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

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): link

DNA extraction lecture and demo (by China Lunde): link

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

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

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

Lecture (by Dr Daniil Prigozhin): link

Exercises: link

Genome editing

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

Good microbes, bad microbes: plant microbiomes

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

 

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