Joe Derisi, PhD

Professor

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

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

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

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

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

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

  1. Spottiswoode N, Tsitsiklis A, Chu VT, Phan HV, DeVoe C, Love C, Ghale R, Bloomstein J, Zha BS, Maguire CP, Glascock A, Sarma A, Mourani PM, Kalantar KL, Detweiler A, Neff N, Haller SC, COMET Consortium, DeRisi JL, Erle DJ, Hendrickson CM, Kangelaris KN, Krummel MF, Matthay MA, Woodruff PG, Calfee CS, Langelier CR. Microbial dynamics and pulmonary immune responses in COVID-19 secondary bacterial pneumonia. 2024. PMID: 39472555


  2. 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, Weiler-Normann C, Lohse AW, DeRisi J, Tana M. Novel autoantibody targets identified in patients with autoimmune hepatitis (AIH) by PhIP-Seq reveals pathogenic insights. 2023. PMID: 37398174


  3. Lydon E, Osborne CM, Wagner BD, Ambroggio L, Harris JK, Reeder R, Carpenter TC, Maddux AB, Leroue MK, Yehya N, DeRisi JL, Hall MW, Zuppa AF, Carcillo J, Meert K, Sapru A, Pollack MM, McQuillen P, Notterman DA, Langelier CR, Mourani PM, Eunice Kennedy Shriver National Institute of Child Health and Human Development Collaborative Pediat. Proteomic profiling of the local and systemic immune response to pediatric respiratory viral infections. 2024. PMID: 39416167


  4. Peter E, Ciano-Petersen NL, Do LD, Perrot J, Ngo T, Pluvinage J, Bartley CM, Zorn KC, Miske R, Scharf M, Villagrán-García M, Farina A, Rogemond V, Antoine JC, Tranchant C, Dubois V, DeRisi JL, Pleasure SJ, Wilson MR, Gelfand JM, Traverse-Glehen A, Honnorat J, Desestret V. Anti-RGS8 paraneoplastic cerebellar ataxia is preferentially associated with a particular subtype of Hodgkin's lymphoma. 2024. PMID: 39207522


  5. Brook CE, Rozins C, Bohl JA, Ahyong V, Chea S, Fahsbender L, Huy R, Lay S, Leang R, Li Y, Lon C, Man S, Oum M, Northrup GR, Oliveira F, Pacheco AR, Parker DM, Young K, Boots M, Tato CM, DeRisi JL, Yek C, Manning JE. Climate, demography, immunology, and virology combine to drive two decades of dengue virus dynamics in Cambodia. 2024. PMID: 39190356


  6. Bodansky A, Mettelman RC, Sabatino JJ, Vazquez SE, Chou J, Novak T, Moffitt KL, Miller HS, Kung AF, Rackaityte E, Zamecnik CR, Rajan JV, Kortbawi H, Mandel-Brehm C, Mitchell A, Wang CY, Saxena A, Zorn K, Yu DJL, Pogorelyy MV, Awad W, Kirk AM, Asaki J, Pluvinage JV, Wilson MR, Zambrano LD, Campbell AP, Overcoming COVID-19 Network Investigators, Thomas PG, Randolph AG, Anderson MS, DeRisi JL. Molecular mimicry in multisystem inflammatory syndrome in children. 2024. PMID: 39112696


  7. 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 MS, DeRisi JL, Sperling AI, Shum AK. Phage Immunoprecipitation-Sequencing Reveals CDHR5 Autoantibodies in Select Patients With Interstitial Lung Disease. 2024. PMID: 38952015


  8. Pluvinage JV, Ngo T, Fouassier C, McDonagh M, Holmes BB, Bartley CM, Kondapavulur S, Hurabielle C, Bodansky A, Pai V, Hinman S, Aslanpour A, Alvarenga BD, Zorn KC, Zamecnik C, McCann A, Asencor AI, Huynh T, Browne W, Tubati A, Haney MS, Douglas VC, Louine M, Cree BAC, Hauser SL, Seeley W, Baranzini SE, Wells JA, Spudich S, Farhadian S, Ramachandran PS, Gillum L, Hales CM, Zikherman J, Anderson MS, Yazdany J, Smith B, Nath A, Suh G, Flanagan EP, Green AJ, Green R, Gelfand JM, DeRisi JL, Pleasure SJ, Wilson MR. Transcobalamin receptor antibodies in autoimmune vitamin B12 central deficiency. 2024. PMID: 38924428


  9. Van Horn KS, Zhao Y, Parvatkar PT, Maier J, Mutka T, Lacrue A, Brockmeier F, Ebert D, Wu W, Casandra DR, Namelikonda N, Yacoub J, Sigal M, Knapp S, Floyd D, Waterson D, Burrows JN, Duffy J, DeRisi JL, Kyle DE, Guy RK, Manetsch R. Optimization of diastereomeric dihydropyridines as antimalarials. 2024. PMID: 38909569


  10. 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, Keating AK, Qayed M, Killinger JS, Fitzgerald JC, Hanna R, Mahadeo KM, Quigg TC, Satwani P, Castillo P, Gertz SJ, Moore TB, Hanisch B, Abdel-Mageed A, Phelan R, Davis DB, Hudspeth MP, Yanik GA, Pulsipher MA, Sulaiman I, Segal LN, Versluys BA, Lindemans CA, Boelens JJ, DeRisi JL, Pediatric Transplantation and Cell Therapy Consortium. Pathobiological signatures of dysbiotic lung injury in pediatric patients undergoing stem cell transplantation. 2024. PMID: 38783139


  11. Bodansky A, Yu DJ, Rallistan AN, Kalaycioglu M, Boonyaratanakornkit J, Green DJ, Gauthier J, Turtle CJ, Zorn KC, O'Donovan B, Mandel-Brehm C, Asaki J, Kortbawi H, Kung AF, Rackaityte E, Wang CY, Saxena A, de Dios K, Masi G, Nowak RJ, O'Connor KC, Li H, Diaz VE, Saloner R, Casaletto KB, Gontrum EQ, Chan BJ, Kramer JH, Wilson MR, Utz PJ, Hill JA, Jackson SW, Anderson MS, DeRisi JL. Unveiling the proteome-wide autoreactome enables enhanced evaluation of emerging CAR-T therapies in autoimmunity. 2024. PMID: 38753445


  12. Zamecnik CR, Sowa GM, Abdelhak A, Dandekar R, Bair RD, Wade KJ, Bartley CM, Kizer K, Augusto DG, Tubati A, Gomez R, Fouassier C, Gerungan C, Caspar CM, Alexander J, Wapniarski AE, Loudermilk RP, Eggers EL, Zorn KC, Ananth K, Jabassini N, Mann SA, Ragan NR, Santaniello A, Henry RG, Baranzini SE, Zamvil SS, Sabatino JJ, Bove RM, Guo CY, Gelfand JM, Cuneo R, von Büdingen HC, Oksenberg JR, Cree BAC, Hollenbach JA, Green AJ, Hauser SL, Wallin MT, DeRisi JL, Wilson MR. An autoantibody signature predictive for multiple sclerosis. 2024. PMID: 38641750


  13. Spottiswoode N, Haston JC, Hanners NW, Gruenberg K, Kim A, DeRisi JL, Wilson MR. Challenges and advances in the medical treatment of granulomatous amebic encephalitis. 2024. PMID: 38312848


  14. 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. The antibiotic resistance reservoir of the lung microbiome expands with age in a population of critically ill patients. 2024. PMID: 38168095


  15. Bastard P, Vazquez S, 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, Salagianni M, Poulakou G, Siouti E, Sahanic S, Tancevski I, Weiss G, Nagl L, Manry J, Duvlis S, Arroyo-Sánchez D, Paz Artal E, Rubio L, Perani C, Bezzi M, Sottini A, Quaresima V, Roussel L, Vinh DC, Reyes LF, Garzaro M, Hatipoglu N, Boutboul D, Tandjaoui-Lambiotte Y, Borghesi A, Aliberti A, Cassaniti I, Venet F, Monneret G, Halwani R, Sharif-Askari NS, Danielson J, Burrel S, Morbieu C, Stepanovskyy Y, Bondarenko A, Volokha A, Boyarchuk O, Gagro A, Neuville M, Neven B, Keles S, Hernu R, Bal A, Novelli A, Novelli G, Saker K, Ailioaie O, Antolí A, Jeziorski E, Rocamora-Blanch G, Teixeira C, Delaunay C, Lhuillier M, Le Turnier P, Zhang Y, Mahevas M, Pan-Hammarström Q, Abolhassani H, Bompoil T, Dorgham K, COVID HGE consortium † , French COVID study group † , COMET consortium † , Gorochov G, Laouenan C, Rodríguez-Gallego C, Ng LFP, Renia L, Pujol A, Belot A, Raffi F, Allende LM, Martinez-Picado J, Ozcelik T, Keles S, Imberti L, Notarangelo LD, Troya J, Solanich X, Zhang SY, Puel A, Wilson MR, Trouillet-Assant S, Abel L, Jouanguy E, Ye CJ, Cobat A, Thompson LM, Andreakos E, Zhang Q, Anderson MS, Casanova JL, DeRisi JL. Vaccine breakthrough hypoxemic COVID-19 pneumonia in patients with auto-Abs neutralizing type I IFNs. 2022. PMID: 35857576


  16. 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 A, de Dios K, Masi G, Nowak RJ, O'Connor KC, Li H, Diaz VE, Casaletto KB, Gontrum EQ, Chan B, Kramer JH, Wilson MR, Utz PJ, Hill JA, Jackson SW, Anderson MS, DeRisi JL. Unveiling the autoreactome: Proteome-wide immunological fingerprints reveal the promise of plasma cell depleting therapy. 2023. PMID: 38196603


  17. Rackaityte E, Proekt I, Miller HS, Ramesh A, Brooks JF, Kung AF, Mandel-Brehm C, Yu DJ, Zamecnik CR, Bair R, Vazquez SE, Sunshine S, Abram CL, Lowell CA, Rizzuto G, Wilson MR, Zikherman J, Anderson MS, DeRisi JL. Validation of a murine proteome-wide phage display library for identification of autoantibody specificities. 2023. PMID: 37934865


  18. 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, Keating AK, Qayed M, Killinger JS, Fitzgerald JC, Hanna R, Mahadeo KM, Quigg TC, Satwani P, Castillo P, Gertz SJ, Moore TB, Hanisch B, Abdel-Mageed A, Phelan R, Davis DB, Hudspeth MP, Yanik GA, Pulsipher MA, Sulaiman I, Segal LN, Versluys BA, Lindemans CA, Boelens JJ, DeRisi JL, Pediatric Transplantation and Cell Therapy Consortium. Pulmonary microbiome and transcriptome signatures reveal distinct pathobiologic states associated with mortality in two cohorts of pediatric stem cell transplant patients. 2023. PMID: 38077035


  19. 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, Maglorius Renkilaraj MRL, Ogishi M, Soudée C, Migaud M, Rozenberg F, Momenilandi M, Riller Q, Imberti L, Delmonte OM, Müller G, Keller B, Orrego J, Franco Gallego WA, Rubin T, Emiroglu M, Parvaneh N, Eriksson D, Aranda-Guillen M, Berrios DI, Vong L, Katelaris CH, Mustillo P, Raedler J, Bohlen J, Bengi Celik J, Astudillo C, Winter S, NF-?B Consortium, COVID Human Genetic Effort, McLean C, Guffroy A, DeRisi JL, Yu D, Miller C, Feng Y, Guichard A, Béziat V, Bustamante J, Pan-Hammarström Q, Zhang Y, Rosen LB, Holland SM, Bosticardo M, Kenney H, Castagnoli R, Slade CA, Boztug K, Mahlaoui N, Latour S, Abraham RS, Lougaris V, Hauck F, Sediva A, Atschekzei F, Sogkas G, Poli MC, Slatter MA, Palterer B, Keller MD, Pinzon-Charry A, Sullivan A, Droney L, Suan D, Wong M, Kane A, Hu H, Ma C, Grombiríková H, Ciznar P, Dalal I, Aladjidi N, Hie M, Lazaro E, Franco J, Keles S, Malphettes M, Pasquet M, Maccari ME, Meinhardt A, Ikinciogullari A, Shahrooei M, Celmeli F, Frosk P, Goodnow CC, Gray PE, Belot A, Kuehn HS, Rosenzweig SD, Miyara M, Licciardi F, Servettaz A, Barlogis V, Le Guenno G, Herrmann VM, Kuijpers T, Ducoux G, Sarrot-Reynauld F, Schuetz C, Cunningham-Rundles C, Rieux-Laucat F, Tangye SG, Sobacchi C, Doffinger R, Warnatz K, Grimbacher B, Fieschi C, Berteloot L, Bryant VL, Trouillet Assant S, Su H, Neven B, Abel L, Zhang Q, Boisson B, Cobat A, Jouanguy E, Kampe O, Bastard P, Roifman CM, Landegren N, Notarangelo LD, Anderson MS, Casanova JL, Puel A. Autoantibodies against type I IFNs in humans with alternative NF-κB pathway deficiency. 2023. PMID: 37938781


  20. 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, Jacobson K. Implementation of California COVIDNet - a multi-sector collaboration for statewide SARS-CoV-2 genomic surveillance. 2023. PMID: 37937074


  21. 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. Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq. 2023. PMID: 37803001


  22. 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, Zuppa AF, Carcillo JA, Meert KL, Pollack MM, McQuillen PS, Notterman DA, DeRisi J, Mourani PM, National Institute for Child Health and Human Development Collaborative Pediatric Critical Care Rese. 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. 2023. PMID: 37732845


  23. 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, Binxia Y, Montalvo Perero MJ, Kung AF, Mann SA, Shah MP, Geschwind MD, Gelfand JM, DeRisi JL, Pittock SJ, Honnorat J, Pleasure SJ, Wilson MR. Detection of High-Risk Paraneoplastic Antibodies Against TRIM9 and TRIM67 proteins. 2023. PMID: 37632288


  24. Langelier C, Chu V, Tsitsiklis A, Mick E, Ambroggio L, Kalantar K, Glascock A, Osborne C, Wagner B, Matthay M, DeRisi J, Calfee C, Mourani P. The antibiotic resistance reservoir of the lung microbiome expands with age. 2023. PMID: 37790384


  25. 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. In host evolution of beta lactam resistance during active treatment for Pseudomonas aeruginosa bacteremia. 2023. PMID: 37712060


  26. Lohse MB, Laurie MT, Levan S, Ziv N, Ennis CL, Nobile CJ, DeRisi J, Johnson AD. Broad susceptibility of Candida auris strains to 8-hydroxyquinolines and mechanisms of resistance. 2023. PMID: 37493629


  27. Popova G, Retallack H, Kim CN, Wang A, Shin D, DeRisi JL, Nowakowski T. Rubella virus tropism and single-cell responses in human primary tissue and microglia-containing organoids. 2023. PMID: 37470786


  28. 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. Viral co-infection, autoimmunity, and CSF HIV antibody profiles in HIV central nervous system escape. 2023. PMID: 37418948


  29. 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. Whole-genome sequencing rule-out of suspected hospital-onset Rhizopus outbreaks. 2023. PMID: 37308466


  30. 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, Hellmuth J, Kelly JD, Martin JN, Anderson MS, Deeks SG, Henrich TJ, DeRisi JL, Peluso MJ. Autoantigen profiling reveals a shared post-COVID signature in fully recovered and long COVID patients. 2023. PMID: 37288661


  31. 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, Jabassini N, Mann SA, Ragan NR, Santaniello A, Henry RG, Baranzini SE, Zamvil SS, Bove RM, Guo CY, Gelfand JM, Cuneo R, von Büdingen HC, Oksenberg JR, Cree BA, Hollenbach JA, Green AJ, Hauser SL, Wallin MT, DeRisi JL, Wilson MR. A Predictive Autoantibody Signature in Multiple Sclerosis. 2023. PMID: 37205595


  32. 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, Sperling AI. Antigenic responses are hallmarks of fibrotic interstitial lung diseases independent of underlying etiologies. 2023. PMID: 37214861


  33. 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. PhIP-Seq uncovers novel autoantibodies and unique endotypes in interstitial lung disease. 2023. PMID: 37163026


  34. 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, DeRisi JL. Validation of a murine proteome-wide phage display library for the identification of autoantibody specificities. 2023. PMID: 37066405


  35. 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, Sim?es EA, Carpenter TC, Wagner BD, DeRisi JL, Ambroggio L, Mourani PM, Langelier CR. Integrated host/microbe metagenomics enables accurate lower respiratory tract infection diagnosis in critically ill children. 2023. PMID: 37009900


  36. 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, Martinez J, Chamie G, Glaser C, Jacobson K, Petersen M, DeRisi J, Havlir DV. Field assessment of BinaxNOW antigen tests as COVID-19 treatment entry point at a community testing site in San Francisco during evolving omicron surges. 2023. PMID: 36961855


  37. 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, Palmore TN, Thurm A, Baker EH, Chang R, Fauni H, Adams D, Macnamara EF, Lau CC, Malicdan MCV, Pusey-Swerdzewski B, Downing R, Bunga S, Thomas JD, Gahl WA, Nath A. Genomic analysis, immunomodulation and deep phenotyping of patients with nodding syndrome. 2022. PMID: 36181424


  38. Lohse MB, Laurie MT, Levan S, Ziv N, Ennis CL, Nobile CJ, DeRisi J, Johnson AD. Broad sensitivity of Candida auris strains to quinolones and mechanisms of resistance. 2023. PMID: 36824717


  39. 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 Structural Biology Consortium, DeRisi J, Kortemme T, Rosenberg OS, Glasgow A, Leung KK, Wells JA, Verba KA. Computational pipeline provides mechanistic understanding of Omicron variant of concern neutralizing engineered ACE2 receptor traps. 2023. PMID: 36805129


  40. 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. Proteome-wide antigenic profiling in Ugandan cohorts identifies associations between age, exposure intensity, and responses to repeat-containing antigens in Plasmodium falciparum. 2023. PMID: 36790168


  41. 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, Kelly JD, Martin JN, Anderson MS, Deeks SG, Henrich TJ, DeRisi JL, Peluso MJ. Autoantigen profiling reveals a shared post-COVID signature in fully recovered and Long COVID patients. 2023. PMID: 36798288


  42. 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 MR, Pleasure SJ. Dual ankyrinG and subpial autoantibodies in a man with well-controlled HIV infection with steroid-responsive meningoencephalitis: A case report. 2023. PMID: 36756346


  43. 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. Low Prevalence of Interferon-α Autoantibodies in People Experiencing Long COVID Symptoms. 2022. PMID: 36089700


  44. 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, Agarwal AK, Li X, Zhu C, Li Q, Oral E, Brown R, Anderson MS, Garg A, DeRisi JL. Autoantibodies to Perilipin-1 Define a Subset of Acquired Generalized Lipodystrophy. 2022. PMID: 35709010


  45. 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. Successful Treatment of Balamuthia mandrillaris Granulomatous Amebic Encephalitis with Nitroxoline. 2023. PMID: 36573629


  46. Ghale R, Spottiswoode N, Anderson MS, Mitchell A, Wang G, Calfee CS, DeRisi JL, Langelier CR. Prevalence of type-1 interferon autoantibodies in adults with non-COVID-19 acute respiratory failure. 2022. PMID: 36527083


  47. 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. A 2-Gene Host Signature for Improved Accuracy of COVID-19 Diagnosis Agnostic to Viral Variants. 2022. PMID: 36507688


  48. 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, Gertz SJ, Rowan CM, Irby K, Sanders RC, Kong M, Schuster JE, Staat MA, Zinter MS, Cvijanovich NZ, Tarquinio KM, Coates BM, Flori HR, Dahmer MK, Crandall H, Cullimore ML, Levy ER, Chatani B, Nofziger R, Overcoming COVID-19 Network Study Group Investigators, Geha RS, DeRisi J, Campbell AP, Anderson M, Randolph AG. NFKB2 haploinsufficiency identified via screening for IFNa2 autoantibodies in children and adolescents hospitalized with SARS-CoV-2-related complications. 2022. PMID: 36509151


  49. 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, Tagi VM, Shimizu C, Tremoulet A, Lynch K, Wilson MR, Kämpe O, Dobbs K, Delmonte OM, Bacchetta R, Notarangelo LD, Burns JC, Casanova JL, Lionakis MS, Torgerson TR, Anderson MS, DeRisi JL. Autoantibody discovery across monogenic, acquired, and COVID-19-associated autoimmunity with scalable PhIP-seq. 2022. PMID: 36300623


  50. 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, Gomez A, Neff N, Pisco A, Doernberg SB, Derisi JL, Matthay MA, Calfee CS, Langelier CR. Integrated host-microbe plasma metagenomics for sepsis diagnosis in a prospective cohort of critically ill adults. 2022. PMID: 36266337


  51. 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 J, Havlir DV. 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. 2022. PMID: 36215069


  52. 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, Brook CE. Discovery and Genomic Characterization of a Novel Henipavirus, Angavokely Virus, from Fruit Bats in Madagascar. 2022. PMID: 36040175


  53. 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, DeRisi J. SARS-CoV-2 transmission dynamics and immune responses in a household of vaccinated persons. 2022. PMID: 35037050


  54. 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 Biology Consortium, DeRisi J, Kortemme T, Rosenberg OS, Glasgow A, Leung KK, Wells JA, Verba KA. Computational pipeline provides mechanistic understanding of Omicron variant of concern neutralizing engineered ACE2 receptor traps. 2022. PMID: 35982665


  55. Yek C, Lay S, Bohl JA, Man S, Chea S, Lon C, Ahyong V, Tato CM, DeRisi JL, Sovannaroth S, Manning JE. Case Report: Cambodian National Malaria Surveillance Program Detection of Plasmodium knowlesi. 2022. PMID: 35895370


  56. 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 CR. Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections. 2022. PMID: 35818068


  57. 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 BD, DeRisi JL, Ambroggio L, Mourani PM, Langelier CR. Upper airway gene expression shows a more robust adaptive immune response to SARS-CoV-2 in children. 2022. PMID: 35803954


  58. Kodani A, Knopp KA, Di Lullo E, Retallack H, Kriegstein AR, DeRisi JL, Reiter JF. Zika virus alters centrosome organization to suppress the innate immune response. 2022. PMID: 35793002


  59. 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. SARS-CoV-2 variant exposures elicit antibody responses with differential cross-neutralization of established and emerging strains including Delta and Omicron. 2022. PMID: 34979030


  60. 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, Seeley WW, Pleasure SJ, Wilson MR, Gorman MP, DeRisi JL. ZSCAN1 autoantibodies are associated with pediatric paraneoplastic ROHHAD. 2022. PMID: 35466441


  61. Bartley CM, Ngo TT, Alvarenga BD, Kung AF, Teliska LH, Sy M, DeRisi JL, Rasband MN, Pittock SJ, Dubey D, Wilson MR, Pleasure SJ. ßIV-Spectrin Autoantibodies in 2 Individuals With Neuropathy of Possible Paraneoplastic Origin: A Case Series. 2022. PMID: 35581007


  62. Liu J, Knopp KA, Rackaityte E, Wang CY, Laurie MT, Sunshine S, Puschnik AS, DeRisi JL. Genome-Wide Knockout Screen Identifies Human Sialomucin CD164 as an Essential Entry Factor for Lymphocytic Choriomeningitis Virus. 2022. PMID: 35502904


  63. 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, Bahr NC, Musubire A, Skipper CP, Fouassier C, Lyden A, Serpa P, Castaneda G, Caldera S, Ahyong V, DeRisi JL, Langelier C, Crawford ED, Boulware DR, Meya DB, Wilson MR. Integrating central nervous system metagenomics and host response for diagnosis of tuberculosis meningitis and its mimics. 2022. PMID: 35354815


  64. 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 JL, Lynch SV, Worodria W, Huang L, Langelier CR. Pneumonia surveillance with culture-independent metatranscriptomics in HIV-positive adults in Uganda: a cross-sectional study. 2022. PMID: 35544096


  65. 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, Lynch K, Wilson MR, Kampe O, Dobbs K, Delmonte OM, Notarangelo LD, Burns JC, Casanova JL, Lionakis MS, Torgerson TR, Anderson MS, DeRisi JL. Autoantibody discovery across monogenic, acquired, and COVID19-associated autoimmunity with scalable PhIP-Seq. 2022. PMID: 35350199


  66. 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, Langelier CR. 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). 2022. PMID: 35311638


  67. Tana MM, Klepper A, Lyden A, Pisco AO, Phelps M, McGee B, Green K, Feng S, DeRisi J, Crawford ED, Lammert CS. Transcriptomic profiling of blood from autoimmune hepatitis patients reveals potential mechanisms with implications for management. 2022. PMID: 35312680


  68. 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. Viral Load Among Vaccinated and Unvaccinated, Asymptomatic and Symptomatic Persons Infected With the SARS-CoV-2 Delta Variant. 2022. PMID: 35479304


  69. 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, Leroue MK, Hall MW, Zuppa AF, Carcillo J, Meert KL, Sapru A, Pollack MM, McQuillen PS, Notterman DA, Dean JM, Zinter MS, Wagner BD, DeRisi JL, Mourani PM, Langelier CR. Lower respiratory tract infections in children requiring mechanical ventilation: a multicentre prospective surveillance study incorporating airway metagenomics. 2022. PMID: 35544065


  70. 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. Pulmonary microbiome and gene expression signatures differentiate lung function in pediatric hematopoietic cell transplant candidates. 2022. PMID: 35263147


  71. 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. Using genomic epidemiology of SARS-CoV-2 to support contact tracing and public health surveillance in rural Humboldt County, California. 2022. PMID: 35255849


  72. 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, Huch C, Kry H, Leang R, Huy R, Lon C, Tato CM, DeRisi JL, Manning JE. Discovering disease-causing pathogens in resource-scarce Southeast Asia using a global metagenomic pathogen monitoring system. 2022. PMID: 35238677


  73. 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 JA, Wilson MR, Zamvil SS, Bove R. Multiple sclerosis therapies differentially affect SARS-CoV-2 vaccine-induced antibody and T cell immunity and function. 2022. PMID: 35030101


  74. 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. Full Genome Nobecovirus Sequences From Malagasy Fruit Bats Define a Unique Evolutionary History for This Coronavirus Clade. 2022. PMID: 35223729


  75. 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, Cotham VC, Ueberheide BM, Aftab BT, Anderson MS, DeRisi JL, Wilson MR, Bashford-Rogers RJM, Platten M, Garcia KC, Steinman L, Robinson WH. Clonally expanded B cells in multiple sclerosis bind EBV EBNA1 and GlialCAM. 2022. PMID: 35073561


  76. Peng J, Liu J, Mann SA, Mitchell AM, Laurie MT, Sunshine S, Pilarowski G, Ayscue P, Kistler A, Vanaerschot M, Li LM, McGeever A, Chow ED, Marquez C, Nakamura R, Rubio L, Chamie G, Jones D, Jacobo J, Rojas S, Rojas S, Tulier-Laiwa V, Black D, Martinez J, Naso J, Schwab J, Petersen M, Havlir D, DeRisi J, IDseq Team. Estimation of secondary household attack rates for emergent spike L452R SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco. 2021. PMID: 33788923


  78. 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. SARS-CoV-2 variant exposures elicit antibody responses with differential cross-neutralization of established and emerging strains including Delta and Omicron. 2021. PMID: 34981075


  79. 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. High Parental Vaccine Motivation at a Neighborhood-Based Vaccine and Testing Site Serving a Predominantly Latinx Community. 2021. PMID: 35018317


  80. 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. Anti-SARS-CoV-2 and Autoantibody Profiles in the Cerebrospinal Fluid of 3 Teenaged Patients With COVID-19 and Subacute Neuropsychiatric Symptoms. 2021. PMID: 34694339


  81. 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. Long-term MRI changes in a patient with Kelch-like protein 11-associated paraneoplastic neurological syndrome. 2021. PMID: 34561925


  82. Tsitsiklis A, Zha BS, Byrne A, Devoe C, Levan S, Rackaityte E, Sunshine S, Mick E, Ghale R, Jauregui A, Sarma A, Neff N, Serpa PH, Deiss TJ, Kistler A, Carrillo S, Ansel KM, Leligdowicz A, Christenson S, Jones N, Wu B, Darmanis S, Matthay MA, Lynch SV, DeRisi JL, COMET Consortium+ , Hendrickson CM, Kangelaris KN, Krummel MF, Woodruff PG, Erle DJ, Rosenberg O, Calfee CS, Langelier CR. Impaired antibacterial immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19. 2021. PMID: 33791731


  83. 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, Usachenko J, Immareddy R, Schmidt BA, O'Connor SL, DeRisi J, Busch MP, Iyer SS, Van Rompay KKA, Hartigan-O'Connor DJ, Miller CJ. SARS-CoV-2 Infection of Rhesus Macaques Treated Early with Human COVID-19 Convalescent Plasma. 2021. PMID: 34817208


  84. 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, Petersen M, DeRisi J, Havlir DV. Field performance and public health response using the BinaxNOW TM Rapid SARS-CoV-2 antigen detection assay during community-based testing. 2020. PMID: 33367619


  85. Gu W, Rauschecker AM, Hsu E, Zorn KC, Sucu Y, Federman S, Gopez A, Arevalo S, Sample HA, Talevich E, Nguyen ED, Gottschall M, Nourbakhsh B, Gold CA, Cree BAC, Douglas VC, Richie MB, Shah MP, Josephson SA, Gelfand JM, Miller S, Wang L, Tihan T, DeRisi JL, Chiu CY, Wilson MR. Detection of Neoplasms by Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid. 2021. PMID: 34515766


  86. 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. Cerebrospinal Fluid Pterins, Pterin-Dependent Neurotransmitters, and Mortality in Pediatric Cerebral Malaria. 2021. PMID: 33617646


  87. Schubert RD, Hawes IA, Ramachandran PS, Ramesh A, Crawford ED, Pak JE, Wu W, Cheung CK, O'Donovan BD, Tato CM, Lyden A, Tan M, Sit R, Sowa GM, Sample HA, Zorn KC, Banerji D, Khan LM, Bove R, Hauser SL, Gelfand AA, Johnson-Kerner BL, Nash K, Krishnamoorthy KS, Chitnis T, Ding JZ, McMillan HJ, Chiu CY, Briggs B, Glaser CA, Yen C, Chu V, Wadford DA, Dominguez SR, Ng TFF, Marine RL, Lopez AS, Nix WA, Soldatos A, Gorman MP, Benson L, Messacar K, Konopka-Anstadt JL, Oberste MS, DeRisi JL, Wilson MR. Author Correction: Pan-viral serology implicates enteroviruses in acute flaccid myelitis. 2021. PMID: 34548659


  88. Marquez C, Kerkhoff AD, Naso J, Contreras MG, Castellanos Diaz E, Rojas S, Peng J, Rubio L, Jones D, Jacobo J, Rojas S, Gonzalez R, Fuchs JD, Black D, Ribeiro S, Nossokoff J, Tulier-Laiwa V, Martinez J, Chamie G, Pilarowski G, DeRisi J, Petersen M, Havlir DV. A multi-component, community-based strategy to facilitate COVID-19 vaccine uptake among Latinx populations: From theory to practice. 2021. PMID: 34543291


  89. 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. Elevated N-Linked Glycosylation of IgG V Regions in Myasthenia Gravis Disease Subtypes. 2021. PMID: 34544801


  90. Sarma A, Christenson SA, Byrne A, Mick E, Pisco AO, DeVoe C, Deiss T, Ghale R, Zha BS, Tsitsiklis A, Jauregui A, Moazed F, Detweiler AM, Spottiswoode N, Sinha P, Neff N, Tan M, Serpa PH, Willmore A, Ansel KM, Wilson JG, Leligdowicz A, Siegel ER, Sirota M, DeRisi JL, Matthay MA, COMET Consortium, Hendrickson CM, Kangelaris KN, Krummel MF, Woodruff PG, Erle DJ, Calfee CS, Langelier CR. Tracheal aspirate RNA sequencing identifies distinct immunological features of COVID-19 ARDS. 2021. PMID: 34446707


  91. Mick E, Tsitsiklis A, Spottiswoode N, Caldera S, Serpa P, Detweiler A, Neff N, Pisco AO, Li L, Retallack H, Ratnasiri K, Williamson K, Soesanto V, Simões E, Kistler A, Wagner B, DeRisi J, Ambroggio L, Mourani P, Langelier C. Upper airway gene expression reveals a more robust innate and adaptive immune response to SARS-CoV-2 in children compared with older adults. 2021. PMID: 34462739


  92. van der Wijst MGP, Vazquez SE, Hartoularos GC, Bastard P, Grant T, Bueno R, Lee DS, Greenland JR, Sun Y, Perez R, Ogorodnikov A, Ward A, Mann SA, Lynch KL, Yun C, Havlir DV, Chamie G, Marquez C, Greenhouse B, Lionakis MS, Norris PJ, Dumont LJ, Kelly K, Zhang P, Zhang Q, Gervais A, Le Voyer T, Whatley A, Si Y, Byrne A, Combes AJ, Rao AA, Song YS, Fragiadakis GK, Kangelaris K, Calfee CS, Erle DJ, Hendrickson C, Krummel MF, Woodruff PG, Langelier CR, Casanova JL, Derisi JL, Anderson MS, Ye CJ, UCSF COMET consortium. Type I interferon autoantibodies are associated with systemic immune alterations in patients with COVID-19. 2021. PMID: 34429372


  93. Ramesh A, Bailey ES, Ahyong V, Langelier C, Phelps M, Neff N, Sit R, Tato C, DeRisi JL, Greer AG, Gray GC. Metagenomic characterization of swine slurry in a North American swine farm operation. 2021. PMID: 34417469


  95. Retallack H, Popova KD, Laurie MT, Sunshine S, DeRisi JL. Persistence of Ambigrammatic Narnaviruses Requires Translation of the Reverse Open Reading Frame. 2021. PMID: 33762418


  96. Gu W, Talevich E, Hsu E, Qi Z, Urisman A, Federman S, Gopez A, Arevalo S, Gottschall M, Liao L, Tung J, Chen L, Lim H, Ho C, Kasowski M, Oak J, Holmes BJ, Yeh I, Yu J, Wang L, Miller S, DeRisi JL, Prakash S, Simko J, Chiu CY. Detection of cryptogenic malignancies from metagenomic whole genome sequencing of body fluids. 2021. PMID: 34074327


  97. Rajan JV, McCracken M, Mandel-Brehm C, Gromowski G, Pollett S, Jarman R, 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. 2021. PMID: 34031504


  98. Vazquez SE, Bastard P, Kelly K, Gervais A, Norris PJ, Dumont LJ, Casanova JL, Anderson MS, DeRisi JL. Neutralizing Autoantibodies to Type I Interferons in COVID-19 Convalescent Donor Plasma. 2021. PMID: 34009544


  99. Song E, Bartley CM, Chow RD, Ngo TT, Jiang R, Zamecnik CR, Dandekar R, Loudermilk RP, Dai Y, Liu F, Sunshine S, Liu J, Wu W, Hawes IA, Alvarenga BD, Huynh T, McAlpine L, Rahman NT, Geng B, Chiarella J, Goldman-Israelow B, Vogels CBF, Grubaugh ND, Casanovas-Massana A, Phinney BS, Salemi M, Alexander JR, Gallego JA, Lencz T, Walsh H, Wapniarski AE, Mohanty S, Lucas C, Klein J, Mao T, Oh J, Ring A, Spudich S, Ko AI, Kleinstein SH, Pak J, DeRisi JL, Iwasaki A, Pleasure SJ, Wilson MR, Farhadian SF. Divergent and self-reactive immune responses in the CNS of COVID-19 patients with neurological symptoms. 2021. PMID: 33969321


  101. Tsitsiklis A, Zha B, Byrne A, DeVoe C, Levan S, Rackaityte E, Sunshine S, Mick E, Ghale R, Jauregui A, Neff N, Sarma A, Serpa P, Deiss T, Kistler A, Carrillo S, Ansel KM, Leligdowicz A, Christenson S, Jones N, Wu B, Darmanis S, Matthay M, Lynch S, DeRisi J, Consortium C, Hendrickson C, Kangelaris K, Krummel M, Woodruff P, Erle D, Rosenberg O, Calfee C, Langelier C. Impaired immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19. 2021. PMID: 34013247


  102. Pilarowski G, Lebel P, Sunshine S, Liu J, Crawford E, Marquez C, Rubio L, Chamie G, Martinez J, Peng J, Black D, Wu W, Pak J, Laurie MT, Jones D, Miller S, Jacobo J, Rojas S, Rojas S, Nakamura R, Tulier-Laiwa V, Petersen M, Havlir DV. Performance characteristics of a rapid SARS-CoV-2 antigen detection assay at a public plaza testing site in San Francisco. 2021. PMID: 33394052


  103. Zylberberg M, Van Hemert C, Handel CM, Liu RM, DeRisi JL. POECIVIRUS IS PRESENT IN INDIVIDUALS WITH BEAK DEFORMITIES IN SEVEN SPECIES OF NORTH AMERICAN BIRDS. 2021. PMID: 33822149


  104. 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. The pulmonary metatranscriptome prior to pediatric HCT identifies post-HCT lung injury. 2021. PMID: 33512420


  105. Mourani PM, Sontag MK, Williamson KM, Harris JK, Reeder R, Locandro C, Carpenter TC, Maddux AB, Ziegler K, Simões EAF, Osborne CM, Ambroggio L, Leroue MK, Robertson CE, Langelier C, DeRisi JL, Kamm J, Hall MW, Zuppa AF, Carcillo J, Meert K, Sapru A, Pollack MM, McQuillen P, Notterman DA, Dean JM, Wagner BD, Eunice Kennedy Shriver National Institute of Child Health and Human Development Collaborative Pediat, Eunice Kennedy Shriver National Institute of Child Health and Human Development Collaborative Pediat. Temporal airway microbiome changes related to ventilator-associated pneumonia in children. 2021. PMID: 33008935


  106. van der Wijst MGP, Vazquez SE, Hartoularos GC, Bastard P, Grant T, Bueno R, Lee DS, Greenland JR, Sun Y, Perez R, Ogorodnikov A, Ward A, Mann SA, Lynch KL, Yun C, Havlir DV, Chamie G, Marquez C, Greenhouse B, Lionakis MS, Norris PJ, Dumont LJ, Kelly K, Zhang P, Zhang Q, Gervais A, Voyer TL, Whatley A, Si Y, Byrne A, Combes AJ, Rao AA, Song YS, UCSF COMET consortium , Fragiadakis GK, Kangelaris K, Calfee CS, Erle DJ, Hendrickson C, Krummel MF, Woodruff PG, Langelier CR, Casanova JL, Derisi JL, Anderson MS, Ye CJ. Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19. 2021. PMID: 33758859


  108. Randremanana RV, Andriamandimby SF, Rakotondramanga JM, Razanajatovo NH, Mangahasimbola RT, Randriambolamanantsoa TH, Ranaivoson HC, Rabemananjara HA, Razanajatovo I, Razafindratsimandresy R, Rabarison JH, Brook CE, Rakotomanana F, Rabetombosoa RM, Razafimanjato H, Ahyong V, Raharinosy V, Raharimanga V, Raharinantoanina SJ, Randrianarisoa MM, Bernardson B, Randrianasolo L, Randriamampionona LBN, Tato CM, DeRisi JL, Dussart P, Vololoniaina MC, Randriatsarafara FM, Randriamanantany ZA, Heraud JM. The COVID-19 epidemic in Madagascar: clinical description and laboratory results of the first wave, march-september 2020. 2021. PMID: 33586912


  109. Madera S, Crawford E, Langelier C, Tran NK, Thornborrow E, Miller S, DeRisi JL. Nasopharyngeal SARS-CoV-2 viral loads in young children do not differ significantly from those in older children and adults. 2021. PMID: 33542262


  110. Sarma A, Christenson S, Mick E, Deiss T, DeVoe C, Pisco A, Ghale R, Jauregui A, Byrne A, Moazed F, Spottiswoode N, Sinha P, Zha B, Neff N, Tan M, Serpa PH, Ansel KM, Wilson J, Leligdowicz A, Seigel E, Sirota M, DeRisi J, Matthay M, Consortium C, Hendrickson C, Kangelaris K, Krummel M, Woodruff P, Erle D, Calfee C, Langelier C. COVID-19 ARDS is characterized by a dysregulated host response that differs from cytokine storm and is modified by dexamethasone. 2021. PMID: 33469573


  112. Vanaerschot M, Mann SA, Webber JT, Kamm J, Bell SM, Bell J, Hong SN, Nguyen MP, Chan LY, Bhatt KD, Tan M, Detweiler AM, Espinosa A, Wu W, Batson J, Dynerman D, Wadford DA, Puschnik AS, Neff N, Ahyong V, Miller S, Ayscue P, Tato CM, Paul S, Kistler AL, DeRisi JL, Crawford ED. Identification of a Polymorphism in the N Gene of SARS-CoV-2 That Adversely Impacts Detection by Reverse Transcription-PCR. 2020. PMID: 33067272


  113. Song E, Bartley CM, Chow RD, Ngo TT, Jiang R, Zamecnik CR, Dandekar R, Loudermilk RP, Dai Y, Liu F, Hawes IA, Alvarenga BD, Huynh T, McAlpine L, Rahman NT, Geng B, Chiarella J, Goldman-Israelow B, Vogels CBF, Grubaugh ND, Casanovas-Massana A, Phinney BS, Salemi M, Alexander J, Gallego JA, Lencz T, Walsh H, Lucas C, Klein J, Mao T, Oh J, Ring A, Spudich S, Ko AI, Kleinstein SH, DeRisi JL, Iwasaki A, Pleasure SJ, Wilson MR, Farhadian SF. Exploratory neuroimmune profiling identifies CNS-specific alterations in COVID-19 patients with neurological involvement. 2020. PMID: 32935102


  114. Fozouni P, Son S, Díaz de León Derby M, Knott GJ, Gray CN, D'Ambrosio MV, Zhao C, Switz NA, Kumar GR, Stephens SI, Boehm D, Tsou CL, Shu J, Bhuiya A, Armstrong M, Harris AR, Chen PY, Osterloh JM, Meyer-Franke A, Joehnk B, Walcott K, Sil A, Langelier C, Pollard KS, Crawford ED, Puschnik AS, Phelps M, Kistler A, DeRisi JL, Doudna JA, Fletcher DA, Ott M. Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy. 2020. PMID: 33306959


  115. Mick E, Kamm J, Pisco AO, Ratnasiri K, Babik JM, Castañeda G, DeRisi JL, Detweiler AM, Hao SL, Kangelaris KN, Kumar GR, Li LM, Mann SA, Neff N, Prasad PA, Serpa PH, Shah SJ, Spottiswoode N, Tan M, Calfee CS, Christenson SA, Kistler A, Langelier C. Upper airway gene expression reveals suppressed immune responses to SARS-CoV-2 compared with other respiratory viruses. 2020. PMID: 33203890


  116. Pilarowski G, Lebel P, Sunshine S, Liu J, Crawford E, Marquez C, Rubio L, Chamie G, Martinez J, Peng J, Black D, Wu W, Pak J, Laurie MT, Jones D, Miller S, Jacobo J, Rojas S, Rojas S, Nakamura R, Tulier-Laiwa V, Petersen M, Havlir DV, DeRisi J. Performance characteristics of a rapid SARS-CoV-2 antigen detection assay at a public plaza testing site in San Francisco. 2020. PMID: 33173911


  117. Gu W, Deng X, Lee M, Sucu YD, Arevalo S, Stryke D, Federman S, Gopez A, Reyes K, Zorn K, Sample H, Yu G, Ishpuniani G, Briggs B, Chow ED, Berger A, Wilson MR, Wang C, Hsu E, Miller S, DeRisi JL, Chiu CY. Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids. 2020. PMID: 33169017


  118. Dubey D, Wilson MR, Clarkson B, Giannini C, Gandhi M, Cheville J, Lennon VA, Eggers S, Devine MF, Mandel-Brehm C, Kryzer T, Hinson SR, Khazaie K, Hales C, Kattah J, Pavelko KD, Andrews P, Eaton JE, Jitprapaikulsan J, Mills JR, Flanagan EP, Zekeridou A, Leibovich B, Fryer J, Torre M, Kaufman C, Thoreson JB, Sagen J, Linnoila JJ, DeRisi JL, Howe CL, McKeon A, Pittock SJ. Expanded Clinical Phenotype, Oncological Associations, and Immunopathologic Insights of Paraneoplastic Kelch-like Protein-11 Encephalitis. 2020. PMID: 32744608


  119. Crawford ED, Acosta I, Ahyong V, Anderson EC, Arevalo S, Asarnow D, Axelrod S, Ayscue P, Azimi CS, Azumaya CM, Bachl S, Bachmutsky I, Bhaduri A, Brown JB, Batson J, Behnert A, Boileau RM, Bollam SR, Bonny AR, Booth D, Borja MJB, Brown D, Buie B, Burnett CE, Byrnes LE, Cabral KA, Cabrera JP, Caldera S, Canales G, Castañeda GR, Chan AP, Chang CR, Charles-Orszag A, Cheung C, Chio U, Chow ED, Citron YR, Cohen A, Cohn LB, Chiu C, Cole MA, Conrad DN, Constantino A, Cote A, Crayton-Hall T, Darmanis S, Detweiler AM, Dial RL, Dong S, Duarte EM, Dynerman D, Egger R, Fanton A, Frumm SM, Fu BXH, Garcia VE, Garcia J, Gladkova C, Goldman M, Gomez-Sjoberg R, Gordon MG, Grove JCR, Gupta S, Haddjeri-Hopkins A, Hadley P, Haliburton J, Hao SL, Hartoularos G, Herrera N, Hilberg M, Ho KYE, Hoppe N, Hosseinzadeh S, Howard CJ, Hussmann JA, Hwang E, Ingebrigtsen D, Jackson JR, Jowhar ZM, Kain D, Kim JYS, Kistler A, Kreutzfeld O, Kulsuptrakul J, Kung AF, Langelier C, Laurie MT, Lee L, Leng K, Leon KE, Leonetti MD, Levan SR, Li S, Li AW, Liu J, Lubin HS, Lyden A, Mann J, Mann S, Margulis G, Marquez DM, Marsh BP, Martyn C, McCarthy EE, McGeever A, Merriman AF, Meyer LK, Miller S, Moore MK, Mowery CT, Mukhtar T, Mwakibete LL, Narez N, Neff NF, Osso LA, Oviedo D, Peng S, Phelps M, Phong K, Picard P, Pieper LM, Pincha N, Pisco AO, Pogson A, Pourmal S, Puccinelli RR, Puschnik AS, Rackaityte E, Raghavan P, Raghavan M, Reese J, Replogle JM, Retallack H, Reyes H, Rose D, Rosenberg MF, Sanchez-Guerrero E, Sattler SM, Savy L, See SK, Sellers KK, Serpa PH, Sheehy M, Sheu J, Silas S, Streithorst JA, Strickland J, Stryke D, Sunshine S, Suslow P, Sutanto R, Tamura S, Tan M, Tan J, Tang A, Tato CM, Taylor JC, Tenvooren I, Thompson EM, Thornborrow EC, Tse E, Tung T, Turner ML, Turner VS, Turnham RE, Turocy MJ, Vaidyanathan TV, Vainchtein ID, Vanaerschot M, Vazquez SE, Wandler AM, Wapniarski A, Webber JT, Weinberg ZY, Westbrook A, Wong AW, Wong E, Worthington G, Xie F, Xu A, Yamamoto T, Yang Y, Yarza F, Zaltsman Y, Zheng T, DeRisi JL. Rapid deployment of SARS-CoV-2 testing: The CLIAHUB. 2020. PMID: 33112933


  120. Kalantar KL, Carvalho T, de Bourcy CFA, Dimitrov B, Dingle G, Egger R, Han J, Holmes OB, Juan YF, King R, Kislyuk A, Lin MF, Mariano M, Morse T, Reynoso LV, Cruz DR, Sheu J, Tang J, Wang J, Zhang MA, Zhong E, Ahyong V, Lay S, Chea S, Bohl JA, Manning JE, Tato CM, DeRisi JL. IDseq-An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring. 2020. PMID: 33057676


  121. Zhou J, Li S, Leung KK, O'Donovan B, Zou JY, DeRisi JL, Wells JA. Deep profiling of protease substrate specificity enabled by dual random and scanned human proteome substrate phage libraries. 2020. PMID: 32973096


  122. Zamecnik CR, Rajan JV, Yamauchi KA, Mann SA, Loudermilk RP, Sowa GM, Zorn KC, Alvarenga BD, Gaebler C, Caskey M, Stone M, Norris PJ, Gu W, Chiu CY, Ng D, Byrnes JR, Zhou XX, Wells JA, Robbiani DF, Nussenzweig MC, DeRisi JL, Wilson MR. ReScan, a Multiplex Diagnostic Pipeline, Pans Human Sera for SARS-CoV-2 Antigens. 2020. PMID: 32995758


  123. Hao S, Abdelghany M, Lyden A, Sit R, Tan M, Tato CM, DeRisi JL, Miller S, Doernberg SB, Langelier C. Genomic Profiling of Evolving Daptomycin Resistance in a Patient with Recurrent Staphylococcus argenteus Sepsis. 2020. PMID: 32601156


  124. Ramesh A, Schubert RD, Greenfield AL, Dandekar R, Loudermilk R, Sabatino JJ, Koelzer MT, Tran EB, Koshal K, Kim K, Pröbstel AK, Banerji D, University of California, San Francisco MS-EPIC Team, Guo CY, Green AJ, Bove RM, DeRisi JL, Gelfand JM, Cree BAC, Zamvil SS, Baranzini SE, Hauser SL, Wilson MR. A pathogenic and clonally expanded B cell transcriptome in active multiple sclerosis. 2020. PMID: 32859762


  125. Shah SJ, Barish PN, Prasad PA, Kistler A, Neff N, Kamm J, Li LM, Chiu CY, Babik JM, Fang MC, Kangelaris KN, Langelier C, Abe-Jones Y, Alipanah N, Alvarez FN, Botvinnik OB, Castaneda G. Clinical features, diagnostics, and outcomes of patients presenting with acute respiratory illness: A retrospective cohort study of patients with and without COVID-19. 2020. PMID: 32864588


  126. Crawford E, Kamm J, Miller S, Li LM, Caldera S, Lyden A, Yokoe D, Nichols A, Tran NK, Barnard SE, Conner PM, Nambiar A, Zinter MS, Moayeri M, Serpa PH, Prince BC, Quan J, Sit R, Tan M, Phelps M, DeRisi JL, Tato CM, Langelier C. Investigating Transfusion-Related Sepsis using Culture-Independent Metagenomic Sequencing. 2019. PMID: 31563940


  127. 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. High-resolution epitope mapping of anti-Hu and anti-Yo autoimmunity by programmable phage display. 2020. PMID: 32954318


  128. DeRisi JL. Erratum. 2020. PMID: 32847662


  129. 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. Complete Genome Sequence of a Novel Coronavirus (SARS-CoV-2) Isolate from Bangladesh. 2020. PMID: 32527780


  130. Mick E, Kamm J, Pisco AO, Ratnasiri K, Babik JM, Calfee CS, Castañeda G, DeRisi JL, Detweiler AM, Hao S, Kangelaris KN, Kumar GR, Li LM, Mann SA, Neff N, Prasad PA, Serpa PH, Shah SJ, Spottiswoode N, Tan M, Christenson SA, Kistler A, Langelier C. Upper airway gene expression differentiates COVID-19 from other acute respiratory illnesses and reveals suppression of innate immune responses by SARS-CoV-2. 2020. PMID: 32511476


  131. Seto J, Horst JA, Parkinson DY, Frachella JC, DeRisi JL. Enhanced Tooth Structure Via Silver Microwires Following Treatment with 38 Percent Silver Diamine Fluoride. 2020. PMID: 32522328


  132. 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. Identification of novel, clinically correlated autoantigens in the monogenic autoimmune syndrome APS1 by proteome-wide PhIP-Seq. 2020. PMID: 32410729


  133. Shah SJ, Barish PN, Prasad PA, Kistler AL, Neff N, Kamm J, Li LM, Chiu CY, Babick JM, Fang MC, Abe-Jones Y, Alipanah N, Alvarez FN, Botvinnik OB, Davis JM, Castenada GD, Consortium C, Dadasovich RM, Deng X, DeRisi JL, Detweiler AM, Federman S, Haliburton JR, Hao SL, Kerkhoff AD, Kumar R, Malcolm K, Mann SA, Martinez SP, Marya R, Mick E, Mwakibete LL, Najafi N, Peluso MJ, Phelps MS, Pisco AO, Ratnasiri K, Rubio LA, Sellas AB, Sherwood KD, Sheu J, Spottiswoode N, Tan M, Yu G, Kangelaris KN, Langelier C. Clinical features, diagnostics, and outcomes of patients presenting with acute respiratory illness: a comparison of patients with and without COVID-19. 2020. PMID: 32511488


  134. 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. Central Nervous System Virus Infection in African Children with Cerebral Malaria. 2020. PMID: 32342847


  135. 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. Identification of anisomycin, prodigiosin and obatoclax as compounds with broad-spectrum anti-parasitic activity. 2020. PMID: 32196500


  136. Leon KE, Schubert RD, Casas-Alba D, Hawes IA, Ramachandran PS, Ramesh A, Pak JE, Wu W, Cheung CK, Crawford ED, Khan LM, Launes C, Sample HA, Zorn KC, Cabrerizo M, Valero-Rello A, Langelier C, Muñoz-Almagro C, DeRisi JL, Wilson MR. Genomic and serologic characterization of enterovirus A71 brainstem encephalitis. 2020. PMID: 32139440


  137. 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. Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia. 2020. PMID: 32511296


  138. Langelier C, Fung M, Caldera S, Deiss T, Lyden A, Prince BC, Hayakawa Serpa P, Moazed F, Chin-Hong P, DeRisi JL, Calfee CS. Detection of Pneumonia Pathogens from Plasma Cell-Free DNA. 2019. PMID: 31647702


  139. Berger A, Matloubian M, Shah NP, Wachter RM, DeRisi JL, Anderson M. The Molecular Medicine Investigation Unit: Linking Patient Care and Scientific Inquiry in Physician-Scientist Training. 2020. PMID: 32089799


  140. Sindhe KMV, Wu W, Legac J, Zhang YK, Easom EE, Cooper RA, Plattner JJ, Freund YR, DeRisi JL, Rosenthal PJ. Plasmodium falciparum Resistance to a Lead Benzoxaborole Due to Blocked Compound Activation and Altered Ubiquitination or Sumoylation. 2020. PMID: 31992618


  142. Saha S, Ramesh A, Kalantar K, Malaker R, Hasanuzzaman M, Khan LM, Mayday MY, Sajib MSI, Li LM, Langelier C, Rahman H, Crawford ED, Tato CM, Islam M, Juan YF, de Bourcy C, Dimitrov B, Wang J, Tang J, Sheu J, Egger R, De Carvalho TR, Wilson MR, Saha SK, DeRisi JL. Unbiased Metagenomic Sequencing for Pediatric Meningitis in Bangladesh Reveals Neuroinvasive Chikungunya Virus Outbreak and Other Unrealized Pathogens. 2019. PMID: 31848287


  143. DeRisi JL, Huber G, Kistler A, Retallack H, Wilkinson M, Yllanes D. An exploration of ambigrammatic sequences in narnaviruses. 2019. PMID: 31784609


  144. 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. 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. 2019. PMID: 31659431


  145. 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 GA, Sample HA, Zorn KC, Banerji D, Khan LM, Bove R, Hauser SL, Gelfand AA, Johnson-Kerner BL, Nash K, Krishnamoorthy KS, Chitnis T, Ding JZ, McMillan HJ, Chiu CY, Briggs B, Glaser CA, Yen C, Chu V, Wadford DA, Dominguez SR, Ng TFF, Marine RL, Lopez AS, Nix WA, Soldatos A, Gorman MP, Benson L, Messacar K, Konopka-Anstadt JL, Oberste MS, DeRisi JL, Wilson MR. Pan-viral serology implicates enteroviruses in acute flaccid myelitis. 2019. PMID: 31636453


  146. Quan J, Langelier C, Kuchta A, Batson J, Teyssier N, Lyden A, Caldera S, McGeever A, Dimitrov B, King R, Wilheim J, Murphy M, Ares LP, Travisano KA, Sit R, Amato R, Mumbengegwi DR, Smith JL, Bennett A, Gosling R, Mourani PM, Calfee CS, Neff NF, Chow ED, Kim PS, Greenhouse B, DeRisi JL, Crawford ED. FLASH: a next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences. 2019. PMID: 31114866


  147. 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. Kelch-like Protein 11 Antibodies in Seminoma-Associated Paraneoplastic Encephalitis. 2019. PMID: 31269365


  148. Mandel-Brehm C, Retallack H, Knudsen GM, Yamana A, Hajj-Ali RA, Calabrese LH, Tihan T, Sample HA, Zorn KC, Gorman MP, Madan Cohen J, Sreih AG, Marcus JF, Josephson SA, Douglas VC, Gelfand JM, Wilson MR, DeRisi JL. Exploratory proteomic analysis implicates the alternative complement cascade in primary CNS vasculitis. 2019. PMID: 31270218


  149. Langelier C, Graves M, Kalantar K, Caldera S, Durrant R, Fisher M, Backman R, Tanner W, DeRisi JL, Leung DT. Microbiome and Antimicrobial Resistance Gene Dynamics in International Travelers. 2019. PMID: 31211676


  150. 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. Metagenomic next-generation sequencing of samples from pediatric febrile illness in Tororo, Uganda. 2019. PMID: 31220115


  151. Wilson MR, Sample HA, Zorn KC, Arevalo S, Yu G, Neuhaus J, Federman S, Stryke D, Briggs B, Langelier C, Berger A, Douglas V, Josephson SA, Chow FC, Fulton BD, DeRisi JL, Gelfand JM, Naccache SN, Bender J, Dien Bard J, Murkey J, Carlson M, Vespa PM, Vijayan T, Allyn PR, Campeau S, Humphries RM, Klausner JD, Ganzon CD, Memar F, Ocampo NA, Zimmermann LL, Cohen SH, Polage CR, DeBiasi RL, Haller B, Dallas R, Maron G, Hayden R, Messacar K, Dominguez SR, Miller S, Chiu CY. Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis. 2019. PMID: 31189036


  152. 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. Sentinel Case of Candida auris in the Western United States Following Prolonged Occult Colonization in a Returned Traveler from India. 2019. PMID: 31163013


  153. Ramachandran PS, Cresswell FV, Meya DB, Langelier C, Crawford ED, DeRisi JL, Boulware DR, Wilson MR. Detection of Cryptococcus DNA by Metagenomic Next-generation Sequencing in Symptomatic Cryptococcal Antigenemia. 2019. PMID: 30535266


  154. Zinter MS, Dvorak CC, Mayday MY, Iwanaga K, Ly NP, McGarry ME, Church GD, Faricy LE, Rowan CM, Hume JR, Steiner ME, Crawford ED, Langelier C, Kalantar K, Chow ED, Miller S, Shimano K, Melton A, Yanik GA, Sapru A, DeRisi JL. Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children. 2019. PMID: 30239621


  156. Zinter MS, Mayday MY, Ryckman KK, Jelliffe-Pawlowski LL, DeRisi JL. Towards precision quantification of contamination in metagenomic sequencing experiments. 2019. PMID: 30992055


  157. 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. Bergeyella cardium: Clinical Characteristics and Draft Genome of an Emerging Pathogen in Native and Prosthetic Valve Endocarditis. 2019. PMID: 31024974


  158. Maes P, Adkins S, Alkhovsky SV, Avšic-Županc T, Ballinger MJ, Bente DA, Beer M, Bergeron É, Blair CD, Briese T, Buchmeier MJ, Burt FJ, Calisher CH, Charrel RN, Choi IR, Clegg JCS, de la Torre JC, de Lamballerie X, DeRisi JL, Digiaro M, Drebot M, Ebihara H, Elbeaino T, Ergünay K, Fulhorst CF, Garrison AR, Gao GF, Gonzalez JJ, Groschup MH, Günther S, Haenni AL, Hall RA, Hewson R, Hughes HR, Jain RK, Jonson MG, Junglen S, Klempa B, Klingström J, Kormelink R, Lambert AJ, Langevin SA, Lukashevich IS, Marklewitz M, Martelli GP, Mielke-Ehret N, Mirazimi A, Mühlbach HP, Naidu R, Nunes MRT, Palacios G, Papa A, Paweska JT, Peters CJ, Plyusnin A, Radoshitzky SR, Resende RO, Romanowski V, Sall AA, Salvato MS, Sasaya T, Schmaljohn C, Shí X, Shirako Y, Simmonds P, Sironi M, Song JW, Spengler JR, Stenglein MD, Tesh RB, Turina M, Wèi T, Whitfield AE, Yeh SD, Zerbini FM, Zhang YZ, Zhou X, Kuhn JH. Taxonomy of the order Bunyavirales: second update 2018. 2019. PMID: 30663021


  159. 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. Metagenomic comparison of tracheal aspirate and mini-bronchial alveolar lavage for assessment of respiratory microbiota. 2019. PMID: 30652494


  160. Mayday MY, Khan LM, Chow ED, Zinter MS, DeRisi JL. Miniaturization and optimization of 384-well compatible RNA sequencing library preparation. 2019. PMID: 30629604


  161. Beck ES, Ramachandran PS, Khan LM, Sample HA, Zorn KC, O'Connell EM, Nash T, Reich DS, Venkatesan A, DeRisi JL, Nath A, Wilson MR. Clinicopathology conference: 41-year-old woman with chronic relapsing meningitis. 2019. PMID: 30565288


  162. Wilson MR, O'Donovan BD, DeRisi JL. Misinterpretation of Study Data-Reply. 2019. PMID: 30477022


  164. 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. Ebola virus, but not Marburg virus, replicates efficiently and without required adaptation in snake cells. 2018. PMID: 30524754


  165. Langelier C, Kalantar KL, Moazed F, Wilson MR, Crawford ED, Deiss T, Belzer A, Bolourchi S, Caldera S, Fung M, Jauregui A, Malcolm K, Lyden A, Khan L, Vessel K, Quan J, Zinter M, Chiu CY, Chow ED, Wilson J, Miller S, Matthay MA, Pollard KS, Christenson S, Calfee CS, DeRisi JL. Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults. 2018. PMID: 30482864


  166. Laurie MT, White CV, Retallack H, Wu W, Moser MS, Sakanari JA, Ang K, Wilson C, Arkin MR, DeRisi JL. Functional Assessment of 2,177 U.S. and International Drugs Identifies the Quinoline Nitroxoline as a Potent Amoebicidal Agent against the Pathogen Balamuthia mandrillaris. 2018. PMID: 30377287


  167. Miller LJ, Fetterer DP, Garza NL, Lackemeyer MG, Donnelly GC, Steffens JT, Van Tongeren SA, Fiallos JO, Moore JL, Marko ST, Lugo-Roman LA, Fedewa G, DeRisi JL, Kuhn JH, Stahl SJ. A fixed moderate-dose combination of tiletamine+zolazepam outperforms midazolam in induction of short-term immobilization of ball pythons (Python regius). 2018. PMID: 30339670


  169. Wilson MR, O'Donovan BD, Gelfand JM, Sample HA, Chow FC, Betjemann JP, Shah MP, Richie MB, Gorman MP, Hajj-Ali RA, Calabrese LH, Zorn KC, Chow ED, Greenlee JE, Blum JH, Green G, Khan LM, Banerji D, Langelier C, Bryson-Cahn C, Harrington W, Lingappa JR, Shanbhag NM, Green AJ, Brew BJ, Soldatos A, Strnad L, Doernberg SB, Jay CA, Douglas V, Josephson SA, DeRisi JL. Chronic Meningitis Investigated via Metagenomic Next-Generation Sequencing. 2018. PMID: 29710329


  170. Mavor D, Barlow KA, Asarnow D, Birman Y, Britain D, Chen W, Green EM, Kenner LR, Mensa B, Morinishi LS, Nelson CA, Poss EM, Suresh P, Tian R, Arhar T, Ary BE, Bauer DP, Bergman ID, Brunetti RM, Chio CM, Dai SA, Dickinson MS, Elledge SK, Helsell CVM, Hendel NL, Kang E, Kern N, Khoroshkin MS, Kirkemo LL, Lewis GR, Lou K, Marin WM, Maxwell AM, McTigue PF, Myers-Turnbull D, Nagy TL, Natale AM, Oltion K, Pourmal S, Reder GK, Rettko NJ, Rohweder PJ, Schwarz DMC, Tan SK, Thomas PV, Tibble RW, Town JP, Tsai MK, Ugur FS, Wassarman DR, Wolff AM, Wu TS, Bogdanoff D, Li J, Thorn KS, O'Conchúir S, Swaney DL, Chow ED, Madhani HD, Redding S, Bolon DN, Kortemme T, DeRisi JL, Kampmann M, Fraser JS. Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance. 2018. PMID: 30037883


  171. Kalantar K, LaHue SC, DeRisi JL, Sample HA, Contag CA, Josephson SA, Wilson MR, Douglas VC. Whole-Genome mRNA Gene Expression Differs Between Patients With and Without Delirium. 2018. PMID: 29991314


  172. Zylberberg M, Van Hemert C, Handel CM, DeRisi JL. Avian keratin disorder of Alaska black-capped chickadees is associated with Poecivirus infection. 2018. PMID: 29903045


  173. Solomon IH, Spera KM, Ryan SL, Helgager J, Andrici J, Zaki SR, Vaitkevicius H, Leon KE, Wilson MR, DeRisi JL, Koo S, Smirnakis SM, De Girolami U. Fatal Powassan Encephalitis (Deer Tick Virus, Lineage II) in a Patient With Fever and Orchitis Receiving Rituximab. 2018. PMID: 29554185


  174. Maes P, Alkhovsky SV, Bào Y, Beer M, Birkhead M, Briese T, Buchmeier MJ, Calisher CH, Charrel RN, Choi IR, Clegg CS, de la Torre JC, Delwart E, DeRisi JL, Di Bello PL, Di Serio F, Digiaro M, Dolja VV, Drosten C, Druciarek TZ, Du J, Ebihara H, Elbeaino T, Gergerich RC, Gillis AN, Gonzalez JJ, Haenni AL, Hepojoki J, Hetzel U, H? T, Hóng N, Jain RK, Jansen van Vuren P, Jin Q, Jonson MG, Junglen S, Keller KE, Kemp A, Kipar A, Kondov NO, Koonin EV, Kormelink R, Korzyukov Y, Krupovic M, Lambert AJ, Laney AG, LeBreton M, Lukashevich IS, Marklewitz M, Markotter W, Martelli GP, Martin RR, Mielke-Ehret N, Mühlbach HP, Navarro B, Ng TFF, Nunes MRT, Palacios G, Paweska JT, Peters CJ, Plyusnin A, Radoshitzky SR, Romanowski V, Salmenperä P, Salvato MS, Sanfaçon H, Sasaya T, Schmaljohn C, Schneider BS, Shirako Y, Siddell S, Sironen TA, Stenglein MD, Storm N, Sudini H, Tesh RB, Tzanetakis IE, Uppala M, Vapalahti O, Vasilakis N, Walker PJ, Wáng G, Wáng L, Wáng Y, Wèi T, Wiley MR, Wolf YI, Wolfe ND, Wú Z, Xú W, Yang L, Yang Z, Yeh SD, Zhang YZ, Zhèng Y, Zhou X, Zhu C, Zirkel F, Kuhn JH. Taxonomy of the family Arenaviridae and the order Bunyavirales: update 2018. 2018. PMID: 29680923


  175. Langelier C, Zinter MS, Kalantar K, Yanik GA, Christenson S, O'Donovan B, White C, Wilson M, Sapru A, Dvorak CC, Miller S, Chiu CY, DeRisi JL. Metagenomic Sequencing Detects Respiratory Pathogens in Hematopoietic Cellular Transplant Patients. Volume 197 of Issue 4. 2018. PMID: 28686513


  176. Bhakta NR, Christenson SA, Nerella S, Solberg OD, Nguyen CP, Choy DF, Jung KL, Garudadri S, Bonser LR, Pollack JL, Zlock LT, Erle DJ, Langelier C, Derisi JL, Arron JR, Fahy JV, Woodruff PG. IFN-stimulated Gene Expression, Type 2 Inflammation, and Endoplasmic Reticulum Stress in Asthma. 2018. PMID: 29064281


  178. Gonzales J, Doan T, Shantha JG, Bloomer M, Wilson MR, DeRisi JL, Acharya N. Metagenomic deep sequencing of aqueous fluid detects intraocular lymphomas. 2017. PMID: 29122821


  179. Hanna ZR, Henderson JB, Wall JD, Emerling CA, Fuchs J, Runckel C, Mindell DP, Bowie RCK, DeRisi JL, Dumbacher JP. Northern Spotted Owl (Strix occidentalis caurina) Genome: Divergence with the Barred Owl (Strix varia) and Characterization of Light-Associated Genes. 2017. PMID: 28992302


  180. Faden DL, Thomas S, Cantalupo PG, Agrawal N, Myers J, DeRisi J. Multi-modality analysis supports APOBEC as a major source of mutations in head and neck squamous cell carcinoma. 2017. PMID: 29103756


  182. Stenglein MD, Sanchez-Migallon Guzman D, Garcia VE, Layton ML, Hoon-Hanks LL, Boback SM, Keel MK, Drazenovich T, Hawkins MG, DeRisi JL. Differential Disease Susceptibilities in Experimentally Reptarenavirus-Infected Boa Constrictors and Ball Pythons. 2017. PMID: 28515291


  183. Wilson MR, Suan D, Duggins A, Schubert RD, Khan LM, Sample HA, Zorn KC, Rodrigues Hoffman A, Blick A, Shingde M, DeRisi JL. A novel cause of chronic viral meningoencephalitis: Cache Valley virus. 2017. PMID: 28628941


  184. Zinter MS, Barrows BD, Ursell PC, Kowalek K, Kalantar K, Cambronero N, DeRisi JL, Oishi P, Dvorak CC. Extracorporeal life support survival in a pediatric hematopoietic cellular transplant recipient with presumed GvHD-related fulminant myocarditis. 2017. PMID: 28581474


  186. Doan T, Acharya NR, Pinsky BA, Sahoo MK, Chow ED, Banaei N, Budvytiene I, Cevallos V, Zhong L, Zhou Z, Lietman TM, DeRisi JL. Metagenomic DNA Sequencing for the Diagnosis of Intraocular Infections. 2017. PMID: 28526549


  187. Postler TS, Clawson AN, Amarasinghe GK, Basler CF, Bavari S, Benko M, Blasdell KR, Briese T, Buchmeier MJ, Bukreyev A, Calisher CH, Chandran K, Charrel R, Clegg CS, Collins PL, Juan Carlos T, Derisi JL, Dietzgen RG, Dolnik O, Dürrwald R, Dye JM, Easton AJ, Emonet S, Formenty P, Fouchier RAM, Ghedin E, Gonzalez JP, Harrach B, Hewson R, Horie M, Jiang D, Kobinger G, Kondo H, Kropinski AM, Krupovic M, Kurath G, Lamb RA, Leroy EM, Lukashevich IS, Maisner A, Mushegian AR, Netesov SV, Nowotny N, Patterson JL, Payne SL, PaWeska JT, Peters CJ, Radoshitzky SR, Rima BK, Romanowski V, Rubbenstroth D, Sabanadzovic S, Sanfaçon H, Salvato MS, Schwemmle M, Smither SJ, Stenglein MD, Stone DM, Takada A, Tesh RB, Tomonaga K, Tordo N, Towner JS, Vasilakis N, Volchkov VE, Wahl-Jensen V, Walker PJ, Wang LF, Varsani A, Whitfield AE, Zerbini FM, Kuhn JH. Possibility and Challenges of Conversion of Current Virus Species Names to Linnaean Binomials. 2017. PMID: 27798405


  188. Ludington WB, Seher TD, Applegate O, Li X, Kliegman JI, Langelier C, Atwill ER, Harter T, DeRisi JL. Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater. 2017. PMID: 28384184


  189. Sonoiki E, Ng CL, Lee MC, Guo D, Zhang YK, Zhou Y, Alley MR, Ahyong V, Sanz LM, Lafuente-Monasterio MJ, Dong C, Schupp PG, Gut J, Legac J, Cooper RA, Gamo FJ, DeRisi J, Freund YR, Fidock DA, Rosenthal PJ. A potent antimalarial benzoxaborole targets a Plasmodium falciparum cleavage and polyadenylation specificity factor homologue. Volume 8. 2017. PMID: 28262680


  191. Medina GN, Knudsen GM, Greninger AL, Kloc A, Díaz-San Segundo F, Rieder E, Grubman MJ, DeRisi JL, de Los Santos T. Interaction between FMDV Lpro and transcription factor ADNP is required for optimal viral replication. 2017. PMID: 28219017


  193. Slabodnick MM, Ruby JG, Reiff SB, Swart EC, Gosai S, Prabakaran S, Witkowska E, Larue GE, Fisher S, Freeman RM, Gunawardena J, Chu W, Stover NA, Gregory BD, Nowacki M, Derisi J, Roy SW, Marshall WF, Sood P. The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell. 2017. PMID: 28190732


  195. Sonoiki E, Nsanzabana C, Legac J, Sindhe KM, DeRisi J, Rosenthal PJ. Altered Plasmodium falciparum Sensitivity to the Antiretroviral Protease Inhibitor Lopinavir Associated with Polymorphisms in pfmdr1. 2016. PMID: 27821443


  196. Retallack H, Di Lullo E, Arias C, Knopp KA, Laurie MT, Sandoval-Espinosa C, Mancia Leon WR, Krencik R, Ullian EM, Spatazza J, Pollen AA, Mandel-Brehm C, Nowakowski TJ, Kriegstein AR, DeRisi JL. Zika virus cell tropism in the developing human brain and inhibition by azithromycin. 2016. PMID: 27911847


  197. Greene TT, Tokuyama M, Knudsen GM, Kunz M, Lin J, Greninger AL, DeFilippis VR, DeRisi JL, Raulet DH, Coscoy L. A Herpesviral induction of RAE-1 NKG2D ligand expression occurs through release of HDAC mediated repression. 2016. PMID: 27874833


  198. Doan T, Wilson MR, Crawford ED, Chow ED, Khan LM, Knopp KA, O'Donovan BD, Xia D, Hacker JK, Stewart JM, Gonzales JA, Acharya NR, DeRisi JL. Erratum to: Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens. 2016. PMID: 27876088


  199. Chang L, Fu D, Stenglein MD, Hernandez JA, DeRisi JL, Jacobson ER. Detection and prevalence of boid inclusion body disease in collections of boas and pythons using immunological assays. 2016. PMID: 27938703


  200. Wilson MR, Zimmermann LL, Crawford ED, Sample HA, Soni PR, Baker AN, Khan LM, DeRisi JL. Acute West Nile Virus Meningoencephalitis Diagnosed Via Metagenomic Deep Sequencing of Cerebrospinal Fluid in a Renal Transplant Patient. 2016. PMID: 27647685


  201. Nguyen HQ, Baxter BC, Brower K, Diaz-Botia CA, DeRisi JL, Fordyce PM, Thorn KS. Programmable Microfluidic Synthesis of Over One Thousand Uniquely Identifiable Spectral Codes. 2016. PMID: 28936383


  202. Nguyen JT, Green A, Wilson MR, DeRisi JL, Gundling K. Neurologic Complications of Common Variable Immunodeficiency. 2016. PMID: 27704236


  203. Faden DL, Arron ST, Heaton CM, DeRisi J, South AP, Wang SJ. Targeted next-generation sequencing of TP53 in oral tongue carcinoma from non-smokers. 2016. PMID: 27640185


  204. Doan T, Wilson MR, Crawford ED, Chow ED, Khan LM, Knopp KA, O'Donovan BD, Xia D, Hacker JK, Stewart JM, Gonzales JA, Acharya NR, DeRisi JL. Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens. 2016. PMID: 27562436


  205. Van Voorhis WC, Adams JH, Adelfio R, Ahyong V, Akabas MH, Alano P, Alday A, Alemán Resto Y, Alsibaee A, Alzualde A, Andrews KT, Avery SV, Avery VM, Ayong L, Baker M, Baker S, Ben Mamoun C, Bhatia S, Bickle Q, Bounaadja L, Bowling T, Bosch J, Boucher LE, Boyom FF, Brea J, Brennan M, Burton A, Caffrey CR, Camarda G, Carrasquilla M, Carter D, Belen Cassera M, Chih-Chien Cheng K, Chindaudomsate W, Chubb A, Colon BL, Colón-López DD, Corbett Y, Crowther GJ, Cowan N, D'Alessandro S, Le Dang N, Delves M, DeRisi JL, Du AY, Duffy S, Abd El-Salam El-Sayed S, Ferdig MT, Fernández Robledo JA, Fidock DA, Florent I, Fokou PV, Galstian A, Gamo FJ, Gokool S, Gold B, Golub T, Goldgof GM, Guha R, Guiguemde WA, Gural N, Guy RK, Hansen MA, Hanson KK, Hemphill A, Hooft van Huijsduijnen R, Horii T, Horrocks P, Hughes TB, Huston C, Igarashi I, Ingram-Sieber K, Itoe MA, Jadhav A, Naranuntarat Jensen A, Jensen LT, Jiang RH, Kaiser A, Keiser J, Ketas T, Kicka S, Kim S, Kirk K, Kumar VP, Kyle DE, Lafuente MJ, Landfear S, Lee N, Lee S, Lehane AM, Li F, Little D, Liu L, Llinás M, Loza MI, Lubar A, Lucantoni L, Lucet I, Maes L, Mancama D, Mansour NR, March S, McGowan S, Medina Vera I, Meister S, Mercer L, Mestres J, Mfopa AN, Misra RN, Moon S, Moore JP, Morais Rodrigues da Costa F, Müller J, Muriana A, Nakazawa Hewitt S, Nare B, Nathan C, Narraidoo N, Nawaratna S, Ojo KK, Ortiz D, Panic G, Papadatos G, Parapini S, Patra K, Pham N, Prats S, Plouffe DM, Poulsen SA, Pradhan A, Quevedo C, Quinn RJ, Rice CA, Abdo Rizk M, Ruecker A, St Onge R, Salgado Ferreira R, Samra J, Robinett NG, Schlecht U, Schmitt M, Silva Villela F, Silvestrini F, Sinden R, Smith DA, Soldati T, Spitzmüller A, Stamm SM, Sullivan DJ, Sullivan W, Suresh S, Suzuki BM, Suzuki Y, Swamidass SJ, Taramelli D, Tchokouaha LR, Theron A, Thomas D, Tonissen KF, Townson S, Tripathi AK, Trofimov V, Udenze KO, Ullah I, Vallieres C, Vigil E, Vinetz JM, Voong Vinh P, Vu H, Watanabe NA, Weatherby K, White PM, Wilks AF, Winzeler EA, Wojcik E, Wree M, Wu W, Yokoyama N, Zollo PH, Abla N, Blasco B, Burrows J, Laleu B, Leroy D, Spangenberg T, Wells T, Willis PA. Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond. 2016. PMID: 27467575


  206. Zylberberg M, Van Hemert C, Dumbacher JP, Handel CM, Tihan T, DeRisi JL. Novel Picornavirus Associated with Avian Keratin Disorder in Alaskan Birds. 2016. PMID: 27460795


  207. Sonoiki E, Palencia A, Guo D, Ahyong V, Dong C, Li X, Hernandez VS, Zhang YK, Choi W, Gut J, Legac J, Cooper R, Alley MR, Freund YR, DeRisi J, Cusack S, Rosenthal PJ. Antimalarial Benzoxaboroles Target Plasmodium falciparum Leucyl-tRNA Synthetase. Volume 60 of Issue 8. 2016. PMID: 27270277


  208. Wilson MR, Fedewa G, Stenglein MD, Olejnik J, Rennick LJ, Nambulli S, Feldmann F, Duprex WP, Connor JH, Mühlberger E, DeRisi JL. Multiplexed Metagenomic Deep Sequencing To Analyze the Composition of High-Priority Pathogen Reagents. 2016. PMID: 27822544


  209. Mavor D, Barlow K, Thompson S, Barad BA, Bonny AR, Cario CL, Gaskins G, Liu Z, Deming L, Axen SD, Caceres E, Chen W, Cuesta A, Gate RE, Green EM, Hulce KR, Ji W, Kenner LR, Mensa B, Morinishi LS, Moss SM, Mravic M, Muir RK, Niekamp S, Nnadi CI, Palovcak E, Poss EM, Ross TD, Salcedo EC, See SK, Subramaniam M, Wong AW, Li J, Thorn KS, Conchúir SÓ, Roscoe BP, Chow ED, DeRisi JL, Kortemme T, Bolon DN, Fraser JS. Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting. 2016. PMID: 27111525


  212. Soupene E, Kao J, Cheng DH, Wang D, Greninger AL, Knudsen GM, DeRisi JL, Kuypers FA. Association of NMT2 with the acyl-CoA carrier ACBD6 protects the N-myristoyltransferase reaction from palmitoyl-CoA. 2015. PMID: 26621918


  213. Hanna ZR, Runckel C, Fuchs J, DeRisi JL, Mindell DP, Van Hemert C, Handel CM, Dumbacher JP. Isolation of a Complete Circular Virus Genome Sequence from an Alaskan Black-Capped Chickadee (Poecile atricapillus) Gastrointestinal Tract Sample. 2015. PMID: 26404604


  214. Wilson MR, Shanbhag NM, Reid MJ, Singhal NS, Gelfand JM, Sample HA, Benkli B, O'Donovan BD, Ali IK, Keating MK, Dunnebacke TH, Wood MD, Bollen A, DeRisi JL. Diagnosing Balamuthia mandrillaris Encephalitis With Metagenomic Deep Sequencing. 2015. PMID: 26290222


  217. Greninger AL, DeRisi JL. Draft Genome Sequence of Tombunodavirus UC1. 2015. PMID: 26139709


  218. Radoshitzky SR, Bào Y, Buchmeier MJ, Charrel RN, Clawson AN, Clegg CS, DeRisi JL, Emonet S, Gonzalez JP, Kuhn JH, Lukashevich IS, Peters CJ, Romanowski V, Salvato MS, Stenglein MD, de la Torre JC. Past, present, and future of arenavirus taxonomy. 2015. PMID: 25935216


  222. Stenglein MD, Jacobson ER, Chang LW, Sanders C, Hawkins MG, Guzman DS, Drazenovich T, Dunker F, Kamaka EK, Fisher D, Reavill DR, Meola LF, Levens G, DeRisi JL. Widespread recombination, reassortment, and transmission of unbalanced compound viral genotypes in natural arenavirus infections. 2015. PMID: 25993603


  223. O'Donoghue AJ, Knudsen GM, Beekman C, Perry JA, Johnson AD, DeRisi JL, Craik CS, Bennett RJ. Destructin-1 is a collagen-degrading endopeptidase secreted by Pseudogymnoascus destructans, the causative agent of white-nose syndrome. 2015. PMID: 25944934


  224. Gerver RE, Gómez-Sjöberg R, Baxter BC, Thorn KS, Fordyce PM, Diaz-Botia CA, Helms BA, DeRisi JL. Correction: Programmable microfluidic synthesis of spectrally encoded microspheres. 2015. PMID: 25619960


  225. Schulze CJ, Navarro G, Ebert D, DeRisi J, Linington RG. Salinipostins A-K, long-chain bicyclic phosphotriesters as a potent and selective antimalarial chemotype. 2015. PMID: 25584395


  227. Kuhn JH, Dürrwald R, Bào Y, Briese T, Carbone K, Clawson AN, deRisi JL, Garten W, Jahrling PB, Kolodziejek J, Rubbenstroth D, Schwemmle M, Stenglein M, Tomonaga K, Weissenböck H, Nowotny N. Taxonomic reorganization of the family Bornaviridae. 2014. PMID: 25449305


  228. Jiménez-Díaz MB, Ebert D, Salinas Y, Pradhan A, Lehane AM, Myrand-Lapierre ME, O'Loughlin KG, Shackleford DM, Justino de Almeida M, Carrillo AK, Clark JA, Dennis AS, Diep J, Deng X, Duffy S, Endsley AN, Fedewa G, Guiguemde WA, Gómez MG, Holbrook G, Horst J, Kim CC, Liu J, Lee MC, Matheny A, Martínez MS, Miller G, Rodríguez-Alejandre A, Sanz L, Sigal M, Spillman NJ, Stein PD, Wang Z, Zhu F, Waterson D, Knapp S, Shelat A, Avery VM, Fidock DA, Gamo FJ, Charman SA, Mirsalis JC, Ma H, Ferrer S, Kirk K, Angulo-Barturen I, Kyle DE, DeRisi JL, Floyd DM, Guy RK. (+)-SJ733, a clinical candidate for malaria that acts through ATP4 to induce rapid host-mediated clearance of Plasmodium. 2014. PMID: 25453091


  230. Stenglein MD, Leavitt EB, Abramovitch MA, McGuire JA, DeRisi JL. Genome Sequence of a Bornavirus Recovered from an African Garter Snake (Elapsoidea loveridgei). 2014. PMID: 25301640


  231. Stenglein MD, Jacobson ER, Wozniak EJ, Wellehan JF, Kincaid A, Gordon M, Porter BF, Baumgartner W, Stahl S, Kelley K, Towner JS, DeRisi JL. Ball python nidovirus: a candidate etiologic agent for severe respiratory disease in Python regius. 2014. PMID: 25205093


  232. Li R, Faden DL, Fakhry C, Langelier C, Jiao Y, Wang Y, Wilkerson MD, Pedamallu CS, Old M, Lang J, Loyo M, Ahn SM, Tan M, Gooi Z, Chan J, Richmon J, Wood LD, Hruban RH, Bishop J, Westra WH, Chung CH, Califano J, Gourin CG, Bettegowda C, Meyerson M, Papadopoulos N, Kinzler KW, Vogelstein B, DeRisi JL, Koch WM, Agrawal N. Clinical, genomic, and metagenomic characterization of oral tongue squamous cell carcinoma in patients who do not smoke. 2014. PMID: 24954188


  233. Skewes-Cox P, Sharpton TJ, Pollard KS, DeRisi JL. Profile hidden Markov models for the detection of viruses within metagenomic sequence data. 2014. PMID: 25140992


  234. Naccache SN, Federman S, Veeraraghavan N, Zaharia M, Lee D, Samayoa E, Bouquet J, Greninger AL, Luk KC, Enge B, Wadford DA, Messenger SL, Genrich GL, Pellegrino K, Grard G, Leroy E, Schneider BS, Fair JN, Martínez MA, Isa P, Crump JA, DeRisi JL, Sittler T, Hackett J, Miller S, Chiu CY. A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Volume 24 of Issue 7. 2014. PMID: 24899342


  235. Wilson MR, Naccache SN, Samayoa E, Biagtan M, Bashir H, Yu G, Salamat SM, Somasekar S, Federman S, Miller S, Sokolic R, Garabedian E, Candotti F, Buckley RH, Reed KD, Meyer TL, Seroogy CM, Galloway R, Henderson SL, Gern JE, DeRisi JL, Chiu CY. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. Volume 370 of Issue 25. 2014. PMID: 24896819


  236. Pérez JC, Fordyce PM, Lohse MB, Hanson-Smith V, DeRisi JL, Johnson AD. How duplicated transcription regulators can diversify to govern the expression of nonoverlapping sets of genes. 2014. PMID: 24874988


  237. Slabodnick MM, Ruby JG, Dunn JG, Feldman JL, DeRisi JL, Marshall WF. The kinase regulator mob1 acts as a patterning protein for stentor morphogenesis. 2014. PMID: 24823688


  238. Parrish JZ, Kim CC, Tang L, Bergquist S, Wang T, Derisi JL, Jan LY, Jan YN, Davis GW. Krüppel mediates the selective rebalancing of ion channel expression. 2014. PMID: 24811378


  239. Runckel C, DeRisi J, Flenniken ML. A draft genome of the honey bee trypanosomatid parasite Crithidia mellificae. 2014. PMID: 24743507


  240. Rubio CA, Weisburd B, Holderfield M, Arias C, Fang E, DeRisi JL, Fanidi A. Transcriptome-wide characterization of the eIF4A signature highlights plasticity in translation regulation. 2014. PMID: 25273840


  241. Szentiks CA, Tsangaras K, Abendroth B, Scheuch M, Stenglein MD, Wohlsein P, Heeger F, Höveler R, Chen W, Sun W, Damiani A, Nikolin V, Gruber AD, Grobbel M, Kalthoff D, Höper D, Czirják GÁ, Derisi J, Mazzoni CJ, Schüle A, Aue A, East ML, Hofer H, Beer M, Osterrieder N, Greenwood AD. Polar bear encephalitis: establishment of a comprehensive next-generation pathogen analysis pipeline for captive and free-living wildlife. 2013. PMID: 24534459


  242. Koellhoffer JF, Dai Z, Malashkevich VN, Stenglein MD, Liu Y, Toro R, S Harrison J, Chandran K, DeRisi JL, Almo SC, Lai JR. Structural characterization of the glycoprotein GP2 core domain from the CAS virus, a novel arenavirus-like species. 2013. PMID: 24333483


  243. Hernday AD, Lohse MB, Fordyce PM, Nobile CJ, DeRisi JL, Johnson AD. Structure of the transcriptional network controlling white-opaque switching in Candida albicans. 2013. PMID: 23855748


  244. Guler JL, Freeman DL, Ahyong V, Patrapuvich R, White J, Gujjar R, Phillips MA, DeRisi J, Rathod PK. Asexual populations of the human malaria parasite, Plasmodium falciparum, use a two-step genomic strategy to acquire accurate, beneficial DNA amplifications. 2013. PMID: 23717205


  247. Lohse MB, Hernday AD, Fordyce PM, Noiman L, Sorrells TR, Hanson-Smith V, Nobile CJ, DeRisi JL, Johnson AD. Identification and characterization of a previously undescribed family of sequence-specific DNA-binding domains. 2013. PMID: 23610392


  248. Greninger AL, Knudsen GM, Betegon M, Burlingame AL, DeRisi JL. ACBD3 interaction with TBC1 domain 22 protein is differentially affected by enteroviral and kobuviral 3A protein binding. 2013. PMID: 23572552


  249. Abromaitis S, Nelson CS, Previte D, Yoon KS, Clark JM, DeRisi JL, Koehler JE. Bartonella quintana deploys host and vector temperature-specific transcriptomes. 2013. PMID: 23554923


  250. Runckel C, Westesson O, Andino R, DeRisi JL. Identification and manipulation of the molecular determinants influencing poliovirus recombination. 2013. PMID: 23408891


  251. Melters DP, Bradnam KR, Young HA, Telis N, May MR, Ruby JG, Sebra R, Peluso P, Eid J, Rank D, Garcia JF, DeRisi JL, Smith T, Tobias C, Ross-Ibarra J, Korf I, Chan SW. Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. 2013. PMID: 23363705


  252. Vale RD, DeRisi J, Phillips R, Mullins RD, Waterman C, Mitchison TJ. Graduate education. Interdisciplinary graduate training in teaching labs. 2012. PMID: 23258877


  253. Gerver RE, Gómez-Sjöberg R, Baxter BC, Thorn KS, Fordyce PM, Diaz-Botia CA, Helms BA, DeRisi JL. Programmable microfluidic synthesis of spectrally encoded microspheres. 2012. PMID: 23042484


  254. Yu G, Greninger AL, Isa P, Phan TG, Martínez MA, de la Luz Sanchez M, Contreras JF, Santos-Preciado JI, Parsonnet J, Miller S, DeRisi JL, Delwart E, Arias CF, Chiu CY. Discovery of a novel polyomavirus in acute diarrheal samples from children. Volume 7 of Issue 11. 2012. PMID: 23166671


  257. Fordyce PM, Pincus D, Kimmig P, Nelson CS, El-Samad H, Walter P, DeRisi JL. Basic leucine zipper transcription factor Hac1 binds DNA in two distinct modes as revealed by microfluidic analyses. 2012. PMID: 23054834


  258. Holmes TC, May AE, Zaleta-Rivera K, Ruby JG, Skewes-Cox P, Fischbach MA, DeRisi JL, Iwatsuki M, Omura S, Khosla C. Molecular insights into the biosynthesis of guadinomine: a type III secretion system inhibitor. 2012. PMID: 23030602


  259. O'Donoghue AJ, Eroy-Reveles AA, Knudsen GM, Ingram J, Zhou M, Statnekov JB, Greninger AL, Hostetter DR, Qu G, Maltby DA, Anderson MO, Derisi JL, McKerrow JH, Burlingame AL, Craik CS. Global identification of peptidase specificity by multiplex substrate profiling. 2012. PMID: 23023596


  260. Stenglein MD, Velazquez E, Greenacre C, Wilkes RP, Ruby JG, Lankton JS, Ganem D, Kennedy MA, DeRisi JL. Complete genome sequence of an astrovirus identified in a domestic rabbit (Oryctolagus cuniculus) with gastroenteritis. 2012. PMID: 22998755


  261. Lee D, Das Gupta J, Gaughan C, Steffen I, Tang N, Luk KC, Qiu X, Urisman A, Fischer N, Molinaro R, Broz M, Schochetman G, Klein EA, Ganem D, Derisi JL, Simmons G, Hackett J, Silverman RH, Chiu CY. In-depth investigation of archival and prospectively collected samples reveals no evidence for XMRV infection in prostate cancer. Volume 7 of Issue 9. 2012. PMID: 23028701


  263. Lowes D, Pradhan A, Iyer LV, Parman T, Gow J, Zhu F, Furimsky A, Lemoff A, Guiguemde WA, Sigal M, Clark JA, Wilson E, Tang L, Connelly MC, Derisi JL, Kyle DE, Mirsalis J, Guy RK. Lead optimization of antimalarial propafenone analogues. 2012. PMID: 22708838


  264. Yozwiak NL, Skewes-Cox P, Stenglein MD, Balmaseda A, Harris E, DeRisi JL. Virus identification in unknown tropical febrile illness cases using deep sequencing. 2012. PMID: 22347512


  266. Greninger AL, Knudsen GM, Betegon M, Burlingame AL, Derisi JL. The 3A protein from multiple picornaviruses utilizes the golgi adaptor protein ACBD3 to recruit PI4KIIIβ. 2012. PMID: 22258260


  267. Core A, Runckel C, Ivers J, Quock C, Siapno T, Denault S, Brown B, Derisi J, Smith CD, Hafernik J. A new threat to honey bees, the parasitic phorid fly Apocephalus borealis. 2012. PMID: 22235317


  268. Anderson CM, Chen SY, Dimon MT, Oke A, DeRisi JL, Fung JC. ReCombine: a suite of programs for detection and analysis of meiotic recombination in whole-genome datasets. 2011. PMID: 22046241


  269. Lowes DJ, Guiguemde WA, Connelly MC, Zhu F, Sigal MS, Clark JA, Lemoff AS, Derisi JL, Wilson EB, Guy RK. Optimization of propafenone analogues as antimalarial leads. 2011. PMID: 21955244


  270. Hwang JY, Kawasuji T, Lowes DJ, Clark JA, Connelly MC, Zhu F, Guiguemde WA, Sigal MS, Wilson EB, Derisi JL, Guy RK. Synthesis and evaluation of 7-substituted 4-aminoquinoline analogues for antimalarial activity. 2011. PMID: 21910466


  271. Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol I, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B. Assemblathon 1: a competitive assessment of de novo short read assembly methods. 2011. PMID: 21926179


  273. Runckel C, Flenniken ML, Engel JC, Ruby JG, Ganem D, Andino R, DeRisi JL. Temporal analysis of the honey bee microbiome reveals four novel viruses and seasonal prevalence of known viruses, Nosema, and Crithidia. 2011. PMID: 21687739


  274. Arron ST, Skewes-Cox P, Do PH, Dybbro E, Da Costa M, Palefsky JM, Derisi JL. Validation of a diagnostic microarray for human papillomavirus: coverage of 102 genotypes. 2011. PMID: 21785699


  275. Chen EC, Miller SA, DeRisi JL, Chiu CY. Using a pan-viral microarray assay (Virochip) to screen clinical samples for viral pathogens. of Issue 50. 2011. PMID: 21559002


  277. Wootton SC, Kim DS, Kondoh Y, Chen E, Lee JS, Song JW, Huh JW, Taniguchi H, Chiu C, Boushey H, Lancaster LH, Wolters PJ, DeRisi J, Ganem D, Collard HR. Viral infection in acute exacerbation of idiopathic pulmonary fibrosis. 2011. PMID: 21471095


  278. Sun JC, Lopez-Verges S, Kim CC, DeRisi JL, Lanier LL. NK cells and immune "memory". 2011. PMID: 21289313


  280. Zhang Y, Anderson M, Weisman JL, Lu M, Choy CJ, Boyd VA, Price J, Sigal M, Clark J, Connelly M, Zhu F, Guiguemde WA, Jeffries C, Yang L, Lemoff A, Liou AP, Webb TR, Derisi JL, Guy RK. Evaluation of Diarylureas for Activity Against Plasmodium falciparum. 2010. PMID: 21243104


  282. Fordyce PM, Gerber D, Tran D, Zheng J, Li H, DeRisi JL, Quake SR. De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis. 2010. PMID: 20802496


  283. Greninger AL, Holtz L, Kang G, Ganem D, Wang D, DeRisi JL. Serological evidence of human klassevirus infection. 2010. PMID: 20739504


  284. Raghav R, Taylor M, Delay J, Ojkic D, Pearl DL, Kistler AL, Derisi JL, Ganem D, Smith DA. Avian bornavirus is present in many tissues of psittacine birds with histopathologic evidence of proventricular dilatation disease. 2010. PMID: 20622218


  285. Yozwiak NL, Skewes-Cox P, Gordon A, Saborio S, Kuan G, Balmaseda A, Ganem D, Harris E, DeRisi JL. Human enterovirus 109: a novel interspecies recombinant enterovirus isolated from a case of acute pediatric respiratory illness in Nicaragua. 2010. PMID: 20592079


  286. Ganem D, Kistler A, DeRisi J. Achalasia and viral infection: new insights from veterinary medicine. 2010. PMID: 20505212


  287. Guiguemde WA, Shelat AA, Bouck D, Duffy S, Crowther GJ, Davis PH, Smithson DC, Connelly M, Clark J, Zhu F, Jiménez-Díaz MB, Martinez MS, Wilson EB, Tripathi AK, Gut J, Sharlow ER, Bathurst I, El Mazouni F, Fowble JW, Forquer I, McGinley PL, Castro S, Angulo-Barturen I, Ferrer S, Rosenthal PJ, Derisi JL, Sullivan DJ, Lazo JS, Roos DS, Riscoe MK, Phillips MA, Rathod PK, Van Voorhis WC, Avery VM, Guy RK. Chemical genetics of Plasmodium falciparum. 2010. PMID: 20485428


  288. Ray S, Madrid PB, Catz P, LeValley SE, Furniss MJ, Rausch LL, Guy RK, DeRisi JL, Iyer LV, Green CE, Mirsalis JC. Development of a new generation of 4-aminoquinoline antimalarial compounds using predictive pharmacokinetic and toxicology models. 2010. PMID: 20361799


  290. Chiu CY, Greninger AL, Chen EC, Haggerty TD, Parsonnet J, Delwart E, Derisi JL, Ganem D. Cultivation and serological characterization of a human Theiler's-like cardiovirus associated with diarrheal disease. Volume 84 of Issue 9. 2010. PMID: 20164225


  291. Kim CC, Wilson EB, DeRisi JL. Improved methods for magnetic purification of malaria parasites and haemozoin. 2010. PMID: 20074366


  294. Webster DR, Hekele AG, Lauring AS, Fischer KF, Li H, Andino R, DeRisi JL. An enhanced single base extension technique for the analysis of complex viral populations. 2009. PMID: 19834618


  296. Arico-Muendel C, Centrella PA, Contonio BD, Morgan BA, O'Donovan G, Paradise CL, Skinner SR, Sluboski B, Svendsen JL, White KF, Debnath A, Gut J, Wilson N, McKerrow JH, DeRisi JL, Rosenthal PJ, Chiang PK. Antiparasitic activities of novel, orally available fumagillin analogs. 2009. PMID: 19648008


  297. Gancz AY, Kistler AL, Greninger AL, Farnoushi Y, Mechani S, Perl S, Berkowitz A, Perez N, Clubb S, DeRisi JL, Ganem D, Lublin A. Experimental induction of proventricular dilatation disease in cockatiels (Nymphicus hollandicus) inoculated with brain homogenates containing avian bornavirus 4. 2009. PMID: 19589169


  298. Greninger AL, Runckel C, Chiu CY, Haggerty T, Parsonnet J, Ganem D, DeRisi JL. The complete genome of klassevirus - a novel picornavirus in pediatric stool. Volume 6. 2009. PMID: 19538752


  299. Sorber K, Chiu C, Webster D, Dimon M, Ruby JG, Hekele A, DeRisi JL. The long march: a sample preparation technique that enhances contig length and coverage by high-throughput short-read sequencing. Volume 3 of Issue 10. 2008. PMID: 18941527


  300. Kim CC, Parikh S, Sun JC, Myrick A, Lanier LL, Rosenthal PJ, DeRisi JL. Experimental malaria infection triggers early expansion of natural killer cells. 2008. PMID: 18824529


  301. Chiu CY, Greninger AL, Kanada K, Kwok T, Fischer KF, Runckel C, Louie JK, Glaser CA, Yagi S, Schnurr DP, Haggerty TD, Parsonnet J, Ganem D, DeRisi JL. Identification of cardioviruses related to Theiler's murine encephalomyelitis virus in human infections. Volume 105 of Issue 37. 2008. PMID: 18768820


  302. Kistler AL, Gancz A, Clubb S, Skewes-Cox P, Fischer K, Sorber K, Chiu CY, Lublin A, Mechani S, Farnoushi Y, Greninger A, Wen CC, Karlene SB, Ganem D, DeRisi JL. Recovery of divergent avian bornaviruses from cases of proventricular dilatation disease: identification of a candidate etiologic agent. Volume 5. 2008. PMID: 18671869


  303. Chang HH, Falick AM, Carlton PM, Sedat JW, DeRisi JL, Marletta MA. N-terminal processing of proteins exported by malaria parasites. 2008. PMID: 18534695


  304. Chiu CY, Urisman A, Greenhow TL, Rouskin S, Yagi S, Schnurr D, Wright C, Drew WL, Wang D, Weintrub PS, Derisi JL, Ganem D. Utility of DNA microarrays for detection of viruses in acute respiratory tract infections in children. Volume 153 of Issue 1. 2008. PMID: 18571541


  305. Kistler A, Avila PC, Rouskin S, Wang D, Ward T, Yagi S, Schnurr D, Ganem D, DeRisi JL, Boushey HA. Pan-viral screening of respiratory tract infections in adults with and without asthma reveals unexpected human coronavirus and human rhinovirus diversity. 2007. PMID: 17703411


  306. Chiu CY, Alizadeh AA, Rouskin S, Merker JD, Yeh E, Yagi S, Schnurr D, Patterson BK, Ganem D, DeRisi JL. Diagnosis of a critical respiratory illness caused by human metapneumovirus by use of a pan-virus microarray. Volume 45 of Issue 7. 2007. PMID: 17494722


  307. Kistler AL, Webster DR, Rouskin S, Magrini V, Credle JJ, Schnurr DP, Boushey HA, Mardis ER, Li H, DeRisi JL. Genome-wide diversity and selective pressure in the human rhinovirus. 2007. PMID: 17477878


  308. Jambhekar A, Derisi JL. Cis-acting determinants of asymmetric, cytoplasmic RNA transport. 2007. PMID: 17449729


  309. Dong B, Kim S, Hong S, Das Gupta J, Malathi K, Klein EA, Ganem D, Derisi JL, Chow SA, Silverman RH. An infectious retrovirus susceptible to an IFN antiviral pathway from human prostate tumors. 2007. PMID: 17234809


  310. Jolly ER, Chin CS, Miller S, Bahgat MM, Lim KC, DeRisi J, McKerrow JH. Gene expression patterns during adaptation of a helminth parasite to different environmental niches. 2007. PMID: 17456242


  313. Xiao M, Phong A, Ha C, Chan TF, Cai D, Leung L, Wan E, Kistler AL, DeRisi JL, Selvin PR, Kwok PY. Rapid DNA mapping by fluorescent single molecule detection. 2006. PMID: 17175538


  314. Chiu CY, Rouskin S, Koshy A, Urisman A, Fischer K, Yagi S, Schnurr D, Eckburg PB, Tompkins LS, Blackburn BG, Merker JD, Patterson BK, Ganem D, DeRisi JL. Microarray detection of human parainfluenzavirus 4 infection associated with respiratory failure in an immunocompetent adult. Volume 43 of Issue 8. 2006. PMID: 16983602


  315. Dahl EL, Shock JL, Shenai BR, Gut J, DeRisi JL, Rosenthal PJ. Tetracyclines specifically target the apicoplast of the malaria parasite Plasmodium falciparum. 2006. PMID: 16940111


  317. Weisman JL, Liou AP, Shelat AA, Cohen FE, Guy RK, DeRisi JL. Searching for new antimalarial therapeutics amongst known drugs. 2006. PMID: 16882315


  318. Newman JR, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, DeRisi JL, Weissman JS. Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. 2006. PMID: 16699522


  319. Urisman A, Molinaro RJ, Fischer N, Plummer SJ, Casey G, Klein EA, Malathi K, Magi-Galluzzi C, Tubbs RR, Ganem D, Silverman RH, DeRisi JL. Identification of a novel Gammaretrovirus in prostate tumors of patients homozygous for R462Q RNASEL variant. 2006. PMID: 16609730


  320. Llinás M, Bozdech Z, Wong ED, Adai AT, DeRisi JL. Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains. 2006. PMID: 16493140


  322. Jambhekar A, McDermott K, Sorber K, Shepard KA, Vale RD, Takizawa PA, DeRisi JL. Unbiased selection of localization elements reveals cis-acting determinants of mRNA bud localization in Saccharomyces cerevisiae. 2005. PMID: 16326802


  323. Anderson MO, Sherrill J, Madrid PB, Liou AP, Weisman JL, DeRisi JL, Guy RK. Parallel synthesis of 9-aminoacridines and their evaluation against chloroquine-resistant Plasmodium falciparum. 2005. PMID: 16216519


  324. Silvestrini F, Bozdech Z, Lanfrancotti A, Di Giulio E, Bultrini E, Picci L, Derisi JL, Pizzi E, Alano P. Genome-wide identification of genes upregulated at the onset of gametocytogenesis in Plasmodium falciparum. 2005. PMID: 16026866


  325. Urisman A, Fischer KF, Chiu CY, Kistler AL, Beck S, Wang D, DeRisi JL. E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns. Volume 6 of Issue 9. 2005. PMID: 16168085


  327. Madrid PB, Sherrill J, Liou AP, Weisman JL, Derisi JL, Guy RK. Synthesis of ring-substituted 4-aminoquinolines and evaluation of their antimalarial activities. 2005. PMID: 15686903


  328. Galgoczy DJ, Cassidy-Stone A, Llinás M, O'Rourke SM, Herskowitz I, DeRisi JL, Johnson AD. Genomic dissection of the cell-type-specification circuit in Saccharomyces cerevisiae. 2004. PMID: 15604142


  330. Glynn EF, Megee PC, Yu HG, Mistrot C, Unal E, Koshland DE, DeRisi JL, Gerton JL. Genome-wide mapping of the cohesin complex in the yeast Saccharomyces cerevisiae. 2004. PMID: 15309048


  331. Weber SA, Gerton JL, Polancic JE, DeRisi JL, Koshland D, Megee PC. The kinetochore is an enhancer of pericentric cohesin binding. 2004. PMID: 15309047


  332. Madrid PB, Wilson NT, DeRisi JL, Guy RK. Parallel synthesis and antimalarial screening of a 4-aminoquinoline library. 2004. PMID: 15132606


  333. Wang D, Urisman A, Liu YT, Springer M, Ksiazek TG, Erdman DD, Mardis ER, Hickenbotham M, Magrini V, Eldred J, Latreille JP, Wilson RK, Ganem D, DeRisi JL. Viral discovery and sequence recovery using DNA microarrays. 2003. PMID: 14624234


  334. Shepard KA, Gerber AP, Jambhekar A, Takizawa PA, Brown PO, Herschlag D, DeRisi JL, Vale RD. Widespread cytoplasmic mRNA transport in yeast: identification of 22 bud-localized transcripts using DNA microarray analysis. 2003. PMID: 13679573


  335. Bozdech Z, Llinás M, Pulliam BL, Wong ED, Zhu J, DeRisi JL. The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. 2003. PMID: 12929205


  336. Rota PA, Oberste MS, Monroe SS, Nix WA, Campagnoli R, Icenogle JP, Peñaranda S, Bankamp B, Maher K, Chen MH, Tong S, Tamin A, Lowe L, Frace M, DeRisi JL, Chen Q, Wang D, Erdman DD, Peret TC, Burns C, Ksiazek TG, Rollin PE, Sanchez A, Liffick S, Holloway B, Limor J, McCaustland K, Olsen-Rasmussen M, Fouchier R, Günther S, Osterhaus AD, Drosten C, Pallansch MA, Anderson LJ, Bellini WJ. Characterization of a novel coronavirus associated with severe acute respiratory syndrome. 2003. PMID: 12730500


  337. Ksiazek TG, Erdman D, Goldsmith CS, Zaki SR, Peret T, Emery S, Tong S, Urbani C, Comer JA, Lim W, Rollin PE, Dowell SF, Ling AE, Humphrey CD, Shieh WJ, Guarner J, Paddock CD, Rota P, Fields B, DeRisi J, Yang JY, Cox N, Hughes JM, LeDuc JW, Bellini WJ, Anderson LJ, SARS Working Group. A novel coronavirus associated with severe acute respiratory syndrome. 2003. PMID: 12690092


  338. Smith CD, Smith DL, DeRisi JL, Blackburn EH. Telomeric protein distributions and remodeling through the cell cycle in Saccharomyces cerevisiae. 2003. PMID: 12589054


  339. Bozdech Z, Zhu J, Joachimiak MP, Cohen FE, Pulliam B, DeRisi JL. Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. 2003. PMID: 12620119


  340. Greenbaum DC, Baruch A, Grainger M, Bozdech Z, Medzihradszky KF, Engel J, DeRisi J, Holder AA, Bogyo M. A role for the protease falcipain 1 in host cell invasion by the human malaria parasite. 2002. PMID: 12471262


  341. Wang D, Coscoy L, Zylberberg M, Avila PC, Boushey HA, Ganem D, DeRisi JL. Microarray-based detection and genotyping of viral pathogens. 2002. PMID: 12429852


  343. Nautiyal S, DeRisi JL, Blackburn EH. The genome-wide expression response to telomerase deletion in Saccharomyces cerevisiae. 2002. PMID: 12084816


  345. Rathod PK, Ganesan K, Hayward RE, Bozdech Z, DeRisi JL. DNA microarrays for malaria. 2002. PMID: 11850013


  346. DeRisi J. Overview of nucleic acid arrays. 2001. PMID: 18428485


  347. Carroll AS, Bishop AC, DeRisi JL, Shokat KM, O'Shea EK. Chemical inhibition of the Pho85 cyclin-dependent kinase reveals a role in the environmental stress response. 2001. PMID: 11675494


  349. Derisi J. Overview of nucleic acid arrays. 2001. PMID: 18265199


  350. Miki R, Kadota K, Bono H, Mizuno Y, Tomaru Y, Carninci P, Itoh M, Shibata K, Kawai J, Konno H, Watanabe S, Sato K, Tokusumi Y, Kikuchi N, Ishii Y, Hamaguchi Y, Nishizuka I, Goto H, Nitanda H, Satomi S, Yoshiki A, Kusakabe M, DeRisi JL, Eisen MB, Iyer VR, Brown PO, Muramatsu M, Shimada H, Okazaki Y, Hayashizaki Y. Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays. 2001. PMID: 11226216


  354. Gerton JL, DeRisi J, Shroff R, Lichten M, Brown PO, Petes TD. Global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae. 2000. PMID: 11027339


  355. Khodursky AB, Peter BJ, Schmid MB, DeRisi J, Botstein D, Brown PO, Cozzarelli NR. Analysis of topoisomerase function in bacterial replication fork movement: use of DNA microarrays. 2000. PMID: 10944214


  356. DeRisi J, van den Hazel B, Marc P, Balzi E, Brown P, Jacq C, Goffeau A. Genome microarray analysis of transcriptional activation in multidrug resistance yeast mutants. 2000. PMID: 10734226


  357. Hayward RE, Derisi JL, Alfadhli S, Kaslow DC, Brown PO, Rathod PK. Shotgun DNA microarrays and stage-specific gene expression in Plasmodium falciparum malaria. 2000. PMID: 10632873


  358. Wilson M, DeRisi J, Kristensen HH, Imboden P, Rane S, Brown PO, Schoolnik GK. Exploring drug-induced alterations in gene expression in Mycobacterium tuberculosis by microarray hybridization. 1999. PMID: 10536008


  359. DeRisi JL, Iyer VR. Genomics and array technology. 1999. PMID: 9914882


  360. Lutfiyya LL, Iyer VR, DeRisi J, DeVit MJ, Brown PO, Johnston M. Characterization of three related glucose repressors and genes they regulate in Saccharomyces cerevisiae. 1998. PMID: 9832517


  361. Marton MJ, DeRisi JL, Bennett HA, Iyer VR, Meyer MR, Roberts CJ, Stoughton R, Burchard J, Slade D, Dai H, Bassett DE, Hartwell LH, Brown PO, Friend SH. Drug target validation and identification of secondary drug target effects using DNA microarrays. 1998. PMID: 9809554


  362. Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown PO, Herskowitz I. The transcriptional program of sporulation in budding yeast. 1998. PMID: 9784122


  364. Lashkari DA, DeRisi JL, McCusker JH, Namath AF, Gentile C, Hwang SY, Brown PO, Davis RW. Yeast microarrays for genome wide parallel genetic and gene expression analysis. 1997. PMID: 9371799


  366. DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, Chen Y, Su YA, Trent JM. Use of a cDNA microarray to analyse gene expression patterns in human cancer. 1996. PMID: 8944026


  367. Peck LJ, Bartilson M, DeRisi JL. Bead-shift isolation of protein--DNA complexes on a 5S RNA gene. 1994. PMID: 8127682