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).

• Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

  PMID 17576681 · PMC1934990 · Nucleic acids research · 2007 · 8 claims · 4 setups

  Full-text index only

  Cryptic 5'ss are best predicted by computational algorithms that accommodate nucleotide dependencies (e.g., Markov model, maximum entropy, maximum dependence decomposition) rather than by weight-matrix models

  disease mammalian compiled literature minigene computational

• Ribosome A and P sites revealed by length analysis of ribosome profiling data.

  PMID 25805170 · PMC4402525 · Nucleic acids research · 2015 · 8 claims · 8 setups

  Has reproduction · 81

  Accounting for ribosome footprint length variation reveals the ribosome aminoacyl (A) and peptidyl (P) site locations within footprints.

  coli saccharomyces ribosome single ribosome mrna-seq sequence

• Detecting transcriptionally active regions using genomic tiling arrays.

  PMID 16859498 · PMC1779562 · Genome biology · 2006 · 8 claims · 4 setups

  Full-text index only

  A non-parametric method (TranscriptionDetector) integrates single-channel p-values from multiple replicate arrays into a multi-channel p-value (MCPV) to identify transcribed probed loci without assumptions about intensity distributions.

  anopheles chromosomes simulated genomic high-density sequence-based

• Rbfox2 controls autoregulation in RNA-binding protein networks.

  PMID 24637117 · PMC3967051 · Genes & development · 2014 · 8 claims · 8 setups

  Has reproduction · 48

  Rbfox2 cross-regulates AS-NMD events within RNA-binding protein genes to alter their expression, tuning autoregulatory splicing networks and placing Rbfox2 at a critical node of a multilayer regulatory network.

  v6.5 fhfox2 top introns iclip sequencing rt-pcr

• Natural selection of protein structural and functional properties: a single nucleotide polymorphism perspective.

  PMID 18397526 · PMC2643940 · Genome biology · 2008 · 8 claims · 8 setups

  Full-text index only

  The SNP A/S ratio is a robust measure of selective constraint, correlating with interspecies Ka/Ks ratios and with protein sequence conservation.

  sequence genes proteins sequences snp interspecies sequence

• Large-scale discovery of insertion hotspots and preferential integration sites of human transposed elements.

  PMID 20008508 · PMC2836564 · Nucleic acids research · 2010 · 8 claims · 6 setups

  Full-text index only

  Most TEs insert within specific 'hotspots' along the targeted TE rather than uniformly.

  genome sequences unique nested chi-square position-specific

• Integrated analysis of post-transcriptional regulations reveals insights into acute myeloid leukemia.

  PMID 41407883 · PMC12712020 · Communications biology · 2025 · 8 claims · 8 setups

  Has reproduction · 32

  PTRs are highly conserved across 44 AML samples and 30 different human tissues, indicating broadly conserved post-transcriptional mechanisms

  blasts aml impaired top integrative proteomics sequencing

• An extensive evaluation of read trimming effects on Illumina NGS data analysis.

  PMID 24376861 · PMC3871669 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  Read trimming increases the quality and reliability of downstream NGS analyses (RNA-Seq mapping, SNP identification, genome assembly) while reducing execution time and computational resources.

  homo arabidopsis prunus saccharomyces rna-seq snp novo