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).

Publications 1.3k Datasets 392.5k Experiments 187

System / cell line: orthologous ✕ Clear

Reconstruction of pathways associated with amino acid metabolism in human mitochondria.

PMID 18267298 · PMC5054205 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 5 setups

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Out of 20 amino acids, the metabolic pathways of 17 utilize mitochondrial enzymes, and dysfunction of these enzymes causes over 40 known human mitochondrial diseases/disorders

mitoproteome orthologous liver mitochondrial sequence-based computational literature
ARED Organism: expansion of ARED reveals AU-rich element cluster variations between human and mouse.

PMID 17984078 · PMC2238997 · Nucleic acids research · 2008 · 6 claims · 4 setups

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ARED Organism and ARED-Integrated are new/updated public databases cataloguing ARE-containing mRNAs/genes in human, mouse and rat

6x6 ortholog 3'utr comparative chi-squared
Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.

PMID 17982176 · PMC2238928 · Nucleic acids research · 2008 · 6 claims · 7 setups

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Evola combines genome synteny-based computational ortholog detection with manual curation of phylogenetic trees by experts to yield more reliable orthologs than automated pairwise methods

genome h-invdb gene sets genome transcript-to-genome coding
Narcisse: a mirror view of conserved syntenies.

PMID 17981845 · PMC2238891 · Nucleic acids research · 2008 · 8 claims · 4 setups

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Narcisse is a database/web tool providing an integrated, multi-level comparative analysis of sequence similarities and conserved chromosomal segments (syntenies) across animal, plant, fungal and bacterial completely sequenced genomes.

annotated genome pairwise pairs sequence nucleic-level conserved
How accurately is ncRNA aligned within whole-genome multiple alignments?

PMID 17963514 · PMC2206062 · BMC bioinformatics · 2007 · 7 claims · 4 setups

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MULTIZ does a fairly accurate job of aligning ncRNA regions across 17 vertebrate genomes, but better alignments exist in some regions.

genome vertebrate nonhuman genomic sequence whole-genome covariance
Inference of transcriptional regulation using gene expression data from the bovine and human genomes.

PMID 17683551 · PMC1978505 · BMC genomics · 2007 · 7 claims · 8 setups

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Using human reference promoter sequences is a useful approach for studying gene expression regulation in species with limited or non-existing genomic sequence, such as cattle.

muscle-specific bovine refseq cardiac novo est blastn
Reconstructing the evolution of the mitochondrial ribosomal proteome.

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

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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
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
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
Evolutionary origins of human apoptosis and genome-stability gene networks.

PMID 18832373 · PMC2577361 · Nucleic acids research · 2008 · 8 claims · 8 setups

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The entanglement of DNA repair, chromosome stability and apoptosis gene networks appears with the caspase gene family and the antiapoptotic gene BCL2.

apoptosis fully same orthologous protein-protein comparative orthology
Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals.

PMID 18826599 · PMC2576242 · BMC evolutionary biology · 2008 · 7 claims · 4 setups

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CpG/non-CpG assignment based on presence/absence of a CpG dinucleotide seriously biases substitution rate estimates, overestimating CpG changes and underestimating non-CpG changes.

randomly real human-chimpanzee simulated simulation comparative
Exhaustive prediction of disease susceptibility to coding base changes in the human genome.

PMID 18793467 · PMC2537574 · BMC bioinformatics · 2008 · 8 claims · 7 setups

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Inter-species conservation is the strongest single predictor of disease-associated coding mutations among the factors tested.

hgmd refseq aligned svm svm reciprocal inter-species
In silico promoters: modelling of cis-regulatory context facilitates target predictio.

PMID 18505473 · PMC3823354 · Journal of cellular and molecular medicine · 2009 · 8 claims · 8 setups

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An integrated 'profiling of transcriptional targets' (PTT) strategy by Freebern et al. identified IGF-1 as a co-modulator of immune cell function genes in mitogen/drug-activated T cells.

serca2 rantes genes podocyte-associated literature-based promoter cross-referenced
In silico discovery of transcription regulatory elements in Plasmodium falciparum.

PMID 18257930 · PMC2268928 · BMC genomics · 2008 · 7 claims · 8 setups

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GEMS, using hypergeometric scoring and PWM parameter optimization, reliably identifies high-confidence cis-regulatory elements in the AT-rich, repeat-rich P. falciparum genome

falciparum plasmodium invasion invasion-related microarray motif comparative
Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

PMID 20003482 · PMC2807441 · BMC genomics · 2009 · 8 claims · 6 setups

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Manual annotation of the mouse Chromosome 8 defensin region identifies 98 gene loci: 54 in the alpha-defensin cluster and 44 in the beta-defensin cluster

c57bl orthologous alpha-defensin defensin manual comparative sequence
Tandem repeats modify the structure of human genes hosted in segmental duplications.

PMID 19954527 · PMC2812944 · Genome biology · 2009 · 8 claims · 6 setups

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Around 7% of primate-specific genes located within segmental duplications contain variable internal tandem repeats (ITRs).

genome genomic est paired genome-wide comparative cnv
Correlation of microsynteny conservation and disease gene distribution in mammalian genomes.

PMID 19909546 · PMC2779822 · BMC genomics · 2009 · 7 claims · 8 setups

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Density of mouse orthologs of human disease genes correlates with regions of conserved microsynteny in the mouse genome

genes autosomes dog genome comparative blat sliding-window
Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness.

PMID 19895688 · PMC3091318 · Genome biology · 2009 · 8 claims · 6 setups

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MacroRNA and lincRNA exons are subject to the same relatively low degree of sequence constraint, contrary to prior reports that lincRNAs are far more conserved

macrorna sequence comparative mouse-human population
MEROPS: the peptidase database.

PMID 19892822 · PMC2808883 · Nucleic acids research · 2010 · 8 claims · 5 setups

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MEROPS is a manually curated hierarchical classification of peptidases and protein inhibitors organized into protein species, families, and clans based on sequence and structural homology.

archaean holotype c-x-c proteins comparative domain substrate
A new procedure for determining the genetic basis of a physiological process in a non-model species, illustrated by cold induced angiogenesis in the carp.

PMID 19852815 · PMC2771047 · BMC genomics · 2009 · 8 claims · 5 setups

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The Conditional Stepped Reciprocal Best Hit (CSRBH) approach, combining direct RBH and zebrafish-stepped RBH (SRBH), outperformed other ortholog assignment methods and attained 8,726 carp-human functional homolog relationships for 16,650 carp contigs

carp randomly zebrafish reciprocal sequence microarray

Experiments

Reconstruction of pathways associated with amino acid metabolism in human mitochondria.

ARED Organism: expansion of ARED reveals AU-rich element cluster variations between human and mouse.

Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.

Narcisse: a mirror view of conserved syntenies.

How accurately is ncRNA aligned within whole-genome multiple alignments?

Inference of transcriptional regulation using gene expression data from the bovine and human genomes.

Reconstructing the evolution of the mitochondrial ribosomal proteome.

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

Improving the specificity of exon prediction using comparative genomics.

Evolutionary origins of human apoptosis and genome-stability gene networks.

Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals.

Exhaustive prediction of disease susceptibility to coding base changes in the human genome.

In silico promoters: modelling of cis-regulatory context facilitates target predictio.

In silico discovery of transcription regulatory elements in Plasmodium falciparum.

Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

Tandem repeats modify the structure of human genes hosted in segmental duplications.

Correlation of microsynteny conservation and disease gene distribution in mammalian genomes.

Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness.

MEROPS: the peptidase database.

A new procedure for determining the genetic basis of a physiological process in a non-model species, illustrated by cold induced angiogenesis in the carp.