Computational Biology

Computational biology uses the techniques of computer programmers and data scientists to approach biological problems. Common areas of focus are computer modeling of biological processes, protein structure and function analysis, genome mapping and function prediction, simulation and design of plant and microbial systems, and the creation of computational tools to facilitate these activities.
Computational biology plays a crucial role in drug discovery research, the design of microbial systems for medical and environmental applications, and the analysis of huge sets of biological data to find patterns and targets for medical treatment.
Research in computational biology has real-world impact in areas like:
The Environment, disease modeling, drug discovery, gene editing, microbiome, personalized medicine.

J. Christopher Anderson
For more information, see: https://andersonlab.qb3.berkeley.edu/
Anderson Lab develops new applications and tools for the Synthetic Biology community. Our goal is to create a computationally-driven platform for the design of genetic organisms that minimizes the uncertainties and errors of such projects. Our platform is built around a computational method for encapsulating the function of biomolecules based on precise chemical models. Our platform aggregates data from various sources, then develops synthesis and verification tools to automatically design engineered organisms with new functions, demonstrated with bacterium that produces acetaminophen.

Adam Arkin
For more information, see: https://arkinlab.bio/
The Arkin Lab focus is how microbes transform, clean, and improve soils, soils that are currently degrading due to climate change, pollution, and poor water use. Near close-loops, low-energy, low-input biomanufacturing programs for food, pharmaceuticals, and building materials at “small village” scale, which are initially designed for a deep-space crewed Mars mission but have applications here on Earth for supporting sustainable agriculture. Another interest is to develop engineering approaches for microbiomes so we can control communities of microbes that drive the earth’s mineral cycles, support our plants and efficiency and stress responses, and impact the health and food-efficiency of a good many living creatures including ourselves.

Leah Guthrie
For more information, see: https://www.theguthrielab.com/
The Guthrie lab investigates the principles that govern microbial metabolism and signaling in the context of kidney homeostasis and disease using mass spectrometry, chemoinformatics, and molecular biology approaches.

Teresa Head-Gordon
For more information, see: https://thglab.berkeley.edu/
The simultaneous revolutions in energy, molecular biology, nanotechnology and advanced scientific computing, is giving rise to new interdisciplinary research opportunities in computational science. The Head-Gordon lab embraces this large scope of science drivers through development of computational models and methodologies applied to molecular liquids, macromolecular assemblies, protein biophysics, and homogeneous, heterogeneous catalysis and biocatalysis. The development and application of complex chemistry models, accelerated sampling methods, coarse graining/multiscale techniques, and machine learning developed in her lab are widely disseminated through many community software codes that scale on high performance computing platforms.

Ian Holmes
For more information, see: https://biowiki.org/IanHolmes
The Holmes Lab brings techniques from machine learning, statistical linguistics, phylogenetics, and web development to bear on the interpretation and analysis of genomic data. Examples include the application of context-free grammars to understanding DNA and RNA structure; the use of phylogenetic methods in genome annotation, and to detect recombination breakpoints; the development of machine learning algorithms for bioinformatics models; the reconstruction of insertion, deletion and transposition events in genome evolutionary histories; statistical algorithms for metagenomics species distribution analysis; and dynamic-HTML web applications for collaborative genomic data analysis.

Patrick Hsu
For more information, see: http://patrickhsulab.org/
The Hsu Lab aims to understand and manipulate the genetic circuits that control brain and immune cell function to improve human health. We explore the rich biological diversity of nature to create new molecular technologies, perturb complex cellular processes at scale, and develop next-generation gene and cell therapies. To do this, our group draws from a palette of experimental and computational techniques including CRISPR-Cas systems, single cell genomics, engineered viruses, brain organoids, and pooled genetic screens. Current interests include 1) inventing novel approaches for editing the postmitotic genome, 2) developing engineered vehicles for therapeutic macromolecule delivery, and 3) leveraging library screens and brain organoids to interrogate human neuroscience at scale.

Liana Lareau
For more information, see: http://www.lareaulab.org/
A single genome produces the huge diversity of cells and tissues needed to make a human by regulating gene expression to turn on and off the right genes at the right times. The final, post-transcriptional steps of gene expression — RNA processing and translation — are essential to the proper outcome. Our goal is to understand how these layers of regulation are encoded in gene sequences and how disruptions to this regulation can cause disease. Our research uses machine learning and other computational methods, coupled with high-throughput experiments, to understand how post-transcriptional regulation leads to robust and flexible control of gene expression.

Mohammad Reza Kaazempur Mofrad
For more information, see: https://biomechanics.berkeley.edu/
Molecular and Multiscale Biomechanics; Bioinformatics and Computational Biology; Statistical Machine Learning; Computational Precision Health; Microbiome; Personalized Medicine

Aaron Streets
For more information, see: https://streetslab.com/
The Streets lab is interested in applying lessons from mathematics, physics, and engineering, to invent tools that help us dissect and quantify complex biological systems. Our goal is to uncover laws that govern the interactions of molecules inside the cell and the interactions between cells in a tissue or organism, by making precision measurements on single cells. In pursuit of this goal, we exploit three core technologies; microfluidics, microscopy, and genomics.
News About: Computational Biology
Arkin Lab receives ARPA-H award for microbiome engineering
Adam Arkin has been granted an award of over $20 million from the Advanced Research Projects Agency for Health (ARPA-H) to pursue microbiome engineering to create probiotic bacterial communities that prevent and treat lung pathogens.
Could a new medical approach fix faulty genes before birth?
Murthy lab and UC Davis have developed a unique mRNA delivery method for in-utero gene editing for neurodevelopmental conditions.
Revealing the Mysteries Within Microbial Genomes
Adam Arkin’s lab has developed a new technique, barcoded overexpression bacterial shotgun library sequencing (Boba-seq), that will make it much easier for researchers to discover the traits or activities encoded by genes of unknown function in microbes.
Bakar ClimatEnginuity Hub: Berkeley’s new home for climate innovation
Professor David Schaffer will lead the new Bakar ClimatEnginuity Hub, an incubator that will provide resources and support to entrepreneurs in renewable energy and clean technology.
Berkeley’s ecosystem of innovation, entrepreneurship combats climate change
Professors John Dueber and David Schaffer are featured in this article highlighting campus research and entrepreneurship in sustainability.
Bolt Threads going public
Bolt Threads, a company co-founded by BioE PhD alumnus David Breslauer, plans to go public in a SPAC deal that values the one-time unicorn at $250 million. Bolt Threads uses synthetic biology and other techniques to sustainably produce engineered biomaterials, including synthetic spider silk and mushroom-based faux leather.
Uncovering the Secrets of the Smallest Phages
In a new paper in Nature Chemical Biology, Professor Adam Arkin and collaborator Vivek Mutalik report advances in understanding phage biology that bring us closer to using these small predators to fight antibiotic-resistant bacteria.
Bacteria for Blastoff: Using Microbes to Make Supercharged New Rocket Fuel
New research led by Professor Jay Keasling took inspiration from an extraordinary antifungal molecule made by Streptomyces bacteria to develop a totally new type of fuel that has projected energy density greater than the most advanced heavy-duty fuels used today, including the rocket fuels used by NASA.
Best Inventions of 2021: Huue
Congratulations BioE startup Huue and founder PhD alumna Tammy Hsu! Huue’s process for creating environmentally friendly indigo dye through synthetic biology has been named one of Time Magazine’s Best Inventions of 2021.
Synthetic biology moves into the realm of the unnatural
Berkeley researchers, including Professor Jay Keasling, have for the first time engineered bacteria to produce a molecule that, until now, could only be synthesized in a laboratory. This advance opens the door to production of a broader range of chemicals from yeast and bacterial fermentation.