Vol. 18: Supplement B

Entire issue

• EMBnet.journal 18 Suppl. B

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ARTICLES

• Editorial

  p. 2

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• BITS Introduction

  p. 3

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• Preface - NETTAB 2012 Workshop on “Integrated Bio-Search”

  pp. 4-7

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• Scientific Programme

  pp. 8-11

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Keynote Lectures

• Integration and analysis of multi-type high-throughput data for biomolecular knowledge discovery

  Erik Bongcam-Rudloff

  p. 13

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• Semantics based biomedical knowledge search, integration and discovery

  Barend Mons

  p. 14

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

  Eric Neumann

  p. 15

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Tutorials

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

  Alexander Kel

  p. 17

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

  Katy Wolstencroft

  p. 18

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Oral Communications

• Rational design of organelle compartments in cells

  Claudio Angione, Giovanni Carapezza, Jole Costanza, Pietro Lió, Giuseppe Nicosia

  pp. 20-22

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• Filtering with alignment free distances for high throughput DNA reads assembly

  Maria C De Cola, Giovanni Felici, Daniele Santoni, Emanuel Weitschek

  pp. 23-25

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• A semantic collaborative system for the management of translational research projects

  Matteo Gabetta, Giuseppe Milani, Cristiana Larizza, Valentina Favalli, Eloisa Arbustini, Riccardo Bellazzi

  pp. 26-28

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• Answering Gene Ontology terms to proteomics questions by supervised macro reading in Medline

  Julien Gobeill, Emilie Pasche, Douglas Teodoro, Anne-Lise Veuthey, Patrick Ruch

  pp. 29-31

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• Using graph theory to analyze gene network coherence

  Francisco Gómez-Vela, Norberto Díaz-Díaz, José A Lagares, José A Sánchez, Jesús S Aguilar-Ruiz

  pp. 32-34

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• 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

  pp. 35-37

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• Network-based gene-disease prioritization using PROPHNET

  Víctor Martínez, Carlos Cano, Armando Blanco

  pp. 38-40

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• QTreds: a flexible LIMS for omics laboratories

  Piergiorgio Palla, Gianfranco Frau, Laura Vargiu, Patricia Rodriguez-Tomé

  pp. 41-43

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• Development of a text search engine for medicinal chemistry patents

  Emilie Pasche, Julien Gobeill, Fatma Oezdemir-Zaech, Therese Vachon, Christian Lovis, Patrick Ruch

  pp. 44-46

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

  Fabio Rinaldi

  pp. 47-49

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• IntelliGenWiki: An Intelligent Semantic Wiki for Life Sciences

  Bahar Sateli, Marie-Jean Meurs, Greg Butler, Justin Powlowski, Adrian Tsang, René Witte

  pp. 50-52

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• ROCK: a resource for integrative breast cancer data analysis

  Saif Ur-Rehman, Costas Mitsopoulos, Marketa Zvelebil

  pp. 53-54

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Technological Industrial Communications

• Extracting knowledge from biomedical data through Logic Learning Machines and Rulex

  Marco Muselli

  pp. 56-58

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• Data modeling: the key to biological data integration

  François Rechenmann

  pp. 59-60

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Short Oral Communications

• BioQuery-ASP: querying biomedical databases and ontologies using answer set programming

  Esra Erdem, Umut Oztok

  pp. 62-64

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• 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

  pp. 65-67

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• Applications of a generic model of genomic variations functional analysis

  Sarah Mapelli, Uberto Pozzoli

  pp. 68-70

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• Ranking-aware integration and explorative search of distributed bio-data

  Marco Masseroli, Matteo Picozzi, Giorgio Ghisalberti

  pp. 71-73

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• DiGSNP: a web tool for Disease-Gene-SNP hierarchical prioritization

  Carmen Navarro, Carlos Cano, Armando Blanco, Fernando García-Alcalde

  pp. 74-76

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• The BioVel Project: Robust phylogenetic workflows running on the GRID

  Saverio Vicario, Bachir Balech, Giacinto Donvito, Pasquale Notarangelo, Graziano Pesole

  pp. 77-79

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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

  pp. 81-83

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• Ordering copy number alteration data to analyze colorectal cancer progression

  Iuliana M. Bocicor, Giulio Caravagna, Alex Graudenzi, Claudia Cava, Giancarlo Mauri, Marco Antoniotti

  pp. 84-86

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• 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

  pp. 87-88

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• Genomic and proteomic data integration for comprehensive biodata search

  Arif Canakoglu, Marco Masseroli

  pp. 89-91

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• 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

  pp. 92-93

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• Simulation of caspases apoptotic signalling pathway in a tuple space-based bioinformatics infrastructure

  Maura Cárdenas-García, Pedro P González-Pérez, Sara Montagna

  pp. 94-96

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• Chromosome instability for tumor progression inference

  Claudia Cava, Italo Zoppis, Manuela Gariboldi, James F. Reid, Marco Antoniotti, Giancarlo Mauri

  pp. 97-99

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• Distilling structure in scientific workflows

  Juiqiang Chen, Christine Froidevaux, Carole Goble, Alan R. Williams, Sarah Cohen-Boulakia

  pp. 100-102

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• 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

  pp. 103-105

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• Business intelligence for biopharmaceutical company

  Anass El Haddadi, Bernard Dousser

  pp. 106-107

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• Biomedical Text Mining for Disease Gene Discovery

  Sarah ElShal, Jesse Davis, Yves Moreau

  pp. 108-109

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• An ontological-based knowledge organization for bioinformatics workflow management system

  Antonino Fiannaca, Massimo La Rosa, Salvatore Gaglio, Riccardo Rizzo, Alfonso Urso

  pp. 110-112

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• 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

  pp. 113-115

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• Prediction and 3D visualization of biological networks using cytological disease mapping

  Björn Sommer, Vladimir Ivanisenko, Patrizio Arrigo, Ralf Hofestädt

  pp. 116-117

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• A Grid-enabled web platform for integrated digital biobanking in paediatrics

  Massimiliano Izzo, Andrea Schenone, Sara Barzaghi, Fabiola Blengio, Marco M Fato, Luigi Varesio

  pp. 118-120

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• 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

  pp. 121-123

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• A multivariate analysis of protein microarrays for signature selection profiles

  Saveria Mazzara, Antonella Sinisi, Angela Cardaci, Sergio Abrignani, Mauro Bombaci

  pp. 124-126

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• Extracting correspondences between terminologies for an easier access to biomedical information

  Adila Merabti, Lina F Soualmia, Stéfan J Darmoni

  pp. 127-129

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• 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

  pp. 130-131

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• Network-based analysis of stem cells differentiation

  Francesca Mulas, Lan Zagar, Blaz Zupan, Riccardo Bellazzi

  pp. 132-134

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• AnnotateGenomicRegions: a web application

  Heiko Muller, Luca Zammataro, Gabriele Bucci

  pp. 135-137

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• G-SNPM - A GPU-based SNP mapping tool

  Alessandro Orro, Andrea Manconi, Emanuele Manca, Giuliano Armano, Luciano Milanesi

  pp. 138-139

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• HARP: an automated platform for targeted resequencing data analysis

  Fernando Palluzzi

  pp. 140-141

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• 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

  pp. 142-144

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• 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

  pp. 145-147

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• Bioinformatics approach for data management about bone cells grown on substitute materials

  Federica Viti, Ivan Merelli, Silvia Scaglione, Luciano Milanesi

  pp. 148-150

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• A first RDF implementation of the COSMIC database on mutations in cancer

  Achille Zappa, Paolo Romano

  pp. 151-153

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