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 481

System / cell line: coding ✕ Clear

Defective DNA repair and increased genomic instability in Artemis-deficient murine cells.

PMID 12615897 · PMC2193825 · The Journal of experimental medicine · 2003 · 8 claims · 8 setups

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Artemis-deficient ES cells are severely impaired in VDJ coding joining but retain relatively normal RS (signal) joining

recombined southern rt-pcr colony
Evaluation of NTHL1, NEIL1, NEIL2, MPG, TDG, UNG and SMUG1 genes in familial colorectal cancer predisposition.

PMID 17029639 · PMC1624846 · BMC cancer · 2006 · 6 claims · 4 setups

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Coding sequences and intron-exon boundaries of NTHL1, NEIL1, NEIL2, MPG, TDG, UNG and SMUG1 were screened in 94 familial CRC cases with known genes excluded

genomic predicted archival mutation targeted functional
Retinitis pigmentosa: mutation analysis of RHO, PRPF31, RP1, and IMPDH1 genes in patients from India.

PMID 18552984 · PMC2426732 · Molecular vision · 2008 · 8 claims · 4 setups

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Coding/flanking regions of RHO, PRPF31, and IMPDH1, plus exons 4F/4G/4H of RP1, were PCR-amplified and directly sequenced in 48 isolated and 53 adRP Indian patients and 75 controls

genomic peripheral probands identified pcr reverse clinical
Systematic Analysis of Long Non-Coding RNA Genes in Nonalcoholic Fatty Liver Disease.

PMID 35893239 · PMC9332188 · Non-coding RNA · 2022 · 6 claims · 5 setups

Has reproduction · 85

Many lncRNAs, like protein-coding genes, are differentially expressed in NAFLD patients compared to healthy normal-weight and obese individuals.

liver huh-7 bulk sirna lipid
Mitotic checkpoint protein hsMAD2 as a marker predicting liver metastasis of human gastric cancers.

PMID 11572763 · PMC5926839 · Japanese journal of cancer research : Gann · 2001 · 8 claims · 4 setups

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No mutations were found in the coding sequence of the hsMAD2 gene in 32 primary gastric cancers

gastric cancer formalin-fixed near-diploid pcr semi-quantitative immunohistochemistry
Human CCS gene: genomic organization and exclusion as a candidate for amyotrophic lateral sclerosis (ALS).

PMID 11991808 · PMC107843 · BMC genetics · 2002 · 6 claims · 5 setups

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The genomic organization of human CCS was characterized, with the 823 bp coding region organized into 8 exons spanning 12798 bp of genomic DNA.

bac heart ccs genomic genomic rt-pcr transcription
Empirical codon substitution matrix.

PMID 15927081 · PMC1173088 · BMC bioinformatics · 2005 · 8 claims · 5 setups

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The authors present the first empirical codon substitution matrix built entirely from alignments of vertebrate coding DNA sequences.

orthologous million codon same pairwise empirical comparative
Sequence changes in predicted promoter elements of STK11/LKB1 are unlikely to contribute to Peutz-Jeghers syndrome.

PMID 15774015 · PMC1084245 · BMC genomics · 2005 · 6 claims · 4 setups

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Integrated phylogenetic foot printing and transcription factor binding site (TFBS) prediction identified a consensus putative STK11/LKB1 promoter region between nucleotides -1090 and -1472

genomic phylogenetic direct high
Comparisons of substitution, insertion and deletion probes for resequencing and mutational analysis using oligonucleotide microarrays.

PMID 15722479 · PMC549431 · Nucleic acids research · 2005 · 7 claims · 4 setups

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Two base deletion probes display the highest average hybridization specificity, followed by single base substitution, single base deletion, and single base insertion probes.

atm hybridized probe oligonucleotide transcription microarray
GeneAlign: a coding exon prediction tool based on phylogenetical comparisons.

PMID 16845010 · PMC1538901 · Nucleic acids research · 2006 · 8 claims · 5 setups

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GeneAlign predicts coding exons by using signal detection (GeneSplicer/WMM) combined with CORAL, a heuristic linear-time alignment tool, to align candidate signal-flanked regions against annotated exons of a homologous organism's genes

homologous human-mouse same gene comparative parameter micro-exon
The secrets of a functional synapse--from a computational and experimental viewpoint.

PMID 16723009 · PMC1810317 · BMC bioinformatics · 2006 · 8 claims · 8 setups

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Kinesin motor proteins move cargo along axonal microtubules to the synapse, with cargo specificity determined by adaptor/linker proteins rather than lipid recognition

mammalian kinesin cholinergic dendrites kinesin sequence-based comparative
Large-scale trends in the evolution of gene structures within 11 animal genomes.

PMID 16518452 · PMC1386723 · PLoS computational biology · 2006 · 8 claims · 5 setups

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Change in intron–exon gene structure is gradual, clock-like, and largely independent of coding-sequence (protein) evolution

annotated animal unannotated comparative all-against-all neighbor-joining
Optineurin coding variants in Ghanaian patients with primary open-angle glaucoma.

PMID 19096531 · PMC2605106 · Molecular vision · 2008 · 8 claims · 4 setups

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OPTN coding variant allele frequencies do not differ significantly between POAG cases and controls in the Ghanaian population.

genomic ghanaian pcr taqman logistic
Cataloging coding sequence variations in human genome databases.

PMID 18974781 · PMC2570488 · PloS one · 2008 · 8 claims · 7 setups

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A significant proportion of CVs overlap between HGMD and dbSNP (4.36% of HGMD CVs registered in dbSNP; 8.11% of dbSNP CVs registered in HGMD), warranting caution when interpreting phenotypic relevance of concurrent CVs.

coding hapmap concurrent nssnps database hapmap amino
Worldwide distribution of NAT2 diversity: implications for NAT2 evolutionary history.

PMID 18304320 · PMC2292740 · BMC genetics · 2008 · 8 claims · 8 setups

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NAT2 coding region sequence variation in the Mandenka and other sub-Saharan African populations is consistent with selective neutrality and constant population size.

mandenka worldwide hapmap nat2 full snp analysis
The pharmacogenomics of membrane transporters project: research at the interface of genomics and transporter pharmacology.

PMID 19940846 · PMC2923224 · Clinical pharmacology and therapeutics · 2010 · 8 claims · 8 setups

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PMT identified sequence variants in 129 membrane transporter genes in the SLC and ABC superfamilies, discovering over 3100 SNPs

sophie mammalian xenopus lymphoblastoid resequencing cellular heterologous
The heterogeneous allelic repertoire of human toll-like receptor (TLR) genes.

PMID 19924287 · PMC2773936 · PloS one · 2009 · 8 claims · 8 setups

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Human TLR genes are unequally polymorphic: TLR2, 4, 7, 8 and 9 are comparatively least diverse, whereas TLR1, 5, 6 and 10 show substantial allelic diversity.

tlr10 tlr5 tlr1 tlr6 pcr-based
Novel SOX2 mutations and genotype-phenotype correlation in anophthalmia and microphthalmia.

PMID 19921648 · PMC2787970 · American journal of medical genetics. Part A · 2009 · 7 claims · 4 setups

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SOX2 coding-region mutations were identified in 10 of 51 (19.6%) unrelated individuals with anophthalmia/microphthalmia

blood parents sox2-mutation-positive pcr parental clinical
Mutation and deletion analysis of GFR alpha-1, encoding the co-receptor for the GDNF/RET complex, in human brain tumours.

PMID 10408842 · PMC2362327 · British journal of cancer · 1999 · 8 claims · 3 setups

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No mutations were found in the coding region of GDNF in any of the 36 brain tumours analysed

sporadic tumour tumour-derived pcr loss semi-quantitative
Absence of mutations in NR2E1 and SNX3 in five patients with MMEP (microcephaly, microphthalmia, ectrodactyly, and prognathism) and related phenotypes.

PMID 17655765 · PMC1950490 · BMC medical genetics · 2007 · 8 claims · 3 setups

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No coding mutations were found in NR2E1 or SNX3 in five patients with MMEP or related phenotypes

patients unaffected sanger restriction

Experiments

Defective DNA repair and increased genomic instability in Artemis-deficient murine cells.

Evaluation of NTHL1, NEIL1, NEIL2, MPG, TDG, UNG and SMUG1 genes in familial colorectal cancer predisposition.

Retinitis pigmentosa: mutation analysis of RHO, PRPF31, RP1, and IMPDH1 genes in patients from India.

Systematic Analysis of Long Non-Coding RNA Genes in Nonalcoholic Fatty Liver Disease.

Mitotic checkpoint protein hsMAD2 as a marker predicting liver metastasis of human gastric cancers.

Human CCS gene: genomic organization and exclusion as a candidate for amyotrophic lateral sclerosis (ALS).

Empirical codon substitution matrix.

Sequence changes in predicted promoter elements of STK11/LKB1 are unlikely to contribute to Peutz-Jeghers syndrome.

Comparisons of substitution, insertion and deletion probes for resequencing and mutational analysis using oligonucleotide microarrays.

GeneAlign: a coding exon prediction tool based on phylogenetical comparisons.

The secrets of a functional synapse--from a computational and experimental viewpoint.

Large-scale trends in the evolution of gene structures within 11 animal genomes.

Optineurin coding variants in Ghanaian patients with primary open-angle glaucoma.

Cataloging coding sequence variations in human genome databases.

Worldwide distribution of NAT2 diversity: implications for NAT2 evolutionary history.

The pharmacogenomics of membrane transporters project: research at the interface of genomics and transporter pharmacology.

The heterogeneous allelic repertoire of human toll-like receptor (TLR) genes.

Novel SOX2 mutations and genotype-phenotype correlation in anophthalmia and microphthalmia.

Mutation and deletion analysis of GFR alpha-1, encoding the co-receptor for the GDNF/RET complex, in human brain tumours.

Absence of mutations in NR2E1 and SNX3 in five patients with MMEP (microcephaly, microphthalmia, ectrodactyly, and prognathism) and related phenotypes.