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).

• Optimizing open data to support one health: best practices to ensure interoperability of genomic data from bacterial pathogens.

  PMID 33103064 · PMC7568946 · One health outlook · 2020 · 8 claims · 3 setups

  Has reproduction · 85

  An open-access pathogen surveillance database (NCBI Pathogen Detection) plus contributor Best Practices enables FAIR, interoperable genomic data across human, animal, food, and environmental sources for One Health surveillance.

  salmonella ncbi-pd illumina empirical coverage

• Optimal scaling of digital transcriptomes.

  PMID 24223126 · PMC3819321 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 67

  Fifteen existing and novel transcript-count normalization algorithms can be compared with two novel, mutually independent metrics: the number of "uniform" genes (sufficiently low coefficient of variation after normalization) and low average Spearman correlation between normalized expression profiles of gene pairs.

  tissues bodymap mapped 16-sample bulk read transcript

• HTSstation: a web application and open-access libraries for high-throughput sequencing data analysis.

  PMID 24475057 · PMC3903476 · PloS one · 2014 · 8 claims · 5 setups

  Has reproduction · 66

  HTSstation is a web application suite coupling simple web forms to modular analysis pipelines for ChIP-seq, RNA-seq, 4C-seq and re-sequencing HTS applications, accessible at http://htsstation.epfl.ch.

  embryonic mycobacterium forebrain rna-seq re-sequencing 4c-seq

• TC-hunter: identification of the insertion site of a transgenic gene within the host genome.

  PMID 35184734 · PMC8859905 · BMC genomics · 2022 · 7 claims · 4 setups

  Has reproduction · 69

  TC-hunter is an open-source Nextflow pipeline that identifies transgene insertion sites using chimeric reads and discordant read pairs from NGS data.

  ppm1d-transgenic genome genome read touchdown-pcr

• Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs.

  PMID 23536903 · PMC3607606 · PloS one · 2013 · 8 claims · 9 setups

  Has reproduction · 45

  Bubbleparse detects sequence variants directly from NGS reads without a reference genome, using the coloured de Bruijn graph implementation of Cortex plus a new depth-first bubble-finding module.

  arabidopsis bubbleparse escherichia col-0 reference-free alignment-based sequence

• The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.

  PMID 24068976 · PMC3778014 · PLoS genetics · 2013 · 8 claims · 8 setups

  Has reproduction · 76

  The 50 Mb P. confluens genome with 13,369 predicted protein-coding genes is more characteristic of higher filamentous ascomycetes than of the large, repeat-rich Tuber melanosporum genome, showing that the truffle's expanded genome is not typical of the Pezizales.

  pyronema confluens fungal whole-genome k-mer rna-seq

• Assessing the gene space in draft genomes.

  PMID 19042974 · PMC2615622 · Nucleic acids research · 2009 · 6 claims · 7 setups

  Full-text index only

  The proportion of mapped CEGs in a draft genome assembly is a useful metric for describing gene space completeness, complementing N50 and x-fold coverage.

  caenorhabditis toxoplasma homo briggsae cegma blast tblastn

• Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level.

  PMID 17090320 · PMC1654190 · BMC evolutionary biology · 2006 · 8 claims · 5 setups

  Full-text index only

  HHpred (HMM-HMM comparison) detects remote homologs in the human proteome with higher sensitivity than hmmpfam (HMMER), giving 10% more functional domain coverage and 20% higher residue coverage against Pfam-A families.

  proteome homo domains hmm-hmm hmm subtractive

• Genomic Description of 'Candidatus Abyssubacteria,' a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes.

  PMID 30210471 · PMC6121073 · Frontiers in microbiology · 2018 · 8 claims · 7 setups

  Has reproduction · 91

  SURF_5 and SURF_17 are the first full genomes of a novel bacterial lineage, 'Candidatus Abyssubacteria,' within the candidate phylum Hydrogenedentes

  deep co-assembled surf_17 surf_5 whole-genome novo 16s

• Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments.

  PMID 36088548 · PMC9487593 · Briefings in bioinformatics · 2022 · 8 claims · 6 setups

  Has reproduction · 94

  Well-established, hierarchically organized pathway annotation systems (e.g. GO, Reactome, KEGG) yield the best overall enrichment performance despite covering much of the human genome only in general terms.

  user-submitted string pubmed protein-coding gene hierarchical text-mining

• Proteomic comparison of two-dimensional gel electrophoresis profiles from human lung squamous carcinoma and normal bronchial epithelial tissues.

  PMID 15626334 · PMC5172349 · Genomics, proteomics & bioinformatics · 2003 · 8 claims · 5 setups

  Full-text index only

  Well-resolved, reproducible 2-DE profiles of human lung squamous carcinoma and normal bronchial epithelial tissues were obtained under optimized conditions (0.75-mg protein load, TCA precipitation)

  lung scanned excised peptide 2-d 2-de maldi-tof-ms

• Comparative Genome Analysis of 16SrXII-A 'Candidatus Phytoplasma solani' POT Transmitted by Hyalesthes obsoletus.

  PMID 41597744 · PMC12843639 · Microorganisms · 2026 · 7 claims · 8 setups

  Has reproduction · 95

  The complete 832,614 bp circular chromosome of the H. obsoletus-transmissible 'Ca. P. solani' 16SrXII-A strain POT was assembled and functionally reconstructed.

  catharanthus pacbio smrt pot experimental endpoint smrt

• 'Genome design' model and multicellular complexity: golden middle.

  PMID 17062620 · PMC1635334 · Nucleic acids research · 2006 · 8 claims · 8 setups

  Full-text index only

  Intermediately expressed human genes are the longest genes genome-wide, in both coding and intronic sequence, longer than housekeeping or tissue-specific genes.

  normal genes proteins encoded oligonucleotide gene functional

• Nucleosome regulatory dynamics in response to TGFβ.

  PMID 24771338 · PMC4066760 · Nucleic acids research · 2014 · 8 claims · 7 setups

  Has reproduction · 59

  SuMMIt, a Bayesian strand-based mixture model requiring support from both ends of sequenced fragments, enables precise nucleosome mid-position calling, fuzziness scoring and between-condition change detection.

  hepatocellular hepg2 130-bp mnase strand-specific taqman

• 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

• Analysis of recent segmental duplications in the bovine genome.

  PMID 19951423 · PMC2796684 · BMC genomics · 2009 · 8 claims · 6 setups

  Full-text index only

  Recently duplicated sequence (≥1 kb, ≥90% identity) comprises 3.11% (94.4 Mb) of the bovine genome assembly (Btau_4.0)

  bos bovine genes cattle genome fluorescent repeat

• Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic.

  PMID 23516341 · PMC3597545 · PLoS computational biology · 2013 · 8 claims · 7 setups

  Has reproduction · 44

  Local sequence context strongly determines position-specific polymerase kinetic rate: roughly 80% of IPD variation is explained by a 10 bp context (7 bases upstream, 2 bases downstream of the incorporation site), saturating at 7 bases upstream.

  plasmid coli wild-type artificial smrt read-mixing distributional

• 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