eugene levy implies the existence of pseudogene levy
July 27, 2026 at 12:23 PM
eugene levy implies the existence of pseudogene levy
Now out in print! Elli Cryan (coadvised by @spicybotrytis.bsky.social) digs deep into the sgtructure and function of hybrid incompatibility loci in maize. Among other things she discovers a conserved, ancient pseudogene haplotype that silences the locus in trans! academic.oup.com/genetics/adv...
May 8, 2025 at 3:29 AM
Now out in print! Elli Cryan (coadvised by @spicybotrytis.bsky.social) digs deep into the sgtructure and function of hybrid incompatibility loci in maize. Among other things she discovers a conserved, ancient pseudogene haplotype that silences the locus in trans! academic.oup.com/genetics/adv...
because we think this pseudogene can turn off the drive locus Kindr, we've taken to calling it sudoKindr instead of pseudo. With apologies to @xkcd.com
December 31, 2024 at 5:51 AM
because we think this pseudogene can turn off the drive locus Kindr, we've taken to calling it sudoKindr instead of pseudo. With apologies to @xkcd.com
High‑throughput long‑read sequencing uncovers how chickens diversify their Ig genes: dominant somatic gene conversion, biased pseudogene usage, and focused CDR‑targeted insertions.
A look into avian antibody evolution: https://bit.ly/45wSe95
A look into avian antibody evolution: https://bit.ly/45wSe95
September 25, 2026 at 11:00 AM
High‑throughput long‑read sequencing uncovers how chickens diversify their Ig genes: dominant somatic gene conversion, biased pseudogene usage, and focused CDR‑targeted insertions.
A look into avian antibody evolution: https://bit.ly/45wSe95
A look into avian antibody evolution: https://bit.ly/45wSe95
unfortunately, also a torment nexus
September 18, 2026 at 2:20 AM
unfortunately, also a torment nexus
playing with BLAST today. pseudogene copies of the meiotic drive gene behind Abnormal chromosome 10 in maize vary widely across lines. Pseudogenes produce siRNA that targets the Ab10 drive gene. Proposing to do crosses with Jonathan Gent at UGA to see if we can epigenetically silence meiotic drive.
December 31, 2024 at 5:48 AM
playing with BLAST today. pseudogene copies of the meiotic drive gene behind Abnormal chromosome 10 in maize vary widely across lines. Pseudogenes produce siRNA that targets the Ab10 drive gene. Proposing to do crosses with Jonathan Gent at UGA to see if we can epigenetically silence meiotic drive.
C01.06 - Stefano Facchini - Gene-pseudogene inversions as a source of missing heritability.
Using long-read (@nanopore)
- historic known IDS1/2 Hunter
- PMS2 (Lynch syn) & SORD (CMT) strong candidates for missing diagnoses
- SORD inversion found frequent but cryptic
#ESHG2025
Using long-read (@nanopore)
- historic known IDS1/2 Hunter
- PMS2 (Lynch syn) & SORD (CMT) strong candidates for missing diagnoses
- SORD inversion found frequent but cryptic
#ESHG2025
May 24, 2025 at 9:57 AM
C01.06 - Stefano Facchini - Gene-pseudogene inversions as a source of missing heritability.
Using long-read (@nanopore)
- historic known IDS1/2 Hunter
- PMS2 (Lynch syn) & SORD (CMT) strong candidates for missing diagnoses
- SORD inversion found frequent but cryptic
#ESHG2025
Using long-read (@nanopore)
- historic known IDS1/2 Hunter
- PMS2 (Lynch syn) & SORD (CMT) strong candidates for missing diagnoses
- SORD inversion found frequent but cryptic
#ESHG2025
Happy to share a preprint—the last chapter of my dissertation with @mcsymbiont.bsky.social and Co—on what happens when bacterial endosymbionts accumulate huge numbers of pseudogenes during early genome reduction.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
February 8, 2026 at 2:08 AM
Happy to share a preprint—the last chapter of my dissertation with @mcsymbiont.bsky.social and Co—on what happens when bacterial endosymbionts accumulate huge numbers of pseudogenes during early genome reduction.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Most mammals make their own vitamin C. Humans have got the gene for manufacturing the vitamin too -- but our gene is a pseudogene, the remnant of the real gene, mutated into uselessness. (Maybe our ancestors ate plenty of fruit and didn't waste energy synthesising a nutrient present in their diet?)
December 14, 2025 at 1:32 AM
Most mammals make their own vitamin C. Humans have got the gene for manufacturing the vitamin too -- but our gene is a pseudogene, the remnant of the real gene, mutated into uselessness. (Maybe our ancestors ate plenty of fruit and didn't waste energy synthesising a nutrient present in their diet?)
Exciting work from neighbor Jörn Coers at Duke identifying a new class of host defense GTPases. Out of a genetic screen they identify the human Giant GTPase GVIN1 (previously annotated as a human pseudogene) in coatomer-based restriction of Burkholderia motility. 1808 aas long!
Human giant GTPase GVIN1 forms an antimicrobial coatomer around the intracellular bacterial pathogen Burkholderia thailandensis
Several human pathogens exploit the kinetic forces generated by polymerizing actin to power their intracellular motility. Human cell-autonomous immune responses activated by the cytokine interferon-ga...
www.biorxiv.org
April 14, 2025 at 4:14 PM
Exciting work from neighbor Jörn Coers at Duke identifying a new class of host defense GTPases. Out of a genetic screen they identify the human Giant GTPase GVIN1 (previously annotated as a human pseudogene) in coatomer-based restriction of Burkholderia motility. 1808 aas long!
Cross-species check across 670 species: gene content variance is systematically lower than pseudogene variance at matched means, and the constraint tightens with selection intensity. Selection is suppressing variance, which is the cross-species signature of bet-hedging.
May 11, 2026 at 9:18 AM
Cross-species check across 670 species: gene content variance is systematically lower than pseudogene variance at matched means, and the constraint tightens with selection intensity. Selection is suppressing variance, which is the cross-species signature of bet-hedging.
#eshg2026 Day 3: Use it or lose it: example of body symmetry in reproductive organs. Pseudogene prevalence across evolution, here avian and reptiles reflects biological changes, including novel factors CIROP+CIROZ.
June 15, 2026 at 9:29 AM
#eshg2026 Day 3: Use it or lose it: example of body symmetry in reproductive organs. Pseudogene prevalence across evolution, here avian and reptiles reflects biological changes, including novel factors CIROP+CIROZ.
The third gene, PpWOX13LC, was considered a pseudogene as it is truncated and was not detected in RT-PCR in several tissue types. This is where out study kicks off... 4/
June 19, 2026 at 7:18 AM
The third gene, PpWOX13LC, was considered a pseudogene as it is truncated and was not detected in RT-PCR in several tissue types. This is where out study kicks off... 4/
Sci-Fi author: In my book I invented the Torment Nexus Destroyer as an optimistic tale
Grant Program: At long last, we have funded the Torment Nexus Destroyer from classic sci-fi novel Please Create The Torment Nexus Destroyer
Grant Program: At long last, we have funded the Torment Nexus Destroyer from classic sci-fi novel Please Create The Torment Nexus Destroyer
February 13, 2024 at 9:55 AM
Sci-Fi author: In my book I invented the Torment Nexus Destroyer as an optimistic tale
Grant Program: At long last, we have funded the Torment Nexus Destroyer from classic sci-fi novel Please Create The Torment Nexus Destroyer
Grant Program: At long last, we have funded the Torment Nexus Destroyer from classic sci-fi novel Please Create The Torment Nexus Destroyer
Michael Behe, the notorious creationist author of Darwin's Black Box, admits that the vitamin C pseudogene found only in the great apes is proof we evolved from a common ancestor.
January 27, 2025 at 12:54 PM
Michael Behe, the notorious creationist author of Darwin's Black Box, admits that the vitamin C pseudogene found only in the great apes is proof we evolved from a common ancestor.
EasyPseudogene: an easy-to-use and multithreaded pipeline for pseudogene detection https://www.biorxiv.org/content/10.64898/2026.03.04.709571v1
March 7, 2026 at 3:50 AM
EasyPseudogene: an easy-to-use and multithreaded pipeline for pseudogene detection https://www.biorxiv.org/content/10.64898/2026.03.04.709571v1
@ironark.bsky.social et al. measured transcript abundance, ribosome-associated RNA, and protein abundance in bacterial endosymbionts, suggesting a mechanism for aberrant pseudogene-derived protein removal.
🔗 doi.org/10.1093/molbev/msag153
#societyjournal #evobio #molbio
🔗 doi.org/10.1093/molbev/msag153
#societyjournal #evobio #molbio
July 13, 2026 at 9:01 AM
@ironark.bsky.social et al. measured transcript abundance, ribosome-associated RNA, and protein abundance in bacterial endosymbionts, suggesting a mechanism for aberrant pseudogene-derived protein removal.
🔗 doi.org/10.1093/molbev/msag153
#societyjournal #evobio #molbio
🔗 doi.org/10.1093/molbev/msag153
#societyjournal #evobio #molbio
A review on pseudogene-derived lncRNAs signaling in cancer stem cell regulation, their classification & functions, and their dysregulation in CSC development, highlighting their potential as #Biomarkers. @TehUofMed
#OpenAccess: doi.org/10.1016/j.ge...
#OpenAccess: doi.org/10.1016/j.ge...
December 10, 2025 at 4:34 PM
A review on pseudogene-derived lncRNAs signaling in cancer stem cell regulation, their classification & functions, and their dysregulation in CSC development, highlighting their potential as #Biomarkers. @TehUofMed
#OpenAccess: doi.org/10.1016/j.ge...
#OpenAccess: doi.org/10.1016/j.ge...
5. Pseudofinder: detects pseudogene candidates from annotated genbank files of bacterial and archaeal genomes. github.com/filip-husnik...
6. GToTree: a user-friendly workflow for phylogenomics intended to give more researchers the capability to easily create phylogenomic trees.
6. GToTree: a user-friendly workflow for phylogenomics intended to give more researchers the capability to easily create phylogenomic trees.
GitHub - filip-husnik/pseudofinder: Detection of pseudogene candidates in bacterial and archaeal genomes.
Detection of pseudogene candidates in bacterial and archaeal genomes. - filip-husnik/pseudofinder
github.com
April 8, 2025 at 12:39 PM
5. Pseudofinder: detects pseudogene candidates from annotated genbank files of bacterial and archaeal genomes. github.com/filip-husnik...
6. GToTree: a user-friendly workflow for phylogenomics intended to give more researchers the capability to easily create phylogenomic trees.
6. GToTree: a user-friendly workflow for phylogenomics intended to give more researchers the capability to easily create phylogenomic trees.
We may have lost some of these genes relatively recently in evolution. One example is TDH, encoding L-threonine dehydrogenase. Prokaryotes to chimps have TDH. But, in us, it may have degenerated into a pseudogene. CCDC162 is another example: chimps have it, but it’s pseudogenized in us. 3/8
December 31, 2025 at 7:31 PM
We may have lost some of these genes relatively recently in evolution. One example is TDH, encoding L-threonine dehydrogenase. Prokaryotes to chimps have TDH. But, in us, it may have degenerated into a pseudogene. CCDC162 is another example: chimps have it, but it’s pseudogenized in us. 3/8
Just like the word "Homeowner" has the word "Meow" in it, the word "Pseudogene" has the word "Dog" in it.
February 27, 2024 at 7:57 PM
Just like the word "Homeowner" has the word "Meow" in it, the word "Pseudogene" has the word "Dog" in it.
Wu et al. explored the dynamics and genetic basis of repeated evolution by experimentally evolving fission yeast populations, suggesting that pseudogene revival is likely an important mechanism underlying repeated evolution.
🔗 doi.org/10.1093/molbev/msag120
#evobio #molbio #yeast
🔗 doi.org/10.1093/molbev/msag120
#evobio #molbio #yeast
Pseudogene revival drives repeated adaptation in fission yeast
Abstract. Repeated (parallel or convergent) evolution is often taken as evidence of adaptation and is relevant to the predictability of evolution. However,
doi.org
May 29, 2026 at 1:22 PM
Wu et al. explored the dynamics and genetic basis of repeated evolution by experimentally evolving fission yeast populations, suggesting that pseudogene revival is likely an important mechanism underlying repeated evolution.
🔗 doi.org/10.1093/molbev/msag120
#evobio #molbio #yeast
🔗 doi.org/10.1093/molbev/msag120
#evobio #molbio #yeast
Your plates are made like stiffened hair
They filter-feed beyond compare
They could be teeth but for a pseudogene
I try to catch my tiny food
But it evades me, it's so rude
And I cannot compete with you, baleen
They filter-feed beyond compare
They could be teeth but for a pseudogene
I try to catch my tiny food
But it evades me, it's so rude
And I cannot compete with you, baleen
April 18, 2026 at 3:27 AM
Your plates are made like stiffened hair
They filter-feed beyond compare
They could be teeth but for a pseudogene
I try to catch my tiny food
But it evades me, it's so rude
And I cannot compete with you, baleen
They filter-feed beyond compare
They could be teeth but for a pseudogene
I try to catch my tiny food
But it evades me, it's so rude
And I cannot compete with you, baleen
The estimated size of the human proteome has been shrinking for decades. At the outset of the human genome project, researchers thought maybe 100K proteins encoded. After it wrapped, perhaps ~23K. Since then, pseudogene removal has cut the count to ~19.5K.
May 6, 2026 at 3:36 PM
The estimated size of the human proteome has been shrinking for decades. At the outset of the human genome project, researchers thought maybe 100K proteins encoded. After it wrapped, perhaps ~23K. Since then, pseudogene removal has cut the count to ~19.5K.
Congrats!! 👏👏 👏 This is an important piece demonstrating paralogous genes newly found in T2T-CHM13 better represents the coding form while the version in hg38 that was conceived as protein coding turned out to be a pseudogene. Also supported by the #HPRC assemblies. #T2Tgenomes
March 12, 2024 at 2:23 PM
Congrats!! 👏👏 👏 This is an important piece demonstrating paralogous genes newly found in T2T-CHM13 better represents the coding form while the version in hg38 that was conceived as protein coding turned out to be a pseudogene. Also supported by the #HPRC assemblies. #T2Tgenomes