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 23

System / cell line: frequency ✕ Assay: homology ✕ Clear

The Proteomic Code: a molecular recognition code for proteins.

PMID 17999762 · PMC2206014 · Theoretical biology & medical modelling · 2007 · 8 claims · 8 setups

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The Proteomic Code is a set of rules by which genetic information is transferred into the physico-chemical properties of amino acids, determining protein-protein interactions and folding; it is part of the redundant Genetic Code.

anti-peptide sequence exon smooth radioimmunoassay pairwise genome-wide
Retropseudogenes derived from the human Ro/SS-A autoantigen-associated hY RNAs.

PMID 15817567 · PMC1074747 · Nucleic acids research · 2005 · 8 claims · 8 setups

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966 pseudogenes derived from the four human Y (hY) RNAs were characterized in the human genome

genome chimpanzee pseudogenes genomic megablast blat sequence
MODBASE, a database of annotated comparative protein structure models and associated resources.

PMID 18948282 · PMC2686492 · Nucleic acids research · 2009 · 8 claims · 8 setups

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MODBASE contains 5,152,695 reliable comparative protein structure models for 1,593,209 unique protein sequences.

sequences chains template chain comparative pairwise ligand
Cryptic loxP sites in mammalian genomes: genome-wide distribution and relevance for the efficiency of BAC/PAC recombineering techniques.

PMID 17284462 · PMC1865043 · Nucleic acids research · 2007 · 6 claims · 6 setups

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Cryptic lox P sites occur frequently and are homogeneously distributed across the mouse genome (1.2 primary sites per megabase).

genome bac coli el350 genome-wide sequence bacterial
SNPmasker: automatic masking of SNPs and repeats across eukaryotic genomes.

PMID 16845091 · PMC1538889 · Nucleic acids research · 2006 · 8 claims · 4 setups

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SNPmasker is a web service combining SNP masking and repeat masking, supporting both coordinate-defined and homology-search-defined input regions, a combination not offered by prior tools

genome reference genomic runtime sequence comparative
Patterns of evolutionary constraints on genes in humans.

PMID 18840274 · PMC2587479 · BMC evolutionary biology · 2008 · 7 claims · 6 setups

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BaseDiver, a novel framework integrating GERP score and derived allele frequency (DAF) at nonsynonymous coding SNPs, can classify GO functional categories by patterns of evolutionary constraint

mammalian hapmap panther significant comparative population chi-square
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
The UCSC Proteome Browser.

PMID 15608236 · PMC540054 · Nucleic acids research · 2005 · 8 claims · 5 setups

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The UCSC Proteome Browser is tightly integrated with the UCSC Genome Browser, giving users simultaneous access to genome and proteome data.

swiss-prot sequence domain isoelectric
Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina.

PMID 14519200 · PMC328454 · Genome biology · 2003 · 8 claims · 5 setups

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Annotation of 8,633 high-quality non-mitochondrial/non-ribosomal ESTs shows 57% represent known genes and 43% are unknown or novel, with M15E having the highest proportion of novel ESTs

embryonic high-quality unique m15e est sequence comparative
Intronic alternative splicing regulators identified by comparative genomics in nematodes.

PMID 16839192 · PMC1500816 · PLoS computational biology · 2006 · 8 claims · 6 setups

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Conserved intronic elements flanking alternative exons occur more often than expected from total intron sequence, consistent with selective pressure for splicing regulation

elegans database transgenic comparative est cross-species
PCP consensus sequences of flaviviruses: correlating variance with vector competence and disease phenotype.

PMID 19969003 · PMC2822003 · Journal of molecular biology · 2010 · 7 claims · 7 setups

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PCP-consensus sequences of E protein show insertions/deletions that distinguish tick-borne, mosquito-borne, no-known-vector (NKV), and yellow fever virus (YFV) Flaviviruses

natural aligned ns3 denv sequence pcp-consensus physicochemical
Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics.

PMID 15601538 · PMC3525068 · Human genomics · 2004 · 8 claims · 8 setups

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An integrated system combining Ensembl, ACeDB, Gbrowse and custom relational databases provides a scalable genome informatics and workflow infrastructure for complex disease gene discovery.

pcr candidate embl clinical snp manual homology
Protein ranking by semi-supervised network propagation.

PMID 16723003 · PMC1810311 · BMC bioinformatics · 2006 · 8 claims · 5 setups

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RankProp, a diffusion-based network propagation algorithm on a PSI-BLAST-derived protein similarity network, significantly outperforms local search methods (BLAST/PSI-BLAST) at detecting remote homologs.

scop similarity same psi-blast rankprop probabilistic
Resequencing PNMT in European hypertensive and normotensive individuals: no common susceptibilily variants for hypertension and purifying selection on intron 1.

PMID 17645789 · PMC1947951 · BMC medical genetics · 2007 · 7 claims · 7 setups

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Resequencing of PNMT found no common susceptibility variants that distinguish hypertensive from normotensive individuals

genomic pnmt promoter pcr population haplotype
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
Genome-wide linkage analysis of an autosomal recessive hypotrichosis identifies a novel P2RY5 mutation.

PMID 18692127 · PMC3341170 · Genomics · 2008 · 8 claims · 7 setups

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Autozygosity mapping identified a highly significant homozygous region on chromosome 13q14.11-q14.3 (Z/LOD=10.41)

family p2ry5 affected snp microsatellite sanger
Comprehensive transcriptome study to develop molecular resources of the copepod Calanus sinicus for their potential ecological applications.

PMID 24982883 · PMC4055022 · BioMed research international · 2014 · 8 claims · 8 setups

Has reproduction · 61

Illumina RNA-Seq with Trinity de novo assembly produced a C. sinicus transcriptome of 69,751 contigs (average 928.8 bp, N50 1,127 bp) from 58.9 million reads.

calanus sinicus genomic rna-seq novo sequence
Comparative genomics and understanding of microbial biology.

PMID 10998382 · PMC2627966 · Emerging infectious diseases · 2000 · 8 claims · 7 setups

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GC content varies widely among prokaryotic genomes (29% in B. burgdorferi to 68% in M. tuberculosis) and shapes codon usage and amino acid composition.

completed same sequenced mycobacterium whole-genome comparative phylogenomic
Whole-genome experimental identification of insertion/deletion polymorphisms of interspersed repeats by a new general approach.

PMID 15673711 · PMC548376 · Nucleic acids research · 2005 · 8 claims · 6 setups

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A new technique combining whole-genome selective PCR amplification and subtractive hybridization can experimentally identify polymorphic retroelement insertions without prior knowledge of RE evolutionary history or sequence

genomic driver coli individual whole-genome subtractive cloning
Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening.

PMID 18655731 · PMC2515324 · BMC genomics · 2008 · 7 claims · 6 setups

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A collection of 132,577 ESTs from four Actinidia species was generated and clustered into 41,858 non-redundant clusters (18,070 TCs and 23,788 singletons)

cdna full-length tentative non-redundant est codon snp

Experiments

The Proteomic Code: a molecular recognition code for proteins.

Retropseudogenes derived from the human Ro/SS-A autoantigen-associated hY RNAs.

MODBASE, a database of annotated comparative protein structure models and associated resources.

Cryptic loxP sites in mammalian genomes: genome-wide distribution and relevance for the efficiency of BAC/PAC recombineering techniques.

SNPmasker: automatic masking of SNPs and repeats across eukaryotic genomes.

Patterns of evolutionary constraints on genes in humans.

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

The UCSC Proteome Browser.

Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina.

Intronic alternative splicing regulators identified by comparative genomics in nematodes.

PCP consensus sequences of flaviviruses: correlating variance with vector competence and disease phenotype.

Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics.

Protein ranking by semi-supervised network propagation.

Resequencing PNMT in European hypertensive and normotensive individuals: no common susceptibilily variants for hypertension and purifying selection on intron 1.

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

Genome-wide linkage analysis of an autosomal recessive hypotrichosis identifies a novel P2RY5 mutation.

Comprehensive transcriptome study to develop molecular resources of the copepod Calanus sinicus for their potential ecological applications.

Comparative genomics and understanding of microbial biology.

Whole-genome experimental identification of insertion/deletion polymorphisms of interspersed repeats by a new general approach.

Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening.