ºÝºÝߣshows by User: suryasaha / http://www.slideshare.net/images/logo.gif ºÝºÝߣshows by User: suryasaha / Tue, 29 Mar 2022 18:20:52 GMT ºÝºÝߣShare feed for ºÝºÝߣshows by User: suryasaha An open access resource portal for arthropod vectors and agricultural pathosystems: Agrivectors.org /slideshow/an-open-access-resource-portal-for-arthropod-vectors-and-agricultural-pathosystems-agrivectorsorg/251464971 sahaagrivectorsmar29-220329182052
Arthropod vectors of plant pathogens cause enormous economic losses and are a fundamental challenge for sustainable food production. To develop more effective control of plant pathogens and pests, data pertaining to disease systems need to be consolidated, made accessible, searchable and amenable to data mining. The AgriVectors™ platform is an open access and comprehensive resource for growers, researchers and industry who are working on insect-vectored plant pathogens. The portal connects established public repositories with ‘pathosystem-specific’ data repositories. Current resources include the Asian citrus psyllid, the potato psyllid and the bacterial pathogens they transmit to citrus and Solanaceous plants. Expansion to include resources for other important Hemipteran vectors (whiteflies, leafhoppers, planthoppers, scale, mealybugs etc.), thrips. and mites is planned. There is also the capacity to set up private and protected databases for protected access as needed. Linking visual data with gene expression profiles using 3D microCT technology will expand the understanding and use of diverse and complex data. The AgriVectors portal will extend this model beyond gene-centric omics-data to the broader Systems Biology Pathosystem-wide information, with integrated pest management, behavior, plant health, soil health and climate data to incorporate rapid phenotyping information from greenhouse and field trials. This will establish a foundation for more effective identification and development of solutions for the control of plant diseases. AgriVectors portal creates a user-friendly platform that fosters interdisciplinary collaborations among researchers of diverse plant pathosystems, to simplify data sharing, ideas, and technologies to develop solutions for managing plant diseases. Presented at https://esa.confex.com/esa/2022seb/meetingapp.cgi/Paper/157059]]>
Arthropod vectors of plant pathogens cause enormous economic losses and are a fundamental challenge for sustainable food production. To develop more effective control of plant pathogens and pests, data pertaining to disease systems need to be consolidated, made accessible, searchable and amenable to data mining. The AgriVectors™ platform is an open access and comprehensive resource for growers, researchers and industry who are working on insect-vectored plant pathogens. The portal connects established public repositories with ‘pathosystem-specific’ data repositories. Current resources include the Asian citrus psyllid, the potato psyllid and the bacterial pathogens they transmit to citrus and Solanaceous plants. Expansion to include resources for other important Hemipteran vectors (whiteflies, leafhoppers, planthoppers, scale, mealybugs etc.), thrips. and mites is planned. There is also the capacity to set up private and protected databases for protected access as needed. Linking visual data with gene expression profiles using 3D microCT technology will expand the understanding and use of diverse and complex data. The AgriVectors portal will extend this model beyond gene-centric omics-data to the broader Systems Biology Pathosystem-wide information, with integrated pest management, behavior, plant health, soil health and climate data to incorporate rapid phenotyping information from greenhouse and field trials. This will establish a foundation for more effective identification and development of solutions for the control of plant diseases. AgriVectors portal creates a user-friendly platform that fosters interdisciplinary collaborations among researchers of diverse plant pathosystems, to simplify data sharing, ideas, and technologies to develop solutions for managing plant diseases. Presented at https://esa.confex.com/esa/2022seb/meetingapp.cgi/Paper/157059]]> Tue, 29 Mar 2022 18:20:52 GMT /slideshow/an-open-access-resource-portal-for-arthropod-vectors-and-agricultural-pathosystems-agrivectorsorg/251464971 suryasaha@slideshare.net(suryasaha) An open access resource portal for arthropod vectors and agricultural pathosystems: Agrivectors.org suryasaha Arthropod vectors of plant pathogens cause enormous economic losses and are a fundamental challenge for sustainable food production. To develop more effective control of plant pathogens and pests, data pertaining to disease systems need to be consolidated, made accessible, searchable and amenable to data mining. The AgriVectors™ platform is an open access and comprehensive resource for growers, researchers and industry who are working on insect-vectored plant pathogens. The portal connects established public repositories with ‘pathosystem-specific’ data repositories. Current resources include the Asian citrus psyllid, the potato psyllid and the bacterial pathogens they transmit to citrus and Solanaceous plants. Expansion to include resources for other important Hemipteran vectors (whiteflies, leafhoppers, planthoppers, scale, mealybugs etc.), thrips. and mites is planned. There is also the capacity to set up private and protected databases for protected access as needed. Linking visual data with gene expression profiles using 3D microCT technology will expand the understanding and use of diverse and complex data. The AgriVectors portal will extend this model beyond gene-centric omics-data to the broader Systems Biology Pathosystem-wide information, with integrated pest management, behavior, plant health, soil health and climate data to incorporate rapid phenotyping information from greenhouse and field trials. This will establish a foundation for more effective identification and development of solutions for the control of plant diseases. AgriVectors portal creates a user-friendly platform that fosters interdisciplinary collaborations among researchers of diverse plant pathosystems, to simplify data sharing, ideas, and technologies to develop solutions for managing plant diseases. Presented at https://esa.confex.com/esa/2022seb/meetingapp.cgi/Paper/157059 <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/sahaagrivectorsmar29-220329182052-thumbnail.jpg?width=120&amp;height=120&amp;fit=bounds" /><br> Arthropod vectors of plant pathogens cause enormous economic losses and are a fundamental challenge for sustainable food production. To develop more effective control of plant pathogens and pests, data pertaining to disease systems need to be consolidated, made accessible, searchable and amenable to data mining. The AgriVectors™ platform is an open access and comprehensive resource for growers, researchers and industry who are working on insect-vectored plant pathogens. The portal connects established public repositories with ‘pathosystem-specific’ data repositories. Current resources include the Asian citrus psyllid, the potato psyllid and the bacterial pathogens they transmit to citrus and Solanaceous plants. Expansion to include resources for other important Hemipteran vectors (whiteflies, leafhoppers, planthoppers, scale, mealybugs etc.), thrips. and mites is planned. There is also the capacity to set up private and protected databases for protected access as needed. Linking visual data with gene expression profiles using 3D microCT technology will expand the understanding and use of diverse and complex data. The AgriVectors portal will extend this model beyond gene-centric omics-data to the broader Systems Biology Pathosystem-wide information, with integrated pest management, behavior, plant health, soil health and climate data to incorporate rapid phenotyping information from greenhouse and field trials. This will establish a foundation for more effective identification and development of solutions for the control of plant diseases. AgriVectors portal creates a user-friendly platform that fosters interdisciplinary collaborations among researchers of diverse plant pathosystems, to simplify data sharing, ideas, and technologies to develop solutions for managing plant diseases. Presented at https://esa.confex.com/esa/2022seb/meetingapp.cgi/Paper/157059
An open access resource portal for arthropod vectors and agricultural pathosystems: Agrivectors.org from Surya Saha
]]> 122 0 https://cdn.slidesharecdn.com/ss_thumbnails/sahaagrivectorsmar29-220329182052-thumbnail.jpg?width=120&height=120&fit=bounds presentation Black http://activitystrea.ms/schema/1.0/post http://activitystrea.ms/schema/1.0/posted 0 Functional annotation of invertebrate genomes /slideshow/functional-annotation-of-invertebrate-genomes/238344753 uoaacbsaug30-2020v1-200831213907
Functional annotation of invertebrate genomes with an application in Asian citrus psyllid]]>
Functional annotation of invertebrate genomes with an application in Asian citrus psyllid]]> Mon, 31 Aug 2020 21:39:07 GMT /slideshow/functional-annotation-of-invertebrate-genomes/238344753 suryasaha@slideshare.net(suryasaha) Functional annotation of invertebrate genomes suryasaha Functional annotation of invertebrate genomes with an application in Asian citrus psyllid <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/uoaacbsaug30-2020v1-200831213907-thumbnail.jpg?width=120&amp;height=120&amp;fit=bounds" /><br> Functional annotation of invertebrate genomes with an application in Asian citrus psyllid
Functional annotation of invertebrate genomes from Surya Saha
]]> 371 0 https://cdn.slidesharecdn.com/ss_thumbnails/uoaacbsaug30-2020v1-200831213907-thumbnail.jpg?width=120&height=120&fit=bounds presentation Black http://activitystrea.ms/schema/1.0/post http://activitystrea.ms/schema/1.0/posted 0 Saha UC Davis Plant Pathology seminar Infrastructure for battling the Citrus Greening (HLB) disease: High quality genomes and an open access integrated systems biology portal /slideshow/saha-uc-davis-plant-pathology-seminar-infrastructure-for-battling-the-citrus-greening-hlb-disease-high-quality-genomes-and-an-open-access-integrated-systems-biology-portal/226807463 sahaucdavisppath-200203164118
Rapidly spreading invasive diseases in systems with little or no prior experimental data or resources pose a unique set of challenges for growers, scientists as well as regulators. As a part of a USDA NIFA CAPS project focused on the psyllid, Diaphorina citri, we have released improved genomics resources including high quality genome assemblies and annotation. We have also created an open access web portal for analyses around the Citrus Greening/Huanglongbing disease complex. Citrusgreening.org includes pathosystem-wide resources and bioinformatics tools for multiple Citrus spp. hosts, the Asian citrus psyllid vector (ACP, Diaphorina citri), and multiple pathogens including Candidatus Liberibacter asiaticus (CLas). To the best of our knowledge, this is the first example of a database to use the pathosystem as a holistic framework to understand an insect transmitted plant disease. Users can submit relevant data sets to enable sharing and allow the community to leverage their data within an integrated system. The system includes the metabolic pathway databases CitrusCyc and DiaphorinaCyc with organism specific pathways that can be used to mine metabolomics, transcriptomics and proteomics results to identify pathways and regulatory mechanisms involved in disease response. The Psyllid Expression Network (PEN) contains expression profiles of ACP genes from multiple life stages, tissues, conditions and hosts. The Citrus Expression Network (CEN) contains public expression data from multiple tissues and conditions for various citrus hosts. All tools connect to a central database. The portal also includes electrical penetration graph (EPG) recordings, information about citrus rootstock trials and metabolomics data in addition to traditional omics data types with a goal of combining and mining all information related to the Huanglongbing pathosystem. User-friendly manual curation tools will allow the continuous improvement of knowledge base as more experimental research is published. The portal can be accessed at https://citrusgreening.org/.]]>
Rapidly spreading invasive diseases in systems with little or no prior experimental data or resources pose a unique set of challenges for growers, scientists as well as regulators. As a part of a USDA NIFA CAPS project focused on the psyllid, Diaphorina citri, we have released improved genomics resources including high quality genome assemblies and annotation. We have also created an open access web portal for analyses around the Citrus Greening/Huanglongbing disease complex. Citrusgreening.org includes pathosystem-wide resources and bioinformatics tools for multiple Citrus spp. hosts, the Asian citrus psyllid vector (ACP, Diaphorina citri), and multiple pathogens including Candidatus Liberibacter asiaticus (CLas). To the best of our knowledge, this is the first example of a database to use the pathosystem as a holistic framework to understand an insect transmitted plant disease. Users can submit relevant data sets to enable sharing and allow the community to leverage their data within an integrated system. The system includes the metabolic pathway databases CitrusCyc and DiaphorinaCyc with organism specific pathways that can be used to mine metabolomics, transcriptomics and proteomics results to identify pathways and regulatory mechanisms involved in disease response. The Psyllid Expression Network (PEN) contains expression profiles of ACP genes from multiple life stages, tissues, conditions and hosts. The Citrus Expression Network (CEN) contains public expression data from multiple tissues and conditions for various citrus hosts. All tools connect to a central database. The portal also includes electrical penetration graph (EPG) recordings, information about citrus rootstock trials and metabolomics data in addition to traditional omics data types with a goal of combining and mining all information related to the Huanglongbing pathosystem. User-friendly manual curation tools will allow the continuous improvement of knowledge base as more experimental research is published. The portal can be accessed at https://citrusgreening.org/.]]> Mon, 03 Feb 2020 16:41:18 GMT /slideshow/saha-uc-davis-plant-pathology-seminar-infrastructure-for-battling-the-citrus-greening-hlb-disease-high-quality-genomes-and-an-open-access-integrated-systems-biology-portal/226807463 suryasaha@slideshare.net(suryasaha) Saha UC Davis Plant Pathology seminar Infrastructure for battling the Citrus Greening (HLB) disease: High quality genomes and an open access integrated systems biology portal suryasaha Rapidly spreading invasive diseases in systems with little or no prior experimental data or resources pose a unique set of challenges for growers, scientists as well as regulators. As a part of a USDA NIFA CAPS project focused on the psyllid, Diaphorina citri, we have released improved genomics resources including high quality genome assemblies and annotation. We have also created an open access web portal for analyses around the Citrus Greening/Huanglongbing disease complex. Citrusgreening.org includes pathosystem-wide resources and bioinformatics tools for multiple Citrus spp. hosts, the Asian citrus psyllid vector (ACP, Diaphorina citri), and multiple pathogens including Candidatus Liberibacter asiaticus (CLas). To the best of our knowledge, this is the first example of a database to use the pathosystem as a holistic framework to understand an insect transmitted plant disease. Users can submit relevant data sets to enable sharing and allow the community to leverage their data within an integrated system. The system includes the metabolic pathway databases CitrusCyc and DiaphorinaCyc with organism specific pathways that can be used to mine metabolomics, transcriptomics and proteomics results to identify pathways and regulatory mechanisms involved in disease response. The Psyllid Expression Network (PEN) contains expression profiles of ACP genes from multiple life stages, tissues, conditions and hosts. The Citrus Expression Network (CEN) contains public expression data from multiple tissues and conditions for various citrus hosts. All tools connect to a central database. The portal also includes electrical penetration graph (EPG) recordings, information about citrus rootstock trials and metabolomics data in addition to traditional omics data types with a goal of combining and mining all information related to the Huanglongbing pathosystem. User-friendly manual curation tools will allow the continuous improvement of knowledge base as more experimental research is published. The portal can be accessed at https://citrusgreening.org/. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/sahaucdavisppath-200203164118-thumbnail.jpg?width=120&amp;height=120&amp;fit=bounds" /><br> Rapidly spreading invasive diseases in systems with little or no prior experimental data or resources pose a unique set of challenges for growers, scientists as well as regulators. As a part of a USDA NIFA CAPS project focused on the psyllid, Diaphorina citri, we have released improved genomics resources including high quality genome assemblies and annotation. We have also created an open access web portal for analyses around the Citrus Greening/Huanglongbing disease complex. Citrusgreening.org includes pathosystem-wide resources and bioinformatics tools for multiple Citrus spp. hosts, the Asian citrus psyllid vector (ACP, Diaphorina citri), and multiple pathogens including Candidatus Liberibacter asiaticus (CLas). To the best of our knowledge, this is the first example of a database to use the pathosystem as a holistic framework to understand an insect transmitted plant disease. Users can submit relevant data sets to enable sharing and allow the community to leverage their data within an integrated system. The system includes the metabolic pathway databases CitrusCyc and DiaphorinaCyc with organism specific pathways that can be used to mine metabolomics, transcriptomics and proteomics results to identify pathways and regulatory mechanisms involved in disease response. The Psyllid Expression Network (PEN) contains expression profiles of ACP genes from multiple life stages, tissues, conditions and hosts. The Citrus Expression Network (CEN) contains public expression data from multiple tissues and conditions for various citrus hosts. All tools connect to a central database. The portal also includes electrical penetration graph (EPG) recordings, information about citrus rootstock trials and metabolomics data in addition to traditional omics data types with a goal of combining and mining all information related to the Huanglongbing pathosystem. User-friendly manual curation tools will allow the continuous improvement of knowledge base as more experimental research is published. The portal can be accessed at https://citrusgreening.org/.
Saha UC Davis Plant Pathology seminar Infrastructure for battling the Citrus Greening (HLB) disease: High quality genomes and an open access integrated systems biology portal from Surya Saha
]]> 146 0 https://cdn.slidesharecdn.com/ss_thumbnails/sahaucdavisppath-200203164118-thumbnail.jpg?width=120&height=120&fit=bounds presentation Black http://activitystrea.ms/schema/1.0/post http://activitystrea.ms/schema/1.0/posted 0 Updates on Citrusgreening.org database from USDA NIFA project meeting /slideshow/updates-on-citrusgreeningorg-database-from-usda-nifa-project-meeting/204518507 obj12019database-191211170543
New resources at the Citrusgreening.org portal and future work Mirella Flores-Gonzalez, Marina Mann, Prashant Hosmani, Lukas Mueller, Surya Saha 5th Annual Meeting Indian River State College Fort Pierce, FL]]>
New resources at the Citrusgreening.org portal and future work Mirella Flores-Gonzalez, Marina Mann, Prashant Hosmani, Lukas Mueller, Surya Saha 5th Annual Meeting Indian River State College Fort Pierce, FL]]> Wed, 11 Dec 2019 17:05:43 GMT /slideshow/updates-on-citrusgreeningorg-database-from-usda-nifa-project-meeting/204518507 suryasaha@slideshare.net(suryasaha) Updates on Citrusgreening.org database from USDA NIFA project meeting suryasaha New resources at the Citrusgreening.org portal and future work Mirella Flores-Gonzalez, Marina Mann, Prashant Hosmani, Lukas Mueller, Surya Saha 5th Annual Meeting Indian River State College Fort Pierce, FL <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/obj12019database-191211170543-thumbnail.jpg?width=120&amp;height=120&amp;fit=bounds" /><br> New resources at the Citrusgreening.org portal and future work Mirella Flores-Gonzalez, Marina Mann, Prashant Hosmani, Lukas Mueller, Surya Saha 5th Annual Meeting Indian River State College Fort Pierce, FL
Updates on Citrusgreening.org database from USDA NIFA project meeting from Surya Saha
]]> 165 1 https://cdn.slidesharecdn.com/ss_thumbnails/obj12019database-191211170543-thumbnail.jpg?width=120&height=120&fit=bounds presentation White http://activitystrea.ms/schema/1.0/post http://activitystrea.ms/schema/1.0/posted 0 Updates on the ACP v3 genome and annotation from USDA NIFA project meeting /slideshow/updates-on-the-acp-v3-genome-and-annotation-from-usda-nifa-project-meeting/204515923 obj12019genomeannotation-191211165753
ACP version 3 genome, official gene set version 3 and Isoseq transcriptome Prashant Hosmani, Mirella Flores-Gonzalez, Lukas Mueller, Surya Saha 5th Annual Meeting Indian River State College Fort Pierce, FL]]>
ACP version 3 genome, official gene set version 3 and Isoseq transcriptome Prashant Hosmani, Mirella Flores-Gonzalez, Lukas Mueller, Surya Saha 5th Annual Meeting Indian River State College Fort Pierce, FL]]> Wed, 11 Dec 2019 16:57:53 GMT /slideshow/updates-on-the-acp-v3-genome-and-annotation-from-usda-nifa-project-meeting/204515923 suryasaha@slideshare.net(suryasaha) Updates on the ACP v3 genome and annotation from USDA NIFA project meeting suryasaha ACP version 3 genome, official gene set version 3 and Isoseq transcriptome Prashant Hosmani, Mirella Flores-Gonzalez, Lukas Mueller, Surya Saha 5th Annual Meeting Indian River State College Fort Pierce, FL <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/obj12019genomeannotation-191211165753-thumbnail.jpg?width=120&amp;height=120&amp;fit=bounds" /><br> ACP version 3 genome, official gene set version 3 and Isoseq transcriptome Prashant Hosmani, Mirella Flores-Gonzalez, Lukas Mueller, Surya Saha 5th Annual Meeting Indian River State College Fort Pierce, FL
Updates on the ACP v3 genome and annotation from USDA NIFA project meeting from Surya Saha
]]> 199 1 https://cdn.slidesharecdn.com/ss_thumbnails/obj12019genomeannotation-191211165753-thumbnail.jpg?width=120&height=120&fit=bounds presentation Black http://activitystrea.ms/schema/1.0/post http://activitystrea.ms/schema/1.0/posted 0 AgriVectors: A Data and Systems Resource for Arthropod Vectors of Plant Diseases /slideshow/agrivectors-a-data-and-systems-resource-for-arthropod-vectors-of-plant-diseases/128179460 pag2019agrivectorsphytobiomes-190116144007
Arthropod vectors of pathogens cause enormous economic losses and are a fundamental challenge for sustainable increases in food production, yet agricultural pathosystems remain an underserved area of research. To more effectively fight plant diseases, data pertaining to a disease system needs to be consolidated, made searchable and amenable to data mining. The AgriVectors platform is an open access and comprehensive resource for growers, researchers and industry working on plant pathogens and pathosystems spread by arthropod vectors. The portal connects established public repositories with pathosystem-specific data repositories. The AgriVectors system will provide tools to enable technologies such as RNAi, CRISPR, screening bioassays, etc. to leverage current and emerging knowledge across disciplines. It will also include private and unpublished data, using passwords and secure protocols for restricted access. The portal will be based on the Citrusgreening.org (https://citrusgreening.org/) community resource that was developed as a model for systems biology of tritrophic disease complexes. Citrusgreening.org provides omics and biology resources for the Huanglongbing pathosystem. In addition, it includes a biochemical pathway database for each organism in this disease complex, and an expression atlas with proteomics and RNAseq data from psyllids (http://pen.citrusgreening.org) and citrus (http://cen.citrusgreening.org) across multiple infection states. The AgriVectors portal will extend this model beyond gene-centric omics data to the broader Pathosystem-wide information, with integrated pest management, behavioral, plant health, soil health and climate data to incorporate rapid phenotyping information from research trials, building a foundation for more effectively identifying solutions to combat plant diseases.]]>
Arthropod vectors of pathogens cause enormous economic losses and are a fundamental challenge for sustainable increases in food production, yet agricultural pathosystems remain an underserved area of research. To more effectively fight plant diseases, data pertaining to a disease system needs to be consolidated, made searchable and amenable to data mining. The AgriVectors platform is an open access and comprehensive resource for growers, researchers and industry working on plant pathogens and pathosystems spread by arthropod vectors. The portal connects established public repositories with pathosystem-specific data repositories. The AgriVectors system will provide tools to enable technologies such as RNAi, CRISPR, screening bioassays, etc. to leverage current and emerging knowledge across disciplines. It will also include private and unpublished data, using passwords and secure protocols for restricted access. The portal will be based on the Citrusgreening.org (https://citrusgreening.org/) community resource that was developed as a model for systems biology of tritrophic disease complexes. Citrusgreening.org provides omics and biology resources for the Huanglongbing pathosystem. In addition, it includes a biochemical pathway database for each organism in this disease complex, and an expression atlas with proteomics and RNAseq data from psyllids (http://pen.citrusgreening.org) and citrus (http://cen.citrusgreening.org) across multiple infection states. The AgriVectors portal will extend this model beyond gene-centric omics data to the broader Pathosystem-wide information, with integrated pest management, behavioral, plant health, soil health and climate data to incorporate rapid phenotyping information from research trials, building a foundation for more effectively identifying solutions to combat plant diseases.]]> Wed, 16 Jan 2019 14:40:07 GMT /slideshow/agrivectors-a-data-and-systems-resource-for-arthropod-vectors-of-plant-diseases/128179460 suryasaha@slideshare.net(suryasaha) AgriVectors: A Data and Systems Resource for Arthropod Vectors of Plant Diseases suryasaha Arthropod vectors of pathogens cause enormous economic losses and are a fundamental challenge for sustainable increases in food production, yet agricultural pathosystems remain an underserved area of research. To more effectively fight plant diseases, data pertaining to a disease system needs to be consolidated, made searchable and amenable to data mining. The AgriVectors platform is an open access and comprehensive resource for growers, researchers and industry working on plant pathogens and pathosystems spread by arthropod vectors. The portal connects established public repositories with pathosystem-specific data repositories. The AgriVectors system will provide tools to enable technologies such as RNAi, CRISPR, screening bioassays, etc. to leverage current and emerging knowledge across disciplines. It will also include private and unpublished data, using passwords and secure protocols for restricted access. The portal will be based on the Citrusgreening.org (https://citrusgreening.org/) community resource that was developed as a model for systems biology of tritrophic disease complexes. Citrusgreening.org provides omics and biology resources for the Huanglongbing pathosystem. In addition, it includes a biochemical pathway database for each organism in this disease complex, and an expression atlas with proteomics and RNAseq data from psyllids (http://pen.citrusgreening.org) and citrus (http://cen.citrusgreening.org) across multiple infection states. The AgriVectors portal will extend this model beyond gene-centric omics data to the broader Pathosystem-wide information, with integrated pest management, behavioral, plant health, soil health and climate data to incorporate rapid phenotyping information from research trials, building a foundation for more effectively identifying solutions to combat plant diseases. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/pag2019agrivectorsphytobiomes-190116144007-thumbnail.jpg?width=120&amp;height=120&amp;fit=bounds" /><br> Arthropod vectors of pathogens cause enormous economic losses and are a fundamental challenge for sustainable increases in food production, yet agricultural pathosystems remain an underserved area of research. To more effectively fight plant diseases, data pertaining to a disease system needs to be consolidated, made searchable and amenable to data mining. The AgriVectors platform is an open access and comprehensive resource for growers, researchers and industry working on plant pathogens and pathosystems spread by arthropod vectors. The portal connects established public repositories with pathosystem-specific data repositories. The AgriVectors system will provide tools to enable technologies such as RNAi, CRISPR, screening bioassays, etc. to leverage current and emerging knowledge across disciplines. It will also include private and unpublished data, using passwords and secure protocols for restricted access. The portal will be based on the Citrusgreening.org (https://citrusgreening.org/) community resource that was developed as a model for systems biology of tritrophic disease complexes. Citrusgreening.org provides omics and biology resources for the Huanglongbing pathosystem. In addition, it includes a biochemical pathway database for each organism in this disease complex, and an expression atlas with proteomics and RNAseq data from psyllids (http://pen.citrusgreening.org) and citrus (http://cen.citrusgreening.org) across multiple infection states. The AgriVectors portal will extend this model beyond gene-centric omics data to the broader Pathosystem-wide information, with integrated pest management, behavioral, plant health, soil health and climate data to incorporate rapid phenotyping information from research trials, building a foundation for more effectively identifying solutions to combat plant diseases.
AgriVectors: A Data and Systems Resource for Arthropod Vectors of Plant Diseases from Surya Saha
]]> 447 3 https://cdn.slidesharecdn.com/ss_thumbnails/pag2019agrivectorsphytobiomes-190116144007-thumbnail.jpg?width=120&height=120&fit=bounds presentation Black http://activitystrea.ms/schema/1.0/post http://activitystrea.ms/schema/1.0/posted 0 Visualization of insect vector-plant pathogen interactions in the citrus greening pathosystem using genomics, transcriptomics and proteomics /suryasaha/visualization-of-insect-vectorplant-pathogen-interactions-in-the-citrus-greening-pathosystem-using-genomics-transcriptomics-and-proteomics pag2019arthropodworkshopacp-190115220811
The Asian citrus psyllid (ACP,Diaphorina citri) is the insect vector of the bacterium Candidatus Liberibacter asiaticus (CLas), the causal agent for citrus greening disease, which threatens the citrus industry worldwide. The Asian citrus psyllid genome project is a coordinated effort to define the psyllid genome, including the identification and annotation of every psyllid gene. This discovery of psyllid genes regulating CLas acquisition and transmission by the psyllid will transform future vector management strategies for controlling citrus greening. Advances in psyllid genome sequencing to improve genome assembly, including using Pacbio and long-range Hi-C scaffolding, resulted in the identification of 13 psyllid chromosomes, the first description of chromosome number for this economically important hemipteran insect vector. Together with Pacbio IsoSeq technology to sequence psyllid transcripts from different life stages and those reared on CLas + and - trees, approximately 20,000 putative full-length protein coding psyllid genes were identified. Student driven annotation resulted in more than 500 high quality models of genes involved in CLas-ACP interactions. New assemblies and annotations of the Florida strains of the ACP bacterial endosymbionts, Wolbachia, Profftella, and Carsonella were also characterized from the genome sequencing data. Finally, we developed a data visualization platform, the Psyllid Expression Network (PEN), which is a user-friendly web-based tool for mining gene and protein expression patterns. PEN enabled us to identify tissue and host plant specific changes in ACP genes in response to CLas at the transcript and proteome level. The availability of a high quality reference genome, endosymbiont genomes and tools for analyzing transcriptomics, proteomics and metabolomics data in an integrated, systems biology approach will enable novel approaches to control the transmission of citrus greening disease. The new ACP genome assembly (Diaci v3), PEN and other tools are available on https://citrusgreening.org/ which is our portal for all omics resources for the citrus greening disease. https://plan.core-apps.com/pag_2019/event/b6da6bc5896fea594de507e257910266]]>
The Asian citrus psyllid (ACP,Diaphorina citri) is the insect vector of the bacterium Candidatus Liberibacter asiaticus (CLas), the causal agent for citrus greening disease, which threatens the citrus industry worldwide. The Asian citrus psyllid genome project is a coordinated effort to define the psyllid genome, including the identification and annotation of every psyllid gene. This discovery of psyllid genes regulating CLas acquisition and transmission by the psyllid will transform future vector management strategies for controlling citrus greening. Advances in psyllid genome sequencing to improve genome assembly, including using Pacbio and long-range Hi-C scaffolding, resulted in the identification of 13 psyllid chromosomes, the first description of chromosome number for this economically important hemipteran insect vector. Together with Pacbio IsoSeq technology to sequence psyllid transcripts from different life stages and those reared on CLas + and - trees, approximately 20,000 putative full-length protein coding psyllid genes were identified. Student driven annotation resulted in more than 500 high quality models of genes involved in CLas-ACP interactions. New assemblies and annotations of the Florida strains of the ACP bacterial endosymbionts, Wolbachia, Profftella, and Carsonella were also characterized from the genome sequencing data. Finally, we developed a data visualization platform, the Psyllid Expression Network (PEN), which is a user-friendly web-based tool for mining gene and protein expression patterns. PEN enabled us to identify tissue and host plant specific changes in ACP genes in response to CLas at the transcript and proteome level. The availability of a high quality reference genome, endosymbiont genomes and tools for analyzing transcriptomics, proteomics and metabolomics data in an integrated, systems biology approach will enable novel approaches to control the transmission of citrus greening disease. The new ACP genome assembly (Diaci v3), PEN and other tools are available on https://citrusgreening.org/ which is our portal for all omics resources for the citrus greening disease. https://plan.core-apps.com/pag_2019/event/b6da6bc5896fea594de507e257910266]]> Tue, 15 Jan 2019 22:08:11 GMT /suryasaha/visualization-of-insect-vectorplant-pathogen-interactions-in-the-citrus-greening-pathosystem-using-genomics-transcriptomics-and-proteomics suryasaha@slideshare.net(suryasaha) Visualization of insect vector-plant pathogen interactions in the citrus greening pathosystem using genomics, transcriptomics and proteomics suryasaha The Asian citrus psyllid (ACP,Diaphorina citri) is the insect vector of the bacterium Candidatus Liberibacter asiaticus (CLas), the causal agent for citrus greening disease, which threatens the citrus industry worldwide. The Asian citrus psyllid genome project is a coordinated effort to define the psyllid genome, including the identification and annotation of every psyllid gene. This discovery of psyllid genes regulating CLas acquisition and transmission by the psyllid will transform future vector management strategies for controlling citrus greening. Advances in psyllid genome sequencing to improve genome assembly, including using Pacbio and long-range Hi-C scaffolding, resulted in the identification of 13 psyllid chromosomes, the first description of chromosome number for this economically important hemipteran insect vector. Together with Pacbio IsoSeq technology to sequence psyllid transcripts from different life stages and those reared on CLas + and - trees, approximately 20,000 putative full-length protein coding psyllid genes were identified. Student driven annotation resulted in more than 500 high quality models of genes involved in CLas-ACP interactions. New assemblies and annotations of the Florida strains of the ACP bacterial endosymbionts, Wolbachia, Profftella, and Carsonella were also characterized from the genome sequencing data. Finally, we developed a data visualization platform, the Psyllid Expression Network (PEN), which is a user-friendly web-based tool for mining gene and protein expression patterns. PEN enabled us to identify tissue and host plant specific changes in ACP genes in response to CLas at the transcript and proteome level. The availability of a high quality reference genome, endosymbiont genomes and tools for analyzing transcriptomics, proteomics and metabolomics data in an integrated, systems biology approach will enable novel approaches to control the transmission of citrus greening disease. The new ACP genome assembly (Diaci v3), PEN and other tools are available on https://citrusgreening.org/ which is our portal for all omics resources for the citrus greening disease. https://plan.core-apps.com/pag_2019/event/b6da6bc5896fea594de507e257910266 <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/pag2019arthropodworkshopacp-190115220811-thumbnail.jpg?width=120&amp;height=120&amp;fit=bounds" /><br> The Asian citrus psyllid (ACP,Diaphorina citri) is the insect vector of the bacterium Candidatus Liberibacter asiaticus (CLas), the causal agent for citrus greening disease, which threatens the citrus industry worldwide. The Asian citrus psyllid genome project is a coordinated effort to define the psyllid genome, including the identification and annotation of every psyllid gene. This discovery of psyllid genes regulating CLas acquisition and transmission by the psyllid will transform future vector management strategies for controlling citrus greening. Advances in psyllid genome sequencing to improve genome assembly, including using Pacbio and long-range Hi-C scaffolding, resulted in the identification of 13 psyllid chromosomes, the first description of chromosome number for this economically important hemipteran insect vector. Together with Pacbio IsoSeq technology to sequence psyllid transcripts from different life stages and those reared on CLas + and - trees, approximately 20,000 putative full-length protein coding psyllid genes were identified. Student driven annotation resulted in more than 500 high quality models of genes involved in CLas-ACP interactions. New assemblies and annotations of the Florida strains of the ACP bacterial endosymbionts, Wolbachia, Profftella, and Carsonella were also characterized from the genome sequencing data. Finally, we developed a data visualization platform, the Psyllid Expression Network (PEN), which is a user-friendly web-based tool for mining gene and protein expression patterns. PEN enabled us to identify tissue and host plant specific changes in ACP genes in response to CLas at the transcript and proteome level. The availability of a high quality reference genome, endosymbiont genomes and tools for analyzing transcriptomics, proteomics and metabolomics data in an integrated, systems biology approach will enable novel approaches to control the transmission of citrus greening disease. The new ACP genome assembly (Diaci v3), PEN and other tools are available on https://citrusgreening.org/ which is our portal for all omics resources for the citrus greening disease. https://plan.core-apps.com/pag_2019/event/b6da6bc5896fea594de507e257910266
Visualization of insect vector-plant pathogen interactions in the citrus greening pathosystem using genomics, transcriptomics and proteomics from Surya Saha
]]> 504 2 https://cdn.slidesharecdn.com/ss_thumbnails/pag2019arthropodworkshopacp-190115220811-thumbnail.jpg?width=120&height=120&fit=bounds presentation Black http://activitystrea.ms/schema/1.0/post http://activitystrea.ms/schema/1.0/posted 0 Deciphering the genome of Diaphorina citri to develop solutions for the citrus greening disease /slideshow/deciphering-the-genome-of-diaphorina-citri-to-develop-solutions-for-the-citrus-greening-disease/86349235 cgproject-entoretreat2018-180118123731
The Asian citrus psyllid (Diaphorina citri Kuwayama) is the insect vector of the bacterium Candidatus Liberibacter asiaticus (CLas), the causal agent for the citrus greening or Huanglongbing disease which threatens citrus industry worldwide. This vector is the primary target of approaches to stop the transmission of the pathogen. Accurate structural and functional annotation of the psyllid’s gene models and understanding its interactions with the pathogenic bacterium, CLas, is required for precise targeting using molecular methods such as RNAi. We opted for manual curation of gene families in the draft genome of D. citri (Diaci v1.1, contig N50 34.4Kb) that have key functional roles in D. citri biology and pathology. The community effort resulted in Official Gene Set v1.0 with more than 500 manually curated gene models across developmental, RNAi regulatory, and immune-related pathways. Single copy marker analysis of the current genome shows a significant proportion of 3,350 markers conserved in Hemipterans to be missing (25%) with only 74% present in full-length copies. The manual genome annotation also identified a number of misassemblies and missing genes in the current genome. This is, in-part, due to the complexity introduced when assembling a heterogeneous sample containing DNA from multiple psyllids and exacerbated by the use of short reads. This challenge is common with insect genomes due to the size of individuals. To improve quality of genome assembly, we generated 36.2Gb of Pacbio long reads with a coverage of 80X for the 450Mb psyllid genome. The Canu assembler followed by Dovetail Chicago-based scaffolding was used to create an improved assembly (Diaci v2.0) with a contig N50 of 758.7kb and 1906 contigs. The assembly was polished with Pacbio and Illumina paired-end reads to remove indel and SNP errors. We are employing Dovetail Chicago and 10X Illumina libraries generated from a single psyllid in conjunction with Bionano optical maps to achieve long-range scaffolding of the genome. We have also generated full-length cDNA transcripts from diseased and healthy tissue from multiple life stages with the Pacbio IsoSeq technology. This will be the first time all these methods have been applied to resolve a complex insect genome from a highly heterogeneous sample. The new assembly will be available on https://citrusgreening.org/ which is our portal for all omics resources for the citrusgreening disease. We are continuing with the manual curation effort using the improved genome. We will also present how the improved genome and annotation is contributing to the development of molecular interdiction methods to disrupt the vectoring ability of D. citri. ]]>
The Asian citrus psyllid (Diaphorina citri Kuwayama) is the insect vector of the bacterium Candidatus Liberibacter asiaticus (CLas), the causal agent for the citrus greening or Huanglongbing disease which threatens citrus industry worldwide. This vector is the primary target of approaches to stop the transmission of the pathogen. Accurate structural and functional annotation of the psyllid’s gene models and understanding its interactions with the pathogenic bacterium, CLas, is required for precise targeting using molecular methods such as RNAi. We opted for manual curation of gene families in the draft genome of D. citri (Diaci v1.1, contig N50 34.4Kb) that have key functional roles in D. citri biology and pathology. The community effort resulted in Official Gene Set v1.0 with more than 500 manually curated gene models across developmental, RNAi regulatory, and immune-related pathways. Single copy marker analysis of the current genome shows a significant proportion of 3,350 markers conserved in Hemipterans to be missing (25%) with only 74% present in full-length copies. The manual genome annotation also identified a number of misassemblies and missing genes in the current genome. This is, in-part, due to the complexity introduced when assembling a heterogeneous sample containing DNA from multiple psyllids and exacerbated by the use of short reads. This challenge is common with insect genomes due to the size of individuals. To improve quality of genome assembly, we generated 36.2Gb of Pacbio long reads with a coverage of 80X for the 450Mb psyllid genome. The Canu assembler followed by Dovetail Chicago-based scaffolding was used to create an improved assembly (Diaci v2.0) with a contig N50 of 758.7kb and 1906 contigs. The assembly was polished with Pacbio and Illumina paired-end reads to remove indel and SNP errors. We are employing Dovetail Chicago and 10X Illumina libraries generated from a single psyllid in conjunction with Bionano optical maps to achieve long-range scaffolding of the genome. We have also generated full-length cDNA transcripts from diseased and healthy tissue from multiple life stages with the Pacbio IsoSeq technology. This will be the first time all these methods have been applied to resolve a complex insect genome from a highly heterogeneous sample. The new assembly will be available on https://citrusgreening.org/ which is our portal for all omics resources for the citrusgreening disease. We are continuing with the manual curation effort using the improved genome. We will also present how the improved genome and annotation is contributing to the development of molecular interdiction methods to disrupt the vectoring ability of D. citri. ]]> Thu, 18 Jan 2018 12:37:31 GMT /slideshow/deciphering-the-genome-of-diaphorina-citri-to-develop-solutions-for-the-citrus-greening-disease/86349235 suryasaha@slideshare.net(suryasaha) Deciphering the genome of Diaphorina citri to develop solutions for the citrus greening disease suryasaha The Asian citrus psyllid (Diaphorina citri Kuwayama) is the insect vector of the bacterium Candidatus Liberibacter asiaticus (CLas), the causal agent for the citrus greening or Huanglongbing disease which threatens citrus industry worldwide. This vector is the primary target of approaches to stop the transmission of the pathogen. Accurate structural and functional annotation of the psyllid’s gene models and understanding its interactions with the pathogenic bacterium, CLas, is required for precise targeting using molecular methods such as RNAi. We opted for manual curation of gene families in the draft genome of D. citri (Diaci v1.1, contig N50 34.4Kb) that have key functional roles in D. citri biology and pathology. The community effort resulted in Official Gene Set v1.0 with more than 500 manually curated gene models across developmental, RNAi regulatory, and immune-related pathways. Single copy marker analysis of the current genome shows a significant proportion of 3,350 markers conserved in Hemipterans to be missing (25%) with only 74% present in full-length copies. The manual genome annotation also identified a number of misassemblies and missing genes in the current genome. This is, in-part, due to the complexity introduced when assembling a heterogeneous sample containing DNA from multiple psyllids and exacerbated by the use of short reads. This challenge is common with insect genomes due to the size of individuals. To improve quality of genome assembly, we generated 36.2Gb of Pacbio long reads with a coverage of 80X for the 450Mb psyllid genome. The Canu assembler followed by Dovetail Chicago-based scaffolding was used to create an improved assembly (Diaci v2.0) with a contig N50 of 758.7kb and 1906 contigs. The assembly was polished with Pacbio and Illumina paired-end reads to remove indel and SNP errors. We are employing Dovetail Chicago and 10X Illumina libraries generated from a single psyllid in conjunction with Bionano optical maps to achieve long-range scaffolding of the genome. We have also generated full-length cDNA transcripts from diseased and healthy tissue from multiple life stages with the Pacbio IsoSeq technology. This will be the first time all these methods have been applied to resolve a complex insect genome from a highly heterogeneous sample. The new assembly will be available on https://citrusgreening.org/ which is our portal for all omics resources for the citrusgreening disease. We are continuing with the manual curation effort using the improved genome. We will also present how the improved genome and annotation is contributing to the development of molecular interdiction methods to disrupt the vectoring ability of D. citri. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/cgproject-entoretreat2018-180118123731-thumbnail.jpg?width=120&amp;height=120&amp;fit=bounds" /><br> The Asian citrus psyllid (Diaphorina citri Kuwayama) is the insect vector of the bacterium Candidatus Liberibacter asiaticus (CLas), the causal agent for the citrus greening or Huanglongbing disease which threatens citrus industry worldwide. This vector is the primary target of approaches to stop the transmission of the pathogen. Accurate structural and functional annotation of the psyllid’s gene models and understanding its interactions with the pathogenic bacterium, CLas, is required for precise targeting using molecular methods such as RNAi. We opted for manual curation of gene families in the draft genome of D. citri (Diaci v1.1, contig N50 34.4Kb) that have key functional roles in D. citri biology and pathology. The community effort resulted in Official Gene Set v1.0 with more than 500 manually curated gene models across developmental, RNAi regulatory, and immune-related pathways. Single copy marker analysis of the current genome shows a significant proportion of 3,350 markers conserved in Hemipterans to be missing (25%) with only 74% present in full-length copies. The manual genome annotation also identified a number of misassemblies and missing genes in the current genome. This is, in-part, due to the complexity introduced when assembling a heterogeneous sample containing DNA from multiple psyllids and exacerbated by the use of short reads. This challenge is common with insect genomes due to the size of individuals. To improve quality of genome assembly, we generated 36.2Gb of Pacbio long reads with a coverage of 80X for the 450Mb psyllid genome. The Canu assembler followed by Dovetail Chicago-based scaffolding was used to create an improved assembly (Diaci v2.0) with a contig N50 of 758.7kb and 1906 contigs. The assembly was polished with Pacbio and Illumina paired-end reads to remove indel and SNP errors. We are employing Dovetail Chicago and 10X Illumina libraries generated from a single psyllid in conjunction with Bionano optical maps to achieve long-range scaffolding of the genome. We have also generated full-length cDNA transcripts from diseased and healthy tissue from multiple life stages with the Pacbio IsoSeq technology. This will be the first time all these methods have been applied to resolve a complex insect genome from a highly heterogeneous sample. The new assembly will be available on https://citrusgreening.org/ which is our portal for all omics resources for the citrusgreening disease. We are continuing with the manual curation effort using the improved genome. We will also present how the improved genome and annotation is contributing to the development of molecular interdiction methods to disrupt the vectoring ability of D. citri.
Deciphering the genome of Diaphorina citri to develop solutions for the citrus greening disease from Surya Saha
]]> 269 5 https://cdn.slidesharecdn.com/ss_thumbnails/cgproject-entoretreat2018-180118123731-thumbnail.jpg?width=120&height=120&fit=bounds presentation Black http://activitystrea.ms/schema/1.0/post http://activitystrea.ms/schema/1.0/posted 0 Quality Control of Sequencing Data /slideshow/quality-control-of-sequencing-data/73804417 seqqaex-170328172217
From our 2017 course https://btiplantbioinfocourse.wordpress.com/]]>
From our 2017 course https://btiplantbioinfocourse.wordpress.com/]]> Tue, 28 Mar 2017 17:22:17 GMT /slideshow/quality-control-of-sequencing-data/73804417 suryasaha@slideshare.net(suryasaha) Quality Control of Sequencing Data suryasaha From our 2017 course https://btiplantbioinfocourse.wordpress.com/ <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/seqqaex-170328172217-thumbnail.jpg?width=120&amp;height=120&amp;fit=bounds" /><br> From our 2017 course https://btiplantbioinfocourse.wordpress.com/
Quality Control of Sequencing Data from Surya Saha
]]> 511 2 https://cdn.slidesharecdn.com/ss_thumbnails/seqqaex-170328172217-thumbnail.jpg?width=120&height=120&fit=bounds presentation Black http://activitystrea.ms/schema/1.0/post http://activitystrea.ms/schema/1.0/posted 0 Sequencing 2017 /slideshow/sequencing-2017/73803940 sequencing2017-170328171419
Overview of major sequencing platforms and data formats Presented at our bioinformatics course https://btiplantbioinfocourse.wordpress.com/ ]]>
Overview of major sequencing platforms and data formats Presented at our bioinformatics course https://btiplantbioinfocourse.wordpress.com/ ]]> Tue, 28 Mar 2017 17:14:19 GMT /slideshow/sequencing-2017/73803940 suryasaha@slideshare.net(suryasaha) Sequencing 2017 suryasaha Overview of major sequencing platforms and data formats Presented at our bioinformatics course https://btiplantbioinfocourse.wordpress.com/ <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/sequencing2017-170328171419-thumbnail.jpg?width=120&amp;height=120&amp;fit=bounds" /><br> Overview of major sequencing platforms and data formats Presented at our bioinformatics course https://btiplantbioinfocourse.wordpress.com/
Sequencing 2017 from Surya Saha
]]> 4549 7 https://cdn.slidesharecdn.com/ss_thumbnails/sequencing2017-170328171419-thumbnail.jpg?width=120&height=120&fit=bounds presentation Black http://activitystrea.ms/schema/1.0/post http://activitystrea.ms/schema/1.0/posted 0 Community resources for all y’all Omics /slideshow/community-resources-for-all-yall-omics/73249996 suryaacpgenomecycspen-170317112353
Community resources for the citrusgreening research presented at IRC HLB meeting in March 2017 in Orlando, FL irchlb.org/hlb.aspx]]>
Community resources for the citrusgreening research presented at IRC HLB meeting in March 2017 in Orlando, FL irchlb.org/hlb.aspx]]> Fri, 17 Mar 2017 11:23:53 GMT /slideshow/community-resources-for-all-yall-omics/73249996 suryasaha@slideshare.net(suryasaha) Community resources for all y’all Omics suryasaha Community resources for the citrusgreening research presented at IRC HLB meeting in March 2017 in Orlando, FL irchlb.org/hlb.aspx <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/suryaacpgenomecycspen-170317112353-thumbnail.jpg?width=120&amp;height=120&amp;fit=bounds" /><br> Community resources for the citrusgreening research presented at IRC HLB meeting in March 2017 in Orlando, FL irchlb.org/hlb.aspx
Community resources for all y’all Omics from Surya Saha
]]> 371 5 https://cdn.slidesharecdn.com/ss_thumbnails/suryaacpgenomecycspen-170317112353-thumbnail.jpg?width=120&height=120&fit=bounds presentation Black http://activitystrea.ms/schema/1.0/post http://activitystrea.ms/schema/1.0/posted 0 CitrusCyc: Metabolic Pathway Databases for the C. clementina and C. sinensis Genomes /slideshow/citruscyc-metabolic-pathway-databases-for-the-c-clementina-and-c-sinensis-genomes/71030027 citruscyc-170115130714
Pathway tools metabolic databases for the 2 citrus references genomes]]>
Pathway tools metabolic databases for the 2 citrus references genomes]]> Sun, 15 Jan 2017 13:07:13 GMT /slideshow/citruscyc-metabolic-pathway-databases-for-the-c-clementina-and-c-sinensis-genomes/71030027 suryasaha@slideshare.net(suryasaha) CitrusCyc: Metabolic Pathway Databases for the C. clementina and C. sinensis Genomes suryasaha Pathway tools metabolic databases for the 2 citrus references genomes <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/citruscyc-170115130714-thumbnail.jpg?width=120&amp;height=120&amp;fit=bounds" /><br> Pathway tools metabolic databases for the 2 citrus references genomes
CitrusCyc: Metabolic Pathway Databases for the C. clementina and C. sinensis Genomes from Surya Saha
]]> 1423 4 https://cdn.slidesharecdn.com/ss_thumbnails/citruscyc-170115130714-thumbnail.jpg?width=120&height=120&fit=bounds presentation 000000 http://activitystrea.ms/schema/1.0/post http://activitystrea.ms/schema/1.0/posted 0 Using Long Reads, Optical Maps and Long-Range Scaffolding to improve the Diaphorina citri Genome: An update /slideshow/using-long-reads-optical-maps-and-longrange-scaffolding-to-improve-the-diaphorina-citri-genome-an-update/71029956 suryaacpgenome-170115130233
Improving Diaci1.1 genome with Pacbio, Dovetail, 10X and BioNano technologies]]>
Improving Diaci1.1 genome with Pacbio, Dovetail, 10X and BioNano technologies]]> Sun, 15 Jan 2017 13:02:32 GMT /slideshow/using-long-reads-optical-maps-and-longrange-scaffolding-to-improve-the-diaphorina-citri-genome-an-update/71029956 suryasaha@slideshare.net(suryasaha) Using Long Reads, Optical Maps and Long-Range Scaffolding to improve the Diaphorina citri Genome: An update suryasaha Improving Diaci1.1 genome with Pacbio, Dovetail, 10X and BioNano technologies <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/suryaacpgenome-170115130233-thumbnail.jpg?width=120&amp;height=120&amp;fit=bounds" /><br> Improving Diaci1.1 genome with Pacbio, Dovetail, 10X and BioNano technologies
Using Long Reads, Optical Maps and Long-Range Scaffolding to improve the Diaphorina citri Genome: An update from Surya Saha
]]> 958 6 https://cdn.slidesharecdn.com/ss_thumbnails/suryaacpgenome-170115130233-thumbnail.jpg?width=120&height=120&fit=bounds presentation 000000 http://activitystrea.ms/schema/1.0/post http://activitystrea.ms/schema/1.0/posted 0 Sequencing 2016 /slideshow/sequencing-2016/60179862 sequencing-160329184311
Overview of major sequencing platforms and data formats]]>
Overview of major sequencing platforms and data formats]]> Tue, 29 Mar 2016 18:43:11 GMT /slideshow/sequencing-2016/60179862 suryasaha@slideshare.net(suryasaha) Sequencing 2016 suryasaha Overview of major sequencing platforms and data formats <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/sequencing-160329184311-thumbnail.jpg?width=120&amp;height=120&amp;fit=bounds" /><br> Overview of major sequencing platforms and data formats
Sequencing 2016 from Surya Saha
]]> 1697 4 https://cdn.slidesharecdn.com/ss_thumbnails/sequencing-160329184311-thumbnail.jpg?width=120&height=120&fit=bounds presentation Black http://activitystrea.ms/schema/1.0/post http://activitystrea.ms/schema/1.0/posted 0 Tomato Genome Build SL3.0 /slideshow/tomato-genome-build-sl30/54377577 sol2015sgnworkshop-151026104358-lva1-app6892
Sol2015 SGN workshop]]>
Sol2015 SGN workshop]]> Mon, 26 Oct 2015 10:43:58 GMT /slideshow/tomato-genome-build-sl30/54377577 suryasaha@slideshare.net(suryasaha) Tomato Genome Build SL3.0 suryasaha Sol2015 SGN workshop <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/sol2015sgnworkshop-151026104358-lva1-app6892-thumbnail.jpg?width=120&amp;height=120&amp;fit=bounds" /><br> Sol2015 SGN workshop
Tomato Genome Build SL3.0 from Surya Saha
]]> 1336 4 https://cdn.slidesharecdn.com/ss_thumbnails/sol2015sgnworkshop-151026104358-lva1-app6892-thumbnail.jpg?width=120&height=120&fit=bounds presentation Black http://activitystrea.ms/schema/1.0/post http://activitystrea.ms/schema/1.0/posted 0 Sequencing and Bioinformatics PGRP Summer 2015 /slideshow/sequencing-and-bioinformatics-pgrp-summer-2015/49270317 sequencingpgrp2015-150611135124-lva1-app6891
ºÝºÝߣs for Bioinformatics Workshop I: Introduction to Sequencing and Bioinformatics BTI PGRP Summer 2015cohort]]>
ºÝºÝߣs for Bioinformatics Workshop I: Introduction to Sequencing and Bioinformatics BTI PGRP Summer 2015cohort]]> Thu, 11 Jun 2015 13:51:24 GMT /slideshow/sequencing-and-bioinformatics-pgrp-summer-2015/49270317 suryasaha@slideshare.net(suryasaha) Sequencing and Bioinformatics PGRP Summer 2015 suryasaha ºÝºÝߣs for Bioinformatics Workshop I: Introduction to Sequencing and Bioinformatics BTI PGRP Summer 2015cohort <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/sequencingpgrp2015-150611135124-lva1-app6891-thumbnail.jpg?width=120&amp;height=120&amp;fit=bounds" /><br> ºÝºÝߣs for Bioinformatics Workshop I: Introduction to Sequencing and Bioinformatics BTI PGRP Summer 2015cohort
Sequencing and Bioinformatics PGRP Summer 2015 from Surya Saha
]]> 881 5 https://cdn.slidesharecdn.com/ss_thumbnails/sequencingpgrp2015-150611135124-lva1-app6891-thumbnail.jpg?width=120&height=120&fit=bounds presentation Black http://activitystrea.ms/schema/1.0/post http://activitystrea.ms/schema/1.0/posted 0 Quality Control of Sequencing Data /slideshow/sequencing-quality-filtering/46505798 bti2015seqqaex-150331132946-conversion-gate01
This was presented on Mar 31, 2015 at Boyce Thompson Institute, Ithaca, NY at the 3rd BTI Bioinformatics Course http://btiplantbioinfocourse.wordpress.com/]]>
This was presented on Mar 31, 2015 at Boyce Thompson Institute, Ithaca, NY at the 3rd BTI Bioinformatics Course http://btiplantbioinfocourse.wordpress.com/]]> Tue, 31 Mar 2015 13:29:25 GMT /slideshow/sequencing-quality-filtering/46505798 suryasaha@slideshare.net(suryasaha) Quality Control of Sequencing Data suryasaha This was presented on Mar 31, 2015 at Boyce Thompson Institute, Ithaca, NY at the 3rd BTI Bioinformatics Course http://btiplantbioinfocourse.wordpress.com/ <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/bti2015seqqaex-150331132946-conversion-gate01-thumbnail.jpg?width=120&amp;height=120&amp;fit=bounds" /><br> This was presented on Mar 31, 2015 at Boyce Thompson Institute, Ithaca, NY at the 3rd BTI Bioinformatics Course http://btiplantbioinfocourse.wordpress.com/
Quality Control of Sequencing Data from Surya Saha
]]> 1587 3 https://cdn.slidesharecdn.com/ss_thumbnails/bti2015seqqaex-150331132946-conversion-gate01-thumbnail.jpg?width=120&height=120&fit=bounds presentation Black http://activitystrea.ms/schema/1.0/post http://activitystrea.ms/schema/1.0/posted 0 Sequencing: The Next Generation 2015 /slideshow/sequencing-46505442/46505442 sequencing-150331132032-conversion-gate01
This was presented on Mar 31, 2015 at Boyce Thompson Institute, Ithaca, NY at the 3rd BTI Bioinformatics Course http://btiplantbioinfocourse.wordpress.com/]]>
This was presented on Mar 31, 2015 at Boyce Thompson Institute, Ithaca, NY at the 3rd BTI Bioinformatics Course http://btiplantbioinfocourse.wordpress.com/]]> Tue, 31 Mar 2015 13:20:31 GMT /slideshow/sequencing-46505442/46505442 suryasaha@slideshare.net(suryasaha) Sequencing: The Next Generation 2015 suryasaha This was presented on Mar 31, 2015 at Boyce Thompson Institute, Ithaca, NY at the 3rd BTI Bioinformatics Course http://btiplantbioinfocourse.wordpress.com/ <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/sequencing-150331132032-conversion-gate01-thumbnail.jpg?width=120&amp;height=120&amp;fit=bounds" /><br> This was presented on Mar 31, 2015 at Boyce Thompson Institute, Ithaca, NY at the 3rd BTI Bioinformatics Course http://btiplantbioinfocourse.wordpress.com/
Sequencing: The Next Generation 2015 from Surya Saha
]]> 6467 6 https://cdn.slidesharecdn.com/ss_thumbnails/sequencing-150331132032-conversion-gate01-thumbnail.jpg?width=120&height=120&fit=bounds presentation Black http://activitystrea.ms/schema/1.0/post http://activitystrea.ms/schema/1.0/posted 0 Tomato Genome SL2.50 and Beyond… /slideshow/tomato-genome-sl250-and-beyond/43474361 pag2015sgnworkshop-150113113421-conversion-gate01
The tomato reference genome is one of the most widely used genomic resources in the Solanaceae as well as the wider plant research community. We frequently receive questions from the community regarding the assembly versions. This session will explain the changes in the current version of the tomato genome (SL2.50). The current tomato genome build contains numerous inter-contig gaps (median 931bp, mean 1869bp) and inter-scaffold gaps (median 210Kbp, mean 525Kbp). Updates will be provided regarding the forthcoming tomato genome build (SL3.0) that will include finished BACs (HTGS phase 3) for closing the gaps.]]>
The tomato reference genome is one of the most widely used genomic resources in the Solanaceae as well as the wider plant research community. We frequently receive questions from the community regarding the assembly versions. This session will explain the changes in the current version of the tomato genome (SL2.50). The current tomato genome build contains numerous inter-contig gaps (median 931bp, mean 1869bp) and inter-scaffold gaps (median 210Kbp, mean 525Kbp). Updates will be provided regarding the forthcoming tomato genome build (SL3.0) that will include finished BACs (HTGS phase 3) for closing the gaps.]]> Tue, 13 Jan 2015 11:34:21 GMT /slideshow/tomato-genome-sl250-and-beyond/43474361 suryasaha@slideshare.net(suryasaha) Tomato Genome SL2.50 and Beyond… suryasaha The tomato reference genome is one of the most widely used genomic resources in the Solanaceae as well as the wider plant research community. We frequently receive questions from the community regarding the assembly versions. This session will explain the changes in the current version of the tomato genome (SL2.50). The current tomato genome build contains numerous inter-contig gaps (median 931bp, mean 1869bp) and inter-scaffold gaps (median 210Kbp, mean 525Kbp). Updates will be provided regarding the forthcoming tomato genome build (SL3.0) that will include finished BACs (HTGS phase 3) for closing the gaps. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/pag2015sgnworkshop-150113113421-conversion-gate01-thumbnail.jpg?width=120&amp;height=120&amp;fit=bounds" /><br> The tomato reference genome is one of the most widely used genomic resources in the Solanaceae as well as the wider plant research community. We frequently receive questions from the community regarding the assembly versions. This session will explain the changes in the current version of the tomato genome (SL2.50). The current tomato genome build contains numerous inter-contig gaps (median 931bp, mean 1869bp) and inter-scaffold gaps (median 210Kbp, mean 525Kbp). Updates will be provided regarding the forthcoming tomato genome build (SL3.0) that will include finished BACs (HTGS phase 3) for closing the gaps.
Tomato Genome SL2.50 and Beyond… from Surya Saha
]]> 1519 3 https://cdn.slidesharecdn.com/ss_thumbnails/pag2015sgnworkshop-150113113421-conversion-gate01-thumbnail.jpg?width=120&height=120&fit=bounds presentation 000000 http://activitystrea.ms/schema/1.0/post http://activitystrea.ms/schema/1.0/posted 0 Sequencing /slideshow/sequencing-bioinfo-interns-2014/36755563 sequencing-bioinfointerns2014-140708111612-phpapp02
Surya Saha Sol Genomics Network (SGN) Boyce Thompson Institute, Ithaca, NY @SahaSurya BTI PGRP Summer Internship Program 2014 ]]>
Surya Saha Sol Genomics Network (SGN) Boyce Thompson Institute, Ithaca, NY @SahaSurya BTI PGRP Summer Internship Program 2014 ]]> Tue, 08 Jul 2014 11:16:12 GMT /slideshow/sequencing-bioinfo-interns-2014/36755563 suryasaha@slideshare.net(suryasaha) Sequencing suryasaha Surya Saha Sol Genomics Network (SGN) Boyce Thompson Institute, Ithaca, NY @SahaSurya BTI PGRP Summer Internship Program 2014 <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/sequencing-bioinfointerns2014-140708111612-phpapp02-thumbnail.jpg?width=120&amp;height=120&amp;fit=bounds" /><br> Surya Saha Sol Genomics Network (SGN) Boyce Thompson Institute, Ithaca, NY @SahaSurya BTI PGRP Summer Internship Program 2014
Sequencing from Surya Saha
]]> 805 3 https://cdn.slidesharecdn.com/ss_thumbnails/sequencing-bioinfointerns2014-140708111612-phpapp02-thumbnail.jpg?width=120&height=120&fit=bounds presentation Black http://activitystrea.ms/schema/1.0/post http://activitystrea.ms/schema/1.0/posted 0 https://cdn.slidesharecdn.com/profile-photo-suryasaha-48x48.jpg?cb=1702643166 Working with a cross-matrixed team of molecular and computational biologists on a variety of vector biology, genome assembly, annotation, proteomics, metagenomics, microbiome and transcriptomics projects. Specialties: Computer Science skills: System administration, Virtualization, Machine learning, Artificial Intelligence, Association rule mining, Open source tools, Object oriented programming, Graph theory, Cloud computing and Cluster computing. Biological domains: Comparative Genomics, RNAseq, Microbiome, Proteomics, Metagenomics, Annotation, Repeat/Transposon discovery and characterization, Assembly, PCR, SSR analysis. Languages and tools: Linux, Perl (BioPerl, DBIx::Class, Moose),... https://cdn.slidesharecdn.com/ss_thumbnails/sahaagrivectorsmar29-220329182052-thumbnail.jpg?width=320&height=320&fit=bounds slideshow/an-open-access-resource-portal-for-arthropod-vectors-and-agricultural-pathosystems-agrivectorsorg/251464971 An open access resourc... https://cdn.slidesharecdn.com/ss_thumbnails/uoaacbsaug30-2020v1-200831213907-thumbnail.jpg?width=320&height=320&fit=bounds slideshow/functional-annotation-of-invertebrate-genomes/238344753 Functional annotation ... https://cdn.slidesharecdn.com/ss_thumbnails/sahaucdavisppath-200203164118-thumbnail.jpg?width=320&height=320&fit=bounds slideshow/saha-uc-davis-plant-pathology-seminar-infrastructure-for-battling-the-citrus-greening-hlb-disease-high-quality-genomes-and-an-open-access-integrated-systems-biology-portal/226807463 Saha UC Davis Plant Pa...