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 22

System / cell line: genome ✕ Assay: mismatch ✕ Clear

EPD in its twentieth year: towards complete promoter coverage of selected model organisms.

PMID 16381980 · PMC1347508 · Nucleic acids research · 2006 · 7 claims · 4 setups

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EPD is an annotated, non-redundant collection of experimentally defined eukaryotic POL II promoters accessed via genome position pointers.

rice preliminary primer sequence quality
Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment.

PMID 16925837 · PMC1810552 · Genome biology · 2006 · 6 claims · 3 setups

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Promoter predictors that combine promoter prediction with gene prediction (N-SCAN, Fprom) achieve better performance than pure ab initio promoter predictors, mainly by reducing the promoter search space and false positives

genome encode computational tss manual
Evolutionarily conserved human targets of adenosine to inosine RNA editing.

PMID 15731336 · PMC549564 · Nucleic acids research · 2005 · 8 claims · 6 setups

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Identified four novel human ADAR editing substrates causing amino acid changes: FLNA, BLCAP, CYFIP2 and IGFBP7

panel brain chicken flna comparative rt-pcr homology
Periodicity of SNP distribution around transcription start sites.

PMID 16579865 · PMC1448210 · BMC genomics · 2006 · 8 claims · 6 setups

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SNP density around TSS shows a 146-nucleotide periodicity

genome human-chimpanzee tss promoter snp sequence cpg
Biologic diversity of polyomavirus BK genomic sequences: Implications for molecular diagnostic laboratories.

PMID 18712842 · PMC2906129 · Journal of medical virology · 2008 · 8 claims · 5 setups

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Coverage of naturally occurring BKV strains varies substantially among current PCR diagnostic assays due to primer/probe mismatches

bkv virus sequence primer cross-reactivity
The sequence and de novo assembly of the giant panda genome.

PMID 20010809 · PMC3951497 · Nature · 2010 · 8 claims · 8 setups

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A draft giant panda genome was successfully generated and assembled de novo using only Illumina Genome Analyser short-read sequencing

giant panda whole-genome novo read
Ensembl 2006.

PMID 16381931 · PMC1347495 · Nucleic acids research · 2006 · 8 claims · 5 setups

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Ensembl now provides annotation for 19 genomes, up from 4 the previous year, including new mammalian (Rhesus macaque, Opossum), chordate (Ciona intestinalis), and yeast genomes.

cow ensembl snps genome gene whole-genome pairwise
Massively parallel genomic perturbations with multi-target CRISPR interrogates Cas9 activity and DNA repair at endogenous sites.

PMID 36064968 · PMC9481459 · Nature cell biology · 2022 · 8 claims · 6 setups

Has reproduction · 98

Multi-target gRNAs (mgRNAs) can direct Cas9 to over a hundred well-mapped endogenous genomic sites simultaneously, enabling massively parallel, high-throughput interrogation of Cas9 activity via short-read sequencing

hg38 hela hek293t induced genome-wide high-throughput chip-seq
Comparative genomics and understanding of microbial biology.

PMID 10998382 · PMC2627966 · Emerging infectious diseases · 2000 · 8 claims · 7 setups

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GC content varies widely among prokaryotic genomes (29% in B. burgdorferi to 68% in M. tuberculosis) and shapes codon usage and amino acid composition.

completed same sequenced mycobacterium whole-genome comparative phylogenomic
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
RiboSubstrates: a web application addressing the cleavage specificities of ribozymes in designated genomes.

PMID 17076887 · PMC1634876 · BMC bioinformatics · 2006 · 7 claims · 4 setups

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RiboSubstrates is a web-based Perl application that scans a cDNA database for all potential substrates of a given ribozyme, including perfect matches, Wobble base-pair matches, and mismatch-containing matches.

homo hcv substrate ribozyme
A missense mutation in the nuclear localization signal sequence of CERKL (p.R106S) causes autosomal recessive retinal degeneration.

PMID 18978954 · PMC2576480 · Molecular vision · 2008 · 8 claims · 6 setups

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A C>A transversion in exon 2 of CERKL (c.316C>A) causes a missense change p.R106S in the nuclear localization signal sequence (KLKRR) of the protein.

patients genomic family cerkl ophthalmic homozygosity multipoint
Predicting failure rate of PCR in large genomes.

PMID 18492719 · PMC2441781 · Nucleic acids research · 2008 · 7 claims · 8 setups

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The number of predicted primer-binding sites in genomic DNA is the most important factor determining PCR failure.

genomic genome pcr combined large-scale exact-match mismatch-tolerant
Kangaroo--a pattern-matching program for biological sequences.

PMID 12150718 · PMC119856 · BMC bioinformatics · 2002 · 7 claims · 2 setups

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Kangaroo is a web-based regular expression pattern-matching program that searches DNA, protein, or coding-region sequences across ten organisms with no restriction on query length or complexity.

coding regular-expression mutation
COMUS: Clinician-Oriented locus-specific MUtation detection and deposition System.

PMID 19958500 · PMC2788389 · BMC genomics · 2009 · 8 claims · 6 setups

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COMUS is a bioinformatics system for detecting and depositing new mutations from patient DNA with a clinician-friendly interface

ab1 fasta mutation hemophilia base-calling sequence known-variant
Human and mouse oligonucleotide-based array CGH.

PMID 16361265 · PMC1316119 · Nucleic acids research · 2005 · 8 claims · 8 setups

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Oligo array CGH detects single copy gains, multi-copy amplifications, and homozygous/heterozygous deletions as small as 100 kb

bt474 normal gm01750 mda-mb-468 array fish
Free energy of DNA duplex formation on short oligonucleotide microarrays.

PMID 17169993 · PMC1807971 · Nucleic acids research · 2007 · 8 claims · 6 setups

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The PDNN model, originally built for DNA/RNA hybridization, can be applied to model DNA/DNA duplex formation on SNP and genome tiling arrays

mapping50k_xba240 dgcr hg-u133a pdnn free correlation
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
ORFer--retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files.

PMID 12493080 · PMC139979 · BMC bioinformatics · 2002 · 6 claims · 6 setups

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ORFer retrieves protein and nucleic acid sequences and annotations from NCBI GenBank using the XML sequence format

sequences parsed bacillus anopheles large-scale sequence orf
Thermodynamic stability and Watson-Crick base pairing in the seed duplex are major determinants of the efficiency of the siRNA-based off-target effect.

PMID 18988625 · PMC2602766 · Nucleic acids research · 2008 · 8 claims · 6 setups

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Thermodynamic stability (Tm and standard free-energy change, ΔG) of the seed duplex is a major determinant of siRNA off-target effect efficiency

hela protein-free dual-luciferase reporter thermodynamic

Experiments

EPD in its twentieth year: towards complete promoter coverage of selected model organisms.

Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment.

Evolutionarily conserved human targets of adenosine to inosine RNA editing.

Periodicity of SNP distribution around transcription start sites.

Biologic diversity of polyomavirus BK genomic sequences: Implications for molecular diagnostic laboratories.

The sequence and de novo assembly of the giant panda genome.

Ensembl 2006.

Massively parallel genomic perturbations with multi-target CRISPR interrogates Cas9 activity and DNA repair at endogenous sites.

Comparative genomics and understanding of microbial biology.

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

RiboSubstrates: a web application addressing the cleavage specificities of ribozymes in designated genomes.

A missense mutation in the nuclear localization signal sequence of CERKL (p.R106S) causes autosomal recessive retinal degeneration.

Predicting failure rate of PCR in large genomes.

Kangaroo--a pattern-matching program for biological sequences.

COMUS: Clinician-Oriented locus-specific MUtation detection and deposition System.

Human and mouse oligonucleotide-based array CGH.

Free energy of DNA duplex formation on short oligonucleotide microarrays.

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

ORFer--retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files.

Thermodynamic stability and Watson-Crick base pairing in the seed duplex are major determinants of the efficiency of the siRNA-based off-target effect.