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).

• binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets.

  PMID 36239393 · PMC9677464 · Briefings in bioinformatics · 2022 · 8 claims · 8 setups

  Has reproduction · 67

  binny outperforms or is highly competitive with commonly used and state-of-the-art binning methods (MetaBAT2, MaxBin2, CONCOCT, VAMB, SemiBin, MetaDecoder)

  cami real-world metagenomic binned genome binning mag

• The MAPPER database: a multi-genome catalog of putative transcription factor binding sites.

  PMID 15608292 · PMC540057 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  Built a library of 1134 HMM models (359 matrix-derived, 718 factor-derived, 57 JASPAR-derived), corresponding to 863 distinct TF names, from TRANSFAC and JASPAR binding site data

  genome drosophila transfac b99 profile sequence case-study

• Reconstructing the evolution of the mitochondrial ribosomal proteome.

  PMID 17604309 · PMC1950548 · Nucleic acids research · 2007 · 8 claims · 6 setups

  Full-text index only

  The ancestral mitoribosome was of alpha-proteobacterial descent and more than doubled its protein content in most eukaryotic lineages.

  proteomes eukaryotic aligned alignments iterative hmm-based neighbor-joining

• SysZNF: the C2H2 zinc finger gene database.

  PMID 18974185 · PMC2686507 · Nucleic acids research · 2009 · 7 claims · 6 setups

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  SysZNF is a database that systematically catalogs C2H2-ZNF genes in human and mouse with physical location, gene models, expression probes, protein domains, homologs, and literature links

  user-defined hmm domain all-to-all

• A model-based approach to selection of tag SNPs.

  PMID 16776821 · PMC1525207 · BMC bioinformatics · 2006 · 7 claims · 5 setups

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  The Li and Stephens hidden Markov model outperforms other tested models (simple Markov, two-state HMM, HMM-4D, greedy GR-1/GR-2) in description code-length, tag set information content, and prediction of tagged SNPs.

  hapmap encode enr112 tag cross-validated entropy tagged

• ADaCGH: A parallelized web-based application and R package for the analysis of aCGH data.

  PMID 17710137 · PMC1940324 · PloS one · 2007 · 8 claims · 4 setups

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  ADaCGH implements eight CNA detection methods, including the best-performing ones from recent reviews (CBS, GLAD, CGHseg, HMM)

  30-node web-based cluster simulated computational web comparison

• Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines.

  PMID 36864379 · PMC9979506 · Genetics, selection, evolution : GSE · 2023 · 6 claims · 8 setups

  Has reproduction · 100

  French LWD and LWS lines have lost approximately 5% of the SNPs that segregated in the 1977 ancestral population.

  boars lwd lws pig whole-genome genetic genome-wide

• Pathway analysis of kidney cancer using proteomics and metabolic profiling.

  PMID 17123452 · PMC1665458 · Molecular cancer · 2006 · 8 claims · 8 setups

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  31 proteins are differentially expressed with high statistical significance (p<0.05) in ccRCC tumor tissue compared to adjacent non-malignant kidney tissue

  ccrcc rcc computational random gel immunoblotting immunohistochemistry

• Local combinational variables: an approach used in DNA-binding helix-turn-helix motif prediction with sequence information.

  PMID 19651875 · PMC2761287 · Nucleic acids research · 2009 · 8 claims · 7 setups

  Full-text index only

  The LCV approach predicts HTH motifs with 93.29% accuracy, 93.93% sensitivity and 92.66% specificity using only primary sequence information

  quintessentialset-88 hth same newly lcs svm traditional

• AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome.

  PMID 16925833 · PMC1810548 · Genome biology · 2006 · 8 claims · 5 setups

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  AUGUSTUS predicted significantly more genes correctly than any other ab initio program in EGASP

  genome human-mouse genes initio comparative extrinsic