iiinova — where your digital self keeps evolving

Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 07/10/2026

News: "TGX in Brno: second half of the ELIXIR exchange with RECETOX" www.maastrichtuniversity.nl/news/tg… #elixirEurope @elixir-nl.bsky.social "From 24 to 28 August, Egon, Denise, Javier and Marvin drove to […] [Original post on social.edu.nl]

Photo of the TGX and RECETOX researchers in front of an entrance of Masarykova Univerzita.

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 02/10/2026

the Dutch Virtual Human Platform 4 Safety (VHP4Safety) project has a series of webinars upcoming. www.sciencrew.com/c/6594/a/33572695… #toxicology #safety #nederlandseWetenschapsAgenda

"Save the date" infographics for the "VHP4Safety Webinar Series" showing three colored hexagons with the three date/times of the three webinars and next to that the three webinar titles. All on a light blue background. Full details:

Introduction to the VHP
14 October 2026, 13:00 to 14:30 CEST

The first webinar will introduce the VHP4Safety project and the Virtual Human Platform. Participants will see how the platform works, explore its tools and learn how it can support safety assessment workflows. The programme will include a live demonstration of the platform and an example of how it was used to address a regulatory question related to thyroid hormone-mediated brain development.

Deep dive into the Parkinson's case study
28 October 2026, 13:00 to 14:30 CET

The second webinar will focus on VHP4Safety’s Parkinson’s case study. Speakers will explain how the Virtual Human Platform brings together in vitro research, Adverse Outcome Pathways, experimental data and available methods to support risk assessment, as demonstrated through the Parkinson’s case study.

From innovation to implementation
18 November 2026, 13:00 to 14:30 CET

The final webinar of the VHP4Safety webinar series will focus on the social side of building the VHP, including user research supporting the development and implementation of the Virtual Human Platform. It will also examine the public acceptance of computational models and artificial intelligence in risk assessment. The webinar will show how stakeholder needs and perspectives can support the development of tools that are scientifically robust, transparent and fit for purpose.

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FAIR4ChemNL @fair4chemnl.social.edu.nl.ap.brid.gy · 25/09/2026

so far, we have been using @elixir_europe's TeSS and the @SURF's taxila.nl for sharing events and (training) materials. Because both can scrape the content using community standards like Bioschemas, we now have a GitHub Pages website […] [Original post on social.edu.nl]

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 04/09/2026

"Discovering life's directed metabolic (sub)paths to interpret human biochemical markers using the DSMN tool" doi.org/10.1039/d3dd00069a #health #aging #biomarker #wikipathways this paper is not getting the attention is deserves: network biology to […] [Original post on social.edu.nl]

Part if Figure 12A: "Network visualization of aging biomarkers found in blood. (A) Overview of directed shortest path calculations for one of the analyzed datasets (MTBLS265) in this study, where relevant metabolites considered to be biomarkers for aging (high CV30 values) have a diamond shape; round nodes depict metabolites needed for connectivity, and hexagons visualize proteins. The thickness of the arrows between the nodes indicates the occurrence of this reaction in different pathways."

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 04/09/2026

Dr Susan Coort was keynote at the NuGOweek 2026 this week: "Connecting the dots: pathways and networks in nutrition research" nugo2026.pan.olsztyn.pl #nutrigenomics #NuGOweek #wikipathways Find more about her research here […] [Original post on social.edu.nl]

Coort on stage in front of one of her slides, showing information about the WikIpathways project.

Photo: All rights reserved, Meike Bünger, Health-RI / ELIXIR-NL.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 31/08/2026

the @SIB hosts this years #ECCB2026 (see mstdn.science/@SIB/1165389559309233…) and Aishwarya Iyer is speaking tomorrow in the 15:15-16:15 session on "Network-based stratification of allele-specific expression reveals patient subgroups in Huntington's disease", see […]

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 29/08/2026

"Network-based stratification of allele-specific expression reveals patient subgroups in Huntington’s disease" doi.org/10.1093/bioinformatics/btag… "Intersection of differentially imbalanced and expressed genes identified FAM181B as a candidate gene […] [Original post on social.edu.nl]

Figure 1Patient clusters identified by network-based stratification of allele-specific expression profiles. (left; A) The heatmap shows the co-cluster frequency for each patient pair over 1000 iterations. Patients are grouped by cluster assignment, indicated by coloured bars (red: cluster 1, green: cluster 2, cyan: cluster 3). (right; B) Network representation of patient clusters. Nodes represent individual patients, coloured by cluster assignments. Edges connect patients with a co-cluster frequency 0.63, with edge width scaling linearly with co-cluster frequency.

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BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 21/08/2026

"BioHackSWAT4HCLS25 report: Towards an interactive mapping experience for data owners" doi.org/10.37044/osf.io/mhvbs_v1 #biohackathon #SWAT4HCLS25 "At the Barcelona SWAT4HCLS 2025 Hackathon, a hacking group familiarized with and worked on improvements for RDFCraft. A tool for a data […]

fediscience.org

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BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 21/08/2026

"INTOXICOM Workshop Report: Making toxicology tools more accessible and interoperable" doi.org/10.37044/osf.io/u3fnh_v1 #biohackathon #toxicology "Here, we here report on the 3rd workshop, titled “Making toxicology tools more accessible and interoperable” which was held from 26 to 27 […]

fediscience.org

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 19/08/2026

new paper: "Dietary Titanium Dioxide (E171) Alters the Colon Transcriptome—Evidence From a Human Dietary Intervention Study" doi.org/10.1002/mnfr.70583 #toxicology #titaniumDioxide #E171 "Systemic oxidative stress increased, evidenced by increased superoxide radical levels in whole […]

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 17/08/2026

new paper: "Genome-Wide Association of Genetic Variants with Intestinal Cholesterol Absorption Markers in a European Population" doi.org/10.3390/nu18162679 "A total of 16 SNPs were identified. Eight SNPs overlapped with both campesterol/TC and […] [Original post on social.edu.nl]

Table of Contents graphics, showing a visualization of the intestinal lumen, along with dietary cholesterol. With 398 data points, this genome-wide association analysis found several SNPs of interest, including rs439976, rs6544713, rs4245791, rs260769, rs5011112, rs4962526, rs2033254, and rs12708980. These are found on chromosomes 2-4, 10, and 16, with nearby genes being ABCG8, ADAM12, and CETP.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 12/08/2026

new paper: "Computational metabolomics at scale: from open data to insight" doi.org/10.1016/j.copbio.2026.103557 #openscience #metabolomics "In this review, we summarize discussions from the “Dagstuhl-Seminar 24181 Computational Metabolomics: Towards Molecules, Models, and their […]

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 12/08/2026

new paper: "Integrating transcriptomics and molecular AOPs to identify T3-dependent regulation of neuronal development in the human neural progenitor test" doi.org/10.1016/j.tox.2026.154542 "This study illustrates the utility of integrating […] [Original post on social.edu.nl]

Table of Contents graphics showing three sections ("Experiment setup", "Transcriptomics response", and "Molecular AOP interpretation"). The first shows the three T3 doses, the middle a Venn diagrem of differential expressed genes, and the last a network with key events and molecular pathways.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 12/08/2026

new paper: "Colonoid-Based Transcriptomics Reveals Conserved and Model-Specific Mechanisms of Doxorubicin-Induced Intestinal Toxicity" doi.org/10.3390/ijms27167072 "Using a parallelogram approach, differential expression, co-expression, pathway mapping […] [Original post on social.edu.nl]

Table of Contents graphics showing two rows, the top one showing depictions of the methods (RNA-seq, DE Seq2, WGCNA, pathway enrichment, ad CTD benchmark(-ing)), and the second (larger) row with the three used models (in vitro human and mouse colonoids and in vivo mouse colon), the core responses (dna damage response, cell-cycle arrest, and intrinsic apoptosis), and the translation/implications to human colon (in vivo). At the bottom the text "gut-relevant candidate markers highlighting CTD gaps across models" is given.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 03/07/2026

new paper: "The Secretome of a Cachexia-Inducing Lung Tumor Impairs Mitochondrial Function and Skeletal Muscle Differentiation" doi.org/10.3390/cancers18132130 "344P tumor-conditioned medium did not induce myotube atrophy, or activation of […] [Original post on social.edu.nl]

Figure 1. Differential expression analysis of genes involved in processes related to proteolysis (A) and myogenesis (B) in gastrocnemius muscles of OLCC mice compared to sham control mice. Upregulated genes are depicted in red; downregulated DEGs are depicted in blue. Directional bias was assessed by Fisher’s exact test (two-tailed) with FDR correction. A literature-based approach for atrophy-related genes yielded 82 genes. A literature-based search for genes related to myogenic processes yielded 56 genes, shown in a regulatory network with interconnecting nodes. Node size indicates the number of log 2-fold changes; green node border indicates DEGs. Edges represent TF–target interactions from TFLink, supported by small-scale evidence or by high-throughput ChIP-seq (C). Edges with at least one small-scale record are drawn thicker (higher confidence). Edges supported only by ChIP-seq are drawn thinner. ** FDR ≤ 0.005, *** FDR ≤ 0.001

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 03/07/2026

new paper: "Genetic variants associated with triglyceride metabolism and fasting triglyceride concentrations: a systematic review and a meta-analysis" doi.org/10.1016/j.jacl.2026.06.019 "Five of those (rs58542926, rs738409, rs320, rs328, and rs1801282) […] [Original post on social.edu.nl]

Table of Contents graphcis, showing the research question at the top, and a flow diagram of the used approached (CC-BY).

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WikiPathways @wikipathways.fosstodon.org.ap.brid.gy · 07/06/2026

a new R package, PinPath, allows mapping experimental data onto pathways, using just R: doi.org/doi:10.18129/B9.bioc.PinPath bioconductor.org/packages/devel/bio… #openscience #bioinformatics #bioconductor

Example SVG from the WikiPathways vignette of the PinPath packages with data mapped onto a pathway. The pathways is from a publication from 2022: https://doi.org/10.3389/fonc.2022.849640 "A Community-Driven, Openly Accessible Molecular Pathway Integrating Knowledge on Malignant Pleural Mesothelioma"

Genes/Proteins are colored by up- or downregulation, blue and red.

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 30/05/2026

Fwd: "New paper: pyBiodatafuse: Extending interoperability of data using modular queries across biomedical resources" doi.org/10.59350/7n2bs-zsm80 "In a recent paper, Yojana Gadiya, Javier Millán Acosta, and Tooba Abbassi-Daloii led a project called […] [Original post on social.edu.nl]

Schematic diagram showing many entities, like Gene, Key Event, Drug, Pathway, function, etc, along with ontology IDs for those types, and in colored arrows lines between them. The diagram is the result of data from multiple databases aggregated with the Python pyBiodatafuse package into a question-specific knowledge graph.

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BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 22/05/2026

"INTOXICOM Workshop Report: Systems Biology Models for Toxicology" doi.org/10.37044/osf.io/zf2qj_v1 "The workshop took place under the INTOXICOM Implementation Study workshop series (Integrating the toxicology community into ELIXIR 2024) and aimed to […] [Original post on fediscience.org]

Schematic with many boxes in various UML types. At the top we see a purple box with various stakeholders (JRC, ELIXIR, OECD, EIRENE, NWO, etc), and a blue box below this with various activities (AOP Wiki, Omics AOP, Methods AOP, AOP-DB, AOPXplorer, etc), supported by a layer reflection data warehouses (without much details). On the right side we see three headers (Macro level: landscape, Meso level: regimes, and Micro level (niches).

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 30/04/2026

new paper: "Multi-omics characterization of developing forebrain organoids unravels the dynamic molecular events of Rett syndrome pathogenesis" doi.org/10.1186/s11689-026-09699-9 "The spatiotemporal transcriptomic analysis revealed alterations in […] [Original post on social.edu.nl]

Table of Contents graphical abstract showing various aspects of the biology, experimental design, and analysis: dorsal brain organoids, iPSC, regulatory networks, validation, and spatiotemporal alterations.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 30/04/2026

new paper: "A dataset of rare copy number variants associated with neurodevelopmental and neuropsychiatric disorders" doi.org/10.1038/s41597-026-07345-6 "We present a curated machine readable dataset, CNVPathwayAtlas, that integrates 38 pathogenic CNVs […] [Original post on social.edu.nl]

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 29/04/2026

vacancy: "Postdoctoral Researcher - Translational Genomics (Nutrigenomics)" vacancies.maastrichtuniversity.nl/j… "What you will do In this role, you investigate how gene–diet interactions […]

social.edu.nl

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 23/04/2026

We are happy to inform you about an exciting five-day course TGX is organising June 22-26 in Maastricht (Randwyck), in collaboration between FHML and FSE. The course is titled “Multi-omics and data sciences in complex diseases” and is aimed at PhD candidates, as well as postdoc and senior […]

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 15/04/2026

On the afternoon of Thursday 28 May, the official launch of the Virtual Human Platform (VHP) will take place, where innovation meets practical application in human-relevant safety assessment. This event promises a dynamic program with something for everyone, including: Three parallel […]

social.edu.nl

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 07/04/2026

new paper: "Reduced NR2F6 expression reshapes the VPA-induced transcriptome in human hepatocytes and increases lipid accumulation" doi.org/10.1016/j.tox.2026.154457 "Functional validation in HepG2 and HepaRG models demonstrated that NR2F6 knockdown […] [Original post on social.edu.nl]

Fig. 6. Mechanistic model of NR2F6 modulation of VPA-induced lipid accumulation. Reduced NR2F6 expression alters hepatocellular responses to VPA by decreasing CPT1A, increasing CPT2, upregulating PLIN2, reducing PLIN4, lowering FASN, and increasing CYP2B6 expression. These coordinated changes shift lipid-droplet composition, modify fatty-acid handling, and enhance susceptibility to VPA-induced steatosis.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 07/04/2026

new paper: "Effects of acute fluctuations of extracellular Zinc on network activity of human iPSC-derived neurons; impact of NMDA Receptor and L-Type Calcium Channel Activation" doi.org/10.1016/j.neuropharm.2026.1… "Addition of nMolar […] [Original post on social.edu.nl]

Fig. 6. Expression analysis of genes encoding various neuronal markers. Analysis of a panel of a–f: MAP2, GRIN1, GRIN2A, GRIN2B, VGLUT1, and CACNA1C in control neurons in the absence and presence of added 200 nM or 5 μM ZnCl2 in the absence or presence of ZX1. Data are presented as fold change relative to the control, which is indicated by the horizontal line. Data are represented as means ± SEM. *p < 0.05, ***p < 0.001 following One-way ANOVA with post hoc comparisons using Dunnett's multiple comparisons test. N = 6 for MAP2 and VGLUT1 and CACNA1C, and 3 for GRIN1, GRIN2A and GRIN2B.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 07/04/2026

new paper: "ToxTempAssistant: using large language models to standardise cell-based toxicological test method descriptions" doi.org/10.1080/2833373X.2026.26380… "This study quantifies the tool’s baseline performance under controlled conditions […] [Original post on social.edu.nl]

Figure 1. Schematic overview of the ToxTempAssistant workflow. The ToxTempAssistant enables automated drafting of ToxTemp templates using a large language model (LLM). Users upload contextual documents along with the assay name and short assay description. For each of the 77 ToxTemp questions across 11 sections (Krebs et al. Citation2020), targeted prompts extract relevant information via the LLM. Deviating from the graphic, the current software implementation allows sending requests to the LLM in parallel. Users validate and edit the draft before exporting the completed template.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 07/04/2026

new paper: "From disease prevention to fertility treatment: rethinking the use of mitochondrial donation for oocyte-related infertility in the light of safety and efficacy" doi.org/10.1093/humrep/deag027 "The paper discusses the regulation of MST/PNT for both applications in relation to […]

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 15/03/2026

Registered the @elixir_europe Toxicology Community Hybrid Meeting 2026 meeting (25/26 June) in Taxila and TeSS: elixir-europe.org/events/toxicology… Local organizers: @Marvin, Danyel Jennen, and me Registration is open! #toxicology #learning #FAIRdata #safety #ELIXIREurope

Since Taxila and ELIXIR TeSS use the same software, the left (Taxila) and right (TeSS) pages for the same linked meeting, the pages look more or less the same (Taxila uses OpenStreetMap, where TeSS uses Google Maps). Otherwise, they both show the meeting title, dates, location, some more metadata (see the linked page), and a description:

"The ELIXIR Toxicology Community hybrid meeting will bring together Community members and partners for two days of presentations, workshops and collaborative discussion. The programme will review lessons learned from the INTOXICOM workshops, reflect on progress since the first Toxicology Community white paper, and outline priorities for the second white paper. Participants will also align Community needs with the new ELIXIR Roadmap and identify next goals and strategic directions. The meeting aims to strengthen collaboration across the Community and ensure continued alignment with ELIXIR strategic priorities."

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 14/03/2026

new paper: "Black carbon is detectable in association with small extracellular vesicles in fetal circulation" doi.org/10.1016/j.envint.2026.110186 "Here we show that black carbon (BC) is detectable in association with small extracellular vesicles […] [Original post on social.edu.nl]

ToC graphics, showing three papels explaining the paper: "Maternal exposure", "Placental interface exchange", and "Fetal circulation & BC-Brain accomodation".

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 14/03/2026

new paper: "Outcomes and future activities of the ‘Pan-European network in Lipidomics and EpiLipidomics – EpiLipidNET’" doi.org/10.1007/s11306-026-02396-7 #lipidomics #metabolism

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 01/03/2026

new paper: "pyBiodatafuse: extending interoperability of data using modular queries across biomedical resources" doi.org/10.1093/bioinformatics/btag… "Additionally, the tool offers plugins for widely used platforms such as Cytoscape, Neo4j, and […] [Original post on social.edu.nl]

Figure 2The property graph data model of the biomedical knowledge graph was generated by pyBiodatafuse.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 01/03/2026

new editorial w @Marvin: "The Environmental Health Language Collaborative (EHLC) Adverse Outcome Pathway (AOP) Standards Workshop Report" doi.org/10.12688/f1000research.1758… "The recent EHLC AOP Standards two-day workshop served as a platform to connect the Adverse Outcome Pathway […]

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 19/02/2026

📣 Save the date! Toxicology Community Face2Face! Maastricht, The Netherlands, Thu-Fri - 25/26 June 2026. Details will follow asap. #elixirEurope #toxicology

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 12/02/2026

🔬 Exciting news! Houman Kahroba et al.'s paper “Small extracellular vesicles: connecting early life exposure outcomes to air pollution during pregnancy to early childhood health” has been selected as an Editor’s Choice 2025 by Environmental Health! 🎉 doi.org/10.1186/s12940-025-01238-8 […]

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 12/02/2026

Our team organized in December the 7th @vhp4safety hackathon in Maastricht. The photo is the hackathon in action. A report is available here: www.sciencrew.com/c/9347/a/33561849… More about the VHP4Safety […] [Original post on social.edu.nl]

Photo of a room of 16 people sitting around tables, laptops open, sideways looking at a presentation given on a large TV screen on the far side of the room.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 12/02/2026

new paper: "Food Additive Titanium Dioxide (E171) Alters Gut Microbial Metabolic Activity and Butyrate Production in the TIM-2 In Vitro Colon Model" doi.org/10.1093/jambio/lxag042 "E171 undergoes distinct physicochemical transformations depending on […] [Original post on social.edu.nl]

Figure 3: Cumulative production (mmol) of SCFAs (acetate, propionate, butyrate) at 24 h, 48 h, D and 72 h for Ctrl-aq, E171-aq, Ctrl-yog, and E171-yog within SIEM. The addition of E171 Edrastically increases butyrate production T in E171-aq and E171-yog settings, with an overall increase in total SCFA production.

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WikiPathways @wikipathways.fosstodon.org.ap.brid.gy · 12/02/2026

February 2026 WikiPathways update: 95 edits by 9 contributorsin the last month. More news at github.com/wikipathways/wikipathway… Accessible via #webservices, #rstats, #pathvisio and #cytoscape. Supported by #awsopen […]

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 18/01/2026

new paper: "Short-term high-dose nicotinamide treatment across glaucoma subtypes reveals increased mtDNA content and minimal metabolomic change in blood" doi.org/10.1016/j.exer.2025.110807 "All groups showed a similar metabolome response to treatment […] [Original post on social.edu.nl]

Fig. 1. Control and glaucoma subtypes have similar plasma metabolomes following oral NAM treatment. A) Analysis by construction of a linear model with covariate adjustment (age, sex) demonstrated that baseline (pre-NAM) plasma metabolomes were similar across all subtypes compared to normal controls, with only ethylmalonic acid demonstrating a small yet significant relative increase in glaucoma. B) Unsupervised hierarchical clustering demonstrated that individual plasma samples clustered into pre- and post-NAM groups based on the metabolome alone, which appears to be largely driven by 4 NAM species metabolites. C) Individual comparisons of responses to NAM treatment (pre vs. post) demonstrated that all conditions respond similarly to high dose NAM treatment. NAM was significantly elevated across all conditions, and methylated NAM species were also detected suggesting active metabolism in the liver. In support of this, betaine (a methyl donor produced predominantly in the liver) was significantly reduced. D) Comparison of these responses by construction of a linear model with covariate adjustment (age, sex) demonstrated that sarcosine was the only metabolite that was significantly different across conditions. Sarcosine was significantly reduced in HTG and NTG patients but not in controls and PEXG. HTG: high tension glaucoma; NAM: nicotinamide; NTG: normal tension glaucoma; PEXG: pseudoexfoliative glaucoma.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 18/01/2026

new preprint: "Fostering and sustaining collaborative innovation: Insights from ELIXIR Europe's life science Communities" doi.org/10.12688/f1000research.1682… "The ELIXIR Communities framework is made up of a suite of tools and processes that ensure […] [Original post on social.edu.nl]

"Figure 1. Stages in the development of ELIXIR Communities.

Timeline to show the progression of each ELIXIR Community through the stages of Community maturity, following the processes outlined along the top row. Once a community has reached the phase of Heads of Nodes approval (i.e. approval by the country-level bioinformatics leads), it becomes an official ELIXIR Community and can begin work on an internal project funded through ELIXIR’s core funds. The most mature Communities are shown in the top right (these were the four ELIXIR-EXCELERATE Use Cases), with the newest Communities shown in the bottom left (Communities portfolio as of December 2023)."

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 18/01/2026

new paper: "Quantitative Adverse Outcome Pathway Modeling of Cisplatin-Induced Nephrotoxicity: Developing In Vitro and In Vivo Models for Predictive Extrapolation" doi.org/10.1093/toxsci/kfaf177 "Here, we focus on the development of ordinary differential equation (ODE)-based qAOPs for […]

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 18/01/2026

new paper: 'Beyond Single Variants: A Pathway-Based Approach to Explore the Genetic Basis of Memory" doi.org/10.1007/s12035-025-05582-1 "We present three independent genome-wide association studies within the Human Connectome Project on a (i) Penn-Word […] [Original post on social.edu.nl]

Figure 1: Manhattan plots for each of the performed GWASs. Orange dots highlight the SNPs with p-value < 1E−5.

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 15/01/2026

new paper: "Single-cell transcriptomics of acetaminophen-induced responses in human 2D and 3D liver microtissues" doi.org/10.1007/s00204-025-04296-6 "Here, we applied single cell RNA sequencing to characterize cellular responses to acetaminophen […] [Original post on social.edu.nl]

Figure 1: Baseline transcriptional and pathway-level differences between 2 and 3D liver cell cultures identified by scRNA-seq.

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ELIXIR-Netherlands @elixir-nl.bsky.social · 17/12/2025

Last month, ELIXIR-Netherlands joined the ELIXIR-Europe BioHackathon, collaborating with hundreds of researchers, developers and infrastructure experts from across Europe. Read the full overview, project highlights and participant reflections on our website: www.health-ri.nl/en/news/elix...

health-ri.nl

ELIXIR BioHackathon 2025 | Health-RI

The ELIXIR BioHackathon brings together experts from across Europe to develop practical solutions for data driven life sciences. This year the event took place from 3 to 7 November in Berlin and gathe...

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 01/12/2025

🚀 BioSB course "Knowledge Graphs in the Life Sciences” 🚀 Don't miss this exciting opportunity for Life Sciences researchers and data enthusiasts. In just 9 weeks, BioSB will host this course: www.dtls.nl/courses/knowledge-graph… 📅 January 5–9, 2025 🗺️ […]

social.edu.nl

Original post on social.edu.nl

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 30/11/2025

new paper: "Small extracellular vesicles: connecting early life exposure outcomes to air pollution during pregnancy to early childhood health" doi.org/10.1186/s12940-025-01238-8 "In this review, we explore mechanisms involving sEVs in transplacental […] [Original post on social.edu.nl]

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 30/11/2025

new paper: "Molecular pathways of kidney development and their applications to clinical research" doi.org/10.1016/j.kint.2025.09.032 "Here, we develop and describe fully machine-readable, well annotated pathways to visualize and analyze key events […] [Original post on social.edu.nl]

Figure 3. Subnetworks derived from kidney development pathways, extended with chemical compound information and annotated with the compounds’ usages in humans. a) Subnetwork showing interactions of known nephrotoxic compounds with kidney development pathway proteins. b) Herbicidal compounds interacting with kidney development pathway proteins. c) Chemical compounds binding to or affecting expression of GDNF.

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