Greg Finak

Summary

Affiliation: Fred Hutchinson Cancer Research Center
Country: USA

Publications

  1. pmc Optimizing transformations for automated, high throughput analysis of flow cytometry data
    Greg Finak
    Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fariview Ave N, Seattle, WA 98109, USA
    BMC Bioinformatics 11:546. 2010
  2. pmc Mixture models for single-cell assays with applications to vaccine studies
    Greg Finak
    Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center FHCRC, Seattle, WA 98109, USA
    Biostatistics 15:87-101. 2014
  3. pmc High-throughput flow cytometry data normalization for clinical trials
    Greg Finak
    Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109
    Cytometry A 85:277-86. 2014
  4. pmc OpenCyto: an open source infrastructure for scalable, robust, reproducible, and automated, end-to-end flow cytometry data analysis
    Greg Finak
    Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
    PLoS Comput Biol 10:e1003806. 2014
  5. pmc Modeling bi-modality improves characterization of cell cycle on gene expression in single cells
    Andrew McDavid
    Department of Statistics, University of Washington, Seattle, Washington, United States of America Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
    PLoS Comput Biol 10:e1003696. 2014
  6. pmc QUAliFiER: an automated pipeline for quality assessment of gated flow cytometry data
    Greg Finak
    Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
    BMC Bioinformatics 13:252. 2012
  7. pmc flowDensity: reproducing manual gating of flow cytometry data by automated density-based cell population identification
    Mehrnoush Malek
    Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, BC V5Z 1L3, Canada, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 1024, USA and Bioinformatics Training Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada
    Bioinformatics 31:606-7. 2015
  8. pmc Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments
    Andrew McDavid
    Department of Statistics, University of Washington, Seattle, WA 98195, USA
    Bioinformatics 29:461-7. 2013

Collaborators

  • Raphael Gottardo
  • Stephen C De Rosa
  • Mario Roederer
  • Andrew McDavid
  • Mehrnoush Malek
  • Lauren Chong
  • Mohammad Jafar Taghiyar
  • Ryan R Brinkman
  • Alice Wang
  • Patrick Danaher
  • Michael Krouse
  • Philippa Webster
  • Joseph Beechem
  • Lucas Dennis
  • Laurie Lamoreaux
  • Steven S Ma
  • Pratip K Chattopadyay
  • Maria Dominguez

Detail Information

Publications8

  1. pmc Optimizing transformations for automated, high throughput analysis of flow cytometry data
    Greg Finak
    Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fariview Ave N, Seattle, WA 98109, USA
    BMC Bioinformatics 11:546. 2010
    ..By making some modelling assumptions about the transformed data, we develop maximum likelihood criteria to optimize parameter choice for these different transformations...
  2. pmc Mixture models for single-cell assays with applications to vaccine studies
    Greg Finak
    Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center FHCRC, Seattle, WA 98109, USA
    Biostatistics 15:87-101. 2014
    ....
  3. pmc High-throughput flow cytometry data normalization for clinical trials
    Greg Finak
    Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109
    Cytometry A 85:277-86. 2014
    ..The normalization framework allows the use of template gates even in the presence of sample-to-sample staining variability, mitigates the subjectivity and bias of manual gating, and decreases the time necessary to analyze large datasets...
  4. pmc OpenCyto: an open source infrastructure for scalable, robust, reproducible, and automated, end-to-end flow cytometry data analysis
    Greg Finak
    Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
    PLoS Comput Biol 10:e1003806. 2014
    ..It can rapidly leverage new developments in computational cytometry and facilitate reproducible analysis in a unified environment. ..
  5. pmc Modeling bi-modality improves characterization of cell cycle on gene expression in single cells
    Andrew McDavid
    Department of Statistics, University of Washington, Seattle, Washington, United States of America Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
    PLoS Comput Biol 10:e1003696. 2014
    ..We find that the cell cycle explains only 5%-17% of expression variability, suggesting that the cell cycle will not tend to be a large nuisance factor in analysis of the single cell transcriptome. ..
  6. pmc QUAliFiER: an automated pipeline for quality assessment of gated flow cytometry data
    Greg Finak
    Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
    BMC Bioinformatics 13:252. 2012
    ..Gated cell populations and their statistics must be monitored within the context of the experimental run, assay, and the overall study...
  7. pmc flowDensity: reproducing manual gating of flow cytometry data by automated density-based cell population identification
    Mehrnoush Malek
    Terry Fox Laboratory, BC Cancer Agency Research Centre, Vancouver, BC V5Z 1L3, Canada, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 1024, USA and Bioinformatics Training Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada
    Bioinformatics 31:606-7. 2015
    ..It chooses the best cut-off for individual markers using characteristics of the density distribution. The Supplementary Material is linked to the online version of the manuscript...
  8. pmc Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments
    Andrew McDavid
    Department of Statistics, University of Washington, Seattle, WA 98195, USA
    Bioinformatics 29:461-7. 2013
    ..However, few analytic tools have been developed specifically for the statistical and analytical challenges of single-cell quantitative polymerase chain reactions data...