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...
Seniski, Gerusa G, Camargo, Anamaria A, Ierardi, Daniela F, Ramos, Edneia AS, Grochoski, Mariana, Ribeiro, Enilze SF, ...
Abstract Background ADAM33 protein is a member of the family of transmembrane glycoproteins composed of multidomains. ADAM family members have different activities, such as proteolysis and adhesion,...
CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens (2009)
Almeida, Luiz Gonzaga, Sakabe, Noboru J., DeOliveira, Alice R., Silva, Maria Cristina C., Mundstein, Alex S., Cohen, Tzeela, ...
The potency of the immune response has still to be harnessed effectively to combat human cancers. However, the discovery of T-cell targets in melanomas and other tumors has raised the possibility...
De Oliveira, João, Fernandes, Flora, Cruz, Angela K, Trombela, Viviane, Monteiro, Elisângela, Camargo, Anamaria A, ...
Abstract Background Leishmania (Leishmania) amazonensis infection in man results in a clinical spectrum of disease manifestations ranging from cutaneous to mucosal or visceral involvement. In the...
Hu, Yanhui, Rolfs, Andreas, Bhullar, Bhupinder, Murthy, Tellamraju V. S., Zhu, Cong, Berger, Michael F., ...
The availability of an annotated genome sequence for the yeast Saccharomyces cerevisiae has made possible the proteome-scale study of protein function and protein–protein interactions. These...
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...
Hu, Yanhui, Rolfs, Andreas, Bhullar, Bhupinder, Murthy, Tellamraju V. S., Zhu, Cong, Berger, Michael F., ...
The availability of an annotated genome sequence for the yeast Saccharomyces cerevisiae has made possible the proteome-scale study of protein function and protein–protein interactions. These...
Anamaria A. Camargo, Ricardo R. Brentani
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...
A Transcript Finishing Initiative for Closing Gaps in the Human Transcriptome (2004)
Sogayar, Mari Cleide, Camargo, Anamaria A.
We report the results of a transcript finishing initiative, undertaken for the purpose of identifying and characterizing novel human transcripts, in which RT-PCR was used to bridge gaps between...
Generation of longer 3' cDNA fragments from massively parallel signature sequencing tags (2004)
Silva, Ana Paula M., Chen, Jianjun, Carraro, Dirce M., Wang, San Ming, Camargo, Anamaria A.
Massively Parallel Signature Sequencing (MPSS) is a powerful technique for genome-wide gene expression analysis, which, similar to SAGE, relies on the production of short tags proximal to the 3′end...
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...
A Transcript Finishing Initiative for Closing Gaps in the Human Transcriptome (2004)
Sogayar, Mari Cleide, Camargo, Anamaria A.
We report the results of a transcript finishing initiative, undertaken for the purpose of identifying and characterizing novel human transcripts, in which RT-PCR was used to bridge gaps between...
CagA status of Helicobacter pylori infection and p53 gene mutations in gastric adenocarcinoma (2003)
Magalhães, Paula P., Queiroz, Dulciene M.M., Camargo, Anamaria A., Simpson, Andrew J.G.
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., ...
Anamaria A. Camargo, Ricardo R. Brentani
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...
Directed Gap Closure in Large-Scale Sequencing Projects (2001)
Frohme, Marcus, Camargo, Anamaria A., Czink, Claudia, Matsukuma, Adriana Y., Simpson, Andrew J.G., Hoheisel, Jörg D., ...
Sertié, Andréa Laurato, Sossi, Vitorio, Camargo, AnaMaria A., Zatz, Mayana, Brahe, Christina, Passos-Bueno, Maria Rita
Knobloch syndrome (KS) is an autosomal recessive disorder defined by the occurrence of high myopia, vitreoretinal degeneration with retinal detachment, macular abnormalities and occipital...
Mapping analysis of the Xylella fastidiosa genome (2000)
Frohme, Marcus, Camargo, Anamaria A., Heber, Steffen, Czink, Claudia, Simpson, Andrew J. D., Hoheisel, Jörg D., ...
A cosmid library was made of the 2.7 Mb genome of the Gram-negative plant pathogenic bacterium Xylella fastidiosa and analysed by hybridisation mapping. Clones taken from the library as well as...
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...
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...
Mapping analysis of the Xylella fastidiosa genome
Frohme, Marcus, Camargo, Anamaria A., Heber, Steffen, Czink, Claudia, Simpson, Andrew J. D., Hoheisel, Jörg D., ...
A cosmid library was made of the 2.7 Mb genome of the Gram-negative plant pathogenic bacterium Xylella fastidiosa and analysed by hybridisation mapping. Clones taken from the library as well as...
Collaborative research networks work
Camargo, Anamaria A., Simpson, Andrew J.G.
Brazil was heralded for completion of the first genome sequence of a plant pathogen following the development of a virtual research center — a collaborative network of laboratories throughout 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...
Directed Gap Closure in Large-Scale Sequencing Projects
Frohme, Marcus, Camargo, Anamaria A., Czink, Claudia, Matsukuma, Adriana Y., Simpson, Andrew J.G., Hoheisel, Jörg D., ...
A problem in many sequencing projects is the final closure of gaps left in the clone libraries, which serve as templates for sequencing, because of uncloned or unclonable genomic areas. By use of the...
A Transcript Finishing Initiative for Closing Gaps in the Human Transcriptome
Sogayar, Mari Cleide, Camargo, Anamaria A.
We report the results of a transcript finishing initiative, undertaken for the purpose of identifying and characterizing novel human transcripts, in which RT-PCR was used to bridge gaps between...
Generation of longer 3′ cDNA fragments from massively parallel signature sequencing tags
Silva, Ana Paula M., Chen, Jianjun, Carraro, Dirce M., Wang, San Ming, Camargo, Anamaria A.
Massively Parallel Signature Sequencing (MPSS) is a powerful technique for genome-wide gene expression analysis, which, similar to SAGE, relies on the production of short tags proximal to the 3′end...
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...
Vasconcelos, Ana Tereza R., Ferreira, Henrique B., Bizarro, Cristiano V., Bonatto, Sandro L., Carvalho, Marcos O., Pinto, Paulo M., ...
This work reports the results of analyses of three complete mycoplasma genomes, a pathogenic (7448) and a nonpathogenic (J) strain of the swine pathogen Mycoplasma hyopneumoniae and a strain of the...
Colorectal Cancer “Methylator Phenotype”: Fact or Artifact?1
Anacleto, Charles, Leopoldino, Andréia M, Rossi, Benedito, Soares, Fernando A, Lopes, Ademar, Rocha, José Cláudio C, ...
It has been proposed that human colorectal tumors can be classified into two groups: one in which methylation is rare, and another with methylation of several loci associated with a “CpG island...
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...
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...
Mapping analysis of the Xylella fastidiosa genome
Frohme, Marcus, Camargo, Anamaria A., Heber, Steffen, Czink, Claudia, Simpson, Andrew J. D., Hoheisel, Jörg D., ...
A cosmid library was made of the 2.7 Mb genome of the Gram-negative plant pathogenic bacterium Xylella fastidiosa and analysed by hybridisation mapping. Clones taken from the library as well as...
Collaborative research networks work
Camargo, Anamaria A., Simpson, Andrew J.G.
Brazil was heralded for completion of the first genome sequence of a plant pathogen following the development of a virtual research center — a collaborative network of laboratories throughout 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...
Directed Gap Closure in Large-Scale Sequencing Projects
Frohme, Marcus, Camargo, Anamaria A., Czink, Claudia, Matsukuma, Adriana Y., Simpson, Andrew J.G., Hoheisel, Jörg D., ...
A problem in many sequencing projects is the final closure of gaps left in the clone libraries, which serve as templates for sequencing, because of uncloned or unclonable genomic areas. By use of the...
A Transcript Finishing Initiative for Closing Gaps in the Human Transcriptome
Sogayar, Mari Cleide, Camargo, Anamaria A.
We report the results of a transcript finishing initiative, undertaken for the purpose of identifying and characterizing novel human transcripts, in which RT-PCR was used to bridge gaps between...
Generation of longer 3′ cDNA fragments from massively parallel signature sequencing tags
Silva, Ana Paula M., Chen, Jianjun, Carraro, Dirce M., Wang, San Ming, Camargo, Anamaria A.
Massively Parallel Signature Sequencing (MPSS) is a powerful technique for genome-wide gene expression analysis, which, similar to SAGE, relies on the production of short tags proximal to the 3′end...
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...
Vasconcelos, Ana Tereza R., Ferreira, Henrique B., Bizarro, Cristiano V., Bonatto, Sandro L., Carvalho, Marcos O., Pinto, Paulo M., ...
This work reports the results of analyses of three complete mycoplasma genomes, a pathogenic (7448) and a nonpathogenic (J) strain of the swine pathogen Mycoplasma hyopneumoniae and a strain of the...
Colorectal Cancer “Methylator Phenotype”: Fact or Artifact?1
Anacleto, Charles, Leopoldino, Andréia M, Rossi, Benedito, Soares, Fernando A, Lopes, Ademar, Rocha, José Cláudio C, ...
It has been proposed that human colorectal tumors can be classified into two groups: one in which methylation is rare, and another with methylation of several loci associated with a “CpG island...
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...
Hu, Yanhui, Rolfs, Andreas, Bhullar, Bhupinder, Murthy, Tellamraju V. S., Zhu, Cong, Berger, Michael F., ...
The availability of an annotated genome sequence for the yeast Saccharomyces cerevisiae has made possible the proteome-scale study of protein function and protein–protein interactions. These...
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...
Seniski, Gerusa G, Camargo, Anamaria A, Ierardi, Daniela F, Ramos, Edneia AS, Grochoski, Mariana, Ribeiro, Enilze SF, ...
CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens
Almeida, Luiz Gonzaga, Sakabe, Noboru J., DeOliveira, Alice R., Silva, Maria Cristina C., Mundstein, Alex S., Cohen, Tzeela, ...
The potency of the immune response has still to be harnessed effectively to combat human cancers. However, the discovery of T-cell targets in melanomas and other tumors has raised the possibility...
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...