Lachlan Coin
@lachlanjmc.bsky.social
Computational biologist working on infectious disease
Reposted by Lachlan Coin
🚨 Update to nohuman 🚨
While testing against the standard Kraken DB, I noticed Kraken was detecting far more human reads than nohuman. I realised Kraken masks low-complexity regions by default during DB construction and that setting had been left on in nohuman, leading to missing human reads.
While testing against the standard Kraken DB, I noticed Kraken was detecting far more human reads than nohuman. I realised Kraken masks low-complexity regions by default during DB construction and that setting had been left on in nohuman, leading to missing human reads.
November 20, 2025 at 6:50 AM
🚨 Update to nohuman 🚨
While testing against the standard Kraken DB, I noticed Kraken was detecting far more human reads than nohuman. I realised Kraken masks low-complexity regions by default during DB construction and that setting had been left on in nohuman, leading to missing human reads.
While testing against the standard Kraken DB, I noticed Kraken was detecting far more human reads than nohuman. I realised Kraken masks low-complexity regions by default during DB construction and that setting had been left on in nohuman, leading to missing human reads.
Huge thanks to Chenxi Zhou for helping scale this approach to human sized genomes!
Our method for genome size estimation from long-read overlaps is now published 🥳
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
Genome size estimation from long read overlaps
AbstractMotivation. Accurate genome size estimation is an important component of genomic analyses such as assembly and coverage calculation, though existin
academic.oup.com
November 7, 2025 at 3:49 AM
Huge thanks to Chenxi Zhou for helping scale this approach to human sized genomes!
Reposted by Lachlan Coin
A paper from @lachlanjmc.bsky.social Lachlan Coin, not active here for the past month, on Using synthetic RNA to benchmark poly(A) length inference from direct RNA sequencing academic.oup.com/gigascience/...
Using synthetic RNA to benchmark poly(A) length inference from direct RNA sequencing
Abstract. Polyadenylation is a dynamic process that is important in cellular physiology, which has implications in messenger RNA decay rates, translation e
academic.oup.com
September 4, 2025 at 9:23 AM
A paper from @lachlanjmc.bsky.social Lachlan Coin, not active here for the past month, on Using synthetic RNA to benchmark poly(A) length inference from direct RNA sequencing academic.oup.com/gigascience/...
Reposted by Lachlan Coin
Louisiana has to build three new natural gas power plants to accommodate the "AI" data center that Meta just crammed through because said center will use *Three Times* as much electricity (and, thus, attendant resources) as the *Entire City Of New Orleans*, every year.
Y'all this isn't sustainable.
Y'all this isn't sustainable.
La. regulators approve Entergy power plants for Meta’s AI data center
Louisiana Public Service Commissioners voted four to one to approve Entergy’s three new gas plants to power Meta’s largest-ever data center.
www.kplctv.com
August 22, 2025 at 5:15 PM
Louisiana has to build three new natural gas power plants to accommodate the "AI" data center that Meta just crammed through because said center will use *Three Times* as much electricity (and, thus, attendant resources) as the *Entire City Of New Orleans*, every year.
Y'all this isn't sustainable.
Y'all this isn't sustainable.
Reposted by Lachlan Coin
Today, our article "The entities enabling scientific fraud at scale are large, resilient, and growing rapidly" is finally published in PNAS. I hope that it proves to be a wake-up-call for the whole scientific community.
reeserichardson.blog/2025/08/04/a...
reeserichardson.blog/2025/08/04/a...
A do-or-die moment for the scientific enterprise
Reflecting on our paper “The entities enabling scientific fraud at scale are large, resilient, and growing rapidly”
reeserichardson.blog
August 4, 2025 at 8:47 PM
Today, our article "The entities enabling scientific fraud at scale are large, resilient, and growing rapidly" is finally published in PNAS. I hope that it proves to be a wake-up-call for the whole scientific community.
reeserichardson.blog/2025/08/04/a...
reeserichardson.blog/2025/08/04/a...
Our latest preprint using long read nanopore sequencing to study Ferret transcriptomic response to infection and interferon stimulation, lead by Rubaiyea Farrukee and Jessie Chang www.biorxiv.org/content/10.1...
Characterizing the transcriptomic response to interferon and infection in European Domestic Ferret respiratory tissues using long-read RNA sequencing
The European domestic ferret (Mustela putorius furo) is considered the gold-standard small animal model for studying human and avian influenza virus infections. However, experimental characterization ...
www.biorxiv.org
July 24, 2025 at 1:08 AM
Our latest preprint using long read nanopore sequencing to study Ferret transcriptomic response to infection and interferon stimulation, lead by Rubaiyea Farrukee and Jessie Chang www.biorxiv.org/content/10.1...
New paper from our lab in collaboration with Blaskovich lab led by former Phd student Anggia Prasetyoputri using in vitro selection to identify drug resistance conferring murations in S. aureus academic.oup.com/jacamr/artic...
Characterisation of in vitro resistance selection against second-/last-line antibiotics in methicillin-resistant Staphylococcus aureus ATCC 43300 strain
AbstractBackground and objectives. The increasing occurrence of MRSA clinical isolates harbouring reduced susceptibility to mainstay antibiotics has escala
academic.oup.com
June 26, 2025 at 4:23 AM
New paper from our lab in collaboration with Blaskovich lab led by former Phd student Anggia Prasetyoputri using in vitro selection to identify drug resistance conferring murations in S. aureus academic.oup.com/jacamr/artic...
New preprint from @aleixcanalda.bsky.social on structural variation in TB and its role in evolution and drug resistance www.biorxiv.org/content/10.1...
May 9, 2025 at 6:30 AM
New preprint from @aleixcanalda.bsky.social on structural variation in TB and its role in evolution and drug resistance www.biorxiv.org/content/10.1...
New preprint from the lab, describing an approach to enrichment of transcript isoforms for nanopore cDNA sequencing, using CRISPR-Cas9 www.biorxiv.org/content/10.1...
Customizable host and viral transcript enrichment using CRISPR-Cas9 long-read sequencing for isoform discovery and validation
Long-read RNA sequencing has been broadly utilized to examine the diversity of transcriptomes, understand differential expression and discover novel transcript isoforms. One of the major limitations o...
www.biorxiv.org
April 15, 2025 at 4:41 AM
New preprint from the lab, describing an approach to enrichment of transcript isoforms for nanopore cDNA sequencing, using CRISPR-Cas9 www.biorxiv.org/content/10.1...
Reposted by Lachlan Coin
Customizable host and viral transcript enrichment using CRISPR-Cas9 long-read sequencing for isoform discovery and validation https://www.biorxiv.org/content/10.1101/2025.04.11.648353v1
April 15, 2025 at 2:33 AM
Customizable host and viral transcript enrichment using CRISPR-Cas9 long-read sequencing for isoform discovery and validation https://www.biorxiv.org/content/10.1101/2025.04.11.648353v1
Reposted by Lachlan Coin
I want to provide an overview and perspective of rare disease genomic testing, which is a real success story of science impacting health - a science which goes back over 100 years and yet is still striding forward and much more to come.
December 19, 2024 at 12:56 PM
I want to provide an overview and perspective of rare disease genomic testing, which is a real success story of science impacting health - a science which goes back over 100 years and yet is still striding forward and much more to come.
Latest preprint from the lab: we asked whether native RNA sequencing (using nanopore sequencing) might be a successor to traditional cDNA sequencing for biomarker discovery in blood.
Utilising Nanopore direct RNA sequencing of blood from patients with sepsis for discovery of co- and post-transcriptional disease biomarkers https://www.medrxiv.org/content/10.1101/2024.12.13.24318230v1
December 15, 2024 at 10:34 AM
Latest preprint from the lab: we asked whether native RNA sequencing (using nanopore sequencing) might be a successor to traditional cDNA sequencing for biomarker discovery in blood.
Reposted by Lachlan Coin
“We don’t value software, data, and methods in the same way we value papers, even though those resources empower millions of scientists” 💯
www.statnews.com/sponsor/2024...
www.statnews.com/sponsor/2024...
New report highlights the scientific impact of open source software
Two of the scientists who won this year’s Nobel Prize for cracking the code of proteins’ intricate structures relied, in part, on a series of computing
www.statnews.com
December 4, 2024 at 12:08 AM
“We don’t value software, data, and methods in the same way we value papers, even though those resources empower millions of scientists” 💯
www.statnews.com/sponsor/2024...
www.statnews.com/sponsor/2024...
Reposted by Lachlan Coin
Genome size estimation from long read overlaps https://www.biorxiv.org/content/10.1101/2024.11.27.625777v1
Genome size estimation from long read overlaps https://www.biorxiv.org/content/10.1101/2024.11.27.625777v1
Summary: Accurate genome size estimation is an important component of genomic analyses, though exist
www.biorxiv.org
December 2, 2024 at 11:46 PM
Genome size estimation from long read overlaps https://www.biorxiv.org/content/10.1101/2024.11.27.625777v1
Reposted by Lachlan Coin
🌟 Excited to share my latest preprint with @lachlanjmc.bsky.social on @biorxivpreprint.bsky.social: "Genome size estimation from long read overlaps”! 🚀
Check it out here: doi.org/10.1101/2024...
And find the code here: github.com/mbhall88/lrge
🧵👇
Check it out here: doi.org/10.1101/2024...
And find the code here: github.com/mbhall88/lrge
🧵👇
doi.org
December 3, 2024 at 1:38 AM
🌟 Excited to share my latest preprint with @lachlanjmc.bsky.social on @biorxivpreprint.bsky.social: "Genome size estimation from long read overlaps”! 🚀
Check it out here: doi.org/10.1101/2024...
And find the code here: github.com/mbhall88/lrge
🧵👇
Check it out here: doi.org/10.1101/2024...
And find the code here: github.com/mbhall88/lrge
🧵👇
Was inspiring to attend the TBunion conference in Bali last week and learn about the great TB research happening all over the world. Probably one of the most international conferences I have been to (in terms of number of countries represented)
November 18, 2024 at 6:03 AM
Was inspiring to attend the TBunion conference in Bali last week and learn about the great TB research happening all over the world. Probably one of the most international conferences I have been to (in terms of number of countries represented)