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 · 67
Optimal scaling of digital transcriptomes.
PMID 24223126 · PMC3819321 · PloS one · 2013 · 8 claims · 8 setups
Fifteen existing and novel transcript-count normalization algorithms can be compared with two novel, mutually independent metrics: the number of "uniform" genes (sufficiently low coefficient of variation after normalization) and low average Spearman correlation between normalized expression profiles of gene pairs.
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Has reproduction · 94
Large-Scale Phylogenomics of the Lactobacillus casei Group Highlights Taxonomic Inconsistencies and Reveals Novel Clade-Associated Features.
PMID 28845461 · PMC5566788 · mSystems · 2017 · 8 claims · 8 setups
Many strains currently classified as L. casei or L. paracasei are taxonomically misclassified; reclassifying them to their closest type strain improves functional predictive power
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Promoting human promoters.
PMID 16760901 · PMC1681504 · Molecular systems biology · 2006 · 8 claims · 5 setups
A computational protocol using MARS on known sequence motifs can quantify transcription factor effects on human gene expression despite noise and data size challenges
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Has reproduction · 78
Protocol for the generation of single-nuclei RNA-seq libraries and quantification of heterogeneous cell types activated during social interaction.
PMID 39423127 · PMC11532268 · STAR protocols · 2024 · 7 claims · 5 setups
A protocol for dissecting mouse PFC, hippocampus, and cerebellum and generating snRNA-seq libraries can identify neuronal populations activated during social interaction.
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Single nucleotide polymorphism discovery and functional assessment of variation in the UDP-glucuronosyltransferase 2B7 gene.
PMID 18622261 · PMC2680356 · Pharmacogenetics and genomics · 2008 · 7 claims · 7 setups
UGT2B7 haplotype 4 is associated with increased enzyme activity (M3G and M6G formation)
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Urinary proteomic profiling for diagnostic bladder cancer biomarkers.
PMID 19811072 · PMC3422861 · Expert review of proteomics · 2009 · 8 claims · 8 setups
Single protein biomarkers (e.g., NMP-22, BTA) suffer from high false-positive rates and none have replaced cystoscopy or cytology for bladder cancer detection.
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Quality control of highly multiplexed proteomic immunostaining with quantum dots: correcting for crosstalk.
PMID 19963937 · PMC5859565 · Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference · 2009 · 8 claims · 5 setups
Crosstalk between multiplexed QD-antibody reporters occurs and can be on the same order of magnitude as the intended signal, varying by tissue and reagent.
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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
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Has reproduction · 38
RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.
PMID 24324815 · PMC3855774 · PloS one · 2013 · 8 claims · 8 setups
A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed field-grown upland cotton root tissues (913 up-regulated, 617 down-regulated).
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Has reproduction · 86
RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.
PMID 22199257 · PMC3315322 · Nucleic acids research · 2012 · 8 claims · 7 setups
RNASEQR is a new RNA-seq mapper/aligner that combines a BWT-based (Bowtie) transcriptomic/genomic alignment with hash-based BLAT local alignment in three sequential steps: transcriptome mapping, novel exon detection, and anchor-and-align novel splice junction identification.
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EGASP: the human ENCODE Genome Annotation Assessment Project.
PMID 16925836 · PMC1810551 · Genome biology · 2006 · 8 claims · 6 setups
Best-performing computational gene prediction methods correctly predict at least one transcript for close to 70% of annotated genes in the ENCODE regions.
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Targeted capture and massively parallel sequencing of 12 human exomes.
PMID 19684571 · PMC2844771 · Nature · 2009 · 8 claims · 8 setups
Targeted exome capture combined with massively parallel sequencing sensitively and specifically identifies rare and common variants across >300 Mb of coding sequence
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DNA sequencing: bench to bedside and beyond.
PMID 17855400 · PMC2094077 · Nucleic acids research · 2007 · 8 claims · 7 setups
DNA sequencing methods derived from Sanger's 1977 dideoxy method have dominated sequencing for 30 years despite being only incrementally refined.
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Genomics, proteomics and bioinformatics: all in the same boat.
PMID 12374575 · PMC244909 · Genome biology · 2002 · 8 claims · 8 setups
Microarray sensitivity has improved enough to analyze clinical samples as small as 10-50 nanograms, and many early microarray experiments may need to be repeated due to data quality issues
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The vertebrate genome annotation (Vega) database.
PMID 18003653 · PMC2238886 · Nucleic acids research · 2008 · 8 claims · 8 setups
Vega is a database for viewing manual genome annotation of human, mouse and zebrafish genomic sequences produced at the Wellcome Trust Sanger Institute.