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Ashar Malik

@proteinmechanic.bsky.social
83 followers 46 following 59 posts

Evolutionary Biologist | Protein Structure Enthusiast | Quantum Programmer | Wannabe Polymath | Science Comm | Life Sciences Programmer | Originally from 🇵🇰

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Ashar Malik @proteinmechanic.bsky.social · 24/08/2026
Setting up for what’s going to be an exciting talk by @masarunobu.bsky.social in the invited Skerman Lecture series
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Ashar Malik @proteinmechanic.bsky.social · 04/08/2026
In the past three months #Claude wrote 80% of its own code. #AGI #ASI
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Ashar Malik @proteinmechanic.bsky.social · 04/08/2026
There's a little beta-test invite hiding in the #bioRxiv sidebar now 👀 Its the new @openrxiv.bsky.social Curvenote Reader. I think I like this. This is what reading preprints should feel like. I couldn't see the AI summaries though. Hope that feature make it in. reader.openrxivlabs.org #Science
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Ashar Malik @proteinmechanic.bsky.social · 10/05/2026
New work: Our earlier work showed that Foldseek characters could be adapted for phylogenetic alignment, treating each character as an evolutionary state. That part holds but there's a hidden assumption baked in that needed unpacking. So lets do that.🧵 #StructuralPhylogenetics #Evolution #Protein
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bioRxivpreprint @biorxivpreprint.bsky.social · 10/05/2026
Know Your Alphabet: Conformational Noise, Latent-Space Encodings, and the Future of Structural Phylogenetics www.biorxiv.org/content/10.64898/20…
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Ashar Malik @proteinmechanic.bsky.social · 26/03/2026
Distance-based #StructuralPhylogenetics is a powerful approach for exploring deep evolutionary relationships. Tools like those in the #Structome suite make this accessible in web workflows — but there's always been a critical missing piece: confidence estimates for the inferred trees. #StrPhy (1/3)
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Spyros Lytras @spyroslytras.bsky.social · 19/02/2026
Plus got to do some advertising for the new lab 👀 👀 #strphy26
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Spyros Lytras @spyroslytras.bsky.social · 19/02/2026
What a great conference!! Leaving Brisbane inspired about the future of structural phylogenetics! Thanks again to the organisers @cpuentelelievre.bsky.social @proteinmechanic.bsky.social and Jordan Douglas for an amazing work putting it all together!
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Caroline Puente-Lelievre @cpuentelelievre.bsky.social · 17/02/2026
Great to chair the session on Virus Evolution at APSPM2026. Thank you to all the speakers for sharing their cool research with us 🦠 Mihnea Bostina, Cinthy Jimenez Silva, @spyroslytras.bsky.social @jonathonmifsud.bsky.social #StryPhy26
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Structural Phylogenetics (StrPhy) @strphy.bsky.social · 16/02/2026
APSPM2026 - Today's session starts with @claudiaalcar.bsky.social Charting the protein universe: Deep evolutionary signals in sequence structure space (remote). She'll present her work on exploring how protein folds emerged and diversified over billions of years. #StrPhy26 #StrPhy
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Ashar Malik @proteinmechanic.bsky.social · 16/02/2026
Amazing talk by @martinsteinegger.bsky.social at the #StructuralPhylogenetics meeting in Brisbane @strphy.bsky.social The meeting is going to be live for the next 2 days. Excited to see what happens next. #Evolution
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Lorne Proteins @lorneproteins.bsky.social · 08/02/2026
Chris Barnes on now! Outpacing RNA viruses. #lorneproteins26 is go 🎆
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Ashar Malik @proteinmechanic.bsky.social · 07/02/2026
Protein structure is more conserved than sequence. Work in 2020 (MBE: academic.oup.com/mbe/article/...), showed 3D data unlocks deeper evolutionary signals. A thought was why not go higher than 3D? 🧵 #Phylogenetics #StructuralBiology #Structome #Evolution #StructuralPhylogenetics #StrPhy
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Ashar Malik @proteinmechanic.bsky.social · 26/01/2026
The program is now live. An excellent global lineup of speakers - AUS, NZ, Korea, India, Laos, UK, Switzerland, France, Finland, Germany, Hungary, Japan, Uruguay, Mexico and USA. Browse abstracts. Just 3 weeks left. Super excited. #StrPhy26 #Science #Evolution #StrPhy #StructuralPhylogenetics
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Ashar Malik @proteinmechanic.bsky.social · 14/01/2026
An interesting way to look at encoded structural characters to build alignments and trees downstream. This takes structural phylogenetics one step further in the post-AlphaFold era. #Evolution #Science #StrPhy On Confidence Assessment in Structure-Aware Alignments doi.org/10.1093/gbe/...
doi.org
Structome-AlignViewer: On Confidence Assessment in Structure-Aware Alignments
Abstract. Protein structure-based comparison provides a framework for uncovering deep evolutionary relationships that can escape conventional sequence-base
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Ashar Malik @proteinmechanic.bsky.social · 21/11/2025
Had an amazing three days hanging out with brilliant minds at #Phylomania 2025. Amazing mathematicians tackling amazing challenges. #Science #Phylogenetics
Phylomania logo
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Ashar Malik @proteinmechanic.bsky.social · 03/11/2025
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
biosig.lab.uq.edu.au
APSPM 2026: Structural Phylogenetics Meeting
A pivotal SMBE regional meeting in Brisbane on the interface of protein structure, function, and evolution.
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Ashar Malik @proteinmechanic.bsky.social · 28/10/2025
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.
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Society for Molecular Biology and Evolution @official-smbe.bsky.social · 22/10/2025
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
biosig.lab.uq.edu.au
APSPM 2026: Structural Phylogenetics Meeting
A pivotal SMBE regional meeting in Brisbane on the interface of protein structure, function, and evolution.
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Ashar Malik @proteinmechanic.bsky.social · 22/10/2025
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
biosig.lab.uq.edu.au
APSPM 2026: Structural Phylogenetics Meeting
A pivotal SMBE regional meeting in Brisbane on the interface of protein structure, function, and evolution.
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Ashar Malik @proteinmechanic.bsky.social · 15/10/2025
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
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Ashar Malik @proteinmechanic.bsky.social · 09/10/2025
We’ve set up a dedicated Bluesky space for structural phylogenetics: @strphy.bsky.social. Follow for community updates. #StrPhy #StructuralPhylogenetics
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Caroline Puente-Lelievre @cpuentelelievre.bsky.social · 04/09/2025
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...
academic.oup.com
search
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Ashar Malik @proteinmechanic.bsky.social · 22/08/2025
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
academic.oup.com
Protein Structural Phylogenetics
Abstract. Protein structural phylogenetics is an interdisciplinary branch of molecular evolution that (i) uses 3D structural data to trace evolutionary his
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bioRxivpreprint @biorxivpreprint.bsky.social · 08/08/2025
Quantome: A Quantum Surrogate Model for Biophysical Landscapes www.biorxiv.org/content/10.1101/202…
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 08/08/2025
Quantome: A Quantum Surrogate Model for Biophysical Landscapes www.biorxiv.org/content/10.1101/202…
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Ashar Malik @proteinmechanic.bsky.social · 07/08/2025
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.
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Ashar Malik @proteinmechanic.bsky.social · 29/06/2025
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
Tagetes lemmonii, also known as Lemmon’s marigold (or mountain marigold according to Google's Brisbane result) is shown against a blurred background (bokeh).
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Ashar Malik @proteinmechanic.bsky.social · 04/06/2025
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
biosig.lab.uq.edu.au
Structome-AlignViewer
Structome-AlignViewer is a tool to assess the quality of structural alignments using 3Di character encoding. It provides interactive visualization, confidence scoring, and downloadable full/trimmed al...
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Ashar Malik @proteinmechanic.bsky.social · 04/06/2025
🧵: 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
biorxiv.org
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...
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Ashar Malik @proteinmechanic.bsky.social · 15/05/2025
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
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Ashar Malik @proteinmechanic.bsky.social · 11/05/2025
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
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Ashar Malik @proteinmechanic.bsky.social · 14/04/2025
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
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Ashar Malik @proteinmechanic.bsky.social · 07/04/2025
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
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Ashar Malik @proteinmechanic.bsky.social · 19/03/2025
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
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Lorne Proteins @lorneproteins.bsky.social · 10/02/2025
Michael Healy is first speaker of the Anders early career investigators session. The scientists of the future (and the present!).
Photo of Michael Healy
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Ashar Malik @proteinmechanic.bsky.social · 09/02/2025
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
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Ashar Malik @proteinmechanic.bsky.social · 09/02/2025
Syd Leach remembered at the 50th #LorneProtein conference. @lorneproteins.bsky.social
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bioRxivpreprint @biorxivpreprint.bsky.social · 08/02/2025
Structome-TM: Complementing dataset assembly for structural phylogenetics by addressing size-based biases www.biorxiv.org/content/10.1101/202…
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Ashar Malik @proteinmechanic.bsky.social · 08/02/2025
Structome-TM preprint now live @ www.biorxiv.org/content/10.1... @biorxivpreprint.bsky.social #Science #Structome #StructuralPhylogenetics
biorxiv.org
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...
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Ashar Malik @proteinmechanic.bsky.social · 22/01/2025
#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/
biosig.lab.uq.edu.au
Structome-Q
Structome-Q: A next-generation platform for structural phylogenetics, enabling protein structure comparison, phylogenetic tree construction, and insights into deep evolutionary relationships.
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Ashar Malik @proteinmechanic.bsky.social · 20/12/2024
This is the green tree python (Morelia viridis), housed at the Queensland Museum, Brisbane. This photo presents an opportunity for a science class. #Python #snake #reptile #QMkurilpa #qldmuseum #nikonphotography #nikonz6ii
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Ashar Malik @proteinmechanic.bsky.social · 30/11/2024
Setting this up for my photography. Hopefully will more time for this soon.
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