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: family ✕ Assay: large ✕ Clear

Ethnically diverse causes of Walker-Warburg syndrome (WWS): FCMD mutations are a more common cause of WWS outside of the Middle East.

PMID 18752264 · PMC2577713 · Human mutation · 2008 · 8 claims · 4 setups

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40% (16/40) of WWS families in this diverse cohort received a molecular diagnosis with mutations in POMT1, POMT2, FKRP or FCMD

genomic pomt2 population genome-wide pcr multiplex
Intragenic deletion in the LARGE gene causes Walker-Warburg syndrome.

PMID 17436019 · PMC1914248 · Human genetics · 2007 · 7 claims · 8 setups

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A homozygous 63.1-kb intragenic deletion in LARGE (exons 9-10) causes Walker-Warburg syndrome in a consanguineous Saudi family

genomic family skeletal blood microsatellite direct multiplex
Protective effect of KCNH2 single nucleotide polymorphism K897T in LQTS families and identification of novel KCNQ1 and KCNH2 mutations.

PMID 18808722 · PMC2570672 · BMC medical genetics · 2008 · 8 claims · 7 setups

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LQTS-associated mutations were identified in 8 of 112 families studied

large lqts family mutation linkage direct single-strand
A procedure for the detection of linkage with high density SNP arrays in a large pedigree with colorectal cancer.

PMID 17222328 · PMC1784097 · BMC cancer · 2007 · 7 claims · 8 setups

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A workflow combining Alohomora, Mega2, MENDEL, SNPLINK and SimWalk2 enables linkage analysis with high-density SNP arrays in large pedigrees (>35-40 bits) that exceed the capacity of single existing programs

peripheral pedigree nuclear family snp two-point multipoint
Managing incidental findings in human subjects research: analysis and recommendations.

PMID 18547191 · PMC2575242 · The Journal of law, medicine & ethics : a journal of the American Society of Law, Medicine & Ethics · 2008 · 8 claims · 5 setups

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Little guidance currently exists on managing research IFs, and no consensus exists on the best approach across genetic/genomic and imaging research domains.

affected large research consent linkage genomic structural
FGF: a web tool for Fishing Gene Family in a whole genome database.

PMID 17584790 · PMC1933194 · Nucleic acids research · 2007 · 6 claims · 3 setups

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FGF efficiently searches and identifies gene families in whole-genome databases and outputs visual phylogenetic trees annotated with gene structure, chromosome position, duplication fate, and selective pressure (Ka/Ks)

genome rice gene large-scale
Comprehensive benchmarking of large language models for RNA secondary structure prediction.

PMID 40205851 · PMC11982019 · Briefings in bioinformatics · 2025 · 7 claims · 4 setups

Has reproduction · 88

Existing RNA-LLMs had not previously been evaluated for secondary structure prediction in a unified, fair experimental setup with the same datasets and prediction model.

archiveii bprna large-scale secondary cross-family self-supervised
Human genome research in China.

PMID 15168679 · PMC7079922 · Journal of molecular medicine (Berlin, Germany) · 2004 · 8 claims · 8 setups

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China completed its assigned 1% share of the international Human Genome Project sequencing effort and contributed ~10% of the HapMap effort

genome chinese high-risk nb4 large-scale mutation positional
Characterization of large rearrangements in autosomal dominant polycystic kidney disease and the PKD1/TSC2 contiguous gene syndrome.

PMID 18818683 · PMC2756756 · Kidney international · 2008 · 8 claims · 8 setups

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Developed an MLPA assay with PKD1 exon 1-33 probes designed at single base-pair mismatches with the six PKD1 pseudogenes to achieve locus specificity

blood-derived blood crisp father mlpa long-range field
Prediction and assessment of splicing alterations: implications for clinical testing.

PMID 18951448 · PMC2832470 · Human mutation · 2008 · 8 claims · 5 setups

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Bioinformatic prediction alone is insufficient; in vitro analysis is needed to confirm or establish splicing aberrations for clinical variant classification

brca1 lymphocytes mammalian large bioinformatic cycloheximide mini-gene
oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets.

PMID 22973536 · PMC3429929 · G3 (Bethesda, Md.) · 2012 · 8 claims · 6 setups

Has reproduction · 49

oPOSSUM-3 is a web-accessible system that identifies over-represented TFBS and TFBS families in DNA sequences of co-expressed genes or in sequences from high-throughput methods such as ChIP-Seq.

hg19 large-scale gene-based jaspar tfbs sequence-based anchored
BRCA1 and BRCA2 mutation predictions using the BOADICEA and BRCAPRO models and penetrance estimation in high-risk French-Canadian families.

PMID 16417652 · PMC1413985 · Breast cancer research : BCR · 2006 · 8 claims · 7 setups

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BOADICEA predicts accurately the number of BRCA1 and BRCA2 mutations across family groups and discriminates well between carriers and noncarriers

french-canadian families brca1-positive same targeted full-length multiplex
How to find soluble proteins: a comprehensive analysis of alpha/beta hydrolases for recombinant expression in E. coli.

PMID 15804363 · PMC1079826 · BMC genomics · 2005 · 7 claims · 7 setups

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Predicted solubility in E. coli (via CV-CV') depends on hydrolase size, phylogenetic origin, homologous family, and superfamily

lipase bacterial small genera cv-cv correlation grouped
Downregulation of death-associated protein kinase 1 (DAPK1) in chronic lymphocytic leukemia.

PMID 17540169 · PMC4647864 · Cell · 2007 · 8 claims · 13 setups

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DAPK1 promoter is epigenetically silenced by DNA methylation in almost all sporadic CLL cases

cd19+ leukemia raji jurkat quantitative cobra chromatin
Ratiocinative screen of eukaryotic integral membrane protein expression and solubilization for structure determination.

PMID 19031011 · PMC2756966 · Journal of structural and functional genomics · 2009 · 8 claims · 6 setups

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A discovery-oriented pipeline using standardized single-condition methods (one expression system, one detergent, one SEC buffer) can efficiently triage large numbers of eukaryotic IMP targets to identify well-behaved candidates for crystallization

cerevisiae ddm-solubilized sec-included tmhmm ligase-independent small-scale
The molecular landscape of ASPM mutations in primary microcephaly.

PMID 19028728 · PMC2658750 · Journal of medical genetics · 2009 · 8 claims · 7 setups

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ASPM mutations are the most common cause of MCPH

consanguineous genomic parents one polymorphic sanger family
Variation in conserved non-coding sequences on chromosome 5q and susceptibility to asthma and atopy.

PMID 16336695 · PMC1325232 · Respiratory research · 2005 · 6 claims · 8 setups

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There is overall little sequence variation in the conserved non-coding elements (CNEs) on 5q31, including none detected in CNE-B/CNS-1

genomic pcr large outbred comparative denaturing pcr
MRPS18CP2 alleles and DEFA3 absence as putative chromosome 8p23.1 modifiers of hearing loss due to mtDNA mutation A1555G in the 12S rRNA gene.

PMID 18154640 · PMC2233610 · BMC medical genetics · 2007 · 8 claims · 6 setups

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Chromosome 8p23.1 has previously been proposed as a nuclear modifier locus for A1555G-associated hearing loss phenotype

blood a1555g lymphoblastoid nuclear pcr-rflp direct rt-pcr
No germline mutations in supposed tumour suppressor genes SAFB1 and SAFB2 in familial breast cancer with linkage to 19p.

PMID 19077293 · PMC2635354 · BMC medical genetics · 2008 · 8 claims · 5 setups

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SAFB1 and SAFB2 had previously been proposed as tumour suppressor genes in breast cancer based on functional properties (ERα repression) and loss of heterozygosity in tumours

germline genomic identified individuals sequencing pcr mlpa
Evaluation of BRCA1 and BRCA2 mutations and risk-prediction models in a typical Asian country (Malaysia) with a relatively low incidence of breast cancer.

PMID 18627636 · PMC2575532 · Breast cancer research : BCR · 2008 · 8 claims · 5 setups

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27 deleterious BRCA1/BRCA2 mutations were detected in 28 breast cancer patients (14 in BRCA1, 13 in BRCA2) among 187 tested

blood-derived family brca1 direct multiplex boadicea

Experiments

Ethnically diverse causes of Walker-Warburg syndrome (WWS): FCMD mutations are a more common cause of WWS outside of the Middle East.

Intragenic deletion in the LARGE gene causes Walker-Warburg syndrome.

Protective effect of KCNH2 single nucleotide polymorphism K897T in LQTS families and identification of novel KCNQ1 and KCNH2 mutations.

A procedure for the detection of linkage with high density SNP arrays in a large pedigree with colorectal cancer.

Managing incidental findings in human subjects research: analysis and recommendations.

FGF: a web tool for Fishing Gene Family in a whole genome database.

Comprehensive benchmarking of large language models for RNA secondary structure prediction.

Human genome research in China.

Characterization of large rearrangements in autosomal dominant polycystic kidney disease and the PKD1/TSC2 contiguous gene syndrome.

Prediction and assessment of splicing alterations: implications for clinical testing.

oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets.

BRCA1 and BRCA2 mutation predictions using the BOADICEA and BRCAPRO models and penetrance estimation in high-risk French-Canadian families.

How to find soluble proteins: a comprehensive analysis of alpha/beta hydrolases for recombinant expression in E. coli.

Downregulation of death-associated protein kinase 1 (DAPK1) in chronic lymphocytic leukemia.

Ratiocinative screen of eukaryotic integral membrane protein expression and solubilization for structure determination.

The molecular landscape of ASPM mutations in primary microcephaly.

Variation in conserved non-coding sequences on chromosome 5q and susceptibility to asthma and atopy.

MRPS18CP2 alleles and DEFA3 absence as putative chromosome 8p23.1 modifiers of hearing loss due to mtDNA mutation A1555G in the 12S rRNA gene.

No germline mutations in supposed tumour suppressor genes SAFB1 and SAFB2 in familial breast cancer with linkage to 19p.

Evaluation of BRCA1 and BRCA2 mutations and risk-prediction models in a typical Asian country (Malaysia) with a relatively low incidence of breast cancer.