Raphael Gottardo

Publications | Mémoires et thèses

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171 publications

En préparation | 2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2004 | 2003 |
En préparation
 
The tidyomics ecosystem: Enhancing omic data analyses.
Hutchison William J., Keyes Timothy J., Crowell Helena L., Serizay Jacques, Soneson Charlotte, Davis Eric S., Sato Noriaki, Moses Lambda, Tarlinton Boyd, Nahid Abdullah A. et al..
[DOI][Pmid][serval:BIB_2E7F8476CE75]
2024
 
Immune modules to guide diagnosis and personalized treatment of inflammatory skin diseases.
Seremet T., Di Domizio J., Girardin A., Yatim A., Jenelten R., Messina F., Saidoune F., Schlapbach C., Bogiatzi S., Minisini F. et al., 2024/12/18. Nature communications, 15 (1) p. 10688. Peer-reviewed.
[DOI][Pmid][serval:BIB_EE04B0E74C9B]
 
Long term T cell response and safety of a tetravalent dengue vaccine in healthy children.
Mandaric S., Friberg H., Saez-Llorens X., Borja-Tabora C., Biswal S., Escudero I., Faccin A., Gottardo R., Brose M., Roubinis N. et al., 2024/10/17. NPJ vaccines, 9 (1) p. 192. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_421259B77384]
 
Histone marks identify novel transcription factors that parse CAR-T subset-of-origin, clinical potential and expansion.
Fiorenza S., Zheng Y., Purushe J., Bock T.J., Sarthy J., Janssens D.H., Sheih A.S., Kimble E.L., Kirchmeier D., Phi T.D. et al., 2024/09/27. Nature communications, 15 (1) p. 8309. Peer-reviewed.
[DOI][Pmid][serval:BIB_63C2526F1F8E]
 
ADTnorm: Robust Integration of Single-cell Protein Measurement across CITE-seq Datasets
Gottardo Raphael, Zheng Ye, Caron Daniel, Kim Ju, Jun Seong, Tian Yuan, Mair Florian, Stuart Kenneth, Sims Peter, 2024/07/08..
[DOI][Pmid][serval:BIB_8A286CBE32FB]
 
Long-term Remissions Following CD20-Directed Chimeric Antigen Receptor-Adoptive T-cell Therapy.
Mo G., Lee S.Y., Coffey D.G., Voillet V., Kirsch I.R., Gottardo R., Smythe K.S., Yeung CCS, Greenbaum A., Green D.J. et al., 2024/07/01. Blood cancer discovery, 5 (4) pp. 258-266. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_F35F15A30130]
 
The tidyomics ecosystem: enhancing omic data analyses.
Hutchison W.J., Keyes T.J., tidyomics Consortium, Crowell H.L., Serizay J., Soneson C., Davis E.S., Sato N., Moses L., Tarlinton B. et al., 2024/07. Nature methods, 21 (7) pp. 1166-1170. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_D2FD0777383A]
An approach for integrating multimodal omics data into sparse and interpretable models.
Dong Y., Gottardo R., 2024/02/26. Cell reports methods, 4 (2) p. 100718. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_FC1B402F5F17]
Signaling via a CD27-TRAF2-SHP-1 axis during naive T cell activation promotes memory-associated gene regulatory networks.
Jaeger-Ruckstuhl C.A., Lo Y., Fulton E., Waltner O.G., Shabaneh T.B., Simon S., Muthuraman P.V., Correnti C.E., Newsom O.J., Engstrom I.A. et al., 2024/02/13. Immunity, 57 (2) pp. 287-302.e12. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_A730B5E1D986]
2023
 
Single-cell protein expression profiling resolves circulating and resident memory T cell diversity across tissues and infection contexts.
Evrard M., Becht E., Fonseca R., Obers A., Park S.L., Ghabdan-Zanluqui N., Schroeder J., Christo S.N., Schienstock D., Lai J. et al., 2023/07/11. Immunity, 56 (7) pp. 1664-1680.e9. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_203407FABD48]
The Statistical Analysis of the Varying Brain.
Chén Oliver Y., Thanh Vũ Duy, Greub Gilbert, Cao Hengyi, He Xingru, Muller Yannick, Petrovas Constantinos, Shou Haochang, Nguyen Viet-Dung, Zhi Bangdong et al., 2023/07/02. IEEE Statistical Signal Processing (SSP). Peer-reviewed.
[URN][DOI][WoS][serval:BIB_C6B3B6AA1F8B]
Differentiation of IL-26+ TH17 intermediates into IL-17A producers via epithelial crosstalk in psoriasis.
Fries A., Saidoune F., Kuonen F., Dupanloup I., Fournier N., Guerra de Souza A.C., Haniffa M., Ma F., Gudjonsson J.E., Roesner L. et al., 2023/06/30. Nature communications, 14 (1) p. 3878. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_F7440A1D7F03]
An information theoretic approach to detecting spatially varying genes.
Jones D.C., Danaher P., Kim Y., Beechem J.M., Gottardo R., Newell E.W., 2023/06/26. Cell reports methods, 3 (6) p. 100507. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_3A146C47077F]
2022
 
Pan-vaccine analysis reveals innate immune endotypes predictive of antibody responses to vaccination.
Fourati S., Tomalin L.E., Mulè M.P., Chawla D.G., Gerritsen B., Rychkov D., Henrich E., Miller HER, Hagan T., Diray-Arce J. et al., 2022/12. Nature immunology, 23 (12) pp. 1777-1787. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_7EDDB1E44F2D]
 
Transcriptional atlas of the human immune response to 13 vaccines reveals a common predictor of vaccine-induced antibody responses.
Hagan T., Gerritsen B., Tomalin L.E., Fourati S., Mulè M.P., Chawla D.G., Rychkov D., Henrich E., Miller HER, Diray-Arce J. et al., 2022/12. Nature immunology, 23 (12) pp. 1788-1798. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_A8FF8D49C962]
The Immune Signatures data resource, a compendium of systems vaccinology datasets.
Diray-Arce J., Miller HER, Henrich E., Gerritsen B., Mulè M.P., Fourati S., Gygi J., Hagan T., Tomalin L., Rychkov D. et al., 2022/10/20. Scientific data, 9 (1) p. 635. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_FDA7293F77B9]
Transcriptional and functional analyses of neoantigen-specific CD4 T cells during a profound response to anti-PD-L1 in metastatic Merkel cell carcinoma.
Church C., Pulliam T., Longino N., Park S.Y., Smythe K.S., Makarov V., Riaz N., Jing L., Amezquita R., Campbell J.S. et al., 2022/09. Journal for immunotherapy of cancer, 10 (9) pp. e005328. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_750977A30F9F]
 
Th2-Biased Transcriptional Profile Predicts HIV Envelope-Specific Polyfunctional CD4+ T Cells That Correlated with Reduced Risk of Infection in RV144 Trial.
Cohen K.W., Tian Y., Thayer C., Seese A., Amezquita R., McElrath M.J., De Rosa S.C., Gottardo R., 2022/08/01. Journal of immunology, 209 (3) pp. 526-534. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_D21FD8190EFD]
Monocyte Transcriptional Responses to Mycobacterium tuberculosis Associate with Resistance to Tuberculin Skin Test and Interferon Gamma Release Assay Conversion.
Simmons J.D., Dill-McFarland K.A., Stein C.M., Van P.T., Chihota V., Ntshiqa T., Maenetje P., Peterson G.J., Benchek P., Nsereko M. et al., 2022/06/29. mSphere, 7 (3) pp. e0015922. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_2FD7AA544175]
Extricating human tumour immune alterations from tissue inflammation.
Mair F., Erickson J.R., Frutoso M., Konecny A.J., Greene E., Voillet V., Maurice N.J., Rongvaux A., Dixon D., Barber B. et al., 2022/05. Nature, 605 (7911) pp. 728-735. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_DEEFAB8708F3]
Humoral Responses Against Variants of Concern by COVID-19 mRNA Vaccines in Immunocompromised Patients.
Obeid M., Suffiotti M., Pellaton C., Bouchaab H., Cairoli A., Salvadé V., Stevenel C., Hottinger R., Pythoud C., Coutechier L. et al., 2022/05/01. JAMA oncology, 8 (5) pp. e220446. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_8956034C5615]
 
Multiple early factors anticipate post-acute COVID-19 sequelae.
Su Y., Yuan D., Chen D.G., Ng R.H., Wang K., Choi J., Li S., Hong S., Zhang R., Xie J. et al., 2022/03/03. Cell, 185 (5) pp. 881-895.e20. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_296B705072A0]
 
Targeting an alternate Wilms' tumor antigen 1 peptide bypasses immunoproteasome dependency.
Lahman M.C., Schmitt T.M., Paulson K.G., Vigneron N., Buenrostro D., Wagener F.D., Voillet V., Martin L., Gottardo R., Bielas J. et al., 2022/02/09. Science translational medicine, 14 (631) pp. eabg8070. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_5583F3C8D203]
IDEAS: individual level differential expression analysis for single-cell RNA-seq data.
Zhang M., Liu S., Miao Z., Han F., Gottardo R., Sun W., 2022/01/24. Genome biology, 23 (1) p. 33. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_B48AF13F6F91]
Transcriptional correlates of malaria in RTS,S/AS01-vaccinated African children: a matched case-control study.
Moncunill G., Carnes J., Chad Young W., Carpp L., De Rosa S., Campo J.J., Nhabomba A., Mpina M., Jairoce C., Finak G. et al., 2022/01/21. eLife, 11 pp. e70393. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_807A74E7EF22]
 
Characterization of the cell-mediated immune response to Takeda's live-attenuated tetravalent dengue vaccine in adolescents participating in a phase 2 randomized controlled trial conducted in a dengue-endemic setting
Tricou V., Gottardo R., Egan M. A., Clement F., Leroux-Roels G., Saez-Llorens X., Borkowski A., Wallace D., Dean H. J., 2022. Vaccine, 40 (8) pp. 1143-1151.
[DOI][Pmid][serval:BIB_B80DB520E3DE]
 
Integrated analysis of plasma and single immune cells uncovers metabolic changes in individuals with COVID-19.
Lee J.W., Su Y., Baloni P., Chen D., Pavlovitch-Bedzyk A.J., Yuan D., Duvvuri V.R., Ng R.H., Choi J., Xie J. et al., 2022/01. Nature biotechnology, 40 (1) pp. 110-120. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_0C32A4C49EAB]
 
Single-cell immunology of SARS-CoV-2 infection.
Tian Y., Carpp L.N., Miller HER, Zager M., Newell E.W., Gottardo R., 2022/01. Nature biotechnology, 40 (1) pp. 30-41. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_F4C681A1F5A5]
The deficiency in Th2-like Tfh cells affects the maturation and quality of HIV-specific B cell response in viremic infection.
Noto A., Suffiotti M., Joo V., Mancarella A., Procopio F.A., Cavet G., Leung Y., Corpataux J.M., Cavassini M., Riva A. et al., 2022. Frontiers in immunology, 13 p. 960120. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_3A9147719CB5]
2021
New interpretable machine-learning method for single-cell data reveals correlates of clinical response to cancer immunotherapy.
Greene E., Finak G., D'Amico L.A., Bhardwaj N., Church C.D., Morishima C., Ramchurren N., Taube J.M., Nghiem P.T., Cheever M.A. et al., 2021/12/10. Patterns, 2 (12) p. 100372. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_4AF9E6EB0D95]
 
A regulatory T cell signature distinguishes the immune landscape of COVID-19 patients from those with other respiratory infections.
Vick S.C., Frutoso M., Mair F., Konecny A.J., Greene E., Wolf C.R., Logue J.K., Franko N.M., Boonyaratanakornkit J., Gottardo R. et al., 2021/11/12. Science advances, 7 (46) pp. eabj0274. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_8E8F91ADD6A0]
 
Spatial transcriptomics at subspot resolution with BayesSpace
Zhao E., Stone M. R., Ren X., Guenthoer J., Smythe K. S., Pulliam T., Williams S. R., Uytingco C. R., Taylor S. E. B., Nghiem P. et al., 2021/11. Nat Biotechnol, 39 (11) pp. 1375-1384.
[DOI][Pmid][serval:BIB_8D92033C8F26]
 
Spatial UMAP and Image Cytometry for Topographic Immuno-oncology Biomarker Discovery
Giraldo N. A., Berry S., Becht E., Ates D., Schenk K. M., Engle E. L., Green B., Nguyen P., Soni A., Stein J. E. et al., 2021/11. Cancer Immunol Res, 9 (11) pp. 1262-1269.
[DOI][Pmid][serval:BIB_B645EB19D1AF]
 
High-throughput single-cell quantification of hundreds of proteins using conventional flow cytometry and machine learning.
Becht E., Tolstrup D., Dutertre C.A., Morawski P.A., Campbell D.J., Ginhoux F., Newell E.W., Gottardo R., Headley M.B., 2021/09/24. Science advances, 7 (39) pp. eabg0505. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_BF60BD88DD8E]
 
Comparative analysis of TCR and CAR signaling informs CAR designs with superior antigen sensitivity and in vivo function.
Salter A.I., Rajan A., Kennedy J.J., Ivey R.G., Shelby S.A., Leung I., Templeton M.L., Muhunthan V., Voillet V., Sommermeyer D. et al., 2021/08/24. Science signaling, 14 (697). Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_4549B78DD27D]
 
Monocyte metabolic transcriptional programs associate with resistance to tuberculin skin test/interferon-γ release assay conversion.
Simmons J.D., Van P.T., Stein C.M., Chihota V., Ntshiqa T., Maenetje P., Peterson G.J., Reynolds A., Benchek P., Velen K. et al., 2021/07/15. The Journal of clinical investigation, 131 (14). Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_9E84874C44D0]
 
Single-cell CUT&Tag analysis of chromatin modifications in differentiation and tumor progression.
Wu S.J., Furlan S.N., Mihalas A.B., Kaya-Okur H.S., Feroze A.H., Emerson S.N., Zheng Y., Carson K., Cimino P.J., Keene C.D. et al., 2021/07. Nature biotechnology, 39 (7) pp. 819-824. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_CE7A12D8A905]
 
The human memory T cell compartment changes across tissues of the female reproductive tract
Woodward Davis A. S., Vick S. C., Pattacini L., Voillet V., Hughes S. M., Lentz G. M., Kirby A. C., Fialkow M. F., Gottardo R., Hladik F. et al., 2021/07. Mucosal Immunol, 14 (4) pp. 862-872.
[DOI][Pmid][serval:BIB_DF1824BE5A58]
 
Safety and immunogenicity of an HIV-1 gp120-CD4 chimeric subunit vaccine in a phase 1a randomized controlled trial.
Chua J.V., Davis C., Husson J.S., Nelson A., Prado I., Flinko R., Lam KWJ, Mutumbi L., Mayer B.T., Dong D. et al., 2021/06/29. Vaccine, 39 (29) pp. 3879-3891. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_BC5E37197EB8]
 
Integrated analysis of multimodal single-cell data.
Hao Y., Hao S., Andersen-Nissen E., Mauck W.M., Zheng S., Butler A., Lee M.J., Wilk A.J., Darby C., Zager M. et al., 2021/06/24. Cell, 184 (13) pp. 3573-3587.e29. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_C664D84081D5]
 
CD101 genetic variants modify regulatory and conventional T cell phenotypes and functions.
Richert-Spuhler L.E., Mar C.M., Shinde P., Wu F., Hong T., Greene E., Hou S., Thomas K., Gottardo R., Mugo N. et al., 2021/06/15. Cell reports. Medicine, 2 (6) p. 100322. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_A95D49E87527]
 
Optimal therapeutic targeting by HDAC inhibition in biopsy-derived treatment-naïve diffuse midline glioma models.
Vitanza N.A., Biery M.C., Myers C., Ferguson E., Zheng Y., Girard E.J., Przystal J.M., Park G., Noll A., Pakiam F. et al., 2021/03/25. Neuro-oncology, 23 (3) pp. 376-386. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_D48BD252D415]
 
Immunogenic Chemotherapy Enhances Recruitment of CAR-T Cells to Lung Tumors and Improves Antitumor Efficacy when Combined with Checkpoint Blockade.
Srivastava S., Furlan S.N., Jaeger-Ruckstuhl C.A., Sarvothama M., Berger C., Smythe K.S., Garrison S.M., Specht J.M., Lee S.M., Amezquita R.A. et al., 2021/02/08. Cancer cell, 39 (2) pp. 193-208.e10. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_45BBFC2841DC]
 
Development of a clinically relevant ovarian cancer model incorporating surgical cytoreduction to evaluate treatment of micro-metastatic disease.
Morse C.B., Voillet V., Bates B.M., Chiu E.Y., Garcia N.M., Gottardo R., Greenberg P.D., Anderson K.G., 2021/02. Gynecologic oncology, 160 (2) pp. 427-437. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_276C9CE59B3C]
 
A differential regulatory T cell signature distinguishes the immune landscape of COVID-19 hospitalized patients from those hospitalized with other respiratory viral infections
Vick Sarah C., Frutoso Marie, Mair Florian, Konecny Andrew J., Greene Evan, Wolf Caitlin R., Logue Jennifer K., Boonyaratanakornkit Jim, Gottardo Raphael, Schiffer Joshua T. et al., 2021..
[DOI][Pmid][serval:BIB_CFF5F3763E69]
 
Comprehensive Data Integration Approach to Assess Immune Responses and Correlates of RTS,S/AS01-Mediated Protection From Malaria Infection in Controlled Human Malaria Infection Trials.
Young W.C., Carpp L.N., Chaudhury S., Regules J.A., Bergmann-Leitner E.S., Ockenhouse C., Wille-Reece U., deCamp A.C., Hughes E., Mahoney C. et al., 2021. Frontiers in big data, 4 p. 672460. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_F94F06DDAEE9]
2020
 
Multi-Omics Resolves a Sharp Disease-State Shift between Mild and Moderate COVID-19.
Su Y., Chen D., Yuan D., Lausted C., Choi J., Dai C.L., Voillet V., Duvvuri V.R., Scherler K., Troisch P. et al., 2020/12/10. Cell, 183 (6) pp. 1479-1495.e20. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_078856281154]
 
PD-1 and TIGIT coexpression identifies a circulating CD8 T cell subset predictive of response to anti-PD-1 therapy.
Simon S., Voillet V., Vignard V., Wu Z., Dabrowski C., Jouand N., Beauvais T., Khammari A., Braudeau C., Josien R. et al., 2020/11. Journal for immunotherapy of cancer, 8 (2). Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_61FA7BC39A7C]
 
A Potent Anti-Malarial Human Monoclonal Antibody Targets Circumsporozoite Protein Minor Repeats and Neutralizes Sporozoites in the Liver.
Wang L.T., Pereira L.S., Flores-Garcia Y., O'Connor J., Flynn B.J., Schön A., Hurlburt N.K., Dillon M., Yang ASP, Fabra-García A. et al., 2020/10/13. Immunity, 53 (4) pp. 733-744.e8. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_3829E3BD3BCE]
 
3M-052, a synthetic TLR-7/8 agonist, induces durable HIV-1 envelope-specific plasma cells and humoral immunity in nonhuman primates.
Kasturi S.P., Rasheed MAU, Havenar-Daughton C., Pham M., Legere T., Sher Z.J., Kovalenkov Y., Gumber S., Huang J.Y., Gottardo R. et al., 2020/06/19. Science immunology, 5 (48). Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_DF43F44F88B5]
 
Aggregating transcript-level analyses for single-cell differential gene expression.
Becht E., Zhao E., Amezquita R., Gottardo R., 2020/06. Nature methods, 17 (6) pp. 583-585. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_4E64E7B37886]
Optimal priming of poxvirus vector (NYVAC)-based HIV vaccine regimens for T cell responses requires three DNA injections. Results of the randomized multicentre EV03/ANRS VAC20 Phase I/II Trial.
Lévy Y., Lacabaratz C., Ellefsen-Lavoie K., Stöhr W., Lelièvre J.D., Bart P.A., Launay O., Weber J., Salzberger B., Wiedemann A. et al., 2020/06. PLoS pathogens, 16 (6) pp. e1008522. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_82AFFC2A801F]
 
A Targeted Multi-omic Analysis Approach Measures Protein Expression and Low-Abundance Transcripts on the Single-Cell Level.
Mair F., Erickson J.R., Voillet V., Simoni Y., Bi T., Tyznik A.J., Martin J., Gottardo R., Newell E.W., Prlic M., 2020/04/07. Cell reports, 31 (1) p. 107499. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_184B65D24AAF]
 
Characterization of two in vivo challenge models to measure functional activity of monoclonal antibodies to Plasmodium falciparum circumsporozoite protein.
Raghunandan R., Mayer B.T., Flores-Garcia Y., Gerber M.W., Gottardo R., Jhun H., Herrera S.M., Perez-Ramos D.W., Locke E., King C.R. et al., 2020/03/17. Malaria journal, 19 (1) p. 113. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_FB500F9FF0CE]
 
Orchestrating single-cell analysis with Bioconductor.
Amezquita R.A., Lun ATL, Becht E., Carey V.J., Carpp L.N., Geistlinger L., Marini F., Rue-Albrecht K., Risso D., Soneson C. et al., 2020/02. Nature methods, 17 (2) pp. 137-145. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_CC67D1B61149]
 
Clonal kinetics and single-cell transcriptional profiling of CAR-T cells in patients undergoing CD19 CAR-T immunotherapy.
Sheih A., Voillet V., Hanafi L.A., DeBerg H.A., Yajima M., Hawkins R., Gersuk V., Riddell S.R., Maloney D.G., Wohlfahrt M.E. et al., 2020/01/10. Nature communications, 11 (1) p. 219. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_530D7646DE87]
 
Multiomic Immunophenotyping of COVID-19 Patients Reveals Early Infection Trajectories
Su Yapeng, Chen Daniel, Lausted Christopher, Yuan Dan, Choi Jongchan, Dai Cheng, Voillet Valentin, Scherler Kelsey, Troisch Pamela, Duvvuri Venkata R. et al., 2020..
[DOI][Pmid][serval:BIB_0C94D0884781]
2019
Recombinant HIV-1 vaccine candidates based on replication-defective flavivirus vector.
Giel-Moloney M., Esteban M., Oakes B.H., Vaine M., Asbach B., Wagner R., Mize G.J., Spies A.G., McElrath J., Perreau M. et al., 2019/12/27. Scientific reports, 9 (1) p. 20005. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_576063A9C68A]
 
BCG revaccination boosts adaptive polyfunctional Th1/Th17 and innate effectors in IGRA+ and IGRA- Indian adults.
Rakshit S., Ahmed A., Adiga V., Sundararaj B.K., Sahoo P.N., Kenneth J., D'Souza G., Bonam W., Johnson C., Franken K.L. et al., 2019/12/19. JCI insight, 4 (24). Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_912C7148B907]
 
A composite immune signature parallels disease progression across T1D subjects.
Speake C., Skinner S.O., Berel D., Whalen E., Dufort M.J., Young W.C., Odegard J.M., Pesenacker A.M., Gorus F.K., James E.A. et al., 2019/12/05. JCI insight, 4 (23). Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_76BC38830B74]
 
Antibody Fc effector functions and IgG3 associate with decreased HIV-1 risk.
Neidich S.D., Fong Y., Li S.S., Geraghty D.E., Williamson B.D., Young W.C., Goodman D., Seaton K.E., Shen X., Sawant S. et al., 2019/11/01. The Journal of clinical investigation, 129 (11) pp. 4838-4849. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_81535AD488CF]
Correction for Kibler et al., "Replication-Competent NYVAC-KC Yields Improved Immunogenicity to HIV-1 Antigens in Rhesus Macaques Compared to Nonreplicating NYVAC".
Kibler K.V., Asbach B., Perdiguero B., García-Arriaza J., Yates N.L., Parks R., Stanfield-Oakley S., Ferrari G., Montefiori D.C., Tomaras G.D. et al., 2019/11/01. Journal of virology, 93 (21). Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_805F4DFC76DE]
 
Engineered Adoptive T-cell Therapy Prolongs Survival in a Preclinical Model of Advanced-Stage Ovarian Cancer.
Anderson K.G., Voillet V., Bates B.M., Chiu E.Y., Burnett M.G., Garcia N.M., Oda S.K., Morse C.B., Stromnes I.M., Drescher C.W. et al., 2019/09. Cancer immunology research, 7 (9) pp. 1412-1425. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_AEBAE9A85F6D]
 
T cell receptor gene therapy targeting WT1 prevents acute myeloid leukemia relapse post-transplant.
Chapuis A.G., Egan D.N., Bar M., Schmitt T.M., McAfee M.S., Paulson K.G., Voillet V., Gottardo R., Ragnarsson G.B., Bleakley M. et al., 2019/07. Nature medicine, 25 (7) pp. 1064-1072. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_D60C7B1DD27D]
Tumor suppression of novel anti-PD-1 antibodies mediated through CD28 costimulatory pathway.
Fenwick C., Loredo-Varela J.L., Joo V., Pellaton C., Farina A., Rajah N., Esteves-Leuenberger L., Decaillon T., Suffiotti M., Noto A. et al., 2019/07/01. The Journal of experimental medicine, 216 (7) pp. 1525-1541. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_0B420592FE76]
 
Graphical Models For Zero-Inflated Single Cell Gene Expression.
McDavid A., Gottardo R., Simon N., Drton M., 2019/06. The annals of applied statistics, 13 (2) pp. 848-873. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_127C7A7CE77A]
 
Integrated systems approach defines the antiviral pathways conferring protection by the RV144 HIV vaccine.
Fourati S., Ribeiro S.P., Blasco Tavares Pereira Lopes F., Talla A., Lefebvre F., Cameron M., Kaewkungwal J., Pitisuttithum P., Nitayaphan S., Rerks-Ngarm S. et al., 2019/02/20. Nature communications, 10 (1) p. 863. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_AE42018B720C]
 
Priming with a Potent HIV-1 DNA Vaccine Frames the Quality of Immune Responses prior to a Poxvirus and Protein Boost.
Asbach B., Kibler K.V., Köstler J., Perdiguero B., Yates N.L., Stanfield-Oakley S., Tomaras G.D., Kao S.F., Foulds K.E., Roederer M. et al., 2019/02/01. Journal of virology, 93 (3). Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_011979DE2022]
 
Replication-Competent NYVAC-KC Yields Improved Immunogenicity to HIV-1 Antigens in Rhesus Macaques Compared to Nonreplicating NYVAC.
Kibler K.V., Asbach B., Perdiguero B., García-Arriaza J., Yates N.L., Parks R., Stanfield-Oakley S., Ferrari G., Montefiori D.C., Tomaras G.D. et al., 2019/02/01. Journal of virology, 93 (3). Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_C7AB149CAD1E]
2018
 
CytoML for cross-platform cytometry data sharing.
Finak G., Jiang W., Gottardo R., 2018/12. Cytometry. Part A, 93 (12) pp. 1189-1196. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_538C4D1288AD]
 
ggCyto: next generation open-source visualization software for cytometry.
Van P., Jiang W., Gottardo R., Finak G., 2018/11/15. Bioinformatics, 34 (22) pp. 3951-3953. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_77593933C51D]
 
cytometree: A binary tree algorithm for automatic gating in cytometry analysis.
Commenges D., Alkhassim C., Gottardo R., Hejblum B., Thiébaut R., 2018/11. Cytometry. Part A, 93 (11) pp. 1132-1140. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_C4E1F1B81793]
 
Effect of Adding Motolimod to Standard Combination Chemotherapy and Cetuximab Treatment of Patients With Squamous Cell Carcinoma of the Head and Neck: The Active8 Randomized Clinical Trial.
Ferris R.L., Saba N.F., Gitlitz B.J., Haddad R., Sukari A., Neupane P., Morris J.C., Misiukiewicz K., Bauman J.E., Fenton M. et al., 2018/11/01. JAMA oncology, 4 (11) pp. 1583-1588. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_A9E4863563CE]
 
T Cell-Dependent Affinity Maturation and Innate Immune Pathways Differentially Drive Autoreactive B Cell Responses in Rheumatoid Arthritis.
Lu D.R., McDavid A.N., Kongpachith S., Lingampalli N., Glanville J., Ju C.H., Gottardo R., Robinson W.H., 2018/11. Arthritis & rheumatology, 70 (11) pp. 1732-1744. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_4D7ADE75440F]
CD32+ and PD-1+ Lymph Node CD4 T Cells Support Persistent HIV-1 Transcription in Treated Aviremic Individuals
Noto A., Procopio F.A., Banga R., Suffiotti M., Corpataux J.M., Cavassini M., Riva A., Fenwick C., Gottardo R., Perreau M. et al., 2018/10/15. Journal of virology, 92 (20). Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_EFF772664CD3]
 
Acquired cancer resistance to combination immunotherapy from transcriptional loss of class I HLA.
Paulson K.G., Voillet V., McAfee M.S., Hunter D.S., Wagener F.D., Perdicchio M., Valente W.J., Koelle S.J., Church C.D., Vandeven N. et al., 2018/09/24. Nature communications, 9 (1) p. 3868. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_CF5BF945549D]
 
Phosphoproteomic analysis of chimeric antigen receptor signaling reveals kinetic and quantitative differences that affect cell function.
Salter A.I., Ivey R.G., Kennedy J.J., Voillet V., Rajan A., Alderman E.J., Voytovich U.J., Lin C., Sommermeyer D., Liu L. et al., 2018/08/21. Science signaling, 11 (544). Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_2C4B58BA246B]
 
Human MAIT cells exit peripheral tissues and recirculate via lymph in steady state conditions.
Voillet V., Buggert M., Slichter C.K., Berkson J.D., Mair F., Addison M.M., Dori Y., Nadolski G., Itkin M.G., Gottardo R. et al., 2018/04/05. JCI insight, 3 (7). Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_CAF34EE5BB0E]
 
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., 2018. Gates open research, 2 p. 31. Peer-reviewed.
[DOI][Pmid][serval:BIB_156956AEE710]
 
Generation and characterization of a bivalent protein boost for future clinical trials: HIV-1 subtypes CR01_AE and B gp120 antigens with a potent adjuvant.
Wen Y., Trinh H.V., Linton C.E., Tani C., Norais N., Martinez-Guzman D., Ramesh P., Sun Y., Situ F., Karaca-Griffin S. et al., 2018. PloS one, 13 (4) pp. e0194266. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_5258142D29D7]
 
Whole blood transcriptome changes following controlled human malaria infection in malaria pre-exposed volunteers correlate with parasite prepatent period.
Rothen J., Murie C., Carnes J., Anupama A., Abdulla S., Chemba M., Mpina M., Tanner M., Lee Sim B.K., Hoffman S.L. et al., 2018. PloS one, 13 (6) pp. e0199392. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_6AAF64480240]
2017
 
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 S.S., Kochar N.K., Elizaga M., Hay C.M., Wilson G.J., Cohen K.W., De Rosa S.C., Xu R., Ota-Setlik A., Morris D. et al., 2017/11. Clinical and vaccine immunology, 24 (11). Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_16C8AA21A97E]
 
Panels of HIV-1 Subtype C Env Reference Strains for Standardized Neutralization Assessments.
Hraber P., Rademeyer C., Williamson C., Seaman M.S., Gottardo R., Tang H., Greene K., Gao H., LaBranche C., Mascola J.R. et al., 2017/10/01. Journal of virology, 91 (19) pp. e00991. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_4C573D25EBC0]
 
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 H.S., Mehr K.T., Backert L., Finak G., Gottardo R., Bica M.A., Garofano A., Koch S.D. et al., 2017/09/23. Lancet, 390 (10101) pp. 1511-1520. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_E90A911DB55F]
 
Multicohort analysis reveals baseline transcriptional predictors of influenza vaccination responses.
HIPC-CHI Signatures Project Team, HIPC-I Consortium, Gottardo R., Khatri P., Kleinstein S.H., Shen-Orr S.S., Tsang J.S., 2017/08/25. Science immunology, 2 (14) pp. eaal4656. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_5EB19C61AAC6]
 
A Functional Toll-Interacting Protein Variant Is Associated with Bacillus Calmette-Guérin-Specific Immune Responses and Tuberculosis.
Shah J.A., Musvosvi M., Shey M., Horne D.J., Wells R.D., Peterson G.J., Cox J.S., Daya M., Hoal E.G., Lin L. et al., 2017/08/15. American journal of respiratory and critical care medicine, 196 (4) pp. 502-511. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_B6F332364300]
 
Controlled Human Malaria Infection Leads to Long-Lasting Changes in Innate and Innate-like Lymphocyte Populations.
Mpina M., Maurice N.J., Yajima M., Slichter C.K., Miller H.W., Dutta M., McElrath M.J., Stuart K.D., De Rosa S.C., McNevin J.P. et al., 2017/07/01. Journal of immunology, 199 (1) pp. 107-118. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_F872E86AA7F8]
 
Single-Cell RNA Sequencing Reveals Expanded Clones of Islet Antigen-Reactive CD4<sup>+</sup> T Cells in Peripheral Blood of Subjects with Type 1 Diabetes.
Cerosaletti K., Barahmand-Pour-Whitman F., Yang J., DeBerg H.A., Dufort M.J., Murray S.A., Israelsson E., Speake C., Gersuk V.H., Eddy J.A. et al., 2017/07/01. Journal of immunology, 199 (1) pp. 323-335. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_541D6BC934DF]
 
Combined single-cell quantitation of host and SIV genes and proteins ex vivo reveals host-pathogen interactions in individual cells.
Bolton D.L., McGinnis K., Finak G., Chattopadhyay P., Gottardo R., Roederer M., 2017/06. PLoS pathogens, 13 (6) pp. e1006445. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_4D34F6518C35]
A phase 2, randomized, double-blind, placebo- controlled study of chemo-immunotherapy combination using motolimod with pegylated liposomal doxorubicin in recurrent or persistent ovarian cancer: a Gynecologic Oncology Group partners study.
Monk B.J., Brady M.F., Aghajanian C., Lankes H.A., Rizack T., Leach J., Fowler J.M., Higgins R., Hanjani P., Morgan M. et al., 2017/05/01. Annals of oncology, 28 (5) pp. 996-1004. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_B4FD453E2DFC]
 
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 H.E., Cohen K.W., Frahm N., De Rosa S.C., Sanchez B., Hural J., Magaret C.A., Karuna S., Bentley C., Gottardo R. et al., 2017/05/01. The Journal of infectious diseases, 215 (9) pp. 1376-1385. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_F73BB0DA3CCA]
 
HIV/AIDS Vaccine Candidates Based on Replication-Competent Recombinant Poxvirus NYVAC-C-KC Expressing Trimeric gp140 and Gag-Derived Virus-Like Particles or Lacking the Viral Molecule B19 That Inhibits Type I Interferon Activate Relevant HIV-1-Specific B and T Cell Immune Functions in Nonhuman Primates.
García-Arriaza J., Perdiguero B., Heeney J.L., Seaman M.S., Montefiori D.C., Yates N.L., Tomaras G.D., Ferrari G., Foulds K.E., Roederer M. et al., 2017/05/01. Journal of virology, 91 (9). Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_4AB7B2C38624]
 
Superiority in Rhesus Macaques of Targeting HIV-1 Env gp140 to CD40 versus LOX-1 in Combination with Replication-Competent NYVAC-KC for Induction of Env-Specific Antibody and T Cell Responses.
Zurawski G., Shen X., Zurawski S., Tomaras G.D., Montefiori D.C., Roederer M., Ferrari G., Lacabaratz C., Klucar P., Wang Z. et al., 2017/05/01. Journal of virology, 91 (9). Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_57668F63DF01]
 
Sieve analysis of breakthrough HIV-1 sequences in HVTN 505 identifies vaccine pressure targeting the CD4 binding site of Env-gp120.
deCamp A.C., Rolland M., Edlefsen P.T., Sanders-Buell E., Hall B., Magaret C.A., Fiore-Gartland A.J., Juraska M., Carpp L.N., Karuna S.T. et al., 2017. PloS one, 12 (11) pp. e0185959. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_500AD4BCECBE]
2016
 
Bayesian hierarchical modeling for subject-level response classification in peptide microarray immunoassays.
Imholte G., Gottardo R., 2016/12. Biometrics, 72 (4) pp. 1206-1215. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_693BA81169A2]
 
The contribution of cell cycle to heterogeneity in single-cell RNA-seq data.
McDavid A., Finak G., Gottardo R., 2016/06/09. Nature biotechnology, 34 (6) pp. 591-593. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_AD05A43FFC7E]
 
Distinct activation thresholds of human conventional and innate-like memory T cells.
Slichter C.K., McDavid A., Miller H.W., Finak G., Seymour B.J., McNevin J.P., Diaz G., Czartoski J.L., McElrath M.J., Gottardo R. et al., 2016/06/02. JCI insight, 1 (8). Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_C70F7FCD5587]
 
Potential To Streamline Heterologous DNA Prime and NYVAC/Protein Boost HIV Vaccine Regimens in Rhesus Macaques by Employing Improved Antigens.
Asbach B., Kliche A., Köstler J., Perdiguero B., Esteban M., Jacobs B.L., Montefiori D.C., LaBranche C.C., Yates N.L., Tomaras G.D. et al., 2016/04. Journal of virology, 90 (8) pp. 4133-4149. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_C0177FF88AB3]
 
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 M.L. et al., 2016/02/10. Scientific reports, 6 p. 20686. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_CB77E8F95B49]
 
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 B.N., Malek M., McLachlan G.J., Qian Y. et al., 2016/01. Cytometry. Part A, 89 (1) pp. 16-21. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_A44139678561]
 
Analyzing Peptide Microarray Data with the R pepStat Package.
Imholte G., Sauteraud R., Gottardo R., 2016. pp. 127-142 dans Methods in molecular biology chap. 10, Springer.
[DOI][WoS][Pmid][serval:BIB_577340325A95]
 
Automated analysis of flow cytometry data comes of age.
Brinkman R.R., Aghaeepour N., Finak G., Gottardo R., Mosmann T., Scheuermann R.H., 2016/01. Cytometry. Part A, 89 (1) pp. 13-15. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_F889056D29E6]
 
Promises and Pitfalls of High-Throughput Biological Assays.
Finak G., Gottardo R., 2016. pp. 225-243 dans Methods in molecular biology chap. 12, Springer.
[DOI][WoS][Pmid][serval:BIB_22E91D3AF3A7]
Targeting HIV-1 Env gp140 to LOX-1 Elicits Immune Responses in Rhesus Macaques.
Zurawski G., Zurawski S., Flamar A.L., Richert L., Wagner R., Tomaras G.D., Montefiori D.C., Roederer M., Ferrari G., Lacabaratz C. et al., 2016. Plos One, 11 (4) pp. e0153484. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_980FC2E7134A]
2015
 
Late-Stage Cancer Patients Remain Highly Responsive to Immune Activation by the Selective TLR8 Agonist Motolimod (VTX-2337).
Dietsch G.N., Randall T.D., Gottardo R., Northfelt D.W., Ramanathan R.K., Cohen P.A., Manjarrez K.L., Newkirk M., Bryan J.K., Hershberg R.M., 2015/12/15. Clinical cancer research, 21 (24) pp. 5445-5452. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_197931E36D5C]
 
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 A.K., Slichter C.K., Miller H.W., McElrath M.J., Prlic M. et al., 2015/12/10. Genome biology, 16 p. 278. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_477F3AB1833A]
 
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. et al., 2015/11/15. Journal of immunology, 195 (10) pp. 4595-4603. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_F155E6F18CFD]
 
Notch-mediated expansion of cord blood progenitors: maintenance of transcriptional and epigenetic fidelity.
Dahlberg A., Woo S., Delaney C., Boyle P., Gnirke A., Bock C., Bernstein B.E., Meissner A., Gottardo R., Bernstein I.D., 2015/09. Leukemia, 29 (9) pp. 1948-1951. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_222B2819BDE1]
 
State-of-the-Art in the Computational Analysis of Cytometry Data.
Brinkman R.R., Aghaeepour N., Finak G., Gottardo R., Mosmann T., Scheuermann R.H., 2015/07. Cytometry. Part A, 87 (7) pp. 591-593. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_317749857B57]
COMPASS identifies T-cell subsets correlated with clinical outcomes.
Lin L., Finak G., Ushey K., Seshadri C., Hawn T.R., Frahm N., Scriba T.J., Mahomed H., Hanekom W., Bart P.A. et al., 2015/06. Nature biotechnology, 33 (6) pp. 610-616. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_8FADB11D7063]
 
flowCL: ontology-based cell population labelling in flow cytometry.
Courtot M., Meskas J., Diehl A.D., Droumeva R., Gottardo R., Jalali A., Taghiyar M.J., Maecker H.T., McCoy J.P., Ruttenberg A. et al., 2015/04/15. Bioinformatics, 31 (8) pp. 1337-1339. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_0119A2481840]
 
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., 2015/02/15. Bioinformatics, 31 (4) pp. 606-607. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_A9D715CBD77F]
 
Mucosal effects of tenofovir 1% gel.
Hladik F., Burgener A., Ballweber L., Gottardo R., Vojtech L., Fourati S., Dai J.Y., Cameron M.J., Strobl J., Hughes S.M. et al., 2015/02/03. eLife, 4. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_66FFD7CCC21C]
 
Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial.
Edlefsen P.T., Rolland M., Hertz T., Tovanabutra S., Gartland A.J., deCamp A.C., Magaret C.A., Ahmed H., Gottardo R., Juraska M. et al., 2015/02. PLoS computational biology, 11 (2) pp. e1003973. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_F93FCA3CDFBF]
 
Orchestrating high-throughput genomic analysis with Bioconductor.
Huber W., Carey V.J., Gentleman R., Anders S., Carlson M., Carvalho B.S., Bravo H.C., Davis S., Gatto L., Girke T. et al., 2015/02. Nature methods, 12 (2) pp. 115-121. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_7FF1BD531420]
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 P.A., Pantaleo G., McElrath J., DeRosa S., Gottardo R., 2015. Cytometry. Part A, 87 (7) pp. 675-682. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_A190F236B1C2]
2014
 
Vaccine-induced Human Antibodies Specific for the Third Variable Region of HIV-1 gp120 Impose Immune Pressure on Infecting Viruses.
Zolla-Pazner S., Edlefsen P.T., Rolland M., Kong X.P., deCamp A., Gottardo R., Williams C., Tovanabutra S., Sharpe-Cohen S., Mullins J.I. et al., 2014/11/01. EBioMedicine, 1 (1) pp. 37-45. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_2989949ED30E]
 
FCGR2C polymorphisms associate with HIV-1 vaccine protection in RV144 trial.
Li S.S., Gilbert P.B., Tomaras G.D., Kijak G., Ferrari G., Thomas R., Pyo C.W., Zolla-Pazner S., Montefiori D., Liao H.X. et al., 2014/09. The Journal of clinical investigation, 124 (9) pp. 3879-3890. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_7DD3C0903CBA]
 
Analysis of HLA A*02 association with vaccine efficacy in the RV144 HIV-1 vaccine trial.
Gartland A.J., Li S., McNevin J., Tomaras G.D., Gottardo R., Janes H., Fong Y., Morris D., Geraghty D.E., Kijak G.H. et al., 2014/08. Journal of virology, 88 (15) pp. 8242-8255. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_37FED32413FC]
 
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 E.W., Ramey J., Davis M.M., Kalams S.A., De Rosa S.C., Gottardo R., 2014/08. PLoS computational biology, 10 (8) pp. e1003806. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_91064CB1A908]
 
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., 2014/07. PLoS computational biology, 10 (7) pp. e1003696. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_5FE69A8B55E0]
 
Exosomes in human semen carry a distinctive repertoire of small non-coding RNAs with potential regulatory functions.
Vojtech L., Woo S., Hughes S., Levy C., Ballweber L., Sauteraud R.P., Strobl J., Westerberg K., Gottardo R., Tewari M. et al., 2014/06. Nucleic acids research, 42 (11) pp. 7290-7304. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_A3AE2E9ABC32]
 
Global panel of HIV-1 Env reference strains for standardized assessments of vaccine-elicited neutralizing antibodies.
deCamp A., Hraber P., Bailer R.T., Seaman M.S., Ochsenbauer C., Kappes J., Gottardo R., Edlefsen P., Self S., Tang H. et al., 2014/03. Journal of virology, 88 (5) pp. 2489-2507. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_FD3D020242EC]
 
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 S.C., Self S., Gottardo R., 2014/03. Cytometry. Part A, 85 (3) pp. 277-286. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_FA4F651A07A4]
 
Computational resources for high-dimensional immune analysis from the Human Immunology Project Consortium.
Brusic V., Gottardo R., Kleinstein S.H., Davis M.M., HIPC steering committee, 2014/02. Nature biotechnology, 32 (2) pp. 146-148. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_A59EE63C532F]
 
Immunological and virological mechanisms of vaccine-mediated protection against SIV and HIV.
Roederer M., Keele B.F., Schmidt S.D., Mason R.D., Welles H.C., Fischer W., Labranche C., Foulds K.E., Louder M.K., Yang Z.Y. et al., 2014/01/23. Nature, 505 (7484) pp. 502-508. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_5501A01A694C]
 
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., 2014/01. Biostatistics, 15 (1) pp. 87-101. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_A80BA72DA74B]
 
The inner foreskin of healthy males at risk of HIV infection harbors epithelial CD4+ CCR5+ cells and has features of an inflamed epidermal barrier.
Lemos M.P., Lama J.R., Karuna S.T., Fong Y., Montano S.M., Ganoza C., Gottardo R., Sanchez J., McElrath M.J., 2014. PloS one, 9 (9) pp. e108954. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_B22F735B726A]
2013
 
iBMQ: a R/Bioconductor package for integrated Bayesian modeling of eQTL data.
Imholte G.C., Scott-Boyer M.P., Labbe A., Deschepper C.F., Gottardo R., 2013/11/01. Bioinformatics, 29 (21) pp. 2797-2798. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_466705C0405C]
 
A computational framework for the analysis of peptide microarray antibody binding data with application to HIV vaccine profiling.
Imholte G.C., Sauteraud R., Korber B., Bailer R.T., Turk E.T., Shen X., Tomaras G.D., Mascola J.R., Koup R.A., Montefiori D.C. et al., 2013/09/30. Journal of immunological methods, 395 (1-2) pp. 1-13. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_C6FB59E34DC7]
 
PING 2.0: an R/Bioconductor package for nucleosome positioning using next-generation sequencing data.
Woo S., Zhang X., Sauteraud R., Robert F., Gottardo R., 2013/08/15. Bioinformatics, 29 (16) pp. 2049-2050. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_C84E1857A37D]
 
Comparability and reproducibility of biomedical data.
Huang Y., Gottardo R., 2013/07. Briefings in bioinformatics, 14 (4) pp. 391-401. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_EF6F0CB028F6]
 
Therapeutic vaccination expands and improves the function of the HIV-specific memory T-cell repertoire.
Casazza J.P., Bowman K.A., Adzaku S., Smith E.C., Enama M.E., Bailer R.T., Price D.A., Gostick E., Gordon I.J., Ambrozak D.R. et al., 2013/06/15. The Journal of infectious diseases, 207 (12) pp. 1829-1840. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_6201A36634D7]
 
Highly multiplexed quantitation of gene expression on single cells.
Dominguez M.H., Chattopadhyay P.K., Ma S., Lamoreaux L., McDavid A., Finak G., Gottardo R., Koup R.A., Roederer M., 2013/05/31. Journal of immunological methods, 391 (1-2) pp. 133-145. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_78C1C9F65885]
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, Dialogue for Reverse Engineering Assessment and Methods (DREAM) Consortium, 2013/03. Nature Methods, 10 (3) pp. 228-238.
[URN][DOI][WoS][Pmid][serval:BIB_86D904679F84]
 
Identification and analysis of murine pancreatic islet enhancers.
Tennant B.R., Robertson A.G., Kramer M., Li L., Zhang X., Beach M., Thiessen N., Chiu R., Mungall K., Whiting C.J. et al., 2013/03. Diabetologia, 56 (3) pp. 542-552. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_E969476E1237]
 
Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments.
McDavid A., Finak G., Chattopadyay P.K., Dominguez M., Lamoreaux L., Ma S.S., Roederer M., Gottardo R., 2013/02/15. Bioinformatics, 29 (4) pp. 461-467. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_A0AFBB3853AF]
 
Analysis of V2 antibody responses induced in vaccinees in the ALVAC/AIDSVAX HIV-1 vaccine efficacy trial.
Zolla-Pazner S., deCamp A.C., Cardozo T., Karasavvas N., Gottardo R., Williams C., Morris D.E., Tomaras G., Rao M., Billings E. et al., 2013. PloS one, 8 (1) pp. e53629. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_D5ECB90D7240]
 
Plasma IgG to linear epitopes in the V2 and V3 regions of HIV-1 gp120 correlate with a reduced risk of infection in the RV144 vaccine efficacy trial.
Gottardo R., Bailer R.T., Korber B.T., Gnanakaran S., Phillips J., Shen X., Tomaras G.D., Turk E., Imholte G., Eckler L. et al., 2013. PloS one, 8 (9) pp. e75665. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_33A24EBAA502]
2012
 
The Thai Phase III HIV Type 1 Vaccine trial (RV144) regimen induces antibodies that target conserved regions within the V2 loop of gp120.
Karasavvas N., Billings E., Rao M., Williams C., Zolla-Pazner S., Bailer R.T., Koup R.A., Madnote S., Arworn D., Shen X. et al., 2012/11. AIDS research and human retroviruses, 28 (11) pp. 1444-1457. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_1E0BD205FEEC]
 
QUAliFiER: an automated pipeline for quality assessment of gated flow cytometry data.
Finak G., Jiang W., Pardo J., Asare A., Gottardo R., 2012/09/28. BMC bioinformatics, 13 p. 252. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_BC703407DBE7]
 
An integrated hierarchical Bayesian model for multivariate eQTL mapping.
Scott-Boyer M.P., Imholte G.C., Tayeb A., Labbe A., Deschepper C.F., Gottardo R., 2012/07/12. Statistical applications in genetics and molecular biology, 11 (4). Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_A73154B339D1]
 
B cells with high side scatter parameter by flow cytometry correlate with inferior survival in diffuse large B-cell lymphoma.
Bashashati A., Johnson N.A., Khodabakhshi A.H., Whiteside M.D., Zare H., Scott D.W., Lo K., Gottardo R., Brinkman F.S., Connors J.M. et al., 2012/05. American journal of clinical pathology, 137 (5) pp. 805-814. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_F37BC32590FA]
 
On-line changepoint detection and parameter estimation with application to genomic data
Caron François, Doucet Arnaud, Gottardo Raphael, 2012/03. Statistics and Computing, 22 (2) pp. 579-595.
[DOI][WoS][serval:BIB_CD2B5EFFC3C8]
 
Flexible mixture modeling via the multivariate t distribution with the Box-Cox transformation: an alternative to the skew-t distribution.
Lo K., Gottardo R., 2012/01/01. Statistics and computing, 22 (1) pp. 33-52. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_1DA76AB4F142]
 
Probabilistic inference for nucleosome positioning with MNase-based or sonicated short-read data.
Zhang X., Robertson G., Woo S., Hoffman B.G., Gottardo R., 2012. PloS one, 7 (2) pp. e32095. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_2703A25EEC93]
2011
 
PICS: probabilistic inference for ChIP-seq.
Zhang X., Robertson G., Krzywinski M., Ning K., Droit A., Jones S., Gottardo R., 2011/03. Biometrics, 67 (1) pp. 151-163. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_38E05B59A639]
 
An integrated pipeline for the genome-wide analysis of transcription factor binding sites from ChIP-Seq.
Mercier E., Droit A., Li L., Robertson G., Zhang X., Gottardo R., 2011/02/16. PloS one, 6 (2) pp. e16432. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_F0EA083988A4]
2010
 
Optimizing transformations for automated, high throughput analysis of flow cytometry data.
Finak G., Perez J.M., Weng A., Gottardo R., 2010/11/04. BMC bioinformatics, 11 p. 546. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_4BC7ECDD2551]
 
Combining Mixture Components for Clustering.
Baudry J.P., Raftery A.E., Celeux G., Lo K., Gottardo R., 2010/06/01. Journal of computational and graphical statistics, 9 (2) pp. 332-353. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_9E08FA638101]
 
An efficient computational approach for prior sensitivity analysis and cross-validation.
Bornn L., Doucet A., Gottardo R., 2010/03. Canadian Journal of Statistics-Revue Canadienne De Statistique, 38 (1) pp. 47-64.
[WoS][serval:BIB_1E8C1F6C8DD2]
 
rMAT--an R/Bioconductor package for analyzing ChIP-chip experiments.
Droit A., Cheung C., Gottardo R., 2010/03/01. Bioinformatics, 26 (5) pp. 678-679. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_5256E8597C63]
 
Grouping priors and the Bayesian elastic net
Bornn Luke, Gottardo Raphael, Doucet Arnaud, 2010..
[DOI][serval:BIB_1C49433ABFB2]
2009
 
A Pipeline for automated analysis of flow cytometry data: Preliminary results on lymphoma sub-type diagnosis
Bashashati A., Lo K., Gottardo R., Gascoyne R.D., Weng A., Brinkman R., 2009/09. dans 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, IEE.
[DOI][WoS][Pmid][serval:BIB_8BADF2BEF9A2]
 
Bayesian robust transformation and variable selection: A unified approach
Gottardo Raphael, Raftery Adrian, 2009/09. Canadian Journal of Statistics, 37 (3) pp. 361-380.
[DOI][WoS][serval:BIB_73AC1151FB55]
 
flowClust: a Bioconductor package for automated gating of flow cytometry data.
Lo K., Hahne F., Brinkman R.R., Gottardo R., 2009/05/14. BMC bioinformatics, 10 p. 145. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_4479D98799C0]
 
Merging mixture components for cell population identification in flow cytometry.
Finak G., Bashashati A., Brinkman R., Gottardo R., 2009. Advances in bioinformatics, 2009 p. 247646. Peer-reviewed.
[DOI][Pmid][serval:BIB_67AF5BA35245]
 
Modeling and analysis of ChIP-chip experiments.
Gottardo R., 2009. pp. 133-143 dans Methods in molecular biology chap. 9, Springer.
[DOI][WoS][Pmid][serval:BIB_3A488A54D922]
 
Recent bioinformatics advances in the analysis of high throughput flow cytometry data.
Gottardo R., Brinkman R.R., Luta G., Wand M.P., 2009. Advances in bioinformatics, 2009 p. 461763. Peer-reviewed.
[DOI][Pmid][serval:BIB_9DFEF14CE7D4]
2008
 
Markov Chain Monte Carlo With Mixtures of Mutually Singular Distributions
Gottardo Raphael, Raftery Adrian E, 2008/12. Journal of Computational and Graphical Statistics, 17 (4) pp. 949-975.
[DOI][WoS][serval:BIB_FF8AE322E5DF]
 
A flexible and powerful bayesian hierarchical model for ChIP-Chip experiments.
Gottardo R., Li W., Johnson W.E., Liu X.S., 2008/06. Biometrics, 64 (2) pp. 468-478. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_A2971578657A]
 
Automated gating of flow cytometry data via robust model-based clustering.
Lo K., Brinkman R.R., Gottardo R., 2008/04. Cytometry. Part A, 73 (4) pp. 321-332. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_AD1E0A7A933A]
 
MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis.
Chu V.T., Gottardo R., Raftery A.E., Bumgarner R.E., Yeung K.Y., 2008. Genome biology, 9 (7) pp. R118. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_7A0CFB76956C]
2007
 
Flexible empirical Bayes models for differential gene expression.
Lo K., Gottardo R., 2007/02/01. Bioinformatics, 23 (3) pp. 328-335. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_C13886118110]
2006
 
Model-based analysis of tiling-arrays for ChIP-chip.
Johnson W.E., Li W., Meyer C.A., Gottardo R., Carroll J.S., Brown M., Liu X.S., 2006/08/15. Proceedings of the National Academy of Sciences of the United States of America, 103 (33) pp. 12457-12462. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_875270FFB30D]
 
Bayesian robust inference for differential gene expression in microarrays with multiple samples.
Gottardo R., Raftery A.E., Yeung K.Y., Bumgarner R.E., 2006/03. Biometrics, 62 (1) pp. 10-18. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_D51D846D05B1]
 
Quality Control and Robust Estimation for cDNA Microarrays With Replicates
Gottardo Raphael, Raftery Adrian E, Yeung Ka Yee, Bumgarner Roger E, 2006/03. Journal of the American Statistical Association, 101 (473) pp. 30-40.
[DOI][WoS][serval:BIB_A12CD43F89D1]
 
Probabilistic segmentation and intensity estimation for microarray images.
Gottardo R., Besag J., Stephens M., Murua A., 2006/01. Biostatistics, 7 (1) pp. 85-99. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_48E4A8BAEB26]
2004
 
Evaluation of the host transcriptional response to human cytomegalovirus infection.
Challacombe J.F., Rechtsteiner A., Gottardo R., Rocha L.M., Browne E.P., Shenk T., Altherr M.R., Brettin T.S., 2004/06/17. Physiological genomics, 18 (1) pp. 51-62. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_F5CDE9E0004F]
2003
 
Statistical analysis of microarray data: a Bayesian approach.
Gottardo R., Pannucci J.A., Kuske C.R., Brettin T., 2003/10. Biostatistics, 4 (4) pp. 597-620. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_5D021BA41873]
 
Lateral gene transfer and ancient paralogy of operons containing redundant copies of tryptophan-pathway genes in Xylella species and in heterocystous cyanobacteria.
Xie G., Bonner C.A., Brettin T., Gottardo R., Keyhani N.O., Jensen R.A., 2003. Genome biology, 4 (2) pp. R14. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_F56AF94C3D28]
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