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 30

System / cell line: genbank ✕ Assay: blast ✕ Clear

Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.

PMID 17010196 · PMC1592491 · BMC genomics · 2006 · 8 claims · 7 setups

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High-throughput 454 sequencing-by-synthesis of LNCaP cDNA can profile transcript abundance across the transcriptome

lncap lncap-derived r1881-treated massively blast blat
A novel optineurin genetic mutation associated with open-angle glaucoma in a Chinese family.

PMID 19710941 · PMC2730747 · Molecular vision · 2009 · 8 claims · 3 setups

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A novel missense mutation A1274G (Lys322Glu) in exon 10 of OPTN was identified in affected members of the family

family peripheral patients microsatellite pcr clinical
Database resources of the National Center for Biotechnology Information.

PMID 17170002 · PMC1781113 · Nucleic acids research · 2007 · 8 claims · 8 setups

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NCBI maintains an integrated suite of database resources (Entrez, PubMed, RefSeq, dbSNP, BLAST, etc.) for molecular biology data retrieval and analysis

genbank genomic eukaryotic completely sequence rapid est
Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins.

PMID 18564434 · PMC2453528 · BMC genomics · 2008 · 8 claims · 6 setups

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Jmjd6 has been misleadingly annotated as a transmembrane receptor for engulfment of apoptotic cells; recent evidence contradicts this transmembrane receptor function

species genomic jmjd6 jmjc reciprocal comparative est
GenBank.

PMID 16381837 · PMC1347519 · Nucleic acids research · 2006 · 8 claims · 8 setups

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GenBank is a comprehensive public database of nucleotide sequences with supporting bibliographic and biological annotation, built and distributed by NCBI.

sapiens organisms genbank large-scale genome expressed blast
Bases and spaces: resources on the web for accessing the draft human genome.

PMID 11178254 · PMC138875 · Genome biology · 2000 · 8 claims · 8 setups

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By combining currently available genomic databases and mapping resources (GenBank/Entrez, UniGene, RH maps, BAC fingerprint maps, Ensembl, NIX), it is possible to devise strategies that fully exploit the fragmentary draft human genome sequence.

bac whole-genome draft submitted bac radiation initio
Human SNPs resulting in premature stop codons and protein truncation.

PMID 16595072 · PMC3500177 · Human genomics · 2006 · 8 claims · 6 setups

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Genome-wide screening of dbSNP identified 28 validated X-SNPs from 28 genes with known minor allele frequencies.

genome transcripts validated x-snp-encoded database blast exon-intron
Sequence, "subtle" alternative splicing and expression of the CYYR1 (cysteine/tyrosine-rich 1) mRNA in human neuroendocrine tumors.

PMID 17442112 · PMC1863428 · BMC cancer · 2007 · 7 claims · 5 setups

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CYYR1 mRNA undergoes a 'subtle' alternative splicing event generating two isoforms (CAG- and CAG+) differing by a single alanine codon at the exon3/exon4 junction

neuroendocrine tumors normal cyyr1 rt-pcr quantitative psti
A new procedure for determining the genetic basis of a physiological process in a non-model species, illustrated by cold induced angiogenesis in the carp.

PMID 19852815 · PMC2771047 · BMC genomics · 2009 · 8 claims · 5 setups

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The Conditional Stepped Reciprocal Best Hit (CSRBH) approach, combining direct RBH and zebrafish-stepped RBH (SRBH), outperformed other ortholog assignment methods and attained 8,726 carp-human functional homolog relationships for 16,650 carp contigs

carp randomly zebrafish reciprocal sequence microarray
SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements.

PMID 18174224 · PMC2238826 · Nucleic acids research · 2008 · 6 claims · 5 setups

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Standard genome annotation pipelines misannotate selenoprotein genes because they rely on UGA as a universal stop codon, failing to recognize its dual role as the selenocysteine-recoding codon.

genomic cdna known sequence homology transcript
Having a BLAST with bioinformatics (and avoiding BLASTphemy).

PMID 11597340 · PMC138974 · Genome biology · 2001 · 8 claims · 4 setups

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BLAST is the most widely used tool for searching biological sequences for regions of local similarity

superfamilies blocks query pairwise phylogenetic sequence heuristic
RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration.

PMID 18954448 · PMC2605478 · BMC genomics · 2008 · 7 claims · 4 setups

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Constructed enhanced protein databases integrating annotated SAPs, PTMs, and disease associations for 17 organisms.

consensus sap query all-against-all blast cross-database
Non-EST based prediction of exon skipping and intron retention events using Pfam information.

PMID 16204458 · PMC1243800 · Nucleic acids research · 2005 · 7 claims · 5 setups

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A novel ab initio method predicts exon skipping and intron retention events using only Pfam domain annotation, via a Viterbi-like dynamic programming algorithm applied to the Pfam alignment.

refseq dbest genome pfam initio est comparative
In silico and in vitro comparative analysis to select, validate and test SNPs for human identification.

PMID 18076761 · PMC2222643 · BMC genomics · 2007 · 8 claims · 7 setups

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A panel of 24 SNPs was selected and validated for human identification using 1,040 unrelated samples from three populations (Italian, Benin Gulf, Mongolian)

genomic genome pan blood snp sequence cross-species
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
AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome.

PMID 16925833 · PMC1810548 · Genome biology · 2006 · 8 claims · 5 setups

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AUGUSTUS predicted significantly more genes correctly than any other ab initio program in EGASP

genome human-mouse genes initio comparative extrinsic
GREM, a technique for genome-wide isolation and quantitative analysis of promoter active repeats.

PMID 16698959 · PMC3303178 · Nucleic acids research · 2006 · 7 claims · 5 setups

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GREM enables genome-wide isolation and quantitative analysis of transcriptionally active (promoter-active) repetitive elements while excluding read-through transcript background

testicular genomic coli grem rt-pcr race
A novel de novo PAX6 mutation in an Ashkenazi-Jewish family with aniridia.

PMID 18334930 · PMC2255027 · Molecular vision · 2008 · 7 claims · 5 setups

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A novel heterozygous de novo PAX6 frameshift mutation (c.577_578insG, insG@Gly72) in exon 6 causes autosomal dominant aniridia with congenital cataract, nystagmus, and glaucoma in this family.

genomic pax6 direct microsatellite blast
Analysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen Pectobacterium aroidearum in Amorphophallus konjac Using Comparative Genomics.

PMID 35910650 · PMC9326479 · Frontiers in microbiology · 2022 · 8 claims · 8 setups

Has reproduction · 100

The causal agent of konjac soft rot in China is Pectobacterium aroidearum, confirmed via in vitro/in vivo pathogenicity tests, ANI, dDDH, and phylogenomic analysis.

amorphophallus 6-month-old bacterial aroidearum pathogenicity pectinolytic 16s
Haplotype analysis of common variants in the BRCA1 gene and risk of sporadic breast cancer.

PMID 15743496 · PMC1064127 · Breast cancer research : BCR · 2005 · 7 claims · 5 setups

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A common BRCA1 haplotype (haplotype 2, C A G G) is associated with a modest increase in sporadic breast cancer risk

individuals nested same nurses whole-gene snp statistical

Experiments

Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.

A novel optineurin genetic mutation associated with open-angle glaucoma in a Chinese family.

Database resources of the National Center for Biotechnology Information.

Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins.

GenBank.

Bases and spaces: resources on the web for accessing the draft human genome.

Human SNPs resulting in premature stop codons and protein truncation.

Sequence, "subtle" alternative splicing and expression of the CYYR1 (cysteine/tyrosine-rich 1) mRNA in human neuroendocrine tumors.

A new procedure for determining the genetic basis of a physiological process in a non-model species, illustrated by cold induced angiogenesis in the carp.

SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements.

Having a BLAST with bioinformatics (and avoiding BLASTphemy).

RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration.

Non-EST based prediction of exon skipping and intron retention events using Pfam information.

In silico and in vitro comparative analysis to select, validate and test SNPs for human identification.

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

AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome.

GREM, a technique for genome-wide isolation and quantitative analysis of promoter active repeats.

A novel de novo PAX6 mutation in an Ashkenazi-Jewish family with aniridia.

Analysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen Pectobacterium aroidearum in Amorphophallus konjac Using Comparative Genomics.

Haplotype analysis of common variants in the BRCA1 gene and risk of sporadic breast cancer.