GCID Outreach: Training the Next Generation of Genomic Scientists

Intro: 

The J. Craig Venter Institute (JCVI) Genomic Center for Infectious Diseases (GCID) was established by the National Institute of Allergy and Infectious Disease (NIAID) to explore disease biology through the application of nucleic acid sequencing and bioinformatics analysis tools. Throughout the history of the program, which is in its third iteration, GCID has been focused on expanding access to these technological platforms through education and outreach. To that end, we have devoted resources to train the next generation of genomic scientists through internship opportunities and by holding seminars and workshops in developing countries, whenever possible. Going forward, the GCID pledges to continue the pursuit of community outreach.

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Visiting Scientist in Virology Department

TrainingFebruary 5-August 15, 2018, Rockville, MD

Patti Erickson PhD, Visiting Scientist

Patti Erickson PhD is a Visiting Scientist from Salisbury University, who is developing a more rapid and simple reverse genetics system for human respiratory syncytial virus (RSV) using a synthetic genomics approach. The improved RSV reverse genetics system is expected to enable researchers to quickly generate clones of clinical samples and advance understanding of the relationship between genotype and phenotype. After the training is completed, Dr. Erickson will use the synthetic genomics knowledge gained through the GCID outreach program in the undergraduate Contemporary Genetics class she teaches at Salisbury University.

Postdoctoral Research Fellow In Virology Department

Post-Doc2016, Rockville, MD

Lauren Oldfield, PhD, Postdoctoral Research Fellow

Dr. Oldfield participated in the development of a QPCR based zika virus detection assay, and assisted with adaption of the viral lab workflows for zika virus sequencing.

Bioinformatics and Metagenomics training

TrainingNovember 30-December 15, 2017, Rockville, MD

Cindy Baburam, PhD student from Vaal University of Technology, South Africa attended Bioinformatics and Metagenomics training at JCVI.

Indian Council of Medical Research (ICMR) Sequencing and Informatics Workshop

WorkshopOctober 15, 2017, La Jolla, CA

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.

Analysis of genome sequencing data generated from T. gondii

TrainingMay 08-September 29, 2017, J. Craig Venter Institute, Rockville, MD

Visiting scientist Bruno BelloPede worked with Dr. Hernan Lorenzi on the analysis of genome sequencing data generated from T. gondii samples that were submitted by collaborator Dr. Solange Gennari, University of Sao Paulo, Brazil. The data was used to identify molecular markers that can be used for T. gondii strain genotyping. He also worked on the improvement of a T. gondii SNP identification pipeline that can be used by the T. gondii scientific community. This was a collaborative effort between Dr. Hernan Lorenzi, Dr. Chunlei Su (University of Tennessee) and Dr. Gennari to investigate T. gondii worldwide diversity, as part of the Parasites GCID project.

La Red Network Viral Informatics Training

TrainingSeptember 13, 2017, Rockville, MD

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.

Translational Health Science and Technology Institute (THSTI) Training

WorkshopSeptember 6-8, 2017, Delhi, India

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.

Everybody is Kung-Flu Fighting: Deep Sequencing of Clinical Influenza A Virus Reveals Patterns of Emerging/ Re-emerging Amino Acid Substitutions

InternshipJune, 2017, J. Craig Venter Institute, Rockville, MD

Intern Emma Roth worked under the guidance of Brett Pickett, PhD, in the Department of Informatics. At the time of her internship, Ms. Roth was pursuing her Bachelor’s in Computer Science at UC San Diego, La Jolla

Infection by influenza A virus (IAV) can occur in birds or swine, and results in approximately 700,000 hospitalizations and 56,000 human deaths each year. Although vaccines exist and are reformulated each year, the rapid mutation rates (antigenic drift) and reassortment (antigenic shift) across the viral subtypes make it difficult to prevent or treat infection consistently. In this study, we examined deep sequencing data of IAV samples collected between 2011-2013 from Santiago, Chile to determine whether amino acid substitutions emerging/re-emerging at the global scale could be identified by observing minor variants in the genomes isolated from multiple patients. We created a workflow that visualizes the locations of minor variants across each segment for these genomes, calculates mutations that stray from the consensus amino acid in that location across all GenBank sequence data for each year, and determines whether the amino acid positions that contain a minor variant are located in known epitope regions from a reference genome.

Postdoctoral Research Fellow in Infectious Diseases Department

Post-Doc2016–2017, Rockville, MD

Harinder Singh, PhD, Postdoctoral Research Fellow

Dr. Singh benchmarked existing AMR-detection software and helped to determine that one search tool outperforms all others.

Postdoctoral Research Fellow In Virology Department

Post-Doc2017, Rockville, MD

Pilar Viedma, PhD, Postdoctoral Research Fellow

Dr. Viedma quantified Zika virus RNA with our custom qRT-PCR primers and probes to determine the lower limit of detection of these reagents in serum and urine using a variety of reverse transcriptase enzymes.

Optimizing Phagehunting Methods to Isolate and Amplify Bacteriophages

InternshipJune, 2017, J. Craig Venter Institute, Rockville, MD

Intern Shriya Singh worked under the guidance of Derrick Fouts, PhD, in the Department of Genomic Medicine. At the time of her internship, Ms. Singh was enrolled in the Science, Math and Computer Science Magnet Program at Poolesville High School, Poolesville, MD

There are an estimated 1031 bacteriophages (phage), viruses that infect bacteria, in the biosphere, thus comprising a significant portion of the biosphere on Earth. Of these, a mere 10,733 phages have been isolated and 2,061 phages have sequenced, complete genomes, with even fewer, only 1,073, presently publicly available in the NCBI GenBank database. “Phagehunting” is the process of isolation, characterization, and genomic analyses of phages that infect bacterial hosts.

Genomic Data Analysis and Visualization for identification and characterization of WGS

InternshipJune, 2017, J. Craig Venter Institute, Rockville, MD

Intern Enrique Garcia-Assad worked under the guidance of Indresh Singh, Manager of Core Informatics Services, in the Department of Informatics. At the time of his internship, Mr. Garcia-Assad was enrolled at Wootton High School in Rockville, MD.

Whole-genome sequencing (WGS) is becoming available as a common place tool for clinical microbiology. If applied directly on clinical samples, this could further reduce diagnostic times and thereby improve control and treatment especially in outbreak events. A major bottleneck is the availability of fast and reliable bioinformatic tools to identify and characterize large numbers of microbial genomes. In this project, I applied NASP for single nucleotide polymorphism (SNP) identification and characterization, and used FigTree and PHYLOBar for phylogenetic analysis and visualization.

Postdoctoral Research Fellow in Infectious Diseases Department

Post-Doc2016–2017, Rockville, MD

Alexander Voorhies, PhD, Postdoctoral Research Fellow

Dr. Voorhies worked on detecting the spread of AMR genes in metagenomic datasets. He also participated in the analysis of 16S taxonomic profiles to investigate the potential role of the intestinal microbiota in malaria immunity and the impact of antimalarial treatments on the human intestinal microbiome.

Postdoctoral Research Fellow in Infectious Diseases Department

Post-Doc2015–2017, La Jolla, CA

Meredith Wright, PhD, Postdoctoral Research Fellow

Dr. Wright performed a myriad of duties, including bioinformatic analysis, detection of AMR genes, and manuscript preparation.

Bioinformatics and Metagenomics training

TrainingApril 01-May 08, 2017, Rockville, MD

Visiting scientist Dr. Naser A Feto from Vaal University of Technology, South Africa attended bioinformatics training at JCVI.

Workshop on Apicomplexan Genome Analysis

WorkshopSeptember, 2016, University of São Paulo, Brazil

In September 2016, Dr. Hernan Lorenzi (JCVI) and collaborators Chunlei Su and Solange Gennary and organized a 5-day workshop on Apicomplexan Genome Analysis in the Department of Preventive Veterinary Medicine at the University of São Paulo, Brazil. Participants in the workshop included 20 scientists, postdoctoral fellows and PhD students from South and Central America. The workshop was supported in part by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health under Award Numbers R13AI126819 and U19AI110819 and the University of São Paulo, Brazil.

Bioinformatics and Metagenomics training

Post-Doc2016-2017, Rockville, MD

Kari Dilley, PhD, Postdoctoral Research Fellow

Dr. Dilley worked on the development and optimization of Sequence Independent Single Primer Amplification (SISPA) methods and its application to the viral sequencing workflows, and on the sequencing and analysis of zika virus samples.

Workshop on MLST determination and analysis from Streptococcus pneumoniae isolates

WorkshopAugust, 2016, University of Capetown

Postodoc students from Mark Nicol’s lab, Clinton Moodley and Katie Lennard visited JCVI from University of Capetown in August 2016 to participate in a training workshop conducted by Meredith Wright and Stephanie Mounaud on MLST determination and analysis from Streptococcus pneumoniae isolates sequenced by JCVI.

Identifying Bacterial Antibiotic Resistance Markers in gut microbes

InternshipJune, 2016, J. Craig Venter Institute, La Jolla, CA

Intern Ian Lamb worked under the guidance of Manolito Torralba, Laboratory Research and Development Manager, in the Department of Genomic Medicine. At the time of his internship, Mr. Lamb was enrolled at La Jolla High School in La Jolla, CA.

The gut microbiome plays a critical role in our health and well-being, but it also facilitates sharing of antibiotic resistance genes. However, antibiotic resistance genes can be identified by distinct markers which we screen in this study. Plasmids pTRACA18, pTRACA20, and pTRACA22 were chosen since they have demonstrated to be present in many gut microbes. This in turn allows the bacteria to spread antibiotic resistance genes to each other through conjugation and other forms of gene transfer. For the study, stool samples were used from a Malian tribe, which we extracted DNA from and screened for presence of plasmids through PCR. When the amplicons were screened, we determined that the amount of anti-microbial plasmids are sporadic because within each individual there are differing levels of abundance for each plasmid due to varying gut microbiomes.

Postdoctoral Research Fellow in Infectious Diseases Department

Post-Doc2016, La Jolla, CA

Aubrie O’Rourke, PhD, Postdoctoral Research Fellow

Dr. O’Rourke received bioinformatics training that ultimately led to her ability to perform bacterial RNAseq expression analysis and Tnseq genetic participation analysis that she has subsequently applied to additional studies of bacterial genomes.

Postdoctoral Research Fellow In Infectious Diseases Department

Post-Doc2015-2016, La Jolla, CA

Qiyun Zhu, PhD, Postdoctoral Research Fellow

Dr. Zhu worked on the detection of AMR genes and AMR reservoirs related to human gut infections.

South Africa Microbiome Analysis Workshops

WorkshopApril 21-22, 2016, Durban, SA; April 25-29, 2016, Cape Town, SA

In April 2016, researchers from JCVI led two microbiome data analysis workshops in South Africa. Both workshops were co-sponsored by the NIAID-funded JCVI Genomic Center for Infectious Disease and the H3Africa Initiative.

The first workshop was held from April 21 - 22 at the Durban University of Technology (DUT). Forty-five participants attended the workshop led by JCVI scientists Alex Voorhies, Ph.D., Derek Harkins, and Andres Gomez, Ph.D.

The second workshop was held from April 25 – 29 at the University of Cape Town (UCT).  The DUT JCVI team was joined by Stephanie Mounaud and partnered with UCT faculty, Gerrit Botha, Ph.D. and Katie Lenard, Ph.D., and UCT PI Mark Nicol to teach a four-day microbiome analysis course. Twenty-two researchers from Nigeria, The Gambia, Malawi, Tunisia, Zimbabwe and South Africa were selected from over 70 applicants to participate.

Postdoctoral Research Fellow In Virology Department

Post-Doc2014-2015, Rockville, MD

Karla Stucker, PhD, Postdoctoral Research Fellow

Dr. Stucker worked extensively on the GCID to provide expertise on the multiplexing and phylogenetic analysis of rotavirus strains.

PanGenome Visualization with JBrowse

InternshipJune, 2015, J. Craig Venter Institute, Rockville, MD

Interns Namita Dongre and Anika Verma worked under the guidance of Indresh Singh, Manager of Core Informatics Services, in the Department of Informatics. At the time of their internship, Ms. Dongre was enrolled at Thomas Jefferson High School for Science Technology in Alexandria, Virginia and Ms. Verma at Wootton high School in Rockville, MD.

The objective of this project was to visually compare genome variations to a single consensus using a genome browser. Our biological data came from the Enterobacter cloacae, strain 34977 and was based on the pan-genomic analysis done by pan-genome ortholog clustering tool (PanOCT) and three other commonly used ortholog-detection methods. Our consensus track contained the 70% common clusters present in the various genomes of E. cloacae. We created GFF-file format tracks for the consensus and individual genomes with Python and imported them into JBrowse, a JavaScript-based genome browser.

Development of a high throughput sequencing and analysis pipeline for West Nile virus

InternshipJune, 2015, J. Craig Venter Institute, Rockville, MD

Intern Emmi Mueller worked under the guidance of Rebecca Halpin, Viral Project Team Lead, in the Department of Infectious Disease. At the time of her internship, Ms. Mueller was pursuing her Bachelor’s in Microbiology at the University of Michigan.

West Nile virus (WNV) is a member of the Flaviviridae family of enveloped, single-stranded RNA viruses with a linear, non-segmented, positive-sense ~11,000bp genome. WNV is an enzootic virus of birds and mosquitos, with humans and other mammals serving as spillover hosts, typically via mosquito bites. In humans, WNV is usually asymptomatic, but ~20% of infected people develop a mild flu-like fever (West Nile fever) and ~1% can develop severe symptoms such as encephalitis or meningitis, which can be fatal. WNV was first isolated from a woman in Uganda in 1937 and first reported in North America in New York City in 1999. Since then, WNV has caused over 39,000 reported human disease cases in the USA contributing to over 1600 deaths. WNV continues to remain a formidable clinical and public health concern in the USA and worldwide.

Phylogenetic Analyses of North American Exhibition Swine Influenza A Viruses from 2009 to 2013

InternshipJune, 2015, J. Craig Venter Institute, Rockville, MD

Intern Alison Schwam worked under the guidance of Karla Stucker, PhD and Suman Das, PhD in the Department of Infectious Disease. At the time of her internship, Ms. Schwam was pursuing her Bachelor’s in Mathematics at the University of Maryland.

We studied the evolution of swine influenza A viruses (IAVs) to gain a better understanding of the movement of IAVs among commercial and exhibition swine, as well as spillover into human hosts. IAV is a segmented, negative-sense RNA virus that is classified by the viral surface proteins hemagglutinin (HA or H) and neuraminidase (NA or N). Of the three species of influenza viruses (A, B and C), IAV is the most virulent human pathogen and causes the majority of outbreaks of severe illness. We analyzed North American swine IAVs circulating since the emergence of the human 2009 H1N1pdm in commercial and exhibition swine, as well as human cases of variant swine-origin influenza infections in the US. Specific fair locations in Ohio where exhibition swine were held were sampled for IAV.

2015 Advanced Genomics Workshop at The University of the West Indies, St Augustine Campus

WorkshopMarch 13, 2015, The University of the West Indies (UWI)

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.

NIAID H3AFRICA WORKSHOP

WorkshopJuly 21-25, 2014, Ibadan, Nigeria

On July 21-25, 2014, the GCID supported the NIAID H3Africa initiative by co-sponsoring Andrey Tovchigrechko for his participation in a workshop held in Ibadan, Nigeria. The workshop was organized by the local H3Africa Bioinformatics Network node. In three days of teaching, Dr. Tovchigrechko taught the students launching and controlling computing instances on Amazon cloud, basics of Python and R programming, MG-RAST Web interface, MG-RAST R package matR and my JCVI R code MGSAT. The students took a great interest in both Python and R programming, skipping coffee breaks to keep moving forward with assignments. The main technical challenge was to provide a uniform computing environment with a complex set of packages for everyone while tolerating slow and unstable Internet access. For this purpose, Dr. Tovchigrechko used through-the-Web client-server programming User Interface for both Python (Python notebooks server) and R (RStudio server). Dr. Tovchigrechko also gave a talk, along with a dozen other speakers, at a one-day symposium at the University of Ibadan that preceded the workshop and included about 200 participants.

Association of KPC Variants with Clinical and Genomic Features in Klebsiella pneumonia

PresentationAugust 30, 2013

ICAAC (Interscience Conference on Antimicrobial Agents and Chemotherapy), Denver

Advanced Bioinformatics Workshop, International Livestock Research Institute, Nairobi, Kenya

WorkshopAugust 22-28, 2013

Advanced bioinformatics workshop was conducted at International Livestock Research Institute, Nairobi, Kenya coverting Primer Design for Microbial Genomes, Molecular Barcoding for Multiplexing,Processing NGS Data - Assembly Strategies,Assembly Exercise,Annotation,Annotation Exercise,Submitting Data to GenBank,Synthetic Genomics and Its Application to Viral Infectious Diseases,Application of Omics Technology to Infectious Diseases and the Human Microbiome,Data Mining: Clustering and Statistical Analysis with MeV,Overview of Next Generation Sequencing (NGS) Technologies,Introduction to Bioinformatics Software and Computing Infrastructures,Synthetic Genomics and its Applications to Bacterial Infectious Diseases,Lessons Learnt from Emerging Viruses,Overview of viral projects: technology, microbiome, phylogenetics, zoonotic infections,Comparative Genomics Analysis to Identify Genetic Determinants of Influenza Virus Human Adaptation,Influenza Research Database & Virus Pathogen Resource Exercises.

BioConference Live Genetics and Genomics

PresentationAugust 21, 2013

Azole resistance in Aspergillus fumigatus clinical isolate screening, culture selection, and genetics

Bioinformatics analyses of Next-generation Sequencing of Bordetella genomes

TrainingJuly 22, 2013

Visiting Scientist Yury V. Ivanov, Penn State University

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

PresentationJuly 20, 2013

CEIRS Annual Meeting, Memphis, TN

PresentationJuly 08, 2013

International Congress on Toxoplasmosis, Oxford, UK.

PresentationJune 22, 2013

Sequence-independent amplification of rotaviruses for high-throughput next-generation sequencing

TrainingJune, 2013

Rotavirus is a segmented dsRNA virus that causes gastroenteritis and is the primary cause of severe pediatric diarrhea, which results in over half a million deaths per year globally. There are eight known species of rotaviruses (A-H) that infect humans and other animals, with Rotavirus A being the leading cause of human disease. Due to their great genetic diversity and broad public health implications, it is essential to increase existing genomic sequence data on rotaviruses. The goal of this project is to develop an in-house method for the sequence-independent amplification of viral dsRNA genomes that will be optimized for high-throughput viral genome sequencing using next generation sequencing platforms already in place at the J. Craig Venter Institute (JCVI).

Generating a library of influenza A virus hemagglutanin and neuraminidase genes

TrainingJune, 2013

Every year, five to twenty percent of the United States population is infected with seasonal influenza, making the construction of a seasonal vaccine of high importance. However, due to antigenic drift among seasonal influenza viruses, the vaccine strains need frequent updating. Antigenic drift occurs as the genes encoding influenza’s major antigenic proteins, hemagglutinin (HA) and neuraminidase (NA), undergo mutations in response to selection pressures exerted by the host immune response. Therefore, careful surveillance of influenza viruses is required to monitor their evolution and determine when the vaccine needs to be updated.

Genomic and antigenic analysis of seasonal H3N2 influenza A virus from 2012-2013

TrainingJune, 2013

Influenza is an acute viral infection of the upper respiratory system that accounts for 3-5 million hospitalizations and 250,000-500,000 deaths annually worldwide (WHO). Influenza A virus is a segmented, negative-sense RNA virus that is classified into various subtypes based on its two main surface glycoproteins, hemagluttinin (HA) and neuraminidase (NA). The two influenza A subtypes that annually circulate in humans are seasonal H1N1 and seasonal H3N2. The 2012-2013 influenza season resulted in a severe epidemic of H3N2 viruses. We hypothesize that this epidemic resulted from genetic changes in the HA that resulted in significant drift and aim to prove this by analyzing 145 human nasopharyngeal isolates that were collected from The Methodist Hospital System in Houston, Texas from November, 2012 through February, 2013

Developed annotation and analysis pipelines for the Aspergillus fumigatus Project

Training2010-2013

Aspergillus fumigatus is the predominant cause of both allergic and invasive aspergillosis possessing particular metabolic capabilities and genetic determinants that differentiate it from most other fungal species. A. fumigatus is also a primary pathogen of the sinuses, lungs, damaged skin, and subcutaneous tissues, and disseminates to other organs including the brain. The key drugs for treating aspergillosis are azoles, especially voriconazole, but unfortunately resistance to these drugs is emerging.

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

Training01-November-2012

Visiting Scientist Venkatesh Moktali, Penn State University

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

PresentationJuly 19, 2012

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

Creating a Reverse Genetics System for A/Swine/Illinois/02860/2008

InternshipJune, 2012

Intern Titas Bera, Wooton High School, Maryland worked in Virology Department

Coronavirus: Amplification of the HE and Spike genes in human coronavirus genomes

InternshipJune, 2012

Intern Sybelle Djikeng, Rosslyn Academy, Kenya worked in Virology Department

Creating a metabolic model of Aspergillus Fumigatus

InternshipJune, 2012

Intern John Zenk, University of Colorado worked in Infectious Diseases Department

Evolution of Burkholderia mallei

PresentationMay 04, 2012

George Mason University, Manassas, VA

Sequencing Toxoplasma gondii, the parasite of love

PresentationApril 25,2012

Improving our understanding of Aspergillus fumigatus

PresentationApril, 2012

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

TrainingFebruary, 2012

Cloud BioLinux provides a platform for developing bioinformatics infrastructures on the cloud. An automated and configurable process builds Virtual Machines, allowing the development of highly customized versions from a shared code base. This shared community toolkit enables application specific analysis platforms on the cloud by minimizing the effort required to prepare and maintain them.

Indentification of Polymerfic HET Markers in Aspergillus Fumigatus

Presentation2012

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

PresentationSeptember 29, 2011

Generating PCR Products for SARS Coronavirus

InternshipJune, 2011

Intern Sybelle Djiken, Rosslyn Academy, Kenya worked in Virology Department

Diversity Within and Evolution of Burkholderia pseudomallei and Burkholderia mallei Species

PresentationSeptember 15, 2011

CDC Meeting on Microbial Evolution and Cutting Edge Tools for Outbreak Investigations, Atlanta, GA

Optimizing Biosynthetic Clusters assemblies in Yeast

InternshipJune, 2011

Intern Julianna Drew, The Bryn Mawr School, Maryland worked in Infectious Diseases Department

Research on New Bioinformatic Algorithms to Determine the Relationship between Families of Proteins

InternshipJune, 2011

Intern Olga Kamneva, University of Wyoming worked in Informatics Department

Expanding Synthetic Biology Technology

InternshipJune, 2011

Intern Vidula Naik, Georgetown University worked in Informatics Department

Improvements of Prokaryotic Annotation Pipeline and Pangenome Pipeline

InternshipJune, 2011

Intern Neha Varghese, Georgia Institute of Technology worked in Informatics Department

Genetics of Burkholderia

PresentationMarch 15, 2011

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

Limitation of Nextgen Sequencing Platforms and Analysis Tools; Deep Sequencing of Yersina pestis D27

PresentationNovember 08, 2010

Microbial Forensics in the Era of Genomics, The Banbury Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY

Reannotation of Aspergillus fumigatus

InternshipJune, 2010

Intern Olukemi Abdolude, Johns Hopkins University worked in Informatics Department

Aspergillus fumigatus: Average Mold or Dangerous Pathogen?

InternshipJune, 2010

Intern Katy Fleming, University of Mary Washington worked in Informatics Department

Sequencing Technology

PresentationFebruary 23, 2010

Pan-Fungal Data Resources Strategy Meeting, Alexandria, VA

Sequencing of Gregarina niphanrodes

Training2010

Visiting Scientist Charlotte Omoto

Sample Preparation in Viral Group

InternshipJune, 2009

Intern Anna Sharova, University of Maryland worked in Virology Department

Study of the Influenza virus and Sequencing Preparation by Amplification

InternshipJune, 2009

Intern Samuel Engel, River Hill High School, Maryland worked in Virology Department

Analysis and tool development for the Influenza Project

Training2009

Visting Scientist Santiago Revale