Vol. 18: Supplement A

Entire issue

• EMBnet.journal 18 Suppl. A

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• The Bioinformatics Italian Society

  p. 3

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• Preface - BITS 2012: Ninth Annual Meeting of the Bioinformatics Italian Society

  pp. 4-7

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• Conference Programme

  pp. 8-11

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Keynote Lectures

• Renato Dulbecco: genes, cancer and epigenomics

  Ileana Zucchi

  p. 13

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• On bioimage informatics and decoding genomes

  Eugene W. Myers

  p. 14

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• Statistical inference in high dimensional spaces of genomics: an RNA structural example

  Charles E. Lawrence

  p. 15

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Oral Presentations

• Next Generation Sequencing, Pharmacogenomics

  EMBnet journal

• 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

  pp. 17-18

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• Next Generation Programming: software tools for NGS tertiary analysis

  U Pozzoli

  p. 19

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• Building an optimized pipeline for whole-exome sequencing

  M D'Antonio, P D'Onorio De Meo, B Elmi, N Sanna, G Pesole, T Castrignanò

  pp. 20-21

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• On the impact of short-reads quality on variants detection

  S Castellana, T Mazza

  pp. 22-23

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• Improving biomarker discovering for chemosensitivity prediction using an integrated approach

  A Visconti, F Cordero, RA Calogero

  p. 24

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• Systems Biology, Molecular Evolution

  EMBnet journal

• The location of T1 Diabetes associated SNPs in regulatory regions

  S Beka, I te Boekhorst, I Abnizova

  p. 25

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• Quasi-cellular systems: stochastic simulation analysis at nanoscale range

  L Calviello, P Stano, F Mavelli, PL Luisi, R Marangoni

  p. 26

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• An analytical spatially-based approach to study cancer cell population evolutions

  F Cordero, M Gribaudo, D Manini

  p. 27

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• 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

  pp. 28-29

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• Drug repositioning through pharmacological spaces integration based on networks projections

  M Re, M Mesiti, G Valentini

  pp. 30-31

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• Cyto-Sevis: semantic similarity-based visualisation of protein interaction networks

  PH Guzzi, M Cannataro

  pp. 32-33

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• Genomics, Transcriptomics, Protein Structure and Function

  EMBnet journal

• Digging in the RNA-seq garbage: evaluating the characteristics of unmapped RNA-seq reads in normal tissues

  M Carrara, R Calogero

  p. 34

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• Alternative splicing as regulator of protein-protein interactions

  A Colantoni, F Ferrè, M Helmer-Citterich

  p. 35

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• Fungal alternative splicing associates with higher cellular complexity and virulence

  K Grützmann, K Szafranski, M Pohl, K Voigt, A Petzold, S Schuster

  p. 36

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• 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

  p. 37

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• 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

  p. 38

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• Algorithms for Bioinformatics, Metagenomics

  EMBnet journal

• 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

  pp. 39-40

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• Regularized Network-Based Algorithm for Predicting Gene Functions with High-Imbalanced Data

  M Frasca, A Bertoni, G Valentini

  pp. 41-42

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• 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

  pp. 43-44

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• 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

  pp. 45-46

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• A greedy and stochastic algorithm for multiple local alignment of interaction networks

  G Micale, A Pulvirenti, R Giugno, A Ferro

  pp. 47-49

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• GAM: Genomic Assemblies Merger

  A Policriti, S Scalabrin, F Vezzi, R Vicedomini

  pp. 50-51

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• 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

  p. 52

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• Biological Databases, Biobanks

  EMBnet journal

• Identification of gene annotations and interactions and protein-protein interaction associated disorders through data integration

  A Canakoglu, P Gangi, S Gennaro, M Masseroli

  pp. 53-54

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• 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

  p. 55

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• A Knowledge Base for fish and fishery products

  AM Pappalardo, F Guarino, A Messina, A Pulvirenti, R Giugno, A Ferro, V De Pinto

  pp. 56-57

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• Micro-Analyzer: a tool for automatic pre-processing of multiple Affymetrix arrays

  PH Guzzi, M Cannataro

  pp. 58-59

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• IGI grid services for the bioinformatics community

  L Gaido, M Bencivenni, D Cesini, G Donvito, P Veronesi

  pp. 60-61

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• FERMI: the most powerful computational resource for Italian scientists

  F Falciano, E Rossi

  p. 62

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Posters

• Algorithms for Bioinformatics

  EMBnet journal

• Devising and experimenting correlation-based metrics for evaluating the effectiveness of input encoding techniques in prediction tasks

  G Armano, E Tamponi

  p. 64

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• Core algorithms to search in biological structured data

  V Bonnici, R Giugno, A Pulvirenti, D Shasha, A Ferro

  pp. 65-66

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• Truncated SVD best rank choice through ROC curves for genomic annotation prediction

  D Chicco, M Masseroli

  p. 67

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• New metaheuristics approaches for biclustering of gene expression Data

  F Musacchia, A Marabotti, A Facchiano, L Milanesi, P. Festa

  p. 68

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• Identification, reconstruction and validation of insertions in resequencing projects with GapFiller

  F Nadalin, F Vezzi, S Scalabrin, A Policriti

  p. 69

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• Biological Databases

  EMBnet journal

• CytokineDB and CytReD@CROM

  S Costantini, A Sharma, R Raucci, F Capone, M Miele, E Guerriero, G Castello, M Di Stasio, G Colonna

  p. 70

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• 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

  pp. 71-72

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• 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

  pp. 73-74

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• 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

  pp. 75-76

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• 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

  pp. 77-78

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• 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

  p. 79

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• OsteoChondroDB: a database about biomolecular chondral- bone development in physiological and diseased conditions

  F Viti, I Merelli, L Milanesi

  pp. 80-81

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• Comparative Genomics

  EMBnet journal

• NumtS footsteps from the past: an interbreed between eukaryotic nucleus and the mitochondrion

  FM Calabrese, DL Balacco, D Simone, M Attimonelli

  p. 82

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• 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

  pp. 83-84

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• Plasmodium phylogenetic profile: an assessment of a predictive tool for protein-protein interactions

  G Sferra, D Santoni, E Pizzi

  p. 85

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• Genomics

  EMBnet journal

• Role of alternative splicing in modulating protein-protein interactions

  V Bianchi, A Colantoni, M Helmer-Citterich, F Ferrè

  pp. 86-87

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• GC content dependency of open reading frame prediction

  M Pohl, G Theißen, S Schuster

  p. 88

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• 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

  p. 89

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• Metagenomics

  EMBnet journal

• 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

  p. 90

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• Molecular Evolution

  EMBnet journal

• Towards an integrated resource for the study of population and disease associated variability of the human mitochondrial genome

  MA Diroma, M Attimonelli

  p. 91

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• Analysis of barcode sequences by means of compression-based methods

  M La Rosa, A Fiannaca, R Rizzo, A Urso

  p. 92

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• Next Generation Sequencing

  EMBnet journal

• NGS TREX: next generation sequences transcriptome profile explorer

  I Boria, G Pesole, F Mignone

  p. 93

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• Integrated analysis of epigenetic and transcriptional circuits in gliomagenesis

  G Bucci, E Signaroldi, P Laise, P-L Germain, L Zammataro, H Muller, G Testa

  pp. 94-95

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• 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

  pp. 96-97

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• Development of pipeline for exome sequencing data analysis

  MR De Filippo, G Giurato, C Cantarella, F Rizzo, F Cirillo, A Weisz

  p. 98

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• RNA sequencing data: biases and normalization

  F Finotello, E Lavezzo, L Barzon, P Fontana, A Si-Ammour, S Toppo, B Di Camillo

  p. 99

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• 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

  pp. 100-101

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• Analysis workflow for the identification allelic variants associated with rare disorders using whole genome sequencing approach

  V Maselli, D Cittaro, E Stupka

  p. 102

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• A software pipeline for the discovery of variations in exome sequencing projects

  E Mattei, PF Gherardini, G Ausiello, M Helmer-Citterich

  pp. 103-104

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• 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

  p. 105

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• AnnotateGenomicRegions: a Web application

  L Zammataro, G Bucci, H Muller

  p. 106

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• Protein Structure and Function

  EMBnet journal

• 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

  p. 107

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• Identification and analysis of conserved pockets on protein surfaces

  M Cammisa, A Correra, T Fioriello, G Andreotti, MV Cubellis

  p. 108

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• A structure based pattern recognition on antibodies

  D Corrada, G Morra, G Colombo

  pp. 109-110

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• Structural studies on the CXCR7 decoy receptor

  T De Vero, S Costantini, G Colonna

  pp. 111-112

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• Modeling and protein function prediction of truncated form of Geobacillus thermocatenulatus lipase (BTL2)

  MA Ghafouri, AA Karkhane, MR Azimi, B Yakhchali, N Goudarzi

  p. 113

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• Analysis of molecular recognition features in membrane proteins

  I Kotta-Loizou, GN Tsaousis, SJ Hamodrakas

  p. 114

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• Assessment of structure-based functional annotation methods on protein 3D models

  I Mangone, M Helmer-Citterich, G Ausiello

  p. 115

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• Application of computational methods for structural and functional characterization of mutants of GALT enzyme

  A Marabotti, A Facchiano, L Milanesi, M Tang, K Lai

  pp. 116-117

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• Identification of molecular targets for mycotoxins related to autism development

  A Marabotti, M Landini, A Mezzelani, L Milanesi, ME Raggi

  pp. 118-119

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• Domain-context information for the improvement of phosphorylation site prediction

  A Palmeri, M Helmer-Citterich, PF Gherardini

  pp. 120-121

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• Computer modeling of human delta opioid receptor

  F Sapundzhi, T Dzimbova, N Pencheva, P Milanov

  p. 122

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• Cooperative fluctuations of PTP1B by an elastic network model analysis

  AC Serdaroglu, AN Ozer

  p. 123

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• Use of BioBlender for all atom morphing of protein structures

  MF Zini, Y Porozov, T Loni, R Andrei, M Zoppè

  p. 124

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• Proteomics

  EMBnet journal

• Geena, a tool for MS spectra filtering, averaging and aligning

  P Romano, A Profumo, R Mangerini, F Ferri, M Rocco, F Boccardo, A Facchiano

  pp. 125-126

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• Systems Biology

  EMBnet journal

• 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

  p. 127

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• mentha: the interactome browser

  A Calderone, G Cesareni

  p. 128

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• 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

  p. 129

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• Transcriptomics

  EMBnet journal

• Discovery of conserved long non-coding RNAs in vertebrates

  S Basu, R Sanges

  pp. 130-131

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• 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

  pp. 132-133

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• An improved procedure for clustering and assembly of large transcriptome data

  E Picardi, V Bevilacqua, F Stoppa, G Pesole

  p. 134

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• miRandola: extracellular circulating microRNAs database

  F Russo, S Di Bella, G Nigita, V Macca, A Laganà, R Giugno, A Pulvirenti, A Ferro

  p. 135

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