Comparative analysis of algorithms for whole-genome assembly of pyrosequencing data. - Francesca Finotello; Enrico Lavezzo; Paolo Fontana; Denis Peruzzo; Alessandro Albiero; Luisa Barzon; Marco Falda; Barbara Di Camillo; Stefano Toppo (Briefings Bioinform., 2012)

Reducing bias in RNA sequencing data: a novel approach to compute counts. - Francesca Finotello; Enrico Lavezzo; Luca Bianco; Luisa Barzon; Paolo Mazzon; Paolo Fontana; Stefano Toppo; Barbara Di Camillo (BMC Bioinform., 2014)

EEG signal features extraction based on fractal dimension. - Francesca Finotello; Fabio Scarpa; Mattia Zanon (EMBC, 2015)

TIminer: NGS data mining pipeline for cancer immunology and immunotherapy. - Elias Tappeiner; Francesca Finotello; Pornpimol Charoentong; Clemens Mayer; Dietmar Rieder; Zlatko Trajanoski (Bioinform., 2017)

Hypoglycemia-induced EEG complexity changes in Type 1 diabetes assessed by fractal analysis algorithm. - Fabio Scarpa; Maria Rubega; Mattia Zanon; Francesca Finotello; Anne-Sophie Sejling; Giovanni Sparacino (Biomed. Signal Process. Control., 2017)

Measuring the diversity of the human microbiota with targeted next-generation sequencing. - Francesca Finotello; Eleonora Mastrorilli; Barbara Di Camillo (Briefings Bioinform., 2018)

Optimizing PCR primers targeting the bacterial 16S ribosomal RNA gene. - Francesco Sambo; Francesca Finotello; Enrico Lavezzo; Giacomo Baruzzo; Giulia Masi; Elektra Peta; Marco Falda; Stefano Toppo; Luisa Barzon; Barbara Di Camillo (BMC Bioinform., 2018)

Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology. - Gregor Sturm; Francesca Finotello; Florent Petitprez; Jitao David Zhang; Jan Baumbach; Wolf-Herman Fridman; Markus List; Tatsiana Aneichyk (Bioinform., 2019)

NeoFuse: predicting fusion neoantigens from RNA sequencing data. - Georgios Fotakis; Dietmar Rieder; Marlene Haider; Zlatko Trajanoski; Francesca Finotello (Bioinform., 2020)

Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data. - Gregor Sturm; Tamás Szabó; Georgios Fotakis; Marlene Haider; Dietmar Rieder; Zlatko Trajanoski; Francesca Finotello (Bioinform., 2020)

Interpretable systems biomarkers predict response to immune-checkpoint inhibitors. - Óscar Lapuente-Santana; Maisa van Genderen; Peter A. J. Hilbers; Francesca Finotello; Federica Eduati (Patterns, 2021)

SimBu: bias-aware simulation of bulk RNA-seq data with variable cell-type composition. - Alexander Dietrich; Gregor Sturm; Lorenzo Merotto; Federico Marini 002; Francesca Finotello; Markus List (Bioinform., 2022)

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction. - Dietmar Rieder; Georgios Fotakis; Markus Ausserhofer; Rene Geyeregger; Wolfgang Paster; Zlatko Trajanoski; Francesca Finotello (Bioinform., 2022)