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 177

System / cell line: presence ✕ Assay: number ✕ Clear

U7 snRNAs: a computational survey.

PMID 18267300 · PMC5054213 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 6 setups

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A computational (BLAST-based) survey identified bona fide U7 snRNA genes with characteristic upstream promoter elements (PSE) across most vertebrate genomes examined, plus numerous pseudogenes.

mammalian drosophilid aligned basal blast sequence consensus
Family history of breast cancer and all-cause mortality after breast cancer diagnosis in the Breast Cancer Family Registry.

PMID 19034644 · PMC2728159 · Breast cancer research and treatment · 2009 · 7 claims · 5 setups

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Family history of breast cancer is not associated with all-cause mortality after breast cancer diagnosis in women without a known germline BRCA1/BRCA2 mutation.

women same breast structured cox germline
New mutations in the PKD1 gene in Czech population with autosomal dominant polycystic kidney disease.

PMID 19686598 · PMC2736583 · BMC medical genetics · 2009 · 8 claims · 7 setups

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DGGE screening of the non-duplicated PKD1 region detects likely pathogenic mutations in Czech ADPKD patients

genomic pcr polycystin-1 czech denaturing sanger family
A comprehensive proteomics and genomics analysis reveals novel transmembrane proteins in human platelets and mouse megakaryocytes including G6b-B, a novel immunoreceptor tyrosine-based inhibitory motif protein.

PMID 17186946 · PMC1860054 · Molecular & cellular proteomics : MCP · 2007 · 8 claims · 8 setups

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Three complementary membrane-enrichment proteomic methods (lectin affinity, biotin/NeutrAvidin affinity, free flow electrophoresis) combined with LC-MS/MS identify 136 transmembrane proteins in human platelets, including many novel ones.

washed platelets tryptic hek293t lc-ms free longsage
Inter-population variability of DEFA3 gene absence: correlation with haplotype structure and population variability.

PMID 17214878 · PMC1779775 · BMC genomics · 2007 · 8 claims · 7 setups

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The proportion of subjects lacking DEFA3 varies significantly by population, from 10% to 37%

genomic hapmap 150-kb alpha-defensin pcr-rflp snp linkage
Design factors that influence PCR amplification success of cross-species primers among 1147 mammalian primer pairs.

PMID 17029642 · PMC1635982 · BMC genomics · 2006 · 8 claims · 7 setups

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The number of index-species (IS) mismatches in a primer pair significantly reduces amplification success, with an estimated 6-8% decrease in success rate per additional mismatch.

dog hamster pcr primer pcr blast sequence
Frequent and multiple mutations at minisatellite loci in sporadic human colorectal and gastric cancers--possible mechanistic differences from microsatellite instability in cancer cells.

PMID 11985787 · PMC5927018 · Japanese journal of cancer research : Gann · 2002 · 6 claims · 3 setups

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MN mutations occur significantly more frequently in sporadic colorectal cancer (56%) than in gastric cancer (25%)

sporadic same multilocus pcr-simple
Programmed genetic instability: a tumor-permissive mechanism for maintaining the evolvability of higher species through methylation-dependent mutation of DNA repair genes in the male germ line.

PMID 18535014 · PMC2464741 · Molecular biology and evolution · 2008 · 8 claims · 7 setups

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Repair genes are numerically less common than apoptosis genes in the genomes of multicellular organisms

yeast familial human-mouse comparative gene mutation
Global variation in copy number in the human genome.

PMID 17122850 · PMC2669898 · Nature · 2006 · 8 claims · 6 setups

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A first-generation CNV map of the human genome was constructed from 270 HapMap individuals across four populations, identifying 1,447 CNV regions covering ~360 Mb (12%) of the genome.

hapmap subset blood snp array karyotyping
Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space.

PMID 16481312 · PMC1373602 · Nucleic acids research · 2006 · 8 claims · 7 setups

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The number of protein families continues to expand steadily as more genomes are sequenced, showing no sign of saturation.

non-identical gene3d cath whole-gene domain transmembrane
Genomic analysis of the clonal origins of relapsed acute lymphoblastic leukemia.

PMID 19039135 · PMC2746051 · Science (New York, N.Y.) · 2008 · 8 claims · 7 setups

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Diagnosis and relapse ALL samples show different patterns of CNAs, with relapse-acquired abnormalities preferentially affecting cell cycle regulation and B-cell development genes

matched bone leukemia diagnosis snp flow quantitative
Copy number variations are a rare cause of non-CMT1A Charcot-Marie-Tooth disease.

PMID 19949810 · PMC2865568 · Journal of neurology · 2010 · 7 claims · 4 setups

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CNVs are a rare cause of non-CMT1A Charcot-Marie-Tooth disease

unrelated genomic mtmr2 array quantitative sanger
Limited copy number-high resolution melting (LCN-HRM) enables the detection and identification by sequencing of low level mutations in cancer biopsies.

PMID 19811662 · PMC2766370 · Molecular cancer · 2009 · 7 claims · 6 setups

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LCN-HRM enables detection and sequencing-based characterisation of low-level mutations that are undetectable by direct sequencing alone

hct116 ffpe genomic tx84 dideoxynucleotide high lcn-hrm
Bayesian prediction of microbial oxygen requirement.

PMID 26913185 · PMC4743139 · F1000Research · 2013 · 7 claims · 8 setups

Has reproduction · 76

A naive Bayesian classifier based on presence/absence of class-associated Pfam-A domains can distinguish three oxygen requirement classes (aerobe, anaerobe, facultative anaerobe) from genome sequence, unlike prior studies that only made pairwise distinctions.

bacterial selected predicted pfam-a genome gene domain
Evolutionary analysis of the highly dynamic CHEK2 duplicon in anthropoids.

PMID 18831734 · PMC2566985 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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CHEK2 is present as a single copy in New World monkeys, Old World monkeys, and gibbons

metaphase chek2 blood-derived y-chromosomal comparative phylogenetic inter-species
Modified H5 promoter improves stability of insert genes while maintaining immunogenicity during extended passage of genetically engineered MVA vaccines.

PMID 19969118 · PMC2821965 · Vaccine · 2010 · 7 claims · 8 setups

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rMVA expressing multiple antigens under the mH5 promoter exhibit remarkable genetic stability and maintain potent immunogenicity after serial passage

rmva-infected individually bhk-21 pbmc qpcr western southern
Genomic view of the evolution of the complement system.

PMID 16896831 · PMC2480602 · Immunogenetics · 2006 · 8 claims · 6 setups

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Bony fish and higher vertebrates share practically the same set of complement genes, indicating most complement gene duplications occurred by the teleost/mammalian divergence (~500 MYA)

chicken complement sponge shark comparative phylogenetic reverse
Analysis of copy number variation using quantitative interspecies competitive PCR.

PMID 18697816 · PMC2553599 · Nucleic acids research · 2008 · 7 claims · 6 setups

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qicPCR uses the entire genome of a single chimpanzee as a competitor, requiring only one reference sample for all assays and enabling large-scale multiplexing

genomic single 22q11ds qicpcr-derived qicpcr mlpa fluorescence
A genome-wide screen for copy number alterations in Aicardi syndrome.

PMID 19760649 · PMC3640635 · American journal of medical genetics. Part A · 2009 · 7 claims · 4 setups

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Aicardi syndrome is thought to result from heterozygous defects in an essential X-linked gene, or from a sex-limited autosomal gene defect, due to its occurrence almost exclusively in females and in 47,XXY males.

genomic subject array quantitative fluorescence
Severe combined immunodeficiency (SCID) and attention deficit hyperactivity disorder (ADHD) associated with a Coronin-1A mutation and a chromosome 16p11.2 deletion.

PMID 19097825 · PMC2692687 · Clinical immunology (Orlando, Fla.) · 2009 · 8 claims · 7 setups

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CORO1A deficiency, caused by a paternal 2bp frameshift mutation combined with a maternal de novo 600kb deletion at chromosome 16p11.2, is the molecular cause of this patient's T-B+NK+ SCID

ebv-transformed genomic father peripheral intracellular snp sequencing

Experiments

U7 snRNAs: a computational survey.

Family history of breast cancer and all-cause mortality after breast cancer diagnosis in the Breast Cancer Family Registry.

New mutations in the PKD1 gene in Czech population with autosomal dominant polycystic kidney disease.

A comprehensive proteomics and genomics analysis reveals novel transmembrane proteins in human platelets and mouse megakaryocytes including G6b-B, a novel immunoreceptor tyrosine-based inhibitory motif protein.

Inter-population variability of DEFA3 gene absence: correlation with haplotype structure and population variability.

Design factors that influence PCR amplification success of cross-species primers among 1147 mammalian primer pairs.

Frequent and multiple mutations at minisatellite loci in sporadic human colorectal and gastric cancers--possible mechanistic differences from microsatellite instability in cancer cells.

Programmed genetic instability: a tumor-permissive mechanism for maintaining the evolvability of higher species through methylation-dependent mutation of DNA repair genes in the male germ line.

Global variation in copy number in the human genome.

Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space.

Genomic analysis of the clonal origins of relapsed acute lymphoblastic leukemia.

Copy number variations are a rare cause of non-CMT1A Charcot-Marie-Tooth disease.

Limited copy number-high resolution melting (LCN-HRM) enables the detection and identification by sequencing of low level mutations in cancer biopsies.

Bayesian prediction of microbial oxygen requirement.

Evolutionary analysis of the highly dynamic CHEK2 duplicon in anthropoids.

Modified H5 promoter improves stability of insert genes while maintaining immunogenicity during extended passage of genetically engineered MVA vaccines.

Genomic view of the evolution of the complement system.

Analysis of copy number variation using quantitative interspecies competitive PCR.

A genome-wide screen for copy number alterations in Aicardi syndrome.

Severe combined immunodeficiency (SCID) and attention deficit hyperactivity disorder (ADHD) associated with a Coronin-1A mutation and a chromosome 16p11.2 deletion.