Joe Derisi, PhD

Title(s)Professor, Biochemistry and Biophysics
SchoolSchool of Medicine
Address1700 4th St
San Francisco CA 94158
Phone415-418-3647
ORCID ORCID Icon0000-0002-4611-9205 Additional info
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    Other Positions
    Title(s)Howard Hughes Investigator


    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 T32EB009383Apr 1, 2009 - Jun 30, 2023
    Role: Principal Investigator
    Pacific Southwest RCE for Biodefense & Emerging Infectious Diseases Research
    NIH U54AI065359May 20, 2005 - Apr 30, 2015
    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 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. to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Anti-SARS-CoV-2 and Autoantibody Profiles in the Cerebrospinal Fluid of 3 Teenaged Patients With COVID-19 and Subacute Neuropsychiatric Symptoms. JAMA Neurol. 2021 Oct 25. Bartley CM, Johns C, Ngo TT, Dandekar R, Loudermilk RL, Alvarenga BD, Hawes IA, Zamecnik CR, Zorn KC, Alexander JR, Wapniarski AE, DeRisi JL, Francisco C, Nash KB, Wietstock SO, Pleasure SJ, Wilson MR. PMID: 34694339.
      View in: PubMed   Mentions:
    2. Long-term MRI changes in a patient with Kelch-like protein 11-associated paraneoplastic neurological syndrome. Eur J Neurol. 2021 Sep 24. Ishikawa H, Mandel-Brehm C, Shindo A, Cady MA, Mann SA, Niwa A, Miyashita K, Ii Y, Zorn KC, Taniguchi A, Maeda M, Wilson MR, DeRisi JL, Tomimoto H. PMID: 34561925.
      View in: PubMed   Mentions:    Fields:    
    3. Author Correction: Pan-viral serology implicates enteroviruses in acute flaccid myelitis. Nat Med. 2021 Sep 21. Schubert RD, Hawes IA, Ramachandran PS, Ramesh A, Crawford ED, Pak JE, Wu W, Cheung CK, O'Donovan BD, Tato CM, Lyden A, Tan M, Sit R, Sowa GM, Sample HA, Zorn KC, Banerji D, Khan LM, Bove R, Hauser SL, Gelfand AA, Johnson-Kerner BL, Nash K, Krishnamoorthy KS, Chitnis T, Ding JZ, McMillan HJ, Chiu CY, Briggs B, Glaser CA, Yen C, Chu V, Wadford DA, Dominguez SR, Ng TFF, Marine RL, Lopez AS, Nix WA, Soldatos A, Gorman MP, Benson L, Messacar K, Konopka-Anstadt JL, Oberste MS, DeRisi JL, Wilson MR. PMID: 34548659.
      View in: PubMed   Mentions:    Fields:    
    4. Elevated N-Linked Glycosylation of IgG V Regions in Myasthenia Gravis Disease Subtypes. J Immunol. 2021 Oct 15; 207(8):2005-2014. Mandel-Brehm C, Fichtner ML, Jiang R, Winton VJ, Vazquez SE, Pham MC, Hoehn KB, Kelleher NL, Nowak RJ, Kleinstein SH, Wilson MR, DeRisi JL, O'Connor KC. PMID: 34544801.
      View in: PubMed   Mentions:    Fields:    
    5. A multi-component, community-based strategy to facilitate COVID-19 vaccine uptake among Latinx populations: From theory to practice. PLoS One. 2021; 16(9):e0257111. Marquez C, Kerkhoff AD, Naso J, Contreras MG, Castellanos Diaz E, Rojas S, Peng J, Rubio L, Jones D, Jacobo J, Rojas S, Gonzalez R, Fuchs JD, Black D, Ribeiro S, Nossokoff J, Tulier-Laiwa V, Martinez J, Chamie G, Pilarowski G, DeRisi J, Petersen M, Havlir DV. PMID: 34543291.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansPHPublic Health
    6. Detection of Neoplasms by Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid. JAMA Neurol. 2021 Sep 13. Gu W, Rauschecker AM, Hsu E, Zorn KC, Sucu Y, Federman S, Gopez A, Arevalo S, Sample HA, Talevich E, Nguyen ED, Gottschall M, Nourbakhsh B, Gold CA, Cree BAC, Douglas VC, Richie MB, Shah MP, Josephson SA, Gelfand JM, Miller S, Wang L, Tihan T, DeRisi JL, Chiu CY, Wilson MR. PMID: 34515766.
      View in: PubMed   Mentions:    Fields:    
    7. Upper airway gene expression reveals a more robust innate and adaptive immune response to SARS-CoV-2 in children compared with older adults. Res Sq. 2021 Aug 26. Mick E, Tsitsiklis A, Spottiswoode N, Caldera S, Serpa P, Detweiler A, Neff N, Pisco AO, Li L, Retallack H, Ratnasiri K, Williamson K, Soesanto V, Simões E, Kistler A, Wagner B, DeRisi J, Ambroggio L, Mourani P, Langelier C. PMID: 34462739.
      View in: PubMed   Mentions:
    8. Tracheal aspirate RNA sequencing identifies distinct immunological features of COVID-19 ARDS. Nat Commun. 2021 08 26; 12(1):5152. Sarma A, Christenson SA, Byrne A, Mick E, Pisco AO, DeVoe C, Deiss T, Ghale R, Zha BS, Tsitsiklis A, Jauregui A, Moazed F, Detweiler AM, Spottiswoode N, Sinha P, Neff N, Tan M, Serpa PH, Willmore A, Ansel KM, Wilson JG, Leligdowicz A, Siegel ER, Sirota M, DeRisi JL, Matthay MA, COMET Consortium , Hendrickson CM, Kangelaris KN, Krummel MF, Woodruff PG, Erle DJ, Calfee CS, Langelier CR. PMID: 34446707.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    9. Type I interferon autoantibodies are associated with systemic immune alterations in patients with COVID-19. Sci Transl Med. 2021 09 22; 13(612):eabh2624. van der Wijst MGP, Vazquez SE, Hartoularos GC, Bastard P, Grant T, Bueno R, Lee DS, Greenland JR, Sun Y, Perez R, Ogorodnikov A, Ward A, Mann SA, Lynch KL, Yun C, Havlir DV, Chamie G, Marquez C, Greenhouse B, Lionakis MS, Norris PJ, Dumont LJ, Kelly K, Zhang P, Zhang Q, Gervais A, Le Voyer T, Whatley A, Si Y, Byrne A, Combes AJ, Rao AA, Song YS, Fragiadakis GK, Kangelaris K, Calfee CS, Erle DJ, Hendrickson C, Krummel MF, Woodruff PG, Langelier CR, Casanova JL, Derisi JL, Anderson MS, Ye CJ, UCSF COMET consortium . PMID: 34429372.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    10. Metagenomic characterization of swine slurry in a North American swine farm operation. Sci Rep. 2021 Aug 20; 11(1):16994. Ramesh A, Bailey ES, Ahyong V, Langelier C, Phelps M, Neff N, Sit R, Tato C, DeRisi JL, Greer AG, Gray GC. PMID: 34417469.
      View in: PubMed   Mentions:    Fields:    
    11. Label-free imaging and classification of live P. falciparum enables high performance parasitemia quantification without fixation or staining. PLoS Comput Biol. 2021 Aug; 17(8):e1009257. Lebel P, Dial R, Vemuri VNP, Garcia V, DeRisi J, Gómez-Sjöberg R. PMID: 34370724.
      View in: PubMed   Mentions:    Fields:    
    12. Persistence of Ambigrammatic Narnaviruses Requires Translation of the Reverse Open Reading Frame. J Virol. 2021 06 10; 95(13):e0010921. Retallack H, Popova KD, Laurie MT, Sunshine S, DeRisi JL. PMID: 33762418.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    13. Detection of cryptogenic malignancies from metagenomic whole genome sequencing of body fluids. Genome Med. 2021 Jun 01; 13(1):98. Gu W, Talevich E, Hsu E, Qi Z, Urisman A, Federman S, Gopez A, Arevalo S, Gottschall M, Liao L, Tung J, Chen L, Lim H, Ho C, Kasowski M, Oak J, Holmes BJ, Yeh I, Yu J, Wang L, Miller S, DeRisi JL, Prakash S, Simko J, Chiu CY. PMID: 34074327.
      View in: PubMed   Mentions:    Fields:    
    14. Phage display demonstrates durable differences in serological profile by route of inoculation in primary infections of non-human primates with Dengue Virus 1. Sci Rep. 2021 05 24; 11(1):10823. Rajan JV, McCracken M, Mandel-Brehm C, Gromowski G, Pollett S, Jarman R, DeRisi JL. PMID: 34031504.
      View in: PubMed   Mentions:    Fields:    
    15. Neutralizing Autoantibodies to Type I Interferons in COVID-19 Convalescent Donor Plasma. J Clin Immunol. 2021 08; 41(6):1169-1171. Vazquez SE, Bastard P, Kelly K, Gervais A, Norris PJ, Dumont LJ, Casanova JL, Anderson MS, DeRisi JL. PMID: 34009544.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    16. Divergent and self-reactive immune responses in the CNS of COVID-19 patients with neurological symptoms. Cell Rep Med. 2021 May 18; 2(5):100288. Song E, Bartley CM, Chow RD, Ngo TT, Jiang R, Zamecnik CR, Dandekar R, Loudermilk RP, Dai Y, Liu F, Sunshine S, Liu J, Wu W, Hawes IA, Alvarenga BD, Huynh T, McAlpine L, Rahman NT, Geng B, Chiarella J, Goldman-Israelow B, Vogels CBF, Grubaugh ND, Casanovas-Massana A, Phinney BS, Salemi M, Alexander JR, Gallego JA, Lencz T, Walsh H, Wapniarski AE, Mohanty S, Lucas C, Klein J, Mao T, Oh J, Ring A, Spudich S, Ko AI, Kleinstein SH, Pak J, DeRisi JL, Iwasaki A, Pleasure SJ, Wilson MR, Farhadian SF. PMID: 33969321.
      View in: PubMed   Mentions: 5  
    17. Use of unbiased metagenomic and transcriptomic analyses to investigate the association between feline calicivirus and feline chronic gingivostomatitis in domestic cats. Am J Vet Res. 2021 May; 82(5):381-394. Fried WA, Soltero-Rivera M, Ramesh A, Lommer MJ, Arzi B, DeRisi JL, Horst JA. PMID: 33904799.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    18. Impaired immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19. Res Sq. 2021 Apr 23. Tsitsiklis A, Zha B, Byrne A, DeVoe C, Levan S, Rackaityte E, Sunshine S, Mick E, Ghale R, Jauregui A, Neff N, Sarma A, Serpa P, Deiss T, Kistler A, Carrillo S, Ansel KM, Leligdowicz A, Christenson S, Jones N, Wu B, Darmanis S, Matthay M, Lynch S, DeRisi J, Consortium C, Hendrickson C, Kangelaris K, Krummel M, Woodruff P, Erle D, Rosenberg O, Calfee C, Langelier C. PMID: 34013247.
      View in: PubMed   Mentions:
    19. Performance Characteristics of a Rapid Severe Acute Respiratory Syndrome Coronavirus 2 Antigen Detection Assay at a Public Plaza Testing Site in San Francisco. J Infect Dis. 2021 04 08; 223(7):1139-1144. Pilarowski G, Lebel P, Sunshine S, Liu J, Crawford E, Marquez C, Rubio L, Chamie G, Martinez J, Peng J, Black D, Wu W, Pak J, Laurie MT, Jones D, Miller S, Jacobo J, Rojas S, Rojas S, Nakamura R, Tulier-Laiwa V, Petersen M, Havlir DV, DeRisi J. PMID: 33394052.
      View in: PubMed   Mentions: 34     Fields:    Translation:Humans
    20. POECIVIRUS IS PRESENT IN INDIVIDUALS WITH BEAK DEFORMITIES IN SEVEN SPECIES OF NORTH AMERICAN BIRDS. J Wildl Dis. 2021 04 01; 57(2):273-281. Zylberberg M, Van Hemert C, Handel CM, Liu RM, DeRisi JL. PMID: 33822149.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    21. Estimation of secondary household attack rates for emergent spike L452R SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco. Clin Infect Dis. 2021 03 31. Peng J, Liu J, Mann SA, Mitchell AM, Laurie MT, Sunshine S, Pilarowski G, Ayscue P, Kistler A, Vanaerschot M, Li LM, McGeever A, Chow ED, Marquez C, Nakamura R, Rubio L, Chamie G, Jones D, Jacobo J, Rojas S, Rojas S, Tulier-Laiwa V, Black D, Martinez J, Naso J, Schwab J, Petersen M, Havlir D, DeRisi J, IDseq Team . PMID: 33788923.
      View in: PubMed   Mentions: 9     Fields:    
    22. Impaired antibacterial immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19. medRxiv. 2021 Mar 26. Tsitsiklis A, Zha BS, Byrne A, Devoe C, Levan S, Rackaityte E, Sunshine S, Mick E, Ghale R, Jauregui A, Sarma A, Neff N, Serpa PH, Deiss TJ, Kistler A, Carrillo S, Ansel KM, Leligdowicz A, Christenson S, Jones N, Wu B, Darmanis S, Matthay MA, Lynch SV, DeRisi JL, COMET Consortium+ , Hendrickson CM, Kangelaris KN, Krummel MF, Woodruff PG, Erle DJ, Rosenberg O, Calfee CS, Langelier CR. PMID: 33791731.
      View in: PubMed   Mentions:
    23. The pulmonary metatranscriptome prior to pediatric HCT identifies post-HCT lung injury. Blood. 2021 03 25; 137(12):1679-1689. Zinter MS, Lindemans CA, Versluys BA, Mayday MY, Sunshine S, Reyes G, Sirota M, Sapru A, Matthay MA, Kharbanda S, Dvorak CC, Boelens JJ, DeRisi JL. PMID: 33512420.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    24. Temporal airway microbiome changes related to ventilator-associated pneumonia in children. Eur Respir J. 2021 03; 57(3). Mourani PM, Sontag MK, Williamson KM, Harris JK, Reeder R, Locandro C, Carpenter TC, Maddux AB, Ziegler K, Simões EAF, Osborne CM, Ambroggio L, Leroue MK, Robertson CE, Langelier C, DeRisi JL, Kamm J, Hall MW, Zuppa AF, Carcillo J, Meert K, Sapru A, Pollack MM, McQuillen P, Notterman DA, Dean JM, Wagner BD, Eunice Kennedy Shriver National Institute of Child Health and Human Development Collaborative Pediat , Eunice Kennedy Shriver National Institute of Child Health and Human Development Collaborative Pediat . PMID: 33008935.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    25. Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19. bioRxiv. 2021 Mar 10. van der Wijst MGP, Vazquez SE, Hartoularos GC, Bastard P, Grant T, Bueno R, Lee DS, Greenland JR, Sun Y, Perez R, Ogorodnikov A, Ward A, Mann SA, Lynch KL, Yun C, Havlir DV, Chamie G, Marquez C, Greenhouse B, Lionakis MS, Norris PJ, Dumont LJ, Kelly K, Zhang P, Zhang Q, Gervais A, Voyer TL, Whatley A, Si Y, Byrne A, Combes AJ, Rao AA, Song YS, UCSF COMET consortium , Fragiadakis GK, Kangelaris K, Calfee CS, Erle DJ, Hendrickson C, Krummel MF, Woodruff PG, Langelier CR, Casanova JL, Derisi JL, Anderson MS, Ye CJ. PMID: 33758859.
      View in: PubMed   Mentions:
    26. Estimation of secondary household attack rates for emergent SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco. medRxiv. 2021 Mar 03. Peng J, Mann SA, Mitchell AM, Liu J, Laurie MT, Sunshine S, Pilarowski G, Ayscue P, Kistler A, Vanaerschot M, Li LM, McGeever A, Chow ED, Team I, Marquez C, Nakamura R, Rubio L, Chamie G, Jones D, Jacobo J, Rojas S, Rojas S, Tulier-Laiwa V, Black D, Martinez J, Naso J, Schwab J, Petersen M, Havlir D, DeRisi J. PMID: 33688689.
      View in: PubMed   Mentions:
    27. Cerebrospinal fluid pterins, pterin-dependent neurotransmitters, and mortality in pediatric cerebral malaria. J Infect Dis. 2021 Feb 22. Rubach MP, Mukemba JP, Florence SM, Lopansri BK, Hyland K, Simmons RA, Langelier C, Nakielny S, DeRisi JL, Yeo TW, Anstey NM, Weinberg JB, Mwaikambo ED, Granger DL. PMID: 33617646.
      View in: PubMed   Mentions:    Fields:    
    28. The COVID-19 epidemic in Madagascar: clinical description and laboratory results of the first wave, march-september 2020. Influenza Other Respir Viruses. 2021 07; 15(4):457-468. Randremanana RV, Andriamandimby SF, Rakotondramanga JM, Razanajatovo NH, Mangahasimbola RT, Randriambolamanantsoa TH, Ranaivoson HC, Rabemananjara HA, Razanajatovo I, Razafindratsimandresy R, Rabarison JH, Brook CE, Rakotomanana F, Rabetombosoa RM, Razafimanjato H, Ahyong V, Raharinosy V, Raharimanga V, Raharinantoanina SJ, Randrianarisoa MM, Bernardson B, Randrianasolo L, Randriamampionona LBN, Tato CM, DeRisi JL, Dussart P, Vololoniaina MC, Randriatsarafara FM, Randriamanantany ZA, Heraud JM. PMID: 33586912.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    29. Nasopharyngeal SARS-CoV-2 viral loads in young children do not differ significantly from those in older children and adults. Sci Rep. 2021 02 04; 11(1):3044. Madera S, Crawford E, Langelier C, Tran NK, Thornborrow E, Miller S, DeRisi JL. PMID: 33542262.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    30. COVID-19 ARDS is characterized by a dysregulated host response that differs from cytokine storm and is modified by dexamethasone. Res Sq. 2021 Jan 14. Sarma A, Christenson S, Mick E, Deiss T, DeVoe C, Pisco A, Ghale R, Jauregui A, Byrne A, Moazed F, Spottiswoode N, Sinha P, Zha B, Neff N, Tan M, Serpa PH, Ansel KM, Wilson J, Leligdowicz A, Seigel E, Sirota M, DeRisi J, Matthay M, Consortium C, Hendrickson C, Kangelaris K, Krummel M, Woodruff P, Erle D, Calfee C, Langelier C. PMID: 33469573.
      View in: PubMed   Mentions:
    31. Genome-Wide Ribosome Profiling of the Plasmodium falciparum Intraerythrocytic Developmental Cycle. Methods Mol Biol. 2021; 2252:57-87. Caro F, DeRisi JL. PMID: 33765271.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    32. Identification of a Polymorphism in the N Gene of SARS-CoV-2 That Adversely Impacts Detection by Reverse Transcription-PCR. J Clin Microbiol. 2020 12 17; 59(1). Vanaerschot M, Mann SA, Webber JT, Kamm J, Bell SM, Bell J, Hong SN, Nguyen MP, Chan LY, Bhatt KD, Tan M, Detweiler AM, Espinosa A, Wu W, Batson J, Dynerman D, Wadford DA, Puschnik AS, Neff N, Ahyong V, Miller S, Ayscue P, Tato CM, Paul S, Kistler AL, DeRisi JL, Crawford ED. PMID: 33067272.
      View in: PubMed   Mentions: 11     Fields:    Translation:Humans
    33. Exploratory neuroimmune profiling identifies CNS-specific alterations in COVID-19 patients with neurological involvement. bioRxiv. 2020 Dec 09. Song E, Bartley CM, Chow RD, Ngo TT, Jiang R, Zamecnik CR, Dandekar R, Loudermilk RP, Dai Y, Liu F, Hawes IA, Alvarenga BD, Huynh T, McAlpine L, Rahman NT, Geng B, Chiarella J, Goldman-Israelow B, Vogels CBF, Grubaugh ND, Casanovas-Massana A, Phinney BS, Salemi M, Alexander J, Gallego JA, Lencz T, Walsh H, Lucas C, Klein J, Mao T, Oh J, Ring A, Spudich S, Ko AI, Kleinstein SH, DeRisi JL, Iwasaki A, Pleasure SJ, Wilson MR, Farhadian SF. PMID: 32935102.
      View in: PubMed   Mentions: 2  
    34. Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy. Cell. 2021 01 21; 184(2):323-333.e9. Fozouni P, Son S, Díaz de León Derby M, Knott GJ, Gray CN, D'Ambrosio MV, Zhao C, Switz NA, Kumar GR, Stephens SI, Boehm D, Tsou CL, Shu J, Bhuiya A, Armstrong M, Harris AR, Chen PY, Osterloh JM, Meyer-Franke A, Joehnk B, Walcott K, Sil A, Langelier C, Pollard KS, Crawford ED, Puschnik AS, Phelps M, Kistler A, DeRisi JL, Doudna JA, Fletcher DA, Ott M. PMID: 33306959.
      View in: PubMed   Mentions: 38     Fields:    Translation:HumansAnimalsCells
    35. Upper airway gene expression reveals suppressed immune responses to SARS-CoV-2 compared with other respiratory viruses. Nat Commun. 2020 11 17; 11(1):5854. Mick E, Kamm J, Pisco AO, Ratnasiri K, Babik JM, Castañeda G, DeRisi JL, Detweiler AM, Hao SL, Kangelaris KN, Kumar GR, Li LM, Mann SA, Neff N, Prasad PA, Serpa PH, Shah SJ, Spottiswoode N, Tan M, Calfee CS, Christenson SA, Kistler A, Langelier C. PMID: 33203890.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansCellsPHPublic Health
    36. Performance characteristics of a rapid SARS-CoV-2 antigen detection assay at a public plaza testing site in San Francisco. medRxiv. 2020 Nov 12. Pilarowski G, Lebel P, Sunshine S, Liu J, Crawford E, Marquez C, Rubio L, Chamie G, Martinez J, Peng J, Black D, Wu W, Pak J, Laurie MT, Jones D, Miller S, Jacobo J, Rojas S, Rojas S, Nakamura R, Tulier-Laiwa V, Petersen M, Havlir DV, CLIAHUB Consortium , DeRisi J. PMID: 33173911.
      View in: PubMed   Mentions: 5  
    37. Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids. Nat Med. 2021 01; 27(1):115-124. Gu W, Deng X, Lee M, Sucu YD, Arevalo S, Stryke D, Federman S, Gopez A, Reyes K, Zorn K, Sample H, Yu G, Ishpuniani G, Briggs B, Chow ED, Berger A, Wilson MR, Wang C, Hsu E, Miller S, DeRisi JL, Chiu CY. PMID: 33169017.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimalsCells
    38. Expanded Clinical Phenotype, Oncological Associations, and Immunopathologic Insights of Paraneoplastic Kelch-like Protein-11 Encephalitis. JAMA Neurol. 2020 11 01; 77(11):1420-1429. Dubey D, Wilson MR, Clarkson B, Giannini C, Gandhi M, Cheville J, Lennon VA, Eggers S, Devine MF, Mandel-Brehm C, Kryzer T, Hinson SR, Khazaie K, Hales C, Kattah J, Pavelko KD, Andrews P, Eaton JE, Jitprapaikulsan J, Mills JR, Flanagan EP, Zekeridou A, Leibovich B, Fryer J, Torre M, Kaufman C, Thoreson JB, Sagen J, Linnoila JJ, DeRisi JL, Howe CL, McKeon A, Pittock SJ. PMID: 32744608.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCells
    39. Rapid deployment of SARS-CoV-2 testing: The CLIAHUB. PLoS Pathog. 2020 10; 16(10):e1008966. Crawford ED, Acosta I, Ahyong V, Anderson EC, Arevalo S, Asarnow D, Axelrod S, Ayscue P, Azimi CS, Azumaya CM, Bachl S, Bachmutsky I, Bhaduri A, Brown JB, Batson J, Behnert A, Boileau RM, Bollam SR, Bonny AR, Booth D, Borja MJB, Brown D, Buie B, Burnett CE, Byrnes LE, Cabral KA, Cabrera JP, Caldera S, Canales G, Castañeda GR, Chan AP, Chang CR, Charles-Orszag A, Cheung C, Chio U, Chow ED, Citron YR, Cohen A, Cohn LB, Chiu C, Cole MA, Conrad DN, Constantino A, Cote A, Crayton-Hall T, Darmanis S, Detweiler AM, Dial RL, Dong S, Duarte EM, Dynerman D, Egger R, Fanton A, Frumm SM, Fu BXH, Garcia VE, Garcia J, Gladkova C, Goldman M, Gomez-Sjoberg R, Gordon MG, Grove JCR, Gupta S, Haddjeri-Hopkins A, Hadley P, Haliburton J, Hao SL, Hartoularos G, Herrera N, Hilberg M, Ho KYE, Hoppe N, Hosseinzadeh S, Howard CJ, Hussmann JA, Hwang E, Ingebrigtsen D, Jackson JR, Jowhar ZM, Kain D, Kim JYS, Kistler A, Kreutzfeld O, Kulsuptrakul J, Kung AF, Langelier C, Laurie MT, Lee L, Leng K, Leon KE, Leonetti MD, Levan SR, Li S, Li AW, Liu J, Lubin HS, Lyden A, Mann J, Mann S, Margulis G, Marquez DM, Marsh BP, Martyn C, McCarthy EE, McGeever A, Merriman AF, Meyer LK, Miller S, Moore MK, Mowery CT, Mukhtar T, Mwakibete LL, Narez N, Neff NF, Osso LA, Oviedo D, Peng S, Phelps M, Phong K, Picard P, Pieper LM, Pincha N, Pisco AO, Pogson A, Pourmal S, Puccinelli RR, Puschnik AS, Rackaityte E, Raghavan P, Raghavan M, Reese J, Replogle JM, Retallack H, Reyes H, Rose D, Rosenberg MF, Sanchez-Guerrero E, Sattler SM, Savy L, See SK, Sellers KK, Serpa PH, Sheehy M, Sheu J, Silas S, Streithorst JA, Strickland J, Stryke D, Sunshine S, Suslow P, Sutanto R, Tamura S, Tan M, Tan J, Tang A, Tato CM, Taylor JC, Tenvooren I, Thompson EM, Thornborrow EC, Tse E, Tung T, Turner ML, Turner VS, Turnham RE, Turocy MJ, Vaidyanathan TV, Vainchtein ID, Vanaerschot M, Vazquez SE, Wandler AM, Wapniarski A, Webber JT, Weinberg ZY, Westbrook A, Wong AW, Wong E, Worthington G, Xie F, Xu A, Yamamoto T, Yang Y, Yarza F, Zaltsman Y, Zheng T, DeRisi JL. PMID: 33112933.
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    40. IDseq-An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring. Gigascience. 2020 10 15; 9(10). Kalantar KL, Carvalho T, de Bourcy CFA, Dimitrov B, Dingle G, Egger R, Han J, Holmes OB, Juan YF, King R, Kislyuk A, Lin MF, Mariano M, Morse T, Reynoso LV, Cruz DR, Sheu J, Tang J, Wang J, Zhang MA, Zhong E, Ahyong V, Lay S, Chea S, Bohl JA, Manning JE, Tato CM, DeRisi JL. PMID: 33057676.
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    41. ReScan, a Multiplex Diagnostic Pipeline, Pans Human Sera for SARS-CoV-2 Antigens. Cell Rep Med. 2020 Oct 20; 1(7):100123. Zamecnik CR, Rajan JV, Yamauchi KA, Mann SA, Loudermilk RP, Sowa GM, Zorn KC, Alvarenga BD, Gaebler C, Caskey M, Stone M, Norris PJ, Gu W, Chiu CY, Ng D, Byrnes JR, Zhou XX, Wells JA, Robbiani DF, Nussenzweig MC, DeRisi JL, Wilson MR. PMID: 32995758.
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    42. Deep profiling of protease substrate specificity enabled by dual random and scanned human proteome substrate phage libraries. Proc Natl Acad Sci U S A. 2020 10 13; 117(41):25464-25475. Zhou J, Li S, Leung KK, O'Donovan B, Zou JY, DeRisi JL, Wells JA. PMID: 32973096.
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    43. Genomic Profiling of Evolving Daptomycin Resistance in a Patient with Recurrent Staphylococcus argenteus Sepsis. Antimicrob Agents Chemother. 2020 09 21; 64(10). Hao S, Abdelghany M, Lyden A, Sit R, Tan M, Tato CM, DeRisi JL, Miller S, Doernberg SB, Langelier C. PMID: 32601156.
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    44. A pathogenic and clonally expanded B cell transcriptome in active multiple sclerosis. Proc Natl Acad Sci U S A. 2020 09 15; 117(37):22932-22943. Ramesh A, Schubert RD, Greenfield AL, Dandekar R, Loudermilk R, Sabatino JJ, Koelzer MT, Tran EB, Koshal K, Kim K, Pröbstel AK, Banerji D, University of California, San Francisco MS-EPIC Team , Guo CY, Green AJ, Bove RM, DeRisi JL, Gelfand JM, Cree BAC, Zamvil SS, Baranzini SE, Hauser SL, Wilson MR. PMID: 32859762.
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    45. Clinical features, diagnostics, and outcomes of patients presenting with acute respiratory illness: A retrospective cohort study of patients with and without COVID-19. EClinicalMedicine. 2020 Oct; 27:100518. Shah SJ, Barish PN, Prasad PA, Kistler A, Neff N, Kamm J, Li LM, Chiu CY, Babik JM, Fang MC, Abe-Jones Y, Alipanah N, Alvarez FN, Botvinnik OB, Castaneda G, CZB CLIAhub Consortium , Dadasovich RM, Davis J, Deng X, DeRisi JL, Detweiler AM, Federman S, Haliburton J, Hao S, Kerkhoff AD, Kumar GR, Malcolm KB, Mann SA, Martinez S, Mary RK, Mick E, Mwakibete L, Najafi N, Peluso MJ, Phelps M, Pisco AO, Ratnasiri K, Rubio LA, Sellas A, Sherwood KD, Sheu J, Spottiswoode N, Tan M, Yu G, Kangelaris KN, Langelier C. PMID: 32864588.
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    46. Investigating Transfusion-related Sepsis Using Culture-Independent Metagenomic Sequencing. Clin Infect Dis. 2020 08 22; 71(5):1179-1185. Crawford E, Kamm J, Miller S, Li LM, Caldera S, Lyden A, Yokoe D, Nichols A, Tran NK, Barnard SE, Conner PM, Nambiar A, Zinter MS, Moayeri M, Serpa PH, Prince BC, Quan J, Sit R, Tan M, Phelps M, Derisi JL, Tato CM, Langelier C. PMID: 31563940.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    47. High-resolution epitope mapping of anti-Hu and anti-Yo autoimmunity by programmable phage display. Brain Commun. 2020; 2(2):fcaa059. O'Donovan B, Mandel-Brehm C, Vazquez SE, Liu J, Parent AV, Anderson MS, Kassimatis T, Zekeridou A, Hauser SL, Pittock SJ, Chow E, Wilson MR, DeRisi JL. PMID: 32954318.
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    48. Erratum. Pediatr Dent. 2020 07 15; 42(4):248. DeRisi JL. PMID: 32847662.
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    49. Complete Genome Sequence of a Novel Coronavirus (SARS-CoV-2) Isolate from Bangladesh. Microbiol Resour Announc. 2020 Jun 11; 9(24). Saha S, Malaker R, Sajib MSI, Hasanuzzaman M, Rahman H, Ahmed ZB, Islam MS, Islam M, Hooda Y, Ahyong V, Vanaerschot M, Batson J, Hao S, Kamm J, Kistler A, Tato CM, DeRisi JL, Saha SK. PMID: 32527780.
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    50. Upper airway gene expression differentiates COVID-19 from other acute respiratory illnesses and reveals suppression of innate immune responses by SARS-CoV-2. medRxiv. 2020 May 19. Mick E, Kamm J, Pisco AO, Ratnasiri K, Babik JM, Calfee CS, Castañeda G, DeRisi JL, Detweiler AM, Hao S, Kangelaris KN, Kumar GR, Li LM, Mann SA, Neff N, Prasad PA, Serpa PH, Shah SJ, Spottiswoode N, Tan M, Christenson SA, Kistler A, Langelier C. PMID: 32511476.
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    51. Identification of novel, clinically correlated autoantigens in the monogenic autoimmune syndrome APS1 by proteome-wide PhIP-Seq. Elife. 2020 05 15; 9. Vazquez SE, Ferré EM, Scheel DW, Sunshine S, Miao B, Mandel-Brehm C, Quandt Z, Chan AY, Cheng M, German M, Lionakis M, DeRisi JL, Anderson MS. PMID: 32410729.
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    52. Enhanced Tooth Structure Via Silver Microwires Following Treatment with 38 Percent Silver Diamine Fluoride. Pediatr Dent. 2020 May 15; 42(3):226-231. Seto J, Horst JA, Parkinson DY, Frachella JC, DeRisi JL. PMID: 32522328.
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    53. Clinical features, diagnostics, and outcomes of patients presenting with acute respiratory illness: a comparison of patients with and without COVID-19. medRxiv. 2020 May 06. Shah SJ, Barish PN, Prasad PA, Kistler AL, Neff N, Kamm J, Li LM, Chiu CY, Babick JM, Fang MC, Abe-Jones Y, Alipanah N, Alvarez FN, Botvinnik OB, Davis JM, Castenada GD, Consortium C, Dadasovich RM, Deng X, DeRisi JL, Detweiler AM, Federman S, Haliburton JR, Hao SL, Kerkhoff AD, Kumar R, Malcolm K, Mann SA, Martinez SP, Marya R, Mick E, Mwakibete LL, Najafi N, Peluso MJ, Phelps MS, Pisco AO, Ratnasiri K, Rubio LA, Sellas AB, Sherwood KD, Sheu J, Spottiswoode N, Tan M, Yu G, Kangelaris KN, Langelier C. PMID: 32511488.
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    54. Central Nervous System Virus Infection in African Children with Cerebral Malaria. Am J Trop Med Hyg. 2020 07; 103(1):200-205. Postels DG, Osei-Tutu L, Seydel KB, Xu Q, Li C, Taylor TE, John CC, Mallewa M, Solomon T, Agbenyega T, Ansong D, Opoka RO, Khan LM, Ramachandran PS, Leon KE, DeRisi JL, Langelier C, Wilson MR. PMID: 32342847.
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    55. Identification of anisomycin, prodigiosin and obatoclax as compounds with broad-spectrum anti-parasitic activity. PLoS Negl Trop Dis. 2020 03; 14(3):e0008150. Ehrenkaufer G, Li P, Stebbins EE, Kangussu-Marcolino MM, Debnath A, White CV, Moser MS, DeRisi J, Gisselberg J, Yeh E, Wang SC, Company AH, Monti L, Caffrey CR, Huston CD, Wang B, Singh U. PMID: 32196500.
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    56. Genomic and serologic characterization of enterovirus A71 brainstem encephalitis. Neurol Neuroimmunol Neuroinflamm. 2020 05; 7(3). Leon KE, Schubert RD, Casas-Alba D, Hawes IA, Ramachandran PS, Ramesh A, Pak JE, Wu W, Cheung CK, Crawford ED, Khan LM, Launes C, Sample HA, Zorn KC, Cabrerizo M, Valero-Rello A, Langelier C, Muñoz-Almagro C, DeRisi JL, Wilson MR. PMID: 32139440.
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    57. Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia. bioRxiv. 2020 Mar 05. Manning JE, Bohl JA, Lay S, Chea S, Sovann L, Sengdoeurn Y, Heng S, Vuthy C, Kalantar K, Ahyong V, Tan M, Sheu J, Tato CM, DeRisi JL, Baril L, Duong V, Dussart P, Karlsson EA. PMID: 32511296.
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    58. Detection of Pneumonia Pathogens from Plasma Cell-Free DNA. Am J Respir Crit Care Med. 2020 02 15; 201(4):491-495. Langelier C, Fung M, Caldera S, Deiss T, Lyden A, Prince BC, Serpa PH, Moazed F, Chin-Hong P, DeRisi JL, Calfee CS. PMID: 31647702.
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    59. The Molecular Medicine Investigation Unit: Linking Patient Care and Scientific Inquiry in Physician-Scientist Training. J Grad Med Educ. 2020 Feb; 12(1):92-97. Berger A, Matloubian M, Shah NP, Wachter RM, DeRisi JL, Anderson M. PMID: 32089799.
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    60. Plasmodium falciparum Resistance to a Lead Benzoxaborole Due to Blocked Compound Activation and Altered Ubiquitination or Sumoylation. mBio. 2020 01 28; 11(1). Sindhe KMV, Wu W, Legac J, Zhang YK, Easom EE, Cooper RA, Plattner JJ, Freund YR, DeRisi JL, Rosenthal PJ. PMID: 31992618.
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    61. Exploratory analysis of the potential for advanced diagnostic testing to reduce healthcare expenditures of patients hospitalized with meningitis or encephalitis. PLoS One. 2020; 15(1):e0226895. Fulton BD, Proudman DG, Sample HA, Gelfand JM, Chiu CY, DeRisi JL, Wilson MR. PMID: 31940319.
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    62. Unbiased Metagenomic Sequencing for Pediatric Meningitis in Bangladesh Reveals Neuroinvasive Chikungunya Virus Outbreak and Other Unrealized Pathogens. mBio. 2019 12 17; 10(6). Saha S, Ramesh A, Kalantar K, Malaker R, Hasanuzzaman M, Khan LM, Mayday MY, Sajib MSI, Li LM, Langelier C, Rahman H, Crawford ED, Tato CM, Islam M, Juan YF, de Bourcy C, Dimitrov B, Wang J, Tang J, Sheu J, Egger R, De Carvalho TR, Wilson MR, Saha SK, DeRisi JL. PMID: 31848287.
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    63. An exploration of ambigrammatic sequences in narnaviruses. Sci Rep. 2019 11 29; 9(1):17982. DeRisi JL, Huber G, Kistler A, Retallack H, Wilkinson M, Yllanes D. PMID: 31784609.
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    64. Neuroglial stem cell-derived inflammatory pseudotumor (n-SCIPT): clinicopathologic characterization of a novel lesion of the lumbosacral spinal cord and nerve roots following intrathecal allogeneic stem cell intervention. Acta Neuropathol. 2019 12; 138(6):1103-1106. Sloan EA, Sampognaro PJ, Junn JC, Chin C, Jacques L, Ramachandran PS, DeRisi JL, Wilson MR, Kriegstein AR, Bollen AW, Solomon DA, Margeta M, Engstrom JW. PMID: 31659431.
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    65. Pan-viral serology implicates enteroviruses in acute flaccid myelitis. Nat Med. 2019 11; 25(11):1748-1752. Schubert RD, Hawes IA, Ramachandran PS, Ramesh A, Crawford ED, Pak JE, Wu W, Cheung CK, O'Donovan BD, Tato CM, Lyden A, Tan M, Sit R, Sowa GM, Sample HA, Zorn KC, Banerji D, Khan LM, Bove R, Hauser SL, Gelfand AA, Johnson-Kerner BL, Nash K, Krishnamoorthy KS, Chitnis T, Ding JZ, McMillan HJ, Chiu CY, Briggs B, Glaser CA, Yen C, Chu V, Wadford DA, Dominguez SR, Ng TFF, Marine RL, Lopez AS, Nix WA, Soldatos A, Gorman MP, Benson L, Messacar K, Konopka-Anstadt JL, Oberste MS, DeRisi JL, Wilson MR. PMID: 31636453.
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    66. FLASH: a next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences. Nucleic Acids Res. 2019 08 22; 47(14):e83. Quan J, Langelier C, Kuchta A, Batson J, Teyssier N, Lyden A, Caldera S, McGeever A, Dimitrov B, King R, Wilheim J, Murphy M, Ares LP, Travisano KA, Sit R, Amato R, Mumbengegwi DR, Smith JL, Bennett A, Gosling R, Mourani PM, Calfee CS, Neff NF, Chow ED, Kim PS, Greenhouse B, DeRisi JL, Crawford ED. PMID: 31114866.
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    67. Kelch-like Protein 11 Antibodies in Seminoma-Associated Paraneoplastic Encephalitis. N Engl J Med. 2019 07 04; 381(1):47-54. Mandel-Brehm C, Dubey D, Kryzer TJ, O'Donovan BD, Tran B, Vazquez SE, Sample HA, Zorn KC, Khan LM, Bledsoe IO, McKeon A, Pleasure SJ, Lennon VA, DeRisi JL, Wilson MR, Pittock SJ. PMID: 31269365.
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    68. Exploratory proteomic analysis implicates the alternative complement cascade in primary CNS vasculitis. Neurology. 2019 07 30; 93(5):e433-e444. Mandel-Brehm C, Retallack H, Knudsen GM, Yamana A, Hajj-Ali RA, Calabrese LH, Tihan T, Sample HA, Zorn KC, Gorman MP, Madan Cohen J, Sreih AG, Marcus JF, Josephson SA, Douglas VC, Gelfand JM, Wilson MR, DeRisi JL. PMID: 31270218.
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    69. Microbiome and Antimicrobial Resistance Gene Dynamics in International Travelers. Emerg Infect Dis. 2019 07; 25(7):1380-1383. Langelier C, Graves M, Kalantar K, Caldera S, Durrant R, Fisher M, Backman R, Tanner W, DeRisi JL, Leung DT. PMID: 31211676.
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    70. Metagenomic next-generation sequencing of samples from pediatric febrile illness in Tororo, Uganda. PLoS One. 2019; 14(6):e0218318. Ramesh A, Nakielny S, Hsu J, Kyohere M, Byaruhanga O, de Bourcy C, Egger R, Dimitrov B, Juan YF, Sheu J, Wang J, Kalantar K, Langelier C, Ruel T, Mpimbaza A, Wilson MR, Rosenthal PJ, DeRisi JL. PMID: 31220115.
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    71. Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis. N Engl J Med. 2019 06 13; 380(24):2327-2340. Wilson MR, Sample HA, Zorn KC, Arevalo S, Yu G, Neuhaus J, Federman S, Stryke D, Briggs B, Langelier C, Berger A, Douglas V, Josephson SA, Chow FC, Fulton BD, DeRisi JL, Gelfand JM, Naccache SN, Bender J, Dien Bard J, Murkey J, Carlson M, Vespa PM, Vijayan T, Allyn PR, Campeau S, Humphries RM, Klausner JD, Ganzon CD, Memar F, Ocampo NA, Zimmermann LL, Cohen SH, Polage CR, DeBiasi RL, Haller B, Dallas R, Maron G, Hayden R, Messacar K, Dominguez SR, Miller S, Chiu CY. PMID: 31189036.
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    72. Sentinel Case of Candida auris in the Western United States Following Prolonged Occult Colonization in a Returned Traveler from India. Microb Drug Resist. 2019 Jun; 25(5):677-680. Woodworth MH, Dynerman D, Crawford ED, Doernberg SB, Ramirez-Avila L, Serpa PH, Nichols A, Li LM, Lyden A, Tato CM, Miller S, Derisi JL, Langelier C. PMID: 31163013.
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    73. Detection of Cryptococcus DNA by Metagenomic Next-generation Sequencing in Symptomatic Cryptococcal Antigenemia. Clin Infect Dis. 2019 05 17; 68(11):1978-1979. Ramachandran PS, Cresswell FV, Meya DB, Langelier C, Crawford ED, DeRisi JL, Boulware DR, Wilson MR. PMID: 30535266.
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    74. Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children. Clin Infect Dis. 2019 05 17; 68(11):1847-1855. Zinter MS, Dvorak CC, Mayday MY, Iwanaga K, Ly NP, McGarry ME, Church GD, Faricy LE, Rowan CM, Hume JR, Steiner ME, Crawford ED, Langelier C, Kalantar K, Chow ED, Miller S, Shimano K, Melton A, Yanik GA, Sapru A, DeRisi JL. PMID: 30239621.
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    75. Genome Sequence of a Divergent Avian Metapneumovirus from a Monk Parakeet (Myiopsitta monachus). Microbiol Resour Announc. 2019 Apr 18; 8(16). Retallack H, Clubb S, DeRisi JL. PMID: 31000555.
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    76. Towards precision quantification of contamination in metagenomic sequencing experiments. Microbiome. 2019 04 16; 7(1):62. Zinter MS, Mayday MY, Ryckman KK, Jelliffe-Pawlowski LL, DeRisi JL. PMID: 30992055.
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    77. Bergeyella cardium: Clinical Characteristics and Draft Genome of an Emerging Pathogen in Native and Prosthetic Valve Endocarditis. Open Forum Infect Dis. 2019 Apr; 6(4):ofz134. Mulliken JS, Langelier C, Budak JZ, Miller S, Dynerman D, Hao S, Li LM, Crawford E, Lyden A, Woodworth MH, DeRisi JL, Desmond E, Browne C, Luu A, Grandis DJ, Grossman W, Deuse T, Melcher GP. PMID: 31024974.
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    78. Taxonomy of the order Bunyavirales: second update 2018. Arch Virol. 2019 Mar; 164(3):927-941. 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. PMID: 30663021.
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    79. Metagenomic comparison of tracheal aspirate and mini-bronchial alveolar lavage for assessment of respiratory microbiota. . 2019 03 01; 316(3):L578-L584. 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. PMID: 30652494.
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    80. Miniaturization and optimization of 384-well compatible RNA sequencing library preparation. PLoS One. 2019; 14(1):e0206194. Mayday MY, Khan LM, Chow ED, Zinter MS, DeRisi JL. PMID: 30629604.
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    81. Clinicopathology conference: 41-year-old woman with chronic relapsing meningitis. Ann Neurol. 2019 02; 85(2):161-169. 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. PMID: 30565288.
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    82. Misinterpretation of Study Data-Reply. JAMA Neurol. 2019 01 01; 76(1):113-114. Wilson MR, O'Donovan BD, DeRisi JL. PMID: 30477022.
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    83. 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. Sheridan CM, Garcia VE, Ahyong V, DeRisi JL. PMID: 30541569.
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    84. Ebola virus, but not Marburg virus, replicates efficiently and without required adaptation in snake cells. Virus Evol. 2018 Jul; 4(2):vey034. Fedewa G, Radoshitzky SR, Chi X, Dong L, Zeng X, Spear M, Strauli N, Ng M, Chandran K, Stenglein MD, Hernandez RD, Jahrling PB, Kuhn JH, DeRisi JL. PMID: 30524754.
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    85. 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 12 26; 115(52):E12353-E12362. 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. PMID: 30482864.
      View in: PubMed   Mentions: 66     Fields:    Translation:HumansCells
    86. 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 10 30; 9(5). Laurie MT, White CV, Retallack H, Wu W, Moser MS, Sakanari JA, Ang K, Wilson C, Arkin MR, DeRisi JL. PMID: 30377287.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    87. 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. 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. PMID: 30339670.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    88. 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. 2019 04; 55(2):375-386. Retallack H, Okihiro MS, Britton E, Sommeran SV, DeRisi JL. PMID: 30289337.
      View in: PubMed   Mentions: 2     Fields:    Translation:Animals
    89. Chronic Meningitis Investigated via Metagenomic Next-Generation Sequencing. JAMA Neurol. 2018 08 01; 75(8):947-955. 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. PMID: 29710329.
      View in: PubMed   Mentions: 55     Fields:    Translation:HumansAnimalsCells
    90. 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). 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. PMID: 30037883.
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    91. Whole-Genome mRNA Gene Expression Differs Between Patients With and Without Delirium. J Geriatr Psychiatry Neurol. 2018 07; 31(4):203-210. Kalantar K, LaHue SC, DeRisi JL, Sample HA, Contag CA, Josephson SA, Wilson MR, Douglas VC. PMID: 29991314.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    92. Avian keratin disorder of Alaska black-capped chickadees is associated with Poecivirus infection. Virol J. 2018 06 15; 15(1):100. Zylberberg M, Van Hemert C, Handel CM, DeRisi JL. PMID: 29903045.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    93. Fatal Powassan Encephalitis (Deer Tick Virus, Lineage II) in a Patient With Fever and Orchitis Receiving Rituximab. JAMA Neurol. 2018 06 01; 75(6):746-750. 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. PMID: 29554185.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    94. Taxonomy of the family Arenaviridae and the order Bunyavirales: update 2018. Arch Virol. 2018 Aug; 163(8):2295-2310. 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. PMID: 29680923.
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    95. Metagenomic Sequencing Detects Respiratory Pathogens in Hematopoietic Cellular Transplant Patients. Am J Respir Crit Care Med. 2018 02 15; 197(4):524-528. 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. PMID: 28686513.
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    96. IFN-stimulated Gene Expression, Type 2 Inflammation, and Endoplasmic Reticulum Stress in Asthma. Am J Respir Crit Care Med. 2018 02 01; 197(3):313-324. 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. PMID: 29064281.
      View in: PubMed   Mentions: 30     Fields:    Translation:HumansCells
    97. 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). Langelier C, White CV, Sontag MK, Mourani PM, DeRisi JL. PMID: 29192071.
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    98. Metagenomic deep sequencing of aqueous fluid detects intraocular lymphomas. Br J Ophthalmol. 2018 01; 102(1):6-8. Gonzales J, Doan T, Shantha JG, Bloomer M, Wilson MR, DeRisi JL, Acharya N. PMID: 29122821.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    99. 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. Hanna ZR, Henderson JB, Wall JD, Emerling CA, Fuchs J, Runckel C, Mindell DP, Bowie RCK, DeRisi JL, Dumbacher JP. PMID: 28992302.
      View in: PubMed   Mentions: 7     Fields:    Translation:AnimalsCells
    100. 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. Faden DL, Thomas S, Cantalupo PG, Agrawal N, Myers J, DeRisi J. PMID: 29103756.
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    101. 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. Milgrom P, Horst JA, Ludwig S, Rothen M, Chaffee BW, Lyalina S, Pollard KS, DeRisi JL, Mancl L. PMID: 28866468.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCellsPHPublic Health
    102. Differential Disease Susceptibilities in Experimentally Reptarenavirus-Infected Boa Constrictors and Ball Pythons. J Virol. 2017 08 01; 91(15). Stenglein MD, Sanchez-Migallon Guzman D, Garcia VE, Layton ML, Hoon-Hanks LL, Boback SM, Keel MK, Drazenovich T, Hawkins MG, DeRisi JL. PMID: 28515291.
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    103. A novel cause of chronic viral meningoencephalitis: Cache Valley virus. Ann Neurol. 2017 Jul; 82(1):105-114. Wilson MR, Suan D, Duggins A, Schubert RD, Khan LM, Sample HA, Zorn KC, Rodrigues Hoffman A, Blick A, Shingde M, DeRisi JL. PMID: 28628941.
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    104. Extracorporeal life support survival in a pediatric hematopoietic cellular transplant recipient with presumed GvHD-related fulminant myocarditis. Bone Marrow Transplant. 2017 09; 52(9):1330-1333. Zinter MS, Barrows BD, Ursell PC, Kowalek K, Kalantar K, Cambronero N, DeRisi JL, Oishi P, Dvorak CC. PMID: 28581474.
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    105. 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. Crawford ED, Quan J, Horst JA, Ebert D, Wu W, DeRisi JL. PMID: 28542423.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    106. Metagenomic DNA Sequencing for the Diagnosis of Intraocular Infections. Ophthalmology. 2017 08; 124(8):1247-1248. Doan T, Acharya NR, Pinsky BA, Sahoo MK, Chow ED, Banaei N, Budvytiene I, Cevallos V, Zhong L, Zhou Z, Lietman TM, DeRisi JL. PMID: 28526549.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansAnimalsCells
    107. Possibility and Challenges of Conversion of Current Virus Species Names to Linnaean Binomials. Syst Biol. 2017 05 01; 66(3):463-473. 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. PMID: 27798405.
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    108. Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater. PLoS One. 2017; 12(4):e0174930. Ludington WB, Seher TD, Applegate O, Li X, Kliegman JI, Langelier C, Atwill ER, Harter T, DeRisi JL. PMID: 28384184.
      View in: PubMed   Mentions: 4     Fields:    Translation:PHPublic Health
    109. A potent antimalarial benzoxaborole targets a Plasmodium falciparum cleavage and polyadenylation specificity factor homologue. Nat Commun. 2017 03 06; 8:14574. 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. PMID: 28262680.
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    110. MinorityReport, software for generalized analysis of causal genetic variants. Malar J. 2017 02 23; 16(1):90. Horst JA, Wu W, DeRisi JL. PMID: 28231785.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimals
    111. Interaction between FMDV Lpro and transcription factor ADNP is required for optimal viral replication. Virology. 2017 05; 505:12-22. Medina GN, Knudsen GM, Greninger AL, Kloc A, Díaz-San Segundo F, Rieder E, Grubman MJ, DeRisi JL, de Los Santos T. PMID: 28219017.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansAnimalsCells
    112. 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. Faden DL, Asthana S, Tihan T, DeRisi J, Kliot M. PMID: 28207875.
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    113. The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell. Curr Biol. 2017 Feb 20; 27(4):569-575. 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. PMID: 28190732.
      View in: PubMed   Mentions: 25     Fields:    Translation:AnimalsCells
    114. Whole Exome Sequencing of Growing and Non-Growing Cutaneous Neurofibromas from a Single Patient with Neurofibromatosis Type 1. PLoS One. 2017; 12(1):e0170348. Faden DL, Asthana S, Tihan T, DeRisi J, Kliot M. PMID: 28099461.
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    115. Altered Plasmodium falciparum Sensitivity to the Antiretroviral Protease Inhibitor Lopinavir Associated with Polymorphisms in pfmdr1. Antimicrob Agents Chemother. 2017 01; 61(1). Sonoiki E, Nsanzabana C, Legac J, Sindhe KM, DeRisi J, Rosenthal PJ. PMID: 27821443.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    116. 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. 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. PMID: 27911847.
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    117. Erratum to: Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens. Genome Med. 2016 11 22; 8(1):123. 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. PMID: 27876088.
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    118. A Herpesviral induction of RAE-1 NKG2D ligand expression occurs through release of HDAC mediated repression. Elife. 2016 11 22; 5. Greene TT, Tokuyama M, Knudsen GM, Kunz M, Lin J, Greninger AL, DeFilippis VR, DeRisi JL, Raulet DH, Coscoy L. PMID: 27874833.
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    119. Detection and prevalence of boid inclusion body disease in collections of boas and pythons using immunological assays. Vet J. 2016 Dec; 218:13-18. Chang L, Fu D, Stenglein MD, Hernandez JA, DeRisi JL, Jacobson ER. PMID: 27938703.
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    120. Acute West Nile Virus Meningoencephalitis Diagnosed Via Metagenomic Deep Sequencing of Cerebrospinal Fluid in a Renal Transplant Patient. Am J Transplant. 2017 03; 17(3):803-808. Wilson MR, Zimmermann LL, Crawford ED, Sample HA, Soni PR, Baker AN, Khan LM, DeRisi JL. PMID: 27647685.
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    121. Programmable Microfluidic Synthesis of Over One Thousand Uniquely Identifiable Spectral Codes. Adv Opt Mater. 2017 Feb 02; 5(3). Nguyen HQ, Baxter BC, Brower K, Diaz-Botia CA, DeRisi JL, Fordyce PM, Thorn KS. PMID: 28936383.
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    122. Neurologic Complications of Common Variable Immunodeficiency. J Clin Immunol. 2016 11; 36(8):793-800. Nguyen JT, Green A, Wilson MR, DeRisi JL, Gundling K. PMID: 27704236.
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    123. Targeted next-generation sequencing of TP53 in oral tongue carcinoma from non-smokers. J Otolaryngol Head Neck Surg. 2016 Sep 17; 45(1):47. Faden DL, Arron ST, Heaton CM, DeRisi J, South AP, Wang SJ. PMID: 27640185.
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    124. Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens. Genome Med. 2016 08 25; 8(1):90. 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. PMID: 27562436.
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    125. Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond. PLoS Pathog. 2016 07; 12(7):e1005763. 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. PMID: 27467575.
      View in: PubMed   Mentions: 79     Fields:    Translation:Humans
    126. Novel Picornavirus Associated with Avian Keratin Disorder in Alaskan Birds. mBio. 2016 07 26; 7(4). Zylberberg M, Van Hemert C, Dumbacher JP, Handel CM, Tihan T, DeRisi JL. PMID: 27460795.
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    127. Antimalarial Benzoxaboroles Target Plasmodium falciparum Leucyl-tRNA Synthetase. Antimicrob Agents Chemother. 2016 08; 60(8):4886-95. 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. PMID: 27270277.
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    128. Multiplexed Metagenomic Deep Sequencing To Analyze the Composition of High-Priority Pathogen Reagents. mSystems. 2016 Jul-Aug; 1(4). Wilson MR, Fedewa G, Stenglein MD, Olejnik J, Rennick LJ, Nambulli S, Feldmann F, Duprex WP, Connor JH, Mühlberger E, DeRisi JL. PMID: 27822544.
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    129. Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting. Elife. 2016 04 25; 5. 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. PMID: 27111525.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansAnimals
    130. 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. Ahyong V, Sheridan CM, Leon KE, Witchley JN, Diep J, DeRisi JL. PMID: 26987601.
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    131. Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications. Genome Biol. 2016 Mar 04; 17:41. Gu W, Crawford ED, O'Donovan BD, Wilson MR, Chow ED, Retallack H, DeRisi JL. PMID: 26944702.
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    132. 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. Soupene E, Kao J, Cheng DH, Wang D, Greninger AL, Knudsen GM, DeRisi JL, Kuypers FA. PMID: 26621918.
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    133. 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). Hanna ZR, Runckel C, Fuchs J, DeRisi JL, Mindell DP, Van Hemert C, Handel CM, Dumbacher JP. PMID: 26404604.
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    134. Diagnosing Balamuthia mandrillaris Encephalitis With Metagenomic Deep Sequencing. Ann Neurol. 2015 Nov; 78(5):722-30. 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. PMID: 26290222.
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    135. Draft Genome Sequence of Picalivirus D Recovered from San Francisco Wastewater. Genome Announc. 2015 Jul 02; 3(4). Greninger AL, DeRisi JL. PMID: 26139708.
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    136. Draft Genome Sequence of Laverivirus UC1, a Dicistrovirus-Like RNA Virus Featuring an Unusual Genome Organization. Genome Announc. 2015 Jul 02; 3(4). Greninger AL, DeRisi JL. PMID: 26139710.
      View in: PubMed   Mentions: 1  
    137. Draft Genome Sequence of Tombunodavirus UC1. Genome Announc. 2015 Jul 02; 3(4). Greninger AL, DeRisi JL. PMID: 26139709.
      View in: PubMed   Mentions: 3  
    138. Past, present, and future of arenavirus taxonomy. Arch Virol. 2015 Jul; 160(7):1851-74. 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. PMID: 25935216.
      View in: PubMed   Mentions: 63     Fields:    Translation:HumansAnimalsCells
    139. Draft Genome Sequences of Leviviridae RNA Phages EC and MB Recovered from San Francisco Wastewater. Genome Announc. 2015 Jun 25; 3(3). Greninger AL, DeRisi JL. PMID: 26112785.
      View in: PubMed   Mentions: 6  
    140. Draft Genome Sequences of Ciliovirus and Brinovirus from San Francisco Wastewater. Genome Announc. 2015 Jun 25; 3(3). Greninger AL, DeRisi JL. PMID: 26112784.
      View in: PubMed   Mentions: 7  
    141. 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). Greninger AL, DeRisi JL. PMID: 26089423.
      View in: PubMed   Mentions: 5  
    142. Widespread recombination, reassortment, and transmission of unbalanced compound viral genotypes in natural arenavirus infections. PLoS Pathog. 2015 May; 11(5):e1004900. 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. PMID: 25993603.
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    143. 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. O'Donoghue AJ, Knudsen GM, Beekman C, Perry JA, Johnson AD, DeRisi JL, Craik CS, Bennett RJ. PMID: 25944934.
      View in: PubMed   Mentions: 30     Fields:    Translation:AnimalsCells
    144. Correction: Programmable microfluidic synthesis of spectrally encoded microspheres. Lab Chip. 2015 Feb 21; 15(4):1213. Gerver RE, Gómez-Sjöberg R, Baxter BC, Thorn KS, Fordyce PM, Diaz-Botia CA, Helms BA, DeRisi JL. PMID: 25619960.
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    145. Salinipostins A-K, long-chain bicyclic phosphotriesters as a potent and selective antimalarial chemotype. J Org Chem. 2015 Feb 06; 80(3):1312-20. Schulze CJ, Navarro G, Ebert D, DeRisi J, Linington RG. PMID: 25584395.
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    146. Genome-wide regulatory dynamics of translation in the Plasmodium falciparum asexual blood stages. Elife. 2014 Dec 10; 3. Caro F, Ahyong V, Betegon M, DeRisi JL. PMID: 25493618.
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    147. Taxonomic reorganization of the family Bornaviridae. Arch Virol. 2015 Feb; 160(2):621-32. 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. PMID: 25449305.
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    148. (+)-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. 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. PMID: 25453091.
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    149. A chemical rescue screen identifies a Plasmodium falciparum apicoplast inhibitor targeting MEP isoprenoid precursor biosynthesis. Antimicrob Agents Chemother. 2015 Jan; 59(1):356-64. Wu W, Herrera Z, Ebert D, Baska K, Cho SH, DeRisi JL, Yeh E. PMID: 25367906.
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    150. Genome Sequence of a Bornavirus Recovered from an African Garter Snake (Elapsoidea loveridgei). Genome Announc. 2014 Oct 09; 2(5). Stenglein MD, Leavitt EB, Abramovitch MA, McGuire JA, DeRisi JL. PMID: 25301640.
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    151. Ball python nidovirus: a candidate etiologic agent for severe respiratory disease in Python regius. mBio. 2014 Sep 09; 5(5):e01484-14. Stenglein MD, Jacobson ER, Wozniak EJ, Wellehan JF, Kincaid A, Gordon M, Porter BF, Baumgartner W, Stahl S, Kelley K, Towner JS, DeRisi JL. PMID: 25205093.
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    152. 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. 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. PMID: 24954188.
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    153. Profile hidden Markov models for the detection of viruses within metagenomic sequence data. PLoS One. 2014; 9(8):e105067. Skewes-Cox P, Sharpton TJ, Pollard KS, DeRisi JL. PMID: 25140992.
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    154. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N Engl J Med. 2014 Jun 19; 370(25):2408-17. 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. PMID: 24896819.
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    155. A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Genome Res. 2014 Jul; 24(7):1180-92. 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. PMID: 24899342.
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    156. How duplicated transcription regulators can diversify to govern the expression of nonoverlapping sets of genes. Genes Dev. 2014 Jun 15; 28(12):1272-7. Pérez JC, Fordyce PM, Lohse MB, Hanson-Smith V, DeRisi JL, Johnson AD. PMID: 24874988.
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    157. The kinase regulator mob1 acts as a patterning protein for stentor morphogenesis. PLoS Biol. 2014 May; 12(5):e1001861. Slabodnick MM, Ruby JG, Dunn JG, Feldman JL, DeRisi JL, Marshall WF. PMID: 24823688.
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    158. Krüppel mediates the selective rebalancing of ion channel expression. Neuron. 2014 May 07; 82(3):537-44. Parrish JZ, Kim CC, Tang L, Bergquist S, Wang T, Derisi JL, Jan LY, Jan YN, Davis GW. PMID: 24811378.
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    159. A draft genome of the honey bee trypanosomatid parasite Crithidia mellificae. PLoS One. 2014; 9(4):e95057. Runckel C, DeRisi J, Flenniken ML. PMID: 24743507.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansAnimals
    160. Transcriptome-wide characterization of the eIF4A signature highlights plasticity in translation regulation. Genome Biol. 2014; 15(10):476. Rubio CA, Weisburd B, Holderfield M, Arias C, Fang E, DeRisi JL, Fanidi A. PMID: 25273840.
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    161. 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. 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. PMID: 24534459.
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    162. 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. Koellhoffer JF, Dai Z, Malashkevich VN, Stenglein MD, Liu Y, Toro R, S Harrison J, Chandran K, DeRisi JL, Almo SC, Lai JR. PMID: 24333483.
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    163. Structure of the transcriptional network controlling white-opaque switching in Candida albicans. Mol Microbiol. 2013 Oct; 90(1):22-35. Hernday AD, Lohse MB, Fordyce PM, Nobile CJ, DeRisi JL, Johnson AD. PMID: 23855748.
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    164. 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. Guler JL, Freeman DL, Ahyong V, Patrapuvich R, White J, Gujjar R, Phillips MA, DeRisi J, Rathod PK. PMID: 23717205.
      View in: PubMed   Mentions: 46     Fields:    Translation:HumansAnimals
    165. PRICE: software for the targeted assembly of components of (Meta) genomic sequence data. G3 (Bethesda). 2013 May 20; 3(5):865-80. Ruby JG, Bellare P, Derisi JL. PMID: 23550143.
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    166. 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. Nelson CS, Fuller CK, Fordyce PM, Greninger AL, Li H, DeRisi JL. PMID: 23625967.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansAnimalsCells
    167. 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. Lohse MB, Hernday AD, Fordyce PM, Noiman L, Sorrells TR, Hanson-Smith V, Nobile CJ, DeRisi JL, Johnson AD. PMID: 23610392.
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    168. 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. Greninger AL, Knudsen GM, Betegon M, Burlingame AL, DeRisi JL. PMID: 23572552.
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    169. Bartonella quintana deploys host and vector temperature-specific transcriptomes. PLoS One. 2013; 8(3):e58773. Abromaitis S, Nelson CS, Previte D, Yoon KS, Clark JM, DeRisi JL, Koehler JE. PMID: 23554923.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    170. Identification and manipulation of the molecular determinants influencing poliovirus recombination. PLoS Pathog. 2013 Feb; 9(2):e1003164. Runckel C, Westesson O, Andino R, DeRisi JL. PMID: 23408891.
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    171. Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. Genome Biol. 2013 Jan 30; 14(1):R10. 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. PMID: 23363705.
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    172. Graduate education. Interdisciplinary graduate training in teaching labs. Science. 2012 Dec 21; 338(6114):1542-3. Vale RD, DeRisi J, Phillips R, Mullins RD, Waterman C, Mitchison TJ. PMID: 23258877.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    173. Programmable microfluidic synthesis of spectrally encoded microspheres. Lab Chip. 2012 Nov 21; 12(22):4716-23. Gerver RE, Gómez-Sjöberg R, Baxter BC, Thorn KS, Fordyce PM, Diaz-Botia CA, Helms BA, DeRisi JL. PMID: 23042484.
      View in: PubMed   Mentions: 18     Fields:    
    174. Discovery of a novel polyomavirus in acute diarrheal samples from children. PLoS One. 2012; 7(11):e49449. 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. PMID: 23166671.
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    175. Systematic characterization of feature dimensions and closing pressures for microfluidic valves produced via photoresist reflow. Lab Chip. 2012 Nov 07; 12(21):4287-95. Fordyce PM, Diaz-Botia CA, DeRisi JL, Gomez-Sjoberg R. PMID: 22930180.
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    176. 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. Kim CC, Nelson CS, Wilson EB, Hou B, DeFranco AL, DeRisi JL. PMID: 23144737.
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    177. 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. Fordyce PM, Pincus D, Kimmig P, Nelson CS, El-Samad H, Walter P, DeRisi JL. PMID: 23054834.
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    178. Molecular insights into the biosynthesis of guadinomine: a type III secretion system inhibitor. J Am Chem Soc. 2012 Oct 24; 134(42):17797-806. Holmes TC, May AE, Zaleta-Rivera K, Ruby JG, Skewes-Cox P, Fischbach MA, DeRisi JL, Iwatsuki M, Omura S, Khosla C. PMID: 23030602.
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    179. Global identification of peptidase specificity by multiplex substrate profiling. Nat Methods. 2012 Nov; 9(11):1095-100. 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. PMID: 23023596.
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    180. Complete genome sequence of an astrovirus identified in a domestic rabbit (Oryctolagus cuniculus) with gastroenteritis. Virol J. 2012 Sep 22; 9:216. Stenglein MD, Velazquez E, Greenacre C, Wilkes RP, Ruby JG, Lankton JS, Ganem D, Kennedy MA, DeRisi JL. PMID: 22998755.
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    181. In-depth investigation of archival and prospectively collected samples reveals no evidence for XMRV infection in prostate cancer. PLoS One. 2012; 7(9):e44954. 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. PMID: 23028701.
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    182. 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. Stenglein MD, Sanders C, Kistler AL, Ruby JG, Franco JY, Reavill DR, Dunker F, Derisi JL. PMID: 22893382.
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    183. Lead optimization of antimalarial propafenone analogues. J Med Chem. 2012 Jul 12; 55(13):6087-93. 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. PMID: 22708838.
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    184. Virus identification in unknown tropical febrile illness cases using deep sequencing. PLoS Negl Trop Dis. 2012; 6(2):e1485. Yozwiak NL, Skewes-Cox P, Stenglein MD, Balmaseda A, Harris E, DeRisi JL. PMID: 22347512.
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    185. Plate-based transfection and culturing technique for genetic manipulation of Plasmodium falciparum. Malar J. 2012 Jan 18; 11:22. Caro F, Miller MG, DeRisi JL. PMID: 22257490.
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    186. The 3A protein from multiple picornaviruses utilizes the golgi adaptor protein ACBD3 to recruit PI4KIIIβ. J Virol. 2012 Apr; 86(7):3605-16. Greninger AL, Knudsen GM, Betegon M, Burlingame AL, Derisi JL. PMID: 22258260.
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    187. A new threat to honey bees, the parasitic phorid fly Apocephalus borealis. PLoS One. 2012; 7(1):e29639. Core A, Runckel C, Ivers J, Quock C, Siapno T, Denault S, Brown B, Derisi J, Smith CD, Hafernik J. PMID: 22235317.
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    188. ReCombine: a suite of programs for detection and analysis of meiotic recombination in whole-genome datasets. PLoS One. 2011; 6(10):e25509. Anderson CM, Chen SY, Dimon MT, Oke A, DeRisi JL, Fung JC. PMID: 22046241.
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    189. Optimization of propafenone analogues as antimalarial leads. J Med Chem. 2011 Nov 10; 54(21):7477-85. Lowes DJ, Guiguemde WA, Connelly MC, Zhu F, Sigal MS, Clark JA, Lemoff AS, Derisi JL, Wilson EB, Guy RK. PMID: 21955244.
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    190. Synthesis and evaluation of 7-substituted 4-aminoquinoline analogues for antimalarial activity. J Med Chem. 2011 Oct 27; 54(20):7084-93. Hwang JY, Kawasuji T, Lowes DJ, Clark JA, Connelly MC, Zhu F, Guiguemde WA, Sigal MS, Wilson EB, Derisi JL, Guy RK. PMID: 21910466.
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    191. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res. 2011 Dec; 21(12):2224-41. 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. PMID: 21926179.
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    192. Chemical rescue of malaria parasites lacking an apicoplast defines organelle function in blood-stage Plasmodium falciparum. PLoS Biol. 2011 Aug; 9(8):e1001138. Yeh E, DeRisi JL. PMID: 21912516.
      View in: PubMed   Mentions: 163     Fields:    Translation:HumansAnimalsCells
    193. 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. Runckel C, Flenniken ML, Engel JC, Ruby JG, Ganem D, Andino R, DeRisi JL. PMID: 21687739.
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    194. Validation of a diagnostic microarray for human papillomavirus: coverage of 102 genotypes. J Nucleic Acids. 2011; 2011:756905. Arron ST, Skewes-Cox P, Do PH, Dybbro E, Da Costa M, Palefsky JM, Derisi JL. PMID: 21785699.
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    195. Using a pan-viral microarray assay (Virochip) to screen clinical samples for viral pathogens. J Vis Exp. 2011 Apr 27; (50). Chen EC, Miller SA, DeRisi JL, Chiu CY. PMID: 21559002.
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    196. Transcriptome sequencing demonstrates that human papillomavirus is not active in cutaneous squamous cell carcinoma. J Invest Dermatol. 2011 Aug; 131(8):1745-53. Arron ST, Ruby JG, Dybbro E, Ganem D, Derisi JL. PMID: 21490616.
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    197. Viral infection in acute exacerbation of idiopathic pulmonary fibrosis. Am J Respir Crit Care Med. 2011 Jun 15; 183(12):1698-702. 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. PMID: 21471095.
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    198. NK cells and immune "memory". J Immunol. 2011 Feb 15; 186(4):1891-7. Sun JC, Lopez-Verges S, Kim CC, DeRisi JL, Lanier LL. PMID: 21289313.
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    199. 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. Sorber K, Dimon MT, DeRisi JL. PMID: 21245033.
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    200. Evaluation of Diarylureas for Activity Against Plasmodium falciparum. ACS Med Chem Lett. 2010 Dec 09; 1(9):460-465. 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. PMID: 21243104.
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    201. 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. Dimon MT, Sorber K, DeRisi JL. PMID: 21079731.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansAnimalsCells
    202. De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis. Nat Biotechnol. 2010 Sep; 28(9):970-5. Fordyce PM, Gerber D, Tran D, Zheng J, Li H, DeRisi JL, Quake SR. PMID: 20802496.
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    203. Serological evidence of human klassevirus infection. Clin Vaccine Immunol. 2010 Oct; 17(10):1584-8. Greninger AL, Holtz L, Kang G, Ganem D, Wang D, DeRisi JL. PMID: 20739504.
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    204. 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. Raghav R, Taylor M, Delay J, Ojkic D, Pearl DL, Kistler AL, Derisi JL, Ganem D, Smith DA. PMID: 20622218.
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    205. 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. Yozwiak NL, Skewes-Cox P, Gordon A, Saborio S, Kuan G, Balmaseda A, Ganem D, Harris E, DeRisi JL. PMID: 20592079.
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    206. Achalasia and viral infection: new insights from veterinary medicine. Sci Transl Med. 2010 May 26; 2(33):33ps24. Hanna RF, Ward TJ, Chow DS, Lagana SM, Moreira RK, Emond JC, Weintraub JL, Prince MR, Ganem D, Kistler A, DeRisi J. PMID: 20505212.
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    207. Chemical genetics of Plasmodium falciparum. Nature. 2010 May 20; 465(7296):311-5. 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. PMID: 20485428.
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    209. 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. Mattiazzi M, Jambhekar A, Kaferle P, Derisi JL, Krizaj I, Petrovic U. PMID: 20379744.
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    210. Cultivation and serological characterization of a human Theiler's-like cardiovirus associated with diarrheal disease. J Virol. 2010 May; 84(9):4407-14. Chiu CY, Greninger AL, Chen EC, Haggerty TD, Parsonnet J, Delwart E, Derisi JL, Ganem D. PMID: 20164225.
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    211. Improved methods for magnetic purification of malaria parasites and haemozoin. Malar J. 2010 Jan 14; 9:17. Kim CC, Wilson EB, DeRisi JL. PMID: 20074366.
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    212. VersaCount: customizable manual tally software for cell counting. Source Code Biol Med. 2010 Jan 13; 5(1):1. Kim CC, Derisi JL. PMID: 20180957.
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    214. An enhanced single base extension technique for the analysis of complex viral populations. PLoS One. 2009 Oct 16; 4(10):e7453. Webster DR, Hekele AG, Lauring AS, Fischer KF, Li H, Andino R, DeRisi JL. PMID: 19834618.
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    215. 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. Niles JC, Derisi JL, Marletta MA. PMID: 19633187.
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    216. Antiparasitic activities of novel, orally available fumagillin analogs. Bioorg Med Chem Lett. 2009 Sep 01; 19(17):5128-31. Hanna RF, Ward TJ, Chow DS, Lagana SM, Moreira RK, Emond JC, Weintraub JL, Prince MR, 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. PMID: 19648008.
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    217. Experimental induction of proventricular dilatation disease in cockatiels (Nymphicus hollandicus) inoculated with brain homogenates containing avian bornavirus 4. Virol J. 2009 Jul 09; 6:100. Gancz AY, Kistler AL, Greninger AL, Farnoushi Y, Mechani S, Perl S, Berkowitz A, Perez N, Clubb S, DeRisi JL, Ganem D, Lublin A. PMID: 19589169.
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    218. The complete genome of klassevirus - a novel picornavirus in pediatric stool. Virol J. 2009 Jun 18; 6:82. Greninger AL, Runckel C, Chiu CY, Haggerty T, Parsonnet J, Ganem D, DeRisi JL. PMID: 19538752.
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    219. 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. Sorber K, Chiu C, Webster D, Dimon M, Ruby JG, Hekele A, DeRisi JL. PMID: 18941527.
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    220. Experimental malaria infection triggers early expansion of natural killer cells. Infect Immun. 2008 Dec; 76(12):5873-82. Kim CC, Parikh S, Sun JC, Myrick A, Lanier LL, Rosenthal PJ, DeRisi JL. PMID: 18824529.
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    221. 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. 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. PMID: 18768820.
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    222. Recovery of divergent avian bornaviruses from cases of proventricular dilatation disease: identification of a candidate etiologic agent. Virol J. 2008 Jul 31; 5:88. 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. PMID: 18671869.
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    223. N-terminal processing of proteins exported by malaria parasites. Mol Biochem Parasitol. 2008 Aug; 160(2):107-15. Chang HH, Falick AM, Carlton PM, Sedat JW, DeRisi JL, Marletta MA. PMID: 18534695.
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    224. Utility of DNA microarrays for detection of viruses in acute respiratory tract infections in children. J Pediatr. 2008 Jul; 153(1):76-83. Chiu CY, Urisman A, Greenhow TL, Rouskin S, Yagi S, Schnurr D, Wright C, Drew WL, Wang D, Weintrub PS, Derisi JL, Ganem D. PMID: 18571541.
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    225. 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. Kistler A, Avila PC, Rouskin S, Wang D, Ward T, Yagi S, Schnurr D, Ganem D, DeRisi JL, Boushey HA. PMID: 17703411.
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    226. 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. Chiu CY, Alizadeh AA, Rouskin S, Merker JD, Yeh E, Yagi S, Schnurr D, Patterson BK, Ganem D, DeRisi JL. PMID: 17494722.
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    227. Genome-wide diversity and selective pressure in the human rhinovirus. Virol J. 2007 May 03; 4:40. Kistler AL, Webster DR, Rouskin S, Magrini V, Credle JJ, Schnurr DP, Boushey HA, Mardis ER, Li H, DeRisi JL. PMID: 17477878.
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    228. Cis-acting determinants of asymmetric, cytoplasmic RNA transport. RNA. 2007 May; 13(5):625-42. Jambhekar A, Derisi JL. PMID: 17449729.
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    229. 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. Dong B, Kim S, Hong S, Das Gupta J, Malathi K, Klein EA, Ganem D, Derisi JL, Chow SA, Silverman RH. PMID: 17234809.
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    230. 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. Shock JL, Fischer KF, DeRisi JL. PMID: 17612404.
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    231. Gene expression patterns during adaptation of a helminth parasite to different environmental niches. Genome Biol. 2007; 8(4):R65. Jolly ER, Chin CS, Miller S, Bahgat MM, Lim KC, DeRisi J, McKerrow JH. PMID: 17456242.
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    232. A Bayesian network driven approach to model the transcriptional response to nitric oxide in Saccharomyces cerevisiae. PLoS One. 2006 Dec 20; 1:e94. Zhu J, Jambhekar A, Sarver A, DeRisi J. PMID: 17183726.
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    233. Rapid DNA mapping by fluorescent single molecule detection. Nucleic Acids Res. 2007; 35(3):e16. Xiao M, Phong A, Ha C, Chan TF, Cai D, Leung L, Wan E, Kistler AL, DeRisi JL, Selvin PR, Kwok PY. PMID: 17175538.
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    234. Tetracyclines specifically target the apicoplast of the malaria parasite Plasmodium falciparum. Antimicrob Agents Chemother. 2006 Sep; 50(9):3124-31. Dahl EL, Shock JL, Shenai BR, Gut J, DeRisi JL, Rosenthal PJ. PMID: 16940111.
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    235. 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. 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. PMID: 16983602.
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    236. 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. Madrid PB, Liou AP, DeRisi JL, Guy RK. PMID: 16854059.
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    237. Searching for new antimalarial therapeutics amongst known drugs. Chem Biol Drug Des. 2006 Jun; 67(6):409-16. Weisman JL, Liou AP, Shelat AA, Cohen FE, Guy RK, DeRisi JL. PMID: 16882315.
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    238. Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature. 2006 Jun 15; 441(7095):840-6. Newman JR, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, DeRisi JL, Weissman JS. PMID: 16699522.
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    239. Identification of a novel Gammaretrovirus in prostate tumors of patients homozygous for R462Q RNASEL variant. PLoS Pathog. 2006 Mar; 2(3):e25. 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. PMID: 16609730.
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    240. Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains. Nucleic Acids Res. 2006; 34(4):1166-73. Llinás M, Bozdech Z, Wong ED, Adai AT, DeRisi JL. PMID: 16493140.
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    241. 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. Green BM, Morreale RJ, Ozaydin B, Derisi JL, Li JJ. PMID: 16481397.
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    242. 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. Jambhekar A, McDermott K, Sorber K, Shepard KA, Vale RD, Takizawa PA, DeRisi JL. PMID: 16326802.
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    243. Parallel synthesis of 9-aminoacridines and their evaluation against chloroquine-resistant Plasmodium falciparum. Bioorg Med Chem. 2006 Jan 15; 14(2):334-43. Anderson MO, Sherrill J, Madrid PB, Liou AP, Weisman JL, DeRisi JL, Guy RK. PMID: 16216519.
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    244. Genome-wide identification of genes upregulated at the onset of gametocytogenesis in Plasmodium falciparum. Mol Biochem Parasitol. 2005 Sep; 143(1):100-10. Silvestrini F, Bozdech Z, Lanfrancotti A, Di Giulio E, Bultrini E, Picci L, Derisi JL, Pizzi E, Alano P. PMID: 16026866.
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    245. E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns. Genome Biol. 2005; 6(9):R78. Urisman A, Fischer KF, Chiu CY, Kistler AL, Beck S, Wang D, DeRisi JL. PMID: 16168085.
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    246. Fzf1p regulates an inducible response to nitrosative stress in Saccharomyces cerevisiae. Mol Biol Cell. 2005 Oct; 16(10):4781-91. Sarver A, DeRisi J. PMID: 16014606.
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    247. Synthesis of ring-substituted 4-aminoquinolines and evaluation of their antimalarial activities. Bioorg Med Chem Lett. 2005 Feb 15; 15(4):1015-8. Madrid PB, Sherrill J, Liou AP, Weisman JL, Derisi JL, Guy RK. PMID: 15686903.
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    248. 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. Galgoczy DJ, Cassidy-Stone A, Llinás M, O'Rourke SM, Herskowitz I, DeRisi JL, Johnson AD. PMID: 15604142.
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    249. Pernicious plans revealed: Plasmodium falciparum genome wide expression analysis. Curr Opin Microbiol. 2004 Aug; 7(4):382-7. Llinás M, DeRisi JL. PMID: 15358256.
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    250. The kinetochore is an enhancer of pericentric cohesin binding. PLoS Biol. 2004 Sep; 2(9):E260. Weber SA, Gerton JL, Polancic JE, DeRisi JL, Koshland D, Megee PC. PMID: 15309047.
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    251. Genome-wide mapping of the cohesin complex in the yeast Saccharomyces cerevisiae. PLoS Biol. 2004 Sep; 2(9):E259. Glynn EF, Megee PC, Yu HG, Mistrot C, Unal E, Koshland DE, DeRisi JL, Gerton JL. PMID: 15309048.
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    252. Parallel synthesis and antimalarial screening of a 4-aminoquinoline library. J Comb Chem. 2004 May-Jun; 6(3):437-42. Madrid PB, Wilson NT, DeRisi JL, Guy RK. PMID: 15132606.
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    253. Viral discovery and sequence recovery using DNA microarrays. PLoS Biol. 2003 Nov; 1(2):E2. 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. PMID: 14624234.
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    254. 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. Shepard KA, Gerber AP, Jambhekar A, Takizawa PA, Brown PO, Herschlag D, DeRisi JL, Vale RD. PMID: 13679573.
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    255. The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol. 2003 Oct; 1(1):E5. Bozdech Z, Llinás M, Pulliam BL, Wong ED, Zhu J, DeRisi JL. PMID: 12929205.
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    256. Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science. 2003 May 30; 300(5624):1394-9. 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. PMID: 12730500.
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    257. A novel coronavirus associated with severe acute respiratory syndrome. N Engl J Med. 2003 May 15; 348(20):1953-66. 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, SARS Working Group . PMID: 12690092.
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    258. Telomeric protein distributions and remodeling through the cell cycle in Saccharomyces cerevisiae. Mol Biol Cell. 2003 Feb; 14(2):556-70. Smith CD, Smith DL, DeRisi JL, Blackburn EH. PMID: 12589054.
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    259. Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biol. 2003; 4(2):R9. Bozdech Z, Zhu J, Joachimiak MP, Cohen FE, Pulliam B, DeRisi JL. PMID: 12620119.
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    260. A role for the protease falcipain 1 in host cell invasion by the human malaria parasite. Science. 2002 Dec 06; 298(5600):2002-6. Greenbaum DC, Baruch A, Grainger M, Bozdech Z, Medzihradszky KF, Engel J, DeRisi J, Holder AA, Bogyo M. PMID: 12471262.
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    261. Microarray-based detection and genotyping of viral pathogens. Proc Natl Acad Sci U S A. 2002 Nov 26; 99(24):15687-92. Wang D, Coscoy L, Zylberberg M, Avila PC, Boushey HA, Ganem D, DeRisi JL. PMID: 12429852.
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    262. 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. Polson AG, Wang D, DeRisi J, Ganem D. PMID: 12154065.
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    263. 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. Nautiyal S, DeRisi JL, Blackburn EH. PMID: 12084816.
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    264. Mnd1p: an evolutionarily conserved protein required for meiotic recombination. Proc Natl Acad Sci U S A. 2002 May 14; 99(10):6895-900. Gerton JL, DeRisi JL. PMID: 12011448.
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    265. DNA microarrays for malaria. Trends Parasitol. 2002 Jan; 18(1):39-45. Rathod PK, Ganesan K, Hayward RE, Bozdech Z, DeRisi JL. PMID: 11850013.
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    266. Overview of nucleic acid arrays. Curr Protoc Neurosci. 2001 Nov; Chapter 4:Unit 4.25. DeRisi J. PMID: 18428485.
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    267. 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. Carroll AS, Bishop AC, DeRisi JL, Shokat KM, O'Shea EK. PMID: 11675494.
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    269. Overview of nucleic acid arrays. Curr Protoc Mol Biol. 2001 May; Chapter 22:Unit 22.1. Derisi J. PMID: 18265199.
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    270. 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. 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. PMID: 11226216.
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    271. 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. Kuhn KM, DeRisi JL, Brown PO, Sarnow P. PMID: 11154278.
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    272. 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. Ogawa N, DeRisi J, Brown PO. PMID: 11102525.
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    273. Plasma membrane compartmentalization in yeast by messenger RNA transport and a septin diffusion barrier. Science. 2000 Oct 13; 290(5490):341-4. Takizawa PA, DeRisi JL, Wilhelm JE, Vale RD. PMID: 11030653.
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    274. 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. Gerton JL, DeRisi J, Shroff R, Lichten M, Brown PO, Petes TD. PMID: 11027339.
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    275. 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. Khodursky AB, Peter BJ, Schmid MB, DeRisi J, Botstein D, Brown PO, Cozzarelli NR. PMID: 10944214.
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    276. Genome microarray analysis of transcriptional activation in multidrug resistance yeast mutants. FEBS Lett. 2000 Mar 24; 470(2):156-60. DeRisi J, van den Hazel B, Marc P, Balzi E, Brown P, Jacq C, Goffeau A. PMID: 10734226.
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    277. Shotgun DNA microarrays and stage-specific gene expression in Plasmodium falciparum malaria. Mol Microbiol. 2000 Jan; 35(1):6-14. Hayward RE, Derisi JL, Alfadhli S, Kaslow DC, Brown PO, Rathod PK. PMID: 10632873.
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    278. 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. Wilson M, DeRisi J, Kristensen HH, Imboden P, Rane S, Brown PO, Schoolnik GK. PMID: 10536008.
      View in: PubMed   Mentions: 144     Fields:    Translation:Cells
    279. Genomics and array technology. Curr Opin Oncol. 1999 Jan; 11(1):76-9. DeRisi JL, Iyer VR. PMID: 9914882.
      View in: PubMed   Mentions: 15     Fields:    
    280. Characterization of three related glucose repressors and genes they regulate in Saccharomyces cerevisiae. Genetics. 1998 Dec; 150(4):1377-91. Lutfiyya LL, Iyer VR, DeRisi J, DeVit MJ, Brown PO, Johnston M. PMID: 9832517.
      View in: PubMed   Mentions: 78     Fields:    Translation:AnimalsCells
    281. Drug target validation and identification of secondary drug target effects using DNA microarrays. Nat Med. 1998 Nov; 4(11):1293-301. 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. PMID: 9809554.
      View in: PubMed   Mentions: 121     Fields:    Translation:AnimalsCells
    282. The transcriptional program of sporulation in budding yeast. Science. 1998 Oct 23; 282(5389):699-705. Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown PO, Herskowitz I. PMID: 9784122.
      View in: PubMed   Mentions: 582     Fields:    Translation:HumansAnimalsCells
    283. 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. Gerton JL, Ohgi S, Olsen M, DeRisi J, Brown PO. PMID: 9573274.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansCells
    284. 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. Lashkari DA, DeRisi JL, McCusker JH, Namath AF, Gentile C, Hwang SY, Brown PO, Davis RW. PMID: 9371799.
      View in: PubMed   Mentions: 130     Fields:    Translation:Animals
    285. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science. 1997 Oct 24; 278(5338):680-6. DeRisi JL, Iyer VR, Brown PO. PMID: 9381177.
      View in: PubMed   Mentions: 1084     Fields:    Translation:AnimalsCells
    286. Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat Genet. 1996 Dec; 14(4):457-60. DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, Chen Y, Su YA, Trent JM. PMID: 8944026.
      View in: PubMed   Mentions: 336     Fields:    Translation:HumansAnimalsCells
    287. Bead-shift isolation of protein--DNA complexes on a 5S RNA gene. Nucleic Acids Res. 1994 Feb 11; 22(3):443-9. Peck LJ, Bartilson M, DeRisi JL. PMID: 8127682.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
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