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).

• Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases.

  PMID 20019805 · PMC2787626 · PLoS computational biology · 2009 · 8 claims · 8 setups

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  A novel semi-parametric meta-analysis method (based on a gene-centric Glass's d effect size) outperforms existing parametric and non-parametric meta-analysis methods at identifying functionally coherent gene pairs across species.

  liver simulated conserved nearly gene simulation kolmogorov-smirnov

• DBTSS provides a tissue specific dynamic view of Transcription Start Sites.

  PMID 19910371 · PMC2808897 · Nucleic acids research · 2010 · 8 claims · 8 setups

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  DBTSS update adds ~330 million new TSS Seq tags from 31 different human/mouse cell types or culture conditions.

  normal dld1 beas2b ramos tss comparative

• Comparative genomics.

  PMID 14624258 · PMC261895 · PLoS biology · 2003 · 8 claims · 7 setups

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  Conserved DNA between species tends to encode shared functional features, while divergent DNA underlies species differences

  caenorhabditis yeast mammalian vertebrate whole-genome comparative interspecies-similarity-informed

• 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

• Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.

  PMID 16536879 · PMC1479377 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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  ENACE, a cross-species EST-to-genome comparison algorithm, can identify novel cassette-on exons and retained introns for EST-scanty species and distinguish conserved vs lineage-specific exons

  presumably orthologous enace genes cross-species rt-pcr-sequencing nonsynonymous-to-synonymous

• Benchmarking ortholog identification methods using functional genomics data.

  PMID 16613613 · PMC1557999 · Genome biology · 2006 · 8 claims · 7 setups

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  InParanoid is the best overall ortholog identification method for identifying functionally equivalent proteins when sensitivity and selectivity are combined into an overall score.

  known human-mouse expression interpro co-expression

• Comparative genomics comes of age.

  PMID 12186641 · PMC139393 · Genome biology · 2002 · 8 claims · 8 setups

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  Only about 50% of conserved sequence elements (exons+introns) in orthologous human-mouse genes correspond to exons, implying substantial non-exonic conservation

  orthologous chromosome chimpanzee somatic-cell comparative targeted tiled

• The post-genomic era for a select few.

  PMID 14759254 · PMC395745 · Genome biology · 2004 · 8 claims · 8 setups

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  The Exofish comparative-genomics tool identifies protein-coding DNA segments by comparing two genome sequences and was used to compare pufferfish (Takifugu, Tetraodon) genomes with mammalian genomes, improving annotation of the human and mouse genomes.

  takifugu physcomitrella coli vibrio comparative genetic dna-microarray

• Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics.

  PMID 15790398 · PMC1082905 · BMC genomics · 2005 · 8 claims · 6 setups

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  Twenty-three chemokine genes and 14 chemokine receptor genes were identified in the chicken genome, including 12 new chemokines and 7 new receptors beyond prior reports.

  chicken comparative amino phylogenetic

• Mining expressed sequence tags identifies cancer markers of clinical interest.

  PMID 17078886 · PMC1635568 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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  An EST-mining approach (Fisher Exact Test on tumor vs. non-tumor library hit counts) identifies differentially expressed transcripts with an estimated false discovery rate below 22% when human and mouse screens are combined.

  dbest cancer gene est human-mouse leave-one-out

• Widespread ectopic expression of olfactory receptor genes.

  PMID 16716209 · PMC1508154 · BMC genomics · 2006 · 8 claims · 6 setups

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  OR genes show widespread, locus-dependent, heterogeneous ectopic expression across dozens of non-olfactory human and mouse tissues

  tissues olfactory intact probesets microarray est custom

• Genome-wide survey for biologically functional pseudogenes.

  PMID 16680195 · PMC1456316 · PLoS computational biology · 2006 · 8 claims · 6 setups

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  A subset of ancient, cross-species-conserved pseudogenes (30 of 1,453 candidate quartets) show evidence consistent with retained biological function

  human-mouse chimpanzee cross-species maximum-likelihood synteny

• 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

• A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database.

  PMID 17521420 · PMC1929158 · Genome biology · 2007 · 7 claims · 6 setups

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  mtcPTM is a hierarchically organized database of human and mouse phosphosites that preserves experimental context, enabling comparison of phosphorylation patterns across conditions

  nonredundant database high-throughput homology

• 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

• Ensembl's 10th year.

  PMID 19906699 · PMC2808936 · Nucleic acids research · 2010 · 8 claims · 8 setups

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  Ensembl provides comprehensive gene annotation and integrated genomic resources (variation, regulation, comparative genomics) across a growing set of chordate genomes

  anole western genome cd4+ whole-genome gene cross-database

• RummaGEO: Automatic mining of human and mouse gene sets from GEO.

  PMID 39569206 · PMC11573963 · Patterns (New York, N.Y.) · 2024 · 8 claims · 7 setups

  Has reproduction · 63

  RummaGEO is a gene expression signature search engine built from automatically mined human and mouse RNA-seq perturbation studies in GEO

  genes rummageo rummageo-derived leiden bulk gene leiden

• Phylogenetic variation and polymorphism at the toll-like receptor 4 locus (TLR4).

  PMID 11104518 · PMC31919 · Genome biology · 2000 · 7 claims · 7 setups

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  The Tlr4 extracellular domain is far more variable than the cytoplasmic domain, both among mouse strains and among species

  tlr4 mus chimpanzee baboon genomic coding sequence

• Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps.

  PMID 15601531 · PMC3525001 · Human genomics · 2003 · 8 claims · 4 setups

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  The MGR algorithm applied to human, mouse, cat and cattle comparative maps can impute an ancestral mammalian genome composed of conserved segments.

  cat mammalian genome grimm-synteny comparative

• Pairagon+N-SCAN_EST: a model-based gene annotation pipeline.

  PMID 16925839 · PMC1810554 · Genome biology · 2006 · 7 claims · 5 setups

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  Pairagon+N-SCAN_EST, using only native alignments, was as accurate as ENSEMBL and ExoGean in the EGASP mRNA/EST evidence assessment

  encode genome cdna-to-genome novo comparative