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 615

Assay: size ✕ Clear

Rubinstein-Taybi Syndrome: spectrum of CREBBP mutations in Italian patients.

PMID 17052327 · PMC1626071 · BMC medical genetics · 2006 · 8 claims · 8 setups

Full-text index only

RSTS is caused by chromosomal microdeletions and point mutations in one copy of CREBBP (16p13.3), consistent with haploinsufficiency of this dosage-sensitive gene

peripheral patient-parent genomic crebbp karyotyping bac microsatellite
Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs.

PMID 23536903 · PMC3607606 · PloS one · 2013 · 8 claims · 9 setups

Has reproduction · 45

Bubbleparse detects sequence variants directly from NGS reads without a reference genome, using the coloured de Bruijn graph implementation of Cortex plus a new depth-first bubble-finding module.

arabidopsis bubbleparse escherichia col-0 reference-free alignment-based sequence
Identification of diagnostic markers for tuberculosis by proteomic fingerprinting of serum.

PMID 16980117 · PMC7159276 · Lancet (London, England) · 2006 · 8 claims · 5 setups

Full-text index only

An SVM classifier trained on serum proteomic profiles discriminated patients with active tuberculosis from controls with clinically overlapping conditions

serum computational kda spin-column seldi-tof supervised peptide
Negative association of endothelial nitric oxide gene polymorphism with hypertension in Turkish patients: effect of ecNOS polymorphism on left ventricular hypertrophy.

PMID 16923191 · PMC1559722 · Cardiovascular ultrasound · 2006 · 7 claims · 4 setups

Full-text index only

ecNOS4a/b gene polymorphism is not associated with hypertension in Turkish patients

genomic hypertensive clinical pcr m-mode pulsed
V-MitoSNP: visualization of human mitochondrial SNPs.

PMID 16907992 · PMC1564046 · BMC bioinformatics · 2006 · 6 claims · 4 setups

Full-text index only

V-MitoSNP integrates RFLP genotyping information with mitochondria-related cancer/disease data in a user-friendly, interactive, color-coded visual web interface

blood blood-derived mtdna standard agarose rflp
The pseudo-mitochondrial genome influences mistakes in heteroplasmy interpretation.

PMID 16859552 · PMC1538596 · BMC genomics · 2006 · 7 claims · 7 setups

Full-text index only

Numts co-amplified with mtDNA during PCR generate false heteroplasmic signals at specific nucleotide positions.

143b ffpe blood cloned southern pcr rt-pcr
Wiggle-predicting functionally flexible regions from primary sequence.

PMID 16839194 · PMC1500818 · PLoS computational biology · 2006 · 7 claims · 6 setups

Full-text index only

A GNM-derived, correlation-weighted 'FF score' can objectively define functionally flexible regions (FFRs) that match experimentally confirmed flexible/functional regions (hinges, recognition loops, catalytic loops).

hiv bovine calmodulin nonredundant gaussian gnm support
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

Full-text index only

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
Comparative genomic mapping of the bovine Fragile Histidine Triad (FHIT) tumour suppressor gene: characterization of a 2 Mb BAC contig covering the locus, complete annotation of the gene, analysis of cDNA and of physiological expression profiles.

PMID 16719907 · PMC1513570 · BMC genomics · 2006 · 8 claims · 5 setups

Full-text index only

A 2 Mb BAC contig of 78 clones was assembled covering the entire bovine FHIT locus

bovine pcr-based comparative rt-pcr
Genetic diversity among five T4-like bacteriophages.

PMID 16716236 · PMC1524935 · Virology journal · 2006 · 8 claims · 8 setups

Full-text index only

A core set of 82 conserved genes (T4-like genes) is present in all five genomes analyzed, clustered in large collinear blocks.

bacteriophages five conserved aeh1 genome orf trna
Genome microevolution of chikungunya viruses causing the Indian Ocean outbreak.

PMID 16700631 · PMC1463904 · PLoS medicine · 2006 · 8 claims · 6 setups

Full-text index only

The Indian Ocean outbreak was initiated by a strain related to East African CHIKV isolates, which subsequently evolved via a traceable microevolution history

chikv partial pseudoscutellaris mosquito nucleotide phylogenetic focus
Four genomic islands that mark post-1995 pandemic Vibrio parahaemolyticus isolates.

PMID 16672049 · PMC1464126 · BMC genomics · 2006 · 8 claims · 7 setups

Full-text index only

Seven genomic islands (VPaI-1 to VPaI-7, 10-81 kb) were identified in V. parahaemolyticus RIMD2210633 by aberrant GC content, presence of integrases/transposases, flanking direct repeats, and absence from related Vibrionaceae genomes.

parahaemolyticus vulnificus clinical ecori-digested bioinformatic comparative pcr
Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms.

PMID 16569258 · PMC1557760 · Genome biology · 2006 · 8 claims · 7 setups

Full-text index only

An exon-gene-union (EGU) algorithm followed by an open-reading-frame-selection algorithm can synthesize ab initio (GENSCAN, GeneMark, SNAP) and comparative (Ensembl/Genewise) predictions into a single, more complete CDS set

anopheles gambiae reanocds05 initio full-length rt-pcr
The fragile breakage versus random breakage models of chromosome evolution.

PMID 16501665 · PMC1378107 · PLoS computational biology · 2006 · 8 claims · 6 setups

Full-text index only

Sankoff and Trinh's synteny block identification algorithm (ST-Synteny) is flawed, producing erroneous block identifications even in small toy examples.

small synthetic synteny random whole-genome
Microsatellite instability analysis in hereditary non-polyposis colon cancer using the Bethesda consensus panel of microsatellite markers in the absence of proband normal tissue.

PMID 16426447 · PMC1373649 · BMC medical genetics · 2006 · 7 claims · 4 setups

Full-text index only

MSI status can be determined in the absence of proband non-tumor tissue by comparing tumor alleles to alleles carried by the proband's progenitors

proband's peripheral hmsh2 microsatellite direct targeted
Mutation analysis of SDHB and SDHC: novel germline mutations in sporadic head and neck paraganglioma and familial paraganglioma and/or pheochromocytoma.

PMID 16405730 · PMC1343542 · BMC medical genetics · 2006 · 8 claims · 4 setups

Full-text index only

Germline mutations of SDHB and SDHC play a minor role in sporadic head and neck paraganglioma

peripheral genomic ebv-transformed conformation pira-pcr rt-pcr
A modified T-test feature selection method and its application on the HapMap genotype data.

PMID 18267305 · PMC5054219 · Genomics, proteomics & bioinformatics · 2007 · 7 claims · 4 setups

Full-text index only

A modified t-test ranking measure, extended to handle nominal SNP genotype data via vector transformation, can effectively rank SNPs by their discriminative capability for population classification.

hapmap modified f-statistics informativeness
Co-circulation and evolution of polioviruses and species C enteroviruses in a district of Madagascar.

PMID 18085822 · PMC2134956 · PLoS pathogens · 2007 · 8 claims · 8 setups

Full-text index only

Madagascar VDPVs are intertypic/interspecies recombinants with Sabin 2-derived sequence in the 5'-half of the genome and HEV-C-derived sequence in the 3'-half

vdpv mad04 pvr-tg21 hep-2c rt-pcr monoclonal plaque
Characterisation and protein expression profiling of annexins in colorectal cancer.

PMID 18071363 · PMC2361450 · British journal of cancer · 2008 · 7 claims · 5 setups

Full-text index only

Annexins A1, A2, A4 and A11 are overexpressed in primary colorectal cancer compared with normal colon

dukes colorectal immunised whole-cell gel immunohistochemistry elisa
Genetic variability of the P120' surface protein gene of Mycoplasma hominis isolates recovered from Tunisian patients with uro-genital and infertility disorders.

PMID 18053243 · PMC2225410 · BMC infectious diseases · 2007 · 7 claims · 5 setups

Full-text index only

The P120' surface-exposed N-terminal region undergoes substantial genetic variability among Tunisian M. hominis clinical isolates

cloned clinical hominis pcr culture sanger

Experiments

Rubinstein-Taybi Syndrome: spectrum of CREBBP mutations in Italian patients.

Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs.

Identification of diagnostic markers for tuberculosis by proteomic fingerprinting of serum.

Negative association of endothelial nitric oxide gene polymorphism with hypertension in Turkish patients: effect of ecNOS polymorphism on left ventricular hypertrophy.

V-MitoSNP: visualization of human mitochondrial SNPs.

The pseudo-mitochondrial genome influences mistakes in heteroplasmy interpretation.

Wiggle-predicting functionally flexible regions from primary sequence.

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

Comparative genomic mapping of the bovine Fragile Histidine Triad (FHIT) tumour suppressor gene: characterization of a 2 Mb BAC contig covering the locus, complete annotation of the gene, analysis of cDNA and of physiological expression profiles.

Genetic diversity among five T4-like bacteriophages.

Genome microevolution of chikungunya viruses causing the Indian Ocean outbreak.

Four genomic islands that mark post-1995 pandemic Vibrio parahaemolyticus isolates.

Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms.

The fragile breakage versus random breakage models of chromosome evolution.

Microsatellite instability analysis in hereditary non-polyposis colon cancer using the Bethesda consensus panel of microsatellite markers in the absence of proband normal tissue.

Mutation analysis of SDHB and SDHC: novel germline mutations in sporadic head and neck paraganglioma and familial paraganglioma and/or pheochromocytoma.

A modified T-test feature selection method and its application on the HapMap genotype data.

Co-circulation and evolution of polioviruses and species C enteroviruses in a district of Madagascar.

Characterisation and protein expression profiling of annexins in colorectal cancer.

Genetic variability of the P120' surface protein gene of Mycoplasma hominis isolates recovered from Tunisian patients with uro-genital and infertility disorders.