex analytical projects, including multi-variate decomposition, bayesian statistical analysis of genomics, pooled population genomics, and multi-omics.
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Manage client contracts and billing across six collaborating universities.
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Secured funding for dedicated high memory compute nodes to support genomics research
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Grew bioinformatic service income by 300% and managed bioinformatics requests for the core.
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Collaborated on 3-4 research projects annually as a contributing author or Co-PI, spanning projects in neurodevelopmental disorders, infectious disease, microbiomes, and soil ecology.
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Designed and implemented courses in CRISPR technologies, spatial and single-cell analyses, machine learning, and applied bioinformatics.
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Designed and built comparative genomics platform with integrated, GUI-based tools to allow exploration of published and novel genomic data on emerging systems.
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Designed, modernized, and managed data transfer, networking, and storage infrastructure supporting high-throughput sequencing workflows and client data delivery.
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Built and led national-scale bioinformatics support infrastructure serving 3000 genomic researchers in all 50 states and Puerto Rico.
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Resolved approximately 300 annual technical support requests involving bioinformatics software, HPC infrastructure, workflow deployment, and genomic data analysis.
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Generated and consulted on 4-6 research projects with over 80 billable hours each, including machine learning projects in ecology, remote sensing, and cancer treatment outcomes.
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Managed ~300 scientific software packages on HPC systems with ~3 million annual uses
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Developed containerized workflow, one of which supported 12 publications and 8 dissertations.
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Led cloud-based training initiatives reaching more than 1200 researchers nationally
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Mentored twelve undergraduate and graduate researchers in bioinformatics, statistical analysis, and computing.
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Managed renewal, reporting, and administration of an approximately $1 million NSF-funded national bioinformatics support program.
Select Technical Projects
Dockerized Comparative Genomics Platform
Designed and developed a fully containerized comparative genomics platform integrating JBrowse2, BLAST, CRISPR guide design, genome annotation, and downstream analysis workflows into a unified web-based resource. The platform automates deployment, configuration, and data integration from NCBI, enabling researchers to rapidly publish and explore new genomic resources.
Documentation, tutorials, and source code are available at
Associated Publications
Amiri et al. (2026). PLOS Biology. https://doi.org/10.1371/journal.pbio.3003896.
Tenger-Trolander et al. (2025). Development. https://doi.org/10.1242/dev.204732
Containerized Transcriptome Assembly Workflow and Workshop
Developed and optimized a combined de novo transcriptome assembly pipeline that merges multiple assemblers and multiple k-mers to increase accuracy and reduce individual biases. The workflow integrates quality control, assembly, annotation, and analysis of differential expression into an end to end analysis framework driven by automatically installed biocontainers. The workflow was used in dozens of projects and collaborations as it substantially decreased computational and analysis time for first time analysts.
The workflow became the foundation of a national workshop series, training 82 participants from 43 institutions over 26 states/territories and two international institutions. Code, presentations, and documentation available at
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https://github.com/kallistaconsulting/Transcriptome_Assembly_Workshop_Spring_2019
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https://ittraining.iu.edu/explore-topics/titles/denovo/index.html
Select Associated Publications
Lomheim et al. (2025). Evolution and Development. https://doi.org/10.1111/ede.70014
McManuset al. (2025). Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2025.1709239
Brooks et al. (2024). Association for Computing Machinery. https://doi.org/10.1145/3626203.3670605
Wenninger et al. (2025). bioRxiv. https://pubmed.ncbi.nlm.nih.gov/40964355/
Containerized Transcriptome Assembly Workflow and Workshop
Developed and optimized a combined de novo transcriptome assembly pipeline that merges multiple assemblers and multiple k-mers to increase accuracy and reduce individual biases. The workflow integrates quality control, assembly, annotation, and analysis of differential expression into an end to end analysis framework driven by automatically installed biocontainers. The workflow was used in dozens of projects and collaborations as it substantially decreased computational and analysis time for first time analysts.
The workflow became the foundation of a national workshop series, training 82 participants from 43 institutions over 26 states/territories and two international institutions. Code, presentations, and documentation available at
-
https://github.com/kallistaconsulting/Transcriptome_Assembly_Workshop_Spring_2019
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https://ittraining.iu.edu/explore-topics/titles/denovo/index.html
Select Associated Publications
Lomheim et al. (2025). Evolution and Development. https://doi.org/10.1111/ede.70014
McManuset al. (2025). Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2025.1709239
Brooks et al. (2024). Association for Computing Machinery. https://doi.org/10.1145/3626203.3670605
Wenninger et al. (2025). bioRxiv. https://pubmed.ncbi.nlm.nih.gov/40964355/
Modeling White Blood Cell Levels to Prevent Radiation-induced Leukopenia
Developed a proof-of-concept machine learning model to predict the risk of clinically significant white blood cell depletion in cancer patients undergoing radiation therapy series. Identified relevant clinical features (e.g. point in series, anatomical target site, and exposure time) to evaluate patient-specific risk using predictive modeling techniques. The project was completed in collaboration with a medical researcher as the capstone for my graduate certificate in Data Science. Source code and data are under embargo.
Bayesian Modeling and Deconvolution of Complex Population Genomics Data
Developed a probabilistic framework to identify genetic factors contributing to survival and adaptation in experimentally evolved populations using pooled sequencing data. The project addressed a common challenge in genomic analysis: separating biological signals from uncertainty caused by sequencing depth, sampling variation, and mixed populations.
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Implemented Bayesian allele frequency models using beta-binomial frameworks to estimate genomic changes with uncertainty rather than relying on single point estimates. Developed Monte Carlo approaches to evaluate allele frequency changes while incorporating confidence intervals and measurement uncertainty.
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Extended the workflow with Bayesian mixture deconvolution to estimate the relative contribution of individual genetic lineages within pooled samples. Combined clone-level genotype information with population-level sequencing data to partition changes in population composition and evaluate contributions from selection, drift, laboratory effects, and experimental conditions.
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This work demonstrates the application of Bayesian statistics, mixture modeling, and reproducible computational workflows to extract interpretable biological signals from noisy, high-dimensional genomic datasets.
Products from this projects are in preparation, but here is a sneak peak at statistical design.
Machine Learning and Neural Framework for Automated Bioacoustic Classification
Designed and led the development of machine learning workflows for automated identification of 14 frog species from acoustic recordings using CNNs, RNNs, and random forest classifiers. Built an end-to-end cloud-based monitoring platform integrating Raspberry Pi data collection, MQTT messaging, automated inference, and visualization dashboards, demonstrating scalable machine learning deployment for remote ecological monitoring.
Select Associated Presentations
Foran et al. (2019). Automated Recognition of Frog Calls. Supercomputing 2019. https://scholarworks.iu.edu/iuswrrest/api/core/bitstreams/3c890609-aa1c-442b-bdcb-bb9295285b4b/content
Foran et al. (2019). Developing a Workflow for Bioacoustic Recording Devices and Frog Call Analysis Within Jetstream. Center of Excellence for Women & Technology. https://scholarworks.iu.edu/iuswrrest/api/core/bitstreams/77a256a3-785a-483f-b756-c7b378775f34/content
Sanders (2019). Teaching Machine Learning to Domain Scientists: Supporting Newcomers to AI on HPC Systems. Supercomputing 2019.
Education
2021
Graduate Certificate
Data Science
Indiana University
​While working at IU, I completed coursework in machine learning and data visualization. I applied these skills to identifying frog calls from recorded data using CNNs and RNNs with undergraduate students, characterize radiation-induced lymphopenia in cancer patients using ML, and produce a business report on the status of NCGAS as I took over as director.
2016
Doctorate
Biology
University of Notre Dame
While studying the genomics of a very strange salamander system local to the Great Lakes, I learned Linux and computational genomics. I also continued my training in teaching and course design, earning a certificate for teaching alongside my doctorate. It was during this time I wrote my first textbook for an introductory linux course I taught, my second large-scale writing project. This text still circulates the department a decade later.
2010
Master's
Biology
University of Texas, Tyler
My thesis ended up being over a hundred and fifty pages, making it my first large-scale writing project and an education in learning to control scope of research projects. I also managed my first grants, permits, and reports during this time.
2007
Bachelor's of Science
Environmental Science and Management
Michigan State University
I completed a second bachelor's degree, this time focused on herpetology. I worked in a neurobiology lab and a hyena behavior lab during this time, and continued to teach supplemental instruction for pre-veterinary students in required courses (e.g. organic chemistry, physics, biology, anatomy and physiology, animal science).
2006
Bachelor's of Science
Zoology
Michigan State University
Having originally planned to become a zoo vet, I finished a pre-veterinary program and then continued onto a degree in Zoo and Aquarium Science. I completed two internships where I trained tigers and painted with elephants. I began teaching pre-veterinary supplemental courses as I completed them and worked in several veterinary clinics. This pursuit gave me a very solid foundation in anatomy and physiology (which I later taught) and medical science.
Additional Training
2026 Conservation Stewardship Program (Michigan DNR; upcoming Aug)
2026 Fossil Preparation (Indiana Dinosaur Museum)
2026 Creative Non-Fiction Writing (Southwestern Michigan College)
2022 Welding Fundamentals (Ivy Technical College)
2020 Sustaining Biological Infrastructure Grantsmenship Course (ESA)
2018 Advanced Linux System Administration (LCI)
2016 Teaching Certificate in Biological Sciences with Teaching Apprenticeship Communication Training
for Scientific and Technology Issues (UND)
2014 Policy Training for Scientists (COMPASS)
2012 Grantsmanship Course (Notre Dame)
2007 20 credits of Veterinary Medical School (switched to research)
Study Abroad
2012 Salamander Biology at University of Guelph, Guelph, Ontario, Canada (Bogart Lab)
2007 Tropical Biology and Social Science at various locations, Panama
2006 Behavioral Ecology at Masai Mara National Reserve, Kenya