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Francesca Finotello
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Pan-cancer immunogenomic analyses reveal genotype-immunophenotype relationships and predictors of response to checkpoint blockade
P Charoentong, F Finotello, M Angelova, C Mayer, M Efremova, D Rieder, ...
Cell reports 18 (1), 248-262, 2017
22432017
Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data
F Finotello, C Mayer, C Plattner, G Laschober, D Rieder, H Hackl, ...
Genome medicine 11 (1), 34, 2019
5482019
Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology
G Sturm, F Finotello, F Petitprez, JD Zhang, J Baumbach, WH Fridman, ...
Bioinformatics 35 (14), i436-i445, 2019
4432019
Global genomic and transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism
J Fadista, P Vikman, EO Laakso, IG Mollet, JL Esguerra, J Taneera, ...
Proceedings of the National Academy of Sciences 111 (38), 13924-13929, 2014
4272014
Quantifying tumor-infiltrating immune cells from transcriptomics data
F Finotello, Z Trajanoski
Cancer Immunology, Immunotherapy 67 (7), 1031-1040, 2018
2562018
Measuring differential gene expression with RNA-seq: challenges and strategies for data analysis
F Finotello, B Di Camillo
Briefings in functional genomics 14 (2), 130-142, 2015
2502015
Computational genomics tools for dissecting tumour-immune cell interactions
H Hackl, P Charoentong, F Finotello, Z Trajanoski
Nature Reviews Genetics 17 (8), 441-458, 2016
2352016
Inferring causal molecular networks: empirical assessment through a community-based effort
SM Hill, LM Heiser, T Cokelaer, M Unger, NK Nesser, DE Carlin, Y Zhang, ...
Nature Methods 13 (4), 310-318, 2016
2202016
Targeting immune checkpoints potentiates immunoediting and changes the dynamics of tumor evolution
M Efremova, D Rieder, V Klepsch, P Charoentong, F Finotello, H Hackl, ...
Nature Communications 9 (1), 32, 2018
2022018
Neoantigens generated by individual mutations and their role in cancer immunity and immunotherapy
M Efremova, F Finotello, D Rieder, Z Trajanoski
Frontiers in immunology 8, 1679, 2017
1702017
Mitochondrial DNA drives abscopal responses to radiation that are inhibited by autophagy
T Yamazaki, A Kirchmair, AI Sato, A Buque, M Rybstein, G Petroni, N Bloy, ...
Nature Immunology 21 (10), 1160-1171, 2020
1682020
Deviations of the immune cell landscape between healthy liver and hepatocellular carcinoma
N Rohr-Udilova, F Klinglmüller, R Schulte-Hermann, J Stift, M Herac, ...
Scientific Reports 8 (1), 6220, 2018
1472018
A genome-wide association study of diabetic kidney disease in subjects with type 2 diabetes
NR Van Zuydam, E Ahlqvist, N Sandholm, H Deshmukh, NW Rayner, ...
Diabetes 67 (7), 1414-1427, 2018
1252018
Next-generation computational tools for interrogating cancer immunity
F Finotello, D Rieder, H Hackl, Z Trajanoski
Nature Reviews Genetics, 1-23, 2019
1032019
Deconvoluting tumor-infiltrating immune cells from RNA-seq data using quanTIseq
C Plattner, F Finotello, D Rieder
Methods in enzymology 636, 261-285, 2020
902020
Immunedeconv: an R package for unified access to computational methods for estimating immune cell fractions from bulk RNA-sequencing data
G Sturm, F Finotello, M List
Bioinformatics for cancer immunotherapy: methods and protocols, 223-232, 2020
782020
Measuring the diversity of the human microbiota with targeted next-generation sequencing
F Finotello, E Mastrorilli, B Di Camillo
Briefings in bioinformatics 19 (4), 679-692, 2018
752018
TIminer: NGS data mining pipeline for cancer immunology and immunotherapy
E Tappeiner, F Finotello, P Charoentong, C Mayer, D Rieder, Z Trajanoski
Bioinformatics 33 (19), 3140-3141, 2017
722017
CD39 Identifies the CD4+ Tumor-Specific T-cell Population in Human CancerCD39 Identifies CD4+ Tumor-Specific T Cells
KE Kortekaas, SJ Santegoets, G Sturm, I Ehsan, SL van Egmond, ...
Cancer Immunology Research 8 (10), 1311-1321, 2020
652020
Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data
G Sturm, T Szabo, G Fotakis, M Haider, D Rieder, Z Trajanoski, F Finotello
Bioinformatics 36 (18), 4817-4818, 2020
612020
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