Systems biology approaches living systems as interactive, multifaceted networks rather than as a collection of individual units. Synthetic biology seeks to build parts, devices, and systems from biological components. The goals of these efforts can include using microorganisms to synthesize materials of medical or industrial value, and even to repurpose bacteria to fight disease.
Efforts within systems biology focus on collection, curation, and analysis of large data sets, including genomic and proteomic information. There is also a significant effort to apply systems-level modeling to organize such data sets, bringing this field in close alignment with computational biology. Increasingly, synthetic biological concepts are being applied in the realm of therapeutics, including “designer” immune cells for the treatment of cancer.
Faculty working in systems & synthetic biology:
J. Christopher Anderson
Associate Professor, Bioengineering
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
Dean A. Richard Newton Memorial Professor, Bioengineering;
Senior Faculty Scientist, Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory;
Director, Center for the Utilization of Bioengineering in Space;
CEO/CSO, DOE Systems Biology Knowledgebase
PI and Co-Director, ENIGMA SFA
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.
Iain Clark
Assistant Professor, Bioengineering
http://clarklab.berkeley.edu/The Clark Lab develops microfluidic and molecular methods for the high throughput analysis of single cells. We use these techniques to study HIV latency in CD4 T cells and profile cellular interactions during central nervous system inflammation.
Irina Conboy
Professor, Bioengineering
https://conboylab.berkeley.edu/Our work has been focused on establishing new paradigms in multi-tissue stem cell aging, rejuvenation and regulation by conserved morphogenic signaling pathways. One of our goals is to define pharmacology for enhancing maintenance and repair of adult tissues in vivo. The spearheaded by us heterochronic parabiosis and blood apheresis studies have established that the process of aging is reversible through modulation of circulatory milieu. Our synthetic biology method of choice focuses on bio-orthogonal non-canonical amino acid tagging (BONCAT) and subsequent identification of age-imposed and disease-causal changes in mammalian proteomes in vivo. Our drug delivery reg medicine projects focus on CRISPR/Cas9 based therapeutics for more effective and safer gene editing.
John Dueber
Lester John and Lynne Dewar Lloyd Distinguished Professor, Bioengineering
https://dueberlab.berkeley.edu/The Dueber Lab develops strategies for introducing designable, modular control over living cells. We are particularly interested in generating technologies for improving engineered metabolic pathway efficiency and directing flux. Our projects have applications in the development of biofuels, specialty chemicals, and environmentally friendly processes.
Leah Guthrie
Assistant Professor
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.
Patrick Hsu
Assistant Professor, Bioengineering
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.
Jay Keasling
Professor, Bioengineering, Philomathia Professor of Alternative Energy at the University of California, Berkeley in the Departments of Bioengineering and Chemical and Biomolecular Engineering, senior faculty scientist at Lawrence Berkeley National Laboratory, and Chief Executive Officer of the Joint BioEnergy Institute (JBEI)
https://keaslinglab.lbl.gov/Metabolic engineering, environmental biotechnology, and biochemical engineering.
Sanjay Kumar
Chancellor’s Professor, Bioengineering & Chemical and Biomolecular Engineering
Director, California Institute for Quantitative Biosciences (QB3) at UC Berkeley
Professor in Residence, Bioengineering and Therapeutic Sciences, UCSF
Faculty Scientist, Biological Systems and Engineering, LBNL
Our lab seeks to understand and engineer mechanical and other biophysical communication between cells and materials. In addition to investigating fundamental aspects of this problem with a variety of micro/nanoscale technologies, we are especially interested in discovering how this signaling regulates tumor and stem cell biology in the central nervous system. Recent directions have included: (1) Engineering new tissue-mimetic culture platforms for biophysical studies, molecular analysis, and screening; (2) Exploring mechanobiological signaling systems as targets for limiting the invasion of brain tumors and enhancing stem cell neurogenesis; and (3) Creating new biomaterials inspired by cellular structural networks.
Liana Lareau
Assistant Professor
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
Professor, Bioengineering
Professor, Mechanical Engineering
Faculty Scientist, Lawrence Berkeley National Lab
Molecular and Multiscale Biomechanics; Bioinformatics and Computational Biology; Statistical Machine Learning; Computational Precision Health; Microbiome; Personalized Medicine
Aaron Streets
Associate Professor, Bioengineering
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.