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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Full-text index only
Shotgun haplotyping: a novel method for surveying allelic sequence variation.
PMID 16221968 · PMC1253838 · Nucleic acids research · 2005 · 8 claims · 7 setups
A novel shotgun haplotyping method generates haplotypic sequences from long PCR products by shotgun sequencing both alleles concurrently and using read-pair information to separate alleles during assembly
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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 · 67
GAVISUNK: genome assembly validation via inter-SUNK distances in Oxford Nanopore reads.
PMID 36321867 · PMC9805576 · Bioinformatics (Oxford, England) · 2023 · 7 claims · 4 setups
GAVISUNK is an open-source pipeline that validates phased diploid HiFi assemblies by assessing concordance of inter-SUNK distances against orthogonal Oxford Nanopore (ONT) reads.
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Has reproduction · 73
Gapless provides combined scaffolding, gap filling, and assembly correction with long reads.
PMID 37142439 · PMC10166144 · Life science alliance · 2023 · 8 claims · 5 setups
gapless is a new tool that combines assembly correction, scaffolding, and gap filling in one pipeline using PacBio or Oxford Nanopore long reads.
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Has reproduction · 86
Plasmid transmission dynamics and evolution of partner quality in a natural population of Rhizobium leguminosarum.
PMID 41212030 · PMC12691615 · mBio · 2025 · 8 claims · 8 setups
Of the four most frequent plasmid types, types II and III have more stable size, larger core genomes, and track the chromosomal phylogeny (more vertical transmission), while types I and IV (pSym) vary in size and gene content with phylogenies consistent with frequent horizontal transmission.
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Has reproduction · 99
A platinum standard pan-genome resource that represents the population structure of Asian rice.
PMID 32265447 · PMC7138821 · Scientific data · 2020 · 6 claims · 6 setups
The 3,000 Rice Genomes (3K-RG) dataset can be subdivided into 15 subpopulations (K=15), refining the previous K=9 population structure.
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Has reproduction · 99
getSequenceInfo: a suite of tools allowing to get genome sequence information from public repositories.
PMID 35804320 · PMC9264741 · BMC bioinformatics · 2022 · 8 claims · 8 setups
getSequenceInfo (gSeqI) allows programmatic (CLI) or GUI-based retrieval of sequence data and metadata from GenBank, RefSeq, and ENA across Linux, MacOS, and Windows.
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Has reproduction · 67
A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome.
PMID 25009556 · PMC4070175 · Frontiers in genetics · 2014 · 8 claims · 8 setups
Multiple k-mer (MK) assemblies are more complete than single k-mer (SK) assemblies, showing higher reads-mapped-back-to-transcripts (RMBT) and higher CEGMA complete-gene percentages for all three tools.
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Has reproduction · 50
Viewing RNA-seq data on the entire human genome.
PMID 28979763 · PMC5605993 · F1000Research · 2017 · 6 claims · 3 setups
RNA-Seq Viewer is a web application that visualizes genome-wide expression data from NCBI's SRA and GEO databases using an ideogram across the entire human genome.
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Has reproduction · 89
A near complete genome for goat genetic and genomic research.
PMID 34507524 · PMC8434745 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups
Saanen_v1 is a high-quality de novo goat genome assembly from a male Saanen buck, including the first goat Y chromosome scaffold.
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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 · 76
Organelle Genomes and Transcriptomes of Nymphaea Reveal the Interplay between Intron Splicing and RNA Editing.
PMID 34576004 · PMC8466565 · International journal of molecular sciences · 2021 · 8 claims · 7 setups
Multiple partially or fully intron-spliced intermediates co-exist within an organelle, and both cis- and trans-splicing introns are spliced randomly (no fixed order), generating diverse intermediates.
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Has reproduction · 69
A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly.
PMID 23496952 · PMC3655071 · BMC genomics · 2013 · 8 claims · 8 setups
Representative de novo transcriptome assemblies are generated with as few as ~20 million reads for single-tissue samples and ~30 million reads for whole animals at the mRNA-coverage level.
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Has reproduction · 92
Chromosome-scale genome sequencing, assembly and annotation of six genomes from subfamily Leishmaniinae.
PMID 34489462 · PMC8421402 · Scientific data · 2021 · 8 claims · 8 setups
Chromosome-scale genomes of six Leishmaniinae species (five L. (Mundinia) species and one Porcisia species) were sequenced, assembled and annotated, providing genome, proteome, transcriptome and GFF outputs for taxa previously lacking public reference genomes
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Has reproduction · 90
Gap-free telomere-to-telomere haplotype assembly of the tomato hind (Cephalopholis sonnerati).
PMID 39578472 · PMC11584678 · Scientific data · 2024 · 8 claims · 8 setups
Two T2T gap-free haplotype assemblies of C. sonnerati (YSFRI_Csonn_HA_1.0 and YSFRI_Csonn_HB_1.0) were successfully generated, each spanning 24 chromosomes with no gaps.
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Has reproduction · 85
Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain).
PMID 37137526 · PMC10214862 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2023 · 8 claims · 8 setups
First high-quality chromosome-level genome assembly and annotation of P. lilfordi, generated via a mixed sequencing strategy (10X linked reads, ONT long reads, Hi-C) plus RNAseq/Iso-Seq
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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.
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Full-text index only
Evolutionary toggling of the MAPT 17q21.31 inversion region.
PMID 19165922 · PMC2684794 · Nature genetics · 2008 · 8 claims · 6 setups
The H2 (inverted) orientation is the most likely ancestral great ape/human configuration at 17q21.31
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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 · 74
MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction.
PMID 34172000 · PMC8235852 · BMC genomics · 2021 · 8 claims · 8 setups
MicroPIPE, an end-to-end Nextflow/Singularity-based pipeline built from systematically validated tool choices, produces high-quality complete bacterial genome assemblies without manual intervention.