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 164

System / cell line: sequence ✕ Assay: same ✕ Clear

Performance of methods for SARS-CoV-2 variant detection and abundance estimation within mixed population samples.

PMID 36721781 · PMC9884472 · PeerJ · 2023 · 8 claims · 4 setups

Has reproduction · 50

Kallisto was the most accurate VCE on simulated data, having the lowest RRMSE, followed by Freyja

sars-cov-2 publicly simulated simulated amplicon-based variant
A comprehensive resequence analysis of the KLK15-KLK3-KLK2 locus on chromosome 19q13.33.

PMID 19823874 · PMC2793378 · Human genetics · 2010 · 7 claims · 7 setups

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Deep resequencing of a 56 kb region on chr19q13.33 identified 555 polymorphic loci, including 116 novel SNPs and 182 novel indels.

individuals sequence resequencing snps targeted sequence genotype
SeqDoC: rapid SNP and mutation detection by direct comparison of DNA sequence chromatograms.

PMID 15927052 · PMC1156871 · BMC bioinformatics · 2005 · 8 claims · 6 setups

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SeqDoC generates a subtracted difference trace between a reference and test chromatogram that highlights single base changes

melanocortin same paired test chromatogram tracediff weak
FeatureScan: revealing property-dependent similarity of nucleotide sequences.

PMID 16845077 · PMC1538849 · Nucleic acids research · 2006 · 6 claims · 5 setups

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FeatureScan transforms nucleotide sequences into numerical signals of physico-chemical/conformational properties and compares them via a convolution/correlation (Fourier transform) method rather than comparing letters

randomly fully same chimpanzee signal-theoretic featurescan blast
A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

PMID 25202605 · PMC4103609 · Applications in plant sciences · 2014 · 8 claims · 8 setups

Has reproduction · 87

A custom sequence capture probe set (9678 baits targeting 1061 orthologous genes) was designed to enrich COS loci across the Compositae.

compositae same species helianthus targeted genome genomic
Sequence analysis of MYOC and CYP1B1 in a Chinese pedigree of juvenile glaucoma with goniodysgenesis.

PMID 19668597 · PMC2722712 · Molecular vision · 2009 · 7 claims · 4 setups

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A heterozygous MYOC mutation c.1109C>T (P370L) in exon 3 cosegregates with disease, present in all 6 affected members and absent in asymptomatic members.

genomic patients pcr clinical genomic
Bayesian coestimation of phylogeny and sequence alignment.

PMID 15804354 · PMC1087833 · BMC bioinformatics · 2005 · 7 claims · 3 setups

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Alignment and phylogenetic inference are mutually dependent, and treating them as separate sequential steps (align then infer tree) is fundamentally flawed and produces biased, overconfident estimates.

globin same four-sequence bayesian mcmc comparison
Molecular epidemiology of O139 Vibrio cholerae: mutation, lateral gene transfer, and founder flush.

PMID 12890320 · PMC3023423 · Emerging infectious diseases · 2003 · 8 claims · 4 setups

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Lateral gene transfer (LGT) produced roughly three times as many nucleotide changes as point mutation among the 96 O139 isolates.

vibrio same novel aligned multilocus pcr blast
Speeding disease gene discovery by sequence based candidate prioritization.

PMID 15766383 · PMC1274252 · BMC bioinformatics · 2005 · 7 claims · 8 setups

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Disease genes (OMIM) differ significantly from non-disease genes in sequence-based features including gene/cDNA/protein size, exon number, homolog conservation, secretion signal, 3' UTR length, CpG islands, and distance to nearest gene.

ensembl training same hgmd comparative machine tenfold
Sequence variation and linkage disequilibrium in the GABA transporter-1 gene (SLC6A1) in five populations: implications for pharmacogenetic research.

PMID 17941974 · PMC2175509 · BMC genetics · 2007 · 8 claims · 7 setups

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SLC6A1 shows low levels of LD and an absence of major LD blocks across all five populations studied

african-american thai same study sanger snp genotyping
Conservation, variability and the modeling of active protein kinases.

PMID 17912359 · PMC1989141 · PloS one · 2007 · 7 claims · 5 setups

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A novel sequence-order independent (fold-independent) structural alignment algorithm was developed that maximizes side-chain similarity to produce a consensus kinase structure.

active-conformation same chak rio2 sequence-order pairwise structural
Heterozygous CAV1 frameshift mutations (MIM 601047) in patients with atypical partial lipodystrophy and hypertriglyceridemia.

PMID 18237401 · PMC2276215 · Lipids in health and disease · 2008 · 8 claims · 4 setups

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Two distinct heterozygous frameshift mutations in CAV1 (I134fsdelA-X137 and -88delC) were identified in patients with atypical partial lipodystrophy and severe hypertriglyceridemia

genomic sequence restriction allele-specific
Multilocus sequence typing supports the hypothesis that Ochrobactrum anthropi displays a human-associated subpopulation.

PMID 20021660 · PMC2810298 · BMC microbiology · 2009 · 8 claims · 6 setups

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A novel Multi-Locus Sequence Typing (MLST) scheme for O. anthropi was developed for the first time, based on 7 genes (3490 nucleotides) evolving mostly by neutral mutations

anthropi same candidate multi-locus pulsed-field antibiotyping
Rapid detection of SMARCB1 sequence variation using high resolution melting.

PMID 20003390 · PMC2801682 · BMC cancer · 2009 · 8 claims · 6 setups

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HRM screening of SMARCB1 amplicons has a zero false negative rate compared to direct sequencing

genomic same tumor rhabdoid high direct hrm
Toward the use of genomics to study microevolutionary change in bacteria.

PMID 19855823 · PMC2756242 · PLoS genetics · 2009 · 7 claims · 5 setups

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The clonal population structure of bacteria, combined with occasional DNA import, provides a powerful context for identifying genetic bases of adaptive phenotypes via association studies.

neisseria campylobacter helicobacter sequence multilocus phylogeny-based
Multilocus sequence typing of Cronobacter sakazakii and Cronobacter malonaticus reveals stable clonal structures with clinical significance which do not correlate with biotypes.

PMID 19852808 · PMC2770063 · BMC microbiology · 2009 · 8 claims · 6 setups

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A seven-locus MLST scheme (atpD, fusA, glnS, gltB, gyrB, infB, pps) reliably identifies and discriminates C. sakazakii and C. malonaticus strains

sakazakii cronobacter sequenced multilocus biotyping phylogenetic
Cotranscriptional RNA strand exchange underlies the gene regulation mechanism in a purine-sensing transcriptional riboswitch.

PMID 35348734 · PMC9756952 · Nucleic acids research · 2022 · 7 claims · 6 setups

Has reproduction · 91

A nascent intermediate central helix forms in the yxjA riboswitch that is mutually exclusive with both the aptamer's P1 helix and the expression platform's intrinsic terminator hairpin.

coli yxja refolded flow bulk cotranscriptional
Molecular characterization of Campylobacter jejuni clones: a basis for epidemiologic investigation.

PMID 12194772 · PMC2732546 · Emerging infectious diseases · 2002 · 8 claims · 5 setups

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Clonal complex, as defined by MLST, is an epidemiologically relevant unit for long- and short-term investigation of C. jejuni epidemiology.

jejuni same clonal mlst multilocus heat-stable flaa
Novel mutations in the BRCA1 and BRCA2 genes in Iranian women with early-onset breast cancer.

PMID 12100744 · PMC116720 · Breast cancer research : BCR · 2002 · 8 claims · 4 setups

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Germline BRCA1 and BRCA2 mutations are present in Iranian women with early-onset breast cancer, including four novel frameshift mutations

genomic pcr-amplified pcr truncation single-strand heteroduplex
Comprehensive search for intra- and inter-specific sequence polymorphisms among coding envelope genes of retroviral origin found in the human genome: genes and pseudogenes.

PMID 16150157 · PMC1236922 · BMC genomics · 2005 · 8 claims · 5 setups

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HERV-W (envW) and HERV-FRD (envFRD) envelope genes, both specifically expressed in placenta, show strong sequence conservation with only two nonsynonymous SNPs identified across 91 individuals

genomic genotype 293t pcr-amplified pcr haplotype cell-cell

Experiments

Performance of methods for SARS-CoV-2 variant detection and abundance estimation within mixed population samples.

A comprehensive resequence analysis of the KLK15-KLK3-KLK2 locus on chromosome 19q13.33.

SeqDoC: rapid SNP and mutation detection by direct comparison of DNA sequence chromatograms.

FeatureScan: revealing property-dependent similarity of nucleotide sequences.

A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

Sequence analysis of MYOC and CYP1B1 in a Chinese pedigree of juvenile glaucoma with goniodysgenesis.

Bayesian coestimation of phylogeny and sequence alignment.

Molecular epidemiology of O139 Vibrio cholerae: mutation, lateral gene transfer, and founder flush.

Speeding disease gene discovery by sequence based candidate prioritization.

Sequence variation and linkage disequilibrium in the GABA transporter-1 gene (SLC6A1) in five populations: implications for pharmacogenetic research.

Conservation, variability and the modeling of active protein kinases.

Heterozygous CAV1 frameshift mutations (MIM 601047) in patients with atypical partial lipodystrophy and hypertriglyceridemia.

Multilocus sequence typing supports the hypothesis that Ochrobactrum anthropi displays a human-associated subpopulation.

Rapid detection of SMARCB1 sequence variation using high resolution melting.

Toward the use of genomics to study microevolutionary change in bacteria.

Multilocus sequence typing of Cronobacter sakazakii and Cronobacter malonaticus reveals stable clonal structures with clinical significance which do not correlate with biotypes.

Cotranscriptional RNA strand exchange underlies the gene regulation mechanism in a purine-sensing transcriptional riboswitch.

Molecular characterization of Campylobacter jejuni clones: a basis for epidemiologic investigation.

Novel mutations in the BRCA1 and BRCA2 genes in Iranian women with early-onset breast cancer.

Comprehensive search for intra- and inter-specific sequence polymorphisms among coding envelope genes of retroviral origin found in the human genome: genes and pseudogenes.