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).

• FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq.

  PMID 23768108 · PMC3691734 · BMC bioinformatics · 2013 · 8 claims · 8 setups

  Has reproduction · 65

  FusionQ is a novel tool that detects gene fusions, constructs chimerical transcript structures, and estimates their abundances from paired-end RNA-Seq data.

  simulated four rna-seq randomly simulated paired-end read-mappability

• An empirical study of choosing efficient discriminative seeds for oligonucleotide design.

  PMID 19958494 · PMC2788383 · BMC genomics · 2009 · 8 claims · 3 setups

  Full-text index only

  The spaced seed is the most efficient discriminative seed for oligonucleotide design among the five algorithms tested.

  simulated pmoa nirs seed

• Bayesian transcriptome assembly.

  PMID 25367074 · PMC4397945 · Genome biology · 2014 · 8 claims · 8 setups

  Has reproduction · 68

  Bayesembler, a probabilistic transcriptome assembler built on a Bayesian model of the RNA sequencing process with Gibbs sampling over expressed candidates, abundances and read assignments, is introduced.

  k562 embryonic dendritic rna-seq simulated paired-end long-read

• Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses.

  PMID 19761607 · PMC2759961 · BMC bioinformatics · 2009 · 8 claims · 5 setups

  Full-text index only

  2LOmb performs an omnibus permutation test on ensembles of two-locus analyses via a four-step algorithm (two-locus analysis, permutation test, global p-value determination, progressive ensemble search)

  simulated same snp type two-locus 2lomb benchmark

• RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.

  PMID 22199257 · PMC3315322 · Nucleic acids research · 2012 · 8 claims · 7 setups

  Has reproduction · 86

  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.

  ccds glioblastoma experimental simulated simulated bulk quality

• Whole genome association mapping by incompatibilities and local perfect phylogenies.

  PMID 17042942 · PMC1624851 · BMC bioinformatics · 2006 · 8 claims · 8 setups

  Full-text index only

  Blossoc scores the perfect phylogenetic tree spanning the largest compatible region around each marker as a decision tree for case/control status to detect association

  coalescent-simulated artificial empirical same perfect-phylogeny hapminer haplotype

• Testing groups of genomic locations for enrichment in disease loci using linkage scan data: a method for hypothesis testing.

  PMID 16848972 · PMC3525155 · Human genomics · 2006 · 8 claims · 2 setups

  Full-text index only

  A method testing enrichment of a group of genomic locations for disease loci by comparing the average NPL score of the group to a null distribution from randomly drawn groups of equal size

  simulated pedigrees simulated real

• On the analysis of glycomics mass spectrometry data via the regularized area under the ROC curve.

  PMID 18076765 · PMC2211327 · BMC bioinformatics · 2007 · 8 claims · 4 setups

  Full-text index only

  The TGDR-AUC algorithm regularizes the empirical AUC by replacing the non-differentiable 0-1 loss with a smooth sigmoid surrogate function and applies constrained threshold gradient descent regularization

  simulated serum preprocessed simulation mass high-resolution

• A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145.

  PMID 17939873 · PMC2222656 · BMC bioinformatics · 2007 · 8 claims · 4 setups

  Full-text index only

  Yu et al.'s original comparison ran RJaCGH's MCMC sampler for a severely insufficient number of iterations (50 burn-in, 500 total)

  simulated same mcmc-based direct original

• Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals.

  PMID 18826599 · PMC2576242 · BMC evolutionary biology · 2008 · 7 claims · 4 setups

  Full-text index only

  CpG/non-CpG assignment based on presence/absence of a CpG dinucleotide seriously biases substitution rate estimates, overestimating CpG changes and underestimating non-CpG changes.

  randomly real human-chimpanzee simulated simulation comparative

• Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes.

  PMID 17158152 · PMC1802574 · Nucleic acids research · 2007 · 8 claims · 8 setups

  Full-text index only

  GLR is a novel maximum-likelihood measure of gene loss rate that probabilistically weighs all possible ancestral phyletic patterns rather than relying on a single parsimonious reconstruction.

  synthetic eukaryotic simulated 16-species analytical comparative simulation

• QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data.

  PMID 17341461 · PMC1874617 · Nucleic acids research · 2007 · 8 claims · 7 setups

  Full-text index only

  QuantiSNP (OB-HMM) provides probabilistic quantification of copy number states and significantly improves accuracy of segmental aneuploidy identification and breakpoint mapping relative to existing tools (BeadStudio/Illumina)

  genomic same pseudo-normal artificially snp fish molecular

• LMAS: evaluating metagenomic short de novo assembly methods through defined communities.

  PMID 36576131 · PMC9795473 · GigaScience · 2022 · 8 claims · 5 setups

  Has reproduction · 86

  LMAS (Last Metagenomic Assembler Standing) is a flexible, Nextflow-based, Docker-containerized automated workflow for benchmarking de novo metagenomic assemblers against defined mock communities, producing an interactive HTML report.

  zymobiomics assembled assembler-generated novo reference-based contig

• The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists.

  PMID 17784955 · PMC2375021 · Genome biology · 2007 · 8 claims · 6 setups

  Full-text index only

  Gene-gene functional similarity can be measured using kappa statistics applied to a binary gene-annotation-term matrix built from 14 annotation categories.

  genome protein-protein genes artificial kappa clustering gene

• Improving the specificity of exon prediction using comparative genomics.

  PMID 18831778 · PMC2559877 · BMC genomics · 2008 · 8 claims · 6 setups

  Full-text index only

  A log-odds ratio scoring method based on codon conservation across human-mouse/human-dog alignments and adjacent-codon dependency can classify putative exons as coding vs non-coding.

  human-mouse human-dog genome simulated comparative single-genome simulated

• Genomic variability within an organism exposes its cell lineage tree.

  PMID 16261192 · PMC1274291 · PLoS computational biology · 2005 · 8 claims · 5 setups

  Full-text index only

  Somatic mutations accumulated during normal development implicitly encode an organism's entire cell lineage tree with very high precision.

  robinia arabidopsis randomly genotyping multiplex computer

• A comparative study of techniques for differential expression analysis on RNA-Seq data.

  PMID 25119138 · PMC4132098 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 58

  edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives.

  brain neurospheres lymphoblastoid simulation single-end paired-end rna-seq

• CGHPRO -- a comprehensive data analysis tool for array CGH.

  PMID 15807904 · PMC1274268 · BMC bioinformatics · 2005 · 8 claims · 3 setups

  Full-text index only

  CGHPRO is a user-friendly, versatile, stand-alone Java tool for normalization, visualization, breakpoint detection and comparative analysis of array-CGH data

  tiling artificially array

• Accurate chromatin marks peak calling with Omnipeak.

  PMID 41521664 · PMC12784980 · Nucleic acids research · 2026 · 8 claims · 6 setups

  Has reproduction · 77

  Omnipeak is a universal unsupervised peak-calling algorithm based on a constrained three-state hidden Markov model (zero, noise, signal states)

  gm12878 roadmap abf immgen chip-seq ultra-low-input atac-seq

• The distribution of SNPs in human gene regulatory regions.

  PMID 16209714 · PMC1260019 · BMC genomics · 2005 · 8 claims · 6 setups

  Full-text index only

  SNPs occur with higher density closer to the transcriptional start site within gene promoter regions than in further upstream regions

  gene mammalian promoter experimentally genome-wide computational binding