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 112

System / cell line: common ✕ Clear

Functional nsSNPs from carcinogenesis-related genes expressed in breast tissue: potential breast cancer risk alleles and their distribution across human populations.

PMID 16595073 · PMC3500178 · Human genomics · 2006 · 7 claims · 5 setups

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A bioinformatics strategy cross-referencing carcinogenesis-related gene lists with breast-tissue expression data can identify candidate breast cancer risk nsSNPs.

breast carcinogenesis-related nssnp-containing african gene snp functional
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
CanPredict: a computational tool for predicting cancer-associated missense mutations.

PMID 17537827 · PMC1933186 · Nucleic acids research · 2007 · 8 claims · 7 setups

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CanPredict is a web application providing public access to a random forest classifier that combines SIFT, LogR.E-value, and GOSS scores to predict whether a missense mutation is cancer-associated

missense observed sjoblom refseq cross-validation recurrence comparative
Relative impact of nucleotide and copy number variation on gene expression phenotypes.

PMID 17289997 · PMC2665772 · Science (New York, N.Y.) · 2007 · 8 claims · 5 setups

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SNPs and CNVs capture largely non-overlapping signals of genetic variation affecting gene expression

lymphoblastoid same computational subset gene snp array
Integrated multi-level quality control for proteomic profiling studies using mass spectrometry.

PMID 19055809 · PMC2657802 · BMC bioinformatics · 2008 · 7 claims · 5 setups

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QC processes for identifying and removing low-quality spectra are often overlooked in proteomic profiling studies

serum pooled duplicate full seldi-tof principal technical
A highly polymorphic insertion in the Y-chromosome amelogenin gene can be used for evolutionary biology, population genetics and sexing in Cetacea and Artiodactyla.

PMID 18925953 · PMC2580767 · BMC genetics · 2008 · 8 claims · 6 setups

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A 460–465 bp insertion is present in intron 4 of the Amel-Y locus in most Cetartiodactyla lineages (cetaceans and ruminants) but absent in pig

cetacea amel-y amel-x cetartiodactyla pcr sanger molecular
Rise of the machines.

PMID 18670625 · PMC2467494 · PLoS genetics · 2008 · 8 claims · 4 setups

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New short-read sequencing platforms (Illumina Genome Analyzer, 454 FLX, ABI SOLiD) enable rapid, scalable whole-genome resequencing that was previously restricted to dedicated sequencing centers using Sanger methods.

bacillus independent subtilis whole-genome read
High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi.

PMID 18660809 · PMC2652037 · Nature genetics · 2008 · 7 claims · 8 setups

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Evolution in the Typhi population is characterized by ongoing loss of gene function (pseudogene accumulation) rather than gain of function or diversifying selection.

salmonella sequenced typhi whole-genome snp-based selection
Distinctive pattern of sequence polymorphism in the NS3 protein of hepatitis C virus type 1b reflects conflicting evolutionary pressures.

PMID 18632963 · PMC2577380 · The Journal of general virology · 2008 · 7 claims · 6 setups

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NS3 shows less evidence of purifying selection acting on its CTL epitopes than the other 9 HCV proteins, while outside the CTL epitopes NS3 is more conserved than the other proteins.

complete hcv-1b sequence nonsynonymous comparative neighbor-joining maximum
Approaching the genomics of risk-taking behavior.

PMID 20109660 · PMC3961474 · Advances in genetics · 2009 · 8 claims · 8 setups

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Candidate genes (e.g., DRD4, SERT, MAOA) explain only a small fraction of total genetic variation in risk-taking-related behaviors, motivating a whole-genome approach.

wild-caught three-spined sticklebacks open-field-like predator repeated-measures
High mitochondrial DNA stability in B-cell chronic lymphocytic leukemia.

PMID 19924307 · PMC2775629 · PloS one · 2009 · 7 claims · 5 setups

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mtDNA control-region instability is not the primary causal factor in B-CLL

lymphocytes paired clinical-pathological pcr autosomal likelihood
Sequence and structure signatures of cancer mutation hotspots in protein kinases.

PMID 19834613 · PMC2759519 · PloS one · 2009 · 8 claims · 6 setups

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Developed CKMD (Composite Kinase Mutation Database), an integrated bioinformatics resource mapping genetic variation in protein kinase genes to sequence, structural, and functional data

kinase common egfr autoinhibited database-driven structure-informed evolutionary
CLEAN: CLustering Enrichment ANalysis.

PMID 19640299 · PMC2734555 · BMC bioinformatics · 2009 · 8 claims · 4 setups

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The gene-specific CLEAN score improves reproducibility of cluster analysis conclusions across independent datasets compared to the traditional cluster-wide score (cwCLEAN).

four breast combined hierarchical cluster csimm-based
PHA4GE quality control contextual data tags: standardized annotations for sharing public health sequence datasets with known quality issues to facilitate testing and training.

PMID 38860884 · PMC11261899 · Microbial genomics · 2024 · 7 claims · 3 setups

Has reproduction · 75

PHA4GE developed a set of standardized contextual data tags (five fields plus controlled-vocabulary terms) for annotating pathogen sequence datasets with known quality issues.

fda pha4ge genomic metagenomic community ontology
Social and ethical implications of genomics, race, ethnicity, and health inequities.

PMID 19000599 · PMC2892396 · Seminars in oncology nursing · 2008 · 8 claims · 5 setups

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Race and ethnicity are increasingly viewed as genetic surrogates for predicting disease risk and treatment response, though directly assessing genomic and environmental factors is more accurate.

population prostate non-small-cell breast genome-wide gene somatic
Threshold-dominated regulation hides genetic variation in gene expression networks.

PMID 18062810 · PMC2238762 · BMC systems biology · 2007 · 8 claims · 2 setups

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Threshold robustness (insensitivity of a singular/regulating variable's equilibrium value to parameter perturbations, except threshold changes) increases with increasing response function steepness and is present even under Michaelis-Menten conditions, not just in the step-function limit.

three-gene illustrative numerical analytical
htSNPer1.0: software for haplotype block partition and htSNPs selection.

PMID 15740612 · PMC1274247 · BMC bioinformatics · 2005 · 6 claims · 1 setups

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The GBB algorithm finds the globally optimal minimal htSNP set with far less computing time than exhaustive/enumeration search.

chromosome haplotype
Ensembl 2007.

PMID 17148474 · PMC1761443 · Nucleic acids research · 2007 · 8 claims · 7 setups

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Ensembl added 18 new chordate genomes this year, increasing total genomes available from 15 to 33, the largest yearly increase to date.

low-coverage cow chicken genome genome standard customized
The detection of regions of our genome under selection has increasingly relied on the use of genome scans.

PMID 16197732 · PMC3525123 · Human genomics · 2005 · 8 claims · 3 setups

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Markers linked to a locus under local adaptation show larger variance in allele frequencies across populations (higher FST) than neutral markers

populations common genome snp comparative
Bioinformatics and system biology approaches to identify pathophysiological impact of COVID-19 to the progression and severity of neurological diseases.

PMID 34601390 · PMC8483812 · Computers in biology and medicine · 2021 · 8 claims · 8 setups

Has reproduction · 69

COVID-19 and neurological diseases (NDs) share pathophysiological connections that influence disease progression and severity

peripheral hippocampal spinal peritumoral microarray protein-protein

Experiments

Functional nsSNPs from carcinogenesis-related genes expressed in breast tissue: potential breast cancer risk alleles and their distribution across human populations.

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

CanPredict: a computational tool for predicting cancer-associated missense mutations.

Relative impact of nucleotide and copy number variation on gene expression phenotypes.

Integrated multi-level quality control for proteomic profiling studies using mass spectrometry.

A highly polymorphic insertion in the Y-chromosome amelogenin gene can be used for evolutionary biology, population genetics and sexing in Cetacea and Artiodactyla.

Rise of the machines.

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi.

Distinctive pattern of sequence polymorphism in the NS3 protein of hepatitis C virus type 1b reflects conflicting evolutionary pressures.

Approaching the genomics of risk-taking behavior.

High mitochondrial DNA stability in B-cell chronic lymphocytic leukemia.

Sequence and structure signatures of cancer mutation hotspots in protein kinases.

CLEAN: CLustering Enrichment ANalysis.

PHA4GE quality control contextual data tags: standardized annotations for sharing public health sequence datasets with known quality issues to facilitate testing and training.

Social and ethical implications of genomics, race, ethnicity, and health inequities.

Threshold-dominated regulation hides genetic variation in gene expression networks.

htSNPer1.0: software for haplotype block partition and htSNPs selection.

Ensembl 2007.

The detection of regions of our genome under selection has increasingly relied on the use of genome scans.

Bioinformatics and system biology approaches to identify pathophysiological impact of COVID-19 to the progression and severity of neurological diseases.