Insights into gliomagenesis: systems biology unravels key pathways (2009)
De Souza, Sandro J, Stransky, Beatriz, Camargo, Anamaria A
Abstract Technological advances have enabled a better characterization of all the genetic alterations in tumors. A picture that emerges is that tumor cells are much more genetically heterogeneous...
Pinheiro, Daniel G, Galante, Pedro AF, De Souza, Sandro J, Zago, Marco A, Silva, Wilson A
Abstract Background High-throughput molecular approaches for gene expression profiling, such as Serial Analysis of Gene Expression (SAGE), Massively Parallel Signature Sequencing (MPSS) or...
Galante, Pedro A. F., Trimarchi, Jeff, Cepko, Constance L., De Souza, Sandro J., Ohno-Machado, Lucila, Kuo, Winston P.
Summary: A critical step in any SAGE, MPSS and SBS data analysis is tag-to-gene assignment. Current available tools are limited by a tag-by-tag annotation process and/or do not provide the dataset...
Sense-antisense pairs in mammals: functional and evolutionary considerations (2007)
Galante, Pedro AF, Vidal, Daniel O, De Souza, Jorge E, Camargo, Anamaria A, De Souza, Sandro J
Abstract Background A significant number of genes in mammalian genomes are being found to have natural antisense transcripts (NATs). These sense-antisense (S-AS) pairs are believed to be involved in...
Galante, Pedro A. F., Trimarchi, Jeff, Cepko, Constance L., De Souza, Sandro J., Ohno-Machado, Lucila, Kuo, Winston P.
Summary: A critical step in any SAGE, MPSS, and SBS data analysis is tag-to-gene assignment. Current available tools are limited by a tag-by-tag annotation process and/or do not provide the dataset...
The impact of SNPs on the interpretation of SAGE and MPSS experimental data (2004)
Silva, Ana Paula M., Galante, Pedro A. F., Riggins, Gregory J., De Souza, Sandro J., Camargo, Anamaria A.
Serial Analysis of Gene Expression (SAGE) and Massively Parallel Signature Sequencing (MPSS) are powerful techniques for gene expression analysis. A crucial step in analyzing SAGE and MPSS data is...
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., ...
Do Introns Favor or Avoid Regions of Amino Acid Conservation? (2002)
Endo, Toshinori, Fedorov, Alexei, De Souza, Sandro J., Gilbert, Walter
Are intron positions correlated with regions of high amino acid conservation? For a set of ancient conserved proteins, with intronless prokaryotic but intron-containing eukaryotic homologs, multiple...
Generation of a database containing discordant intron positions in eukaryotic genes (MIDB) (2001)
Sakharkar, Meena K., Tan, Tin Wee, De Souza, Sandro J.
Motivation: Intron sliding is the relocation of intron–exon boundaries over short distances and is often also referred to as intron slippage or intron migration or intron drift. We have generated a...
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...
Relationship between “proto-splice sites” and intron phases: Evidence from dicodon analysis
Long, Manyuan, De Souza, Sandro J., Rosenberg, Carl, Gilbert, Walter
The coding sequence at the boundaries of exons flanking nuclear introns shows some degree of conservation. To the extent that such sequences might be recognized by the splicing machinery, this...
Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags
De Souza, Sandro J., Camargo, Anamaria A., Briones, Marcelo R. S., Costa, Fernando F., Nagai, Maria Aparecida, Verjovski-Almeida, Sergio, ...
Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of...
De Souza, Sandro J., Long, Manyuan, Klein, Robert J., Roy, Scott, Lin, Shin, Gilbert, Walter
We present evidence that a well defined subset of intron positions shows a non-random distribution in ancient genes. We analyze a database of ancient conserved regions drawn from GenBank 101 to...
Gilbert, Walter, De Souza, Sandro J., Long, Manyuan
We discuss two tests of the hypothesis that the first genes were assembled from exons. The hypothesis of exon shuffling in the progenote predicts that intron phases will be correlated so that exons...
The contribution of 700,000 ORF sequence tags to the definition of the human transcriptome
Camargo, Anamaria A., Samaia, Helena P. B., Dias-Neto, Emmanuel, Simão, Daniel F., Migotto, Italo A., Briones, Marcelo R. S., ...
Open reading frame expressed sequences tags (ORESTES) differ from conventional ESTs by providing sequence data from the central protein coding portion of transcripts. We generated a total of 696,745...
Fedorov, Alexei, Cao, Xiaohong, Saxonov, Serge, De Souza, Sandro J., Roy, Scott W., Gilbert, Walter
Do introns delineate elements of protein tertiary structure? This issue is crucial to the debate about the role and origin of introns. We present an analysis of the full set of proteins with known...
An anatomy of normal and malignant gene expression
Boon, Kathy, Osório, Elisson C., Greenhut, Susan F., Schaefer, Carl F., Shoemaker, Jennifer, Polyak, Kornelia, ...
A gene's expression pattern provides clues to its role in normal physiology and disease. To provide quantitative expression levels on a genome-wide scale, the Cancer Genome Anatomy Project (CGAP)...
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...
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones
Imanishi, Tadashi, Itoh, Takeshi, Suzuki, Yutaka, O'Donovan, Claire, Fukuchi, Satoshi, Koyanagi, Kanako O, ...
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this...
The impact of SNPs on the interpretation of SAGE and MPSS experimental data
Silva, Ana Paula M., Galante, Pedro A. F., Riggins, Gregory J., De Souza, Sandro J., Camargo, Anamaria A.
Serial Analysis of Gene Expression (SAGE) and Massively Parallel Signature Sequencing (MPSS) are powerful techniques for gene expression analysis. A crucial step in analyzing SAGE and MPSS data is...
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...
Relationship between “proto-splice sites” and intron phases: Evidence from dicodon analysis
Long, Manyuan, De Souza, Sandro J., Rosenberg, Carl, Gilbert, Walter
The coding sequence at the boundaries of exons flanking nuclear introns shows some degree of conservation. To the extent that such sequences might be recognized by the splicing machinery, this...
Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags
De Souza, Sandro J., Camargo, Anamaria A., Briones, Marcelo R. S., Costa, Fernando F., Nagai, Maria Aparecida, Verjovski-Almeida, Sergio, ...
Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of...
De Souza, Sandro J., Long, Manyuan, Klein, Robert J., Roy, Scott, Lin, Shin, Gilbert, Walter
We present evidence that a well defined subset of intron positions shows a non-random distribution in ancient genes. We analyze a database of ancient conserved regions drawn from GenBank 101 to...
Gilbert, Walter, De Souza, Sandro J., Long, Manyuan
We discuss two tests of the hypothesis that the first genes were assembled from exons. The hypothesis of exon shuffling in the progenote predicts that intron phases will be correlated so that exons...
The contribution of 700,000 ORF sequence tags to the definition of the human transcriptome
Camargo, Anamaria A., Samaia, Helena P. B., Dias-Neto, Emmanuel, Simão, Daniel F., Migotto, Italo A., Briones, Marcelo R. S., ...
Open reading frame expressed sequences tags (ORESTES) differ from conventional ESTs by providing sequence data from the central protein coding portion of transcripts. We generated a total of 696,745...
Fedorov, Alexei, Cao, Xiaohong, Saxonov, Serge, De Souza, Sandro J., Roy, Scott W., Gilbert, Walter
Do introns delineate elements of protein tertiary structure? This issue is crucial to the debate about the role and origin of introns. We present an analysis of the full set of proteins with known...
An anatomy of normal and malignant gene expression
Boon, Kathy, Osório, Elisson C., Greenhut, Susan F., Schaefer, Carl F., Shoemaker, Jennifer, Polyak, Kornelia, ...
A gene's expression pattern provides clues to its role in normal physiology and disease. To provide quantitative expression levels on a genome-wide scale, the Cancer Genome Anatomy Project (CGAP)...
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...
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones
Imanishi, Tadashi, Itoh, Takeshi, Suzuki, Yutaka, O'Donovan, Claire, Fukuchi, Satoshi, Koyanagi, Kanako O, ...
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this...
The impact of SNPs on the interpretation of SAGE and MPSS experimental data
Silva, Ana Paula M., Galante, Pedro A. F., Riggins, Gregory J., De Souza, Sandro J., Camargo, Anamaria A.
Serial Analysis of Gene Expression (SAGE) and Massively Parallel Signature Sequencing (MPSS) are powerful techniques for gene expression analysis. A crucial step in analyzing SAGE and MPSS data is...
Sense-antisense pairs in mammals: functional and evolutionary considerations
Galante, Pedro AF, Vidal, Daniel O, De Souza, Jorge E, Camargo, Anamaria A, De Souza, Sandro J
Analysis of a catalog of S-AS pairs in the human and mouse genomes revealed several putative roles for natural antisense transcripts and showed that some are artifacts of cDNA library construction.
Parmigiani, Raphael B., Bettoni, Fabiana, Vibranovski, Maria D., Lopes, Marilene H., Martins, Waleska K., Cunha, Isabela W., ...
Cancer/testis (CT) antigens are immunogenic proteins expressed in normal gametogenic tissues and in different types of tumors. CT antigens are promising candidates for cancer immunotherapy, and the...
Definition of the Gene Content of the Human Genome: The Need for Deep Experimental Verification
Simpson, Andrew J. G., De Souza, Sandro J., Camargo, Anamaria A., Brentani, Ricardo R.
Based on the analysis of the drafts of the human genome sequence, it is being speculated that our species may possess an unexpectedly low number of genes. The quality of the drafts, the impossibility...
Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line
Zhao, Qi, Caballero, Otavia L., Levy, Samuel, Stevenson, Brian J., Iseli, Christian, De Souza, Sandro J., ...
We have identified new genomic alterations in the breast cancer cell line HCC1954, using high-throughput transcriptome sequencing. With 120 Mb of cDNA sequences, we were able to identify genomic...
Insights into gliomagenesis: systems biology unravels key pathways
De Souza, Sandro J, Stransky, Beatriz, Camargo, Anamaria A
Technological advances have enabled a better characterization of all the genetic alterations in tumors. A picture that emerges is that tumor cells are much more genetically heterogeneous than...