Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

Publications 1.3k Datasets 392.5k Experiments 497

System / cell line: family ✕ Clear

Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease.

PMID 41781332 · PMC13138337 · Genome research · 2026 · 8 claims · 7 setups

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Single-nucleus multiome (RNA+ATAC) sequencing of mouse substantia nigra across four age stages (2, 6, 12, 18 months) yields a 40,125-cell atlas spanning 27 cell subclasses

substantia allen five oligodendrocyte single-nucleus scrna-seq single-cell
Genome evolution and regulatory dynamics underlying salt stress tolerance in the halophyte Halogeton arachnoideus.

PMID 41803406 · PMC13103082 · Communications biology · 2026 · 8 claims · 8 setups

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A high-quality, chromosome-scale genome assembly of H. arachnoideus was generated using PacBio HiFi and Hi-C sequencing.

arachnoideus pacbio high-throughput illumina
SMARCA4/2 loss reduces BCL-xL expression and confers a druggable MCL1 dependency in cancer.

PMID 41807550 · PMC13249849 · NPJ precision oncology · 2026 · 8 claims · 8 setups

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MCL1 inhibition is synthetic lethal with SMARCA4/2 loss in SCCOHT and NSCLC cells

nsclc lung smarca4 bin-67 genome-wide drug colony
Insights into karyotype evolution and flower color variation from the genome assembly of wallflower (Erysimum cheiri).

PMID 41824659 · PMC13089509 · Plant physiology · 2026 · 7 claims · 8 setups

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A near-complete telomere-to-telomere genome assembly of E. cheiri was generated (244.33 Mb, 6 chromosomes)

cheiri brassicaceae illumina pacbio hi-c
Developmental reprogramming underlies chemotherapy resistance in favorable-histology Wilms tumor.

PMID 41850280 · PMC13103949 · Cell reports · 2026 · 8 claims · 8 setups

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Chemotherapy-resistant KT-47R tumors show blastemal predominance and reduced stromal content compared to pre-treatment KT-47PT

kt-47 kt-47pt histology whole-exome cut&tag
Signatures of Innovation and Selection in the Extremotolerant Yeast Kluyveromyces marxianus.

PMID 41874284 · PMC13011806 · Genome biology and evolution · 2026 · 8 claims · 9 setups

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K. marxianus shows a unique stress-resistance syndrome (heat, ethanol, caffeine, propidium iodide, MMS) relative to other Kluyveromyces species

kluyveromyces marxianus one-to-one liquid heat-shock stress
Centromeric retrotransposons shape chromosomal evolution beyond pericentromeric regions.

PMID 41923128 · PMC13169781 · Mobile DNA · 2026 · 8 claims · 8 setups

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Specialized CRM retrotransposon elements specifically target active centromeres and are surrounded by Athila element copies

biscutella varia austriaca unassembled long-read short-read hi-c
Integrating co-expression network analysis and machine learning to reveal the regulatory landscape of GPD genes in Chlamydomonas reinhardtii under salinity stress.

PMID 42004709 · PMC13089224 · PeerJ · 2026 · 8 claims · 8 setups

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GPD2 and GPD3 cluster into distinct WGCNA co-expression modules (magenta and black, respectively) with contrasting temporal expression profiles

chlamydomonas genes normalized gpd bulk weighted gene
Transcriptome analysis and characterization of cathepsin B-like protein in Melanaphis sorghi in response to resistant sorghum.

PMID 42117064 · PMC13157386 · Molecular breeding : new strategies in plant improvement · 2026 · 8 claims · 8 setups

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RNA-seq identified 1,388 differentially expressed genes (DEGs) in M. sorghi aphids feeding on resistant sorghum HN16

melanaphis sorghi nicotiana benthamiana rna-seq aphid weighted
Polymorphic repeat in AIB1 does not alter breast cancer risk.

PMID 11056690 · PMC13920 · Breast cancer research : BCR · 2000 · 7 claims · 3 setups

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AIB1 alleles with 26 or fewer glutamine repeats are not associated with increased breast cancer risk in the general population

peripheral cohort plasma pcr nested plasma
Rare germline mutations in the BRCA2 gene are associated with early-onset prostate cancer.

PMID 17700570 · PMC2360390 · British journal of cancer · 2007 · 8 claims · 3 setups

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Germline protein-truncating BRCA2 mutations confer an elevated relative risk (~7.8-fold) of early-onset prostate cancer in Caucasian men

peripheral population-based same germline epidemiological genotype-phenotype
Putting science over supposition in the arena of personalized genomics.

PMID 18665132 · PMC2531214 · Nature genetics · 2008 · 6 claims · 3 setups

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There is a rapidly widening gap between gene-disease association discovery and research into the public health/clinical utility of that information.

adults same tested baseline multiplex telephone-based
Polymorphisms of delta-aminolevulinic acid dehydratase (ALAD) and peptide transporter 2 (PEPT2) genes in children with low-level lead exposure.

PMID 19723536 · PMC2789866 · Neurotoxicology · 2009 · 7 claims · 3 setups

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Children homozygous for the PEPT2*2 polymorphism have significantly higher blood lead levels than heterozygous or non-carrier children.

mexican-american buccal parents blood genetic demographic
Ensembl 2013.

PMID 23203987 · PMC3531136 · Nucleic acids research · 2013 · 8 claims · 8 setups

Has reproduction · 85

Ensembl (http://www.ensembl.org) provides genome information for sequenced chordate genomes, currently supporting 70 species with a focus on human, mouse, zebrafish and rat.

genome species supported variants evidence-based rna-seq chip-seq
The changing face of genomics.

PMID 15128443 · PMC416465 · Genome biology · 2004 · 8 claims · 8 setups

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Genome-wide ChIP-chip mapping of ~200 yeast transcriptional regulators across environmental conditions reveals general principles of promoter architecture and regulatory response types

yeast drosophila zebrafish elegans chip-chip comparative insertional
Splicing bioinformatics to biology.

PMID 16732900 · PMC1779529 · Genome biology · 2006 · 8 claims · 8 setups

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Mutually exclusive selection of Dscam exon 6 variants is governed by base pairing between a conserved intronic docking site and selector sequences adjacent to each alternative exon.

dscam alternative heterologous expressing comparative dicodon reporter
MODBASE: a database of annotated comparative protein structure models and associated resources.

PMID 16381869 · PMC1347422 · Nucleic acids research · 2006 · 8 claims · 7 setups

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MODBASE is a database of automatically calculated comparative protein structure models covering all UniProt sequences matchable to a known structure

uniprot non-redundant complexes saccharomyces comparative pairwise domain-domain
Web-based resources for comparative genomics.

PMID 16197736 · PMC3525128 · Human genomics · 2005 · 8 claims · 8 setups

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Comparative genomics is an indispensable tool for identifying functional genome elements and exploring evolutionary genome dynamics

yeast chimpanzee mammalian protein-coding comparative genome maximum-likelihood
Basic and applied biology of the primate reproductive tract--a symposium in honor of the career of Dr Robert M Brenner: introduction and overview.

PMID 17118166 · PMC1775062 · Reproductive biology and endocrinology : RB&E · 2006 · 8 claims · 6 setups

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A critical ~36-hour window exists after progesterone withdrawal in macaques during which menstruation can still be blocked by progesterone add-back, after which it becomes inevitable

ovariectomized baboon endometrium macaque hormone laparoscopic immunohistochemistry
Complete Genome Sequencing of Lactobacillus plantarum ZLP001, a Potential Probiotic That Enhances Intestinal Epithelial Barrier Function and Defense Against Pathogens in Pigs.

PMID 30542296 · PMC6277807 · Frontiers in physiology · 2018 · 8 claims · 8 setups

Has reproduction · 68

The complete genome of L. plantarum ZLP001 was sequenced and compared with 18 other L. plantarum genomes to identify genomic features underlying its gut-health-promoting probiotic properties.

lactobacillus plantarum whole-genome gene comparative

Experiments

Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease.

Genome evolution and regulatory dynamics underlying salt stress tolerance in the halophyte Halogeton arachnoideus.

SMARCA4/2 loss reduces BCL-xL expression and confers a druggable MCL1 dependency in cancer.

Insights into karyotype evolution and flower color variation from the genome assembly of wallflower (Erysimum cheiri).

Developmental reprogramming underlies chemotherapy resistance in favorable-histology Wilms tumor.

Signatures of Innovation and Selection in the Extremotolerant Yeast Kluyveromyces marxianus.

Centromeric retrotransposons shape chromosomal evolution beyond pericentromeric regions.

Integrating co-expression network analysis and machine learning to reveal the regulatory landscape of GPD genes in Chlamydomonas reinhardtii under salinity stress.

Transcriptome analysis and characterization of cathepsin B-like protein in Melanaphis sorghi in response to resistant sorghum.

Polymorphic repeat in AIB1 does not alter breast cancer risk.

Rare germline mutations in the BRCA2 gene are associated with early-onset prostate cancer.

Putting science over supposition in the arena of personalized genomics.

Polymorphisms of delta-aminolevulinic acid dehydratase (ALAD) and peptide transporter 2 (PEPT2) genes in children with low-level lead exposure.

Ensembl 2013.

The changing face of genomics.

Splicing bioinformatics to biology.

MODBASE: a database of annotated comparative protein structure models and associated resources.

Web-based resources for comparative genomics.

Basic and applied biology of the primate reproductive tract--a symposium in honor of the career of Dr Robert M Brenner: introduction and overview.

Complete Genome Sequencing of Lactobacillus plantarum ZLP001, a Potential Probiotic That Enhances Intestinal Epithelial Barrier Function and Defense Against Pathogens in Pigs.