The i5k Webinar Series


Details
Current Schedule
Previous Presentations

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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.

To connect, please refer to these instructions for the WebEx teleconference software:

Connection TypeDetails
Web Conference ConnectionThis connection will allow you to view the video.
You can join your audio through your computer or, if your computer does not support an audio connection, you can connect the audio portion of the webinar via a telephone (see Audio Connection option for details).

1. Connect to the Web Conference using the WebEx application
Using the link above, enter your name and email then select “Join Meeting” to download the application, which will launch once installed.

2. Connect through your WEB BROWSER without downloading the WebEx application
Using the link above, enter your name and email then select “Join by browser”.

The options described can only be selected after entering a name and valid email.
Audio Connection via TelephoneOnce logged in either through the application or a web browser, you can select the option to have WebEx call your phone to establish an audio connection or you can use the information below to call in separately.

1. USA Access
USA Toll-Free: 888-844-9904, then enter Code: 5909637#
USA Caller Paid: 816-423-4261, then enter Code: 5909637#

2. International Access Numbers
A number in your country or in a country close to you (may not be toll free).

3. When prompted, enter the Meeting Access Code: 5909637#

Note: All parties are muted on entry and expected to remain muted throughout the meeting. If you wish to speak, temporarily un-mute on your computer or use “*6” on your telephone keypad, if not linked to your computer. If you have problems connecting, please refer to this WebEx help page.

Current Schedule

DateTalk Information
July 11th
Note this date is one week later than normal due to the US Federal Holiday on July 4th

Speaker: Dr. Brian J. Henson, Sr. Sequencing Specialist, Mid-Atlantic, Illumina, Inc.

Title: Using Illumina’s NGS Technology to Empower Genetic Discovery

Summary: This seminar will focus on how Illumina’s SBS (sequencing by synthesis) technology can be used to drive genomic discovery. We will present an overview of how NGS works and discuss our different platforms. We will also discuss whole genome sequencing with a focus on our Nextera DNA Flex library prep kit.

Will slides be made available: Yes
Will the presentation be recorded: TBD

August 1st
Speaker: Rosa Fernández, Bioinformatics & Genomics Unit, Center for Genomic Regulation, Barcelona (Spain)

Title: The ‘other’ arthropods: a phylotranscriptomics approach to species tree reconstruction.

Summary: In this seminar, I will discuss the latest efforts to shed light on some recalcitrant systematic conundrums in non-insect arthropods (namely arachnids and myriapods), as well as provide an overall view of methodologies and sensitivity analyses commonly used to test hypothesis robustness in species tree reconstruction.

Will slides be made available: Yes
Will the presentation be recorded: No

September 5th
Speaker: Gregg Thomas

Title:

Summary:

Will slides be made available:
Will the presentation be recorded:

Previous Presentations

Date     Talk Information
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.

Slides
Video Recording

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.

Slides
Video Recording

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.

Video Recording

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.

Slides
Video Recording

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.

Slides
Video Recording

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.

Slides
Video Recording

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.

Slides
Video Recording

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

Slides
Video Recording

September 6th, 2017
CANCELED
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.

Slides
Video Recording

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…

Slides
Video Recording

December 5th, 2017On hiatus - There was no December 2017 webinar
January 3rd, 2018On 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.

Slides
Video Recording

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.

Slides
Video Recording

April 4th 2018
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.

Slides
Video recording coming soon

May 2nd, 2018
Speaker: Ben Busby, Genomic Outreach Coordinator and Bioinformatics Training Lead, NCBI

Title: NCBI Resources in the Data Science Era!

Summary: Ben will discuss a number of NCBI databases, submissions, finding, extracting and analyzing data. After a brief introduction, he will work through a use case. At the end, he will talk about some research projects which use similar workflows that were prototyped in a hackathon setting (one example with a collaborator from i5k).

Slides
Video recording coming soon

June 6th, 2018
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.