Micah Olivas
mbolivas [at] stanford.edu
I’m a fourth-year Genetics PhD student studying enzyme evolution at Stanford University. I am a member of Polly Fordyce's group in the Departments of Genetics and Bioengineering, and Sarafan ChEM-H. I am grateful to be supported by a NRSA F31 fellowship from the National Human Genome Research Institute of the NIH.
In my research, I use high-throughput microfluidics experiments to dissect how enzymatic properties like substrate specificity and thermostability are encoded in the amino acid sequences of natural proteins. Through this work, I hope to improve sequence-to-function prediction in both natural and engineered proteins.
Here are my Google Scholar, Twitter, Github, and CV.
Current Research Interests
- High-throughput assay development for kinetic measurements of proteins
- Inferring catalytic properties from evolutionary sequence data
- Connecting statistical coupling from enzyme phylogenies with energetic coupling in structures
News
- August 2023 I had a great time presenting my work on characterizing designed acylphosphatases at the Current Issues in Genetics (CIG) seminar series in the Stanford Genetics Department.
- July 2023 I'm very grateful to receive a NRSA F31 fellowship from the National Human Genome Research Institute
to support my research on sequence-to-function relationships in enzymes!
- December 2022 During the NeurIPS Learning Meaningful Representations of Life workshop Clara Wong-Fannjiang and I presented our work on using protein language models to enhance thermostability and activity of acylphosphatases (Poster).
- September 2022 At this year's Genetics Department retreat, I presented a strategy to characterize a large library of enzymes designed by a newly-described protein language model (PDF).
- November 2021 I passed my qualifying exam in the Genetics Department!
- September 2021 I presented my rotation project in the Fordyce lab, in which I generated high-throughput kinetic measurements of human acylphosphatases (PDF) at the
Stanford Genetics Department Retreat.
- July 2021 I am thrilled to join Polly Fordyce's group in the Departments of Genetics
and Bioengineering! I will continue to work with the high-throughput enzymology team on a project I started at
the beginning of my rotation in May.
- April 2021 After spending the winter quarter with
Serena Sanulli's group,
I will be moving on to another rotation with Polly Fordyce's group. It was great to witness the
formative weeks of Serena's lab at Stanford.
- February 2021 My rotation in the
Steinmetz Lab has come to an end. I had a great time working on
the TAP-seq pipeline with Andreas Gschwind, Dan Schraivogel, and others.
- May 2020 I was awarded a
graduate fellowship from the Honor Society of Phi Kappa Phi!
- April 2020 After a round of socially-distanced interviews, I accepted an
offer to join 23andMe Therapeutics as a Target Biology Intern
for Summer 2020.
- March 2020 New work on pooled CRISPR screens in an organoid model of lung
cancer is out now in Nature! We demonstrate that 3D "spheroid" cultures of
lung adenocarcinoma resolve phenotypic defects that arise in 2D monoloayer cell culture and
apply genome-wide forward screens in these models to identify genes implicated in tumor growth regulation.
Papers, Talks, and Posters
2023
Talk Beyond Structure: Exploring the Language of Enzyme Function with HT-MEK.
Current Issues in Genetics Seminar Series. Stanford Genetics Department. August 4th, 2023
2022
Poster Leveraging novel protein language models to understand constraints on enzyme function and design. [PDF]
Olivas M.*, Wong-Fannjiang C.*, Markin C., Naik N., and Fordyce P.M.
Quantitative Biology Institute Bay Area Chemical Biology Symposium. San Francisco, CA. 2022
Paper Designing active and thermostable enzymes with sequence-only predictive models. [Paper]
Wong-Fannjiang C.*, Olivas M.*, Greene E.R., Markin C.J., Wallace B., Krause B., Pinney M., Fraser J., Fordyce P.M., Madani A., and Naik N.
Neural Information Processing Systems (NeurIPS) Learning Meaningful Representations of Life Workshop. 2022
2021
Talk Developing predictive models of enzyme function from physics and phylogeny.
Genetics Department Annual Retreat. Stanford, CA, 2021
2020
Paper CRISPR screens in cancer spheroids identify 3D growth-specific vulnerabilities. [PDF]
Kyuho Han, Sarah E. Pierce, Amy Li, Kaitlyn Spees, Gray R. Anderson, Jose A. Seoane, Yuan-Hung Lo, Michael Dubreuil, Micah Olivas, Roarke A. Kamber, Michael Wainberg, Kaja Kostyrko, Marcus R. Kelly, Maryam Yousefi, Scott W. Simpkins, David Yao, Keonil Lee, Calvin J. Kuo, Peter K. Jackson, Alejandro Sweet-Cordero, Anshul Kundaje, Andrew J. Gentles, Christina Curtis, Monte M. Winslow and Michael C. Bassik.
Nature 2020.
2019
Poster Genome-wide CRISPR screens in 3D tumor spheroids reveal IGF1R processing dependencies in lung adenocarcinoma.
Olivas M*, Han K, Anderson G, and Bassik MC.
Stanford Summer Research Program Symposium. Stanford, CA. 08/2019
Poster Development of an inducible Cas9 for temporally controlled gene editing in mammary adenocarcinoma. [PDF]
Olivas M*, Fox D, and Alvarez J.
American Society for Pharmacology and Experimental Therapeutics meeting. Orlando, FL. 04/2019
Poster Study of the chemical and signaling bases of ambient particulate matter-induced oxidative stress in alveolar macrophages.
Olivas M*, Flores D*, Waterston A, Dejean L, and Hasson A.
California State University Program for Education and Research in Biotechnology (CSUPERB) meeting. Garden Grove, CA. 01/2019
2018
Talk Chemical and signaling bases of PM-mediated ROS production in alveolar macrophages.
Olivas M*, Flores D*, Waterston A, Dejean L, and Hasson A.
American Society for Cell Biology meeting. San Diego, CA. 12/2018
Talk Development of an inducible Cas9 for temporally controlled gene editing. Selected for symposium review.
Olivas M*, Fox D, and Alvarez J.
BioCoRE symposium. Durham, NC. 07/2018
Poster PM2.5 Exposure and ROS Production in NR8383 Alveolar Macrophages.
Olivas M*, Waterston A, Dejean L, and Hasson A.
California State University Honors Research Conference. Northridge, CA. 04/2018
Poster PM2.5 Exposure and ROS Production in NR8383 Alveolar Macrophages. [PDF]
Olivas M*, Waterston A, Dejean L, and Hasson A.
California State University Program for Education and Research in Biotechnology (CSUPERB). Santa Clara, CA. 01/2018
2017
Poster Effects of particulate matter aerosols on ROS production in alveolar macrophage cells. [PDF]
Castillo J*, Olivas M*, Waterston A, Dejean L, and Hasson A.
Central California Research Symposium. Fresno, CA. 04/2017
- August 2023 I had a great time presenting my work on characterizing designed acylphosphatases at the Current Issues in Genetics (CIG) seminar series in the Stanford Genetics Department.
- July 2023 I'm very grateful to receive a NRSA F31 fellowship from the National Human Genome Research Institute to support my research on sequence-to-function relationships in enzymes!
- December 2022 During the NeurIPS Learning Meaningful Representations of Life workshop Clara Wong-Fannjiang and I presented our work on using protein language models to enhance thermostability and activity of acylphosphatases (Poster).
- September 2022 At this year's Genetics Department retreat, I presented a strategy to characterize a large library of enzymes designed by a newly-described protein language model (PDF).
- November 2021 I passed my qualifying exam in the Genetics Department!
- September 2021 I presented my rotation project in the Fordyce lab, in which I generated high-throughput kinetic measurements of human acylphosphatases (PDF) at the Stanford Genetics Department Retreat.
- July 2021 I am thrilled to join Polly Fordyce's group in the Departments of Genetics and Bioengineering! I will continue to work with the high-throughput enzymology team on a project I started at the beginning of my rotation in May.
- April 2021 After spending the winter quarter with Serena Sanulli's group, I will be moving on to another rotation with Polly Fordyce's group. It was great to witness the formative weeks of Serena's lab at Stanford.
- February 2021 My rotation in the Steinmetz Lab has come to an end. I had a great time working on the TAP-seq pipeline with Andreas Gschwind, Dan Schraivogel, and others.
- May 2020 I was awarded a graduate fellowship from the Honor Society of Phi Kappa Phi!
- April 2020 After a round of socially-distanced interviews, I accepted an offer to join 23andMe Therapeutics as a Target Biology Intern for Summer 2020.
- March 2020 New work on pooled CRISPR screens in an organoid model of lung cancer is out now in Nature! We demonstrate that 3D "spheroid" cultures of lung adenocarcinoma resolve phenotypic defects that arise in 2D monoloayer cell culture and apply genome-wide forward screens in these models to identify genes implicated in tumor growth regulation.
Papers, Talks, and Posters
2023
Talk Beyond Structure: Exploring the Language of Enzyme Function with HT-MEK.
Current Issues in Genetics Seminar Series. Stanford Genetics Department. August 4th, 2023
2022
Poster Leveraging novel protein language models to understand constraints on enzyme function and design. [PDF]
Olivas M.*, Wong-Fannjiang C.*, Markin C., Naik N., and Fordyce P.M.
Quantitative Biology Institute Bay Area Chemical Biology Symposium. San Francisco, CA. 2022
Paper Designing active and thermostable enzymes with sequence-only predictive models. [Paper]
Wong-Fannjiang C.*, Olivas M.*, Greene E.R., Markin C.J., Wallace B., Krause B., Pinney M., Fraser J., Fordyce P.M., Madani A., and Naik N.
Neural Information Processing Systems (NeurIPS) Learning Meaningful Representations of Life Workshop. 2022
2021
Talk Developing predictive models of enzyme function from physics and phylogeny.
Genetics Department Annual Retreat. Stanford, CA, 2021
2020
Paper CRISPR screens in cancer spheroids identify 3D growth-specific vulnerabilities. [PDF]
Kyuho Han, Sarah E. Pierce, Amy Li, Kaitlyn Spees, Gray R. Anderson, Jose A. Seoane, Yuan-Hung Lo, Michael Dubreuil, Micah Olivas, Roarke A. Kamber, Michael Wainberg, Kaja Kostyrko, Marcus R. Kelly, Maryam Yousefi, Scott W. Simpkins, David Yao, Keonil Lee, Calvin J. Kuo, Peter K. Jackson, Alejandro Sweet-Cordero, Anshul Kundaje, Andrew J. Gentles, Christina Curtis, Monte M. Winslow and Michael C. Bassik.
Nature 2020.
2019
Poster Genome-wide CRISPR screens in 3D tumor spheroids reveal IGF1R processing dependencies in lung adenocarcinoma.
Olivas M*, Han K, Anderson G, and Bassik MC.
Stanford Summer Research Program Symposium. Stanford, CA. 08/2019
Poster Development of an inducible Cas9 for temporally controlled gene editing in mammary adenocarcinoma. [PDF]
Olivas M*, Fox D, and Alvarez J.
American Society for Pharmacology and Experimental Therapeutics meeting. Orlando, FL. 04/2019
Poster Study of the chemical and signaling bases of ambient particulate matter-induced oxidative stress in alveolar macrophages.
Olivas M*, Flores D*, Waterston A, Dejean L, and Hasson A.
California State University Program for Education and Research in Biotechnology (CSUPERB) meeting. Garden Grove, CA. 01/2019
2018
Talk Chemical and signaling bases of PM-mediated ROS production in alveolar macrophages.
Olivas M*, Flores D*, Waterston A, Dejean L, and Hasson A.
American Society for Cell Biology meeting. San Diego, CA. 12/2018
Talk Development of an inducible Cas9 for temporally controlled gene editing. Selected for symposium review.
Olivas M*, Fox D, and Alvarez J.
BioCoRE symposium. Durham, NC. 07/2018
Poster PM2.5 Exposure and ROS Production in NR8383 Alveolar Macrophages.
Olivas M*, Waterston A, Dejean L, and Hasson A.
California State University Honors Research Conference. Northridge, CA. 04/2018
Poster PM2.5 Exposure and ROS Production in NR8383 Alveolar Macrophages. [PDF]
Olivas M*, Waterston A, Dejean L, and Hasson A.
California State University Program for Education and Research in Biotechnology (CSUPERB). Santa Clara, CA. 01/2018
2017
Poster Effects of particulate matter aerosols on ROS production in alveolar macrophage cells. [PDF]
Castillo J*, Olivas M*, Waterston A, Dejean L, and Hasson A.
Central California Research Symposium. Fresno, CA. 04/2017