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 294

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Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches.

PMID 19773805 · PMC2958924 · Nature reviews. Molecular cell biology · 2009 · 8 claims · 6 setups

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Alternative splicing occurs in the expression of nearly 95% of human multi-exon genes

gria2 drosophila nova1 cd45 splicing sirna hits-clip
Compound heterozygosity for a novel and a recurrent MFRP gene mutation in a family with the nanophthalmos-retinitis pigmentosa complex.

PMID 19753314 · PMC2742641 · Molecular vision · 2009 · 8 claims · 8 setups

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Compound heterozygosity for two distinct MFRP mutations (a novel nonsense mutation and a recurrent frameshift mutation) causes the nanophthalmos-retinitis pigmentosa-foveoschisis-optic disc drusen complex in this sibling pair

patients eyes genomic ophthalmological a-mode electroretinogram
A pre-S gene chip to detect pre-S deletions in hepatitis B virus large surface antigen as a predictive marker for hepatoma risk in chronic hepatitis B virus carriers.

PMID 19751529 · PMC2755474 · Journal of biomedical science · 2009 · 8 claims · 5 setups

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Pre-S1 and pre-S2 deletion mutants of the HBV LHBS gene are highly associated with HBV-related HCC

serum plasmids coli pcr oligonucleotide chip
Personalized copy number and segmental duplication maps using next-generation sequencing.

PMID 19718026 · PMC2875196 · Nature genetics · 2009 · 5 claims · 5 setups

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mrFAST maps short reads to all possible locations in the reference genome, enabling read-depth-based prediction of absolute copy number in both unique and duplicated sequence, including discrimination between highly identical gene paralogs.

genomes genomic interphase na18507 whole-genome array fluorescence
Protocadherin PCDH10, involved in tumor progression, is a frequent and early target of promoter hypermethylation in cervical cancer.

PMID 19681120 · PMC3430375 · Genes, chromosomes & cancer · 2009 · 8 claims · 5 setups

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PCDH10 promoter hypermethylation is a frequent event in invasive cervical cancer

invasive lines normal cervical snp methylation-specific bisulphite
BreakDancer: an algorithm for high-resolution mapping of genomic structural variation.

PMID 19668202 · PMC3661775 · Nature methods · 2009 · 8 claims · 8 setups

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BreakDancer (BreakDancerMax + BreakDancerMini) is a software package that predicts a wide variety of structural variants including deletions, insertions, inversions, and intra/inter-chromosomal translocations from paired-end short-insert sequencing reads.

reads yoruban cytogenetically predicted simulated paired-end whole-genome
Discovery and characterization of gene-by-environment and epistatic genetic effects in a vertebrate model.

PMID 41672067 · PMC13174225 · Cell genomics · 2026 · 7 claims · 7 setups

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A segregation analysis in an F2 medaka cross identified 16 QTLs linked to embryonic heart rate variation across temperatures

mikk medaka discovered informed high-throughput heart shallow
Env-antibody coevolution identifies B cell priming as the principal bottleneck to HIV V2 apex broadly neutralizing antibody development.

PMID 41686912 · PMC13015429 · Science immunology · 2026 · 8 claims · 8 setups

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Efficiency of B cell priming, not complexity of Env-guided affinity maturation, is the primary obstacle to V2 apex bNAb elicitation in SHIV-infected macaques.

shiv-infected plasma igg+ rhesus plasma single-genome next-generation
Whole genomes reveal subpopulations and isolation-by-distance patterns in the Norwegian lemming.

PMID 41787358 · PMC13064042 · BMC biology · 2026 · 8 claims · 8 setups

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The Norwegian lemming population is geographically structured into distinct subpopulations showing an isolation-by-distance pattern, contrary to earlier microsatellite-based findings of weak structure

lemmus single norwegian lemmings whole-genome novo principal
Beyond blacklists: a critical assessment of exclusion set generation strategies and alternative approaches.

PMID 41826793 · PMC13020910 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 8 setups

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Pre-generated Blacklist exclusion sets were difficult to reproduce due to sensitivity to input BAM data, aligner choice, and read length

hg38 gm12878 gse235167 syo-1 chip-seq rna-seq atac-seq
Pseudoalteromonas is a symbiont of marine invertebrates that exhibits broad patterns of phylosymbiosis.

PMID 42007585 · PMC13245728 · The ISME journal · 2026 · 8 claims · 8 setups

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Pseudoalteromonas is a symbiont with substantial evidence of phylosymbiosis across at least three marine invertebrate phyla (Nematoda, Mollusca, and Cnidaria)

pseudoalteromonas mollusca individual live pangenomic core-genome average
Probing the zooarchaeological record across time and space for ancient pathogen DNA.

PMID 42062273 · PMC13133277 · Nature communications · 2026 · 6 claims · 4 setups

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Palaeopathological lesions provide guidance for selecting specimens likely to yield ancient pathogen DNA

bones extracts ancient macroscopic shotgun metagenomic
Transcriptional landscape of repetitive elements in normal and cancer human cells.

PMID 25012247 · PMC4122776 · BMC genomics · 2014 · 8 claims · 8 setups

Has reproduction · 76

RepEnrich, a computational method that uses all mapping reads (uniquely mapping plus multi-mapping reads assigned to repetitive element subfamily assemblies/pseudogenomes), quantifies genome-wide repetitive element enrichment

chromosomes lines imr-90 prostate simulated pol chip-seq
scXDR: drug response prediction across single-cell datasets via heterogeneous network transfer learning.

PMID 41507436 · PMC12859067 · Communications biology · 2026 · 7 claims · 7 setups

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scXDR outperforms seven methods that transfer drug response information from bulk RNA-seq to single-cell data, across all four evaluated scenarios

single-cell scrna-seq scxdr gse117872 heterogeneous benchmarking type
Transcriptome- and phenotype-based epistasis analysis in Caenorhabditis elegans reveals daf-16/FoxO-dependent and independent effects of daf-2/InsR in L1 starvation and recovery.

PMID 41528819 · PMC12958807 · G3 (Bethesda, Md.) · 2026 · 7 claims · 8 setups

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Differential gene expression caused by disruption of daf-2/InsR during L1 starvation is daf-16-dependent.

elegans bulk principal hierarchical
Development of a split-toxin CRISPR screening platform to systematically identify regulators of human myoblast fusion.

PMID 41540035 · PMC12808753 · Nature communications · 2026 · 8 claims · 7 setups

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A CRISPR screening platform combining human myoblast models, a custom muscle-targeted gRNA library (MyoCRISPR-KO Lib), and a split-toxin selection system enables quantitative enrichment of fusion-defective myocytes.

myoblasts myoblast time-course immunostaining gene
Af-CUT&Tag: a sensitive and antibody-free chromatin profiling method using genetically encoded tags and high-affinity binders fused to Tn5.

PMID 41547832 · PMC12914055 · Nature communications · 2026 · 8 claims · 8 setups

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Af-CUT&Tag eliminates dependence on conventional target antibodies by using CRISPR-integrated HiBiT/ALFA-tags recognized by LgBiT/NbALFA-Tn5 fusion proteins

recombinant sw480 lysates genomic bio-layer chemiluminescent co-immunoprecipitation
Redefinition of the toll-like receptor repertoire in Ciona robusta through genomic, structural, and expression analyses.

PMID 41568004 · PMC12816324 · Frontiers in cellular and infection microbiology · 2025 · 8 claims · 8 setups

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CiTLR13 is a redundant annotation of CiTLR1 (same genomic locus, >94% sequence identity), so it is not a distinct TLR gene

ciona six lrr tlr blastp domain nucleotide
The RNA-binding protein SRSF3 controls epicardial formation by regulating splicing and proliferation.

PMID 41601313 · PMC13006530 · Development (Cambridge, England) · 2026 · 8 claims · 8 setups

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SRSF3 is highly expressed in the proepicardial organ and early epicardium, declining after E11.5 and remaining low postnatally

embryo heart e11.5 proepicardium immunofluorescence qrt-pcr conditional
ERGA-BGE Genomes of Culex laticinctus, Culex modestus, Culex perexiguus, and Culex theileri: Unveiling the Genomes of the Key Vectors of West Nile Virus in the Mediterranean Basin.

PMID 41626876 · PMC12862641 · Genome biology and evolution · 2026 · 7 claims · 8 setups

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High-quality chromosome-level reference genomes were assembled for four previously unsequenced Culex species

whole-organism assembled annotated individual pacbio hi-c poly

Experiments

Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches.

Compound heterozygosity for a novel and a recurrent MFRP gene mutation in a family with the nanophthalmos-retinitis pigmentosa complex.

A pre-S gene chip to detect pre-S deletions in hepatitis B virus large surface antigen as a predictive marker for hepatoma risk in chronic hepatitis B virus carriers.

Personalized copy number and segmental duplication maps using next-generation sequencing.

Protocadherin PCDH10, involved in tumor progression, is a frequent and early target of promoter hypermethylation in cervical cancer.

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation.

Discovery and characterization of gene-by-environment and epistatic genetic effects in a vertebrate model.

Env-antibody coevolution identifies B cell priming as the principal bottleneck to HIV V2 apex broadly neutralizing antibody development.

Whole genomes reveal subpopulations and isolation-by-distance patterns in the Norwegian lemming.

Beyond blacklists: a critical assessment of exclusion set generation strategies and alternative approaches.

Pseudoalteromonas is a symbiont of marine invertebrates that exhibits broad patterns of phylosymbiosis.

Probing the zooarchaeological record across time and space for ancient pathogen DNA.

Transcriptional landscape of repetitive elements in normal and cancer human cells.

scXDR: drug response prediction across single-cell datasets via heterogeneous network transfer learning.

Transcriptome- and phenotype-based epistasis analysis in Caenorhabditis elegans reveals daf-16/FoxO-dependent and independent effects of daf-2/InsR in L1 starvation and recovery.

Development of a split-toxin CRISPR screening platform to systematically identify regulators of human myoblast fusion.

Af-CUT&Tag: a sensitive and antibody-free chromatin profiling method using genetically encoded tags and high-affinity binders fused to Tn5.

Redefinition of the toll-like receptor repertoire in Ciona robusta through genomic, structural, and expression analyses.

The RNA-binding protein SRSF3 controls epicardial formation by regulating splicing and proliferation.

ERGA-BGE Genomes of Culex laticinctus, Culex modestus, Culex perexiguus, and Culex theileri: Unveiling the Genomes of the Key Vectors of West Nile Virus in the Mediterranean Basin.