Bay Area Virus Network

We connect thousands of top level researchers to share insights and spark collaboration.

About

The Bay Area Virus Network represents a constellation of scientists, engineers, and clinician researchers in the San Francisco Bay Area who are working to understand, prevent, and control human and animal viral infections. It is a platform for connecting investigators at universities, biotechnology and pharmaceutical companies, and research institutes throughout the region.

BAY AREA COVID-19 LABORATORY RESOURCES

Here you can find a comprehensive list of facilities within the Bay Area Virus Network and associated laboratories that can be utilized in response to the Covid-19 pandemic.

OPEN NETWORK SPREADSHEET

Collaboration on COVID-19 pandemic

Are you working on or interested in collaborating in response to the COVID-19 pandemic? Please reach out to Julia Schaletzky at jschaletzky@berkeley.edu.

Resources About Affiliated Labs Projects News & Events FAQs

Resources

The SF Bay Area provides access to a broad array of shared facilities, incubator space, translation opportunities, and specialized training. This web portal provides static listings of resources in the bay area, including lab protocols, software packages, and other tools provided by the community.For a digest of new and transient funding opportunities, jobs, and other resources for virus researchers in the San Francisco bay area, please join our listserv.

To add your resources to this listing please contact Isabelle Charles at i.m.charles@berkeley.edu

Protocols

Bioinformatic Tools

Web based

http://www.ebi.ac.uk/Tools/emboss/cpgplot/
Plots GC content across input DNA sequences and identifies CpG rich regions.
Phylogenomic Analysis Tools (Sjolander Group, UC Berkeley)
Malaria Strain Comparison DB

Software

About the Network

The SF Bay Area offers a unique ecology for virus research, with its long tradition of innovation. Our diverse community of investigators is led by distinguished scientists like Jay Levy at UCSF, who co-discovered the AIDS virus in 1983, and Edward Penhoet at UC Berkeley, who discovered the Hepatitis C virus and went on to found Chiron (which developed the first vaccine against Hepatitis B).

CEND continues to serve as an administrative home for the network, with new co-sponsors including:

Organizations that sponsor the network benefit from participation in bayviro.org symposia and seminars, access to recruiting tools and networking events, and opportunities to interact directly with leading bay area researchers. To join as a sponsor, please email cend@berkeley.edu.

Major Participating Institutions

UC Berkeley

UC Berkeley excels in basic science research and possesses state-of-the-art facilities for conducting experiments involving next generation sequencing, proteomics, biomolecular structure determination, advanced microscopy, and transgenic animals. The virology community at UC Berkeley spans a number of departments and disciplines including Molecular and Cell Biology, Plant and Microbial Biology, Integrative Biology, Infectious Disease, Public Health, Bioengineering, Chemical Engineering, and Environmental Science, Policy and Management. The collaborative atmosphere in virology at UC Berkeley is apparent in the multiple interest groups and organizations devoted to bringing together disparate techniques towards the goal of understanding virus-host interactions and the development of novel treatment approaches. The Center for Emerging and Neglected Diseases (CEND) is a cornerstone to the UC Berkeley virology community and acts to encourage interest in virology research by providing funding opportunities and arranging symposia on topics of current interest in the field. Collaborations with other Bay Area universities, the nearby Lawrence Berkeley National Labs (LBNL), and industry partners make UC Berkeley an epicenter for the study of viruses as well as their relation to humanity.

UCSF University of California, San Francisco is a UC campus devoted to health and life sciences. It is a powerhouse of scientific research and home to several virology labs. Its graduate programs offer an outstanding grounding in a wide variety of fields and approaches to biology. Biomedical Sciences Graduate Program (BMS) and Program in Biological Sciences (PIBS) and are particularly relevant to anyone interested in virology.

UCSF

Several symposia of interest to the virology community are held at UCSF annually: note the Bay Area RNA Club (BARC) and Bay Area Microbial Pathogenesis Symposium (BAMPS).

UCSF boasts an incredibly vigorous seminar series. Virology topics often come up in the seminars for Immunology and Biochemistry & Molecular Biology, Cell Biology, Developmental Biology, & Genetics.

The UCSF-affiliated Gladstone Institute also houses an active virology community.

For information regarding UCSF, contact Leonid Gitlin (leonid.gitlin@ucsf.edu).

Gladstone Institute of Virology and Immunology

The Gladstone Institute of Virology and Immunology is a research institute dedicated to the study of virology and immunology with a focus on HIV and AIDS. Founded in April of 1993, GIVI conducts a full range of basic and clinical research on HIV/AIDS, in addition to viruses such as HCV, Epstein-Barr, and CMV. Our research also encompasses other areas of human health, highlighting our strategy to give scientists the freedom to follow their research wherever it leads. GIVI laboratories are headed by Drs. Warner Greene, Gilad Doitsh, Robert Grant, Nevan Krogan, JJ Miranda, Melanie Ott, Shomyseh Sanjabi, Eric Verdin, and Leor Weinberger. With faculty appointments within UCSF, GIVI Investigators participate in a wide range of university activities such as the Program in Biological Sciences (PIBS) and Biomedical Sciences (BMS) graduate student programs. GIVI Seminars frequent external speakers of renown in the areas of virology and immunology. The numerous resources and rich scientific environment at Gladstone is reflected in the institute’s having been ranked #1 by The Scientist as the best place to work in academia in 2011 and 2012, and illustrates our standing as an excellent place for pre- or postdoctoral training. GIVI has also partnered with UCSF for the federally sponsored UCSF-GIVI Center for AIDS Research (CFAR), which is co-directed by Drs. Warner Greene and Paul Volberding.

For information regarding GIVI, contact Renuka Kumar (renuka.kumar@gladstone.ucsf.edu).

UC Davis

The mission of the University of California, Davis is to advance the human condition through improving the quality of life for all. This institution uses a framework that connects its land-grant history to a transformative vision for the 21st century with the aim of making global impact in many scientific and social areas. UC Davis is composed of 4 colleges (Agricultural and Environmental Sciences, Biological Sciences, Engineering, Letters and Science) and 6 professional schools (Education, Law, Management, Medicine, Veterinary Medicine and the Betty Irene Moore School of Nursing), with a total number of 33,000 students. There are 101 undergraduate majors and 90 graduate programs, and many of these are in the biological sciences. Infectious disease research at UC Davis covers a broad range of pathogens in humans, animals (including invertebrates), and plants, and about 55 faculty members pursue research and teaching in virology.

For information regarding UC Davis, contact Paul Luciw (paluciw@ucdavis.edu).

Affiliated Labs

If you wish to be added to this list, please contact Isabelle Charles at i.m.charles@berkeley.edu with information about your lab.

Investigator	Affiliation	Interests	Keywords

Peter A. Barry	UC Davis	Mechanisms of cytomegalovirus (CMV) persistence and pathogenesis; Nonhuman primate models of human CMV; Modeling of human CMV vaccine strategies in a nonhuman primate model
Paul A. Luciw	UC Davis	Viral Pathogenesis and Therapy (HIV and AIDS) Biomarkers for Infectious Diseases and Cancer	Retroviruses, Persistent Infection, Nonhuman Primate Models, HIV and AIDS
Raul Andino	UCSF	RNA virus replication, virus population dynamics and evolution	RNA virus, virus detection by host, RNAi, antiviral response.
Jody Baron	UCSF	Innate and adaptive immunity to viral pathogens.	Immune response, Hepatitis B
Nichole Baumgarth	UC Davis	We are interested in understanding the regulation of immunity to influenza virus with particular emphasis on the regulation of the local B cell responses by innate signals and the B cell subsets that are contributing to immune defense against respirato	Immune regulation; antiviral immunity; humoral immunity; respiratory tract immunity; B cell subset responses; B-1 cells; natural antibodies
Monica Borucki	Lawrence Livermore National Lab	evolution, quasispecies, forensics	evolution, quasispecies, forensics
Gertrude Buehring	UC Berkeley	My area of research is oncogenic viruses--viruses that cause human cancer.	molecular epidemiology, oncogenic viruses and human cancers
Jan Carette	Stanford	Research focuses on identification of host genes using haploid genetic screens in human cells; obtain fundamental insights on how viruses hijack cellular processes and on host defense mechanisms; facilitate the development of new therapeutic strategies.	virology, immunology, genetics, influenza
Charles Chiu	UCSF	Metagenomics-Based Technologies for Virus Detection and Discovery	Viral Detection and Discovery, Clinical Diagnostics, Pathogen Detection Microarrays, Deep Sequencing, Metagenomics
Jinah Choi	UC Merced	HCV, oxidative stress, mutation, interferon
Candice Clay	California National Primate Research Center	Our lab has largely focused on understanding the development of asthma, exploring the relationship between childhood asthma and exposure to allergens and environmental air pollution.	Respiratory syncytial virus, Rhinovirus, influenza, Tobacco, side stream cigarette smoke, asthma
Lark Coffey	UC Davis	viral molecular evolution, viral genetic factors that promote mosquito-borne virus emergence and disease	mosquito-borne viruses, virus mutations, Zika virus, chikungunya virus
Laurent Coscoy	UC Berkeley		herpesvirus, innate immune response
Charles Craik	UCSF	The Craik lab focuses on viral proteases with a current emphasis on HIV and the human herpesviruses. Specifically, we are interested in host-virus interactions involving proteases as well as small molecules and biologics for the modulation of protease act	small-molecule allosteric inhibition, protein-protein interaction, host-virus interaction, restriction factor identification, structure-function characterization, proteases
Joseph DeRisi	UCSF	Genomics, proteomics, informatics, etc.	Viral discovery, RNA viruses, metagenomics, viral-host interactions, viral recombination
Jerome Deval	Alios BioPharma	Alios is a biotechnology company located in South San Francisco, California, that is developing novel medicines to treat viral diseases. Alios has two platform technologies: novel nucleoside/nucleotide chemistries and small molecule activators of the RN	Antivirals, RNA polymerases, drug discovery, HCV, Influenza virus, RSV, nucleoside, RNase L
Rebecca DuBois	UC Santa Cruz	The DuBois Lab seeks to understand the molecular mechanisms of virus infections, and to use this information to develop new vaccines and antiviral therapeutics.	Structural virology, vaccine design, antiviral antibody therapies
James E.K. Hildreth	UC Davis	My laboratory research is focused on understanding mechanisms by which HIV subverts host pathways and molecules during its replication cycle. We are particularly interested in the role of cholesterol and cholesterol homeostatic pathways in virus entry, vi	HIV-1, cholesterol, HIV-1 and co-infecting viruses
Shirit Einav	Stanford	Focuses on better understanding interactions of Flaviviridae with the human host and their inhibition.	Flaviviridae, viral-host protein-protein interactions, antivirals, assembly, budding
Bryce Falk	UC Davis	Work with plant viruses; their biology and molecular biology, and engineering plants for resistance against virus infections.
Margaret Feeney	UCSF	Immunopathogenesis of HIV and malaria in childhood	Immunopathogenesis, HIV, malaria, T-cell response, immune response
Ellen Fiss	Roche Molecular Systems	Diagnostic assays for the detection of viruses.	diagnostic, assay, detection
Alan Frankel	UCSF	Assembly and evolution of RNA-protein complexes and virus-host interactions. HIV – Tat and Rev proteins: their biochemistry, structure and interactions.	RNA-protein, HIV, Tat protein, Rev protein, virus-host interaction
Scott Geller	Bay Genomics	With a background in molecular neuroscience, animal models of disease, and especially dangerous pathogen handling and detection, Bay Genomics is a private lab and scientific resource for the greater San Francisco Bay Area, committed to helping local sci	cell culture, molecular biology, immunology, microscopy, and genomics studies
Britt Glaunsinger	UC Berkeley	Studying how viruses interface with host gene expression machinery; emphasis on gammaherpesviruses.	herpesvirus, RNA turnover, host shutoff
Harry Greenberg	Stanford	Long-standing interests in rotavirus, influenza, hepatitis B and C and Noroviruses. Interests in viral immunity (innate and acquired), pathogenesis and vaccines	Rotavirus, influenza, hepatitis B and C, notaviruses, viral immunity, pathogensis, vaccines
John Gross	UCSF	The control of eukaryotic gene expression at the level of mRNA metabolism. Biology of HIV-host complexes.	gene expression, mRNA metabolism, HIV-host
Eva Harris	UC Berkeley		Correlate of protection of vaccines, cross-reactive B cell response
Laura Hertel	CHORI, Center for Immunobiology and Vaccine Development	Mechanisms regulating human cytomegalovirus (CMV) tropism and latency, in particular, how CMV gains access to specific cells of the innate immune system, the dendritic cells, and how the CMV genome is maintained within the host bone marrow cells for life.	Human Cytomegalovirus, CMV, tropism, latency, vaccine, innate immune system
Christopher J. Miller	UC Davis	My laboratory utilizes non-human primate models of AIDS and influenza A virus infection to define the pathogenesis of these viral infections, study the nature of protective antiviral immunity, and test vaccines and immunotherapeutic strategies to preven	Viral Pathogenesis Anti-viral Immunity Mucosal Immunology RNA viruses
Hong Jin	MedImmune	Negative strand RNA viruses
Nevan Krogan	UCSF	High-troughput analysis of host-pathogen interactions in HIV, enteroviruses, dengue virus	host-pathogen interaction, HIV, enterovirus, dengue virus
Desiree LaBeaud	Stanford	Explore the risk factors of arthropod-borne viral diseases (Rift Valley fever (RVFV), dengue (DENV) and chikungunya (CHIKV) viruses) to understand transmission, optimize prevention and control, and estimate the proportion of acute febrile illness.	anthropod-borne viral diseases, Rift Valley fever, RVFV, dengue, DENV, chikungunya, CHIKV, transmission, epidemiology, diagnostics
Jennifer Lavail	UCSF	Axonal Transport Mechanisms of Herpes Simplex Virus in CNS Neurons	axonal transport, herpes simplex virus, CNS neurons
Jay Levy	UCSF	Research in our laboratory deals with virologic, immunologic and molecular studies of HIV pathogenesis and vaccine development. Specific attention is given to the innate immune response against HIV including that of dendritic cells and CD8+ lymph	Innate immunity, HIV, non-cytotoxic CD8+ cell antiviral activity, HIV vaccine development
Zengji Li	BN ImmunoTherapeutics		Poxvirus vector cancer vaccine
Patricia LiWang	UC Merced	The LiWang Lab research interests include structural biology of chemokines, applications to HIV and inflammatory diseases.	HIV inhibition and inflammation.
Uri Lopatin	Assembly Pharmaceuticals	HBV, drug development, immunology, allostery
Susan Lynch	UCSF	Human microbiome,including its perturbations in HIV patients. Chronic inflammatory disease.	human microbiome, HIV, chornic inflammatory disease
Stephanie Mandl	BN ImmunoTherapeutics	BN ImmunoTherapeutics is a biotech company that is developing poxvirus based immunotherapies for cancer.	Tumor immunology, breaking tolerance, vaccine development, immunotherapy
B. Matija Peterlin	UCSF	Study the molecular biology of HIV and endogenous retroviruses with special emphasis on transcription, restriction and proviral latency; focus is on Tat:P-TEFb, Nef, Vif:APOBEC, and aspects of other accessory proteins.	Transcription, latency, reservoir, restriction, integration, silencing, replication
Mehrdad Matloubian	UCSF	Lymphocyte migration and autoimmune disease as revealed by the lymphocytic choreomeningitis virus	lymphocyte migration, autoimmune disease, lymphocytic choreomeningitis virus
Alison McCormick	Touro University, California		Vaccines, Virology, Public Health
Mike McCune	UCSF	Pathogenic Mechanisms, Treatment, and Prevention of HIV Disease	pathogenic mechanisms, treatment, prevention, HIV
Mohammad Mofrad	UC Berkeley (Bioengineering)	Using computational models to shed light on the process by which HIV Rev oligomerizes on the Rev Response Element (RRE) sequence of the viral genome and recruits crm1 (chromosome region maintenance 1; also referred to as exportin1) to export this genome.	HIV, HIV replication, viral genome, bioengineering.
Brian Murphy	UC Davis	Interested in retroviral promoter function/regulation and how it relates to viral pathogenesis (FIV, SIV, CAEV, ENTV, JSRV).	transcriptional regulation and latency- host:viral cross-regulation
Doug Nixon	UCSF	Cellular immune responses to HIV	cellular immune responses, HIV, immunity
Philip Norris	Blood Systems Research Institute	Understanding the role CD4+T helper cells play in the body's immune defense against viral infections, such as HIV. Understanding acute immune response to West Nile virus and other flavivirus infection. Defining the types and mechanisms of immune reactio	T-cell immunology, cytokine networks, human viral pathogenesis
Patricia Pesavento	School of Veterinary Medicine, UC Davis	We divide our research time between enigmatic cases of disease in group-housed (shelter) animals, and a basic research program on host:viral pathogen interactions. What unites all of our work is our desire to study natural disease and to help make sense,	virus, pathology, oncogenesis
Daniel Portnoy	UC Berkeley	Pathogen immune evasion, pathogenesis	Immune evasion, pathogenesis
Mary Premenko-Lanier	SRI	Cellular immune dysfunction during persistent viral infections	cellular immune dysfunction, viral infection, immunity
David Raulet	UC Berkeley	We are interested in how natural killer cells recognize virus-infected cells. A specific focus concerns how viral infections induce expression in infected cells of cell surface ligands recognized by NK cell activating receptors, such as NKG2D.	Immune activation, innate immunity
Peter Sarnow	Stanford	Virus-host interactions, cellular and viral translation, miRNA regulation of gene expression
David Schaffer	UC Berkeley	Stem Cells, Gene therapy and HIV	gene therapy, RNA viruses, HIV-1, viral latency
Barbara Shacklett	UC Davis	Mucosal immunity to HIV and SIV (gastrointestinal and reproductive mucosa). Trafficking of antigen-specific T-cells to mucosal tissues and the central nervous system. Natural Killer cells and non-classical effector cells in mucosal tissues.	Mucosal immunity Cytotoxic T-cells Host Responses Adaptive immunity
Mina Sun	UC Berkeley	Virus DNA packaging mechanisms	virus, DNA, virology
Jane Sykes	UC Davis	Viral infections of dogs and cats	Clinical virology
Julian Symons	Alios BioPharma Inc.	Alios BioPharma is a biotechnology company located in South San Francisco, California, that is developing novel medicines aimed at the treatment of viral diseases. Alios is developing direct acting antiviral agents against several human viral pathogens of	Chronic hepatitis C, hepatotropic viruses, respiratory viruses, RNase L, direct acting antiviral agents.
Cristina Tato	CZ Biohub		Global health and infectious diseases
Russell Vance	UC Berkeley	Innate immunity, host-pathogen biology, inflammasome activation
Jonatahn Weissman	UCSF	Global monitoring of protein translation and mRNA transcription, including in viral systems	protein translation, mRNA transcription, viral systems
JoAnn Yee	UC Davis	Infectious Disease in Animal Models	Infectious Disease in Nonhuman primates.

Projects

Projects coming soon! If you have a project you would like to feature, please reach out to Isabelle Charles at i.m.charles@berkeley.edu

Upcoming Events

VIRTUAL Coronavirus Diagnostic Hackathon – March 25th and 26th

Many events in the Bay Area have been cancelled due to the current threat of the covid-19 pandemic.

If you have an event you would like to advertise, please reach out to Isabelle Charles at i.m.charles@berkeley.edu

Questions

Who is included in the Bay Area Viruses Network?

The bayviro.org web platform features profiles of more than 40 research labs and programs located in the San Francisco bay area. These include academic investigator labs, as well as research programs at local companies, government agencies (like the Department of Energy National Labs), and non-profit research institutes. In addition, bayviro.org maintains a listserv with more than 400 subscribers.

How can I join the network?

The first step in joining BayViro is to sign up for our listserv. The list provides a digest of upcoming events, funding opportunities, and jobs for virus researchers in the San Francisco bay area. Members are invited to share notices and other information with the broader network by contacting Isabelle Charles at i.m.charles@berkeley.ed, who maintains the listserv.

Who runs the network?

We are a community-organized resource maintained by scientists at UC Berkeley, UC Davis, UCSF, and Stanford University. Researchers on each campus collect information to disseminate to the broader network. Our events are organized by staff and volunteers at each university.

How was the Bay Area Virus Network established?

Bayviro was launched in 2012, after a successful first meeting of nearly 400 virus researchers in the San Francisco bay area. At the meeting, a need was identified for a portal to link researchers with scientific resources, potential collaborators, and event listings in the Northern California region. The network was established by the Henry Wheeler Center for Emerging and Neglected Diseases at UC Berkeley, with support from our sponsors.

Projects

Projects coming soon! If you have a project you would like to feature, please reach out to Isabelle Charles at i.m.charles@berkeley.edu