Joseph Walker

As a computational biologist my interests fall at the intersection of biology and computer science. In this growing field, I focus on comparing large genomic datasets across species in order to identify historical processes that occurred millions of years ago. This includes examining genome datasets for signatures of gene and whole genome duplications, ancient hybridization, and genomic changes associated with rapid speciation events. By inferring these processes, we can begin to understand how species are related to each other, why traits are unevenly distributed across the tree of life, and what genes are associated with specific adaptations.

Although genomic data has incredible potential to provide insight about biology, processing it requires unprecedented memory and computing power. The exponential rate at which sequencing data is produced is beginning to outpace our ability to store and process this data in an efficient manner. As such, my research advances the study of genomes by developing novel methods and programs to process and analyze sequencing data. Specifically, I aim to create fast, memory efficient, and biologically informed procedures to help ease the burden that large scale sequencing projects have on our current computing infrastructure.

(Complete list of publications on Google Scholar)

1. LC Wheeler, JF Walker, J Ng, R Deanna, A Dunbar-Wallis, A Backes, PH Pezzi, M Palchetti, †HM Robertson, A Monaghan, L Brandão de Freitas, GE Barboza, E Moyroud, SD Smith. Transcription factors evolve faster than their structural gene targets in the flavonoid pigment pathway (2022). Molecular Biology and Evolution. 39:3.
2. JF Walker, SA Smith, RGJ Hodel, and E Moyroud. Concordance-based approaches for the inference of relationships and molecular rates with phylogenomic datasets (2021). Advanced access. Systematic Biology.
3. G Reeves, A Tripathi, P Singh, MRW Jones, AK Nanda, C Musseau, M Craze, S Bowden, JF Walker, AR Bentley, CW Melnyk, JM Hibberd. Monocotyledonous plants graft at the embryonic root–shoot interface. Nature (2021). https://doi.org/10.1038/s41586-021-04247-y
4. SA Smith, JF Walker and N Walker-Hale. Intragenic conflict in phylogenomic datasets (2020). Molecular Biology and Evolution. 37:11.
5. DA Larson, JF Walker, OM Vargas and SA Smith. A consensus phylogenomic approach highlights the ancient rapid radiation of the Ericales (2020). American Journal of Botany. 105:5.
6. SA Smith, N Walker-Hale, JF Walker and JW Brown. Phylogenetic Conflicts, Combinability, and Deep Phylogenomics in Plants (2020).  Systematic Biology. 69:3.
7. JF Walker, N Walker-Hale, DA Larson, OM Vargas and GW Characterizing gene tree conflict and systematic error in plastome-inferred phylogenies (2019). PeerJ. 7:7747.
8. S Tittes, JF Walker, L Torres-Martinez and N Grow where you thrive or where only you can survive? A Bayesian analysis of tolerance curve evolution in a clade with diverse habitat affinities (2019). The American Naturalist. 193:4.
9. N Wang, Y Yang, MJ Moore, SF Brockington, JF Walker, JW Brown, T Feng, A Timoneda, C Edwards, L Majure, R Puente, U Eggli, B Liang and SA Evolution of Portulacineae marked by adaptation to harsh environments, gene tree conflict, and gene family expansion (2019). Molecular Biology and Evolution, 36:1.
10. SA Smith and JF PyPHLAWD: A python package for phylogenetic dataset construction (2019). Methods in Ecology and Evolution, 10:1.
11. T Casey, JF Walker, K Bhide, J Thimmapuram and J Global transcriptome difference in myokine and inflammatory genes in muscle of mature steer progeny is related to maternal lactation diet and muscle composition (2018). Physiological Genomics, 50:10.
12. JF Walker, JW Brown and SA Analyzing contentious relationships and outlier genes in phylogenomics (2018). Systematic Biology, 67:5.
13. SA Smith, JW Brown and JF Walker. So many genes, so little time: A practical approach to divergence time estimation in the genomic era (2018). PLOS ONE, 13:5.
14. JF Walker, Y Yang, T Feng, A Timoneda, J Mikenas, V Hutchison, C Edwards, N Wang, S Ahluwalia, J Olivieri, N Walker-Hale, LC Majure, R Puente, G Kadereit, M Lauterbach, U Eggli, H Flores-Olvera, H Ochoterena, SF Brockington, MJ Moore and SA From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provides further insight to the evolution of Caryophyllales (2018). American Journal of Botany, 105:3.
15. JB Pease, JW Brown, JF Walker, CE Hinchliff and SA Quartet sampling distinguishes lack of support from conflicting support in plant tree of life (2018). American Journal of Botany, 105:3.
16. Y Yang, MJ Moore, SF Brockington, J Mikenas, J Olivieri, JF Walker and SA Improved transcriptome sampling pinpoints 26 paleopolyploidy events in Caryophyllales, including two paleo-allopolyploidy events (2018). New Phytologist, 217:2.
17. SA Smith, JW Brown, Y Yang, R Bruenn, CP Drummond, SF Brockington, JF Walker, N Last, NA Douglas and MJ Disparity, diversity, and duplications in the Caryophyllales (2018). New Phytologist, 217:2.
18. JF Walker, Y Yang, MJ Moore, J Mikenas, SF Brockington, A Timoneda and SA Widespread paleopolyploidy, gene tree conflict and recalcitrant relationships among the carnivorous Caryophyllales (2017). American Journal of Botany, 104:6.
19. JW Brown, JF Walker and SA Smith (2017). Phyx: Phylogenetic tools for Bioinformatics, 33:12.
20. Y Yang, MJ Moore, SF Brockington, A Timoneda, T Feng, H Marx, JF Walker and SA Smith (2017). An efficient field and laboratory workflow for plant phylotranscriptomic projects. Applications in Plant Sciences, 5:3.
21. JF Walker, RK Jansen, MJ Zanis and NC Emery (2015). Sources of inversion variation in the small single copy (SSC) region of chloroplast American Journal of Botany, 102:11.
22. JF Walker, MJ Zanis and NC Emery (2014). Comparative analysis of Complete Chloroplast Genome Sequence and Inversion Variation in Lasthenia Burkei (Madieae, Asteraceae). American Journal of Botany, 101:4.
23. AM Stoehr, JF Walker and A Monteiro (2013). Spalt expression and the development of melanic color patterns in pierid EvoDevo, 4:6.

Ph.D. Ecology and Evolutionary Biology, University of Michigan, 2018
M.S. Botany, Purdue University, 2014
B.S. Genetics, Purdue University, 2012
B.S. Neurology and Physiology, Purdue University, 2012