Philosophy for 1.7.x: In order to reduce the number of dependencies, we are actively encouraging ... more Philosophy for 1.7.x: In order to reduce the number of dependencies, we are actively encouraging developers wanting to submit new code with additional dependencies to release code in a separate repository and release it on CPAN. We can help assist in this process and can also place this under the 'bioperl' Github organization (and similarly under the bioperl umbrella account in CPAN), though this is not required. We will also be moving additonal code to other repositories and will release them separately on CPAN. Modules considered obsolute (relies on a dead web service or utilizes strict dependencies that are also considered obsolete) will be removed. 1.7.0 - "Disney" <code>[New site] * We have migrated to Github Pages. This was actually planned, but the recent OBF server compromise forced our hand. Brian Osborne [bosborne] took this under his wing to move docs and has done a tremendous amount of work formatting the site and working out some of the idiosyncr...
Bars 1–7 correspond to all West tumor libraries (CGAP_MD_HG7, CGAP_MD_HS29, CGAP_MD_G329, GSM757,... more Bars 1–7 correspond to all West tumor libraries (CGAP_MD_HG7, CGAP_MD_HS29, CGAP_MD_G329, GSM757, GSM758, GSM14760, GSM2385 and bars 8–10 correspond to all East tumor libraries (GSM7800, GSM8505, GSM8867). The tag normalized expression level appears in the CGAP format value (Tags per 200,000) plotted in a logarithmic scale.<b>Copyright information:</b>Taken from "In Silico analysis of Gastric carcinoma Serial Analysis of Gene Expression libraries reveals different profiles associated with ethnicity"http://www.molecular-cancer.com/content/7/1/22Molecular Cancer 2008;7():22-22.Published online 27 Feb 2008PMCID:PMC2323622.
To the left and shown in orange color, the significant tags with higher expression in the West tu... more To the left and shown in orange color, the significant tags with higher expression in the West tumor libraries; to the right and shown in blue color, the significant tags with higher expression in the East tumor libraries.<b>Copyright information:</b>Taken from "In Silico analysis of Gastric carcinoma Serial Analysis of Gene Expression libraries reveals different profiles associated with ethnicity"http://www.molecular-cancer.com/content/7/1/22Molecular Cancer 2008;7():22-22.Published online 27 Feb 2008PMCID:PMC2323622.
To the left and shown in green color, the significant tags with higher expression in the normal l... more To the left and shown in green color, the significant tags with higher expression in the normal libraries; to the right and shown in red color, the significant tags with higher expression in the tumor libraries.<b>Copyright information:</b>Taken from "In Silico analysis of Gastric carcinoma Serial Analysis of Gene Expression libraries reveals different profiles associated with ethnicity"http://www.molecular-cancer.com/content/7/1/22Molecular Cancer 2008;7():22-22.Published online 27 Feb 2008PMCID:PMC2323622.
In (A) blue line is the East cell line (MKN45) and red line is the West cell line (N87). In (B) b... more In (A) blue line is the East cell line (MKN45) and red line is the West cell line (N87). In (B) blue line is the East cell line (MKN45) and red line is the West cell line (AGS). Both genes are over-expressed in the East (MKN45) cell line.<b>Copyright information:</b>Taken from "In Silico analysis of Gastric carcinoma Serial Analysis of Gene Expression libraries reveals different profiles associated with ethnicity"http://www.molecular-cancer.com/content/7/1/22Molecular Cancer 2008;7():22-22.Published online 27 Feb 2008PMCID:PMC2323622.
Lanes 1–4 normal libraries (CGAP_MD_13S, GSM784, CGAP_MD_14S, GSM14780), lanes 5–11 West tumor li... more Lanes 1–4 normal libraries (CGAP_MD_13S, GSM784, CGAP_MD_14S, GSM14780), lanes 5–11 West tumor libraries (CGAP_MD_HG7, CGAP_MD_HS29, CGAP_MD_G329, GSM757, GSM758, GSM14760, GSM2385) and lanes 12–14 East tumor libraries (GSM7800, GSM8505, and GSM8867). Only the top of the dendrogram is shown here. The full dendrogram appear in Additional File .<b>Copyright information:</b>Taken from "In Silico analysis of Gastric carcinoma Serial Analysis of Gene Expression libraries reveals different profiles associated with ethnicity"http://www.molecular-cancer.com/content/7/1/22Molecular Cancer 2008;7():22-22.Published online 27 Feb 2008PMCID:PMC2323622.
Database : the journal of biological databases and curation, 2016
Eukaryotic genes are typically interrupted by intragenic, noncoding sequences termed introns. How... more Eukaryotic genes are typically interrupted by intragenic, noncoding sequences termed introns. However, some genes lack introns in their coding sequence (CDS) and are generally known as 'single exon genes' (SEGs). In this work, a SEG is defined as a nuclear, protein-coding gene that lacks introns in its CDS. Whereas, many public databases of Eukaryotic multi-exon genes are available, there are only two specialized databases for SEGs. The present work addresses the need for a more extensive and diverse database by creating SinEx DB, a publicly available, searchable database of predicted SEGs from 10 completely sequenced mammalian genomes including human. SinEx DB houses the DNA and protein sequence information of these SEGs and includes their functional predictions (KOG) and the relative distribution of these functions within species. The information is stored in a relational database built with My SQL Server 5.1.33 and the complete dataset of SEG sequences and their functiona...
Metagenomic analysis reveals adaptations to a psychrotrophic lifestyle in a low temperature acid ... more Metagenomic analysis reveals adaptations to a psychrotrophic lifestyle in a low temperature acid mine drainage stream
The present invention concerns a connecting device comprising a connector having an inner sleeve ... more The present invention concerns a connecting device comprising a connector having an inner sleeve and an outer cylindrical sleeve sliding axially in relation to the inner sleeve. The inner sleeve has on its outside a very wide V-shaped groove defining two ramps. The outer sleeve has a series of protuberances resting against the side walls of the groove and biased inwardly by a split ring. The protuberances may be integral with the split ring.
Objetivo: La introduccion del Antigeno Prostatico Especifico (APE) como herramienta de uso masivo... more Objetivo: La introduccion del Antigeno Prostatico Especifico (APE) como herramienta de uso masivo en la deteccion precoz de cancer prostatico (CaP), parece ser al menos parcialmente responsable de la disminucion en la mortalidad observada en el ultimo tiempo. Sin embargo, el APE tiene una baja especificidad como marcador de cancer, especialmente en el rango de 4 a 10 ng/ml donde existe una alta sobreposicion con otras patologias de mayor prevalencia como por ejemplo, Hiperplasia Prostatica Benigna (HPB). Es por esto, que existe una busqueda constante de nuevos marcadores. Nuestro objetivo fue caracterizar el perfil de expresion genica del CaP utilizando microarray. Material y metodos: Doce casos de CaP con PSA 10 ng/ml fueron seleccionados prospectivamente para analisis de microarray para 96 genes caracteristicos de tejido prostatico. Los analisis se efectuaron por el metodo de Hierarchical Clustering y se realizo Transcripcion Reversa y Reaccion de Polimerasa en Cadena para confirm...
The composition of the vaginal microbiome, including both the presence of pathogens involved in s... more The composition of the vaginal microbiome, including both the presence of pathogens involved in sexually transmitted infections (STI) as well as commensal microbiota, has been shown to have important associations for a woman’s reproductive and general health. Currently, healthcare providers cannot offer comprehensive vaginal microbiome screening, but are limited to the detection of individual pathogens, such as high-risk human papillomavirus (hrHPV), the predominant cause of cervical cancer. There is no single test on the market that combines HPV, STI, and microbiome screening. Here, we describe a novel inclusive women’s health assay that combines self-sampling with sequencing-based HPV detection and genotyping, vaginal microbiome analysis, and STI-associated pathogen detection. The assay includes genotyping and detection of 14 hrHPV types, 5 low-risk HPV types (lrHPV), as well as the relative abundance of 32 bacterial taxa of clinical importance, including Lactobacillus, Sneathia, ...
Philosophy for 1.7.x: In order to reduce the number of dependencies, we are actively encouraging ... more Philosophy for 1.7.x: In order to reduce the number of dependencies, we are actively encouraging developers wanting to submit new code with additional dependencies to release code in a separate repository and release it on CPAN. We can help assist in this process and can also place this under the 'bioperl' Github organization (and similarly under the bioperl umbrella account in CPAN), though this is not required. We will also be moving additonal code to other repositories and will release them separately on CPAN. Modules considered obsolute (relies on a dead web service or utilizes strict dependencies that are also considered obsolete) will be removed. 1.7.0 - "Disney" <code>[New site] * We have migrated to Github Pages. This was actually planned, but the recent OBF server compromise forced our hand. Brian Osborne [bosborne] took this under his wing to move docs and has done a tremendous amount of work formatting the site and working out some of the idiosyncr...
Bars 1–7 correspond to all West tumor libraries (CGAP_MD_HG7, CGAP_MD_HS29, CGAP_MD_G329, GSM757,... more Bars 1–7 correspond to all West tumor libraries (CGAP_MD_HG7, CGAP_MD_HS29, CGAP_MD_G329, GSM757, GSM758, GSM14760, GSM2385 and bars 8–10 correspond to all East tumor libraries (GSM7800, GSM8505, GSM8867). The tag normalized expression level appears in the CGAP format value (Tags per 200,000) plotted in a logarithmic scale.<b>Copyright information:</b>Taken from "In Silico analysis of Gastric carcinoma Serial Analysis of Gene Expression libraries reveals different profiles associated with ethnicity"http://www.molecular-cancer.com/content/7/1/22Molecular Cancer 2008;7():22-22.Published online 27 Feb 2008PMCID:PMC2323622.
To the left and shown in orange color, the significant tags with higher expression in the West tu... more To the left and shown in orange color, the significant tags with higher expression in the West tumor libraries; to the right and shown in blue color, the significant tags with higher expression in the East tumor libraries.<b>Copyright information:</b>Taken from "In Silico analysis of Gastric carcinoma Serial Analysis of Gene Expression libraries reveals different profiles associated with ethnicity"http://www.molecular-cancer.com/content/7/1/22Molecular Cancer 2008;7():22-22.Published online 27 Feb 2008PMCID:PMC2323622.
To the left and shown in green color, the significant tags with higher expression in the normal l... more To the left and shown in green color, the significant tags with higher expression in the normal libraries; to the right and shown in red color, the significant tags with higher expression in the tumor libraries.<b>Copyright information:</b>Taken from "In Silico analysis of Gastric carcinoma Serial Analysis of Gene Expression libraries reveals different profiles associated with ethnicity"http://www.molecular-cancer.com/content/7/1/22Molecular Cancer 2008;7():22-22.Published online 27 Feb 2008PMCID:PMC2323622.
In (A) blue line is the East cell line (MKN45) and red line is the West cell line (N87). In (B) b... more In (A) blue line is the East cell line (MKN45) and red line is the West cell line (N87). In (B) blue line is the East cell line (MKN45) and red line is the West cell line (AGS). Both genes are over-expressed in the East (MKN45) cell line.<b>Copyright information:</b>Taken from "In Silico analysis of Gastric carcinoma Serial Analysis of Gene Expression libraries reveals different profiles associated with ethnicity"http://www.molecular-cancer.com/content/7/1/22Molecular Cancer 2008;7():22-22.Published online 27 Feb 2008PMCID:PMC2323622.
Lanes 1–4 normal libraries (CGAP_MD_13S, GSM784, CGAP_MD_14S, GSM14780), lanes 5–11 West tumor li... more Lanes 1–4 normal libraries (CGAP_MD_13S, GSM784, CGAP_MD_14S, GSM14780), lanes 5–11 West tumor libraries (CGAP_MD_HG7, CGAP_MD_HS29, CGAP_MD_G329, GSM757, GSM758, GSM14760, GSM2385) and lanes 12–14 East tumor libraries (GSM7800, GSM8505, and GSM8867). Only the top of the dendrogram is shown here. The full dendrogram appear in Additional File .<b>Copyright information:</b>Taken from "In Silico analysis of Gastric carcinoma Serial Analysis of Gene Expression libraries reveals different profiles associated with ethnicity"http://www.molecular-cancer.com/content/7/1/22Molecular Cancer 2008;7():22-22.Published online 27 Feb 2008PMCID:PMC2323622.
Database : the journal of biological databases and curation, 2016
Eukaryotic genes are typically interrupted by intragenic, noncoding sequences termed introns. How... more Eukaryotic genes are typically interrupted by intragenic, noncoding sequences termed introns. However, some genes lack introns in their coding sequence (CDS) and are generally known as 'single exon genes' (SEGs). In this work, a SEG is defined as a nuclear, protein-coding gene that lacks introns in its CDS. Whereas, many public databases of Eukaryotic multi-exon genes are available, there are only two specialized databases for SEGs. The present work addresses the need for a more extensive and diverse database by creating SinEx DB, a publicly available, searchable database of predicted SEGs from 10 completely sequenced mammalian genomes including human. SinEx DB houses the DNA and protein sequence information of these SEGs and includes their functional predictions (KOG) and the relative distribution of these functions within species. The information is stored in a relational database built with My SQL Server 5.1.33 and the complete dataset of SEG sequences and their functiona...
Metagenomic analysis reveals adaptations to a psychrotrophic lifestyle in a low temperature acid ... more Metagenomic analysis reveals adaptations to a psychrotrophic lifestyle in a low temperature acid mine drainage stream
The present invention concerns a connecting device comprising a connector having an inner sleeve ... more The present invention concerns a connecting device comprising a connector having an inner sleeve and an outer cylindrical sleeve sliding axially in relation to the inner sleeve. The inner sleeve has on its outside a very wide V-shaped groove defining two ramps. The outer sleeve has a series of protuberances resting against the side walls of the groove and biased inwardly by a split ring. The protuberances may be integral with the split ring.
Objetivo: La introduccion del Antigeno Prostatico Especifico (APE) como herramienta de uso masivo... more Objetivo: La introduccion del Antigeno Prostatico Especifico (APE) como herramienta de uso masivo en la deteccion precoz de cancer prostatico (CaP), parece ser al menos parcialmente responsable de la disminucion en la mortalidad observada en el ultimo tiempo. Sin embargo, el APE tiene una baja especificidad como marcador de cancer, especialmente en el rango de 4 a 10 ng/ml donde existe una alta sobreposicion con otras patologias de mayor prevalencia como por ejemplo, Hiperplasia Prostatica Benigna (HPB). Es por esto, que existe una busqueda constante de nuevos marcadores. Nuestro objetivo fue caracterizar el perfil de expresion genica del CaP utilizando microarray. Material y metodos: Doce casos de CaP con PSA 10 ng/ml fueron seleccionados prospectivamente para analisis de microarray para 96 genes caracteristicos de tejido prostatico. Los analisis se efectuaron por el metodo de Hierarchical Clustering y se realizo Transcripcion Reversa y Reaccion de Polimerasa en Cadena para confirm...
The composition of the vaginal microbiome, including both the presence of pathogens involved in s... more The composition of the vaginal microbiome, including both the presence of pathogens involved in sexually transmitted infections (STI) as well as commensal microbiota, has been shown to have important associations for a woman’s reproductive and general health. Currently, healthcare providers cannot offer comprehensive vaginal microbiome screening, but are limited to the detection of individual pathogens, such as high-risk human papillomavirus (hrHPV), the predominant cause of cervical cancer. There is no single test on the market that combines HPV, STI, and microbiome screening. Here, we describe a novel inclusive women’s health assay that combines self-sampling with sequencing-based HPV detection and genotyping, vaginal microbiome analysis, and STI-associated pathogen detection. The assay includes genotyping and detection of 14 hrHPV types, 5 low-risk HPV types (lrHPV), as well as the relative abundance of 32 bacterial taxa of clinical importance, including Lactobacillus, Sneathia, ...
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