Vol 18

Supplement A

Table of Contents

Entire issue

EMBnet.journal 18 Suppl. A PDF
The Bioinformatics Italian Society HTML PDF
Manuela Helmer-Citterich, Paolo Romano p. 3
Preface - BITS 2012: Ninth Annual Meeting of the Bioinformatics Italian Society HTML PDF
Alfredo Ferro, Rosalba Giugno, Alfredo Pulvirenti, Domenica D'Elia, Manuela Helmer-Citterich, Paolo Romano pp. 4-7
Conference Programme PDF
  pp. 8-11

Keynote Lectures

Renato Dulbecco: genes, cancer and epigenomics PDF
Ileana Zucchi p. 13
On bioimage informatics and decoding genomes PDF
Eugene W. Myers p. 14
Statistical inference in high dimensional spaces of genomics: an RNA structural example PDF
Charles E. Lawrence p. 15

Oral Presentations

Next Generation Sequencing, Pharmacogenomics
Integrated cloud environment for characterization of genotype specific transcriptome from next generation sequencing data PDF
R Giugno, F Abate, N Bombieri, M Delledonne, A Ferrarini, E Ficarra, A Pulvirenti, A Acquaviva pp. 17-18
Next Generation Programming: software tools for NGS tertiary analysis PDF
U Pozzoli p. 19
Building an optimized pipeline for whole-exome sequencing PDF
M D'Antonio, P D'Onorio De Meo, B Elmi, N Sanna, G Pesole, T Castrignanò pp. 20-21
On the impact of short-reads quality on variants detection PDF
S Castellana, T Mazza pp. 22-23
Improving biomarker discovering for chemosensitivity prediction using an integrated approach PDF
A Visconti, F Cordero, RA Calogero p. 24

Systems Biology, Molecular Evolution
The location of T1 Diabetes associated SNPs in regulatory regions PDF
S Beka, I te Boekhorst, I Abnizova p. 25
Quasi-cellular systems: stochastic simulation analysis at nanoscale range PDF
L Calviello, P Stano, F Mavelli, PL Luisi, R Marangoni p. 26
An analytical spatially-based approach to study cancer cell population evolutions PDF
F Cordero, M Gribaudo, D Manini p. 27
A combined computational/experimental strategy to map phosphatases on growth pathways PDF
PF Gherardini, F Sacco, S Paoluzi, J Saez-Rodriguez, M Helmer-Citterich, A Ragnini-Wilson, L Castagnoli, G Cesareni pp. 28-29
Drug repositioning through pharmacological spaces integration based on networks projections PDF
M Re, M Mesiti, G Valentini pp. 30-31
Cyto-Sevis: semantic similarity-based visualisation of protein interaction networks PDF
PH Guzzi, M Cannataro 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 PDF
M Carrara, R Calogero p. 34
Alternative splicing as regulator of protein-protein interactions PDF
A Colantoni, F Ferrè, M Helmer-Citterich p. 35
Fungal alternative splicing associates with higher cellular complexity and virulence PDF
K Grützmann, K Szafranski, M Pohl, K Voigt, A Petzold, S Schuster 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 PDF
C Romano, P Buffa, A Pandini, M Massimino, E Tirrò, L Manzella, F Fraternali, P Vigneri p. 37
The role of transposable elements in shaping the combinatorial interaction of transcription factors PDF
A Testori, L Caizzi, S Cutrupi, O Friard, M De Bortoli, D Corà, M Caselle p. 38

Algorithms for Bioinformatics, Metagenomics
Translation of a Robust, Biology-Driven, Prognostic Classifier of Cancer Patients' Outcome into Clinically Relevant Rules PDF
D Cangelosi, M Muselli, F Blengio, R Versteeg, A Eggert, A Schramm, A Garaventa, C Gambini, L Varesio pp. 39-40
Regularized Network-Based Algorithm for Predicting Gene Functions with High-Imbalanced Data PDF
M Frasca, A Bertoni, G Valentini pp. 41-42
A novel biclustering algorithm for the discovery of meaningful biological correlations between miRNAs and mRNAs PDF
G Pio, M Ceci, D D'Elia, C Loglisci, D Malerba pp. 43-44
A bioinformatics framework for the identification of active regulatory elements through the integrative analysis of high-throughput genomic data PDF
G Malagoli Tagliazucchi, A Miccio, A Cavazza, V Poletti, C Peano, G De Bellis, F Mavillo, S Bicciato pp. 45-46
A greedy and stochastic algorithm for multiple local alignment of interaction networks PDF
G Micale, A Pulvirenti, R Giugno, A Ferro pp. 47-49
GAM: Genomic Assemblies Merger PDF
A Policriti, S Scalabrin, F Vezzi, R Vicedomini pp. 50-51
SARMA: a web resource for species assignment of high-throughput sequencing reads from metagenomics analysis PDF
M D'Antonio, D Paoletti, M Santamaria, T Castrignanò, G Pesole p. 52

Biological Databases, Biobanks
Identification of gene annotations and interactions and protein-protein interaction associated disorders through data integration PDF
A Canakoglu, P Gangi, S Gennaro, M Masseroli pp. 53-54
HUPHO: the human phosphatase portal PDF
S Liberti, A Calderone, F Sacco, L Perfetto, M Iannuccelli, S Panni, E Santonico, A Palma, AP Nardozza, L Castagnoli, G Cesareni p. 55
A Knowledge Base for fish and fishery products PDF
AM Pappalardo, F Guarino, A Messina, A Pulvirenti, R Giugno, A Ferro, V De Pinto pp. 56-57
Micro-Analyzer: a tool for automatic pre-processing of multiple Affymetrix arrays PDF
PH Guzzi, M Cannataro pp. 58-59
IGI grid services for the bioinformatics community PDF
L Gaido, M Bencivenni, D Cesini, G Donvito, P Veronesi pp. 60-61
FERMI: the most powerful computational resource for Italian scientists PDF
F Falciano, E Rossi p. 62


Algorithms for Bioinformatics
Devising and experimenting correlation-based metrics for evaluating the effectiveness of input encoding techniques in prediction tasks PDF
G Armano, E Tamponi p. 64
Core algorithms to search in biological structured data PDF
V Bonnici, R Giugno, A Pulvirenti, D Shasha, A Ferro pp. 65-66
Truncated SVD best rank choice through ROC curves for genomic annotation prediction PDF
D Chicco, M Masseroli p. 67
New metaheuristics approaches for biclustering of gene expression Data PDF
F Musacchia, A Marabotti, A Facchiano, L Milanesi, P. Festa p. 68
Identification, reconstruction and validation of insertions in resequencing projects with GapFiller PDF
F Nadalin, F Vezzi, S Scalabrin, A Policriti p. 69

Biological Databases
CytokineDB and CytReD@CROM PDF
S Costantini, A Sharma, R Raucci, F Capone, M Miele, E Guerriero, G Castello, M Di Stasio, G Colonna p. 70
VIRES: visualization and identification of A-to-I RNA editing sites in genomic sequences PDF
R Distefano, G Nigita, V Macca, R Giugno, A Pulvirenti, A Ferro pp. 71-72
SpliceAid-F: a database of human splicing factors and their RNA binding sites PDF
M Giulietti, F Piva, M D'Antonio, P D'Onorio De Meo, T Castrignanò, G Pavesi, G Pesole pp. 73-74
An integrated system for mining relations among microRNAs, drugs and phenotypes PDF
A Pulvirenti, R Giugno, S Di Bella, G Nigita, V Macca, A Giummarra, D Garofalo, G Caruso, V Bonnici, A Ferro pp. 75-76
A comprehensive 16 loci-based DNA fingerprinting dataset of a broad tumor cell line panel for cancer research PDF
A Somaschini, E Scacheri, A Nuzzo, N Amboldi, D Ballinari, G Ukmar, A Isacchi, R Bosotti pp. 77-78
An interactive tool enabling a comparative analysis of STR profiles PDF
G Ukmar, R Bosotti, A Somaschini, J Malysko, L Raddrizzani, G Masetti, E Scacheri, A Isacchi, A Nuzzo p. 79
OsteoChondroDB: a database about biomolecular chondral- bone development in physiological and diseased conditions PDF
F Viti, I Merelli, L Milanesi pp. 80-81

Comparative Genomics
NumtS footsteps from the past: an interbreed between eukaryotic nucleus and the mitochondrion PDF
FM Calabrese, DL Balacco, D Simone, M Attimonelli 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 PDF
D Catalano, F Cillo, M Finetti-Sialer pp. 83-84
Plasmodium phylogenetic profile: an assessment of a predictive tool for protein-protein interactions PDF
G Sferra, D Santoni, E Pizzi p. 85

Role of alternative splicing in modulating protein-protein interactions PDF
V Bianchi, A Colantoni, M Helmer-Citterich, F Ferrè pp. 86-87
GC content dependency of open reading frame prediction PDF
M Pohl, G Theißen, S Schuster p. 88
Whole genome sequencing, assembly and annotation of Halomonas smyrnensis, a levan producing halophilic bacterium PDF
E Sogutcu, Z Emrence, M Arikan, A Cakiris, N Abaci, E Toksoy Oner, D Ustek, KY Arga p. 89

ITSoneDB: a specialized ITS1 database for amplicon-based metagenomic characterization of environmental fungal communities PDF
B Fosso, M Santamaria, A Consiglio, G De Caro, G Grillo, F Licciuli, S Liuni, M Marzano, G Pesole p. 90

Molecular Evolution
Towards an integrated resource for the study of population and disease associated variability of the human mitochondrial genome PDF
MA Diroma, M Attimonelli p. 91
Analysis of barcode sequences by means of compression-based methods PDF
M La Rosa, A Fiannaca, R Rizzo, A Urso p. 92

Next Generation Sequencing
NGS TREX: next generation sequences transcriptome profile explorer PDF
I Boria, G Pesole, F Mignone p. 93
Integrated analysis of epigenetic and transcriptional circuits in gliomagenesis PDF
G Bucci, E Signaroldi, P Laise, P-L Germain, L Zammataro, H Muller, G Testa pp. 94-95
A next generation sequencing-based approach to identify piRNAs in breast cancer cells PDF
C Cantarella, C Stellato, G Giurato, MR De Filippo, R Tarallo, A Weisz pp. 96-97
Development of pipeline for exome sequencing data analysis PDF
MR De Filippo, G Giurato, C Cantarella, F Rizzo, F Cirillo, A Weisz p. 98
RNA sequencing data: biases and normalization PDF
F Finotello, E Lavezzo, L Barzon, P Fontana, A Si-Ammour, S Toppo, B Di Camillo p. 99
An accurate pipeline for analysis of NGS data of small non-coding RNA PDF
G Giurato, MR De Filippo, C Cantarella, G Nassa, M Ravo, E Nola, A Weisz pp. 100-101
Analysis workflow for the identification allelic variants associated with rare disorders using whole genome sequencing approach PDF
V Maselli, D Cittaro, E Stupka p. 102
A software pipeline for the discovery of variations in exome sequencing projects PDF
E Mattei, PF Gherardini, G Ausiello, M Helmer-Citterich pp. 103-104
De novo detection of A-To-I RNA editing sites in human mRNAs by massive transcriptome sequencing PDF
E Picardi, A Gallo, S Raho, F Galeano, G Pesole p. 105
AnnotateGenomicRegions: a Web application PDF
L Zammataro, G Bucci, H Muller p. 106

Protein Structure and Function
Molecular dynamics simulations reveal the role of five BCR-ABL kinase domain critical residues in TKIS binding PDF
P Buffa, C Romano, A Pandini, P Vigneri, F Fraternali p. 107
Identification and analysis of conserved pockets on protein surfaces PDF
M Cammisa, A Correra, T Fioriello, G Andreotti, MV Cubellis p. 108
A structure based pattern recognition on antibodies PDF
D Corrada, G Morra, G Colombo pp. 109-110
Structural studies on the CXCR7 decoy receptor PDF
T De Vero, S Costantini, G Colonna pp. 111-112
Modeling and protein function prediction of truncated form of Geobacillus thermocatenulatus lipase (BTL2) PDF
MA Ghafouri, AA Karkhane, MR Azimi, B Yakhchali, N Goudarzi p. 113
Analysis of molecular recognition features in membrane proteins PDF
I Kotta-Loizou, GN Tsaousis, SJ Hamodrakas p. 114
Assessment of structure-based functional annotation methods on protein 3D models PDF
I Mangone, M Helmer-Citterich, G Ausiello p. 115
Application of computational methods for structural and functional characterization of mutants of GALT enzyme PDF
A Marabotti, A Facchiano, L Milanesi, M Tang, K Lai pp. 116-117
Identification of molecular targets for mycotoxins related to autism development PDF
A Marabotti, M Landini, A Mezzelani, L Milanesi, ME Raggi pp. 118-119
Domain-context information for the improvement of phosphorylation site prediction PDF
A Palmeri, M Helmer-Citterich, PF Gherardini pp. 120-121
Computer modeling of human delta opioid receptor PDF
F Sapundzhi, T Dzimbova, N Pencheva, P Milanov p. 122
Cooperative fluctuations of PTP1B by an elastic network model analysis PDF
AC Serdaroglu, AN Ozer p. 123
Use of BioBlender for all atom morphing of protein structures PDF
MF Zini, Y Porozov, T Loni, R Andrei, M Zoppè p. 124

Geena, a tool for MS spectra filtering, averaging and aligning PDF
P Romano, A Profumo, R Mangerini, F Ferri, M Rocco, F Boccardo, A Facchiano pp. 125-126

Systems Biology
Topological analysis of co-expression networks in neoplastic tissues PDF
R Anglani, TM Creanza, VC Liuzzi, PF Stifanelli, R Maglietta, A Piepoli, S Mukherjee, FP Schena, N Ancona p. 127
mentha: the interactome browser PDF
A Calderone, G Cesareni p. 128
miRNA-mRNA integrated pathway analysis: an application to colorectal cancer PDF
TM Creanza, R Maglietta, VC Liuzzi, R Anglani, PF Stifanelli, A Piepoli, S Mukherjee, FP Schena, N Ancona p. 129

Discovery of conserved long non-coding RNAs in vertebrates PDF
S Basu, R Sanges pp. 130-131
Non-coding RNA bioinformatics platform for full backing of the high-throughput sequencing experiments generated by next-generation sequencing technologies PDF
F Licciulli, A Consiglio, G De Caro, A Gisel, G Grillo, A Tulipano, S Liuni pp. 132-133
An improved procedure for clustering and assembly of large transcriptome data PDF
E Picardi, V Bevilacqua, F Stoppa, G Pesole p. 134
miRandola: extracellular circulating microRNAs database PDF
F Russo, S Di Bella, G Nigita, V Macca, A Laganà, R Giugno, A Pulvirenti, A Ferro p. 135

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ISSN: 2226-6089