IL-6 underlies microenvironment immunosuppression and resistance to therapy in glioblastoma
Young JS, Cho NW, Lucas CG, Najem H, Mirchia K, Chen WC, Seo K, Zakimi N, Daggubati V, Casey-Clyde T, Nguyen MP, Chen A, Phillips JJ, Ozawa T, Aghi MK, Taylor JW, DeRisi JL, Bhaduri A, Berger MS, Heimberger AB, Butowski N, Spitzer MH, Raleigh DR

bioRxiv, 2025

A Trypanosoma cruzi Trans-Sialidase Peptide Demonstrates High Serological Prevalence Among Infected Populations Across Endemic Regions of Latin America
Kortbawi HM, Marczak RJ, Rajan JV, Bulaong NL, Pak JE, Wu W, Wang G, Mitchell A, Saxena A, Maheshwari A, Fleischmann CJ, Kelly EA, Teal E, Townsend RL, Stramer SL, Okamoto EE, Sherbuk JE, Clark EH, Gilman RH, Colanzi R, Gennatas ED, Bern C, DeRisi JL, Whitman JD

medRxiv, 2025

Proteomic profiling of the local and systemic immune response to pediatric respiratory viral infections
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

American Society for Microbiology, 2025

Endogenous antigens shape the transcriptome and TCR repertoire in an autoimmune arthritis model
McCarthy EE, Yu S, Perlmutter N, Nakao Y, Naito R, Lin C, Riekher V, DeRisi J, Ye CJ, Weiss A, Ashouri JF

The Journal of Clinical Investigation, 2024

Total Syntheses of Cyclomarin and Metamarin Natural Products
Fan FeiShichun LunAditi SaxenaMadhura RaghavanJoseph L. DeRisiWilliam R. BishaiJason K. Sello

Organic Letters, 2024

Remoscope: a label-free imaging cytometer for malaria diagnostics
Lebel PM, Jeyakumar I, Khoo MWL, Charlton C, Saxena A, Jacobsen A, James E, Huynh E, Wu W, Courville G, Fu PC, Raghavan M, Puccinelli R, Peter O, Dorsey G, Rosenthal P, DeRisi J, Gomez-Sjoberg R

medRxiv, 2025

Microbial dynamics and pulmonary immune responses in COVID-19 secondary bacterial pneumonia
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.

Nature Portfolio, 2024

Climate, demography, immunology, and virology combine to drive two decades of dengue virus dynamics in Cambodia
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

PNAS, 2024

Anti-RGS8 paraneoplastic cerebellar ataxia is preferentially associated with a particular subtype of Hodgkin's lymphoma
Elise Peter, Nicolas Lundahl Ciano-Petersen, Le-Duy Do, Jimmy Perrot, Thomas Ngo, John Pluvinage, Christopher M. Bartley, Kelsey C. Zorn, Ramona Miske, Madeleine Scharf, Macarena Villagrán-García, Antonio Farina, Véronique Rogemond, Jean-Christophe Antoine, Christine Tranchant, Valérie Dubois, Joseph L. DeRisi, Samuel J. Pleasure, Michael R. Wilson, Jeffrey M. Gelfand, Alexandra Traverse-Glehen, Jérôme Honnorat & Virginie Desestret

Springer Nature, 2024

Molecular mimicry in multisystem inflammatory syndrome in children
Aaron Bodansky, Robert C. Mettelman, Joseph J. Sabatino, Jr, Sara E. Vazquez, Janet Chou, Tanya Novak, Kristin L. Moffitt, Haleigh S. Miller, Andrew F. Kung, Elze Rackaityte, Colin R. Zamecnik, Jayant V. Rajan, Hannah Kortbawi, Caleigh Mandel-Brehm, Anthea Mitchell, Chung-Yu Wang, Aditi Saxena, Kelsey Zorn, David J. L. Yu, Mikhail V. Pogorelyy, Walid Awad, Allison M. Kirk, James Asaki, John V. Pluvinage, Michael R. Wilson, Laura D. Zambrano, Angela P. Campbell, Overcoming COVID-19 Network Investigators, Paul G. Thomas, Adrienne G. Randolph, Mark S. Anderson, corresponding author and Joseph L. DeRisi corresponding author

Nature Portfolio, 2024

Phage Immunoprecipitation-Sequencing Reveals CDHR5 Autoantibodies in Select Patients With Interstitial Lung Disease
Vaibhav Upadhyay, Young me Yoon, Sara E. Vazquez, Tania E. Velez, Kirk D. Jones, Cathryn T. Lee, Christopher S. Law, Paul J. Wolters, Seoyeon Lee, Monica M. Yang, Erica Farrand, Imre Noth, Mary E. Strek, Mark S. Anderson, Joseph L. DeRisi, Anne I. Sperling, Anthony K. Shum

American College of Rheumatology, 2024

Transcobalamin receptor antibodies in autoimmune vitamin B12 central deficiency
John V. Pluvinage,, Thomas Ngo,, Camille Fouassier,, Maura McDonagh,, Brandon B. Holmes,, Christopher M. Bartley,†, Sravani Kondapavulur,, Charlotte Hurabielle, Aaron Bodansky, Vincent Pai, Sam Hinman, Ava Aslanpour, Bonny D. Alvarenga,, Kelsey C. Zorn, Colin Zamecnik,, Adrian McCann, Andoni I. Asencor,, Trung Huynh,, Weston Browne,, Asritha Tubati,, Michael S. Haney, Vanja C. Douglas,, Martineau Louine,, Bruce A.C. Cree,, Stephen L. Hauser,, William Seeley,, Sergio E. Baranzini,, James A. Wells, Serena Spudich, Shelli Farhadian, Prashanth S. Ramachandran,, Leslie Gillum, Chadwick M. Hales, Julie Zikherman, Mark S. Anderson,, Jinoos Yazdany, Bryan Smith, Avindra Nath, Gina Suh, Eoin P. Flanagan, Ari J. Green,, Ralph Green, Jeffrey M. Gelfand,, Joseph L. DeRisi,, Samuel J. Pleasure,, Michael R. Wilson

Sci Tran Med 2024

Optimization of diastereomeric dihydropyridines as antimalarials
Kurt S Van Horn, Yingzhao Zhao, Prakash T Parvatkar, Julie Maier, Tina Mutka, Alexis Lacrue, Fabian Brockmeier, Daniel Ebert, Wesley Wu, Debora R Casandra, Niranjan Namelikonda, Jeanine Yacoub, Martina Sigal, Spencer Knapp, David Floyd, David Waterson, Jeremy N Burrows, James Duffy, Joseph L DeRisi, Dennis E Kyle, R Kiplin Guy, Roman Manetsch

Elsevier, 2024

Pathobiological signatures of dysbiotic lung injury in pediatric patients undergoing stem cell transplantation
Matt S. Zinter, Christopher C. Dvorak, Madeline Y. Mayday, Gustavo Reyes, Miriam R. Simon, Emma M. Pearce, Hanna Kim, Peter J. Shaw, Courtney M. Rowan, Jeffrey J. Auletta, Paul L. Martin, Kamar Godder, Christine N. Duncan, Nahal R. Lalefar, Erin M. Kreml, Janet R. Hume, Hisham Abdel-Azim, Caitlin Hurley, Geoffrey D. E. Cuvelier, Amy K. Keating, Muna Qayed, James S. Killinger, Julie C. Fitzgerald, Rabi Hanna, the Pediatric Transplantation and Cell Therapy Consortium

Nature Portfolio, 2024

Unveiling the proteome-wide autoreactome enables enhanced evaluation of emerging CAR T cell therapies in autoimmunity
Aaron Bodansky, David Jl Yu, Alysa Rallistan, Muge Kalaycioglu, Jim Boonyaratanakornkit, Damian J Green, Jordan Gauthier, Cameron J Turtle, Kelsey Zorn, Brian O'Donovan, Caleigh Mandel-Brehm, James Asaki, Hannah Kortbawi, Andrew F Kung, Elze Rackaityte, Chung-Yu Wang, Aditi Saxena, Kimberly de Dios, Gianvito Masi, Richard J Nowak, Kevin C O'Connor, Hao Li, Valentina E Diaz, Rowan Saloner, Kaitlin B Casaletto, Eva Q Gontrum, Brandon Chan, Joel H Kramer, Michael R Wilson, Paul J Utz, Joshua A Hill, Shaun W Jackson,Mark S Anderson, Joseph L DeRisi

J Clin Invest 2024

An autoantibody signature predictive for multiple sclerosis
Colin R Zamecnik , Gavin M Sowa , Ahmed Abdelhak, Ravi Dandekar, Rebecca D Bair, Kristen J Wade, Christopher M Bartley, Kerry Kizer, Danillo G Augusto, Asritha Tubati, Refujia Gomez, Camille Fouassier, Chloe Gerungan, Colette M Caspar, Jessica Alexander, Anne E Wapniarski, Rita P Loudermilk, Erica L Eggers, Kelsey C Zorn, Kirtana Ananth, Nora Jabassini, Sabrina A Mann, Nicholas R Ragan, Adam Santaniello, Roland G Henry, Sergio E Baranzini, Scott S Zamvil, Joseph J Sabatino Jr, Riley M Bove, Chu-Yueh Guo, Jeffrey M Gelfand, Richard Cuneo, H-Christian von Büdingen, Jorge R Oksenberg, Bruce A C Cree, Jill A Hollenbach, Ari J Green, Stephen L Hauser, Mitchell T Wallin, Joseph L DeRisi, Michael R Wilson

Nat Med 2024

Phage Immunoprecipitation-Sequencing Reveals CDHR5 Autoantibodies in Select Patients With Interstitial Lung Disease
Vaibhav Upadhyay, Young me Yoon, Sara E. Vazquez, Tania E. Velez, Kirk D. Jones, Cathryn T. Lee, Christopher S. Law, Paul J. Wolters, Seoyeon Lee, Monica M. Yang, Erica Farrand, Imre Noth, Mary E. Strek, Mark S. Anderson, Joseph L. DeRisi, Anne I. Sperling, Anthony K. Shum

American College of Rheumatology, 2024

An autoantibody signature predictive for multiple sclerosis
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 Jr, 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

Nature Medicine, 2024

Challenges and advances in the medical treatment of granulomatous amebic encephalitis
Natasha Spottiswoode, Julia C. Haston, Natasha W. Hanners, Katherine Gruenberg , Annie Kim, Joseph L. DeRisi and Michael R. Wilson

Sage Journals, 2024

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
Christina M Osborne, Charles Langelier Jack Kamm, Kayla Williamson, Lilliam Ambroggio, Ron W Reeder, Christopher Locandro, J Kirk Harris, Brandie D Wagner, Aline B Maddux, Saharai Caldera, Amy Lyden, Victoria Soesanto, Eric A F Simoes 2, Matthew K Leroue, Todd C Carpenter, Mark W Hall, Athena F Zuppa, Joseph A Carcillo, Kathleen L Meert, Murray M Pollack, Patrick S McQuillen, Daniel A Notterman, Joseph DeRisi, Peter M Mourani, National Institute for Child Health and Human Development Collaborative Pediatric Critical Care Research Network

Society of Pediatric Critical Care Medicine, 2024

The antibiotic resistance reservoir of the lung microbiome expands with age in a population of critically ill patients
Victoria T. Chu, Alexandra Tsitsiklis, Eran Mick, Lilliam Ambroggio, Katrina L. Kalantar, Abigail Glascock, Christina M. Osborne, Brandie D. Wagner, Michael A. Matthay, Joseph L. DeRisi, Carolyn S. Calfee, Peter M. Mourani & Charles R. Langelier

Nature Journal, 2023

Vaccine breakthrough hypoxemic COVID-19 pneumonia in patients with auto-Abs neutralizing type I IFNs
Paul Bastard, Sara E Vazquez, Jamin Liu, Matthew T Laurie,...... Joseph L DeRisi

Science Immunology, 2023

Detection of High-Risk Paraneoplastic Antibodies against TRIM9 and TRIM67 Proteins
Christopher M. Bartley MD, PhD, Thomas T. Ngo BS, Le Duy Do PhD, Anastasia Zekeridou MD, PhD, Ravi Dandekar BS, MS, Sergio Muñiz-Castrillo MD, PhD, Bonny D. Alvarenga BA, Kelsey C. Zorn BA, MHS, Asritha Tubati BS, Anne-Laurie Pinto MSc, Weston D. Browne BS, Patrick W. Hullett MD, PhD, Mark Terrelonge MD, MPH, Ryan D. Schubert MD, Amanda L. Piquet MD, Binxia Yang PhD, Mayra Montalvo MD, Andrew F. Kung BA, Sabrina A. Mann BS, Maulik P. Shah MD, MHS, Michael D. Geschwind MD, PhD, Jeffrey M. Gelfand MD, MAS, Joseph L. DeRisi PhD, Sean J. Pittock MD, Jérôme Honnorat MD, PhD, Samuel J. Pleasure MD, PhD, Michael R. Wilson MD, PhD

Annuls of Neurology, 2023

Validation of a murine proteome-wide phage display library for identification of autoantibody specificities
Elze Rackaityte, Irina Proekt, Haleigh S. Miller, Akshaya Ramesh, Jeremy F. Brooks, Andrew F. Kung, Caleigh Mandel-Brehm, David Yu, Colin R. Zamecnik, Rebecca Bair, Sara E. Vazquez, Sara Sunshine, Clare L. Abram, Clifford A. Lowell, Gabrielle Rizzuto, Michael R. Wilson, Julie Zikherman, Mark S. Anderson, and Joseph L. DeRis

JCI Insight, 2023

Whole-genome sequencing rule-out of suspected hospital-onset Rhizopus outbreaks
Victoria T. Chu Open the ORCID record for Victoria T. Chu[Opens in a new window] , Saba Nafees Open the ORCID record for Saba Nafees[Opens in a new window] , Eric Waltari Open the ORCID record for Eric Waltari[Opens in a new window] , Nicole McNeil Open the ORCID record for Nicole McNeil[Opens in a new window] , Carolyn Caughell , Estella Sanchez-Guerrero , Lusha Wang , Kim Stanley , Gail Cunningham , Joan Wong Open the ORCID record for Joan Wong[Opens in a new window] , Maíra Phelps , Cristina M. Tato , Steve Miller , Joseph L. DeRisi , Deborah S. Yokoe , Lynn Ramirez-Avila and Charles R. Langelier

Cambridge University Press, 2023

Implementation of California COVIDNet - a multi-sector collaboration for statewide SARS-CoV-2 genomic surveillance
Debra A Wadford, Nikki Baumrind, Elizabeth F Baylis, John M Bell, Ellen L Bouchard, Megan Crumpler, Eric M Foote, Sabrina Gilliam, Carol A Glaser, Jill K Hacker, Katya Ledin, Sharon L Messenger, Christina Morales, Emily A Smith, Joel R Sevinsky, Russell B Corbett-Detig, Joseph DeRisi, Kathleen Jacobson

Frontiers in Public Health, 2023

Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq.
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.

Nature Communications, 2023

Broad susceptibility of Candida auris strains to 8-hydroxyquinolines and mechanisms of resistance
Matthew B Lohse, Matthew T Laurie, Sophia Levan 3, Naomi Ziv, Craig L Ennis, Clarissa J Nobile, Joseph DeRisi, Alexander D Johnson

American Society for Microbiology, 2023

Viral co-infection, autoimmunity, and CSF HIV antibody profiles in HIV central nervous system escape
I A Hawes, B D Alvarenga, W Browne, A Wapniarski, R Dandekar, C M Bartley, G M Sowa, J L DeRisi, P Cinque, A N Dravid, S J Pleasure, M Gisslen, R W Price, M R Wilson

Elsevier, 2023

In host evolution of beta lactam resistance during active treatment for Pseudomonas aeruginosa bacteremia
Natasha Spottiswoode, Samantha Hao, Estella Sanchez-Guerrero, Angela M Detweiler, Honey Mekonen, Norma Neff, Henriette Macmillan, Brian S Schwartz, Joanne Engel, Joseph L DeRisi, Steven A Miller, Charles R Langelier

Frontiers, 2023

Rubella virus tropism and single-cell responses in human primary tissue and microglia-containing organoids
Galina Popova, Hanna Retallack, Chang N Kim, Albert WangDavid Shin, Joseph L DeRisi, Tomasz Nowakowsk

eLife, 2023

Autoantigen profiling reveals a shared post-COVID signature in fully recovered and long COVID patients
Aaron Bodansky, Chung-Yu Wang, Aditi Saxena, Anthea Mitchell, Andrew F. Kung, Saki Takahashi, Khamal Anglin, Beatrice Huang, Rebecca Hoh, Scott Lu, Sarah A. Goldberg, Justin Romero, Brandon Tran, Raushun Kirtikar, Halle Grebe, Matthew So, Bryan Greenhouse, Matthew S. Durstenfeld, Priscilla Y. Hsue, Joanna Hellmuth, J. Daniel Kelly, Jeffrey N. Martin, Mark S. Anderson, Steven G. Deeks, Timothy J. Henrich, Joseph L. DeRisi, Michael J. Peluso

JCI Insight, 2023

Integrated host/microbe metagenomics enables accurate lower respiratory tract infection diagnosis in critically ill children
Eran Mick, Alexandra Tsitsiklis, Jack Kamm, Katrina L Kalantar, Saharai Caldera, Amy Lyden, Michelle Tan 1, Angela M Detweiler 1, Norma Neff 1, Christina M Osborne 5, Kayla M Williamson 6, Victoria Soesanto 6, Matthew Leroue 5, Aline B Maddux 5, Eric Af Simões 5, Todd C Carpenter 5, Brandie D Wagner 5 6, Joseph L DeRisi 1 7, Lilliam Ambroggio 5, Peter M Mourani 5 8, Charles R Langelier

JCI, 2023

Field assessment of BinaxNOW antigen tests as COVID-19 treatment entry point at a community testing site in San Francisco during evolving omicron surges
John Schrom, Carina Marquez, Chung-Yu Wang, Aditi Saxena, Anthea M. Mitchell, Salu Ribeiro, Genay Pilarowski, Robert Nakamura, Susana Rojas, Douglas Black, Maria G. Contreras Oseguera, Edgar Castellanos Diaz, Joselin Payan, Susy Rojas, Diane Jones, Valerie Tulier-Laiwa, Aleks Zavaleta, Jacqueline Martinez, Gabriel Chamie, Carol Glaser, Kathy Jacobson, Maya Petersen, Joseph DeRisi, Diane V. Havlir

PLOS One, 2023

Computational pipeline provides mechanistic understanding of Omicron variant of concern neutralizing engineered ACE2 receptor traps
Soumya G Remesh, Gregory E Merz, Axel F Brilot, Un Seng Chio, Alexandrea N Rizo, Thomas H Pospiech Jr, Irene Lui, Mathew T Laurie, Jeff Glasgow, Chau Q Le, Yun Zhang, Devan Diwanji, Evelyn Hernandez, Jocelyne Lopez, Hevatib Mehmood, Komal Ishwar Pawar, Sergei Pourmal, Amber M Smith, Fengbo Zhou; QCRG Structural Biology Consortium; Joseph DeRisi, Tanja Kortemme, Oren S Rosenberg, Anum Glasgow, Kevin K Leung, James A Wells, Kliment A Verba

Science Direct, 2023

Antibodies to repeat-containing antigens in Plasmodium falciparum are exposure-dependent and short-lived in children in natural malaria infections
Madhura Raghavan, Katrina L Kalantar, Elias Duarte, Noam Teyssier, Saki Takahashi, Andrew F Kung, Jayant V RajanJ, John Rek, Kevin KA Tetteh, Chris Drakeley, Isaac Ssewanyana, Isabel Rodriguez-Barraquer, Bryan Greenhouse, Joseph L DeRisi

eLife, 2023

Successful Treatment of Balamuthia mandrillaris Granulomatous Amebic Encephalitis with Nitroxoline
Natasha Spottiswoode, Douglas Pet, Annie Kim, Katherine Gruenberg, Maulik Shah, Amrutha Ramachandran, Matthew T Laurie, Maham Zia, Camille Fouassier, Christine L Boutros, Rufei Lu, Yueyuan Zhang, Venice Servellita, Andrew Bollen, Charles Y Chiu, Michael R Wilson, Liza Valdivia, Joseph L DeRisi

Emerging Infectious Diseases, 2023

Dual ankyrinG and subpial autoantibodies in a man with well-controlled HIV infection with steroid-responsive meningoencephalitis: A case report
Christopher M Bartley, Thomas T Ngo, Cathryn R Cadwell, Adil Harroud, Ryan D Schubert, Bonny D Alvarenga, Isobel A Hawes, Kelsey C Zorn, Trung Hunyh, Lindsay H Teliska, Andrew F Kung, Shailee Shah, Jeffrey M Gelfand, Felicia C Chow, Matthew N Rasband, Divyanshu Dubey, Sean J Pittock, Joseph L DeRisi, Michael R Wilson, Samuel J Pleasure

Frontiers, 2023

Low Prevalence of Interferon alpha Autoantibodies in People with Long COVID
Michael J. Peluso, Anthea Mitchell, Chung Yu Wang, Saki Takahashi, Rebecca Hoh, Viva Tai, Matthew S. Durstenfeld, Priscilla Y. Hsue, J. Daniel Kelly, Jeffrey N. Martin,Michael R. Wilson, Bryan Greenhouse, Steven G. Deeks, Joseph L. DeRisi, and Timothy J. Henrich

JID 2023

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)
Sharline Madera, Nicole McNeil , Paula Hayakawa Serpa, Jack Kamm, Christy Pak , Carolyn Caughell , Amy Nichols , David Dynerman, Lucy M. Li, Estella Sanchez-Guerrero, Maira S. Phelps, Angela M. Detweiler, Norma Neff, Helen Reyes , Steve A. Miller , Deborah S. Yokoe , Joseph L. DeRisi , Lynn Ramirez-Avila and Charles R. Langelier

Cambridge University Press, 2023

Autoantibodies to Perilipin-1 Define a Subset of Acquired Generalized Lipodystrophy
Caleigh Mandel-Brehm, Sara E. Vazquez,, Christopher Liverman, Mickie Cheng, Zoe Quandt,, Andrew F. Kung, Audrey Parent, Brenda Miao,, Emmanuel Disse,, Christine Cugnet-Anceau,, Stephane Dalle,, Elizaveta Orlova, Elena Frolova, Diana Alba,, Aaron Michels, Bergithe E. Oftedal,, Michail S. Lionakis, Eystein S. Husebye,, Anil K. Agarwal, Xilong Li, Chengsong Zhu, Quan Li, Elif Oral, Rebecca Brown, Mark S. Anderson,, Abhimanyu Garg, and Joseph L. DeRisi

Diabetes, Jan 2023

Prevalence of type-1 interferon autoantibodies in adults with non-COVID-19 acute respiratory failure
Rajani Ghale, Natasha Spottiswoode, Mark S. Anderson, Anthea Mitchell, Grace Wang, Carolyn S. Calfee, Joseph L. DeRisi and Charles R. Langelier

BMC, 2022

A 2-Gene Host Signature for Improved Accuracy of COVID-19 Diagnosis Agnostic to Viral Variants
Jack Albright, Eran Mick, Estella Sanchez-Guerrero, Jack Kamm, Anthea Mitchell, Angela M. Detweiler, Norma Neff, Alexandra Tsitsiklis, Paula Hayakawa Serpa, Kalani Ratnasiri, Diane Havlir, Amy Kistler, Joseph L. DeRisi, Angela Oliveira Pisco, Charles R. Langelier

American Society for Microbiology, 2023

NFKB2 haploinsufficiency identified via screening for IFN-a2 autoantibodies in children and adolescents hospitalized with SARS-CoV-2–related complications
Aaron Bodansky, Sara E Vazquez, Janet Chou, Tanya Novak, Amer Al-Musa, Cameron Young, Margaret Newhams, Suden Kucukak, Laura D Zambrano, Anthea Mitchell, Chung-Yu Wang, Kristin Moffitt, Natasha B Halasa, Laura L Loftis, Stephanie P Schwartz, Tracie C Walker, Elizabeth H Mack, Julie C Fitzgerald, Shira J Gertz, Courtney M Rowan, Katherine Irby, Ronald C Sanders Jr, Michele Kong, Jennifer E Schuster, Mary A Staat, Matt S Zinter, Natalie Z Cvijanovich, Keiko M Tarquinio, Bria M Coates, Heidi R Flori, Mary K Dahmer, Hillary Crandall, Melissa L Cullimore, Emily R Levy, Brandon Chatani, Ryan Nofziger; Overcoming COVID-19 Network Study Group Investigators,; Raif S Geha, Joseph DeRisi, Angela P Campbell, Mark Anderson, Adrienne G Randolph

Journal of Allergy and Clinical Immunology, 2022

Reproducibility and implementation of a rapid, community-based COVID-19 test and respond model
Gabriel Chamie , Patric Prado , Yolanda Oviedo , Tatiana Vizcaíno , Carina Arechiga , Kara Marson , Omar Carrera , Manuel J Alvarado 3, Claudia G Corchado 3, Monica Gomez 3, Marilyn Mochel , Irene de Leon , Kesia K Garibay , Arturo Durazo , Maria-Elena De Trinidad Young , Irene H Yen , John Sauceda , Susana Rojas , Joe DeRisi , Maya Petersen , Diane V Havlir , Carina Marquez

PLOS One, 2022

Autoantibody discovery across monogenic, acquired, and COVID-19-associated autoimmunity with scalable PhIP-seq
Sara E Vazquez, Sabrina A Mann, Aaron Bodansky, Andrew F Kung, Zoe Quandt, Elise MN Ferré, Nils Landegren, Daniel Eriksson, Paul Bastard, Shen-Ying Zhang, Jamin Liu, Anthea Mitchell, Irina Proekt, David Yu, Caleigh Mandel-Brehm, Chung-Yu Wang, Brenda Miao, Gavin Sowa, Kelsey Zorn, Alice Y Chan, Veronica M Tagi, Chisato Shimizu, Adriana Tremoulet, Kara Lynch, Michael R Wilson, Olle Kämpe, Kerry Dobbs, Ottavia M Delmonte, Rosa Bacchetta, Luigi D Notarangelo, Jane C Burns, Jean-Laurent Casanova, Michail S Lionakis, Troy R Torgerson, Mark S Anderson, Joseph L DeRisi

Elife, 2022

Integrated host-microbe plasma metagenomics for sepsis diagnosis in a prospective cohort of critically ill adults
Katrina L. Kalantar, Lucile Neyton, Mazin Abdelghany, Eran Mick, Alejandra Jauregui, Saharai Caldera, Paula Hayakawa Serpa, Rajani Ghale, Jack Albright, Aartik Sarma, Alexandra Tsitsiklis, Aleksandra Leligdowicz, Stephanie A. Christenson, Kathleen Liu, Kirsten N. Kangelaris, Carolyn Hendrickson, Pratik Sinha, Antonio Gomez, Norma Neff, Angela Pisco, Sarah B. Doernberg, Joseph L. Derisi, Michael A. Matthay, Carolyn S. Calfee & Charles R. Langelier

Nature Microbiology, 2022

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
Carina Marquez, MD, MPH; Andrew D. Kerkhoff, MD, PhD; John Schrom, MPH; Susana Rojas; Douglas Black, BA; Anthea Mitchell, BA; Chung-Yu Wang, BA; Genay Pilarowski, PhD; Salustiano Ribeiro, MS; Diane Jones, RN; Joselin Payan; Simone Manganelli, MS; Susy Rojas, BS; Jonathan Lemus, BA; Vivek Jain, MD; Gabriel Chamie, MD; Valerie Tulier-Laiwa, JD; Maya Petersen, MD, PhD; Joseph DeRisi, PhD; Diane V. Havlir, MD

JAMA Network, 2022

Genomic analysis, immunomodulation and deep phenotyping of patients with nodding syndrome
Ariane Soldatos, Thomas B Nutman, Tory Johnson, Scott F Dowell, James J Sejvar, Michael R Wilson, Joseph L DeRisi, Sara K Inati, Catherine Groden, Colleen Evans, Elise M O’Connell, Bernard Opar Toliva, Jane R Aceng, Josephine Aryek-Kwe, Camilo Toro, Constantine A Stratakis, A Gretchen Buckler, Cathy Cantilena, Tara N Palmore, Audrey Thurm, Eva H Baker, Richard Chang, Harper Fauni, David Adams, Ellen F Macnamara, C Christopher Lau, May Christine V Malicdan, Barbara Pusey-Swerdzewski, Robert Downing, Sudhir Bunga, Jerry D Thomas, William A Gahl, and Avindra Nath

Oxford Academic, 2022

Discovery and Genomic Characterization of a Novel Henipavirus, Angavokely Virus, from Fruit Bats in Madagascar
Sharline Madera, Amy Kistler, Hafaliana C. Ranaivoson, Vida Ahyong, Angelo Andrianiaina, Santino Andry, Vololoniaina Raharinosy, Tsiry H. Randriambolamanantsoa, Ny Anjara Fifi Ravelomanantsoa, Cristina M. Tato, Joseph L. DeRisi, Hector C. Aguilar, Vincent Lacoste, Philippe Dussart, Jean-Michel Heraud, Cara E. Brook

Journal of Virology, 2022

Zika virus alters centrosome organization to suppress the innate immune response
Andrew Kodani, Kristeene A Knopp, Elizabeth Di Lullo, Hanna Retallack, Arnold R Kriegstein, Joseph L DeRisi, Jeremy F Reiter

EMBO Press, 2022

Lower respiratory tract infections in children requiring mechanical ventilation: a multicentre prospective surveillance study incorporating airway metagenomics
Alexandra Tsitsiklis, Christina M Osborne, Jack Kamm, Kayla Williamson, Katrina Kalantar, Gytis Dudas, Saharai Caldera, Amy Lyden, Michelle Tan, Norma Neff, Victoria Soesanto, J Kirk Harris, Lilliam Ambroggio, Aline B Maddux, Todd C Carpenter, Ron W Reeder, Chris Locandro, Eric A F Simões, Matthew K Leroue, Mark W Hall, Athena F Zuppa, Joseph Carcillo, Kathleen L Meert, Anil Sapru, Murray M Pollack, Patrick S McQuillen, Daniel A Notterman, J Michael Dean, Matt S Zinter, Brandie D Wagner, Joseph L DeRisi, Peter M Mourani*, Charles R Langelier

The Lancet Microbe, 2022

Case Report: Cambodian National Malaria Surveillance Program Detection of Plasmodium knowlesi
Christina Yek, Sreyngim Lay, Jennifer A. Bohl, Somnang Man, Sophana Chea, Chanthap Lon, Vida Ahyong, Cristina M. Tato, Joseph L. DeRisi, Siv Sovannaroth, and Jessica E. Manning

ASTMH, 2022

Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections
Paula Hayakawa Serpa, Xianding Deng, Mazin Abdelghany, Emily Crawford, Katherine Malcolm, Saharai Caldera, Monica Fung, Aaron McGeever, Katrina L. Kalantar, Amy Lyden, Rajani Ghale, Thomas Deiss, Norma Neff, Steven A. Miller, Sarah B. Doernberg, Charles Y. Chiu, Joseph L. DeRisi, Carolyn S. Calfee & Charles R. Langelier

BMC, 2022

Genome-Wide Knockout Screen Identifies Human Sialomucin CD164 as an Essential Entry Factor for Lymphocytic Choriomeningitis Virus
Jamin Liu, Kristeene A. Knoppa, Elze Rackaityte, Chung Yu Wangc, Matthew T. Laurie, Sara Sunshine, Andreas S. Puschnik, Joseph L. DeRisi

American Society for Microbiology, 2022

Vaccine breakthrough hypoxemic COVID-19 pneumonia in patients with auto-Abs neutralizing type I IFNs
astard P, Vazquez SE, Liu J, Laurie MT, Wang CY, Gervais A, Le Voyer T, Bizien L, Zamecnik C, Philippot Q, Rosain J, Catherinot E, Willmore A, Mitchell AM, Bair R, Garçon P, Kenney H, Fekkar A, 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, Imberti L, Notarangelo LD, Troya J, Solanich X, Zhang SY, Puel A, Wilson MR, Trouillet-Assant S, Laurent Abel, Emmanuelle Jouanguy, Chun Jimmie Ye, Aurélie Cobat, Leslie M Thompson, Evangelos Andreakos, Qian Zhang, Mark S Anderson, Jean-Laurent Casanova, Joseph L DeRisi

Science Immunology, 2022

BIV-Spectrin Autoantibodies in 2 Individuals With Neuropathy of Possible Paraneoplastic Origin: A Case Series
Christopher M. Bartley, MD,* Thomas T. Ngo, BS,* Bonny D. Alvarenga, BA, Andrew F. Kung, BA, Lindsay H. Teliska, BS, Michael Sy, MD, Joseph L. DeRisi, PhD, Matthew N. Rasband, PhD, Sean J. Pittock, MD, Divyanshu Dubey, MBBS, Michael R. Wilson, MD, MAS, and Samuel J. Pleasure, MD, PhD

Neurology Journals, 2022

Comparison of SARS-CoV-2 Reverse Transcriptase Polymerase Chain Reaction and BinaxNOW Rapid Antigen Tests at a Community Site During an Omicron Surge : A Cross-Sectional Study
John Schrom, MPH; Carina Marquez, MD; Genay Pilarowski, PhD; Chung-Yu Wang, MS; Anthea Mitchell, BS;Robert Puccinelli, BS; Doug Black, BA; Susana Rojas; Salustiano Ribeiro, MS; Valerie Tulier-Laiwa, JD; Jacqueline Martinez, BA;Joselin Payan; Susy Rojas, BS; Diane Jones, BSN; Daniel Martinez, JD; Robert Nakamura, PhD; Gabriel Chamie, MD;Vivek Jain, MD; Maya Petersen, MD, PhD; Joe DeRisi, PhD; and Diane Havlir, MD

Annals of Internal Medicine, 2022

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

medRxiv, 2021

Genome-Wide Knockout Screen Identifies Human Sialomucin CD164 as an Essential Entry Factor for Lymphocytic Choriomeningitis Virus
Jamin Liu, Kristeene A. Knopp, Elze Rackaityte, Chung Yu Wang, Matthew T. Laurie, Sara Sunshine, Andreas S. Puschnik, Joseph L. DeRisi

American Society for Microbiology, 2022

Pneumonia surveillance with culture-independent metatranscriptomics in HIV-positive adults in Uganda: a cross-sectional study
Natasha Spottiswoode, Joshua D Bloomstein, Saharai Caldera, Abdul Sessolo, Kathryn McCauley, Patrick Byanyima, Josephine Zawedde, Katrina Kalantar, Sylvia Kaswabuli, Rachel L Rutishauser, Monica K Lieng, J Lucian Davis, Julia Moore, Amanda Jan, Shoko Iwai, Meera Shenoy, Ingvar Sanyu, Joseph L DeRisi, Susan V Lynch, William Worodria, Laurence Huang, Charles R Langelier

The Lancet, 2022

ZSCAN1 autoantibodies are associated with pediatric paraneoplastic ROHHAD
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.

Annals of Neurology, 2022

Integrating central nervous system metagenomics and host response for diagnosis of tuberculosis meningitis and its mimics
P. S. Ramachandran, A. Ramesh, F. V. Creswell, A. Wapniarski, R. Narendra, C. M. Quinn, E. B. Tran, M. K. Rutakingirwa, A. S. Bangdiwala, E. Kagimu, K. T. Kandole, K. C. Zorn, L. Tugume, J. Kasibante, K. Ssebambulidde, M. Okirwoth, N. C. Bahr, A. Musubire, C. P. Skipper, C. Fouassier, A. Lyden, P. Serpa, G. Castaneda, S. Caldera, V. Ahyong, J. L. DeRisi, C. Langelier, E. D. Crawford, D. R. Boulware, D. B. Meya & M. R. Wilson

Nature Communications, 2022

Autoantibody discovery across monogenic, acquired, and COVID19-associated autoimmunity with scalable PhIP-seq
Sara E Vazquez*, Sabrina A Mann*, Aaron Bodansky*, Andrew F Kung, Zoe Quandt, Elise M. N. Ferré, Nils Landegren, Daniel Eriksson, Paul Bastard, Shen-Ying Zhang, Jamin Liu, Anthea Mitchell, Caleigh Mandel-Brehm, Brenda Miao, Gavin Sowa, Kelsey Zorn, Alice Y. Chan, Chisato Shimizu, Adriana Tremoulet, Kara Lynch, Michael R. Wilson, Olle Kampe, Kerry Dobbs, Ottavia M. Delmonte, Luigi D. Notarangelo, Jane C. Burns, Jean-Laurent Casanova, Michael S. Lionakis, Troy R. Torgerson, Mark S Anderson#, Joseph L DeRisi

BiorRxiv, 2022

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)
Sharline Madera, Nicole McNeil, Paula Hayakawa Serpa, Jack Kamm, Christy Pak, Carolyn Caughell, Amy Nichols, David Dynerman, Lucy M Li, Estella Sanchez-Guerrero, Maira S Phelps, Angela M Detweiler, Norma Neff, Helen Reyes, Steve A Miller, Deborah S Yokoe, Joseph L DeRisi, Lynn Ramirez-Avila, Charles R Langelier

Cambridge University Press, 2022

Transcriptomic profiling of blood from autoimmune hepatitis patients reveals potential mechanisms with implications for management
Michele May-Sien Tana , Arielle Klepper, Amy Lyden, Angela Oliveira Pisco, Maira Phelps, Breann McGee, Kelsey Green, Sandy Feng, Joseph DeRisi, Emily Dawn Crawford, Craig S. Lammert

PLOS One, 2022

Viral Load Among Vaccinated and Unvaccinated, Asymptomatic and Symptomatic Persons Infected With the SARS-CoV-2 Delta Variant
Charlotte B Acharya, John Schrom, Anthea M Mitchell, David A Coil, Carina Marquez, Susana Rojas, Chung Yu Wang, Jamin Liu, Genay Pilarowski, Leslie Solis, Elizabeth Georgian, Sheri Belafsky, Maya Petersen, Joseph DeRisi, Richard Michelmore, Diane Havlir

Infectious Disease Society of America, 2022

Pulmonary microbiome and gene expression signatures differentiate lung function in pediatric hematopoietic cell transplant candidates
MATT S. ZINTER, A. BIRGITTA VERSLUYS, CAROLINE A. LINDEMANS, MADELINE Y. MAYDAY, GUSTAVO REYES, SARA SUNSHINE, MARILYNN CHAN, ELIZABETH K. FIORINO, MARIA CANCIO, SABINE PREVAES, MARINA SIROTA, MICHAEL A. MATTHAY, SANDHYA KHARBANDA, CHRISTOPHER C. DVORAK, JAAP J. BOELENS, AND JOSEPH L. DERISI

Science Translational Medicine, 2022

Using genomic epidemiology of SARS-CoV-2 to support contact tracing and public health surveillance in rural Humboldt County, California
Gunnar Stoddard, Allison Black, Patrick Ayscue, Dan Lu, Jack Kamm, Karan Bhatt, Lienna Cha, Amy L Kistler, Joshua Batson, Angela Detweiler , Michelle Tan , Norma Nef, Joseph L DeRisi. and Jeremy Corrigan

BMC Public Health, 2022

Discovering disease-causing pathogens in resource-scarce Southeast Asia using a global metagenomic pathogen monitoring system
Jennifer A Bohl, Sreyngim Lay, Sophana Chea, Vida Ahyong, Daniel M Parker, Shannon Gallagher, Jonathan Fintzi, Somnang Man, Aiyana Ponce, Sokunthea Sreng, Dara Kong, Fabiano Oliveira, Katrina Kalantar, Michelle Tan, Liz Fahsbender, Jonathan Sheu, Norma Neff, Angela M Detweiler, Christina Yek, Sokna Ly, Rathanak Sath, Chea Huch, Hok Kry, Rithea Leang, Rekol Huy, Chanthap Lon, Cristina M Tato, Joseph L DeRisi, Jessica E Manning

PNAS, 2022

Clonally expanded B cells in multiple sclerosis bind EBV EBNA1 and GlialCAM
Tobias V. Lanz, R. Camille Brewer, Peggy P. Ho, Jae-Seung Moon, Kevin M. Jude, Daniel Fernandez, Ricardo A. Fernandes, Alejandro M. Gomez, Gabriel-Stefan Nadj, Christopher M. Bartley, Ryan D. Schubert, Isobel A. Hawes, Sara E. Vazquez, Manasi Iyer, J. Bradley Zuchero, Bianca Teegen, Jeffrey E. Dunn, Christopher B. Lock, Lucas B. Kipp, Victoria C. Cotham, Beatrix M. Ueberheide, Blake T. Aftab, Mark S. Anderson, Joseph L. DeRisi, …William H. Robinson

Nature, 2022

Full Genome Nobecovirus Sequences From Malagasy Fruit Bats Define a Unique Evolutionary History for This Coronavirus Clade
Gwenddolen Kettenburg, Amy Kistler, Hafaliana Christian Ranaivoson, Vida Ahyong, Angelo Andrianiaina, Santino Andry, Joseph L DeRisi, Anecia Gentles, Vololoniaina Raharinosy, Tsiry Hasina Randriambolamanantsoa, Ny Anjara Fifi Ravelomanantsoa, Cristina M Tato, Philippe Dussart, Jean-Michel Heraud, Cara E Brook

Frontiers, 2022

Clonally expanded B cells in multiple sclerosis bind EBV EBNA1 and GlialCAM
Tobias V. Lanz, R. Camille Brewer, Peggy P. Ho, Jae-Seung Moon, Kevin M. Jude, Daniel Fernandez, Ricardo A. Fernandes, Alejandro M. Gomez, Gabriel-Stefan Nadj, Christopher M. Bartley, Ryan D. Schubert, Isobel A. Hawes, Sara E. Vazquez, Manasi Iyer, J. Bradley Zuchero, Bianca Teegen, Jeffrey E. Dunn, Christopher B. Lock, Lucas B. Kipp, Victoria C. Cotham, Beatrix M. Ueberheide, Blake T. Aftab, Mark S. Anderson, Joseph L. DeRisi, …William H. Robinson

Nature, 2022

Functional characterization of 5' UTR cis-acting sequence elements that modulate translational efficiency in Plasmodium falciparum and humans
Valentina E Garcia, Rebekah Dial, Joseph L DeRisi

Malaria Journal, 2022

Community Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 Disproportionately Affects the Latinx Population During Shelter-in-Place in San Francisco
Chamie G, Marquez C, Crawford E, Peng J, Petersen M, Schwab D, Schwab J, Martinez J, Jones D, Black D, Gandhi M, Kerkhoff AD, Jain V, Sergi F, Jacobo J, Rojas S, Tulier-Laiwa V, Gallardo-Brown T, Appa A, Chiu C, Rodgers M, Hackett J; CLIAhub Consortium, Kistler A, Hao S, Kamm J, Dynerman D, Batson J, Greenhouse B, DeRisi J, Havlir DV

Oxford University Press, 2021

Persistence of Ambigrammatic Narnaviruses Requires Translation of the Reverse Open Reading Frame
Hanna Retallack, Katerina D. Popova, Matthew T. Laurie, Sara Sunshine, Joseph L. DeRisi

Journal of Virology, 2021

Est. of secondary household attack rates for emergent spike L452R SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in SF
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.

Clin Infect Dis. 2021

Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy
Parinaz Fozouni , Sungmin Son, María Díaz de León Derb , Gavin J Knott , Carley N Gray, Michael V D'Ambrosio , Chunyu Zhao , Neil A Switz , G Renuka Kumar, Stephanie I Stephens , Daniela Boehm , Chia-Lin Tsou, Jeffrey Shu, Abdul Bhuiya, Maxim Armstrong , Andrew R Harris , Pei-Yi Chen , Jeannette M Osterloh, Anke Meyer-Franke, Bastian Joehnk , Keith Walcott, Anita Sil , Charles Langelier, Katherine S Pollard , Emily D Crawford , Andreas S Puschnik , Maira Phelps, Amy Kistler , Joseph L DeRisi , Jennifer A Doudna , Daniel A Fletcher, Melanie Ott

Cell 2021

Performance Characteristics of a Rapid SARS-CoV-2 Antigen Detection Assay at a Public Plaza Testing Site in San Francisco
Genay Pilarowski, et al.

J. of Infect. Disease, 2020

Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids
Wei Gu, Xianding Deng, Marco Lee, Yasemin D Sucu, Shaun Arevalo, Doug Stryke, Scot Federman, Allan Gopez, Kevin Reyes, Kelsey Zorn, Hannah Sample, Guixia Yu, Gurpreet Ishpuniani, Benjamin Briggs, Eric D Chow , Amy Berger, Michael R Wilson, Candace Wang, Elaine Hsu, Steve Miller, Joseph L DeRisi, Charles Y Chiu

Nature Medicine, 2021

Expanded Clinical Phenotype, Oncological Associations, and Immunopathologic Insights of Paraneoplastic Kelch-like Protein-11 Encephalitis
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.

JAMA Neurology, 2020

IDseq-An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring
Katrina L Kalantar, Tiago Carvalho, Charles F A de Bourcy, Boris Dimitrov, Greg Dingle, Rebecca Egger, Julie Han, Olivia B Holmes, Yun-Fang Juan, Ryan King, Andrey Kislyuk, Michael F Lin, Maria Mariano, Todd Morse, Lucia V Reynoso, David Rissato Cruz, Jonathan Sheu, Jennifer Tang, James Wang, Mark A Zhang, Emily Zhong, Vida Ahyong, Sreyngim Lay, Sophana Chea, Jennifer A Bohl, Jessica E Manning, Cristina M Tato, Joseph L DeRisi

Oxford Academic, 2020

Rapid deployment of SARS-CoV-2 testing: The CLIAHUB
Emily Crawford and the CLIAHUB Consortium

PLOS Pathogens, 2020

Temporal airway microbiome changes related to ventilator associated pneumonia in children
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 Pediatric Critical Care Research Network (CPCCRN)

European Respiratory Journal, 2020

Deep profiling of protease substrate specificity enabled by dual random and scanned human proteome substrate phage libraries
Jie Zhou, Shantao Li, Kevin K Leung, Brian O'Donovan, James Y Zou, Joseph L DeRisi, James A Wells

PNAS, 2020

ReScan, a Multiplex Diagnostic Pipeline, Pans Human Sera for SARS-CoV-2 Antigens
Colin R. Zamecnik, Jayant V. Rajan, Kevin A. Yamauchi, Michel C. Nussenzweig, Joseph L. DeRisi, Michael R. Wilson

Cell Reports Medicine, 2020

Auto-antibodies against type I IFNs in patients with life-threatening COVID-19
Bastard P, Rosen LB, Zhang Q, Michailidis E, Hoffmann HH, Zhang Y, Dorgham K, Philippot Q, Rosain J, Béziat V, Manry J, Shaw E, Haljasmägi L, Peterson P, Lorenzo L, Bizien L, Trouillet-Assant S, Dobbs K, de Jesus AA, Belot A, Kallaste A, Catherinot E, Tandjaoui-Lambiotte Y, Le Pen J, Kerner G, Bigio B, Seeleuthner Y, Yang R, Bolze A, Spaan AN, Delmonte OM, Abers MS, Aiuti A, Casari G, Lampasona V, Piemonti L, Ciceri F, Bilguvar K, Lifton RP, Vasse M, Smadja DM, Migaud M, Hadjadj J, Terrier B, Duffy D, Quintana-Murci L, van de Beek D, Roussel L, Vinh DC, Tangye SG, Haerynck F, Dalmau D, Martinez-Picado J, Brodin P, Nussenzweig MC, Boisson-Dupuis S, Rodríguez-Gallego C, Vogt G, Mogensen TH, Oler AJ, Gu J, Burbelo PD, Cohen J, Biondi A, Bettini LR, D'Angio M, Bonfanti P, Rossignol P, Mayaux J, Rieux-Laucat F, Husebye ES, Fusco F, Ursini MV, Imberti L, Sottini A, Paghera S, Quiros-Roldan E, Rossi C, Castagnoli R, Montagna D, Licari A, Marseglia GL, Duval X, Ghosn J; HGID Lab; NIAID-USUHS Immune Response to COVID Group; COVID Clinicians; COVID-STORM Clinicians; Imagine COVID Group; French COVID Cohort Study Group; Milieu Intérieur Consortium; CoV-Contact Cohort; Amsterdam UMC Covid-19 Biobank; COVID Human Genetic Effort, Tsang JS, Goldbach-Mansky R, Kisand K, Lionakis MS, Puel A, Zhang SY, Holland SM, Gorochov G, Jouanguy E, Rice CM, Cobat A, Notarangelo LD, Abel L, Su HC, Casanova JL

Science, 2020

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

American Society for Microbiology, 2020

A pathogenic and clonally expanded B cell transcriptome in active multiple sclerosis
Ramesh A, Schubert RD, Greenfield AL, Dandekar R, Loudermilk R, Sabatino JJ Jr, 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.

PNAS,2020

Investigating Transfusion-related Sepsis Using Culture-Independent Metagenomic Sequencing.
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.

Infectious Disease Journal of America, 2020

Community Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 Disproportionately Affects the Latinx Population During Shelter-in-Place in San Francisco
Gabriel Chamie, Carina Marquez, Emily Crawford, James Peng, Maya Petersen, Daniel Schwab, Joshua Schwab, Jackie Martinez, Diane Jon Es, Douglas Black, Monica Gandhi, Andrew D Kerkhoff, Vivek Jain, Francesco Sergi, Jon Jacobo, Susana Rojas, Valerie Tulier-Laiwa, Tracy Gallardo-Brown, Ayesha Appa, Charles Chiu, Mary Rodgers, John Hackett, Amy Kistler, Samantha Hao, Jack Kamm, David Dynerman, Joshua Batson, Bryan Greenhouse, Joe DeRisi, Diane V Havlir, CLIAhub Consortium

Infectious Disease Society of America, 2020

Central Nervous System Virus Infection in African Children with Cerebral Malaria.
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.

American Journal of Tropical Medicine and Hygiene, 2020

Complete Genome Sequence of a Novel Coronavirus (SARS-CoV-2) Isolate from Bangladesh
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.

American Society for Microbiology, 2020

High resolution epitope mapping of anti-Hu and anti-Yo autoimmunity by programmable phage display
Brian O’Donovan, Caleigh Mandel-Brehm, Sara E Vazquez, Jamin Liu, Audrey V Parent, Mark S Anderson, Travis Kassimatis, Anastasia Zekeridou, Stephen L Hauser, Sean J Pittock, Eric Chow, Michael R Wilson, Joseph L DeRisi

Oxford Academic, 2020

Upper airway gene expression differentiates COVID-19 from other acute respiratory illnesses and reveals suppression of innate immune responses by SARS-CoV-2.
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.

medRvix, 2020

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

eLife, 2020

Clinical features, diagnostics, and outcomes of patients presenting with acute respiratory illness: a comparison of patients with and without COVID-19.
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.

medRvix, 2020

Integrating central nervous system metagenomics and host response for diagnosis of tuberculosis meningitis and its mimics
P S Ramachandran, A Ramesh, F V Creswell, A Wapniarski, R Narendra, C M Quinn, E B Tran, M K Rutakingirwa, A S Bangdiwala, E Kagimu, K T Kandole, K C Zorn, L Tugume, J Kasibante, K Ssebambulidde M Okirwoth, N C Bahr, A Musubire 6, C P Skipper, C Fouassiu, A Lyden, P Serpa, G Castaneda, S Caldera, V Ahyong, J L DeRisi, C Langelier, E D Crawford, D R Boulware, D B Meya, M R Wilson

Nature Communications, 2020

Identification of anisomycin, prodigiosin and obatoclax as compounds with broad-spectrum anti-parasitic activity
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.

PLOS, Neglected Tropical Diseases, 2020

Genomic and serologic characterization of enterovirus A71 brainstem encephalitis
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

American Academy of Neurology, 2020

Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia
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.

bioRxiv, 2020

Detection of Pneumonia Pathogens from PlasmaCell-Free DNA
Langelier C, Fung M, Caldera S, Deiss T, Lyden A, Prince BC, Serpa PH, Moazed F, Chin-Hong P, DeRisi JL, Calfee CS

American Journal of Respiratory Critical Care, 2020

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

Journal of Graduate Medical Education, 2020

Plasmodium falciparum Resistance to a Lead Benzoxaborole Due to Blocked Compound Activation and Altered Ubiquitination or Sumoylation
Kirthana M. V. Sindhe, Wesley Wu, Jenny Legac, Yong-Kang Zhang, Eric E. Easom, Roland A. Cooper, Jacob J. Plattner, Yvonne R. Freund, Joseph L. DeRisi, Philip J. Rosenthal

American Society of Microbiology, 2020

Pan-viral serology implicates enteroviruses in acute flaccid myelitis
Ryan D. Schubert, Isobel A. Hawes, Prashanth S. Ramachandran, Akshaya Ramesh, Emily D. Crawford, John E. Pak, Wesley Wu, Carly K. Cheung, Brian D. O’Donovan, Cristina M. Tato, Amy Lyden, Michelle Tan, Rene Sit, Gavin A. Sowa, Hannah A. Sample, Kelsey C. Zorn, Debarko Banerji, Lillian M. Khan, Riley Bove, Stephen L. Hauser, Amy A. Gelfand, Bethany L. Johnson-Kerner, Kendall Nash, Kalpathy S. Krishnamoorthy, Tanuja Chitnis, Joy Z. Ding, Hugh J. McMillan, Charles Y. Chiu, Benjamin Briggs, Carol A. Glaser, Cynthia Yen, Victoria Chu, Debra A. Wadford, Samuel R. Dominguez, Terry Fei Fan Ng, Rachel L. Marine, Adriana S. Lopez, W. Allan Nix, Ariane Soldatos, Mark P. Gorman, Leslie Benson, Kevin Messacar, Jennifer L. Konopka-Anstadt, M. Steven Oberste, Joseph L. DeRisi, and Michael R. Wilson

Nature Medicine, 2020

Exploratory analysis of the potential for advanced diagnostic testing to reduce healthcare expenditures of patients hospitalized with meningitis or encephalitis
Fulton BD, Proudman DG, Sample HA, Gelfand JM, Chiu CY, DeRisi JL, Wilson MR

PLoS One, 2020

Unbiased Metagenomic Sequencing for Pediatric Meningitis in Bangladesh Reveals Neuroinvasive Chikungunya Virus Outbreak and Other Unrealized Pathogens
Saha S, Ramesh A, Kalantar, Malaker, Hasanuzzaman, Khan LM, Mayday MY, Sajib MS, Li, 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

American Society of Microbiology, 2019

An exploration of ambigrammatic sequences in narnaviruses
DeRisi JL, Huber G, Kistler A, Retallack H, Wilkinson M, Yllanes D

Scientific Reports, 2020

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
Emily A. Sloan, Paul J. Sampognaro, Jacqueline C. Junn, Cynthia Chin, Line Jacques, Prashanth S. Ramachandran, Joseph L. DeRisi, Michael R. Wilson, Arnold R. Kriegstein, Andrew W. Bollen, David A. Solomon, Marta Margeta & John W. Engstrom

Springer Link, 2020

FLASH: a next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences
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

Nucleic Acid Research, 2019

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

Emerging Infectious Diseases, 2019

Kelch-like Protein 11 Seminoma-associated Paraneoplastic Encephalitis
Caleigh Mandel-Brehm, Ph.D., Divyanshu Dubey, M.D., Thomas J. Kryzer, A.S., Brian D. O’Donovan, Ph.D., Baouyen Tran, Ph.D., Sara E. Vazquez, B.S., Hannah A. Sample, B.S., Kelsey C. Zorn, M.H.S., Lillian M. Khan, B.S., Ian O. Bledsoe, M.D., Andrew McKeon, M.D., Samuel J. Pleasure, M.D., Ph.D., Vanda A. Lennon, M.D., Ph.D., Joseph L. DeRisi, Ph.D., Michael R. Wilson, M.D., and Sean J. Pittock, M.D.

NEJM 2019

Exploratory proteomic analysis implicates thealternative complement cascade in primary CNS vasculitis
Caleigh Mandel-Brehm, PhD,* Hanna Retallack, AB,* Giselle M. Knudsen, PhD, Alex Yamana, BS,Rula A. Hajj-Ali, MD, Leonard H. Calabrese, DO, Tarik Tihan, MD, PhD, Hannah A. Sample, BS,Kelsey C. Zorn, MHS, Mark P. Gorman, MD, Jennifer Madan Cohen, MD, Antoine G. Sreih, MD,Jacqueline F. Marcus, MD, S. Andrew Josephson, MD, Vanja C. Douglas, MD, Jeffrey M. Gelfand, MD,Michael R. Wilson, MD, and Joseph L. DeRisi, PhD

Neurology, 2019

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

Microbial Drug Resistance, 2019

Metagenomic next-generation sequencing of samples from pediatric febrile illness in Tororo, Uganda
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.

PLOS One, 2019

Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis
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.

New England Journal of Medicine, 2019

Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children
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

Oxford Academic, 2019

Towards precision quantification of contamination in metagenomic sequencing experiments
M. S. Zinter, M. Y. Mayday, K. K. Ryckman, L. L. Jelliffe-Pawlowski, and J. L. DeRisi5

Microbiome, 2019

METAGENOMIC NEXT-GENERATION SEQUENCING REVEALS MIAMIENSIS AVIDUS (CILIOPHORA: SCUTICOCILIATIDA) IN THE 2017 EPIZOOTIC OF LEOPARD SHARKS ( TRIAKIS SEMIFASCIATA) IN SAN FRANCISCO BAY, CALIFORNIA, USA
Retallack H, Okihiro MS, Britton E, Sommeran SV, DeRisi JL.

Journal of Wildlife Disease, 2019

Metagenomic comparison of tracheal aspirate and mini-bronchial alveolar lavage for assessment of respiratory microbiota
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

American Journal of Physiology, 2019

Miniaturization and optimization of 384-well compatible RNA sequencing library preparation
Mayday MY, Khan LM, Chow ED, Zinter MS, DeRisi JL

PLOS One, 2019

Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults
Langelier C, Kalantar KL, Moazed F4 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

PNAS, 2018

Clinicopathology conference: 41‐year‐old woman with chronic relapsing meningitis
Erin S. Beck MD, PhD Prashanth S. Ramachandran MBBS, BMedSci Lillian M. Khan BS Hannah A. Sample BS Kelsey C. Zorn MHS Elise M. O'Connell MD Theodore Nash MD Daniel S. Reich MD, PhD Arun Venkatesan MD, PhD Joseph L. DeRisi PhD Avindra Nath MD Michael R. Wilson MD, MAS

Annuls of Neurology, 2018

The Plasmodium falciparum cytoplasmic translation apparatus: a promising therapeutic target not yet exploited by clinically approved anti-malarials
Christine Moore Sheridan , Valentina E. Garcia , Vida Ahyong and Joseph L. DeRisi

Malaria Journal, 2018

Detection of Cryptococcus DNA by Metagenomic Next-generation Sequencing in Symptomatic Cryptococcal Antigenemia
Ramachandran PS, Cresswell FV, Meya DB, Crawford ED, DeRisi JL, Boulware DR, Wilson MR

Clinical Infectious Diseases, 2018

Ebola virus, but not Marburg virus, replicates efficiently and without required adaptation in snake cells
Greg Fedewa, Sheli R. Radoshitzky, Xiaolı` Chı¯, Lia´nDong, Xiankun Zeng, Melissa Spear, Nicolas Strauli, Melinda Ng, Kartik Chandran, Mark D. Stenglein, Ryan D. Hernandez, Peter B. Jahrling, Jens H. Kuhn, and Joseph L. DeRisi

Virus Evolution, 2018

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

American Society for Microbiology, 2018

Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance
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

Biology Open, 2018

Whole-Genome mRNA Gene Expression Differs Between Patients With and Without Delirium
Kalantar K, LaHue SC, DeRisi J, Sample HA, Contag CA, Josephson SA, Wilson MR, Douglas VC

Sage Journals, 2018

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

Virology Journal, 2018

Low-cost touchscreen driven programmable dual syringe pump for life Science Applications
Valentina E. Garcia, Jamin Liu, Joseph L. DeRisi

Science Direct, 2018

Metagenomic next-generation sequencing reveals Miamiensis avidus (Ciliophora: Scuticociliatida) in the 2017 epizootic of leopard sharks (Triakis semifasciata) in San Francisco Bay, California
Hanna Retallack, Mark S. Okihiro, Elliot Britton, Sean Van Sommeran, Joseph L. DeRisi

BioOne Complete

Chronic Meningitis Investigated via Metagenomic Next-Generation Sequencing
Michael R. Wilson, MD, MAS; Brian D. O’Donovan, MS; JeffreyM. Gelfand, MD, MAS; Hannah A. Sample, BS; Felicia C. Chow, MD, MAS; John P. Betjemann, MD; Maulik P. Shah, MD; Megan B. Richie, MD; Mark P. Gorman, MD; Rula A. Hajj-Ali, MD; Leonard H. Calabrese, DO; Kelsey C. Zorn, MHS; Eric D. Chow, PhD; John E. Greenlee, MD; Jonathan H. Blum, MD, PhD; Gary Green, MD; Lillian M. Khan, BS; Debarko Banerji, BS; Charles Langelier,MD, PhD; Chloe Bryson-Cahn, MD; Whitney Harrington, MD, PhD; Jairam R. Lingappa, MD, PhD; Niraj M. Shanbhag, MD, PhD; Ari J. Green, MD, MAS; Bruce J. Brew, MBBS, DMedSci, DSc; Ariane Soldatos, MD; Luke Strnad, MD; Sarah B. Doernberg, MD, MAS; Cheryl A. Jay, MD; Vanja Douglas, MD; S. Andrew Josephson, MD; Joseph L. DeRisi, PhD

JAMA Network, 2018

Metagenomic Sequencing Detects Respiratory Pathogens in Hematopoietic Cellular Transplant Patients
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

American Journal of Respiratory and Critical Care Medicine, 2018

Complete Genome Sequence of a Divergent Human Rhinovirus C Isolate from an Infant with Severe Community- Acquired Pneumonia in Colorado, USA
Charles Langelier, Corin V. White, Marci K. Sontag, Peter M. Mourani, Joseph L. DeRisi

ASM, 2017

IFN-stimulated Gene Expression, Type 2 Inflammation, and Endoplasmic Reticulum Stress in Asthma
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

ATS Journals, 2017

Metagenomic deep sequencing of aqueous fluid detects intraocular lymphomas
John Gonzales, Thuy Doan, Jessica G Shantha, Michele Bloomer, Michael R Wilson, Joseph L DeRisi, Nisha Acharya

Innovations, 2017

Topical silver diamine fluoride for dental caries arrest in preschool children: A randomized controlled trial and microbiological analysis of caries associated microbes and resistance gene expression
Milgrom P, Horst JA, Ludwig S, Rothen M, Chaffee BW, Lyalina S, Pollard KS, DeRisi JL, Mancl L.

Journal of Dentistry, 2017

A Novel Cause of Chronic Viral Meningoencephalitis: Cache Valley Virus
Michael R. Wilson, M.D., M.A.S., Dan Suan, M.B.B.S., PhD, Andrew Duggins, M.B.B.S., Ph.D., Ryan D. Schubert, M.D., Lillian M. Khan, B.S., Hannah A. Sample, B.S., Kelsey C. Zorn, M.H.S., Aline Rodrigues Hoffman, D.V.M., Ph.D., Anna Blick, B.S., Meena Shingde, F.R.C.P.A., Joseph L. DeRisi, Ph.D.

Annals of Neurology, 2017

Plasmid-free CRISPR/Cas9 genome editing in Plasmodium falciparum confirms mutations conferring resistance to the dihydroisoquinolone clinical candidate SJ733
Emily D. Crawford, Jenai Quan, Jeremy A. Horst, Daniel Ebert Wesley Wu, Joseph L. DeRisi

PLoS One, 2017

Zika virus cell tropism in the developing human brain and inhibition by azithromycin
Hanna Retallack, Elizabeth Di Lullo, Carolina Arias Kristeene A. Knopp, Matthew T. Laurie, Carmen Sandoval-Espinosa, Walter R. Mancia Leon, Robert Krencik, Erik M. Ullian, Julien Spatazza, Alex A. Pollen, Caleigh Mandel-Brehm, Tomasz J. Nowakowski, Arnold R. Kriegstein, and Joseph L. DeRisi

PNAS, 2017

Differential disease susceptibility in experimentally reptarenavirus infected boa constrictors and ball pythons
Mark D. Stenglein , David Sanchez-Migallon Guzman , Valentina E. Garcia , Marylee L. Layton , Laura L. Hoon-Hanks , Scott M. Boback , M. Kevin Keel , Tracy Drazenovich , Michelle G. Hawkins, Joseph L. DeRisi

Journal of Virology, 2017

Metagenomic DNA Sequencing for the Diagnosis of Intraocular Infections
Thuy Doan, MD, PhD, Nisha R. Acharya, MD, MS, Benjamin A. Pinsky, MD, PhD, Malaya K. Sahoo, PhD, Eric D. Chow, PhD, Niaz Banaei, MD, Indre Budvytiene, MS, CLS, Vicky Cevallos, MT, Lina Zhong, BS, Zhaoxia Zhou, BS, Thomas M. Lietman, MD, Joseph L. DeRisi, PhD

American Academy of Ophthamology, 2017

MinorityReport, software for generalized analysis of causal genetic variants
Horst JA, Wu W, DeRisi JL

Malaria Journal, 2017

A Herpesviral induction of RAE-1 NKG2D ligand expression occurs through release of HDAC mediated repression
Trever T Greene, Maria Tokuyama, Giselle M Knudsen, Michele Kunz, James Lin, Alexander L Greninger, Victor R DeFilippis, Joseph L DeRisi, David H Raulet, Laurent Coscoy

eLIFE, 2016

Acute West Nile virus meningoencephalitis diagnosed via metagenomic deep sequencing of cerebrospinal fluid in a renal transplant patient
Michael R. Wilson, M.D., Lara L. Zimmermann, M.D., Emily D. Crawford, Ph.D., Hannah A. Sample, B.S., Priya Soni, M.D., Amira Baker, M.D., Lillian M. Khan, B.S., Joseph L. DeRisi, Ph.D.

American Journal of Transplantation, 2016

Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens
Thuy Doan, Michael R. Wilson, Emily D. Crawford, Eric D. Chow, Lillian M. Khan, Kristeene A. Knopp, Brian D. O ’ Donovan, Dongxiang Xia, Jill K. Hacker, Jay M. Stewart, John A. Gonzales, Nisha R. Acharya and Joseph L. DeRisi

Genome Medicine, 2016

Multiplexed Metagenomic Deep Sequencing To Analyze the Composition of High-Priority Pathogen Reagents
Michael R. Wilson, Greg Fedewa, Mark D. Stenglein, Judith Olejnik, Linda J. Rennick, Sham Nambulli, Friederike Feldmann, W. Paul Duprex, John H. Connor, Elke Mühlberger, Joseph L. DeRisi

ASM mSystems, 2016

Novel Picornavirus Associated with Avian Keratin Disorder in Alaskan Birds
Maxine Zylberberg, Caroline Van Hemert, John P. Dumbacher, Colleen M. Handel, Tarik Tihan, Joseph L. DeRisi

mBio 2016

Anti-malarial benzoxaboroles target P. falciparum leucyl-tRNA synthetase
Ebere Sonoiki, Andres Palencia, Denghui Guo, Vida Ahyong, Chen Dong, Xianfeng Li, Vincent S. Hernandez, Yong-Kang Zhang, Wai Choi, Jiri Gut, Jenny Legac, Roland Cooper, M.R.K Alley, Yvonne R. Freund, Joseph DeRisi, Stephen Cusack, Philip J. Rosenthal

AAC, 2016

Identification of Plasmodium falciparum specific translation inhibitors from the MMV Malaria Box using a high throughput in vitro translation screen
Vida Ahyong, Christine M. Sheridan, Kristoffer E. Leon, Jessica N. Witchley, Jonathan Diep, and Joseph L. DeRisi

Malaria Journal, 2016

Depletion of Abundant Sequences by Hybridization (DASH): Using Cas9 to remove unwanted highabundance species in sequencing libraries and molecular counting applications
Gu W*, Crawford ED*, O’Donovan BD, Wilson MR, Chow ED, Retallack H, DeRisi JL (*These authors contributed equally)

BioRxiv, 2015 and Genome Biology, 2016

Diagnosing Balamuthia mandrillaris Encephalitis With Metagenomic Deep Sequencing
Michael R. Wilson MD, Niraj M. Shanbhag MD, PhD, Michael J. Reid MD, Neel S. Singhal MD, PhD, Jeffrey M. Gelfand MD, MAS, Hannah A. Sample BS, Barlas Benkli BA, Brian D. O’Donovan MS, Ibne K.M. Ali PhD, M. Kelly Keating DVM, Thelma H. Dunnebacke PhD, Matthew D. Wood MD, PhD, Andrew Bollen MD, and Joseph L. DeRisi PhD

Annals of Neurology, 2015

Genome Announcements Collection 2: Tombunodavirus UC1; Picalivirus D; Laverivirus UC1
Alexander L. Greninger, Joseph L. DeRisi

Genome Announcements, 2015

Genome Announcements Collection 1: Ciliovirus, Brinovirus; Marine RNA Viruses SF-1, SF-2, SF-3; Leviviridae RNA Phages EC and MB
Alexander L. Greninger, Joseph L. DeRisi

Genome Announcements, 2015

Widespread Recombination, Reassortment, and Transmission of Unbalanced Compound Viral Genotypes in Natural Arenavirus Infections
Mark D. Stenglein, Elliott R. Jacobson, Li-Wen Chang, Chris Sanders, Michelle G. Hawkins, David S-M. Guzman, Tracy Drazenovich, Freeland Dunker, Elizabeth K. Kamaka, Debbie Fisher, Drury R. Reavill, Linda F. Meola, Gregory Levens, Joseph L. DeRisi

PLoS, 2015

Destructin-1 is a Collagen-Degrading Endopeptidase Secreted by P. destructans, the Causative Agent of White-Nose Syndrome
Anthony J. O’Donoghue, Giselle M. Knudsen, Chapman Beekman, Jenna Perry, Alexander D. Johnson, Joseph L. DeRisi, Charles S. Craik, and Richard J. Bennett

PNAS, 2015

A chemical rescue screen identifies a P.falcip. apicoplast inhibitor targeting MEP isoprenoid precursor biosynthesis
Wesley Wu, Zachary Herrera, Danny Ebert, Katie Baska, Seok H. Cho, Joseph L. DeRisi, Ellen Yeh

AAC, 2014

Genome-wide regulatory dynamics of translation in the Plasmodium falciparum asexual blood stages
Florence Caro, Vida Ahyong, Miguel Betegon, Joseph L DeRisi

eLife, 2014

SJ733, a clinical candidate for malaria that acts through ATP4 to induce rapid host-mediated clearance of Plasmodium
Jiménez-Díaz MB, Ebert D, and many more authors.

PNAS, 2014

Ball Python Nidovirus: a Candidate Etiologic Agent for Severe Respiratory Disease in Python regius
Mark D. Stenglein, Elliott R. Jacobson, Edward J. Wozniak, James F. X. Wellehan, Anne Kincaid, Marcus Gordon, Brian F. Porter, Wes Baumgartner, Scott Stahl, Karen Kelley, Jonathan S. Towner, Joseph L. DeRisi

mBio, 2014

Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing
Wilson, Naccache, Samayoa, Biagtan, Bashir, Yu, Salamat, Somasekar, Federman, Miller, Sokolic, Garabedian, Candotti, Buckley, Reed, Meyer, Seroogy, Galloway, Henderson, Gern, DeRisi, Chiu

NEJM, 2014

The Kinase Regulator Mob1 Acts as a Patterning Protein for Stentor Morphogenesis
Mark M. Slabodnick, J. Graham Ruby, Joshua G. Dunn, Jessica L. Feldman, Joseph L. DeRisi, Wallace F. Marshall

PLoS Biology, 2014

Kruppel Mediates the Selective Rebalancing of Ion Channel Expression
Jay Z. Parrish, Charles C. Kim, Lamont Tang, Sharon Bergquist, Tingting Wang, Joseph L. DeRisi, Lily Yeh Jan, Yuh Nung Jan, and Graeme W. Davis

Neuron, 2014

Structural Characterization of the Glycoprotein GP2 Core Domain from the CAS Virus, a Novel Arenavirus
Jayne F. Koellhoffer, Zhou Dai, Vladimir N. Malashkevich, Mark D. Stenglein, Yanyun Liu, Rafael Toro, Joseph S. Harrison, Kartik Chandran, Joseph L. DeRisi, Steven C. Almo and Jonathan R. Lai

J. Mol. Bio., 2014

Structure of the transcriptional network controlling white-opaque switching in Candida albicans
Hernday AD, Lohse MB, Fordyce PM, Nobile CJ, Derisi JL, Johnson AD

Mol Microbiol, 2013

Asexual populations of the malaria parasite, P.falcip, use a 2-step genomic strategy to acquire beneficial DNA amplifications
Guler JL, Freeman DL, Ahyong V, Patrapuvich R, White J, Gujjar R, Phillips MA, DeRisi J, Rathod PK

PLoS Pathog., 2013

PRICE: software for the targeted assembly of components of (Meta) genomic sequence data
Ruby JG, Bellare P, Derisi JL

G3 (Bethesda), 2013

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

PNAS, 2013

Microfluidic affinity and ChIP-seq analyses converge on a conserved FOXP2-binding motif in chimp and human...
Christopher S. Nelson1, Chris K. Fuller, Polly M. Fordyce, Alexander L. Greninger, Hao Li, and Joseph L. DeRisi

NAR, 2013

ACBD3 Interaction with TBC1 Domain 22 Protein Is Differentially Affected by Enteroviral and Kobuviral 3A Protein Binding
Alexander L. Greninger, Giselle M. Knudsen, Miguel Betegon, Alma L. Burlingame, Joseph L. DeRisi

mBio, 2013

Bartonella quintana Deploys Host and Vector Temperature-Specific Transcriptomes
Stephanie Abromaitis, Christopher S. Nelson, Domenic Previte, Kyong S. Yoon, J. Marshall Clark, Joseph L. DeRisi, Jane E. Koehler

PLos One 2013

Identification and manipulation of the molecular determinants influencing poliovirus recombination.
Charles Runckel, Oscar Westesson, Raul Andino, Joseph DeRisi

PLoS Pathogen, 2013

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution
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

Genome Biol., 2013

Splenic Red Pulp Macrophages Produce Type I Interferons as Early Sentinels of Malaria Infection...
Charles C. Kim, Christopher S. Nelson, Emily B. Wilson, Baidong Hou, Anthony L. DeFranco, Joseph L. DeRisi

PLoS One 2012

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

J Am Chem Soc., 2012

Global identification of peptidase specificity by multiplex substrate profiling
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.

Nat Methods, 2012

Complete genome sequence of an astrovirus identified in a domestic rabbit with gastroenteritis
Stenglein MD, Velazquez E, Greenacre C, Wilkes RP, Ruby JG, Lankton JS, Ganem D, Kennedy MA, DeRisi JL

Virol J., 2012

Programmable microfluidic synthesis of spectrally encoded microspheres
Rachel E. Gerver, Rafael Gomez-Sjoberg, Brian C. Baxter, Kurt S. Thorn, Polly M. Fordyce, Camilo A. Diaz-Botia, Brett A. Helms and Joe L. DeRisi

Lab on a Chip 2012

Basic leucine zipper transcription factor Hac1 binds DNA in two distinct modes as revealed by microfluidic analyses
Polly M. Fordyce, David Pincus, Philipp Kimmig, Christopher S. Nelson, Hana El-Samad, Peter Walter, and Joseph L. DeRisi

PNAS 2012

Identification, Characterization, and In Vitro Culture of Highly Divergent Arenaviruses from Boa Constrictors
Mark D. Stenglein, Chris Sanders, Amy L. Kistler, J. Graham Ruby, Jessica Y. Franco, Drury R. Reavill, Freeland Dunker, and Joseph L. DeRisi

mBio, 2012

Lead optimization of antimalarial propafenone analogues
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

J Med Chem, 2012

Systematic characterization of feature dimensions and closing pressures for microfluidic valves produced via photoresist reflow
Polly M. Fordyce, Camilo A. Diaz-Botia, Joe L. DeRisi, and Rafael Gomez-Sjoberg

Lab on a Chip 2012

Virus Identification in Unknown Tropical Febrile Illness Cases Using Deep Sequencing
Nathan L. Yozwiak., Peter Skewes-Cox, Mark D. Stenglein., Angel Balmaseda, Eva Harris, Joseph L. DeRisi

PLoS Neglected Tropical Diseases, 2012

The 3A protein from multiple picornaviruses utilizes the Golgi Adaptor Protein ACBD3 to Recruit PI4KIIIβ
Alexander L. Greninger, Giselle M. Knudsen, Miguel Betegon, Alma L. Burlingame and Joseph L. DeRisi

Journal of Virology, 2012

Plate-based transfection and culturing technique for genetic manipulation of Plasmodium falciparum
Florence Caro, Mathew G. Miller and Joseph L. DeRisi

Malaria Journal 2012

Chemical Rescue of Malaria Parasites Lacking an Apicoplast Defines Organelle Function in Blood-Stage P.falciparum
Ellen Yeh and Joseph DeRisi

PLoS Biology 2011

Temporal Analysis of the Honey Bee Microbiome Reveals Four Novel Viruses and Seasonal Prevalence of Known Viruses, Nosema, and Crithidia
Charles Runckel, Michelle L. Flenniken, Juan C. Engel, J. Graham Ruby, Donald Ganem, Raul Andino, Joseph L. DeRisi

PLoS ONE. 2011

Transcriptome Sequencing Demonstrates that Human Papillomavirus Is Not Active in Cutaneous Squamous Cell Carcinoma.
Arron ST, Ruby JG, Dybbro E, Ganem D, Derisi JL.

J Invest Dermatol. 2011

Viral Infection in Acute Exacerbation of Idiopathic Pulmonary Fibrosis
Sharon Chao Wootton, Dong Soon Kim, Yasuhiro Kondoh, Eunice Chen, Joyce S Lee, Jin Woo Song, Jin Won Huh, Hiroyuki Taniguchi, Charles Chiu, Homer Boushey, Lisa H Lancaster, Paul J Wolters, Joseph DeRisi, Don Ganem, and Harold R Collard

Am. J. Respir. Crit. Care Med. 2011

RNA-Seq analysis of splicing in P.falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts
Katherine Sorber, Michelle T. Dimon and Joseph L. DeRisi

Nuc. Acids Res. 2010

HMMSplicer: A Tool for Efficient and Sensitive Discovery of Known and Novel Splice Junctions in RNA-Seq Data
Dimon MT, Sorber K, Derisi JL

PLoS One 2010

De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis
Polly M Fordyce, Doron Gerber, Danh Tran, Jiashun Zheng, Hao Li, Joseph L DeRisi & Stephen R Quake

Nat Biotech. 2010

Serological evidence of human klassevirus infection
Greninger AL, Holtz L, Kang G, Ganem D, Wang D, Derisi JL

Clin Vaccine Immunol. 2010

Human Enterovirus 109: a novel inter-species recombinant enterovirus discovered in acute pediatric respiratory illness in Nicaragua
Yozwiak NL, Skewes-Cox P, Gordon A, Saborio S, Kuan G, Balmaseda A, Ganem D, Harris E, Derisi JL

J Virol. 2010

Chemical genetics of Plasmodium falciparum.
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.

Nature. 2010

Cultivation and serological characterization of a human Theilers like cardiovirus
Chiu CY, Greninger AL, Chen EC, Haggerty TD, Parsonnet J, Delwart E, Derisi JL, Ganem D.

J Virol. 2010

Genetic interactions between a phospholipase A(2) and the Rim101 pathway components in S. cerevisiae reveal a role for this pathway in response to changes in membrane composition and shape.
Mattiazzi M, Jambhekar A, Kaferle P, Derisi JL, Kri?aj I, Petrovič U

Mol Genet Genomics. 2010

Development of a New Generation of 4-Aminoquinoline Antimalarial Compounds Using Predictive Pharmacokinetic and Toxicology Models.
Ray S, Madrid PB, Catz P, Levalley SE, Furniss MJ, Rausch LL, Guy RK, Derisi JL, Iyer LV, Green CE, Mirsalis JC.

J Med Chem. 2010

Analysis of Naturally Occurring Avian Bornavirus Infection and Transmission during an Outbreak of Proventricular Dilatation Disease among Captive Psittacine Birds
Kistler AL, Smith JM, Greninger AL, Derisi JL, Ganem D.

J Virol. 2010 Feb

Improved methods for magnetic purification of malaria parasites and haemozoin.
Kim CC, Wilson EB, DeRisi JL.

Malar J. 2010 Jan

VersaCount: customizable manual tally software for cell counting.
Kim CC, Derisi JL.

Source Code Biol Med. 2010 Jan

An Enhanced Single Base Extension Technique for the Analysis of Complex Viral Populations
Webster DR, Hekele AG, Lauring AS, Fischer KF, Li H, Andino R, DeRisi JL.

PLoS One. 2009 Oct

Antiparasitic activities of novel, orally available fumagillin analogs
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.

Bioorg Med Chem Lett. 2009 Sep

Inhibiting Plasmodium falciparum growth and heme detoxification pathway using heme-binding DNA aptamers.
Niles JC, Derisi JL, Marletta MA.

Proc Natl Acad Sci U S A. 2009 Aug

Experimental induction of proventricular dilatation disease in cockatiels inoculated with brain homogenates containing AVB 4.
Gancz AY, Kistler AL, Greninger AL, Farnoushi Y, Mechani S, Perl S, Berkowitz A, Perez N, Clubb S, DeRisi JL, Ganem D, Lublin A

Virol J. 2009 Jul 9;6:100

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

Virol J. 2009 Jun 18;6:82

Recovery of divergent avian bornaviruses from cases of proventricular dilatation disease: identification of a candidate etiologic agent
Amy L Kistler , Ady Gancz , Susan Clubb , Peter Skewes-Cox , Kael Fischer , Katherine Sorber , Charles Y. Chiu , Avishai Lublin , Sara Mechani , Yigal Farnoushi , Alexander Greninger , Christopher C. Wen , Scott B. Karlene , Don Ganem and Joseph L. DeRisi

Virology Journal 2008

The Long March: A Sample Preparation Technique that Enhances Contig Length and Coverage by High-Throughput Short-Read Sequencing
Katherine Sorber1#, Charles Chiu1,4#, Dale Webster1,2¶, Michelle Dimon1,2¶, J. Graham Ruby1, Armin Hekele3, Joseph L. DeRisi1,5*

PLoS ONE 2008

Experimental Malaria Infection Triggers Early Expansion of Natural Killer Cells
Charles C. Kim, Sunil Parikh, Joseph C. Sun, Alissa Myrick, Lewis L. Lanier, Philip J. Rosenthal, and Joseph L. DeRisi*

Infect. Immun. 2008

Identification of cardioviruses related to Theilers murine encephalomyelitis virus in human infections.
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.

PNAS. 2008

Dynamics and design principles of a basic regulatory architecture controlling metabolic pathways.
Chin CS, Chubukov V, Jolly ER, DeRisi J, Li H.

PLoS Biol. 2008

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

Mol Biochem Parasitol. 2008

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

J Pediatr. 2008

Whole-genome analysis of mRNA decay in P.falciparum reveals a global lengthening of mRNA half-life
Jennifer Shock, Kael Fischer and Joseph L DeRisi

Genome Biology 2007

Pan-Viral Screening of Respiratory Tract Infections in Adults with and without Asthma Reveals Unexpected Diversity
Amy Kistler, Pedro Avila, Silvi Rouskin, David Wang, Theresa Ward, Shigeo Yagi, David Schnurr, Don Ganem, Joseph DeRisi and Homer Boushey

JID 2007

Diagnosis of a Critical Respiratory Illness from Human Metapneumovirus Using a Pan-Viral Microarray
Chiu, Alizadeh, Rouskin, Merker, Yeh, Yagi, Schnurr, Patterson, Ganem, Derisi

J Clin Micro 2007

Genome-wide diversity and selective pressure in the human rhinovirus
Amy L Kistler, Dale R Webster, Silvi Rouskin, Vince Magrini, Joel J Credle, David P Schnurr, Homer A Boushey, Elaine R Mardis, Hao Li, Joseph L DeRisi

Virology Journal 2007

Cis-acting determinants of asymmetric, cytoplasmic RNA transport.
Jambhekar A, Derisi JL

RNA. 2007

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

Genome Biol 2007

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

PNAS 2007

A Bayesian network driven approach to model the transcriptional response to NO in S cerevisiae
Zhu J, Jambhekar A, Sarver A, DeRisi J.

PLoS ONE 2006

Microarray detection of human parainfluenzavirus-4 infection associated with respiratory failure
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

Clin Infect Dis 2006

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

Chem Biol Drug Des. 2006

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

Nature. 2006

Tetracyclines specifically target the apicoplast of the malaria parasite P. falciparum
Dahl EL, Shock JL, Shenai BR, Gut J, DeRisi JL, Rosenthal PJ.

Antimicrobial Agts Chemother 2006

Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains
Llinas M, Bozdech Z, Wong ED, Adai AT, DeRisi JL

Nucl Acids Res 2006

Incorporation of an intramolecular hydrogen-bonding motif in the side chain of 4-aminoquinolines enhances activity against drug-resistant P. falciparum.
Madrid PB, Liou AP, DeRisi JL, Guy RK.

J Med Chem. 2006

Genome-wide map of DNA synthesis in Sc reveals mechanisms preventing reinitiation of DNA replication are not redundant.
Green BM, Morreale RJ, Ozaydin B, DeRisi JL, Li JJ

Mol Biol Cell 2006

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

Proc Natl Acad Sci U S A. 2005

Parallel synthesis of 9-aminoacridines and evaluation against chloroquine-resistant falciparum
Anderson MO, Sherrill J, Madrid PB, Liou AP, Weisman JL, DeRisi JL, Guy RK.

Bioorg Med Chem 2006

Genome-wide identification of genes upregulated at onset of gametocytogenesis in P. falciparum
Silvestrini F, Bozdech Z, Lanfrancotti A, Di Giulio E, Bultrini E, Picci L, DeRisi JL, Pizzi E, Alano P.

Mol Biochem Parasitol 2005

E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns.
Urisman A, Fischer KF, Chiu CY, Kistler AL, Beck S, Wang D, DeRisi JL.

Genome Biol. 2005

Fzf1p regulates an inducible response to nitrosative stress in Saccharomyces cerevisiae
Sarver A, DeRisi J.

Mol Biol Cell 2005

Synthesis of ring-substituted 4-aminoquinolines and evaluation of their antimalarial activities
Madrid PB, Sherrill J, Liou AP, Weisman JL, DeRisi JL, Guy RK.

Bioorg Med Chem Lett 2005

Genome-scale approaches for discovering novel nonconventional splicing substrates of the Ire1 nuclease
Niwa M, Patil CK, DeRisi J, Walter P.

Genome Biol 2005

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

Proc Natl Acad Sci U S A. 2004

Pernicious plans revealed: Plasmodium falciparum genome wide expression analysis
Llinas M, DeRisi JL.

Curr Opin Microbiol 2004

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

PLoS Biol 2004

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

PLoS Biol 2004

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

Bioorg Med Chem. 2006

Viral discovery and sequence recovery using DNA microarrays.
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.

PLoS Biology 2003

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

Proc Natl Acad Sci U S A. 2003

The transcriptome of the intraerythrocytic developmental cycle of P falciparum
Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL.

PLoS Biol 2003

Characterization of a novel coronavirus associated with severe acute respiratory syndrome.
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.

Science. 2003

A novel coronavirus associated with severe acute respiratory syndrome.
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

N Engl J Med 2003

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

Mol Biol Cell. 2003

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

Genome Biol 2003

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

Science. 2002

Microarray-based detection and genotyping of viral pathogens
Wang D, Coscoy L, Zylberberg M, Avila PC, Boushey HA, Ganem D, DeRisi JL

Proc Natl Acad Sci U S A. 2002

Modulation of host gene expression by the constitutively active G protein-coupled receptor of Kaposi's sarcoma-associated herpesvirus.
Polson AG, Wang D, DeRisi J, Ganem D.

Cancer Res. 2002

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

PNAS 2002

Mnd1p: an evolutionarily conserved protein required for meiotic recombination.
Gerton JL, DeRisi JL.

Proc Natl Acad Sci U S A. 2002

DNA microarrays for malaria.
Rathod PK, Ganesan K, Hayward RE, Bozdech Z, DeRisi JL.

Trends Parasitol. 2002

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

Proc Natl Acad Sci U S A. 2001

Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays
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.

Proc Natl Acad Sci U S A. 2001

Functional genomic analysis of a commercial wine strain of Saccharomyces cerevisiae under differing nitrogen conditions.
Backhus LE, DeRisi J, Bisson LF.

FEMS Yeast Res. 2001

New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis.
Ogawa N, DeRisi J, Brown PO.

Mol Biol Cell. 2000

Plasma membrane compartmentalization in yeast by messenger RNA transport and a septin diffusion barrier
Takizawa PA, DeRisi JL, Wilhelm JE, Vale RD

Science. 2000

Global and specific translational regulation in the genomic response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source.
Kuhn KM, DeRisi JL, Brown PO, Sarnow P.

Mol Cell Biol. 2001

Inaugural article: global mapping of meiotic recombination hotspots and coldspots in the yeast S. cerevisiae
Gerton JL, DeRisi J, Shroff R, Lichten M, Brown PO, Petes TD.

PNAS 2000

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

Proc Natl Acad Sci U S A. 2000

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

FEBS Lett. 2000

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

Mol Microbiol. 2000

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

Proc Natl Acad Sci U S A. 1999

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

Genetics 1998

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

Nature Med 1998

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

Science 1998

Effects of mutations in residues near the active site of HIV type 1 integrase on specific enzyme-substrate interactions.
Gerton JL, Ohgi S, Olsen M, DeRisi J, Brown PO.

J Virology 1998

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

PNAS 1997

Exploring the metabolic and genetic control of gene expression on a genomic scale.
DeRisi JL, Iyer VR, Brown PO

Science. 1997

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

Nature Genetics 1996

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

Nucleic Acids Res. 1994

Clinical features, diagnostics, and outcomes of patients presenting with acute respiratory illness: A retrospective cohort study of patients with and without COVID-19
Shah SJ, Barish PN, Prasad PA, Kistler A, Neff N, Kamm J, Li LM, Chiu CY, Babik JM, Fang MC, Abe-Jones Y, Alipanah N, Alvarez FN, Botvinnik OB, Castaneda G; CZB CLIAhub Consortium, Dadasovich RM, Davis J, Deng X, DeRisi JL, Detweiler AM, Federman S, Haliburton J, Hao S, Kerkhoff AD, Kumar GR, Malcolm KB, Mann SA, Martinez S, Mary RK, Mick E, Mwakibete L, Najafi N, Peluso MJ, Phelps M, Pisco AO, Ratnasiri K, Rubio LA, Sellas A, Sherwood KD, Sheu J, Spottiswoode N, Tan M, Yu G, Kangelaris KN, Langelier C.

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