List of works - Greg Finak

A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes.

scientific article published on 08 October 2015

Automated analysis of flow cytometry data comes of age.

scientific article published in January 2016

COMPASS identifies T-cell subsets correlated with clinical outcomes

scientific article

Circulating Mycobacterium tuberculosis DosR latency antigen-specific, polyfunctional, regulatory IL10+ Th17 CD4 T-cells differentiate latent from active tuberculosis

scientific article published on 20 September 2017

Combined single-cell quantitation of host and SIV genes and proteins ex vivo reveals host-pathogen interactions in individual cells

scientific article

CytoML for cross-platform cytometry data sharing.

scientific article

DNA Priming Increases Frequency of T-Cell Responses to a Vesicular Stomatitis Virus HIV Vaccine with Specific Enhancement of CD8+ T-Cell Responses by Interleukin-12 Plasmid DNA.

scientific article published on 20 September 2017

Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments.

scientific article

Gene expression signatures of morphologically normal breast tissue identify basal-like tumors

scientific article

Gene-expression profiling of microdissected breast cancer microvasculature identifies distinct tumor vascular subtypes ⬇️

scientific article published on August 20, 2012

High-throughput flow cytometry data normalization for clinical trials.

scientific article

Higher T-Cell Responses Induced by DNA/rAd5 HIV-1 Preventive Vaccine Are Associated With Lower HIV-1 Infection Risk in an Efficacy Trial

scientific article published on 12 February 2017

Hypoxia promotes ligand-independent EGF receptor signaling via hypoxia-inducible factor-mediated upregulation of caveolin-1

scientific article published on 12 March 2012

Identification and visualization of multidimensional antigen-specific T-cell populations in polychromatic cytometry data.

scientific article

In silico ascription of gene expression differences to tumor and stromal cells in a model to study impact on breast cancer outcome

scientific article

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data

scientific article

Merging mixture components for cell population identification in flow cytometry

scientific article

Modeling bi-modality improves characterization of cell cycle on gene expression in single cells

scientific article (publication date: July 2014)

Multidimensional analyses reveal modulation of adaptive and innate immune subsets by tuberculosis vaccines

scientific article published on 09 October 2020

OpenCyto: an open source infrastructure for scalable, robust, reproducible, and automated, end-to-end flow cytometry data analysis

scientific article

QUAliFiER: an automated pipeline for quality assessment of gated flow cytometry data.

scientific article

Regulation of endocytosis via the oxygen-sensing pathway

scientific article

State-of-the-Art in the Computational Analysis of Cytometry Data.

scientific article published in July 2015

Stromal gene expression predicts clinical outcome in breast cancer

scientific article

The Computational article format: Software as a research output

scientific article published on 01 December 2018

Thinking outside the gate: single-cell assessments in multiple dimensions

scientific article published on April 2015

Vaccination induces HIV broadly neutralizing antibody precursors in humans ⬇️

journal article published in 2022

[The tumor microenvironment: a new tool to predict breast cancer outcome].

scientific article published in May 2009

flowDensity: reproducing manual gating of flow cytometry data by automated density-based cell population identification.

scientific article

ggCyto: next generation open-source visualization software for cytometry

scientific article published on 01 November 2018

List of works by Greg Finak

A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes.

Automated analysis of flow cytometry data comes of age.

COMPASS identifies T-cell subsets correlated with clinical outcomes

Circulating Mycobacterium tuberculosis DosR latency antigen-specific, polyfunctional, regulatory IL10+ Th17 CD4 T-cells differentiate latent from active tuberculosis

Combined single-cell quantitation of host and SIV genes and proteins ex vivo reveals host-pathogen interactions in individual cells

CytoML for cross-platform cytometry data sharing.

DNA Priming Increases Frequency of T-Cell Responses to a Vesicular Stomatitis Virus HIV Vaccine with Specific Enhancement of CD8+ T-Cell Responses by Interleukin-12 Plasmid DNA.

Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments.

Gene expression signatures of morphologically normal breast tissue identify basal-like tumors

Gene-expression profiling of microdissected breast cancer microvasculature identifies distinct tumor vascular subtypes ⬇️

High-throughput flow cytometry data normalization for clinical trials.

Higher T-Cell Responses Induced by DNA/rAd5 HIV-1 Preventive Vaccine Are Associated With Lower HIV-1 Infection Risk in an Efficacy Trial

Hypoxia promotes ligand-independent EGF receptor signaling via hypoxia-inducible factor-mediated upregulation of caveolin-1

Identification and visualization of multidimensional antigen-specific T-cell populations in polychromatic cytometry data.

In silico ascription of gene expression differences to tumor and stromal cells in a model to study impact on breast cancer outcome

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data

Merging mixture components for cell population identification in flow cytometry

Modeling bi-modality improves characterization of cell cycle on gene expression in single cells

Multidimensional analyses reveal modulation of adaptive and innate immune subsets by tuberculosis vaccines

OpenCyto: an open source infrastructure for scalable, robust, reproducible, and automated, end-to-end flow cytometry data analysis

QUAliFiER: an automated pipeline for quality assessment of gated flow cytometry data.

Regulation of endocytosis via the oxygen-sensing pathway

State-of-the-Art in the Computational Analysis of Cytometry Data.

Stromal gene expression predicts clinical outcome in breast cancer

The Computational article format: Software as a research output

Thinking outside the gate: single-cell assessments in multiple dimensions

Vaccination induces HIV broadly neutralizing antibody precursors in humans ⬇️

[The tumor microenvironment: a new tool to predict breast cancer outcome].

flowDensity: reproducing manual gating of flow cytometry data by automated density-based cell population identification.

ggCyto: next generation open-source visualization software for cytometry