Logan Walker
Senior Bioinformatics Scientist
Cell and Developmental Biology, University of Michigan
Research Interests
Microscopy and Image Analysis
I am interested in developing high throughput microscopy tools and methods for analyzing microscopy images.
Neuroscience
Our microscopy tools are used to study the development and function of the brain through the lens of 3D neuron tracing and morphology reconstruction.
Genomics
I am interested in using high throughput sequencing technologies to interrogate the function of genes and their interactions.
Experience
Senior Bioinformatics Scientist
Cell and Developmental Biology, Michigan Medicine
2023 - Present
Ann Arbor, MI
- Continuing work begun during my thesis research.
- Currently developing an improved version of our lab's line confocal microscopy hardware.
Graduate Student Research Assistant/Fellow
Biophysics, University of Michigan
2018 - 2023
Ann Arbor, MI
- Performed thesis research in neuroscience methods development, requiring the development of bioinformatics software, building custom microscopy hardware, and constructing a bespoke compute cluster under Dr. Dawen Cai.
- Managed creation of the nGauge, nTracer2, and SISF software platforms.
- Developed custom microscopy hardware and control software, used in the lab for the Parallel Line Confocal
- Recieved the Rackham Predoctoral Fellowship.
Research Assistant/Fellow
Physics and Medical Center, The Ohio State University
2014 - 2018
Columbus, OH
- Performed bioinformatics data analysis, manuscript preparation, and laboratory management for Illumina next-generation sequencing experiments in the Genomics Shared Resource (GSR) lab under Dr. Pearlly Yan and Dr. Ralf Bundschuh.
- Specifically focused on data from single cell and small RNA sequencing experiments.
- Recieved the Pelotonia Fellowship.
Publications
A browser-based platform for storage, visualization, and analysis of large-scale 3D images in HPC environments
Preprint on BioRxiv 2024.10.04.616591 (2024)
Non-linear Quantization and Automated Compression Artifact Minimization Facilitate Image Analysis with High Compression Ratio
Preprint on BioRxiv 2024.07.17.603794 (2024)
Optimized neuron tracing using post hoc reanalysis
IEEE 20th International Symposium on Biomedical Imaging (ISBI) 1-5 (2023)
A Comparison of Lossless Compression Methods in Microscopy Data Storage Applications
6th International Conference on Software Engineering and Information Management (ICSIM) 154-159 (2023)
Post-explant profiling of subcellular-scale carbon fiber intracortical electrodes and surrounding neurons enables modeling of recorded electrophysiology
Journal of Neural Engineering 20, 026019 (2023)
A low-cost and robust microscope hardware trigger interface board
Preprint on OSF preprints fcb3t (2023)
Genome-wide DNA hypermethylation opposes healing in patients with chronic wounds by impairing epithelial-mesenchymal transition
Journal of Clinical Investigation (JCI) 132(17), E157279 (2022)
Robust transcriptional profiling and identification of differentially expressed genes with low input RNA sequencing of adult hippocampal neural stem and progenitor populations
Frontiers In Molecular Neuroscience 15:810722 (2022)
Leukemia-initiating HSCs in chronic lymphocytic leukemia reveal clonal leukemogenesis and differential drug sensitivity
Cell Reports 40(3), 111115 (2022)
PP2A is a therapeutically targetable driver of cell fate decisions via a c-Myc/p21 axis in Acute Myeloid Leukemia
Blood 139(9), 1340–1358 (2022)
nGauge: Integrated and extensible neuron morphology analysis in Python
Neuroinformatics 20, 755–764 (2022)
Teaching Python for Data Science: Collaborative development of a modular & interactive curriculum
Journal of Open Source Education 4(46), 138 (2021)
Bitbow enables highly efficient neuronal lineage tracing and morphology reconstruction in single Drosophila brains
Frontiers in Neural Circuits 15:732183 (2021)
The molecular landscape of neural differentiation in the developing Drosophila brain revealed by targeted scRNA-seq and multi-informatic analysis
Cell Reports 35(4), 109039 (2021)
Unsupervised Neural Tracing in Densely Labeled Multispectral Brainbow Images
IEEE 18th International Symposium on Biomedical Imaging (ISBI) 1122–1126 (2021)
Light microscopy based approach for mapping connectivity with molecular specificity
Nature Communications 11, 4632 (2020)
CLEAR: Coverage-based Limiting-cell Experiment Analysis for RNA-seq
Journal of Translational Medicine 18(1), 63 (2020)
TraceMontage: a Method for Merging Multiple Independent Neuronal Traces
Journal of Neuroscience Methods 332, 108560 (2020)
ROR1-targeted delivery of miR-29b induces cell cycle arrest and therapeutic benefit in vivo in CLL mouse model
Blood 134(5), 432-444 (2019)
Whole Transcriptome Analysis of Renal Intercalated Cells Predicts Lipopolysaccharide Mediated Inhibition of Retinoid X Receptor alpha Function
Scientific Reports 9(1), 545 (2019)
Education
Ph.D. in Biophysics
University of Michigan
2018 - 2023
Ann Arbor, MI
Thesis: A microscopy and bioinformatics toolkit for high-throughput connectomics studies.
M.S. in Bioinformatics
University of Michigan
2020 - 2023
Ann Arbor, MI
M.S. in Biophysics
University of Michigan
2018 - 2020
Ann Arbor, MI
B.S. in Physics, Astronomy and Astrophysics
The Ohio State University
2014 - 2018
Columbus, OH
Minor: Computational Sciences
Teaching Experience
Biophysics 370
Graduate Student InstructorUniversity of Michigan Biophysics
Fall 2020
CSE 2221: Java Programming
Instructional AssistantOhio State University CSE
Fall 2015