Information technologies incentivizing scholastic fruition (2009)
KAZANCIGIL, MUSTAFA ASIM, VALLE, GIORGIO, FOLGIERI, RAFFAELLA
Information technologies incentivizing scholastic fruition / F. Epifania, G. Valle, R. Folgieri, M. A. Kazancigil. - In: Proceedings of Society for Information Technology and Teacher Education...
Muscle Research and Gene Ontology: New standards for improved data integration (2009)
Feltrin, Erika, Campanaro, Stefano, Diehl, Alexander D, Ehler, Elisabeth, Faulkner, Georgine, Fordham, Jennifer, ...
Abstract Background The Gene Ontology Project provides structured controlled vocabularies for molecular biology that can be used for the functional annotation of genes and gene products. In a...
Information technologies incentivizing scholastic fruition (2009)
KAZANCIGIL, MUSTAFA ASIM, VALLE, GIORGIO, FOLGIERI, RAFFAELLA
Information technologies incentivizing scholastic fruition / F. Epifania, G. Valle, R. Folgieri, M.A. Kazancigil. - In: Proceedings of Society for Information Technology and Teacher Education...
VALLE, GIORGIO, FOLGIERI, RAFFAELLA, A. Andronico, L. Colazzo
UN ESPERIMENTO DI APPRENDIMENTO COLLETTIVO, ATTRAVERSO L’USO DI STRUMENTI WEB 2.0, PRESSO L’UNIVERSITA’ STATALE DI MILANO. / R. Folgieri, F. Epifania, G. Valle. - In: Didamatica 2009 -...
PASS: a program to align short sequences (2009)
Campagna, Davide, Albiero, Alessandro, Bilardi, Alessandra, Caniato, Elisa, Forcato, Claudio, Manavski, Svetlin, ...
Summary: Standard DNA alignment programs are inadequate to manage the data produced by new generation DNA sequencers. To answer this problem, we developed PASS with the objective of improving...
A snapshot of the emerging tomato genome sequence (2009)
Mueller, Lukas, Klein Lankhorst, René, Tanksley, Steven D., Giovannoni, James J., White, Ruth, Vrebalov, Julia, ...
The genome of tomato (Solanum lycopersicum L.) is being sequenced by an international consortium of 10 countries (Korea, China, the United Kingdom, India, the Netherlands, France, Japan, Spain,...
Annotating genomes with massive-scale RNA sequencing (2008)
Denoeud, France, Aury, Jean-Marc, Da Silva, Corinne, Noel, Benjamin, Rogier, Odile, Delledonne, Massimo, ...
Abstract Next generation technologies enable massive-scale cDNA sequencing (so-called RNA-Seq). Mainly because of the difficulty of aligning short reads on exon-exon junctions, no attempts have been...
Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society (2008)
Bmc Bioinformatics, Manuela Helmer-citterich, Rita Casadio, Ro Guffanti, Giancarlo Mauri, Luciano Milanesi, ...
Protein evolution in deep sea bacteria: an analysis of amino acids substitution rates (2008)
Campanaro, Stefano, Treu, Laura, Valle, Giorgio
Abstract Background Abyssal microorganisms have evolved particular features that enable them to grow in their extreme habitat. Genes belonging to specific functional categories are known to be...
Paolo Fontana, Riccardo Velasco, Giorgio Valle
We present a novel fold recognition method based on the combination of detailed sequence searches and structural information. Presently the protocol implements two different approaches to assign the...
Manavski, Svetlin A, Valle, Giorgio
Abstract Background Searching for similarities in protein and DNA databases has become a routine procedure in Molecular Biology. The Smith-Waterman algorithm has been available for more than 25...
An Interactive VideoJournal to complement Learning & Training (2008)
VALLE, GIORGIO, G. Valle, F. Epifania, T. Bastiaens, S. Caeliner
An Interactive VideoJournal to complement Learning & Training / G. Valle, F. Epifania. - In: Proceedings of World Conference on Educational Multimedia, Hypermedia and Telecommunications 2008 ; T....
Bmc Bioinformatics, Svetlin A Manavski, Giorgio Valle
CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment
Manavski, Svetlin A, Valle, Giorgio
Background Searching for similarities in protein and DNA databases has become a routine procedure in Molecular Biology. The Smith-Waterman algorithm has been available for more than 25 years. It is...
Erika Feltrin, Stefano Campanaro, Alexander D. Diehl, Elisabeth Ehler, Georgine Faulkner, Jennifer Fordham, ...
PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. Muscle Research and Gene Ontology: New standards for...
BMC Bioinformatics BioMed Central Open Access BMC 32002, (2007)
Rehannah Ha Borup, Yi-wen Chen, Tanya M Teslovich, Gerolamo Lanfranchi, Giorgio Valle, Eric P Hoffman, ...
Research article Development and production of an oligonucleotide MuscleChip: use for validation of ambiguous ESTs
Nicola Cannata, Chiara Romualdi, Paolo Laveder, Gerolamo Lanfranchi, Giorgio Valle
TRAIT [1] is a knowledgebase integrating information on human transcripts to related data from genome, proteins, ortholog genes, gene ontology, diseases and expression data based both on ESTs...
Campanaro, Stefano, Picelli, Simone, Torregrossa, Rossella, Colluto, Laura, Ceol, Monica, Del Prete, Dorella, ...
Abstract Background Understanding how mesenchymal cells arise from epithelial cells could have a strong impact in unveiling mechanisms of epithelial cell plasticity underlying kidney regeneration and...
A global gene evolution analysis on Vibrionaceaefamily using phylogenetic profile (2007)
Vitulo, Nicola, Vezzi, Alessandro, Romualdi, Chiara, Campanaro, Stefano, Valle, Giorgio
Abstract Background Vibrionaceae represent a significant portion of the cultivable heterotrophic sea bacteria; they strongly affect nutrient cycling and some species are devastating pathogens. In...
Nicola Vitulo, Alessandro Vezzi, Giulio Galla, Sandra Citterio, Giada Marino, Benedetto Ruperti, ...
The MOB family includes a group of cell cycle-associated proteins highly conserved throughout eukaryotes, whose founding members are implicated in mitotic exit and co-ordination of cell cycle...
Campanaro, Stefano, Picelli, Simone, Terragrossa, Rossella, Colluto, Laura, Ceol, Monica, Del Prete, Dorella, ...
Background Understanding how mesenchymal cells arise from epithelial cells could have a strong impact in unveiling mechanisms of epithelial cell plasticity underlying kidney regeneration and repair....
A global gene evolution analysis on Vibrionaceae family using phylogenetic profile (2007)
Vitulo, Nicola, Vezzi, Alessandro, Romualdi, Chiara, Campanaro, Stefano, Valle, Giorgio
Background Vibrionaceae represent a significant portion of the cultivable heterotrophic sea bacteria; they strongly affect nutrient cycling and some species are devastating pathogens. In this work we...
Bmc Genomics, Stefano Campanaro, Simone Picelli, Rossella Torregrossa, Laura Colluto, Monica Ceol, ...
Research article Genes involved in TGFβ1-driven epithelial-mesenchymal transition of renal epithelial cells are topologically related in the human interactome map
The LGI1/Epitempin gene encodes two protein isoforms differentially expressed in human brain (2006)
Furlan, Sandra, Roncaroli, Federico, Forner, Francesca, Vitiello, Libero, Calabria, Elisa, Piquer-Sirerol, Salomé, ...
7 pages, 5 figures.-- PMID: 16787412 [PubMed].
Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society (2005)
Helmer-Citterich, Manuela, Casadio, Rita, Guffanti, Alessandro, Mauri, Giancarlo, Milanesi, Luciano, Pesole, Graziano, ...
Abstract The BITS2005 Conference brought together about 200 Italian scientists working in the field of Bioinformatics, students in Biology, Computer Science and Bioinformatics on March 17–19 2005,...
Campanaro, Stefano, Vezzi, Alessandro, Vitulo, Nicola, Lauro, Federico M, D'Angelo, Michela, Simonato, Francesca, ...
Abstract Background Oceans cover approximately 70% of the Earth's surface with an average depth of 3800 m and a pressure of 38 MPa, thus a large part of the biosphere is occupied by high pressure...
The SSEA server for protein secondary structure alignment (2005)
Paolo Fontana, Eckart Bindewald, Riccardo Velasco, Giorgio Valle, Via E. Mach
Campanaro, Stefano, Vezzi, Alessandro, Vitulo, Nicola, Lauro, Federico M, D'Angelo, Michela, Simonato, Francesca, ...
Background Oceans cover approximately 70% of the Earth's surface with an average depth of 3800 m and a pressure of 38 MPa, thus a large part of the biosphere is occupied by high pressure...
Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society (2005)
Helmer-Citterich, Manuela, Casadio, Rita, Guffanti, Alessandro, Mauri, Giancarlo, Milanesi, Luciano, Pesole, Graziano, ...
The BITS2005 Conference brought together about 200 Italian scientists working in the field of Bioinformatics, students in Biology, Computer Science and Bioinformatics on March 17–19 2005, in Milan....
RAP: a new computer program for de novo identification of repeated sequences in whole genomes (2005)
Campagna, Davide, Romualdi, Chiara, Vitulo, Nicola, Del Favero, Micky, Lexa, Matej, Cannata, Nicola, ...
Motivation: DNA repeats are a common feature of most genomic sequences. Their de novo identification is still difficult despite being a crucial step in genomic analysis and oligonucleotides design....
The SSEA server for protein secondary structure alignment (2005)
Fontana, Paolo, Bindewald, Eckart, Toppo, Stefano, Velasco, Riccardo, Valle, Giorgio, Tosatto, Silvio C. E.
Summary: We present a web server that computes alignments of protein secondary structures. The server supports both performing pairwise alignments and searching a secondary structure against a...
FOLGIERI, RAFFAELLA, VALLE, GIORGIO, Giorgio Valle, Raffaella Folgieri
Continuous Learning Relaxing Time & Location Constraints In a Regular Curricula Degree Offered by University of Milan. / Giorgio Valle, Raffaella Folgieri. - (Volume 2004, issue 1). - In: Proceedings...
Davide Campagna, Chiara Romualdi, Nicola Vitulo, Micky Del Favero, Matej Lexa, Nicola Cannata, ...
Motivation: DNA repeats are a common feature of most genomic sequences. Their de novo identification is still difficult despite being a crucial step in genomic analysis and oligonucleotides design....
Negrisolo, Enrico, Minelli, Alessandro, Valle, Giorgio
Recent advances in molecular phylogenetics are continuously changing our perception of the phylogenetic relationships among the main arthropod lineages: crustaceans, hexapods, chelicerates and...
The SSEA server for protein secondary structure alignment (2004)
Fontana, Paolo, Bindewald, Eckart, Toppo, Stefano, Velasco, Riccardo, Valle, Giorgio, Tosatto, Silvio C. E.
Summary: We present a web server which computes alignments of protein secondary structures. The server supports both performing pairwise alignments and searching a secondary structure against a...
RAP: a new computer program for de novo identification of repeated sequences in whole genomes (2004)
Campagna, Davide, Romualdi, Chiara, Vitulo, Nicola, Del Favero, Micky, Lexa, Matej, Cannata, Nicola, ...
Motivation: DNA repeats are a common feature of most genomic sequences. Their de novo identification is still difficult despite being a crucial step in genomic analysis and oligonucleotides design....
Negrisolo, Enrico, Minelli, Alessandro, Valle, Giorgio
Recent advances in molecular phylogenetics are continuously changing our perception of the phylogenetic relationships among the main arthropod lineages: crustaceans, hexapods, chelicerates, and...
Negrisolo, Enrico, Minelli, Alessandro, Valle, Giorgio
Recent advances in molecular phylogenetics are continuously changing our perception of the phylogenetic relationships among the main arthropod lineages: crustaceans, hexapods, chelicerates and...
The SSEA server for protein secondary structure alignment (2004)
Fontana, Paolo, Bindewald, Eckart, Toppo, Stefano, Velasco, Riccardo, Valle, Giorgio, Tosatto, Silvio C. E.
Summary: We present a web server which computes alignments of protein secondary structures. The server supports both performing pairwise alignments and searching a secondary structure against a...
RAP: a new computer program for de novo identification of repeated sequences in whole genomes (2004)
Campagna, Davide, Romualdi, Chiara, Vitulo, Nicola, Del Favero, Micky, Lexa, Matej, Cannata, Nicola, ...
Motivation: DNA repeats are a common feature of most genomic sequences. Their de novo identification is still difficult despite being a crucial step in genomic analysis and oligonucleotides design....
Simple consensus procedures are effective and sufficient in secondary structure prediction (2003)
Albrecht,Mario, Tosatto,Silvio C.E., Lengauer,Thomas, Valle,Giorgio
Simple consensus procedures are effective and sufficient in secondary structure prediction (2003)
Albrecht, Mario, Tosatto, Silvio C.E., Lengauer, Thomas, Valle, Giorgio
PRIMEX: rapid identification of oligonucleotide matches in whole genomes (2003)
Summary: PRIMEX (PRImer Match EXtractor) can detect oligonucleotide sequences in whole genomes, allowing for mismatches. Using a word lookup table and server functionality, PRIMEX accepts queries...
TRAIT (TRAnscript Integrated Table): a knowledgebase of human skeletal muscle transcripts (2003)
Toppo, Stefano, Cannata, Nicola, Fontana, Paolo, Romualdi, Chiara, Laveder, Paolo, Bertocco, Emanuela, ...
Summary: TRAIT is a knowledgebase integrating information on transcripts with related data from genome, proteins, ortholog genes and diseases. It was initially built as a system to manage an...
Simple consensus procedures are effective and sufficient in secondary structure prediction (2003)
Albrecht, Mario, Tosatto, Silvio C.E., Lengauer, Thomas, Valle, Giorgio
We have analyzed the performance of majority voting on minimal combination sets of three state‐of‐the‐art secondary structure prediction methods in order to obtain a consensus...
Romualdi, Chiara, Campanaro, Stefano, Campagna, Davide, Celegato, Barbara, Cannata, Nicola, Toppo, Stefano, ...
Large-scale parallel measurements of the expression of many thousands genes are now available with high-density array made with collections of cDNA fragments, or oligonucleotide corresponding to...
Borup, Rehannah HA, Toppo, Stefano, Chen, Yi-Wen, Teslovich, Tanya M, Lanfranchi, Gerolamo, Valle, Giorgio, ...
Abstract Background We describe the development, validation, and use of a highly redundant 120,000 oligonucleotide microarray (MuscleChip) containing 4,601 probe sets representing 1,150 known genes...
Chiara Romualdi, Stefano Campanaro, Davide Campagna, Barbara Celegato, Nicola Cannata, Giorgio Valle, ...
Pattern recognition in gene expression profiling
Borup, Rehannah HA, Toppo, Stefano, Chen, Yi-Wen, Teslovich, Tanya M, Lanfranchi, Gerolamo, Valle, Giorgio, ...
Background We describe the development, validation, and use of a highly redundant 120,000 oligonucleotide microarray (MuscleChip) containing 4,601 probe sets representing 1,150 known genes expressed...
Gene expression profiling in dysferlinopathies using a dedicated muscle microarray (2002)
Campanaro, Stefano, Romualdi, Chiara, Fanin, Marina, Celegato, Barbara, Pacchioni, Beniamina, Trevisan, Silvia, ...
We have performed expression profiling to define the molecular changes in dysferlinopathy using a novel dedicated microarray platform made with 3′-end skeletal muscle cDNAs. Eight dysferlinopathy...
Cannata, Nicola, Toppo, Stefano, Romualdi, Chiara, Valle, Giorgio
Motivation: Protein and DNA are generally represented by sequences of letters. In a number of circumstances simplified alphabets (where one or more letters would be represented by the same symbol)...
A two-step strategy for constructing specifically self-subtracted cDNA libraries (2002)
Laveder, Paolo, De Pittà, Cristiano, Toppo, Stefano, Valle, Giorgio, Lanfranchi, Gerolamo
We have developed a new strategy for producing subtracted cDNA libraries that is optimized for connective and epithelial tissues, where a few exceptionally abundant (super-prevalent) RNA species...
A Comprehensive, High-Resolution Genomic Transcript Map of Human Skeletal Muscle (1998)
Bortoluzzi, Stefania, Rampoldi, Luca, Simionati, Barbara, Zimbello, Rosanna, Barbon, Alessandro, D'Alessi, Fabio, ...
Discover 1: a new program to search for unusually represented DNA motifs (1993)
DISCOVER1 (Distribution COunter VERsion 1) is a new program that can identify DNA motifs occurring with a high deviation from the expected frequency. The program generates families of patterns, each...
A two-step strategy for constructing specifically self-subtracted cDNA libraries
Laveder, Paolo, De Pittà, Cristiano, Toppo, Stefano, Valle, Giorgio, Lanfranchi, Gerolamo
We have developed a new strategy for producing subtracted cDNA libraries that is optimized for connective and epithelial tissues, where a few exceptionally abundant (super-prevalent) RNA species...
Development and production of an oligonucleotide MuscleChip: use for validation of ambiguous ESTs
Borup, Rehannah HA, Toppo, Stefano, Chen, Yi-Wen, Teslovich, Tanya M, Lanfranchi, Gerolamo, Valle, Giorgio, ...
A Comprehensive, High-Resolution Genomic Transcript Map of Human Skeletal Muscle
Bortoluzzi, Stefania, Rampoldi, Luca, Simionati, Barbara, Zimbello, Rosanna, Barbon, Alessandro, D’Alessi, Fabio, ...
We present the Human Muscle Gene Map (HMGM), the first comprehensive and updated high-resolution expression map of human skeletal muscle. The 1078 entries of the map were obtained by merging data...
Do the Four Clades of the mtDNA Haplogroup L2 Evolve at Different Rates?
Torroni, Antonio, Rengo, Chiara, Guida, Valentina, Cruciani, Fulvio, Sellitto, Daniele, Coppa, Alfredo, ...
Forty-seven mtDNAs collected in the Dominican Republic and belonging to the African-specific haplogroup L2 were studied by high-resolution RFLP and control-region sequence analyses. Four sets of...
Laterally transferred elements and high pressure adaptation in Photobacterium profundum strains
Campanaro, Stefano, Vezzi, Alessandro, Vitulo, Nicola, Lauro, Federico M, D'Angelo, Michela, Simonato, Francesca, ...
Carelli, Valerio, Achilli, Alessandro, Valentino, Maria Lucia, Rengo, Chiara, Semino, Ornella, Pala, Maria, ...
The mitochondrial DNA (mtDNA) of 87 index cases with Leber hereditary optic neuropathy (LHON) sequentially diagnosed in Italy, including an extremely large Brazilian family of Italian maternal...
A two-step strategy for constructing specifically self-subtracted cDNA libraries
Laveder, Paolo, De Pittà, Cristiano, Toppo, Stefano, Valle, Giorgio, Lanfranchi, Gerolamo
We have developed a new strategy for producing subtracted cDNA libraries that is optimized for connective and epithelial tissues, where a few exceptionally abundant (super-prevalent) RNA species...
Development and production of an oligonucleotide MuscleChip: use for validation of ambiguous ESTs
Borup, Rehannah HA, Toppo, Stefano, Chen, Yi-Wen, Teslovich, Tanya M, Lanfranchi, Gerolamo, Valle, Giorgio, ...
A Comprehensive, High-Resolution Genomic Transcript Map of Human Skeletal Muscle
Bortoluzzi, Stefania, Rampoldi, Luca, Simionati, Barbara, Zimbello, Rosanna, Barbon, Alessandro, D’Alessi, Fabio, ...
We present the Human Muscle Gene Map (HMGM), the first comprehensive and updated high-resolution expression map of human skeletal muscle. The 1078 entries of the map were obtained by merging data...
Do the Four Clades of the mtDNA Haplogroup L2 Evolve at Different Rates?
Torroni, Antonio, Rengo, Chiara, Guida, Valentina, Cruciani, Fulvio, Sellitto, Daniele, Coppa, Alfredo, ...
Forty-seven mtDNAs collected in the Dominican Republic and belonging to the African-specific haplogroup L2 were studied by high-resolution RFLP and control-region sequence analyses. Four sets of...
Laterally transferred elements and high pressure adaptation in Photobacterium profundum strains
Campanaro, Stefano, Vezzi, Alessandro, Vitulo, Nicola, Lauro, Federico M, D'Angelo, Michela, Simonato, Francesca, ...
Carelli, Valerio, Achilli, Alessandro, Valentino, Maria Lucia, Rengo, Chiara, Semino, Ornella, Pala, Maria, ...
The mitochondrial DNA (mtDNA) of 87 index cases with Leber hereditary optic neuropathy (LHON) sequentially diagnosed in Italy, including an extremely large Brazilian family of Italian maternal...
Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society
Helmer-Citterich, Manuela, Casadio, Rita, Guffanti, Alessandro, Mauri, Giancarlo, Milanesi, Luciano, Pesole, Graziano, ...
The BITS2005 Conference brought together about 200 Italian scientists working in the field of Bioinformatics, students in Biology, Computer Science and Bioinformatics on March 17–19 2005, in Milan....
A global gene evolution analysis on Vibrionaceae family using phylogenetic profile
Vitulo, Nicola, Vezzi, Alessandro, Romualdi, Chiara, Campanaro, Stefano, Valle, Giorgio
Campanaro, Stefano, Picelli, Simone, Torregrossa, Rossella, Colluto, Laura, Ceol, Monica, Del Prete, Dorella, ...
DeMarini, Douglas J., Adams, Alison E.M., Fares, Hanna, Virgilio, Claudio De, Valle, Giorgio, Chuang, John S., ...
Just before bud emergence, a Saccharomyces cerevisiae cell forms a ring of chitin in its cell wall; this ring remains at the base of the bud as the bud grows and ultimately forms part of the bud scar...
Lauro, Federico M., Tran, Khiem, Vezzi, Alessandro, Vitulo, Nicola, Valle, Giorgio, Bartlett, Douglas H.
Microorganisms adapted to piezopsychrophilic growth dominate the majority of the biosphere that is at relatively constant low temperatures and high pressures, but the genetic bases for the...
Annotating genomes with massive-scale RNA sequencing
Denoeud, France, Aury, Jean-Marc, Da Silva, Corinne, Noel, Benjamin, Rogier, Odile, Delledonne, Massimo, ...
A method for de novo genome annotation using high-throughput cDNA sequencing data.
Muscle Research and Gene Ontology: New standards for improved data integration
Feltrin, Erika, Campanaro, Stefano, Diehl, Alexander D, Ehler, Elisabeth, Faulkner, Georgine, Fordham, Jennifer, ...
Vitulo, Nicola, Vezzi, Alessandro, Galla, Giulio, Citterio, Sandra, Marino, Giada, Ruperti, Benedetto, ...
The MOB family includes a group of cell cycle-associated proteins highly conserved throughout eukaryotes, whose founding members are implicated in mitotic exit and co-ordination of cell cycle...
Von Nandelstadh, Pernilla, Ismail, Mohamed, Gardin, Chiara, Suila, Heli, Zara, Ivano, Belgrano, Anna, ...
Interactions between Z-disc proteins regulate muscle functions and disruption of these interactions results in muscle disorders. Mutations in Z-disc components myotilin, ZASP/Cypher, and FATZ-2...