Genomes and Plant Health 2021

Summer workshops for the Undergraduate Researchers and for High School Students.

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*The images (left to right): A wild tomato Solanum habrochaites that harbors many disease resistance genes. (c) ksenia; A Nepenthes pitcher plant (c) boyan xu; A DNA sequencing device MinION that can operate from USB port in any computer (c) china lunde; A visual representation of computational approach to mine genomic information of plant pathogens and deduce their protein structures (c) kyungyong seong

"Genomes and Plant Health" course (virtual format) will give introduction to the following topics:

  • Genomics and computational biology
  • Practical skills in biological data analyses
  • Good microbes and bad microbes: decoding microbial communities
  • Genome editing and its application to plant health
  • Majoring and performing research in Biology, Data Science and related disciplines.

This class will require that you have access to the computer, stable internet and capability to install some software.

Information and registration

Undergraduate Research Students

July 6-7th

Participants: For all undergraduate students involved in research.

Format: virtual (by zoom, the link will be provided after the enrollment confirmation - two weeks ahead of the course)

Student fee: None, these are free to all students

Registration: this class is full

We will need your electronic signature on the video and audio release consent forms. Please, contact us if this is an issue.

Please, contact us (genomesplanthealth@gmail.com) if you need to drop your registration, so we can let someone from the waitlist to attend.

We will confirm whether we are able to offer you a place in the course this year and send you zoom details two weeks ahead of the course.

Class size: 30 students

High School Students:

July 14-15th

Participants: Grades 11-12 only , High School Biology required as a prerequisite.

Format: virtual (by zoom, the link will be provided after the enrollment confirmation - two weeks ahead of the course)

Student fee: None, these are free to all students

Registration: here

For those under 18, you will need parent's electronic signature on the video and audio release consent forms.

Please, contact us (genomesplanthealth@gmail.com) if you need to drop your registration, so we can let someone from the waitlist to attend.

We will confirm whether we are able to offer you a place in the course this year and send you zoom details two weeks ahead of the course.

Class size: 30 students

Schedule

Day 1 Genomics and Computational Biology (9am-2pm with a break for lunch)

  • Introductions (30 min)
  • Decoding genomes: DNA extraction, sequencing technologies, genome databases (lecture and practical, 1hr)
  • Genome assembly, annotation, and the ins and outs of computational biology (lecture and practical, 1hr)
  • From genes to proteins: protein domain architectures and families, structures (lecture and practical, 1hr)

Day 2 Applications to Plant Health (9am-2pm with a break for lunch)

  • check in and social (30 min)
  • Good microbes, bad microbes: plant microbiomes (lecture and practical, 1hr)
  • Genome editing (lecture and practical, 1hr)
  • Career discussion panel with all instructors (1 hr)

Funding

Our workshops are supported by The National Science Foundation and the United States Department of Agriculture - National Institute of Food and Agriculture.

If you would like to provide additional support, please, contact us at genomesplanthealth@gmail.com or Prof Ksenia Krasileva directly at kseniak@berkeley.edu

Instructors

Prof Ksenia Krasileva is an Assistant Professor in the Department of Plant and Microbial Biology as well as Innovative Genomics Institute and the Center for Computational Biology, UC Berkeley. She is an expert in plant genomes and genome databases, next generation sequencing technologies and protein family analyses. Ksenia will be present at all course sessions, she will lead the topic "Decoding genomes: DNA extraction, sequencing technologies, genome databases" and co-teach "From genes to proteins: protein domain architectures and families, structures" as well as "Genome editing" in both workshops. You can read more about her research on this website.

China Lunde Shaw is a Laboratory manager in the Krasileva Lab, UC Berkeley. She is an expert in genetics and genomics, including but not limited to DNA extraction workflows, DNA quality control for sequencing, Oxford Nanopore sequencing. China provides administrative support for the workshops and will co-teach "Decoding genomes: DNA extraction, sequencing technologies, genome databases". China is involved in many research projects described here: link

Pierre Joubert is a PhD candidate in Microbiology with Designated Emphasis in Genomics and Computational Biology in the Krasileva Lab, UC Berkeley. He is an expert in genomics and computational biology. Pierre will lead "Genome assembly, annotation, and the ins and outs of computational biology" topic for undergraduate workshop and co-teach "Good microbes, bad microbes: plant microbiomes". You can find more information about his research here: link

Boyan Xu is a PhD Student in Mathematics with Designated Emphasis in Genomics and Computational Biology in the Krasileva Lab, UC Berkeley. He is an expert in computational biology, data science, and protein sequence analyses. Boyan will lead "Genome assembly, annotation, and the ins and outs of computational biology" topic for the high school workshop, illustrating how we can use computational biology to understand plant biodiversity. You can find more information about his research here: link

Dr Michael Gomez is a postdoctoral researcher in plant biology in the Staskawicz Lab, UC Berkeley and Innovative Genomics Institute. He is an expert in genome engineering from selective breeding to CRISPR, CRISPR strategies for virus-resistant plants, improving crops for plant health and human health. Michael will lead a section on "Genome editing". You can find more information about his research here: link

Reena Debray is a PhD student in Integrative Biology in the Kostkella lab, UC Berkeley. She is an expert in plant microbiomes, bacterial genomics and plant health. Reena will lead a section on "Good microbes, bad microbes: plant microbiomes". You can find more about her research here: link

Dr Daniil Prigozhin is a Staff Beam line Scientist at the Advanced Light Source at the Lawrence Berkeley National Laboratory and UC Berkeley. He is an expert in genomics, protein sequence analyses, protein structure analyses. Daniil will lead the topic "From genes to proteins: protein domain architectures and families, structures". You can find more about his research here: link