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).
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Using comparative genomics to reorder the human genome sequence into a virtual sheep genome.
PMID 17663790 · PMC2323240 · Genome biology · 2007 · 8 claims · 6 setups
A sheep BAC library (CHORI-243) with ~13.5-fold genome coverage was constructed and end-sequenced.
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Has reproduction · 27
Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing.
PMID 23840502 · PMC3688795 · PloS one · 2013 · 8 claims · 5 setups
A de novo radish root transcriptome of 68,940 assembled transcripts including 33,337 unigenes was generated, providing the first comprehensive molecular characterization of the radish root response to Pb stress.
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Has reproduction · 86
The selection of software and database for metagenomics sequence analysis impacts the outcome of microbial profiling and pathogen detection.
PMID 37027361 · PMC10081788 · PloS one · 2023 · 7 claims · 7 setups
Obtaining an accurate species-level microbial profile using current direct-read metagenomics profiling software is still a challenging task.
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Has reproduction · 99
Free circular introns with an unusual branchpoint in neuronal projections.
PMID 31697236 · PMC6879206 · eLife · 2019 · 8 claims · 7 setups
A set of free circular introns with a non-canonical (C) branchpoint is enriched in distal neuronal projections; these appear to be tailless lariats that escape debranching.
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ChromAcS: an automated and flexible GUI for end-to-end reproducible ATAC-seq analysis across multiple species.
PMID 41639613 · PMC12973882 · BMC bioinformatics · 2026 · 8 claims · 8 setups
ChromAcS is a comprehensive open-source, GUI-based ATAC-seq analysis pipeline supporting multi-species genomes with real-time progress monitoring and modular re-execution.
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Has reproduction · 87
Insights into the Evolution of the New World Diploid Cottons (Gossypium, Subgenus Houzingenia) Based on Genome Sequencing.
PMID 30476109 · PMC6320677 · Genome biology and evolution · 2019 · 8 claims · 8 setups
Subgenus Houzingenia likely originated via transoceanic dispersal from Africa about 6.6 Ma
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Has reproduction · 80
Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA.
PMID 22466171 · PMC3371705 · Genome research · 2012 · 8 claims · 8 setups
BisChIP-seq — bisulfite sequencing of chromatin immunoprecipitated DNA — enables direct genome-wide, base-resolution interrogation of DNA methylation on histone-modified DNA molecules
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Has reproduction · 83
Taxonomic and functional metagenomic assessment of a Dolichospermum bloom in a large and deep lake south of the Alps.
PMID 39227168 · PMC11412076 · FEMS microbiology ecology · 2024 · 7 claims · 8 setups
Phylogenomic analysis of the MAG clarified the taxonomic position of D. lemmermannii within the genus Dolichospermum and the ADA (Anabaena/Dolichospermum/Aphanizomenon) group
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Has reproduction · 87
Reconstruction of 2,965 Microbial Genomes from Mangrove Sediments across Guangxi, China.
PMID 41419779 · PMC12858935 · Scientific data · 2025 · 7 claims · 8 setups
A standardized assembly, binning, and dereplication pipeline was used to reconstruct 2,965 non-redundant MAGs from 38 mangrove sediment samples across six sites in Guangxi
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Has reproduction · 66
RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties.
PMID 36159175 · PMC9492272 · NAR genomics and bioinformatics · 2022 · 8 claims · 6 setups
RiboTaxa, combining BBTools, FastQC, SortMeRNA, MetaRib, EMIRGE, VSEARCH, BBMap and QIIME 2's Sklearn classifier, was built as a pipeline for SSU rRNA-based taxonomic profiling of metagenomics data.
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Haplotype-resolved and near telomere-to-telomere assembly of the autotetraploid potato genome.
PMID 41634861 · PMC12955163 · Genome biology · 2026 · 8 claims · 8 setups
PHap is a new pipeline that enables haplotype-resolved, near-T2T assembly of autopolyploid genomes using only standard HiFi, ONT-UL, and Hi-C sequencing data
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Genome evolution and regulatory dynamics underlying salt stress tolerance in the halophyte Halogeton arachnoideus.
PMID 41803406 · PMC13103082 · Communications biology · 2026 · 8 claims · 8 setups
A high-quality, chromosome-scale genome assembly of H. arachnoideus was generated using PacBio HiFi and Hi-C sequencing.
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Centromere organization and epigenetic regulation in Aristolochia fimbriata.
PMID 41761339 · PMC13049873 · Genome biology · 2026 · 8 claims · 8 setups
A complete gapless telomere-to-telomere (T2T) genome assembly of A. fimbriata was constructed, substantially improving on the previous v1 assembly.
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ENCODE whole-genome data in the UCSC Genome Browser.
PMID 19920125 · PMC2808953 · Nucleic acids research · 2010 · 7 claims · 8 setups
The UCSC ENCODE Data Coordination Center serves as the primary repository for ENCODE experimental results, providing access via Genome Browser, Table Browser, and FTP download.