Eric Chow, PhD
Associate Professor
Biochemistry and Biophysics
School of Medicine

Over the past decade, the CAT has been a hub for new NGS methods, with a focus on single cell sequencing, spatial genomics, and infectious disease detection and diagnostics. He received his BA in Molecular and Cell Biology from the University of California, Berkeley, and his PhD in Biochemistry studying Mycobacterium tuberculosis with genomic and lipidomic tools at UCSF.

• SCITO-seq: single-cell combinatorial indexed cytometry sequencing.
  Nature methods 2021 Hwang B, Lee DS, Tamaki W, Sun Y, Ogorodnikov A, Hartoularos GC, Winters A, Yeung BZ, Nazor KL, Song YS, Chow ED, Spitzer MH, Ye CJ
• XYZeq: Spatially resolved single-cell RNA sequencing reveals expression heterogeneity in the tumor microenvironment.
  Science advances 2021 Lee Y, Bogdanoff D, Wang Y, Hartoularos GC, Woo JM, Mowery CT, Nisonoff HM, Lee DS, Sun Y, Lee J, Mehdizadeh S, Cantlon J, Shifrut E, Ngyuen DN, Roth TL, Song YS, Marson A, Chow ED, Ye CJ
• 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, …
• Macrolide and Nonmacrolide Resistance with Mass Azithromycin Distribution.
  The New England journal of medicine 2020 Doan T, Worden L, Hinterwirth A, Arzika AM, Maliki R, Abdou A, Zhong L, Chen C, Cook C, Lebas E, O'Brien KS, Oldenburg CE, Chow ED, Porco TC, Lipsitch M, Keenan JD, Lietman TM
• Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids.
  Nature medicine 2020 Gu W, Deng X, Lee M, Sucu YD, Arevalo S, Stryke D, Federman S, Gopez A, Reyes K, Zorn K, Sample H, Yu G, Ishpuniani G, Briggs B, Chow ED, Berger A, Wilson MR, Wang C, Hsu E, Miller S, DeRisi JL, Chiu …
• 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, …
• Robust Sequence Determinants of α-Synuclein Toxicity in Yeast Implicate Membrane Binding.
  ACS chemical biology 2020 Newberry RW, Arhar T, Costello J, Hartoularos GC, Maxwell AM, Naing ZZC, Pittman M, Reddy NR, Schwarz DMC, Wassarman DR, Wu TS, Barrero D, Caggiano C, Catching A, Cavazos TB, Estes LS, Faust B, Fink …
• High-resolution epitope mapping of anti-Hu and anti-Yo autoimmunity by programmable phage display.
  Brain communications 2020 O'Donovan B, Mandel-Brehm C, Vazquez SE, Liu J, Parent AV, Anderson MS, Kassimatis T, Zekeridou A, Hauser SL, Pittock SJ, Chow E, Wilson MR, DeRisi JL
• The DNA methylation landscape of advanced prostate cancer.
  Nature genetics 2020 Zhao SG, Chen WS, Li H, Foye A, Zhang M, Sjöström M, Aggarwal R, Playdle D, Liao A, Alumkal JJ, Das R, Chou J, Hua JT, Barnard TJ, Bailey AM, Chow ED, Perry MD, Dang HX, Yang R, Moussavi-Baygi R, …
• ZipSeq: barcoding for real-time mapping of single cell transcriptomes.
  Nature methods 2020 Hu KH, Eichorst JP, McGinnis CS, Patterson DM, Chow ED, Kersten K, Jameson SC, Gartner ZJ, Rao AA, Krummel MF
• Intratumoral CD4+ T Cells Mediate Anti-tumor Cytotoxicity in Human Bladder Cancer.
  Cell 2020 Oh DY, Kwek SS, Raju SS, Li T, McCarthy E, Chow E, Aran D, Ilano A, Pai CS, Rancan C, Allaire K, Burra A, Sun Y, Spitzer MH, Mangul S, Porten S, Meng MV, Friedlander TW, Ye CJ, Fong L
• Deep mutational scanning reveals the structural basis for α-synuclein activity.
  Nature chemical biology 2020 Newberry RW, Leong JT, Chow ED, Kampmann M, DeGrado WF
• FLASH: a next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences.
  Nucleic acids research 2019 Quan J, Langelier C, Kuchta A, Batson J, Teyssier N, Lyden A, Caldera S, McGeever A, Dimitrov B, King R, Wilheim J, Murphy M, Ares LP, Travisano KA, Sit R, Amato R, Mumbengegwi DR, Smith JL, Bennett A…
• Gut microbiome alteration in MORDOR I: a community-randomized trial of mass azithromycin distribution.
  Nature medicine 2019 Doan T, Hinterwirth A, Worden L, Arzika AM, Maliki R, Abdou A, Kane S, Zhong L, Cummings ME, Sakar S, Chen C, Cook C, Lebas E, Chow ED, Nachamkin I, Porco TC, Keenan JD, Lietman TM
• MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices.
  Nature methods 2019 McGinnis CS, Patterson DM, Winkler J, Conrad DN, Hein MY, Srivastava V, Hu JL, Murrow LM, Weissman JS, Werb Z, Chow ED, Gartner ZJ
• Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children.
  Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2019 Zinter MS, Dvorak CC, Mayday MY, Iwanaga K, Ly NP, McGarry ME, Church GD, Faricy LE, Rowan CM, Hume JR, Steiner ME, Crawford ED, Langelier C, Kalantar K, Chow ED, Miller S, Shimano K, Melton A, Yanik …
• Predicting Splicing from Primary Sequence with Deep Learning.
  Cell 2019 Jaganathan K, Kyriazopoulou Panagiotopoulou S, McRae JF, Darbandi SF, Knowles D, Li YI, Kosmicki JA, Arbelaez J, Cui W, Schwartz GB, Chow ED, Kanterakis E, Gao H, Kia A, Batzoglou S, Sanders SJ, Farh …
• Miniaturization and optimization of 384-well compatible RNA sequencing library preparation.
  PloS one 2019 Mayday MY, Khan LM, Chow ED, Zinter MS, DeRisi JL
• Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults.
  Proceedings of the National Academy of Sciences of the United States of America 2018 Langelier C, Kalantar KL, Moazed F, Wilson MR, Crawford ED, Deiss T, Belzer A, Bolourchi S, Caldera S, Fung M, Jauregui A, Malcolm K, Lyden A, Khan L, Vessel K, Quan J, Zinter M, Chiu CY, Chow ED, …
• Chronic Meningitis Investigated via Metagenomic Next-Generation Sequencing.
  JAMA neurology 2018 Wilson MR, O'Donovan BD, Gelfand JM, Sample HA, Chow FC, Betjemann JP, Shah MP, Richie MB, Gorman MP, Hajj-Ali RA, Calabrese LH, Zorn KC, Chow ED, Greenlee JE, Blum JH, Green G, Khan LM, Banerji D, …
• Mass Azithromycin Distribution and Community Microbiome: A Cluster-Randomized Trial.
  Open forum infectious diseases 2018 Doan T, Hinterwirth A, Arzika AM, Cotter SY, Ray KJ, O'Brien KS, Zhong L, Chow ED, Zhou Z, Cummings SL, Fry D, Oldenburg CE, Worden L, Porco TC, Keenan JD, Lietman TM
• Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance.
  Biology open 2018 Mavor D, Barlow KA, Asarnow D, Birman Y, Britain D, Chen W, Green EM, Kenner LR, Mensa B, Morinishi LS, Nelson CA, Poss EM, Suresh P, Tian R, Arhar T, Ary BE, Bauer DP, Bergman ID, Brunetti RM, Chio …
• Mapping the Genetic Landscape of Human Cells.
  Cell 2018 Horlbeck MA, Xu A, Wang M, Bennett NK, Park CY, Bogdanoff D, Adamson B, Chow ED, Kampmann M, Peterson TR, Nakamura K, Fischbach MA, Weissman JS, Gilbert LA
• Metagenomic DNA Sequencing for the Diagnosis of Intraocular Infections.
  Ophthalmology 2017 Doan T, Acharya NR, Pinsky BA, Sahoo MK, Chow ED, Banaei N, Budvytiene I, Cevallos V, Zhong L, Zhou Z, Lietman TM, DeRisi JL
• UDP-galactose and acetyl-CoA transporters as Plasmodium multidrug resistance genes.
  Nature microbiology 2016 Lim MY, LaMonte G, Lee MCS, Reimer C, Tan BH, Corey V, Tjahjadi BF, Chua A, Nachon M, Wintjens R, Gedeck P, Malleret B, Renia L, Bonamy GMC, Ho PC, Yeung BKS, Chow ED, Lim L, Fidock DA, Diagana TT, …
• Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens.
  Genome medicine 2016 Doan T, Wilson MR, Crawford ED, Chow ED, Khan LM, Knopp KA, O'Donovan BD, Xia D, Hacker JK, Stewart JM, Gonzales JA, Acharya NR, DeRisi JL
• Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting.
  eLife 2016 Mavor D, Barlow K, Thompson S, Barad BA, Bonny AR, Cario CL, Gaskins G, Liu Z, Deming L, Axen SD, Caceres E, Chen W, Cuesta A, Gate RE, Green EM, Hulce KR, Ji W, Kenner LR, Mensa B, Morinishi LS, Moss…
• Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications.
  Genome biology 2016 Gu W, Crawford ED, O'Donovan BD, Wilson MR, Chow ED, Retallack H, DeRisi JL
• Subclonal mutations in SETBP1 confer a poor prognosis in juvenile myelomonocytic leukemia.
  Blood 2014 Stieglitz E, Troup CB, Gelston LC, Haliburton J, Chow ED, Yu KB, Akutagawa J, Taylor-Weiner AN, Liu YL, Wang YD, Beckman K, Emanuel PD, Braun BS, Abate A, Gerbing RB, Alonzo TA, Loh ML
• A cysteine protease inhibitor rescues mice from a lethal Cryptosporidium parvum infection.
  Antimicrobial agents and chemotherapy 2013 Ndao M, Nath-Chowdhury M, Sajid M, Marcus V, Mashiyama ST, Sakanari J, Chow E, Mackey Z, Land KM, Jacobson MP, Kalyanaraman C, McKerrow JH, Arrowood MJ, Caffrey CR
• Genetic and mass spectrometric tools for elucidating the physiological function(s) of cytochrome P450 enzymes from Mycobacterium tuberculosis.
  Methods in molecular biology (Clifton, N.J.) 2013 Ouellet H, Chow ED, Guan S, Cox JS, Burlingame AL, de Montellano PR
• TB lipidomics--the final frontier.
  Chemistry & biology 2011 Chow ED, Cox JS
• Mycobacterium tuberculosis CYP125A1, a steroid C27 monooxygenase that detoxifies intracellularly generated cholest-4-en-3-one.
  Molecular microbiology 2010 Ouellet H, Guan S, Johnston JB, Chow ED, Kells PM, Burlingame AL, Cox JS, Podust LM, de Montellano PR
• Systematic genetic analysis of virulence in the human fungal pathogen Cryptococcus neoformans.
  Cell 2008 Liu OW, Chun CD, Chow ED, Chen C, Madhani HD, Noble SM
• Exploration of whole-genome responses of the human AIDS-associated yeast pathogen Cryptococcus neoformans var grubii: nitric oxide stress and body temperature.
  Current genetics 2007 Chow ED, Liu OW, O'Brien S, Madhani HD
• Parallel beta-helix proteins required for accurate capsule polysaccharide synthesis and virulence in the yeast Cryptococcus neoformans.
  Eukaryotic cell 2007 Liu OW, Kelly MJ, Chow ED, Madhani HD