Best Transcriptomics Podcasts (2025)

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

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3d ago17:07

17:07

️ 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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Episode 439: Transcriptome Expression and Treatment Sensitivity in Prostate Cancer 41:24

21d ago41:24

41:24

Gert Attard joins the show to discuss his recent Cell publication looking at tumor transcriptome-wide expression classifiers in advanced prostate cancer.

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

8h ago15:56

15:56

️ 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

1d ago22:35

22:35

️ 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

2d ago14:32

14:32

️ 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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Episode 443: ESMO 2025 Bladder Cancer Preview 32:09

4d ago32:09

32:09

Tom and Brian preview the practice-changing bladder cancer data to be presented at ESMO 2025 in Berlin

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

4d 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

5d ago20:05

20:05

️ 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

6d 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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Episode 441: The History of IO in Urothelial Cancer - Part 2 33:16

7d ago33:16

33:16

Jonathan Rosenberg returns to finish this two-part series on IO drug development in urothelial cancer

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

7d ago16:53

16:53

️ 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

8d 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

9d 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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QOL and cognitive functioning in patients with oligodendroglioma 18:22

10d ago18:22

18:22

Dr. Iyad Alnahhas interviews Drs. Florien Boele and Martin Klein about their recent manuscript entitled: “Health-related quality of life and cognitive functioning in survivors of oligodendroglioma: An international cross-sectional investigation”, published online in Neuro-Oncology in July 2025.By Drs. Iyad Alnahhas, Florien Boele, Martin Klein

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

10d ago15:04

15:04

️ 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

11d ago14:44

14:44

️ 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

12d 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

13d ago15:56

15:56

️ 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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Episode 440: The History of IO in Urothelial Cancer - Part 1 45:39

14d ago45:39

45:39

Jonathan Rosenberg joins in this 2-part series on the history of IO-based therapy in Urothelial Cancer

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

14d ago16:59

16:59

️ 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

15d 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

16d 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

17d 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

18d ago26:12

26:12

️ 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

19d ago20:18

20:18

️ 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

20d 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

21d ago19:43

19:43

️ 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

22d 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

23d ago14:48

14:48

️ 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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Post-operative radiation in recurrent grade 1 meningiomas 19:39

24d ago19:39

19:39

Dr. Iyad Alnahhas interviews Drs. Felix Sahm and Maximilian Deng about their recent manuscript entitled: "Postoperative radiotherapy in subtotally-resected recurrent WHO grade 1 meningiomas with intermediate/ high-risk molecular profiles", published online in Neuro-Oncology in May 2025.By Drs. Felix Sahm, Maximilian Deng, Iyad Alnahhas

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

24d ago14:26

14:26

️ 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

25d ago15:47

15:47

️ 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

26d ago24:31

24:31

️ 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

27d ago20:35

20:35

️ 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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Episode 438: The History of Testis Cancer Treatment 39:22

28d ago39:22

39:22

Christian Kollmannsberger joins us to walk through decades of advances in advanced testis cancer.

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

28d ago17:59

17:59

️ 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

29d 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

22:11

️ 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

15:26

️ 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

17:36

️ 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

20:59

️ 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

22:46

️ 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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Episode 437: Uromigos Japan - バルバーサ (Erdafitinib)を実臨床でどう使うか！ 44:36

1M ago44:36

44:36

Erdafitinibがついに承認されましたが、依然として多くのCQが残されています。日常診療に役立つ最新のデータをもとに、その活用法についてディスカッションしました。

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

1M ago23:47

23:47

️ 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

1M ago18:12

18:12

️ 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

1M ago19:57

19:57

️ 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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mRNA CAR T against GD2 in high-grade glioma models 29:43

1M ago29:43

29:43

Dr. Maya Graham interviews Dr. Jessica Foster about her and her team's recent manuscript, entitled "Transient mRNA CAR T cells targeting GD2 provide dose-adjusted efficacy against diffuse midline glioma and high-grade glioma models". This work was published online in Neuro-Oncology in May 2025.By Drs Maya Graham, Jessica Foster, Iyad Alnahhas

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

1M ago19:02

19:02

️ 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

1M ago22:30

22:30

️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

1M ago18:35

18:35

️ 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…