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

L. A. Walker*, W. J. Lee*, B. Duan, M. Weatherspoon, Y. Li, F. Y. Shen, M.-C. Cheng, X. Niu, J. Eggerd, B. Xie, H. P. J. Cheng, H. Xu, X.-X. Zhong, H. Jiang, M. Cui, Y. Yan, and D. Cai

Preprint on BioRxiv 2024.10.04.616591 (2024)

Non-linear Quantization and Automated Compression Artifact Minimization Facilitate Image Analysis with High Compression Ratio

B. Duan, L. A. Walker, B. Xie, W. J. Lee, A. Lin, Y. Yan, and D. Cai

Preprint on BioRxiv 2024.07.17.603794 (2024)

Scalable Image Storage Format

D. Cai and L. A. Walker

US Patent Application 18/378,485 (2024)

Optimized neuron tracing using post hoc reanalysis

S. Azzouz*, L. A. Walker*, A. Doerner, K. L. Geisel, A. K. Rodrıguez Rivera, Y. Li, D. H. Roossien, and D. Cai

IEEE 20th International Symposium on Biomedical Imaging (ISBI) 1-5 (2023)

A Comparison of Lossless Compression Methods in Microscopy Data Storage Applications

L. A. Walker, Y. Li, M. McGlothlin, and D. Cai

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

J. G. Letner, P. R. Patel, J.-C. Hsieh, I. M. S. Flores, E. D. Valle, L. A. Walker, J. D. Weiland, C. A. Chestek#, and D. Cai#

Journal of Neural Engineering 20, 026019 (2023)

A low-cost and robust microscope hardware trigger interface board

L. A. Walker, N. S. Michki, and D. Cai

Preprint on OSF preprints fcb3t (2023)

Genome-wide DNA hypermethylation opposes healing in patients with chronic wounds by impairing epithelial-mesenchymal transition

K. Singh, Y. Rustagi, A. S. Abouhashem, S. Tabasum, P. Verma, E. Hernandez, D. Pal, D. K. Khona, S. K. Mohanty, M. Kumar, R. Srivastava, P. R. Guda, S. S. Verma, S. Mahajan, J. A. Killian, L. A. Walker, S. Ghatak, S. S. Mathew-Steiner, K. E. Wanczyk, S. Liu, J. Wan, P. Yan, R. Bundschuh, S. Khanna, G. M. Gordillo, M. P. Murphy, S. Roy, and C. K. Sen

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

J. K. Denninger, L. A. Walker, X. Chen, A. Turkoglu, A. Pan, Z. Tapp, S. Senthilvelan, R. Rindani, O. Kokiko-Cochran, R. Bundschuh, P. Yan, and E. D. Kirby

Frontiers In Molecular Neuroscience 15:810722 (2022)

Leukemia-initiating HSCs in chronic lymphocytic leukemia reveal clonal leukemogenesis and differential drug sensitivity

C.-L. Chiang, E. Y. Hu, L. Chang, J. Labanowska, K. Zapolnik, X. Mo, J. Shi, T.-J. Doong, A. Lozanski, P. Yan, R. Bundschuh, L. A. Walker, D. Gallego-Perez, W. Lu, M. Long, S. Kim, N. A. Heerema, G. Lozanski, J. A. Woyach, J. C. Byrd, L. J. Lee, and N. Muthusamy

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

S. Goswami, R. Mani, J. Nunes, C.-L. Chiang, K. Zapolnik, E. Hu, F. Frissora, X. Mo, L. A. Walker, P. Yan, R. Bundschuh, L. Beaver, R. Devine, Y.-T. Tsai, A. Ventura, Z. Xie, Z. Xie, M. Chen, R. Lapalombella, A. Walker, A. Mims, K. Larkin, C. Bennett, M. Phelps, E. Hertleine, G. Behbehani, S. Vasu, J. C. Byrd and N. Muthusamy

Blood 139(9), 1340–1358 (2022)

nGauge: Integrated and extensible neuron morphology analysis in Python

L. A. Walker*, J. S. Williams*, Y. Li, D. Roossien, W. J. Lee, N. S. Michki, and D. Cai

Neuroinformatics 20, 755–764 (2022)

Teaching Python for Data Science: Collaborative development of a modular & interactive curriculum

M. Duda, K. L. Sovacool, N. Farzaneh, V. Nguyen, S. Haynes, H. Falk, K. L. Furman, L. A. Walker, R. Diao, M. Oneka, A. Drotos, A. Woloshin, G. Dotson, A. Kriebel, L. Meng, S. Thiede, S. Ramdas, Z. Lapp#, and B. N. Wolford#

Journal of Open Source Education 4(46), 138 (2021)

Bitbow enables highly efficient neuronal lineage tracing and morphology reconstruction in single Drosophila brains

Y. Li, L. A. Walker, Y. Zhao, E. M. Edwards, N. S. Michki, H. J. Cheng, M. Ghazzi, T. Y. Chen, M. Chen, D. H. Roossien, and D. Cai

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

N. S. Michki, Y. Li, K. Sanjasaz, Y. Zhao, F. Shen, L. A. Walker, W. Cao, C.-Y. Lee, and D. Cai

Cell Reports 35(4), 109039 (2021)

Unsupervised Neural Tracing in Densely Labeled Multispectral Brainbow Images

B. Duan, L. A. Walker, D. Roossien, F. Shen, D. Cai#, and Y. Yan#

IEEE 18th International Symposium on Biomedical Imaging (ISBI) 1122–1126 (2021)

Light microscopy based approach for mapping connectivity with molecular specificity

F. Shen, M. Harrington, L. A. Walker, H. J. Chen, E. S. Boyden, and D. Cai

Nature Communications 11, 4632 (2020)

CLEAR: Coverage-based Limiting-cell Experiment Analysis for RNA-seq

L. A. Walker, M. G. Sovic, C.-L. Chiang, E. Hu, J. K. Denninger, X. Chen, E. D. Kirby, J. C. Byrd, N. Muthusamy, R. Bundschuh, and P. Yan

Journal of Translational Medicine 18(1), 63 (2020)

TraceMontage: a Method for Merging Multiple Independent Neuronal Traces

S. A. Dizaji, L. A. Walker, and D. Cai

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

C.-L. Chiang, S. Goswami, F. W. Frissora, Z. Xie, P. Yan, R. A. Bundschuh, L. A. Walker, X. Huang, R. Mani, X. Mo, S. Baskar, C. Rader, M. A. Phelps, G. Marcucci, J. C. Byrd, L. Lee, and N. Muthusamy

Blood 134(5), 432-444 (2019)

Whole Transcriptome Analysis of Renal Intercalated Cells Predicts Lipopolysaccharide Mediated Inhibition of Retinoid X Receptor alpha Function

V. Saxena, J. Fitch, J. Ketz, P. White, A. Wetzel, M. A. Chanley, J. D. Spencer, B. Becknell, K. R. Pierce, S. W. Arregui, R. D. Nelson, G. J. Schwartz, V. Velazquez, L. A. Walker, X. Chen, P. Yan, D. S. Hains, and A. L. Schwaderer

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

Neurons Can Fly

Instructor

Summer 2023 - present

Biophysics 370

Graduate Student Instructor

University of Michigan Biophysics

Fall 2020

NIH Outreach Core

Program Assistant

Ohio State University

Summers 2017 - 2018

CSE 2221: Java Programming

Instructional Assistant

Ohio State University CSE

Fall 2015