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).

• RNAmountAlign: Efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure alignment.

  PMID 31978147 · PMC6980424 · PloS one · 2020 · 8 claims · 6 setups

  Has reproduction · 71

  RNAmountAlign is the first RNA sequence/structure pairwise alignment algorithm based on incremental ensemble mountain distance, running in O(n^3) time and O(n^2) space for two sequences of length n.

  sequences sequence trna target pairwise global single

• StatsDB: platform-agnostic storage and understanding of next generation sequencing run metrics.

  PMID 24627795 · PMC3938176 · F1000Research · 2013 · 8 claims · 6 setups

  Has reproduction · 43

  StatsDB is an open-source software package for storage and analysis of next generation sequencing run metrics, backed by an SQL (MySQL) database with Perl and Java APIs.

  fastq mysql perl java fastqc relational programmatic

• Divergence of exonic splicing elements after gene duplication and the impact on gene structures.

  PMID 19883501 · PMC3091315 · Genome biology · 2009 · 8 claims · 7 setups

  Full-text index only

  ESEs and ESSs diverge especially fast shortly after gene duplication, correlating with time since duplication (Ks)

  paralogous human-mouse duplicated comparative ortholog binomial

• Viroporin potential of the lentivirus lytic peptide (LLP) domains of the HIV-1 gp41 protein.

  PMID 18028545 · PMC2211469 · Virology journal · 2007 · 8 claims · 4 setups

  Full-text index only

  Synthetic peptides corresponding to LLP-1, LLP-2, and LLP-3 domains partition into POPC:POPG lipid membranes and adopt amphipathic α-helical secondary structure

  hiv-1 synthetic nbd 90%popc wimley-white circular tryptophan

• Analysis of concordance of different haplotype block partitioning algorithms.

  PMID 16356172 · PMC1343594 · BMC bioinformatics · 2005 · 7 claims · 7 setups

  Full-text index only

  Each block partitioning algorithm infers blocks differing in number, size, and coverage under different SNP density and allele frequency conditions.

  simulated subsamples coalescent diversity-based ld-based