Ellis Torrance
@ellistorrance.bsky.social
Computational biologist stopping to study the little things in life! 🦠🧬🔬🧪👩🔬🖥️ | genetics | microbiology | evolution | bioinformatics | hpc . Reposts are on my "to read" list!
Reposted by Ellis Torrance
🚨 New postdoc opportunity in Aotearoa 🇳🇿 with @drhhnz.bsky.social
RA / Postdoctoral Fellow in honeybee bacteriophages, microbial genetics & molecular evolution at the University of Canterbury (Christchurch).
3-year position, starts March 2026.
🔗 jobs.canterbury.ac.nz/jobdetails/a...
RA / Postdoctoral Fellow in honeybee bacteriophages, microbial genetics & molecular evolution at the University of Canterbury (Christchurch).
3-year position, starts March 2026.
🔗 jobs.canterbury.ac.nz/jobdetails/a...
Research Associate / Postdoctoral Fellow - Honeybee Bacteriophages and Advanced Biotechnology -
University of Canterbury | Te Whare Wānanga o Waitaha
jobs.canterbury.ac.nz
January 12, 2026 at 3:38 AM
🚨 New postdoc opportunity in Aotearoa 🇳🇿 with @drhhnz.bsky.social
RA / Postdoctoral Fellow in honeybee bacteriophages, microbial genetics & molecular evolution at the University of Canterbury (Christchurch).
3-year position, starts March 2026.
🔗 jobs.canterbury.ac.nz/jobdetails/a...
RA / Postdoctoral Fellow in honeybee bacteriophages, microbial genetics & molecular evolution at the University of Canterbury (Christchurch).
3-year position, starts March 2026.
🔗 jobs.canterbury.ac.nz/jobdetails/a...
Reposted by Ellis Torrance
Fresh news on de novo genes! Happy to present our latest work published in Nature communications: www.nature.com/articles/s41...
Keywords not in specific order: intergenic ORFs, de novo genes, GC content, foldability, genetic code, ancestral sequence reconstruction and more :)
Keywords not in specific order: intergenic ORFs, de novo genes, GC content, foldability, genetic code, ancestral sequence reconstruction and more :)
January 11, 2026 at 7:43 PM
Fresh news on de novo genes! Happy to present our latest work published in Nature communications: www.nature.com/articles/s41...
Keywords not in specific order: intergenic ORFs, de novo genes, GC content, foldability, genetic code, ancestral sequence reconstruction and more :)
Keywords not in specific order: intergenic ORFs, de novo genes, GC content, foldability, genetic code, ancestral sequence reconstruction and more :)
Reposted by Ellis Torrance
We discovered a universal scaling law linking copy number and plasmid size, which can be used to predict the PCN of your favorite plasmid! 6/7
July 2, 2025 at 10:12 AM
We discovered a universal scaling law linking copy number and plasmid size, which can be used to predict the PCN of your favorite plasmid! 6/7
Reposted by Ellis Torrance
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 9:02 AM
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...
Reposted by Ellis Torrance
We're hiring for several positions (a post-bac researcher in #transcriptomics, a #phage #postdoc, a senior researcher (broad topics) and a graduate student to work on #ciliates) - find info here: www.marine.usf.edu/genomics/app...
Apply - Genomics
www.marine.usf.edu
October 2, 2025 at 5:29 PM
We're hiring for several positions (a post-bac researcher in #transcriptomics, a #phage #postdoc, a senior researcher (broad topics) and a graduate student to work on #ciliates) - find info here: www.marine.usf.edu/genomics/app...
Reposted by Ellis Torrance
Recent paper from the lab studying predictors of phage cocktail efficacy against complex clinical Pseudomonas populations
royalsocietypublishing.org/doi/epdf/10....
Led by Rosanna Wright with extraordinary MSc (PhD) student Maisie Czernuska
royalsocietypublishing.org/doi/epdf/10....
Led by Rosanna Wright with extraordinary MSc (PhD) student Maisie Czernuska
Bacteria–phage infection network structure and genomic defence system content predict efficacy of a phage therapy cocktail against Pseudomonas aeruginosa from chronic lung infections
royalsocietypublishing.org
September 25, 2025 at 1:55 PM
Recent paper from the lab studying predictors of phage cocktail efficacy against complex clinical Pseudomonas populations
royalsocietypublishing.org/doi/epdf/10....
Led by Rosanna Wright with extraordinary MSc (PhD) student Maisie Czernuska
royalsocietypublishing.org/doi/epdf/10....
Led by Rosanna Wright with extraordinary MSc (PhD) student Maisie Czernuska
Reposted by Ellis Torrance
The Peters lab is looking for a new team member! The role transposons play in evolution, basic mechanisms regulating transposition, and applying transposons as tools for genome modification with a special focus on guide RNA-directed transposition. cornell.wd1.myworkdayjobs.com/CornellCaree...
Technician III - Department of Microbiology
Position Summary This position will be in the lab of Dr. Joseph E. Peters in the Department of Microbiology. Research in the Peters’ lab broadly involves deciphering mechanisms in genome stability and...
cornell.wd1.myworkdayjobs.com
October 3, 2025 at 1:01 PM
The Peters lab is looking for a new team member! The role transposons play in evolution, basic mechanisms regulating transposition, and applying transposons as tools for genome modification with a special focus on guide RNA-directed transposition. cornell.wd1.myworkdayjobs.com/CornellCaree...
Reposted by Ellis Torrance
EvANI benchmarking workflow for evolutionary distance estimation academic.oup.com/bib/article/...
An great teamwork by @mohsenzakeri.bsky.social, @stephenhwang.bsky.social and me, with the excellent mentorship of @benlangmead.bsky.social
An great teamwork by @mohsenzakeri.bsky.social, @stephenhwang.bsky.social and me, with the excellent mentorship of @benlangmead.bsky.social
EvANI benchmarking workflow for evolutionary distance estimation
Abstract. Advances in long-read sequencing technology have led to a rapid increase in high-quality genome assemblies. These make it possible to compare gen
academic.oup.com
September 21, 2025 at 3:26 PM
EvANI benchmarking workflow for evolutionary distance estimation academic.oup.com/bib/article/...
An great teamwork by @mohsenzakeri.bsky.social, @stephenhwang.bsky.social and me, with the excellent mentorship of @benlangmead.bsky.social
An great teamwork by @mohsenzakeri.bsky.social, @stephenhwang.bsky.social and me, with the excellent mentorship of @benlangmead.bsky.social
Reposted by Ellis Torrance
The LSRF post-doc fellowship is open (due Oct 31)!
The LSRF is a supportive and kind community. We *always* celebrate each other.
On a personal level, they've always greeted me with open arms and an abundance of kindness.
If you are thinking of applying and have questions, feel free to reach out!
The LSRF is a supportive and kind community. We *always* celebrate each other.
On a personal level, they've always greeted me with open arms and an abundance of kindness.
If you are thinking of applying and have questions, feel free to reach out!
September 9, 2025 at 4:11 PM
The LSRF post-doc fellowship is open (due Oct 31)!
The LSRF is a supportive and kind community. We *always* celebrate each other.
On a personal level, they've always greeted me with open arms and an abundance of kindness.
If you are thinking of applying and have questions, feel free to reach out!
The LSRF is a supportive and kind community. We *always* celebrate each other.
On a personal level, they've always greeted me with open arms and an abundance of kindness.
If you are thinking of applying and have questions, feel free to reach out!
Reposted by Ellis Torrance
Bacteria–phage infection network structure and genomic defence system content predict efficacy of a phage therapy cocktail against Pseudomonas aeruginosa from chronic lung infections
#phage #phagesky #microsky
royalsocietypublishing.org/doi/10.1098/...
#phage #phagesky #microsky
royalsocietypublishing.org/doi/10.1098/...
Bacteria–phage infection network structure and genomic defence system content predict efficacy of a phage therapy cocktail against Pseudomonas aeruginosa from chronic lung infections | Philosophical T...
Pseudomonas aeruginosa chronic lung infections pose serious challenges for phage therapy due to high between-patient
strain diversity and rapid within-patient phenotypic and genetic diversification,
n...
royalsocietypublishing.org
September 8, 2025 at 6:24 AM
Bacteria–phage infection network structure and genomic defence system content predict efficacy of a phage therapy cocktail against Pseudomonas aeruginosa from chronic lung infections
#phage #phagesky #microsky
royalsocietypublishing.org/doi/10.1098/...
#phage #phagesky #microsky
royalsocietypublishing.org/doi/10.1098/...
Reposted by Ellis Torrance
Gene co-occurrence and its association with phage infectivity in bacterial pangenomes
#phage #phagesky #microsky
royalsocietypublishing.org/doi/10.1098/...
#phage #phagesky #microsky
royalsocietypublishing.org/doi/10.1098/...
Gene co-occurrence and its association with phage infectivity in bacterial pangenomes | Philosophical Transactions of the Royal Society B: Biological Sciences
Phages infect bacteria and have recently re-emerged as a promising strategy to combat bacterial infections. However, there is a lack of methods to predict whether and why a particular phage can or cannot infect a bacterial strain based on their genome ...
royalsocietypublishing.org
September 8, 2025 at 6:26 AM
Gene co-occurrence and its association with phage infectivity in bacterial pangenomes
#phage #phagesky #microsky
royalsocietypublishing.org/doi/10.1098/...
#phage #phagesky #microsky
royalsocietypublishing.org/doi/10.1098/...
Reposted by Ellis Torrance
Do you love phage? I have an opening for a postdoc in my lab at the University of South Florida College of Marine Science (@cmarinescience.bsky.social) looking at interactions between marine phage and iron, which is an important limiting trace metal in the oceans (1/5) 🧵#phagesky 🦠🌊
August 1, 2025 at 1:45 PM
Do you love phage? I have an opening for a postdoc in my lab at the University of South Florida College of Marine Science (@cmarinescience.bsky.social) looking at interactions between marine phage and iron, which is an important limiting trace metal in the oceans (1/5) 🧵#phagesky 🦠🌊
Reposted by Ellis Torrance
Excited to share new #program, STEPS, which can simulate #dynamics of the E. coli Long-Term Evolution Experiment (#LTEE) or other microbes in serial transfer regime.
telliamedrevisited.wordpress.com/2025/08/12/s...
STEPS developed by @devinmlake.bsky.social, Zachary Matson, Minako Izutsu, and me.
telliamedrevisited.wordpress.com/2025/08/12/s...
STEPS developed by @devinmlake.bsky.social, Zachary Matson, Minako Izutsu, and me.
STEPS To It
Announcing a new program, called STEPS, to simulate the dynamics of evolving microbial populations.
telliamedrevisited.wordpress.com
August 12, 2025 at 3:53 PM
Excited to share new #program, STEPS, which can simulate #dynamics of the E. coli Long-Term Evolution Experiment (#LTEE) or other microbes in serial transfer regime.
telliamedrevisited.wordpress.com/2025/08/12/s...
STEPS developed by @devinmlake.bsky.social, Zachary Matson, Minako Izutsu, and me.
telliamedrevisited.wordpress.com/2025/08/12/s...
STEPS developed by @devinmlake.bsky.social, Zachary Matson, Minako Izutsu, and me.
Reposted by Ellis Torrance
Tn7 family transposons that include all of the guide RNA-directed transposons (CAST) are common in bacteria. We now find diverse representatives across archaea, with many in the Asgard group. Reviving an Asgard element confirmed the exciting behaviors of the family #MicroSky #TESky
Tn7 family bacterial transposons known for tightly controlled target site selection are distributed across Asgard and archaeal groups https://www.biorxiv.org/content/10.1101/2025.07.27.667033v1
July 30, 2025 at 8:31 PM
Reposted by Ellis Torrance
We made structural predictions of representatives of each #PHROG from #phage genomes, and put the whole lot online. You can browse through montages or go to your favourite phrog directly and download its PDB.
💻🧬 #phagesky
linsalrob.github.io/PHROG_struct...
💻🧬 #phagesky
linsalrob.github.io/PHROG_struct...
PHROG Structure Gallery
linsalrob.github.io
July 7, 2025 at 8:28 AM
We made structural predictions of representatives of each #PHROG from #phage genomes, and put the whole lot online. You can browse through montages or go to your favourite phrog directly and download its PDB.
💻🧬 #phagesky
linsalrob.github.io/PHROG_struct...
💻🧬 #phagesky
linsalrob.github.io/PHROG_struct...
Reposted by Ellis Torrance
Go work for @linsalrob.bsky.social ! I would if I could!!!
PhD opportunities at @flindersuniversity.bsky.social in Adelaide, Australia's most liveable city, to study genetics in #phage
We will also have genetics #postdoc positions too!
#microsky #phagesky
www.linkedin.com/pulse/phd-pr...
We will also have genetics #postdoc positions too!
#microsky #phagesky
www.linkedin.com/pulse/phd-pr...
PhD Project: Discovering Novel Mechanisms of Phage Genome Evolution
We are looking for an awesome PhD student to join our research team to investigate how bacteriophages (phages) generate targeted mutations that enable them to evolve and infect new bacterial hosts. Yo...
www.linkedin.com
July 7, 2025 at 10:52 AM
Go work for @linsalrob.bsky.social ! I would if I could!!!
Reposted by Ellis Torrance
Reposted by Ellis Torrance
A @csisingapore.bsky.social team showed D-I-Tasser can outperform AlphaFold2/3, elevating high-accuracy protein structure & function predictions. We wonder if this moves us closer to resolving protein–protein complex structure prediction? @natbiotech.nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
July 1, 2025 at 2:15 PM
A @csisingapore.bsky.social team showed D-I-Tasser can outperform AlphaFold2/3, elevating high-accuracy protein structure & function predictions. We wonder if this moves us closer to resolving protein–protein complex structure prediction? @natbiotech.nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Ellis Torrance
Scihub stopped uploading new articles. SciDB is a continuing effort which has the entire scihub collection AND new papers.
annas-archive.org/scidb
annas-archive.org/scidb
🧬 SciDB - Anna’s Archive
The world’s largest open-source open-data library. Mirrors Sci-Hub, Library Genesis, Z-Library, and more.
annas-archive.org
July 2, 2025 at 5:14 AM
Scihub stopped uploading new articles. SciDB is a continuing effort which has the entire scihub collection AND new papers.
annas-archive.org/scidb
annas-archive.org/scidb
Reposted by Ellis Torrance
Now published: Systematic comparison of protein language models for transfer learning.
Key points:
- You don't need gigantic models. The two smaller ESM C variants work great.
- There is huge variability in performance across datasets. We have no idea why.
www.nature.com/articles/s41...
Key points:
- You don't need gigantic models. The two smaller ESM C variants work great.
- There is huge variability in performance across datasets. We have no idea why.
www.nature.com/articles/s41...
July 1, 2025 at 11:34 PM
Now published: Systematic comparison of protein language models for transfer learning.
Key points:
- You don't need gigantic models. The two smaller ESM C variants work great.
- There is huge variability in performance across datasets. We have no idea why.
www.nature.com/articles/s41...
Key points:
- You don't need gigantic models. The two smaller ESM C variants work great.
- There is huge variability in performance across datasets. We have no idea why.
www.nature.com/articles/s41...
Reposted by Ellis Torrance
Alignment-free Bacterial Taxonomy Classification with Genomic Language Models www.biorxiv.org/content/10.1... #jcampubs
June 30, 2025 at 1:56 PM
Alignment-free Bacterial Taxonomy Classification with Genomic Language Models www.biorxiv.org/content/10.1... #jcampubs
Reposted by Ellis Torrance
An assessment of DNA language models concludes:
◼️ They do not offer compelling gains over baseline models
Their performance is inconsistent and requires much more compute.
arxiv.org/abs/2412.05430
◼️ They do not offer compelling gains over baseline models
Their performance is inconsistent and requires much more compute.
arxiv.org/abs/2412.05430
June 23, 2025 at 8:21 PM
An assessment of DNA language models concludes:
◼️ They do not offer compelling gains over baseline models
Their performance is inconsistent and requires much more compute.
arxiv.org/abs/2412.05430
◼️ They do not offer compelling gains over baseline models
Their performance is inconsistent and requires much more compute.
arxiv.org/abs/2412.05430
Reposted by Ellis Torrance
New pre-print out \o/ All about CRISPR, metagenomes, and what you learn when you collect (a lot of) spacers from natural communities, with @apcamargo.bsky.social @urineri.bsky.social @lhug.bsky.social but also Uri Gophna, Nikhil George (not on Bsky I think) & others at JGI doi.org/10.1101/2025...
doi.org
June 13, 2025 at 8:22 PM
New pre-print out \o/ All about CRISPR, metagenomes, and what you learn when you collect (a lot of) spacers from natural communities, with @apcamargo.bsky.social @urineri.bsky.social @lhug.bsky.social but also Uri Gophna, Nikhil George (not on Bsky I think) & others at JGI doi.org/10.1101/2025...
Reposted by Ellis Torrance
The Koonin Law of Computatoinal Biology:
Whenever you think you have a great idea in computational or evolutionary biology, it will already have been published by Eugene Koonin in the mid 90ies.
Whenever you think you have a great idea in computational or evolutionary biology, it will already have been published by Eugene Koonin in the mid 90ies.
June 3, 2025 at 12:31 PM
The Koonin Law of Computatoinal Biology:
Whenever you think you have a great idea in computational or evolutionary biology, it will already have been published by Eugene Koonin in the mid 90ies.
Whenever you think you have a great idea in computational or evolutionary biology, it will already have been published by Eugene Koonin in the mid 90ies.
Reposted by Ellis Torrance
Evolution of gene order in prokaryotes is driven primarily by gene gain and loss www.pnas.org/doi/abs/10.1... #jcampubs 🌊
Evolution of gene order in prokaryotes is driven primarily by gene gain and loss | PNAS
Evolution of bacterial and archaeal genomes is highly dynamic, including extensive
gene gain via horizontal gene transfer (HGT) and gene loss as we...
www.pnas.org
June 12, 2025 at 3:07 PM
Evolution of gene order in prokaryotes is driven primarily by gene gain and loss www.pnas.org/doi/abs/10.1... #jcampubs 🌊