EMBnet.journal

• Home
• About
• Login
• Register
• Search
• Current
• Archives
• Announcements
• Books For Review
• Archives (EMBnet.news)
• Submission
• Contact

Home > Archives > Vol 18

Table of Contents

Entire issue

EMBnet.journal 18 Suppl. B

PDF

ARTICLES

Editorial

HTML PDF p. 2

BITS Introduction

HTML PDF p. 3

Preface - NETTAB 2012 Workshop on “Integrated Bio-Search” Marco Masseroli, Paolo Romano, Frédérique Lisacek

HTML PDF pp. 4-7

Scientific Programme

PDF pp. 8-11

Keynote Lectures

Integration and analysis of multi-type high-throughput data for biomolecular knowledge discovery Erik Bongcam-Rudloff

PDF p. 13

Semantics based biomedical knowledge search, integration and discovery Barend Mons

PDF p. 14

Clinical and genomic data integration in support of biomedical research and clinical practice Eric Neumann

PDF p. 15

Tutorials

Multi-scale data integration and virtual exploration from promoters, through networks to drug targets Alexander Kel

PDF p. 17

The Taverna Workbench: Integrating and analysing biological and clinical data with computerised workflows Katy Wolstencroft

PDF p. 18

Oral Communications

Rational design of organelle compartments in cells Claudio Angione, Giovanni Carapezza, Jole Costanza, Pietro Lió, Giuseppe Nicosia

PDF pp. 20-22

Filtering with alignment free distances for high throughput DNA reads assembly Maria C De Cola, Giovanni Felici, Daniele Santoni, Emanuel Weitschek

PDF pp. 23-25

A semantic collaborative system for the management of translational research projects Matteo Gabetta, Giuseppe Milani, Cristiana Larizza, Valentina Favalli, Eloisa Arbustini, Riccardo Bellazzi

PDF pp. 26-28

Answering Gene Ontology terms to proteomics questions by supervised macro reading in Medline Julien Gobeill, Emilie Pasche, Douglas Teodoro, Anne-Lise Veuthey, Patrick Ruch

PDF pp. 29-31

Using graph theory to analyze gene network coherence Francisco Gómez-Vela, Norberto Díaz-Díaz, José A Lagares, José A Sánchez, Jesús S Aguilar-Ruiz

PDF pp. 32-34

The open source ISA software suite and its international user community: knowledge management of experimental data Alejandra González-Beltrán, Eamonn Maguire, Philippe Rocca-Serra, Susanna-Assunta Sansone

PDF pp. 35-37

Network-based gene-disease prioritization using PROPHNET Víctor Martínez, Carlos Cano, Armando Blanco

PDF pp. 38-40

QTreds: a flexible LIMS for omics laboratories Piergiorgio Palla, Gianfranco Frau, Laura Vargiu, Patricia Rodriguez-Tomé

PDF pp. 41-43

Development of a text search engine for medicinal chemistry patents Emilie Pasche, Julien Gobeill, Fatma Oezdemir-Zaech, Therese Vachon, Christian Lovis, Patrick Ruch

PDF pp. 44-46

The ontogene system: an advanced information extraction application for biological literature Fabio Rinaldi

PDF pp. 47-49

IntelliGenWiki: An Intelligent Semantic Wiki for Life Sciences Bahar Sateli, Marie-Jean Meurs, Greg Butler, Justin Powlowski, Adrian Tsang, René Witte

PDF pp. 50-52

ROCK: a resource for integrative breast cancer data analysis Saif Ur-Rehman, Costas Mitsopoulos, Marketa Zvelebil

PDF pp. 53-54

Technological Industrial Communications

Extracting knowledge from biomedical data through Logic Learning Machines and Rulex Marco Muselli

PDF pp. 56-58

Data modeling: the key to biological data integration François Rechenmann

PDF pp. 59-60

Short Oral Communications

BioQuery-ASP: querying biomedical databases and ontologies using answer set programming Esra Erdem, Umut Oztok

PDF pp. 62-64

A strategy to reduce technical variability and bias in RNA sequencing data Francesca Finotello, Enrico Lavezzo, Luisa Barzon, Paolo Mazzon, Paolo Fontana, Stefano Toppo, Barbara Di Camillo

PDF pp. 65-67

Applications of a generic model of genomic variations functional analysis Sarah Mapelli, Uberto Pozzoli

PDF pp. 68-70

Ranking-aware integration and explorative search of distributed bio-data Marco Masseroli, Matteo Picozzi, Giorgio Ghisalberti

PDF pp. 71-73

DiGSNP: a web tool for Disease-Gene-SNP hierarchical prioritization Carmen Navarro, Carlos Cano, Armando Blanco, Fernando García-Alcalde

PDF pp. 74-76

The BioVel Project: Robust phylogenetic workflows running on the GRID Saverio Vicario, Bachir Balech, Giacinto Donvito, Pasquale Notarangelo, Graziano Pesole

PDF pp. 77-79

Posters

Empowering web portal users with personalized text mining services Fedor Bakalov, Marie-Jean Meurs, Birgitta König-Ries, Bahar Sateli, Rene Witte, Greg Butler, Adrian Tsang

PDF pp. 81-83

Ordering copy number alteration data to analyze colorectal cancer progression Iuliana M. Bocicor, Giulio Caravagna, Alex Graudenzi, Claudia Cava, Giancarlo Mauri, Marco Antoniotti

PDF pp. 84-86

Glycans, the forgotten biomolecular actors of the big picture Matthew P. Campbell, Julien A. Mariethoz, Catherine M. Hayes, Pauline G. Rudd, Niclas G. Karlsson, Nicki H. Packer, Frédérique Lisacek

PDF pp. 87-88

Genomic and proteomic data integration for comprehensive biodata search Arif Canakoglu, Marco Masseroli

PDF pp. 89-91

Generation of explicit rules predicting neuroblastoma patients’ outcome Davide Cangelosi, Fabiola Blengio, Rogier Versteeg, Angelika Eggert, Alberto Garaventa, Claudio Gambini, Massimo Conte, Alessandra Eva, Luigi Varesio

PDF pp. 92-93

Simulation of caspases apoptotic signalling pathway in a tuple space-based bioinformatics infrastructure Maura Cárdenas-García, Pedro P González-Pérez, Sara Montagna

PDF pp. 94-96

Chromosome instability for tumor progression inference Claudia Cava, Italo Zoppis, Manuela Gariboldi, James F. Reid, Marco Antoniotti, Giancarlo Mauri

PDF pp. 97-99

Distilling structure in scientific workflows Juiqiang Chen, Christine Froidevaux, Carole Goble, Alan R. Williams, Sarah Cohen-Boulakia

PDF pp. 100-102

CorrelaGenes: a new tool for the interpretation of the human transcriptome Paolo Cremaschi, Sergio Rovida, Lucia Sacchi, Antonella Lisa, Alessandra Montecucco, Giuseppe Biamonti, Silvia Bione, Gianni Sacchi

PDF pp. 103-105

Business intelligence for biopharmaceutical company Anass El Haddadi, Bernard Dousser

PDF pp. 106-107

Biomedical Text Mining for Disease Gene Discovery Sarah ElShal, Jesse Davis, Yves Moreau

PDF pp. 108-109

An ontological-based knowledge organization for bioinformatics workflow management system Antonino Fiannaca, Massimo La Rosa, Salvatore Gaglio, Riccardo Rizzo, Alfonso Urso

PDF pp. 110-112

A tool for the extraction of new disease biomarkers from ex vivo and in vivo data Francesca Gallivanone, Carla Canevari, Isabella Sassi, Alberto Marassi, Maria Picchio, Maria C Gilardi, Isabella Castiglioni

PDF pp. 113-115

Prediction and 3D visualization of biological networks using cytological disease mapping Björn Sommer, Vladimir Ivanisenko, Patrizio Arrigo, Ralf Hofestädt

PDF pp. 116-117

A Grid-enabled web platform for integrated digital biobanking in paediatrics Massimiliano Izzo, Andrea Schenone, Sara Barzaghi, Fabiola Blengio, Marco M Fato, Luigi Varesio

PDF pp. 118-120

MBLabDB: a social database for molecular biodiversity data Flavio Licciulli, Domenico Catalano, Domenica D'Elia, Giorgio De Caro, Giorgio Grillo, Pietro Leo, Giuseppina Mulè, Paolo Pannarale, Graziano Pappadà, Francesco Rubino, Antonella Susca, Saverio Vicario, Gaetano Scioscia

PDF pp. 121-123

A multivariate analysis of protein microarrays for signature selection profiles Saveria Mazzara, Antonella Sinisi, Angela Cardaci, Sergio Abrignani, Mauro Bombaci

PDF pp. 124-126

Extracting correspondences between terminologies for an easier access to biomedical information Adila Merabti, Lina F Soualmia, Stéfan J Darmoni

PDF pp. 127-129

Detection of allele-specific gene expression on Next Generation Sequencing data Vladan Mijatovic, Luciano Xumerle, Alberto Ferrarini, Ilaria Iacobucci, Chiara Pighi, Antonio Mori, Chiara Zusi, Paola Prandini, Elisabetta Trabetti, Massimo Delledonne, Giovanni Martinelli, Alberto Zamò, Pier F Pignatti, Giovanni Malerba

PDF pp. 130-131

Network-based analysis of stem cells differentiation Francesca Mulas, Lan Zagar, Blaz Zupan, Riccardo Bellazzi

PDF pp. 132-134

AnnotateGenomicRegions: a web application Heiko Muller, Luca Zammataro, Gabriele Bucci

PDF pp. 135-137

G-SNPM - A GPU-based SNP mapping tool Alessandro Orro, Andrea Manconi, Emanuele Manca, Giuliano Armano, Luciano Milanesi

PDF pp. 138-139

HARP: an automated platform for targeted resequencing data analysis Fernando Palluzzi

PDF pp. 140-141

The integration of microRNA target data by biclustering techniques opens new roads for signaling networks analysis Gianvito Pio, Michelangelo Ceci, Corrado Loglisci, Donato Malerba, Domenica D'Elia

PDF pp. 142-144

ONCO-i2b2: improve patients selection through CBR techniques with heterogeneous distance functions Daniele Segagni, Matteo Gabetta, Valentina Tibollo, Arianna Dagliati, Alberto Zambelli, Cristiana Larizza, Silvia G Priori, Riccardo G Bellazzi

PDF pp. 145-147

Bioinformatics approach for data management about bone cells grown on substitute materials Federica Viti, Ivan Merelli, Silvia Scaglione, Luciano Milanesi

PDF pp. 148-150

A first RDF implementation of the COSMIC database on mutations in cancer Achille Zappa, Paolo Romano

PDF pp. 151-153