Martin Smith
@martinalexsmith.bsky.social
🧬 Genomics | RNA Biology | AI & Nanopore Sequencing | Biotech & Innovation
🔬 Director @ramacgenomics.bsky.social | A/Prof @ UNSW BABS | RNA Institute
🌍 Exploring genomes, RNA, & the future of precision medicine
🏕️🥾🎣🚴 Science, adventure & good coffee
🔬 Director @ramacgenomics.bsky.social | A/Prof @ UNSW BABS | RNA Institute
🌍 Exploring genomes, RNA, & the future of precision medicine
🏕️🥾🎣🚴 Science, adventure & good coffee
Zheng Su presents kiloBrains.com, an AI-powered biodata analysis platform.
A virtual bioinformatics assistant
#AGTA2025
A virtual bioinformatics assistant
#AGTA2025
October 14, 2025 at 12:38 AM
Zheng Su presents kiloBrains.com, an AI-powered biodata analysis platform.
A virtual bioinformatics assistant
#AGTA2025
A virtual bioinformatics assistant
#AGTA2025
Cornetto from @hasindu2008.bsky.social presented by Ira Deveson: T2T assembly of human genomes with @nanoporetech.com adaptive sampling by rejecting the "boring bits". 27/46 chromosomes fully assembled from one flowcell. Can also be used on saliva!
#AGTA2025
github.com/hasindu2008/...
#AGTA2025
github.com/hasindu2008/...
October 13, 2025 at 11:53 PM
Cornetto from @hasindu2008.bsky.social presented by Ira Deveson: T2T assembly of human genomes with @nanoporetech.com adaptive sampling by rejecting the "boring bits". 27/46 chromosomes fully assembled from one flowcell. Can also be used on saliva!
#AGTA2025
github.com/hasindu2008/...
#AGTA2025
github.com/hasindu2008/...
Check out his team's online ressources for long read songle-cell sequencing
kinnex-documentation-external.readthedocs.io/en/latest/in...
And keep an eye out for LRAA...
kinnex-documentation-external.readthedocs.io/en/latest/in...
And keep an eye out for LRAA...
October 13, 2025 at 4:34 AM
Check out his team's online ressources for long read songle-cell sequencing
kinnex-documentation-external.readthedocs.io/en/latest/in...
And keep an eye out for LRAA...
kinnex-documentation-external.readthedocs.io/en/latest/in...
And keep an eye out for LRAA...
"Isoforms are important; how come we're not studying them?"
#AGTA2025 keynote @azizalkhafaji.bsky.social mentions that we are now at am I flection point, where 100s of millions of reads are produced per run.
#AGTA2025 keynote @azizalkhafaji.bsky.social mentions that we are now at am I flection point, where 100s of millions of reads are produced per run.
October 13, 2025 at 4:14 AM
"Isoforms are important; how come we're not studying them?"
#AGTA2025 keynote @azizalkhafaji.bsky.social mentions that we are now at am I flection point, where 100s of millions of reads are produced per run.
#AGTA2025 keynote @azizalkhafaji.bsky.social mentions that we are now at am I flection point, where 100s of millions of reads are produced per run.
The great Prof Vanessa Hayes, who sequenced the first African Genome, states "the closer we get to ancestral populations, the more diversity we see in genomes".
Presents genomic data from WGS of Khoe-San populations, interesting phylogenetic split between Khoe (hunters) and San (gatherers) #agta2025
Presents genomic data from WGS of Khoe-San populations, interesting phylogenetic split between Khoe (hunters) and San (gatherers) #agta2025
October 13, 2025 at 2:45 AM
The great Prof Vanessa Hayes, who sequenced the first African Genome, states "the closer we get to ancestral populations, the more diversity we see in genomes".
Presents genomic data from WGS of Khoe-San populations, interesting phylogenetic split between Khoe (hunters) and San (gatherers) #agta2025
Presents genomic data from WGS of Khoe-San populations, interesting phylogenetic split between Khoe (hunters) and San (gatherers) #agta2025
October 13, 2025 at 2:31 AM
Prof Sean Grimmong from PeterMac Genomic Cancer Medicine on the entire workflow for #cancer #diagnosis, and how to deal with dilemmas, like the 5% of Australians without a clear diagnosis #agta2025
October 12, 2025 at 11:49 PM
Prof Sean Grimmong from PeterMac Genomic Cancer Medicine on the entire workflow for #cancer #diagnosis, and how to deal with dilemmas, like the 5% of Australians without a clear diagnosis #agta2025
October 12, 2025 at 11:34 PM
Adaptive sampling #WGS is moving from bench to bedside. Our work delivers SNV, structural & methylation insights on @nanoporetech.com with molecular signals emerging in minutes, not days. Watch this space 👀 #cancer #genomicAI #MultiOmics #bioinformatics @cra-chusj.bsky.social
tinyurl.com/4d337djb
tinyurl.com/4d337djb
October 7, 2025 at 1:59 AM
Adaptive sampling #WGS is moving from bench to bedside. Our work delivers SNV, structural & methylation insights on @nanoporetech.com with molecular signals emerging in minutes, not days. Watch this space 👀 #cancer #genomicAI #MultiOmics #bioinformatics @cra-chusj.bsky.social
tinyurl.com/4d337djb
tinyurl.com/4d337djb
Some exciting #SingleCell events with #ParseBio coming up this month at @ramacgenomics.bsky.social 🧬
9 Sept: SPLiT-Seq Tech Showcase Seminar 🔗 tinyurl.com/bddc5zc3
15 Sept: Application deadline for discounted Parse Evercode WT Mini v3 Kit promotion 🔗 tinyurl.com/yc84zmfm
📩 [email protected]
9 Sept: SPLiT-Seq Tech Showcase Seminar 🔗 tinyurl.com/bddc5zc3
15 Sept: Application deadline for discounted Parse Evercode WT Mini v3 Kit promotion 🔗 tinyurl.com/yc84zmfm
📩 [email protected]
September 5, 2025 at 12:58 AM
Some exciting #SingleCell events with #ParseBio coming up this month at @ramacgenomics.bsky.social 🧬
9 Sept: SPLiT-Seq Tech Showcase Seminar 🔗 tinyurl.com/bddc5zc3
15 Sept: Application deadline for discounted Parse Evercode WT Mini v3 Kit promotion 🔗 tinyurl.com/yc84zmfm
📩 [email protected]
9 Sept: SPLiT-Seq Tech Showcase Seminar 🔗 tinyurl.com/bddc5zc3
15 Sept: Application deadline for discounted Parse Evercode WT Mini v3 Kit promotion 🔗 tinyurl.com/yc84zmfm
📩 [email protected]
Congratulations to @hasindu2008.bsky.social form #UNSW Computer Science and Engineering for wearing a tuxedo last night 👏🏻
Also for being awarded the #EurekaPrize for outstanding early career researcher, showcase his pioneering and impacftful research in #bioinformatics software
Also for being awarded the #EurekaPrize for outstanding early career researcher, showcase his pioneering and impacftful research in #bioinformatics software
September 4, 2025 at 6:07 AM
Congratulations to @hasindu2008.bsky.social form #UNSW Computer Science and Engineering for wearing a tuxedo last night 👏🏻
Also for being awarded the #EurekaPrize for outstanding early career researcher, showcase his pioneering and impacftful research in #bioinformatics software
Also for being awarded the #EurekaPrize for outstanding early career researcher, showcase his pioneering and impacftful research in #bioinformatics software
Prof Cecile King finishing her #ARNASydney2025 talk on biomolecular condensates by promoting the upcoming (free) symposium on the topic in November
September 3, 2025 at 5:44 AM
Prof Cecile King finishing her #ARNASydney2025 talk on biomolecular condensates by promoting the upcoming (free) symposium on the topic in November
Early bird deadline extended for #AGTA #AGTA2025
This year will be quite different, with a big focus on tech, low cost Rego, digital engagement, and in a central location.
Don't miss the ECR events, exhibitor lounges (à la AGBT) and two lightning talk sessions, open to industry members: agta2025.com
This year will be quite different, with a big focus on tech, low cost Rego, digital engagement, and in a central location.
Don't miss the ECR events, exhibitor lounges (à la AGBT) and two lightning talk sessions, open to industry members: agta2025.com
September 2, 2025 at 3:16 AM
Early bird deadline extended for #AGTA #AGTA2025
This year will be quite different, with a big focus on tech, low cost Rego, digital engagement, and in a central location.
Don't miss the ECR events, exhibitor lounges (à la AGBT) and two lightning talk sessions, open to industry members: agta2025.com
This year will be quite different, with a big focus on tech, low cost Rego, digital engagement, and in a central location.
Don't miss the ECR events, exhibitor lounges (à la AGBT) and two lightning talk sessions, open to industry members: agta2025.com
Prof Nils Walter from U.Michigan back in Sydney, mentions it's his favourite place!
Opening up the #ARNASydney2025 structure, chemistry and dynamics session.
Opening up the #ARNASydney2025 structure, chemistry and dynamics session.
September 2, 2025 at 1:11 AM
Prof Nils Walter from U.Michigan back in Sydney, mentions it's his favourite place!
Opening up the #ARNASydney2025 structure, chemistry and dynamics session.
Opening up the #ARNASydney2025 structure, chemistry and dynamics session.
(7/8) To test our approach, we applied ECSFinder to one of the few lncRNAs with experimentally validated structure: hTERC, the RNA template of telomerase.
The framework correctly recovered its conserved structural features — showing the power of combining benchmarking + ML-selected signals.
The framework correctly recovered its conserved structural features — showing the power of combining benchmarking + ML-selected signals.
August 25, 2025 at 3:02 AM
(7/8) To test our approach, we applied ECSFinder to one of the few lncRNAs with experimentally validated structure: hTERC, the RNA template of telomerase.
The framework correctly recovered its conserved structural features — showing the power of combining benchmarking + ML-selected signals.
The framework correctly recovered its conserved structural features — showing the power of combining benchmarking + ML-selected signals.
(6/8) We then used #MachineLearning + feature selection to identify which covariation and conservation features truly help.
By integrating the best-performing ones into ML models, we improved their ability to predict conserved RNA structures, as implemented in a new #bioinformatics tool: ECSfinder.
By integrating the best-performing ones into ML models, we improved their ability to predict conserved RNA structures, as implemented in a new #bioinformatics tool: ECSfinder.
August 25, 2025 at 3:02 AM
(6/8) We then used #MachineLearning + feature selection to identify which covariation and conservation features truly help.
By integrating the best-performing ones into ML models, we improved their ability to predict conserved RNA structures, as implemented in a new #bioinformatics tool: ECSfinder.
By integrating the best-performing ones into ML models, we improved their ability to predict conserved RNA structures, as implemented in a new #bioinformatics tool: ECSfinder.
(5/8) The challenge? Covariation is subtle, noisy, and measured in many ways.
Methods disagree, and benchmarking has been inconsistent.
We built a framework that simulates the experimental conditions under which conserved RNA structures are predicted, allowing fair side-by-side comparisons.
Methods disagree, and benchmarking has been inconsistent.
We built a framework that simulates the experimental conditions under which conserved RNA structures are predicted, allowing fair side-by-side comparisons.
August 25, 2025 at 3:02 AM
(5/8) The challenge? Covariation is subtle, noisy, and measured in many ways.
Methods disagree, and benchmarking has been inconsistent.
We built a framework that simulates the experimental conditions under which conserved RNA structures are predicted, allowing fair side-by-side comparisons.
Methods disagree, and benchmarking has been inconsistent.
We built a framework that simulates the experimental conditions under which conserved RNA structures are predicted, allowing fair side-by-side comparisons.
(4/8) This is especially important for lncRNAs.
The number of #lncRNA genes has exploded with long read sequencing — now outpacing protein-coding genes.
Yet their functions remain poorly understood.
Identifying where they form conserved structures is one way to unlock their biology.
The number of #lncRNA genes has exploded with long read sequencing — now outpacing protein-coding genes.
Yet their functions remain poorly understood.
Identifying where they form conserved structures is one way to unlock their biology.
August 25, 2025 at 3:02 AM
(4/8) This is especially important for lncRNAs.
The number of #lncRNA genes has exploded with long read sequencing — now outpacing protein-coding genes.
Yet their functions remain poorly understood.
Identifying where they form conserved structures is one way to unlock their biology.
The number of #lncRNA genes has exploded with long read sequencing — now outpacing protein-coding genes.
Yet their functions remain poorly understood.
Identifying where they form conserved structures is one way to unlock their biology.
(3/8) At the 2D level — the helices and loops formed by base-pairing — prediction is much more tractable.
Here, covariation across species is the key signal: when two nucleotides evolve together to preserve structure, like in this mitochondrial tRNA for glutamine (Figure 2 of paper).
Here, covariation across species is the key signal: when two nucleotides evolve together to preserve structure, like in this mitochondrial tRNA for glutamine (Figure 2 of paper).
August 25, 2025 at 3:02 AM
(3/8) At the 2D level — the helices and loops formed by base-pairing — prediction is much more tractable.
Here, covariation across species is the key signal: when two nucleotides evolve together to preserve structure, like in this mitochondrial tRNA for glutamine (Figure 2 of paper).
Here, covariation across species is the key signal: when two nucleotides evolve together to preserve structure, like in this mitochondrial tRNA for glutamine (Figure 2 of paper).
(2/8) Predicting full 3D #RNAstructure remains extremely hard — even with AI.
Recent benchmarks show deep-learning tools still struggle on novel RNAs (c.f. Bahai et al, 2024, PLoS Comp Bio)
And while AlphaFold 3 can model RNA, its accuracy lags far behind proteins: www.ebi.ac.uk/training/onl...
Recent benchmarks show deep-learning tools still struggle on novel RNAs (c.f. Bahai et al, 2024, PLoS Comp Bio)
And while AlphaFold 3 can model RNA, its accuracy lags far behind proteins: www.ebi.ac.uk/training/onl...
August 25, 2025 at 3:02 AM
(2/8) Predicting full 3D #RNAstructure remains extremely hard — even with AI.
Recent benchmarks show deep-learning tools still struggle on novel RNAs (c.f. Bahai et al, 2024, PLoS Comp Bio)
And while AlphaFold 3 can model RNA, its accuracy lags far behind proteins: www.ebi.ac.uk/training/onl...
Recent benchmarks show deep-learning tools still struggle on novel RNAs (c.f. Bahai et al, 2024, PLoS Comp Bio)
And while AlphaFold 3 can model RNA, its accuracy lags far behind proteins: www.ebi.ac.uk/training/onl...
RNA is far more than a messenger.
Its structures regulate, evolve, and catalyze — carrying out functions DNA alone cannot.
But predicting #RNA structure from sequence is still extremely difficult.
In our recently published paper in @narjournal.bsky.social we present a way forward.
🧵 ⤵️
Its structures regulate, evolve, and catalyze — carrying out functions DNA alone cannot.
But predicting #RNA structure from sequence is still extremely difficult.
In our recently published paper in @narjournal.bsky.social we present a way forward.
🧵 ⤵️
August 25, 2025 at 3:02 AM
RNA is far more than a messenger.
Its structures regulate, evolve, and catalyze — carrying out functions DNA alone cannot.
But predicting #RNA structure from sequence is still extremely difficult.
In our recently published paper in @narjournal.bsky.social we present a way forward.
🧵 ⤵️
Its structures regulate, evolve, and catalyze — carrying out functions DNA alone cannot.
But predicting #RNA structure from sequence is still extremely difficult.
In our recently published paper in @narjournal.bsky.social we present a way forward.
🧵 ⤵️
🥱 Bored during #ScienceWeek2025?
🥼 Want to go on an adventure from the comfort of your pyjamas?
🧪🧬Why not go on an immersive & interactive virtual tour of a #Genomics #Lab?
Wander around the @ramacgenomics.bsky.social Centre with impunity here ➡️ tinyurl.com/mr2cj4rj
#UNSWscience
🥼 Want to go on an adventure from the comfort of your pyjamas?
🧪🧬Why not go on an immersive & interactive virtual tour of a #Genomics #Lab?
Wander around the @ramacgenomics.bsky.social Centre with impunity here ➡️ tinyurl.com/mr2cj4rj
#UNSWscience
August 12, 2025 at 2:53 AM
🥱 Bored during #ScienceWeek2025?
🥼 Want to go on an adventure from the comfort of your pyjamas?
🧪🧬Why not go on an immersive & interactive virtual tour of a #Genomics #Lab?
Wander around the @ramacgenomics.bsky.social Centre with impunity here ➡️ tinyurl.com/mr2cj4rj
#UNSWscience
🥼 Want to go on an adventure from the comfort of your pyjamas?
🧪🧬Why not go on an immersive & interactive virtual tour of a #Genomics #Lab?
Wander around the @ramacgenomics.bsky.social Centre with impunity here ➡️ tinyurl.com/mr2cj4rj
#UNSWscience
The P6 buzzing alone peacefully, discretely filling up hard drives 🧬
July 26, 2025 at 1:17 AM
The P6 buzzing alone peacefully, discretely filling up hard drives 🧬
🌅🐦⬛Early bird Registration for #AGTA2025 is live!
Submit your abstract 📝 and check-out the awesome 🗓️ program here ➡️ agta2025.org
Submit your abstract 📝 and check-out the awesome 🗓️ program here ➡️ agta2025.org
July 8, 2025 at 5:55 AM
🌅🐦⬛Early bird Registration for #AGTA2025 is live!
Submit your abstract 📝 and check-out the awesome 🗓️ program here ➡️ agta2025.org
Submit your abstract 📝 and check-out the awesome 🗓️ program here ➡️ agta2025.org
