Matthew K. Howard

Last updated: November 2025

about

Hello! My name is Matt. I am a PhD candidate at UCSF working in the Coyote-Maestas and Manglik labs. My current work uses deep mutational scanning and other library-based approaches to understand GPCR function, pharmacology, and evolution. I dabble in and collaborate widely across many disciplines including: structural biology & biophysics, molecular simulation, molecular pharmacology, machine learning, and various other "-omics". If you're interested to hear the latest, please reach out!

Prior to UCSF, I graduated from Washington University in St. Louis with degrees in chemistry and biology. At WashU, I worked in the Jackrel lab where I investigated structure-function relationships in the disaggregase Hsp104 and amyloid proteins that comprise microbial biofilms

I can be found the following places: email me, Twitter(X), Bluesky, Github, Linkedin, Google Scholar, Orcid.

publications

Please find a list of my publications below. My Google Scholar may be more current. Please email me if you run into paywall issues.

PhD work at UCSF

• [in prep] Howard MK et al (2026) Deep mutational pharmacology reveals the molecular basis of opioid agonism.
• [Submitted - in review] Howard MK & Coyote-Maestas W (2026) Mechanistic mutational scanning to uncover the secret life of proteins. Annual Reviews Biomedical Data Science.
• Tedman A, Goel M, Shah S, Howard MK, Chamness LM, Bonifasi A, Adams I, Gallagher JM, Penn WD, Nemec K, McDonald EF, Corman BN, Robinson JP, Post CB, Clark PL, Babu MM, Manglik AM, Kuntz CP, Coyote-Maestas W, Schlebach JP (2025) Deep Receptor Scanning Reveals General Sequence Constraints on GPCR Biosynthesis. bioRxiv. https://doi.org/10.1101/2025.09.19.677468
• Freudenberg J, Rao J, Howard MK, Macdonald C, Greenwald NF, et al. (2025) Accurate variant effect estimation in FACS-based deep mutational scanning data with Lilace. bioRxiv. https://doi.org/10.1101/2025.06.24.661380
• Rao J, Wang M, Howard MK, Coyote-Maestas W, Pimentel H (2025) Cosmos: A Position-Resolution Causal Model for Direct and Indirect Effects in Protein Functions. bioRxiv. https://doi.org/10.1101/2025.08.01.667517
• Rao J, Wang M, Howard MK, Macdonald C, Fraser JS, Coyote-Maestas W, Pimentel H (2025) Rosace-AA: Enhancing interpretation of deep mutational scanning data with amino acid substitution and position-specific insights. Bioinformatics Advances. https://doi.org/10.1093/bioadv/vbaf218
• Macdonald C, Nedrud D, Grimes PR, Trinidad D, Shin C, Greenwald N, Howard MK, Fraser J, Coyote-Maestas (2025) DIMPLE library generation and assembly protocol V6. protocol.io. https://doi.org/10.1101/2024.10.10.617568
• Naghipourfar M, Chen S, Howard MK, Macdonald CB, Saberi A, Hagen T, Mofrad MRK, Coyote-Maestas W, Growald M (2024) A Suite of Foundation Models Captures the Contextual Interplay Between Codons. bioRxiv. https://doi.org/10.1101/2024.10.10.617568
• 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 (2024) Molecular basis of proton-sensing by G protein-coupled receptors. Cell. https://doi.org/10.1016/j.cell.2024.11.036
• 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
• 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 activated μ-opioid receptor. Nature Chemical Biology. https://doi.org/10.1038/s41589-024-01588-3

From WUSTL

• Chen S, Puri A, Bell B, Fritsche J, Palacios HH, Balch M, Sprunger ML, Howard MK, Patterson JN, Patti GJ, Davis AA, Jackrel ME (2024) HtrA1 disaggregates α-synuclein amyloid fibrils and converts them into non-toxic and seeding incompetent species. Nature Communications. https://doi.org/10.1038/s41467-024-46538-8
• 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 Adjuvant Potential for use as DNA Vaccines. Acta Biomaterialia. https://doi.org/10.1016/j.actbio.2023.08.015
• Howard MK, Miller KR, Sohn BS, Ryan JJ, 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
• Howard MK, Sohn BS, von Borcke J, Xu A, Jackrel ME (2020) Functional analysis of proposed substrate-binding residues of Hsp104. PLoS ONE. https://doi.org/10.1371/journal.pone.0230198

news

• May 2024: Jingyou's paper is out in Genome Biology
• April 2024: Matt's paper is out on Biorxiv
• March 2024: Matt gives an invited talk at the 2024 Ligand Gating and Molecular Recognition GRS and a poster at the GRC (Ventura, CA)
• March 2024: Andy's paper is out in Nature Communications
• December 2023: Ruth's μOR-APEX paper is out on Biorxiv
• October 2023: Jingyou's ROSACE paper is out on Biorxiv
• June 2023: Matt presents a poster at the 2023 Membrane Protein Folding GRC
• June 2023: Matt is awarded the UCSF Julius R. and Patricia A. Krevans Fellowship
• April 2023: Matt presents ongoing work at the UCSF GPCR Supergroup monthly meeting (San Francisco, CA)
• April 2023: Matt's paper from the Jackrel Lab studying the PSMα peptides is accepted at mBio!
• April 2023: Matt gives an invited talk at the UCSF Cell Engineering & Synthetic Biology seminar series (San Francisco, CA)
• January 2023: Matt gives an invited short talk and poster presentation at the 2023 GPCR Workshop (Kona, HI) and is supported by the UCSF Graduate Division Travel Award
• October 2022: Matt gives a talk and poster presentation at the CZ Biohub Inter-lab Confab (San Francisco, CA)
• October 2022: Matt give a poster presentation on his work at the annual UCSF Tetrad retreat (Tahoe, CA)
• June 2022: Matt Joins the Willow Coyote-Maestas and Manglik Labs
• April 2022: 3rd rotation with the Mordes Lab
• January 2022: 2nd rotation with Willow Coyote-Maestas and the Manglik Lab
• September 2021: 1st lab rotation in the Fraser Lab
• September 2021: First day at UCSF!
• April 2021: Matt accepts an offer to join the Tetrad Program at UCSF!
• January 2021: Matt serves as a TA for Introduction to Biochemistry (Bio406)
• March 2020: COVID-19 starts to turn the world inside-out
• March 2020: Matt's work on Hsp104 pore loops is published in PLOS One
• November 2019: Matt presents a poster at the Center for Science & Engineering of Living Systems (CSELS) meeting
• May 2019: Matt graduates from Washington University in St. Louis with majors in both Biology and Chemistry: concentration in Biochemistry
• May 2019: Matt receives the Lipkin Award for outstanding undergraduate research in chemistry
• May 2019: Matt receives the Outstanding PLTL Award for excellence in academic mentorship
• April 2019: Matt presents a poster on his work from the Jackrel Lab and another poster from his work in Bio4522 at the Undergraduate Research Symposium
• November 2018: Matt presents his work from the Jackrel Lab at the Undergraduate Research Symposium
• August 2018: Matt serves as a TA for General Biochemistry I (Chem481/Bio4810)
• July 2018: Matt attends the Alpha Chi Sigma Chemistry Fraternity Conclave in Pittsburgh, PA
• April 2018: Matt received a BioSURF award to fund his summer research in the Jackrel Lab
• August 2017: Matt starts work as an undergraduate research assistant in the Jackrel Lab at Washington University in St. Louis
• January 2017: Matt starts work as a undergraduate research assistant in the Wayne Barnes Lab at the Washington University School of Medicine
• August 2016: Matt starts work as a General Chemistry (Chem111/112) Peer-Led Team Learning (PLTL) Leader
• June 2016: Matt starts a summer research internship with the Carolinas Laparoscopic and Advanced Surgery Program (CLASP) at Carolinas Healthcare System
• August 2015: Matt starts his undergraduate degree at Washington University in St. Louis
• June 2015: Matt graduates from Providence Day School (Charlotte, NC)
• March 2013: Matt received an honorable mention by the Toshiba|NSTA Exploravision competition for his project "Utilizing an Automatically Titrating Therapeutic Oxygen Delivery Device (ATTODD) to Improve Individualized Patient Care"
• June 2012: Matt, Alex, and Christian win 1st at the state and regional level and travel to Washington, DC to compete for the national eCybermission title
• February 2012: Matt, Emily, and Alexander are invited to the White House Science Fair to present their eCybermission project on water filtration
• June 2011: Matt, Emily, and Alexander win 1st at the state and regional level and travel to Washington, DC to compete for the national eCybermission title