Alexander L Greninger

Summary

Publications

  1. pmc Draft Genome Sequences of Marine RNA Viruses SF-1, SF-2, and SF-3 Recovered from San Francisco Wastewater
    Alexander L Greninger
    Genome Announc 3:. 2015
  2. pmc Draft Genome Sequences of Leviviridae RNA Phages EC and MB Recovered from San Francisco Wastewater
    Alexander L Greninger
    Genome Announc 3:. 2015
  3. pmc Draft Genome Sequence of Tombunodavirus UC1
    Alexander L Greninger
    Genome Announc 3:. 2015
  4. pmc Draft Genome Sequence of Goose Dicistrovirus
    Alexander L Greninger
    Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
    Genome Announc 4:. 2016
  5. pmc Draft Genome Sequences of Ciliovirus and Brinovirus from San Francisco Wastewater
    Alexander L Greninger
    Department of Biochemistry and Biophysics, UCSF, San Francisco, California, USA Howard Hughes Medical Institute, UCSF, San Francisco, California, USA
    Genome Announc 3:. 2015
  6. pmc Draft Genome Sequence of Picalivirus D Recovered from San Francisco Wastewater
    Alexander L Greninger
    Genome Announc 3:. 2015
  7. pmc Draft Genome Sequence of Laverivirus UC1, a Dicistrovirus-Like RNA Virus Featuring an Unusual Genome Organization
    Alexander L Greninger
    Genome Announc 3:. 2015
  8. doi request reprint Picornavirus--host interactions to construct viral secretory membranes
    Alexander L Greninger
    School of Medicine, University of California, San Francisco, California, USA Electronic address
    Prog Mol Biol Transl Sci 129:189-212. 2015
  9. pmc The complete genome of klassevirus - a novel picornavirus in pediatric stool
    Alexander L Greninger
    Howard Hughes Medical Institute, Departments of Medicine, Biochemistry, and Microbiology, University of California, San Francisco, California 94143, USA
    Virol J 6:82. 2009
  10. pmc ACBD3 interaction with TBC1 domain 22 protein is differentially affected by enteroviral and kobuviral 3A protein binding
    Alexander L Greninger
    Howard Hughes Medical Institute, San Francisco, California, USA
    MBio 4:e00098-13. 2013

Collaborators

Detail Information

Publications29

  1. pmc Draft Genome Sequences of Marine RNA Viruses SF-1, SF-2, and SF-3 Recovered from San Francisco Wastewater
    Alexander L Greninger
    Genome Announc 3:. 2015
    ..These viruses were most closely related to marine RNA virus JP-B and algae viruses. ..
  2. pmc Draft Genome Sequences of Leviviridae RNA Phages EC and MB Recovered from San Francisco Wastewater
    Alexander L Greninger
    Genome Announc 3:. 2015
    ..These phages showed moderate translated amino acid identity to other enterobacteria phages and appear to constitute novel members of the Leviviridae family. ..
  3. pmc Draft Genome Sequence of Tombunodavirus UC1
    Alexander L Greninger
    Genome Announc 3:. 2015
    ..This virus shares hallmarks of members of the Tombusviridae and the nodavirus-like Plasmopara halstedii and Sclerophthora macrospora viruses. ..
  4. pmc Draft Genome Sequence of Goose Dicistrovirus
    Alexander L Greninger
    Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
    Genome Announc 4:. 2016
    ..The 9.1-kb dicistronic RNA virus falls within the family Dicistroviridae; however, it shares <33% translated amino acid sequence within the nonstructural open reading frame (ORF) from aparavirus or cripavirus. ..
  5. pmc Draft Genome Sequences of Ciliovirus and Brinovirus from San Francisco Wastewater
    Alexander L Greninger
    Department of Biochemistry and Biophysics, UCSF, San Francisco, California, USA Howard Hughes Medical Institute, UCSF, San Francisco, California, USA
    Genome Announc 3:. 2015
    ..Based on sequence alignments and a nonuniversal genetic code, we believe these to be the first described RNA viruses of ciliates; however, more work is necessary to confirm their host. ..
  6. pmc Draft Genome Sequence of Picalivirus D Recovered from San Francisco Wastewater
    Alexander L Greninger
    Genome Announc 3:. 2015
    ..This virus likely constitutes a novel genus within the picalivirus family. ..
  7. pmc Draft Genome Sequence of Laverivirus UC1, a Dicistrovirus-Like RNA Virus Featuring an Unusual Genome Organization
    Alexander L Greninger
    Genome Announc 3:. 2015
    ..This dicistronic RNA virus bears some similarity to dicistroviruses; however, it appears to have a unique genome organization relative to all other known RNA viruses. ..
  8. doi request reprint Picornavirus--host interactions to construct viral secretory membranes
    Alexander L Greninger
    School of Medicine, University of California, San Francisco, California, USA Electronic address
    Prog Mol Biol Transl Sci 129:189-212. 2015
    ..This chapter reviews the major discoveries associating picornavirus pathogenic interactions with the secretory system and highlights important questions and opportunities for future study. ..
  9. pmc The complete genome of klassevirus - a novel picornavirus in pediatric stool
    Alexander L Greninger
    Howard Hughes Medical Institute, Departments of Medicine, Biochemistry, and Microbiology, University of California, San Francisco, California 94143, USA
    Virol J 6:82. 2009
    ..Modern technologies, especially deep sequencing, allow rapid, high-throughput screening of clinical samples such as stool for new infectious agents associated with human disease...
  10. pmc ACBD3 interaction with TBC1 domain 22 protein is differentially affected by enteroviral and kobuviral 3A protein binding
    Alexander L Greninger
    Howard Hughes Medical Institute, San Francisco, California, USA
    MBio 4:e00098-13. 2013
    ..These data reinforce the notion that ACBD3 organizes numerous cellular functionalities and that RNA virus replication proteins likely modulate these interactions by more than one mechanism...
  11. pmc Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
    Alexander L Greninger
    Department of Laboratory Medicine, University of California, San Francisco, CA, 94107, USA
    Genome Med 7:99. 2015
    ....
  12. pmc Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing
    Alexander L Greninger
    Department of Laboratory Medicine, University of California, 185 Berry Street, Box 0134, San Francisco, CA, 94107, USA
    Genome Med 7:113. 2015
    ..Primary amoebic meningoencephalitis (PAM) is a rare, often lethal, cause of encephalitis, for which early diagnosis and prompt initiation of combination antimicrobials may improve clinical outcomes...
  13. doi request reprint A novel outbreak enterovirus D68 strain associated with acute flaccid myelitis cases in the USA (2012-14): a retrospective cohort study
    Alexander L Greninger
    Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA UCSF Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
    Lancet Infect Dis 15:671-82. 2015
    ..We aimed to investigate the association between enterovirus D68 infection and acute flaccid myelitis during the 2014 enterovirus D68 respiratory outbreak in the USA...
  14. pmc Discovery of a novel polyomavirus in acute diarrheal samples from children
    Guixia Yu
    Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, USA
    PLoS ONE 7:e49449. 2012
    ..Further studies will be important to determine the association, if any, of MXPyV with disease in humans...
  15. pmc The 3A protein from multiple picornaviruses utilizes the golgi adaptor protein ACBD3 to recruit PI4KIII╬▓
    Alexander L Greninger
    Howard Hughes Medical Institute and the Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California, USA
    J Virol 86:3605-16. 2012
    ....
  16. pmc Identification of cardioviruses related to Theiler's murine encephalomyelitis virus in human infections
    Charles Y Chiu
    Department of Biochemistry and Biophysics, University of California, 1700 4th Street, Box 2542, San Francisco, CA 94143, USA
    Proc Natl Acad Sci U S A 105:14124-9. 2008
    ....
  17. pmc Serological evidence of human klassevirus infection
    Alexander L Greninger
    Departments of Molecular Microbiology and Pathology and Immunology, Howard Hughes Medical Institute, Washington University, St Louis, MO 63110, USA
    Clin Vaccine Immunol 17:1584-8. 2010
    ..Additional screening of 353 samples from an age-banded serological cohort from two St. Louis hospitals indicated a seroprevalence of 6.8%...
  18. pmc Enhanced arbovirus surveillance with deep sequencing: Identification of novel rhabdoviruses and bunyaviruses in Australian mosquitoes
    Lark L Coffey
    Blood Systems Research Institute, University of California, San Francisco, USA Department of Laboratory Medicine, University of California, 270 Masonic Avenue, San Francisco, CA 94118, USA
    Virology 448:146-58. 2014
    ..Follow-up epidemiological studies are required to determine whether the novel viruses infect humans...
  19. pmc First Draft Genome Sequences of Neisseria sp. Strain 83E34 and Neisseria sp. Strain 74A18, Previously Identified as CDC Eugonic Fermenter 4b Species
    Alexander L Greninger
    Department of Laboratory Medicine, UCSF, San Francisco, California, USA
    Genome Announc 4:. 2016
    ..83E34 and Neisseria sp. 74A18. Both strains were isolated from patients with animal bites and likely constitute novel genomospecies with average nucleotide identities of <95% to other sequenced strains...
  20. pmc Two Rapidly Growing Mycobacterial Species Isolated from a Brain Abscess: First Whole-Genome Sequences of Mycobacterium immunogenum and Mycobacterium llatzerense
    Alexander L Greninger
    Department of Laboratory Medicine, University of California, San Francisco, California, USA UCSF Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
    J Clin Microbiol 53:2374-7. 2015
    ..immunogenum and M. llatzerense. The Mycobacterium isolates were distinguishable by molecular methods, and whole-genome sequencing showed <60% pairwise nucleotide identity. ..
  21. pmc A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples
    Samia N Naccache
    Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA UCSF Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA
    Genome Res 24:1180-92. 2014
    ....
  22. pmc The perils of pathogen discovery: origin of a novel parvovirus-like hybrid genome traced to nucleic acid extraction spin columns
    Samia N Naccache
    Department of Laboratory Medicine, University of California, San Francisco, California, USA
    J Virol 87:11966-77. 2013
    ....
  23. pmc Global identification of peptidase specificity by multiplex substrate profiling
    Anthony J O'Donoghue
    Department of Pharmaceutical Chemistry, University of California, San Francisco, USA
    Nat Methods 9:1095-100. 2012
    ..Additionally, the proteolytic secretions from schistosome parasitic flatworm larvae and a pancreatic cancer cell line were deconvoluted in a subtractive strategy using class-specific peptidase inhibitors...
  24. pmc Analysis of naturally occurring avian bornavirus infection and transmission during an outbreak of proventricular dilatation disease among captive psittacine birds
    Amy L Kistler
    Howard Hughes Medical Institute and UCSF Biochemistry and Biophysics, 1700 4th St, QB3 Room 403, San Francisco, CA 94143 2542, USA
    J Virol 84:2176-9. 2010
    ..These findings demonstrate that ABV infection precedes the development of PDD. ABV-specific Western blotting and reverse transcription-PCR indicate that ABV2 is not strictly neurotropic...
  25. pmc Rapid metagenomic next-generation sequencing during an investigation of hospital-acquired human parainfluenza virus 3 infections
    Alexander L Greninger
    Department of Laboratory Medicine, University of Washington, Seattle, WA
    J Clin Microbiol . 2016
    ..Adequate sequence coverage was not recovered for the third case. This work demonstrates the promise of mNGS to provide rapid information for infection prevention in addition to microbial detection...
  26. ncbi request reprint Copy number heterogeneity of JC virus standards
    Alexander L Greninger
    Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
    J Clin Microbiol . 2016
    ..In summary, targeting of different regions of the same international standard could result in up to an 8-fold difference in quantitation. We recommend the use of next-generation sequencing to validate standards in clinical virology...
  27. pmc Whole-Genome Sequencing of Methicillin-Resistant Staphylococcus aureus Resistant to Fifth-Generation Cephalosporins Reveals Potential Non-mecA Mechanisms of Resistance
    Alexander L Greninger
    Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
    PLoS ONE 11:e0149541. 2016
    ..These genomic findings suggest that non-mecA mechanisms, while yet to be encountered in the clinical setting, may also be important in mediating resistance to 5th-generation cephalosporins. ..
  28. pmc Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions
    John H Morris
    Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
    Nat Protoc 9:2539-54. 2014
    ..Similarly, the network analysis and visualization protocol in Cytoscape takes 2-4 h to complete with the provided sample data, but we recommend taking days or even weeks to explore one's data and find the right questions. ..
  29. pmc Microfluidic affinity and ChIP-seq analyses converge on a conserved FOXP2-binding motif in chimp and human, which enables the detection of evolutionarily novel targets
    Christopher S Nelson
    Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94131, USA
    Nucleic Acids Res 41:5991-6004. 2013
    ..Combined, these data present a comprehensive portrait of FOXP2's-binding properties and imply that although its sequence specificity has been conserved, some of its genomic binding sites are newly evolved. ..