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).

• Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

  PMID 17452356 · PMC1904267 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  PASE (Prediction of Alternative Signaling Exons) is a computational algorithm combining Markov splice-site models, a Bayesian classifier, species conservation, and Scansite motif scoring to identify novel alternative cassette exons involved in cell signaling.

  elegans pooled pcr known semi-nested cloning initio

• Detecting natural selection by empirical comparison to random regions of the genome.

  PMID 19783549 · PMC2778377 · Human molecular genetics · 2009 · 8 claims · 5 setups

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  Comparing candidate loci to empirically matched random genomic regions (ENCODE data) avoids the strong demographic/mutation assumptions required by theoretical neutral models and provides a robust test for selection

  ceu genomic simulated long-read snp population

• Diagnostic proteomics: serum proteomic patterns for the detection of early stage cancers.

  PMID 15258335 · PMC3851082 · Disease markers · 2003 · 8 claims · 8 setups

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  Proteomic pattern analysis of serum mass spectra, without identifying the underlying proteins, can distinguish cancer patients from healthy controls with high sensitivity and specificity.

  serum frozen ig-depleted clinical seldi-tof maldi lc-ms

• 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

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  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

• Construction and use of spotted large-insert clone DNA microarrays for the detection of genomic copy number changes.

  PMID 17406619 · PMC2688820 · Nature protocols · 2007 · 8 claims · 7 setups

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  Combining three human-optimized DOP-PCR primers before a secondary amino-labeled PCR increases array hybridization sensitivity and reproducibility sixfold compared to the standard 6MW DOP-PCR primer

  large-insert patients test genomic array-cgh manual automated

• 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

• JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions.

  PMID 16925843 · PMC1810558 · Genome biology · 2006 · 8 claims · 4 setups

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  Adding model states for specific biological features (signal peptides, CpG islands, etc.) to non-comparative GHMM gene finders did little or nothing to enhance predictive accuracy, sometimes reducing it.

  encode genes invertebrate initio comparative training

• Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA.

  PMID 16925841 · PMC1810556 · Genome biology · 2006 · 8 claims · 5 setups

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  Exogean is a framework using directed acyclic coloured multigraphs (DACMs) to represent biological objects (mRNA, ESTs, protein alignments, exons) and iteratively combine them into complex protein-coding transcript models.

  genome sequences automatic manual sequence

• AceView: a comprehensive cDNA-supported gene and transcripts annotation.

  PMID 16925834 · PMC1810549 · Genome biology · 2006 · 8 claims · 4 setups

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  At the mRNA level, AceView transcripts are the closest match to Gencode transcripts among all evaluated methods, including alternative splice variants

  genome encode caenorhabditis comparative n-to-n cds

• The cancer secretome: a reservoir of biomarkers.

  PMID 18796163 · PMC2562990 · Journal of translational medicine · 2008 · 8 claims · 8 setups

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  Cancer secretome analysis is a promising reservoir for identifying novel, non-invasive cancer biomarkers, addressing limitations of whole blood/serum proteomics

  a549 m-be sw480 neoplastic 2-de dige icat

• Unlocking the microbial studies through computational approaches: how far have we reached?

  PMID 36920617 · PMC10016191 · Environmental science and pollution research international · 2023 · 8 claims · 8 setups

  Has reproduction

  Metagenomics enables culture-independent study of microbial communities directly from their natural environments, bypassing the need for clonal isolation.

  clinical bacteriophage vaginal hbv ngs random whole-genome

• Analysis of protein sequence and interaction data for candidate disease gene prediction.

  PMID 17020920 · PMC1636487 · Nucleic acids research · 2006 · 8 claims · 7 setups

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  Combining CPS and CMP using known disease genes as input achieves sensitivity 0.52 and specificity 0.97, reducing candidate lists 13-fold

  ophid biocarta kegg pfam-annotated common benchmarking multiple-interval

• Identification of diagnostic markers for tuberculosis by proteomic fingerprinting of serum.

  PMID 16980117 · PMC7159276 · Lancet (London, England) · 2006 · 8 claims · 5 setups

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  An SVM classifier trained on serum proteomic profiles discriminated patients with active tuberculosis from controls with clinically overlapping conditions

  serum computational kda spin-column seldi-tof supervised peptide

• Reference based annotation with GeneMapper.

  PMID 16600017 · PMC1557983 · Genome biology · 2006 · 7 claims · 6 setups

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  GeneMapper transfers reference gene annotations to target genomes with higher accuracy than GeneWise and Projector

  orthologous human-mouse chicken encode reference-based multi-species reciprocal

• Detection of venous thromboembolism by proteomic serum biomarkers.

  PMID 17579716 · PMC1891085 · PloS one · 2007 · 5 claims · 8 setups

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  A neural network-based classifier built from direct MALDI-TOF MS serum protein expression profiles can diagnose VTE with sensitivity/specificity that exceeds D-dimer assays

  serum anova-selected citrated depleted direct artificial d-dimer

• Pol II promoter prediction using characteristic 4-mer motifs: a machine learning approach.

  PMID 18834544 · PMC2575220 · BMC bioinformatics · 2008 · 8 claims · 8 setups

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  128 discriminating 4-mer motifs combined with an SVM (RBF kernel, LIBSVM) can distinguish promoter from non-promoter DNA sequences

  plant drosophila promoter same 4-mer tata blast

• DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight.

  PMID 18628296 · PMC2504308 · Nucleic acids research · 2008 · 8 claims · 6 setups

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  Digital PCR compartmentalizes individual bisulfite-converted DNA template molecules into separate wells, enabling single-molecule DNA methylation analysis

  fresh-frozen same sssi-methylated mixture digital conventional classic

• Filtering high-throughput protein-protein interaction data using a combination of genomic features.

  PMID 15833142 · PMC1127019 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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  A combination of three genomic features (interacting Pfam domains, GO annotations, sequence homology) using naive Bayesian networks predicts true protein-protein interactions with high sensitivity and good specificity.

  saccharomyces bank caenorhabditis homo yeast mass naive

• Biomarkers that discriminate multiple myeloma patients with or without skeletal involvement detected using SELDI-TOF mass spectrometry and statistical and machine learning tools.

  PMID 17124346 · PMC3862287 · Disease markers · 2006 · 8 claims · 5 setups

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  SELDI-TOF MS serum profiling can discriminate MM patients with vs without skeletal (bone lesion) involvement using peak biomarkers

  serum seldi seldi-tof serum univariate

• Design and analysis issues in genome-wide somatic mutation studies of cancer.

  PMID 18692126 · PMC2820387 · Genomics · 2009 · 6 claims · 4 setups

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  Two-stage (discovery + validation) sequencing designs efficiently allocate resources and can produce highly informative candidate driver gene lists even with relatively small sample sizes.

  hypothetical panel colorectal germline simulation targeted genome-wide