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 40

System / cell line: families ✕ Assay: size ✕ Clear

Long-term trends in evolution of indels in protein sequences.

PMID 17298668 · PMC1805498 · BMC evolutionary biology · 2007 · 8 claims · 5 setups

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More than one third of protein domains show a statistically significant tendency to increase or decrease in size over evolutionary distance.

curated individual cdd linear pearson binomial
Association between the ACCN1 gene and multiple sclerosis in Central East Sardinia.

PMID 17534430 · PMC1868958 · PloS one · 2007 · 8 claims · 6 setups

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Microsatellite D17S798 in the 17q11.2 region shows significant association with MS

nuclear accn1 genetic genotype microsatellite direct snp
A chromosome-level genome assembly provides insights into the environmental adaptability and outbreaks of Chlorops oryzae.

PMID 36028584 · PMC9418232 · Communications biology · 2022 · 8 claims · 8 setups

Has reproduction · 80

A high-quality chromosome-level genome assembly of C. oryzae was generated using PacBio, Illumina, and Hi-C sequencing

oryzae whole-genome genome orthology
Insights into vertebrate evolution from the chicken genome sequence.

PMID 15693954 · PMC551526 · Genome biology · 2005 · 8 claims · 6 setups

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Chicken has expanded gene families involved in egg production (e.g., avidin) and feather/scale/claw formation (avian-specific keratins) not present or lost in mammals

red chicken whole-genome comparative synteny
Genetic variants of surfactant proteins A, B, C, and D in bronchopulmonary dysplasia.

PMID 17264398 · PMC3850613 · Disease markers · 2006 · 7 claims · 4 setups

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Significant associations (p ≤ 0.01) were found between BPD subgroups and alleles of SP-B and SP-B-linked microsatellite markers, and haplotypes of SP-A, SP-D, and SP-B

greek genomic family-based pyrosequencing pcr
Analysis of cancer risk and BRCA1 and BRCA2 mutation prevalence in the kConFab familial breast cancer resource.

PMID 16507150 · PMC1413975 · Breast cancer research : BCR · 2006 · 6 claims · 7 setups

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kConFab is a collaborative resource providing epidemiological, clinical, and biospecimen data from high-risk familial breast/ovarian cancer families, available to researchers worldwide for ethically approved, peer-reviewed projects.

germline unaffected index randomly brca1 tyrer-cuzick strp
Genomic analysis of a heterogeneous Mendelian phenotype: multiple novel alleles for inherited hearing loss in the Palestinian population.

PMID 16460646 · PMC3525152 · Human genomics · 2006 · 8 claims · 8 setups

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GJB2 (connexin 26) mutations account for hearing loss in only 17 of 156 families (11%), a smaller fraction than reported in other populations.

palestinian genomic probands lymphoblasts targeted sanger pcr
Significance of the parkin and PINK1 gene in Jordanian families with incidences of young-onset and juvenile parkinsonism.

PMID 19087301 · PMC2635385 · BMC neurology · 2008 · 8 claims · 8 setups

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A parkin exon 4 deletion segregates with disease in a three-generation family (Family F), homozygous in both affected individuals

consanguineous same affected family sanger multiplex microsatellite
Identification of SLC26A4 gene mutations in Iranian families with hereditary hearing impairment.

PMID 18813951 · PMC4428656 · European journal of pediatrics · 2009 · 7 claims · 6 setups

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SLC26A4 mutations are the most prevalent cause of syndromic hereditary hearing loss (Pendred syndrome) in Iran

affected short pcr perchlorate
Efficient algorithms for probing the RNA mutation landscape.

PMID 18688270 · PMC2475669 · PLoS computational biology · 2008 · 8 claims · 4 setups

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RNAmutants generalizes McCaskill's partition function algorithm to sum over the grand canonical ensemble of all secondary structures of all k-point mutants, simultaneously computing MFE(k) and Z(k) for each k

element hepatitis hiv utr partition deleterious mutation
Mutations in the formin gene INF2 cause focal segmental glomerulosclerosis.

PMID 20023659 · PMC2980844 · Nature genetics · 2010 · 8 claims · 8 setups

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Mutations in INF2, a formin family actin-regulating protein, cause autosomal dominant focal segmental glomerulosclerosis (FSGS)

families genes individuals kidney genome-wide sanger resequencing
SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology.

PMID 19793867 · PMC2808975 · Nucleic acids research · 2010 · 8 claims · 8 setups

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A new 8.5x-coverage silkworm genome assembly with N50 scaffold size of ~3.7 Mb over a 432 Mb genome represents a significant quality improvement over the prior draft.

bombyx whole-genome snp novo
Identification of HNPCC by molecular analysis of colorectal and endometrial tumors.

PMID 15528786 · PMC3839268 · Disease markers · 2004 · 8 claims · 5 setups

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The Bethesda criteria, with a few modifications, are appropriate to identify families eligible for MMR mutation genetic testing

colorectal endometrial microsatellite immunohistochemistry germline
Novel and de novo PKD1 mutations identified by multiple restriction fragment-single strand conformation polymorphism (MRF-SSCP).

PMID 15018634 · PMC356914 · BMC medical genetics · 2004 · 6 claims · 7 setups

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MRF-SSCP method (using combined restriction digestion plus SSCP with silver staining) was developed to screen PKD1 mutations in full-length cDNA fractionated into nine overlapping nested-PCR segments

blood pkd1 pcr-purified genomic long nested-pcr mrf-sscp
PKD1 and PKD2 mutations in Slovenian families with autosomal dominant polycystic kidney disease.

PMID 16430766 · PMC1434729 · BMC medical genetics · 2006 · 7 claims · 8 setups

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Linkage analysis can pre-select which gene (PKD1 or PKD2) to screen for mutations in ADPKD families with sufficient samples

genomic pcr additional cat linkage direct heteroduplex
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
PAX6 gene variations associated with aniridia in south India.

PMID 15086958 · PMC419353 · BMC medical genetics · 2004 · 7 claims · 5 setups

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Mutations in PAX6 cause the aniridia phenotype via haploinsufficiency (loss-of-function/null alleles)

genomic pcr aniridia sscp automated allele-specific
Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties.

PMID 16790052 · PMC1534064 · BMC bioinformatics · 2006 · 8 claims · 7 setups

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The Sequential Minimal Optimization (SMO) SVM algorithm was the best-performing classifier among 26 WEKA classifiers for predicting catalytic residues

benchmarking same pirsf pdb supervised wrapper sequence
Identification of two novel OPA1 mutations in Chinese families with autosomal dominant optic atrophy.

PMID 19112530 · PMC2610289 · Molecular vision · 2008 · 8 claims · 5 setups

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Two novel heterozygous OPA1 mutations were identified: a splice-site mutation c.985-2A>G in family F1 and a nonsense mutation c.2197C>T (p.R733X) in family F2

genomic available leukocytes affected linkage pcr single
Complete Genome Sequencing of Lactobacillus plantarum ZLP001, a Potential Probiotic That Enhances Intestinal Epithelial Barrier Function and Defense Against Pathogens in Pigs.

PMID 30542296 · PMC6277807 · Frontiers in physiology · 2018 · 8 claims · 8 setups

Has reproduction · 68

The complete genome of L. plantarum ZLP001 was sequenced and compared with 18 other L. plantarum genomes to identify genomic features underlying its gut-health-promoting probiotic properties.

lactobacillus plantarum whole-genome gene comparative

Experiments

Long-term trends in evolution of indels in protein sequences.

Association between the ACCN1 gene and multiple sclerosis in Central East Sardinia.

A chromosome-level genome assembly provides insights into the environmental adaptability and outbreaks of Chlorops oryzae.

Insights into vertebrate evolution from the chicken genome sequence.

Genetic variants of surfactant proteins A, B, C, and D in bronchopulmonary dysplasia.

Analysis of cancer risk and BRCA1 and BRCA2 mutation prevalence in the kConFab familial breast cancer resource.

Genomic analysis of a heterogeneous Mendelian phenotype: multiple novel alleles for inherited hearing loss in the Palestinian population.

Significance of the parkin and PINK1 gene in Jordanian families with incidences of young-onset and juvenile parkinsonism.

Identification of SLC26A4 gene mutations in Iranian families with hereditary hearing impairment.

Efficient algorithms for probing the RNA mutation landscape.

Mutations in the formin gene INF2 cause focal segmental glomerulosclerosis.

SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology.

Identification of HNPCC by molecular analysis of colorectal and endometrial tumors.

Novel and de novo PKD1 mutations identified by multiple restriction fragment-single strand conformation polymorphism (MRF-SSCP).

PKD1 and PKD2 mutations in Slovenian families with autosomal dominant polycystic kidney disease.

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

PAX6 gene variations associated with aniridia in south India.

Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties.

Identification of two novel OPA1 mutations in Chinese families with autosomal dominant optic atrophy.

Complete Genome Sequencing of Lactobacillus plantarum ZLP001, a Potential Probiotic That Enhances Intestinal Epithelial Barrier Function and Defense Against Pathogens in Pigs.