Joe Derisi, PhD
Professor
Biochemistry and Biophysics
School of Medicine
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:
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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.
Websites
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- Derisi Lab (derisilab.ucsf.edu)
Grants and Projects
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- Integrative Program in Complex Biological System (ipCBS), NIH, 2009-2023
- Intracellular pathogens and innate immunity, NIH, 2004-2021
- Protein homeostasis mechanisms underlying enterovirus replication and evolution, NIH, 2011-2016
- Bio-Organic Biomedical Mass Spectrometry Resource, NIH, 1982-2015
- Pacific Southwest RCE for Biodefense & Emerging Infectious Diseases Research, NIH, 2005-2015
- Novel Anti-Malarials by Combinatorial Pharmacogenomics, NIH, 2002-2008
Publications (353)
Top publication keywords:
Respiratory Tract InfectionsSequence Analysis, DNARNA, ViralAutoantibodiesHigh-Throughput Nucleotide SequencingPicornaviridaeBalamuthia mandrillarisMetagenomeAntimalarialsBoidaePicornaviridae InfectionsPlasmodium falciparumBird DiseasesGenome, ViralMetagenomics
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Challenges and advances in the medical treatment of granulomatous amebic encephalitis.
Therapeutic advances in infectious disease 2024 Spottiswoode N, Haston JC, Hanners NW, Gruenberg K, Kim A, DeRisi JL, Wilson MR -
The antibiotic resistance reservoir of the lung microbiome expands with age in a population of critically ill patients.
Nature communications 2024 Chu VT, Tsitsiklis A, Mick E, Ambroggio L, Kalantar KL, Glascock A, Osborne CM, Wagner BD, Matthay MA, DeRisi JL, Calfee CS, Mourani PM, Langelier CR -
Vaccine breakthrough hypoxemic COVID-19 pneumonia in patients with auto-Abs neutralizing type I IFNs.
Science immunology 2023 Bastard P, Vazquez SE, Liu J, Laurie MT, Wang CY, Gervais A, Le Voyer T, Bizien L, Zamecnik C, Philippot Q, Rosain J, Catherinot E, Willmore A, Mitchell AM, Bair R, Garçon P, Kenney H, Fekkar A, … -
Unveiling the autoreactome: Proteome-wide immunological fingerprints reveal the promise of plasma cell depleting therapy.
medRxiv : the preprint server for health sciences 2023 Bodansky A, Yu DJ, Rallistan A, Kalaycioglu M, Boonyaratanakornkit J, Green DJ, Gauthier J, Turtle CJ, Zorn K, O'Donovan B, Mandel-Brehm C, Asaki J, Kortbawi H, Kung AF, Rackaityte E, Wang CY, Saxena … -
Validation of a murine proteome-wide phage display library for identification of autoantibody specificities.
JCI insight 2023 Rackaityte E, Proekt I, Miller HS, Ramesh A, Brooks JF, Kung AF, Mandel-Brehm C, Yu D, Zamecnik CR, Bair R, Vazquez SE, Sunshine S, Abram CL, Lowell CA, Rizzuto G, Wilson MR, Zikherman J, Anderson MS,…
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Pulmonary microbiome and transcriptome signatures reveal distinct pathobiologic states associated with mortality in two cohorts of pediatric stem cell transplant patients.
medRxiv : the preprint server for health sciences 2023 Zinter MS, Dvorak CC, Mayday MY, Reyes G, Simon MR, Pearce EM, Kim H, Shaw PJ, Rowan CM, Auletta JJ, Martin PL, Godder K, Duncan CN, Lalefar NR, Kreml EM, Hume JR, Abdel-Azim H, Hurley C, Cuvelier GDE… -
Autoantibodies against type I IFNs in humans with alternative NF-κB pathway deficiency.
Nature 2023 Le Voyer T, Parent AV, Liu X, Cederholm A, Gervais A, Rosain J, Nguyen T, Perez Lorenzo M, Rackaityte E, Rinchai D, Zhang P, Bizien L, Hancioglu G, Ghillani-Dalbin P, Charuel JL, Philippot Q, Gueye MS… -
Implementation of California COVIDNet - a multi-sector collaboration for statewide SARS-CoV-2 genomic surveillance.
Frontiers in public health 2023 Wadford DA, Baumrind N, Baylis EF, Bell JM, Bouchard EL, Crumpler M, Foote EM, Gilliam S, Glaser CA, Hacker JK, Ledin K, Messenger SL, Morales C, Smith EA, Sevinsky JR, Corbett-Detig RB, DeRisi J, … -
Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq.
Nature communications 2023 Sunshine S, Puschnik AS, Replogle JM, Laurie MT, Liu J, Zha BS, Nuñez JK, Byrum JR, McMorrow AH, Frieman MB, Winkler J, Qiu X, Rosenberg OS, Leonetti MD, Ye CJ, Weissman JS, DeRisi JL, Hein MY -
Viral Detection by Reverse Transcriptase Polymerase Chain Reaction in Upper Respiratory Tract and Metagenomic RNA Sequencing in Lower Respiratory Tract in Critically Ill Children With Suspected Lower Respiratory Tract Infection.
Pediatric critical care medicine : a journal of the Society of Critical Care Medicine and the World Federation of Pediatric Intensive and Critical Care Societies 2023 Osborne CM, Langelier C, Kamm J, Williamson K, Ambroggio L, Reeder RW, Locandro C, Kirk Harris J, Wagner BD, Maddux AB, Caldera S, Lyden A, Soesanto V, Simões EAF, Leroue MK, Carpenter TC, Hall MW, … -
Detection of High-Risk Paraneoplastic Antibodies against TRIM9 and TRIM67 Proteins.
Annals of neurology 2023 Bartley CM, Ngo TT, Do LD, Zekeridou A, Dandekar R, Muñiz-Castrillo S, Alvarenga BD, Zorn KC, Tubati A, Pinto AL, Browne WD, Hullett PW, Terrelonge M, Schubert RD, Piquet AL, Yang B, Montalvo M, Kung … -
The antibiotic resistance reservoir of the lung microbiome expands with age.
Research square 2023 Chu VT, Tsitsiklis A, Mick E, Ambroggio L, Kalantar KL, Glascock A, Osborne CM, Wagner BD, Matthay MA, DeRisi JL, Calfee CS, Mourani PM, Langelier CR -
In host evolution of beta lactam resistance during active treatment for Pseudomonas aeruginosa bacteremia.
Frontiers in cellular and infection microbiology 2023 Spottiswoode N, Hao S, Sanchez-Guerrero E, Detweiler AM, Mekonen H, Neff N, Macmillan H, Schwartz BS, Engel J, DeRisi JL, Miller SA, Langelier CR -
Broad susceptibility of Candida auris strains to 8-hydroxyquinolines and mechanisms of resistance.
mBio 2023 Lohse MB, Laurie MT, Levan S, Ziv N, Ennis CL, Nobile CJ, DeRisi J, Johnson AD -
Rubella virus tropism and single-cell responses in human primary tissue and microglia-containing organoids.
eLife 2023 Popova G, Retallack H, Kim CN, Wang A, Shin D, DeRisi JL, Nowakowski T -
Viral co-infection, autoimmunity, and CSF HIV antibody profiles in HIV central nervous system escape.
Journal of neuroimmunology 2023 Hawes IA, Alvarenga BD, Browne W, Wapniarski A, Dandekar R, Bartley CM, Sowa GM, DeRisi JL, Cinque P, Dravid AN, Pleasure SJ, Gisslen M, Price RW, Wilson MR -
Novel autoantibody targets identified in patients with autoimmune hepatitis (AIH) by PhIP-Seq reveals pathogenic insights.
medRxiv : the preprint server for health sciences 2023 Klepper A, Kung A, Vazquez SE, Mitchell A, Mann S, Zorn K, Avila-Vargas I, Kari S, Tekeste M, Castro J, Lee B, Duarte M, Khalili M, Yang M, Wolters P, Price J, Perito E, Feng S, Maher JJ, Lai J, … -
Whole-genome sequencing rule-out of suspected hospital-onset Rhizopus outbreaks.
Infection control and hospital epidemiology 2023 Chu VT, Nafees S, Waltari E, McNeil N, Caughell C, Sanchez-Guerrero E, Wang L, Stanley K, Cunningham G, Wong J, Phelps M, Tato CM, Miller S, DeRisi JL, Yokoe DS, Ramirez-Avila L, Langelier CR -
Autoantigen profiling reveals a shared post-COVID signature in fully recovered and long COVID patients.
JCI insight 2023 Bodansky A, Wang CY, Saxena A, Mitchell A, Kung AF, Takahashi S, Anglin K, Huang B, Hoh R, Lu S, Goldberg SA, Romero J, Tran B, Kirtikar R, Grebe H, So M, Greenhouse B, Durstenfeld MS, Hsue PY, … -
A Predictive Autoantibody Signature in Multiple Sclerosis.
medRxiv : the preprint server for health sciences 2023 Zamecnik CR, Sowa GM, Abdelhak A, Dandekar R, Bair RD, Wade KJ, Bartley CM, Tubati A, Gomez R, Fouassier C, Gerungan C, Alexander J, Wapniarski AE, Loudermilk RP, Eggers EL, Zorn KC, Ananth K, … -
Antigenic responses are hallmarks of fibrotic interstitial lung diseases independent of underlying etiologies.
medRxiv : the preprint server for health sciences 2023 Yoon YM, Velez TE, Upadhyay V, Vazquez SE, Lee CT, Selvan KC, Law CS, Blaine KM, Hollinger MK, Decker DC, Clark MR, Strek ME, Guzy RD, Adegunsoye A, Noth I, Wolters PJ, Anderson M, DeRisi JL, Shum AK,… -
PhIP-Seq uncovers novel autoantibodies and unique endotypes in interstitial lung disease.
bioRxiv : the preprint server for biology 2023 Upadhyay V, Yoon YM, Vazquez SE, Velez TE, Jones KD, Lee CT, Law CS, Wolters PJ, Lee S, Yang MM, Farrand E, Noth I, Strek ME, Anderson M, DeRisi J, Sperling AI, Shum AK -
Validation of a murine proteome-wide phage display library for the identification of autoantibody specificities.
bioRxiv : the preprint server for biology 2023 Rackaityte E, Proekt I, Miller HS, Ramesh A, Brooks JF, Kung AF, Mandel-Brehm C, Yu D, Zamecnik C, Bair R, Vazquez SE, Sunshine S, Abram CL, Lowell CA, Rizzuto G, Wilson MR, Zikherman J, Anderson MS, … -
Integrated host/microbe metagenomics enables accurate lower respiratory tract infection diagnosis in critically ill children.
The Journal of clinical investigation 2023 Mick E, Tsitsiklis A, Kamm J, Kalantar KL, Caldera S, Lyden A, Tan M, Detweiler AM, Neff N, Osborne CM, Williamson KM, Soesanto V, Leroue M, Maddux AB, Simões EA, Carpenter TC, Wagner BD, DeRisi JL, … -
Field assessment of BinaxNOW antigen tests as COVID-19 treatment entry point at a community testing site in San Francisco during evolving omicron surges.
PloS one 2023 Schrom J, Marquez C, Wang CY, Saxena A, Mitchell AM, Ribeiro S, Pilarowski G, Nakamura R, Rojas S, Black D, Contreras Oseguera MG, Diaz EC, Payan J, Rojas S, Jones D, Tulier-Laiwa V, Zavaleta A, … -
Genomic analysis, immunomodulation and deep phenotyping of patients with nodding syndrome.
Brain : a journal of neurology 2023 Soldatos A, Nutman TB, Johnson T, Dowell SF, Sejvar JJ, Wilson MR, DeRisi JL, Inati SK, Groden C, Evans C, O'Connell EM, Toliva BO, Aceng JR, Aryek-Kwe J, Toro C, Stratakis CA, Buckler AG, Cantilena C… -
Broad sensitivity of Candida auris strains to quinolones and mechanisms of resistance.
bioRxiv : the preprint server for biology 2023 Lohse MB, Laurie MT, Levan S, Ziv N, Ennis CL, Nobile CJ, DeRisi J, Johnson AD -
Computational pipeline provides mechanistic understanding of Omicron variant of concern neutralizing engineered ACE2 receptor traps.
Structure (London, England : 1993) 2023 Remesh SG, Merz GE, Brilot AF, Chio US, Rizo AN, Pospiech TH, Lui I, Laurie MT, Glasgow J, Le CQ, Zhang Y, Diwanji D, Hernandez E, Lopez J, Mehmood H, Pawar KI, Pourmal S, Smith AM, Zhou F, QCRG … -
Antibodies to repeat-containing antigens in Plasmodium falciparum are exposure-dependent and short-lived in children in natural malaria infections.
eLife 2023 Raghavan M, Kalantar KL, Duarte E, Teyssier N, Takahashi S, Kung AF, Rajan JV, Rek J, Tetteh KKA, Drakeley C, Ssewanyana I, Rodriguez-Barraquer I, Greenhouse B, DeRisi JL -
Autoantigen profiling reveals a shared post-COVID signature in fully recovered and Long COVID patients.
medRxiv : the preprint server for health sciences 2023 Bodansky A, Wang CY, Saxena A, Mitchell A, Takahashi S, Anglin K, Huang B, Hoh R, Lu S, Goldberg SA, Romero J, Tran B, Kirtikar R, Grebe H, So M, Greenhouse B, Durstenfeld MS, Hsue PY, Hellmuth J, … -
Dual ankyrinG and subpial autoantibodies in a man with well-controlled HIV infection with steroid-responsive meningoencephalitis: A case report.
Frontiers in neurology 2023 Bartley CM, Ngo TT, Cadwell CR, Harroud A, Schubert RD, Alvarenga BD, Hawes IA, Zorn KC, Hunyh T, Teliska LH, Kung AF, Shah S, Gelfand JM, Chow FC, Rasband MN, Dubey D, Pittock SJ, DeRisi JL, Wilson … -
Low Prevalence of Interferon α Autoantibodies in People Experiencing Symptoms of Post-Coronavirus Disease 2019 (COVID-19) Conditions, or Long COVID.
The Journal of infectious diseases 2023 Peluso MJ, Mitchell A, Wang CY, Takahashi S, Hoh R, Tai V, Durstenfeld MS, Hsue PY, Kelly JD, Martin JN, Wilson MR, Greenhouse B, Deeks SG, DeRisi JL, Henrich TJ -
Autoantibodies to Perilipin-1 Define a Subset of Acquired Generalized Lipodystrophy.
Diabetes 2023 Mandel-Brehm C, Vazquez SE, Liverman C, Cheng M, Quandt Z, Kung AF, Parent A, Miao B, Disse E, Cugnet-Anceau C, Dalle S, Orlova E, Frolova E, Alba D, Michels A, Oftedal BE, Lionakis MS, Husebye ES, … -
Successful Treatment of Balamuthia mandrillaris Granulomatous Amebic Encephalitis with Nitroxoline.
Emerging infectious diseases 2023 Spottiswoode N, Pet D, Kim A, Gruenberg K, Shah M, Ramachandran A, Laurie MT, Zia M, Fouassier C, Boutros CL, Lu R, Zhang Y, Servellita V, Bollen A, Chiu CY, Wilson MR, Valdivia L, DeRisi JL -
Prevalence of type-1 interferon autoantibodies in adults with non-COVID-19 acute respiratory failure.
Respiratory research 2022 Ghale R, Spottiswoode N, Anderson MS, Mitchell A, Wang G, Calfee CS, DeRisi JL, Langelier CR -
A 2-Gene Host Signature for Improved Accuracy of COVID-19 Diagnosis Agnostic to Viral Variants.
mSystems 2022 Albright J, Mick E, Sanchez-Guerrero E, Kamm J, Mitchell A, Detweiler AM, Neff N, Tsitsiklis A, Hayakawa Serpa P, Ratnasiri K, Havlir D, Kistler A, DeRisi JL, Pisco AO, Langelier CR -
NFKB2 haploinsufficiency identified via screening for IFN-α2 autoantibodies in children and adolescents hospitalized with SARS-CoV-2-related complications.
The Journal of allergy and clinical immunology 2022 Bodansky A, Vazquez SE, Chou J, Novak T, Al-Musa A, Young C, Newhams M, Kucukak S, Zambrano LD, Mitchell A, Wang CY, Moffitt K, Halasa NB, Loftis LL, Schwartz SP, Walker TC, Mack EH, Fitzgerald JC, … -
Autoantibody discovery across monogenic, acquired, and COVID-19-associated autoimmunity with scalable PhIP-seq.
eLife 2022 Vazquez SE, Mann SA, Bodansky A, Kung AF, Quandt Z, Ferré EMN, Landegren N, Eriksson D, Bastard P, Zhang SY, Liu J, Mitchell A, Proekt I, Yu D, Mandel-Brehm C, Wang CY, Miao B, Sowa G, Zorn K, Chan AY… -
Integrated host-microbe plasma metagenomics for sepsis diagnosis in a prospective cohort of critically ill adults.
Nature microbiology 2022 Kalantar KL, Neyton L, Abdelghany M, Mick E, Jauregui A, Caldera S, Serpa PH, Ghale R, Albright J, Sarma A, Tsitsiklis A, Leligdowicz A, Christenson SA, Liu K, Kangelaris KN, Hendrickson C, Sinha P, … -
COVID-19 Symptoms and Duration of Rapid Antigen Test Positivity at a Community Testing and Surveillance Site During Pre-Delta, Delta, and Omicron BA.1 Periods.
JAMA network open 2022 Marquez C, Kerkhoff AD, Schrom J, Rojas S, Black D, Mitchell A, Wang CY, Pilarowski G, Ribeiro S, Jones D, Payan J, Manganelli S, Rojas S, Lemus J, Jain V, Chamie G, Tulier-Laiwa V, Petersen M, DeRisi… -
Discovery and Genomic Characterization of a Novel Henipavirus, Angavokely Virus, from Fruit Bats in Madagascar.
Journal of virology 2022 Madera S, Kistler A, Ranaivoson HC, Ahyong V, Andrianiaina A, Andry S, Raharinosy V, Randriambolamanantsoa TH, Ravelomanantsoa NAF, Tato CM, DeRisi JL, Aguilar HC, Lacoste V, Dussart P, Heraud JM, … -
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Transmission Dynamics and Immune Responses in a Household of Vaccinated Persons.
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2022 Liu J, Laurie MT, Rubio L, Vazquez SE, Sunshine S, Mitchell AM, Hapte-Selassie M, Mann SA, Pilarowski G, Black D, Marquez C, Rojas S, Lionakis MS, Petersen M, Whitman JD, Jain V, Anderson M, Havlir D,… -
Computational pipeline provides mechanistic understanding of Omicron variant of concern neutralizing engineered ACE2 receptor traps.
bioRxiv : the preprint server for biology 2022 Remesh SG, Merz GE, Brilot AF, Chio US, Rizo AN, Pospiech TH, Lui I, Laurie MT, Glasgow J, Le CQ, Zhang Y, Diwanji D, Hernandez E, Lopez J, Pawar KI, Pourmal S, Smith AM, Zhou F, QCRG Structural … -
Case Report: Cambodian National Malaria Surveillance Program Detection of Plasmodium knowlesi.
The American journal of tropical medicine and hygiene 2022 Yek C, Lay S, Bohl JA, Man S, Chea S, Lon C, Ahyong V, Tato CM, DeRisi JL, Sovannaroth S, Manning JE -
Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections.
Genome medicine 2022 Serpa PH, Deng X, Abdelghany M, Crawford E, Malcolm K, Caldera S, Fung M, McGeever A, Kalantar KL, Lyden A, Ghale R, Deiss T, Neff N, Miller SA, Doernberg SB, Chiu CY, DeRisi JL, Calfee CS, Langelier … -
Upper airway gene expression shows a more robust adaptive immune response to SARS-CoV-2 in children.
Nature communications 2022 Mick E, Tsitsiklis A, Spottiswoode N, Caldera S, Serpa PH, Detweiler AM, Neff N, Pisco AO, Li LM, Retallack H, Ratnasiri K, Williamson KM, Soesanto V, Simões EAF, Smith C, Abuogi L, Kistler A, Wagner … -
Zika virus alters centrosome organization to suppress the innate immune response.
EMBO reports 2022 Kodani A, Knopp KA, Di Lullo E, Retallack H, Kriegstein AR, DeRisi JL, Reiter JF -
SARS-CoV-2 Variant Exposures Elicit Antibody Responses With Differential Cross-Neutralization of Established and Emerging Strains Including Delta and Omicron.
The Journal of infectious diseases 2022 Laurie MT, Liu J, Sunshine S, Peng J, Black D, Mitchell AM, Mann SA, Pilarowski G, Zorn KC, Rubio L, Bravo S, Marquez C, Sabatino JJ, Mittl K, Petersen M, Havlir D, DeRisi J -
ZSCAN1 Autoantibodies Are Associated with Pediatric Paraneoplastic ROHHAD.
Annals of neurology 2022 Mandel-Brehm C, Benson LA, Tran B, Kung AF, Mann SA, Vazquez SE, Retallack H, Sample HA, Zorn KC, Khan LM, Kerr LM, McAlpine PL, Zhang L, McCarthy F, Elias JE, Katwa U, Astley CM, Tomko S, Dalmau J, … -
βIV-Spectrin Autoantibodies in 2 Individuals With Neuropathy of Possible Paraneoplastic Origin: A Case Series.
Neurology(R) neuroimmunology & neuroinflammation 2022 Bartley CM, Ngo TT, Alvarenga BD, Kung AF, Teliska LH, Sy M, DeRisi JL, Rasband MN, Pittock SJ, Dubey D, Wilson MR, Pleasure SJ -
Genome-Wide Knockout Screen Identifies Human Sialomucin CD164 as an Essential Entry Factor for Lymphocytic Choriomeningitis Virus.
mBio 2022 Liu J, Knopp KA, Rackaityte E, Wang CY, Laurie MT, Sunshine S, Puschnik AS, DeRisi JL -
Integrating central nervous system metagenomics and host response for diagnosis of tuberculosis meningitis and its mimics.
Nature communications 2022 Ramachandran PS, Ramesh A, Creswell FV, Wapniarski A, Narendra R, Quinn CM, Tran EB, Rutakingirwa MK, Bangdiwala AS, Kagimu E, Kandole KT, Zorn KC, Tugume L, Kasibante J, Ssebambulidde K, Okirwoth M, … -
Pneumonia surveillance with culture-independent metatranscriptomics in HIV-positive adults in Uganda: a cross-sectional study.
The Lancet. Microbe 2022 Spottiswoode N, Bloomstein JD, Caldera S, Sessolo A, McCauley K, Byanyima P, Zawedde J, Kalantar K, Kaswabuli S, Rutishauser RL, Lieng MK, Davis JL, Moore J, Jan A, Iwai S, Shenoy M, Sanyu I, DeRisi … -
Autoantibody discovery across monogenic, acquired, and COVID19-associated autoimmunity with scalable PhIP-Seq.
bioRxiv : the preprint server for biology 2022 Vazquez SE, Mann SA, Bodansky A, Kung AF, Quandt Z, Ferré EMN, Landegren N, Eriksson D, Bastard P, Zhang SY, Liu J, Mitchell A, Mandel-Brehm C, Miao B, Sowa G, Zorn K, Chan AY, Shimizu C, Tremoulet A,… -
Prolonged silent carriage, genomic virulence potential and transmission between staff and patients characterize a neonatal intensive care unit (NICU) outbreak of methicillin-resistant Staphylococcus aureus (MRSA).
Infection control and hospital epidemiology 2022 Madera S, McNeil N, Serpa PH, Kamm J, Pak C, Caughell C, Nichols A, Dynerman D, Li LM, Sanchez-Guerrero E, Phelps MS, Detweiler AM, Neff N, Reyes H, Miller SA, Yokoe DS, DeRisi JL, Ramirez-Avila L, … -
Transcriptomic profiling of blood from autoimmune hepatitis patients reveals potential mechanisms with implications for management.
PloS one 2022 Tana MM, Klepper A, Lyden A, Pisco AO, Phelps M, McGee B, Green K, Feng S, DeRisi J, Crawford ED, Lammert CS -
Viral Load Among Vaccinated and Unvaccinated, Asymptomatic and Symptomatic Persons Infected With the SARS-CoV-2 Delta Variant.
Open forum infectious diseases 2022 Acharya CB, Schrom J, Mitchell AM, Coil DA, Marquez C, Rojas S, Wang CY, Liu J, Pilarowski G, Solis L, Georgian E, Belafsky S, Petersen M, DeRisi J, Michelmore R, Havlir D -
Lower respiratory tract infections in children requiring mechanical ventilation: a multicentre prospective surveillance study incorporating airway metagenomics.
The Lancet. Microbe 2022 Tsitsiklis A, Osborne CM, Kamm J, Williamson K, Kalantar K, Dudas G, Caldera S, Lyden A, Tan M, Neff N, Soesanto V, Harris JK, Ambroggio L, Maddux AB, Carpenter TC, Reeder RW, Locandro C, Simões EAF, … -
Pulmonary microbiome and gene expression signatures differentiate lung function in pediatric hematopoietic cell transplant candidates.
Science translational medicine 2022 Zinter MS, Versluys AB, Lindemans CA, Mayday MY, Reyes G, Sunshine S, Chan M, Fiorino EK, Cancio M, Prevaes S, Sirota M, Matthay MA, Kharbanda S, Dvorak CC, Boelens JJ, DeRisi JL -
Using genomic epidemiology of SARS-CoV-2 to support contact tracing and public health surveillance in rural Humboldt County, California.
BMC public health 2022 Stoddard G, Black A, Ayscue P, Lu D, Kamm J, Bhatt K, Chan L, Kistler AL, Batson J, Detweiler A, Tan M, Neff N, DeRisi JL, Corrigan J -
Discovering disease-causing pathogens in resource-scarce Southeast Asia using a global metagenomic pathogen monitoring system.
Proceedings of the National Academy of Sciences of the United States of America 2022 Bohl JA, Lay S, Chea S, Ahyong V, Parker DM, Gallagher S, Fintzi J, Man S, Ponce A, Sreng S, Kong D, Oliveira F, Kalantar K, Tan M, Fahsbender L, Sheu J, Neff N, Detweiler AM, Yek C, Ly S, Sath R, … -
Multiple sclerosis therapies differentially affect SARS-CoV-2 vaccine-induced antibody and T cell immunity and function.
JCI insight 2022 Sabatino JJ, Mittl K, Rowles WM, McPolin K, Rajan JV, Laurie MT, Zamecnik CR, Dandekar R, Alvarenga BD, Loudermilk RP, Gerungan C, Spencer CM, Sagan SA, Augusto DG, Alexander JR, DeRisi JL, Hollenbach… -
Full Genome Nobecovirus Sequences From Malagasy Fruit Bats Define a Unique Evolutionary History for This Coronavirus Clade.
Frontiers in public health 2022 Kettenburg G, Kistler A, Ranaivoson HC, Ahyong V, Andrianiaina A, Andry S, DeRisi JL, Gentles A, Raharinosy V, Randriambolamanantsoa TH, Ravelomanantsoa NAF, Tato CM, Dussart P, Heraud JM, Brook CE -
Clonally expanded B cells in multiple sclerosis bind EBV EBNA1 and GlialCAM.
Nature 2022 Lanz TV, Brewer RC, Ho PP, Moon JS, Jude KM, Fernandez D, Fernandes RA, Gomez AM, Nadj GS, Bartley CM, Schubert RD, Hawes IA, Vazquez SE, Iyer M, Zuchero JB, Teegen B, Dunn JE, Lock CB, Kipp LB, … -
Estimation of Secondary Household Attack Rates for Emergent Spike L452R Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants Detected by Genomic Surveillance at a Community-Based Testing Site in San Francisco.
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2022 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, … -
Functional characterization of 5' UTR cis-acting sequence elements that modulate translational efficiency in Plasmodium falciparum and humans.
Malaria journal 2022 Garcia VE, Dial R, DeRisi JL -
SARS-CoV-2 variant exposures elicit antibody responses with differential cross-neutralization of established and emerging strains including Delta and Omicron.
medRxiv : the preprint server for health sciences 2021 Laurie MT, Liu J, Sunshine S, Peng J, Black D, Mitchell AM, Mann SA, Pilarowski G, Zorn KC, Rubio L, Bravo S, Marquez C, Sabatino JJ, Mittl K, Petersen M, Havlir D, DeRisi J -
High Parental Vaccine Motivation at a Neighborhood-Based Vaccine and Testing Site Serving a Predominantly Latinx Community.
Health equity 2021 Naso J, Rojas S, Peng J, Marquez C, Contreras M, Castellanos E, Rojas S, Rubio L, Jones D, Jacobo J, Black D, Tulier-Laiwa V, Martinez J, Chamie G, Pilarowski G, DeRisi J, Havlir D, Petersen M -
Anti-SARS-CoV-2 and Autoantibody Profiles in the Cerebrospinal Fluid of 3 Teenaged Patients With COVID-19 and Subacute Neuropsychiatric Symptoms.
JAMA neurology 2021 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 -
Long-term MRI changes in a patient with Kelch-like protein 11-associated paraneoplastic neurological syndrome.
European journal of neurology 2021 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 -
Impaired immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19.
medRxiv : the preprint server for health sciences 2021 Tsitsiklis A, Zha BS, Byrne A, DeVoe C, Rackaityte E, Levan S, Sunshine S, Mick E, Ghale R, Love C, Tarashansky AJ, Pisco A, Albright J, Jauregui A, Sarma A, Neff N, Serpa PH, Deiss TJ, Kistler A, … -
SARS-CoV-2 Infection of Rhesus Macaques Treated Early with Human COVID-19 Convalescent Plasma.
Microbiology spectrum 2021 Deere JD, Carroll TD, Dutra J, Fritts L, Sammak RL, Yee JL, Olstad KJ, Reader JR, Kistler A, Kamm J, Di Germanio C, Shaan Lakshmanappa Y, Elizaldi SR, Roh JW, Simmons G, Watanabe J, Pollard RE, … -
Field Performance and Public Health Response Using the BinaxNOWTM Rapid Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Antigen Detection Assay During Community-Based Testing.
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 Pilarowski G, Marquez C, Rubio L, Peng J, Martinez J, Black D, Chamie G, Jones D, Jacobo J, Tulier-Laiwa V, Rojas S, Rojas S, Cox C, Nakamura R, Petersen M, DeRisi J, Havlir DV -
Detection of Neoplasms by Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid.
JAMA neurology 2021 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… -
Cerebrospinal Fluid Pterins, Pterin-Dependent Neurotransmitters, and Mortality in Pediatric Cerebral Malaria.
The Journal of infectious diseases 2021 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 -
Author Correction: Pan-viral serology implicates enteroviruses in acute flaccid myelitis.
Nature medicine 2021 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… -
A multi-component, community-based strategy to facilitate COVID-19 vaccine uptake among Latinx populations: From theory to practice.
PloS one 2021 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 … -
Elevated N-Linked Glycosylation of IgG V Regions in Myasthenia Gravis Disease Subtypes.
Journal of immunology (Baltimore, Md. : 1950) 2021 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 -
Tracheal aspirate RNA sequencing identifies distinct immunological features of COVID-19 ARDS.
Nature communications 2021 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, … -
Upper airway gene expression reveals a more robust innate and adaptive immune response to SARS-CoV-2 in children compared with older adults.
Research square 2021 Mick E, Tsitsiklis A, Spottiswoode N, Caldera S, Serpa PH, Detweiler AM, Neff N, Pisco AO, Li LM, Retallack H, Ratnasiri K, Williamson KM, Soesanto V, Simões EAF, Kistler A, Wagner BD, DeRisi JL, … -
Type I interferon autoantibodies are associated with systemic immune alterations in patients with COVID-19.
Science translational medicine 2021 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, … -
Metagenomic characterization of swine slurry in a North American swine farm operation.
Scientific reports 2021 Ramesh A, Bailey ES, Ahyong V, Langelier C, Phelps M, Neff N, Sit R, Tato C, DeRisi JL, Greer AG, Gray GC -
Label-free imaging and classification of live P. falciparum enables high performance parasitemia quantification without fixation or staining.
PLoS computational biology 2021 Lebel P, Dial R, Vemuri VNP, Garcia V, DeRisi J, Gómez-Sjöberg R -
Persistence of Ambigrammatic Narnaviruses Requires Translation of the Reverse Open Reading Frame.
Journal of virology 2021 Retallack H, Popova KD, Laurie MT, Sunshine S, DeRisi JL -
Detection of cryptogenic malignancies from metagenomic whole genome sequencing of body fluids.
Genome medicine 2021 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, … -
Phage display demonstrates durable differences in serological profile by route of inoculation in primary infections of non-human primates with Dengue Virus 1.
Scientific reports 2021 Rajan JV, McCracken M, Mandel-Brehm C, Gromowski G, Pollett S, Jarman R, DeRisi JL -
Neutralizing Autoantibodies to Type I Interferons in COVID-19 Convalescent Donor Plasma.
Journal of clinical immunology 2021 Vazquez SE, Bastard P, Kelly K, Gervais A, Norris PJ, Dumont LJ, Casanova JL, Anderson MS, DeRisi JL -
Divergent and self-reactive immune responses in the CNS of COVID-19 patients with neurological symptoms.
Cell reports. Medicine 2021 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… -
Use of unbiased metagenomic and transcriptomic analyses to investigate the association between feline calicivirus and feline chronic gingivostomatitis in domestic cats.
American journal of veterinary research 2021 Fried WA, Soltero-Rivera M, Ramesh A, Lommer MJ, Arzi B, DeRisi JL, Horst JA -
Impaired immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19.
Research square 2021 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… -
Performance Characteristics of a Rapid Severe Acute Respiratory Syndrome Coronavirus 2 Antigen Detection Assay at a Public Plaza Testing Site in San Francisco.
The Journal of infectious diseases 2021 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, … -
POECIVIRUS IS PRESENT IN INDIVIDUALS WITH BEAK DEFORMITIES IN SEVEN SPECIES OF NORTH AMERICAN BIRDS.
Journal of wildlife diseases 2021 Zylberberg M, Van Hemert C, Handel CM, Liu RM, DeRisi JL -
The pulmonary metatranscriptome prior to pediatric HCT identifies post-HCT lung injury.
Blood 2021 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 -
Temporal airway microbiome changes related to ventilator-associated pneumonia in children.
The European respiratory journal 2021 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,… -
Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19: Anti-IFN antibodies in critical COVID-19 correlate with poor ISG response and upregulation of LAIR1 surface protein in PBMCs.
bioRxiv : the preprint server for biology 2021 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, … -
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 : the preprint server for health sciences 2021 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, … -
The COVID-19 epidemic in Madagascar: clinical description and laboratory results of the first wave, march-september 2020.
Influenza and other respiratory viruses 2021 Randremanana RV, Andriamandimby SF, Rakotondramanga JM, Razanajatovo NH, Mangahasimbola RT, Randriambolamanantsoa TH, Ranaivoson HC, Rabemananjara HA, Razanajatovo I, Razafindratsimandresy R, … -
Nasopharyngeal SARS-CoV-2 viral loads in young children do not differ significantly from those in older children and adults.
Scientific reports 2021 Madera S, Crawford E, Langelier C, Tran NK, Thornborrow E, Miller S, DeRisi JL -
COVID-19 ARDS is characterized by a dysregulated host response that differs from cytokine storm and is modified by dexamethasone.
Research square 2021 Sarma A, Christenson SA, Mick E, DeVoe C, Deiss T, Pisco AO, Ghale R, Jauregui A, Byrne A, Moazed F, Spottiswoode N, Sinha P, Zha BS, Neff N, Tan M, Serpa PH, Ansel KM, Wilson JG, Leligdowicz A, … -
Genome-Wide Ribosome Profiling of the Plasmodium falciparum Intraerythrocytic Developmental Cycle.
Methods in molecular biology (Clifton, N.J.) 2021 Caro F, DeRisi JL -
Identification of a Polymorphism in the N Gene of SARS-CoV-2 That Adversely Impacts Detection by Reverse Transcription-PCR.
Journal of clinical microbiology 2020 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 … -
Exploratory neuroimmune profiling identifies CNS-specific alterations in COVID-19 patients with neurological involvement.
bioRxiv : the preprint server for biology 2020 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, … -
Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy.
Cell 2020 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, … -
Upper airway gene expression reveals suppressed immune responses to SARS-CoV-2 compared with other respiratory viruses.
Nature communications 2020 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, … -
Performance characteristics of a rapid SARS-CoV-2 antigen detection assay at a public plaza testing site in San Francisco.
medRxiv : the preprint server for health sciences 2020 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, … -
Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids.
Nature medicine 2020 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 … -
Expanded Clinical Phenotype, Oncological Associations, and Immunopathologic Insights of Paraneoplastic Kelch-like Protein-11 Encephalitis.
JAMA neurology 2020 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, … -
Rapid deployment of SARS-CoV-2 testing: The CLIAHUB.
PLoS pathogens 2020 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, … -
IDseq-An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring.
GigaScience 2020 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, … -
Deep profiling of protease substrate specificity enabled by dual random and scanned human proteome substrate phage libraries.
Proceedings of the National Academy of Sciences of the United States of America 2020 Zhou J, Li S, Leung KK, O'Donovan B, Zou JY, DeRisi JL, Wells JA -
ReScan, a Multiplex Diagnostic Pipeline, Pans Human Sera for SARS-CoV-2 Antigens.
Cell reports. Medicine 2020 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, … -
Genomic Profiling of Evolving Daptomycin Resistance in a Patient with Recurrent Staphylococcus argenteus Sepsis.
Antimicrobial agents and chemotherapy 2020 Hao S, Abdelghany M, Lyden A, Sit R, Tan M, Tato CM, DeRisi JL, Miller S, Doernberg SB, Langelier C -
A pathogenic and clonally expanded B cell transcriptome in active multiple sclerosis.
Proceedings of the National Academy of Sciences of the United States of America 2020 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,… -
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 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, … -
Investigating Transfusion-related Sepsis Using Culture-Independent Metagenomic Sequencing.
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 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, … -
High-resolution epitope mapping of anti-Hu and anti-Yo autoimmunity by programmable phage display.
Brain communications 2020 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 -
Erratum.
Pediatric dentistry 2020 DeRisi JL -
Complete Genome Sequence of a Novel Coronavirus (SARS-CoV-2) Isolate from Bangladesh.
Microbiology resource announcements 2020 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 -
Upper airway gene expression differentiates COVID-19 from other acute respiratory illnesses and reveals suppression of innate immune responses by SARS-CoV-2.
medRxiv : the preprint server for health sciences 2020 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, … -
Enhanced Tooth Structure Via Silver Microwires Following Treatment with 38 Percent Silver Diamine Fluoride.
Pediatric dentistry 2020 Seto J, Horst JA, Parkinson DY, Frachella JC, DeRisi JL -
Identification of novel, clinically correlated autoantigens in the monogenic autoimmune syndrome APS1 by proteome-wide PhIP-Seq.
eLife 2020 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 -
Clinical features, diagnostics, and outcomes of patients presenting with acute respiratory illness: a comparison of patients with and without COVID-19.
medRxiv : the preprint server for health sciences 2020 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, … -
Central Nervous System Virus Infection in African Children with Cerebral Malaria.
The American journal of tropical medicine and hygiene 2020 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 -
Identification of anisomycin, prodigiosin and obatoclax as compounds with broad-spectrum anti-parasitic activity.
PLoS neglected tropical diseases 2020 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 -
Genomic and serologic characterization of enterovirus A71 brainstem encephalitis.
Neurology(R) neuroimmunology & neuroinflammation 2020 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-… -
Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia.
bioRxiv : the preprint server for biology 2020 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 -
Detection of Pneumonia Pathogens from Plasma Cell-Free DNA.
American journal of respiratory and critical care medicine 2020 Langelier C, Fung M, Caldera S, Deiss T, Lyden A, Prince BC, Serpa PH, Moazed F, Chin-Hong P, DeRisi JL, Calfee CS -
The Molecular Medicine Investigation Unit: Linking Patient Care and Scientific Inquiry in Physician-Scientist Training.
Journal of graduate medical education 2020 Berger A, Matloubian M, Shah NP, Wachter RM, DeRisi JL, Anderson M -
Plasmodium falciparum Resistance to a Lead Benzoxaborole Due to Blocked Compound Activation and Altered Ubiquitination or Sumoylation.
mBio 2020 Sindhe KMV, Wu W, Legac J, Zhang YK, Easom EE, Cooper RA, Plattner JJ, Freund YR, DeRisi JL, Rosenthal PJ -
Exploratory analysis of the potential for advanced diagnostic testing to reduce healthcare expenditures of patients hospitalized with meningitis or encephalitis.
PloS one 2020 Fulton BD, Proudman DG, Sample HA, Gelfand JM, Chiu CY, DeRisi JL, Wilson MR -
Unbiased Metagenomic Sequencing for Pediatric Meningitis in Bangladesh Reveals Neuroinvasive Chikungunya Virus Outbreak and Other Unrealized Pathogens.
mBio 2019 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, … -
An exploration of ambigrammatic sequences in narnaviruses.
Scientific reports 2019 DeRisi JL, Huber G, Kistler A, Retallack H, Wilkinson M, Yllanes D -
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 neuropathologica 2019 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 -
Pan-viral serology implicates enteroviruses in acute flaccid myelitis.
Nature medicine 2019 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… -
FLASH: a next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences.
Nucleic acids research 2019 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… -
Kelch-like Protein 11 Antibodies in Seminoma-Associated Paraneoplastic Encephalitis.
The New England journal of medicine 2019 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 -
Exploratory proteomic analysis implicates the alternative complement cascade in primary CNS vasculitis.
Neurology 2019 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 … -
Microbiome and Antimicrobial Resistance Gene Dynamics in International Travelers.
Emerging infectious diseases 2019 Langelier C, Graves M, Kalantar K, Caldera S, Durrant R, Fisher M, Backman R, Tanner W, DeRisi JL, Leung DT -
Metagenomic next-generation sequencing of samples from pediatric febrile illness in Tororo, Uganda.
PloS one 2019 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 -
Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis.
The New England journal of medicine 2019 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, … -
Sentinel Case of Candida auris in the Western United States Following Prolonged Occult Colonization in a Returned Traveler from India.
Microbial drug resistance (Larchmont, N.Y.) 2019 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 -
Detection of Cryptococcus DNA by Metagenomic Next-generation Sequencing in Symptomatic Cryptococcal Antigenemia.
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 Ramachandran PS, Cresswell FV, Meya DB, Langelier C, Crawford ED, DeRisi JL, Boulware DR, Wilson MR -
Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children.
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 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 … -
Genome Sequence of a Divergent Avian Metapneumovirus from a Monk Parakeet (Myiopsitta monachus).
Microbiology resource announcements 2019 Retallack H, Clubb S, DeRisi JL -
Towards precision quantification of contamination in metagenomic sequencing experiments.
Microbiome 2019 Zinter MS, Mayday MY, Ryckman KK, Jelliffe-Pawlowski LL, DeRisi JL -
Bergeyella cardium: Clinical Characteristics and Draft Genome of an Emerging Pathogen in Native and Prosthetic Valve Endocarditis.
Open forum infectious diseases 2019 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 -
Taxonomy of the order Bunyavirales: second update 2018.
Archives of virology 2019 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 … -
Metagenomic comparison of tracheal aspirate and mini-bronchial alveolar lavage for assessment of respiratory microbiota.
American journal of physiology. Lung cellular and molecular physiology 2019 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 -
Miniaturization and optimization of 384-well compatible RNA sequencing library preparation.
PloS one 2019 Mayday MY, Khan LM, Chow ED, Zinter MS, DeRisi JL -
Clinicopathology conference: 41-year-old woman with chronic relapsing meningitis.
Annals of neurology 2019 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 -
Misinterpretation of Study Data-Reply.
JAMA neurology 2019 Wilson MR, O'Donovan BD, DeRisi JL -
The Plasmodium falciparum cytoplasmic translation apparatus: a promising therapeutic target not yet exploited by clinically approved anti-malarials.
Malaria journal 2018 Sheridan CM, Garcia VE, Ahyong V, DeRisi JL -
Ebola virus, but not Marburg virus, replicates efficiently and without required adaptation in snake cells.
Virus evolution 2018 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 -
Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults.
Proceedings of the National Academy of Sciences of the United States of America 2018 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, … -
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 Laurie MT, White CV, Retallack H, Wu W, Moser MS, Sakanari JA, Ang K, Wilson C, Arkin MR, DeRisi JL -
A fixed moderate-dose combination of tiletamine+zolazepam outperforms midazolam in induction of short-term immobilization of ball pythons (Python regius).
PloS one 2018 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 -
METAGENOMIC NEXT-GENERATION SEQUENCING REVEALS MIAMIENSIS AVIDUS (CILIOPHORA: SCUTICOCILIATIDA) IN THE 2017 EPIZOOTIC OF LEOPARD SHARKS ( TRIAKIS SEMIFASCIATA) IN SAN FRANCISCO BAY, CALIFORNIA, USA.
Journal of wildlife diseases 2018 Retallack H, Okihiro MS, Britton E, Sommeran SV, DeRisi JL -
Chronic Meningitis Investigated via Metagenomic Next-Generation Sequencing.
JAMA neurology 2018 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, … -
Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance.
Biology open 2018 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 … -
Whole-Genome mRNA Gene Expression Differs Between Patients With and Without Delirium.
Journal of geriatric psychiatry and neurology 2018 Kalantar K, LaHue SC, DeRisi JL, Sample HA, Contag CA, Josephson SA, Wilson MR, Douglas VC -
Avian keratin disorder of Alaska black-capped chickadees is associated with Poecivirus infection.
Virology journal 2018 Zylberberg M, Van Hemert C, Handel CM, DeRisi JL -
Fatal Powassan Encephalitis (Deer Tick Virus, Lineage II) in a Patient With Fever and Orchitis Receiving Rituximab.
JAMA neurology 2018 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 -
Taxonomy of the family Arenaviridae and the order Bunyavirales: update 2018.
Archives of virology 2018 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,… -
Metagenomic Sequencing Detects Respiratory Pathogens in Hematopoietic Cellular Transplant Patients.
American journal of respiratory and critical care medicine 2018 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 -
IFN-stimulated Gene Expression, Type 2 Inflammation, and Endoplasmic Reticulum Stress in Asthma.
American journal of respiratory and critical care medicine 2018 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 -
Complete Genome Sequence of a Divergent Human Rhinovirus C Isolate from an Infant with Severe Community-Acquired Pneumonia in Colorado, USA.
Genome announcements 2017 Langelier C, White CV, Sontag MK, Mourani PM, DeRisi JL -
Metagenomic deep sequencing of aqueous fluid detects intraocular lymphomas.
The British journal of ophthalmology 2017 Gonzales J, Doan T, Shantha JG, Bloomer M, Wilson MR, DeRisi JL, Acharya N -
Northern Spotted Owl (Strix occidentalis caurina) Genome: Divergence with the Barred Owl (Strix varia) and Characterization of Light-Associated Genes.
Genome biology and evolution 2017 Hanna ZR, Henderson JB, Wall JD, Emerling CA, Fuchs J, Runckel C, Mindell DP, Bowie RCK, DeRisi JL, Dumbacher JP -
Multi-modality analysis supports APOBEC as a major source of mutations in head and neck squamous cell carcinoma.
Oral oncology 2017 Faden DL, Thomas S, Cantalupo PG, Agrawal N, Myers J, DeRisi J -
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.
Journal of dentistry 2017 Milgrom P, Horst JA, Ludwig S, Rothen M, Chaffee BW, Lyalina S, Pollard KS, DeRisi JL, Mancl L -
Differential Disease Susceptibilities in Experimentally Reptarenavirus-Infected Boa Constrictors and Ball Pythons.
Journal of virology 2017 Stenglein MD, Sanchez-Migallon Guzman D, Garcia VE, Layton ML, Hoon-Hanks LL, Boback SM, Keel MK, Drazenovich T, Hawkins MG, DeRisi JL -
A novel cause of chronic viral meningoencephalitis: Cache Valley virus.
Annals of neurology 2017 Wilson MR, Suan D, Duggins A, Schubert RD, Khan LM, Sample HA, Zorn KC, Rodrigues Hoffman A, Blick A, Shingde M, DeRisi JL -
Extracorporeal life support survival in a pediatric hematopoietic cellular transplant recipient with presumed GvHD-related fulminant myocarditis.
Bone marrow transplantation 2017 Zinter MS, Barrows BD, Ursell PC, Kowalek K, Kalantar K, Cambronero N, DeRisi JL, Oishi P, Dvorak CC -
Plasmid-free CRISPR/Cas9 genome editing in Plasmodium falciparum confirms mutations conferring resistance to the dihydroisoquinolone clinical candidate SJ733.
PloS one 2017 Crawford ED, Quan J, Horst JA, Ebert D, Wu W, DeRisi JL -
Metagenomic DNA Sequencing for the Diagnosis of Intraocular Infections.
Ophthalmology 2017 Doan T, Acharya NR, Pinsky BA, Sahoo MK, Chow ED, Banaei N, Budvytiene I, Cevallos V, Zhong L, Zhou Z, Lietman TM, DeRisi JL -
Possibility and Challenges of Conversion of Current Virus Species Names to Linnaean Binomials.
Systematic biology 2017 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 … -
Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater.
PloS one 2017 Ludington WB, Seher TD, Applegate O, Li X, Kliegman JI, Langelier C, Atwill ER, Harter T, DeRisi JL -
A potent antimalarial benzoxaborole targets a Plasmodium falciparum cleavage and polyadenylation specificity factor homologue.
Nature communications 2017 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… -
MinorityReport, software for generalized analysis of causal genetic variants.
Malaria journal 2017 Horst JA, Wu W, DeRisi JL -
Interaction between FMDV Lpro and transcription factor ADNP is required for optimal viral replication.
Virology 2017 Medina GN, Knudsen GM, Greninger AL, Kloc A, Díaz-San Segundo F, Rieder E, Grubman MJ, DeRisi JL, de Los Santos T -
Correction: Whole Exome Sequencing of Growing and Non-Growing Cutaneous Neurofibromas from a Single Patient with Neurofibromatosis Type 1.
PloS one 2017 Faden DL, Asthana S, Tihan T, DeRisi J, Kliot M -
The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell.
Current biology : CB 2017 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, … -
Whole Exome Sequencing of Growing and Non-Growing Cutaneous Neurofibromas from a Single Patient with Neurofibromatosis Type 1.
PloS one 2017 Faden DL, Asthana S, Tihan T, DeRisi J, Kliot M -
Altered Plasmodium falciparum Sensitivity to the Antiretroviral Protease Inhibitor Lopinavir Associated with Polymorphisms in pfmdr1.
Antimicrobial agents and chemotherapy 2016 Sonoiki E, Nsanzabana C, Legac J, Sindhe KM, DeRisi J, Rosenthal PJ -
Zika virus cell tropism in the developing human brain and inhibition by azithromycin.
Proceedings of the National Academy of Sciences of the United States of America 2016 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 -
A Herpesviral induction of RAE-1 NKG2D ligand expression occurs through release of HDAC mediated repression.
eLife 2016 Greene TT, Tokuyama M, Knudsen GM, Kunz M, Lin J, Greninger AL, DeFilippis VR, DeRisi JL, Raulet DH, Coscoy L -
Erratum to: Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens.
Genome medicine 2016 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 -
Detection and prevalence of boid inclusion body disease in collections of boas and pythons using immunological assays.
Veterinary journal (London, England : 1997) 2016 Chang L, Fu D, Stenglein MD, Hernandez JA, DeRisi JL, Jacobson ER -
Acute West Nile Virus Meningoencephalitis Diagnosed Via Metagenomic Deep Sequencing of Cerebrospinal Fluid in a Renal Transplant Patient.
American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons 2016 Wilson MR, Zimmermann LL, Crawford ED, Sample HA, Soni PR, Baker AN, Khan LM, DeRisi JL -
Programmable Microfluidic Synthesis of Over One Thousand Uniquely Identifiable Spectral Codes.
Advanced optical materials 2016 Nguyen HQ, Baxter BC, Brower K, Diaz-Botia CA, DeRisi JL, Fordyce PM, Thorn KS -
Neurologic Complications of Common Variable Immunodeficiency.
Journal of clinical immunology 2016 Nguyen JT, Green A, Wilson MR, DeRisi JL, Gundling K -
Targeted next-generation sequencing of TP53 in oral tongue carcinoma from non-smokers.
Journal of otolaryngology - head & neck surgery = Le Journal d'oto-rhino-laryngologie et de chirurgie cervico-faciale 2016 Faden DL, Arron ST, Heaton CM, DeRisi J, South AP, Wang SJ -
Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens.
Genome medicine 2016 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 -
Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond.
PLoS pathogens 2016 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, … -
Novel Picornavirus Associated with Avian Keratin Disorder in Alaskan Birds.
mBio 2016 Zylberberg M, Van Hemert C, Dumbacher JP, Handel CM, Tihan T, DeRisi JL -
Antimalarial Benzoxaboroles Target Plasmodium falciparum Leucyl-tRNA Synthetase.
Antimicrobial agents and chemotherapy 2016 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 -
Multiplexed Metagenomic Deep Sequencing To Analyze the Composition of High-Priority Pathogen Reagents.
mSystems 2016 Wilson MR, Fedewa G, Stenglein MD, Olejnik J, Rennick LJ, Nambulli S, Feldmann F, Duprex WP, Connor JH, Mühlberger E, DeRisi JL -
Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting.
eLife 2016 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… -
Identification of Plasmodium falciparum specific translation inhibitors from the MMV Malaria Box using a high throughput in vitro translation screen.
Malaria journal 2016 Ahyong V, Sheridan CM, Leon KE, Witchley JN, Diep J, DeRisi JL -
Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications.
Genome biology 2016 Gu W, Crawford ED, O'Donovan BD, Wilson MR, Chow ED, Retallack H, DeRisi JL -
Association of NMT2 with the acyl-CoA carrier ACBD6 protects the N-myristoyltransferase reaction from palmitoyl-CoA.
Journal of lipid research 2015 Soupene E, Kao J, Cheng DH, Wang D, Greninger AL, Knudsen GM, DeRisi JL, Kuypers FA -
Isolation of a Complete Circular Virus Genome Sequence from an Alaskan Black-Capped Chickadee (Poecile atricapillus) Gastrointestinal Tract Sample.
Genome announcements 2015 Hanna ZR, Runckel C, Fuchs J, DeRisi JL, Mindell DP, Van Hemert C, Handel CM, Dumbacher JP -
Diagnosing Balamuthia mandrillaris Encephalitis With Metagenomic Deep Sequencing.
Annals of neurology 2015 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 -
Draft Genome Sequence of Laverivirus UC1, a Dicistrovirus-Like RNA Virus Featuring an Unusual Genome Organization.
Genome announcements 2015 Greninger AL, DeRisi JL -
Draft Genome Sequence of Picalivirus D Recovered from San Francisco Wastewater.
Genome announcements 2015 Greninger AL, DeRisi JL -
Draft Genome Sequence of Tombunodavirus UC1.
Genome announcements 2015 Greninger AL, DeRisi JL -
Past, present, and future of arenavirus taxonomy.
Archives of virology 2015 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 -
Draft Genome Sequences of Ciliovirus and Brinovirus from San Francisco Wastewater.
Genome announcements 2015 Greninger AL, DeRisi JL -
Draft Genome Sequences of Leviviridae RNA Phages EC and MB Recovered from San Francisco Wastewater.
Genome announcements 2015 Greninger AL, DeRisi JL -
Draft Genome Sequences of Marine RNA Viruses SF-1, SF-2, and SF-3 Recovered from San Francisco Wastewater.
Genome announcements 2015 Greninger AL, DeRisi JL -
Widespread recombination, reassortment, and transmission of unbalanced compound viral genotypes in natural arenavirus infections.
PLoS pathogens 2015 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 -
Destructin-1 is a collagen-degrading endopeptidase secreted by Pseudogymnoascus destructans, the causative agent of white-nose syndrome.
Proceedings of the National Academy of Sciences of the United States of America 2015 O'Donoghue AJ, Knudsen GM, Beekman C, Perry JA, Johnson AD, DeRisi JL, Craik CS, Bennett RJ -
Correction: Programmable microfluidic synthesis of spectrally encoded microspheres.
Lab on a chip 2015 Gerver RE, Gómez-Sjöberg R, Baxter BC, Thorn KS, Fordyce PM, Diaz-Botia CA, Helms BA, DeRisi JL -
Salinipostins A-K, long-chain bicyclic phosphotriesters as a potent and selective antimalarial chemotype.
The Journal of organic chemistry 2015 Schulze CJ, Navarro G, Ebert D, DeRisi J, Linington RG -
Genome-wide regulatory dynamics of translation in the Plasmodium falciparum asexual blood stages.
eLife 2014 Caro F, Ahyong V, Betegon M, DeRisi JL -
Taxonomic reorganization of the family Bornaviridae.
Archives of virology 2014 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 -
(+)-SJ733, a clinical candidate for malaria that acts through ATP4 to induce rapid host-mediated clearance of Plasmodium.
Proceedings of the National Academy of Sciences of the United States of America 2014 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 … -
A chemical rescue screen identifies a Plasmodium falciparum apicoplast inhibitor targeting MEP isoprenoid precursor biosynthesis.
Antimicrobial agents and chemotherapy 2014 Wu W, Herrera Z, Ebert D, Baska K, Cho SH, DeRisi JL, Yeh E -
Genome Sequence of a Bornavirus Recovered from an African Garter Snake (Elapsoidea loveridgei).
Genome announcements 2014 Stenglein MD, Leavitt EB, Abramovitch MA, McGuire JA, DeRisi JL -
Ball python nidovirus: a candidate etiologic agent for severe respiratory disease in Python regius.
mBio 2014 Stenglein MD, Jacobson ER, Wozniak EJ, Wellehan JF, Kincaid A, Gordon M, Porter BF, Baumgartner W, Stahl S, Kelley K, Towner JS, DeRisi JL -
Clinical, genomic, and metagenomic characterization of oral tongue squamous cell carcinoma in patients who do not smoke.
Head & neck 2014 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, … -
Profile hidden Markov models for the detection of viruses within metagenomic sequence data.
PloS one 2014 Skewes-Cox P, Sharpton TJ, Pollard KS, DeRisi JL -
A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples.
Genome research 2014 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… -
Actionable diagnosis of neuroleptospirosis by next-generation sequencing.
The New England journal of medicine 2014 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,… -
How duplicated transcription regulators can diversify to govern the expression of nonoverlapping sets of genes.
Genes & development 2014 Pérez JC, Fordyce PM, Lohse MB, Hanson-Smith V, DeRisi JL, Johnson AD -
The kinase regulator mob1 acts as a patterning protein for stentor morphogenesis.
PLoS biology 2014 Slabodnick MM, Ruby JG, Dunn JG, Feldman JL, DeRisi JL, Marshall WF -
Krüppel mediates the selective rebalancing of ion channel expression.
Neuron 2014 Parrish JZ, Kim CC, Tang L, Bergquist S, Wang T, Derisi JL, Jan LY, Jan YN, Davis GW -
A draft genome of the honey bee trypanosomatid parasite Crithidia mellificae.
PloS one 2014 Runckel C, DeRisi J, Flenniken ML -
Transcriptome-wide characterization of the eIF4A signature highlights plasticity in translation regulation.
Genome biology 2014 Rubio CA, Weisburd B, Holderfield M, Arias C, Fang E, DeRisi JL, Fanidi A -
Polar bear encephalitis: establishment of a comprehensive next-generation pathogen analysis pipeline for captive and free-living wildlife.
Journal of comparative pathology 2013 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, … -
Structural characterization of the glycoprotein GP2 core domain from the CAS virus, a novel arenavirus-like species.
Journal of molecular biology 2013 Koellhoffer JF, Dai Z, Malashkevich VN, Stenglein MD, Liu Y, Toro R, S Harrison J, Chandran K, DeRisi JL, Almo SC, Lai JR -
Structure of the transcriptional network controlling white-opaque switching in Candida albicans.
Molecular microbiology 2013 Hernday AD, Lohse MB, Fordyce PM, Nobile CJ, DeRisi JL, Johnson AD -
Asexual populations of the human malaria parasite, Plasmodium falciparum, use a two-step genomic strategy to acquire accurate, beneficial DNA amplifications.
PLoS pathogens 2013 Guler JL, Freeman DL, Ahyong V, Patrapuvich R, White J, Gujjar R, Phillips MA, DeRisi J, Rathod PK -
PRICE: software for the targeted assembly of components of (Meta) genomic sequence data.
G3 (Bethesda, Md.) 2013 Ruby JG, Bellare P, Derisi JL -
Microfluidic affinity and ChIP-seq analyses converge on a conserved FOXP2-binding motif in chimp and human, which enables the detection of evolutionarily novel targets.
Nucleic acids research 2013 Nelson CS, Fuller CK, Fordyce PM, Greninger AL, Li H, DeRisi JL -
Identification and characterization of a previously undescribed family of sequence-specific DNA-binding domains.
Proceedings of the National Academy of Sciences of the United States of America 2013 Lohse MB, Hernday AD, Fordyce PM, Noiman L, Sorrells TR, Hanson-Smith V, Nobile CJ, DeRisi JL, Johnson AD -
ACBD3 interaction with TBC1 domain 22 protein is differentially affected by enteroviral and kobuviral 3A protein binding.
mBio 2013 Greninger AL, Knudsen GM, Betegon M, Burlingame AL, DeRisi JL -
Bartonella quintana deploys host and vector temperature-specific transcriptomes.
PloS one 2013 Abromaitis S, Nelson CS, Previte D, Yoon KS, Clark JM, DeRisi JL, Koehler JE -
Identification and manipulation of the molecular determinants influencing poliovirus recombination.
PLoS pathogens 2013 Runckel C, Westesson O, Andino R, DeRisi JL -
Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution.
Genome biology 2013 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 -
Graduate education. Interdisciplinary graduate training in teaching labs.
Science (New York, N.Y.) 2012 Vale RD, DeRisi J, Phillips R, Mullins RD, Waterman C, Mitchison TJ -
Programmable microfluidic synthesis of spectrally encoded microspheres.
Lab on a chip 2012 Gerver RE, Gómez-Sjöberg R, Baxter BC, Thorn KS, Fordyce PM, Diaz-Botia CA, Helms BA, DeRisi JL -
Discovery of a novel polyomavirus in acute diarrheal samples from children.
PloS one 2012 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 -
Systematic characterization of feature dimensions and closing pressures for microfluidic valves produced via photoresist reflow.
Lab on a chip 2012 Fordyce PM, Diaz-Botia CA, DeRisi JL, Gomez-Sjoberg R -
Splenic red pulp macrophages produce type I interferons as early sentinels of malaria infection but are dispensable for control.
PloS one 2012 Kim CC, Nelson CS, Wilson EB, Hou B, DeFranco AL, DeRisi JL -
Basic leucine zipper transcription factor Hac1 binds DNA in two distinct modes as revealed by microfluidic analyses.
Proceedings of the National Academy of Sciences of the United States of America 2012 Fordyce PM, Pincus D, Kimmig P, Nelson CS, El-Samad H, Walter P, DeRisi JL -
Molecular insights into the biosynthesis of guadinomine: a type III secretion system inhibitor.
Journal of the American Chemical Society 2012 Holmes TC, May AE, Zaleta-Rivera K, Ruby JG, Skewes-Cox P, Fischbach MA, DeRisi JL, Iwatsuki M, Omura S, Khosla C -
Global identification of peptidase specificity by multiplex substrate profiling.
Nature methods 2012 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 -
Complete genome sequence of an astrovirus identified in a domestic rabbit (Oryctolagus cuniculus) with gastroenteritis.
Virology journal 2012 Stenglein MD, Velazquez E, Greenacre C, Wilkes RP, Ruby JG, Lankton JS, Ganem D, Kennedy MA, DeRisi JL -
In-depth investigation of archival and prospectively collected samples reveals no evidence for XMRV infection in prostate cancer.
PloS one 2012 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 -
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 Stenglein MD, Sanders C, Kistler AL, Ruby JG, Franco JY, Reavill DR, Dunker F, Derisi JL -
Lead optimization of antimalarial propafenone analogues.
Journal of medicinal chemistry 2012 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 -
Virus identification in unknown tropical febrile illness cases using deep sequencing.
PLoS neglected tropical diseases 2012 Yozwiak NL, Skewes-Cox P, Stenglein MD, Balmaseda A, Harris E, DeRisi JL -
Plate-based transfection and culturing technique for genetic manipulation of Plasmodium falciparum.
Malaria journal 2012 Caro F, Miller MG, DeRisi JL -
The 3A protein from multiple picornaviruses utilizes the golgi adaptor protein ACBD3 to recruit PI4KIIIβ.
Journal of virology 2012 Greninger AL, Knudsen GM, Betegon M, Burlingame AL, Derisi JL -
A new threat to honey bees, the parasitic phorid fly Apocephalus borealis.
PloS one 2012 Core A, Runckel C, Ivers J, Quock C, Siapno T, Denault S, Brown B, Derisi J, Smith CD, Hafernik J -
ReCombine: a suite of programs for detection and analysis of meiotic recombination in whole-genome datasets.
PloS one 2011 Anderson CM, Chen SY, Dimon MT, Oke A, DeRisi JL, Fung JC -
Optimization of propafenone analogues as antimalarial leads.
Journal of medicinal chemistry 2011 Lowes DJ, Guiguemde WA, Connelly MC, Zhu F, Sigal MS, Clark JA, Lemoff AS, Derisi JL, Wilson EB, Guy RK -
Synthesis and evaluation of 7-substituted 4-aminoquinoline analogues for antimalarial activity.
Journal of medicinal chemistry 2011 Hwang JY, Kawasuji T, Lowes DJ, Clark JA, Connelly MC, Zhu F, Guiguemde WA, Sigal MS, Wilson EB, Derisi JL, Guy RK -
Assemblathon 1: a competitive assessment of de novo short read assembly methods.
Genome research 2011 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… -
Chemical rescue of malaria parasites lacking an apicoplast defines organelle function in blood-stage Plasmodium falciparum.
PLoS biology 2011 Yeh E, DeRisi JL -
Temporal analysis of the honey bee microbiome reveals four novel viruses and seasonal prevalence of known viruses, Nosema, and Crithidia.
PloS one 2011 Runckel C, Flenniken ML, Engel JC, Ruby JG, Ganem D, Andino R, DeRisi JL -
Validation of a diagnostic microarray for human papillomavirus: coverage of 102 genotypes.
Journal of nucleic acids 2011 Arron ST, Skewes-Cox P, Do PH, Dybbro E, Da Costa M, Palefsky JM, Derisi JL -
Using a pan-viral microarray assay (Virochip) to screen clinical samples for viral pathogens.
Journal of visualized experiments : JoVE 2011 Chen EC, Miller SA, DeRisi JL, Chiu CY -
Transcriptome sequencing demonstrates that human papillomavirus is not active in cutaneous squamous cell carcinoma.
The Journal of investigative dermatology 2011 Arron ST, Ruby JG, Dybbro E, Ganem D, Derisi JL -
Viral infection in acute exacerbation of idiopathic pulmonary fibrosis.
American journal of respiratory and critical care medicine 2011 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 -
NK cells and immune "memory".
Journal of immunology (Baltimore, Md. : 1950) 2011 Sun JC, Lopez-Verges S, Kim CC, DeRisi JL, Lanier LL -
RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts.
Nucleic acids research 2011 Sorber K, Dimon MT, DeRisi JL -
Evaluation of Diarylureas for Activity Against Plasmodium falciparum.
ACS medicinal chemistry letters 2010 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 -
HMMSplicer: a tool for efficient and sensitive discovery of known and novel splice junctions in RNA-Seq data.
PloS one 2010 Dimon MT, Sorber K, DeRisi JL -
De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis.
Nature biotechnology 2010 Fordyce PM, Gerber D, Tran D, Zheng J, Li H, DeRisi JL, Quake SR -
Serological evidence of human klassevirus infection.
Clinical and vaccine immunology : CVI 2010 Greninger AL, Holtz L, Kang G, Ganem D, Wang D, DeRisi JL -
Avian bornavirus is present in many tissues of psittacine birds with histopathologic evidence of proventricular dilatation disease.
Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc 2010 Raghav R, Taylor M, Delay J, Ojkic D, Pearl DL, Kistler AL, Derisi JL, Ganem D, Smith DA -
Human enterovirus 109: a novel interspecies recombinant enterovirus isolated from a case of acute pediatric respiratory illness in Nicaragua.
Journal of virology 2010 Yozwiak NL, Skewes-Cox P, Gordon A, Saborio S, Kuan G, Balmaseda A, Ganem D, Harris E, DeRisi JL -
Achalasia and viral infection: new insights from veterinary medicine.
Science translational medicine 2010 Ganem D, Kistler A, DeRisi J -
Chemical genetics of Plasmodium falciparum.
Nature 2010 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 … -
Development of a new generation of 4-aminoquinoline antimalarial compounds using predictive pharmacokinetic and toxicology models.
Journal of medicinal chemistry 2010 Ray S, Madrid PB, Catz P, LeValley SE, Furniss MJ, Rausch LL, Guy RK, DeRisi JL, Iyer LV, Green CE, Mirsalis JC -
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.
Molecular genetics and genomics : MGG 2010 Mattiazzi M, Jambhekar A, Kaferle P, Derisi JL, Krizaj I, Petrovic U -
Cultivation and serological characterization of a human Theiler's-like cardiovirus associated with diarrheal disease.
Journal of virology 2010 Chiu CY, Greninger AL, Chen EC, Haggerty TD, Parsonnet J, Delwart E, Derisi JL, Ganem D -
Improved methods for magnetic purification of malaria parasites and haemozoin.
Malaria journal 2010 Kim CC, Wilson EB, DeRisi JL -
VersaCount: customizable manual tally software for cell counting.
Source code for biology and medicine 2010 Kim CC, Derisi JL -
Analysis of naturally occurring avian bornavirus infection and transmission during an outbreak of proventricular dilatation disease among captive psittacine birds.
Journal of virology 2009 Kistler AL, Smith JM, Greninger AL, Derisi JL, Ganem D -
An enhanced single base extension technique for the analysis of complex viral populations.
PloS one 2009 Webster DR, Hekele AG, Lauring AS, Fischer KF, Li H, Andino R, DeRisi JL -
Inhibiting Plasmodium falciparum growth and heme detoxification pathway using heme-binding DNA aptamers.
Proceedings of the National Academy of Sciences of the United States of America 2009 Niles JC, Derisi JL, Marletta MA -
Antiparasitic activities of novel, orally available fumagillin analogs.
Bioorganic & medicinal chemistry letters 2009 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… -
Experimental induction of proventricular dilatation disease in cockatiels (Nymphicus hollandicus) inoculated with brain homogenates containing avian bornavirus 4.
Virology journal 2009 Gancz AY, Kistler AL, Greninger AL, Farnoushi Y, Mechani S, Perl S, Berkowitz A, Perez N, Clubb S, DeRisi JL, Ganem D, Lublin A -
The complete genome of klassevirus - a novel picornavirus in pediatric stool.
Virology journal 2009 Greninger AL, Runckel C, Chiu CY, Haggerty T, Parsonnet J, Ganem D, DeRisi JL -
The long march: a sample preparation technique that enhances contig length and coverage by high-throughput short-read sequencing.
PloS one 2008 Sorber K, Chiu C, Webster D, Dimon M, Ruby JG, Hekele A, DeRisi JL -
Experimental malaria infection triggers early expansion of natural killer cells.
Infection and immunity 2008 Kim CC, Parikh S, Sun JC, Myrick A, Lanier LL, Rosenthal PJ, DeRisi JL -
Identification of cardioviruses related to Theiler's murine encephalomyelitis virus in human infections.
Proceedings of the National Academy of Sciences of the United States of America 2008 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 -
Recovery of divergent avian bornaviruses from cases of proventricular dilatation disease: identification of a candidate etiologic agent.
Virology journal 2008 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 -
N-terminal processing of proteins exported by malaria parasites.
Molecular and biochemical parasitology 2008 Chang HH, Falick AM, Carlton PM, Sedat JW, DeRisi JL, Marletta MA -
Utility of DNA microarrays for detection of viruses in acute respiratory tract infections in children.
The Journal of pediatrics 2008 Chiu CY, Urisman A, Greenhow TL, Rouskin S, Yagi S, Schnurr D, Wright C, Drew WL, Wang D, Weintrub PS, Derisi JL, Ganem D -
Pan-viral screening of respiratory tract infections in adults with and without asthma reveals unexpected human coronavirus and human rhinovirus diversity.
The Journal of infectious diseases 2007 Kistler A, Avila PC, Rouskin S, Wang D, Ward T, Yagi S, Schnurr D, Ganem D, DeRisi JL, Boushey HA -
Diagnosis of a critical respiratory illness caused by human metapneumovirus by use of a pan-virus microarray.
Journal of clinical microbiology 2007 Chiu CY, Alizadeh AA, Rouskin S, Merker JD, Yeh E, Yagi S, Schnurr D, Patterson BK, Ganem D, DeRisi JL -
Genome-wide diversity and selective pressure in the human rhinovirus.
Virology journal 2007 Kistler AL, Webster DR, Rouskin S, Magrini V, Credle JJ, Schnurr DP, Boushey HA, Mardis ER, Li H, DeRisi JL -
Cis-acting determinants of asymmetric, cytoplasmic RNA transport.
RNA (New York, N.Y.) 2007 Jambhekar A, Derisi JL -
An infectious retrovirus susceptible to an IFN antiviral pathway from human prostate tumors.
Proceedings of the National Academy of Sciences of the United States of America 2007 Dong B, Kim S, Hong S, Das Gupta J, Malathi K, Klein EA, Ganem D, Derisi JL, Chow SA, Silverman RH -
Gene expression patterns during adaptation of a helminth parasite to different environmental niches.
Genome biology 2007 Jolly ER, Chin CS, Miller S, Bahgat MM, Lim KC, DeRisi J, McKerrow JH -
Whole-genome analysis of mRNA decay in Plasmodium falciparum reveals a global lengthening of mRNA half-life during the intra-erythrocytic development cycle.
Genome biology 2007 Shock JL, Fischer KF, DeRisi JL -
A Bayesian network driven approach to model the transcriptional response to nitric oxide in Saccharomyces cerevisiae.
PloS one 2006 Zhu J, Jambhekar A, Sarver A, DeRisi J -
Rapid DNA mapping by fluorescent single molecule detection.
Nucleic acids research 2006 Xiao M, Phong A, Ha C, Chan TF, Cai D, Leung L, Wan E, Kistler AL, DeRisi JL, Selvin PR, Kwok PY -
Microarray detection of human parainfluenzavirus 4 infection associated with respiratory failure in an immunocompetent adult.
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2006 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 -
Tetracyclines specifically target the apicoplast of the malaria parasite Plasmodium falciparum.
Antimicrobial agents and chemotherapy 2006 Dahl EL, Shock JL, Shenai BR, Gut J, DeRisi JL, Rosenthal PJ -
Incorporation of an intramolecular hydrogen-bonding motif in the side chain of 4-aminoquinolines enhances activity against drug-resistant P. falciparum.
Journal of medicinal chemistry 2006 Madrid PB, Liou AP, DeRisi JL, Guy RK -
Searching for new antimalarial therapeutics amongst known drugs.
Chemical biology & drug design 2006 Weisman JL, Liou AP, Shelat AA, Cohen FE, Guy RK, DeRisi JL -
Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise.
Nature 2006 Newman JR, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, DeRisi JL, Weissman JS -
Identification of a novel Gammaretrovirus in prostate tumors of patients homozygous for R462Q RNASEL variant.
PLoS pathogens 2006 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 -
Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains.
Nucleic acids research 2006 Llinás M, Bozdech Z, Wong ED, Adai AT, DeRisi JL -
Genome-wide mapping of DNA synthesis in Saccharomyces cerevisiae reveals that mechanisms preventing reinitiation of DNA replication are not redundant.
Molecular biology of the cell 2006 Green BM, Morreale RJ, Ozaydin B, Derisi JL, Li JJ -
Unbiased selection of localization elements reveals cis-acting determinants of mRNA bud localization in Saccharomyces cerevisiae.
Proceedings of the National Academy of Sciences of the United States of America 2005 Jambhekar A, McDermott K, Sorber K, Shepard KA, Vale RD, Takizawa PA, DeRisi JL -
Parallel synthesis of 9-aminoacridines and their evaluation against chloroquine-resistant Plasmodium falciparum.
Bioorganic & medicinal chemistry 2005 Anderson MO, Sherrill J, Madrid PB, Liou AP, Weisman JL, DeRisi JL, Guy RK -
Genome-wide identification of genes upregulated at the onset of gametocytogenesis in Plasmodium falciparum.
Molecular and biochemical parasitology 2005 Silvestrini F, Bozdech Z, Lanfrancotti A, Di Giulio E, Bultrini E, Picci L, Derisi JL, Pizzi E, Alano P -
E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns.
Genome biology 2005 Urisman A, Fischer KF, Chiu CY, Kistler AL, Beck S, Wang D, DeRisi JL -
Fzf1p regulates an inducible response to nitrosative stress in Saccharomyces cerevisiae.
Molecular biology of the cell 2005 Sarver A, DeRisi J -
Synthesis of ring-substituted 4-aminoquinolines and evaluation of their antimalarial activities.
Bioorganic & medicinal chemistry letters 2005 Madrid PB, Sherrill J, Liou AP, Weisman JL, Derisi JL, Guy RK -
Genomic dissection of the cell-type-specification circuit in Saccharomyces cerevisiae.
Proceedings of the National Academy of Sciences of the United States of America 2004 Galgoczy DJ, Cassidy-Stone A, Llinás M, O'Rourke SM, Herskowitz I, DeRisi JL, Johnson AD -
Pernicious plans revealed: Plasmodium falciparum genome wide expression analysis.
Current opinion in microbiology 2004 Llinás M, DeRisi JL -
Genome-wide mapping of the cohesin complex in the yeast Saccharomyces cerevisiae.
PLoS biology 2004 Glynn EF, Megee PC, Yu HG, Mistrot C, Unal E, Koshland DE, DeRisi JL, Gerton JL -
The kinetochore is an enhancer of pericentric cohesin binding.
PLoS biology 2004 Weber SA, Gerton JL, Polancic JE, DeRisi JL, Koshland D, Megee PC -
Parallel synthesis and antimalarial screening of a 4-aminoquinoline library.
Journal of combinatorial chemistry 2004 Madrid PB, Wilson NT, DeRisi JL, Guy RK -
Viral discovery and sequence recovery using DNA microarrays.
PLoS biology 2003 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 -
Widespread cytoplasmic mRNA transport in yeast: identification of 22 bud-localized transcripts using DNA microarray analysis.
Proceedings of the National Academy of Sciences of the United States of America 2003 Shepard KA, Gerber AP, Jambhekar A, Takizawa PA, Brown PO, Herschlag D, DeRisi JL, Vale RD -
The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum.
PLoS biology 2003 Bozdech Z, Llinás M, Pulliam BL, Wong ED, Zhu J, DeRisi JL -
Characterization of a novel coronavirus associated with severe acute respiratory syndrome.
Science (New York, N.Y.) 2003 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, … -
A novel coronavirus associated with severe acute respiratory syndrome.
The New England journal of medicine 2003 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 … -
Telomeric protein distributions and remodeling through the cell cycle in Saccharomyces cerevisiae.
Molecular biology of the cell 2003 Smith CD, Smith DL, DeRisi JL, Blackburn EH -
Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray.
Genome biology 2003 Bozdech Z, Zhu J, Joachimiak MP, Cohen FE, Pulliam B, DeRisi JL -
A role for the protease falcipain 1 in host cell invasion by the human malaria parasite.
Science (New York, N.Y.) 2002 Greenbaum DC, Baruch A, Grainger M, Bozdech Z, Medzihradszky KF, Engel J, DeRisi J, Holder AA, Bogyo M -
Modulation of host gene expression by the constitutively active G protein-coupled receptor of Kaposi's sarcoma-associated herpesvirus.
Cancer research 2002 Polson AG, Wang D, DeRisi J, Ganem D -
The genome-wide expression response to telomerase deletion in Saccharomyces cerevisiae.
Proceedings of the National Academy of Sciences of the United States of America 2002 Nautiyal S, DeRisi JL, Blackburn EH -
Mnd1p: an evolutionarily conserved protein required for meiotic recombination.
Proceedings of the National Academy of Sciences of the United States of America 2002 Gerton JL, DeRisi JL -
Overview of nucleic acid arrays.
Current protocols in neuroscience 2001 DeRisi J -
Functional genomic analysis of a commercial wine strain of Saccharomyces cerevisiae under differing nitrogen conditions.
FEMS yeast research 2001 Backhus LE, DeRisi J, Bisson LF -
Overview of nucleic acid arrays.
Current protocols in molecular biology 2001 Derisi J -
Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays.
Proceedings of the National Academy of Sciences of the United States of America 2001 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… -
Global and specific translational regulation in the genomic response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source.
Molecular and cellular biology 2001 Kuhn KM, DeRisi JL, Brown PO, Sarnow P -
New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis.
Molecular biology of the cell 2000 Ogawa N, DeRisi J, Brown PO -
Plasma membrane compartmentalization in yeast by messenger RNA transport and a septin diffusion barrier.
Science (New York, N.Y.) 2000 Takizawa PA, DeRisi JL, Wilhelm JE, Vale RD -
Global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae.
Proceedings of the National Academy of Sciences of the United States of America 2000 Gerton JL, DeRisi J, Shroff R, Lichten M, Brown PO, Petes TD -
Analysis of topoisomerase function in bacterial replication fork movement: use of DNA microarrays.
Proceedings of the National Academy of Sciences of the United States of America 2000 Khodursky AB, Peter BJ, Schmid MB, DeRisi J, Botstein D, Brown PO, Cozzarelli NR -
Genome microarray analysis of transcriptional activation in multidrug resistance yeast mutants.
FEBS letters 2000 DeRisi J, van den Hazel B, Marc P, Balzi E, Brown P, Jacq C, Goffeau A -
Shotgun DNA microarrays and stage-specific gene expression in Plasmodium falciparum malaria.
Molecular microbiology 2000 Hayward RE, Derisi JL, Alfadhli S, Kaslow DC, Brown PO, Rathod PK -
Exploring drug-induced alterations in gene expression in Mycobacterium tuberculosis by microarray hybridization.
Proceedings of the National Academy of Sciences of the United States of America 1999 Wilson M, DeRisi J, Kristensen HH, Imboden P, Rane S, Brown PO, Schoolnik GK -
Genomics and array technology.
Current opinion in oncology 1999 DeRisi JL, Iyer VR -
Characterization of three related glucose repressors and genes they regulate in Saccharomyces cerevisiae.
Genetics 1998 Lutfiyya LL, Iyer VR, DeRisi J, DeVit MJ, Brown PO, Johnston M -
Drug target validation and identification of secondary drug target effects using DNA microarrays.
Nature medicine 1998 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 -
The transcriptional program of sporulation in budding yeast.
Science (New York, N.Y.) 1998 Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown PO, Herskowitz I -
Effects of mutations in residues near the active site of human immunodeficiency virus type 1 integrase on specific enzyme-substrate interactions.
Journal of virology 1998 Gerton JL, Ohgi S, Olsen M, DeRisi J, Brown PO -
Yeast microarrays for genome wide parallel genetic and gene expression analysis.
Proceedings of the National Academy of Sciences of the United States of America 1997 Lashkari DA, DeRisi JL, McCusker JH, Namath AF, Gentile C, Hwang SY, Brown PO, Davis RW -
Exploring the metabolic and genetic control of gene expression on a genomic scale.
Science (New York, N.Y.) 1997 DeRisi JL, Iyer VR, Brown PO -
Use of a cDNA microarray to analyse gene expression patterns in human cancer.
Nature genetics 1996 DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, Chen Y, Su YA, Trent JM -
Bead-shift isolation of protein--DNA complexes on a 5S RNA gene.
Nucleic acids research 1994 Peck LJ, Bartilson M, DeRisi JL