Research Areas

Biochemistry, Structural & Molecular Cell Biology

Biochemistry & Biophysics
Molecular and Cellular Biology
Structural Biology

Developmental Biology & Genetics

Developmental Biology
Genetics

Microbiology & Immunology

Environmental Microbial Interactions (EMI)
Immunology
Microbial Molecular & Cellular Biology (MMBR)
Synthetic & Quantitative Microbial Biology (SQMB)

Systems Biology

Circuit Biology
Molecular Programming & Synthetic Biology
Network Biology, Genomics, & Computational Biology
Systems Development Biology

Biological Engineering (Also see Bioengineering PhD Option)

Biodevices
Bioimaging
Bioinspired Design
Biomechanics
Biomedical Engineering
Cell and Tissue Engineering
Molecular Medicine
Molecular Programming
Synthetic Biology
Systems Biology

Neurobiology (Also see Neurobiology PhD Option)

Molecules to Neurons
Neurons to Behavior
Neuroscience of Brain Disorders
Neuroengineering


Biochemistry, Structural & Molecular Cell Biology

Biochemistry & Biophysics
(Aravin, Bjorkman, Campbell, Dunphy, Hay, Kennedy, Shan, Varshavsky, Voorhees)
Laboratories in this research area are broadly interested in molecular mechanisms underlying DNA replication, DNA repair, gene expression, regulation of cell division, protein trafficking, protein degradation, cell-cell interaction, and synapse formation. The approaches used include structural, biochemical, and single-molecule approaches to understand the function and regulation of individual protein and RNA molecules, molecular pathways and circuits.

Molecular and Cellular Biology
(Aravin, Baltimore, Campbell, Chan, Dunphy, Elowitz, Fejes Toth, Goentoro, Guttman, Hay, Jensen, Kennedy, Lois, Newman, Shan, Varshavsky, Voorhees)
Molecular and Cellular Biology laboratories are investigating the underlying molecular mechanisms of fundamental cellular and organismal processes including the replication, expression, and repair of the genome, transduction of signals from the cell surface to the nucleus in response to diffusible signals or cell-cell interaction, protein trafficking and organellar biogenesis, and protein homeostasis. These laboratories use biochemistry, genetics, structural biology, genomics, high-resolution microscopy, proteomics, and computational approaches, among others, to gain insights into a broad range of fundamental questions.

Structural Biology
(Bjorkman, Clemons, HoelzJensen, Mayo, Rees, Shan, Voorhees)
Laboratories with a major emphasis in this area are interested in the structural basis of fundamental biological processes. The approaches used are broad and include X-ray crystallography, cryo-electron microscopy, high-resolution optical methods, and computational analysis.

Developmental Biology & Genetics

Developmental Biology
(Anderson, Bronner, Elowitz, Goentoro, Guttman, Hay, Lois, Mazmanian, Meyerowitz, Newman, Pachter, Parker, Rothenberg, Stathopoulos, Sternberg, Thomson, Varshavsky, Wold, Zinn)
Laboratories that work in this area seek to understand how a multicellular organism arises from a single cell, the fertilized egg.  Research in this area spans a broad range of topics, approaches, and experimental systems, including sea urchin development, muscle specification in mice, neural crest development in vertebrates, postembryonic nematode development, Arabidopsis development, mouse T-cell development, Drosophila mesoderm development, Xenopus signaling pathways, stem cell regulatory circuits, genomics and bioinformatics of stem cells, and evolution of development.

Genetics
(Bronner, Hay, Lois, Meyerowitz, Pachter, Parker, Prober, Sternberg, Thomson, Varshavsky, Zinn)
Genetics underlies all of biology and much biological inquiry. We build on our rich history in genetics, in which Caltech geneticists such as Morgan, Beadle, Delbruck, Benzer, Wood, Lewis and Hood laid down the foundations of our understanding of genes, gene function, genetic pathways and genome sequences. Current research on Genetics at Caltech includes modern developmental and behavioral genetics using flies, worms, mice, yeast, Arabidopsis, and zebrafish to elucidate the genetic control of development, physiology and behavior.

Microbiology & Immunology

Environmental Microbial Interactions (EMI)
(FischerIsmagilov, Leadbetter, Mazmanian, Newman, Orphan, Phillips, Sessions, Sternberg)
EMI laboratories are focused on understanding how complex microbial communities have co-evolved with Earth and its animal and plant inhabitants. Employing approaches that span analytical chemistry, animal models, genetics, genomics, imaging, immunology, and custom microfluidics, these labs strive to achieve an integrated understanding of the microbial role in ecosystems that are important in human or planetary health and disease.

Immunology
(Baltimore, Bjorkman, Mazmanian, Rothenberg)
The immune system is our defense against pathogenic microorganisms. It involves an innate branch that recognizes generic aspects of pathogens and an adaptive branch that recognizes specific molecules on pathogens. Caltech laboratories are using structural biology, molecular biology, and mouse genetics to study how the immune system develops, how the immune system interacts with microbes that naturally reside in our bodies and are not pathogens, and how signals are transduced in both the innate and adaptive branches of the immune system. In addition, there is a strong translational medicine effort, with a focus on pathologies of the immune system including cancer, engineering antibodies to produce more potent vaccines, and engineering immune cells to attack cancer.

Microbial Molecular and Cellular Biology (MMBR)
(Aravin, Cai, Clemons, Elowitz, Jensen, Mazmanian, Newman, Rees)
Because they can grow rapidly, have small genomes, and are amenable to many types of molecular analyses, microbes provide outstanding model systems in which to study fundamental cellular processes. MMBR laboratories draw on techniques including cryo-electron and fluorescence microscopy, protein crystallography, genetics, and biochemistry to study the bioenergetics, regulation of gene expression, protein trafficking, lipid-protein interactions, and ultrastructure of diverse organisms.

Synthetic and Quantitative Microbial Biology (SQMB)
(Arnold, Cai, Elowitz, JensenIsmagilovPhillips)
SQMB laboratories are working to understand the quantitative basis for fundamental capabilities of microbes, and to learn how to reprogram microbes both to better understand how they work and to develop novel industrial and biomedical capabilities. Techniques include directed evolution, custom microfluidics, quantitative time-lapse imaging of single cells, and mathematical modeling, and the research involves a variety of model and non-model microbial species.

Systems Biology

Circuit Biology
(Cai, Doyle, Elowitz, Goentoro, Gradinaru, Hay, Lois, Murray, Phillips)
Biological circuits underlie most aspects of cell and organismal biology. Circuit biology seeks to understand "mechanisms," the precise structures and interactions of biological parts—be they genes, cells or organisms—that ultimately produce biological function. Circuit biology often involves computational modeling of potential mechanisms, coupled with quantitative tests of the predictions of models by cell biological, molecular biological, and biophysical techniques.

Molecular Programming and Synthetic Biology
(Gradinaru, Hay, MayoMurray, Phillips, Winfree, Thomson)
Knowledge of biological parts, circuits, and networks allows us to build or alter existing biological molecules, macromolecular complexes, and circuits. This synthetic approach not only tests our knowledge but also has many practical implications

Network Biology, Genomics, and Computational Biology
(Aravin, Guttman, Hay, Kennedy, Pachter, Sternberg, Thomson, Wold)
Part of understanding biological systems involves defining the relevant parts and measuring how they change in a quantitative and comprehensive fashion as they carry out their functions. This task is the domain of genomics, proteomics, metabolomics, functional genomics, and bioinformatics, among other disciplines.

Systems Development Biology
(Bronner, Cai, Elowitz, Goentoro, Hay, Lois, Meyerowitz, Rothenberg, Stathopoulos)
One particularly stunning feature of organisms is their ability to develop from a single fertilized egg; thus, Systems Developmental Biology is an important theme of our program. This theme involves the study of developing organisms by a wide variety of molecular, cellular, and genomic techniques.

Biological Engineering

(Also see Bioengineering PhD Option)
Bioimaging

(Cai, Gharib, GuoLois, MeyerowitzPierce, ShapiroYang)
Biophotonics, advanced imaging technologies, computational image analysis, noninvasive biomedical imaging, single-molecule technologies, flow-field imaging technologies, in situ amplification.

Bioinspired Design
(Gharib, Greer, HajimiriIsmagilov, Murray, Shapiro, TirrellWinfree)
Engineering physiological machines, engineering self-powered technologies, control systems, synthetic heteropolymers, and self-healing circuits and systems.

Biomechanics
(Bhattacharya, Gharib, Greer, Guo, MeyerowitzPhillipsRoukes)
Molecular and cellular biophysics, cardiovascular mechanics, muscle and membrane mechanics, physiology and mechanics of flapping flight, multicellular morphodynamics, cell-biomaterial interactions.

Cell and Tissue Engineering
(ArnoldElowitz, GharibGradinaru, GuoIsmagilov, Lois, ShapiroTirrell)
Multicellular morphodynamics, principles of feedback between tissue mechanics and genetic expression, non-natural protein biomaterials, cell-biomaterial interactions, developmental patterning.

Molecular Medicine
(Baltimore, Bjorkman, Davis, Gradinaru, HayIsmagilov, Lester, MazmanianPierce)
Engineering immunity, cancer vaccines, AIDS vaccine, novel anti-cancer therapeutics, Parkinson's disease, nicotine addiction, microbiome perturbations in disease, molecular basis of autism, programmable chemotherapies, conditional chemotherapies, nanoparticle drug delivery.

Molecular Programming
(Aravin, Murray, Pierce, Qian, Rothemund, Winfree)
Abstractions, languages, algorithms and compilers for programming nucleic acid function, molecular information processing, molecular complexity theory, free energy landscapes, metastable systems, self-assembly across length scales, algorithmic self-assembly, synthetic molecular motors, in vitro and in vivo nucleic acid circuits.

Synthetic Biology
(Aravin, Arnold, Elowitz, Gradinaru, Hay, Ismagilov, Lois, Murray, Pierce, Qian, Rothemund, ShapiroTirrell Winfree)
Principles of biological circuit design, genetic circuits, protein engineering, noncanonical amino acids, nucleic acid engineering, rational design, directed evolution, metabolic engineering, biofuels, biocatalysts, elucidation of systems biology principles using synthetic systems.

Systems Biology
(Aravin, Cai, Doyle, Elowitz, Goentoro, Guo, Ismagilov, Lester, MeisterMeyerowitz, Murray, Phillips, Sternberg, Winfree)
Roles of circuit architecture and stochasticity in cellular decision making, feedback, control and complexity in biological networks, multicellular morphodynamics, principles of developmental circuitry including signal integration and coordination, spatial patterning, and organ formation, principles of feedback between tissue mechanics and genetic expression, neural development and disease.

Neurobiology

(Also see Neurobiology PhD Option)
Molecules to Neurons

(Anderson, Bronner, Gradinaru, Kennedy, Lester, Lois, Prober, Sternberg, Zinn)
Molecular mechanisms of nervous-system development; neural crest development; axon guidance and synaptogenesis; ion channels, transporters, and receptors; structure and function of synapses; genetic tools for activating, silencing, and tracing neural circuits; molecular genetics of behavior.


Neurons to Behavior

(Adolphs, Allman, Andersen, Anderson, Gradinaru, Lois, Meister, Prober, Shimojo, Siapas, Sternberg, Tsao)
Function of neural circuits; neural coding of information; visual processing; object recognition; perception of space and motion in primates; neural mechanisms of emotional behavior; mechanisms of sleep; learning and memory; psychophysics of human perception, cognition, and action; social behavior in humans; complexity and control in brain architecture; evolution of brain and behavior in primates.

Neuroscience of Brain Disorders
(Adolphs, Allman, Andersen, Gradinaru, Lester)
Human brain imaging and neuropsychiatric disease; neural prosthetics; deep brain stimulation; interactions of brain and immune system; mouse models of neurological disease.

Neuroengineering
(Andersen, Anderson, Dickinson, Gradinaru, Lois, Meister, Siapas)
Genetic tools for activating, silencing, and tracing neural circuits; optogenetic applications; multi-electrode devices; wireless recording; large-scale data analysis; computational modeling.