Genomes and Plant Health

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 (in person, UC Berkeley) will give introduction to the following topics:

  • Genomics and computational biology
  • Practical skills in DNA extractions, real time sequencing with Oxford Nanopore, biological data analyses
  • Genome editing and its application to plant health
  • Majoring and performing research in Biology, Data Science and related disciplines.

The course will be delivered in person at the University of California Berkeley, some sections will be broadcasted live.

We are currently planning to deliver two courses as last year: one oriented at research undergraduates and another at high school students, however if not enough students sign up, the courses might be combined.

The course will be free to all participants.

Undergraduate Research Students

June 27-28th, 2022

Participants: For all undergraduate students involved in research.

Format: in person, lunch provided.

Parts of the course will also be available as Webinar on zoom.

Student fee: Workshops are free to all students, small (up to $100) scholarships to cover transportation are available.

In person attendance registration: link

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.

In person class size: 30 students

Webinar attendance registration: link

A link to the webinar will be emailed a few days ahead of the course.

High School Students:

June 29th-30th, 2022

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

Format: in person, lunch provided

Parts of the course will also be available as Webinar on zoom.

Student fee: Workshops are free to all students, small (up to $100) scholarships to cover transportation are available.

In person attendance registration: link

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.

In person class size: 30 students

Webinar attendance registration: link

A link to the webinar will be emailed a few days ahead of the course.

Teaching and learning resources from "Genomes and Plant Health" 2021 course (virtual format)

Slides and tutorials

Decoding genomes: DNA extraction, sequencing technologies, genome databases

Lecture and tutorial (by Dr Ksenia Krasileva): Video cliplink to slides

DNA extraction lecture and demo (by China Lunde): Video cliplink to slides

Genome assembly, annotation, and the ins and outs of computational biology

Lecture and coding exercises (Google CoLab, by Pierre Joubert and Boyan Xu): link to slides and Google Colab

From genes to proteins: protein domain architectures and families, structures

Lecture (by Dr Daniil Prigozhin): link to slides 

Exercises: link

Genome editing

Lecture and tutorial (by Dr Michael Gomez and Dr Ksenia Krasileva): link to slides

Good microbes, bad microbes: plant microbiomes

Lecture and coding exercise (Google CoLab, by Reena Debray): link to slides and Google Colab

 

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

This year 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

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 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


Chandler Sutherland is is a PhD candidate in Plant Biology with Designated Emphasis in Genomics and Computational Biology in the Krasileva Lab, UC Berkeley. She is an expert in genomics, next generation sequencing and sequence analyses. Chandler will lead Genome Sequencing topic with hands on demonstration of Oxford Nanopore sequencing. You can find more information about her research here: link

Anne Nakamoto is a post-baccalaureate scientist in the Krasileva Lab, UC Berkeley. She obtained BSc in Molecular and Cellular Biology with Minor in Computer Science in May 2022 and is an expert in computational biology, data science and evolutionary biology. Anne will lead genome and protein family analyses topic. You can find more information about her research here: link


Evan Groover is a PhD candidate at UC Berkeley and is an expert in plant gene editing and metabolism. He is developing CRISPR tools to understand and improve photosynthesis, and is advised by David Savage and Brian Staskawicz. You can find more information about his research here: link


Enrico Calvanese is a second-year PhD student at UC Berkeley. Enrico uses CRISPR technology as a reverse genetics tool to investigate protein degradation pathways in plants. He is mentored by Dr. Yangnan Gu. You can find more information about the Gu lab and Enrico's research here: link