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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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
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Has reproduction · 89
TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches.
PMID 37013657 · PMC10069131 · Genome biology · 2023 · 6 claims · 6 setups
TrEMOLO combines an assembly-based INSIDER module and a mapping-based OUTSIDER module to detect TE insertions/deletions from long-read sequencing data and estimate their allele frequency
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Has reproduction · 100
Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency.
PMID 24131564 · PMC3875859 · Genome research · 2014 · 8 claims · 8 setups
TSscan, a computational pipeline integrating long- and short-read transcriptome sequencing from multiple hESC lines, can detect trans-splicing while minimizing false positives from experimental artifacts and genetic rearrangements.
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Has reproduction · 71
polishCLR: A Nextflow Workflow for Polishing PacBio CLR Genome Assemblies.
PMID 36792366 · PMC9985148 · Genome biology and evolution · 2023 · 8 claims · 8 setups
polishCLR is a reproducible, containerized Nextflow workflow that implements best practices for polishing PacBio CLR genome assemblies.
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Has reproduction · 92
Acquisition and loss of CTX-M plasmids in Shigella species associated with MSM transmission in the UK.
PMID 34427554 · PMC8549364 · Microbial genomics · 2021 · 8 claims · 8 setups
bla_CTX-M-27 is located on IncFII pKSR100-like plasmids, flanked by IS26 and IS903B
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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
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Has reproduction · 90
The COMBAT-TB Workbench: Making Powerful Mycobacterium tuberculosis Bioinformatics Accessible.
PMID 35138128 · PMC8827006 · mSphere · 2022 · 8 claims · 5 setups
The COMBAT-TB Workbench combines the IRIDA web platform and the Galaxy workflow platform into a single easy-to-install, Docker-based application
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The sequence and de novo assembly of the giant panda genome.
PMID 20010809 · PMC3951497 · Nature · 2010 · 8 claims · 8 setups
A draft giant panda genome was successfully generated and assembled de novo using only Illumina Genome Analyser short-read sequencing
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Has reproduction · 55
Natural clines and human management impact the genetic structure of Algerian honey bee populations.
PMID 38114899 · PMC10729559 · Genetics, selection, evolution : GSE · 2023 · 7 claims · 8 setups
No significant admixture from European subspecies was detected in Algerian honey bees, suggesting large-scale queen imports have not occurred in Algeria.
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Has reproduction · 93
Firefly genomes illuminate parallel origins of bioluminescence in beetles.
PMID 30324905 · PMC6191289 · eLife · 2018 · 8 claims · 8 setups
Bioluminescence evolved independently at least twice in beetles: once in the firefly ancestor and once in the bioluminescent click beetle ancestor.
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Has reproduction · 100
poreCov-An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction via Nanopore Sequencing.
PMID 34394197 · PMC8355734 · Frontiers in genetics · 2021 · 8 claims · 8 setups
poreCov is an easy-to-use, fast, and robust Nextflow-based workflow for reference-based SARS-CoV-2 genome reconstruction and lineage determination from nanopore sequencing data
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Has reproduction · 67
binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets.
PMID 36239393 · PMC9677464 · Briefings in bioinformatics · 2022 · 8 claims · 8 setups
binny outperforms or is highly competitive with commonly used and state-of-the-art binning methods (MetaBAT2, MaxBin2, CONCOCT, VAMB, SemiBin, MetaDecoder)
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PigGIS: Pig Genomic Informatics System.
PMID 17090590 · PMC1669765 · Nucleic acids research · 2007 · 7 claims · 7 setups
PigGIS identified 15,700 pig consensus sequences covering 18.5 Mb of homologous human exons
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Has reproduction · 58
Revised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group.
PMID 25273863 · PMC4267930 · G3 (Bethesda, Md.) · 2014 · 8 claims · 6 setups
Revised RNA-seq-based gene models for D. ananassae, D. yakuba, and D. simulans include UTRs, empirically verified intron-exon boundaries, and previously unannotated novel exons, improving on r1.3 comparative-genomics annotations that lack UTRs.
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Has reproduction
Genome-wide signatures of convergent evolution in echolocating mammals.
PMID 24005325 · PMC3836225 · Nature · 2013 · 8 claims · 8 setups
Genome-wide convergent sequence evolution between echolocating lineages is not rare but widespread and continuously distributed, with signatures consistent with convergence in nearly 200 loci out of 2,326 examined.