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...
Wang, Xiaosong, Zhao, Haitao, Xu, Qingwen, Jin, Weibo, Liu, Changning, Zhang, Huagang, ...
Tumor-associated antigens (TAAs) have been the most actively employed targets in the clinical diagnosis and treatment of human carcinoma, such as PSA in the diagnosis of prostate cancer and NY-ESO-1...
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...
Spatz, Linus, Kissinger, Jessica C., Redondo, Rodrigo A. F., Pires, Edina C. R., Simpson, Andrew J. G., ...
The first and second internal transcribed spacer regions (ITS1 and ITS2) of the ribosomal DNA of Biomphalaria tenagophila complex (B. tenagophila, B. occidentalis, and B. t. guaibensis) were...
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., ...
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., ...
Terra,Ana Paula Sarreta, Silva-Vergara,Mario León, Gomes,Roseli Aparecida S., Pereira,Carla Lisandra L., Simpson,Andrew J.G., Caballero,Otávia Luísa
O citomegalovirus é um patógeno importante em indivíduos infectados pelo vírus da imunodeficiência humana (HIV). A carga viral do CMV parece ser preditora da sintomatologia das infecções...
Pereira,Rinaldo W., Pires,Edina R., Duarte,Ana P.M., Moura,Ricardo P. De, Monteiro,Elisangela, Torloni,Humberto, ...
The identification of a 32-bp deletion in the cc-chemokine receptor-5 gene (CCR5delta32 allele) that renders homozygous individuals highly resistant to HIV infection has prompted worldwide...
Bevilacqua,Roberta A.U., Corvello,Cassandra M., Duarte,Ana Paula, Simpson,Andrew J.G.
A crucial role for the adenomatous polyposis colonic (APC) gene in colorectal carcinogenesis has been conclusively established, but, the role of APC in gastric tumors remains controversial. APC...
Sturzeneker, Rosane, Bevilacqua, Roberta A.U., Haddad, Luciana A., Simpson, Andrew J.G., Pena, Sérgio D.J.
We screened 42 sporadic gastric tumors and found that seven of them had significant microsatellite instability. These were then studied at 26 microsatellite loci, comprising di-, tri- and...
Low stringency-PCR (LS-PCR) allows entirely internally standardized DNA quantitation (1995)
Caballero, Otavia L., Villa, Luisa L., Simpson, Andrew J. G.
Sex determination by low stringency PCR (LS-PCR) (1993)
Neto, Emmanuel Dias, Santos, Fabricio Rodrigues, Pena, Sergio D. J., Simpson, Andrew J. G.
Pena, Sergio D.J., Macedo, Andrea M., Braga, Vania M.M., Rumjanek, Franklin D., Simpson, Andrew J.G.
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...
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...
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...
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...
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...
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...
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...
HPtaa database-potential target genes for clinical diagnosis and immunotherapy of human carcinoma
Wang, Xiaosong, Zhao, Haitao, Xu, Qingwen, Jin, Weibo, Liu, Changning, Zhang, Huagang, ...
Tumor-associated antigens (TAAs) have been the most actively employed targets in the clinical diagnosis and treatment of human carcinoma, such as PSA in the diagnosis of prostate cancer and NY-ESO-1...
Sequence survey of receptor tyrosine kinases reveals mutations in glioblastomas
Rand, Vikki, Huang, Jiaqi, Stockwell, Tim, Ferriera, Steve, Buzko, Oleksandr, Levy, Samuel, ...
It is now clear that tyrosine kinases represent attractive targets for therapeutic intervention in cancer. Recent advances in DNA sequencing technology now provide the opportunity to survey...
Transferable anticancer innate immunity in spontaneous regression/complete resistance mice
Hicks, Amy M., Riedlinger, Gregory, Willingham, Mark C., Alexander-Miller, Martha A., Pettenati, Mark J., ...
Spontaneous regression/complete resistance (SR/CR) mice resist very high doses of cancer cells that are lethal to WT mice even at low doses. In this study, we show that this resistance is mediated by...
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...
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...
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...
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...
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...
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...
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...
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...
Sequence survey of receptor tyrosine kinases reveals mutations in glioblastomas
Rand, Vikki, Huang, Jiaqi, Stockwell, Tim, Ferriera, Steve, Buzko, Oleksandr, Levy, Samuel, ...
It is now clear that tyrosine kinases represent attractive targets for therapeutic intervention in cancer. Recent advances in DNA sequencing technology now provide the opportunity to survey...
HPtaa database-potential target genes for clinical diagnosis and immunotherapy of human carcinoma
Wang, Xiaosong, Zhao, Haitao, Xu, Qingwen, Jin, Weibo, Liu, Changning, Zhang, Huagang, ...
Tumor-associated antigens (TAAs) have been the most actively employed targets in the clinical diagnosis and treatment of human carcinoma, such as PSA in the diagnosis of prostate cancer and NY-ESO-1...
Transferable anticancer innate immunity in spontaneous regression/complete resistance mice
Hicks, Amy M., Riedlinger, Gregory, Willingham, Mark C., Alexander-Miller, Martha A., Pettenati, Mark J., ...
Spontaneous regression/complete resistance (SR/CR) mice resist very high doses of cancer cells that are lethal to WT mice even at low doses. In this study, we show that this resistance is mediated by...
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...
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...
Spisek, Radek, Kukreja, Anjli, Chen, Lin-Chi, Matthews, Phillip, Mazumder, Amitabha, Vesole, David, ...
Specific targets of cellular immunity in human premalignancy are largely unknown. Monoclonal gammopathy of undetermined significance (MGUS) represents a precursor lesion to myeloma (MM). We show that...
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...
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...
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...
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...
CT-X antigen expression in human breast cancer
Grigoriadis, Anita, Caballero, Otavia L., Hoek, Keith S., Da Silva, Leonard, Chen, Yao-Tseng, Shin, Sandra J., ...
Cancer/testis (CT) genes are predominantly expressed in human germ line cells, but not somatic tissues, and frequently become activated in different cancer types. Several CT antigens have already...