Ksenia Krasileva
@kseniakrasileva
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Solving puzzles in genomics and plant immunity. Assistant Prof at Berkeley. She/Her.
Berkeley, CA
Joined August 2009
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Pinned Tweet
New preprint from the lab on NLR engineering led by
@KyungyongS
👇🧵
A new preprint from
@kseniakrasileva
lab: resurrecting an NLR to recognize its effector escape mutant!
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I reached the point in my career where I go to lab and do experiments as procrastination from doing paperwork
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Tenured 😀✅
Grateful to the lab members, colleagues and friends for sharing this journey 🫶🥂
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Out today! "Prediction of effector protein structures from fungal phytopathogens enables evolutionary analyses" - awesome work by
@KyungyongS
📜
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I am honored to receive
@NIH
Director's award! I could not wish for a better group of scholars to work with than people in our lab. Getting this award is a tribute to them
Just found a very exciting project funded by NIH Director's New Innovator Award. Congratulations
@kseniakrasileva
!
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Friends ask if anti-Russian sentiments affect me and my family. I am and will be ok, that’s the least of my worries. My lab, university, and friends show support and compassion. I beg you to
#stopthewar
, support Ukraine, and brave Russians who are speaking up.
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Krasileva Lab is moving to Berkeley, July 2018!
After 3.5 years as Group Leader in Norwich, I'll be an Assistant Professor
@PMB_Berkeley
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New preprint from the lab!
@KyungyongS
used the latest machine learning algorithms to model 1,854 secreted proteins from the fungal pathogen M. oryzae. Here is what we learned from this computational structural genomics project (1/n):
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Congratulations
@GittaCoaker
on Noel T Keen Award for Research Excellence in Molecular Plant Pathology 📸👏
#PlantHealth2022
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I am honored and excited to receive this grant. I look forward to meeting the cohort of other scientists and learning what they do.
#MooreInventors
Congrats to prof. Ksenia Krasivela, plant genomics researcher, on being named a
@MooreFound
’s Moore Inventor Fellow! Krasivela was recognized for her work as a scientist and her dedication to reducing
#foodinsecurity
.
#MooreInventors
@UCBerkeley
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If you had invited me to give a scientific talk in next few days or weeks, expect that I would ask permission to voice my support for
#stopthewar
at the beginning of each presentation. It is otherwise simply impossible for me as a human being to speak about my science right now.
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'Life of a plant' can also be told in memes. I find this one especially funny.
by Kenda Rauscher, UC Berkeley.
#sciencecomminication
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I am very excited to be part of this ambitious project!
IGI researchers
@bstask
&
@kseniakrasileva
have been awarded $3.2 million for fighting diseases in wheat crops. We are excited about what we can do with this generous support from
@FoundationFAR
&
@2blades
!
Learn more:
@UCBerkeley
@PMB_Berkeley
@Cal
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Duckweeds can be resistant or susceptible to common plant pathogens, but they have lost many immune genes key to disease resistance in other plants. We wondered how Duckweeds survive in a soup of microbes without being diseased? New preprint from the lab:
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Is it too egocentric to announce that I give myself tenure? This is the 1st year when I am confident that I want to and can successfully lead a research lab for the next 30 years or so. We will make many discoveries. Keep in mind, I have not submitted even a mid-term review yet.
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Congratulations to Dr
@erinbaggs1
for a superb finishing talk. I am proud of the first Krasileva Lab graduate student 👩🎓 🧪 🧬 💻 who made several discoveries & established a new pathosystem. Any place that’s hiring: Dr Baggs has a great research program to start her own lab
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Now might be the best time to pick up some bioinformatics skills. We have a tutorial on protein family analyses available online:
Galaxy has some of the best training resources for NGS:
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We surveyed plant genomes and discovered convergent evolution among aquatic flowering plants - rewiring of plant immunity and drought response. Fantastic work by
@erinbaggs_
- read and peer-review it openly today at
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Dear community,
We release chromosome level genome of pasta wheat T turgidum Kronos, a model organism, founder of the sequenced reverse genetics resource, highly amenable to transformation.
The genome is released here under Toronto agreement
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I am proud of
@erinbaggs_
for having her first study published
@ThePlantCell
and for putting her discovery on
@biorxivpreprint
many months before. She is a true leader in our community! I'm grateful to all colleagues and reviewers who worked with us
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Happy to see this out in press! Congrats
@chandler_suth
!
Ksenia Krasileva
@kseniakrasileva
and co-workers
@UCBerkeley
show that high allelic diversity in
#Arabidopsis
#NLRs
is associated with distinct genomic features.
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Plant and Microbial Biology IPA - made by grad students
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A plant on my mind today is Triticum (wheat). It has a large complex genome, 5x larger than human genome. Decoding wheat pivoted from efforts of international consortia to democratization of sequencing any specific variety. This has been key to understand disease resistance.
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When students from the lab get independently invited (I have nothing to do with it) to present, it makes me proud and happy. This is how I measure success.
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New preprint from the lab! Pathogens evolve as fast as their hosts. We looked into which genomic features are associated with rapid gene presence absence variation.
Read new
@pmjoubert
study to find out more.
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We are looking for a postdoc to join
#projectwheat
What you bring: expertise in wheat, genomics, genetics, plant pathology.
What you'll have access to: unique germplasm (you can take it with you to start a lab), lot's of funding, fun lab
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New preprint! Genome of a duckweed Wolffia reveals a single canonical NLR (plus 2 non-canonical) in its reductionist immune system great collaboration, NLR analysis by
@erinbaggs_
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It is happening! We launched and we will be teaching two workshops this summer on Genomes and Plant Health, our goal is to expose research undergraduates and high school students to genomics, bioinformatics and how to use them to improve plant health.
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What did McClintock study when she discovered TEs? - this is an exam question in a grad module I teach. Few people know she pioneered genome instability research, formulating hypotheses about innate processes actively controlling instability. TEs is one of them.
Barbara McClintock changed genetics when she discovered that individual genes can change places in chromosomes. Since the discovery was contradictory to genetics theory at the time, it took 40yrs until her findings were accepted & she was awarded the
#NobelPrize
.
#WomenInScience
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Today is a blueberry muffin type of morning. Blueberry genome is 1.6 Gb (half the human genome) with 48 chromosomes and 2 distinct sub-genomes. Antioxidants vary 20x across varieties, coupled with tandem array duplication of biosynthesis genes.
#AwesomePowerOfGenomes
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This year as a lab, we mentored 5 rotation students and 2 undergraduates despite fires, pandemics, exams, teaching and all that jazz. This is a huge success for a relatively small lab. I am so proud of us!
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New from the lab! Comparative computational structural genomics allowed
@KyungyongS
to investigate evolution of elusive pathogen effectors across many fungal pathogens and non-pathogenic sister groups! We learned a lot! See 🧵👇
Structure prediction with
#AlphaFold
and fungal pathogen secretome? Not just one pathogen but many! Check out a new preprint from
@kseniakrasileva
lab! 1/19
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It's online! Altering specificity and auto-activity of plant immune receptors Sr33 and Sr50 via a rational engineering approach by
@JaninaTamborski
@KyungyongS
together with
@FurongLiu
@bstask
you all saw it first
@biorxivpreprint
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I explained a generalized linear regression to the 1st year grad students in plant biology this morning (did not plan to).
While it may not be rocket science, I consider this is one of the highest points in my teaching career so far in making computational biology accessible.
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A week ago, I incorporated ChatGPT in teaching. The assignment was to ask ChatGPT questions about course materials, then critically review and grade the answers. Overall, I am really impressed how throughout and critical students' evaluations are. 🎯
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Yesterday at a playground:
“Plants have an immune system? Is this for real?
Is this what you are studying?”
A few minutes later “Are all of our bananas going to die?”
We are working to solve this.
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Fancy doing postdoc at Berkeley in Plant Genomics and/or Immunity? Send me your expression of interest and CV. Ability to identify postdoc fellowships is ++
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Science Art: two wheat pathogens drawn by postdoc in our lab
@Lorena_B_Parra
Can you guess which ones?
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New position in our department - Assistant Professor in Fungal biology.
We welcome applicants from all fields of fungal biology: genetics, biochemistry, development, metabolism, ecology, and their relevance in agriculture, industry, and/or biomedicine.
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I now get all the ‘wow moments’ people post about
@Nanopore
runs. Watching 100kb wheat reads of our favorite research line produced real time is pure joy... I still remember a reference genome with most assembled contigs being 2kb just a few years ago.
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New from our lab: "Evolution of Plant NLRs: From Natural History to Precise Modifications" by
@JaninaTamborski
and me. Several people to thank for great discussions that led to this review
@erinbaggs_
@daniilprigozhin
@Eli_Thynne
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Thank you those who hosted me for seminars and all who heard my
#nowarinUkraine
statements. I’m asked if I see hostility to myself as Russian-American. No, friends, I received hugs from Ukrainian women. It’s not about a name or a title, it’s what you do that matters.
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Today we bid farewell and wish very best to the first Krasileva lab @ Berkeley postdoc
@JaninaTamborski
Stay tuned for an exciting preprint on NLR engineering coming here very soon.
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We are looking for a postdoc to work on protein engineering and/or directed evolution of plant immune receptors. Collaboration with
@igisci
. Please, help spread the word. Candidates can DM/email me.
@chang_c_liu
@nicolabiologist
@pdhsu
@Jenny_Mortimer1
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In our latest pre-print,
@pmjoubert
describes extra chromosomal circular DNA (eccDNA) from a filamentous fungus, plant pathogen extraordinaire - Magnaporthe oryzae.
What are eccDNAs? [1/9]
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In print today! Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions.
Great collaboration
@PaulBailey70
@MatthewMoscou
@erinbaggsEI
@cpt_bwt
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Flashback to 10 years ago. This was the "Successful PhD student guide" that I kept on my Desktop. I adhered to the rules. I disputed the rules. I never removed the guide.
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My department
@PMB_Berkeley
has an open position for an Assistant Professor in Plant Developmental Biology
The environment is supportive and collegial, the grad student program is outstanding and.. we are overall very happy! Join us🌱🧬🔬💻🌎
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Pomegranate season is at its peak in California. The genome of this berry is only 320 Mb (10% of ours, but has the same number of genes). Many pomegranate varieties have been sequenced, it helped identify the genes that humans selected (hard vs soft seed).
#AwesomePowerOfGenomes
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I’m happy to see not 1 but 10 researchers, programs and labs highlighted!
It is an honor to be among them.
Rising Stars in Plant Sciences 2023 (RSPS2023) | Finalist Oral Presentation Contest | May 30 13:00-15:30pm & May 31 13:00-15:30pm (GMT/UTC) | FREE to Watch the Live Streaming via YouTube ()
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We make an observation that recognition of modified self in plants is an evolutionary byproduct of recognition of non-self. A subset of plant innate immune receptors is responsible for diversity generation, preempting plant ability to recognize any molecule.
Our latest preprint is online with an update on evolution of plant NLRs
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It is an honor to give a seminar today at St Petersburg State University. I had first introduction to biology here when I was 10 years old from Prof Tikhodeev who is hosting me today.
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Immune receptors with exogenous domain fusions form evolutionary hotspots in grass genomes. Our first pre-print!
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With 2 small kids and no real daycare options, me and my husband moved to a 2 shift system: 7am-3pm and 3pm-10pm to ensure we can work remotely. These are the hours when our kids are awake! I explained it to my lab. Q: do I need to put this in an email signature?
#WorkLifeBalance
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We opened the 7th Krasileva Lab retreat with a happy hour on a beach and DEIB discussions. I look forward to the next three days of research planning, topic discussion (mentorship, careers, SWOT), socials (music, pub quiz) and enjoying Asilomar.
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Congratulations to Cara Haney for
#2023ISMPMI
Achievement Award!! She reminds us that science is symbiotic, love this slide.
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I cannot believe that my last day at
@EarlhamInst
and
@TheSainsburyLab
- June 29th is coming up and so fast. Such amazing four years in Norwich. I am grateful to all who helped me develop as a scientist and a group leader.
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My first lecture
@UCBerkeley
today as an Assist Prof. It was great to see enthusiastic students eager to learn about genomics and plants
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I am really proud of my department
@PMB_Berkeley
@UCBerkeley
as I was almost 9 months pregnant during the interview and no one blinked an eye (except for one faculty giving me an extra bag of snacks in case I needed them throughout the day)
Please don't ask women if they plan to have a baby during a job interview.
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/Opening Twitter looking for new hot science to see yet another discussion on what a professor should or should not look like/Apologies, to all. I have a unix machine to fix out of emergency boot mode first thing Monday morning. -Sincerely, Prof Krasileva
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Our latest preprint is online with an update on evolution of plant NLRs
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National Academy of Sciences Elects New Members — Including a Record Number of Women — and International Members. Congratulations for two of them from
@PMB_Berkeley
Prof Louise Glass and Prof Barbara Baker 👏
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If you are curious to know more about Krasileva lab, how it came about and my thoughts on doing research, read this BMC Biology piece:
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We have an exiting postdoc position available in my lab to work on protein engineering. Please, RT widely!
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I cannot believe that it is
@erinbaggs1
last week in the lab! Erin is an awesome contemporary that I was lucky to work with and I look forward to all she does next.
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I’m celebrating return to office by decorating it with our study organisms. Here are
#duckweeds
Spirodela and Lemna.
@erinbaggs1
studies how these tiny plants that lack a canonical immune system are able to colonize all continents except Antarctica.
#biodiversity
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Such an inspiring and rational talk by
@pcronald
#PlantBio19
you can also listed to her TED talk on engineering our crops
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Preprint! 📜
We developed structure-guided method for solenoid protein repeat annotation. We tested and applied it to Leucine Rich Repeat (these look like "slinky" in 3D). Boyan Xu, PhD candidate in our lab led the work together with colleagues.
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New from the lab! We used iterative synbio approach in combination with structure modeling to resurrect wheat NLR Sr50.
@KyungyongS
will post a🧵today
Engineering the plant intracellular immune receptor Sr50 to restore recognition of the AvrSr50 escape mutant
#biorxiv_plants
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New from the lab!
@JaninaTamborski
successfully designed a synthetic hvNLR with changed ligand binding specifity. Spoiler alert: we also found how to keep it in the proper OFF state.
We created a synthetic NLR Sr33syn, that recognizes AvrSr50 - the cognate effector of Sr50. How many amino acid changes did this require? Fewer than we suspected! Very excited to share the preprint of my postdoctoral work with
@kseniakrasileva
!
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@schwessinger
@PlantTeaching
I outline our lab's policy in the lab charter: For joined projects, it is always good to discuss what would be determining factors ahead of time.
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2700 mutant wheat lines, 10,000,000 mutations in genes - yours to use.
#WheatAsModelOrganism
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Our new version of Magnaporthe oryzae secreted proteins dataset with structures predicted by AlphaFold is now available from Zenodo!
@KyungyongS
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Thank you for this opportunity to share our published and unpublished results and all of you who connected to listen from around the world! I am proud to be a member of
@ASPB
Don't forget to register for this week's
#PlantaePresents
webinar with Graham Farquhar and Ksenia Krasileva (
@kseniakrasileva
)! It starts in less than 5 hours.
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This can be a game changing strategy to engineer NLRs with synthetic IDs
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Dominant integration locus drives diversification of plant immune receptors w/ exogenous domains. New NLR-ID results
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New postdoc opportunity in Dangl lab (if you apply based on this tweet, tell Jeff so he considers joining twitter)
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« There is greater pathogen diversity in wild vs agricultural systems. More diversity means more balanced frequencies of pathogen strains » - Talia Karasov
#ICPP2023
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Must read: how can two innate immune receptors next to each other undergo drastically distinct evolution? One is prone to structural variation and new domain fusions while other keeps still and does signaling tasks.
A genetically linked pair of NLR immune receptors show contrasting patterns of evolution
#bioRxiv
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In a new preprint from the lab,
@anne_nakamoto
and
@pmjoubert
present a new project in our lab that they designed - analysis of the TE content across M oryzae lineages that infect different hosts (wheat, rice, grasses).
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"Genomes and Plant Health" workshops are happening again this summer.
These are free 2 day in person workshops at UCB for high schoolers and undergraduates. We cover a range of topics in genomics and gene editing with hands on and coding demos. It's fun!
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NLRs are TEs, look how well their are jumping. Bravi! This is fantastic visualization 👏
I'm working with 2 talented undergrads this summer. They created these great chromosome maps showing NLR gene location across the maize NAM-pangenome 😍
NLR annotation was done by
@erinbaggs1
and
@kseniakrasileva
as part of
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Wheat and maize are becoming my two favorite species. Their genomes are wonderfully related yet contrasting. Wheat is messy, complicated, diverse in all dimensions. Maize keeps everything in order like a true model organism.
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I am so proud of
@erinbaggs_
3 talks to finish off 3rd year of PhD, including invited seminar from
@PlantEvolution
Stimulating seminar today by
@erinbaggs_
from
@kseniakrasileva
lab on convergent loss of immune genes in aquatic monocots & dicots
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Good news come as busses. I am looking for a postdoc to join our protein engineering efforts. An ideal candidate should have experience in yeast genetics and protein biochemistry (no plant experience needed). DM me if interested. RT and help to spread the word!
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I want to dedicate this to the memory of Tatiana Novikova, my school teacher who passed away last week, and all teachers around the globe
Krasileva Lab is moving to Berkeley, July 2018!
After 3.5 years as Group Leader in Norwich, I'll be an Assistant Professor
@PMB_Berkeley
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Personally, I am very humbled and honored to be closing
#wheatswomen2018
with Carlotta Award talk on Wheat Genomics and Immunity.
My slides are online:
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With our most recent publication on hvNLRs, we made analyses available through CoLab. Did you clone a resistance gene from maize, soybean or Arabidopsis? You can now place it in pan-NLRome tree, get info on variability and key sites that might be evolving for ligand binding.
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I had a luxury to see Vavilov Institute during an invited seminar trip to St Petersburg (where I grew up). This story is about a genius from the past, one of my heroes. People working there now are as dedicated, bright & talented. My seminar was followed by 45min of Q&A.
I enjoyed reading
@LeeDugatkin
's piece on Vavilov this morning with coffee. Vavilov's story is part adventure as he collected seeds from around the world, full of fascinating theories on domestication and genetics, and then tragedy during Lysenko's era.
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PhD students finishing
#2023ISMPMI
talks with « I’m looking for a postdoc position»! We are doing something special as the community!
I hope soon to hear « I’m looking for industry job, I’m starting a biotech company, I want to be an editor, a policy maker» & getting the support.
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I'm thrilled to present work of fantastic graduate (
@KyungyongS
@pmjoubert
) and undergraduate (Anne Nakamoto) students who inspire me with their curiosity and excitement about fungal genomics. *this talk is certified 100% NLR-free
Thank you
@UNL_PlantPath
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Earlier this week we had a lab retreat, our 6th annual gathering to discuss science, reflect on the past year and make new plans. It is our personal conference and for me a great source of joy, motivation.
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Found this on my door step. Who could be possibly reading this in my family?
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Remember us? While everyone (including us) are playing with AlphaFold2 I want to remind that breakthrough in structure modeling happened 2 years ago, a qualitative change allowing computational structural genomics. I'll talk about old and new data and future plans
@ISMPMI
in Sept
New preprint from the lab!
@KyungyongS
used the latest machine learning algorithms to model 1,854 secreted proteins from the fungal pathogen M. oryzae. Here is what we learned from this computational structural genomics project (1/n):
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I will give a talk on "evolution in overdrive" in NLRs and effectors on Thursday July 20th.
(I'll mostly focus on preprinted unpublished work).
For more details on structural genomics of effectors, see talk by
@KyungyongS
Thursday morning.
#2023ISMPMI
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