BIOINFORMATICS APPLICATIONS NOTE (2008)
Genome Analysis, Florence Arm, C. Victor Jongeneel, Edward E. Farmer
Rapid and selective surveillance of Arabidopsis thaliana
Christian Iseli, C. Victor Jongeneel
One of the problems associated with the large-scale analysis of unannotated, low quality EST sequences is the detection of coding regions and the correction of frameshift errors that they often...
Retelska, Dorota, Beaudoing, Emmanuel, Notredame, Cédric, Jongeneel, C Victor, Bucher, Philipp
Abstract Background The comparison of complete genomes has revealed surprisingly large numbers of conserved non-protein-coding (CNC) DNA regions. However, the biological function of CNC remains...
MyHits: improvements to an interactive resource for analyzing protein sequences (2007)
Pagni, Marco, Ioannidis, Vassilios, Cerutti, Lorenzo, Zahn-Zabal, Monique, Jongeneel, C. Victor, Hau, Jörg, ...
The MyHits web site (http://myhits.isb-sib.ch) is an integrated service dedicated to the analysis of protein sequences. Since its first description in 2004, both the user interface and the back end...
Rapid evolution of cancer/testis genes on the X chromosome (2007)
Stevenson, Brian J, Iseli, Christian, Panji, Sumir, Zahn-Zabal, Monique, Hide, Winston, Old, Lloyd J, ...
Abstract Background Cancer/testis (CT) genes are normally expressed only in germ cells, but can be activated in the cancer state. This unusual property, together with the finding that many CT...
Marco Pagni, Vassilios Ioannidis, Lorenzo Cerutti, Monique Zahn-zabal, C. Victor Jongeneel, Jörg Hau, ...
improvements to an interactive resource for
Grigoriadis, Anita, Mackay, Alan, Reis-Filho, Jorge S, Steele, Dawn, Iseli, Christian, Stevenson, Brian J, ...
Abstract Introduction Diverse microarray and sequencing technologies have been widely used to characterise the molecular changes in malignant epithelial cells in breast cancers. Such gene expression...
Similarities and differences of polyadenylation signals in human and fly (2006)
Retelska, Dorota, Iseli, Christian, Bucher, Philipp, Jongeneel, C Victor, Naef, Felix
Abstract Background Cleavage of messenger RNA (mRNA) precursors is an essential step in mRNA maturation. The signal recognized by the cleavage enzyme complex has been characterized as an A rich...
Bioinformatics: decoding the genome (2005)
Jongeneel, C Victor, Deutsch, Sam, Michielin, Olivier, Thomas, Arthur, Descombes, Patrick
Extracting the fundamental genomic sequence from the DNA From Genome to Sequence : Biology in the early 21st century has been radically transformed by the availability of the full genome sequences of...
Rapid and selective surveillance of Arabidopsis thaliana genome annotations with Centrifuge. (2005)
Florence Arm, C. Victor Jongeneel, Edward E
Summary: Centrifuge is a user-friendly system with which to simultaneously access Arabidopsis gene annotations and intra- and inter-organism sequence comparison data. The tool allows rapid retrieval...
Deutsch, Samuel, Lyle, Robert, Dermitzakis, Emmanouil T., Attar, Homa, Subrahmanyan, Lakshman, Gehrig, Corinne, ...
Inter-individual differences in gene expression are likely to account for an important fraction of phenotypic differences, including susceptibility to common disorders. Recent studies have shown...
An atlas of human gene expression from massively parallel signature sequencing (MPSS) (2005)
Jongeneel, C. Victor, Delorenzi, Mauro, Iseli, Christian, Zhou, Daixing, Haudenschild, Christian D., Khrebtukova, Irina, ...
We have used massively parallel signature sequencing (MPSS) to sample the transcriptomes of 32 normal human tissues to an unprecedented depth, thus documenting the patterns of expression of almost...
Rapid and selective surveillance of Arabidopsis thaliana genome annotations with Centrifuge (2005)
Armand, Florence, Bucher, Philipp, Jongeneel, C. Victor, Farmer, Edward E.
Summary: Centrifuge is a user-friendly system to simultaneously access Arabidopsis gene annotations and intra- and inter-organism sequence comparison data. The tool allows rapid retrieval of...
Rapid and selective surveillance of Arabidopsis thaliana genome annotations with Centrifuge (2005)
Armand, Florence, Bucher, Philipp, Jongeneel, C. Victor, Farmer, Edward E.
Summary: Centrifuge is a user-friendly system with which to simultaneously access Arabidopsis gene annotations and intra- and inter-organism sequence comparison data. The tool allows rapid retrieval...
Deutsch, Samuel, Lyle, Robert, Dermitzakis, Emmanouil T., Attar, Homa, Subrahmanyan, Lakshman, Gehrig, Corinne, ...
Inter-individual differences in gene expression are likely to account for an important fraction of phenotypic differences, including susceptibility to common disorders. Recent studies have shown...
MyHits: a new interactive resource for protein annotation and domain identification (2004)
Marco Pagni, Vassilios Ioannidis, Lorenzo Cerutti, Monique Zahn-zabal, C. Victor Jongeneel, Laurent Falquet
The MyHits web server
MyHits: a new interactive resource for protein annotation and domain identification (2004)
Pagni, Marco, Ioannidis, Vassilios, Cerutti, Lorenzo, Zahn-Zabal, Monique, Jongeneel, C. Victor, Falquet, Laurent
The MyHits web server (http://myhits.isb-sib.ch) is a new integrated service dedicated to the annotation of protein sequences and to the analysis of their domains and signatures. Guest users can use...
trome, trEST and trGEN: databases of predicted protein sequences (2004)
Sperisen, Peter, Iseli, Christian, Pagni, Marco, Stevenson, Brian J., Bucher, Philipp, Jongeneel, C. Victor
We previously introduced two new protein databases (trEST and trGEN) of hypothetical protein sequences predicted from EST and HTG sequences, respectively. Here, we present the updates made on these...
Swiss EMBnet node web server (2003)
Laurent Falquet, Lorenza Bordoli, Vassilios Ioannidis, Marco Pagni, C. Victor Jongeneel
EMBnet is a consortium of collaborating bioinformatics groups located mainly within Europe
eVOC: A Controlled Vocabulary for Unifying Gene Expression Data (2003)
Kelso, Janet, Visagie, Johann, Theiler, Gregory, Christoffels, Alan, Bardien, Soraya, Smedley, Damian, ...
Expression data contribute significantly to the biological value of the sequenced human genome,providing extensive information about gene structure and the pattern of gene expression. ESTs,together...
Swiss EMBnet node web server (2003)
Falquet, Laurent, Bordoli, Lorenza, Ioannidis, Vassilios, Pagni, Marco, Jongeneel, C. Victor
EMBnet is a consortium of collaborating bioinformatics groups located mainly within Europe (http://www.embnet.org). Each member country is represented by a ‘node’, a group responsible for the...
Long-Range Heterogeneity at the 3' Ends of Human mRNAs (2002)
Iseli, Christian, Stevenson, Brian J., De Souza, Sandro J., Samaia, Helena B., Camargo, Anamaria A., Buetow, Kenneth H., ...
Long-Range Heterogeneity at the 3' Ends of Human mRNAs (2002)
Iseli, Christian, Stevenson, Brian J., De Souza, Sandro J., Samaia, Helena B., Camargo, Anamaria A., Buetow, Kenneth H., ...
Making sense of score statistics for sequence alignments (2001)
Pagni, Marco, Jongeneel, C. Victor
The search for similarity between two biological sequences lies at the core of many applications in bioinformatics. This paper aims to highlight a few of the principles that should be kept in mind...
Searching the expressed sequence tag (EST) databases: Panning for genes (2000)
The genomes of living organisms contain many elements, including genes coding for proteins. The portions of the genes expressed as mature mRNA, collectively known as the transcriptome, represent only...
Lisby, Steen, Müller, Kai M., Jongeneel, C. Victor, Saurat, Jean-Hilaire, Hauser, Conrad, Borst, J.
A critical role of tumor necrosis factor (TNF)-α in irritant contact dermatitis and in the challenge phase of allergic contact dermatitis has recently been demonstrated in vivo. As in situ...
Peitsch, Manuel C., Jongeneel, C. Victor, Arai, K.
Based on the similarity in primary structure between the newly characterized ligand for CD40 (CD40L) and the tumor necrosis factors (TNFs), we have modeled a detailed 3-D structure for CD40L. We used...
Replication of herpes simplex virus type I DNA in permeabilized infected cells (1980)
Jongeneel, C. Victor, Bachenheimer, Steven L.
Herpes simplex type 1 (HSV)-infected Vero cells can be permeabilized by a combination of hypotonic shock and a mild emulsifier, gum arabic. Permeabilized cells will incorporate triphosphate...
Shotgun sequencing of the human transcriptome with ORF expressed sequence tags
Dias Neto, Emmanuel, Garcia Correa, Ricardo, Verjovski-Almeida, Sergio, Briones, Marcelo R. S., Nagai, Maria Aparecida, Da Silva, Wilson, ...
Theoretical considerations predict that amplification of expressed gene transcripts by reverse transcription–PCR using arbitrarily chosen primers will result in the preferential amplification of...
Jongeneel, C. Victor, Iseli, Christian, Stevenson, Brian J., Riggins, Gregory J., Lal, Anita, Mackay, Alan, ...
Whereas information is rapidly accumulating about the structure and position of genes encoded in the human genome, less is known about the complexity and relative abundance of their expression in...
Falquet, Laurent, Bordoli, Lorenza, Ioannidis, Vassilios, Pagni, Marco, Jongeneel, C. Victor
EMBnet is a consortium of collaborating bioinformatics groups located mainly within Europe (http://www.embnet.org). Each member country is represented by a ‘node’, a group responsible for the...
Long-Range Heterogeneity at the 3′ Ends of Human mRNAs
Iseli, Christian, Stevenson, Brian J., De Souza, Sandro J., Samaia, Helena B., Camargo, Anamaria A., Buetow, Kenneth H., ...
The publication of a draft of the human genome and of large collections of transcribed sequences has made it possible to study the complex relationship between the transcriptome and the genome. In...
Brentani, Helena, Caballero, Otávia L., Camargo, Anamaria A., Da Silva, Aline M., Da Silva, Wilson Araújo, Neto, Emmanuel Dias, ...
Whereas genome sequencing defines the genetic potential of an organism, transcript sequencing defines the utilization of this potential and links the genome with most areas of biology. To exploit the...
trome, trEST and trGEN: databases of predicted protein sequences
Sperisen, Peter, Iseli, Christian, Pagni, Marco, Stevenson, Brian J., Bucher, Philipp, Jongeneel, C. Victor
We previously introduced two new protein databases (trEST and trGEN) of hypothetical protein sequences predicted from EST and HTG sequences, respectively. Here, we present the updates made on these...
eVOC: A Controlled Vocabulary for Unifying Gene Expression Data
Kelso, Janet, Visagie, Johann, Theiler, Gregory, Christoffels, Alan, Bardien, Soraya, Smedley, Damian, ...
Expression data contribute significantly to the biological value of the sequenced human genome,providing extensive information about gene structure and the pattern of gene expression. ESTs,together...
MyHits: a new interactive resource for protein annotation and domain identification
Pagni, Marco, Ioannidis, Vassilios, Cerutti, Lorenzo, Zahn-Zabal, Monique, Jongeneel, C. Victor, Falquet, Laurent
The MyHits web server (http://myhits.isb-sib.ch) is a new integrated service dedicated to the annotation of protein sequences and to the analysis of their domains and signatures. Guest users can use...
Identification of cancer/testis-antigen genes by massively parallel signature sequencing
Chen, Yao-Tseng, Scanlan, Matthew J., Venditti, Charis A., Chua, Ramon, Theiler, Gregory, Stevenson, Brian J., ...
Massively parallel signature sequencing (MPSS) generates millions of short sequence tags corresponding to transcripts from a single RNA preparation. Most MPSS tags can be unambiguously assigned to...
An atlas of human gene expression from massively parallel signature sequencing (MPSS)
Jongeneel, C. Victor, Delorenzi, Mauro, Iseli, Christian, Zhou, Daixing, Haudenschild, Christian D., Khrebtukova, Irina, ...
We have used massively parallel signature sequencing (MPSS) to sample the transcriptomes of 32 normal human tissues to an unprecedented depth, thus documenting the patterns of expression of almost...
Similarities and differences of polyadenylation signals in human and fly
Retelska, Dorota, Iseli, Christian, Bucher, Philipp, Jongeneel, C Victor, Naef, Felix
Shotgun sequencing of the human transcriptome with ORF expressed sequence tags
Dias Neto, Emmanuel, Garcia Correa, Ricardo, Verjovski-Almeida, Sergio, Briones, Marcelo R. S., Nagai, Maria Aparecida, Da Silva, Wilson, ...
Theoretical considerations predict that amplification of expressed gene transcripts by reverse transcription–PCR using arbitrarily chosen primers will result in the preferential amplification of...
Jongeneel, C. Victor, Iseli, Christian, Stevenson, Brian J., Riggins, Gregory J., Lal, Anita, Mackay, Alan, ...
Whereas information is rapidly accumulating about the structure and position of genes encoded in the human genome, less is known about the complexity and relative abundance of their expression in...
Falquet, Laurent, Bordoli, Lorenza, Ioannidis, Vassilios, Pagni, Marco, Jongeneel, C. Victor
EMBnet is a consortium of collaborating bioinformatics groups located mainly within Europe (http://www.embnet.org). Each member country is represented by a ‘node’, a group responsible for the...
Long-Range Heterogeneity at the 3′ Ends of Human mRNAs
Iseli, Christian, Stevenson, Brian J., De Souza, Sandro J., Samaia, Helena B., Camargo, Anamaria A., Buetow, Kenneth H., ...
The publication of a draft of the human genome and of large collections of transcribed sequences has made it possible to study the complex relationship between the transcriptome and the genome. In...
Brentani, Helena, Caballero, Otávia L., Camargo, Anamaria A., Da Silva, Aline M., Da Silva, Wilson Araújo, Neto, Emmanuel Dias, ...
Whereas genome sequencing defines the genetic potential of an organism, transcript sequencing defines the utilization of this potential and links the genome with most areas of biology. To exploit the...
trome, trEST and trGEN: databases of predicted protein sequences
Sperisen, Peter, Iseli, Christian, Pagni, Marco, Stevenson, Brian J., Bucher, Philipp, Jongeneel, C. Victor
We previously introduced two new protein databases (trEST and trGEN) of hypothetical protein sequences predicted from EST and HTG sequences, respectively. Here, we present the updates made on these...
eVOC: A Controlled Vocabulary for Unifying Gene Expression Data
Kelso, Janet, Visagie, Johann, Theiler, Gregory, Christoffels, Alan, Bardien, Soraya, Smedley, Damian, ...
Expression data contribute significantly to the biological value of the sequenced human genome,providing extensive information about gene structure and the pattern of gene expression. ESTs,together...
MyHits: a new interactive resource for protein annotation and domain identification
Pagni, Marco, Ioannidis, Vassilios, Cerutti, Lorenzo, Zahn-Zabal, Monique, Jongeneel, C. Victor, Falquet, Laurent
The MyHits web server (http://myhits.isb-sib.ch) is a new integrated service dedicated to the annotation of protein sequences and to the analysis of their domains and signatures. Guest users can use...
Identification of cancer/testis-antigen genes by massively parallel signature sequencing
Chen, Yao-Tseng, Scanlan, Matthew J., Venditti, Charis A., Chua, Ramon, Theiler, Gregory, Stevenson, Brian J., ...
Massively parallel signature sequencing (MPSS) generates millions of short sequence tags corresponding to transcripts from a single RNA preparation. Most MPSS tags can be unambiguously assigned to...
An atlas of human gene expression from massively parallel signature sequencing (MPSS)
Jongeneel, C. Victor, Delorenzi, Mauro, Iseli, Christian, Zhou, Daixing, Haudenschild, Christian D., Khrebtukova, Irina, ...
We have used massively parallel signature sequencing (MPSS) to sample the transcriptomes of 32 normal human tissues to an unprecedented depth, thus documenting the patterns of expression of almost...
Similarities and differences of polyadenylation signals in human and fly
Retelska, Dorota, Iseli, Christian, Bucher, Philipp, Jongeneel, C Victor, Naef, Felix
Grigoriadis, Anita, Mackay, Alan, Reis-Filho, Jorge S, Steele, Dawn, Iseli, Christian, Stevenson, Brian J, ...
Rapid evolution of cancer/testis genes on the X chromosome
Stevenson, Brian J, Iseli, Christian, Panji, Sumir, Zahn-Zabal, Monique, Hide, Winston, Old, Lloyd J, ...
Indexing Strategies for Rapid Searches of Short Words in Genome Sequences
Iseli, Christian, Ambrosini, Giovanna, Bucher, Philipp, Jongeneel, C. Victor
Searching for matches between large collections of short (14–30 nucleotides) words and sequence databases comprising full genomes or transcriptomes is a common task in biological sequence analysis....
MyHits: improvements to an interactive resource for analyzing protein sequences
Pagni, Marco, Ioannidis, Vassilios, Cerutti, Lorenzo, Zahn-Zabal, Monique, Jongeneel, C. Victor, Hau, Jörg, ...
The MyHits web site (http://myhits.isb-sib.ch) is an integrated service dedicated to the analysis of protein sequences. Since its first description in 2004, both the user interface and the back end...
Genome-wide analysis of cancer/testis gene expression
Hofmann, Oliver, Caballero, Otavia L., Stevenson, Brian J., Chen, Yao-Tseng, Cohen, Tzeela, Chua, Ramon, ...
Cancer/Testis (CT) genes, normally expressed in germ line cells but also activated in a wide range of cancer types, often encode antigens that are immunogenic in cancer patients, and present...