Saima Shahid
@psaima.bsky.social
Interested in #SmallRNA #Transposons #ParasiticPlants #InterspeciesRNAi #plantscience. Lecturer @sheffielduni.bsky.social. Lab: shahidlab.github.io
Pinned
BBSRC Yorkshire Bioscience DLA Programme - Decoding the epigenetic language shaping root parasite-host communication at University of Sheffield on FindAPhD.com
PhD Project - BBSRC Yorkshire Bioscience DLA Programme - Decoding the epigenetic language shaping root parasite-host communication at University of Sheffield, listed on FindAPhD.com
www.findaphd.com
Interested in dissecting the epigenetic code of a cereal killer? Apply for our fully-funded @yorkshirebiodtp.bsky.social #PhD project on Striga epigenomics at Sheffield by 7th Jan 2026:
www.findaphd.com/search/Proje...
Open to UK/International students.
#ParasiticPlant @sheffieldpps.bsky.social
www.findaphd.com/search/Proje...
Open to UK/International students.
#ParasiticPlant @sheffieldpps.bsky.social
Reposted by Saima Shahid
We are looking for undergrads to visit us over the next summer!
If you study in the UK, USA, or Canada, you might be eligible for the DAAD-RISE program 🇩🇪🧬
Learn more 👉 www.izmb.uni-bonn.de/en/pbb/news#DR
Do excellent science in Bonn next summer!
@puckerlab.bsky.social @unibonn.bsky.social
If you study in the UK, USA, or Canada, you might be eligible for the DAAD-RISE program 🇩🇪🧬
Learn more 👉 www.izmb.uni-bonn.de/en/pbb/news#DR
Do excellent science in Bonn next summer!
@puckerlab.bsky.social @unibonn.bsky.social
November 18, 2025 at 10:35 AM
We are looking for undergrads to visit us over the next summer!
If you study in the UK, USA, or Canada, you might be eligible for the DAAD-RISE program 🇩🇪🧬
Learn more 👉 www.izmb.uni-bonn.de/en/pbb/news#DR
Do excellent science in Bonn next summer!
@puckerlab.bsky.social @unibonn.bsky.social
If you study in the UK, USA, or Canada, you might be eligible for the DAAD-RISE program 🇩🇪🧬
Learn more 👉 www.izmb.uni-bonn.de/en/pbb/news#DR
Do excellent science in Bonn next summer!
@puckerlab.bsky.social @unibonn.bsky.social
Reposted by Saima Shahid
Thrilled to share our new review in Current Opinion in Genetics & Development on TE driven innovation in gene regulation🤘. I am honored to be part of this with two major TE aficionados @cedricfeschotte.bsky.social and @trono-lab.bsky.social
#TEsky #TEworldwide
authors.elsevier.com/c/1m6MC,LqAZ...
#TEsky #TEworldwide
authors.elsevier.com/c/1m6MC,LqAZ...
November 15, 2025 at 5:23 PM
Thrilled to share our new review in Current Opinion in Genetics & Development on TE driven innovation in gene regulation🤘. I am honored to be part of this with two major TE aficionados @cedricfeschotte.bsky.social and @trono-lab.bsky.social
#TEsky #TEworldwide
authors.elsevier.com/c/1m6MC,LqAZ...
#TEsky #TEworldwide
authors.elsevier.com/c/1m6MC,LqAZ...
Reposted by Saima Shahid
piRNA-directed DNA methylation may not be a mammalian invention, but can already be found in the germline of axolotl salamanders
Donal O’Carroll and coworkers
www.embopress.org/doi/full/10....
Donal O’Carroll and coworkers
www.embopress.org/doi/full/10....
November 13, 2025 at 11:54 AM
piRNA-directed DNA methylation may not be a mammalian invention, but can already be found in the germline of axolotl salamanders
Donal O’Carroll and coworkers
www.embopress.org/doi/full/10....
Donal O’Carroll and coworkers
www.embopress.org/doi/full/10....
Reposted by Saima Shahid
Out today, our take on 6-methyladenine #6mA evolution in Eukaryotes @natgenet.nature.com. We asked a simple question, is really DNA 6mA common across the eukaryotes? The answer is "yes" if you're a unicellular eukaryote 🦠, not so if you're multicellular 🐝🌱🍄. www.nature.com/articles/s41... 1/9
Adenine DNA methylation associated with transcriptionally permissive chromatin is widespread across eukaryotes - Nature Genetics
Long-read sequencing in 18 unicellular eukaryotes reveals that 6mA is widespread across eukaryotes and is enriched at transcriptionally permissive regions, which are also marked by H3K4me3.
www.nature.com
November 19, 2025 at 9:48 AM
Reposted by Saima Shahid
Interested in dissecting the epigenetic code of a cereal killer? Apply for our fully-funded @yorkshirebiodtp.bsky.social #PhD project on Striga epigenomics at Sheffield by 7th Jan 2026:
www.findaphd.com/search/Proje...
Open to UK/International students.
#ParasiticPlant @sheffieldpps.bsky.social
www.findaphd.com/search/Proje...
Open to UK/International students.
#ParasiticPlant @sheffieldpps.bsky.social
BBSRC Yorkshire Bioscience DLA Programme - Decoding the epigenetic language shaping root parasite-host communication at University of Sheffield on FindAPhD.com
PhD Project - BBSRC Yorkshire Bioscience DLA Programme - Decoding the epigenetic language shaping root parasite-host communication at University of Sheffield, listed on FindAPhD.com
www.findaphd.com
November 4, 2025 at 1:52 PM
Interested in dissecting the epigenetic code of a cereal killer? Apply for our fully-funded @yorkshirebiodtp.bsky.social #PhD project on Striga epigenomics at Sheffield by 7th Jan 2026:
www.findaphd.com/search/Proje...
Open to UK/International students.
#ParasiticPlant @sheffieldpps.bsky.social
www.findaphd.com/search/Proje...
Open to UK/International students.
#ParasiticPlant @sheffieldpps.bsky.social
Reposted by Saima Shahid
Few Plant science programmes are left in the UK and they are critical to train the next generation.
This move by @uniofnottingham.bsky.social goes against recommendations made in the recent PS Education manifesto. Big mistake! Sign the petition! nph.onlinelibrary.wiley.com/doi/10.1002/...
This move by @uniofnottingham.bsky.social goes against recommendations made in the recent PS Education manifesto. Big mistake! Sign the petition! nph.onlinelibrary.wiley.com/doi/10.1002/...
November 9, 2025 at 9:30 AM
Few Plant science programmes are left in the UK and they are critical to train the next generation.
This move by @uniofnottingham.bsky.social goes against recommendations made in the recent PS Education manifesto. Big mistake! Sign the petition! nph.onlinelibrary.wiley.com/doi/10.1002/...
This move by @uniofnottingham.bsky.social goes against recommendations made in the recent PS Education manifesto. Big mistake! Sign the petition! nph.onlinelibrary.wiley.com/doi/10.1002/...
Reposted by Saima Shahid
How is epigenetic information inherited? We found that CDCA7 proteins are critical players in the inheritance of DNA methylation at CG sites in plants, and this is true both in the lab and in the wild. How does this work? 🧵👇
New paper! Work led by @p-bourguet.bsky.social and Frédéric Berger at the GMI of the @oeaw.bsky.social and @esasaki007.bsky.social identified how protein CDCA7 helps plants stably maintain epigenetic modifications across generations.
Read more: www.oeaw.ac.at/gmi/detail/n...
Read more: www.oeaw.ac.at/gmi/detail/n...
November 7, 2025 at 5:05 PM
How is epigenetic information inherited? We found that CDCA7 proteins are critical players in the inheritance of DNA methylation at CG sites in plants, and this is true both in the lab and in the wild. How does this work? 🧵👇
Reposted by Saima Shahid
Plz RP. Come join us at @slcuplants.bsky.social @cam.ac.uk to study effector-targeted plant processes impacting plant cell biology and development.
www.cam.ac.uk/jobs/post-do...
www.schornacklab.net
www.cam.ac.uk/jobs/post-do...
www.schornacklab.net
November 6, 2025 at 6:51 PM
Plz RP. Come join us at @slcuplants.bsky.social @cam.ac.uk to study effector-targeted plant processes impacting plant cell biology and development.
www.cam.ac.uk/jobs/post-do...
www.schornacklab.net
www.cam.ac.uk/jobs/post-do...
www.schornacklab.net
Reposted by Saima Shahid
Very happy that our research on TE dynamics accross cotton evolution at @cragenomica.bsky.social and in collaboration with @jonathanfwendel.bsky.social et al. is now published in Genome Biology!: genomebiology.biomedcentral.com/articles/10....
Differential LTR-retrotransposon dynamics across polyploidization, speciation, domestication, and improvement of cotton (Gossypium) - Genome Biology
Background Transposable elements are major components of plant genomes and major drivers of plant genome evolution. The cotton genus (Gossypium) is an excellent evolutionary model for polyploidization...
genomebiology.biomedcentral.com
October 31, 2025 at 1:30 PM
Very happy that our research on TE dynamics accross cotton evolution at @cragenomica.bsky.social and in collaboration with @jonathanfwendel.bsky.social et al. is now published in Genome Biology!: genomebiology.biomedcentral.com/articles/10....
Interested in dissecting the epigenetic code of a cereal killer? Apply for our fully-funded @yorkshirebiodtp.bsky.social #PhD project on Striga epigenomics at Sheffield by 7th Jan 2026:
www.findaphd.com/search/Proje...
Open to UK/International students.
#ParasiticPlant @sheffieldpps.bsky.social
www.findaphd.com/search/Proje...
Open to UK/International students.
#ParasiticPlant @sheffieldpps.bsky.social
BBSRC Yorkshire Bioscience DLA Programme - Decoding the epigenetic language shaping root parasite-host communication at University of Sheffield on FindAPhD.com
PhD Project - BBSRC Yorkshire Bioscience DLA Programme - Decoding the epigenetic language shaping root parasite-host communication at University of Sheffield, listed on FindAPhD.com
www.findaphd.com
November 4, 2025 at 1:52 PM
Interested in dissecting the epigenetic code of a cereal killer? Apply for our fully-funded @yorkshirebiodtp.bsky.social #PhD project on Striga epigenomics at Sheffield by 7th Jan 2026:
www.findaphd.com/search/Proje...
Open to UK/International students.
#ParasiticPlant @sheffieldpps.bsky.social
www.findaphd.com/search/Proje...
Open to UK/International students.
#ParasiticPlant @sheffieldpps.bsky.social
Reposted by Saima Shahid
@tobybarilbio.bsky.social and I are very excited to release MycoMobilome! A very extensive effort to discover, QC and annotate TEs across the fungal kingdom.
👉 Ready-to-use for your own genome with a simple tutorial!
👉 Metadata about TEs discovered in your genome!
👉 Contribute and get recognition!
👉 Ready-to-use for your own genome with a simple tutorial!
👉 Metadata about TEs discovered in your genome!
👉 Contribute and get recognition!
1/ Ever needed to annotate TEs in a fungal genome, but didn't know where to start?
We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes!
www.biorxiv.org/content/10.1...
We have released #MycoMobilome, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes!
www.biorxiv.org/content/10.1...
October 29, 2025 at 4:32 PM
@tobybarilbio.bsky.social and I are very excited to release MycoMobilome! A very extensive effort to discover, QC and annotate TEs across the fungal kingdom.
👉 Ready-to-use for your own genome with a simple tutorial!
👉 Metadata about TEs discovered in your genome!
👉 Contribute and get recognition!
👉 Ready-to-use for your own genome with a simple tutorial!
👉 Metadata about TEs discovered in your genome!
👉 Contribute and get recognition!
Reposted by Saima Shahid
Hey Yaniv Brandvain is not on Bluesky but his most recent biostats ebook is live ybrandvain.github.io/biostats/. His stats resources have been so helpful to me as I develop my own stats course, so check it out. Github repo here: github.com/ybrandvain/b...
Applied Biostatistics
ybrandvain.github.io
October 24, 2025 at 2:47 PM
Hey Yaniv Brandvain is not on Bluesky but his most recent biostats ebook is live ybrandvain.github.io/biostats/. His stats resources have been so helpful to me as I develop my own stats course, so check it out. Github repo here: github.com/ybrandvain/b...
Reposted by Saima Shahid
🦖 Something HUGE just hatched.
Plasmidsaurus now offers RNA sequencing for gene expression analysis:
• As fast as 3 day turnaround
• $50/sample for academia, $80 for industry
• Up to ~10M unique transcript 3’ end reads per sample
• Interactive results
Explore Plasmidsaurus RNA-Seq today.
Plasmidsaurus now offers RNA sequencing for gene expression analysis:
• As fast as 3 day turnaround
• $50/sample for academia, $80 for industry
• Up to ~10M unique transcript 3’ end reads per sample
• Interactive results
Explore Plasmidsaurus RNA-Seq today.
October 15, 2025 at 4:02 PM
🦖 Something HUGE just hatched.
Plasmidsaurus now offers RNA sequencing for gene expression analysis:
• As fast as 3 day turnaround
• $50/sample for academia, $80 for industry
• Up to ~10M unique transcript 3’ end reads per sample
• Interactive results
Explore Plasmidsaurus RNA-Seq today.
Plasmidsaurus now offers RNA sequencing for gene expression analysis:
• As fast as 3 day turnaround
• $50/sample for academia, $80 for industry
• Up to ~10M unique transcript 3’ end reads per sample
• Interactive results
Explore Plasmidsaurus RNA-Seq today.
Reposted by Saima Shahid
This work was led by Young Jun Kim, a very talented student in the lab. If you have ONT data and want to investigate DNA methylation, DMRcaller would be able to provide you more information than what was previously possible.
October 14, 2025 at 8:21 AM
This work was led by Young Jun Kim, a very talented student in the lab. If you have ONT data and want to investigate DNA methylation, DMRcaller would be able to provide you more information than what was previously possible.
It was a pleasure to be part of this collaboration with the amazing @benebachelot.bsky.social and Parker Bartz, excited for the next manuscript stemming from this study!
Our study on warming and free-living nitrogen fixation is out! Great work led by one of the lab alumni, Parker Bartz, the @forestwarming.bsky.social team and @psaima.bsky.social
nph.onlinelibrary.wiley.com/doi/10.1111/...
nph.onlinelibrary.wiley.com/doi/10.1111/...
Experimental warming alters free‐living nitrogen fixation in a humid tropical forest
Microbial nitrogen (N) fixation accounts for c. 97% of natural N inputs to terrestrial ecosystems. These microbes can be free-living in the soil and leaf litter (asymbiotic) or in symbiosis with pla...
nph.onlinelibrary.wiley.com
October 9, 2025 at 5:42 PM
It was a pleasure to be part of this collaboration with the amazing @benebachelot.bsky.social and Parker Bartz, excited for the next manuscript stemming from this study!
Reposted by Saima Shahid
New #PhD opportunities! NorthWestBio projects now online for 2026! Including a #photosynthesis project w/ @marjorielundgren.bsky.social looking at how photosynthetic diversity may affect future crop nutrient quality. Plant projects and the full set of projects available here: tinyurl.com/529yz4jd
FindAPhD : NorthWestBio Fully Funded Doctoral Training Programme Studentship 2026 at University of Glasgow
Apply for a PhD: NorthWestBio Fully Funded Doctoral Training Programme Studentship 2026 at University of Glasgow
tinyurl.com
September 30, 2025 at 3:04 PM
New #PhD opportunities! NorthWestBio projects now online for 2026! Including a #photosynthesis project w/ @marjorielundgren.bsky.social looking at how photosynthetic diversity may affect future crop nutrient quality. Plant projects and the full set of projects available here: tinyurl.com/529yz4jd
Great to have Mike Axtell at Sheffield for a fantastic PPS cluster seminar on Cuscuta trans-species microRNAs- looking forward to seeing more exciting research from Mike’s group! #parasitic_plants
September 30, 2025 at 2:47 PM
Great to have Mike Axtell at Sheffield for a fantastic PPS cluster seminar on Cuscuta trans-species microRNAs- looking forward to seeing more exciting research from Mike’s group! #parasitic_plants
Reposted by Saima Shahid
🚀 Today is the day! Excited to talk about our nanopore sequencing activities in Freiburg 🌱🧬 Including our plant genome sequencing workflow 👉 www.doi.org/10.20944/pre...
@puckerlab.bsky.social @pietzenuk.bsky.social
@puckerlab.bsky.social @pietzenuk.bsky.social
September 30, 2025 at 4:09 AM
🚀 Today is the day! Excited to talk about our nanopore sequencing activities in Freiburg 🌱🧬 Including our plant genome sequencing workflow 👉 www.doi.org/10.20944/pre...
@puckerlab.bsky.social @pietzenuk.bsky.social
@puckerlab.bsky.social @pietzenuk.bsky.social
Reposted by Saima Shahid
TEtrimmer: a tool to automate the manual curation of transposable elements. #TransposableElements #ManualCuration #Genomics #Bioinformatics @natcomms.nature.com 🧬 🖥️
www.nature.com/articles/s41...
www.nature.com/articles/s41...
September 27, 2025 at 6:05 PM
TEtrimmer: a tool to automate the manual curation of transposable elements. #TransposableElements #ManualCuration #Genomics #Bioinformatics @natcomms.nature.com 🧬 🖥️
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Saima Shahid
The postdoc position is open until filled, but I will start reviewing applicants this coming Monday. If you know someone who is looking, please share.
careers.msu.edu/jobs/researc...
careers.msu.edu/jobs/researc...
September 19, 2025 at 12:43 PM
The postdoc position is open until filled, but I will start reviewing applicants this coming Monday. If you know someone who is looking, please share.
careers.msu.edu/jobs/researc...
careers.msu.edu/jobs/researc...
Reposted by Saima Shahid
PIWI clade Argonautes are essential for transposon silencing. Without them, animals are sterile due to massive transposon activity.
But how does piRNA-guided target interaction translate into silencing?
PhD student Júlia Portell Montserrat has an intriguing answer
www.cell.com/molecular-ce...
But how does piRNA-guided target interaction translate into silencing?
PhD student Júlia Portell Montserrat has an intriguing answer
www.cell.com/molecular-ce...
September 17, 2025 at 10:39 AM
PIWI clade Argonautes are essential for transposon silencing. Without them, animals are sterile due to massive transposon activity.
But how does piRNA-guided target interaction translate into silencing?
PhD student Júlia Portell Montserrat has an intriguing answer
www.cell.com/molecular-ce...
But how does piRNA-guided target interaction translate into silencing?
PhD student Júlia Portell Montserrat has an intriguing answer
www.cell.com/molecular-ce...
Reposted by Saima Shahid
"Honey, what did Bastian @frommlab.bsky.social and Eric do to the miRNAs?!?" +special shout-out @katsutomookamura.bsky.social for initiating this work in 2011. as always, everything Katsutomo did was way ahead of its time.
read about giant miRNA hairpin precursors here! www.cell.com/cell-reports...
read about giant miRNA hairpin precursors here! www.cell.com/cell-reports...
September 12, 2025 at 12:36 PM
"Honey, what did Bastian @frommlab.bsky.social and Eric do to the miRNAs?!?" +special shout-out @katsutomookamura.bsky.social for initiating this work in 2011. as always, everything Katsutomo did was way ahead of its time.
read about giant miRNA hairpin precursors here! www.cell.com/cell-reports...
read about giant miRNA hairpin precursors here! www.cell.com/cell-reports...
Reposted by Saima Shahid
Very excited to finally share the main findings from my PhD, now out as a preprint!
We developed an epigenetic system to understand how plants remember and forget past infections - a phenomenon known as immune memory 🌱🧬🧠
Highlights below! 1/9
www.biorxiv.org/content/10.1...
We developed an epigenetic system to understand how plants remember and forget past infections - a phenomenon known as immune memory 🌱🧬🧠
Highlights below! 1/9
www.biorxiv.org/content/10.1...
From recall to reset: the role of DNA (de)methylation in modulating plant immune memory
Epigenetic reprogramming is increasingly recognised as a driver of plant immune memory, yet its molecular basis remains poorly understood. Using a chemically inducible transgene in Arabidopsis, we tra...
www.biorxiv.org
August 19, 2025 at 8:02 PM
Very excited to finally share the main findings from my PhD, now out as a preprint!
We developed an epigenetic system to understand how plants remember and forget past infections - a phenomenon known as immune memory 🌱🧬🧠
Highlights below! 1/9
www.biorxiv.org/content/10.1...
We developed an epigenetic system to understand how plants remember and forget past infections - a phenomenon known as immune memory 🌱🧬🧠
Highlights below! 1/9
www.biorxiv.org/content/10.1...
Reposted by Saima Shahid
The first in a coming array of papers looking at the co-transcriptome of 72 Botrytis genotype in 10 different host plants is out. Summary is the pathogen uses a combination of general virulence and host specific plasticity (not new genes) to infect dicots. www.biorxiv.org/content/10.1...
Combined generalist and host-specific transcriptional strategies enable host generalism in the fungal pathogen Botrytis cinerea
How generalist pathogens infect phylogenetically diverse hosts remains a central question in plant-pathogen biology. In particular, the extent to which broad host range is enabled by genetic variation...
www.biorxiv.org
July 29, 2025 at 3:19 AM
The first in a coming array of papers looking at the co-transcriptome of 72 Botrytis genotype in 10 different host plants is out. Summary is the pathogen uses a combination of general virulence and host specific plasticity (not new genes) to infect dicots. www.biorxiv.org/content/10.1...
I’m missing out on the amazing science at #Botany2025, but super happy that my student Megan Adler is giving her first talk!
July 29, TUE, 9 AM (PDT):
“Dynamic DNA (de)methylation underpins parasitic #Cuscuta-host plant communication”
If you are attending, don’t miss Megan’s talk!
July 29, TUE, 9 AM (PDT):
“Dynamic DNA (de)methylation underpins parasitic #Cuscuta-host plant communication”
If you are attending, don’t miss Megan’s talk!
July 28, 2025 at 10:00 AM
I’m missing out on the amazing science at #Botany2025, but super happy that my student Megan Adler is giving her first talk!
July 29, TUE, 9 AM (PDT):
“Dynamic DNA (de)methylation underpins parasitic #Cuscuta-host plant communication”
If you are attending, don’t miss Megan’s talk!
July 29, TUE, 9 AM (PDT):
“Dynamic DNA (de)methylation underpins parasitic #Cuscuta-host plant communication”
If you are attending, don’t miss Megan’s talk!