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 1.7k

Assay: sequence ✕ Clear

Evolutionary comparison provides evidence for pathogenicity of RMRP mutations.

PMID 16244706 · PMC1262189 · PLoS genetics · 2005 · 7 claims · 5 setups

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Putative pathogenic RMRP mutations are located in highly conserved nucleotides across mammals, whereas polymorphisms are located in non-conserved positions.

genomic rmrp family non-finnish sequencing comparative microsatellite
Chimp genome: branching out.

PMID 16136102 · PMC7420934 · Nature · 2005 · 8 claims · 8 setups

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The Chimpanzee Sequencing and Analysis Consortium published the initial draft chimpanzee genome sequence and compared it to the human genome.

chimpanzee primate rhesus fossil whole-genome phylogenetic genome
Functional coverage of the human genome by existing structures, structural genomics targets, and homology models.

PMID 16118666 · PMC1188274 · PLoS computational biology · 2005 · 8 claims · 5 setups

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Existing PDB structures provide single-domain coverage for 37% of functional classes in the human genome and complete (whole-protein) structure coverage for 25%.

genome functional registered omim comparative kendall's homology
Phosphorylation states of cell cycle and DNA repair proteins can be altered by the nsSNPs.

PMID 16111488 · PMC1208866 · BMC cancer · 2005 · 8 claims · 4 setups

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15 of 89 nsSNPs (16.9%) studied were predicted to abolish or create phosphorylation sites in 14 of 32 proteins (44.0%)

orthologues repair case-control phosphorylation cross-species database
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
Protein coding potential of retroviruses and other transposable elements in vertebrate genomes.

PMID 15716312 · PMC549403 · Nucleic acids research · 2005 · 8 claims · 5 setups

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About 1000 genes across four vertebrate gene sets analyzed contain at least one RETRA marker protein domain

predicted non-masked genome interpro hmm tblastn inter-species
G, N, and P gene-based analysis of Chandipura viruses, India.

PMID 15705335 · PMC3294343 · Emerging infectious diseases · 2005 · 8 claims · 4 setups

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The 2003 epidemic CHPV isolates are closely related to, and not very divergent from, the 1965 isolate, indicating the outbreak was not associated with extensive mutations in the G, N, and P genes.

chpv partial rt-pcr sequence phylogenetic
Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach.

PMID 15693947 · PMC551538 · Genome biology · 2005 · 7 claims · 8 setups

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FastCompare, a non-alignment-based, linear-time algorithm, computes a genome-wide conservation score for all k-mers (7-9 nt) between two genomes to identify conserved regulatory elements

cerevisiae elegans randomized computational randomized microarray
The MAPPER database: a multi-genome catalog of putative transcription factor binding sites.

PMID 15608292 · PMC540057 · Nucleic acids research · 2005 · 8 claims · 6 setups

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Built a library of 1134 HMM models (359 matrix-derived, 718 factor-derived, 57 JASPAR-derived), corresponding to 863 distinct TF names, from TRANSFAC and JASPAR binding site data

genome drosophila transfac b99 profile sequence case-study
GeneTide--Terra Incognita Discovery Endeavor: a new transcriptome focused member of the GeneCards/GeneNote suite of databases.

PMID 15608261 · PMC540076 · Nucleic acids research · 2005 · 8 claims · 7 setups

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GeneTide integrates UniGene, DoTS, AceView, BLAT/GeneLoc genomic alignment, and GeneAnnot probe-set data into a unified Consensus/Uniqueness/Score scheme to associate ESTs with GeneCards genes

transcriptome genome spliced transcripts est genomic splice-orientation
'Genome design' model and multicellular complexity: golden middle.

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

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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
Genomes of Helicobacter pylori from native Peruvians suggest admixture of ancestral and modern lineages and reveal a western type cag-pathogenicity island.

PMID 16872520 · PMC1553449 · BMC genomics · 2006 · 8 claims · 7 setups

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Native Peruvian H. pylori strains comprise two lineages: predominant hp-Europe and ~20% hsp-Amerind (Amerindian ancestry, closer to Alaska strains)

pylori peruvian spanish fluorescent multilocus oipa
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
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
Four genomic islands that mark post-1995 pandemic Vibrio parahaemolyticus isolates.

PMID 16672049 · PMC1464126 · BMC genomics · 2006 · 8 claims · 7 setups

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Seven genomic islands (VPaI-1 to VPaI-7, 10-81 kb) were identified in V. parahaemolyticus RIMD2210633 by aberrant GC content, presence of integrases/transposases, flanking direct repeats, and absence from related Vibrionaceae genomes.

parahaemolyticus vulnificus clinical ecori-digested bioinformatic comparative pcr
Human SNPs resulting in premature stop codons and protein truncation.

PMID 16595072 · PMC3500177 · Human genomics · 2006 · 8 claims · 6 setups

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Genome-wide screening of dbSNP identified 28 validated X-SNPs from 28 genes with known minor allele frequencies.

genome transcripts validated x-snp-encoded database blast exon-intron
Application of machine learning in SNP discovery.

PMID 16398931 · PMC1955739 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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PolyBayes produces high false-positive SNP predictions even with stringent parameters

diverse soybean candidate same sts polybayes polyphred
ABS: a database of Annotated regulatory Binding Sites from orthologous promoters.

PMID 16381947 · PMC1347478 · Nucleic acids research · 2006 · 7 claims · 6 setups

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ABS is a public database of experimentally identified TF binding sites conserved in orthologous vertebrate gene promoters, manually curated from the literature.

orthologous literature sequence pairwise
In silico and in vitro comparative analysis to select, validate and test SNPs for human identification.

PMID 18076761 · PMC2222643 · BMC genomics · 2007 · 8 claims · 7 setups

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A panel of 24 SNPs was selected and validated for human identification using 1,040 unrelated samples from three populations (Italian, Benin Gulf, Mongolian)

genomic genome pan blood snp sequence cross-species
Restriction landmark genomic scanning (RLGS) spot identification by second generation virtual RLGS in multiple genomes with multiple enzyme combinations.

PMID 18053125 · PMC2235865 · BMC genomics · 2007 · 7 claims · 4 setups

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A second-generation virtual RLGS (vRLGS) system predicts DNA fragment migration using sequence characteristics plus fragment length, and is applicable to any sequenced genome and enzyme combination

peripheral genome restriction virtual

Experiments

Evolutionary comparison provides evidence for pathogenicity of RMRP mutations.

Chimp genome: branching out.

Functional coverage of the human genome by existing structures, structural genomics targets, and homology models.

Phosphorylation states of cell cycle and DNA repair proteins can be altered by the nsSNPs.

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

Protein coding potential of retroviruses and other transposable elements in vertebrate genomes.

G, N, and P gene-based analysis of Chandipura viruses, India.

Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach.

The MAPPER database: a multi-genome catalog of putative transcription factor binding sites.

GeneTide--Terra Incognita Discovery Endeavor: a new transcriptome focused member of the GeneCards/GeneNote suite of databases.

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

Genomes of Helicobacter pylori from native Peruvians suggest admixture of ancestral and modern lineages and reveal a western type cag-pathogenicity island.

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

Genome-wide survey for biologically functional pseudogenes.

Four genomic islands that mark post-1995 pandemic Vibrio parahaemolyticus isolates.

Human SNPs resulting in premature stop codons and protein truncation.

Application of machine learning in SNP discovery.

ABS: a database of Annotated regulatory Binding Sites from orthologous promoters.

In silico and in vitro comparative analysis to select, validate and test SNPs for human identification.

Restriction landmark genomic scanning (RLGS) spot identification by second generation virtual RLGS in multiple genomes with multiple enzyme combinations.