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).

• Multiple whole genome alignments and novel biomedical applications at the VISTA portal.

  PMID 17488840 · PMC1933192 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  A novel multiple whole-genome alignment algorithm treats all genomes symmetrically, avoiding dependence on a single base/reference genome

  genome vertebrate multi-species whole-genome conservation non-synonymous

• Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data.

  PMID 15921519 · PMC1166541 · BMC bioinformatics · 2005 · 6 claims · 4 setups

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  A minimum evolution algorithm (implemented in software 'phyrex') can reconstruct ancestral states of continuous characters like gene expression or splicing levels along a phylogeny

  gene upstream chimpanzee reconstructed minimum sequence ancestral

• Viewing RNA-seq data on the entire human genome.

  PMID 28979763 · PMC5605993 · F1000Research · 2017 · 6 claims · 3 setups

  Has reproduction · 50

  RNA-Seq Viewer is a web application that visualizes genome-wide expression data from NCBI's SRA and GEO databases using an ideogram across the entire human genome.

  homo genome chrome rna-seq genomic web-page

• Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.

  PMID 22064864 · PMC3245177 · Nucleic acids research · 2012 · 8 claims · 5 setups

  Has reproduction · 83

  Gene Expression Atlas is an added-value database providing curated, re-annotated and statistically analysed gene expression data across cell types, organism parts, developmental stages, disease states and other biological/experimental conditions, derived from ArrayExpress Archive and the European Nucleotide Archive.

  species microrna atlas microarray rna-seq microrna

• Identifying synonymous regulatory elements in vertebrate genomes.

  PMID 15980499 · PMC1160227 · Nucleic acids research · 2005 · 7 claims · 4 setups

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  SynoR is a tool that performs de novo genome-wide identification of synonymous regulatory elements (SREs) using evolutionarily conserved TFBS modules as seeds

  genome genes genome-wide gene tissue-specificity

• Curation of over 10 000 transcriptomic studies to enable data reuse.

  PMID 33599246 · PMC7904053 · Database : the journal of biological databases and curation · 2021 · 8 claims · 6 setups

  Has reproduction · 80

  Gemma is a curated database and bioinformatics system that addresses metadata, probe annotation, and expression data inconsistencies in GEO to enable transcriptomic data reuse

  microarray curated geo microarray rna-sequencing probe-to-gene

• snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome.

  PMID 16990247 · PMC1636440 · Nucleic acids research · 2006 · 8 claims · 5 setups

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  snoSeeker (comprising CDseeker and ACAseeker) is a computational package that can screen for both guide and orphan snoRNA genes, unlike prior programs limited to guide snoRNAs

  whole-genome genome computational gene northern

• CoMoDis: composite motif discovery in mammalian genomes.

  PMID 17130158 · PMC1702496 · Nucleic acids research · 2007 · 7 claims · 4 setups

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  CoMoDis is a new bioinformatics tool that streamlines computational identification of novel regulatory modules starting from a single seed motif

  ncbi35 gata-1 gene imr90 computational microarray seed-motif-anchored

• Systematic identification of pseudogenes through whole genome expression evidence profiling.

  PMID 16945953 · PMC1636364 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  Developed a novel bioinformatics method that identifies pseudogenes by profiling whole-genome transcript and protein expression evidence

  genome ensembl vega celera spliced protein-to-genome pseudogene

• The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets.

  PMID 19654113 · PMC2759552 · Bioinformatics (Oxford, England) · 2009 · 7 claims · 2 setups

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  IGB is an open-source, Java-based desktop genome browser supporting real-time zooming/panning, moveable tiered feature layout, incremental or genome-scale data loading, and dynamic genome graphs

  arabidopsis pyrosequencing expression

• 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

• Natural selection of protein structural and functional properties: a single nucleotide polymorphism perspective.

  PMID 18397526 · PMC2643940 · Genome biology · 2008 · 8 claims · 8 setups

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  The SNP A/S ratio is a robust measure of selective constraint, correlating with interspecies Ka/Ks ratios and with protein sequence conservation.

  sequence genes proteins sequences snp interspecies sequence

• TFBScluster web server for the identification of mammalian composite regulatory elements.

  PMID 16845063 · PMC1538905 · Nucleic acids research · 2006 · 7 claims · 5 setups

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  TFBScluster is a web server that identifies genome-wide clusters of TFBSs conserved in multiple mammalian species using human or mouse as the reference genome.

  imr90 tissues dog transgenic microarray-based gene

• Phylogenetic analysis of higher-level relationships within Hydroidolina (Cnidaria: Hydrozoa) using mitochondrial genome data and insight into their mitochondrial transcription.

  PMID 26618080 · PMC4655093 · PeerJ · 2015 · 6 claims · 6 setups

  Has reproduction · 68

  Phylogenetic analyses of full mitochondrial gene sets recover siphonophores as the first diverging clade within Hydroidolina, a well-supported Leptothecata–Filifera III–IV clade, and a second clade of Aplanulata–Capitata s.s.–Filifera I–II.

  hydrozoan nanomia liriope concatenated long-range rna-seq dna-seq

• CompMoby: comparative MobyDick for detection of cis-regulatory motifs.

  PMID 18950538 · PMC2605473 · BMC bioinformatics · 2008 · 7 claims · 4 setups

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  CompMoby identifies cis-regulatory binding sites at both transcriptional and post-transcriptional levels in metazoans without prior knowledge of the trans-acting factor

  embryonic hela novo genome-wide

• Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta.

  PMID 18294402 · PMC2287170 · BMC genomics · 2008 · 8 claims · 6 setups

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  Constructed full-length-enriched cDNA libraries and determined 85,721 EST sequences and 9407 full-insert sequences from cynomolgus macaque brain (7 regions), testis, and liver

  cynomolgus 3-year-old macaque est full-insert oligonucleotide

• The UCSC Genome Browser Database: update 2006.

  PMID 16381938 · PMC1347506 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  The UCSC Genome Browser Database (GBD) provides integrated sequence and annotation data, with web tools (Genome Browser, Table Browser, Proteome Browser, Gene Sorter, BLAT, In Silico PCR) for visualizing and querying genomes of about a dozen vertebrate species and several model organisms.

  dog vertebrate encode genome comparative automated cross-species

• A global change in RNA polymerase II pausing during the Drosophila midblastula transition.

  PMID 23951546 · PMC3743134 · eLife · 2013 · 8 claims · 8 setups

  Has reproduction · 71

  Massive de novo recruitment of Pol II (and TBP) with widespread pausing occurs during the Drosophila midblastula transition, at 4007 promoters (~one third of all genes).

  hand-sorted drosophila chip-seq immunostaining dapi

• Genome-wide signatures of convergent evolution in echolocating mammals.

  PMID 24005325 · PMC3836225 · Nature · 2013 · 8 claims · 8 setups

  Has reproduction

  Genome-wide convergent sequence evolution between echolocating lineages is not rare but widespread and continuously distributed, with signatures consistent with convergence in nearly 200 loci out of 2,326 examined.

  four raw orthologous mammalian whole-genome novo homology-based

• Genomic analysis of a heterogeneous Mendelian phenotype: multiple novel alleles for inherited hearing loss in the Palestinian population.

  PMID 16460646 · PMC3525152 · Human genomics · 2006 · 8 claims · 8 setups

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  GJB2 (connexin 26) mutations account for hearing loss in only 17 of 156 families (11%), a smaller fraction than reported in other populations.

  palestinian genomic probands lymphoblasts targeted sanger pcr