BIOENGINEERING & OMICS RESOURCES

See also resources in data science and modeling, structural biology and imaging, chemistry and sustainability


The DOE Joint Genome Institute (JGI) unites the expertise at Lawrence Berkeley National Laboratory, Lawrence Livermore National Laboratory, and the HudsonAlpha Institute for Biotechnology and is located in Walnut Creek, California. JGI is operated by the University of California for the U.S. Department of Energy and the facility provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges.is the global leader in generating genome sequences of plants, fungi, microbes, and metagenomes. The institute’s comparative analysis systems have matured over the past years and are recognized as important resources for conducting genome and metagenome studies, empowering scientists around the world to conduct studies that otherwise would be very expensive or out of reach.

The Department of Energy Systems Biology Knowledgebase (KBase) is a large-scale software and data platform designed to meet the grand challenge of systems biology: predicting and ultimately designing biological function. KBase enables secure sharing of data, tools, and conclusions in a unified, extensible system that allows researchers to collaboratively generate, test, and share hypotheses about molecular and cellular functions. Users can perform large-scale analyses on KBase’s scalable computing infrastructure and combine multiple lines of evidence to model with increasing accuracy plant and microbial physiology and community dynamics. The new KBase Narrative interface enables researchers to create interactive, reproducible records of the data, computational steps, and thought processes underpinning their results and to share these records as “active papers” that let others repeat the computational experiment, even altering parameters or input data to achieve different or improved results.

QB3 has research facilities at the University of California Berkeley, the University of California Santa Cruz and the University of California San Francisco.


The Functional Genomics Laboratory
The Functional Genomics Laboratory enables researchers to conduct state-of-the-art research in functional genomics, with a focus on using DNA microarray technologies. FGL specializes in the fabrication, use, and analysis of DNA microarrays for large-scale gene expression profiling and genetic profiling, and provides full core lab services for Affymetrix GeneChip arrays and Agilent DNA microarrays.


QB3 MacroLab
The QB3 MacroLab is a core facility administered QB3. Located at UC Berkeley the QB3 MacroLab offers an automated gene cloning and recombinant protein expression and purification services.


QB3 also has facilities for material science, imaging and spectroscopy



The Synthetic Biology Engineering Research Center (SynBERC) at the University of California Berkeley is a multi-institution research effort to lay the foundation for the emerging field of synthetic biology. SynBERC’s vision is to catalyze biology as an engineering discipline by developing the foundational understanding and technologies to allow researchers to design and build standardized, integrated biological systems to accomplish many particular tasks. In essence, we are making biology easier to engineer.

The Molecular Foundry is a Department of Energy-funded nanoscience research facility housed at Lawrence Berkeley National Laboratory. The foundry provides users from around the world with access to cutting-edge expertise and instrumentation in a collaborative, multidisciplinary environment. This facility studies the synthesis, analysis and mimicry of biological nanostructures. Expertise and capabilities are available to develop new materials based on the folding and assembly of sequence-defined, bioinspired polymers (including peptides,,nucleic acids, and peptoids). New biocompatible imaging probes based on organic dyes and functionalized inorganic nanocrystals are being developed and are available to facilitate state-of-the-art bioimaging studies. Synthetic biology techniques are used to re-engineer organisms and create hybrid biomolecules to interface with devices. Additional capabilities include synthesis, purification and characterization of bio- and biomimetic polymers, bioconjugation, and combinatorial peptide and peptoid library synthesis and screening. Protein expression, microbial and eukaryotic cell culture, phage display, cellular engineering and biological microscopy, including total internal reflection, confocal and single molecule imaging are offered.

The Synthetic Biology Institute (SBI) at the University of California Berkeley is working to make the engineering of new complex function in cells vastly more efficient, reliable, predictable, and safe. Its breakthroughs will speed the development of biologically engineered solutions to pressing global problems related to health, materials, energy, environment, and security. The Synthetic Biology Institute at UC Berkeley (SBI) was established in 2010 to clear a path to the widespread production of new biological systems to benefit society. Through the combined effort of its researchers, partners and Industry Members, SBI is developing the standards and technologies needed to create transformative applications in energy, materials, pharmaceuticals, chemicals, food products, security, and other industries that affect our daily lives.

The Plant Gene Expression Center (PGEC) is is a unique collaboration of the Agricultural Research Service of the U.S. Department of Agriculture and the Plant & Microbial Biology Department of the University of California Berkeley. The PGEC conducts fundamental research in plant molecular biology. Researchers are elucidating the signal transduction pathways responsible for the perception of environmental and cellular cues. We are exploring disease resistance, light perception, the circadian clock, vegetative growth, and reproduction. Essential genes and the networks within which they operate are elucidated using molecular, genetic and biochemical approaches.

The Superfund Research Program at the University of California Berkeley focuses on using state-of-the-art technology, including ‘omics’ and nanotechnology to achieve the following specific objectives of the program


  • Develop and apply novel biomarkers in studies of human populations.
  • Enhance our knowledge of the toxic effects of benzene and arsenic, especially in early life.
  • Identify genes that confer susceptibility to Superfund chemicals through the application of functional genomics.
  • Expand our ability to remediate toxic waste sites at a lower cost using bioremediation and persulfate oxidation.
  • Improve our ability to measure Superfund chemicals in the environment using nanotechnology.
  • Promote the exchange of information among scientists, regulators, and other interested parties in order to translate basic research findings into appropriate policies and public health interventions




 

The Gene Targeting Facility at the University of California Berkeley has generated hundreds of transgenic mice and made numerous gene-targeted mice. Recently, the facility has shifted to using Cas9/CRISPR-mediated gene targeting as this offers the ability to produce gene-targeted mice with unprecedented speed and ease.

The Flow Cytometry Research Facility is part of the Cancer Research Laboratory at the University of California Berkeley. The Facility provides Berkeley and local researchers with access to cutting-edge flow cytometry instruments and expertise. This core houses two cell sorters: a BD Influx (LSA) and a Beckman-Coulter Moflo. In addition, the LSA facility houses four analyzers: BD LSR II, BD LSR Fortessa, BD LSR Fortessa X20, and a Beckman-Coulter FC500.

Ecosystems and Networks Integrated with Genes and Molecular Assemblies  at  Lawrence Berkeley National Laboratory is a multi-institutional consortium funded by the U.S. Department of Energy (DOE) through its Scientific Focus Area (SFA) grant program and managed by DOE’s Lawrence Berkeley National Laboratory (Berkeley Lab). Established in 2009, ENIGMA researchers seek to advance our understanding of microbial biology and the impact of microbial communities on their ecosystems. Team members collaborate closely to generate detailed quantitative understanding across scales — from molecular to cellular to community-level.  We have the technological and scientific arsenal to link environmental microbiological field-studies to both highly advanced field and laboratory meta-functional genomic and genetics tools. This capability, the ability rapidly to assess gene content and expressed functions of environmental microbes and bring them to model-organism status in the laboratory, is ripe for application to microbial communities. These studies will likely provide unprecedented views into the pathways that link the functioning of diverse genomes in the context of their environment and thereby deliver a mechanistic understanding of complex environmental bioprocesses.

The mission of the Carl R. Woese Institute for Genomic Biology (IGB) is to advance life science research at the University of Illinois at Urbana-Champaign and to stimulate bio-economic development in the state of Illinois. To achieve that mission, our research themes capitalize on recent advances in genome science and technology.

Research at the IGB include:

  • Systems Biology
  • Cellular and Metabolic Engineering
  • Genome Technology
  • Biocomplexity
  • Biosystems Design
  • Business, Economics and Law of Genomic Biology
  • Cellular Decision Making in Cancer
  • Genomic Ecology of Global Change
  • Gene Networks in Neural & Developmental Plasticity
  • Mining Microbial Genomes

The Innovative Genomics Institute (IGI) at the University of California Berkeley is committed to advancing our understanding of the ways in which genomic information is harnessed to produce complex phenotypes, and our overarching long-term goal is to bring about fundamental change in biological and biomedical research by enabling scientists to read and write in genomes with equal ease.