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 · 78
Fungal metabarcoding data integration framework for the MycoDiversity DataBase (MDDB).
PMID 32463383 · PMC7734503 · Journal of integrative bioinformatics · 2020 · 6 claims · 5 setups
The MycoDiversity DataBase (MDDB) is a curated repository integrating public fungal metabarcoding data of environmental samples to study fungal biodiversity patterns in space and time.
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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 · 74
Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.
PMID 23555231 · PMC3610916 · PLoS computational biology · 2013 · 8 claims · 8 setups
Most of the G. intestinalis genome is transcribed in in vitro-grown trophozoites, but at vastly different expression levels.
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GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs.
PMID 17178752 · PMC1781107 · Nucleic acids research · 2007 · 8 claims · 5 setups
GenomeTrafac is a web-accessible database enabling genome-wide detection of conserved cis-element clusters in human-mouse gene orthologs, covering both conventional and microRNA genes
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CapsID: a web-based tool for developing parsimonious sets of CAPS molecular markers for genotyping.
PMID 16686952 · PMC1471797 · BMC genetics · 2006 · 7 claims · 1 setups
CapsID identifies snip-SNPs (SNPs that alter restriction endonuclease recognition sites) within reference sequence alignments and designs PCR primers around them
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Has reproduction · 95
The archives are half-empty: an assessment of the availability of microbial community sequencing data.
PMID 32859925 · PMC7455719 · Communications biology · 2020 · 8 claims · 5 setups
More than half of surveyed amplicon sequencing studies were affected by lack of data deposition, improper file formatting, or inconsistent labeling that impede reuse.
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RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration.
PMID 18954448 · PMC2605478 · BMC genomics · 2008 · 7 claims · 4 setups
Constructed enhanced protein databases integrating annotated SAPs, PTMs, and disease associations for 17 organisms.
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Has reproduction · 57
KARAJ: An Efficient Adaptive Multi-Processor Tool to Streamline Genomic and Transcriptomic Sequence Data Acquisition.
PMID 36430895 · PMC9694301 · International journal of molecular sciences · 2022 · 8 claims · 6 setups
KARAJ automates end-to-end querying and downloading of genomic/transcriptomic sequence data from a list of PMCIDs, URLs, or accession numbers
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In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip technology.
PMID 15871745 · PMC1156887 · BMC genomics · 2005 · 7 claims · 6 setups
Only 14±2% of canine transcripts were detected by U133A probe sets versus 49±6% of human transcripts when hybridized to the same chip
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SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis.
PMID 17338820 · PMC1839109 · BMC bioinformatics · 2007 · 6 claims · 4 setups
EVDB is a comprehensive, non-redundant relational database of known human splice variants built from NCBI Entrez Gene and Evidence Viewer data
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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 · 100
Structure of a mitochondrial ribosome with fragmented rRNA in complex with membrane-targeting elements.
PMID 36253367 · PMC9576764 · Nature communications · 2022 · 8 claims · 4 setups
The P. magna mitoribosome contains rRNA split into 13 fragments (LSU1-8, SSU1-4, mt-5S)
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Benchmarking ortholog identification methods using functional genomics data.
PMID 16613613 · PMC1557999 · Genome biology · 2006 · 8 claims · 7 setups
InParanoid is the best overall ortholog identification method for identifying functionally equivalent proteins when sensitivity and selectivity are combined into an overall score.
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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 originated via transoceanic dispersal from Africa ~6.6 Ma, with most biodiversity arising from rapid mid-Pleistocene (0.5–2.0 Ma) diversification plus multiple long-distance dispersals.