Susan E. Celniker
Retiree Affiliate, formerly Biochemist Senior Scientist
Building: Potter Street (977), Room 160
Mail Stop: 977
Phone: (510) 486-6258
Fax: (510) 486-6798
SECelniker@lbl.gov
Divisions
Biological Systems and Engineering
- BioEngineering & BioMedical Sciences
Secondary Affiliation:
Environmental Genomics and Systems Biology
- Comparative and Functional Genomics
Biography
Dr. Celniker graduated from Pitzer College with a B.A. in Biology and Anthropology, followed by two years at the City of Hope National Medical Center in the Department of Medical Genetics studying brain proteins from Huntington’s patients. After completing her dissertation at Caltech, she received her Ph.D. in Biochemistry from the University of North Carolina, Chapel Hill. She accepted an NIH Postdoctoral Service Award (1983-1986) to work with E.B. Lewis (Nobel Laureate, 1995) conducting a genetic analysis of the bithorax complex, homeotic gene, Abdominal-B. She continued to work with Dr. Lewis until 1996, when she was hired as a Staff Scientist at Berkeley Lab. In 2001, she was a co-recipient of the AAAS Newcomb Cleveland Prize for “The Genome Sequence of Drosophila melanogaster.”
She led the effort to characterize the Drosophila transcriptome for NHGRI’s modENCODE (Encyclopedia of DNA Elements) project. She is an advisor to FlyBase (2007-present), on the editorial boards of BMC Genomics (2009-present) and G3 (2011-present), and a fellow of the American Association for the Advancement of Science. Previously, she served as the Deputy Director of the Life Sciences Division as well as the Biological Systems and Engineering Division from 2016-2021.
Recent Publications
Related News
Researchers Aid in Quest to Identify GMOs
Biosciences Area researchers led testing and evaluation of technologies developed to quickly distinguish genetically modified organisms from naturally occurring ones. They designed and produced biological samples of increasing complexity to assess how well the tools performed.
Microbes to the Rescue
A team of researchers from the Biosciences Area at Berkeley Lab and the University of Birmingham in the United Kingdom found one particular organism in the fly’s microbiome that helps protect it from atrazine, an herbicide toxic to flies that is commonly used in agriculture.
A Laser-powered Upgrade to Cancer Treatment
Proof-of-principle experiments on normal human cells and tumor cells were the first to show that FLASH radiotherapy doses can be delivered by laser-driven accelerators. These radiation bursts resulted in higher survival of normal cells compared with cancerous cells.
Building: 977, Room 291
Mail Stop: 977
Phone: (510) 495-2262
HChang@lbl.gov
http://bmihub.org/users/hang-chang
Links
Divisions
Biological Systems and Engineering
- BioEngineering & BioMedical Sciences
Secondary Affiliation:
Molecular Biophysics and Integrated Bioimaging
- Cellular and Tissue Imaging
Research Interests
The research interests in my lab are primarily centered at interfaces between engineering, computation and biology. Our current research focus is on knowledge discovery and inference from large scale scientific data with applications to computational biology and biomedical informatics, including,
- Identification of imaging bio-markers towards personalized therapy; and,
- Development of a big data oriented open-source Information Technology (IT) solution for domain adaptive biomedical informatics.
Recent Publications
Related News
Toward a Genetic Understanding of Variability in Radiation Sensitivity
Injury to immune-system and blood-forming cells is a common side effect of radiation therapy, which more than half of all cancer patients receive as part of their treatment. Biosciences Area researchers and their collaborators used a genetically diverse mouse population to model individual differences in sensitivity to radiation exposure.
Genetic Background Influences Cancer Risk of Thirdhand Smoke Exposure
A new study investigating the effect of thirdhand smoke (THS) in a mouse model system specially designed to mimic the genetic diversity of human populations has shed new light on how genetic predispositions contribute to an individual's cancer risk. This work is an instrumental step towards building a more realistic understanding of how tobacco smoke residue could impact cancer risk in people.
Machine Learning Helps Link Chemical Exposure and Obesity
Scientists at Berkeley Lab and their collaborators developed a machine learning technique to discover obesity-related mixed chemical exposure patterns associated with environmental health risk in the general U.S. population. To assess this, they used indicators like body mass index and waist circumference.
Research Interests
Our research laboratory utilizes the approaches of mechanistic biochemistry, molecular and cell biology, metabolic engineering, and synthetic biology to address problems in energy and human health. We design and create new biosynthetic pathways in microbial hosts for in vivo production of biofuels from abundant crop feedstocks and pharmaceuticals from natural products or natural product scaffolds. A unifying theme of all of our projects is a focus on gaining a detailed molecular understanding of how living cells control enzymatic processes within the context of the entire metabolic network. Specific projects under current investigation include (i) the in vivo production of biofuels from plant biomass, and (ii) the development of new biosynthetic methods for selective, catalytic C-F bond formation under mild conditions.
Recent Publications
Related News
Biosciences Area FY17 LDRD Projects
The projects of 13 Biosciences Area scientists and engineers received funding through the FY17 Laboratory Directed Research and Development (LDRD) program. The funded projects cover a broad range of topics including the study of microbiomes in relation to their environment, plants, and gut health; catalysis for solar conversion to energy; and genomic expression in tissue. Among them were three projects related to Lab-wide initiatives. Together, these efforts account for 17.5% of the $25.2 million allocated. Lab-wide, a total of 88 projects were selected from a field of 166 proposals.
Biosciences Area FY16 LDRD Projects
The projects of eleven Biosciences Area scientists and engineers received funding through the FY2016 Laboratory Directed Research and Development (LDRD) program. These projects cover a broad range of topics, including energy science technology applications, novel computing technologies, and mechanistic understanding of multi-scale interactions among molecules, microbes, plants, metazoans, the abiotic environment, and their feedbacks. Together, these efforts account for nearly 14% of the $25.3 million allocated. Lab-wide, 84 proposals were selected from a field of 179.
LDRD Update: Six PBD Researchers Awarded FY15 Funding and FY16 Announcement
The projects of six Physical Biosciences Scientists and Engineers received funding through the FY2015 Laboratory Directed Research and Development (LDRD) program. These projects cover a broad range of topics, including energy, biomanufacturing, and technology and tool development. Together, these efforts account for nearly 15% of the $24.9 million allocated. Eighty-two proposals were selected from a field of 169. There was an equal distribution of new and continuing projects among the selected PBD proposals.
Research Interests
Professor Clark’s research is in the field of biochemical engineering, with particular emphasis on enzyme technology, biomaterials, and bioenergy. Current projects include the structural characterization and activation of enzymes in non-aqueous media, the development of metabolic biochips for high-throughput catalysis and bioactivity screening, protein design and assembly for the development of advanced biomaterials, and enhanced conversion of lignocellulosic feedstocks to biofuels.
Recent Publications
Related News
A New Way to Make Chemicals Not Found in Nature
Synthetic biologists have successfully engineered microbes to make chemicals cheaply and more sustainably. However, researchers have been limited by the fact that microbes can only make molecules using chemical reactions seen in nature. A collaboration between scientists at Berkeley Lab and UC Berkeley has engineered the microbe E. coli to produce a molecule that, until now, could only be synthesized in a laboratory.
Douglas Clark tapped to be next College of Chemistry Dean
Doug Clark of the Physical Biosciences Division has been named the dean of UC Berkeley’s College of Chemistry. Clark is a pioneering researcher in the field of biochemical engineering, with particular emphasis on enzyme technology, biomaterials, extremophiles and all areas of biofuels research.
Research Interests
- Structure of Biological Macromolecules
- Beamline Control Systems
- Automation
- Artificial Intelligence and Machine Learning
Programs & Initiatives
Recent Publications
Related News
SIBYLS Team Recognized with Innovative Instrumentation Award
The Structurally Integrated BiologY for the Life Sciences (SIBYLS) team received the 2025 Klaus Halbach Award for Innovative Instrumentation at the 2025 Advanced Light Source (ALS) User Meeting in August.
A Fast Track for Visualizing RNA Structures
Scientists have combined multiple AI tools into a single streamlined process that predicts the atomic structures of RNA molecules.
Programming Proteins to Pair Perfectly
Bioscientists at the Advanced Light Source (ALS) at Berkeley Lab lent their expertise to a project led by scientists at the University of Washington to design proteins in the lab that zip together like DNA. The technique could enable the design of protein nanomachines to help diagnose and treat disease, allow for more precise engineering of cells, and perform a variety of other tasks.
Recent Publications
Related News
Commemorating Judy Campisi
Judith (Judy) Campisi, a leader in the field of cell senescence and a researcher at Berkeley Lab for just over 30 years, died on January 19, 2024. She was 75.
Enigmatic Protein Sculpts DNA to Repair Damage
Biosciences Area researchers and their collaborators have determined how a protein called XPG binds to and reshapes damaged DNA, illuminating its role in averting genetic disease and cancer.
Scientists Discover Protein’s Starring Role in Genome Stability, and Possibly Cancer Prevention
If you have a soft spot for unsung heroes, you'll love a DNA repair protein called XPG. Berkeley Lab scientists discovered that XPG plays a previously unknown and critical role helping to maintain genome stability in human cells. Their findings also raise the possibility that the protein helps prevent breast, ovarian, and other cancers associated with defective BRCA genes. The work, which is published online January 28 in the journal Molecular Cell, indicates XPG is essential to our health in ways far beyond it's been given credit for. Priscilla Cooper of the Biological Systems and Engineering Division conducted the research with Kelly Trego and several others at Berkeley Lab, as well as scientists from Colorado State University, Yale University, and Erasmus University Medical Center in the Netherlands. Read more at the Berkeley Lab News Center.
Divisions
Environmental Genomics and Systems Biology
- Biosystems Data Science
Secondary Affiliation:
Biological Systems and Engineering
- BioEngineering & BioMedical Sciences
Recent Publications
Related News
Foundational AI Models to Accelerate Biological Discovery
Berkeley Lab is helping build AI models for autonomous research that will enable prediction and precise design of biological systems.
Biography
Adam Deutschbauer has a background in Microbial systems biology. As part of the Virtual Institute of Microbial Stress and Survival, he develops next-generation tools for microbial functional genomics. As the Biotechnology Component Deputy Director, he will help drive the development of experimental and computational approaches to develop models of microbial metabolism, gene regulation, and signal transduction. He will ensure the teams can meet project goals, encourage integration and collaboration between groups.
Recent Publications
Related News
EcoFABs Could Help Fuel AI in Agriculture
A first-of-its-kind global study showed that EcoFABs can deliver consistent results across labs on three continents, supported by open protocols, tools, and datasets. The reliable, large-scale data EcoFABs generate are ideal for training AI, which could help accelerate discoveries in crop development, soil health, and agriculture.
Revealing the Mysteries Within Microbial Genomes
A new technique developed by Biosciences Area researchers will make it much easier to discover the traits or activities encoded by genes of unknown function in microbes—a key step toward understanding the roles and impact of individual species.
Dub-seq Used to Screen Phage Proteins for Antibiotic Properties
A team of researchers from Berkeley Lab, UC Berkeley, and Texas A&M University worked together on a high-throughput genetic screen to identify which part of the bacteria bacteriophage viruses were targeting.
Research Interests
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.
Recent Publications
Related News
Using Nature’s Blueprint for Sustainable Indigo Dyeing Process
Indigo has been prized since antiquity for its vibrancy and deep blue hue and, for more than a century, its unique properties have been leveraged to produce the popular textile blue denim. However, the dyeing process requires chemical steps that are environmentally damaging. A team of researchers in the Molecular Biophysics and Integrated Bioimaging (MBIB) and Biological Systems and Engineering (BSE) Divisions, at JBEI, and UC Berkeley have developed a promising sustainable indigo dyeing process that relies on genetically engineered bacteria, mimicking the natural biochemical protecting group strategy employed by the Japanese indigo plant Polygonum tinctorium.
Research Interests
Our group uses and develops advanced multidimensional ultrafast spectroscopic methods to study complex systems such as natural photosynthetic complexes, liquids, solution, and nanoscale systems such as single-walled carbon nanotubes.
In natural photosynthetic systems we aim to define the design principles underlying their remarkable .quantum efficiencies, and to use these principles to aid in the design of robust and efficient artificial photosynthetic devices. Natural systems are also regulated in response to external conditions, such as light levels, and one of the key components of Photosystem II is regularly repaired. We plan to understand the control system at the molecular level by combining molecular genetics biochemistry, modeling, and ultrafast spectroscopy through collaboration with Professor K. K. Niyogi. We have recently shown, using two-dimensional electronic spectroscopy, that long lived electronic quantum coherence exists in photosynthetic light harvesting complexes. We are exploring the implications of quantum coherence for photosynthesis and for quantum information science.
The electronic properties and excited state dynamics of nanoscale materials with significant quantum confinement effects yield a rich range of properties and potential applications. We aim to understand these properties with a particular current emphasis on single-walled carbon nanotubes via non-linear ultrafast spectroscopy and theoretical modeling.
The modern theoretical description of photochemical processes, in particular what determines which products are formed, has at its core relaxation through conical intersections. Yet very little experimental information is available on such processes. Two dimensional electronic spectroscopy has the potential to provide a window into these processes and experiments to explore conical intersection dynamics are under development.
Ultrafast multidimensional electronic spectroscopy is in its infancy with many potential ways to enhance resolution, sharpen the information content and extract specific dynamical pathways (e.g., those that involve only coherence). My group continues to develop new spectroscopic methods and the theoretical tools for their analysis.
Recent Publications
Related News
Congratulations to Biosciences Area Director’s Award Recipients
Each year, the Berkeley Lab Director’s Achievement Award program recognizes outstanding contributions by employees to all aspects of Lab activities. Several Biosciences Area personnel are among the 2025 honorees.
How Plants Manage Light: New Insights Into Nature’s Oxygen-making Machinery
A series of breakthroughs from scientists at Berkeley Lab and their collaborators provides a new understanding of how energy flows through one of nature’s most important molecular machines, the photosystem II supercomplex (PSII).
How Algae Use Memory to Adapt to Sudden Changes in Sunlight
A new study co-led by Graham Fleming a senior faculty scientist in the Molecular Biophysics and Integrated Bioimaging (MBIB) Division, and Krishna Niyogi, a faculty scientist in MBIB, reveals the precise molecular machinery that underpins photoprotective memory in green algae. The results may help scientists develop more productive plants and improve crop yields.
Building: 922, Room 608
Mail Stop: STANLEY
Phone: (510) 643-5624
DAFletcher@lbl.gov
http://fletchlab.berkeley.edu
Links
Research Interests
My laboratory studies the mechanics and dynamics of cell movements on the purified protein, single cell, and tissue levels. For these studies, we are developing new instruments to quantify cell and molecular mechanics based on optical microscopy, force microscopy, and microfabrication.
Recent Publications
Related News
Fletcher Elected to the National Academy of Medicine
Dan Fletcher is being recognized for the development of a mobile phone–based microscopy tool and greater contributions to our understanding of cell movement.
Congratulations 2021 Chan Zuckerberg Biohub Investigators
Four faculty scientists in the Biosciences Area were included in The Chan Zuckerberg Biohub Investigator Program, awarding $21 million to 21 University of California, Berkeley researchers.
Nitric Oxide Is the Key for Building Breast Tissue from Single Cells in 3-Dimensions
Building on four decades of research, Mina Bissell, Distinguished Scientist in Biological Systems and Engineering (BSE) Division and her colleagues have demonstrated a dynamic reciprocity between the extracellular matrix (ECM) and cell nucleus for tissue-specific gene expression. Using the 3D ECM gel to study signaling from outside the cell to the nucleus they have unraveled a dozen different pathways critical for the formation of phenotypically normal breast tissue. The signaling between the ECM and the nucleus is pivotal, bidirectional, and intricate. In two papers published in eLife this week, Bissell and Dan Fletcher, BSE faculty scientist and Purnendu Chatterjee Professor and Chair of Bioengineering at UC Berkeley, shed new light on how the extracellular matrix communicates with breast cells to generate nitric oxide, forming a loop that influences the pathway a single cell takes to form breast tissue.
Biography
Matt Francis is the Department of Chemistry Chair and the T.Z. and Irmgard Chu Distinguished Professor in Chemistry at UC Berkeley. Matt was born in Ohio and received his undergraduate degree in Chemistry from Miami University in Oxford, OH in 1994. From 1994-1999 he attended graduate school at Harvard University, working in the lab of Prof. Eric Jacobsen. His Ph.D. research involved the development of combinatorial strategies for the discovery and optimization of new transition metal catalysts. He then moved to UC Berkeley, where he was a Postdoctoral Fellow in the Miller Institute for Basic Research in Science. He worked under the guidance of Prof. Jean Fréchet, focusing on the development of DNA-based methods for the assembly of polymeric materials and the application of dendrimers for drug delivery. Matt started his independent career in the UC Berkeley Chemistry Department in 2001, and has built a research program involving the development of new organic reactions for protein modification. These new chemical tools have then been used to modify biomolecular assemblies to prepare new materials for diagnostic imaging, wastewater treatment, and solar cell development. For his research accomplishments, Matt has received the Dreyfus Foundation New Faculty Award, an NSF Career Award, a GlaxoSmithKline Young Investigator Award, the 2017 Bioconjugate Chemistry Lectureship Award from the American Chemical Society, and the 2019 Arthur C. Cope Scholar Award from the American Chemical Society. Matt became the chair of the chemistry department at UC Berkeley in 2018. Matt has also received the UC Berkeley Departmental Teaching Award on three occasions, the Noyce Prize for Excellence in Undergraduate Teaching, and the 2009 University Distinguished Teaching Award.
Research Interests
Research in the Francis group is focused on the development of new synthetic methods for the construction of nanoscale materials. The central strategy involves the attachment of new functional components to specific locations on structural proteins, and the subsequent self-assembly of these conjugates into new types of materials with useful electronic and biological functions.
Controlled Growth of Nanocrystalline Arrays Using Cytoskeletal Proteins
Modern synthetic methods for the preparation of inorganic nanocrystals have yielded promising new components for optical and electronic device construction. However, the organization of these materials into functional assemblies remains extremely difficult, in part because the small size of nanocrystals (2-10 nm) is well below the spatial resolution of most lithographic techniques. An alternative approach could be provided by attaching these nanocrystals to specific sites on the surfaces of fiber-forming cytoskeletal proteins, such as actin. By controlling the polymerization of the actin conjugates with additional proteins and small molecule natural products, specified locations could be connected with wire-like arrays of functional materials. Once constructed, the arrays could be converted into conductive linkages, thus providing an entirely new method for nanoscale circuit construction.
Modified Viral Capsids for the Assembly of Core/Shell Materials
A second research area involves the synthesis of three-dimensional nanostructures from the self-assembling proteins that form the outer coats of viruses. For example, by selectively modifying the top and bottom faces of the satellite panicum mosaic virus capsid protein, new types of core/shell materials could be obtained after assembly. These structures could be developed into particles capable of targeting desired tissue types and releasing their cargo of drug molecules. Functionalized viral capsids could also provide new tools for the investigation of multivalent binding interactions that occur in biological systems.
New Methods for Site-Selective Protein Modification
A central theme in this research program is the modification of structural proteins in specific locations in order to achieve homogeneous and predictable assembly. Site-directed mutagenesis provides a powerful set of tools for this purpose, and will be used extensively. However, there are limitations associated with this technique, and therefore the development of new chemical approaches for protein modification will be pursued as well. This research will take advantage of the rapidly expanding set of organic reactions that can proceed in aqueous solution, and will utilize asymmetric ligands and catalysts to enhance the selectivity of protein modifications. Combinatorial reaction libraries will play an important role in this research area.
