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).
-
Has reproduction · 85
High performance imputation of structural and single nucleotide variants using low-coverage whole genome sequencing.
PMID 40155798 · PMC11951665 · Genetics, selection, evolution : GSE · 2025 · 7 claims · 6 setups
SNVs are imputed with high accuracy and recall across all tested WGS depths (1-4x), including in samples external to the reference panel.
-
Has reproduction · 61
TEMP: a computational method for analyzing transposable element polymorphism in populations.
PMID 24753423 · PMC4066757 · Nucleic acids research · 2014 · 8 claims · 8 setups
TEMP combines pair-end (discordant) read and split (soft-clipped) read information to identify both presence and absence of TE insertions in genomic DNA from heterogeneous/pooled samples.
-
Has reproduction · 86
Assessing Bos taurus introgression in the UOA Bos indicus assembly.
PMID 34922445 · PMC8684283 · Genetics, selection, evolution : GSE · 2021 · 7 claims · 6 setups
Aligning divergent (cross-subspecies) sequence data detects substantially more SNVs than aligning to a same-subspecies reference, indicating reference/assembly bias in variant calling.
-
Has reproduction · 49
oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets.
PMID 22973536 · PMC3429929 · G3 (Bethesda, Md.) · 2012 · 8 claims · 6 setups
oPOSSUM-3 is a web-accessible system that identifies over-represented TFBS and TFBS families in DNA sequences of co-expressed genes or in sequences from high-throughput methods such as ChIP-Seq.
-
Full-text index only
A SNP-centric database for the investigation of the human genome.
PMID 15046636 · PMC395999 · BMC bioinformatics · 2004 · 8 claims · 3 setups
SNPper is a web-based, integrated SNP database combining dbSNP, the Human Genome sequence (Goldenpath), LocusLink, GeneOntology, and SWISS-PROT data with querying, visualization, and export tools.
-
Has reproduction · 58
HGA: de novo genome assembly method for bacterial genomes using high coverage short sequencing reads.
PMID 26945881 · PMC4779561 · BMC genomics · 2016 · 8 claims · 7 setups
HGA leads to significant improvement in assembly quality (N50 and corrected N50) for all 7 evaluated GAGE-B bacterial datasets using most of the 8 evaluated assemblers
-
Has reproduction · 71
Single-Cell Transcriptomic Landscape of Right-Sided Colon Cancer Reveals Cellular and Molecular Features of Metastatic Potential.
PMID 41898210 · PMC13024220 · Biomedicines · 2026 · 8 claims · 8 setups
Liver metastatic potential in RCC is marked by stem-like tumor states, metabolic plasticity, and microenvironmental remodeling.
-
Has reproduction · 92
Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration.
PMID 34773081 · PMC8589952 · Communications biology · 2021 · 8 claims · 7 setups
Large-scale integration of 111 sc/snRNAseq datasets captures rare, transitional myogenic progenitor states (commitment and fusion) that are poorly represented in individual datasets.
-
Has reproduction · 67
snpQT: flexible, reproducible, and comprehensive quality control and imputation of genomic data.
PMID 34900230 · PMC8637247 · F1000Research · 2021 · 8 claims · 4 setups
snpQT is a scalable, stand-alone software pipeline using nextflow and BioContainers for comprehensive, reproducible, interactive QC of human genomic data.
-
Has reproduction · 75
Genomic regions and candidate genes selected during the breeding of rice in Vietnam.
PMID 35899250 · PMC9309459 · Evolutionary applications · 2022 · 8 claims · 7 setups
XP-CLR and FST scans identify genomic regions with distorted allele frequency/differentiation patterns resulting from differential selective pressures between Vietnamese rice subpopulations
-
Has reproduction · 73
Vespucci: a system for building annotated databases of nascent transcripts.
PMID 24304890 · PMC3936758 · Nucleic acids research · 2014 · 8 claims · 7 setups
Existing ChIP-seq and RNA-seq analysis platforms (e.g. Cufflinks, peak callers) are unsuited to GRO-seq because they assume spliced/exonic reads, uniform density and paired-end data, and cannot identify transcriptional units de novo across the whole genome.
-
Full-text index only
Ensembl 2007.
PMID 17148474 · PMC1761443 · Nucleic acids research · 2007 · 8 claims · 7 setups
Ensembl added 18 new chordate genomes this year, increasing total genomes available from 15 to 33, the largest yearly increase to date.
-
Full-text index only
The vertebrate genome annotation (Vega) database.
PMID 18003653 · PMC2238886 · Nucleic acids research · 2008 · 8 claims · 8 setups
Vega is a database for viewing manual genome annotation of human, mouse and zebrafish genomic sequences produced at the Wellcome Trust Sanger Institute.
-
Has reproduction · 85
Integration of multi-omics and machine learning strategies identifies immune related candidate biomarkers in inflammation-associated hypertrophic cardiomyopathy.
PMID 41080564 · PMC12510942 · Frontiers in immunology · 2025 · 8 claims · 8 setups
Seven key immune-related genes (RNF165, SNCA, SRGN, MARCO, STEAP4, SIGLEC9, TKT) were identified for HCM by intersecting DEGs with MR-derived HCM-associated eQTLs.