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Matthew Collins

@matthewcollins.bsky.social

Archaeology, University of Cambridge | The Globe, University of Copenhagen Ancient Proteins | Medieval Manuscripts | Proteomics and AI | πŸ‡ΊπŸ‡¦

4,746 Followers  |  4,981 Following  |  575 Posts  |  Joined: 22.09.2023
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Posts by Matthew Collins (@matthewcollins.bsky.social)

This is a really interesting paper and, if I may, particularly well written.

28.02.2026 12:03 β€” πŸ‘ 55    πŸ” 11    πŸ’¬ 2    πŸ“Œ 0
ARK Introduction to Maritime Archaeology - 2026/2027 KΓΈbenhavns Universitet er med cirka 40.000 studerende og 9.000 medarbejdere en af Nordens stΓΈrste forsknings- og uddannelsesinstitutioner.

🌊 Dive into History! 🚒

Join HARKS2026U: Maritime Archaeology at UCPH & the Viking Ship Museum. Explore shipwrecks, submerged settlements, and 3D scanning in Roskilde.

πŸ“ 7.5 ECTS
πŸ“… Apply by April 9 (Intl) / June 1 (DK)
βš“οΈ Ships, sailing, & science!

Apply via KUnet. #Archaeology #Vikings

26.02.2026 15:59 β€” πŸ‘ 1    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0

Key findings:
πŸ”ΉSPPV has threatened Eurasian food security for nearly 4 millennia.
πŸ”ΉMajor lineages diverged ~11,500–3,700 years ago, coinciding with sheep domestication.

26.02.2026 11:41 β€” πŸ‘ 5    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0

In a scientific first, they successfully retrieved #pathogen genomes from medieval #parchment and paper #manuscripts πŸ“– - revealing that historical documents are an under-recognised source of ancient #disease data. (3/4)
+1

26.02.2026 11:41 β€” πŸ‘ 10    πŸ” 0    πŸ’¬ 1    πŸ“Œ 1

The team recovered 21 novel ancient sheeppox virus (SPPV) genomes, dating back as far as ~3,700 years to the #Bronze Age. These are currently the oldest Poxviridae genomes ever recovered. (2/4)

26.02.2026 11:41 β€” πŸ‘ 5    πŸ” 0    πŸ’¬ 1    πŸ“Œ 0
Phylogenetic and dating analysis of ancient and modern sheeppox virus. A. 
Maximum-likelihood phylogeny of ancient and modern SPPV genomes with β‰₯5Γ— coverage, rooted 
using LSDV and GTPV. Nodes with bootstrap support of 100 are indicated by blue circles; other 
bootstrap values are shown at the corresponding nodes. Clades composed exclusively of modern 
genomes are collapsed and shown as triangles, and branches corresponding to ancient genomes are  highlighted in pink. The grey box delineates the SPPV clade. B. Maximum-likelihood phylogeny of 
SPPV genomes with placement of low-coverage ancient samples using PathPhynder (Martiniano et 
al., 2022). For clarity, only the SPPV portion of the phylogeny is shown. Samples are coloured by 
material type, and low-coverage genomes (<5Γ—) placed using PathPhynder are indicated by red 
triangles. Nodes with bootstrap support of 100 are marked with blue circles; other values are shown at  the corresponding nodes. Tip labels indicate sampling location and calibrated historical date. Host 
species, sequencing coverage, and sample age are shown as a heatmap adjacent to the tips. C. 
Time-calibrated Bayesian phylogeny of the SPPV clade, with samples coloured according to material  type.

Phylogenetic and dating analysis of ancient and modern sheeppox virus. A. Maximum-likelihood phylogeny of ancient and modern SPPV genomes with β‰₯5Γ— coverage, rooted using LSDV and GTPV. Nodes with bootstrap support of 100 are indicated by blue circles; other bootstrap values are shown at the corresponding nodes. Clades composed exclusively of modern genomes are collapsed and shown as triangles, and branches corresponding to ancient genomes are highlighted in pink. The grey box delineates the SPPV clade. B. Maximum-likelihood phylogeny of SPPV genomes with placement of low-coverage ancient samples using PathPhynder (Martiniano et al., 2022). For clarity, only the SPPV portion of the phylogeny is shown. Samples are coloured by material type, and low-coverage genomes (<5Γ—) placed using PathPhynder are indicated by red triangles. Nodes with bootstrap support of 100 are marked with blue circles; other values are shown at the corresponding nodes. Tip labels indicate sampling location and calibrated historical date. Host species, sequencing coverage, and sample age are shown as a heatmap adjacent to the tips. C. Time-calibrated Bayesian phylogeny of the SPPV clade, with samples coloured according to material type.

Biopathocodicology?? πŸ¦ πŸ§¬πŸ‘ (1/4)

Check out this groundbreaking new #aDNA #pathology paper by @louis-lhote.bsky.social @gingerhowley.bsky.social and colleagues!

www.biorxiv.org/content/10.6...

26.02.2026 11:41 β€” πŸ‘ 19    πŸ” 5    πŸ’¬ 1    πŸ“Œ 4

I am pleased to share that on December 18, I received the Award for the Best Researcher of the Year at Vilnius University in the Open Science category. This recognition was granted for my work on untargeted #paleoproteomics for the biological sex identification of archaeological remains

19.12.2025 15:03 β€” πŸ‘ 14    πŸ” 3    πŸ’¬ 0    πŸ“Œ 0

High-throughput targeted paleoproteomics sex estimation on medieval Great Moravia individuals using MALDI-CASI-FTICR mass spectrometry https://www.biorxiv.org/content/10.64898/2026.02.17.706309v1

19.02.2026 05:31 β€” πŸ‘ 1    πŸ” 2    πŸ’¬ 0    πŸ“Œ 0

🦷 A new study by @marinemorvan.bsky.social

High-throughput paleoproteomics method using MALDI-CASI-FTICR mass spectrometry to estimate biological sex from tooth enamel.
Great success on 130 individuals from medieval Great Moravia.

#Bioarchaeology #Archaeology #Proteomics #TooMS πŸ˜‰ #Teammasspec

22.02.2026 12:59 β€” πŸ‘ 18    πŸ” 7    πŸ’¬ 0    πŸ“Œ 0
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CODICUM - News and Events We are hiring: Doctoral Researcher in Medieval Manuscript Studies

www.codicum.eu/news-and-eve...

Tuomas HeikkilΓ€ is hiring a 4-year fully funded PhD in Medieval Manuscript Studies at the University of Helsinki within the ERC Synergy Project CODICUM. Interested in medieval studies, philology, history, art history, etc!

20.02.2026 14:14 β€” πŸ‘ 10    πŸ” 14    πŸ’¬ 0    πŸ“Œ 0

Were the Sea Peoples agents of change?

15.02.2026 16:42 β€” πŸ‘ 1    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0

The displaced white-collar workers? πŸ˜€

15.02.2026 15:50 β€” πŸ‘ 1    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0

The displaced hordes of white-collar workers... πŸ˜…

15.02.2026 15:48 β€” πŸ‘ 1    πŸ” 0    πŸ’¬ 1    πŸ“Œ 0

Thanks πŸ‘

15.02.2026 09:16 β€” πŸ‘ 1    πŸ” 0    πŸ’¬ 1    πŸ“Œ 0

9/ The Lesson for the C-Suite: Archaeology teaches us that complexity is a subsidy of stability. If you build your entire strategy on a "Palatial" supply chain (Nvidia/TSMC), you are vulnerable to a 1200 BCE-style collapse.

15.02.2026 08:35 β€” πŸ‘ 26    πŸ” 1    πŸ’¬ 3    πŸ“Œ 0

8/ Innovation through Constraint.
Will we are seeing the same "accidental" toughening. Because we can't all afford $40k H100s, developers outside USA / China are forced to use "charcoal" methods:

A more resiliant 'steel AI' would impact markets and change workpatterns

15.02.2026 08:35 β€” πŸ‘ 13    πŸ” 0    πŸ’¬ 1    πŸ“Œ 0

7/ The "Steel" of AI is a happy accident. Steel wasn't a deliberate inventionβ€”it was a byproduct of struggle. Smiths couldn't melt iron like bronze; they had to work it in charcoal fires. That charcoal "accidentally" introduced carbon, making the metal tougher and lighter than the "elite" bronze.

15.02.2026 08:35 β€” πŸ‘ 13    πŸ” 0    πŸ’¬ 1    πŸ“Œ 0

6/ The "Steel" of AI.
Bronze was brittle. Iron (and eventually steel) was resilient. The "Steel" of AI isn't a massive, fragile LLM in a single data centerβ€”it’s a million small, locally-tuned models running on "gaming PCs."

Resilience beats Scale when the environment gets harsh.

15.02.2026 08:35 β€” πŸ‘ 16    πŸ” 0    πŸ’¬ 1    πŸ“Œ 0

5/ Small Language Models (SLMs) are the new Iron.
If global trade or energy crises make 100,000-GPU clusters unsustainable, we move to the "Artisanal" era.

Quantisation: Making models smaller/faster.
LoRA: Efficient fine-tuning.
Edge Computing: AI running on ARM, Gaming PC not server farms.

15.02.2026 08:35 β€” πŸ‘ 17    πŸ” 0    πŸ’¬ 2    πŸ“Œ 0

4/ The "Iron Age" Pivot.
When the Bronze Age collapsed, the "Democratic" technology of Iron took over. Why? Because iron ore is everywhere. It didn't need a 2,000-mile trade route; it just needed a local blacksmith with the right "recipe."

15.02.2026 08:35 β€” πŸ‘ 15    πŸ” 1    πŸ’¬ 1    πŸ“Œ 0

3/ Palatial vs. Artisanal Economies.
Bronze Age empires were "Palatial"β€”highly centralized, elite-controlled, and fragile.

We are currently in the Palatial AI era: Power is concentrated in a few "Hyperscalers" (Big Tech/Foundries). Only "Palaces" (the data center) have the tech.

15.02.2026 08:35 β€” πŸ‘ 17    πŸ” 1    πŸ’¬ 1    πŸ“Œ 0

2/ The Dependency Trap
Bronze wasn't a "local" tech. It required Copper (common) + Tin (rare). Tin traveled 1000s of km to reach the Mediterranean.

Today’s "Bronze" is Compute. High-end AI requires specialized GPUs + HBM memory. If that hyper-centralized supply chain snaps, the "empire" halts.

15.02.2026 08:35 β€” πŸ‘ 17    πŸ” 1    πŸ’¬ 1    πŸ“Œ 0

The Bronze Age vs The AI Age
1/ Can archaeology predict the future of Big Tech?

Economists usually look back 50-150 years; archaeologists look back further.
When you look at the Bronze Age Collapse (c. 1200 BCE), are there any parallels to our current AI trajectory?
#AI #TechHistory #Archaeology

15.02.2026 08:35 β€” πŸ‘ 77    πŸ” 26    πŸ’¬ 6    πŸ“Œ 10
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Minimally Destructive Radiocarbon Dating of Bone Rationale Bone is commonly used in radiocarbon dating in archaeology and other disciplines. Despite advances in collagen extraction protocols, the process remains destructive, requiring sawing, dril.....

We have a new paper out in Rapid Comms in Mass Spectrometry about 14C dating bone using a minimally destructive approach.
analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/...

31.01.2026 06:51 β€” πŸ‘ 31    πŸ” 15    πŸ’¬ 2    πŸ“Œ 3
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Good news everyone, _Nature_ has published 66 Open Access articles to date in 2026!

This means Springer-Nature has gobbled up USD$837,540 of science funding this year.

I'm sure we couldn't think of anything better to do with that money.

#OpenScience

30.01.2026 00:53 β€” πŸ‘ 33    πŸ” 11    πŸ’¬ 1    πŸ“Œ 1
Graduate School of health and Medical Sciences RadEditor - please enable JavaScript to use the rich text editor.

Registration OPEN for Practical Palaeoproteomics Summer School Copenhagen! 🦴πŸ§ͺ

πŸ—“οΈ Aug 12–21, 2026 πŸ“ Copenhagen (In-person + 3-day remote option) πŸŽ“ 6 ECTS credits ⏳ Deadline: April 1st

Apply here: phdcourses.ku.dk/detailkursus...

#Palaeoproteomics #BioArch #Archaeology #Proteomics #PhDLife

26.01.2026 10:13 β€” πŸ‘ 18    πŸ” 19    πŸ’¬ 0    πŸ“Œ 1
Infographic titled "ZooMS: Unlocking the Past with Protein Fingerprinting." The top section illustrates the Peptide Mass Fingerprinting process: extracting collagen from a sample, using trypsin enzymes to digest it into peptides, and analyzing it via MALDI-TOF mass spectrometry to create a unique spectrum for species identification. The bottom left section shows how ZooMS identifies fragmented archaeological bones (like Neanderthal remains). The bottom right section depicts the non-destructive "eZooMS" technique for medieval parchment, using a PVC eraser to collect protein samples without damaging manuscripts to identify calf, sheep, or goat skins.

Infographic titled "ZooMS: Unlocking the Past with Protein Fingerprinting." The top section illustrates the Peptide Mass Fingerprinting process: extracting collagen from a sample, using trypsin enzymes to digest it into peptides, and analyzing it via MALDI-TOF mass spectrometry to create a unique spectrum for species identification. The bottom left section shows how ZooMS identifies fragmented archaeological bones (like Neanderthal remains). The bottom right section depicts the non-destructive "eZooMS" technique for medieval parchment, using a PVC eraser to collect protein samples without damaging manuscripts to identify calf, sheep, or goat skins.

#ZooMS infographic and ALT generated from a spoken prompt "Can you explain what zooms is and how this is used to identify archaeological bone? and medieval parchment?" πŸ¦΄πŸ“œ #Archaeology. Slightly scary, as while it is clearly AI, my net intellectual contribution was 18 spoken words.

21.01.2026 00:49 β€” πŸ‘ 12    πŸ” 4    πŸ’¬ 0    πŸ“Œ 2
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πŸ“£ Work with us! πŸ“£

We are seeking to appoint a part-time, permanent Biomolecular Research Laboratory Technician!

Hear a bit more about the role from @matthewcollins.bsky.social

πŸ“… Closing date: 2 February

www.cam.ac.uk/jobs/biomole...

15.01.2026 16:20 β€” πŸ‘ 22    πŸ” 9    πŸ’¬ 0    πŸ“Œ 0
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1/5🧡
🚨 New open access paper out today🚨
The Demodifier: a tool for screening modification-induced alternate peptide taxonomy in palaeoproteomics.
doi.org/10.1371/jour...
#palaeoproteomics

13.01.2026 10:03 β€” πŸ‘ 22    πŸ” 9    πŸ’¬ 2    πŸ“Œ 0
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🧬 New study co-authored by #ICArEHB’s Carli Peters identifies collagen markers from New Guinea faunaβ€”improving bone ID in tropical regions: doi.org/10.1098/rsos...
#Proteomics #Archaeology

12.01.2026 15:33 β€” πŸ‘ 12    πŸ” 3    πŸ’¬ 0    πŸ“Œ 0