Joseph DeRisi

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc An enhanced single base extension technique for the analysis of complex viral populations
    Dale R Webster
    Biological and Medical Informatics Program, University of California San Francisco, San Francisco, California, United States of America
    PLoS ONE 4:e7453. 2009
  2. pmc Identification and manipulation of the molecular determinants influencing poliovirus recombination
    Charles Runckel
    Howard Hughes Medical Institute, Bethesda, Maryland, United States of America
    PLoS Pathog 9:e1003164. 2013
  3. pmc Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains
    Manuel Llinas
    Department of Molecular Biology, Lewis Sigler Institute for Integrative Genomics, Princeton University, 246 Carl Icahn Laboratory, Princeton, NJ 08544, USA
    Nucleic Acids Res 34:1166-73. 2006
  4. pmc Splenic red pulp macrophages produce type I interferons as early sentinels of malaria infection but are dispensable for control
    Charles C Kim
    Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
    PLoS ONE 7:e48126. 2012
  5. pmc ACBD3 interaction with TBC1 domain 22 protein is differentially affected by enteroviral and kobuviral 3A protein binding
    Alexander L Greninger
    Howard Hughes Medical Institute, San Francisco, California, USA
    MBio 4:e00098-13. 2013
  6. pmc HMMSplicer: a tool for efficient and sensitive discovery of known and novel splice junctions in RNA-Seq data
    Michelle T Dimon
    Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
    PLoS ONE 5:e13875. 2010
  7. pmc RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts
    Katherine Sorber
    Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
    Nucleic Acids Res 39:3820-35. 2011
  8. pmc Transcriptome sequencing demonstrates that human papillomavirus is not active in cutaneous squamous cell carcinoma
    Sarah T Arron
    Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA
    J Invest Dermatol 131:1745-53. 2011
  9. pmc Temporal analysis of the honey bee microbiome reveals four novel viruses and seasonal prevalence of known viruses, Nosema, and Crithidia
    Charles Runckel
    Howard Hughes Medical Institute, Bethesda, Maryland, United State of America
    PLoS ONE 6:e20656. 2011
  10. pmc Virus identification in unknown tropical febrile illness cases using deep sequencing
    Nathan L Yozwiak
    Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, United States of America
    PLoS Negl Trop Dis 6:e1485. 2012

Research Grants

Collaborators

Detail Information

Publications35

  1. pmc An enhanced single base extension technique for the analysis of complex viral populations
    Dale R Webster
    Biological and Medical Informatics Program, University of California San Francisco, San Francisco, California, United States of America
    PLoS ONE 4:e7453. 2009
    ....
  2. pmc Identification and manipulation of the molecular determinants influencing poliovirus recombination
    Charles Runckel
    Howard Hughes Medical Institute, Bethesda, Maryland, United States of America
    PLoS Pathog 9:e1003164. 2013
    ..Our results imply that modification of these motifs could be extended to whole genome re-designs for the development of recombination-deficient, genetically stable live vaccine strains...
  3. pmc Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains
    Manuel Llinas
    Department of Molecular Biology, Lewis Sigler Institute for Integrative Genomics, Princeton University, 246 Carl Icahn Laboratory, Princeton, NJ 08544, USA
    Nucleic Acids Res 34:1166-73. 2006
    ..The majority of these genes are uncharacterized and have no homology to other species. These tractable transcriptional differences provide important phenotypes for these otherwise highly related strains of Plasmodium...
  4. pmc Splenic red pulp macrophages produce type I interferons as early sentinels of malaria infection but are dispensable for control
    Charles C Kim
    Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
    PLoS ONE 7:e48126. 2012
    ..Our results reveal that RPMs are early sentinels of malaria infection, but that effector mechanisms previously attributed to RPMs are not essential for control...
  5. pmc ACBD3 interaction with TBC1 domain 22 protein is differentially affected by enteroviral and kobuviral 3A protein binding
    Alexander L Greninger
    Howard Hughes Medical Institute, San Francisco, California, USA
    MBio 4:e00098-13. 2013
    ..These data reinforce the notion that ACBD3 organizes numerous cellular functionalities and that RNA virus replication proteins likely modulate these interactions by more than one mechanism...
  6. pmc HMMSplicer: a tool for efficient and sensitive discovery of known and novel splice junctions in RNA-Seq data
    Michelle T Dimon
    Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
    PLoS ONE 5:e13875. 2010
    ..However, transcriptome sequencing creates a new class of alignment problem: mapping short reads that span exon-exon junctions back to the reference genome, especially in the case where a splice junction is previously unknown...
  7. pmc RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts
    Katherine Sorber
    Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
    Nucleic Acids Res 39:3820-35. 2011
    ..Thus, this largest assemblage of new and alternative splicing events to date in Plasmodium falciparum provides a more precise, dynamic view of the parasite's transcriptome...
  8. pmc Transcriptome sequencing demonstrates that human papillomavirus is not active in cutaneous squamous cell carcinoma
    Sarah T Arron
    Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA
    J Invest Dermatol 131:1745-53. 2011
    ..In contrast, HPV16 and HPV18 mRNA transcripts were readily identified in primary cervical and periungual cancers and HeLa cells. These data demonstrate that papillomavirus mRNA expression is not a factor in the maintenance of cuSCCs...
  9. pmc Temporal analysis of the honey bee microbiome reveals four novel viruses and seasonal prevalence of known viruses, Nosema, and Crithidia
    Charles Runckel
    Howard Hughes Medical Institute, Bethesda, Maryland, United State of America
    PLoS ONE 6:e20656. 2011
    ..Peak infection of common honey bee viruses and Nosema occurred in the summer, whereas levels of the trypanosomatid Crithidia mellificae and Lake Sinai virus 2, a novel virus, peaked in January...
  10. pmc Virus identification in unknown tropical febrile illness cases using deep sequencing
    Nathan L Yozwiak
    Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, United States of America
    PLoS Negl Trop Dis 6:e1485. 2012
    ..These results demonstrate the utility of unbiased metagenomic approaches in the detection of known and divergent viruses in the study of tropical febrile illness...
  11. pmc The long march: a sample preparation technique that enhances contig length and coverage by high-throughput short-read sequencing
    Katherine Sorber
    Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
    PLoS ONE 3:e3495. 2008
    ..We also offer a theoretical optimization of the long march for de novo sequence assembly...
  12. pmc Complete genome sequence of an astrovirus identified in a domestic rabbit (Oryctolagus cuniculus) with gastroenteritis
    Mark D Stenglein
    Department of Medicine, University of California San Francisco, San Francisco, CA, USA
    Virol J 9:216. 2012
    ..This study therefore defines a viral species and a potential rabbit pathogen...
  13. pmc The 3A protein from multiple picornaviruses utilizes the golgi adaptor protein ACBD3 to recruit PI4KIII╬▓
    Alexander L Greninger
    Howard Hughes Medical Institute and the Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California, USA
    J Virol 86:3605-16. 2012
    ....
  14. pmc Plate-based transfection and culturing technique for genetic manipulation of Plasmodium falciparum
    Florence Caro
    Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
    Malar J 11:22. 2012
    ..The methods and tools presented here will facilitate genome-scale genetic manipulation of P. falciparum...
  15. pmc Experimental induction of proventricular dilatation disease in cockatiels (Nymphicus hollandicus) inoculated with brain homogenates containing avian bornavirus 4
    Ady Y Gancz
    The Exotic Clinic, Herzlyia, Israel
    Virol J 6:100. 2009
    ..However, it remains unclear whether ABV infection actually causes PDD. To address this question, we examined the impact of ABV inoculation on the cockatiel (Nymphicus hollandicus)...
  16. pmc Genome-wide diversity and selective pressure in the human rhinovirus
    Amy L Kistler
    Department of Microbiology and Immunology, University of California, San Francisco, California, USA
    Virol J 4:40. 2007
    ..Previous comparative genome sequence analyses indicate that recombination drives diversification in multiple genera of the picornavirus family, yet it remains unclear if this holds for HRV...
  17. pmc Recovery of divergent avian bornaviruses from cases of proventricular dilatation disease: identification of a candidate etiologic agent
    Amy L Kistler
    Departments of Biochemistry, Microbiology and Medicine, Howard Hughes Medical Institute, University of California, San Francisco, 94143, USA
    Virol J 5:88. 2008
    ..For almost 40 years, a viral etiology for PDD has been suspected, but to date no candidate etiologic agent has been reproducibly linked to the disease...
  18. pmc The complete genome of klassevirus - a novel picornavirus in pediatric stool
    Alexander L Greninger
    Howard Hughes Medical Institute, Departments of Medicine, Biochemistry, and Microbiology, University of California, San Francisco, California 94143, USA
    Virol J 6:82. 2009
    ..Modern technologies, especially deep sequencing, allow rapid, high-throughput screening of clinical samples such as stool for new infectious agents associated with human disease...
  19. pmc Viral discovery and sequence recovery using DNA microarrays
    David Wang
    Department of Biochemistry and Biophysics, University of California San Francisco, USA
    PLoS Biol 1:E2. 2003
    ..This combination of array hybridization followed by direct viral sequence recovery should prove to be a general strategy for the rapid identification and characterization of novel viruses and emerging infectious disease...
  20. pmc The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum
    Zbynek Bozdech
    Department of Biochemistry and Biophysics, University of California, San Francisco, USA
    PLoS Biol 1:E5. 2003
    ..falciparum and provide a resource for the identification of new chemotherapeutic and vaccine candidates...
  21. pmc Improved methods for magnetic purification of malaria parasites and haemozoin
    Charles C Kim
    Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
    Malar J 9:17. 2010
    ..As these methods are not necessarily optimized for parasite purification, the relationship between magnetic field strength and the quantity and quality of yield during parasite purification was explored...
  22. pmc Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray
    Zbynek Bozdech
    Department of Biochemistry and Biophysics, University of California San Francisco, 513 Parnassus Ave, San Francisco, CA 94143 0448, USA
    Genome Biol 4:R9. 2003
    ..The P. falciparum sequencing project has brought new opportunities for identifying molecular targets for antimalarial drug and vaccine development...
  23. pmc Whole-genome analysis of mRNA decay in Plasmodium falciparum reveals a global lengthening of mRNA half-life during the intra-erythrocytic development cycle
    Jennifer L Shock
    Department of Biochemistry and Biophysics, University of California San Francisco, 1700 4th Street, San Francisco, California 94158 2330, USA
    Genome Biol 8:R134. 2007
    ..Previously, studies in several organisms found that the specific half-life of each mRNA is precisely related to its physiologic role, and plays an important role in determining levels of gene expression...
  24. pmc Genome-scale approaches for discovering novel nonconventional splicing substrates of the Ire1 nuclease
    Maho Niwa
    Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94143 2200, USA
    Genome Biol 6:R3. 2005
    ..Because only the spliced mRNA is translated, splicing is the key regulatory step of the UPR...
  25. pmc E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns
    Anatoly Urisman
    Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94143, USA
    Genome Biol 6:R78. 2005
    ..We demonstrate the application of the algorithm to viral detection in a set of clinical samples and discuss its relevance to other metagenomic applications...
  26. pmc VersaCount: customizable manual tally software for cell counting
    Charles C Kim
    Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
    Source Code Biol Med 5:1. 2010
    ..Traditionally, hand tally counters have been used to track event counts. Although this method is adequate, there are a number of inefficiencies which arise when managing large numbers of samples or large sample sizes...
  27. pmc Viral infection in acute exacerbation of idiopathic pulmonary fibrosis
    Sharon Chao Wootton
    UC San Francisco UC Berkeley Joint Graduate Group in Bioengineering, University of California, Berkeley, California, USA
    Am J Respir Crit Care Med 183:1698-702. 2011
    ..An acute exacerbation of idiopathic pulmonary fibrosis is an episode of acute respiratory worsening without an identifiable etiology. Occult viral infection has been proposed as a possible cause of acute exacerbation...
  28. pmc A new threat to honey bees, the parasitic phorid fly Apocephalus borealis
    Andrew Core
    Department of Biology, San Francisco State University, San Francisco, California, United States of America
    PLoS ONE 7:e29639. 2012
    ..Understanding details of phorid infection may shed light on similar hive abandonment behaviors seen in CCD...
  29. pmc Gene expression patterns during adaptation of a helminth parasite to different environmental niches
    Emmitt R Jolly
    California Institute for Quantitative Biomedical Research QB3 of the University of California, San Francisco, San Francisco, CA 94158 USA
    Genome Biol 8:R65. 2007
    ..We report a global transcriptional analysis of how this parasite alters gene regulation to adapt to three distinct environments...
  30. ncbi request reprint A role for the protease falcipain 1 in host cell invasion by the human malaria parasite
    Doron C Greenbaum
    Department of Pharmaceutical Chemistry, Veterans Affairs Medical Center, University of California, San Francisco, CA 94143, USA
    Science 298:2002-6. 2002
    ..These results demonstrate a specific role for falcipain 1 in host cell invasion and establish a potential new target for antimalarial therapeutics...
  31. ncbi request reprint Modulation of host gene expression by the constitutively active G protein-coupled receptor of Kaposi's sarcoma-associated herpesvirus
    Andrew G Polson
    Department of Microbiology and Immunology, University of California, San Francisco, California 94143 0414, USA
    Cancer Res 62:4525-30. 2002
    ....
  32. ncbi request reprint Achalasia and viral infection: new insights from veterinary medicine
    Don Ganem
    Department of Medicine, University of California, San Francisco, CA 94143, USA
    Sci Transl Med 2:33ps24. 2010
    ..These findings demonstrate that viruses can induce achalasia-like pathophysiology and have renewed interest in the search for infectious agents in this enigmatic human disease...
  33. pmc A draft genome of the honey bee trypanosomatid parasite Crithidia mellificae
    Charles Runckel
    Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
    PLoS ONE 9:e95057. 2014
    ..This draft genome will facilitate additional investigations of the impact of C. mellificae infection on honey bee health and provide insight into the evolution of this unique family. ..
  34. pmc Fzf1p regulates an inducible response to nitrosative stress in Saccharomyces cerevisiae
    Aaron Sarver
    Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
    Mol Biol Cell 16:4781-91. 2005
    ..Our results suggest that the presence of *NO or *NO derivatives activates Fzf1p leading to transcriptional induction of a discrete set of target genes that function to protect the cell from *NO-mediated stress...

Research Grants2

  1. Novel Anti-Malarials by Combinatorial Pharmacogenomics
    Joseph DeRisi; Fiscal Year: 2006
    ..The work will be accomplished by the cooperation of of two academic labs, Kip Guy and Joseph DeRisi, and two industrial partners, GenoSpectra, Inc., and Stanford Research Institute (SRI), Inc...