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 450

Assay: distribution ✕ Clear

Genome comparison without alignment using shortest unique substrings.

PMID 15910684 · PMC1166540 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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A number of sequence comparison tasks, including detection of unique genomic regions, can be accomplished efficiently without an alignment step using shortest unique substrings.

caenorhabditis genome mycoplasma shuffled genome-wide upstream-region local
Blood Pressure Sunday: introducing genomics to the community through family history.

PMID 15888234 · PMC1327717 · Preventing chronic disease · 2005 · 7 claims · 5 setups

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Family history is a significant, longstanding risk factor for high blood pressure and can serve as a practical 'genomic tool' for public health given that routine DNA-based risk testing is not yet available.

family detroit u.s parish readability community national
Alternative polyadenylation of cyclooxygenase-2.

PMID 15872218 · PMC1088970 · Nucleic acids research · 2005 · 8 claims · 5 setups

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The human COX-2 gene undergoes alternative polyadenylation using proximal and distal polyadenylation signals

cox-2 ht29 hela bioinformatics western rnase
How to find soluble proteins: a comprehensive analysis of alpha/beta hydrolases for recombinant expression in E. coli.

PMID 15804363 · PMC1079826 · BMC genomics · 2005 · 7 claims · 7 setups

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Predicted solubility in E. coli (via CV-CV') depends on hydrolase size, phylogenetic origin, homologous family, and superfamily

lipase bacterial small genera cv-cv correlation grouped
The cell cycle and virus infection.

PMID 15576934 · PMC7120536 · Methods in molecular biology (Clifton, N.J.) · 2005 · 8 claims · 7 setups

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Viruses interfere with the host cell cycle to increase efficiency of virus replication

vero chick nucleoli mammalian flow indirect northern
Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform.

PMID 17000641 · PMC1636412 · Nucleic acids research · 2006 · 8 claims · 6 setups

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An anonymous SHyP oligonucleotide microarray can capture genomic signatures of DNA sequence variation from any organism, including a previously unsequenced species

genomic gonystylus subset restriction-digested custom self-self blast
Comparative genomics of Drosophila and human core promoters.

PMID 16827941 · PMC1779564 · Genome biology · 2006 · 8 claims · 6 setups

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Drosophila core promoters contain 298 highly significant (p≤1e-16) non-randomly positioned 8-mers within 100 bp of the TSS, grouped into 15 distinct DNA motifs

drosophila core genome-wide mono gene
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
Coverage and characteristics of the Affymetrix GeneChip Human Mapping 100K SNP set.

PMID 16680197 · PMC1456318 · PLoS genetics · 2006 · 7 claims · 7 setups

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SNPs in the Affymetrix 100K set are undersampled from coding regions (both synonymous and nonsynonymous) and oversampled from regions outside genes, relative to HapMap SNPs

genome autosomal hapmap chromosome snp chromosomal minor
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
Bias of selection on human copy-number variants.

PMID 16482228 · PMC1366494 · PLoS genetics · 2006 · 8 claims · 8 setups

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Human CNVs are significantly overrepresented near telomeres and centromeres and enriched in simple tandem repeats relative to the genome as a whole

genome human-mouse cnv-encompassed inbred comparative randomization molecular
Detection of chromosomal structural alterations in single cells by SNP arrays: a systematic survey of amplification bias and optimized workflow.

PMID 18074030 · PMC2111048 · PloS one · 2007 · 8 claims · 7 setups

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MDA-based single-cell whole-genome amplification (S-WGA) products show large variability in amplification bias, including allele dropout and preferential amplification.

lymphoblastoid lcl cmk11-5 gel taqman oligonucleotide
Gene-centric characteristics of genome-wide association studies.

PMID 18060058 · PMC2092383 · PloS one · 2007 · 8 claims · 5 setups

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High-density SNP chips using either direct or indirect selection approaches provide very high coverage in genic regions and capture most known common disease variants under the HapMap framework.

phase omim snps snp disease genomic
The Edinburgh human metabolic network reconstruction and its functional analysis.

PMID 17882155 · PMC2013923 · Molecular systems biology · 2007 · 8 claims · 7 setups

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EHMN is a high-quality, manually curated human metabolic network combining genome-based and literature-based (EMP) reconstruction, containing nearly 3000 reactions and over 2000 metabolic genes.

enzyme emp kegg humancyc genome literature-based comparative
The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists.

PMID 17784955 · PMC2375021 · Genome biology · 2007 · 8 claims · 6 setups

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Gene-gene functional similarity can be measured using kappa statistics applied to a binary gene-annotation-term matrix built from 14 annotation categories.

genome protein-protein genes artificial kappa clustering gene
Genomic expression during human myelopoiesis.

PMID 17683550 · PMC2045681 · BMC genomics · 2007 · 8 claims · 5 setups

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An integrated myelopoiesis expression dataset of 9,425 genes, each mapped to a unique genomic position, was generated from 24 microarray experiments across 8 myeloid cell types.

myeloid same cd34+ gene microarray unsupervised sam
Using comparative genomics to reorder the human genome sequence into a virtual sheep genome.

PMID 17663790 · PMC2323240 · Genome biology · 2007 · 8 claims · 6 setups

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A sheep BAC library (CHORI-243) with ~13.5-fold genome coverage was constructed and end-sequenced.

sheep genome bac sequence randomization
Sequence polymorphisms cause many false cis eQTLs.

PMID 17637838 · PMC1906859 · PloS one · 2007 · 8 claims · 7 setups

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Many reported local/cis eQTLs are false positives caused by probe-region sequence polymorphisms affecting hybridization rather than true cis-regulatory expression differences.

lymphoblastoid hematopoietic caenorhabditis genome anova-based sanger eqtl
Effects of DNA-targeted ionizing radiation produced by 5-[125I]iodo-2'-deoxyuridine on global gene expression in primary human cells.

PMID 17594496 · PMC1934370 · BMC genomics · 2007 · 8 claims · 7 setups

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125I-IUdR-induced DNA damage alters expression of only a limited subset of genes in primary human cells

ag09319 gm05388 nhfk whole-genome quantitative dna-associated
A novel variable number of tandem repeat of the natriuretic peptide precursor B gene's 5'-flanking region is associated with essential hypertension among Japanese females.

PMID 17554401 · PMC1885554 · International journal of medical sciences · 2007 · 8 claims · 6 setups

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A novel VNTR polymorphism (TTTC repeat) was discovered at -1241 nucleotides in the 5'-flanking region of NPPB, with 8 alleles ranging from 9 to 19 repeats.

genomic plasma serum n=317 pcr-sscp nucleotide genotyping

Experiments

Genome comparison without alignment using shortest unique substrings.

Blood Pressure Sunday: introducing genomics to the community through family history.

Alternative polyadenylation of cyclooxygenase-2.

How to find soluble proteins: a comprehensive analysis of alpha/beta hydrolases for recombinant expression in E. coli.

The cell cycle and virus infection.

Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform.

Comparative genomics of Drosophila and human core promoters.

Widespread ectopic expression of olfactory receptor genes.

Coverage and characteristics of the Affymetrix GeneChip Human Mapping 100K SNP set.

Human SNPs resulting in premature stop codons and protein truncation.

Bias of selection on human copy-number variants.

Detection of chromosomal structural alterations in single cells by SNP arrays: a systematic survey of amplification bias and optimized workflow.

Gene-centric characteristics of genome-wide association studies.

The Edinburgh human metabolic network reconstruction and its functional analysis.

The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists.

Genomic expression during human myelopoiesis.

Using comparative genomics to reorder the human genome sequence into a virtual sheep genome.

Sequence polymorphisms cause many false cis eQTLs.

Effects of DNA-targeted ionizing radiation produced by 5-[125I]iodo-2'-deoxyuridine on global gene expression in primary human cells.

A novel variable number of tandem repeat of the natriuretic peptide precursor B gene's 5'-flanking region is associated with essential hypertension among Japanese females.