Abstract

Authors

Title

1

Alberti S, Trerotola M, Emerson A, Rossi E

An automated approach to the in-silico identification of chimeric mRNAs

3

Angeletti M, Baldoncini A, Cannata N, Corradini F, Culmone R, Forcato C, Mattioni M, Merelli E, Piergallini R

Orion: a spatial Multi Agent System framework for Computational Cellular Dynamics of metabolic pathways

4

Angeletti M, Bartocci E, Merelli E

A workflow for an orthology-based prediction of protein-protein interaction

5

Annese V, Latiano A, Palmieri O, D'Addabbo A, Maglietta R, Liuni S, Pesole G, Ancona N

Multiple Single Nucleotide Polymorphisms analysis of candidate genes in Inflammatory Bowel Diseases by using RLS classifiers

6

Anselmo A, Iacono M, Felice B, Guffanti A, Pesole G

Computational detection of cancer-specific splice sites

7

Arcangeli C, Gianese G, Paparcone R, Sperandei M, Cantale C, Galeffi P, Rosato V

Setting a procedure for "in silico" evaluation of immunoconjugates for cancer therapy

8

Armano G, Manconi A, Vargiu E

Automatic Extraction and Classification of Bioinformatics Publications through a MultiAgent System

9

Armano G, Saba M, Vargiu E

A Graphical Tool for Protein Sequences Analysis

10

Attimonelli M, Accetturo M, Jastrzebski JP, Lascaro D, Santamaria M, Zanchetta De Pasquale L

HmtDB, the Human Mitochondrial Genomic Resource: developments in 2006

11

Barbarini N, Magni P, Bellazzi R

A new approach for the analysis of mass spectrometry data for biomarker discovery

12

Bartocci E, Cannata N, Corradini F, Merelli E, Milanesi L, Romano P

A multilayer architecture to support bioinformaticians of today and tomorrow

13

Bartocci E, Corradini F, Merelli E, Scortichini L

BioWMS: a web based Workflow Management System for Bioinformatics

14

Bartocci E, Merelli E, Möller S

A DAS view of agent-based workflows

15

Beltrame F, Corradi L, Milanesi L, Papadimitropoulos A, Porro I, Scaglione S, Schenone A, Torterolo L, Viti F

A Grid based solution for Management and Analysis of Microarrays in distributed Bone Marrow Stem Cells experiments

16

Bernaschi M, Castiglione F, Ferranti A, Gavrila C, Cesareni G

Dynamic simulation of protein interaction networks

18

Bosotti R, Locatelli G, Healy S, Scacheri E, Calogero R, Isacchi A

Multiplatform approach for robust gene identification

20

Brilli M, Fondi M, Fani R

Analysis of operon genes using a compendium of expression data

21

Brilli M, Mengoni A, Fani R

Network analysis of plasmids encoded proteins

22

Brozzi A, Pelicci PG, Luzi L

Natural cis-antisense of human tumor suppressor genes

23

Cannata N, Corradini F, Di Berardini MR, Mariani F, Merelli E, Trivelli M, Ubaldi M

Modelling and simulation of the E.coli-Lambda interactions

24

Cannata N, Corradini F, La Terza A, Merelli E, Miceli C

Modelling of the eukariotic heat-shock response with probabilistic timed automata

25

Cannata N, Corradini F, Leoni L, Merelli E, Piersigilli F

A resource ontology for bioinformatics Resourceomes

26

Cannataro M, Veltri P

MS-Analyzer: Composing and Executing Preprocessing and Data Mining Services for Proteomics Applications

27

Capobianco E

Entropic Embedding in High-Dimensional Biological Systems

28

Cappadona S, Pattini L, Levander F, James P, Cerutti S

A systematic approach for noise characterization in ESI-Q-TOF spectra

29

Caprera A, Cosentino C, Viotti A, Stella A, Milanesi L, Lazzari B

ESTuber db: a tool for Tuber borchii EST sequence management

30

Capriotti E, Fariselli P, Rossi I, Casadio R

Improving the quality of the predictions of protein stability changes upon mutation using a multi-class predictor

31

Carreras M, Bosotti R

A new interactive and fully automated tool for parsing BLAST output

32

Casadio R, Fariselli P, Margara L, Filippo M, Vassura M

Improving the selection of close-native protein structures in decoy sets using a graph theory-based approach

34

Chiappori F, Ferrario MG, Gaiji N, Fantucci P

Design of Selective Compounds for the Estrogen Receptors: A Molecular Docking and Machine Learning Study

36

Chiusano ML, D'Agostino N, Traini A, Raimondo E, Aversano M, Frusciante L

An integrated platform for solanaceae genomics

37

Cameron G, Clark D, Beltrame F, Coatrieux JL, Del Hoyo Barbolla E, 

Martin-Sanchez F, Milanesi L, Tollis Ioannis G, Van der Lei J

SYMBiomatics: Synergies in Medical Informatics and Bioinformatics

39

Corsi C, Ferragina P, Marangoni R

The bioPrompt-box: an ontology-based clustering tool for searching in biological databases

40

Costantini S, Colonna G, Facchiano AM

Amino acid propensities for secondary structures

41

Cozzuto L, Petrillo M, Silvestro G, Di Nocera PP, Paolella G

Systematic identification of stem-loop containing sequence families in bacterial genomes

42

D'Agostino N, Aversano M, Frusciante L, Chiusano ML

TOMATEST DB: a database of expressed sequences to mine on Tomato functional genomics

43

Damasco C Grassi E Ala U Gatti M Di Cunto F

Identification of new putative mitotic genes through coexpression analysis

44

Di Camillo B, Toffolo G, Cobelli C

Significance analysis of microarray transcript levels in time series experiments

45

D'Ursi P, Marino F, Caprera A, Milanesi L, Faioni E, Rovida E

3D-protein C mutation database: integration of structural, functional and clinical data of natural protein C mutants

46

Emerson A, Rossi E

Immunogrid - The European Virtual Human Immune System Project

47

Farina L, Marcatili P, Uva P, Busiello V, Morelli G, Ruberti I

Dynamic Regulation of Gene Expression

49

Ferrario MG, Chiappori F, Gaiji N, Fantucci P

Alpha and Beta Estrogen Receptors: Molecular Modelling and Conformational Analysis through Molecular Dynamics

51

Ferrazzi F, Sebastiani P, Kohane IS, Ramoni MF, Bellazzi R

Bayesian approaches for reverse engineering of cellular networks: a performance evaluation on simulated data

52

Ferrè F, Clote P, Ausiello G, Via A, Cesareni G, Helmer-Citterich M

Mining the human interactome through gene expression time series analysis

53

Finocchiaro G, Mancuso F, Muller H

Publime: a new tool for meta-analysis of cancer-related microarray experiments

55

Fogolari F, Pieri L, Bortolussi L, Dovier A

A statistical empirical energy function for proteins

56

Fondi M, Brilli M, Fani R

On the origin and evolution of biosynthetic pathways: integrating microarray data with gene structure and organization

57

Fontana P, De Mattè L, Cestaro A, Segala C, Velasco R, Toppo S

GORetriever: a novel Gene Ontology annotation tool based on semantic similaritiy for knowledge discovery in database

59

Gissi C, San Mauro D, Pesole G, Zardoya R

Mitochondrial phylogeny of Anura (Amphibia): a case study of congruent phylogenetic reconstruction using amino acid and nucleotide characters

61

Horner D, Re M, Nasi C, Pesole G

Improving the capacity of the CSTMiner algorithm to correctly classify conserved sequences

62

Iacono M, Mignone F, Anselmo A, Pesole G

ESTissue: A novel method to identify gene expression profile EST based

63

Iannelli F, Griggio F, Pesole G, Gissi C

Reshaping the mtDNA circle: new insights from four newly sequenced ascidian genomes

65

Maglietta R, D'Addabbo A, Piepoli A, Perri F, Liuni S, Pesole G, Ancona N

Selection and ranking of genes relevant for cancer diagnosis based on the classification ability of their expression pattern

67

Marabotti A, Festa M, D'Acierno A, Facchiano A

GALT-Prot database: a database of the structural features of GALT enzyme and its mutations

68

Marino F, Morra G, D'Ursi P, Salvi E, Milanesi L, Faioni E, Rovida E

Molecular dynamics and docking simulation of the G216D mutation in the catalytic domain of activated protein C

69

Masseroli M, Bellistri E, Pinciroli F

Logistic regression of controlled functional annotations of classified genes

70

Masseroli M, Franceschini A, Maffezzoli A, Pinciroli F

Genomic annotation and statistical analysis of protein families and domains for functional investigation of gene lists

71

Menconi G, Dionisi F, Marangoni R

Extraction of recurrent motifs synthetic genomic sequences via dictionary-based compression

72

Mereghetti P, Papaleo E, Fantucci P, Tiranti V, Zeviani M, Mineri R, De Gioia L

Evaluation of protein models quality using neural networks. Application to the ETHE1 protein

73

Merelli I, D'Agostino D, Clematis A, Milanesi L

Analysis system for Protein Surface Recognition

74

Mignone F, Re M, Horner D, Pesole G

A new strategy to identify novel genes and gene isoforms: whole genome comparison of human and mouse

76

Milanesi L, Andreas G, Arlandini C, Beltrame F, Bishop C, Breton V, Ernest P, Jacq N, Legre Y, Liò P, Liuni S, Mazzuccato M, Maggi G, Meloni G, Merelli I, Morra G, Orro A, Porro I, Sanger M, Shuai S, Trombetti G

BioinfoGRID: EU Bioinfomatics GRID Project

77

Mittempergher L, Picelli S, Feltrin E, Colluto L, Nofrate V, Caldara F, Millino C, Campanaro S, Valle G

Contribution to the ontology and system biology of muscle genes and application to microarray expression studies

78

Mizugushi K, Sele M, Cubellis MV

Environment specific substitution tables for thermophilic proteins

79

Morra G, Milanesi L

Molecular dynamics simulations of TBP complexed with diverse TATA variants

81

Muselli M, Romeo F, Pfeffer U

Clustering techniques for classification of splice sites of human exons

82

Mutarelli M, Scafoglio C, Cicatiello L, Colonna G, Facchiano A, Weisz A

Getting the most out of comparative microarray data analysis: analysis of the estrogen-responsive transcriptome from breast cancer cells with four different microarray platforms

83

Nicodemi M, Prisco A

A computer model of X-inactivation

84

Orro A, Armano G, Vargiu E, Milanesi L

FunGenAgent: An Agent-Based Approach for Workflow Composition in Homology Functional Genomics

86

Papaleo E, Pandini A, De Gioia L, Bonati L

A fast conformational sampling approach to investigate enzymatic cold-adaptation mechanisms

87

Papaleo E, Riccardi L, Pasi M, Gonella Diaza R, Smalas AO, Brandsdal BO, Fantucci P, De Gioia L

Comparative molecular dynamics simulations of homologous enzymes to investigate enzymatic cold-adaptation: a family-centred point of view

89

Pavesi G, Valentini G, Mauri G, Pesole G

Motif based classification of coexpressed genes

90

Peluso D, Via A, Ausiello G, Helmer-Citterich M

Mapping OMIM mutated residues on PDB protein structures

92

Piccolis M, Medico E

The genomic signature for in vitro-induced invasive growth is enriched in genes correlated with human cancer aggressiveness

93

Pizzi E, Bultrini E, Silvestrini F, Alano P

Genomic analysis of gene structure and expression of Plasmodium falciparum rifins

94

Pozzoli U, Menozzi G, Cereda M, Comi GP, Sironi M

Expression levels and gene function influence transposon occurrence in mammalian introns

95

Raimondo E, Chiusano ML

Pattern Discovery: a web based interface for exhaustive analyses on multiple biological sequences

97

Rampone S, Aloisio A, Izzo V

FPGA implementation of a greedy scheme for Bioinformatics applications

98

Remondini D, Neretti N, Milanesi L, Tatar M, Sedivy JM, Franceschi C, Castellani GC

Correlation analysis of gene expression time series at multiple scales: from the entire genome to metabolic and signalling pathways

99

Romano P, Bartocci E, Bertolini G, De Paoli F, Marra D, Mauri G, Merelli, Milanesi L

Biowep: a workflow enactment portal for bioinformatics applications

101

Sbisà E, Catalano D, Gisel A, Grillo G, Licciulli F, Turi A, Liuni S, Pesole G, De Grassi A, Caratozzolo MF, D'Erchia AM, Navarro B, Tullo A, Saccone C

p53FamTaG : a database resource of human p53, p63 and p73 direct target genes combining in silico prediction and microarray data

102

Scalabrin S, Policriti A, Morgante M

Stem-loop structure search

103

Sironi M, Menozzi G, Fumagalli M, Comi GP, Pozzoli U

Introns containing conserved elements are evolutionary preserved in size

104

Splendiani A, Brandizi B, Even G, Ottavio B, Pavelka N, Pelizzola M, Mayhaus M, Foti M, Mauri G, Ricciardi-Castagnoli P

The Genopolis Microarray Database

107

Tosatto SCE, Battistutta R, Albiero A

Local protein structure validation revisited

108

Traini A, Chiusano ML

On the experimental annotation of tomato BACs sequences: reliable alignment for useful genomic analyses

109

Trombetti GA, Bonnal RJP, Rizzi E, De Bellis G, Milanesi L

Data handling strategies for high throughput pyrosequencers

111

Tulipano A, Marangi C, Angelini L, Pellicoro M, Donvito G, Maggi G, Gisel A

Genes clustering on large, mixed microarray data sets

112

Via A, Gherardini F, Ferraro E, Scalia Tomba G, Ausiello G, Helmer-Citterich M

False occurrences of functional motifs on protein sequences highlight evolutionary constraints

113

Viti F, Merelli I, Porro I, Papadimitropoulos A, Milanesi L

Valuation study of available genomic data storage platforms

115

Zanzoni A, Gherardini F, Ausiello G, Via A, Helmer-Citterich M

A bioinformatic approach for a structural analysis of protein phosphorylation sites