Article PDFs and links are listed – please contact me directly if there are broken links or paywalls that get in your way! My Google Scholar profile may be more up-to-date.
*, # equal contribution, † corresponding author
Preprints:
Rao J, Wang M, Howard MK, Macdonald C, Fraser J, Coyote-Maestas W, Pimentel, H (2025) Rosace-AA: Enhancing interpretation of deep mutational scanning data with amino acid substitution and position-specific insights. Pre-print available on Biorxiv
Naghipourfar M, Chen S, Howard MK, Macdonald CB, Saberi A, Hagen T, Mofrad MRK†, Coyote-Maestas W†, Goodarzi H† (2024) A Suite of Foundation Models Captures the Contextual Interplay Between Codons. Pre-print available on Biorxiv
2025
Howard MK*, Hoppe N*, Huang XP#, Mitrovic D#, Billesbølle CB, Macdonald CB, Mehrotra E, Rockefeller Grimes P, Trinidad DD, Delemotte L, English J, Coyote-Maestas W†, Manglik A†. (2025) Molecular basis of proton-sensing by G protein-coupled receptors. Cell. https://doi.org/10.1016/j.cell.2024.11.036 Link Pre-print on Biorxiv PDF
2024
Rao J, Xin R*, Macdonald C*, Howard MK, Estevam GO, Yee SW, Wang M, Fraser JS, Coyote-Maestas W†, Pimentel H† (2024) Rosace: a robust deep mutational scanning analysis framework employing position and mean-variance shrinkage. Genome Biology. https://doi.org/10.1186/s13059-024-03279-7 Link Biorxiv preprint PDF
Polacco BJ*, Lobingier BT*, Blythe EE, Abreu N, Khare P, Howard MK, Gonzalez-Hernandez AJ, Xu J, Li Q, Novy B, Naing ZZC, Shoichet BK, Coyote-Maestas W, Levitz J, Krogan NJ, Zastrow MV†, Hüttenhain R† (2024) Profiling the proximal proteome of the mu opioid receptor identifies novel regulators of receptor signaling and trafficking. Nature Chemical biology. https://doi.org/10.1038/s41589-024-01588-3 Link Biorxiv preprint PDF
Chen S, Puri A, Bell B, Fritsche J, Palacios HH, Balch M, Sprunger ML, Howard MK, Patterson JN, Patti GJ, Davis AA, and Jackrel ME† (2024) HtrA1 prevents and reverses α-synuclein aggregation, rendering it non-toxic and seeding incompetent. Nature Communications. https://doi.org/10.1038/s41467-024-46538-8 Link Research Square preprint PDF
2023
Shrimali PC, Chen S*, Das A*, Dreher R*, Howard MK*, Ryan J, Buck J, Kim D, Sprunger M, Rudra JS†, Jackrel ME† (2023) Amyloidogenic Propensity of Self-Assembling Peptides and their Adjuvent Potential for use as DNA Vaccines. Acta Biomaterialia. https://doi.org/10.1016/j.actbio.2023.08.015 Link Biorxiv preprint PDF
Howard MK, Miller KR, Sohn BS, Ryan JR, Xu A, Jackrel ME† (2023) Probing the drivers of Staphylococcus aureus biofilm protein amyloidogenesis and disrupting biofilms with engineered protein disaggregases. mBio. https://doi.org/10.1128/mbio.00587-23 PDF Link
2020
Howard MK, Sohn BS, von Borcke J, Xu A, Jackrel ME† (2020) Functional analysis of proposed substrate-binding residues of Hsp104. PLoS ONE. 15(3):e0230198. https://doi.org/10.1371/journal.pone.0230198 PDF Link