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 25

System / cell line: snp ✕ Assay: fold ✕ Clear

Assessing the utility of whole-genome amplified serum DNA for array-based high throughput genotyping.

PMID 20021669 · PMC2803178 · BMC genetics · 2009 · 8 claims · 8 setups

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WGA DNA from archived serum samples produced low genotyping call rates and is unsuitable for high-resolution genotyping on SNP 6.0 arrays

wga non-amplified archived serum-derived snp purification whole-genome
Searching for SNPs with cloud computing.

PMID 19930550 · PMC3091327 · Genome biology · 2009 · 8 claims · 4 setups

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Crossbow combines the Bowtie short-read aligner and SOAPsnp SNP caller into a seamless, automatic Hadoop/MapReduce pipeline for whole-genome resequencing analysis

han local short simulated whole-genome cloud
High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling.

PMID 16893952 · PMC1540726 · Nucleic acids research · 2006 · 7 claims · 6 setups

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Ecotilling can be adapted to accurately discover and genotype human SNPs, with error rates low relative to resequencing

genomic ecotilling non-synonymous ecotilling sanger universal-primer
Integrated analysis of genetic and proteomic data identifies biomarkers associated with adverse events following smallpox vaccination.

PMID 18923431 · PMC2692715 · Genes and immunity · 2009 · 7 claims · 6 setups

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A two-stage strategy (Random Forest filtering followed by decision tree modeling) can integrate categorical genetic and continuous proteomic data to identify biomarkers of AE risk

ebv-transformed serum combined rf-filtered snp serum random
Primase-based whole genome amplification.

PMID 18559358 · PMC2490742 · Nucleic acids research · 2008 · 8 claims · 6 setups

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A primase-based Whole Genome Amplification (pWGA) method was developed using T7 gp4 primase to synthesize primers on-template, removing the requirement for synthetic primers

genomic plasmids circular agarose picogreen dye-terminator
Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness.

PMID 19895688 · PMC3091318 · Genome biology · 2009 · 8 claims · 6 setups

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MacroRNA and lincRNA exons are subject to the same relatively low degree of sequence constraint, contrary to prior reports that lincRNAs are far more conserved

macrorna sequence comparative mouse-human population
Exome sequencing of a multigenerational human pedigree.

PMID 20011588 · PMC2788131 · PloS one · 2009 · 8 claims · 6 setups

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Microarray-based exome capture combined with 454 GS FLX NGS is an efficient and reliable method to enrich for chromosomal regions of interest, validated on eight individuals from a three-generation pedigree

genomic eluted captured pcr microarray-based qpcr next-generation
Identification of deleterious non-synonymous single nucleotide polymorphisms using sequence-derived information.

PMID 18588693 · PMC2446391 · BMC bioinformatics · 2008 · 8 claims · 5 setups

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A decision tree built on 10 selected sequence-derived features classifies SAPs as Disease or Polymorphism with 82.6% accuracy and 0.607 MCC in cross-validation.

sap sequence-derived humvar same decision independent greedy
Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method.

PMID 16026601 · PMC1637030 · BMC bioinformatics · 2005 · 8 claims · 2 setups

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DF-SNPs, a novel adaptation of the Decision Forest method, can classify esophageal cancer cases vs. controls based on SNP genotype data with high concordance, sensitivity, and specificity.

genomic snp high-throughput decision
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
A comparison of classification methods for predicting Chronic Fatigue Syndrome based on genetic data.

PMID 19772600 · PMC2765429 · Journal of translational medicine · 2009 · 7 claims · 3 setups

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The naive Bayes model with the wrapper-based feature selection approach performed best among all predictive models tested for distinguishing CFS from controls.

subjects naive svm c4.5
Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools.

PMID 16912992 · PMC1538848 · Nucleic acids research · 2006 · 7 claims · 8 setups

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PANTHER HMMs built from family/subfamily multiple sequence alignments can classify novel protein sequences into functional groups based on statistically significant HMM match scores

input gene genome-wide genes sequence gene numerical
Machine-learning approaches for classifying haplogroup from Y chromosome STR data.

PMID 18551166 · PMC2396484 · PLoS computational biology · 2008 · 8 claims · 5 setups

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Y-STR allelic variability is partitioned more by differences among haplogroups than by differences among populations, suggesting Y-STRs carry haplogroup information

globally same computational publicly y-str snp supervised
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
A genome-wide association analysis identifies 16 novel susceptibility loci for carpal tunnel syndrome.

PMID 30833571 · PMC6399342 · Nature communications · 2019 · 8 claims · 8 setups

Has reproduction · 90

16 genome-wide significant susceptibility loci for CTS were identified in UK Biobank

biobank surgically gtex height gwas bulk summary
Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs.

PMID 38594607 · PMC11003151 · Genetics, selection, evolution : GSE · 2024 · 8 claims · 8 setups

Has reproduction · 100

H3K27ac ChIP-seq and RNA-seq were used to construct eRNA expression profiles across multiple tissues in Enshi Black (ES) and Duroc pigs, revealing tissue-level eRNA regulatory landscapes

longissimus muscle snps pig h3k27ac strand-specific starr-seq
Environmental genome project: a positive sequence of events.

PMID 11171540 · PMC1242069 · Environmental health perspectives · 2001 · 8 claims · 5 setups

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Exposure to alkylating agents evokes at least threefold expression changes in about one-third of the yeast genome (~2,000 genes), far beyond DNA repair genes alone

yeast genes population microarray time-course resequencing
Analysis of sequence conservation at nucleotide resolution.

PMID 18166073 · PMC2230682 · PLoS computational biology · 2007 · 8 claims · 4 setups

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SCONE (Sequence CONservation Evaluation) is a novel method that estimates evolutionary rate and a neutrality p-value for individual nucleotide positions in a multiple sequence alignment.

encode population comparative snp functional
MLGA--a rapid and cost-efficient assay for gene copy-number analysis.

PMID 17823203 · PMC2034490 · Nucleic acids research · 2007 · 8 claims · 4 setups

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MLGA is a novel selector-based technique using multiplex ligation-dependent circularization of genomic DNA fragments for copy-number analysis

pooled genomic aneuploid dog mlga
RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.

PMID 24926665 · PMC4057123 · PloS one · 2014 · 8 claims · 8 setups

Has reproduction · 87

Dexamethasone treatment (1 µM, 18 h) of primary human ASM cells differentially regulates 316 genes, including both known and previously uninvestigated glucocorticoid-responsive genes.

airway asm most single rna-seq quantitative qrt-pcr

Experiments

Assessing the utility of whole-genome amplified serum DNA for array-based high throughput genotyping.

Searching for SNPs with cloud computing.

High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling.

Integrated analysis of genetic and proteomic data identifies biomarkers associated with adverse events following smallpox vaccination.

Primase-based whole genome amplification.

Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness.

Exome sequencing of a multigenerational human pedigree.

Identification of deleterious non-synonymous single nucleotide polymorphisms using sequence-derived information.

Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method.

Predicting failure rate of PCR in large genomes.

A comparison of classification methods for predicting Chronic Fatigue Syndrome based on genetic data.

Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools.

Machine-learning approaches for classifying haplogroup from Y chromosome STR data.

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

A genome-wide association analysis identifies 16 novel susceptibility loci for carpal tunnel syndrome.

Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs.

Environmental genome project: a positive sequence of events.

Analysis of sequence conservation at nucleotide resolution.

MLGA--a rapid and cost-efficient assay for gene copy-number analysis.

RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.