biological ontologies,biological data integration,sequence analysis,comparative genomics,molecular evolution

Bioinformatics Pipelines Development
Evolution of the Nervous System in Intelligent Organisms
Complexity in Simple (?) Organisms
Mobile Elements Activity in the Tree of Life

Russo MT, Vitale L, Entrambasaguas L, Anestis K, Fattorini N, Romano F,
Minucci C, De Luca P, Biffali E, Vyverman W, Sanges R, Montresor M, Ferrante MI.
MRP3 is a sex determining gene in the diatom Pseudo-nitzschia multistriata. Nat
Commun. 2018 Nov 28;9(1):5050. doi: 10.1038/s41467-018-07496-0. PubMed PMID:
30487611; PubMed Central PMCID: PMC6261938.

Volpe M, Miralto M, Gustincich S, Sanges R. ClusterScan: simple and
generalistic identification of genomic clusters. Bioinformatics. 2018 Nov
15;34(22):3921-3923. doi: 10.1093/bioinformatics/bty486. PubMed PMID: 29912285.

Basu S, Patil S, Mapleson D, Russo MT, Vitale L, Fevola C, Maumus F, Casotti
R, Mock T, Caccamo M, Montresor M, Sanges R, Ferrante MI. Finding a partner in
the ocean: molecular and evolutionary bases of the response to sexual cues in a
planktonic diatom. New Phytol. 2017 Jul;215(1):140-156. doi: 10.1111/nph.14557.
Epub 2017 Apr 21. PubMed PMID: 28429538; PubMed Central PMCID: PMC5485032.

Mock T, Otillar RP, Strauss J, McMullan M, Paajanen P, Schmutz J, Salamov A,
Sanges R, Toseland A, Ward BJ, Allen AE, Dupont CL, Frickenhaus S, Maumus F,
Veluchamy A, Wu T, Barry KW, Falciatore A, Ferrante MI, Fortunato AE, Glöckner G,
Gruber A, Hipkin R, Janech MG, Kroth PG, Leese F, Lindquist EA, Lyon BR, Martin
J, Mayer C, Parker M, Quesneville H, Raymond JA, Uhlig C, Valas RE, Valentin KU,
Worden AZ, Armbrust EV, Clark MD, Bowler C, Green BR, Moulton V, van Oosterhout
C, Grigoriev IV. Evolutionary genomics of the cold-adapted diatom Fragilariopsis
cylindrus. Nature. 2017 Jan 26;541(7638):536-540. doi: 10.1038/nature20803. Epub
2017 Jan 16. PubMed PMID: 28092920.

Basu S, Hadzhiev Y, Petrosino G, Nepal C, Gehrig J, Armant O, Ferg M, Strahle
U, Sanges R, Müller F. The Tetraodon nigroviridis reference transcriptome:
developmental transition, length retention and microsynteny of long non-coding
RNAs in a compact vertebrate genome. Sci Rep. 2016 Sep 15;6:33210. doi:
10.1038/srep33210. PubMed PMID: 27628538; PubMed Central PMCID: PMC5024134.

Musacchia F, Basu S, Petrosino G, Salvemini M, Sanges R. Annocript: a flexible
pipeline for the annotation of transcriptomes able to identify putative long
noncoding RNAs. Bioinformatics. 2015 Jul 1;31(13):2199-201. doi:
10.1093/bioinformatics/btv106. Epub 2015 Feb 19. PubMed PMID: 25701574.

Zucchelli S, Cotella D, Takahashi H, Carrieri C, Cimatti L, Fasolo F, Jones
MH, Sblattero D, Sanges R, Santoro C, Persichetti F, Carninci P, Gustincich S.
SINEUPs: A new class of natural and synthetic antisense long non-coding RNAs that
activate translation. RNA Biol. 2015;12(8):771-9. doi:
10.1080/15476286.2015.1060395. Review. PubMed PMID: 26259533; PubMed Central
PMCID: PMC4615742.

Dvořák P, Casamatta DA, Poulíčková A, Hašler P, Ondřej V, Sanges R.
Synechococcus: 3 billion years of global dominance. Mol Ecol. 2014
Nov;23(22):5538-51. doi: 10.1111/mec.12948. Epub 2014 Oct 21. PubMed PMID:
25283338.

Racioppi C, Kamal AK, Razy-Krajka F, Gambardella G, Zanetti L, di Bernardo D,
Sanges R, Christiaen LA, Ristoratore F. Fibroblast growth factor signalling
controls nervous system patterning and pigment cell formation in Ciona
intestinalis. Nat Commun. 2014 Sep 5;5:4830. doi: 10.1038/ncomms5830. PubMed
PMID: 25189217; PubMed Central PMCID: PMC4164782.

Sanges R, Hadzhiev Y, Gueroult-Bellone M, Roure A, Ferg M, Meola N, Amore G,
Basu S, Brown ER, De Simone M, Petrera F, Licastro D, Strähle U, Banfi S, Lemaire
P, Birney E, Müller F, Stupka E. Highly conserved elements discovered in
vertebrates are present in non-syntenic loci of tunicates, act as enhancers and
can be transcribed during development. Nucleic Acids Res. 2013 Apr
1;41(6):3600-18. doi: 10.1093/nar/gkt030. Epub 2013 Feb 7. PubMed PMID: 23393190;
PubMed Central PMCID: PMC3616699.

Basu S, Müller F, Sanges R. Examples of sequence conservation analyses
capture a subset of mouse long non-coding RNAs sharing homology with fish
conserved genomic elements. BMC Bioinformatics. 2013;14 Suppl 7:S14. doi:
10.1186/1471-2105-14-S7-S14. Epub 2013 Apr 22. PubMed PMID: 23815359; PubMed
Central PMCID: PMC3633045.


Gennarino VA, D'Angelo G, Dharmalingam G, Fernandez S, Russolillo G, Sanges
R, Mutarelli M, Belcastro V, Ballabio A, Verde P, Sardiello M, Banfi S.
Identification of microRNA-regulated gene networks by expression analysis of
target genes. Genome Res. 2012 Jun;22(6):1163-72. doi: 10.1101/gr.130435.111.
Epub 2012 Feb 24. PubMed PMID: 22345618; PubMed Central PMCID: PMC3371699.

Roma G, Sardiello M, Cobellis G, Cruz P, Lago G, Sanges R, Stupka E. The
UniTrap resource: tools for the biologist enabling optimized use of gene trap
clones. Nucleic Acids Res. 2008 Jan;36(Database issue):D741-6. Epub 2007 Oct 16.
PubMed PMID: 17942430; PubMed Central PMCID: PMC2238955.

Sanges R, Cordero F, Calogero RA. oneChannelGUI: a graphical interface to
Bioconductor tools, designed for life scientists who are not familiar with R
language. Bioinformatics. 2007 Dec 15;23(24):3406-8. Epub 2007 Sep 17. PubMed
PMID: 17875544.

Ferg M, Sanges R, Gehrig J, Kiss J, Bauer M, Lovas A, Szabo M, Yang L,
Straehle U, Pankratz MJ, Olasz F, Stupka E, Müller F. The TATA-binding protein
regulates maternal mRNA degradation and differential zygotic transcription in
zebrafish. EMBO J. 2007 Sep 5;26(17):3945-56. Epub 2007 Aug 16. PubMed PMID:
17703193; PubMed Central PMCID: PMC1950726.

Sanges R, Kalmar E, Claudiani P, D'Amato M, Muller F, Stupka E. Shuffling of
cis-regulatory elements is a pervasive feature of the vertebrate lineage. Genome
Biol. 2006;7(7):R56. PubMed PMID: 16859531; PubMed Central PMCID: PMC1779573.

Gianfrancesco F, Sanges R, Esposito T, Tempesta S, Rao E, Rappold G,
Archidiacono N, Graves JA, Forabosco A, D'Urso M. Differential divergence of
three human pseudoautosomal genes and their mouse homologs: implications for sex
chromosome evolution. Genome Res. 2001 Dec;11(12):2095-100. PubMed PMID:
11731500; PubMed Central PMCID: PMC311231.

Professor of the "Transcriptomics data analysis and mining" course in the PhD program in Structural and Functional Genomics at SISSA

Professor of the "Bioinformatics" course at the Laurea Magistrale in Data science and scientific computing at the University of Trieste