Depletion of Abundant Sequences by Hybridization (DASH): Using Cas9 to remove unwanted highabundance species in sequencing libraries and molecular counting applicationsBioRxiv, 2015
Diagnosing Balamuthia mandrillaris Encephalitis With Metagenomic Deep SequencingAnnals of Neurology, 2015
Genome Announcements Collection 2: Tombunodavirus UC1; Picalivirus D; Laverivirus UC1Genome Announcements, 2015
Genome Announcements Collection 1: Ciliovirus, Brinovirus; Marine RNA Viruses SF-1, SF-2, SF-3; Leviviridae RNA Phages EC and MBGenome Announcements, 2015
Widespread Recombination, Reassortment, and Transmission of Unbalanced Compound Viral Genotypes in Natural Arenavirus InfectionsPLoS, 2015
Destructin-1 is a Collagen-Degrading Endopeptidase Secreted by P. destructans, the Causative Agent of White-Nose SyndromePNAS, 2015
Genome-wide regulatory dynamics of translation in the Plasmodium falciparum asexual blood stageseLife, 2014
Jennifer Mann is the manager for the DeRisi lab. She holds an MSE in Mechanical Engineering from the University of Michigan, and her responsibilities include lab logistics, part design, 3D printing, and laser etching.
Manny is a research analyst level II who is currently working with the DeRisi and Weissman laboratories.
Eric is the Director of the Center for Advanced Technology at UCSF (cat.ucsf.edu). He has been working with groups at UCSF, including the DeRisi Lab, to develop new NGS library preparation methods and find research applications for new technologies.UCSF Center for Advanced Technology
Brian is: (1) an organic/polymer chemist by training, (2) currently working on lanthanide nanophosphor and polymer development for the proteome-scale bead-based linear peptide array project in the DeRisi Lab, and (3) back in academia as a post-doc after an 11-year stint in industry. He currently splits time between the UCSF, Mission Bay campus and the Molecular Foundry at the Lawrence Berkeley National Laboratory where he has a User affiliation in conjunction with this project.
Wesley is a post-doctoral researcher working on malaria drug screens and apicoplast proteomics. He received his Ph.D from UC Berkeley in the lab of Matt Francis.
Maxine first joined the DeRisi lab as a technician working on the
Virus Chip project. She went on to get her PhD at UC Davis, with a
focus on avian disease ecology, and has rejoined the lab as a
postdoctoral research fellow. She is currently working on viral
discovery in a range of avian species.Maxine Zylberberg
Emily is a postdoc working on developing methods for genome engineering in Plasmodium falciparum. She received her PhD in 2012 from Jim Wells' lab at UCSF, where she used proteomics to study the biology of apoptosis.
Huy is a post-doctoral researcher, with specialization in carbohydrate/lipids/phosphoramidite/peptide chemistry, investigating methods for the development of low-cost diagnostic devices with applications in immunoassays and profiling enzyme specificity.
Kristeene is a Postdoc with a broad interest in virology and host-pathogen interactions. She is currently working on methods for identifying host factors that influence arenavirus replication.
Carolina is a postdoctoral researcher in the DeRisi Lab.
Giselle Knudsen is an Assistant Adjunct Professor in the Dept. of Pharmaceutical Chemistry, and is a member of the UCSF Mass Spectrometry Facility. She is interested in using proteomic methods to study host-pathogen interactions, such as affinity-purification mass spectrometry (AP-MS) for discovery of novel interactions and protease activity screening to characterize specific proteases involved at the interface of infectious organisms such as fungi and parasites with their hosts. She is also collaborating on a new project for antigen identification in autoimmune neuroencephalitis patient samples.UCSF Mass Spectrometry Facility
Jeremy is a post-doctoral fellow and practicing pediatric dentist focusing on genome-wide analyses of sugar bugs (bacteria that cause dental caries). His work in the DeRisi Lab focuses on characterizing the heterogeneity of lactobacilli in the dental plaque, and finding safe compounds to prevent and treat dental caries through genome-wide computational drug discovery techniques he is developing with the Samudrala and Sali labs.
Michael is an Assistant Adjunct Professor in the UCSF Department of Neurology where he is a practicing neurologist in the Multiple Sclerosis and Neuroinflammation Center. He is doing a post-doctoral fellowship in the DeRisi Lab where he works on pathogen discovery and host transcriptomics in meningitis and encephalitis as well as characterizing virus-host protein-protein interactions of neuroinvasive paramyxoviruses and arenaviruses.
Dan is Resident in the Department of Otolaryngology-Head and Neck Surgery at UCSF. His work in the DeRisi lab focuses on the genomics and metagenomics of Oral Tongue cancer in patients who lack traditional risk factors.
Chaz is a Fellow in the Division of Infectious Diseases at UCSF. His research involves using metagenomics to identify known and novel pathogens responsible for severe respiratory and neurologic infections in both local and global patient populations. He is also interested in understanding the role of the respiratory microbiome in pulmonary disease and the mechanisms by which environmental exposures modulate respiratory infection severity and susceptibility.
Thuy is a Clinical Instructor at the F.I. Proctor Foundation/UCSF Department of Ophthalmology where she takes care of patients with complex ocular inflammatory diseases. Her research in the DeRisi Lab focuses on the identification of infectious and autoimmune causes of uveitis.
Matt Zinter is a fellow in the UCSF Benioff Children's Hospital pediatric intensive care unit. He studies infectious and alloreactive lung injury in critically ill pediatric hematopoietic stem cell transplant patients.
Greg is currently working on the transcriptional regulation of one parasite that causes malaria, Plasmodium falciparum. He is also interested in using ultra-high throughput sequencing in novel ways to do other ultra-high throughput experiments.
Brian is a PhD candidate in the iPQB program. He is interested in the identification of rare and novel pathogens in metagenomic datasets as well as clinical applications of NGS technologies to improve patient outcomes.
Chris is a graduate student in the Biomedical Sciences (BMS) program. She is studying the biology of malaria infections caused by the parasite Plasmodium falciparum during pregnancy. Chris has a particular interest in issues of global health surrounding infectious disease in developing countries.
Valentina is a TETRAD graduate student. She is currently studying translation in Plasmodium falciparum.
Hanna is a graduate student in the DeRisi Lab.
Hannah Sample is a research coordinator for the pathogen and autoantibody discovery study. She has a B.S. in Biology and Global Studies. Her favorite parasite is Dracunculus medinensis.
Jenai is a research technician in the DeRisi Lab.
Lillian is a research associate that works on bio-specimen databasing and preparations of sequencing libraries for the pathogen and autoantibody discovery study. She has a passion for infectious diseases, and is fascinated by all nerdy things.
Joe is a postdoctoral fellow working on viral pathogen discovery, microbial ecology of aquatic systems, and the influence of enteric bacteria on neurotransmitters. Joe obtained his PhD studying cancer signaling pathways in the lab of Dr. Kevan Shokat.
Michael is a senior at Gunn High School in Palo Alto, and volunteered in the DeRisi Lab for the summer of 2013. His work involved using bioinformatics to analyze the feasibility of using Illumina sequencing of RNA to find well-represented genes, as well as studying the genome and phylogeny of a novel reptilian bornavirus.
Mark is a post doctoral fellow working on the discovery of viral pathogens in a broad range of human diseases. Mark received his Ph.D from the University of Minnesota and is co-mentored by Dr. Don Ganem.
Adrienne Ng was a summer student from U.C. Davis in the 2013 UCSF Summer Research Training Program. She worked on a project to utilize the CRISPR/Cas9 system to genetically engineer P. falciparum.
Eli volunteered in the DeRisi lab for Summer 2013. He studied bioinformatic techniques to understand the feasibility of creating a robust phylogenetic tree from random total rna sequencing of reptile samples, and to discover and assemble new viruses from these samples. He is currently a student at Harvard University.
Kristoffer worked on recombination of snake Arenaviruses with Mark Stenglein for three months as part of the HHMI EXROP program. He was attempting to prove that recombination was occurring in snakes infected by multiple viruses using DNA and RNA manipulation in emulsions.
Polly Fordyce received her PhD from Stanford (lab of Steve Block) and is now a postdoctoral researcher focused on developing new microfluidic tools for investigating protein binding interactions. During her postdoctoral research, she has developed a technique (MITOMI 2.0) for characterizing transcription factor binding specificities and applied it to a variety of proteins, including transcription factors from S. cerevisiae, C. albicans, and H. sapiens. She is also currently working on developing a new platform for the production of low-cost, programmable, proteome-scale peptide arrays.
Rachel is a graduate student in the joint UCSF and UCB Bioengineering Program. She is currently in the laboratory of Amy Herr at UCB.
Charlie Kim, Ph.D. is currently an assistant professor in the department of Experimental Medicine at the University of California, San Francisco.
Sara, a research specialist in the lab, is a biochemist with training in infectious disease epidemiology. Sara works on novel pathogen discovery in a wide range of human diseases, with a particular interest in immunocompromised populations.
Victoria Newman was a Tetrad graduate student studying mechanisms of resistance to quinoline-based drugs in malaria and yeast. She graduated in 2010 and currently working in London for a science journal.
Daniel Ebert is a technician in the DeRisi laboratory working on malaria drug screens.
Miguel was a computer programmer in the DeRisi laboratory. He is currently a graduate student in the iPQB program here at UCSF.
Vida is a graduate student in the Tetrad Program at UCSF. She is studying mechanisms of post-transcriptional regulation in the human malaria parasite, Plasmodium falciparum, as well as various malaria drug resistance studies by deep sequencing.
Sharon Chao is a Bioengineering graduate student worked on ultra-high throughput sequencing for viral detection. She currently works at ABI.
Michelle Dimon was a Biomedical Informatics graduate student and graduated in 2010. She is the author of HMMSplicer, which is featured on our software page.
Sajeev Batra is currently employed at Lawrence Berkeley National Labs as a software developer.
Camilo is a Junior Specialist at the DeRisi Lab working on microfluidic technologies. The main project he is part of is the development of a fully programmable proteome-scale peptide synthesizer. He's also working on developing other microfluidic tools that will help automate some of the tasks performed daily in the DeRisi lab.
Katherine Sorber was a member of the Tetrad graduate program and graduated in 2010. She studied mechanisms of RNA metabolism in malaria by deep sequencing and worked closely with Michelle Dimon. Katherine is now working at the National Science Resource Center in Washington, DC.
Elfadil is an undergraduate HHMI Summer EXROP student currently studying at the University of Maryland. He is studying post-transcriptional regulation mechanisms in the malaria parasite Plasmodium Falciparum
Amy Kistler was a postdoctoral fellow working on the discovery of viral pathogens in a broad range of human and animal diseases. Amy was co-mentored by Dr. Don Ganem, and currently is a member of the viral genomics team at the J.Craig Venter Institute. While in our labs, Amy discovered Avian Bornavirus, the causative agent of PDD in parrots.
Flor was a graduate student from Argentina working on global translation dynamics of the P. falciparum blood stages. Flor also developed a high-throughput transfection protocol to generate transient and stable transfectants as well as gene knockouts in this parasite. She is now doing a postdoc in the Mekalanos lab.
Ellen was a visiting scientist and post doctoral fellow from the Pathology Department at Stanford University. Her research focuses on the apicoplast in malaria. She now has a faculty position at Stanford University. Yeh Lab Website
Kyoko is a summer student from Macalester College in Saint Paul, MN. She works on a project to sequence a novel virus in cats that is associated with kidney disease, and characterize its relationships to other viruses in its family.
Alexandra is learning bioinformatics and data analysis through Python's programming language in order to assist with the Balamuthia research and other sequencing projects. She also catches ants.
Veda is a summer student from Rice University in Houston, TX. She is working on a project to interpret the results of the gene sequencer and visualize the taxonomy of the Balamuthia Amoeba.
Peter was a graduate student in UCSF Bioinformatics Program. He is currently a staff scientist at Novartis, Inc.
Sarah is an HS Assistant Clinical Professor and the Director, of The High Risk Skin Cancer Program in the Department of Dermatology at UCSF. She is currently investigating the relationship between skin cancer and viruses. Please visit the Arron Laboratory at UCSF for more details.
Graham is a postdoctoral fellow who writes software for the de novo assembly of genomes or sub-genomic fragments from complex metagenomic large-scale/short-read datasets. He applies that software to discovery of infectious disease-causing pathogens and genes of interest from diverse non-model organisms.
Charles was a graduate student in the Tetrad program at UCSF. He was studying recombination in enteroviruses as well as bee pathogens. He currently owns and operates his own genomics company in Oregon.
Chris is a graduate student in the Biomedical Science program at UCSF. In the DeRisi lab, he worked on using microfluidic devices to analyze transcription factors. He is currently a postdoc at UCB.
Lara is a student assisting Dr.Crawford with her work developing methods for genome engineering in malaria (Plasmodium Falciparum). She will be attending NYU in the fall.
Emily is currently taking a year off to travel the world before attending Medical School in the fall.
Alex is an MD/PhD student at UCSF. He studies viral discovery and viral-host protein-protein interaction discovery with a focus on the picornaviruses. Alex graduated in 2013 and is now finishing his clinical training. Despite his clinical duties, he continues to find time to come back to lab to continue his virology work.
Tara was a lab manager and logistics coordinator for the DeRisi laboratory from 2008-2013. She has since relocated to Chicago.
Nathan is currently pursuing an postdoctoral fellowship in policy at The National Academy of Arts and Sciences.
Sichen is a rising second year medical student at Eastern Virginia Medical School. As a HHMI Summer Medical Fellow, he is working on discovering new anti-malarial drug targets in Plasmodium Falciparum.
Dale was a member of the Biomedical Informatics program and earned his PhD in 2008. He was immediately hired by Pacific Biosciences, a deep sequencing startup company. Pacific Biosciences
Zbynek, or "ZB" to folks in lab, was instrumental in booting up our malaria culture system, including the use of bioreactors for growth of P. falciparum. ZB was also became famous at UCSF after burning down a tissue culture hood. After our malaria transcriptome paper was published in PLoS Biology, ZB was hired by Nanyang Technolgical University in Singapore where he is currently an assistant professor. ZB Lab Page in Singapore
Anatoly Urisman was a member of the MSTP and Biomedical Sciences (BMS) graduate program. He graduated in 2005 and has since returned to the clinic to finish his MD degree. Anatoly helped pioneer our virus chip technology and worked on a variety of projects in this area, including E-Predict, XMRV, and SARS.
Jenni Weissman graduated from Stanford University and joined the DeRisi lab and the lab of Dr. Fred Cohen (co-mentor) in 2003. Jenni received a AP Giannini Fellowship and she worked on various anti-malarial drug screening projects and methodologies. She is now pursuing policy work in Washington DC.
Manuel graduated from UC Berkeley and joined the DeRisi Lab as a postdoctoral fellow in 2001. During his postdoc, Manuel worked on gene regulation in both Plasmodium falciparum
and yeast. He now is an assistant professor at the Lewis Sigler Institute for Genomics at Princeton University.Manuel Llinas Laboratory
Jenny graduated from the DeRisi Lab in June 2008. Her thesis worked was focused on mRNA decay in Plasmodium falciparum
. Shortly after graduating, Jenny was hired by the biofuels startup company Codexis. Codexis.com
Takeshi graduated in the summer of 2007 and was a member of the MSTP program (Tetrad). He led a heroic effort to characterize and purify transcription factors from Plasmodium falciparum
. He is currently back in the clinic here at UCSF.
Silvi was a staff research assistant that worked on our viral discovery project. In Fall of 2008, Silvi joined the Tetrad graduate program here at UCSF.
Ally was a staff research assistant. She participated in many of our drug screening efforts and is now taking classes in preparation for a career in pharmacy.
Charles Chiu was a Molecular Medicine Fellow and has since become a faculty member in the department of Lab Medicine here at UCSF. He was also hired as the Director of the Viral Diagnostic and Discovery Center, based at China Basin, near Mission Bay.
Mathew Miller pursued his postdoctoral research in the DeRisi lab as a Damon Runyon fellow. He now works at a local biofuel company.
Kael Fischer served as the lab scientific programmer working on computational and experimental methods associated with our viral discovery efforts. He secured a faculty position at the University of Utah in 2008.
Adam Carroll earned his PhD in the lab of Erin O'Shea at UCSF. After graduating, Adam became the first director of the UCSF Center for Advanced Technology (CAT). Adam successfully managed and evolved the CAT into its present day form. He is now an employ at:Bend Research
Ashwini joined the Tetrad program after working on yeast meiosis at Harvard. She briefly continued in this area when she was Jennifer Gerton's rotation student. After joining the DeRisi lab, she worked closely with Kelley Sheppard and Ron Vale to characterize mRNA transport in yeast. After graduating, joined Angelika Amon's lab at MIT where she studied sporulation. She is now a postdoc in Mike Blower's lab at MIT.
Brian Pulliam was originally hired by the DeRisi Lab to help construct a new microarray database, called NOMAD. During his time in the lab, Brian contributed to several projects, including significant work on the malaria transcriptome paper. Brian is due to graduate from the biophysics program at Harvard in 2008, after which he plans to work at a nonprofit.
After graduating from UBC and completing his residency training in Toronto, Patrick conducted a two year post doc in the laboratories of Drs. Don Ganem and Joseph DeRisi at UCSF where he studied viruses in various malignancies. Patrick is currently an Principal Investigator at the BC Centre for Disease Control.Patrick Tang's lab page at BC Centre for Disease Control
David graduated from Massachusetts Institute of Technology and joined the Don Ganem's laboratory in 1998 as a postdoctoral fellow working hepatitis and KSHV. Dave then began a long collaboration with the DeRisi Lab to pursue viral discovery in a broad range of human diseases. David is currently an Assistant Professor at Washington University in St. LouisDavid Wang
Mary Kate Alexandar was a postdoctoral fellow originally in Barbara Panning's lab, and then in the DeRisi lab where she worked on CQ resistance in malaria. She is now a researcher at Genentech.
Yu-Tsueng, or "YT" as he was known in the lab, participated in the early phases of the Virochip project and also helped during the SARS episode. YT subsequently was hired at UC San Diego where he is an assistant project scientist in the medical genetics program. Visit his site here:YT at UCSD
Terry Minn, originally from Burma, was hired as a technician to help set up our malaria program in early 2001. Terry graduated from medical school in New Jersey and is currently practicing in Antioch, CA.Terry Minn, MD
Nicole was a postdoctoral fellow working on the discovery of viral pathogens for a broad range of human and animal diseases. She now heads her own research group at the Universitatsklinikum Hamburg - Eppendorf where she continues her work on XMRV, a novel gammaretrovirus. You can visit her lab here:Nicole Fischer's Research Group
Jennifer Gerton earned her PhD with Patrick O. Brown at Stanford University and then did a postdoc with Tom Petes. She continued her postdoctoral work at UCSF in the DeRisi Lab. Jennifer worked on a variety of meiosis related projects and was subsequently hired by the Stowers Institute. You can visit her lab here:The Gerton Lab at the Stowers Institute
Holly Bennett did her undergraduate work at University of Washington, Seattle. Holly worked with Joe at Stanford in the late 90s and then worked for Rosetta. She later came back to work with Joe at UCSF as the first employee in the lab. She was instrumental in setting up the lab and launching the malaria work. Last we heard, she was living in Santa Barbara.
Edith Wong earned her PhD from UC Davis and joined the DeRisi Lab soon afterward to work on malaria. She worked on CGH methods for comparing falciparum genomes on arrays. She is now employed at:The Saccharomyces cerevisiae Genome Database
Dara Friedman graduated from Ron Vale's laboratory here at Stanford and became the DeRisi Lab's first ever postdoc. She worked on methods to isolate membrane associated polysomes in malaria. Dara went on to work at the CDC, and then to the equivalent organization in Canada.
George Ngondi completed a certificate program in the DeRisi Lab working on metagenomics and human disease.
He is currently an assistant professor at -- University, Kenya.