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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

00:18:41

224: AntennAlive — wireless in-body sensing with...

Base by Base ·

2025/12/10

️ Episode 224: AntennAlive — wireless in-body sensing with engineered bacteria In this episode of PaperCast Base by Base, we explore A bio-hybrid, battery-free implant converts engineered bacterial activity into microwave backscatter signals by controlled degradation of a biodegradable antenna Study Highlights:The AntennAlive system uses a magnesium split-ring passive implant antenna coupled with genetically engineered Escherichia coli that accelerate

en-us

00:18:41

224: AntennAlive — wireless in-body sensing with...

Base by Base ·

2025/12/10

️ Episode 224: AntennAlive — wireless in-body sensing with engineered bacteria In this episode of PaperCast Base by Base, we explore A bio-hybrid, battery-free implant converts engineered bacterial activity into microwave backscatter signals by controlled degradation of a biodegradable antenna Study Highlights:The AntennAlive system uses a magnesium split-ring passive implant antenna coupled with genetically engineered Escherichia coli that accelerate

en-us

00:16:26

223: Torsion Regulates DNA Replication Stalling and...

Base by Base ·

2025/12/09

️ Episode 223: Torsion Regulates DNA Replication Stalling and Restart In this episode of PaperCast Base by Base, we explore New single-molecule angular optical trap assays reveal that DNA torsion directly controls T7 replisome stalling and reactivation Study Highlights:A high-resolution, label-free angular optical trap (AOT) assay was developed to track T7 replisome-driven DNA rotation and torsional slowing in real time. The combined helicase–DNA

en-us

00:16:26

223: Torsion Regulates DNA Replication Stalling and...

Base by Base ·

2025/12/09

️ Episode 223: Torsion Regulates DNA Replication Stalling and Restart In this episode of PaperCast Base by Base, we explore New single-molecule angular optical trap assays reveal that DNA torsion directly controls T7 replisome stalling and reactivation Study Highlights:A high-resolution, label-free angular optical trap (AOT) assay was developed to track T7 replisome-driven DNA rotation and torsional slowing in real time. The combined helicase–DNA

en-us

00:17:57

222: snaR-A hijacks splicing to drive proliferation

Base by Base ·

2025/12/08

️ Episode 222: snaR-A hijacks splicing to drive proliferation In this episode of PaperCast Base by Base, we explore This episode examines how the cancer-associated Pol III transcript snaR-A binds core splicing factors, localizes near nuclear speckles, perturbs U2-dependent splicing to increase intron retention, and promotes cell proliferation linked to poorer patient outcomes Study Highlights:Proteomic pull-downs and CLIP analyses reveal snaR-A

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00:20:23

221: Allele-resolved nanopore tour of the human...

Base by Base ·

2025/12/07

️ Episode 221: Allele-resolved nanopore tour of the human placental methylome In this episode of PaperCast Base by Base, we explore Using phased long-read nanopore and short-read sequencing across eight trios, the study maps allele-specific DNA methylation and transcription in female human placentas, identifies hundreds of DMRs and novel imprinted genes, and reports somatic placental variants Study Highlights:The authors combined >20x Oxford Nanopore

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00:15:48

220: The AML cellular state space reveals NPM1 immune...

Base by Base ·

2025/12/06

️Episode 220: The AML cellular state space reveals NPM1 immune evasion subtypes In this episode of PaperCast Base by Base, we explore Single-cell and bulk sequencing of 120 AML cases reveal two NPM1-mutated subtypes with distinct immune evasion mechanisms and divergent responses to hematopoietic stem cell transplantation Study Highlights:Bulk RNA-seq profiles are strongly confounded by variable mature cell-type signatures that can conceal subtype-specific

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00:15:48

220: The AML cellular state space reveals NPM1 immune...

Base by Base ·

2025/12/06

️Episode 220: The AML cellular state space reveals NPM1 immune evasion subtypes In this episode of PaperCast Base by Base, we explore Single-cell and bulk sequencing of 120 AML cases reveal two NPM1-mutated subtypes with distinct immune evasion mechanisms and divergent responses to hematopoietic stem cell transplantation Study Highlights:Bulk RNA-seq profiles are strongly confounded by variable mature cell-type signatures that can conceal subtype-specific

en-us

00:16:41

219: Multi-omic mapping of lipid dysregulation in...

Base by Base ·

2025/12/05

️Episode 219: Multi-omic mapping of lipid dysregulation in Parkinson’s brain In this episode of PaperCast Base by Base, we explore 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 Study Highlights: The study quantified 146 lipid species across eight anatomically distinct post-mortem brain regions in controls and mid-

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00:19:37

218: SIM1 and the multi-ancestry genomics of erectile...

Base by Base ·

2025/12/04

️Episode 218: SIM1 and the multi-ancestry genomics of erectile dysfunction In this episode of PaperCast Base by Base, we explore 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 Study Highlights: Meta-analysis of 913,194 European and 125,315 African ancestry individuals

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00:19:37

218: SIM1 and the multi-ancestry genomics of erectile...

Base by Base ·

2025/12/04

️Episode 218: SIM1 and the multi-ancestry genomics of erectile dysfunction In this episode of PaperCast Base by Base, we explore 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 Study Highlights: Meta-analysis of 913,194 European and 125,315 African ancestry individuals

en-us

00:17:47

217: Multiscale triads of meiotic crossover patterning

Base by Base ·

2025/12/03

️Episode 217: Multiscale triads of meiotic crossover patterning In this episode of PaperCast Base by Base, we explore 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 Study Highlights: Quantitative fluorescence profiles and Fourier analysis identify two

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00:17:47

217: Multiscale triads of meiotic crossover patterning

Base by Base ·

2025/12/03

️Episode 217: Multiscale triads of meiotic crossover patterning In this episode of PaperCast Base by Base, we explore 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 Study Highlights: Quantitative fluorescence profiles and Fourier analysis identify two

en-us

00:18:27

216: 53BP1-RIF1 and DNA-PKcs: distinct interactions...

Base by Base ·

2025/12/02

️ Episode 216: 53BP1-RIF1 and DNA-PKcs: distinct interactions in chromosomal break repair In this episode of PaperCast Base by Base, we explore 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 Study Highlights:Using EJ7-GFP and MA-del reporters in HEK293 cells, loss of 53BP1 alone did not reduce blunt No Indel EJ but amplified the

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00:20:07

215: Protein Set Transformer for high-diversity viromics

Base by Base ·

2025/12/01

️ Episode 215: Protein Set Transformer for high-diversity viromics In this episode of PaperCast Base by Base, we explore 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 Study Highlights:PST embeds proteins with ESM2, concatenates positional and strand vectors, contextualizes proteins with a multi-head attention

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00:18:21

214: PI(4,5)P2 Asymmetry Enables Rapid FGF2 Secretion

Base by Base ·

2025/11/30

️ Episode 214: PI(4,5)P2 Asymmetry Enables Rapid FGF2 Secretion In this episode of PaperCast Base by Base, we explore This study shows that an asymmetric transbilayer distribution of PI(4,5)P2 lowers the energy barrier for lipidic pore formation and accelerates unconventional secretion of Fibroblast Growth Factor 2 Study Highlights:The authors generated asymmetric LUVs and GUVs by enzymatically converting outer-leaflet PI(4)P to PI(4,5)P2 using PIP5K1C

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00:20:29

213: BRAIN-MAGNET: a functional atlas for non-coding...

Base by Base ·

2025/11/29

️ Episode 213: BRAIN-MAGNET: a functional atlas for non-coding variants In this episode of PaperCast Base by Base, we explore 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 Study Highlights:The authors generated an activity-ranked functional genomics atlas of 148,198 non-coding regulatory

en-us

00:20:29

213: BRAIN-MAGNET: a functional atlas for non-coding...

Base by Base ·

2025/11/29

️ Episode 213: BRAIN-MAGNET: a functional atlas for non-coding variants In this episode of PaperCast Base by Base, we explore 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 Study Highlights:The authors generated an activity-ranked functional genomics atlas of 148,198 non-coding regulatory

en-us

00:16:47

212: Zonal control of mutant β-catenin tumorigenesis

Base by Base ·

2025/11/28

️ Episode 212: Zonal control of mutant β-catenin tumorigenesis 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 Study Highlights:β-catenin exon 3 mutations cooperate with exogenous MYC to produce a proliferative translatome that supports tumour outgrowth. Differentiation to

en-us

00:16:47

212: Zonal control of mutant β-catenin tumorigenesis

Base by Base ·

2025/11/28

️ Episode 212: Zonal control of mutant β-catenin tumorigenesis 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 Study Highlights:β-catenin exon 3 mutations cooperate with exogenous MYC to produce a proliferative translatome that supports tumour outgrowth. Differentiation to

en-us

452 results

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