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).

• Ab initio identification of putative human transcription factor binding sites by comparative genomics.

  PMID 15865625 · PMC1097714 · BMC bioinformatics · 2005 · 8 claims · 5 setups

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  An integrated algorithm combining human-mouse genomic comparison, motif overrepresentation, and coregulation filters (GO annotation and microarray coexpression) can identify candidate transcription factor binding sites genome-wide

  human-mouse conserved gene consensus comparative statistical gene

• Sequence changes in predicted promoter elements of STK11/LKB1 are unlikely to contribute to Peutz-Jeghers syndrome.

  PMID 15774015 · PMC1084245 · BMC genomics · 2005 · 6 claims · 4 setups

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  Integrated phylogenetic foot printing and transcription factor binding site (TFBS) prediction identified a consensus putative STK11/LKB1 promoter region between nucleotides -1090 and -1472

  genomic phylogenetic direct high

• The DNA sequence of the human X chromosome.

  PMID 15772651 · PMC2665286 · Nature · 2005 · 8 claims · 8 setups

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  The euchromatic sequence of the human X chromosome was determined to 99.3% completeness (~155 Mb total)

  pac selected chromosome clone-based shotgun comparative

• The secrets of a functional synapse--from a computational and experimental viewpoint.

  PMID 16723009 · PMC1810317 · BMC bioinformatics · 2006 · 8 claims · 8 setups

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  Kinesin motor proteins move cargo along axonal microtubules to the synapse, with cargo specificity determined by adaptor/linker proteins rather than lipid recognition

  mammalian kinesin cholinergic dendrites kinesin sequence-based comparative

• Population genomics of human gene expression.

  PMID 17873874 · PMC2683249 · Nature genetics · 2007 · 8 claims · 8 setups

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  Gene expression levels in lymphoblastoid cell lines are a heritable trait

  ebv-transformed ceu lymphoblastoid unrelated genome-wide custom cis-eqtl

• Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult.

  PMID 18931093 · PMC2608844 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2008 · 8 claims · 6 setups

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  The SE11 genome comprises a 4.8 Mb chromosome encoding 4679 protein-coding genes and six plasmids encoding 323 protein-coding genes

  coli se11 rapd whole-genome gene

• Improving the specificity of exon prediction using comparative genomics.

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

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  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

• Performance of mitochondrial DNA mutations detecting early stage cancer.

  PMID 18834532 · PMC2572633 · BMC cancer · 2008 · 8 claims · 6 setups

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  The Affymetrix MitoChip resequencing array is a high-throughput, higher-resolution alternative to capillary sequencing for detecting mtDNA point mutations and heteroplasmy in clinical specimens.

  matched blood mtdna low-quantity mitochondrial capillary str

• Novel mutations in TARDBP (TDP-43) in patients with familial amyotrophic lateral sclerosis.

  PMID 18802454 · PMC2527686 · PLoS genetics · 2008 · 8 claims · 6 setups

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  Three heterozygous missense mutations (p.M337V, p.N345K, p.I383V) in exon 6 of TARDBP were identified in familial ALS patients

  patients nd10588 lymphoblastoid neuroglioma sanger taqman copy-number

• Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons.

  PMID 19969543 · PMC2831330 · Nucleic acids research · 2010 · 8 claims · 8 setups

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  38 candidate cis-regulatory coding exons (RCEs) with predicted target genes were identified genome-wide

  hg18 zebrafish bystander human-mouse comparative synteny orthologous

• Identifying cis-regulatory sequences by word profile similarity.

  PMID 19730735 · PMC2731932 · PloS one · 2009 · 8 claims · 8 setups

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  WPH-finder identifies putative co-regulated CRMs by scanning the genome for sequences with word profiles similar to a known CRM, without explicitly defining binding sites

  stripe pair-rule nrsf-bound eve genome-wide chip-chip chip-seq

• miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems.

  PMID 32374865 · PMC7319446 · Nucleic acids research · 2020 · 8 claims · 3 setups

  Has reproduction · 61

  miEAA 2.0 supports miRNA/precursor enrichment input from ten frequently investigated organisms, expanding beyond the human-only first release.

  kidney breast blood mirna-seq mirna small

• The many uses of a genome sequence.

  PMID 11423005 · PMC138940 · Genome biology · 2001 · 8 claims · 8 setups

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  Solved protein structures from structural genomics efforts can be used to model many other proteins by homology, aiding function prediction

  recombinant mammalian chromosome chimpanzee x-ray quantitative tiling

• MitoVariome: a variome database of human mitochondrial DNA.

  PMID 19958475 · PMC2788364 · BMC genomics · 2009 · 8 claims · 5 setups

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  MitoVariome is a web-based, integrated variome database for human mitochondrial DNA that unifies sequence variation, haplogroup, and disease annotation information not jointly available in prior databases (MITOMAP, mtDB, Mitome, MitoRes).

  mitochondrial korean sequence short restriction

• Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution.

  PMID 29041914 · PMC5644144 · BMC genomics · 2017 · 8 claims · 8 setups

  Has reproduction · 72

  A high-quality ~375 Mbp draft genome and transcriptome of Holacanthella duospinosa was assembled and annotated, providing a genomic resource for hexapod evolution.

  holacanthella duospinosa whole-genome transcriptome genome

• A Deluge of Complex Repeats: The Solanum Genome.

  PMID 26241045 · PMC4524691 · PloS one · 2015 · 8 claims · 7 setups

  Has reproduction · 94

  ~50–60% of the S. tuberosum and S. lycopersicum genomes are composed of repetitive elements

  tuberosum orthologous identified de-novo genome-wide transcriptional

• Physiology engages with functional genomics - at last.

  PMID 16086845 · PMC1273626 · Genome biology · 2005 · 8 claims · 8 setups

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  Large-scale QTL phenotyping in rat strains reveals that most hypertension-related traits are sexually dimorphic

  wild-type caenorhabditis kidney pcr qtl enu copas

• Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

  PMID 15103394 · PMC393292 · PLoS biology · 2004 · 8 claims · 5 setups

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  41,118 full-length human cDNAs from six high-throughput sequencing projects were exhaustively integratively characterized

  genome transcriptome gene genes full-length genome cdna

• Impact of genomics on animal agriculture and opportunities for animal health.

  PMID 18022262 · PMC7114270 · Trends in biotechnology · 2008 · 8 claims · 7 setups

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  Genomics tools (single-gene tests, SNP chips, genomic selection) will speed genetic improvement of livestock production traits

  cattle chicken pig snp whole-genome transgenic

• miRBase: tools for microRNA genomics.

  PMID 17991681 · PMC2238936 · Nucleic acids research · 2008 · 8 claims · 6 setups

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  miRBase release 10.0 contains 5071 miRNA hairpin loci from 58 species, expressing 5922 distinct mature miRNA sequences, a growth of over 2000 sequences in 2 years

  species utrs genomic chromosome genome-wide target transcription