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@zymergen.com
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Alexander Shearer is listed as Quantitative Bio, Synthetic Bio, and Biological Learning based in San Francisco, California, United States. AeroLeads shows a work email signal at zymergen.com, phone signal with area code 650, 310, 408, 858, 619, and a matched LinkedIn profile for Alexander Shearer.
Alexander Shearer previously worked as Software Architect, Biologic Learning at Berkeley Lights, Inc. and Biology Design Consultant at Berkeley Lights, Inc.. Alexander Shearer holds Phd, Biology from University Of California, San Diego.
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I'm a biologist working in quantitative biology, systems biology, and synthetic biology.My work focuses on closely coordinated computational and laboratory efforts. I apply novel combinations of existing and new methods to engineer living systems. I have extensive experience with biological networks, picking the best proteins (and protein parts) for the job, and expanding the reach of what we can manufacture biologically, whether the endpoint is a small molecule or the protein itself.Things I've done lately: Making complex proteins - Building out a platform for data-driven design of complex, typically multidomain proteins for therapeutic and other applications. Living Foundries, Bioreachables, & Products - My most recent work at Zymergen included architecting bioreachable prediction methods ("What can we build?") and pathway design approaches ("How do we build it?) - and then using these methods to build pathways to reach high-value small molecules for material and other uses. The Orphan Enzymes Project - My NIH R01-funded project that used a combination of literature, computational, and lab methods to find sequences for 275 orphan enzymes, opening up new areas of biological engineeringI began at the bench and transitioned into computational methods, so I have experience on "both sides" of the fence - I'm comfortable making predictions at the computer and then walking over to the lab to test them out. I'm used to rapidly picking up new methods and systems, and have worked with mice, frogs, flies, E. coli, yeast, and photosynthetic microbes.
Listed skills include Bioinformatics, Genomics, Computational Biology, Science, and 31 others.
A career timeline built from the work history available for this profile.
• Finding new ways to predict cell behavior at scale based on single-cell phenotypic data from the powerful BLI Beacon platform• Providing quantitative biology assists to highly interdisciplinary project teams
• Completely redesigned data structure to power learning, maintain the security of client data, and support automated design of complex, multi domain proteins• Cleaned up and unified existing data consisting of several thousand protein domains collected from a variety of sources of highly variable data quality• Developed method for combining wildly different quantitative and qualitative outcome data for learning• Set up pipeline for consistent intake of outsourced data collection
San Francisco Bay Area
• Architected pathway design infrastructure for making novel products• Designed pathways for biological production of over a hundred high-value small molecules (see patents below for a few examples)• Created novel approach for predicting which molecules can be made biologically, yielding a reliable “catalog” of “bioreachable” molecules (see bioreachable patent below)• Developed methods for prioritizing genetic modifications for high-throughput analysis• Carried out due diligence on potential acquisitions (including Radiant Genomics, which was acquired by Zymergen)• Worked with business development team to support client communications and determine viability of potential company projects
San Francisco Bay Area
• Bioinformatics - Predicted whole-organism phenotypes from metabolic network data. Inferred biomedically significant relationships from large datasets (genomics, proteomics, patient data).• Resolving the problem of orphan enzyme activities (NIH R01) - Principal Investigator on an enzyme genomics project that combined literature, computational, and laboratory methods to resolve a critical gap in our knowledge of how enzyme function connects to protein sequence. We identified sequences for over 275 "orphan" enzymes, cutting the information gap down by over 25%. This was a multi-center project, at various times involving groups in the Bay Area, Virginia, at Texas A&M, and the University of Toronto.
Biologist in the Artificial Intelligence Center at SRI International.• Resolving the problem of orphan enzyme activities (NIH R01) - Principal Investigator on an enzyme genomics project that combined literature, computational, and laboratory methods to resolve a critical gap in our knowledge of how enzyme function connects to protein sequence. We identified sequences for over 275 "orphan" enzymes, cutting the information gap down by over 25%. This has been a multi-center project, at various times involving groups in the Bay Area, Virginia, at Texas A&M, and the University of Toronto.• Metabolic engineering - Designed and developed approaches to biologically generate high-value and commodity chemicals. Worked with an interdisciplinary team of biologists and chemists to make genetically modified microbes to produce a suite of target commodity chemicals.• Interdisciplinary applications of bioinformatics - Collaborated with Luciana Ferrer to apply natural language processing (NLP) methods to the identification of functional gene groups from genome sequence data.• Predictive computational biology - Collaborated on prediction of bacterial growth requirements based on genome sequence data. Developed the metabolic model and then adapted classic microbial assays for high-throughput evaluated of predicted growth in the lab.• PortEco - Assisted in the development of the PortEco multi-strain E. coli resource (a project led by Paul Thomas at USC).• EcoCyc - Developed content and design of the EcoCyc comprehensive E. coli database which serves a community of thousands of researchers. Work in this period included developing formal representations of high-throughput growth, "essentiality," and Biolog data to allow easy visual and computational access by bench and computational biologists. I also continued to produce educational videos for our user base.
Biologist in the Artificial Intelligence Center at SRI International.• Predictive computational biology - Predicted bacterial growth requirements based on genome sequence data in collaboration with members of SRI's Computer Science Laboratory. Developed the metabolic model and then adapted classic microbial assays for high-throughput evaluated of predicted growth in the lab.• Photosynthetic biofuels - Designed and developed approaches to generate photosynthetic biofuels as part of an interdisciplinary team including chemists, engineers, and microbiologists. My work on this project was end-to-end, starting designing the approach and continuing through my work at the bench developing genetically modified Synechococcus elongatus (a photosynthetic bacterium).• EcoCyc - Developed content and design of the EcoCyc comprehensive E. coli database. Work included large-scale literature review covering thousands of papers and development of both informal and formalized representations of biological knowledge in an accessible database format. I also designed our video instructional and outreach series, and made the first three years of videos for the series.•BioCyc - Developed the BioCyc workflow and user experience in collaborating with scientific software engineers, as well as designing automated quality checking methods for the automatically generated BioCyc collection of thousands of model organism databases.
Researched regulated protein degradation in the lab of Randy Hampton. I developed a novel structural transition assay and an aggregation assay, and used those in combination with flow cytometry, fluorescence, and epitope tagging to identify how a small molecule induced a "broken" conformation in the statin target HMG-CoA Reductase, priming it for degradation.
Evaluated the role of the product of the Su(Hw) gene in the action of the Gypsy insulator system, using the X. laevis oocyte system as the primary experimental tool (in the lab of Marietta Dunaway).
Anatomical and molecular analysis of Drosophila mutants in the sog (short gastrulation) developmental gene. Work included maintenance of lab fly strains, fixing and light microscopy of fly wings, and restriction analysis of sog constructs (in the lab of Ethan Bier).
Researched regulated protein degradation in the lab of Randy Hampton UCSD Cell and Molecular Genetics Training Grant Fellow (NIH T32.
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Alexander Shearer is listed as Quantitative Bio, Synthetic Bio, and Biological Learning.
AeroLeads has found 1 work email signal at @zymergen.com for Alexander Shearer.
AeroLeads has found 7 phone signal(s) with area code 650, 310, 408, 858, 619 for Alexander Shearer.
Alexander Shearer is based in San Francisco, California, United States.
Alexander Shearer has worked for Berkeley Lights, Inc., Serotiny, Zymergen, Inc., Independent, and Sri International.
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Alexander Shearer holds Phd, Biology from University Of California, San Diego.
Alexander Shearer is listed with skills including Bioinformatics, Genomics, Computational Biology, Science, Biology, Molecular Biology, Microbiology, and Chemistry.
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