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PODCAST

Base by Base

Base by Base explores advances in genetics and genomics, with a focus on gene-disease associations, variant interpretation, protein structure, and insights from exome and genome sequencing. Each episode breaks down key studies and their clinical relevance—one base at a time. Powered by AI, Base by Base offers a new way to learn on the go. Special thanks to authors who publish under CC BY 4.0, making open-access science faster to share and easier to explore.

science life sciences

All Episodes

00:15:47

134: Single-Cell Maps Link Intestinal Metaplasia to...

Base by Base ·

2025/09/11

️ Episode 134: Single-Cell Maps Link Intestinal Metaplasia to Esophageal Adenocarcinoma Risk In this episode of PaperCast Base by Base, we explore how single-cell RNA sequencing of Barrett’s esophagus (BE), esophageal adenocarcinoma (EAC), and matched normal tissues reveals which cell types carry germline-linked risk and shape progression toward cancer. Study Highlights:The authors profiled epithelial, stromal, endothelial, and immune cells with 10x

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00:24:31

133: Culture-Independent Meta‑Pangenomics Reveals Gut...

Base by Base ·

2025/09/10

️ Episode 133: Culture-Independent Meta‑Pangenomics Reveals Gut Genome Links to Child Growth In this episode of PaperCast Base by Base, we explore how long‑read metagenomics enables recovery of complete metagenome‑assembled genomes directly from fecal samples of Malawian toddlers and applies meta‑pangenomics and microbial GWAS to connect microbial genetics with pediatric linear growth and breastfeeding status. Study Highlights:Long‑read sequencing with

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00:24:31

133: Culture-Independent Meta‑Pangenomics Reveals Gut...

Base by Base ·

2025/09/10

️ Episode 133: Culture-Independent Meta‑Pangenomics Reveals Gut Genome Links to Child Growth In this episode of PaperCast Base by Base, we explore how long‑read metagenomics enables recovery of complete metagenome‑assembled genomes directly from fecal samples of Malawian toddlers and applies meta‑pangenomics and microbial GWAS to connect microbial genetics with pediatric linear growth and breastfeeding status. Study Highlights:Long‑read sequencing with

en-us

00:20:35

132: Tumor transcriptome classifiers predict...

Base by Base ·

2025/09/09

️ Episode 132: Tumor transcriptome classifiers predict treatment sensitivity in advanced prostate cancer In this episode of PaperCast Base by Base, we explore how transcriptome-wide RNA expression classifiers from advanced prostate cancers can inform treatment selection and improve patient outcomes. Study Highlights:Researchers analyzed tumor transcriptome profiles and immunohistochemistry markers from 1,523 patients enrolled in landmark phase 3 trials

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00:17:59

131: pBI143: The Human Gut’s Hidden Heavyweight

Base by Base ·

2025/09/08

️ Episode 131: pBI143: The Human Gut’s Hidden Heavyweight In this episode of PaperCast Base by Base, we explore how a tiny 2.7 kb cryptic plasmid, pBI143, emerges as one of the most numerous genetic elements in industrialized human gut microbiomes, mobilizes across Bacteroidales, persists as monoclonal lineages with vertical transmission, and increases its copy number under stress and in inflammatory bowel disease. Study Highlights:The authors surveyed

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00:20:24

130: Combining Evidence from Human Genetic and...

Base by Base ·

2025/09/07

️ Episode 130: Combining Evidence from Human Genetic and Functional Screens to Identify Pathways Altering Obesity and Fat Distribution In this episode of PaperCast Base by Base, we explore a large-scale study that integrates genetic association testing with functional CRISPR experiments in human adipocytes to uncover mechanisms influencing obesity and body fat distribution. By analyzing data from more than 400,000 individuals in the UK Biobank and

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00:22:11

129: Structural variation and diversification of the...

Base by Base ·

2025/09/06

️ Episode 129: Structural variation and diversification of the NPIP gene family from the human pangenome In this episode of PaperCast Base by Base, we explore how long-read sequencing technologies reveal the structural variation, evolutionary pressures, and expression patterns of the NPIP gene family, one of the most positively selected gene families in humans and African apes. Study Highlights:Using long-read assemblies of 169 human haplotypes,

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00:15:26

128: LINE‑1 Promoters Orchestrate Early Human Brain...

Base by Base ·

2025/09/05

️ Episode 128: LINE‑1 Promoters Orchestrate Early Human Brain Development In this episode of PaperCast Base by Base, we explore how evolutionarily young LINE‑1 retrotransposons are actively expressed in human induced pluripotent stem cells and function as cis‑acting promoters that shape primate‑ and human‑specific transcript isoforms during early neural differentiation. Study Highlights:The authors combine short‑ and long‑read RNA‑seq with CUT&RUN

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00:17:36

127: In silico generation of synthetic cancer genomes...

Base by Base ·

2025/09/04

️ Episode 127: In silico generation of synthetic cancer genomes using generative AI In this episode of PaperCast Base by Base, we explore OncoGAN, a generative AI pipeline designed to produce highly realistic synthetic cancer genomes. The study addresses the challenge of limited access to real cancer genomes due to privacy concerns by creating shareable, simulated datasets that preserve donor confidentiality. Study Highlights:The authors developed

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00:17:36

127: In silico generation of synthetic cancer genomes...

Base by Base ·

2025/09/04

️ Episode 127: In silico generation of synthetic cancer genomes using generative AI In this episode of PaperCast Base by Base, we explore OncoGAN, a generative AI pipeline designed to produce highly realistic synthetic cancer genomes. The study addresses the challenge of limited access to real cancer genomes due to privacy concerns by creating shareable, simulated datasets that preserve donor confidentiality. Study Highlights:The authors developed

en-us

00:20:59

126: Molecular and developmental deficits in...

Base by Base ·

2025/09/03

️ Episode 126: Molecular and developmental deficits in Smith-Magenis syndrome human stem cell-derived cortical neural models In this episode of PaperCast Base by Base, we explore a study that investigates the molecular and developmental mechanisms underlying Smith-Magenis syndrome (SMS) using human induced pluripotent stem cell (hiPSC)-derived cortical models. The research focuses on how the deletion at chromosome 17p11.2 disrupts cortical development

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00:20:59

126: Molecular and developmental deficits in...

Base by Base ·

2025/09/03

️ Episode 126: Molecular and developmental deficits in Smith-Magenis syndrome human stem cell-derived cortical neural models In this episode of PaperCast Base by Base, we explore a study that investigates the molecular and developmental mechanisms underlying Smith-Magenis syndrome (SMS) using human induced pluripotent stem cell (hiPSC)-derived cortical models. The research focuses on how the deletion at chromosome 17p11.2 disrupts cortical development

en-us

00:22:46

125: Tackling a disease on a global scale, the Global...

Base by Base ·

2025/09/02

️ Episode 125: Tackling a disease on a global scale, the Global Parkinson’s Genetics Program, GP2: A new generation of opportunities In this episode of PaperCast Base by Base, we explore how the Global Parkinson’s Genetics Program (GP2) is addressing the critical lack of diversity in Parkinson’s disease genetics research. The article outlines the program’s mission to establish a global hub for recruitment, data generation, and collaborative discovery,

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00:23:47

124: Exploring the Omnigenic Architecture of Selected...

Base by Base ·

2025/09/01

️ Episode 124: Exploring the Omnigenic Architecture of Selected Complex Traits In this episode of PaperCast Base by Base, we explore how researchers are uncovering the organizational principles behind complex traits through the lens of the omnigenic model. The study focuses on ulcerative colitis as a case example and investigates how core and peripheral genes interact within multi-modal molecular networks to shape disease risk and regulation. Study

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00:23:47

124: Exploring the Omnigenic Architecture of Selected...

Base by Base ·

2025/09/01

️ Episode 124: Exploring the Omnigenic Architecture of Selected Complex Traits In this episode of PaperCast Base by Base, we explore how researchers are uncovering the organizational principles behind complex traits through the lens of the omnigenic model. The study focuses on ulcerative colitis as a case example and investigates how core and peripheral genes interact within multi-modal molecular networks to shape disease risk and regulation. Study

en-us

00:18:12

123: Dominant‑Negative ATP5F1A Variants Uncouple...

Base by Base ·

2025/08/31

️ Episode 123: Dominant‑Negative ATP5F1A Variants Uncouple Complex V and Drive Neurological Disease In this episode of PaperCast Base by Base, we explore how de novo heterozygous ATP5F1A missense variants disrupt mitochondrial ATP synthase and manifest as pediatric neurological disorders, revealing a dominant‑negative mechanism and an isolated Complex V defect. Study Highlights:The authors describe six probands with developmental delay, dystonia,

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00:19:57

122: Patient Stratification Reveals the Molecular...

Base by Base ·

2025/08/30

️ Episode 122: Patient Stratification Reveals the Molecular Basis of Disease Co-Occurrences In this episode of PaperCast Base by Base, we explore a study that investigates the molecular underpinnings of why certain diseases tend to co-occur. By using large-scale RNA sequencing data, the authors present a novel approach to identify disease co-occurrences, revealing a shared molecular basis in many comorbidities, particularly involving the immune system

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00:19:57

122: Patient Stratification Reveals the Molecular...

Base by Base ·

2025/08/30

️ Episode 122: Patient Stratification Reveals the Molecular Basis of Disease Co-Occurrences In this episode of PaperCast Base by Base, we explore a study that investigates the molecular underpinnings of why certain diseases tend to co-occur. By using large-scale RNA sequencing data, the authors present a novel approach to identify disease co-occurrences, revealing a shared molecular basis in many comorbidities, particularly involving the immune system

en-us

00:19:02

121: G-quadruplexes as a Source of Vulnerability in...

Base by Base ·

2025/08/29

️ Episode 121: G-quadruplexes as a Source of Vulnerability in BRCA2-deficient Granule Cell Progenitors and Medulloblastoma In this episode of PaperCast Base by Base, we explore how DNA secondary structures called G-quadruplexes (G4s) contribute to genome instability and tumor development in BRCA2-deficient cerebellar granule cell progenitors, leading to medulloblastoma. Study Highlights:Using a mouse model with Brca2 deletion in the nervous system and

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00:22:30

120: Rare BMAL1 Variants Link the Circadian Clock to...

Base by Base ·

2025/08/28

️Episode 120: Rare BMAL1 Variants Link the Circadian Clock to Neurodevelopment In this episode of PaperCast Base by Base, we explore how ultrarare heterozygous variants in BMAL1—a core circadian clock gene—are associated with a neurodevelopmental syndrome featuring developmental delay, autism spectrum disorder, and musculoskeletal findings. Study Highlights:The authors identified ten individuals carrying very rare BMAL1 variants, five of which were de

en-us

456 results

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