Full papers


F. Scarpa, M. Rubega, M. Zanon, F. Finotello, A.. S. Sejling, G. Sparacino. Hypoglycemia-induced EEG complexity changes in Type 1 diabetes assessed by fractal analysis algorithm. Biomedical Signal Processing and Control, 38, 2017. [ View Article ]


E. Tappeiner, F. Finotello, P. Charoentong, C. Mayer, D. Rieder, Z. Trajanoski. TIminer: NGS data mining pipeline for cancer immunology and immunotherapy. Bioinformatics, Epub ahead of print. [ View Article ]


F. Finotello and Z. Trajanoski. New strategies for cancer immunotherapy: targeting regulatory T cells. Genome Medicine, 9:10, 2017. [ View Article ]


P. Charoentong*, F. Finotello*, M. Angelova*, C. Mayer, M. Efremova, D. Rieder, H. Hackl, Z. Trajanoski. Pan-cancer immunogenomic analyses reveal genotype-immunophenotype relationships and predictors of response to checkpoint blockade. Cell Reports, 18(1): 248-262, 2017. [ View Article ]


F. Finotello†, E. Mastrorilli, B. Di Camillo†. Measuring the diversity of the human microbiota with targeted next-generation sequencing. Briefings in Bioinformatics, 2016. Epub ahead of print. [ View Article ]


H. Hackl*, P. Charoentong*, F. Finotello*, Z. Trajanoski. Computational genomics tools for dissecting tumour-immune cell interactions. Nature Reviews Genetics, 17(8): 441-458, 2016. [ View Article ]


S.M. Hill, L.M. Heiser, T. Cokelaer, M. Unger, N.K. Nesser, D.E. Carlin, Y. Zhang, A. Sokolov, E.O. Paull, C.K. Wong, K. Graim, A. Bivol, H. Wang, F. Zhu, B. Afsari, L.V. Danilova, A.V. Favorov, W.S. Lee, D. Taylor, C.W. Hu, B.L. Long, D.P. Noren, A.J. Bisberg, The. HPN-DREAM. Consortium (including F. Finotello), G.B. Mills, J.W. Gray, M. Kellen, T. Norman, S. Friend, A.A. Qutub, E.J. Fertig, Y. Guan, M. Song, J.M. Stuart, P.T. Spellman, H. Koeppl, G. Stolovitzky, J. Saez-Rodriguez, S. Mukherjee. Inferring causal molecular networks: empirical assessment through a community-based effort. Nature Methods, 13(4), 2016. [ View Article ]


T. Sanavia, F. Finotello, B. Di Camillo. FunPat: function-based pattern analysis on RNA-seq time series data. BMC Genomics, 16(Suppl 6):S2, 2015. [ View Article ]


F. Finotello† and B. Di Camillo. Measuring differential gene expression with RNA-seq: challenges and strategies for data analysis. Briefings in Functional Genomics 4 (2): 130-142, 2015. [ View Article ]


J. Fadista, P. Vikman, E. Ottosson Laakso, I. Mollet, P. Osmark, J. Esguerra, J. Taneera, C. Ladenvall, K. Hansson, F. Finotello, U. Krus, B. Di Camillo, L. Eliasson, A. Rosengren, E. Renström, C.B. Wollheim, L. Groop. Global transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism. PNAS, 111(38): 13924-13929, 2014. [ View Article ]


F. Finotello, E. Lavezzo, L. Bianco, L. Barzon, P. Mazzon, P. Fontana, S. Toppo, B. Di Camillo. Reducing bias in RNA sequencing data: a novel approach to compute counts. BMC Bioinformatics 15(1):1-12, 2014. [ View Article ] [ About Maxcounts ]


E. Lavezzo, S. Toppo, E. Franchin, B. Di Camillo, F. Finotello, M. Falda, R. Manganelli, G. Palù, L. Barzon. Genomic comparative analysis and gene function prediction in infectious diseases: application to the investigation of a meningitidis outbreak. BMC Infectious Diseases 13(1):554, 2013. [ View Article ]


F. Finotello*, E. Lavezzo*, P. Fontana, D. Peruzzo, A. Albiero, L. Barzon, M. Falda, B. Di Camillo, S. Toppo. Comparative analysis of algorithms for whole-genome assembly of pyrosequencing data. Briefings in Bioinformatics, 13(3):269-280, 2012. [ View Article ]


E. Lavezzo, S. Toppo, L. Barzon, C. Cobelli, B. Di Camillo, F. Finotello, E. Franchin, D. Peruzzo, G.M. Toffolo, M. Trevisan, G. Palù. Draft genome sequences of two Neisseria meningitidis serogroup C clinical isolates. Journal of bacteriology, 192(19):5270-5271, 2010. [ View Article ]


* co-first authors
† corresponding author(s)



Abstracts and short papers


C. Torroja, F. Finotello, Z. Trajanoski, F. Sánchez-Cabo Deconvolution-based approaches to quantify TILs from bulk RNA-Seq. Quantitative Approaches in Immuno-Oncology. March 1, 2017, New York, USA.


P. Charoentong, F. Finotello, M. Angelova, C. Mayer, E. Tappeiner, M. Efremova, D. Rieder, H. Hackl, Z. Trajanoski Pan-cancer immunogenomic analyses reveal genotype-immunophenotype relationships and predictors of response to checkpoint blockade. Keystone Symposia. Cancer Immunology and Immunotherapy: Taking a Place in Mainstream Oncology. March 19-23, 2017, Whistler, Canada.


F. Finotello, C. Mayer, D. Rieder, P. Charoentong, H. Hackl, U. Sahin, J.G. Hengstler, M. Schmidt, T. Bukur, V. Bukur, G. Schmidt, S. Althammer, Z. Trajanoski. Quantification of tumor-infiltrating lymphocyte subpopulations using imaging and sequencing data. Keystone Symposia. Cancer Immunotherapy: Immunity and Immunosuppression Meet Targeted Therapies. January 24-28, 2016, Vancouver, Canada. Oral Communication.


P. Charoentong, F. Finotello, M. Angelova, C. Mayer, G. Schmidt, S. Althammer, D. Rieder, H. Hackl, Z. Trajanoski. Immunophenotypes and antigenomes of solid cancers. Keystone Symposia. Cancer Immunotherapy: Immunity and Immunosuppression Meet Targeted Therapies. January 24-28, 2016, Vancouver, Canada.


F. Finotello, F. Scarpa, M. Zanon. EEG signal features extraction based on fractal dimension. 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society. August 25-29, 2015, Milan, Italy. [ View Article ]


L. Pierri, P. Saggese, R. Savastano, M. Poeta, S. Guercio Nuzio, G. Massa, M. Di Stasi, V. Ciccone, F. Finotello, O. D'Amico, B. Di Camillo, A. Weisz, P. Vajro. Microbiota and Gut-Liver Axis in Obesity Related Liver Disease: a pediatric Pilot Study. 48th annual Meeting ESPGHAN. May 9-6, 2015, Amsterdam, Netherland.


G. Baruzzo, F. Finotello, E. Lavezzo, A. Serafini, R. Provvedi, S. Toppo, L. Barzon, R. Manganelli, B. Di Camillo. Benchmarking RNA-seq mapping strategies for paired-end reads. NETTAB 2014, from structural bioinformatics to integrative systems biology, October 15-17, 2014, Turin, Italy.


F. Finotello, E. Lavezzo, S. Toppo, L. Barzon, B. Di Camillo. Reverse engineering the human microbiota. NETTAB 2014, from structural bioinformatics to integrative systems biology, October 15-17, 2014, Turin, Italy.


F. Finotello, E. Lavezzo, A. Zandonà, S. Toppo, L. Barzon, B. Di Camillo. Modelling differences and interactions in the human microbiota. GNB 2014, IV National Congress of Bioengineering, June 25-27, 2014. Pavia, Italy. Oral communication.


T. Sanavia, F. Finotello, B. Di Camillo. FunPat: a function-based pattern analysis framework for RNA-seq time-series data. GNB 2014, IV National Congress of Bioengineering, June 25-27, 2014. Pavia, Italy.


A. Benguría, F. Finotello, S. Callejas, R. Álvarez, F. Sánchez-Cabo, B. Di Camillo, C. Hernández-Chico, A. Dopazo. Analysis of whole blood transcriptome of Spinal Muscular Atrophy patients using RNA-seq. Next Generation Sequencing Conference 2014, June 2-4, 2014. Barcelona, Spain.


M. Scarpa, L. Barzon, G. Costanzi, E. Lavezzo, F. Finotello, F. Erroi, L. Dallagnese, S. Basato, P. Brun, S. Toppo, B. Di Camillo, C. Castoro, I. Castagliuolo. Colonic microbiota and gene methylation in colonic carcinogenesis. In SSAT 55th annual meeting, Digestive Disease Week, May 2-6, 2014. Chicago, Illinois, USA.


T. Sanavia, F. Finotello, B. Di Camillo. FunPat: a function-based pattern analysis pipeline for RNA-seq time-series data. In BITS annual meeting 2014, February 26-28, 2014. Rome, Italy. Oral communication.


F. Finotello, E. Lavezzo, L. Barzon, P. Fontana, S. Toppo, B. Di Camillo. Characterization and reduction of biases in RNA sequencing data. Oral communication in IDAMAP, Intelligent data analysis in biomedicine and pharmacology, November 22, 2012.


F. Finotello, E. Lavezzo, L. Barzon, P. Mazzon, P. Fontana, S. Toppo, B. Di Camillo. A strategy to reduce technical variability and bias in RNA sequencing data. EMBnet. journal, 18(B):pp-65, 2012. Oral communication in NETTAB 2012. [ View Abstract ]


F. Finotello, E. Lavezzo, L. Barzon, P. Fontana, A. Si-Ammour, S. Toppo, B. Di Camillo. RNA sequencing data: biases and normalization. EMBnet. journal, 18(A):p-99, 2012. [ View Abstract ]


F. Finotello, E. Lavezzo, L. Barzon, P. Fontana, A. Si-Ammour, S. Toppo, B. Di Camillo. Comparison of parametric methods for detecting differential expression in RNA sequencing data. In Third National Congress of Italian Group of Bioengineering, June 26-29, 2012.


F. Finotello, D. Peruzzo, E. Lavezzo, B. Di Camillo, G. M. Toffolo, C. Cobelli, S. Toppo. Complete and comparative analysis of algorithms for whole genome shotgun assembly. Oral communication in BITS 2010. VII Annual meeting of the bioinformatics italian society, pages 157-159. Progredit, April 14-16, 2010.


Book chapters


D. Rieder and F. Finotello. Analysis of High-Throughput RNA Bisulfite Sequencing Data. RNA Methylation: Methods and Protocols (2017): 143-154. [ View Chapter ]