Outreach, Training and Presentations

ICMR Sequencing and Informatics Workshop, October 15-17, 2017
Five physician scientists from the Indian Council of Medical Research (ICMR) travelled to the JCVI facility in La Jolla, CA for a training workshop on October 15-17, 2017. JCVI instructors included Dr. Derrick Fouts, Dr. Granger Sutton, Mr. Indresh Singh, Ms. Lauren Brinkac, Dr. Todd Michael, Dr. Tim Motley and Ms. Kelly Colt. The visiting scientists were led through practical lab tutorials covering DNA extraction, library preparation and execution of sequencing runs on the Illumina and MinIon platforms. Focused discussions were held on cross-platform sequencing strategies and AMR detection. Hands-on informatics exercises covered many areas such as Unix training, post-run QC, assembly, SNP analysis and AMR gene prediction. The JCVI PanACEA Visualization tool, 16S and full metagenomic analysis were also demonstrated during the workshop.
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La Red Network Viral Informatics Training, September 13-15, 2017
Dr. Karina del Carmen Trujillo Murillo and Maria del Pilar Ramos Cervantes visited the Rockville, MD campus of the JCVI from Sept. 13-15, 2017. They are researchers from Mexico, associated with the La Red Network. La Red is a collaboration between the National Institutes of Allergy and Infectious Diseases (NIAID), and the Mexican Ministry of Health, created to conduct clinical research addressing emerging threats, increase scientific knowledge, and directly contribute to improved clinical management of infectious diseases of public health importance. La Red provided Zika virus samples from Mexico for sequencing, which was facilitated by Dr. John Beigel, who manages the La Red program at NIAID.
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THSTI Training For GCID, September 6-8, 2017
In September 6-8, 2017, Translational Health Science and Technology Institute (THSTI), NIAID Division of Microbiology and Infectious Diseases (DMID) , NIAID PATRIC Bioinformatics Resource Center/University of Chicago and NIAID Genomic Center for Infectious Diseases at J. Craig Venter Institute participated in three days training in Delhi, India for Indo-US Workshop on Genomics and Bioinformatics to Explore Human Microbiome Ecology in Health and Diseases. The Translational Health Science and Technology Institute (THSTI) hosted the workshop. Representatives from NIAID and PATRIC also participated in the event. The JCVI team gave an overview of the GCID, and seminars on Sequencing and Data QC, Genome Typing and PanGenome Analysis, Microbiome (16S and ITS) Data Analysis, and Analysis of Shotgun Metagenomic Data. The team also participated in one-on-one sessions to analyze THSTI datasets. The workshop is the latest in the outreach and training program of the GCID (and its predecessor awards, MSCID & GSCID), and strengthens the growing relationship between NIAID, JCVI and research institutions in India.
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South Africa Microbiome Analysis Workshops (April 21-22, 2016, Durban, SA) (April 25-29, 2016, Cape Town, SA)
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2015 Advanced Genomics Workshop @ The University of the West Indies, St Augustine Campus
The University of the West Indies (UWI), in conjunction with the JCVI Genomic Center for Infectious Diseases (GCID) and the National Institutes of Allergy and Infectious Diseases, is hosting the 2015 Advanced Genomics, Metagenomics and Bioinformatics Workshop. This is second UWI-JCVI bioinformatics training workshop. The workshop targets researchers involved or interested in carrying out genomic, metagenomic and bioinformatic analyses. Participation can be on site at the UWI St. Augustine Campus or via WebEx.
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NIAID H3Africa Workshop (July 21-25, 2014, Ibadan, Nigeria)
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ICAAC (Interscience Conference on Antimicrobial Agents and Chemotherapy), Denver
Association of KPC Variants with Clinical and Genomic Features in Klebsiella pneumonia

BioConference Live Genetics and Genomics
Azole resistance in Aspergillus fumigatus clinical isolate screening, culture selection, and genetics

August 22-28, 2013: Advanced Bioinformatics Workshop, International Livestock Research Institute, Nairobi, Kenya

Visting Scientist Yury V. Ivanov, Penn State University
Bioinformatics analyses of Next-generation Sequencing of Bordetella genomes

American Society for Virology (ASV) Annual Meeting, State College, PA

CEIRS Annual Meeting, Memphis, TN

International Congress on Toxoplasmosis, Oxford, UK.

Intern: Anthony Bennici, College of William and Mary, Virginia
Sequence-independent amplification of rotaviruses for high-throughput next-generation sequencing

Intern: Titas Bera, Wooton High School, Maryland
Generating a library of influenza A virus hemagglutanin and neuraminidase genes

Intern: Haley Hochstein, Johns Hopkins University
Genomic and antigenic analysis of seasonal H3N2 influenza A virus from 2012-2013

Visting Scientist Suchitra Pakala, Montgomery College
Developed annotation and analysis pipelines for the Aspergillus fumigatus Project

Clinicopathologic Grand Rounds - Novel, Insidious, Progressive, and Fatal: The Discovery of Aspergillus Tanneri

Ferret Microbiome Project Update: Characterization of the changes in the microbial diversity and microbiome expression in the upper respiratory track of ferrets (Mustela putorius furo) during influenza virus infection

Intern: Titas Bera, Wooton High School, Maryland
Creating a Reverse Genetics System for A/Swine/Illinois/02860/2008

Intern: Sybelle Djikeng, Rosslyn Academy, Kenya
Coronavirus: Amplification of the HE and Spike genes in human coronavirus genomes

Intern: John Zenk, University of Colorado
Creating a metabolic model of Aspergillus Fumigatus

George Mason University, Manassas, VA
Evolution of Burkholderia mallei

Improving our understanding of Aspergillus fumigatus

Sequencing Toxoplasma gondii, the parasite of love

Cloud BioLinux: Pre-configured and On-demand Bioinformatics Computing for the Genomics Community

Visting Scientist Venkatesh Moktali, Penn State University
Indentification of Polymerfic HET Markers in Aspergillus Fumigatus

Joint GSC Webinar on Plasmodium Projects: Molecular Hallmarks of Naturally Acquired Immunity to Malaria

CDC Meeting on Microbial Evolution and Cutting Edge Tools for Outbreak Investigations, Atlanta, GA
Diversity Within and Evolution of Burkholderia pseudomallei and Burkholderia mallei Species

Intern: Sybelle Djiken, Rosslyn Academy, Kenya
Generating PCR Products for SARS Coronavirus

Intern: Julianna Drew, The Bryn Mawr School, Maryland
Optimizing Biosynthetic Clusters ssemblies in Yeast

Intern: Olga Kamneva, University of Wyoming
Research on New Bioinformatic Algorithms to Determine the Relationship between Families of Proteins

Intern: Vidula Naik, Georgetown University
Expanding Synthetic Biology Technology

Intern: Neha Varghese, Georgia Institute of Technology
Improvements of Prokaryotic Annotation Pipeline and Pangenome Pipeline

Gordon Conference on Chemical and Biological Terrorism Defense, Marriott Hotel, Ventura, CA
Genetics of Burkholderia

Microbial Forensics in the Era of Genomics, The Banbury Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
Limitation of Nextgen Sequencing Platforms and Analysis Tools; Deep Sequencing of Yersina pestis D27

Visting Scientist Charlotte Omoto
Sequencing of Gregarina niphanrodes

Intern: Olukemi Abdolude, Johns Hopkins University
Reannotation of Aspergillus fumigatus

Intern: Katy Fleming, University of Mary Washington
Aspergillus fumigatus: Average Mold or Dangerous Pathogen?

Visting Scientist Santiago Revale
Analysis and tool development for the Influenza Project

Intern: Anna Sharova, University of Maryland
Sample Preparation in Viral Group

Intern: Samuel Engel, River Hill High School, Maryland
Study of the Influenza virus and Sequencing Preparation by Amplification

Pan-Fungal Data Resources Strategy Meeting, Alexandria, VA
Sequencing Technology

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