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 · 91
Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye.
PMID 30010758 · PMC6065499 · GigaScience · 2018 · 8 claims · 6 setups
A draft genome (Ogye_1.1) was assembled using a hybrid de novo method combining high-depth Illumina short reads (376.6X) and low-depth PacBio long reads (9.7X)
-
Has reproduction · 71
Newborn sex-specific transcriptome signatures and gestational exposure to fine particles: findings from the ENVIRONAGE birth cohort.
PMID 28583124 · PMC5458481 · Environmental health : a global access science source · 2017 · 8 claims · 6 setups
Gestational PM2.5 exposure is associated with sex-specific transcriptome signatures in cord blood, with a significant sex-by-exposure interaction for many genes.
-
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 B. taurus samples to UOA_Brahman_1 detects up to 5 million more SNVs than aligning to ARS_UCD1.2, and aligning B. indicus samples to ARS_UCD1.2 detects 1.5 million more SNVs than aligning to UOA_Brahman_1, demonstrating reference-genome bias.
-
Has reproduction · 82
Whole-genome analysis of a multidrug-resistant Klebsiella michiganensis environmental isolate from an orthopedic ward in Mwanza, Tanzania reveals IncF-family plasmid replicon signatures associated with resistance determinants.
PMID 41957580 · PMC13173886 · BMC genomics · 2026 · 8 claims · 8 setups
An isolate phenotypically identified as K. oxytoca was reclassified by genome-based taxonomy (GTDB-Tk, ANI, BLAST) as Klebsiella michiganensis
-
Has reproduction · 86
Prediction of Antibiotic Susceptibility Profiles of Vibrio cholerae Isolates From Whole Genome Illumina and Nanopore Sequencing Data: CholerAegon.
PMID 35814690 · PMC9257098 · Frontiers in microbiology · 2022 · 6 claims · 6 setups
CholerAegon, a Nextflow-based pipeline, predicts AMR profiles of V. cholerae from assembled genomes using CARD ontology
-
Has reproduction · 91
Comparative Genomics of Listeria monocytogenes Isolates from Ruminant Listeriosis Cases in the Midwest United States.
PMID 36314928 · PMC9769944 · Microbiology spectrum · 2022 · 8 claims · 6 setups
73 ruminant listeriosis isolates classified by WGS/cgMLST fall into three lineages: 31.5% lineage 1, 53.4% lineage 2, 15.1% lineage 3
-
Has reproduction · 79
RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing data.
PMID 36339261 · PMC9626663 · iScience · 2022 · 8 claims · 4 setups
RetroSnake is an end-to-end, modular, computationally efficient Snakemake pipeline for detecting HERV-K insertions in short-read NGS data, from raw alignment files to an annotated interactive HTML report
-
Has reproduction · 88
Wochenende - modular and flexible alignment-based shotgun metagenome analysis.
PMID 36368923 · PMC9650795 · BMC genomics · 2022 · 8 claims · 6 setups
Wochenende is a modular, transparent alignment-based pipeline for shotgun metagenome analysis supporting short and long reads across all kingdoms of life
-
Has reproduction · 86
LMAS: evaluating metagenomic short de novo assembly methods through defined communities.
PMID 36576131 · PMC9795473 · GigaScience · 2022 · 8 claims · 5 setups
LMAS (Last Metagenomic Assembler Standing) is a flexible, Nextflow-based, Docker-containerized automated workflow for benchmarking de novo metagenomic assemblers against defined mock communities, producing an interactive HTML report.
-
Has reproduction · 90
An improved assembly of the pearl millet reference genome using Oxford Nanopore long reads and optical mapping.
PMID 36891809 · PMC10151396 · G3 (Bethesda, Md.) · 2023 · 8 claims · 8 setups
Combining ONT long reads with Bionano optical maps produced a substantially more complete and contiguous pearl millet Tift 23D2B1-P1-P5 assembly than the prior short-read assembly.
-
Full-text index only
Differentiation of core promoter architecture between plants and mammals revealed by LDSS analysis.
PMID 17855401 · PMC2094075 · Nucleic acids research · 2007 · 7 claims · 8 setups
LDSS analysis identifies octamer sequences with localized distribution profiles as promoter constituents, classifiable into groups (REG, TATA, Inr, Kozak, CpG, Y Patch)
-
Full-text index only
Searching for SNPs with cloud computing.
PMID 19930550 · PMC3091327 · Genome biology · 2009 · 8 claims · 4 setups
Crossbow combines the Bowtie short-read aligner and SOAPsnp SNP caller into a seamless, automatic Hadoop/MapReduce pipeline for whole-genome resequencing analysis
-
Full-text index only
TEPEAK: A novel method for identifying and characterizing polymorphic transposable elements in non-model species populations.
PMID 41494038 · PMC12788660 · PLoS computational biology · 2026 · 8 claims · 6 setups
TEPEAK identifies and characterizes polymorphic TEs in populations without any prior TE sequence or loci information, using only a chromosome-level reference assembly.
-
Has reproduction · 100
nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning.
PMID 35118380 · PMC8808542 · NAR genomics and bioinformatics · 2022 · 8 claims · 7 setups
nf-core/mag is a Nextflow/nf-core pipeline for hybrid metagenome assembly, binning and taxonomic classification of MAGs.
-
Full-text index only
Cleanifier: contamination removal from microbial sequences using spaced seeds of a human pangenome index.
PMID 41252442 · PMC12758600 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 4 setups
Cleanifier is a fast, memory-frugal alignment-free tool for detecting and removing human contamination using gapped k-mers (spaced seeds) and a human pangenome index.
-
Has reproduction · 80
Chromosome-Scale Assembly of the Complete Genome Sequence of Leishmania (Mundinia) enriettii, Isolate CUR178, Strain LV763.
PMID 34498918 · PMC8428246 · Microbiology resource announcements · 2021 · 7 claims · 7 setups
Complete chromosome-scale genome sequence of Leishmania (Mundinia) enriettii isolate CUR178, strain LV763 was assembled using combined short-read and long-read sequencing
-
Full-text index only
Whole genome sequences of Yersinia pestis strains of ancient phylogenetic branch 0.ANT5 isolated in the 21st century in the Tien-Shan in Kyrgyzstan.
PMID 39206953 · PMC11478111 · Microbiology resource announcements · 2024 · 6 claims · 5 setups
Eleven Yersinia pestis strains of the ancient phylogenetic branch 0.ANT5, isolated in the Tien Shan focus (Kyrgyzstan) in 1952, 1971, and 2013–2023, were hybrid-sequenced (MGI short reads + ONT long reads)
-
Has reproduction · 93
Firefly genomes illuminate parallel origins of bioluminescence in beetles.
PMID 30324905 · PMC6191289 · eLife · 2018 · 7 claims · 8 setups
Bioluminescence arose independently (parallel/convergent origins) in fireflies and click beetles rather than from a single common ancestral origin.
-
Has reproduction · 97
CRISPRbuilder-TB: "CRISPR-builder for tuberculosis". Exhaustive reconstruction of the CRISPR locus in mycobacterium tuberculosis complex using SRA.
PMID 33667225 · PMC7968741 · PLoS computational biology · 2021 · 8 claims · 7 setups
CRISPRbuilder-TB is a new pipeline that reconstructs MTC CRISPR-Cas loci directly from short SRA reads without requiring genome assembly
-
Has reproduction · 93
Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster.
PMID 23284297 · PMC3527207 · PLoS genetics · 2012 · 8 claims · 8 setups
Wolbachia infection status can be accurately predicted in silico from whole-genome shotgun sequence of individual host strains, showing 99% concordance with diagnostic PCR.