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Items: 40

1.

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

Finak G, Mayer B, Fulp W, Obrecht P, Sato A, Chung E, Holman D, Gottardo R.

Gates Open Res. 2018 Jul 10;2:31. doi: 10.12688/gatesopenres.12832.2.

2.

ggCyto: next generation open-source visualization software for cytometry.

Van P, Jiang W, Gottardo R, Finak G.

Bioinformatics. 2018 Nov 15;34(22):3951-3953. doi: 10.1093/bioinformatics/bty441.

3.

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

Rakshit S, Adiga V, Nayak S, Sahoo PN, Sharma PK, van Meijgaarden KE, Uk J AJ, Dhar C, Souza GD, Finak G, De Rosa SC, Ottenhoff THM, Vyakarnam A.

Sci Rep. 2017 Sep 20;7(1):11948. doi: 10.1038/s41598-017-10773-5.

4.

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.

Li SS, Kochar NK, Elizaga M, Hay CM, Wilson GJ, Cohen KW, De Rosa SC, Xu R, Ota-Setlik A, Morris D, Finak G, Allen M, Tieu HV, Frank I, Sobieszczyk ME, Hannaman D, Gottardo R, Gilbert PB, Tomaras GD, Corey L, Clarke DK, Egan MA, Eldridge JH, McElrath MJ, Frahm N; NIAID HIV Vaccine Trials Network.

Clin Vaccine Immunol. 2017 Nov 6;24(11). pii: e00263-17. doi: 10.1128/CVI.00263-17. Print 2017 Nov.

5.

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 M, Gnad-Vogt U, Hong HS, Mehr KT, Backert L, Finak G, Gottardo R, Bica MA, Garofano A, Koch SD, Fotin-Mleczek M, Hoerr I, Clemens R, von Sonnenburg F.

Lancet. 2017 Sep 23;390(10101):1511-1520. doi: 10.1016/S0140-6736(17)31665-3. Epub 2017 Jul 25.

PMID:
28754494
6.

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

Bolton DL, McGinnis K, Finak G, Chattopadhyay P, Gottardo R, Roederer M.

PLoS Pathog. 2017 Jun 27;13(6):e1006445. doi: 10.1371/journal.ppat.1006445. eCollection 2017 Jun.

7.

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 HE, Cohen KW, Frahm N, De Rosa SC, Sanchez B, Hural J, Magaret CA, Karuna S, Bentley C, Gottardo R, Finak G, Grove D, Shen M, Graham BS, Koup RA, Mulligan MJ, Koblin B, Buchbinder SP, Keefer MC, Adams E, Anude C, Corey L, Sobieszczyk M, Hammer SM, Gilbert PB, McElrath MJ.

J Infect Dis. 2017 May 1;215(9):1376-1385. doi: 10.1093/infdis/jix086.

8.

Distinct activation thresholds of human conventional and innate-like memory T cells.

Slichter CK, McDavid A, Miller HW, Finak G, Seymour BJ, McNevin JP, Diaz G, Czartoski JL, McElrath MJ, Gottardo R, Prlic M.

JCI Insight. 2016 Jun 2;1(8). pii: e86292.

9.

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

McDavid A, Finak G, Gottardo R.

Nat Biotechnol. 2016 Jun 9;34(6):591-3. doi: 10.1038/nbt.3498. No abstract available.

10.

Promises and Pitfalls of High-Throughput Biological Assays.

Finak G, Gottardo R.

Methods Mol Biol. 2016;1415:225-43. doi: 10.1007/978-1-4939-3572-7_12.

PMID:
27115636
11.

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.

Fiore-Gartland A, Manso BA, Friedrich DP, Gabriel EE, Finak G, Moodie Z, Hertz T, De Rosa SC, Frahm N, Gilbert PB, McElrath MJ.

PLoS One. 2016 Feb 10;11(2):e0147812. doi: 10.1371/journal.pone.0147812. eCollection 2016.

12.

Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium.

Finak G, Langweiler M, Jaimes M, Malek M, Taghiyar J, Korin Y, Raddassi K, Devine L, Obermoser G, Pekalski ML, Pontikos N, Diaz A, Heck S, Villanova F, Terrazzini N, Kern F, Qian Y, Stanton R, Wang K, Brandes A, Ramey J, Aghaeepour N, Mosmann T, Scheuermann RH, Reed E, Palucka K, Pascual V, Blomberg BB, Nestle F, Nussenblatt RB, Brinkman RR, Gottardo R, Maecker H, McCoy JP.

Sci Rep. 2016 Feb 10;6:20686. doi: 10.1038/srep20686.

13.

Automated analysis of flow cytometry data comes of age.

Brinkman RR, Aghaeepour N, Finak G, Gottardo R, Mosmann T, Scheuermann RH.

Cytometry A. 2016 Jan;89(1):13-5. doi: 10.1002/cyto.a.22810. No abstract available.

14.

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

Finak G, McDavid A, Yajima M, Deng J, Gersuk V, Shalek AK, Slichter CK, Miller HW, McElrath MJ, Prlic M, Linsley PS, Gottardo R.

Genome Biol. 2015 Dec 10;16:278. doi: 10.1186/s13059-015-0844-5.

15.

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

Seshadri C, Lin L, Scriba TJ, Peterson G, Freidrich D, Frahm N, DeRosa SC, Moody DB, Prandi J, Gilleron M, Mahomed H, Jiang W, Finak G, Hanekom WA, Gottardo R, McElrath MJ, Hawn TR.

J Immunol. 2015 Nov 15;195(10):4595-603. doi: 10.4049/jimmunol.1501285. Epub 2015 Oct 14.

16.

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

Aghaeepour N, Chattopadhyay P, Chikina M, Dhaene T, Van Gassen S, Kursa M, Lambrecht BN, Malek M, McLachlan GJ, Qian Y, Qiu P, Saeys Y, Stanton R, Tong D, Vens C, Walkowiak S, Wang K, Finak G, Gottardo R, Mosmann T, Nolan GP, Scheuermann RH, Brinkman RR.

Cytometry A. 2016 Jan;89(1):16-21. doi: 10.1002/cyto.a.22732. Epub 2015 Oct 8.

17.

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

Brinkman RR, Aghaeepour N, Finak G, Gottardo R, Mosmann T, Scheuermann RH.

Cytometry A. 2015 Jul;87(7):591-3. doi: 10.1002/cyto.a.22707. No abstract available.

18.

COMPASS identifies T-cell subsets correlated with clinical outcomes.

Lin L, Finak G, Ushey K, Seshadri C, Hawn TR, Frahm N, Scriba TJ, Mahomed H, Hanekom W, Bart PA, Pantaleo G, Tomaras GD, Rerks-Ngarm S, Kaewkungwal J, Nitayaphan S, Pitisuttithum P, Michael NL, Kim JH, Robb ML, O'Connell RJ, Karasavvas N, Gilbert P, C De Rosa S, McElrath MJ, Gottardo R.

Nat Biotechnol. 2015 Jun;33(6):610-6. doi: 10.1038/nbt.3187. Epub 2015 May 25.

19.

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

Lin L, Frelinger J, Jiang W, Finak G, Seshadri C, Bart PA, Pantaleo G, McElrath J, DeRosa S, Gottardo R.

Cytometry A. 2015 Jul;87(7):675-82. doi: 10.1002/cyto.a.22623. Epub 2015 Apr 23.

20.

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

Kvistborg P, Gouttefangeas C, Aghaeepour N, Cazaly A, Chattopadhyay PK, Chan C, Eckl J, Finak G, Hadrup SR, Maecker HT, Maurer D, Mosmann T, Qiu P, Scheuermann RH, Welters MJ, Ferrari G, Brinkman RR, Britten CM.

Immunity. 2015 Apr 21;42(4):591-2. doi: 10.1016/j.immuni.2015.04.006. No abstract available.

21.

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

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

Bioinformatics. 2015 Feb 15;31(4):606-7. doi: 10.1093/bioinformatics/btu677. Epub 2014 Oct 16.

22.

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

Finak G, Frelinger J, Jiang W, Newell EW, Ramey J, Davis MM, Kalams SA, De Rosa SC, Gottardo R.

PLoS Comput Biol. 2014 Aug 28;10(8):e1003806. doi: 10.1371/journal.pcbi.1003806. eCollection 2014 Aug.

23.

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

McDavid A, Dennis L, Danaher P, Finak G, Krouse M, Wang A, Webster P, Beechem J, Gottardo R.

PLoS Comput Biol. 2014 Jul 17;10(7):e1003696. doi: 10.1371/journal.pcbi.1003696. eCollection 2014 Jul.

24.

High-throughput flow cytometry data normalization for clinical trials.

Finak G, Jiang W, Krouse K, Wei C, Sanz I, Phippard D, Asare A, De Rosa SC, Self S, Gottardo R.

Cytometry A. 2014 Mar;85(3):277-86. doi: 10.1002/cyto.a.22433. Epub 2013 Dec 31.

25.

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.

Biostatistics. 2014 Jan;15(1):87-101. doi: 10.1093/biostatistics/kxt024. Epub 2013 Jul 24.

26.

Highly multiplexed quantitation of gene expression on single cells.

Dominguez MH, Chattopadhyay PK, Ma S, Lamoreaux L, McDavid A, Finak G, Gottardo R, Koup RA, Roederer M.

J Immunol Methods. 2013 May 31;391(1-2):133-45. doi: 10.1016/j.jim.2013.03.002. Epub 2013 Mar 13.

27.

Critical assessment of automated flow cytometry data analysis techniques.

Aghaeepour N, Finak G; FlowCAP Consortium; DREAM Consortium, Hoos H, Mosmann TR, Brinkman R, Gottardo R, Scheuermann RH.

Nat Methods. 2013 Mar;10(3):228-38. doi: 10.1038/nmeth.2365. Epub 2013 Feb 10. Erratum in: Nat Methods. 2013 May;10(5):445.

28.

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

McDavid A, Finak G, Chattopadyay PK, Dominguez M, Lamoreaux L, Ma SS, Roederer M, Gottardo R.

Bioinformatics. 2013 Feb 15;29(4):461-7. doi: 10.1093/bioinformatics/bts714. Epub 2012 Dec 24.

29.

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

Finak G, Jiang W, Pardo J, Asare A, Gottardo R.

BMC Bioinformatics. 2012 Sep 28;13:252. doi: 10.1186/1471-2105-13-252.

30.

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

Pepin F, Bertos N, Laferrière J, Sadekova S, Souleimanova M, Zhao H, Finak G, Meterissian S, Hallett MT, Park M.

Breast Cancer Res. 2012 Aug 20;14(4):R120. doi: 10.1186/bcr3246.

31.

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

Wang Y, Roche O, Xu C, Moriyama EH, Heir P, Chung J, Roos FC, Chen Y, Finak G, Milosevic M, Wilson BC, Teh BT, Park M, Irwin MS, Ohh M.

Proc Natl Acad Sci U S A. 2012 Mar 27;109(13):4892-7. doi: 10.1073/pnas.1112129109. Epub 2012 Mar 12.

32.

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

Myhre S, Mohammed H, Tramm T, Alsner J, Finak G, Park M, Overgaard J, Børresen-Dale AL, Frigessi A, Sørlie T.

PLoS One. 2010 Nov 19;5(11):e14002. doi: 10.1371/journal.pone.0014002.

33.

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

Finak G, Perez JM, Weng A, Gottardo R.

BMC Bioinformatics. 2010 Nov 4;11:546. doi: 10.1186/1471-2105-11-546.

34.

Merging mixture components for cell population identification in flow cytometry.

Finak G, Bashashati A, Brinkman R, Gottardo R.

Adv Bioinformatics. 2009:247646. doi: 10.1155/2009/247646. Epub 2009 Nov 12.

35.

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

Finak G, Laferrière J, Hallett M, Park M.

Med Sci (Paris). 2009 May;25(5):439-41. doi: 10.1051/medsci/2009255439. French. No abstract available.

36.

Regulation of endocytosis via the oxygen-sensing pathway.

Wang Y, Roche O, Yan MS, Finak G, Evans AJ, Metcalf JL, Hast BE, Hanna SC, Wondergem B, Furge KA, Irwin MS, Kim WY, Teh BT, Grinstein S, Park M, Marsden PA, Ohh M.

Nat Med. 2009 Mar;15(3):319-24. doi: 10.1038/nm.1922. Epub 2009 Mar 1.

PMID:
19252501
37.

Stromal gene expression predicts clinical outcome in breast cancer.

Finak G, Bertos N, Pepin F, Sadekova S, Souleimanova M, Zhao H, Chen H, Omeroglu G, Meterissian S, Omeroglu A, Hallett M, Park M.

Nat Med. 2008 May;14(5):518-27. doi: 10.1038/nm1764. Epub 2008 Apr 27.

PMID:
18438415
38.

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

Finak G, Sadekova S, Pepin F, Hallett M, Meterissian S, Halwani F, Khetani K, Souleimanova M, Zabolotny B, Omeroglu A, Park M.

Breast Cancer Res. 2006;8(5):R58.

39.

BIAS: Bioinformatics Integrated Application Software.

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

Bioinformatics. 2005 Apr 15;21(8):1745-6. Epub 2004 Nov 30.

PMID:
15572471
40.

An NMR approach to structural proteomics.

Yee A, Chang X, Pineda-Lucena A, Wu B, Semesi A, Le B, Ramelot T, Lee GM, Bhattacharyya S, Gutierrez P, Denisov A, Lee CH, Cort JR, Kozlov G, Liao J, Finak G, Chen L, Wishart D, Lee W, McIntosh LP, Gehring K, Kennedy MA, Edwards AM, Arrowsmith CH.

Proc Natl Acad Sci U S A. 2002 Feb 19;99(4):1825-30.

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