iRF_LOOPy
High-performance Python package for inferring Gene Regulatory Networks (GRNs) using Iterative Random Forest (iRF).
Posts by Collection
portfolio
metnet-direct-auxiliary
Codebase for analyzing the link between fungal metabolomic outputs and exogenous treatment triggers.
RWRtoolkit
Command-line and R toolkit for performing Random Walk with Restart (RWR) analyses on multiplex biological networks.
Using Bipartite Networks to Determine Interactions Between Analytes and Chemical Treatments
Patent on a bipartite network-based system for ranking metabolite–treatment relationships from LC/MS data using network centrality.
publications
Eyeing the patterns: Data visualization using doubly‑seriated color heatmaps
Published in Advances in Computers, 2020
Book chapter on advanced data visualization techniques using doubly‑seriated heatmaps.
Recommended citation: Lane, M., Maiocco, A., Bhatia, S.K., Climer, S. (2020). “Eyeing the patterns: Data visualization using doubly‑seriated color heatmaps.” Advances in Computers.
Download Paper | Download Slides | Download Bibtex
Synchronized genetic activities in Alzheimer’s brains revealed by heterogeneity‑capturing network analysis
Published in bioRxiv, 2020
Preprint using network heterogeneity analysis to reveal genetic synchrony in Alzheimer’s disease.
Recommended citation: Climer, S., Templeton, A.R., Garvin, M., Jacobson, D., Lane, M., et al. (2020). “Synchronized genetic activities in Alzheimer’s brains revealed by heterogeneity‑capturing network analysis.” bioRxiv.
Download Paper | Download Slides | Download Bibtex
Antiviral Strategies Against SARS‑CoV‑2: A Systems Biology Approach
Published in Methods in Molecular Biology, 2022
Book chapter describing systems biology approaches to antiviral strategies against SARS-CoV-2.
Recommended citation: Prates, E. T., Garvin, M. R., Jones, P., … Lane, M. (2022). “Antiviral Strategies Against SARS‑CoV‑2: A Systems Biology Approach.” Methods in Molecular Biology.
Download Paper | Download Slides | Download Bibtex
Lipo‑Chitooligosaccharides Induce Specialized Fungal Metabolite Profiles That Modulate Bacterial Growth
Published in mSystems, 2022
mSystems article on how lipo-chitooligosaccharides affect fungal metabolite profiles and microbial interactions.
Recommended citation: Rush, T. A., Tannous, J., Lane, M. J., … Ané, J.-M. (2022). “Lipo‑Chitooligosaccharides Induce Specialized Fungal Metabolite Profiles That Modulate Bacterial Growth.” mSystems.
Download Paper | Download Slides | Download Bibtex
Exploring the role of plant lysin motif receptor‑like kinases in regulating plant‑microbe interactions in the bioenergy crop Populus
Published in Computational and Structural Biotechnology Journal, 2023
Journal article on plant lysin motif receptor-like kinases and their role in plant-microbe interactions in Populus.
Recommended citation: Cope, K. R., Prates, E. T., Miller, J. I., … Lane, M. (2023). “Exploring the role of plant lysin motif receptor‑like kinases in regulating plant‑microbe interactions in the bioenergy crop Populus.” Computational and Structural Biotechnology Journal.
Download Paper | Download Slides | Download Bibtex
Genetics of varicose veins reveals polygenic architecture and genetic overlap with arterial and venous disease
Published in Nature Cardiovascular Research, 2023
Nature Cardiovascular Research article detailing the polygenic architecture of varicose veins.
Recommended citation: Levin, M. G., Huffman, J. E., Verma, A., … Lane, M. (2023). “Genetics of varicose veins reveals polygenic architecture and genetic overlap with arterial and venous disease.” Nature Cardiovascular Research.
Download Paper | Download Slides | Download Bibtex
Identification of novel, replicable genetic risk loci for suicidal thoughts and behaviors among US military veterans
Published in JAMA Psychiatry, 2023
JAMA Psychiatry study identifying replicable genomic loci for suicidal thoughts and behaviors among 633,778 US military veterans through large-scale GWAS.
Recommended citation: Kimbrel, N. A., Ashley-Koch, A. E., Qin, X. J., Lindquist, J. H., … Lane, M. J., et al. (2023). “Identification of novel, replicable genetic risk loci for suicidal thoughts and behaviors among US military veterans.” JAMA Psychiatry, 80(2), 135–145.
Download Paper | Download Slides | Download Bibtex
Longitudinal Effects on Plant Species Involved in Agriculture and Pandemic Emergence Undergoing Changes in Abiotic Stress
Published in ACM Conference, 2023
Conference paper studying abiotic stress impacts on agriculture and pandemic risk in plant species over time.
Recommended citation: Cashman, M., Vergara, V. G. M., Lane, M., et al. (2023). “Longitudinal Effects on Plant Species Involved in Agriculture and Pandemic Emergence Undergoing Changes in Abiotic Stress.” ACM Conference.
Download Paper | Download Slides | Download Bibtex
A glimpse into the fungal metabolomic abyss: Novel network analysis reveals relationships between exogenous compounds and their outputs
Published in PNAS Nexus, 2023
PNAS Nexus article unveiling fungal metabolomic networks and compound relationships via network analysis.
Recommended citation: Meena, M. G., Lane, M. J., Tannous, J., et al. (2023). “A glimpse into the fungal metabolomic abyss: Novel network analysis reveals relationships between exogenous compounds and their outputs.” PNAS Nexus.
Download Paper | Download Slides | Download Bibtex
Climate adaptation in P. trichocarpa: key adaptive loci identified for stomata and leaf traits
Published in bioRxiv, 2024
Preprint identifying genetic loci underlying climate-adaptive stomatal and leaf traits in Populus trichocarpa through GWAS and predictive modeling across over 1,300 genotypes.
Recommended citation: Klein, M. C., Meng, Z., Bailey-Bale, J., Milner, S., Shi, P., Muchero, W., … Lane, M., et al. (2024). “Climate adaptation in P. trichocarpa: key adaptive loci identified for stomata and leaf traits.” bioRxiv. https://doi.org/10.1101/2024.07.11.603099
Download Paper | Download Slides | Download Bibtex
MENTOR: Multiplex Embedding of Networks for Team‑Based Omics Research
Published in bioRxiv, 2024
Preprint presenting MENTOR, a multiplex network embedding framework for collaborative omics studies.
Recommended citation: Sullivan, K. A., Miller, J. I., Townsend, A., … Lane, M. (2024). “MENTOR: Multiplex Embedding of Networks for Team‑Based Omics Research.” bioRxiv.
Download Paper | Download Slides | Download Bibtex
Analyses of GWAS signal using GRIN identify additional genes contributing to suicidal behavior
Published in Communications Biology, 2024
Peer-reviewed study introducing GRIN, a method for refining GWAS results using biological networks to uncover additional genes contributing to suicidal behavior across cohorts.
Recommended citation: Sullivan, K. A., Lane, M., Cashman, M., Miller, J. I., Pavicic, M., Walker, A. M., et al. (2024). “Analyses of GWAS signal using GRIN identify additional genes contributing to suicidal behavior.” Communications Biology, 7(1), 1360. https://doi.org/10.1038/s42003-024-06943-7
Download Paper | Download Slides | Download Bibtex
Multi‑omic network analysis identifies dysregulated neurobiological pathways in opioid addiction
Published in Biological Psychiatry, 2024
Biological Psychiatry paper identifying neurobiological pathways related to opioid addiction via multi-omic network analysis.
Recommended citation: Sullivan, K. A., Kainer, D., Lane, M., et al. (2024). “Multi‑omic network analysis identifies dysregulated neurobiological pathways in opioid addiction.” Biological Psychiatry.
Download Paper | Download Slides | Download Bibtex
RWRtoolkit: multi‑omic network analysis using random walks on multiplex networks in any species
Published in GigaScience, 2025
GigaScience article introducing RWRtoolkit, a toolkit for random-walk restart analytics on multiplex biological networks.
Recommended citation: Kainer, D., Lane, M., Sullivan, K. A., et al. (2025). “RWRtoolkit: multi‑omic network analysis using random walks on multiplex networks in any species.” GigaScience.
Download Paper | Download Slides | Download Bibtex
Population and adaptation history of 739 Thlaspi arvense natural accessions
Published in bioRxiv, 2025
Preprint describing the genomic and phenotypic analysis of 739 pennycress accessions to guide climate-resilient domestication efforts.
Recommended citation: Wu, X., Epstein, R., Esfahanian, M., Gautam, B., Griffiths, M., Perez, J., … Lane, M., et al. (2025). “Population and adaptation history of 739 Thlaspi arvense natural accessions.” bioRxiv. https://doi.org/10.1101/2025.03.21.644658
Download Paper | Download Slides | Download Bibtex
Genome shuffling enables quantitative trait locus mapping in Bacillus subtilis
Published in bioRxiv, 2025
Preprint describing the use of iterative genome shuffling to enable bacterial QTL mapping in Bacillus subtilis, revealing genotype–phenotype associations through recombination-enabled linkage analysis.
Recommended citation: Vasileva, D. P., Chhetri, H. B., Hochanadel, L. H., Streich, J. C., Lagergren, J. H., Lane, M. J., et al. (2025). “Genome shuffling enables quantitative trait locus mapping in Bacillus subtilis.” bioRxiv. https://doi.org/10.1101/2025.07.14.664384
Download Paper | Download Slides | Download Bibtex
Climate adaptation in Populus trichocarpa: key adaptive loci identified for stomata and leaf traits
Published in New Phytologist, 2025
This study identifies genetic and physiological traits underpinning drought adaptation in Populus trichocarpa, a key bioenergy crop. By examining over 1300 genotypes in a large-scale field experiment, the authors reveal that stomatal and leaf traits—especially a major locus on chromosome 10—are tightly linked to climatic origin and are likely to evolve under future arid conditions. Their findings provide crucial targets for breeding resilient trees to meet biofuel demands on marginal lands in a changing climate.
Recommended citation: Klein, M. C., Meng, Z., Bailey‐Bale, J., Milner, S., Shi, P., Muchero, W., Chen, J., Tschaplinski, T. J., Jacobson, D., Lagergren, J., Lane, M., O’Brien, C., Chhetri, H., Abeyratne, C. R., Shu, M., Freer‐Smith, P., Buckley, T. N., Magney, T. S., Monroe, J. G., … Taylor, G. (2025). Climate adaptation in Populus trichocarpa: key adaptive loci identified for stomata and leaf traits. New Phytologist. https://doi.org/10.1111/nph.70343
Download Paper | Download Slides | Download Bibtex
talks
teaching
Introduction to Computing with C++
Undergraduate course, University of Missouri - St. Louis, Department of Computer Science, 2019
An introductory computer science course (CS1250) for students with no prior programming background. This course builds a foundation in computational thinking and procedural programming using C++.
Introduction to Web Programming: HTML, Javascript, and PHP
Undergraduate course, University of Missouri - St. Louis, Department of Computer Science, 2019
This course (CS3010) introduces students to the foundational technologies behind the web.
Advanced Web Programming with Javascript
Undergraduate course, University of Missouri - St. Louis, Department of Computer Science, 2020
Course material for CS4140, covering modern JavaScript frameworks and backend development techniques.
Introduction to Object Oriented Programming with Java
Undergraduate course, University of Missouri - St. Louis, Department of Computer Science, 2020
Course material for CS2261, covering Java fundamentals, objects, interfaces, abstract classes, and object-oriented programming principles.
Linux Systems Programming: Bash && C
Undergraduate course, University of Missouri - St. Louis, Department of Computer Science, 2020
This course (CS2700) is an introduction to Linux systems and system-level programming in C and Bash.