M
Matthew Brehove
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Lead Scientist at Chromologic
Pasadena, California, United States
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USD120k/year
Résumé
Jobs
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- CLead ScientistChromoLogic LLCOct 2019 - Current (7 years)Won over $2M in government funding to develop innovative solutions to a wide range of problems. Lead a team of engineers in developing a novel imaging method for non-invasive in-line cell culture monitoring using optical coherence tomography. The resulting device proved capable of quantifying cell concentration and viability in bioreactors reducing the labor needed for monitoring. The technology has attracted the interest of multiple bioreactor manufacturers as it solves a key quality control problem. Trained deep convolutional neural networks to extract biometric data from electroencephalograph (EEG) traces. Developed neuromorphic computing algorithms to convert deep neural networks into spiking neural networks that could be executed on In
Postdoctoral FellowCity of HopeApr 2017 - Oct 2019 (2 years 7 months)Wrote novel algorithms that could extract clustering information from 3D super-resolution microscopy images. A key innovation from this work was the development of a clustering algorithm that calculated aggregate cluster properties including number of molecules per cluster without needing to assign individual molecule localizations to specific clusters. This is necessary because individual molecules create many localizations during imaging that may overlap with nearby molecules. Rewrote a clustering algorithm based on Voronoi tessellation to reduce complexity and achieve a ~100x speedup which enabled publication deadlines to be met Completed Andrew Ng’s Deep Learning Specialization course on Coursera Adapted a cholesterol binding protein fo- Teaching AssistantThe Ohio State UniversitySep 2010 - Dec 2012 (2 years 4 months)- Taught introductory physics discussion sections and labs.
- Reasearch AssistantThe Ohio State UniversitySep 2010 - Dec 2016 (6 years 4 months)- Applied ensemble and single-molecule fluorescence techniques to study DNA-protein complexes. - Outlined, designed, executed, and evaluated the results, which lead to three publications - Developed image analysis software in Matlab to reduced manual analysis time by 50%. - Applied Hidden Markov Modeling to analyze single molecule fluorescence traces. - Developed instrument control software in LabVIEW to automate experimental data acquisition. - Improved our microscope’s temporal resolution 100x by developing and aligning new optics. - Collaborated with researchers outside of my field. - Trained undergraduates and new graduate students in laboratory techniques. - Presented my work at biological and biophysical conferences.
- UUndergraduate Research AssistantUCSB Department of PhysicsJan 2009 - Jun 2010 (1 year 6 months)- Built and aligned a fiber-optic coupler for illuminating a sample inside of a cryogenic apparatus. - Performed photoconductivity measurements on nitrogen impurities in diamond under high magnetic field and low temperature. - Accelerated experimental throughput by writing Lab-VIEW drivers and instrument control software to automate the experiment - Produced new 3D structure in flat samples using focused ion beam lithography.
Education
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- Doctor of Philosophy - PhD, PhysicsThe Ohio State UniversityJan 2010 - Jan 2016 (6 years 1 month)
- Bachelor’s Degree, PhysicsUC Santa BarbaraJan 2006 - Jan 2010 (4 years 1 month)Activities and Societies: St. Marks Parish Council, Amnesty International, Real Life
Projects (professional or personal)
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Awards
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- KKeystone Symposia ScholarshipKeystone SymposiaFeb 2016$1200 Scholarship to cover travel expenses related to the Keystone Symposia Chromatin and Epigenetics of Transcription. Awarded based on the quality of my submitted abstract.
Publications
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- NDNA sequence influences hexasome orientation to regulate DNA accessibilityNucleic Acids ResearchApr 2019Nucleosomes, the fundamental organizing units of eukaryotic genomes, contain ∼146 base pairs of DNA wrapped around a histone H3–H4 tetramer and two histone H2A–H2B dimers. Converting nucleosomes into hexasomes by removal of a H2A–H2B dimer is an important regulatory event, but its regulation and functional consequences are not well-understood. To investigate the influence of hexasomes on DNA accessibility, we used the property of the Widom-601 Nucleosome Positioning Sequence (NPS) to form homogeneously oriented hexasomes in vitro. We find that DNA accessibility to transcription factors (TF) on the hexasome H2A–H2B distal side is identical to naked DNA, while the accessibility on the H2A–H2B proximal side is reduced by 2-fold, which is due t
- MMethods for Investigating DNA Accessibility with Single NucleosomesMethods in enzymologyJan 2016Nucleosomes are the fundamental organizing unit of all eukaryotic genomes. Understanding how proteins gain access to DNA-binding sites located within nucleosomes is important for understanding DNA processing including transcription, replication, and repair. Single-molecule total internal reflection fluorescence (smTIRF) microscopy measurements can provide key insight into how proteins gain and maintain access to DNA sites within nucleosomes. Here, we describe methods for smTIRF experiments including the preparation of fluorophore-labeled nucleosomes, the smTIRF system, data acquisition, analysis, and controls. These methods are presented for investigating transcription factor binding within nucleosomes. However, they are applicable for inve
- JHistone core phosphorylation regulates DNA accessibilityJournal of BiochemistrySep 2015Background: Transcription and DNA replication are regulated by histone core phosphorylation. Results: Histone phosphorylation near the DNA entry-exit region of the nucleosome increases DNA unwrapping and accessibility, which is further enhanced when combined with histone acetylation. Conclusion: Histone core phosphorylation regulates DNA accessibility. Significance: Histone phosphorylation and acetylation function together to regulate occupancy of DNA regulatory complexes.