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    Joe Derisi, PhD

    TitleProfessor
    SchoolUCSF School of Medicine
    DepartmentBiochemistry and Biophysics
    Address1700 4th Street
    San Francisco CA 94158
    Phone415-418-3059
      Other Positions
      TitleHoward Hughes Investigator


       Overview 
       Overview
      Our lab exploits whole genome approaches to tackle problems in yeast molecular biology and human infectious disease. These projects can be classified into three separate areas:

      Functional genomics of Plasmodium falciparum, the causative agent of human malaria.
      Malaria is one of the most deadly and profound human health problems in existence and results in approximately 1.5 to 2.7 million deaths annually. The most fatal and prevalent form of malaria is caused by the blood-borne pathogen Plasmodium falciparum. Beyond the lives this parasite claims every year, hundreds of millions of people will become clinically ill. The socioeconomic impact of this disease to developing countries, especially those on the African continent, is beyond measure. There exist no vaccines with an operational impact and resistance of the parasite to current anti-malarial drugs has spread worldwide. Because the vast majority of malaria occurs in poor nations, there is little profit incentive for large western and European drug companies to pursue new anti-malarial therapies, yet novel approaches are in desperate need

      The paucity of new anti-malarial medications is partly attributable to the lack of validated drug targets. Indeed, all currently approved drugs and those in development are directed against only a handful of gene products and processes. Unlike many bacterial pathogens, both genetic and molecular biological approaches have been difficult in Plasmodia. Fortunately, the completion of the Plasmodium falciparum sequencing project will inherently broaden the range of potential drug targets by identifying all possible open reading frames. Although a great deal of functional annotation may be accomplished by sequence based homology comparisons, this information will not be sufficient to determine whether a gene product actually participates in a function or process at any given time during the development of the parasite. In addition, the majority of gene products discovered through the sequencing of the genome will not reveal significant sequence homology and therefore will remain hypothetical and uncharacterized. We are utilizing the full potential of the completed sequence by implementing a functional genomics approach to the elucidation of metabolic and stage specific gene expression. This is being accomplished by systematic perturbation of P. falciparum cultures in conjunction with genome wide gene expression profiling, exhaustive homology based sequence comparison, pathway analysis, and functional characterization.

      Whole genome approaches to the molecular biology of Saccharomyces cerevisiae
      We are using DNA microarrays to investigate several different aspects of yeast biology. These include chromatin immunoprecipitation techniques to reconstruct the protein-DNA topology of the genome, gene expression profiles to investigate the action of small molecule drugs, and immunoprecipitation of RNA binding proteins to screen for novel regulatory mechanisms. Other yeast-based projects in the lab seek to elucidate the mechanisms responsible for the various steps of meiotic recombination through genetics and biochemistry.

      Searching for a link between asthma and viral infection.
      The notion that acute asthma attacks are frequently precipitated by respiratory infection is part of the training of every physician and is well supported in general terms by numerous clinical investigations. However, the prevalence of respiratory infection in acute asthma and the identities of the responsible pathogen(s) have been more controversial. Studies based upon culture and/or viral antigen detection in respiratory secretions of asthmatics have generally recorded rates of infection between 20-40%; these studies typically identify rhinoviruses, coronaviruses, adenoviruses, influenza and parainfluenza viruses. This is likely to be an underestimate and likely define a minimal estimate of the contribution of viral infection to acute asthma attacks.

      We are constructing and using a viral DNA microarray based system customized for the goal of detecting and differentiating between pathogens commonly found in the respiratory tract. This technology will allow us to investigate whether there is a positive correlation between viral infection and asthma attacks, if so, which viral types are so associated. To accomplish this goal, we are actively collaborating with an on-going clinical research study of asthma here at UCSF.


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       Bibliographic 
       Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
      List All   |   Timeline
      1. Stenglein MD, Leavitt EB, Abramovitch MA, McGuire JA, DeRisi JL. Genome Sequence of a Bornavirus Recovered from an African Garter Snake (Elapsoidea loveridgei). Genome Announc. 2014; 2(5).
        View in: PubMed
      2. Stenglein MD, Jacobson ER, Wozniak EJ, Wellehan JF, Kincaid A, Gordon M, Porter BF, Baumgartner W, Stahl S, Kelley K, Towner JS, DeRisi JL. Ball Python Nidovirus: a Candidate Etiologic Agent for Severe Respiratory Disease in Python regius. MBio. 2014; 5(5).
        View in: PubMed
      3. Skewes-Cox P, Sharpton TJ, Pollard KS, DeRisi JL. Profile Hidden Markov Models for the Detection of Viruses within Metagenomic Sequence Data. PLoS One. 2014; 9(8):e105067.
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      4. Skewes-Cox P, Sharpton TJ, Pollard KS, DeRisi JL. Profile Hidden Markov Models for the Detection of Viruses within Metagenomic Sequence Data. PLoS One. 2014; 9(8):e105067.
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      5. Wilson MR, Naccache SN, Samayoa E, Biagtan M, Bashir H, Yu G, Salamat SM, Somasekar S, Federman S, Miller S, Sokolic R, Garabedian E, Candotti F, Buckley RH, Reed KD, Meyer TL, Seroogy CM, Galloway R, Henderson SL, Gern JE, DeRisi JL, Chiu CY. Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing. N Engl J Med. 2014 Jun 4.
        View in: PubMed
      6. Naccache SN, Federman S, Veeeraraghavan N, Zaharia M, Lee D, Samayoa E, Bouquet J, Greninger AL, Luk KC, Enge B, Wadford DA, Messenger SL, Genrich GL, Pellegrino K, Grard G, Leroy E, Schneider BS, Fair JN, Martínez MA, Isa P, Crump JA, DeRisi JL, Sittler T, Hackett J, Miller S, Chiu CY. A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Genome Res. 2014 Jun 4.
        View in: PubMed
      7. Pérez JC, Fordyce PM, Lohse MB, Hanson-Smith V, DeRisi JL, Johnson AD. How duplicated transcription regulators can diversify to govern the expression of nonoverlapping sets of genes. Genes Dev. 2014 Jun 15; 28(12):1272-7.
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      8. Slabodnick MM, Ruby JG, Dunn JG, Feldman JL, DeRisi JL, Marshall WF. The kinase regulator mob1 acts as a patterning protein for stentor morphogenesis. PLoS Biol. 2014 May; 12(5):e1001861.
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      9. Parrish JZ, Kim CC, Tang L, Bergquist S, Wang T, Derisi JL, Jan LY, Jan YN, Davis GW. Krüppel mediates the selective rebalancing of ion channel expression. Neuron. 2014 May 7; 82(3):537-44.
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      10. Runckel C, Derisi J, Flenniken ML. A Draft Genome of the Honey Bee Trypanosomatid Parasite Crithidia mellificae. PLoS One. 2014; 9(4):e95057.
        View in: PubMed
      11. Szentiks CA, Tsangaras K, Abendroth B, Scheuch M, Stenglein MD, Wohlsein P, Heeger F, Höveler R, Chen W, Sun W, Damiani A, Nikolin V, Gruber AD, Grobbel M, Kalthoff D, Höper D, Czirják GÁ, Derisi J, Mazzoni CJ, Schüle A, Aue A, East ML, Hofer H, Beer M, Osterrieder N, Greenwood AD. Polar Bear Encephalitis: Establishment of a Comprehensive Next-generation Pathogen Analysis Pipeline for Captive and Free-living Wildlife. J Comp Pathol. 2014 May; 150(4):474-88.
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      12. Koellhoffer JF, Dai Z, Malashkevich VN, Stenglein MD, Liu Y, Toro R, S Harrison J, Chandran K, Derisi JL, Almo SC, Lai JR. Structural Characterization of the Glycoprotein GP2 Core Domain from the CAS Virus, a Novel Arenavirus-Like Species. J Mol Biol. 2014 Apr 3; 426(7):1452-68.
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      13. Hernday AD, Lohse MB, Fordyce PM, Nobile CJ, DeRisi JL, Johnson AD. Structure of the transcriptional network controlling white-opaque switching in Candida albicans. Mol Microbiol. 2013 Oct; 90(1):22-35.
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      14. Guler JL, Freeman DL, Ahyong V, Patrapuvich R, White J, Gujjar R, Phillips MA, DeRisi J, Rathod PK. Asexual populations of the human malaria parasite, Plasmodium falciparum, use a two-step genomic strategy to acquire accurate, beneficial DNA amplifications. PLoS Pathog. 2013; 9(5):e1003375.
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      15. Ruby JG, Bellare P, Derisi JL. PRICE: software for the targeted assembly of components of (Meta) genomic sequence data. G3 (Bethesda). 2013 May; 3(5):865-80.
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      16. Nelson CS, Fuller CK, Fordyce PM, Greninger AL, Li H, DeRisi JL. Microfluidic affinity and ChIP-seq analyses converge on a conserved FOXP2-binding motif in chimp and human, which enables the detection of evolutionarily novel targets. Nucleic Acids Res. 2013 Jul; 41(12):5991-6004.
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      17. Lohse MB, Hernday AD, Fordyce PM, Noiman L, Sorrells TR, Hanson-Smith V, Nobile CJ, DeRisi JL, Johnson AD. Identification and characterization of a previously undescribed family of sequence-specific DNA-binding domains. Proc Natl Acad Sci U S A. 2013 May 7; 110(19):7660-5.
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      18. Greninger AL, Knudsen GM, Betegon M, Burlingame AL, DeRisi JL. ACBD3 interaction with TBC1 domain 22 protein is differentially affected by enteroviral and kobuviral 3A protein binding. MBio. 2013; 4(2):e00098-13.
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      19. Abromaitis S, Nelson CS, Previte D, Yoon KS, Clark JM, DeRisi JL, Koehler JE. Bartonella quintana deploys host and vector temperature-specific transcriptomes. PLoS One. 2013; 8(3):e58773.
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      20. Runckel C, Westesson O, Andino R, DeRisi JL. Identification and manipulation of the molecular determinants influencing poliovirus recombination. PLoS Pathog. 2013 Feb; 9(2):e1003164.
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      21. Melters DP, Bradnam KR, Young HA, Telis N, May MR, Ruby JG, Sebra R, Peluso P, Eid J, Rank D, Garcia JF, DeRisi JL, Smith T, Tobias C, Ross-Ibarra J, Korf I, Chan SW. Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. Genome Biol. 2013; 14(1):R10.
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      22. Vale RD, DeRisi J, Phillips R, Mullins RD, Waterman C, Mitchison TJ. Graduate education. Interdisciplinary graduate training in teaching labs. Science. 2012 Dec 21; 338(6114):1542-3.
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      23. Gerver RE, Gómez-Sjöberg R, Baxter BC, Thorn KS, Fordyce PM, Diaz-Botia CA, Helms BA, DeRisi JL. Programmable microfluidic synthesis of spectrally encoded microspheres. Lab Chip. 2012 Nov 21; 12(22):4716-23.
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      24. Yu G, Greninger AL, Isa P, Phan TG, Martínez MA, de la Luz Sanchez M, Contreras JF, Santos-Preciado JI, Parsonnet J, Miller S, DeRisi JL, Delwart E, Arias CF, Chiu CY. Discovery of a novel polyomavirus in acute diarrheal samples from children. PLoS One. 2012; 7(11):e49449.
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      25. Fordyce PM, Diaz-Botia CA, DeRisi JL, Gomez-Sjoberg R. Systematic characterization of feature dimensions and closing pressures for microfluidic valves produced via photoresist reflow. Lab Chip. 2012 Nov 7; 12(21):4287-95.
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      26. Kim CC, Nelson CS, Wilson EB, Hou B, DeFranco AL, DeRisi JL. Splenic red pulp macrophages produce type I interferons as early sentinels of malaria infection but are dispensable for control. PLoS One. 2012; 7(10):e48126.
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      27. Holmes TC, May AE, Zaleta-Rivera K, Ruby JG, Skewes-Cox P, Fischbach MA, DeRisi JL, Iwatsuki M, Omura S, Khosla C. Molecular insights into the biosynthesis of guadinomine: a type III secretion system inhibitor. J Am Chem Soc. 2012 Oct 24; 134(42):17797-806.
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      28. Fordyce PM, Pincus D, Kimmig P, Nelson CS, El-Samad H, Walter P, DeRisi JL. Basic leucine zipper transcription factor Hac1 binds DNA in two distinct modes as revealed by microfluidic analyses. Proc Natl Acad Sci U S A. 2012 Nov 6; 109(45):E3084-93.
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      29. O'Donoghue AJ, Eroy-Reveles AA, Knudsen GM, Ingram J, Zhou M, Statnekov JB, Greninger AL, Hostetter DR, Qu G, Maltby DA, Anderson MO, Derisi JL, McKerrow JH, Burlingame AL, Craik CS. Global identification of peptidase specificity by multiplex substrate profiling. Nat Methods. 2012 Nov; 9(11):1095-100.
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      30. Stenglein MD, Velazquez E, Greenacre C, Wilkes RP, Ruby JG, Lankton JS, Ganem D, Kennedy MA, DeRisi JL. Complete genome sequence of an astrovirus identified in a domestic rabbit (Oryctolagus cuniculus) with gastroenteritis. Virol J. 2012; 9:216.
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      31. Lee D, Das Gupta J, Gaughan C, Steffen I, Tang N, Luk KC, Qiu X, Urisman A, Fischer N, Molinaro R, Broz M, Schochetman G, Klein EA, Ganem D, Derisi JL, Simmons G, Hackett J, Silverman RH, Chiu CY. In-depth investigation of archival and prospectively collected samples reveals no evidence for XMRV infection in prostate cancer. PLoS One. 2012; 7(9):e44954.
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      32. Stenglein MD, Sanders C, Kistler AL, Ruby JG, Franco JY, Reavill DR, Dunker F, Derisi JL. Identification, characterization, and in vitro culture of highly divergent arenaviruses from boa constrictors and annulated tree boas: candidate etiological agents for snake inclusion body disease. MBio. 2012; 3(4):e00180-12.
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      33. Lowes D, Pradhan A, Iyer LV, Parman T, Gow J, Zhu F, Furimsky A, Lemoff A, Guiguemde WA, Sigal M, Clark JA, Wilson E, Tang L, Connelly MC, Derisi JL, Kyle DE, Mirsalis J, Guy RK. Lead optimization of antimalarial propafenone analogues. J Med Chem. 2012 Jul 12; 55(13):6087-93.
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      34. Yozwiak NL, Skewes-Cox P, Stenglein MD, Balmaseda A, Harris E, DeRisi JL. Virus identification in unknown tropical febrile illness cases using deep sequencing. PLoS Negl Trop Dis. 2012; 6(2):e1485.
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      35. Caro F, Miller MG, DeRisi JL. Plate-based transfection and culturing technique for genetic manipulation of Plasmodium falciparum. Malar J. 2012; 11:22.
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      36. Greninger AL, Knudsen GM, Betegon M, Burlingame AL, Derisi JL. The 3A protein from multiple picornaviruses utilizes the golgi adaptor protein ACBD3 to recruit PI4KIIIß. J Virol. 2012 Apr; 86(7):3605-16.
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      37. Core A, Runckel C, Ivers J, Quock C, Siapno T, Denault S, Brown B, Derisi J, Smith CD, Hafernik J. A new threat to honey bees, the parasitic phorid fly Apocephalus borealis. PLoS One. 2012; 7(1):e29639.
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      38. Anderson CM, Chen SY, Dimon MT, Oke A, DeRisi JL, Fung JC. ReCombine: a suite of programs for detection and analysis of meiotic recombination in whole-genome datasets. PLoS One. 2011; 6(10):e25509.
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      39. Lowes DJ, Guiguemde WA, Connelly MC, Zhu F, Sigal MS, Clark JA, Lemoff AS, Derisi JL, Wilson EB, Guy RK. Optimization of propafenone analogues as antimalarial leads. J Med Chem. 2011 Nov 10; 54(21):7477-85.
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      40. Hwang JY, Kawasuji T, Lowes DJ, Clark JA, Connelly MC, Zhu F, Guiguemde WA, Sigal MS, Wilson EB, Derisi JL, Guy RK. Synthesis and evaluation of 7-substituted 4-aminoquinoline analogues for antimalarial activity. J Med Chem. 2011 Oct 27; 54(20):7084-93.
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      41. Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol I, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res. 2011 Dec; 21(12):2224-41.
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      42. Yeh E, DeRisi JL. Chemical rescue of malaria parasites lacking an apicoplast defines organelle function in blood-stage Plasmodium falciparum. PLoS Biol. 2011 Aug; 9(8):e1001138.
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      43. Runckel C, Flenniken ML, Engel JC, Ruby JG, Ganem D, Andino R, DeRisi JL. Temporal analysis of the honey bee microbiome reveals four novel viruses and seasonal prevalence of known viruses, Nosema, and Crithidia. PLoS One. 2011; 6(6):e20656.
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      44. Arron ST, Skewes-Cox P, Do PH, Dybbro E, Da Costa M, Palefsky JM, Derisi JL. Validation of a diagnostic microarray for human papillomavirus: coverage of 102 genotypes. J Nucleic Acids. 2011; 2011:756905.
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      45. Chen EC, Miller SA, DeRisi JL, Chiu CY. Using a pan-viral microarray assay (Virochip) to screen clinical samples for viral pathogens. J Vis Exp. 2011; (50).
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      46. Arron ST, Ruby JG, Dybbro E, Ganem D, Derisi JL. Transcriptome sequencing demonstrates that human papillomavirus is not active in cutaneous squamous cell carcinoma. J Invest Dermatol. 2011 Aug; 131(8):1745-53.
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      47. Wootton SC, Kim DS, Kondoh Y, Chen E, Lee JS, Song JW, Huh JW, Taniguchi H, Chiu C, Boushey H, Lancaster LH, Wolters PJ, DeRisi J, Ganem D, Collard HR. Viral infection in acute exacerbation of idiopathic pulmonary fibrosis. Am J Respir Crit Care Med. 2011 Jun 15; 183(12):1698-702.
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      48. Sun JC, Lopez-Verges S, Kim CC, DeRisi JL, Lanier LL. NK cells and immune "memory". J Immunol. 2011 Feb 15; 186(4):1891-7.
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      49. Sorber K, Dimon MT, DeRisi JL. RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts. Nucleic Acids Res. 2011 May; 39(9):3820-35.
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      50. Dimon MT, Sorber K, DeRisi JL. HMMSplicer: a tool for efficient and sensitive discovery of known and novel splice junctions in RNA-Seq data. PLoS One. 2010; 5(11):e13875.
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      51. Fordyce PM, Gerber D, Tran D, Zheng J, Li H, DeRisi JL, Quake SR. De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis. Nat Biotechnol. 2010 Sep; 28(9):970-5.
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      52. Greninger AL, Holtz L, Kang G, Ganem D, Wang D, DeRisi JL. Serological evidence of human klassevirus infection. Clin Vaccine Immunol. 2010 Oct; 17(10):1584-8.
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      53. Raghav R, Taylor M, Delay J, Ojkic D, Pearl DL, Kistler AL, Derisi JL, Ganem D, Smith DA. Avian bornavirus is present in many tissues of psittacine birds with histopathologic evidence of proventricular dilatation disease. J Vet Diagn Invest. 2010 Jul; 22(4):495-508.
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      54. Yozwiak NL, Skewes-Cox P, Gordon A, Saborio S, Kuan G, Balmaseda A, Ganem D, Harris E, DeRisi JL. Human enterovirus 109: a novel interspecies recombinant enterovirus isolated from a case of acute pediatric respiratory illness in Nicaragua. J Virol. 2010 Sep; 84(18):9047-58.
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      55. Ganem D, Kistler A, DeRisi J. Achalasia and viral infection: new insights from veterinary medicine. Sci Transl Med. 2010 May 26; 2(33):33ps24.
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      56. Guiguemde WA, Shelat AA, Bouck D, Duffy S, Crowther GJ, Davis PH, Smithson DC, Connelly M, Clark J, Zhu F, Jiménez-Díaz MB, Martinez MS, Wilson EB, Tripathi AK, Gut J, Sharlow ER, Bathurst I, El Mazouni F, Fowble JW, Forquer I, McGinley PL, Castro S, Angulo-Barturen I, Ferrer S, Rosenthal PJ, Derisi JL, Sullivan DJ, Lazo JS, Roos DS, Riscoe MK, Phillips MA, Rathod PK, Van Voorhis WC, Avery VM, Guy RK. Chemical genetics of Plasmodium falciparum. Nature. 2010 May 20; 465(7296):311-5.
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      57. Ray S, Madrid PB, Catz P, LeValley SE, Furniss MJ, Rausch LL, Guy RK, DeRisi JL, Iyer LV, Green CE, Mirsalis JC. Development of a new generation of 4-aminoquinoline antimalarial compounds using predictive pharmacokinetic and toxicology models. J Med Chem. 2010 May 13; 53(9):3685-95.
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      58. Mattiazzi M, Jambhekar A, Kaferle P, Derisi JL, Krizaj I, Petrovic U. Genetic interactions between a phospholipase A2 and the Rim101 pathway components in S. cerevisiae reveal a role for this pathway in response to changes in membrane composition and shape. Mol Genet Genomics. 2010 Jun; 283(6):519-30.
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      59. Chiu CY, Greninger AL, Chen EC, Haggerty TD, Parsonnet J, Delwart E, Derisi JL, Ganem D. Cultivation and serological characterization of a human Theiler's-like cardiovirus associated with diarrheal disease. J Virol. 2010 May; 84(9):4407-14.
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      60. Kim CC, Wilson EB, DeRisi JL. Improved methods for magnetic purification of malaria parasites and haemozoin. Malar J. 2010; 9:17.
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      61. Kim CC, Derisi JL. VersaCount: customizable manual tally software for cell counting. Source Code Biol Med. 2010; 5(1):1.
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      62. Kistler AL, Smith JM, Greninger AL, Derisi JL, Ganem D. Analysis of naturally occurring avian bornavirus infection and transmission during an outbreak of proventricular dilatation disease among captive psittacine birds. J Virol. 2010 Feb; 84(4):2176-9.
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      63. Webster DR, Hekele AG, Lauring AS, Fischer KF, Li H, Andino R, DeRisi JL. An enhanced single base extension technique for the analysis of complex viral populations. PLoS One. 2009; 4(10):e7453.
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      64. Niles JC, Derisi JL, Marletta MA. Inhibiting Plasmodium falciparum growth and heme detoxification pathway using heme-binding DNA aptamers. Proc Natl Acad Sci U S A. 2009 Aug 11; 106(32):13266-71.
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      65. Arico-Muendel C, Centrella PA, Contonio BD, Morgan BA, O'Donovan G, Paradise CL, Skinner SR, Sluboski B, Svendsen JL, White KF, Debnath A, Gut J, Wilson N, McKerrow JH, DeRisi JL, Rosenthal PJ, Chiang PK. Antiparasitic activities of novel, orally available fumagillin analogs. Bioorg Med Chem Lett. 2009 Sep 1; 19(17):5128-31.
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      66. Gancz AY, Kistler AL, Greninger AL, Farnoushi Y, Mechani S, Perl S, Berkowitz A, Perez N, Clubb S, DeRisi JL, Ganem D, Lublin A. Experimental induction of proventricular dilatation disease in cockatiels (Nymphicus hollandicus) inoculated with brain homogenates containing avian bornavirus 4. Virol J. 2009; 6:100.
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      67. Greninger AL, Runckel C, Chiu CY, Haggerty T, Parsonnet J, Ganem D, DeRisi JL. The complete genome of klassevirus - a novel picornavirus in pediatric stool. Virol J. 2009; 6:82.
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      68. Sorber K, Chiu C, Webster D, Dimon M, Ruby JG, Hekele A, DeRisi JL. The long march: a sample preparation technique that enhances contig length and coverage by high-throughput short-read sequencing. PLoS One. 2008; 3(10):e3495.
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      69. Kim CC, Parikh S, Sun JC, Myrick A, Lanier LL, Rosenthal PJ, DeRisi JL. Experimental malaria infection triggers early expansion of natural killer cells. Infect Immun. 2008 Dec; 76(12):5873-82.
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      70. Chiu CY, Greninger AL, Kanada K, Kwok T, Fischer KF, Runckel C, Louie JK, Glaser CA, Yagi S, Schnurr DP, Haggerty TD, Parsonnet J, Ganem D, DeRisi JL. Identification of cardioviruses related to Theiler's murine encephalomyelitis virus in human infections. Proc Natl Acad Sci U S A. 2008 Sep 16; 105(37):14124-9.
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      71. Kistler AL, Gancz A, Clubb S, Skewes-Cox P, Fischer K, Sorber K, Chiu CY, Lublin A, Mechani S, Farnoushi Y, Greninger A, Wen CC, Karlene SB, Ganem D, DeRisi JL. Recovery of divergent avian bornaviruses from cases of proventricular dilatation disease: identification of a candidate etiologic agent. Virol J. 2008; 5:88.
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      72. Chang HH, Falick AM, Carlton PM, Sedat JW, DeRisi JL, Marletta MA. N-terminal processing of proteins exported by malaria parasites. Mol Biochem Parasitol. 2008 Aug; 160(2):107-15.
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      73. Chiu CY, Urisman A, Greenhow TL, Rouskin S, Yagi S, Schnurr D, Wright C, Drew WL, Wang D, Weintrub PS, Derisi JL, Ganem D. Utility of DNA microarrays for detection of viruses in acute respiratory tract infections in children. J Pediatr. 2008 Jul; 153(1):76-83.
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      74. Kistler A, Avila PC, Rouskin S, Wang D, Ward T, Yagi S, Schnurr D, Ganem D, DeRisi JL, Boushey HA. Pan-viral screening of respiratory tract infections in adults with and without asthma reveals unexpected human coronavirus and human rhinovirus diversity. J Infect Dis. 2007 Sep 15; 196(6):817-25.
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      75. Chiu CY, Alizadeh AA, Rouskin S, Merker JD, Yeh E, Yagi S, Schnurr D, Patterson BK, Ganem D, DeRisi JL. Diagnosis of a critical respiratory illness caused by human metapneumovirus by use of a pan-virus microarray. J Clin Microbiol. 2007 Jul; 45(7):2340-3.
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      76. Kistler AL, Webster DR, Rouskin S, Magrini V, Credle JJ, Schnurr DP, Boushey HA, Mardis ER, Li H, DeRisi JL. Genome-wide diversity and selective pressure in the human rhinovirus. Virol J. 2007; 4:40.
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      77. Jambhekar A, Derisi JL. Cis-acting determinants of asymmetric, cytoplasmic RNA transport. RNA. 2007 May; 13(5):625-42.
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      78. Dong B, Kim S, Hong S, Das Gupta J, Malathi K, Klein EA, Ganem D, Derisi JL, Chow SA, Silverman RH. An infectious retrovirus susceptible to an IFN antiviral pathway from human prostate tumors. Proc Natl Acad Sci U S A. 2007 Jan 30; 104(5):1655-60.
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      79. Shock JL, Fischer KF, DeRisi JL. Whole-genome analysis of mRNA decay in Plasmodium falciparum reveals a global lengthening of mRNA half-life during the intra-erythrocytic development cycle. Genome Biol. 2007; 8(7):R134.
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      80. Jolly ER, Chin CS, Miller S, Bahgat MM, Lim KC, DeRisi J, McKerrow JH. Gene expression patterns during adaptation of a helminth parasite to different environmental niches. Genome Biol. 2007; 8(4):R65.
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      81. Zhu J, Jambhekar A, Sarver A, DeRisi J. A Bayesian network driven approach to model the transcriptional response to nitric oxide in Saccharomyces cerevisiae. PLoS One. 2006; 1:e94.
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      82. Xiao M, Phong A, Ha C, Chan TF, Cai D, Leung L, Wan E, Kistler AL, DeRisi JL, Selvin PR, Kwok PY. Rapid DNA mapping by fluorescent single molecule detection. Nucleic Acids Res. 2007; 35(3):e16.
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      83. Dahl EL, Shock JL, Shenai BR, Gut J, DeRisi JL, Rosenthal PJ. Tetracyclines specifically target the apicoplast of the malaria parasite Plasmodium falciparum. Antimicrob Agents Chemother. 2006 Sep; 50(9):3124-31.
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      84. Chiu CY, Rouskin S, Koshy A, Urisman A, Fischer K, Yagi S, Schnurr D, Eckburg PB, Tompkins LS, Blackburn BG, Merker JD, Patterson BK, Ganem D, DeRisi JL. Microarray detection of human parainfluenzavirus 4 infection associated with respiratory failure in an immunocompetent adult. Clin Infect Dis. 2006 Oct 15; 43(8):e71-6.
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      85. Madrid PB, Liou AP, DeRisi JL, Guy RK. Incorporation of an intramolecular hydrogen-bonding motif in the side chain of 4-aminoquinolines enhances activity against drug-resistant P. falciparum. J Med Chem. 2006 Jul 27; 49(15):4535-43.
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      86. Weisman JL, Liou AP, Shelat AA, Cohen FE, Guy RK, DeRisi JL. Searching for new antimalarial therapeutics amongst known drugs. Chem Biol Drug Des. 2006 Jun; 67(6):409-16.
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      87. Newman JR, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, DeRisi JL, Weissman JS. Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature. 2006 Jun 15; 441(7095):840-6.
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      88. Urisman A, Molinaro RJ, Fischer N, Plummer SJ, Casey G, Klein EA, Malathi K, Magi-Galluzzi C, Tubbs RR, Ganem D, Silverman RH, DeRisi JL. Identification of a novel Gammaretrovirus in prostate tumors of patients homozygous for R462Q RNASEL variant. PLoS Pathog. 2006 Mar; 2(3):e25.
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      89. Llinás M, Bozdech Z, Wong ED, Adai AT, DeRisi JL. Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains. Nucleic Acids Res. 2006; 34(4):1166-73.
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      90. Green BM, Morreale RJ, Ozaydin B, Derisi JL, Li JJ. Genome-wide mapping of DNA synthesis in Saccharomyces cerevisiae reveals that mechanisms preventing reinitiation of DNA replication are not redundant. Mol Biol Cell. 2006 May; 17(5):2401-14.
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      91. Jambhekar A, McDermott K, Sorber K, Shepard KA, Vale RD, Takizawa PA, DeRisi JL. Unbiased selection of localization elements reveals cis-acting determinants of mRNA bud localization in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2005 Dec 13; 102(50):18005-10.
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      92. Anderson MO, Sherrill J, Madrid PB, Liou AP, Weisman JL, DeRisi JL, Guy RK. Parallel synthesis of 9-aminoacridines and their evaluation against chloroquine-resistant Plasmodium falciparum. Bioorg Med Chem. 2006 Jan 15; 14(2):334-43.
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      93. Silvestrini F, Bozdech Z, Lanfrancotti A, Di Giulio E, Bultrini E, Picci L, Derisi JL, Pizzi E, Alano P. Genome-wide identification of genes upregulated at the onset of gametocytogenesis in Plasmodium falciparum. Mol Biochem Parasitol. 2005 Sep; 143(1):100-10.
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      94. Urisman A, Fischer KF, Chiu CY, Kistler AL, Beck S, Wang D, DeRisi JL. E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns. Genome Biol. 2005; 6(9):R78.
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      95. Sarver A, DeRisi J. Fzf1p regulates an inducible response to nitrosative stress in Saccharomyces cerevisiae. Mol Biol Cell. 2005 Oct; 16(10):4781-91.
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      96. Madrid PB, Sherrill J, Liou AP, Weisman JL, Derisi JL, Guy RK. Synthesis of ring-substituted 4-aminoquinolines and evaluation of their antimalarial activities. Bioorg Med Chem Lett. 2005 Feb 15; 15(4):1015-8.
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      97. Galgoczy DJ, Cassidy-Stone A, Llinás M, O'Rourke SM, Herskowitz I, DeRisi JL, Johnson AD. Genomic dissection of the cell-type-specification circuit in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2004 Dec 28; 101(52):18069-74.
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      98. Llinás M, DeRisi JL. Pernicious plans revealed: Plasmodium falciparum genome wide expression analysis. Curr Opin Microbiol. 2004 Aug; 7(4):382-7.
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      99. Glynn EF, Megee PC, Yu HG, Mistrot C, Unal E, Koshland DE, DeRisi JL, Gerton JL. Genome-wide mapping of the cohesin complex in the yeast Saccharomyces cerevisiae. PLoS Biol. 2004 Sep; 2(9):E259.
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      100. Weber SA, Gerton JL, Polancic JE, DeRisi JL, Koshland D, Megee PC. The kinetochore is an enhancer of pericentric cohesin binding. PLoS Biol. 2004 Sep; 2(9):E260.
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      101. Madrid PB, Wilson NT, DeRisi JL, Guy RK. Parallel synthesis and antimalarial screening of a 4-aminoquinoline library. J Comb Chem. 2004 May-Jun; 6(3):437-42.
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      102. Wang D, Urisman A, Liu YT, Springer M, Ksiazek TG, Erdman DD, Mardis ER, Hickenbotham M, Magrini V, Eldred J, Latreille JP, Wilson RK, Ganem D, DeRisi JL. Viral discovery and sequence recovery using DNA microarrays. PLoS Biol. 2003 Nov; 1(2):E2.
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      103. Shepard KA, Gerber AP, Jambhekar A, Takizawa PA, Brown PO, Herschlag D, DeRisi JL, Vale RD. Widespread cytoplasmic mRNA transport in yeast: identification of 22 bud-localized transcripts using DNA microarray analysis. Proc Natl Acad Sci U S A. 2003 Sep 30; 100(20):11429-34.
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      104. Bozdech Z, Llinás M, Pulliam BL, Wong ED, Zhu J, DeRisi JL. The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol. 2003 Oct; 1(1):E5.
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      105. Rota PA, Oberste MS, Monroe SS, Nix WA, Campagnoli R, Icenogle JP, Peñaranda S, Bankamp B, Maher K, Chen MH, Tong S, Tamin A, Lowe L, Frace M, DeRisi JL, Chen Q, Wang D, Erdman DD, Peret TC, Burns C, Ksiazek TG, Rollin PE, Sanchez A, Liffick S, Holloway B, Limor J, McCaustland K, Olsen-Rasmussen M, Fouchier R, Günther S, Osterhaus AD, Drosten C, Pallansch MA, Anderson LJ, Bellini WJ. Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science. 2003 May 30; 300(5624):1394-9.
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      106. Ksiazek TG, Erdman D, Goldsmith CS, Zaki SR, Peret T, Emery S, Tong S, Urbani C, Comer JA, Lim W, Rollin PE, Dowell SF, Ling AE, Humphrey CD, Shieh WJ, Guarner J, Paddock CD, Rota P, Fields B, DeRisi J, Yang JY, Cox N, Hughes JM, LeDuc JW, Bellini WJ, Anderson LJ. A novel coronavirus associated with severe acute respiratory syndrome. N Engl J Med. 2003 May 15; 348(20):1953-66.
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      107. Smith CD, Smith DL, DeRisi JL, Blackburn EH. Telomeric protein distributions and remodeling through the cell cycle in Saccharomyces cerevisiae. Mol Biol Cell. 2003 Feb; 14(2):556-70.
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      108. Bozdech Z, Zhu J, Joachimiak MP, Cohen FE, Pulliam B, DeRisi JL. Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biol. 2003; 4(2):R9.
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      109. Greenbaum DC, Baruch A, Grainger M, Bozdech Z, Medzihradszky KF, Engel J, DeRisi J, Holder AA, Bogyo M. A role for the protease falcipain 1 in host cell invasion by the human malaria parasite. Science. 2002 Dec 6; 298(5600):2002-6.
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      110. Wang D, Coscoy L, Zylberberg M, Avila PC, Boushey HA, Ganem D, DeRisi JL. Microarray-based detection and genotyping of viral pathogens. Proc Natl Acad Sci U S A. 2002 Nov 26; 99(24):15687-92.
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      111. Polson AG, Wang D, DeRisi J, Ganem D. Modulation of host gene expression by the constitutively active G protein-coupled receptor of Kaposi's sarcoma-associated herpesvirus. Cancer Res. 2002 Aug 1; 62(15):4525-30.
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      112. Nautiyal S, DeRisi JL, Blackburn EH. The genome-wide expression response to telomerase deletion in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2002 Jul 9; 99(14):9316-21.
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      113. Gerton JL, DeRisi JL. Mnd1p: an evolutionarily conserved protein required for meiotic recombination. Proc Natl Acad Sci U S A. 2002 May 14; 99(10):6895-900.
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      114. Rathod PK, Ganesan K, Hayward RE, Bozdech Z, DeRisi JL. DNA microarrays for malaria. Trends Parasitol. 2002 Jan; 18(1):39-45.
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      115. DeRisi J. Overview of nucleic acid arrays. Curr Protoc Neurosci. 2001 Nov; Chapter 4:Unit 4.25.
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      116. Carroll AS, Bishop AC, DeRisi JL, Shokat KM, O'Shea EK. Chemical inhibition of the Pho85 cyclin-dependent kinase reveals a role in the environmental stress response. Proc Natl Acad Sci U S A. 2001 Oct 23; 98(22):12578-83.
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      117. Backhus LE, DeRisi J, Bisson LF. Functional genomic analysis of a commercial wine strain of Saccharomyces cerevisiae under differing nitrogen conditions. FEMS Yeast Res. 2001 Jul; 1(2):111-25.
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      118. Derisi J. Overview of nucleic acid arrays. Curr Protoc Mol Biol. 2001 May; Chapter 22:Unit 22.1.
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      119. Miki R, Kadota K, Bono H, Mizuno Y, Tomaru Y, Carninci P, Itoh M, Shibata K, Kawai J, Konno H, Watanabe S, Sato K, Tokusumi Y, Kikuchi N, Ishii Y, Hamaguchi Y, Nishizuka I, Goto H, Nitanda H, Satomi S, Yoshiki A, Kusakabe M, DeRisi JL, Eisen MB, Iyer VR, Brown PO, Muramatsu M, Shimada H, Okazaki Y, Hayashizaki Y. Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays. Proc Natl Acad Sci U S A. 2001 Feb 27; 98(5):2199-204.
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      120. Kuhn KM, DeRisi JL, Brown PO, Sarnow P. Global and specific translational regulation in the genomic response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source. Mol Cell Biol. 2001 Feb; 21(3):916-27.
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      121. Ogawa N, DeRisi J, Brown PO. New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis. Mol Biol Cell. 2000 Dec; 11(12):4309-21.
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      122. Takizawa PA, DeRisi JL, Wilhelm JE, Vale RD. Plasma membrane compartmentalization in yeast by messenger RNA transport and a septin diffusion barrier. Science. 2000 Oct 13; 290(5490):341-4.
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      123. Gerton JL, DeRisi J, Shroff R, Lichten M, Brown PO, Petes TD. Global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2000 Oct 10; 97(21):11383-90.
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      124. Khodursky AB, Peter BJ, Schmid MB, DeRisi J, Botstein D, Brown PO, Cozzarelli NR. Analysis of topoisomerase function in bacterial replication fork movement: use of DNA microarrays. Proc Natl Acad Sci U S A. 2000 Aug 15; 97(17):9419-24.
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      125. DeRisi J, van den Hazel B, Marc P, Balzi E, Brown P, Jacq C, Goffeau A. Genome microarray analysis of transcriptional activation in multidrug resistance yeast mutants. FEBS Lett. 2000 Mar 24; 470(2):156-60.
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      126. Hayward RE, Derisi JL, Alfadhli S, Kaslow DC, Brown PO, Rathod PK. Shotgun DNA microarrays and stage-specific gene expression in Plasmodium falciparum malaria. Mol Microbiol. 2000 Jan; 35(1):6-14.
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      127. Wilson M, DeRisi J, Kristensen HH, Imboden P, Rane S, Brown PO, Schoolnik GK. Exploring drug-induced alterations in gene expression in Mycobacterium tuberculosis by microarray hybridization. Proc Natl Acad Sci U S A. 1999 Oct 26; 96(22):12833-8.
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      128. DeRisi JL, Iyer VR. Genomics and array technology. Curr Opin Oncol. 1999 Jan; 11(1):76-9.
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      129. Lutfiyya LL, Iyer VR, DeRisi J, DeVit MJ, Brown PO, Johnston M. Characterization of three related glucose repressors and genes they regulate in Saccharomyces cerevisiae. Genetics. 1998 Dec; 150(4):1377-91.
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      130. Marton MJ, DeRisi JL, Bennett HA, Iyer VR, Meyer MR, Roberts CJ, Stoughton R, Burchard J, Slade D, Dai H, Bassett DE, Hartwell LH, Brown PO, Friend SH. Drug target validation and identification of secondary drug target effects using DNA microarrays. Nat Med. 1998 Nov; 4(11):1293-301.
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      131. Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown PO, Herskowitz I. The transcriptional program of sporulation in budding yeast. Science. 1998 Oct 23; 282(5389):699-705.
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      132. Gerton JL, Ohgi S, Olsen M, DeRisi J, Brown PO. Effects of mutations in residues near the active site of human immunodeficiency virus type 1 integrase on specific enzyme-substrate interactions. J Virol. 1998 Jun; 72(6):5046-55.
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      133. Lashkari DA, DeRisi JL, McCusker JH, Namath AF, Gentile C, Hwang SY, Brown PO, Davis RW. Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc Natl Acad Sci U S A. 1997 Nov 25; 94(24):13057-62.
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      134. DeRisi JL, Iyer VR, Brown PO. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science. 1997 Oct 24; 278(5338):680-6.
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      135. DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, Chen Y, Su YA, Trent JM. Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat Genet. 1996 Dec; 14(4):457-60.
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      136. Peck LJ, Bartilson M, DeRisi JL. Bead-shift isolation of protein--DNA complexes on a 5S RNA gene. Nucleic Acids Res. 1994 Feb 11; 22(3):443-9.
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