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Training and education are central to the i5k mission, promoting the adoption of best practices for methodologies, informatics and standards. Our goal for the webinar series is to provide outreach and education by introducing researchers to a variety of techniques, technologies and best practices to help move their research forward. Bring your questions and help us have a lively discussion with our speakers.
When: First Wednesday of each month from 11am to 12 noon EDT
Event times vary relative to your timezone. Please click the date in the schedule below to confirm the time in your location.
Webinars will be 1 hour long, but presentations will be kept short enough to allow plenty of time for participants to ask questions.
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|Web Conference Connection||This connection will allow you to view the video.|
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Speaker: Carson Holt, Research Associate, USTAR Center for Genetic Discovery, University of Utah
Title: Automated Genome Annotation and Analysis
Summary: Introduction to gene prediction and genome annotation methods, organism specific considerations that can affect the annotation process, and a brief example of using automated pipelines such as MAKER for structural and functional annotation of a genome.
Will slides be released: Yes
Will the presentation be recorded: Yes
No webinar in June to accomodate those attending the 11th Annual Arthropod Genomics Symposium June 7-9 at the University of Illinois at Urbana-Champaign.
Note this date is one week later than normal due to the US Federal Holiday on July 4th
Speaker: Rosa Fernández
|October 5, 2016|
Speaker: Jonas Korlach, Chief Scientific Officer, and Sarah Kingan, Senior Scientist Bioinformatics, Pacific Biosciences
Title: High-Quality De Novo Insect Genome Assemblies using PacBio Sequencing
Summary: PacBio Sequencing is characterized by very long sequence reads (average >10,000 bases), lack of GC-bias, and high consensus accuracy. These features have allowed the method to provide a new gold standard in de novo genome assemblies, producing highly contiguous (contig N50 > 1 Mb) and accurate (> QV 50) genome assemblies. We will briefly describe the technology and then highlight the full workflow, from sample preparation through sequencing to data analysis, on examples of insect genome assemblies, and illustrate the difference these high-quality genomes represent with regard to biological insights, compared to fragmented draft assemblies generated by short-read sequencing.
|November 2, 2016|
Speaker: Dr. Anup Parikh, Director of Product Marketing, 10x Genomics
Title: De Novo assembly with 10x Genomics
Summary: Discuss limitations in the current ways we approach genome analysis. Specifically discuss the state of de-novo assembly for genome analysis and demonstrate a straightforward and low-cost method for creating true diploid de novo assemblies with 10x Genomics.
|December 7, 2016|
Speaker: Dr. Ivan Liachko, CEO/CSO, Phase Genomics Inc., Seattle, WA; Dept. of Genome Sciences, University of Washington, Seattle, WA
Title: A rapid method for end-to-end genome assembly, pathogen discovery, and metagenomic deconvolution
Summary: I will describe the Hi-C method and its adaptation toward scaffolding of genomes and metagenomic deconvolution. I will give examples of our work scaffolding large genomes (plant/animal/fungal) as well as assembling prokaryotic and eukaryotic genomes from mixed microbial communities.
|January 4, 2017|
Speaker: Dr. Scott Emrich, UND Director of Bioinformatics; Depts. of Computer Science and Engineering and Biological Sciences (concurrent), University of Notre Dame; contact PI, NIH/NIAID VectorBase, a Bioinformatics Resource Center (BRC)
Title: Non-model arthropod assembly: past, present and future
Summary: Over 40 important arthropod vectors have been sequenced and placed into VectorBase. I will present general principles of genome assembly and analysis ranging from (inbred) colonies to more recent work on field-sourced individuals. Based on these multiple consortium efforts, I will provide information on how to take full advantage of informatics resources available, including but not limited to VectorBase and overcoming potential road-blocks finding or submitting non-model genome data. Finally, I will share emerging results efforts, including my own, to improve genome assemblies of important mosquito vectors using data discussed in other i5K webinars in this series.
|February 1, 2017|
Speaker: Prof. Evgeny M. Zdobnov and Dr Robert M. Waterhouse, University of Geneva Medical School & Swiss Institute of Bioinformatics, Geneva, Switzerland
Title: OrthoDB: an evolutionary perspective to interpreting genomics data
Summary: Orthology is a cornerstone of comparative genomics, and such approaches are well-established as immensely valuable for gene discovery and characterization, offering evolutionarily-qualified hypotheses on gene function by identifying “equivalent” genes in different species.
The OrthoDB hierarchical catalogue of orthologues represents a comprehensive resource of comparative genomics data that delineates the evolutionary histories of millions of genes from thousands of species.
OrthoDB resources and tools enable extensive orthology-based genome annotation and interpretation in a comparative genomics framework that incorporates the growing numbers of sequenced genomes.
|March 1, 2017|
Speaker: Dr. Sven Bocklandt, Senior Application Specialist, Bionano Genomics
Title: Improve genome accuracy and contiguity using Bionano Next-Generation Mapping
Summary: Generating high quality finished genomes remains challenging. Many genomes are highly repetitive, and NGS has led to incomplete assemblies that contain large numbers of contigs and limited long-range information.
Bionano images extremely long molecules, from 150 kbp to megabase pairs in length, to reveal the true long-range structure of the genome. We will discuss how Bionano’s de novo genome maps can increase the contiguity of assemblies up to 100-fold over NGS alone. Because it is the only non-sequencing based scaffolding method, it can error correct assemblies. We will also discuss the difficulties and recent progress in detecting large structural variation.
|April 5, 2017|
Speaker: Dr. Keith R. Hopper, Research Entomologist, Beneficial Insect Introductions Research Unit, USDA-ARS, Newark, Delaware
Title: Phylogenetics and quantitative genetics of host specificity in aphid parasitoids in the genus Aphelinus
Summary: Differences in parasitism success among potential host species can provide strong selection for divergence and speciation in parasitic Hymenoptera. Here we report research on the genomics and genetics of host specificity in Aphelinus species. We have sequenced, assembled, and annotated the genomes and transcriptomes of >10 Aphelinus species. Using coding sequences, we developed a robust phylogeny, onto which we mapped parasitism of diverse species of aphids. For some aphid species, parasitism was phylogenetically conserved, with closely related parasitoids showing similar levels of parasitism. For other aphid species, parasitism diverged between closely related parasitoids, consistent with host-driven speciation. To explore the genetic architecture of differences in host specificity, we crossed and backcrossed A. atriplicis, which readily parasitizes Diuraphis noxia, with A. certus, which rarely parasitizes this aphid. Using genetic markers from reduced-representation genomic libraries, we mapped quantitative trait loci (QTL) affecting parasitism of D. noxia. We found eight QTL (six of which interacted in their effects) that explained 39% of the variation in parasitism D. noxia among backcross females. To help identify candidate genes, we compared the genomes and transcriptomes of these parasitoid species to find proteins that diverged in sequence or expression, and we tested whether these divergent loci mapped to QTL affecting parasitism of D. noxia. So far, we have found 15 divergent genes that mapped to parasitism QTL or significantly affected parasitism by themselves. These are among the first results on the genetic architecture of host specificity in parasitic wasps.
|May 3, 2017|
Speaker: Dr. Kevin Hackett, i5k Co-chair
Summary: Discussion of the Earth BioGenome Project (EBP) including: 1) How getting folks to identify with i5K and EBP can lift all boats; 2) Why we need to invest in genomics infrastructure such as i5K and EBP, in contrast to spending all funding in hypothesis-driven research.
|June 7, 2017|
Wonderful to see everyone at the 10th Annual Arthropod Genomics Symposium and VectorBase Workshop, which was held from June 7 - June 10, 2017 at the University of Notre Dame.
|July 5, 2017|
Speaker: Gerard Coyne, Senior Technical Applications Specialist, Oxford Nanopore Technologies
Title: Real time DNA sequencing using Oxford Nanopore Technologies ‘nanopore sensing’ platform
Summary: Oxford Nanopore Technologies has developed a disruptive platform for the direct, electronic analysis of single molecules. Our instruments the MinION (TM) and the PromethION (TM) are adaptable for the detection and analysis of a range of analytes that include DNA, RNA, proteins and small molecules. At the heart of our platform is a biological protein called a ‘nanopore’. A single nanopore create a hole in a membrane made from a proprietary synthetic polymer. An electric potential is applied across the membrane resulting in a current flowing only through the aperture of the nanopore. Single molecules that enter the nanopore cause characteristic disruptions in the current, by measuring these disruptions single molecules from a sample are identified. The MinION is a small device that is designed for portability and simplicity of its workflow. The MinION plugs into a standard PC or laptop using the USB port. The PromethION is a standalone high throughput benchtop instrument that provides the flexibility to run 100’s of samples in an asynchronous manner. This allows for large projects that requires the flexibility and throughput to interrogate complex eukaryotic genomes. Oxford Nanopore is integrating the data produced by the MinION and PromethION into a cloud-based analytics company, Metrichor. Metrichor is powered by its EPI2ME platform. Metrichor is providing tools to automate data analysis workflows to help people track, trend and predict biological data resulting in real time actionable interpretation of their data. Users of the technology have access to our ‘Nanopore Community’. The Nanopore Community helps new users get started with technical documentation as well as user driven forums and encourages discussion and collaborative experimentation using our technology. There is a growing list of publications on the many uses for our nanopore sensing platform that include field based applications, real time pathogen detection and surveillance, metagenomics analysis, anti-microbial resistance detection, education and many more including sequencing on the International Space Station.
No slides or presentation recording made available.
|August 2nd, 2017|
Speaker: Brandon Rice, Head of Development and Strategy, Dovetail Genomics
Title: Heaps of Chromosomes, New Scales and Evolving Paradigms in Genome Assembly
Summary: The field of genomics has arrived at an inflection point in its history for its most fundamental resource: genome assemblies. Genome assembly is increasingly stream-lined and the results of increasingly outstanding quality, with chromosome-scale assemblies as the new standard. At Dovetail we aim to drive genome assemblies to full commoditization; focus on your science, not on the vagaries of sequencing technologies and analysis approaches. Come hear about the tool-kit and processes we have assembled and those we’re developing to increase focus on science over assembly as the focus of genomics for every organism.
Bonus Presentation from User Perspective
Speaker: Dr. Brenda Oppert, Research Molecular Biologist, Center for Grain and Animal Health Research, Stored Product Insect and Engineering Research Unit, USDA-ARS, Manhattan, Kansas
Title: Reading through the repeats: Dovetail technology improves assembly of insect genomes
|September 6th, 2017|
Speaker: Illumina’s Applied Genomics group
|October 4th, 2017|
Speaker: Monica Poelchau and Christopher Childers, USDA-ARS-NAL
Title: The i5k Workspace@NAL: a pan-Arthropoda genome database
Summary: The i5k Workspace@NAL mission is to support any arthropod genome project by supplying tools and resources to help further applied genomics research. Each genome project has search, gene annotation and visualization tools. We will give an introduction to the workspace, highlighting our resources and services with an emphasis on some of our newer features, such as the new system for starting a project and uploading data and the post annotation QC and Official Gene Set creation pipeline.
|November 1st, 2017|
Speaker: Jonathan Coddington, Director, Global Genome Initiative and Senior Scientist, National Museum of Natural History, Smithsonian Institution
Title: Not Too Much Life: the Global Genome Initiative and the Global Genome Biodiversity Network
Summary: How much life is there and how is it structured? What strategy will best “illuminate” the dark spaces of genomic knowledge across the tree of life? What progress have we made? What resources are rate-limiting? In particular, how can collections-based institutions help i5k? Bioinformatics contributions…
|December 5th, 2017||On hiatus - There was no December 2017 webinar|
|January 3rd, 2018||On hiatus - There was no January 2018 webinar|
|February 7th, 2018|
Speaker: Adam M. Phillippy, Investigator, National Human Genome Research Institute
Title: The pleasures and perils of assembling insect genomes
Summary: Many insect species present a formidable genome assembly challenge due to their small body size and highly diverse and repetitive genomes. Emerging technologies such as long-read sequencing, linked read clouds, Hi-C mapping, and optical mapping are helping to address these challenges, but present some new challenges of their own. I will present the common pitfalls of insect genome assembly, and review my recent experience assembling various Aedes and Anopheles mosquito genomes using these technologies.
|March 7th, 2018|
Speaker: Ning Jiang, Professor, Dept. of Horticulture, Michigan State University
Title: Construction of custom repeat libraries for genome annotation
Summary: Introduction of background, rationale, and methods for building transposon library prior to gene annotation.
Video Recording coming soon