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1

Safety and immunogenicity of a mRNA rabies vaccine in healthy adults: an open-label, non-randomised, prospective, first-in-human phase 1 clinical trial

Alberer, Martin, Gnad-Vogt, Ulrike, Hong, Henoch Sangjoon, Mehr, Keyvan Tadjalli, Backert, Linus, Finak, Greg, Gottardo, Raphael, Bica, Mihai Alexandru, Garofano, Aurelio, Koch, Sven Dominik, Fotin-Ml

Journal:

Lancet (London, England)

Year:

2017

Language:

english

File:

PDF, 455 KB

english, 2017

2

Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium

Finak, Greg, Langweiler, Marc, Jaimes, Maria, Malek, Mehrnoush, Taghiyar, Jafar, Korin, Yael, Raddassi, Khadir, Devine, Lesley, Obermoser, Gerlinde, Pekalski, Marcin L., Pontikos, Nikolas, Diaz, Alain

Journal:

Scientific Reports

Year:

2016

Language:

english

File:

PDF, 855 KB

english, 2016

3

Optimizing transformations for automated, high throughput analysis of flow cytometry data

Greg Finak, Juan-Manuel Perez, Andrew Weng, Raphael Gottardo

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 4.47 MB

english, 2010

4

Mixture models for single-cell assays with applications to vaccine studies

Finak, G., McDavid, A., Chattopadhyay, P., Dominguez, M., De Rosa, S., Roederer, M., Gottardo, R.

Journal:

Year:

2014

Language:

english

File:

PDF, 689 KB

english, 2014

5

Critical assessment of automated flow cytometry data analysis techniques

Aghaeepour, Nima, Finak, Greg, Dougall, David, Khodabakhshi, Alireza Hadj, Mah, Phillip, Obermoser, Gerlinde, Spidlen, Josef, Taylor, Ian, Wuensch, Sherry A, Bramson, Jonathan, Eaves, Connie, Weng, An

Journal:

Year:

2013

Language:

english

File:

PDF, 1.63 MB

english, 2013

6

COMPASS identifies T-cell subsets correlated with clinical outcomes

Lin, Lin, Finak, Greg, Ushey, Kevin, Seshadri, Chetan, Hawn, Thomas R, Frahm, Nicole, Scriba, Thomas J, Mahomed, Hassan, Hanekom, Willem, Bart, Pierre-Alexandre, Pantaleo, Giuseppe, Tomaras, Georgia D

Journal:

Nature Biotechnology

Year:

2015

Language:

english

File:

PDF, 1.18 MB

english, 2015

7

The contribution of cell cycle to heterogeneity in single-cell RNA-seq data

McDavid, Andrew, Finak, Greg, Gottardo, Raphael

Journal:

Nature Biotechnology

Year:

2016

Language:

english

File:

PDF, 342 KB

english, 2016

8

DataPackageR: Reproducible data preprocessing, standardization and sharing using R/Bioconductor for collaborative data analysis

Finak, Greg, Mayer, Bryan, Fulp, William, Obrecht, Paul, Sato, Alicia, Chung, Eva, Holman, Drienna, Gottardo, Raphael

Journal:

Gates Open Research

Year:

2018

Language:

english

File:

PDF, 862 KB

english, 2018

9

Regulation of endocytosis via the oxygen-sensing pathway

Wang, Yi, Roche, Olga, Yan, Mathew S, Finak, Greg, Evans, Andrew J, Metcalf, Julie L, Hast, Bridgid E, Hanna, Sara C, Wondergem, Bill, Furge, Kyle A

Journal:

Nature Medicine

Year:

2009

Language:

english

File:

PDF, 669 KB

english, 2009

10

Stromal signature identifies basal breast cancers

Finak, Greg, Bertos, Nicholas, Hallett, Michael, Park, Morag

Journal:

Nature Medicine

Year:

2009

Language:

english

File:

PDF, 82 KB

english, 2009

11

Stromal gene expression predicts clinical outcome in breast cancer

Finak, Greg, Bertos, Nicholas, Pepin, Francois, Sadekova, Svetlana, Souleimanova, Margarita, Zhao, Hong, Chen, Haiying, Omeroglu, Gulbeyaz, Meterissian, Sarkis, Omeroglu, Atilla

Journal:

Nature Medicine

Year:

2008

Language:

english

File:

PDF, 867 KB

english, 2008

12

Directional-coupler power divider by two-step K^+-ion exchange

Yip, G. L., Finak, J.

Journal:

Year:

1984

Language:

english

File:

PDF, 397 KB

english, 1984

13

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

Pepin François, Nicholas Bertos, Julie Laferrière, Svetlana Sadekova, Margarita Souleimanova, Hong Zhao, Greg Finak, Sarkis Meterissian, Michael T Hallett, Morag Park

Journal:

Breast Cancer Research

Year:

2012

Language:

english

File:

PDF, 576 KB

english, 2012

14

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

Greg Finak, Wenxin Jiang, Jorge Pardo, Adam Asare, Raphael Gottardo

Journal:

BMC Bioinformatics

Year:

2012

Language:

english

File:

PDF, 1.10 MB

english, 2012

15

Highly multiplexed quantitation of gene expression on single cells

Dominguez, Maria H., Chattopadhyay, Pratip K., Ma, Steven, Lamoreaux, Laurie, McDavid, Andrew, Finak, Greg, Gottardo, Raphael, Koup, Richard A., Roederer, Mario

Journal:

Journal of Immunological Methods

Year:

2013

Language:

english

File:

PDF, 1.19 MB

english, 2013

16

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

Greg Finak, Svetlana Sadekova, Francois Pepin, Michael Hallett…

Journal:

Breast Cancer Research

Year:

2006

Language:

english

File:

PDF, 4.03 MB

english, 2006

17

High-throughput flow cytometry data normalization for clinical trials

Finak, Greg, Jiang, Wenxin, Krouse, Kevin, Wei, Chungwen, Sanz, Ignacio, Phippard, Deborah, Asare, Adam, De Rosa, Stephen C., Self, Steve, Gottardo, Raphael

Journal:

Cytometry Part A

Year:

2014

Language:

english

File:

PDF, 1.08 MB

english, 2014

18

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

Wang, Y., Roche, O., Xu, C., Moriyama, E. H., Heir, P., Chung, J., Roos, F. C., Chen, Y., Finak, G., Milosevic, M., Wilson, B. C., Teh, B. T., Park, M., Irwin, M. S., Ohh, M.

Journal:

Proceedings of the National Academy of Sciences

Year:

2012

Language:

english

File:

PDF, 998 KB

english, 2012

19

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

Malek, M., Taghiyar, M. J., Chong, L., Finak, G., Gottardo, R., Brinkman, R. R.

Journal:

Year:

2015

Language:

english

File:

PDF, 321 KB

english, 2015

20

Critical assessment of automated flow cytometry data analysis techniques

Aghaeepour, Nima, Finak, Greg, Hoos, Holger, Mosmann, Tim R, Brinkman, Ryan, Gottardo, Raphael, Scheuermann, Richard H

Journal:

Year:

2013

Language:

english

File:

PDF, 82 KB

english, 2013

21

Critical assessment of automated flow cytometry data analysis techniques

Aghaeepour, Nima, Finak, Greg, Hoos, Holger, Mosmann, Tim R, Brinkman, Ryan, Gottardo, Raphael, Scheuermann, Richard H

Journal:

Year:

2013

Language:

english

File:

PDF, 76 KB

english, 2013

22

Thinking Outside the Gate: Single-Cell Assessments in Multiple Dimensions

Kvistborg, Pia, Gouttefangeas, Cécile, Aghaeepour, Nima, Cazaly, Angelica, Chattopadhyay, Pratip K., Chan, Cliburn, Eckl, Judith, Finak, Greg, Hadrup, Sine Reker, Maecker, Holden T., Maurer, Dominik,

Journal:

Year:

2015

Language:

english

File:

PDF, 162 KB

english, 2015

23

An NMR approach to structural proteomics

Yee, A., Chang, X., Pineda-Lucena, A., Wu, B., Semesi, A., Le, B., Ramelot, T., Lee, G. M., Bhattacharyya, S., Gutierrez, P., Denisov, A., Lee, C.-H., Cort, J. R., Kozlov, G., Liao, J., Finak, G., Che

Journal:

Proceedings of the National Academy of Sciences

Year:

2002

Language:

english

File:

PDF, 515 KB

english, 2002

24

Modeling Bi-modality Improves Characterization of Cell Cycle on Gene Expression in Single Cells

McDavid, Andrew, Dennis, Lucas, Danaher, Patrick, Finak, Greg, Krouse, Michael, Wang, Alice, Webster, Philippa, Beechem, Joseph, Gottardo, Raphael, Zhong, Sheng

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 924 KB

english, 2014

25

OpenCyto: An Open Source Infrastructure for Scalable, Robust, Reproducible, and Automated, End-to-End Flow Cytometry Data Analysis

Finak, Greg, Frelinger, Jacob, Jiang, Wenxin, Newell, Evan W., Ramey, John, Davis, Mark M., Kalams, Spyros A., De Rosa, Stephen C., Gottardo, Raphael, Prlic, Andreas

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 2.37 MB

english, 2014

26

BIAS: Bioinformatics Integrated Application Software

Finak, G., Godin, N., Hallett, M., Pepin, F., Rajabi, Z., Srivastava, V., Tang, Z.

Journal:

Year:

2005

Language:

english

File:

PDF, 47 KB

english, 2005

27

T Cell Responses against Mycobacterial Lipids and Proteins Are Poorly Correlated in South African Adolescents

Seshadri, C., Lin, L., Scriba, T. J., Peterson, G., Freidrich, D., Frahm, N., DeRosa, S. C., Moody, D. B., Prandi, J., Gilleron, M., Mahomed, H., Jiang, W., Finak, G., Hanekom, W. A., Gottardo, R., Mc

Journal:

The Journal of Immunology

Year:

2015

Language:

english

File:

PDF, 1.20 MB

english, 2015

28

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

Finak, Greg, McDavid, Andrew, Yajima, Masanao, Deng, Jingyuan, Gersuk, Vivian, Shalek, Alex K., Slichter, Chloe K., Miller, Hannah W., McElrath, M. Juliana, Prlic, Martin, Linsley, Peter S., Gottardo,

Journal:

Year:

2015

Language:

english

File:

PDF, 3.57 MB

english, 2015

29

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

Lin, Lin, Frelinger, Jacob, Jiang, Wenxin, Finak, Greg, Seshadri, Chetan, Bart, Pierre-Alexandre, Pantaleo, Giuseppe, McElrath, Julie, DeRosa, Steve, Gottardo, Raphael

Journal:

Cytometry Part A

Year:

2015

Language:

english

File:

PDF, 3.19 MB

english, 2015

30

Automated analysis of flow cytometry data comes of age

Brinkman, Ryan R., Aghaeepour, Nima, Finak, Greg, Gottardo, Raphael, Mosmann, Tim, Scheuermann, Richard H.

Journal:

Cytometry Part A

Year:

2016

Language:

english

File:

PDF, 69 KB

english, 2016

31

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

Brinkman, Ryan R., Aghaeepour, Nima, Finak, Greg, Gottardo, Raphael, Mosmann, Tim, Scheuermann, Richard H.

Journal:

Cytometry Part A

Year:

2015

Language:

english

File:

PDF, 78 KB

english, 2015

32

Higher T cell responses induced by DNA/rAd5 HIV-1 preventive vaccine are associated with lower HIV-1 infection risk in an efficacy trial

Janes, Holly E., Cohen, Kristen W., Frahm, Nicole, De Rosa, Stephen C., Sanchez, Brittany, Hural, John, Magaret, Craig A., Karuna, Shelly, Bentley, Carter, Gottardo, Raphael, Finak, Greg, Grove, Dougl

Journal:

The Journal of Infectious Diseases

Year:

2017

Language:

english

File:

PDF, 1.08 MB

english, 2017

33

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

Rakshit, Srabanti, Adiga, Vasista, Nayak, Soumya, Sahoo, Pravat Nalini, Sharma, Prabhat Kumar, van Meijgaarden, Krista E., UK J., Anto Jesuraj, Dhar, Chirag, Souza, George D., Finak, Greg, De Rosa, St

Journal:

Scientific Reports

Year:

2017

Language:

english

File:

PDF, 4.76 MB

english, 2017

34

ggCyto: Next Generation Open-Source Visualization Software for Cytometry

Van, Phu, Jiang, Wenxin, Gottardo, Raphael, Finak, Greg

Journal:

Year:

2018

Language:

english

File:

PDF, 506 KB

english, 2018

35

In Silico Ascription of Gene Expression Differences to Tumor and Stromal Cells in a Model to Study Impact on Breast Cancer Outcome

Myhre, Simen, Mohammed, Hayat, Tramm, Trine, Alsner, Jan, Finak, Greg, Park, Morag, Overgaard, Jens, Børresen-Dale, Anne-Lise, Frigessi, Arnoldo, Sørlie, Therese, Algül, Hana

Journal:

Year:

2010

Language:

english

File:

PDF, 2.88 MB

english, 2010

36

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

Bolton, Diane L., McGinnis, Kathleen, Finak, Greg, Chattopadhyay, Pratip, Gottardo, Raphael, Roederer, Mario, Cullen, Bryan R.

Journal:

Year:

2017

Language:

english

File:

PDF, 1.55 MB

english, 2017

37

Le microenvironnement tumoral

Finak, Greg, Laferrièe, Julie, Hallett, Michael, Park, Morag

Journal:

médecine/sciences

Year:

2009

Language:

french

File:

PDF, 95 KB

french, 2009

38

CytoML for cross‐platform cytometry data sharing

Finak, Greg, Jiang, Wenxin, Gottardo, Raphael

Journal:

Cytometry Part A

Year:

2018

File:

PDF, 1.63 MB

2018

39

The Computational article format: Software as a research output

Journal:

Cytometry Part A

Year:

2018

File:

PDF, 149 KB

2018

40

CytoML for cross‐platform cytometry data sharing

Finak, Greg, Jiang, Wenxin, Gottardo, Raphael

Journal:

Cytometry Part A

Year:

2018

Language:

english

File:

PDF, 1.63 MB

english, 2018

41

The Computational article format: Software as a research output

Journal:

Cytometry Part A

Year:

2018

Language:

english

File:

PDF, 149 KB

english, 2018

42

Special Issue on Machine Learning for Single Cell Data

Saeys, Yvan, Finak, Greg

Journal:

Cytometry Part A

Year:

2020

File:

PDF, 622 KB

2020

43

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

Rozot, Virginie, Nemes, Elisa, Geldenhuys, Hennie, Musvosvi, Munyaradzi, Toefy, Asma, Rantangee, Frances, Makhethe, Lebohang, Erasmus, Mzwandile, Bilek, Nicole, Mabwe, Simbarashe, Finak, Greg, Fulp, W

Journal:

Communications Biology

Year:

2020

File:

PDF, 2.51 MB

2020