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Home > Archives > Vol 18

Table of Contents

Entire issue

EMBnet.journal 18 Suppl. A

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The Bioinformatics Italian Society Manuela Helmer-Citterich, Paolo Romano

HTML PDF p. 3

Preface - BITS 2012: Ninth Annual Meeting of the Bioinformatics Italian Society Alfredo Ferro, Rosalba Giugno, Alfredo Pulvirenti, Domenica D'Elia, Manuela Helmer-Citterich, Paolo Romano

HTML PDF pp. 4-7

Conference Programme

PDF pp. 8-11

Keynote Lectures

Renato Dulbecco: genes, cancer and epigenomics Ileana Zucchi

PDF p. 13

On bioimage informatics and decoding genomes Eugene W. Myers

PDF p. 14

Statistical inference in high dimensional spaces of genomics: an RNA structural example Charles E. Lawrence

PDF p. 15

Oral Presentations

Next Generation Sequencing, Pharmacogenomics

Integrated cloud environment for characterization of genotype specific transcriptome from next generation sequencing data R Giugno, F Abate, N Bombieri, M Delledonne, A Ferrarini, E Ficarra, A Pulvirenti, A Acquaviva

PDF pp. 17-18

Next Generation Programming: software tools for NGS tertiary analysis U Pozzoli

PDF p. 19

Building an optimized pipeline for whole-exome sequencing M D'Antonio, P D'Onorio De Meo, B Elmi, N Sanna, G Pesole, T Castrignanò

PDF pp. 20-21

On the impact of short-reads quality on variants detection S Castellana, T Mazza

PDF pp. 22-23

Improving biomarker discovering for chemosensitivity prediction using an integrated approach A Visconti, F Cordero, RA Calogero

PDF p. 24

Systems Biology, Molecular Evolution

The location of T1 Diabetes associated SNPs in regulatory regions S Beka, I te Boekhorst, I Abnizova

PDF p. 25

Quasi-cellular systems: stochastic simulation analysis at nanoscale range L Calviello, P Stano, F Mavelli, PL Luisi, R Marangoni

PDF p. 26

An analytical spatially-based approach to study cancer cell population evolutions F Cordero, M Gribaudo, D Manini

PDF p. 27

A combined computational/experimental strategy to map phosphatases on growth pathways PF Gherardini, F Sacco, S Paoluzi, J Saez-Rodriguez, M Helmer-Citterich, A Ragnini-Wilson, L Castagnoli, G Cesareni

PDF pp. 28-29

Drug repositioning through pharmacological spaces integration based on networks projections M Re, M Mesiti, G Valentini

PDF pp. 30-31

Cyto-Sevis: semantic similarity-based visualisation of protein interaction networks PH Guzzi, M Cannataro

PDF pp. 32-33

Genomics, Transcriptomics, Protein Structure and Function

Digging in the RNA-seq garbage: evaluating the characteristics of unmapped RNA-seq reads in normal tissues M Carrara, R Calogero

PDF p. 34

Alternative splicing as regulator of protein-protein interactions A Colantoni, F Ferrè, M Helmer-Citterich

PDF p. 35

Fungal alternative splicing associates with higher cellular complexity and virulence K Grützmann, K Szafranski, M Pohl, K Voigt, A Petzold, S Schuster

PDF p. 36

Computational and experimental characterization of critical amino acidic residues in the BCR-ABL kinase domain explaining TKIS resistance in patients with chronic myeloid leukemia C Romano, P Buffa, A Pandini, M Massimino, E Tirrò, L Manzella, F Fraternali, P Vigneri

PDF p. 37

The role of transposable elements in shaping the combinatorial interaction of transcription factors A Testori, L Caizzi, S Cutrupi, O Friard, M De Bortoli, D Corà, M Caselle

PDF p. 38

Algorithms for Bioinformatics, Metagenomics

Translation of a Robust, Biology-Driven, Prognostic Classifier of Cancer Patients' Outcome into Clinically Relevant Rules D Cangelosi, M Muselli, F Blengio, R Versteeg, A Eggert, A Schramm, A Garaventa, C Gambini, L Varesio

PDF pp. 39-40

Regularized Network-Based Algorithm for Predicting Gene Functions with High-Imbalanced Data M Frasca, A Bertoni, G Valentini

PDF pp. 41-42

A novel biclustering algorithm for the discovery of meaningful biological correlations between miRNAs and mRNAs G Pio, M Ceci, D D'Elia, C Loglisci, D Malerba

PDF pp. 43-44

A bioinformatics framework for the identification of active regulatory elements through the integrative analysis of high-throughput genomic data G Malagoli Tagliazucchi, A Miccio, A Cavazza, V Poletti, C Peano, G De Bellis, F Mavillo, S Bicciato

PDF pp. 45-46

A greedy and stochastic algorithm for multiple local alignment of interaction networks G Micale, A Pulvirenti, R Giugno, A Ferro

PDF pp. 47-49

GAM: Genomic Assemblies Merger A Policriti, S Scalabrin, F Vezzi, R Vicedomini

PDF pp. 50-51

SARMA: a web resource for species assignment of high-throughput sequencing reads from metagenomics analysis M D'Antonio, D Paoletti, M Santamaria, T Castrignanò, G Pesole

PDF p. 52

Biological Databases, Biobanks

Identification of gene annotations and interactions and protein-protein interaction associated disorders through data integration A Canakoglu, P Gangi, S Gennaro, M Masseroli

PDF pp. 53-54

HUPHO: the human phosphatase portal S Liberti, A Calderone, F Sacco, L Perfetto, M Iannuccelli, S Panni, E Santonico, A Palma, AP Nardozza, L Castagnoli, G Cesareni

PDF p. 55

A Knowledge Base for fish and fishery products AM Pappalardo, F Guarino, A Messina, A Pulvirenti, R Giugno, A Ferro, V De Pinto

PDF pp. 56-57

Micro-Analyzer: a tool for automatic pre-processing of multiple Affymetrix arrays PH Guzzi, M Cannataro

PDF pp. 58-59

IGI grid services for the bioinformatics community L Gaido, M Bencivenni, D Cesini, G Donvito, P Veronesi

PDF pp. 60-61

FERMI: the most powerful computational resource for Italian scientists F Falciano, E Rossi

PDF p. 62

Posters

Algorithms for Bioinformatics

Devising and experimenting correlation-based metrics for evaluating the effectiveness of input encoding techniques in prediction tasks G Armano, E Tamponi

PDF p. 64

Core algorithms to search in biological structured data V Bonnici, R Giugno, A Pulvirenti, D Shasha, A Ferro

PDF pp. 65-66

Truncated SVD best rank choice through ROC curves for genomic annotation prediction D Chicco, M Masseroli

PDF p. 67

New metaheuristics approaches for biclustering of gene expression Data F Musacchia, A Marabotti, A Facchiano, L Milanesi, P. Festa

PDF p. 68

Identification, reconstruction and validation of insertions in resequencing projects with GapFiller F Nadalin, F Vezzi, S Scalabrin, A Policriti

PDF p. 69

Biological Databases

CytokineDB and CytReD@CROM S Costantini, A Sharma, R Raucci, F Capone, M Miele, E Guerriero, G Castello, M Di Stasio, G Colonna

PDF p. 70

VIRES: visualization and identification of A-to-I RNA editing sites in genomic sequences R Distefano, G Nigita, V Macca, R Giugno, A Pulvirenti, A Ferro

PDF pp. 71-72

SpliceAid-F: a database of human splicing factors and their RNA binding sites M Giulietti, F Piva, M D'Antonio, P D'Onorio De Meo, T Castrignanò, G Pavesi, G Pesole

PDF pp. 73-74

An integrated system for mining relations among microRNAs, drugs and phenotypes A Pulvirenti, R Giugno, S Di Bella, G Nigita, V Macca, A Giummarra, D Garofalo, G Caruso, V Bonnici, A Ferro

PDF pp. 75-76

A comprehensive 16 loci-based DNA fingerprinting dataset of a broad tumor cell line panel for cancer research A Somaschini, E Scacheri, A Nuzzo, N Amboldi, D Ballinari, G Ukmar, A Isacchi, R Bosotti

PDF pp. 77-78

An interactive tool enabling a comparative analysis of STR profiles G Ukmar, R Bosotti, A Somaschini, J Malysko, L Raddrizzani, G Masetti, E Scacheri, A Isacchi, A Nuzzo

PDF p. 79

OsteoChondroDB: a database about biomolecular chondral- bone development in physiological and diseased conditions F Viti, I Merelli, L Milanesi

PDF pp. 80-81

Comparative Genomics

NumtS footsteps from the past: an interbreed between eukaryotic nucleus and the mitochondrion FM Calabrese, DL Balacco, D Simone, M Attimonelli

PDF p. 82

In silico prediction of virus-derived small interfering RNAs and their putative host messenger targets in Solanum lycopersicum infected by different potato virus Y isolates D Catalano, F Cillo, M Finetti-Sialer

PDF pp. 83-84

Plasmodium phylogenetic profile: an assessment of a predictive tool for protein-protein interactions G Sferra, D Santoni, E Pizzi

PDF p. 85

Genomics

Role of alternative splicing in modulating protein-protein interactions V Bianchi, A Colantoni, M Helmer-Citterich, F Ferrè

PDF pp. 86-87

GC content dependency of open reading frame prediction M Pohl, G Theißen, S Schuster

PDF p. 88

Whole genome sequencing, assembly and annotation of Halomonas smyrnensis, a levan producing halophilic bacterium E Sogutcu, Z Emrence, M Arikan, A Cakiris, N Abaci, E Toksoy Oner, D Ustek, KY Arga

PDF p. 89

Metagenomics

ITSoneDB: a specialized ITS1 database for amplicon-based metagenomic characterization of environmental fungal communities B Fosso, M Santamaria, A Consiglio, G De Caro, G Grillo, F Licciuli, S Liuni, M Marzano, G Pesole

PDF p. 90

Molecular Evolution

Towards an integrated resource for the study of population and disease associated variability of the human mitochondrial genome MA Diroma, M Attimonelli

PDF p. 91

Analysis of barcode sequences by means of compression-based methods M La Rosa, A Fiannaca, R Rizzo, A Urso

PDF p. 92

Next Generation Sequencing

NGS TREX: next generation sequences transcriptome profile explorer I Boria, G Pesole, F Mignone

PDF p. 93

Integrated analysis of epigenetic and transcriptional circuits in gliomagenesis G Bucci, E Signaroldi, P Laise, P-L Germain, L Zammataro, H Muller, G Testa

PDF pp. 94-95

A next generation sequencing-based approach to identify piRNAs in breast cancer cells C Cantarella, C Stellato, G Giurato, MR De Filippo, R Tarallo, A Weisz

PDF pp. 96-97

Development of pipeline for exome sequencing data analysis MR De Filippo, G Giurato, C Cantarella, F Rizzo, F Cirillo, A Weisz

PDF p. 98

RNA sequencing data: biases and normalization F Finotello, E Lavezzo, L Barzon, P Fontana, A Si-Ammour, S Toppo, B Di Camillo

PDF p. 99

An accurate pipeline for analysis of NGS data of small non-coding RNA G Giurato, MR De Filippo, C Cantarella, G Nassa, M Ravo, E Nola, A Weisz

PDF pp. 100-101

Analysis workflow for the identification allelic variants associated with rare disorders using whole genome sequencing approach V Maselli, D Cittaro, E Stupka

PDF p. 102

A software pipeline for the discovery of variations in exome sequencing projects E Mattei, PF Gherardini, G Ausiello, M Helmer-Citterich

PDF pp. 103-104

De novo detection of A-To-I RNA editing sites in human mRNAs by massive transcriptome sequencing E Picardi, A Gallo, S Raho, F Galeano, G Pesole

PDF p. 105

AnnotateGenomicRegions: a Web application L Zammataro, G Bucci, H Muller

PDF p. 106

Protein Structure and Function

Molecular dynamics simulations reveal the role of five BCR-ABL kinase domain critical residues in TKIS binding P Buffa, C Romano, A Pandini, P Vigneri, F Fraternali

PDF p. 107

Identification and analysis of conserved pockets on protein surfaces M Cammisa, A Correra, T Fioriello, G Andreotti, MV Cubellis

PDF p. 108

A structure based pattern recognition on antibodies D Corrada, G Morra, G Colombo

PDF pp. 109-110

Structural studies on the CXCR7 decoy receptor T De Vero, S Costantini, G Colonna

PDF pp. 111-112

Modeling and protein function prediction of truncated form of Geobacillus thermocatenulatus lipase (BTL2) MA Ghafouri, AA Karkhane, MR Azimi, B Yakhchali, N Goudarzi

PDF p. 113

Analysis of molecular recognition features in membrane proteins I Kotta-Loizou, GN Tsaousis, SJ Hamodrakas

PDF p. 114

Assessment of structure-based functional annotation methods on protein 3D models I Mangone, M Helmer-Citterich, G Ausiello

PDF p. 115

Application of computational methods for structural and functional characterization of mutants of GALT enzyme A Marabotti, A Facchiano, L Milanesi, M Tang, K Lai

PDF pp. 116-117

Identification of molecular targets for mycotoxins related to autism development A Marabotti, M Landini, A Mezzelani, L Milanesi, ME Raggi

PDF pp. 118-119

Domain-context information for the improvement of phosphorylation site prediction A Palmeri, M Helmer-Citterich, PF Gherardini

PDF pp. 120-121

Computer modeling of human delta opioid receptor F Sapundzhi, T Dzimbova, N Pencheva, P Milanov

PDF p. 122

Cooperative fluctuations of PTP1B by an elastic network model analysis AC Serdaroglu, AN Ozer

PDF p. 123

Use of BioBlender for all atom morphing of protein structures MF Zini, Y Porozov, T Loni, R Andrei, M Zoppè

PDF p. 124

Proteomics

Geena, a tool for MS spectra filtering, averaging and aligning P Romano, A Profumo, R Mangerini, F Ferri, M Rocco, F Boccardo, A Facchiano

PDF pp. 125-126

Systems Biology

Topological analysis of co-expression networks in neoplastic tissues R Anglani, TM Creanza, VC Liuzzi, PF Stifanelli, R Maglietta, A Piepoli, S Mukherjee, FP Schena, N Ancona

PDF p. 127

mentha: the interactome browser A Calderone, G Cesareni

PDF p. 128

miRNA-mRNA integrated pathway analysis: an application to colorectal cancer TM Creanza, R Maglietta, VC Liuzzi, R Anglani, PF Stifanelli, A Piepoli, S Mukherjee, FP Schena, N Ancona

PDF p. 129

Transcriptomics

Discovery of conserved long non-coding RNAs in vertebrates S Basu, R Sanges

PDF pp. 130-131

Non-coding RNA bioinformatics platform for full backing of the high-throughput sequencing experiments generated by next-generation sequencing technologies F Licciulli, A Consiglio, G De Caro, A Gisel, G Grillo, A Tulipano, S Liuni

PDF pp. 132-133

An improved procedure for clustering and assembly of large transcriptome data E Picardi, V Bevilacqua, F Stoppa, G Pesole

PDF p. 134

miRandola: extracellular circulating microRNAs database F Russo, S Di Bella, G Nigita, V Macca, A Laganà, R Giugno, A Pulvirenti, A Ferro

PDF p. 135