Santiago Carmona

Publications | Mémoires et thèses

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43 publications

En préparation
 
NFAT5 induction by the tumor microenvironment enforces CD8 T cell exhaustion
Tillé Laure, Cropp Daniela, Bodley Gabrielle, Andreatta Massimo, Charmoy Mélanie, Crespo Isaac, Nassiri Sina, Lourenco Joao, Leblond Marine, Lopez-Rodriguez Cristina et al..
[DOI][serval:BIB_3D15B154D604]
2024
 
IL-10-expressing CAR T cells resist dysfunction and mediate durable clearance of solid tumors and metastases.
Zhao Y., Chen J., Andreatta M., Feng B., Xie Y.Q., Wenes M., Wang Y., Gao M., Hu X., Romero P. et al., 2024/11. Nature biotechnology, 42 (11) pp. 1693-1704. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_3468BE259407]
Semi-supervised integration of single-cell transcriptomics data.
Andreatta M., Hérault L., Gueguen P., Gfeller D., Berenstein A.J., Carmona S.J., 2024/01/29. Nature communications, 15 (1) p. 872. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_E4C01949C6C2]
2023
Activation of the transcription factor NFAT5 in the tumor microenvironment enforces CD8+ T cell exhaustion.
Tillé L., Cropp D., Charmoy M., Reichenbach P., Andreatta M., Wyss T., Bodley G., Crespo I., Nassiri S., Lourenco J. et al., 2023/10. Nature immunology, 24 (10) pp. 1645-1653. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_9B944FAF7B77]
T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps.
Andreatta M., Gueguen P., Borcherding N., Carmona S.J., 2023/08/20. Bio-protocol, 13 (16) pp. e4735. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_5A2CCFDDD06A]
A CSF-1R-blocking antibody/IL-10 fusion protein increases anti-tumor immunity by effectuating tumor-resident CD8<sup>+</sup> T cells.
Chang Y.W., Hsiao H.W., Chen J.P., Tzeng S.F., Tsai C.H., Wu C.Y., Hsieh H.H., Carmona S.J., Andreatta M., Di Conza G. et al., 2023/08/15. Cell reports. Medicine, 4 (8) p. 101154. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_21D296C123A7]
Orthogonal cytokine engineering enables novel synthetic effector states escaping canonical exhaustion in tumor-rejecting CD8+ T cells.
Corria-Osorio J., Carmona S.J., Stefanidis E., Andreatta M., Ortiz-Miranda Y., Muller T., Rota I.A., Crespo I., Seijo B., Castro W. et al., 2023/05. Nature immunology, 24 (5) pp. 869-883. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_B6529135A8DD]
2022
 
Metacells untangle large and complex single-cell transcriptome networks.
Bilous M., Tran L., Cianciaruso C., Gabriel A., Michel H., Carmona S.J., Pittet M.J., Gfeller D., 2022/08/13. BMC bioinformatics, 23 (1) p. 336. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_E86958E5440A]
A CD4+ T cell reference map delineates subtype-specific adaptation during acute and chronic viral infections.
Andreatta M., Tjitropranoto A., Sherman Z., Kelly M.C., Ciucci T., Carmona S.J., 2022/07/13. eLife, 11 pp. e76339. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_0B25A9B1D7B9]
 
Dissecting the treatment-naive ecosystem of human melanoma brain metastasis.
Biermann J., Melms J.C., Amin A.D., Wang Y., Caprio L.A., Karz A., Tagore S., Barrera I., Ibarra-Arellano M.A., Andreatta M. et al., 2022/07/07. Cell, 185 (14) pp. 2591-2608.e30. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_10AEEAB455A8]
scGate: marker-based purification of cell types from heterogeneous single-cell RNA-seq datasets.
Andreatta M., Berenstein A.J., Carmona S.J., 2022/04/28. Bioinformatics, 38 (9) pp. 2642-2644. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_241F222A7909]
 
Characterization of ADAT2/3 molecules in Trypanosoma cruzi and regulation of mucin gene expression by tRNA editing.
Bertotti Santiago, Fleming Ian, Cámara María de los Milagros, Centeno Cameán Camila, Carmona Santiago J., Agüero Fernán, Balouz Virginia, Zahn Astrid, Di Noia Javier M., Alfonzo Juan D. et al., 2022/02/25. Biochemical Journal, 479 (4) pp. 561-580.
[DOI][WoS][Pmid][serval:BIB_50A177B21DFE]
SPICA: Swiss portal for immune cell analysis.
Andreatta M., David FPA, Iseli C., Guex N., Carmona S.J., 2022/01/07. Nucleic acids research, 50 (D1) pp. D1109-D1114. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_1425D341196A]
Low-Dose Radiotherapy Reverses Tumor Immune Desertification and Resistance to Immunotherapy.
Herrera F.G., Ronet C., Ochoa de Olza M., Barras D., Crespo I., Andreatta M., Corria-Osorio J., Spill A., Benedetti F., Genolet R. et al., 2022/01. Cancer discovery, 12 (1) pp. 108-133. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_D82928F3BB2B]
2021
Myeloid antigen-presenting cell niches sustain antitumor T cells and license PD-1 blockade via CD28 costimulation.
Duraiswamy J., Turrini R., Minasyan A., Barras D., Crespo I., Grimm A.J., Casado J., Genolet R., Benedetti F., Wicky A. et al., 2021/12/13. Cancer cell, 39 (12) pp. 1623-1642.e20. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_4A546D8AF05A]
Interpretation of T cell states from single-cell transcriptomics data using reference atlases.
Andreatta M., Corria-Osorio J., Müller S., Cubas R., Coukos G., Carmona S.J., 2021/05/20. Nature communications, 12 (1) p. 2965. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_BE1D257DF142]
STACAS: Sub-Type Anchor Correction for Alignment in Seurat to integrate single-cell RNA-seq data.
Andreatta M., Carmona S.J., 2021/05/05. Bioinformatics, 37 (6) pp. 882-884. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_D3F01C447F08]
Prediction of neo-epitope immunogenicity reveals TCR recognition determinants and provides insight into immunoediting.
Schmidt J., Smith A.R., Magnin M., Racle J., Devlin J.R., Bobisse S., Cesbron J., Bonnet V., Carmona S.J., Huber F. et al., 2021/02/16. Cell reports. Medicine, 2 (2) p. 100194. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_9AA90BD897A9]
 
APRANK: Computational Prioritization of Antigenic Proteins and Peptides From Complete Pathogen Proteomes.
Ricci A.D., Brunner M., Ramoa D., Carmona S.J., Nielsen M., Agüero F., 2021. Frontiers in immunology, 12 p. 702552. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_9B32BC560C23]
UCell: Robust and scalable single-cell gene signature scoring.
Andreatta M., Carmona S.J., 2021. Computational and structural biotechnology journal, 19 pp. 3796-3798. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_ADC3FAC598DC]
2020
Projecting single-cell transcriptomics data onto a reference T cell atlas to interpret immune responses
Andreatta Massimo, Corria-Osorio Jesus, Müller Sören, Cubas Rafael, Coukos George, Carmona Santiago J., 2020/06/24..
[URN][DOI][serval:BIB_2A40AFE9A2C6]
Deciphering the transcriptomic landscape of tumor-infiltrating CD8 lymphocytes in B16 melanoma tumors with single-cell RNA-Seq
Carmona Santiago J., Siddiqui Imran, Bilous Mariia, Held Werner, Gfeller David, 2020/01/01. OncoImmunology, 9 (1) p. 1737369. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_EDA6E7092CF7]
Enhanced Phenotype Definition for Precision Isolation of Precursor Exhausted Tumor-Infiltrating CD8 T Cells.
Martinez-Usatorre A., Carmona S.J., Godfroid C., Yacoub Maroun C., Labiano S., Romero P., 2020. Frontiers in immunology, 11 p. 340. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_8D693EC9FE6D]
2019
 
MicroRNA-155 Expression Is Enhanced by T-cell Receptor Stimulation Strength and Correlates with Improved Tumor Control in Melanoma.
Martinez-Usatorre A., Sempere L.F., Carmona S.J., Carretero-Iglesia L., Monnot G., Speiser D.E., Rufer N., Donda A., Zehn D., Jandus C. et al., 2019/06. Cancer immunology research, 7 (6) pp. 1013-1024. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_4CB1877985DB]
 
Molecular and antigenic characterization of Trypanosoma cruzi TolT proteins.
Lobo M, Balouz V, Melli L, Carlevaro G, Cortina ME, Cámara MLM, Cánepa GE, Carmona SJ, Altcheh J, Campetella O et al., 2019/03. PLoS neglected tropical diseases.
[DOI][Pmid][serval:BIB_AA1DC716237E]
Intratumoral Tcf1+PD-1+CD8+ T Cells with Stem-like Properties Promote Tumor Control in Response to Vaccination and Checkpoint Blockade Immunotherapy.
Siddiqui I., Schaeuble K., Chennupati V., Fuertes Marraco S.A., Calderon-Copete S., Pais Ferreira D., Carmona S.J., Scarpellino L., Gfeller D., Pradervand S. et al., 2019/01/15. Immunity, 50 (1) pp. 195-211.e10. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_8DBCBF3E53B5]
2018
 
Novel biotechnological platform based on baculovirus occlusion bodies carrying Babesia bovis small antigenic peptides for the design of a diagnostic enzyme-linked immunosorbent assay (ELISA).
López M.G., Pallarés H.M., Alfonso V., Carmona S.J., Farber M., Taboga O., Wilkowsky S.E., 2018/01. Applied microbiology and biotechnology, 102 (2) pp. 885-896. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_99D6DD379AF0]
2017
 
Next-generation ELISA diagnostic assay for Chagas Disease based on the combination of short peptidic epitopes.
Carmona Santiago, 2017/10. PLoS neglected tropical diseases.
[DOI][Pmid][serval:BIB_0DAC9662F97A]
 
High-resolution profiling of linear B-cell epitopes from mucin-associated surface proteins (MASPs) of Trypanosoma cruzi during human infections.
Carmona Santiago, 2017/09. PLoS neglected tropical diseases.
[DOI][Pmid][serval:BIB_ED41DF728B39]
 
Identification of innate lymphoid cells in single-cell RNA-Seq data.
Suffiotti M., Carmona S.J., Jandus C., Gfeller D., 2017/07. Immunogenetics, 69 (7) pp. 439-450. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_746D02A9A722]
Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types.
Carmona S.J., Teichmann S.A., Ferreira L., Macaulay I.C., Stubbington M.J., Cvejic A., Gfeller D., 2017/03. Genome research, 27 (3) pp. 451-461. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_9293ADF6E6AC]
2015
 
Towards High-throughput Immunomics for Infectious Diseases: Use of Next-generation Peptide Microarrays for Rapid Discovery and Mapping of Antigenic Determinants
Carmona Santiago J., Nielsen Morten, Schafer-Nielsen Claus, Mucci Juan, Altcheh Jaime, Balouz Virginia, Tekiel Valeria, Frasch Alberto C., Campetella Oscar, Buscaglia Carlos A. et al., 2015/07. Molecular &amp; Cellular Proteomics, 14 (7) pp. 1871-1884.
[DOI][WoS][Pmid][serval:BIB_C5212F741516]
 
Mapping Antigenic Motifs in the Trypomastigote Small Surface Antigen from Trypanosoma cruzi
Balouz Virginia, Cámara María de los Milagros, Cánepa Gaspar E., Carmona Santiago J., Volcovich Romina, Gonzalez Nicolás, Altcheh Jaime, Agüero Fernán, Buscaglia Carlos A., 2015/03. Clinical and Vaccine Immunology, 22 (3) pp. 304-312.
[DOI][WoS][Pmid][serval:BIB_2511FA14DAD6]
2014
 
Characterization of Toxoplasma gondii subtelomeric-like regions: identification of a long-range compositional bias that is also associated with gene-poor regions
Dalmasso María C, Carmona Santiago J, Angel Sergio O, Agüero Fernán, 2014/12. BMC Genomics, 15 (1) p. 21.
[DOI][WoS][Pmid][serval:BIB_E1697329D840]
2013
 
Genome-wide analysis of 3′-untranslated regions supports the existence of post-transcriptional regulons controlling gene expression in trypanosomes
De Gaudenzi Javier G., Carmona Santiago J., Agüero Fernán, Frasch Alberto C., 2013/07/30. PeerJ, 1 pp. e118.
[DOI][WoS][Pmid][serval:BIB_4B6A66C1CBB7]
2012
 
Diagnostic Peptide Discovery: Prioritization of Pathogen Diagnostic Markers Using Multiple Features
Carmona Santiago J., Sartor Paula A., Leguizamón María S., Campetella Oscar E., Agüero Fernán, 2012/12/14. PLoS ONE, 7 (12) pp. e50748.
[DOI][WoS][Pmid][serval:BIB_E76BE83AE046]
 
Chapter 3: Integrating and Mining Helminth Genomes to Discover and Prioritize Novel Therapeutic Targets
Shanmugam Dhanasekaran, Ralph Stuart A., Carmona Santiago J., Crowther Gregory J., Roos David S., Agüero Fernán, 2012/08/23. pp. 43-59 dans Parasitic Helminths chap. 3, Wiley.
[DOI][serval:BIB_5D57142FF802]
 
TDR Targets: a chemogenomics resource for neglected diseases
Magarinos M. P., Carmona S. J., Crowther G. J., Ralph S. A., Roos D. S., Shanmugam D., Van Voorhis W. C., Aguero F., 2012/01/01. Nucleic Acids Research, 40 (D1) pp. D1118-D1127.
[DOI][WoS][Pmid][serval:BIB_27E04B6F30AB]
2010
 
A computational pipeline for diagnostic biomarker discovery in the human pathogen Trypanosoma cruzi
Carmona Santiago J, Sartor Paula, Leguizamón Maria Susana, Campetella Oscar, Agüero Fernán, 2010/12. BMC Bioinformatics, 11 pp. S10.
[DOI][serval:BIB_14F8342419F1]
 
Designing and implementing chemoinformatic approaches in TDR Targets Database: linking genes to chemical compounds in tropical disease causing pathogens
Magariños María Paula, Overington John, Carmona Santiago, Shanmugam Dhanasekaran, Doyle Maria, Ralph Stuart, Crowther Greg, Hertz-Fowler Christiane, Nwaka Solomon, Berriman Matt et al., 2010/12. BMC Bioinformatics, 11 (S10).
[DOI][serval:BIB_428EFEB40FF5]
 
Identification of Attractive Drug Targets in Neglected-Disease Pathogens Using an In Silico Approach
Crowther Gregory J., Shanmugam Dhanasekaran, Carmona Santiago J., Doyle Maria A., Hertz-Fowler Christiane, Berriman Matthew, Nwaka Solomon, Ralph Stuart A., Roos David S., Van Voorhis Wesley C. et al., 2010/08/24. PLoS Neglected Tropical Diseases, 4 (8) pp. e804.
[DOI][WoS][Pmid][serval:BIB_148697296DD6]
2009
 
TcSNP: a database of genetic variation in Trypanosoma cruzi
Ackermann A. A., Carmona S. J., Aguero F., 2009/01/01. Nucleic Acids Research, 37 (Database) pp. D544-D549.
[DOI][WoS][Pmid][serval:BIB_7BA7EC8AE0D4]
2008
 
Genomic-scale prioritization of drug targets: the TDR Targets database
Agüero Fernán, Al-Lazikani Bissan, Aslett Martin, Berriman Matthew, Buckner Frederick S., Campbell Robert K., Carmona Santiago, Carruthers Ian M., Chan A. W. Edith, Chen Feng et al., 2008/11. Nature Reviews Drug Discovery, 7 (11) pp. 900-907.
[DOI][WoS][Pmid][serval:BIB_5F71FF2333B4]
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