Isabel Meister

Two decades of induced pluripotent stem cell research: From discovery to diverse applications Since the discovery of induced pluripotent stem cells (iPSCs) 20 years ago, iPSC technology has transformed stem cell research and regenerative medicine. This perspective reviews key advances in repro...

Two decades of iPSCs - a timely overview from Shinya Yamanaka.
www.cell.com/cell-stem-ce...

The mass range of tandem mass spectra can be categorized into three main regions. For glycopeptides, the lower mass range contains mainly oxonium ions, the middle range contains mainly peptide fragments, and the high range contains charge-reduced fragments. All regions contain valuable fragment ion information, but they can only be simultaneously accessed by breaking the 5–10–15 rule.

MS/MS scan range can be an afterthought that doesn't receive attention in method design, but improper settings can affect experimental outcomes. This is especially true in glycoproteomics.

A #glycotime thread about a new #JASMS paper on this idea from @riley-research.bsky.social

1/10

Decoding cancer across scales with metabolomics - Nature Reviews Cancer In this Review, Rowles and Patti present metabolomics workflows to study cancer across scales. They explore the nutrient demands of cancer cells and how those needs can be fulfilled through metabolic interactions within the tumour microenvironment or systemic crosstalk with distant tissues, and discuss the opportunities and challenges of each approach and offer insights into future research directions.

Review🚨
Rowles and Patti decode cancer with #metabolomics across scales. They discuss opportunities and challenges of metabolimics approaches to explore how cancer cells' nutrient demands are met through metabolic interactions in the TME or systemic crosstalk.
📖👇

I'm a cognitive scientist with an interest in epistemic vigilance, and this essay that's been going around gave me pause.

I don't think it's straightforward to apply the concept of epistemic vigilance to interactions with LLMs, as this essay does.

🧵/

sbgeoaiphd.github.io/rotating_the...

Awesome paper and super useful resource of CRISPR-based screens to identify regulators of #LipidDroplet biology under different metabolic conditions: crisprlipid.org

The Lipid Interactome: an interactive and open access platform for exploring cellular lipid–protein interactions AbstractSummary. Lipid–protein interactions play essential roles in cellular signaling and membrane dynamics, yet their systematic characterization has lon

This is SO COOL!!!

academic.oup.com/bioinformati...

Circular heatmap of placenta metabolites. Identified metabolites with p-value below 0.05 in any comparison between the study groups are shown. CONT = Control group, EE = Early Exposure group, i.e., placental samples from pregnancies where the woman positive cotinine levels in 1st trimester serum samples but no cotinine in the placental sample, and CE = Continuous Exposure group, i.e., placental samples from pregnancies where both the 1st trimester and placental sample had high cotinine levels. Z-scores are shown for each group, and Cohen’s d effect sizes are shown for each group comparison. *, p-value < 0.05. Metabolite of AALA, metabolite of amino acid local anesthetic; EDAB, ethyl-4-dimethylaminobenzoate; t⁶A, N⁶ threonylcarbamoyladenosine, 17-OHP, 17α-Hydroxyprogesterone.

🚨New preprint!

Masvosva et al. An exploratory investigation of placental metabolomic alterations associated with maternal smoking

doi.org/10.64898/202...

Mucosal vaccination clears Clostridioides difficile colonization - Nature Mucosal administration of a multivalent, adjuvanted vaccine against Clostridioides difficile promoted bacterial clearance and&nbsp;protected against morbidity, mortality, tissue damage and recurrence ...

#NatMicroPicks

C. diff vaccine! 🦠💉

A protective mucosal vaccine formulation that provides sterilizing immunity to clear C. difficile from the host.

#MicroSky

www.nature.com/articles/s41...

Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor - Nature Sequencing of marine sediments finds 136 newly identified Heimdallarchaeia and several novel lineages, and indicates that Heimdallarchaeia evolved distinct metabolic capabilities from other&nbsp;Asgar...

#NatMicroPicks

Aerobic archaeal-eukaryotic ancestor? 🦠🫁

The ancestor of eukaryotes may have combined hydrogen metabolism with aerobic respiration, shaping early cellular complexity.

#MicroSky

www.nature.com/articles/s41...

Mechanisms of node of Ranvier assembly - Nature Reviews Neuroscience The formation of the nodes of Ranvier in myelinated axons involves a specific clustering of ion channels. In this Review, Rasband and Peles describe two independent, glia-directed mechanisms that conv...

14/ NF155 is expressed on Schwann cells and plays a critical role in establishing the structure and integrity of the node of Ranvier. See this excellent review from @mattrasband.bsky.social (www.nature.com/articles/s41...)

[ASAP] Profiling of Low-Abundance Branched-Chain Fatty Acids via Radical Directed Dissociation Tandem Mass Spectrometry Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.6c00001

(JASMS) [ASAP] Profiling of Low-Abundance Branched-Chain Fatty Acids via Radical Directed Dissociation Tandem Mass Spectrometry: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.6c00001 (RSS) #MassSpecRSS #JASMS

There's an art to representing MS-based bioinformatics, and these authors have done an amazing job.

Academics vying for a spot in Epstein‘s world. There are so many. I feel the need to make a thread, so I don’t keep confusing them. 1/

Mechanistic study on the sulfate migration in glycosaminoglycans during MS fragmentation - Communications Chemistry Glycosaminoglycans encode binding specificity through positional sulfation, but understanding these patterns is challenging due to sulfate migration during mass spectrometry (MS). Here, the authors use ion-mobility MS to investigate the isomerization reaction of heparin sulfate disaccharides in the gas phase, providing insights into the resulting isomeric products and potential rearrangement mechanisms of sulfate migration.

Mechanistic study on the sulfate migration in glycosaminoglycans during MS fragmentation #nature #MassSpecRSS

We’ve all had samples where BCA/qubit quant correlates poorly with LC-MS TIC.
Looks like those assays aren’t always needed:
“protein quantification and physical normalization steps can be omitted…without incurring an unacceptable increase in measurement variability after computational normalization”

What happened to Science Goodreads and how do we rebuild it? A 65 million dollar question (at least) - CAIROS Blog The story of the rise and fall of Mendeley

1/ Finally wrote up “The Story of Mendeley”! Most people know the tool, few know about its rise and fall. The Mendeley story provides important clues for how to build self-sustaining AND non-extractive knowledge commons, which is why I think it deserves more attention 🧵

Mendelian randomization links 4 metabolites with 2 enzymes, unveiling metabolic networks & potential therapeutic targets. #Metabolomics PMID:41650937, Am J Hum Genet 2026, @AJHGNews https://www.cell.com/ajhg/fulltext/S0002-9297(25)00484-7 #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪

[ASAP] Regarding Emitter Positioning for Nanoflow Electrospray Ionization with a High-Capacity Inlet Capillary Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00441

(JASMS) [ASAP] Regarding Emitter Positioning for Nanoflow Electrospray Ionization with a High-Capacity Inlet Capillary: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00441 (RSS) #MassSpecRSS #JASMS

News and views from Olivia Seidel in my lab on this important paper from the Baskin lab from last month www.nature.com/articles/s41...

Redefining lipid biology from droplets to ferroptosis - Ireland When most people think of lipids, they think of fat. James Olzmann thinks of life itself — how cells store energy, maintain balance and decide when to die.

Redefining lipid biology from droplets to ferroptosis

https://www.europesays.com/ie/321196/

When most people think of lipids, they think of fat. James Olzmann thinks of life itself — how…

Evolution and diversity of oxidoreductases involved in redox balance and energy conservation - Nature Ecology & Evolution HORBEC are protein complexes involved in the regulation of redox balance and energy conservation. The authors develop a bioinformatic tool for HORBEC annotation in bacterial and archaeal genomes and r...

Passioned by #bioenergetics? Do not miss our new article on the evolutionary history of oxidoreductases with G. Borrel and @sgribaldo.bsky.social @archaeal.bsky.social @valdeanda.bsky.social @pasteur.fr @cnrs.fr @cnrsbiologie.bsky.social @natecoevo.nature.com (www.nature.com/articles/s41...).

l'un de mes livres de chevet 🙂

Thx for @mollyherring.bsky.social for featuring our recent work with @centriolelab.bsky.social and our quest with @gautamdey.bsky.social & the support of the @moorefound.bsky.social to look for the beauty in every #eukaryote out there using #Expansion #Microscopy #UExM

Cell membranes sustain phospholipid imbalance via cholesterol asymmetry This work challenges a major assumption in cell biology by showing that lipid bilayers can have drastically different phospholipid abundances between their two leaflets. This lipid abundance asymmetry...

interesting read😯
www.cell.com/cell/abstrac...

The Dependency Layer in Digital Sovereignty David Eaves recently argued that the path to tech sovereignty runs through commodification, not duplication. Europe shouldn’t try to build its own AWS. Instead, governments should use procurement power to enforce interoperability standards. The S3 API became a de facto standard that lets you move between providers, reducing switching costs. If governments required that kind of compatibility as a condition for contracts, smaller providers could compete. Sovereignty through standards rather than state-owned infrastructure. The same logic applies to the software supply chain, though that layer gets less attention in sovereignty discussions than cloud and storage. Most git forges are US-based: Forge | Owner | Country ---|---|--- GitHub | Microsoft | US GitLab | GitLab Inc | US Gitea | Gitea Ltd | US HuggingFace | Hugging Face Inc | US The dependency intelligence layer built on top of these forges is almost entirely US-based: Service | Owner | Country ---|---|--- Snyk | Snyk Ltd | US Socket | Socket Inc | US Sonatype | Sonatype Inc | US Veracode | Veracode Inc | US Black Duck | Synopsys | US Dependabot | Microsoft | US Renovate | Mend.io | US deps.dev | Google | US GitHub Dependency Graph | Microsoft | US GitHub Advisory Database | Microsoft | US NVD | NIST | US Sigstore | Google/OpenSSF | US JFrog Artifactory | JFrog | US GitHub Packages | Microsoft | US AWS CodeArtifact | Amazon | US Azure Artifacts | Microsoft | US Google Artifact Registry | Google | US Docker Hub | Docker Inc | US Amazon ECR | Amazon | US Quay | Red Hat/IBM | US The package registries follow a similar pattern, with a few European exceptions: Registry | Owner | Country ---|---|--- npm | Microsoft | US PyPI | Python Software Foundation | US RubyGems | Ruby Central | US Maven Central | Sonatype | US NuGet | Microsoft | US Crates.io | Rust Foundation | US Go module proxy | Google | US Docker Hub | Docker Inc | US Conda/Anaconda | Anaconda Inc | US CocoaPods | CocoaPods | US Pub.dev | Google | US CPAN | Perl Foundation | US Homebrew | Homebrew | US Hex.pm | Six Colors AB | Sweden Packagist | Private Packagist | Netherlands CRAN | R Foundation | Austria Clojars | Clojars | Germany The security and metadata tooling built on top of these registries tends to be US-based regardless of where the registry itself is hosted. A European company running Forgejo for code hosting still typically uses US services for dependency updates, vulnerability scanning, license compliance, and SBOM generation. Self-hosting the forge doesn’t change the intelligence layer. Ploum made a related point: Europe doesn’t need a European Google. The European contribution to software has been infrastructure that serves as collective commons: the web, Linux, Git, VLC, OpenStreetMap. “We don’t want a European Google Maps! We want our institutions at all levels to contribute to OpenStreetMap.” The same framing applies to dependency tooling. Rather than building European alternatives to each US service, invest in open infrastructure that anyone can use. Dries Buytaert extended this to procurement: governments buy from system integrators who package and resell open source, but that money doesn’t reach the maintainers who build it. If procurement scoring rewarded upstream contributions, money would flow differently. Open source is “the only software you can run without permission” and therefore useful for sovereignty, but it needs funding to work. ### Where standards exist and where they don’t Eaves’s commodification argument depends on standards to reduce switching costs. In the package management landscape, some de facto standards have emerged. Git is nearly universal for source hosting. Semver is the dominant versioning scheme, even if ecosystems interpret it differently. Lockfile formats vary by ecosystem, but they’ve become standards in practice: every dependency scanning company builds the same set of parsers to extract dependency information from all of them. Syft, bibliothecary, gemnasium, osv-scalibr, and others all parse the same formats. I made a dataset covering manifest and lockfile examples across ecosystems, and a similar collection of OpenAPI schemas for registry APIs. These are what made git-pkgs come together quickly. Beyond those de facto standards, some areas have formal specifications. PURL provides a standardized way to reference packages across ecosystems. OSV and OpenVEX let advisory data flow between systems. CycloneDX and SPDX handle SBOMs. SLSA, in-toto, and TUF cover provenance. OCI standardizes container images. Other areas don’t, which keeps switching costs high. Dependency graph APIs vary by platform, vulnerability scanning integration is proprietary per forge, Dependabot and Renovate each have their own config format, and package metadata APIs differ across registries. Most standards work in this space focuses on compliance artifacts: SBOMs for the Cyber Resilience Act, attestations for procurement requirements. Less attention goes to the underlying tools developers actually use. The dependency graph that feeds the SBOM generator, the metadata lookup that powers vulnerability scanning, the notification when a new version ships. The gap between these columns is where standardization would reduce switching costs. Not building a European deps.dev, but defining a common dependency graph API. Not building a European Dependabot, but standardizing how dependency updates get proposed. A protocol for package management could let different implementations compete on the same interfaces. GitHub and GitLab bundle dependency features into their platforms: dependency graphs, vulnerability alerts, automated updates. A self-hosted Forgejo or Gitea instance doesn’t have equivalent tooling. But if those features were built on open standards and open data sources, switching forges wouldn’t mean losing supply chain visibility. The dependency intelligence could come from any provider that implements the same interfaces, rather than being locked to the forge vendor. Some gaps need new standards rather than adoption of existing ones. There’s no good specification for package version history across registries. Codemeta describes a package at a point in time, not its release history. PkgFed proposes using ActivityPub to federate release announcements, similar to how ForgeFed handles forge events. ### What governments and funders could do The strategy is to unbundle the parts of a package manager and standardize them individually. Registry APIs, dependency graphs, vulnerability feeds, update notifications. Each piece can be commodified without replacing entire systems. Eat the elephant one bite at a time. Treat dependency intelligence as infrastructure worth funding directly. The Sovereign Tech Fund model applies: direct funding to open source projects that serve as foundations. Ecosyste.ms, VulnerableCode, OSV, PURL implementations, CycloneDX/SPDX tooling, Forgejo’s dependency features all fit this category. Procurement requirements could include open supply chain tooling. If an agency requires SBOMs, they could also require that generation doesn’t depend on proprietary services. If they require vulnerability scanning, the scanner could consume open advisory databases. Germany’s ZenDiS and openCode.de initiatives are relevant here. Connecting them with existing open solutions would be more efficient than starting fresh. Supporting Forgejo with work on dependency features would help too. The goal would be feature parity with GitHub and GitLab so self-hosted forges work with the same security tooling. Package management is a wicked problem, but the dependency intelligence layer is more tractable. Standards exist (PURL, OSV, CycloneDX), open implementations exist (ecosyste.ms, VulnerableCode). What’s missing is the investment.

I didn’t realise just how US centric all of package management was until I made these tables 😅

The Dependency Layer in Digital Sovereignty: https://nesbitt.io/2026/01/28/the-dependency-layer-in-digital-sovereignty.html

Resurrected nitrogenases recapitulate canonical N-isotope biosignatures over two billion years - Nature Communications The study shows that nitrogenase enzymes have maintained stable isotope signatures over billions of years, revealing how ancient microbes shaped Earth’s nitrogen cycle and offering a new experimental ...

Our new paper, out today! We resurrected ancient nitrogenases first used by life on Earth 3 billion years ago. We combined synthetic biology and geology & validated their chemical #biosignature in rocks that helps reveal ancient life on Earth!(and beyond!)

Link: www.nature.com/articles/s41...

The evolution of gene regulation in mammalian cerebellum development Gene regulatory changes are considered major drivers of evolutionary innovations, including the cerebellum’s expansion during human evolution, yet they remain largely unexplored. In this study, we com...

Outstanding @science.org study on the evolution of gene regulation shaping
#cerebellum development 🧪🧠🧬
@ioansarr.bsky.social @marisepp.bsky.social @tyamadat.bsky.social @steinaerts.bsky.social @kaessmannlab.bsky.social
www.science.org/doi/10.1126/...

Improving atlas-scale single-cell annotation models with hierarchical cross-entropy loss - Nature Computational Science A hierarchical cross-entropy loss is presented, which incorporates ontology structure into training and improves the out-of-distribution performance of large-scale single-cell annotation models withou...

📢Out now! Sebastiano Cultrera di Montesano, Peter S. Winter, @lcrawford.bsky.social, and colleagues present a hierarchical cross-entropy loss that improves performance of single-cell annotation models. www.nature.com/articles/s43... 🖥️ 🧬

I recommend this as a great summary of the debates and the state of play in eukaryotic regulation. I particularly commend the discussion of causation.

Advancing regulatory variant effect prediction with AlphaGenome - Nature AlphaGenome, a deep learning model that inputs 1-Mb DNA sequence to predict functional genomic tracks at single-base resolution across diverse modalities, outperforms existing models in variant effect...

I had intended to post something about this new Google DeepMind paper that appeared yesterday in Nature, but the press coverage has added to what there is to say. So this is a long 🧵
www.nature.com/articles/s41...