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).

• Comparative genomics of Drosophila and human core promoters.

  PMID 16827941 · PMC1779564 · Genome biology · 2006 · 8 claims · 6 setups

  Full-text index only

  Drosophila core promoters contain 298 highly significant (p≤1e-16) non-randomly positioned 8-mers within 100 bp of the TSS, grouped into 15 distinct DNA motifs

  drosophila core genome-wide mono gene

• Tri-nucleotide threading for parallel amplification of minute amounts of genomic DNA.

  PMID 16582098 · PMC1421508 · Nucleic acids research · 2006 · 6 claims · 5 setups

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  TnT enables parallel amplification of 75 SNPs from sub-nanogram amounts of genomic DNA

  genomic dbsnp tnt duplex bioinformatic

• Ab initio identification of human microRNAs based on structure motifs.

  PMID 18088431 · PMC2238772 · BMC bioinformatics · 2007 · 8 claims · 7 setups

  Full-text index only

  MiRPred predicts miRNA precursors ab initio using only predicted secondary structure motifs, ignoring nucleotide sequence

  genome mirna hairpins chromosome secondary linear five-fold

• Skittle: a 2-dimensional genome visualization tool.

  PMID 20042093 · PMC2817707 · BMC bioinformatics · 2009 · 7 claims · 6 setups

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  Skittle is a 2D genome visualization tool combining a color-coded Nucleotide Display, a Repeat Map, a Repeat Overview, and an Alignment Cylinder to reveal genomic patterns at multiple scales

  chromosome random alpha genome nucleotide repeat alignment

• CorGen--measuring and generating long-range correlations for DNA sequence analysis.

  PMID 16845099 · PMC1538783 · Nucleic acids research · 2006 · 8 claims · 3 setups

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  CorGen is a web server that measures long-range correlations in DNA sequences and generates random sequences with the same (or user-specified) correlation and composition parameters

  chromosome query synthetic long-range sequence

• Spontaneous symmetry breaking in genome evolution.

  PMID 18367477 · PMC2377439 · Nucleic acids research · 2008 · 6 claims · 3 setups

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  Exon size distributions in sequenced genomes follow a lognormal pattern typical of a random Kolmogoroff fractioning process

  animal homo model genome-wide alternatively computational

• Topological signatures in regulatory network enable phenotypic heterogeneity in small cell lung cancer.

  PMID 33729159 · PMC8012062 · eLife · 2021 · 7 claims · 6 setups

  Has reproduction · 94

  Discrete (Boolean/Ising) and continuous (RACIPE) simulations of the SCLC regulatory network yield similar multistable phenotypic distributions, with four dominant steady states (X1-X4) that map onto experimentally observed SCLC molecular subtypes.

  sclc randomized mutant boolean racipe network

• Machine learning algorithm predicts fibrosis-related blood diagnosis markers of intervertebral disc degeneration.

  PMID 37915003 · PMC10619283 · BMC medical genomics · 2023 · 7 claims · 7 setups

  Has reproduction · 68

  CEP120 and SPDL1 are fibrosis-related diagnostic genes for IDD, identified via a random forest model from 29 differentially expressed fibrosis-related genes

  blood gse150408 prediction pbmcs bulk machine roc

• Predicting favorable landing pads for targeted integrations in Chinese hamster ovary cell lines by learning stability characteristics from random transgene integrations.

  PMID 33304461 · PMC7710658 · Computational and structural biotechnology journal · 2020 · 7 claims · 6 setups

  Has reproduction

  Expression stability in CHO cell lines is controlled at three levels: choice of integration site, integrity/concatemerization pattern of the transgene, and stress-related cellular processes.

  horizon six cho-k1 cho genome rna-seq targeted

• GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning.

  PMID 34461978 · PMC8407037 · Genome medicine · 2021 · 8 claims · 6 setups

  Has reproduction · 78

  GenTB is a free, open, web-based application offering two ML predictors (Random Forest and WDNN) that predict resistance to 13 and 10 anti-TB drugs, respectively.

  clinical tuberculosis registered whole-genome targeted retraining

• Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences.

  PMID 16759380 · PMC1525190 · BMC genomics · 2006 · 8 claims · 6 setups

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  Overall pairwise genomic divergences among cattle, dog and human are relatively constant (0.32–0.37 change/site)

  orthologous random cattle aligned three-way pairwise bac

• Allelic drop-out may occur with a primer binding site polymorphism for the commonly used RFLP assay for the -1131T>C polymorphism of the Apolipoprotein AV gene.

  PMID 16670016 · PMC1513378 · Lipids in health and disease · 2006 · 8 claims · 6 setups

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  A -987C>T polymorphism located 4bp from the 3' end of the MseI RFLP forward primer causes allelic drop-out, producing incorrect -1131T>C genotypes.

  asian random subjects unrelated arms-pcr msei sanger

• A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation.

  PMID 16423292 · PMC1382217 · BMC genomics · 2006 · 7 claims · 6 setups

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  Expression context is largely conserved between orthologs across four eukaryote species.

  elegans pairwise orthologs cerevisiae microarray ortholog functional

• Predicting preferential DNA vector insertion sites: implications for functional genomics and gene therapy.

  PMID 18047689 · PMC2106846 · Genome biology · 2007 · 8 claims · 6 setups

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  Vector insertion site preferences differ substantially between viral vectors and transposons, affecting both oncogenic risk in gene therapy and utility for functional genomics

  hela liver gene peripheral retroviral transposon hydrodynamic

• Environmental Burkholderia cepacia complex isolates in human infections.

  PMID 17552100 · PMC2725883 · Emerging infectious diseases · 2007 · 6 claims · 4 setups

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  More than 20% of clinical Bcc isolates examined are indistinguishable by MLST from environmental isolates, linking the natural environment to emergence of clinical infections

  clinical environmental subset stabilis multilocus cloning pulsed-field

• Predicting failure rate of PCR in large genomes.

  PMID 18492719 · PMC2441781 · Nucleic acids research · 2008 · 7 claims · 8 setups

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  The number of predicted primer-binding sites in genomic DNA is the most important factor determining PCR failure.

  genomic genome pcr combined large-scale exact-match mismatch-tolerant

• CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes.

  PMID 19854943 · PMC2800233 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  Functional ('bona fide') CGIs show distinct average/cumulative mutual information (AMI/CMI) distributions of neighboring CpG distances compared to non-functional CGIs and random genome segments

  genome random cd4+ six average mutual chip-seq

• Sequencing of human genomes with nanopore technology.

  PMID 31015479 · PMC6478738 · Nature communications · 2019 · 8 claims · 7 setups

  Has reproduction · 75

  A novel single-sample, reference panel-free, read-based phasing algorithm built on the STITCH model improves nanopore SNV calling from modest baseline levels.

  gm12878 na12878 clinical whole-genome snv read-based

• Gene signature discovery and systematic validation across diverse clinical cohorts for TB prognosis and response to treatment.

  PMID 37471455 · PMC10393163 · PLoS computational biology · 2023 · 8 claims · 8 setups

  Has reproduction · 100

  A network-based meta-analysis across studies identifies a common 45-gene signature specific to active TB disease that accounts for cohort/population heterogeneity

  n×m common independent viral blood gene random

• Prediction of prognostic signatures in triple-negative breast cancer based on the differential expression analysis via NanoString nCounter immune panel.

  PMID 33138797 · PMC7607642 · BMC cancer · 2020 · 8 claims · 7 setups

  Has reproduction · 72

  edgeR identifies 9 DEGs associated with pCR and 13 DEGs associated with relapse from 579 immune genes in a small TNBC sample set (n=55)

  ffpe same nanostring training nanostring immunohistochemistry differential