Base by Base

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...

️ Episode 194: Bayesian History of Science: Watson and Crick and the Structure of DNA In this episode of PaperCast Base by Base, we explore how Bayesian reasoning can be used to reconstruct the famous discovery of the DNA double helix by James Watson and Francis Crick, following the sequence of structural models proposed in the early 1950s and the evolving evidence that supported or undermined eac...

️Episode 193: SARM1, DNA, and the Death Signal In this episode of PaperCast Base by Base, we explore how the axon-degenerating enzyme SARM1 acts as a double-stranded DNA sensor that triggers NAD+ loss, cell death, and chemotherapy-induced neuropathy, opening up new possibilities for neuroprotective therapies. Study Highlights: The authors show that the immune adaptor SARM1 directly binds double-st...

️Episode 192: At Base-Pair Resolution: Chromatin’s Cis-Regulatory Conversations In this episode of PaperCast Base by Base, we explore how base-pair resolution maps of chromatin contacts reveal a unified, biophysical model of communication between enhancers, promoters, and other cis-regulatory elements in mammalian cells. Study Highlights: Using Micro Capture-C ultra (MCCu), the authors generate mu...