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Items: 26

1.

NeoFuse: predicting fusion neoantigens from RNA sequencing data.

Fotakis G, Rieder D, Haider M, Trajanoski Z, Finotello F.

Bioinformatics. 2019 Nov 22. pii: btz879. doi: 10.1093/bioinformatics/btz879. [Epub ahead of print]

PMID:
31755900
2.

Guadecitabine Plus Ipilimumab in Unresectable Melanoma: The NIBIT-M4 Clinical Trial.

Di Giacomo AM, Covre A, Finotello F, Rieder D, Danielli R, Sigalotti L, Giannarelli D, Petitprez F, Lacroix L, Valente M, Cutaia O, Fazio C, Amato G, Lazzeri A, Monterisi S, Miracco C, Coral S, Anichini A, Bock C, Nemc A, Oganesian A, Lowder J, Azab M, Fridman WH, Sautès-Fridman C, Trajanoski Z, Maio M.

Clin Cancer Res. 2019 Dec 15;25(24):7351-7362. doi: 10.1158/1078-0432.CCR-19-1335. Epub 2019 Sep 17.

PMID:
31530631
3.

Next-generation computational tools for interrogating cancer immunity.

Finotello F, Rieder D, Hackl H, Trajanoski Z.

Nat Rev Genet. 2019 Dec;20(12):724-746. doi: 10.1038/s41576-019-0166-7. Epub 2019 Sep 12. Review.

PMID:
31515541
4.

Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology.

Sturm G, Finotello F, Petitprez F, Zhang JD, Baumbach J, Fridman WH, List M, Aneichyk T.

Bioinformatics. 2019 Jul 15;35(14):i436-i445. doi: 10.1093/bioinformatics/btz363.

5.

Correction to: Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data.

Finotello F, Mayer C, Plattner C, Laschober G, Rieder D, Hackl H, Krogsdam A, Loncova Z, Posch W, Wilflingseder D, Sopper S, Ijsselsteijn M, Brouwer TP, Johnson D, Xu Y, Wang Y, Sanders ME, Estrada MV, Ericsson-Gonzalez P, Charoentong P, Balko J, da Cunha Carvalho de Miranda NF, Trajanoski Z.

Genome Med. 2019 Jul 29;11(1):50. doi: 10.1186/s13073-019-0655-5.

6.

Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data.

Finotello F, Mayer C, Plattner C, Laschober G, Rieder D, Hackl H, Krogsdam A, Loncova Z, Posch W, Wilflingseder D, Sopper S, Ijsselsteijn M, Brouwer TP, Johnson D, Xu Y, Wang Y, Sanders ME, Estrada MV, Ericsson-Gonzalez P, Charoentong P, Balko J, de Miranda NFDCC, Trajanoski Z.

Genome Med. 2019 May 24;11(1):34. doi: 10.1186/s13073-019-0638-6. Erratum in: Genome Med. 2019 Jul 29;11(1):50.

7.

Multi-Omics Profiling of the Tumor Microenvironment: Paving the Way to Precision Immuno-Oncology.

Finotello F, Eduati F.

Front Oncol. 2018 Oct 5;8:430. doi: 10.3389/fonc.2018.00430. eCollection 2018. Review.

8.

Optimizing PCR primers targeting the bacterial 16S ribosomal RNA gene.

Sambo F, Finotello F, Lavezzo E, Baruzzo G, Masi G, Peta E, Falda M, Toppo S, Barzon L, Di Camillo B.

BMC Bioinformatics. 2018 Sep 29;19(1):343. doi: 10.1186/s12859-018-2360-6.

9.

Deviations of the immune cell landscape between healthy liver and hepatocellular carcinoma.

Rohr-Udilova N, Klinglmüller F, Schulte-Hermann R, Stift J, Herac M, Salzmann M, Finotello F, Timelthaler G, Oberhuber G, Pinter M, Reiberger T, Jensen-Jarolim E, Eferl R, Trauner M.

Sci Rep. 2018 Apr 18;8(1):6220. doi: 10.1038/s41598-018-24437-5.

10.

Quantifying tumor-infiltrating immune cells from transcriptomics data.

Finotello F, Trajanoski Z.

Cancer Immunol Immunother. 2018 Jul;67(7):1031-1040. doi: 10.1007/s00262-018-2150-z. Epub 2018 Mar 14. Review.

11.

Targeting immune checkpoints potentiates immunoediting and changes the dynamics of tumor evolution.

Efremova M, Rieder D, Klepsch V, Charoentong P, Finotello F, Hackl H, Hermann-Kleiter N, Löwer M, Baier G, Krogsdam A, Trajanoski Z.

Nat Commun. 2018 Jan 2;9(1):32. doi: 10.1038/s41467-017-02424-0.

12.

Neoantigens Generated by Individual Mutations and Their Role in Cancer Immunity and Immunotherapy.

Efremova M, Finotello F, Rieder D, Trajanoski Z.

Front Immunol. 2017 Nov 28;8:1679. doi: 10.3389/fimmu.2017.01679. eCollection 2017. Review.

13.

TIminer: NGS data mining pipeline for cancer immunology and immunotherapy.

Tappeiner E, Finotello F, Charoentong P, Mayer C, Rieder D, Trajanoski Z.

Bioinformatics. 2017 Oct 1;33(19):3140-3141. doi: 10.1093/bioinformatics/btx377.

14.

Analysis of High-Throughput RNA Bisulfite Sequencing Data.

Rieder D, Finotello F.

Methods Mol Biol. 2017;1562:143-154. doi: 10.1007/978-1-4939-6807-7_10.

PMID:
28349459
15.

New strategies for cancer immunotherapy: targeting regulatory T cells.

Finotello F, Trajanoski Z.

Genome Med. 2017 Jan 27;9(1):10. doi: 10.1186/s13073-017-0402-8.

16.

Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade.

Charoentong P, Finotello F, Angelova M, Mayer C, Efremova M, Rieder D, Hackl H, Trajanoski Z.

Cell Rep. 2017 Jan 3;18(1):248-262. doi: 10.1016/j.celrep.2016.12.019.

17.

Measuring the diversity of the human microbiota with targeted next-generation sequencing.

Finotello F, Mastrorilli E, Di Camillo B.

Brief Bioinform. 2018 Jul 20;19(4):679-692. doi: 10.1093/bib/bbw119.

PMID:
28025179
18.

Computational genomics tools for dissecting tumour-immune cell interactions.

Hackl H, Charoentong P, Finotello F, Trajanoski Z.

Nat Rev Genet. 2016 Jul 4;17(8):441-58. doi: 10.1038/nrg.2016.67. Review.

PMID:
27376489
19.

EEG signal features extraction based on fractal dimension.

Finotello F, Scarpa F, Zanon M.

Conf Proc IEEE Eng Med Biol Soc. 2015;2015:4154-7. doi: 10.1109/EMBC.2015.7319309.

PMID:
26737209
20.

FunPat: function-based pattern analysis on RNA-seq time series data.

Sanavia T, Finotello F, Di Camillo B.

BMC Genomics. 2015;16:S2. doi: 10.1186/1471-2164-16-S6-S2. Epub 2015 Jun 1.

21.

Measuring differential gene expression with RNA-seq: challenges and strategies for data analysis.

Finotello F, Di Camillo B.

Brief Funct Genomics. 2015 Mar;14(2):130-42. doi: 10.1093/bfgp/elu035. Epub 2014 Sep 18. Review.

PMID:
25240000
22.

Global genomic and transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism.

Fadista J, Vikman P, Laakso EO, Mollet IG, Esguerra JL, Taneera J, Storm P, Osmark P, Ladenvall C, Prasad RB, Hansson KB, Finotello F, Uvebrant K, Ofori JK, Di Camillo B, Krus U, Cilio CM, Hansson O, Eliasson L, Rosengren AH, Renström E, Wollheim CB, Groop L.

Proc Natl Acad Sci U S A. 2014 Sep 23;111(38):13924-9. doi: 10.1073/pnas.1402665111. Epub 2014 Sep 8.

23.

Reducing bias in RNA sequencing data: a novel approach to compute counts.

Finotello F, Lavezzo E, Bianco L, Barzon L, Mazzon P, Fontana P, Toppo S, Di Camillo B.

BMC Bioinformatics. 2014;15 Suppl 1:S7. doi: 10.1186/1471-2105-15-S1-S7. Epub 2014 Jan 10.

24.

Genomic comparative analysis and gene function prediction in infectious diseases: application to the investigation of a meningitis outbreak.

Lavezzo E, Toppo S, Franchin E, Di Camillo B, Finotello F, Falda M, Manganelli R, Palù G, Barzon L.

BMC Infect Dis. 2013 Nov 19;13:554. doi: 10.1186/1471-2334-13-554.

25.

Comparative analysis of algorithms for whole-genome assembly of pyrosequencing data.

Finotello F, Lavezzo E, Fontana P, Peruzzo D, Albiero A, Barzon L, Falda M, Di Camillo B, Toppo S.

Brief Bioinform. 2012 May;13(3):269-80. doi: 10.1093/bib/bbr063. Epub 2011 Oct 21. Review.

PMID:
22021898
26.

Draft genome sequences of two Neisseria meningitidis serogroup C clinical isolates.

Lavezzo E, Toppo S, Barzon L, Cobelli C, Di Camillo B, Finotello F, Franchin E, Peruzzo D, Toffolo GM, Trevisan M, Palù G.

J Bacteriol. 2010 Oct;192(19):5270-1. doi: 10.1128/JB.00789-10. Epub 2010 Jul 30.

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