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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

00:17:17

206: Wild Birds and the North American H5N1 Epizootic

Base by Base ·

2025/11/22

️ Episode 206: Wild Birds and the North American H5N1 Epizootic In this episode of PaperCast Base by Base, we explore how wild migratory birds have shaped the ecology and spread of the 2021–2023 highly pathogenic H5N1 epizootic across North America, and what this means for wildlife conservation and poultry health. Study Highlights:Using 1,818 haemagglutinin gene sequences from wild birds, domestic birds, and mammals collected across North America, the

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00:17:17

206: Wild Birds and the North American H5N1 Epizootic

Base by Base ·

2025/11/22

️ Episode 206: Wild Birds and the North American H5N1 Epizootic In this episode of PaperCast Base by Base, we explore how wild migratory birds have shaped the ecology and spread of the 2021–2023 highly pathogenic H5N1 epizootic across North America, and what this means for wildlife conservation and poultry health. Study Highlights:Using 1,818 haemagglutinin gene sequences from wild birds, domestic birds, and mammals collected across North America, the

en-us

00:17:19

205: Ancient RNA Expression Profiles from the Woolly...

Base by Base ·

2025/11/21

️ Episode 205: Ancient RNA Expression Profiles from the Woolly Mammoth In this episode of PaperCast Base by Base, we explore how ancient RNA preserved in permafrost can reveal tissue-specific gene expression and regulatory dynamics in the extinct woolly mammoth. Study Highlights:Researchers analyzed skeletal muscle and skin from ten Late Pleistocene woolly mammoths preserved in Siberian permafrost, extracting both ancient DNA and RNA to assess the

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00:17:19

205: Ancient RNA Expression Profiles from the Woolly...

Base by Base ·

2025/11/21

️ Episode 205: Ancient RNA Expression Profiles from the Woolly Mammoth In this episode of PaperCast Base by Base, we explore how ancient RNA preserved in permafrost can reveal tissue-specific gene expression and regulatory dynamics in the extinct woolly mammoth. Study Highlights:Researchers analyzed skeletal muscle and skin from ten Late Pleistocene woolly mammoths preserved in Siberian permafrost, extracting both ancient DNA and RNA to assess the

en-us

00:16:39

204: StealTHY CRISPR: Revealing Hidden Metastasis...

Base by Base ·

2025/11/20

️ Episode 204: StealTHY CRISPR: Revealing Hidden Metastasis Regulators In this episode of PaperCast Base by Base, we explore how the StealTHY CRISPR platform sidesteps Cas9 immunogenicity to uncover metastasis drivers in immunocompetent and humanized cancer models. Study Highlights:Researchers show that standard CRISPR-Cas9 tools and xenogeneic reporters provoke strong T cell responses in syngeneic and humanized mice, reshaping clonal architecture and

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00:16:39

204: StealTHY CRISPR: Revealing Hidden Metastasis...

Base by Base ·

2025/11/20

️ Episode 204: StealTHY CRISPR: Revealing Hidden Metastasis Regulators In this episode of PaperCast Base by Base, we explore how the StealTHY CRISPR platform sidesteps Cas9 immunogenicity to uncover metastasis drivers in immunocompetent and humanized cancer models. Study Highlights:Researchers show that standard CRISPR-Cas9 tools and xenogeneic reporters provoke strong T cell responses in syngeneic and humanized mice, reshaping clonal architecture and

en-us

00:18:08

203: Divergent Evolutionary Dynamics of Benign and...

Base by Base ·

2025/11/19

️ Episode 203: Divergent Evolutionary Dynamics of Benign and Malignant Tumors In this episode of PaperCast Base by Base, we explore how benign and malignant tumors follow different evolutionary trajectories across birds and mammals, and what this reveals about cancer defenses across the tree of life. Study Highlights:The authors combine necropsy data on tumor prevalence from hundreds of bird and mammal species with Bayesian multivariate phylogenetic

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00:18:08

203: Divergent Evolutionary Dynamics of Benign and...

Base by Base ·

2025/11/19

️ Episode 203: Divergent Evolutionary Dynamics of Benign and Malignant Tumors In this episode of PaperCast Base by Base, we explore how benign and malignant tumors follow different evolutionary trajectories across birds and mammals, and what this reveals about cancer defenses across the tree of life. Study Highlights:The authors combine necropsy data on tumor prevalence from hundreds of bird and mammal species with Bayesian multivariate phylogenetic

en-us

00:17:08

202: Stereo-seq V2: Spatial Total RNA Mapping in FFPE...

Base by Base ·

2025/11/19

️ Episode 202: Stereo-seq V2: Spatial Total RNA Mapping in FFPE Tissues In this episode of PaperCast Base by Base, we explore how Stereo-seq V2 delivers high-resolution spatial mapping of total RNA in FFPE samples, from mouse brain to breast cancer and tuberculosis lung tissue. Study Highlights:The authors introduce Stereo-seq V2, a random-priming spatial transcriptomics platform that captures total RNA in situ on FFPE sections at single-cell

en-us

00:17:08

202: Stereo-seq V2: Spatial Total RNA Mapping in FFPE...

Base by Base ·

2025/11/19

️ Episode 202: Stereo-seq V2: Spatial Total RNA Mapping in FFPE Tissues In this episode of PaperCast Base by Base, we explore how Stereo-seq V2 delivers high-resolution spatial mapping of total RNA in FFPE samples, from mouse brain to breast cancer and tuberculosis lung tissue. Study Highlights:The authors introduce Stereo-seq V2, a random-priming spatial transcriptomics platform that captures total RNA in situ on FFPE sections at single-cell

en-us

00:14:52

201: Sex, Smoking, and Somatic Selection in the Bladder

Base by Base ·

2025/11/17

️ Episode 201: Sex, Smoking, and Somatic Selection in the Bladder In this episode of PaperCast Base by Base, we explore how ultradeep duplex DNA sequencing of normal human bladder tissue reveals sex- and smoking-related biases in the selection of somatic mutations and cancer driver clones. Study Highlights:Researchers applied ultradeep duplex DNA sequencing at around 5,000× coverage to 79 normal bladder urothelium samples from 45 deceased donors,

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00:18:48

200: Sperm Sequencing Reveals Extensive Positive...

Base by Base ·

2025/11/16

️ Episode 200: Sperm Sequencing Reveals Extensive Positive Selection in the Male Germline In this episode of PaperCast Base by Base, we explore how ultra-accurate duplex sequencing of human sperm reveals widespread positive selection in the male germline and its consequences for mutation burden and disease risk in offspring. Study Highlights:This Nature study uses NanoSeq duplex whole-genome and exome sequencing on sperm and matched blood samples from

en-us

00:18:48

200: Sperm Sequencing Reveals Extensive Positive...

Base by Base ·

2025/11/16

️ Episode 200: Sperm Sequencing Reveals Extensive Positive Selection in the Male Germline In this episode of PaperCast Base by Base, we explore how ultra-accurate duplex sequencing of human sperm reveals widespread positive selection in the male germline and its consequences for mutation burden and disease risk in offspring. Study Highlights:This Nature study uses NanoSeq duplex whole-genome and exome sequencing on sperm and matched blood samples from

en-us

00:13:57

199: PLD4 Deficiency and Lupus: When Nuclease Failure...

Base by Base ·

2025/11/15

️ Episode 199: PLD4 Deficiency and Lupus: When Nuclease Failure Ignites Autoimmunity In this episode of PaperCast Base by Base, we explore how loss-of-function mutations in the endolysosomal exonuclease PLD4 cause a monogenic form of systemic lupus erythematosus, reshaping our understanding of nucleic acid sensing and interferon-driven autoimmunity. Study Highlights:This study identifies biallelic loss-of-function PLD4 mutations in five patients with

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00:15:47

198: Mechanical Confinement and the Shape-Shifting...

Base by Base ·

2025/11/14

️ Episode 198: Mechanical Confinement and the Shape-Shifting Life of Melanoma Cells In this episode of PaperCast Base by Base, we explore how physical forces in the tumor microenvironment can push melanoma cells to switch from a pigment-producing, proliferative state into an invasive, drug-tolerant one, focusing on new work that links mechanical confinement, chromatin remodeling, and neuronal-like programs in cancer. Study Highlights:Using a zebrafish

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00:15:11

197: Somatic Mutation and Selection at Population Scale

Base by Base ·

2025/11/13

️ Episode 197: Somatic Mutation and Selection at Population Scale In this episode of PaperCast Base by Base, we explore how ultra-accurate NanoSeq duplex sequencing reveals the hidden landscape of somatic mutations and clonal selection across blood and oral epithelium in over a thousand adults. Study Highlights:This study introduces improved whole-genome and targeted versions of NanoSeq, a duplex sequencing method with error rates below five mutations

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00:16:37

196: Impact of Chromatin Accessibility QTLs Across...

Base by Base ·

2025/11/12

️ Episode 196: Impact of Chromatin Accessibility QTLs Across Immune Contexts In this episode of PaperCast Base by Base, we explore how single-cell chromatin accessibility QTLs (caQTLs) reshape the interpretation of immune disease genetics by mapping regulatory variation across major immune cell types and disease-relevant states. Study Highlights:The authors harmonized ∼280,000 PBMC scATAC-seq profiles from 48 individuals—including healthy donors and

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00:18:22

195: Tiny Shields: Lymphoid Microglia in Alzheimer’s...

Base by Base ·

2025/11/11

️ Episode 195: Tiny Shields: Lymphoid Microglia in Alzheimer’s Disease In this episode of PaperCast Base by Base, we explore how a subset of brain immune cells adopts a lymphoid-like program that helps contain inflammation and protect neural circuits in Alzheimer’s disease models. Study Highlights: Using mouse models of amyloid pathology and human Alzheimer’s brain tissue, the authors identify plaque-associated microglia with reduced PU.1 expression

en-us

00:14:29

194: Bayesian History of Science: Watson and Crick...

Base by Base ·

2025/11/10

️ 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 each hypothesis. Study Highlights:The author applies a naïve

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00:15:00

193: SARM1, DNA, and the Death Signal

Base by Base ·

2025/11/09

️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-stranded DNA via its TIR domain and, once activated, rapidly

en-us

424 results

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