iiinova — where your digital self keeps evolving

Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

Brett Phinney @ucdproteomics.bsky.social · 30/09/2026

I asked Claude to make podcast where a statistician and biologist discuss the proteomics results run through my claude proteomics skill and while it's not as good as @benneely.com podcast, but it's not bad either :) it's in the newest version of the skill github.com/bsphinney/DE...

github.com

GitHub - bsphinney/DE-LIMP: LIMPA DAVIS Proteomics Pipeline

LIMPA DAVIS Proteomics Pipeline. Contribute to bsphinney/DE-LIMP development by creating an account on GitHub.

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Bharath A. B. Nair (ഭരത് എ. ബി. നായർ) @bharathabnair.bsky.social · 28/09/2026

1/n Chuffed to have contributed to this new study: We exposed mice to urban air pollution and aircraft noise, alone and combined, then used proteomics to map how the lungs, brain, and heart responded at the protein level. Link below: www.sciencedirect.com/science/arti...

sciencedirect.com

Acute co-exposure to urban particulate matter and aircraft noise elicits lung-centered immune-redox proteomic remodeling in mice

Particulate air pollution and transportation noise frequently co-occur, but their combined molecular effects are poorly defined. We used data-independ…

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

Matthew Collins @matthewcollins.bsky.social · 28/08/2026

There is fun to be had in *not* reviewing a manuscript. @pciarchaeology.bsky.social @cos.io #openaccess

Thank you for your invitation to review a manuscript. While I value the scholarly community's efforts to disseminate research, I have growing concerns about the publishing model many commercial publishers, including Springer Nature, employ. In my view, the current system heavily relies on taxpayer-funded research, often conducted at public institutions, yet places the resulting work behind expensive paywalls. This practice limits access for scientists and the general public in the Global South, who often cannot afford subscription fees or open-access charges.

To put this in perspective, Springer Nature's most recent financial results (for the fiscal year ending December 2025) show total revenue of €1,926.4 million, adjusted operating profit of €543.6 million, and net income of €356 million. The Research division, which includes its journals, generated €1,517.2 million of that revenue. Shareholders received dividends of approximately €25.9 million, a significant increase from the previous year. These figures show that the current model is highly profitable, but much of that profit goes to investor returns rather than making research accessible to the global scientific community.

I have worked unpaid for you in the past, but this unpaid labour, combined with publicly funded research, generates enormous profits for a publishing industry that gives back relatively little to the public or to scientists in under-resourced regions. I do not believe this is fair or sustainable. I therefore have become a champion of Diamond Open Access and an editor at PCI.

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

Carl T. Bergstrom @carlbergstrom.com · 04/02/2025

Modern-Day Oracles or Bullshit Machines? Jevin West (@jevinwest.bsky.social) and I have spent the last eight months developing the course on large language models (LLMs) that we think every college freshman needs to take. thebullshitmachines.com

thebullshitmachines.com

INTRODUCTION

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

Ethan Mollick @emollick.bsky.social · 16/09/2026

Study from Google about AI use in science, complex impacts: acceleration (7 hours saved per week) along with shifts in the kind of work (more verification) and what research gets done (possibly safer topics). Also a good diagram of the jagged frontier in science right now. ai.google/static/docum...

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

Sam Brown @drsambrown.bsky.social · 09/09/2026

We have four invited speakers joining us at IZAZ next week, to share their thoughts on the theme of our workshop, Integrating ZooMS and Zooarchaeology! They are Tiina Manne, Sharada Visweswara Channarayapatna, Anneke Janzen, and Britt Starkovich! 🦴🦬👩🏼‍🔬 Register here: docs.google.com/forms/d/e/1F...

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

EMBO @embo.org · 28/08/2026

This week, we welcomed 20 master students, PhD students and postdoctoral researchers brought by DANEMO from #Denmark to the EMBO/EMBL campus. 🧪 The visit's topic was “#AI in #LifeScience: Data, Discovery, and #Collaboration" and participants were able to learn about different EMBO opportunities.

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Bharath A. B. Nair (ഭരത് എ. ബി. നായർ) @bharathabnair.bsky.social · 27/08/2026

Great fun @embl.org with fellow ECRs from Danish universities. Many thanks @danemoinforms.bsky.social @embl.org @embo.org. Already looking forward to my next visit :D

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

Owen Davies @odavies9.bsky.social · 01/08/2026

So a whole lot of my talented Humanities colleagues are now unemployed as of today. A lot of understandable concern over Exeter. But for over two decades my Hums colleagues were in the top quartile for their research contribution to society. History top 10. Now gone with only a national whisper.

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

Bhavna Ahlawat @bhavnaahlawat.bsky.social · 17/07/2026

We warmly invite students, ECRs, experienced researchers working in zooarchaeology and related disciplines to submit an abstract for our session. 🦏🦓🦙 For session details and abstract submission information,visit: sway.cloud.microsoft/BFTVh4FAbfX6... @bharathabnair.bsky.social @icaz-news.bsky.social

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

HigherJobz @higherjobz.bsky.social · 16/07/2026

Viking Age Archaeology Postdoc | University of York | UK ZooMS | Proteomics | Viking Age | Biomolecular Archaeology Help uncover Viking-Age trade and resource networks using advanced proteomic techniques. higherjobz.com/viking-age-a... #Postdoc #Archaeology #ResearchJobs #Acadhiring @york.ac.uk

higherjobz.com

Viking Age Archaeology Postdoc | University of York UK

Apply for the Viking Age Archaeology Postdoc at University of York, UK. Open to PhD researchers in archaeology and biomolecular research.

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 15/07/2026

Join us in a fun, crazy and interesting interdisciplinary research project that combines protein biophysics, evolutionary genomics, biomolecular archaeology, and textile research to resolve species identity and post-translational modifications in the structural proteins collagen and keratin

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

PAASTA Community @paastacommunity.bsky.social · 06/07/2026

REMINDER: Next 🍝PAASTA🍝 talk this Wednesday! Message us for the link 🔗

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

Tressie McMillan Cottom @tressiemcphd.bsky.social · 01/07/2026

I am once again listening to my partner’s TED talk about why Bone Thugs N Harmony are criminally under appreciated as an historically important bridge between funk and rap.

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

Ben Phillips @benphillips1989.bsky.social · 23/06/2026

A statement from Exeter UCU branch @ucu.org.uk - please share far and wide.

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

Jackson Cahn @jkbcahn.bsky.social · 07/05/2026

This is the big one! So proud to have played a part on this team. www.science.org/doi/10.1126/... Enlicitide is an exciting potential molecule for cardiovascular disease, but if we were going to make it on a commercial scale, existing chemical techniques just weren't going to cut it.

science.org

Biocatalytic cascades enable manufacture of the macrocyclic peptide enlicitide

Historically, many compelling therapeutic targets have been accessible only by injectable biologic drugs. Macrocyclic peptides, such as the proprotein convertase subtilisin/kexin type 9 inhibitor enli...

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

PAASTA Community @paastacommunity.bsky.social · 08/05/2026

Applications are now open for the PAASTA Bioinformatics Summer School 💻 Lessons will cover theory and practical exercises on a variety of palaeoproteomic analyses, including ZooMS, amelogenin sex estimation and shotgun proteomics. Deadline: 1 June 2026 Registration form: forms.gle/pqmecUpD7Xay...

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

Nature Biotechnology @natbiotech.nature.com · 01/05/2026

A transformer model is used to construct the DreaMS Atlas—a molecular network of 201 million MS/MS spectra go.nature.com/4k1n5iC rdcu.be/feuB9

go.nature.com

Self-supervised learning of molecular representations from millions of tandem mass spectra using DreaMS - Nature Biotechnology

A transformer model is used to construct the DreaMS Atlas—a molecular network of 201 million MS/MS spectra.

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

Jan H. Jensen @janhjensen.bsky.social · 08/05/2026

I am organising a 2 day workshop on explainable AI as applied to (bio)chemistry in Copenhagen, June 15-16, 2026. Everyone is invited. No need to register, but lunch is at your own expense. #compchem

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

Zandra Fagernäs @zandraselina.bsky.social · 04/05/2026

Good resources for creating scientific illustrations, instead of using AI!

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

MARKOPOLO EU Project @markersofpollution.bsky.social · 19/03/2026

Two productive days of our 2nd General Assembly Meeting have come to a close. 👏 Thank you to everyone who joined us in Cyprus and online. Safe travels home, and we look forward to the next meeting. 👋 #MarkersOfPollution #EUfunded

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

Phil W @pwilmarth.bsky.social · 17/03/2026

Unlocking the silent proteome?? Are silent proteins the products of silenced genes? Maybe they are just real quiet and you can't hear them over the rough pump noise? Are they withdrawn because of early translation trauma? Are they non-interacting? Who locked them up? So many questions for AI...

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

archaeotina.bsky.social @archaeotina.bsky.social · 16/03/2026

Very interesting find! 😊🏺

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

Simon J. Greenhill @simongreenhill.bsky.social · 30/01/2026

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

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

Umberto Albarella STOP THE GENOCIDE! @umbertoalbarella.bsky.social · 01/02/2026

The International Council of Archaeozoology www.alexandriaarchive.org/icaz/ has published a statement to condemn the Gaza genocide. You can download it here (Newsletter p.7): www.alexandriaarchive.org/icaz/publica... @archagainstaparth.bsky.social @blacktrowel.bsky.social @icaz-news.bsky.social

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

Cambridge Archaeology @cam-archaeology.bsky.social · 15/01/2026

📣 Work with us! 📣 We are seeking to appoint a part-time, permanent Biomolecular Research Laboratory Technician! Hear a bit more about the role from @matthewcollins.bsky.social 📅 Closing date: 2 February www.cam.ac.uk/jobs/biomole...

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

Matthew Collins @matthewcollins.bsky.social · 21/01/2026

#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?" 🦴📜 #Archaeology. Slightly scary, as while it is clearly AI, my net intellectual contribution was 18 spoken words.

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.

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

Rebecca R Helm @rebeccarhelm.bsky.social · 21/01/2026

This is brilliant.

Monk 1: What are you drawing?
Monk 2: A poor soul being dragged to hell by demons
Monk 1: Cool! And what are you planning to use as a border?
Monk 2: I'm thinking freshwater mussels.
Monk 1: That's really perfect

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

ypic.bsky.social @ypic.bsky.social · 21/01/2026

🧪 Online (Zoom) 📅 23 April 2026 ⏰ 14:00–16:00 CEST ✅ Free registration is mandatory! 👉More information in comments! 🔗 ECR Day Registration: docs.google.com/forms/d/e/1F... 🔗 Science Slam Registration: docs.google.com/forms/d/e/1F... #Proteomics #EarlyCareerResearchers #YPIC #EuPA#EuBIC

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PastelBio @pastelbio.bsky.social · 29/12/2025

Remember, once in a Blue Moon, to visit Pastel BioScience's resource pages ... t.ly/EP3hr to see updated list of new #proteomics software packages (153) in 2025 &, t.ly/Mlk39 for Conferences/Symposia/Webinars etc (11) already available in 2026 --- #proteomics #prot-other

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Vivian Scheinsohn @arqueoscheinsohn.bsky.social · 23/12/2025

Scientists against Milei's cuts of funds for basic science. Buenos Aires, Argentina.

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

Takumi Tsutaya @tsutatsuta.bsky.social · 20/11/2025

The Python script reported in Mackie et al. 2018 (Angew Chem Int 57:736–7374) for calculating N and Q deamidation rates from proteomic results has now been ported to the R environment. GitHub github.com/tsutatsuta/r... Zenodo doi.org/10.5281/zeno...

github.com

GitHub - tsutatsuta/rdeamidation: Calculates deamidation rates of N and Q for proteomic results

Calculates deamidation rates of N and Q for proteomic results - tsutatsuta/rdeamidation

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

Yasset Perez-Riverol @ypriverol.bsky.social · 29/10/2025

Vladimir Gorshkov manage to put in place the first release for #ThermoRawFileParser (TRFP) with dotnet support, not need for mono anymore. This is TRFP 2.0dev, if you are using this tool, please test/test, we want to release 2.0 including #bioconda and #biocontainer github.com/CompOmics/Th...

github.com

Release v2.0.0-dev · CompOmics/ThermoRawFileParser

Development release of version 2.0.0 for public testing Code is fully migrated to .NET 8, thus, Mono dependency is obsolete Added an action for automatic building and testing on all code changes A...

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

Yasset Perez-Riverol @ypriverol.bsky.social · 23/10/2025

Looking for feedback. How do you guys does feature intensity normalization? Median across entire experiment? Median by sample, it depends of the experiments?

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

Tobias Kroniger @kronigert.bsky.social · 15/10/2025

Struggling to compare Bruker timsTOF methods or extract window schemes from raw .d files? I developed a free desktop tool to solve this: timsCompare! 🚀 It automates the manual work of extracting method parameters, presenting them in a structured and comparable view. (A thread 🧵)

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

Aparna Nair @disabilitystor1.bsky.social · 24/09/2025

lol what? This just tells me how bad Marriott's reading and media consumption habits are, because it feels like more academics are doing public scholarship than ever! Maybe they're not all "Great White Scholar" types, but they're there, and doing the work.

Academics are also disappearing from public life. In my teens it was possible to assemble virtually a whole amateur curriculum via Mary Beard (classics), Steven Pinker (psychology), Richard Dawkins (biology), John Carey (literature). Now I struggle to name any prominent academics under 50, let alone under 40.

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

Ben Neely @benneely.com · 03/09/2025

Alright, help from my "wider" mass tolerance peeps ( @pwilmarth.bsky.social @ypriverol.bsky.social @michaellazear.bsky.social): I have confirmed what you all said that 1.25 Da MS1 and 20 ppm MS2 is a winning DDA combination. But I see in MSFragger I can do an upper and lower. Do +- 1.25 Da on MS1?

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

Prachee Avasthi @pracheeac.bsky.social · 08/09/2025

While journal publishing has always been deeply problematic, hurting both the pace and trajectory of science, something is happening in this moment that is finally causing the system to crumble under its own weight and cost. 1/

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

HigherJobz @higherjobz.bsky.social · 06/09/2025

Advanced Technician (Archaeological Laboratories) – Durham University, UK Permanent archaeology lab technician role Eligibility: Degree in Archaeology Deadline: 17 Sept 2025 Details: higherjobz.com/archaeology-... #AcademicJobs #ArchaeologyCareers #UKJobs #PermanentRole #ResearchJobs

higherjobz.com

Archaeology Lab Technician Job at Durham University | HigherJobz

Apply now for Archaeology Lab Technician at Durham University, UK. Full-time permanent role in Archaeology. Deadline: 17 Sept 2025.

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Bharath A. B. Nair (ഭരത് എ. ബി. നായർ) @bharathabnair.bsky.social · 03/09/2025

Chuffed to have participated in the Nordic Conference on Mass Spectrometry and Proteomics 2025 in Odense - "the birth place of proteomics". Also, massive congrats to Amalie to winning the Best Poster Award. @markersofpollution.bsky.social - grateful for the support!

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

Physalia-courses@ONLINE @physaliacourses.bsky.social · 02/09/2025

We would like to inform you that only four seats are left for the in-person course, “Machine Learning for Multi-Omics Integration,” with @oskolkov.bsky.social taking place on 15–17 December at the University of Barcelona @irbio-ub.bsky.social www.physalia-courses.org/courses-work...

physalia-courses.org

Machine Learning for Multi-Omics Integration

15-17 December 2025 Dept. Evolutionary Biology, Ecology & Environmental Sciences Faculty of Biology, University of Barcelona Institut de Recerca de la Biodiversitat (IRBio) Av. Diagonal, 643, Les ...

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Reposted by Bharath A. B. Nair (ഭരത് എ. ബി. നായർ)

PAASTA Community @paastacommunity.bsky.social · 02/09/2025

Following a marvelous time at ISBA11 and our PAASTA conference, we're back to sharing the work of our community with you here! @ipatramanis.bsky.social PAASTA talk from March about PaleoProPhyler a tool for #phylogenies from ancient proteins is now live on our YouTube youtu.be/2gVEQyinL4A

youtu.be

PAASTA Seminar Series - Ioannis Patramanis

YouTube video by PAASTA community

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