Amy Kistler, PhD
Associate Professor
Biochemistry and Biophysics
School of Medicine

Publications (55)

Top publication keywords:
Bird DiseasesDengue VirusBornaviridaeHost-Pathogen InteractionsCRISPR-Cas SystemsChiropteraRepliconRhinovirusFlaviviridaeProventriculusGenome, ViralMononegavirales InfectionsVirus ReplicationHepatitis, Viral, AnimalFlaviviridae Infections

• Discovery of a novel bandavirus using metagenomic sequencing in a retrospective analysis of an unresolved 2020 mortality event involving wild black vultures in the northeastern United States.
  Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc 2026 Mwakibete L, Hoarau AOG, Ahyong V, Waltari E, Bender SJ, Davison S, Niedringhaus KD, Gibison ML, Gagne RB, Miller EA, Murphy LA, Kistler AL, Tato CM
• Implementation and outcomes of a rapid response genomic hospital epidemiology programme at an academic medical centre over 7 years.
  The Lancet. Microbe 2026 Chu VT, Spottiswoode N, Ward R, Yokoe DS, Ramirez-Avila L, Phelps MS, Glascock A, Crawford ED, Kamm J, Hao S, Li L, Dynerman D, Waltari E, Nafees S, Kalantar KL, Caldera S, Madera S, Guerrero ES, …
• Replicon-based genome-wide CRISPR knockout screening for the identification of host factors involved in viral replication.
  Nature communications 2025 Cheng KW, Bhave M, Markhard AL, Peng D, Bhatt KD, Travisano KA, Medicielo JV, Anaya A, Lembirik S, Njoya L, Anantpadma M, Kuhn JH, Puschnik AS, Kistler AL
• Evidence for Maternal Autoantibodies in the Pathogenesis of Preterm Birth.
  medRxiv : the preprint server for health sciences 2025 Rackaityte E, Borges B, Kortbawi HM, Miller HS, Shao SJ, Zorn KC, Caspar C, Wong R, McCarthy F, Creery JS, Mayer M, Kouame E, Puccinelli RR, Kistler AL, Yu DJL, Ganem SR, DeRisi A, Kawaja Q, Wang CY, …
• Correction: Detection, characterization, and phylogenetic analysis of novel astroviruses from endemic Malagasy fruit bats.
  Virology journal 2024 Horigan S, Kettenburg G, Kistler A, Ranaivoson HC, Andrianiaina A, Andry S, Raharinosy V, Randriambolamanantsoa TH, Tato CM, Lacoste V, Heraud JM, Dussart P, Brook CE

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• Detection, characterization, and phylogenetic analysis of novel astroviruses from endemic Malagasy fruit bats.
  Virology journal 2024 Horigan S, Kettenburg G, Kistler A, Ranaivoson HC, Andrianiaina A, Andry S, Raharinosy V, Randriambolamanantsoa TH, Tato CM, Lacoste V, Heraud JM, Dussart P, Brook CE
• Metatranscriptomic investigation of single Ixodes pacificus ticks reveals diverse microbes, viruses, and novel mRNA-like endogenous viral elements.
  mSystems 2024 Martyn C, Hayes BM, Lauko D, Midthun E, Castaneda G, Bosco-Lauth A, Salkeld DJ, Kistler A, Pollard KS, Chou S
• A 2-Gene Host Signature for Improved Accuracy of COVID-19 Diagnosis Agnostic to Viral Variants.
  mSystems 2022 Albright J, Mick E, Sanchez-Guerrero E, Kamm J, Mitchell A, Detweiler AM, Neff N, Tsitsiklis A, Hayakawa Serpa P, Ratnasiri K, Havlir D, Kistler A, DeRisi JL, Pisco AO, Langelier CR
• Deconvoluting complex correlates of COVID-19 severity with a multi-omic pandemic tracking strategy.
  Nature communications 2022 Parikh VN, Ioannidis AG, Jimenez-Morales D, Gorzynski JE, De Jong HN, Liu X, Roque J, Cepeda-Espinoza VP, Osoegawa K, Hughes C, Sutton SC, Youlton N, Joshi R, Amar D, Tanigawa Y, Russo D, Wong J, …
• Discovery and Genomic Characterization of a Novel Henipavirus, Angavokely Virus, from Fruit Bats in Madagascar.
  Journal of virology 2022 Madera S, Kistler A, Ranaivoson HC, Ahyong V, Andrianiaina A, Andry S, Raharinosy V, Randriambolamanantsoa TH, Ravelomanantsoa NAF, Tato CM, DeRisi JL, Aguilar HC, Lacoste V, Dussart P, Heraud JM, …
• Quantitative reverse transcription PCR assay to detect a genetic marker of pyrethroid resistance in Culex mosquitoes.
  PloS one 2022 Hager KM, Gaona E, Kistler A, Ratnasiri K, Retallack H, Barretto M, Wheeler SS, Hoover CM, Haas-Stapleton EJ
• Anti-nucleocapsid antibody levels and pulmonary comorbid conditions are linked to post-COVID-19 syndrome.
  JCI insight 2022 Jia X, Cao S, Lee AS, Manohar M, Sindher SB, Ahuja N, Artandi M, Blish CA, Blomkalns AL, Chang I, Collins WJ, Desai M, Din HN, Do E, Fernandes A, Geng LN, Rosenberg-Hasson Y, Mahoney MR, Glascock AL, …
• Upper airway gene expression shows a more robust adaptive immune response to SARS-CoV-2 in children.
  Nature communications 2022 Mick E, Tsitsiklis A, Spottiswoode N, Caldera S, Serpa PH, Detweiler AM, Neff N, Pisco AO, Li LM, Retallack H, Ratnasiri K, Williamson KM, Soesanto V, Simões EAF, Smith C, Abuogi L, Kistler A, Wagner …
• Genomic Epidemiology and Transmission Dynamics of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Congregate Healthcare Facilities in Santa Clara County, California.
  Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2022 MacCannell T, Batson J, Bonin B, Astha KC, Quenelle R, Strong B, Lin W, Rudman SL, Dynerman D, Ayscue P, Han G, Kistler A, Villarino ME, Chan Zuckerberg Biohub COVIDTracker Consortium and the Santa …
• Using genomic epidemiology of SARS-CoV-2 to support contact tracing and public health surveillance in rural Humboldt County, California.
  BMC public health 2022 Stoddard G, Black A, Ayscue P, Lu D, Kamm J, Bhatt K, Chan L, Kistler AL, Batson J, Detweiler A, Tan M, Neff N, DeRisi JL, Corrigan J
• Full Genome Nobecovirus Sequences From Malagasy Fruit Bats Define a Unique Evolutionary History for This Coronavirus Clade.
  Frontiers in public health 2022 Kettenburg G, Kistler A, Ranaivoson HC, Ahyong V, Andrianiaina A, Andry S, DeRisi JL, Gentles A, Raharinosy V, Randriambolamanantsoa TH, Ravelomanantsoa NAF, Tato CM, Dussart P, Heraud JM, Brook CE
• Estimation of Secondary Household Attack Rates for Emergent Spike L452R Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants Detected by Genomic Surveillance at a Community-Based Testing Site in San Francisco.
  Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2022 Peng J, Liu J, Mann SA, Mitchell AM, Laurie MT, Sunshine S, Pilarowski G, Ayscue P, Kistler A, Vanaerschot M, Li LM, McGeever A, Chow ED, Marquez C, Nakamura R, Rubio L, Chamie G, Jones D, Jacobo J, …
• Impaired immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19.
  medRxiv : the preprint server for health sciences 2021 Tsitsiklis A, Zha BS, Byrne A, DeVoe C, Rackaityte E, Levan S, Sunshine S, Mick E, Ghale R, Love C, Tarashansky AJ, Pisco A, Albright J, Jauregui A, Sarma A, Neff N, Serpa PH, Deiss TJ, Kistler A, …
• SARS-CoV-2 Infection of Rhesus Macaques Treated Early with Human COVID-19 Convalescent Plasma.
  Microbiology spectrum 2021 Deere JD, Carroll TD, Dutra J, Fritts L, Sammak RL, Yee JL, Olstad KJ, Reader JR, Kistler A, Kamm J, Di Germanio C, Shaan Lakshmanappa Y, Elizaldi SR, Roh JW, Simmons G, Watanabe J, Pollard RE, …
• Upper airway gene expression reveals a more robust innate and adaptive immune response to SARS-CoV-2 in children compared with older adults.
  Research square 2021 Mick E, Tsitsiklis A, Spottiswoode N, Caldera S, Serpa PH, Detweiler AM, Neff N, Pisco AO, Li LM, Retallack H, Ratnasiri K, Williamson KM, Soesanto V, Simões EAF, Kistler A, Wagner BD, DeRisi JL, …
• Community Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 Disproportionately Affects the Latinx Population During Shelter-in-Place in San Francisco.
  Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 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…
• Single mosquito metatranscriptomics identifies vectors, emerging pathogens and reservoirs in one assay.
  eLife 2021 Batson J, Dudas G, Haas-Stapleton E, Kistler AL, Li LM, Logan P, Ratnasiri K, Retallack H
• Impaired immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19.
  Research square 2021 Tsitsiklis A, Zha BS, Byrne A, Devoe C, Levan S, Rackaityte E, Sunshine S, Mick E, Ghale R, Jauregui A, Sarma A, Neff N, Serpa PH, Deiss TJ, Kistler A, Carrillo S, Ansel KM, Leligdowicz A, Christenson…
• Estimation of secondary household attack rates for emergent SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco.
  medRxiv : the preprint server for health sciences 2021 Peng J, Mann SA, Mitchell AM, Liu J, Laurie MT, Sunshine S, Pilarowski G, Ayscue P, Kistler A, Vanaerschot M, Li LM, McGeever A, Chow ED, Team I, Marquez C, Nakamura R, Rubio L, Chamie G, Jones D, …
• Identification of a Polymorphism in the N Gene of SARS-CoV-2 That Adversely Impacts Detection by Reverse Transcription-PCR.
  Journal of clinical microbiology 2020 Vanaerschot M, Mann SA, Webber JT, Kamm J, Bell SM, Bell J, Hong SN, Nguyen MP, Chan LY, Bhatt KD, Tan M, Detweiler AM, Espinosa A, Wu W, Batson J, Dynerman D, Wadford DA, Puschnik AS, Neff N, Ahyong …
• Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy.
  Cell 2020 Fozouni P, Son S, Díaz de León Derby M, Knott GJ, Gray CN, D'Ambrosio MV, Zhao C, Switz NA, Kumar GR, Stephens SI, Boehm D, Tsou CL, Shu J, Bhuiya A, Armstrong M, Harris AR, Chen PY, Osterloh JM, …
• Upper airway gene expression reveals suppressed immune responses to SARS-CoV-2 compared with other respiratory viruses.
  Nature communications 2020 Mick E, Kamm J, Pisco AO, Ratnasiri K, Babik JM, Castañeda G, DeRisi JL, Detweiler AM, Hao SL, Kangelaris KN, Kumar GR, Li LM, Mann SA, Neff N, Prasad PA, Serpa PH, Shah SJ, Spottiswoode N, Tan M, …
• Rapid deployment of SARS-CoV-2 testing: The CLIAHUB.
  PLoS pathogens 2020 Crawford ED, Acosta I, Ahyong V, Anderson EC, Arevalo S, Asarnow D, Axelrod S, Ayscue P, Azimi CS, Azumaya CM, Bachl S, Bachmutsky I, Bhaduri A, Brown JB, Batson J, Behnert A, Boileau RM, Bollam SR, …
• High-throughput SARS-CoV-2 and host genome sequencing from single nasopharyngeal swabs.
  medRxiv : the preprint server for health sciences 2020 Gorzynski JE, De Jong HN, Amar D, Hughes CR, Ioannidis A, Bierman R, Liu D, Tanigawa Y, Kistler A, Kamm J, Kim J, Cappello L, Neff NF, Rubinacci S, Delaneau O, Shoura MJ, Seo K, Kirillova A, Raja A, …
• Clinical features, diagnostics, and outcomes of patients presenting with acute respiratory illness: A retrospective cohort study of patients with and without COVID-19.
  EClinicalMedicine 2020 Shah SJ, Barish PN, Prasad PA, Kistler A, Neff N, Kamm J, Li LM, Chiu CY, Babik JM, Fang MC, Abe-Jones Y, Alipanah N, Alvarez FN, Botvinnik OB, Castaneda G, CZB CLIAhub Consortium, Dadasovich RM, …
• Complete Genome Sequence of a Novel Coronavirus (SARS-CoV-2) Isolate from Bangladesh.
  Microbiology resource announcements 2020 Saha S, Malaker R, Sajib MSI, Hasanuzzaman M, Rahman H, Ahmed ZB, Islam MS, Islam M, Hooda Y, Ahyong V, Vanaerschot M, Batson J, Hao S, Kamm J, Kistler A, Tato CM, DeRisi JL, Saha SK
• Upper airway gene expression differentiates COVID-19 from other acute respiratory illnesses and reveals suppression of innate immune responses by SARS-CoV-2.
  medRxiv : the preprint server for health sciences 2020 Mick E, Kamm J, Pisco AO, Ratnasiri K, Babik JM, Calfee CS, Castañeda G, DeRisi JL, Detweiler AM, Hao S, Kangelaris KN, Kumar GR, Li LM, Mann SA, Neff N, Prasad PA, Serpa PH, Shah SJ, Spottiswoode N, …
• Clinical features, diagnostics, and outcomes of patients presenting with acute respiratory illness: a comparison of patients with and without COVID-19.
  medRxiv : the preprint server for health sciences 2020 Shah SJ, Barish PN, Prasad PA, Kistler AL, Neff N, Kamm J, Li LM, Chiu CY, Babick JM, Fang MC, Abe-Jones Y, Alipanah N, Alvarez FN, Botvinnik OB, Davis JM, Castenada GD, Consortium C, Dadasovich RM, …
• An exploration of ambigrammatic sequences in narnaviruses.
  Scientific reports 2019 DeRisi JL, Huber G, Kistler A, Retallack H, Wilkinson M, Yllanes D
• A Toolkit for Rapid Modular Construction of Biological Circuits in Mammalian Cells.
  ACS synthetic biology 2019 Fonseca JP, Bonny AR, Kumar GR, Ng AH, Town J, Wu QC, Aslankoohi E, Chen SY, Dods G, Harrigan P, Osimiri LC, Kistler AL, El-Samad H
• JC polyoma viruria associates with protection from chronic kidney disease independently from apolipoprotein L1 genotype in African Americans.
  Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association 2018 Freedman BI, Kistler AL, Skewes-Cox P, Ganem D, Spainhour M, Turner J, Divers J, Langefeld CD, Murea M, Hicks PJ, Hemal AK, Snipes JA, Zhao L, Abend JR, Lyles DS, Ma L, Skorecki KL
• Correlation of BK Virus Neutralizing Serostatus With the Incidence of BK Viremia in Kidney Transplant Recipients.
  Transplantation 2017 Abend JR, Changala M, Sathe A, Casey F, Kistler A, Chandran S, Howard A, Wojciechowski D
• Identification of a previously undescribed divergent virus from the Flaviviridae family in an outbreak of equine serum hepatitis.
  Proceedings of the National Academy of Sciences of the United States of America 2013 Chandriani S, Skewes-Cox P, Zhong W, Ganem DE, Divers TJ, Van Blaricum AJ, Tennant BC, Kistler AL
• Identification, characterization, and in vitro culture of highly divergent arenaviruses from boa constrictors and annulated tree boas: candidate etiological agents for snake inclusion body disease.
  mBio 2012 Stenglein MD, Sanders C, Kistler AL, Ruby JG, Franco JY, Reavill DR, Dunker F, Derisi JL
• Avian bornavirus is present in many tissues of psittacine birds with histopathologic evidence of proventricular dilatation disease.
  Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc 2010 Raghav R, Taylor M, Delay J, Ojkic D, Pearl DL, Kistler AL, Derisi JL, Ganem D, Smith DA
• Achalasia and viral infection: new insights from veterinary medicine.
  Science translational medicine 2010 Ganem D, Kistler A, DeRisi J
• Analysis of naturally occurring avian bornavirus infection and transmission during an outbreak of proventricular dilatation disease among captive psittacine birds.
  Journal of virology 2009 Kistler AL, Smith JM, Greninger AL, Derisi JL, Ganem D
• Experimental induction of proventricular dilatation disease in cockatiels (Nymphicus hollandicus) inoculated with brain homogenates containing avian bornavirus 4.
  Virology journal 2009 Gancz AY, Kistler AL, Greninger AL, Farnoushi Y, Mechani S, Perl S, Berkowitz A, Perez N, Clubb S, DeRisi JL, Ganem D, Lublin A
• Recovery of divergent avian bornaviruses from cases of proventricular dilatation disease: identification of a candidate etiologic agent.
  Virology journal 2008 Kistler AL, Gancz A, Clubb S, Skewes-Cox P, Fischer K, Sorber K, Chiu CY, Lublin A, Mechani S, Farnoushi Y, Greninger A, Wen CC, Karlene SB, Ganem D, DeRisi JL
• Dichotomy and perceptual distortions in absolute pitch ability.
  Proceedings of the National Academy of Sciences of the United States of America 2007 Athos EA, Levinson B, Kistler A, Zemansky J, Bostrom A, Freimer N, Gitschier J
• Pan-viral screening of respiratory tract infections in adults with and without asthma reveals unexpected human coronavirus and human rhinovirus diversity.
  The Journal of infectious diseases 2007 Kistler A, Avila PC, Rouskin S, Wang D, Ward T, Yagi S, Schnurr D, Ganem D, DeRisi JL, Boushey HA
• Genome-wide diversity and selective pressure in the human rhinovirus.
  Virology journal 2007 Kistler AL, Webster DR, Rouskin S, Magrini V, Credle JJ, Schnurr DP, Boushey HA, Mardis ER, Li H, DeRisi JL
• Rapid DNA mapping by fluorescent single molecule detection.
  Nucleic acids research 2006 Xiao M, Phong A, Ha C, Chan TF, Cai D, Leung L, Wan E, Kistler AL, DeRisi JL, Selvin PR, Kwok PY
• E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns.
  Genome biology 2005 Urisman A, Fischer KF, Chiu CY, Kistler AL, Beck S, Wang D, DeRisi JL
• The cyclic GMP-dependent protein kinase EGL-4 regulates olfactory adaptation in C. elegans.
  Neuron 2002 L'Etoile ND, Coburn CM, Eastham J, Kistler A, Gallegos G, Bargmann CI
• Deletion of MUD2, the yeast homolog of U2AF65, can bypass the requirement for sub2, an essential spliceosomal ATPase.
  Genes & development 2001 Kistler AL, Guthrie C
• Therapeutic dilemma: crescentic mesangiocapillary glomerulonephritis type 1 in a patient on antituberculous therapy with rifampicin.
  Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association 1999 Kistler A, Lappin DW, Coward RA
• Silent information regulator protein complexes in Saccharomyces cerevisiae: a SIR2/SIR4 complex and evidence for a regulatory domain in SIR4 that inhibits its interaction with SIR3.
  Proceedings of the National Academy of Sciences of the United States of America 1997 Moazed D, Kistler A, Axelrod A, Rine J, Johnson AD
• Mapping and sequencing of two yeast genes belonging to the ATP-binding cassette superfamily.
  Yeast (Chichester, England) 1994 Dean M, Allikmets R, Gerrard B, Stewart C, Kistler A, Shafer B, Michaelis S, Strathern J
• Biogenesis of yeast a-factor involves prenylation, methylation and a novel export mechanism.
  Antonie van Leeuwenhoek 1992 Michaelis S, Chen P, Berkower C, Sapperstein S, Kistler A