Center-Authored Papers

Filters: Author is Finak, Greg  [Clear All Filters]
2010
Finak G, Perez J-M, Weng A, Gottardo R.  2010.  Optimizing transformations for automated, high throughput analysis of flow cytometry data.. BMC bioinformatics. 11:546. Abstract
2012
Pepin F, Bertos N, Laferriere J, Sadekova S, Souleimanova M, Zhao H, Finak G, Meterissian S, Hallett MT, Park M.  2012.  Gene expression profiling of microdissected breast cancer microvasculature identifies distinct tumor vascular subtypes.. Breast cancer research : BCR. 14(4):R120. Abstract
Finak G, Jiang W, Pardo J, Asare A, Gottardo R.  2012.  QUAliFiER: An automated pipeline for quality assessment of gated flow cytometry data.. BMC bioinformatics. 13(1):252. Abstract
2013
Finak G, Jiang W, Krouse K, Wei C, Sanz I, Phippard D, Asare A, De Rosa SC, Self S, Gottardo R.  2013.  High-throughput flow cytometry data normalization for clinical trials.. Cytometry. Part A : the journal of the International Society for Analytical Cytology. Abstract
Finak G, McDavid A, Chattopadhyay P, Dominguez M, De Rosa S, Roederer M, Gottardo R.  2013.  Mixture models for single-cell assays with applications to vaccine studies.. Biostatistics (Oxford, England). Abstract
Aghaeepour N, Finak G, Hoos H, Mosmann TR, Brinkman R, Gottardo R, Scheuermann RH.  2013.  Critical assessment of automated flow cytometry data analysis techniques.. Nature methods. 10(3):228-38. Abstract
Dominguez MH, Chattopadhyay PK, Ma S, Lamoreaux L, McDavid A, Finak G, Gottardo R, Koup RA, Roederer M.  2013.  Highly multiplexed quantitation of gene expression on single cells.. Journal of immunological methods. 391(1-2):133-45. Abstract
2014
McDavid A, Dennis L, Danaher P, Finak G, Krouse M, Wang A, Webster P, Beechem J, Gottardo R.  2014.  Modeling Bi-modality Improves Characterization of Cell Cycle on Gene Expression in Single Cells.. PLoS computational biology. 10(7):e1003696. Abstract
2015
Kvistborg P, Gouttefangeas C, Aghaeepour N, Cazaly A, Chattopadhyay PK, Chan C, Eckl J, Finak G, Hadrup SR, Maecker HT et al..  2015.  Thinking outside the gate: single-cell assessments in multiple dimensions.. Immunity. 42(4):591-2.
Lin L, Frelinger J, Jiang W, Finak G, Seshadri C, Bart P-A, Pantaleo G, McElrath J, De Rosa S, Gottardo R.  2015.  Identification and visualization of multidimensional antigen-specific T-cell populations in polychromatic cytometry data.. Cytometry. Part A : the journal of the International Society for Analytical Cytology. Abstract
Finak G, McDavid A, Yajima M, Deng J, Gersuk V, Shalek AK, Slichter CK, Miller HW, McElrath MJ, Prlic M et al..  2015.  MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.. Genome biology. 16:278. Abstract
Malek M, Taghiyar MJ, Chong L, Finak G, Gottardo R, Brinkman RR.  2015.  flowDensity: reproducing manual gating of flow cytometry data by automated density-based cell population identification.. Bioinformatics (Oxford, England). 31(4):606-7. Abstract
Brinkman RR, Aghaeepour N, Finak G, Gottardo R, Mosmann T, Scheuermann RH.  2015.  State-of-the-Art in the Computational Analysis of Cytometry Data.. Cytometry. Part A : the journal of the International Society for Analytical Cytology. 87(7):591-3.
Lin L, Finak G, Ushey K, Seshadri C, Hawn TR, Frahm N, Scriba TJ, Mahomed H, Hanekom W, Bart P-A et al..  2015.  COMPASS identifies T-cell subsets correlated with clinical outcomes.. Nature biotechnology. 33(6):610-6. Abstract
Seshadri C, Lin L, Scriba TJ, Peterson G, Freidrich D, Frahm N, De Rosa SC, Moody BD, Prandi J, Gilleron M et al..  2015.  T Cell Responses against Mycobacterial Lipids and Proteins Are Poorly Correlated in South African Adolescents.. Journal of immunology (Baltimore, Md. : 1950). 195(10):4595-4603. Abstract
Aghaeepour N, Chattopadhyay P, Chikina M, Dhaene T, Van Gassen S, Kursa M, Lambrecht BN, Malek M, Qian Y, Qiu P et al..  2015.  A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes.. Cytometry. Part A : the journal of the International Society for Analytical Cytology. Abstract
2016
Fiore-Gartland A, Manso BA, Friedrich DP, Gabriel EE, Finak G, Moodie Z, Hertz T, De Rosa SC, Frahm N, Gilbert PB et al..  2016.  Pooled-Peptide Epitope Mapping Strategies Are Efficient and Highly Sensitive: An Evaluation of Methods for Identifying Human T Cell Epitope Specificities in Large-Scale HIV Vaccine Efficacy Trials.. PloS one. 11(2):e0147812. Abstract
Finak G, Gottardo R.  2016.  Promises and Pitfalls of High-Throughput Biological Assays.. Methods in molecular biology (Clifton, N.J.). 1415:225-43. Abstract
Finak G, Langweiler M, Jaimes M, Malek M, Taghiyar J, Korin Y, Raddassi K, Devine L, Obermoser G, Pekalski ML et al..  2016.  Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium.. Scientific reports. 6:20686. Abstract
Brinkman RR, Aghaeepour N, Finak G, Gottardo R, Mosmann T, Scheuermann RH.  2016.  Automated analysis of flow cytometry data comes of age.. Cytometry. Part A : the journal of the International Society for Analytical Cytology. 89(1):13-5.
Aghaeepour N, Chattopadhyay P, Chikina M, Dhaene T, Van Gassen S, Kursa M, Lambrecht BN, Malek M, McLachlan GJ, Qian Y et al..  2016.  A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes.. Cytometry. Part A : the journal of the International Society for Analytical Cytology. 89(1):16-21. Abstract
Slichter CK, McDavid A, Miller HW, Finak G, Seymour BJ, McNevin JP, Diaz G, Czartoski JL, McElrath MJ, Gottardo R et al..  2016.  Distinct activation thresholds of human conventional and innate-like memory T cells.. JCI insight. 1(8) Abstract
McDavid A, Finak G, Gottardo R.  2016.  The contribution of cell cycle to heterogeneity in single-cell RNA-seq data.. Nature biotechnology. 34(6):591-3.
2017
Janes HE, Cohen KW, Frahm N, De Rosa SC, Sanchez B, Hural J, Magaret CA, Karuna S, Bentley C, Gottardo R et al..  2017.  Higher T cell responses induced by DNA/rAd5 HIV-1 preventive vaccine are associated with lower HIV-1 infection risk in an efficacy trial.. The Journal of infectious diseases.
Alberer M, Gnad-Vogt U, Hong HS, Mehr KT, Backert L, Finak G, Gottardo R, Bica MA, Garofano A, Koch SD et al..  2017.  Safety and immunogenicity of a mRNA rabies vaccine in healthy adults: an open-label, non-randomised, prospective, first-in-human phase 1 clinical trial.. Lancet (London, England). Abstract