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 15

System / cell line: sequences ✕ Assay: masking ✕ Clear

Coiled-coil protein composition of 22 proteomes--differences and common themes in subcellular infrastructure and traffic control.

PMID 16288662 · PMC1322226 · BMC evolutionary biology · 2005 · 7 claims · 5 setups

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Proteins with extended coiled-coil domains (>250 amino acids) are largely absent from bacterial genomes but present in archaea and eukaryotes.

proteomes predicted long prokaryotic coiled-coil all-against-all sequence
PigGIS: Pig Genomic Informatics System.

PMID 17090590 · PMC1669765 · Nucleic acids research · 2007 · 7 claims · 7 setups

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PigGIS identified 15,700 pig consensus sequences covering 18.5 Mb of homologous human exons

million pig matched wgs blastx repeat sequence
Computational comparison of two mouse draft genomes and the human golden path.

PMID 12537546 · PMC151282 · Genome biology · 2003 · 8 claims · 7 setups

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The Celera and public mouse genome assemblies differ in about 10% of the mouse genome, with complementary strengths (Celera higher base-pair accuracy and overall coverage; public assembly higher quality in some finished BAC regions and freely accessible)

newly genome chromosome genomic blat blastn repeat
A statistical approach designed for finding mathematically defined repeats in shotgun data and determining the length distribution of clone-inserts.

PMID 15626332 · PMC5172250 · Genomics, proteomics & bioinformatics · 2003 · 8 claims · 6 setups

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Repeats of different copy number have distinct probabilities of appearance in shotgun data, which can be modeled statistically to define recognition thresholds (MDRs) at different shotgun coverages.

simulated same repeat whole-genome genome
BLASTO: a tool for searching orthologous groups.

PMID 17483516 · PMC1933156 · Nucleic acids research · 2007 · 7 claims · 2 setups

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BLASTO treats each orthologous group as a unit and outputs a ranked list of orthologous groups instead of single sequences

randomly sequences blast blasto
Pegasys: software for executing and integrating analyses of biological sequences.

PMID 15096276 · PMC406494 · BMC bioinformatics · 2004 · 8 claims · 7 setups

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Pegasys is a flexible, modular, customizable software system for executing and integrating heterogeneous biological sequence analysis tools

eukaryotic formatted genomic input initio sequence gene
Combining comparative genomics with de novo motif discovery to identify human transcription factor DNA-binding motifs.

PMID 17217514 · PMC1780116 · BMC bioinformatics · 2006 · 6 claims · 4 setups

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A novel method combining 8-species comparative genomics with de novo motif discovery identifies human TF DNA-binding motifs overrepresented and conserved in upstream regions of co-regulated genes

muscle-specific novo comparative
Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing.

PMID 15885146 · PMC1142312 · BMC genomics · 2005 · 8 claims · 7 setups

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Pig sequence is closer to human than mouse is, across exons, UTRs, introns, intergenic regions, ultra-conserved elements, and miRNAs

sus pig concatenated three-species whole-genome repeat comparative
Expoldb: expression linked polymorphism database with inbuilt tools for analysis of expression and simple repeats.

PMID 17038195 · PMC1618849 · BMC genomics · 2006 · 8 claims · 6 setups

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EXPOLDB is a novel database integrating human gene expression variability data (including monozygotic twin comparisons) with (TG/CA)n repeat polymorphism information

blood genomic genes housekeeping microarray repeat est-based
A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome.

PMID 16670430 · PMC1456330 · Nucleic acids research · 2006 · 8 claims · 7 setups

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Highly-degenerate RE1 sites are significantly enriched in promoters of validated and putative REST target genes compared to control promoters

orthologous randomized high-score promoters pssm-based comparative motif
Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes.

PMID 18187510 · PMC2275096 · Nucleic acids research · 2008 · 8 claims · 6 setups

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G-richness downstream of the TSS is strand-biased, concentrated on the nontemplate strand, with a peak at +200 to +300 bp

refseq chicken random genome-wide quadparser regulatory
A genome-wide survey of segmental duplications that mediate common human genetic variation of chromosomal architecture.

PMID 15588494 · PMC3525102 · Human genomics · 2004 · 8 claims · 5 setups

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PSD-mediated genomic architecture analogous to the 8p23/4p16 inversion regions is not unique to those loci but recurs genome-wide.

genomic genome extracted pairwise online genome-wide
'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
Comparative genomic study reveals a transition from TA richness in invertebrates to GC richness in vertebrates at CpG flanking sites: an indication for context-dependent mutagenicity of methylated CpG sites.

PMID 19329065 · PMC5054122 · Genomics, proteomics & bioinformatics · 2008 · 8 claims · 8 setups

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Nucleotide preference at CpG flanking sites transitions from 5' T (invertebrates) to 5' A (vertebrates) at the invertebrate-vertebrate boundary

genomes same pufferfish elegans nucleotide genome-wide kruskal-wallis
Predicting failure rate of PCR in large genomes.

PMID 18492719 · PMC2441781 · Nucleic acids research · 2008 · 7 claims · 8 setups

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The number of predicted primer-binding sites in genomic DNA is the most important factor determining PCR failure.

genomic genome pcr combined large-scale exact-match mismatch-tolerant

Experiments

Coiled-coil protein composition of 22 proteomes--differences and common themes in subcellular infrastructure and traffic control.

PigGIS: Pig Genomic Informatics System.

Computational comparison of two mouse draft genomes and the human golden path.

A statistical approach designed for finding mathematically defined repeats in shotgun data and determining the length distribution of clone-inserts.

BLASTO: a tool for searching orthologous groups.

Pegasys: software for executing and integrating analyses of biological sequences.

Combining comparative genomics with de novo motif discovery to identify human transcription factor DNA-binding motifs.

Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing.

Expoldb: expression linked polymorphism database with inbuilt tools for analysis of expression and simple repeats.

A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome.

Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes.

A genome-wide survey of segmental duplications that mediate common human genetic variation of chromosomal architecture.

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

Comparative genomic study reveals a transition from TA richness in invertebrates to GC richness in vertebrates at CpG flanking sites: an indication for context-dependent mutagenicity of methylated CpG sites.

Predicting failure rate of PCR in large genomes.