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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...

️ Episode 191: CATphishing: Synthetic Learning as an Alternative to Federated Learning in MRI In this episode of PaperCast Base by Base, we explore a Nature Communications study that proposes CATphishing—an approach that uses latent diffusion models to generate site-specific synthetic 3D brain MRIs for collaborative training without sharing raw data. The work spans seven institutions and 2,491 pat...

Martínez‑López JA et al et al., Nature Communications - This episode examines a Nature Communications study that introduces differential Gene Coordination Network Analysis (dGCNA) applied to deep Smart-seq2 single-cell RNA-seq of human pancreatic islets from 16 T2D and 16 non‑T2D donors. The method uncovers cell type‑specific networks altered in T2D, validates mechanistic roles for CEBPG and TMEM1...

️ Episode 189: DNA methylation patterns facilitate tracing the origin of neuroendocrine neoplasms In this episode of PaperCast Base by Base, we explore how genome-wide DNA methylation profiling can pinpoint the organ of origin for neuroendocrine neoplasms (NEN), with a special focus on lesions detected in the liver and long-debated “primary hepatic NEN”. Study Highlights: Using two independent coh...