The document describes the National Human Genome Center at Howard University and its services. It provides contact information for the Director, Associate Director and Core Laboratory Director. The services described include developing research designs and protocols, processing biological samples for DNA and RNA extraction, genotyping using pyrosequencing and direct sequencing, HLA genotyping, and maintaining a biorepository.
Updates on Citrusgreening.org database from USDA NIFA project meetingSurya Saha
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
Visualization of insect vector-plant pathogen interactions in the citrus gree...Surya Saha
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
RefSeq curation in-depth. Examples of targeted transcript and protein curation, presented at the 8th International Biocuration conference (April, 2015).
Updates on Citrusgreening.org database from USDA NIFA project meetingSurya Saha
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
Visualization of insect vector-plant pathogen interactions in the citrus gree...Surya Saha
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
RefSeq curation in-depth. Examples of targeted transcript and protein curation, presented at the 8th International Biocuration conference (April, 2015).
NCBI has developed a powerful suite of online biomedical and bioinformatics resources, including old friends like PubMed and OMIM and newer resources such as Genome. This collection of databases and tools are widely used by scientists and medical professionals across the world. With such a wealth of information, it is easy to get overwhelmed. Join us for an overview to NCBI resources for the information professional with an emphasis on biodata connectivity. No science degree required!
Development of FDA MicroDB: A Regulatory-Grade Microbial Reference DatabaseNathan Olson
"Development of FDA MicroDB: A Regulatory-Grade
Microbial Reference Database" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by the National Institute for Standards and Technology October 2014 by Heike Sichtig, PhD from the FDA and Luke Tallon from IGS UMSOM.
Cold Spring Harbor. Single Cell Analyses Meeting. November 11 - 14, 2015. Slides for talk: PAGODA—Pathway and gene set overdispersion analysis characterizes single cell transcriptional heterogeneity.
NCBI; Introduction, Homepage and about
Tools and database of NCBI
BLAST; Introduction, Homepage and types of BLAST
Some databases of NCBI
References
Acknowledgements
Next Generation Sequencing for Identification and Subtyping of Foodborne Pat...Nathan Olson
"Next Generation Sequencing for Identification and Subtyping of Foodborne Pathogens" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by the National Institute for Standards and Technology October 2014 by Rebecca Lindsey, PhD from Enteric Diseases Laboratory Branch of the CDC.
How bioinformatic and sequencing data might inform the regulatory process - O...OECD Environment
24 June 2019: This OECD seminar presented and discussed the potential use of genome sequence, bioinformatic tools and databases in a regulatory decision process for microbial pesticides.
High-throughput sequencing data of microorganisms opens new perspectives for ...OECD Environment
24 June 2019: This OECD seminar presented and discussed the potential use of genome sequence, bioinformatic tools and databases in a regulatory decision process for microbial pesticides.
How can Whole Genome Sequencing information be used to address data requireme...OECD Environment
24 June 2019: This OECD seminar presented and discussed the potential use of genome sequence, bioinformatic tools and databases in a regulatory decision process for microbial pesticides.
Course: Bioinformatics for Biomedical Research (2014).
Session: 2.1.3- Next Generation Sequencing. Technologies and Applications. Part III: NGS Applications II.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
NCBI has developed a powerful suite of online biomedical and bioinformatics resources, including old friends like PubMed and OMIM and newer resources such as Genome. This collection of databases and tools are widely used by scientists and medical professionals across the world. With such a wealth of information, it is easy to get overwhelmed. Join us for an overview to NCBI resources for the information professional with an emphasis on biodata connectivity. No science degree required!
Development of FDA MicroDB: A Regulatory-Grade Microbial Reference DatabaseNathan Olson
"Development of FDA MicroDB: A Regulatory-Grade
Microbial Reference Database" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by the National Institute for Standards and Technology October 2014 by Heike Sichtig, PhD from the FDA and Luke Tallon from IGS UMSOM.
Cold Spring Harbor. Single Cell Analyses Meeting. November 11 - 14, 2015. Slides for talk: PAGODA—Pathway and gene set overdispersion analysis characterizes single cell transcriptional heterogeneity.
NCBI; Introduction, Homepage and about
Tools and database of NCBI
BLAST; Introduction, Homepage and types of BLAST
Some databases of NCBI
References
Acknowledgements
Next Generation Sequencing for Identification and Subtyping of Foodborne Pat...Nathan Olson
"Next Generation Sequencing for Identification and Subtyping of Foodborne Pathogens" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by the National Institute for Standards and Technology October 2014 by Rebecca Lindsey, PhD from Enteric Diseases Laboratory Branch of the CDC.
How bioinformatic and sequencing data might inform the regulatory process - O...OECD Environment
24 June 2019: This OECD seminar presented and discussed the potential use of genome sequence, bioinformatic tools and databases in a regulatory decision process for microbial pesticides.
High-throughput sequencing data of microorganisms opens new perspectives for ...OECD Environment
24 June 2019: This OECD seminar presented and discussed the potential use of genome sequence, bioinformatic tools and databases in a regulatory decision process for microbial pesticides.
How can Whole Genome Sequencing information be used to address data requireme...OECD Environment
24 June 2019: This OECD seminar presented and discussed the potential use of genome sequence, bioinformatic tools and databases in a regulatory decision process for microbial pesticides.
Course: Bioinformatics for Biomedical Research (2014).
Session: 2.1.3- Next Generation Sequencing. Technologies and Applications. Part III: NGS Applications II.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
Current CV .
My objective is to obtain a rewarding and challenging research scientist position where my background and experience will contribute to the success of a growing company or research center.
Currently, I am a Senior Associate Scientist at Amgen Inc. and certified Molecular Biologist with the American Society of Clinical Pathology MB (ASCP). I have more than 10 years of experience in the biotechnology/ pharmaceutical industry. I am highly proficient in various lab techniques, technologies, and automation. I demonstrated consistent success in the execution of assay development and method validation activities supporting clinical stage programs within GCP and GLP regulated environments. I possess extensive experience in optimization and validation of drug potency assays (ELISA and cell based assays), protein purification and characterization, and DNA/RNA extraction and quantitation. I am a subject matter expertise in the areas of human and rodent cell lines propagation and tissue dis-aggregation. I have proven operational capabilities in the establishment of standard operating procedures to ensure our laboratory meets regulatory and business requirements.
I am a self-motivated professional who works effectively as an individual contributor or within a team matrix. As a quick learner, I can efficiently deliver results, easily adapt to changing environment and provide fresh ideas. My strengths include statistical analysis/guidance, report writing, and communication.
Thank you in advance for your consideration. Please feel free to call me at (805-990-6258), or by e-mail at (mahawally46@gmail.com) if you have questions or would like a list of references.
Sincerely,
Maha Rizk
Discover new cases studies giving you unprecedented access to both the data and results of how RNA-Seq is being applied successfully from bench to bedside
Gain new insights into RNA-Seq for the study of toxicity, IO, host-viral interactions and more from companies such as BMS, Janssen, Pfizer, Merck, UCSC and Stanford
CRISPR Gene Editing Congress, 25-27 February 2015 in Boston, MADiane McKenna
Key industry leaders will gather at the inaugural CRISPR Precision Gene Editing Congress with an ultimate purpose of addressing the importance of overcoming specificity, efficiency and delivery challenges associated with the CRISPR/Cas9 system. Pioneers will showcase the expanding biomedical and therapeutic potential of gene editing tools for drug discovery and development.
2nd CRISPR Precision Genome Editing congress Berlin 2017 AgendaDiane McKenna
2nd CRISPR Europe Congress is back with the key technology and industry developments uncovering more innovative applications. From basic research to therapeutic development, this end to end CRISPR Congress in Berlin will optimise your CRISPR workflow. Fully experience the value of this technology in base editing, primary cell editing, in vivo delivery, antiviral drugs & gene therapies.
A recognized expert with 16 years of experience on translational bioinformatics, genomics, and genetics, specialized on developing databases, genome repositories, pipeline, clinical application, and commercial products to analyze next generation sequencing data, and interpret personal genomes and electronic medical records for clinical diagnosis, therapeutics, precision medicine, and predictive disease risk.
RNA-Seq Boston (23-25 June 2015) AgendaDiane McKenna
RNA-Seq Boston 2015 will enable scientists to overcome the data bottleneck by applying the most appropriate bioinformatics tools and develop a unified, integrated approach for analysis and interpretation of huge data sets, which in turn can positively impact therapeutic and clinical developments.
1. http://www.genomecenter.howard.edu/ National Human Genome Center Molecular Genetics Georgia M. Dunston, PhD Mezbah U. Faruque, MD, PhD Director Associate Director Yuanxiu Chen, MD, PhD Paulette Furbert-Harris, PhD CTSA Laboratory Director Core Laboratory Director Muneer Abbas, PhD Tshela Mason, MS Laboratory Manager Operations Supervisor Luisel Ricks-Santi, PhD Biorepository Coordinator Contact Mezbah Faruque at 202-806-4780 or e-mail at mfaruque@howard.edu
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5. http://www.genomecenter.howard.edu/ Three PSQ™HS 96 sequencers with built-in robotic mechanism for transfer of ten 96-well plates for high throughput SNP genotyping. Platform compatible primers are designed using PSQ assay design software. Current throughput for the pyrosequencers in our labs exceeds 12,000 genotypes per day. High-throughput pyrosequencing for SNP genotyping
6. http://www.genomecenter.howard.edu/ Performed on ABI 3100 automated DNA sequencers using big dye terminator chemistry . Custom primer designing for amplification and sequencing of up to 500 bp of bi-directional reads. Direct DNA Sequencing
7. http://www.genomecenter.howard.edu/ HLA genotyping HLA genotyping after reverse PCR-SSO using Luminex Technology that offers a microspehere based assay with multiplexed data acquisition and analyses. High resolution sequence based typing of HLA-B, HLA-DRB1 and HLA-DQB1 to identify new HLA alleles as well as to assign allele calls by comparing sequences with reference databases.