Best basebybase.podcast@gmail.com (Gustavo Barra Podcasts (2025)

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167: DeepScence: Detecting Senescent Cells at Single-Cell and Spatial Resolution 21:40

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1d ago21:40

21:40

️ Episode 167: DeepScence: Detecting Senescent Cells at Single-Cell and Spatial Resolution In this episode of PaperCast Base by Base, we explore a Cell Genomics study introducing DeepScence, a deep-learning autoencoder that leverages a compact “CoreScence” gene set to identify senescent cells across single-cell and spatial transcriptomics data, out…

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166: Molecular Squeezing: How Coronin, Cofilin, and AIP1 Rapidly Disassemble Actin Filaments 13:37

3d ago13:37

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️ Episode 166: Molecular Squeezing: How Coronin, Cofilin, and AIP1 Rapidly Disassemble Actin Filaments In this episode of PaperCast Base by Base, we explore a Cell study that uses single-particle cryo-EM to reveal the stepwise, synergistic mechanism by which coronin, cofilin, and AIP1 drive rapid actin filament disassembly in eukaryotic cells. Stud…

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165: Protist Genomics: Key to Understanding Eukaryotic Evolution 19:24

4d ago19:24

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️ Episode 165: Protist Genomics: Key to Understanding Eukaryotic Evolution In this episode of PaperCast Base by Base, we explore how accelerating protist genomics—spanning single-cell approaches, metagenomics, and long-read assemblies—unlocks deep insights into eukaryotic evolution, symbiosis, organelle origins, ecosystem dynamics, and the methodol…

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164: m6A in the coding sequence: linking deposition, translation, and decay 14:46

5d ago14:46

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️ Episode 164: m6A in the coding sequence: linking deposition, translation, and decay In this episode of PaperCast Base by Base, we explore how N6-methyladenosine (m6A) marks within coding sequences orchestrate a fast, translation-coupled route to mRNA decay, and how splicing- and chromatin-linked mechanisms shape where those marks are placed acros…

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163: Animal origins: looping back in time 14:18

6d ago14:18

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️ Episode 163: Animal origins: looping back in time In this episode of PaperCast Base by Base, we explore how chromatin folding mechanisms emerged alongside animal evolution, focusing on a Spotlight article that synthesizes high-resolution 3D genome maps across unicellular relatives of animals and early-branching metazoans to probe when enhancer–pr…

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162: Spatially Resolved microRNA Expression in Tissues: Technologies, Challenges, and Opportunities 20:15

7d ago20:15

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️ Episode 162: Spatially Resolved microRNA Expression in Tissues: Technologies, Challenges, and Opportunities In this episode of PaperCast Base by Base, we explore how emerging “spatial miRNomics” methods map microRNA expression directly within intact tissues, revealing cell- and region-specific regulatory patterns that bulk and even single-cell as…

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161: Decoding Genomic Landscapes of Introgression 20:55

8d ago20:55

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️ Episode 161: Decoding Genomic Landscapes of Introgression In this episode of PaperCast Base by Base, we explore how modern population genetics dissects the genomic footprints of introgression across species, reviewing summary statistic approaches, probabilistic modeling, and supervised learning, and showing how these methods reveal adaptive and g…

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160: The Long‑Read Leap in Single‑Cell Omics 15:36

9d ago15:36

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By Gustavo Barra

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159: The Untapped Potential of Short‑Read Sequencing in Biodiversity Research 15:56

10d ago15:56

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️ Episode 159: The Untapped Potential of Short‑Read Sequencing in Biodiversity Research In this episode of PaperCast Base by Base, we explore how modern short‑read sequencing and genome skimming are reshaping biodiversity science—from rapid species identification and biomass estimation to scalable phylogenomics and holobiont studies—while keeping c…

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158: Interruptions in Repeat Expansion Diseases: How Are They Gained and Lost? 22:35

11d ago22:35

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️ Episode 158: Interruptions in Repeat Expansion Diseases: How Are They Gained and Lost? In this episode of PaperCast Base by Base, we explore how small sequence changes—“interruptions”—within expanded tandem repeats shape the onset and severity of repeat expansion disorders, and a new mechanistic model that may explain how these interruptions are …

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157: Synthetic gametes and the non-identity problem: the babies of tomorrow 14:32

12d ago14:32

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️ Episode 157: Synthetic gametes and the non-identity problem: the babies of tomorrow In this episode of PaperCast Base by Base, we explore how synthetic DNA technologies may enable the creation of synthetic gametes and why this possibility forces a rethinking of identity, harm, and responsibility in human reproduction. Study Highlights: The author…

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156: RAEFISH: Sequencing-free whole-genome spatial transcriptomics at single-molecule resolution 17:07

13d ago17:07

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️ Episode 156: RAEFISH: Sequencing-free whole-genome spatial transcriptomics at single-molecule resolution In this episode of PaperCast Base by Base, we explore RAEFISH, a reverse-padlock amplicon-encoding FISH method that delivers whole-transcriptome imaging at single-molecule resolution without sequencing. The study demonstrates genome-scale cove…

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155: EIF3A/EIF3B Loss-of-Function: A Cardiocraniofacial Neurodevelopmental Syndrome 15:53

14d ago15:53

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️ Episode 155: EIF3A/EIF3B Loss-of-Function: A Cardiocraniofacial Neurodevelopmental Syndrome In this episode of PaperCast Base by Base, we explore how loss-of-function variants in EIF3A and EIF3B—core components of the eIF3 translation initiation complex—cause a multisystem disorder marked by congenital heart defects, craniofacial differences, and…

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154: Multiple-testing corrections in selection scans using identity-by-descent segments 20:05

15d ago20:05

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️ Episode 154: Multiple-testing corrections in selection scans using identity-by-descent segments In this episode of PaperCast Base by Base, we explore how Temple and Browning develop principled genome-wide significance thresholds for IBD-based scans of recent positive selection by explicitly modeling correlation along the genome. Study Highlights:…

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153: Skeletal muscle eQTL meta-analysis implicates genes in the genetic architecture of muscular and cardiometabolic traits 15:13

16d ago15:13

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️ Episode 153: Skeletal muscle eQTL meta-analysis implicates genes in the genetic architecture of muscular and cardiometabolic traits In this episode of PaperCast Base by Base, we explore a large skeletal muscle eQTL meta-analysis that integrates GTEx and FUSION data to pinpoint regulatory variants and genes underlying muscular and cardiometabolic …

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152: One-Well Multiplex ddPCR for Hereditary Alpha Tryptasemia 16:53

17d ago16:53

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️ Episode 152: One-Well Multiplex ddPCR for Hereditary Alpha Tryptasemia In this episode of PaperCast Base by Base, we explore a validated single‑well multiplex digital droplet PCR (ddPCR) assay that reconstructs the TPSAB1 locus by quantifying α‑ and β‑tryptase copy numbers to diagnose hereditary alpha tryptasemia (HαT) in symptomatic patients. St…

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151: EQA of ctDNA Mutation Testing Across the COIN Consortium 16:21

18d ago16:21

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️ Episode 151: EQA of ctDNA Mutation Testing Across the COIN Consortium In this episode of PaperCast Base by Base, we explore how 16 Dutch laboratories evaluated their real‑world workflows for circulating tumor DNA (ctDNA) mutation testing across BRAF, EGFR, and KRAS using a coordinated external quality assessment within the COIN consortium. Study …

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150: Patrilineal segmentary systems and the post‑Neolithic Y‑chromosome bottleneck 17:52

19d ago17:52

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️ Episode 150: Patrilineal segmentary systems and the post‑Neolithic Y‑chromosome bottleneck In this episode of PaperCast Base by Base, we explore a Nature Communications study that proposes a peaceful, socio‑cultural explanation for the sharp decline in male effective population size observed 3,000–5,000 years ago. Instead of widespread violence, …

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149: Cultural Hitchhiking and the Post‑Neolithic Y‑Chromosome Bottleneck 15:04

20d ago15:04

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️ Episode 149: Cultural Hitchhiking and the Post‑Neolithic Y‑Chromosome Bottleneck In this episode of PaperCast Base by Base, we explore how patrilineal social structures and intergroup competition can reshape genetic diversity, offering a cultural explanation for the striking male‑specific bottleneck observed 5,000–7,000 years ago across the Old W…

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148: Systematic Minigene-Based Splicing Analysis and Tentative Clinical Classification of 52 CHEK2 Splice-Site Variants 14:44

21d ago14:44

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️ Episode 148: Systematic Minigene-Based Splicing Analysis and Tentative Clinical Classification of 52 CHEK2 Splice-Site Variants In this episode of PaperCast Base by Base, we explore a comprehensive functional assessment of splice-site variants in CHEK2 using reporter minigenes, revealing how disrupted pre-mRNA splicing contributes to hereditary b…

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147: Comprehensive Annotation of Complete ABO Alleles and Resolution of ABO Variants 15:37

22d ago15:37

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️ Episode 147: Comprehensive Annotation of Complete ABO Alleles and Resolution of ABO Variants In this episode of PaperCast Base by Base, we explore a groundbreaking study that introduces an improved long-read sequencing method to fully resolve ABO haplotypes, spanning from the 5′ to the 3′ untranslated regions. This work addresses a major gap in b…

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146: Automated and Decentralized Genomic Profiling of Plasma Cell-Free DNA in Solid Tumors 15:56

23d ago15:56

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️ Episode 146: Automated and Decentralized Genomic Profiling of Plasma Cell-Free DNA in Solid Tumors In this episode of PaperCast Base by Base, we explore the clinical feasibility of an automated and decentralized cfDNA sequencing system designed to identify actionable and resistance alterations in advanced solid tumors. Study Highlights: Researche…

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145: A Validated Highly Sensitive Microsatellite Instability Assay Identifies PMS2 Variants in CMMRD 16:59

24d ago16:59

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️ Episode 145: A Validated Highly Sensitive Microsatellite Instability Assay Identifies PMS2 Variants in CMMRD In this episode of PaperCast Base by Base, we explore a study that validates a next-generation sequencing-based highly sensitive microsatellite instability (hs-MSI) assay for the diagnosis of constitutional mismatch repair deficiency (CMMR…

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144: Revised time estimation of the ancestral human chromosome 2 fusion 17:10

25d ago17:10

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️ Episode 144: Revised time estimation of the ancestral human chromosome 2 fusion In this episode of PaperCast Base by Base, we explore a study that revisits one of the most defining events in human evolution: the fusion that gave rise to chromosome 2. This work refines previous estimates and provides a clearer timeline for when this pivotal genomi…

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143: The genetic history of the Southern Caucasus: 5,000 years of continuity despite high mobility 18:56

26d ago18:56

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️ Episode 143: The genetic history of the Southern Caucasus: 5,000 years of continuity despite high mobility In this episode of PaperCast Base by Base, we explore a comprehensive archaeogenomic study tracing 230 ancient individuals from Georgia and Armenia over 5,000 years, from the Bronze Age to the Early Middle Ages. The research investigates how…

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142: Specifications of the ACMG/AMP Guidelines for PALB2 Variant Interpretation 16:35

27d ago16:35

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️ Episode 142: Specifications of the ACMG/AMP Guidelines for PALB2 Variant Interpretation In this episode of PaperCast Base by Base, we explore how the Hereditary Breast, Ovarian, and Pancreatic Cancer Variant Curation Expert Panel (HBOP VCEP) developed gene-specific ACMG/AMP guidelines for the interpretation of PALB2 germline sequence variants, a …

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141: RetiGene, a comprehensive gene atlas for inherited retinal diseases 26:12

28d ago26:12

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️ Episode 141: RetiGene, a comprehensive gene atlas for inherited retinal diseases In this episode of PaperCast Base by Base, we explore RetiGene, an expert-curated resource that consolidates genetic, transcriptomic, and functional information on inherited retinal diseases (IRDs). The study highlights the urgent need for a unified gene catalog to g…

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140: Landscapes of missense variant impact for human superoxide dismutase 1 20:18

29d ago20:18

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️ Episode 140: Landscapes of missense variant impact for human superoxide dismutase 1 In this episode of PaperCast Base by Base, we explore a large-scale functional analysis of missense variants in SOD1, a key gene implicated in amyotrophic lateral sclerosis (ALS). The study addresses the challenge of classifying variants of uncertain significance …

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139: MosCoverY: A new method to estimate mosaic loss of Y chromosome from sequencing coverage data 14:03

30d ago14:03

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️ Episode 139: MosCoverY: A new method to estimate mosaic loss of Y chromosome from sequencing coverage data In this episode of PaperCast Base by Base, we explore the development of MosCoverY, a computational method designed to detect and quantify mosaic loss of the Y chromosome (mLOY) from exome and whole-genome sequencing data. This condition, th…

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138: Social exposome and brain health outcomes of dementia across Latin America 19:43

1M ago19:43

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️ Episode 138: Social exposome and brain health outcomes of dementia across Latin America In this episode of PaperCast Base by Base, we explore how a multidimensional social exposome across the lifespan—covering education, food insecurity, financial status, assets, access to healthcare, childhood labor, subjective socioeconomic status, childhood ex…

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137: Rethinking RNA-binding proteins: Riboregulation challenges prevailing views 25:11

1M ago25:11

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️ Episode 137: Rethinking RNA-binding proteins: Riboregulation challenges prevailing views In this episode of PaperCast Base by Base, we explore how a sweeping expansion of the RNA-binding proteome has reframed long‑held assumptions about RNA–protein interactions, spotlighting ‘non‑canonical’ RBPs and the emerging concept of riboregulation—RNA dire…

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136: Gene Context Drift Identifies Drug Targets to Mitigate Cancer Treatment Resistance 14:48

1M ago14:48

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️ Episode 136: Gene Context Drift Identifies Drug Targets to Mitigate Cancer Treatment Resistance In this episode of PaperCast Base by Base, we explore RECODR, a graph‑embedding pipeline that reads single‑cell and single‑nucleus transcriptomes as co‑expression networks to quantify “gene context drift” during therapy and expose druggable vulnerabili…

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135: Global impact of micronutrients in modern human evolution 14:26

1M ago14:26

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️ Episode 135: Global impact of micronutrients in modern human evolution In this episode of PaperCast Base by Base, we explore how dietary micronutrients have influenced modern human evolution. The study investigates the role of essential minerals in shaping genetic adaptation and highlights the health risks posed by imbalances in micronutrient ava…

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134: Single-Cell Maps Link Intestinal Metaplasia to Esophageal Adenocarcinoma Risk 15:47

1M ago15:47

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️ 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 ca…

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133: Culture-Independent Meta‑Pangenomics Reveals Gut Genome Links to Child Growth 24:31

1M ago24:31

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️ 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 …

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132: Tumor transcriptome classifiers predict treatment sensitivity in advanced prostate cancer 20:35

1M ago20:35

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️ 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 tran…

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131: pBI143: The Human Gut’s Hidden Heavyweight 17:59

1M ago17:59

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️ 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 incre…

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130: Combining Evidence from Human Genetic and Functional Screens to Identify Pathways Altering Obesity and Fat Distribution 20:24

1M ago20:24

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️ 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 …

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129: Structural variation and diversification of the NPIP gene family from the human pangenome 22:11

1M ago22:11

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️ 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 famili…

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128: LINE‑1 Promoters Orchestrate Early Human Brain Development 15:26

1M ago15:26

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️ 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 n…

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127: In silico generation of synthetic cancer genomes using generative AI 17:36

1M ago17:36

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️ 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 shar…

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126: Molecular and developmental deficits in Smith-Magenis syndrome human stem cell-derived cortical neural models 20:59

1M ago20:59

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️ 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 cort…

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125: Tackling a disease on a global scale, the Global Parkinson’s Genetics Program, GP2: A new generation of opportunities 22:46

1M ago22:46

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️ 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 p…

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124: Exploring the Omnigenic Architecture of Selected Complex Traits 23:47

1M ago23:47

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️ 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 perip…

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123: Dominant‑Negative ATP5F1A Variants Uncouple Complex V and Drive Neurological Disease 18:12

2M ago18:12

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️ 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 Comp…

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122: Patient Stratification Reveals the Molecular Basis of Disease Co-Occurrences 19:57

2M ago19:57

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️ 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-occurr…

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121: G-quadruplexes as a Source of Vulnerability in BRCA2-deficient Granule Cell Progenitors and Medulloblastoma 19:02

2M ago19:02

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️ 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, leadi…

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120: Rare BMAL1 Variants Link the Circadian Clock to Neurodevelopment 22:30

2M ago22:30

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️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 H…

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119: G‑Quadruplex Stabilization Triggers Pericentromeric DNA Breaks in B Cells 18:35

2M ago18:35

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️ Episode 119: G‑Quadruplex Stabilization Triggers Pericentromeric DNA Breaks in B Cells In this episode of PaperCast Base by Base, we explore how stabilizing G‑quadruplex DNA structures with small molecules reshapes genome stability in B lymphocytes, revealing fragile hotspots in pericentromeric repeats and ribosomal DNA and exposing checkpoint-de…

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118: Cancer cells subvert the primate-specific KRAB zinc finger protein ZNF93 to control APOBEC3B 19:11

2M ago19:11

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️ Episode 118: Cancer cells subvert the primate-specific KRAB zinc finger protein ZNF93 to control APOBEC3B In this episode of PaperCast Base by Base, we explore how cancer cells co-opt a primate-specific KRAB zinc finger protein, ZNF93, to fine-tune the mutagenic enzyme APOBEC3B and manage replication stress. Study Highlights: Using genome-wide KZ…

[email protected] (Gustavo Barra