A SHORT OVERVIEW OF THE
BIOINFORMATICS CORE
Bioinformatics core expertises
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Training in bioinformatics and statistics (all of us)
Statistical data analysis (Annamaria&Luisa)
Image analysis and processing (Annamaria)
Gemonics and proteomics analysis (Veer&Diego C&Margherita)
Next Generation Sequencing (Margherita & Veer)
Maintainance and development of bioinformatics databases and software (Diego C&Gennaro)
Veer
Anna
Marghe
Gennaro
Diego C
Luisa
http://bioinformatics.tigem.it
Databases and software development and maintenance
Tools available on the BC website:
• Microarray Analysis Pipeline
• Mode of Action by NeTwoRk Analysis (MANTRA)
• Local UCSC genome browser
• Local CLUSTALW
• NetView
• Cometa
Coming Soon:
MANTRA2 (SQUARED)
SERVICE DESK
Training: Internal courses calendar
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07 November
Basic Statistic: summary statistics (mean, standard error, histograms etc.) and
hypothesis testing in excel (T-test, Anova, Chisquare etc.)
Deadline: 04 November
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21 November
Microarray analysis: Microarray Pipeline, Gene ontology annotation with David
and Array Express
Deadline: 16 November
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05 December
Gene List functional annotation: transcription factor binding sites with Transfac,
gene set enrichment analysis with GSEA tool and basic usage of Ingenuity
pathway analysis tool
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17 December
Image Analysis: Image Analysis with ImageJ and CellProfiler
Register at bioinformatics.tigem.it
Statistical Analysis
Please make
replicates.
Clustering and network analysis
Time series analysis
Image Analysis and processing
Cell number : 522
Wt
M631 -/- untreated
M631 -/- phenylbutyrate treated
Bioinformatics and Genomics analyses
Next Generation Sequencing
• support in planning NGS experiments
• keep up-to-date with literature and
analysis tools
• development of ad-hoc analysis pipelines
• support in visualization and interpretation
of results
NGS Applications:
- RNA seq
- small RNA seq
- ChIP seq
- Exome / Targeted seq
Hardware resources: a new Computer Cluster
Nodes
Storage
• ProLiant DL380 G7
• CPU: 2 x Intel Xeon E5649
2.53GHz
• 2 x Proliant DL360 G7
• CPU: 2 x Intel Xeon E5645
2.40GHz
– 2 x 8 CORE, 16 Thread, 64 bit
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Memory: 24GB
Disk: 146GB
8 x ProLiant BL280c G6
CPU: 2 x Intel Xeon X5675
3.07GHz
– 2 x 8 CORE, 16 Thread, 64 bit
• Memory: 48GB
• Disk: 500GB
– 2 x 8 CORE, 16 Thread, 64 bit
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Memory: 36GB
Disk: 146GB
OS: LINUX CentOS 6
Storage Area Network
Disk: 5TB SAS + 20 TB SATA
Interconnect: 8Gbs Fibre
Channel
Publications
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Licastro D, Mutarelli M, Peluso I, Neveling K, Wieskamp N, Rispoli R, Vozzi D, Athanasakis E, D'Eustacchio A, Pizzo M,
D'Amico F, Ziviello C, Simonelli F, Fabretto A, Scheffer H, Gasparini P, Banfi S, Nigro V (2012) Molecular diagnosis of usher
syndrome: application of two different next generation sequencing-based procedures. PLoS One, 2012;7(8):e43799. Epub
2012 Aug 29.
Cutillo L, Carissimo A, Figini S (2012) Network Selection: A Method for Ranked Lists Selection. PLoS ONE 7(8): e43678.
doi:10.1371/journal.pone.0043678
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 (2012) Identification of microRNA-regulated gene networks by expression analysis of target
genes. Genome Res., 22: 1163-1172.
Gennarino VA, Sardiello M, Mutarelli M, Dharmalingam G, Maselli V, Lago G, Banfi S. (2011) HOCTARdb: a unique
resource for microRNA target prediction. Gene, Jul 1;480(1-2):51-8.
Costa V, Angelini C, D’Apice L, Mutarelli M, Casamassimi A, Rienzo M, Sommese L, Gallo MA, Aprile M, Esposito R, Leone
L, Donizetti A, Crispi S, Sarubbi B, Calabrò R, Picardi M, Salvatore P, De Berardinis P, Napoli C, Ciccodicola A (2011)
Massive-Scale RNA-Seq Analysis of Non Ribosomal Transcriptome in Human Trisomy 21. PLoS ONE 6(4):e18493.
Cutillo L, Carissimo A, Di Bernardo D (2010) Optimal length choice in top k ordered lists aggregation. GFKL – CLADAG
2010 proceedings.
Vitiello C, Faraso S, Sorrentino N.C, Di Salvo G, Nusco E, Nigro G, Cutillo L, Calabrò R, Auricchio A, Nigro V (2009) Disease
Rescue and Increased Lifespan in a Model of Cardiomyopathy and Muscular Dystrophy by Combined AAV Treatments.
PLoS ONE, 4:1932-6203.
Gennarino VA, Sardiello M, Avellino R, Meola N, Maselli V, Anand S, Cutillo L, Ballabio A, Banfi S (2009) MicroRNA target
prediction by expression analysis of host genes. Genome Res., 19:481-90.
Allocca M, Doria M, Petrillo M, Colella P, Garcia-Hoyos M, Gibbs D, Kim SR, Maguire A, Rex TS, Di Vicino U, Cutillo L,
Sparrow JR, Williams DS, Bennett J, Auricchio A (2008) Serotype-dependent packaging of large genes in adeno-associated
viral vectors results in effective gene delivery in mice. J Clin Invest., 118:1955-64.
Angelini C, Cutillo L, De Canditiis D, Mutarelli M, Pensky M (2008) BATS: a Bayesian user-friendly software for Analyzing
Time Series microarray experiments. BMC Bioinformatics, 9:415.
Lanza A, Cirillo N, Rossiello R, Rienzo M, Cutillo L, Casamassimi A, de Nigris F, Schiano C, Rossiello L, Femiano F, Gombos
F, Napoli C (2008) Evidence of key role of Cdk2 overexpression in pemphigus vulgaris. J Biol Chem., 283:8736-45.
Bioinformatics Core Team
Supervisor:
Diego di Bernardo
Annamaria Carissimo
Diego Carrella
Luisa Cutillo
Veer Singh Marwah
Margherita Mutarelli
Gennaro Oliva