Timothy Fuqua
@timothyfuqua.bsky.social
Postdoc in Claudia Bank’s group at the University of Bern. Promoters, emergence, fitness landscapes, dogs 🐶 and triathlon 🏊 🚲 🏃. He/him 🏳🌈.
timothyfuqua.com
timothyfuqua.com
Pinned
Timothy Fuqua
@timothyfuqua.bsky.social
· May 22
The latent cis-regulatory potential of mobile DNA in Escherichia coli - Nature Communications
The mechanism and extent to which transposons can alter the gene expression of their hosts is not well understood. This study finds that in the IS3 family of transposable elements in E.coli, de-novo p...
www.nature.com
Happy to announce that our study on the latent cis-regulatory potential of mobile DNA is officially published!
TLDR: mobile DNA in bacteria (Insertion Sequences) have a proclivity for evolving new promoters. At least 25% of them probably already encode functional promoters as well.
TLDR: mobile DNA in bacteria (Insertion Sequences) have a proclivity for evolving new promoters. At least 25% of them probably already encode functional promoters as well.
Reposted by Timothy Fuqua
De-novo promoters emerge more readily from random DNA than from genomic DNA
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
February 10, 2026 at 11:17 AM
De-novo promoters emerge more readily from random DNA than from genomic DNA
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
I'm looking for a Swiss department to host me for an SNSF Starting Grant.
I research how gene expression evolves and emerges by combining wet lab + computational work in a variety of model systems (E. coli, Drosophila, yeast). More: timothyfuqua.com
If your department might be a match, let’s chat!
I research how gene expression evolves and emerges by combining wet lab + computational work in a variety of model systems (E. coli, Drosophila, yeast). More: timothyfuqua.com
If your department might be a match, let’s chat!
Home | Timothy Fuqua
timothyfuqua.com
February 10, 2026 at 10:42 AM
I'm looking for a Swiss department to host me for an SNSF Starting Grant.
I research how gene expression evolves and emerges by combining wet lab + computational work in a variety of model systems (E. coli, Drosophila, yeast). More: timothyfuqua.com
If your department might be a match, let’s chat!
I research how gene expression evolves and emerges by combining wet lab + computational work in a variety of model systems (E. coli, Drosophila, yeast). More: timothyfuqua.com
If your department might be a match, let’s chat!
Reposted by Timothy Fuqua
Can you infer cause and effect between genes without disturbing the cell? 🧬
This study shows how natural “noise” in gene expression can reveal directed gene–gene interactions.
buff.ly/mruUeLZ
This study shows how natural “noise” in gene expression can reveal directed gene–gene interactions.
buff.ly/mruUeLZ
February 5, 2026 at 11:28 PM
Can you infer cause and effect between genes without disturbing the cell? 🧬
This study shows how natural “noise” in gene expression can reveal directed gene–gene interactions.
buff.ly/mruUeLZ
This study shows how natural “noise” in gene expression can reveal directed gene–gene interactions.
buff.ly/mruUeLZ
Reposted by Timothy Fuqua
February 6, 2026 at 7:22 AM
Reposted by Timothy Fuqua
Wanna read about yeasts and heat waves? 🥵 Check out our new preprint with @jennifermolinet.bsky.social and @stelkens.bsky.social!
doi.org/10.64898/202...
doi.org/10.64898/202...
doi.org
February 5, 2026 at 8:38 PM
Wanna read about yeasts and heat waves? 🥵 Check out our new preprint with @jennifermolinet.bsky.social and @stelkens.bsky.social!
doi.org/10.64898/202...
doi.org/10.64898/202...
Reposted by Timothy Fuqua
New preprint from the lab! We identify the ZnF protein Mulberry as a condensation-dependent structural regulator of genome topology that organizes “multi-way regulatory hubs” in early Drosophila embryos.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
February 5, 2026 at 10:56 AM
New preprint from the lab! We identify the ZnF protein Mulberry as a condensation-dependent structural regulator of genome topology that organizes “multi-way regulatory hubs” in early Drosophila embryos.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
I just did my first tetrad dissection! 🍞🧫 Am I a yeast person now?
February 3, 2026 at 1:59 PM
I just did my first tetrad dissection! 🍞🧫 Am I a yeast person now?
Reposted by Timothy Fuqua
New online! Emergence and evolution of protein-coding de novo genes
Emergence and evolution of protein-coding de novo genes
Nature Reviews Genetics, Published online: 28 January 2026; doi:10.1038/s41576-025-00929-9De novo gene evolution entails the birth of new genes from previously non-coding DNA. In this Review, Bornberg-Bauer and Eicholt overview how protein-coding de novo genes are identified, the mechanistic and evolutionary processes underlying their emergence and evolution, and the patterns in their encoded protein structures.
dlvr.it
January 28, 2026 at 9:43 PM
New online! Emergence and evolution of protein-coding de novo genes
Reposted by Timothy Fuqua
2026 has just begun and we are looking forward to welcoming you to EMBL for another year of groundbreaking science.
Our programme now features even more events, check it out ➡️ s.embl.org/2026-poster
Our programme now features even more events, check it out ➡️ s.embl.org/2026-poster
January 27, 2026 at 11:40 AM
2026 has just begun and we are looking forward to welcoming you to EMBL for another year of groundbreaking science.
Our programme now features even more events, check it out ➡️ s.embl.org/2026-poster
Our programme now features even more events, check it out ➡️ s.embl.org/2026-poster
Claudia Bank's (@cbank.bsky.social) research group, Theoretical Ecology and Evolution (THEE) is now on Bluesky! I posted a thread showing some of the group's publications from 2025 to get the account going. Please consider following the group for updates related to ecology and evolution 😀
🧬 Our 2025 review is here!
A (very belated) Happy New Year from the THEE group! From transcription factor evolution to microbiomes, epistasis, biodiversity, and antimicrobial resistance — here’s a thread highlighting our group’s contributions to research in 2025 👇
A (very belated) Happy New Year from the THEE group! From transcription factor evolution to microbiomes, epistasis, biodiversity, and antimicrobial resistance — here’s a thread highlighting our group’s contributions to research in 2025 👇
January 22, 2026 at 2:13 PM
Claudia Bank's (@cbank.bsky.social) research group, Theoretical Ecology and Evolution (THEE) is now on Bluesky! I posted a thread showing some of the group's publications from 2025 to get the account going. Please consider following the group for updates related to ecology and evolution 😀
Reposted by Timothy Fuqua
very sad news. Peer Bork was one of the leaders of our field, a wonderful scientist, and he's much too young to be gone. www.embl.org/news/embl-an...
In remembrance of Peer Bork | EMBL
EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.
www.embl.org
January 16, 2026 at 6:33 PM
very sad news. Peer Bork was one of the leaders of our field, a wonderful scientist, and he's much too young to be gone. www.embl.org/news/embl-an...
We lost a legend…
For many years, Peer Bork organised Bio-IT retreats to bring together the bioinformaticians across EMBL, in Garmisch-Partenkirchen and later Feldberg. Days out on the mountain followed by forward-looking and meta-science oriented sessions in the hut that fueled many projects and careers.
January 17, 2026 at 10:24 PM
We lost a legend…
Reposted by Timothy Fuqua
TF-MINDI is out! A new method to learn cis-regulatory codes through rich embeddings of TF binding sites. TF-MINDI decomposes motif neighbourhoods, and works downstream of any sequence-to-function deep learning model. We deeply study the enhancer code in human neural development, check out the thread
January 15, 2026 at 12:32 PM
TF-MINDI is out! A new method to learn cis-regulatory codes through rich embeddings of TF binding sites. TF-MINDI decomposes motif neighbourhoods, and works downstream of any sequence-to-function deep learning model. We deeply study the enhancer code in human neural development, check out the thread
Reposted by Timothy Fuqua
One of the most-viewed PNAS articles in the last week is “The variability of evolvability: Properties of dynamic fitness landscapes determine how phenotypic variability evolves.” Explore now: https://ow.ly/XouU50XWiiV
For more trending articles, visit https://ow.ly/AiXL50XWi81.
For more trending articles, visit https://ow.ly/AiXL50XWi81.
January 13, 2026 at 10:00 PM
One of the most-viewed PNAS articles in the last week is “The variability of evolvability: Properties of dynamic fitness landscapes determine how phenotypic variability evolves.” Explore now: https://ow.ly/XouU50XWiiV
For more trending articles, visit https://ow.ly/AiXL50XWi81.
For more trending articles, visit https://ow.ly/AiXL50XWi81.
Reposted by Timothy Fuqua
📣 #EMBOEvoEco returns in 2026 to uncover the mechanistic foundations of ecological and evolutionary change!
Keynote lectures will spotlight the ecology and evolution of symbiosis.
Submit your abstract for the EMBO Workshop: https://s.embl.org/eae26-01-bl!
Keynote lectures will spotlight the ecology and evolution of symbiosis.
Submit your abstract for the EMBO Workshop: https://s.embl.org/eae26-01-bl!
January 13, 2026 at 12:26 PM
📣 #EMBOEvoEco returns in 2026 to uncover the mechanistic foundations of ecological and evolutionary change!
Keynote lectures will spotlight the ecology and evolution of symbiosis.
Submit your abstract for the EMBO Workshop: https://s.embl.org/eae26-01-bl!
Keynote lectures will spotlight the ecology and evolution of symbiosis.
Submit your abstract for the EMBO Workshop: https://s.embl.org/eae26-01-bl!
Come to my talk today :)
If you're at the Karolinska @ki.se next Monday and are interested in #transcription or #generegulation then consider coming to my guest talk, "The biases and mechanisms of regulatory DNA evolution and emergence." Cheers!
More info here: news.ki.se/calendar/the...
More info here: news.ki.se/calendar/the...
The biases and mechanisms of regulatory DNA evolution and emergence
Welcome to a seminar with Dr Timothy Fuqua from the University of Bern.
news.ki.se
January 12, 2026 at 5:13 AM
Come to my talk today :)
Reposted by Timothy Fuqua
If you're at the Karolinska @ki.se next Monday and are interested in #transcription or #generegulation then consider coming to my guest talk, "The biases and mechanisms of regulatory DNA evolution and emergence." Cheers!
More info here: news.ki.se/calendar/the...
More info here: news.ki.se/calendar/the...
The biases and mechanisms of regulatory DNA evolution and emergence
Welcome to a seminar with Dr Timothy Fuqua from the University of Bern.
news.ki.se
January 7, 2026 at 2:09 PM
If you're at the Karolinska @ki.se next Monday and are interested in #transcription or #generegulation then consider coming to my guest talk, "The biases and mechanisms of regulatory DNA evolution and emergence." Cheers!
More info here: news.ki.se/calendar/the...
More info here: news.ki.se/calendar/the...
Reposted by Timothy Fuqua
New year, new conferences! Consider submitting to the symposium on Fitness landscapes and Genotype-phenotype maps, linking computational and experimental approaches (organising with @n-martin.bsky.social; @dbajic.bsky.social invited spreaker) at SMBE (28/6-2/7)! Abstract deadline February 3rd!
SMBE2026 Symposium 20 | Mapping fitness landscapes with mechanistic models, machine learning and experiments
📨 Abstract submission
smbe2026.org/abstracts
📋 Programme details
smbe2026.org/programme
#SMBE2026
📨 Abstract submission
smbe2026.org/abstracts
📋 Programme details
smbe2026.org/programme
#SMBE2026
January 9, 2026 at 10:37 AM
New year, new conferences! Consider submitting to the symposium on Fitness landscapes and Genotype-phenotype maps, linking computational and experimental approaches (organising with @n-martin.bsky.social; @dbajic.bsky.social invited spreaker) at SMBE (28/6-2/7)! Abstract deadline February 3rd!
Reposted by Timothy Fuqua
Our paper on the newest version of the Registry of candidate cis-Regulatory Elements (cCREs) is out 🧬
Huge thanks to the many collaborators, experimentalists, analysts and software developers who made this work possible — truly a team effort!
A "meme-torial" of the science is coming soon 👀
Huge thanks to the many collaborators, experimentalists, analysts and software developers who made this work possible — truly a team effort!
A "meme-torial" of the science is coming soon 👀
An expanded registry of candidate cis-regulatory elements - Nature
The existing ENCODE registry of candidate human and mouse cis-regulatory elements is expanded with the addition of new ENCODE data, integrating new functional data as well as new cell and tissue types...
www.nature.com
January 7, 2026 at 6:47 PM
Our paper on the newest version of the Registry of candidate cis-Regulatory Elements (cCREs) is out 🧬
Huge thanks to the many collaborators, experimentalists, analysts and software developers who made this work possible — truly a team effort!
A "meme-torial" of the science is coming soon 👀
Huge thanks to the many collaborators, experimentalists, analysts and software developers who made this work possible — truly a team effort!
A "meme-torial" of the science is coming soon 👀
If you're at the Karolinska @ki.se next Monday and are interested in #transcription or #generegulation then consider coming to my guest talk, "The biases and mechanisms of regulatory DNA evolution and emergence." Cheers!
More info here: news.ki.se/calendar/the...
More info here: news.ki.se/calendar/the...
The biases and mechanisms of regulatory DNA evolution and emergence
Welcome to a seminar with Dr Timothy Fuqua from the University of Bern.
news.ki.se
January 7, 2026 at 2:09 PM
If you're at the Karolinska @ki.se next Monday and are interested in #transcription or #generegulation then consider coming to my guest talk, "The biases and mechanisms of regulatory DNA evolution and emergence." Cheers!
More info here: news.ki.se/calendar/the...
More info here: news.ki.se/calendar/the...
Thanks @bryangitschlag.bsky.social for answering my question about mitochondrial genes! Nice little thread below:
Awesome questions! I was asked some of these in my qualifying exam 😅
To your first question, it’s often more the former, especially for Electron Transport Chain components (some proteins that localize to mitochondria, involving immunity for example, likely had a nuclear origin to my knowledge)
1/6
To your first question, it’s often more the former, especially for Electron Transport Chain components (some proteins that localize to mitochondria, involving immunity for example, likely had a nuclear origin to my knowledge)
1/6
December 15, 2025 at 7:59 AM
Thanks @bryangitschlag.bsky.social for answering my question about mitochondrial genes! Nice little thread below:
Question for #mitochondria people:
Many mitochondrial genes are encoded in the nuclear genome. How? Did these genes originate in ancestral mitochondria and horizontally transfer to the nucleus, or did they emerge de novo in the nuclear genome and replace their mitochondrial counterparts? Plz RT.
Many mitochondrial genes are encoded in the nuclear genome. How? Did these genes originate in ancestral mitochondria and horizontally transfer to the nucleus, or did they emerge de novo in the nuclear genome and replace their mitochondrial counterparts? Plz RT.
December 12, 2025 at 9:25 AM
Question for #mitochondria people:
Many mitochondrial genes are encoded in the nuclear genome. How? Did these genes originate in ancestral mitochondria and horizontally transfer to the nucleus, or did they emerge de novo in the nuclear genome and replace their mitochondrial counterparts? Plz RT.
Many mitochondrial genes are encoded in the nuclear genome. How? Did these genes originate in ancestral mitochondria and horizontally transfer to the nucleus, or did they emerge de novo in the nuclear genome and replace their mitochondrial counterparts? Plz RT.
Reposted by Timothy Fuqua
“this structure has been resolved!! your image is in the database!!”
the image in the database:
the image in the database:
December 11, 2025 at 10:26 PM
“this structure has been resolved!! your image is in the database!!”
the image in the database:
the image in the database:
Reposted by Timothy Fuqua
After a huge amount of work w/ @alex-stark.bsky.social's group, a new version of our Ledidi preprint is now out!
In an era of AI-designed proteins, the next leap will be controlling when, where, and how much of these proteins are expressed in living cells.
www.biorxiv.org/content/10.1...
In an era of AI-designed proteins, the next leap will be controlling when, where, and how much of these proteins are expressed in living cells.
www.biorxiv.org/content/10.1...
Programmatic design and editing of cis-regulatory elements
The development of modern genome editing and DNA synthesis has enabled researchers to edit DNA sequences with high precision but has left unsolved the problem of designing these edits. We introduce Le...
www.biorxiv.org
December 10, 2025 at 3:18 PM
After a huge amount of work w/ @alex-stark.bsky.social's group, a new version of our Ledidi preprint is now out!
In an era of AI-designed proteins, the next leap will be controlling when, where, and how much of these proteins are expressed in living cells.
www.biorxiv.org/content/10.1...
In an era of AI-designed proteins, the next leap will be controlling when, where, and how much of these proteins are expressed in living cells.
www.biorxiv.org/content/10.1...
Reposted by Timothy Fuqua
this is amazing
they show some compelling evidence for 3' to 5' translation
#RNASky #RNABiology 🧪
www.biorxiv.org/content/10.6...
they show some compelling evidence for 3' to 5' translation
#RNASky #RNABiology 🧪
www.biorxiv.org/content/10.6...
3' to 5' Translation of Circular RNAs?
For decades, the 5' to 3' direction of translation has been a central dogma of molecular biology. Here we present evidence that eukaryotic circular RNAs (circRNAs) can serve as templates for 3' to 5' ...
www.biorxiv.org
December 10, 2025 at 6:07 AM
this is amazing
they show some compelling evidence for 3' to 5' translation
#RNASky #RNABiology 🧪
www.biorxiv.org/content/10.6...
they show some compelling evidence for 3' to 5' translation
#RNASky #RNABiology 🧪
www.biorxiv.org/content/10.6...