Ashar Malik
@proteinmechanic.bsky.social
Evolutionary Biologist | Protein Structure Enthusiast | Quantum Programmer | Wannabe Polymath | Science Comm | Life Sciences Programmer | Originally from 🇵🇰
We have had some amazing abstracts submitted to the free
@official-smbe.bsky.social APSPM meeting. To help you make up your mind, here is a sneak peek. Join for what will be an amazing meeting. biosig.lab.uq.edu.au/strphy26/sneakpeek/ . #StrPhy26 @strphy.bsky.social #Evolution #Science
@official-smbe.bsky.social APSPM meeting. To help you make up your mind, here is a sneak peek. Join for what will be an amazing meeting. biosig.lab.uq.edu.au/strphy26/sneakpeek/ . #StrPhy26 @strphy.bsky.social #Evolution #Science
APSPM 2026: Structural Phylogenetics Meeting
A pivotal SMBE regional meeting in Brisbane on the interface of protein structure, function, and evolution.
biosig.lab.uq.edu.au
November 3, 2025 at 4:21 AM
We have had some amazing abstracts submitted to the free
@official-smbe.bsky.social APSPM meeting. To help you make up your mind, here is a sneak peek. Join for what will be an amazing meeting. biosig.lab.uq.edu.au/strphy26/sneakpeek/ . #StrPhy26 @strphy.bsky.social #Evolution #Science
@official-smbe.bsky.social APSPM meeting. To help you make up your mind, here is a sneak peek. Join for what will be an amazing meeting. biosig.lab.uq.edu.au/strphy26/sneakpeek/ . #StrPhy26 @strphy.bsky.social #Evolution #Science
Taking a break from the usual #Phylogenetic exploration to spend a little time on the #Quantum computing side of my work.
Hanging out with #Queensland Quantum community at the
Qx | Advanced Technologies for Life and Planet.
Hanging out with #Queensland Quantum community at the
Qx | Advanced Technologies for Life and Planet.
October 28, 2025 at 2:43 AM
Taking a break from the usual #Phylogenetic exploration to spend a little time on the #Quantum computing side of my work.
Hanging out with #Queensland Quantum community at the
Qx | Advanced Technologies for Life and Planet.
Hanging out with #Queensland Quantum community at the
Qx | Advanced Technologies for Life and Planet.
Reposted by Ashar Malik
We are excited to announce APSPM 2026 - the SMBE Australasian Protein Structural Phylogenetics Meeting!
🗓️ 15-18 Feb. 2026
🌏 Brisbane, Australia
🔗 biosig.lab.uq.edu.au/strphy26/
📄 Abstract submission: 28.11.2025
✈️ Travel grant application: 28.11.2025
✏️ Registration: 15.01.2026
#StrPhy26
🗓️ 15-18 Feb. 2026
🌏 Brisbane, Australia
🔗 biosig.lab.uq.edu.au/strphy26/
📄 Abstract submission: 28.11.2025
✈️ Travel grant application: 28.11.2025
✏️ Registration: 15.01.2026
#StrPhy26
APSPM 2026: Structural Phylogenetics Meeting
A pivotal SMBE regional meeting in Brisbane on the interface of protein structure, function, and evolution.
biosig.lab.uq.edu.au
October 22, 2025 at 10:17 AM
We are excited to announce APSPM 2026 - the SMBE Australasian Protein Structural Phylogenetics Meeting!
🗓️ 15-18 Feb. 2026
🌏 Brisbane, Australia
🔗 biosig.lab.uq.edu.au/strphy26/
📄 Abstract submission: 28.11.2025
✈️ Travel grant application: 28.11.2025
✏️ Registration: 15.01.2026
#StrPhy26
🗓️ 15-18 Feb. 2026
🌏 Brisbane, Australia
🔗 biosig.lab.uq.edu.au/strphy26/
📄 Abstract submission: 28.11.2025
✈️ Travel grant application: 28.11.2025
✏️ Registration: 15.01.2026
#StrPhy26
Announcing @official-smbe.bsky.social Australasian Protein Structural Phylogenetics Meeting in Brisbane Feb 15-18, 2026. FREE registration. Join for exciting talks & workshops at the interface of protein structure, function & evolution. biosig.lab.uq.edu.au/strphy26/ #StrPhy26 @strphy.bsky.social
APSPM 2026: Structural Phylogenetics Meeting
A pivotal SMBE regional meeting in Brisbane on the interface of protein structure, function, and evolution.
biosig.lab.uq.edu.au
October 22, 2025 at 7:56 AM
Announcing @official-smbe.bsky.social Australasian Protein Structural Phylogenetics Meeting in Brisbane Feb 15-18, 2026. FREE registration. Join for exciting talks & workshops at the interface of protein structure, function & evolution. biosig.lab.uq.edu.au/strphy26/ #StrPhy26 @strphy.bsky.social
Attending a fascinating talk by
Prof Begona Heras on “Structural insights into the function and inhibition of bacterial virulence proteins. “
Looking for overlaps with methods we are putting together in the Structural Phylogenetics space. #StrPhy #StructuralPhylogenetics @strphy.bsky.social
Prof Begona Heras on “Structural insights into the function and inhibition of bacterial virulence proteins. “
Looking for overlaps with methods we are putting together in the Structural Phylogenetics space. #StrPhy #StructuralPhylogenetics @strphy.bsky.social
October 15, 2025 at 2:05 AM
Attending a fascinating talk by
Prof Begona Heras on “Structural insights into the function and inhibition of bacterial virulence proteins. “
Looking for overlaps with methods we are putting together in the Structural Phylogenetics space. #StrPhy #StructuralPhylogenetics @strphy.bsky.social
Prof Begona Heras on “Structural insights into the function and inhibition of bacterial virulence proteins. “
Looking for overlaps with methods we are putting together in the Structural Phylogenetics space. #StrPhy #StructuralPhylogenetics @strphy.bsky.social
We’ve set up a dedicated Bluesky space for structural phylogenetics: @strphy.bsky.social. Follow for community updates.
#StrPhy #StructuralPhylogenetics
#StrPhy #StructuralPhylogenetics
October 9, 2025 at 4:04 AM
We’ve set up a dedicated Bluesky space for structural phylogenetics: @strphy.bsky.social. Follow for community updates.
#StrPhy #StructuralPhylogenetics
#StrPhy #StructuralPhylogenetics
Reposted by Ashar Malik
Special Section in GBE: Structural Phylogenetics
Here we showcase novel work on how 3D protein structures can reshape evolutionary biology, from methods to applications.
More papers coming out soon!
@genomebiolevol.bsky.social @proteinmechanic.bsky.social
academic.oup.com/gbe/search-r...
Here we showcase novel work on how 3D protein structures can reshape evolutionary biology, from methods to applications.
More papers coming out soon!
@genomebiolevol.bsky.social @proteinmechanic.bsky.social
academic.oup.com/gbe/search-r...
search
academic.oup.com
September 4, 2025 at 1:53 AM
Special Section in GBE: Structural Phylogenetics
Here we showcase novel work on how 3D protein structures can reshape evolutionary biology, from methods to applications.
More papers coming out soon!
@genomebiolevol.bsky.social @proteinmechanic.bsky.social
academic.oup.com/gbe/search-r...
Here we showcase novel work on how 3D protein structures can reshape evolutionary biology, from methods to applications.
More papers coming out soon!
@genomebiolevol.bsky.social @proteinmechanic.bsky.social
academic.oup.com/gbe/search-r...
Third Era of Phylogenetics!
1️⃣ Era 1: Morphology 🦴
2️⃣ Era 2: Sequences 🧬
3️⃣ Era 3: 3D Structures ⚛️
Solving deep evolutionary puzzles like never before. Our new review in GBE explores what's next in #phylogenetics
academic.oup.com/gbe/article/...
#structuralbiology #evolution #AlphaFold #SciSky
1️⃣ Era 1: Morphology 🦴
2️⃣ Era 2: Sequences 🧬
3️⃣ Era 3: 3D Structures ⚛️
Solving deep evolutionary puzzles like never before. Our new review in GBE explores what's next in #phylogenetics
academic.oup.com/gbe/article/...
#structuralbiology #evolution #AlphaFold #SciSky
Protein Structural Phylogenetics
Abstract. Protein structural phylogenetics is an interdisciplinary branch of molecular evolution that (i) uses 3D structural data to trace evolutionary his
academic.oup.com
August 22, 2025 at 12:40 AM
Third Era of Phylogenetics!
1️⃣ Era 1: Morphology 🦴
2️⃣ Era 2: Sequences 🧬
3️⃣ Era 3: 3D Structures ⚛️
Solving deep evolutionary puzzles like never before. Our new review in GBE explores what's next in #phylogenetics
academic.oup.com/gbe/article/...
#structuralbiology #evolution #AlphaFold #SciSky
1️⃣ Era 1: Morphology 🦴
2️⃣ Era 2: Sequences 🧬
3️⃣ Era 3: 3D Structures ⚛️
Solving deep evolutionary puzzles like never before. Our new review in GBE explores what's next in #phylogenetics
academic.oup.com/gbe/article/...
#structuralbiology #evolution #AlphaFold #SciSky
Reposted by Ashar Malik
Quantome: A Quantum Surrogate Model for Biophysical Landscapes https://www.biorxiv.org/content/10.1101/2025.08.06.668871v1
August 8, 2025 at 8:47 PM
Quantome: A Quantum Surrogate Model for Biophysical Landscapes https://www.biorxiv.org/content/10.1101/2025.08.06.668871v1
Reposted by Ashar Malik
Quantome: A Quantum Surrogate Model for Biophysical Landscapes https://www.biorxiv.org/content/10.1101/2025.08.06.668871v1
August 8, 2025 at 8:47 PM
Quantome: A Quantum Surrogate Model for Biophysical Landscapes https://www.biorxiv.org/content/10.1101/2025.08.06.668871v1
Playing around with quantum-styled math on trivial biological problems before tackling the really hard questions. Initial signs are good, with the math behaving as expected. Next leg would be using a non-trivial dataset like missense variants.
On a quantum-inspired kernel for classifying protein torsion angles https://www.biorxiv.org/content/10.1101/2025.08.05.668681v1
August 7, 2025 at 1:11 PM
Playing around with quantum-styled math on trivial biological problems before tackling the really hard questions. Initial signs are good, with the math behaving as expected. Next leg would be using a non-trivial dataset like missense variants.
Within Tagetes lemmonii, (Lemmon’s marigold) are defence molecules called thiophenes which become highly toxic when exposed to sunlight, damaging pests at the cellular level. An elegant example of how plants weaponize light to survive.
#Brisbane #nature #nikon #naturephotography #SciComm
#Brisbane #nature #nikon #naturephotography #SciComm
June 29, 2025 at 3:22 PM
Within Tagetes lemmonii, (Lemmon’s marigold) are defence molecules called thiophenes which become highly toxic when exposed to sunlight, damaging pests at the cellular level. An elegant example of how plants weaponize light to survive.
#Brisbane #nature #nikon #naturephotography #SciComm
#Brisbane #nature #nikon #naturephotography #SciComm
If you do deep evolutionary analysis - structure-aware characters can help. To ensure correct alignments - give it a try: biosig.lab.uq.edu.au/structome_al...
If you would like any features added, drop a message and will give it a shot.
#Science #Evolution #MolecularEvolution #DeepEvolution
If you would like any features added, drop a message and will give it a shot.
#Science #Evolution #MolecularEvolution #DeepEvolution
June 4, 2025 at 12:31 AM
If you do deep evolutionary analysis - structure-aware characters can help. To ensure correct alignments - give it a try: biosig.lab.uq.edu.au/structome_al...
If you would like any features added, drop a message and will give it a shot.
#Science #Evolution #MolecularEvolution #DeepEvolution
If you would like any features added, drop a message and will give it a shot.
#Science #Evolution #MolecularEvolution #DeepEvolution
🧵: It's out. Structome-AlignViewer, a web-based resource for evaluating protein structure-aware sequence alignments. It maps alignment columns directly onto structures and helps identify conserved regions. Feedback encouraged. www.biorxiv.org/content/10.1...
#Evolution #MolecularEvolution #Science
#Evolution #MolecularEvolution #Science
Structome-AlignViewer: On Confidence Assessment in Structure-Aware Alignments
Protein structure-based comparison provides a framework for uncovering deep evolutionary relationships that can escape conventional sequence-based approaches. Encoding three-dimensional protein struct...
www.biorxiv.org
June 4, 2025 at 12:10 AM
🧵: It's out. Structome-AlignViewer, a web-based resource for evaluating protein structure-aware sequence alignments. It maps alignment columns directly onto structures and helps identify conserved regions. Feedback encouraged. www.biorxiv.org/content/10.1...
#Evolution #MolecularEvolution #Science
#Evolution #MolecularEvolution #Science
In a talk today thinking that science isn’t just a collection of facts it’s a method and sometimes, a philosophical tightrope.
Emeritus Professor Ross Bernard at #UQ exploring how science proceeds - via falsifiability. Not everyone agrees but a conversation worth having.
#Science #Philosophy
Emeritus Professor Ross Bernard at #UQ exploring how science proceeds - via falsifiability. Not everyone agrees but a conversation worth having.
#Science #Philosophy
May 15, 2025 at 5:51 AM
In a talk today thinking that science isn’t just a collection of facts it’s a method and sometimes, a philosophical tightrope.
Emeritus Professor Ross Bernard at #UQ exploring how science proceeds - via falsifiability. Not everyone agrees but a conversation worth having.
#Science #Philosophy
Emeritus Professor Ross Bernard at #UQ exploring how science proceeds - via falsifiability. Not everyone agrees but a conversation worth having.
#Science #Philosophy
I am speaking soon about #Evolution at a public talk series in #Brisbane (Ticket $10). Many other talks covering a range of topics. Interested in havin a fun science evening with family?
For more information vIsit and tickets: pintofscience.com.au/events/brisb...
#pintofscience #Pint25 #PintAU25
For more information vIsit and tickets: pintofscience.com.au/events/brisb...
#pintofscience #Pint25 #PintAU25
May 11, 2025 at 9:02 AM
I am speaking soon about #Evolution at a public talk series in #Brisbane (Ticket $10). Many other talks covering a range of topics. Interested in havin a fun science evening with family?
For more information vIsit and tickets: pintofscience.com.au/events/brisb...
#pintofscience #Pint25 #PintAU25
For more information vIsit and tickets: pintofscience.com.au/events/brisb...
#pintofscience #Pint25 #PintAU25
Oldest reference I’ve ever seen while reviewing — 1667, Antonie van Leeuwenhoek.
From the first observation of bacteria under a handcrafted microscope to modern phylogenetics. Science stands on the shoulders of giants — even from 400 years ago.
#Science #Evolution #AcademicLife
From the first observation of bacteria under a handcrafted microscope to modern phylogenetics. Science stands on the shoulders of giants — even from 400 years ago.
#Science #Evolution #AcademicLife
April 14, 2025 at 12:29 PM
Oldest reference I’ve ever seen while reviewing — 1667, Antonie van Leeuwenhoek.
From the first observation of bacteria under a handcrafted microscope to modern phylogenetics. Science stands on the shoulders of giants — even from 400 years ago.
#Science #Evolution #AcademicLife
From the first observation of bacteria under a handcrafted microscope to modern phylogenetics. Science stands on the shoulders of giants — even from 400 years ago.
#Science #Evolution #AcademicLife
Just attending a talk by Professor Warwick from QUBIC at #BrisScience on
“Bringing Quantum to Life: How Quantum technologies may shape the future of society”.
Exciting times ahead as quantum algorithm unravel mysteries of life.
#Quantum #Science
“Bringing Quantum to Life: How Quantum technologies may shape the future of society”.
Exciting times ahead as quantum algorithm unravel mysteries of life.
#Quantum #Science
April 7, 2025 at 10:08 AM
Just attending a talk by Professor Warwick from QUBIC at #BrisScience on
“Bringing Quantum to Life: How Quantum technologies may shape the future of society”.
Exciting times ahead as quantum algorithm unravel mysteries of life.
#Quantum #Science
“Bringing Quantum to Life: How Quantum technologies may shape the future of society”.
Exciting times ahead as quantum algorithm unravel mysteries of life.
#Quantum #Science
Missense mutations impact protein function, but no single predictor is perfect. MissenseViewer integrates AlphaMissense, ESM1b, and VESPA predictions, mapping them onto protein structures to provide a richer, more interpretable view of mutation effects.
#science #health #precisionmedicine #AI
#science #health #precisionmedicine #AI
On interactive spatial visualisation of pathogenicity predictions https://www.biorxiv.org/content/10.1101/2025.03.19.644131v1
March 19, 2025 at 10:59 PM
Missense mutations impact protein function, but no single predictor is perfect. MissenseViewer integrates AlphaMissense, ESM1b, and VESPA predictions, mapping them onto protein structures to provide a richer, more interpretable view of mutation effects.
#science #health #precisionmedicine #AI
#science #health #precisionmedicine #AI
Reposted by Ashar Malik
Michael Healy is first speaker of the Anders early career investigators session. The scientists of the future (and the present!).
February 10, 2025 at 8:55 AM
Michael Healy is first speaker of the Anders early career investigators session. The scientists of the future (and the present!).
Professor Frances Separovic documents her tough journey in #Science. A trailblazing scientist who defied the odds and carved her path in a time when women in science faced unimaginable barriers. Her story is a testament to the power of determination.
#WomenInScience @lorneproteins.bsky.social
#WomenInScience @lorneproteins.bsky.social
February 9, 2025 at 9:37 AM
Professor Frances Separovic documents her tough journey in #Science. A trailblazing scientist who defied the odds and carved her path in a time when women in science faced unimaginable barriers. Her story is a testament to the power of determination.
#WomenInScience @lorneproteins.bsky.social
#WomenInScience @lorneproteins.bsky.social
February 9, 2025 at 8:45 AM
Reposted by Ashar Malik
Structome-TM: Complementing dataset assembly for structural phylogenetics by addressing size-based biases https://www.biorxiv.org/content/10.1101/2025.02.08.637224v1
February 8, 2025 at 6:47 PM
Structome-TM: Complementing dataset assembly for structural phylogenetics by addressing size-based biases https://www.biorxiv.org/content/10.1101/2025.02.08.637224v1
Structome-TM preprint now live @ www.biorxiv.org/content/10.1...
@biorxivpreprint.bsky.social
#Science #Structome #StructuralPhylogenetics
@biorxivpreprint.bsky.social
#Science #Structome #StructuralPhylogenetics
Structome-TM: Complementing dataset assembly for structural phylogenetics by addressing size-based biases
The increasing availability of protein structures presents new opportunities for detecting homologous proteins. While global alignment methods are widely used and generally effective, they often strug...
www.biorxiv.org
February 8, 2025 at 9:10 PM
Structome-TM preprint now live @ www.biorxiv.org/content/10.1...
@biorxivpreprint.bsky.social
#Science #Structome #StructuralPhylogenetics
@biorxivpreprint.bsky.social
#Science #Structome #StructuralPhylogenetics
#Structome began as an initiative to explore #evolutionary signals from #proteins sharing a structural neighborhood. It uses Q-score to rapidly gather datasets & build NJ trees. To highlight usage of Q-score, the tool is now called Structome-Q. App available here: biosig.lab.uq.edu.au/structome_q/
Structome-Q
Structome-Q: A next-generation platform for structural phylogenetics, enabling protein structure comparison, phylogenetic tree construction, and insights into deep evolutionary relationships.
biosig.lab.uq.edu.au
January 22, 2025 at 8:33 AM
#Structome began as an initiative to explore #evolutionary signals from #proteins sharing a structural neighborhood. It uses Q-score to rapidly gather datasets & build NJ trees. To highlight usage of Q-score, the tool is now called Structome-Q. App available here: biosig.lab.uq.edu.au/structome_q/