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Hällqvist J et al., Nature Communications - Targeted multi-region lipidomics with proteomic and mitochondrial data reveals region- and stage-specific lipid alterations in Parkinson’s disease that converge on mitochondrial dysfunction. Key terms: lipids, parkinsons disease, putamen, ceramide, plasmalogens. Study Highlights: The study quantified 146 lipid species across eight anatomically distinct p...

Bright U et al., Nat Commun - A large multi-ancestry GWAS meta-analysis identifies a dominant SIM1-linked locus and multiple genetic connections between electronic health record-defined erectile dysfunction and cardiometabolic, psychiatric, and substance-use traits. Key terms: erectile dysfunction, GWAS, SIM1, obesity, polygenic risk. Study Highlights: Meta-analysis of 913,194 European and 125,315...

White MA et al., Nature Communications - FFT and inverse-FFT analysis of Zip3/Zip2, Hop1 and Zip1 on yeast pachytene chromosomes reveals two interdigitated tiers of evenly spaced protein triads that correspond to canonical and minority crossovers and are differentially regulated by Pch2/TRIP13. Key terms: crossover interference, meiotic chromosomes, Zip3/Zip2, Hop1, Pch2. Study Highlights: Quantit...

Makins K et al., Nature Communications - This episode reviews a study showing that 53BP1-RIF1 and DNA-PKcs have different genetic relationships across blunt end joining, deletion patterns, HDR, and radiosensitivity. Key terms: 53BP1, DNA-PKcs, RIF1, non-homologous end joining, microhomology. Study Highlights: Using EJ7-GFP and MA-del reporters in HEK293 cells, loss of 53BP1 alone did not reduce bl...

Martin et al., Nat Commun (2025) - Protein Set Transformer (PST) is a protein-based genome language model that represents genomes as sets of proteins to improve genome and protein representations across diverse viral datasets. Key terms: viromics, protein-language-model, genome-embeddings, triplet-loss, host-prediction. Study Highlights: PST embeds proteins with ESM2, concatenates positional and s...

Kaur M et al., Nature Communications - Reconstitution of asymmetric membranes and matched cell experiments show that transbilayer asymmetry of PI(4,5)P2 lowers the energetic barrier for FGF2-driven lipidic pore formation and enables rapid unconventional secretion. Disrupting PI(4,5)P2 asymmetry in cells blocks FGF2 export. Key terms: FGF2, PI(4,5)P2, membrane asymmetry, unconventional secretion, l...

Deng R et al. - BRAIN-MAGNET couples a ChIP-STARR-seq atlas of 148,198 neural regulatory elements with a validated convolutional neural network to predict enhancer activity and prioritize disease-relevant non-coding variants. Key terms: enhancers, neural stem cells, convolutional neural network, non-coding variants, functional genomics. Study Highlights: The authors generated an activity-ranked fu...

Raven A et al. - This study shows that hepatic zonation determines whether mutant β-catenin drives proliferation and liver cancer by forcing differentiation to a non-permissive zone 3 fate or, when reversed, enabling MAPK- and mTOR-dependent growth. Key terms: hepatic zonation, beta-catenin, MYC, mTOR, IGFBP2. Study Highlights: β-catenin exon 3 mutations cooperate with exogenous MYC to produce a p...

Sankar et al. - This episode explores the discovery of genetic elements that promote the retention of extrachromosomal DNA (ecDNA) in cancer cells, enhancing their survival and evolution. Key terms: ecDNA, retention elements, cancer cells, genomic elements, oncogenes. Study Highlights: Researchers identified a family of genomic elements known as retention elements that tether ecDNA to mitotic chro...

Tumour-Reactive CD8 T Cell Clusters in Human Melanoma Music: Enjoy the music based on this article at the end of the episode. DOI: 10.1038/s41586-025-09754-w License: This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support: Base by Base – Stripe donations: https://d...

PERT: Prime Editing tRNAs for Nonsense Mutations Music: Enjoy the music based on this article at the end of the episode. DOI: 10.1038/s41586-025-09732-2 License: This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support: Base by Base – Stripe donations: https://donate...

ZAK, Collided Ribosomes, and the Stress Switch Music: Enjoy the music based on this article at the end of the episode. DOI: 10.1038/s41586-025-09772-8 License: This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support: Base by Base – Stripe donations: https://donate.s...

Semantic Design of de novo Genes with Evo Music: Enjoy the music based on this article at the end of the episode. DOI: 10.1038/s41586-025-09749-7 License: This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support: Base by Base – Stripe donations: https://donate.stripe...

Wild Birds and the North American H5N1 Epizootic Music: Enjoy the music based on this article at the end of the episode. License: This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support: Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gE...

Ancient RNA Expression Profiles from the Woolly Mammoth Music: Enjoy the music based on this article at the end of the episode. License: This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support: Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3...

StealTHY CRISPR: Revealing Hidden Metastasis Regulators Music: Enjoy the music based on this article at the end of the episode. License: CC BY 4.0 International License (CC BY 4.0) Support: Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics,...

Divergent Evolutionary Dynamics of Benign and Malignant Tumors Music: Enjoy the music based on this article at the end of the episode. License: This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support: Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz...

Stereo-seq V2: Spatial Total RNA Mapping in FFPE Tissues Music: Enjoy the music based on this article at the end of the episode. License: CC BY 4.0 International License (CC BY 4.0) Support: Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics,...

Music: Enjoy the music based on this article at the end of the episode. DOI: 10.1038/s41586-025-09521-x License: This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support: Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official webs...

Music: Enjoy the music based on this article at the end of the episode. DOI: 10.1038/s41586-025-09448-3 License: This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support: Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official webs...

PLD4 Deficiency and Lupus: When Nuclease Failure Ignites Autoimmunity Music: Enjoy the music based on this article at the end of the episode. License: This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support: Base by Base – Stripe donations: https://donate.stripe.com...

Mechanical Confinement and the Shape-Shifting Life of Melanoma Cells Music: Enjoy the music based on this article at the end of the episode. License: This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support: Base by Base – Stripe donations: https://donate.stripe.com/...

Somatic Mutation and Selection at Population Scale Music: Enjoy the music based on this article at the end of the episode. License: This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support: Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5...

Impact of Chromatin Accessibility QTLs Across Immune Contexts Music: Enjoy the music based on this article at the end of the episode. License: This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support: Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz7...

Music: Enjoy the music based on this article at the end of the episode. Support: Base by Base is independent and ad-free — no sponsors, no paywall. If an episode was worth your time, chip in and keep the papers audited and the original songs coming: ❤️ Support monthly: https://buy.stripe.com/cNifZhclVebvagk2JDgEg01 ☕ One-time donation: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 More at bas...