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Detailed Information

Program of Study

The University of California, San Diego (UCSD), Division of Biological Sciences, in association with the Salk Institute for Biological Studies, offers a program of graduate studies leading to the Ph.D. degree in biology. The program provides an extraordinary setting for highly motivated students interested in training with distinguished faculty members. The major areas of faculty research are biochemistry and biophysics; bioinformatics; cell and developmental biology; ecology, behavior, and evolution; genetics; immunology, virology, and cancer biology; molecular biology; neurobiology; plant molecular biology; plant systems biology; and signal transduction.

During the first year, students complete four to six 6-week research internships (rotations) in laboratories that the student determines to be of interest. To promote a diversity of research experiences and help initiate new students into the community of advanced graduate study and research, students are encouraged to pursue rotations in at least one lab not directly related to their thesis research interests. Following the rotation period, students select a faculty adviser and lab for their thesis research.

First-year students are also expected to enroll in a graduate biology course sequence. Specific course sequences are determined by the student’s area of specialization. The first year concludes with the administration of a qualifying exam that is given in conjunction with the first-year course sequence.

Subsequent years are composed primarily of thesis-oriented research (the thesis proposal is presented at the end of the second year), teaching assistant responsibilities (one year total), and meetings with the 5-member Thesis Committee until the thesis defense, typically after 5.5 years.

Research Facilities

Students have access to more than 100 modern and fully equipped research laboratories in the Division of Biological Sciences and the Salk Institute. The Division is also associated with three organized research groups: the Center for Molecular Genetics, the Kavli Institute for Brain and Mind, and the San Diego Center for Molecular Agriculture. Campus research facilities and tools include the San Diego Supercomputer Center, the Biomedical Genomics Microarray Center, the Protein Sequencing Facility, the Biomolecular Mass Spectrometry Facility, a DNA sequencer, and confocal, electron, and photon microscopes. By July 2010, the campus will house a $115-million San Diego Consortium for Regenerative Medicine facility dedicated to stem cell research.

Financial Aid

All Ph.D. students in good standing receive full financial support (tuition, fees, and health insurance) for five years. In addition, students receive an annual stipend. For the 2009–10 academic year, the stipend level is $28,000.

Cost of Study

The cost of study is detailed in the Financial Aid section.

Living and Housing Costs

Limited affordable on-campus housing is available for both single and married graduate students. A new graduate student housing facility opened for fall 2007. There are also several off-campus housing options for graduate students in neighborhoods near or easily accessible to campus. The housing and dining office (http://hds.ucsd.edu/housing/) maintains current information on rental options.

Student Group

In fall 2008, there were 22,518 undergraduate and 5,682 graduate and medical students at UCSD. There are approximately 215 doctoral students from across the United States and from several other countries in the Division of Biological Sciences.

Location

The University and the Salk Institute are located on the Torrey Pines Mesa, along the San Diego coast, overlooking the Pacific Ocean. The campus is also an easy drive from several mountain and desert locales. Along with San Diego’s dry, temperate climate, UCSD is ideally situated to offer its students year-round outdoor recreational opportunities. The area also shares a rich heritage with its neighbor, Mexico, and supports many cultural events.

The Torrey Pines Mesa is the setting of a world-class scientific and research community as well. This community includes the UCSD School of Medicine, the Scripps Institution of Oceanography, the Scripps Research Institute, the Neurosciences Institute, the La Jolla Institute for Allergy and Immunology, the Burnham Institute for Medical Research, the Sidney Kimmel Cancer Center, and hundreds of biotechnology research firms.

The University

The University of California, San Diego, is one of the nation’s most accomplished research universities, widely acknowledged for its local impact, national influence, and global reach. A leader in climate science research, UC San Diego is one of the greenest universities in the U.S. and works with communities, governments, businesses, and organizations to promote sustainability solutions throughout the region and the world.

With a majestic view of the Pacific Ocean, this distinctively beautiful campus is both a magnet and a catalyst for acclaimed institutes and Nobel laureates. The University’s award-winning scholars are experts at the forefront of their fields, with an impressive track record for achieving scientific, medical, and technological breakthroughs. Renowned for its collaborative, diverse, and cross-disciplinary ethos that transcends traditional boundaries in science, arts, and the humanities, UC San Diego attracts like-minded faculty members, stellar students, and staff.

Applying

Inquiries concerning application procedures should be directed to the Biology Graduate Admissions Coordinator. Applications are accepted for fall enrollment only and are due in mid-December. GRE General Test scores are required. GRE Subject Test scores are recommended.

International applicants must first complete a pre-application available for download from the Biology Graduate Admissions Web site. If the pre-application is deemed competitive, the applicant is invited to complete the official online application. TOEFL scores are also required for international applicants whose first language is not English.

Competitive applicants must demonstrate strong performance in the physical sciences and mathematics. Research experience is also considered desirable. The program encourages applications from members of underrepresented groups.

The Faculty and Their Research

• University of California, San Diego
• Steve Kay, Dean: how circadian clocks are built inside of cells, using molecular, genetic, and genomic approaches in three model systems: mouse, Arabidopsis, and Drosophila.
• Eric Allen: genetic potential; ecology; evolution of marine microbial populations using environmentally derived community genome sequence information.
• Raffi Aroian: relationship between cellular architecture (cytoskeleton) and cellular function.
• Tim Baker: cryoelectron microscopy; three-dimensional computer reconstruction of macromolecules.
• Darwin K. Berg: molecular and cellular neurobiology; regulation of synaptic components on neurons.
• Ethan Bier: Drosophila neural development.
• Steven Briggs: embryonic stem cell fate; plant resistance to infectious disease.
• Stuart Brody: biochemical genetics of circadian rhythms.
• Gert Cauwenberghs: analog and digital VLSI microsystems for adaptive neural computation and sensory information processing.
• Lin Chao: evolutionary processes in microbes; bacteria and their viruses.
• Andrew Chisholm: morphogenesis of cell, tissues, and organs in C. elegans.
• Elsa Cleland: plant ecology; impact of global environmental changes on plant communities and plant species phenology.
• Nigel M. Crawford: plant molecular biology; control of gene expression and ion transport.
• Michael David: mechanisms by which interferons and other cytokines activate the transcription of early response genes.
• Russell F. Doolittle: evolution of protein structure-function.
• Mark Estelle: understanding the molecular mechanisms of plant hormone action.
• Gen-Sheng Feng: deciphering molecular signaling mechanisms in embryonic and adult stem cells.
• Richard A. Firtel: mechanisms regulating gene expression and cell differentiation during development.
• Douglass Forbes: nuclear transport in vitro; nuclear pore structure.
• E. Peter Geiduschek: biochemical and genetic approaches to control of gene activity.
• Anirvan Ghosh: molecular neurobiology; mechanisms of cortical development and plasticity.
• Partho Ghosh: mechanisms of bacterial and protozoan pathogenesis; host response against infectious microbes.
• James Golden: molecular genetics of cyanobacterial development and nitrogen fixation.
• Susan Golden: circadian rhythms of gene expression in cyanobacteria.
• Ananda Goldrath: generation and maintenance of T-cell immunity.
• Shelley Halpain: activity-dependent regulation of neuronal structure; neural development; neurite initiation; synapse formation and stability; dendritic branching and spine formation; synaptic mechanisms; aging-related changes in synaptic plasticity; neurological and neuropsychiatric diseases.
• Randy Hampton: genetics and molecular biology of protein degradation in yeast.
• Jeff Hasty: development of an engineering-based methodology for the design and construction of synthetic gene regulatory networks.
• Stephen M. Hedrick: immune recognition and development.
• Donald R. Helinski: regulation of plasmid DNA replication and plasmid DNA partitioning.
• David Holway: ecological basis of invasive species; Argentine ants; California fire ants.
• Colin Jamora: cell biology of morphogenesis; molecular mechanisms of organ development in mice.
• Yishi Jin: basic processes underlying synapse formation, using the nematode C. elegans.
• Randall Johnson: regulation of response to hypoxia and other microenvironmental stresses in vivo.
• Tracy Johnson: mechanisms of pre-mRNA splicing; mRNA synthesis and processing.
• James T. Kadonaga: transcriptional regulation in eukaryotes.
• Amy Kiger: cellular morphogenesis; functional genomic analysis of cell shape changes in Drosophila development.
• Joshua Kohn: plant population biology; mating system evolution; ecological genetics.
• William B. Kristan: neurobiology of simple nervous systems.
• Mitchell Kronenberg: presentation of peptide and nonpeptide antigens to T lymphocytes and mucosal immunity.
• Jill Leutgeb: biology of memory; encoding of new information in hippocampal neural networks.
• Stefan Leutgeb: loss of function in hippocampus region and effect on memory storage; Alzheimer’s disease.
• William F. Loomis Jr.: developmental biology of Dictyostelium.
• Vicki Lundblad: seeks to understand the unique properties of telomeres, the specialized structures found at the ends of linear chromosomes.
• Jens Lykke-Andersen: molecular biology of regulation of mammalian gene expression; regulation of RNA turnover.
• Eduardo Macagno: cellular and molecular mechanisms underlying the specification of neuronal identity and the generation of neuronal arbors.
• Roberto Malinow: neurobiology; physiology of rodent synapses in memory function and dysfunction.
• Therese Markow: speciation and adaptation to novel environments; mating system evolution; Drosophila evolutionary genetics.
• Stephen Mayfield: regulation of mRNA translation in green plants, especially how light activates the interaction of proteins, mRNAs, and the ribosome.
• William McGinnis: molecular genetics of early Drosophila embryogenesis.
• Mauricio Montal: molecular basis of electrical excitability and signal transduction in neural membranes.
• Cornelis Murre: helix-loop-helix proteins in B-cell development and oncogenesis.
• James Nieh: evolution of animal language: symbolic communication in highly social bees; sensory physiology and mechanisms of multimodal communication; bioacoustics; cyborg bee project.
• Maho Niwa: signal transduction pathways that regulate the functional capacity of organelles.
• Amy Pasquinelli: genetic and molecular approaches for understanding how tiny regulatory RNAs control gene expression.
• Gentry Patrick: neurobiology; the ubiquitin-proteasome system (UPS), one of the major cellular pathways controlling protein turnover in mammalian cells.
• Lorraine Pillus: chromosome structure and function; genetics and epigenetics of transcription; position effects and transcriptional repression.
• Joe Pogliano: DNA segregation in prokaryotes.
• Kit Pogliano: how the progeny of a single cell division assume differing fates.
• James W. Posakony: pattern formation and gene expression in Drosophila development.
• Paul A. Price: analysis of protein structure and physiological function; posttranslational protein modification.
• Pamela Reinagel: neural coding of visual information by thalamic neurons; temporal and population coding, natural scenes, and visual behavior.
• Scott Rifkin: understanding how the structure and mechanics of developmental and physiological processes dampen or amplify genetic, environmental, and stochastic variation and channel their effects.
• Kaustuv Roy: physical and biotic controls on the distribution and diversity of species in benthic marine ecosystems.
• Oliver Ryder: genetics of endangered species; zoo biology.
• Milton H. Saier: transmembrane transport and the regulation of cellular physiology and transcription.
• Massimo Scanziani: developmental neurobiology.
• Immo Scheffler: interest in all aspects of mitochondrial biology.
• Robert J. Schmidt: plant molecular biology; mechanisms of tissue-specific gene expression in maize.
• Julian I. Schroeder: plant cell and molecular biology; signal transduction and ion channels in higher plant cells.
• Terrence J. Sejnowski: computational models of the nervous system; mechanisms for synaptic plasticity.
• Jonathan Shurin: connections among population, community, and ecosystem ecology.
• Laurie Smith: molecular genetic analysis of plant cell division and morphogenesis.
• Deborah Spector: human cytomegalovirus (HCMV); determining at the molecular level how the interplay of viral and host functions relates to in vivo pathogenesis and using this information to develop effective strategies for treatment and prevention of disease.
• Nicholas C. Spitzer: control of expression of neuronal phenotypes.
• Suresh Subramani: organelle homeostasis; peroxisome function and biogenesis; peroxisomal disorders; peroxisomal protein import; peroxisome turnover by autophagy.
• David Traver: vertebrate blood cell development; biology of hematopoietic stem and progenitor cells.
• Emily Troemel: understanding defenses against pathogen infection in C. elegans.
• Jean Y. J. Wang: understanding how cells recognize, assess, and respond to lesions in DNA; molecular mechanisms by which a damaged cell can distinguish between continued proliferation, permanent growth arrest, and suicide.
• Jing W. Wang: systems neurobiology; representation and processing of olfactory information in simple olfactory system.
• Carl Ware: immune regulation by TNF-related cytokines and viral evasion strategies.
• Steven A. Wasserman: molecular genetic analysis of patterning, cell-cycle control, and signal transduction in Drosophila development.
• James Wilhelm: mRNA localization, translation, and membrane trafficking in Drosophila.
• David S. Woodruff: conservation and evolutionary biology; speciation; genetics of endangered species.
• Yang Xu: lymphocyte development and signaling pathways in response to DNA damage.
• Martin F. Yanofsky: molecular and genetic analyses of flower development.
• Deborah Yelon: understand the molecular and cellular mechanisms that specify the size and shape of each cardiac chamber; identification of genes that regulate chamber formation is likely to illuminate the etiology of common types of congenital heart disease.
• Dong-Er Zhang: molecular pathology of cancer development, progression, and treatment.
• Yunde Zhao: plant biology; molecular mechanisms of auxin homeostasis; signal transduction.
• Yimin Zou: molecular and cellular mechanisms of axon pathfinding, target specification, and neuronal migration in nervous system development.
• Elina Zuniga: innate and adaptive immunity.
• Salk Institute
• Senyon Choe: X-ray crystallography of biological macromolecules.
• Joanne Chory: genes that control light-regulated gene expression in Arabidopsis.
• Andrew Dillin: pathways that regulate the aging process.
• Joseph Ecker: molecular genetics of Arabidopsis.
• Beverly Emerson: transcriptional regulation in differentiation and disease.
• Ron Evans: molecular analysis of neuroendocrine function.
• Fred Gage: regeneration in the adult mammalian nervous system.
• Martyn Goulding: homeobox genes in neural development.
• Martin Hetzer: organization and assembly of the nuclear envelope during development and cell proliferation.
• Tony Hunter: role of protein phosphorylation in oncogenesis and cell-cycle regulation.
• Katherine Jones: HIV transcriptional regulation in vitro.
• Leanne Jones: mechanisms controlling stem cell behavior.
• Jan Karlseder: structure and function of mammalian telomeres.
• Chris Kintner: molecular biology of neurogenesis in amphibian embryos.
• Nathaniel Landau: understand how the HIV coreceptor mediates infection and how it affects the rate at which infected individuals progress to disease.
• Kuo-Fen Lee: study of neural development and function using gene targeting.
• Jeffrey Long: understanding apical/basal polarity in plants.
• Marc Montminy: characterization of the structure, regulation of nuclear factors which stimulate gene expression.
• Joseph Noel: stereochemical principles governing biological processes; emphasis on signal transduction.
• Dennis O’Leary: development of the vertebrate nervous system.
• Clodagh O’Shea: using adenovirus to both understand and treat cancer.
• Satchin Panda: molecular mechanism of the biological clock in a mouse model system.
• Samuel Pfaff: molecular mechanisms that control vertebrate motor axon pathfinding.
• Michael G. Rosenfeld: transcriptional regulation of development in the endocrine and neural systems.
• Reuben Shaw: signal transduction pathways that underlie the development of cancer as well as type 2 diabetes.
• Paul Slesinger: molecular gates regulating movement of ions in and out of a cell.
• John Thomas: molecular genetics of neuronal development in Drosophila.
• Jim Umen: control of cell size and organelle DNA inheritance.
• Wylie Vale: brain hormones, in particular, small proteins called peptides.
• Inder Verma: oncogenes, proto-oncogenes, and gene transfer.
• Geoff Wahl: genome remodeling in mammalian cells.
• Lei Wang: strategies for molecular evolution and molecular imaging.
• Matthew Weitzman: virus replication and the development of viral vectors for gene therapy.
• John Young: mechanisms of retroviral and anthrax toxin entry into cells.

Correspondence and Information

University of California, San Diego
Biology Graduate Admissions Coordinator
Division of Biological Sciences, 0348
9500 Gilman Drive
La Jolla, California 92093-0348
Telephone: 858-534-8983
Fax: 858-534-4459
Email: gradprog@biology.ucsd.edu