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Joe Derisi, PhD

Title(s)Professor, Biochemistry and Biophysics
SchoolSchool of Medicine
Phone415-418-3059
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    Other Positions
    Title(s)Howard Hughes Investigator, Biochemistry and Biophysics


    Collapse Overview 
    Collapse 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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    Collapse Research Activities and Funding
    Protein homeostasis mechanisms underlying enterovirus replication and evolution
    NIH P01AI091575Jul 13, 2011 - Jun 30, 2016
    Role: Co-Investigator
    Integrative Program in Complex Biological System (ipCBS)
    NIH/NIBIB T32EB009383Apr 1, 2009 - Aug 31, 2019
    Role: Principal Investigator
    Pacific Southwest RCE for Biodefense &Emerging Infectious Diseases Research
    NIH/NIAID U54AI065359May 20, 2005 - Apr 30, 2014
    Role: Co-Investigator
    Intracellular pathogens and innate immunity
    NIH P01AI063302Sep 30, 2004 - Jun 30, 2021
    Role: Co-Investigator
    Novel Anti-Malarials by Combinatorial Pharmacogenomics
    NIH U01AI053862Sep 30, 2002 - Jul 31, 2008
    Role: Principal Investigator
    Bio-Organic Biomedical Mass Spectrometry Resource
    NIH P41RR001614Mar 1, 1982 - May 31, 2015
    Role: Co-Investigator

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    Collapse Bibliographic 
    Collapse 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.
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    1. Maes P, Adkins S, Alkhovsky SV, Avšic-Županc T, Ballinger MJ, Bente DA, Beer M, Bergeron É, Blair CD, Briese T, Buchmeier MJ, Burt FJ, Calisher CH, Charrel RN, Choi IR, Clegg JCS, de la Torre JC, de Lamballerie X, DeRisi JL, Digiaro M, Drebot M, Ebihara H, Elbeaino T, Ergünay K, Fulhorst CF, Garrison AR, Gao GF, Gonzalez JJ, Groschup MH, Günther S, Haenni AL, Hall RA, Hewson R, Hughes HR, Jain RK, Jonson MG, Junglen S, Klempa B, Klingström J, Kormelink R, Lambert AJ, Langevin SA, Lukashevich IS, Marklewitz M, Martelli GP, Mielke-Ehret N, Mirazimi A, Mühlbach HP, Naidu R, Nunes MRT, Palacios G, Papa A, Paweska JT, Peters CJ, Plyusnin A, Radoshitzky SR, Resende RO, Romanowski V, Sall AA, Salvato MS, Sasaya T, Schmaljohn C, Shí X, Shirako Y, Simmonds P, Sironi M, Song JW, Spengler JR, Stenglein MD, Tesh RB, Turina M, Wèi T, Whitfield AE, Yeh SD, Zerbini FM, Zhang YZ, Zhou X, Kuhn JH. Taxonomy of the order Bunyavirales: second update 2018. Arch Virol. 2019 Jan 20. PMID: 30663021.
      View in: PubMed
    2. Kalantar KL, Moazed F, Christenson SC, Wilson J, Deiss T, Belzer A, Vessel K, Caldera S, Jauregui A, Bolourchi S, DeRisi JL, Calfee CS, Langelier C. A Metagenomic Comparison of Tracheal Aspirate and Mini-Bronchial Alveolar Lavage for Assessment of Respiratory Microbiota. Am J Physiol Lung Cell Mol Physiol. 2019 Jan 17. PMID: 30652494.
      View in: PubMed
    3. Mayday MY, Khan LM, Chow ED, Zinter MS, DeRisi JL. Miniaturization and optimization of 384-well compatible RNA sequencing library preparation. PLoS One. 2019; 14(1):e0206194. PMID: 30629604.
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    4. Wilson MR, O'Donovan BD, DeRisi JL. Misinterpretation of Study Data-Reply. JAMA Neurol. 2019 Jan 01; 76(1):113-114. PMID: 30477022.
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    5. Beck ES, Ramachandran PS, Khan LM, Sample HA, Zorn KC, O'Connell EM, Nash T, Reich DS, Venkatesan A, DeRisi JL, Nath A, Wilson MR. Clinicopathology Conference: 41 year old woman with chronic relapsing meningitis. Ann Neurol. 2018 Dec 19. PMID: 30565288.
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    6. Sheridan CM, Garcia VE, Ahyong V, DeRisi JL. The Plasmodium falciparum cytoplasmic translation apparatus: a promising therapeutic target not yet exploited by clinically approved anti-malarials. Malar J. 2018 Dec 12; 17(1):465. PMID: 30541569.
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    7. Ramachandran PS, Cresswell FV, Meya DB, Crawford ED, DeRisi JL, Boulware DR, Wilson MR. Detection of Cryptococcus DNA by metagenomic next-generation sequencing in symptomatic cryptococcal antigenemia. Clin Infect Dis. 2018 Dec 08. PMID: 30535266.
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    8. Langelier C, Kalantar KL, Moazed F, Wilson MR, Crawford ED, Deiss T, Belzer A, Bolourchi S, Caldera S, Fung M, Jauregui A, Malcolm K, Lyden A, Khan L, Vessel K, Quan J, Zinter M, Chiu CY, Chow ED, Wilson J, Miller S, Matthay MA, Pollard KS, Christenson S, Calfee CS, DeRisi JL. Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults. Proc Natl Acad Sci U S A. 2018 Dec 26; 115(52):E12353-E12362. PMID: 30482864.
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    9. Laurie MT, White CV, Retallack H, Wu W, Moser MS, Sakanari JA, Ang K, Wilson C, Arkin MR, DeRisi JL. Functional Assessment of 2,177 U.S. and International Drugs Identifies the Quinoline Nitroxoline as a Potent Amoebicidal Agent against the Pathogen Balamuthia mandrillaris. MBio. 2018 Oct 30; 9(5). PMID: 30377287.
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    10. Miller LJ, Fetterer DP, Garza NL, Lackemeyer MG, Donnelly GC, Steffens JT, Van Tongeren SA, Fiallos JO, Moore JL, Marko ST, Lugo-Roman LA, Fedewa G, DeRisi JL, Kuhn JH, Stahl SJ. A fixed moderate-dose combination of tiletamine+zolazepam outperforms midazolam in induction of short-term immobilization of ball pythons (Python regius). PLoS One. 2018; 13(10):e0199339. PMID: 30339670.
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    11. Retallack H, Okihiro MS, Britton E, Van Sommeran S, DeRisi JL. Metagenomic Next-Generation Sequencing Reveals Miamiensis avidus (Ciliophora: Scuticociliatida) In the 2017 Epizootic of Leopard Sharks ( Triakis semifasciata) In San Francisco Bay, California, USA. J Wildl Dis. 2018 Oct 05. PMID: 30289337.
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    12. Wilson MR, O'Donovan BD, Gelfand JM, Sample HA, Chow FC, Betjemann JP, Shah MP, Richie MB, Gorman MP, Hajj-Ali RA, Calabrese LH, Zorn KC, Chow ED, Greenlee JE, Blum JH, Green G, Khan LM, Banerji D, Langelier C, Bryson-Cahn C, Harrington W, Lingappa JR, Shanbhag NM, Green AJ, Brew BJ, Soldatos A, Strnad L, Doernberg SB, Jay CA, Douglas V, Josephson SA, DeRisi JL. Chronic Meningitis Investigated via Metagenomic Next-Generation Sequencing. JAMA Neurol. 2018 Aug 01; 75(8):947-955. PMID: 29710329.
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    13. Mavor D, Barlow KA, Asarnow D, Birman Y, Britain D, Chen W, Green EM, Kenner LR, Mensa B, Morinishi LS, Nelson CA, Poss EM, Suresh P, Tian R, Arhar T, Ary BE, Bauer DP, Bergman ID, Brunetti RM, Chio CM, Dai SA, Dickinson MS, Elledge SK, Helsell CVM, Hendel NL, Kang E, Kern N, Khoroshkin MS, Kirkemo LL, Lewis GR, Lou K, Marin WM, Maxwell AM, McTigue PF, Myers-Turnbull D, Nagy TL, Natale AM, Oltion K, Pourmal S, Reder GK, Rettko NJ, Rohweder PJ, Schwarz DMC, Tan SK, Thomas PV, Tibble RW, Town JP, Tsai MK, Ugur FS, Wassarman DR, Wolff AM, Wu TS, Bogdanoff D, Li J, Thorn KS, O'Conchúir S, Swaney DL, Chow ED, Madhani HD, Redding S, Bolon DN, Kortemme T, DeRisi JL, Kampmann M, Fraser JS. Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance. Biol Open. 2018 Jul 23; 7(7). PMID: 30037883.
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    14. Kalantar K, LaHue SC, DeRisi JL, Sample HA, Contag CA, Josephson SA, Wilson MR, Douglas VC. Whole-Genome mRNA Gene Expression Differs Between Patients With and Without Delirium. J Geriatr Psychiatry Neurol. 2018 Jul; 31(4):203-210. PMID: 29991314.
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    15. Zylberberg M, Van Hemert C, Handel CM, DeRisi JL. Avian keratin disorder of Alaska black-capped chickadees is associated with Poecivirus infection. Virol J. 2018 06 15; 15(1):100. PMID: 29903045.
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    16. Solomon IH, Spera KM, Ryan SL, Helgager J, Andrici J, Zaki SR, Vaitkevicius H, Leon KE, Wilson MR, DeRisi JL, Koo S, Smirnakis SM, De Girolami U. Fatal Powassan Encephalitis (Deer Tick Virus, Lineage II) in a Patient With Fever and Orchitis Receiving Rituximab. JAMA Neurol. 2018 Jun 01; 75(6):746-750. PMID: 29554185.
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    17. Maes P, Alkhovsky SV, Bào Y, Beer M, Birkhead M, Briese T, Buchmeier MJ, Calisher CH, Charrel RN, Choi IR, Clegg CS, de la Torre JC, Delwart E, DeRisi JL, Di Bello PL, Di Serio F, Digiaro M, Dolja VV, Drosten C, Druciarek TZ, Du J, Ebihara H, Elbeaino T, Gergerich RC, Gillis AN, Gonzalez JJ, Haenni AL, Hepojoki J, Hetzel U, H? T, Hóng N, Jain RK, Jansen van Vuren P, Jin Q, Jonson MG, Junglen S, Keller KE, Kemp A, Kipar A, Kondov NO, Koonin EV, Kormelink R, Korzyukov Y, Krupovic M, Lambert AJ, Laney AG, LeBreton M, Lukashevich IS, Marklewitz M, Markotter W, Martelli GP, Martin RR, Mielke-Ehret N, Mühlbach HP, Navarro B, Ng TFF, Nunes MRT, Palacios G, Paweska JT, Peters CJ, Plyusnin A, Radoshitzky SR, Romanowski V, Salmenperä P, Salvato MS, Sanfaçon H, Sasaya T, Schmaljohn C, Schneider BS, Shirako Y, Siddell S, Sironen TA, Stenglein MD, Storm N, Sudini H, Tesh RB, Tzanetakis IE, Uppala M, Vapalahti O, Vasilakis N, Walker PJ, Wáng G, Wáng L, Wáng Y, Wèi T, Wiley MR, Wolf YI, Wolfe ND, Wú Z, Xú W, Yang L, Yang Z, Yeh SD, Zhang YZ, Zhèng Y, Zhou X, Zhu C, Zirkel F, Kuhn JH. Taxonomy of the family Arenaviridae and the order Bunyavirales: update 2018. Arch Virol. 2018 Aug; 163(8):2295-2310. PMID: 29680923.
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    18. Langelier C, Zinter MS, Kalantar K, Yanik GA, Christenson S, O'Donovan B, White C, Wilson M, Sapru A, Dvorak CC, Miller S, Chiu CY, DeRisi JL. Metagenomic Sequencing Detects Respiratory Pathogens in Hematopoietic Cellular Transplant Patients. Am J Respir Crit Care Med. 2018 Feb 15; 197(4):524-528. PMID: 28686513.
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    19. Bhakta NR, Christenson SA, Nerella S, Solberg OD, Nguyen CP, Choy DF, Jung KL, Garudadri S, Bonser LR, Pollack JL, Zlock LT, Erle DJ, Langelier C, Derisi JL, Arron JR, Fahy JV, Woodruff PG. IFN-stimulated Gene Expression, Type 2 Inflammation, and Endoplasmic Reticulum Stress in Asthma. Am J Respir Crit Care Med. 2018 Feb 01; 197(3):313-324. PMID: 29064281.
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    20. Langelier C, White CV, Sontag MK, Mourani PM, DeRisi JL. Complete Genome Sequence of a Divergent Human Rhinovirus C Isolate from an Infant with Severe Community-Acquired Pneumonia in Colorado, USA. Genome Announc. 2017 Nov 30; 5(48). PMID: 29192071.
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    21. Gonzales J, Doan T, Shantha JG, Bloomer M, Wilson MR, DeRisi JL, Acharya N. Metagenomic deep sequencing of aqueous fluid detects intraocular lymphomas. Br J Ophthalmol. 2018 01; 102(1):6-8. PMID: 29122821.
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    22. Hanna ZR, Henderson JB, Wall JD, Emerling CA, Fuchs J, Runckel C, Mindell DP, Bowie RCK, DeRisi JL, Dumbacher JP. Northern Spotted Owl (Strix occidentalis caurina) Genome: Divergence with the Barred Owl (Strix varia) and Characterization of Light-Associated Genes. Genome Biol Evol. 2017 10 01; 9(10):2522-2545. PMID: 28992302.
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    23. Faden DL, Thomas S, Cantalupo PG, Agrawal N, Myers J, DeRisi J. Multi-modality analysis supports APOBEC as a major source of mutations in head and neck squamous cell carcinoma. Oral Oncol. 2017 11; 74:8-14. PMID: 29103756.
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    24. Milgrom P, Horst JA, Ludwig S, Rothen M, Chaffee BW, Lyalina S, Pollard KS, DeRisi JL, Mancl L. Topical silver diamine fluoride for dental caries arrest in preschool children: A randomized controlled trial and microbiological analysis of caries associated microbes and resistance gene expression. J Dent. 2018 01; 68:72-78. PMID: 28866468.
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    25. Stenglein MD, Sanchez-Migallon Guzman D, Garcia VE, Layton ML, Hoon-Hanks LL, Boback SM, Keel MK, Drazenovich T, Hawkins MG, DeRisi JL. Differential Disease Susceptibilities in Experimentally Reptarenavirus-Infected Boa Constrictors and Ball Pythons. J Virol. 2017 08 01; 91(15). PMID: 28515291.
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    26. Wilson MR, Suan D, Duggins A, Schubert RD, Khan LM, Sample HA, Zorn KC, Rodrigues Hoffman A, Blick A, Shingde M, DeRisi JL. A novel cause of chronic viral meningoencephalitis: Cache Valley virus. Ann Neurol. 2017 Jul; 82(1):105-114. PMID: 28628941.
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    27. Crawford ED, Quan J, Horst JA, Ebert D, Wu W, DeRisi JL. Plasmid-free CRISPR/Cas9 genome editing in Plasmodium falciparum confirms mutations conferring resistance to the dihydroisoquinolone clinical candidate SJ733. PLoS One. 2017; 12(5):e0178163. PMID: 28542423.
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    28. Doan T, Acharya NR, Pinsky BA, Sahoo MK, Chow ED, Banaei N, Budvytiene I, Cevallos V, Zhong L, Zhou Z, Lietman TM, DeRisi JL. Metagenomic DNA Sequencing for the Diagnosis of Intraocular Infections. Ophthalmology. 2017 08; 124(8):1247-1248. PMID: 28526549.
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    29. Postler TS, Clawson AN, Amarasinghe GK, Basler CF, Bavari S, Benko M, Blasdell KR, Briese T, Buchmeier MJ, Bukreyev A, Calisher CH, Chandran K, Charrel R, Clegg CS, Collins PL, Juan Carlos T, Derisi JL, Dietzgen RG, Dolnik O, Dürrwald R, Dye JM, Easton AJ, Emonet S, Formenty P, Fouchier RAM, Ghedin E, Gonzalez JP, Harrach B, Hewson R, Horie M, Jiang D, Kobinger G, Kondo H, Kropinski AM, Krupovic M, Kurath G, Lamb RA, Leroy EM, Lukashevich IS, Maisner A, Mushegian AR, Netesov SV, Nowotny N, Patterson JL, Payne SL, PaWeska JT, Peters CJ, Radoshitzky SR, Rima BK, Romanowski V, Rubbenstroth D, Sabanadzovic S, Sanfaçon H, Salvato MS, Schwemmle M, Smither SJ, Stenglein MD, Stone DM, Takada A, Tesh RB, Tomonaga K, Tordo N, Towner JS, Vasilakis N, Volchkov VE, Wahl-Jensen V, Walker PJ, Wang LF, Varsani A, Whitfield AE, Zerbini FM, Kuhn JH. Possibility and Challenges of Conversion of Current Virus Species Names to Linnaean Binomials. Syst Biol. 2017 05 01; 66(3):463-473. PMID: 27798405.
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    30. Ludington WB, Seher TD, Applegate O, Li X, Kliegman JI, Langelier C, Atwill ER, Harter T, DeRisi JL. Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater. PLoS One. 2017; 12(4):e0174930. PMID: 28384184.
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    31. Sonoiki E, Ng CL, Lee MC, Guo D, Zhang YK, Zhou Y, Alley MR, Ahyong V, Sanz LM, Lafuente-Monasterio MJ, Dong C, Schupp PG, Gut J, Legac J, Cooper RA, Gamo FJ, DeRisi J, Freund YR, Fidock DA, Rosenthal PJ. A potent antimalarial benzoxaborole targets a Plasmodium falciparum cleavage and polyadenylation specificity factor homologue. Nat Commun. 2017 03 06; 8:14574. PMID: 28262680.
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    32. Horst JA, Wu W, DeRisi JL. MinorityReport, software for generalized analysis of causal genetic variants. Malar J. 2017 02 23; 16(1):90. PMID: 28231785.
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    33. Medina GN, Knudsen GM, Greninger AL, Kloc A, Díaz-San Segundo F, Rieder E, Grubman MJ, DeRisi JL, de Los Santos T. Interaction between FMDV Lpro and transcription factor ADNP is required for optimal viral replication. Virology. 2017 05; 505:12-22. PMID: 28219017.
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    34. Faden DL, Asthana S, Tihan T, DeRisi J, Kliot M. Correction: Whole Exome Sequencing of Growing and Non-Growing Cutaneous Neurofibromas from a Single Patient with Neurofibromatosis Type 1. PLoS One. 2017; 12(2):e0172620. PMID: 28207875.
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    35. Slabodnick MM, Ruby JG, Reiff SB, Swart EC, Gosai S, Prabakaran S, Witkowska E, Larue GE, Fisher S, Freeman RM, Gunawardena J, Chu W, Stover NA, Gregory BD, Nowacki M, Derisi J, Roy SW, Marshall WF, Sood P. The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell. Curr Biol. 2017 Feb 20; 27(4):569-575. PMID: 28190732.
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    36. Faden DL, Asthana S, Tihan T, DeRisi J, Kliot M. Whole Exome Sequencing of Growing and Non-Growing Cutaneous Neurofibromas from a Single Patient with Neurofibromatosis Type 1. PLoS One. 2017; 12(1):e0170348. PMID: 28099461.
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    37. Sonoiki E, Nsanzabana C, Legac J, Sindhe KM, DeRisi J, Rosenthal PJ. Altered Plasmodium falciparum Sensitivity to the Antiretroviral Protease Inhibitor Lopinavir Associated with Polymorphisms in pfmdr1. Antimicrob Agents Chemother. 2017 01; 61(1). PMID: 27821443.
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    38. Retallack H, Di Lullo E, Arias C, Knopp KA, Laurie MT, Sandoval-Espinosa C, Mancia Leon WR, Krencik R, Ullian EM, Spatazza J, Pollen AA, Mandel-Brehm C, Nowakowski TJ, Kriegstein AR, DeRisi JL. Zika virus cell tropism in the developing human brain and inhibition by azithromycin. Proc Natl Acad Sci U S A. 2016 12 13; 113(50):14408-14413. PMID: 27911847.
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    39. Doan T, Wilson MR, Crawford ED, Chow ED, Khan LM, Knopp KA, O'Donovan BD, Xia D, Hacker JK, Stewart JM, Gonzales JA, Acharya NR, DeRisi JL. Erratum to: Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens. Genome Med. 2016 11 22; 8(1):123. PMID: 27876088.
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    40. Greene TT, Tokuyama M, Knudsen GM, Kunz M, Lin J, Greninger AL, DeFilippis VR, DeRisi JL, Raulet DH, Coscoy L. A Herpesviral induction of RAE-1 NKG2D ligand expression occurs through release of HDAC mediated repression. Elife. 2016 11 22; 5. PMID: 27874833.
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    41. Nguyen JT, Green A, Wilson MR, DeRisi JL, Gundling K. Neurologic Complications of Common Variable Immunodeficiency. J Clin Immunol. 2016 11; 36(8):793-800. PMID: 27704236.
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    42. Faden DL, Arron ST, Heaton CM, DeRisi J, South AP, Wang SJ. Targeted next-generation sequencing of TP53 in oral tongue carcinoma from non-smokers. J Otolaryngol Head Neck Surg. 2016 Sep 17; 45(1):47. PMID: 27640185; PMCID: PMC5027093.
    43. Doan T, Wilson MR, Crawford ED, Chow ED, Khan LM, Knopp KA, O'Donovan BD, Xia D, Hacker JK, Stewart JM, Gonzales JA, Acharya NR, DeRisi JL. Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens. Genome Med. 2016 08 25; 8(1):90. PMID: 27562436.
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    44. Van Voorhis WC, Adams JH, Adelfio R, Ahyong V, Akabas MH, Alano P, Alday A, Alemán Resto Y, Alsibaee A, Alzualde A, Andrews KT, Avery SV, Avery VM, Ayong L, Baker M, Baker S, Ben Mamoun C, Bhatia S, Bickle Q, Bounaadja L, Bowling T, Bosch J, Boucher LE, Boyom FF, Brea J, Brennan M, Burton A, Caffrey CR, Camarda G, Carrasquilla M, Carter D, Belen Cassera M, Chih-Chien Cheng K, Chindaudomsate W, Chubb A, Colon BL, Colón-López DD, Corbett Y, Crowther GJ, Cowan N, D'Alessandro S, Le Dang N, Delves M, DeRisi JL, Du AY, Duffy S, Abd El-Salam El-Sayed S, Ferdig MT, Fernández Robledo JA, Fidock DA, Florent I, Fokou PV, Galstian A, Gamo FJ, Gokool S, Gold B, Golub T, Goldgof GM, Guha R, Guiguemde WA, Gural N, Guy RK, Hansen MA, Hanson KK, Hemphill A, Hooft van Huijsduijnen R, Horii T, Horrocks P, Hughes TB, Huston C, Igarashi I, Ingram-Sieber K, Itoe MA, Jadhav A, Naranuntarat Jensen A, Jensen LT, Jiang RH, Kaiser A, Keiser J, Ketas T, Kicka S, Kim S, Kirk K, Kumar VP, Kyle DE, Lafuente MJ, Landfear S, Lee N, Lee S, Lehane AM, Li F, Little D, Liu L, Llinás M, Loza MI, Lubar A, Lucantoni L, Lucet I, Maes L, Mancama D, Mansour NR, March S, McGowan S, Medina Vera I, Meister S, Mercer L, Mestres J, Mfopa AN, Misra RN, Moon S, Moore JP, Morais Rodrigues da Costa F, Müller J, Muriana A, Nakazawa Hewitt S, Nare B, Nathan C, Narraidoo N, Nawaratna S, Ojo KK, Ortiz D, Panic G, Papadatos G, Parapini S, Patra K, Pham N, Prats S, Plouffe DM, Poulsen SA, Pradhan A, Quevedo C, Quinn RJ, Rice CA, Abdo Rizk M, Ruecker A, St Onge R, Salgado Ferreira R, Samra J, Robinett NG, Schlecht U, Schmitt M, Silva Villela F, Silvestrini F, Sinden R, Smith DA, Soldati T, Spitzmüller A, Stamm SM, Sullivan DJ, Sullivan W, Suresh S, Suzuki BM, Suzuki Y, Swamidass SJ, Taramelli D, Tchokouaha LR, Theron A, Thomas D, Tonissen KF, Townson S, Tripathi AK, Trofimov V, Udenze KO, Ullah I, Vallieres C, Vigil E, Vinetz JM, Voong Vinh P, Vu H, Watanabe NA, Weatherby K, White PM, Wilks AF, Winzeler EA, Wojcik E, Wree M, Wu W, Yokoyama N, Zollo PH, Abla N, Blasco B, Burrows J, Laleu B, Leroy D, Spangenberg T, Wells T, Willis PA. Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond. PLoS Pathog. 2016 07; 12(7):e1005763. PMID: 27467575.
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    45. Zylberberg M, Van Hemert C, Dumbacher JP, Handel CM, Tihan T, DeRisi JL. Novel Picornavirus Associated with Avian Keratin Disorder in Alaskan Birds. MBio. 2016 07 26; 7(4). PMID: 27460795; PMCID: PMC4958255.
    46. Sonoiki E, Palencia A, Guo D, Ahyong V, Dong C, Li X, Hernandez VS, Zhang YK, Choi W, Gut J, Legac J, Cooper R, Alley MR, Freund YR, DeRisi J, Cusack S, Rosenthal PJ. Antimalarial Benzoxaboroles Target Plasmodium falciparum Leucyl-tRNA Synthetase. Antimicrob Agents Chemother. 2016 08; 60(8):4886-95. PMID: 27270277.
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    47. Wilson MR, Fedewa G, Stenglein MD, Olejnik J, Rennick LJ, Nambulli S, Feldmann F, Duprex WP, Connor JH, Mühlberger E, DeRisi JL. Multiplexed Metagenomic Deep Sequencing To Analyze the Composition of High-Priority Pathogen Reagents. mSystems. 2016 Jul-Aug; 1(4). PMID: 27822544.
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    48. Mavor D, Barlow K, Thompson S, Barad BA, Bonny AR, Cario CL, Gaskins G, Liu Z, Deming L, Axen SD, Caceres E, Chen W, Cuesta A, Gate RE, Green EM, Hulce KR, Ji W, Kenner LR, Mensa B, Morinishi LS, Moss SM, Mravic M, Muir RK, Niekamp S, Nnadi CI, Palovcak E, Poss EM, Ross TD, Salcedo EC, See SK, Subramaniam M, Wong AW, Li J, Thorn KS, Conchúir SÓ, Roscoe BP, Chow ED, DeRisi JL, Kortemme T, Bolon DN, Fraser JS. Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting. Elife. 2016 04 25; 5. PMID: 27111525; PMCID: PMC4862753.
    49. Ahyong V, Sheridan CM, Leon KE, Witchley JN, Diep J, DeRisi JL. Identification of Plasmodium falciparum specific translation inhibitors from the MMV Malaria Box using a high throughput in vitro translation screen. Malar J. 2016 Mar 17; 15:173. PMID: 26987601; PMCID: PMC4794828.
    50. Soupene E, Kao J, Cheng DH, Wang D, Greninger AL, Knudsen GM, DeRisi JL, Kuypers FA. Association of NMT2 with the acyl-CoA carrier ACBD6 protects the N-myristoyltransferase reaction from palmitoyl-CoA. J Lipid Res. 2016 Feb; 57(2):288-98. PMID: 26621918; PMCID: PMC4727424 [Available on 02/01/17].
    51. Hanna ZR, Runckel C, Fuchs J, DeRisi JL, Mindell DP, Van Hemert C, Handel CM, Dumbacher JP. Isolation of a Complete Circular Virus Genome Sequence from an Alaskan Black-Capped Chickadee (Poecile atricapillus) Gastrointestinal Tract Sample. Genome Announc. 2015 Sep 24; 3(5). PMID: 26404604; PMCID: PMC4582580.
    52. Wilson MR, Shanbhag NM, Reid MJ, Singhal NS, Gelfand JM, Sample HA, Benkli B, O'Donovan BD, Ali IK, Keating MK, Dunnebacke TH, Wood MD, Bollen A, DeRisi JL. Diagnosing Balamuthia mandrillaris Encephalitis With Metagenomic Deep Sequencing. Ann Neurol. 2015 Nov; 78(5):722-30. PMID: 26290222; PMCID: PMC4624031 [Available on 11/01/16].
    53. Greninger AL, DeRisi JL. Draft Genome Sequence of Laverivirus UC1, a Dicistrovirus-Like RNA Virus Featuring an Unusual Genome Organization. Genome Announc. 2015 Jul 02; 3(4). PMID: 26139710; PMCID: PMC4490838.
    54. Greninger AL, DeRisi JL. Draft Genome Sequence of Picalivirus D Recovered from San Francisco Wastewater. Genome Announc. 2015 Jul 02; 3(4). PMID: 26139708; PMCID: PMC4490836.
    55. Greninger AL, DeRisi JL. Draft Genome Sequence of Tombunodavirus UC1. Genome Announc. 2015 Jul 02; 3(4). PMID: 26139709; PMCID: PMC4490837.
    56. Radoshitzky SR, Bào Y, Buchmeier MJ, Charrel RN, Clawson AN, Clegg CS, DeRisi JL, Emonet S, Gonzalez JP, Kuhn JH, Lukashevich IS, Peters CJ, Romanowski V, Salvato MS, Stenglein MD, de la Torre JC. Past, present, and future of arenavirus taxonomy. Arch Virol. 2015 Jul; 160(7):1851-74. PMID: 25935216.
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    57. Greninger AL, DeRisi JL. Draft Genome Sequences of Leviviridae RNA Phages EC and MB Recovered from San Francisco Wastewater. Genome Announc. 2015 Jun 25; 3(3). PMID: 26112785; PMCID: PMC4481283.
    58. Greninger AL, DeRisi JL. Draft Genome Sequences of Ciliovirus and Brinovirus from San Francisco Wastewater. Genome Announc. 2015 Jun 25; 3(3). PMID: 26112784; PMCID: PMC4481282.
    59. Greninger AL, DeRisi JL. Draft Genome Sequences of Marine RNA Viruses SF-1, SF-2, and SF-3 Recovered from San Francisco Wastewater. Genome Announc. 2015 Jun 18; 3(3). PMID: 26089423; PMCID: PMC4472900.
    60. Stenglein MD, Jacobson ER, Chang LW, Sanders C, Hawkins MG, Guzman DS, Drazenovich T, Dunker F, Kamaka EK, Fisher D, Reavill DR, Meola LF, Levens G, DeRisi JL. Widespread recombination, reassortment, and transmission of unbalanced compound viral genotypes in natural arenavirus infections. PLoS Pathog. 2015 May; 11(5):e1004900. PMID: 25993603; PMCID: PMC4438980.
    61. O'Donoghue AJ, Knudsen GM, Beekman C, Perry JA, Johnson AD, DeRisi JL, Craik CS, Bennett RJ. Destructin-1 is a collagen-degrading endopeptidase secreted by Pseudogymnoascus destructans, the causative agent of white-nose syndrome. Proc Natl Acad Sci U S A. 2015 Jun 16; 112(24):7478-83. PMID: 25944934.
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    62. Schulze CJ, Navarro G, Ebert D, DeRisi J, Linington RG. Salinipostins A-K, long-chain bicyclic phosphotriesters as a potent and selective antimalarial chemotype. J Org Chem. 2015 Feb 06; 80(3):1312-20. PMID: 25584395.
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    63. Caro F, Ahyong V, Betegon M, DeRisi JL. Genome-wide regulatory dynamics of translation in the Plasmodium falciparum asexual blood stages. Elife. 2014 Dec 10; 3. PMID: 25493618.
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    64. Kuhn JH, Dürrwald R, Bào Y, Briese T, Carbone K, Clawson AN, deRisi JL, Garten W, Jahrling PB, Kolodziejek J, Rubbenstroth D, Schwemmle M, Stenglein M, Tomonaga K, Weissenböck H, Nowotny N. Taxonomic reorganization of the family Bornaviridae. Arch Virol. 2015 Feb; 160(2):621-32. PMID: 25449305.
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    65. Jiménez-Díaz MB, Ebert D, Salinas Y, Pradhan A, Lehane AM, Myrand-Lapierre ME, O'Loughlin KG, Shackleford DM, Justino de Almeida M, Carrillo AK, Clark JA, Dennis AS, Diep J, Deng X, Duffy S, Endsley AN, Fedewa G, Guiguemde WA, Gómez MG, Holbrook G, Horst J, Kim CC, Liu J, Lee MC, Matheny A, Martínez MS, Miller G, Rodríguez-Alejandre A, Sanz L, Sigal M, Spillman NJ, Stein PD, Wang Z, Zhu F, Waterson D, Knapp S, Shelat A, Avery VM, Fidock DA, Gamo FJ, Charman SA, Mirsalis JC, Ma H, Ferrer S, Kirk K, Angulo-Barturen I, Kyle DE, DeRisi JL, Floyd DM, Guy RK. (+)-SJ733, a clinical candidate for malaria that acts through ATP4 to induce rapid host-mediated clearance of Plasmodium. Proc Natl Acad Sci U S A. 2014 Dec 16; 111(50):E5455-62. PMID: 25453091; PMCID: PMC4273362.
    66. Wu W, Herrera Z, Ebert D, Baska K, Cho SH, DeRisi JL, Yeh E. A chemical rescue screen identifies a Plasmodium falciparum apicoplast inhibitor targeting MEP isoprenoid precursor biosynthesis. Antimicrob Agents Chemother. 2015 Jan; 59(1):356-64. PMID: 25367906; PMCID: PMC4291372.
    67. 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 Oct 09; 2(5). PMID: 25301640; PMCID: PMC4192372.
    68. 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 Sep 09; 5(5):e01484-14. PMID: 25205093.
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    69. Li R, Faden DL, Fakhry C, Langelier C, Jiao Y, Wang Y, Wilkerson MD, Pedamallu CS, Old M, Lang J, Loyo M, Ahn SM, Tan M, Gooi Z, Chan J, Richmon J, Wood LD, Hruban RH, Bishop J, Westra WH, Chung CH, Califano J, Gourin CG, Bettegowda C, Meyerson M, Papadopoulos N, Kinzler KW, Vogelstein B, DeRisi JL, Koch WM, Agrawal N. Clinical, genomic, and metagenomic characterization of oral tongue squamous cell carcinoma in patients who do not smoke. Head Neck. 2015 Nov; 37(11):1642-9. PMID: 24954188; PMCID: PMC4272912 [Available on 11/01/16].
    70. 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. PMID: 25140992; PMCID: PMC4139300.
    71. 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 19; 370(25):2408-17. PMID: 24896819; PMCID: PMC4134948.
    72. Naccache SN, Federman S, Veeraraghavan 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 Jul; 24(7):1180-92. PMID: 24899342; PMCID: PMC4079973.
    73. 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. PMID: 24874988; PMCID: PMC4066398.
    74. 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. PMID: 24823688; PMCID: PMC4019465.
    75. 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 07; 82(3):537-44. PMID: 24811378; PMCID: PMC4104505.
    76. Runckel C, DeRisi J, Flenniken ML. A draft genome of the honey bee trypanosomatid parasite Crithidia mellificae. PLoS One. 2014; 9(4):e95057. PMID: 24743507; PMCID: PMC3990616.
    77. Rubio CA, Weisburd B, Holderfield M, Arias C, Fang E, DeRisi JL, Fanidi A. Transcriptome-wide characterization of the eIF4A signature highlights plasticity in translation regulation. Genome Biol. 2014; 15(10):476. PMID: 25273840; PMCID: PMC4203936.
    78. 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 03; 426(7):1452-68. PMID: 24333483.
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    79. 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. PMID: 23855748; PMCID: PMC3888361.
    80. 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. PMID: 23717205; PMCID: PMC3662640.
    81. Ruby JG, Bellare P, Derisi JL. PRICE: software for the targeted assembly of components of (Meta) genomic sequence data. G3 (Bethesda). 2013 May 20; 3(5):865-80. PMID: 23550143; PMCID: PMC3656733.
    82. 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. PMID: 23625967; PMCID: PMC3695516.
    83. 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 07; 110(19):7660-5. PMID: 23610392; PMCID: PMC3651432.
    84. 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 Apr 09; 4(2):e00098-13. PMID: 23572552.
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    85. 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. PMID: 23554923; PMCID: PMC3595295.
    86. 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. PMID: 23408891; PMCID: PMC3567174.
    87. 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 Jan 30; 14(1):R10. PMID: 23363705.
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    88. 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. PMID: 23258877.
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    89. 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. PMID: 23166671; PMCID: PMC3498111.
    90. 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. PMID: 23144737; PMCID: PMC3483282.
    91. 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 06; 109(45):E3084-93. PMID: 23054834; PMCID: PMC3494901.
    92. 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. PMID: 23030602; PMCID: PMC3483642.
    93. 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. PMID: 23023596; PMCID: PMC3707110.
    94. 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 Sep 22; 9:216. PMID: 22998755.
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    95. 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. PMID: 23028701; PMCID: PMC3445615.
    96. 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. PMID: 22893382; PMCID: PMC3419519.
    97. 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. PMID: 22708838; PMCID: PMC4408918.
    98. 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. PMID: 22347512; PMCID: PMC3274504.
    99. Caro F, Miller MG, DeRisi JL. Plate-based transfection and culturing technique for genetic manipulation of Plasmodium falciparum. Malar J. 2012 Jan 18; 11:22. PMID: 22257490; PMCID: PMC3293776.
    100. 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. PMID: 22258260.
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    101. 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. PMID: 22235317; PMCID: PMC3250467.
    102. 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. PMID: 22046241; PMCID: PMC3201961.
    103. 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. PMID: 21955244; PMCID: PMC3208124.
    104. 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. PMID: 21910466; PMCID: PMC3697074.
    105. 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. PMID: 21926179; PMCID: PMC3227110.
    106. 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. PMID: 21912516; PMCID: PMC3166167.
    107. 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. PMID: 21687739; PMCID: PMC3110205.
    108. 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. PMID: 21785699; PMCID: PMC3139178.
    109. 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 Apr 27; (50). PMID: 21559002; PMCID: PMC3169278.
    110. 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. PMID: 21490616; PMCID: PMC3136639.
    111. 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. PMID: 21471095; PMCID: PMC3136996.
    112. 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. PMID: 21289313; PMCID: PMC4410097.
    113. 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. PMID: 21245033; PMCID: PMC3089446.
    114. Zhang Y, Anderson M, Weisman JL, Lu M, Choy CJ, Boyd VA, Price J, Sigal M, Clark J, Connelly M, Zhu F, Guiguemde WA, Jeffries C, Yang L, Lemoff A, Liou AP, Webb TR, Derisi JL, Guy RK. Evaluation of Diarylureas for Activity Against Plasmodium falciparum. ACS Med Chem Lett. 2010 Dec 09; 1(9):460-465. PMID: 21243104.
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    115. 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 Nov 08; 5(11):e13875. PMID: 21079731; PMCID: PMC2975632.
    116. 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. PMID: 20802496; PMCID: PMC2937095.
    117. 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. PMID: 20739504; PMCID: PMC2952992.
    118. 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. PMID: 20622218.
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    119. 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. PMID: 20592079; PMCID: PMC2937614.
    120. Ganem D, Kistler A, DeRisi J. Achalasia and viral infection: new insights from veterinary medicine. Sci Transl Med. 2010 May 26; 2(33):33ps24. PMID: 20505212.
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    121. 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. PMID: 20485428; PMCID: PMC2874979.
    122. 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. PMID: 20361799; PMCID: PMC2866084.
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    171. 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. PMID: 12429852; PMCID: PMC137777.
    172. 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 01; 62(15):4525-30. PMID: 12154065.
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    173. 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 09; 99(14):9316-21. PMID: 12084816.
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