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 108

System / cell line: sites ✕ Assay: comparison ✕ Clear

Importance sampling for the infinite sites model.

PMID 18976228 · PMC2832804 · Statistical applications in genetics and molecular biology · 2008 · 7 claims · 2 setups

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A new importance sampling proposal distribution for the ISM, derived from a new result on exact sampling from a single segregating site, generally shows greater efficiency than the GT and SD proposals.

simulated empirical computational reanalysis
Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome.

PMID 15534692 · PMC526178 · PLoS biology · 2004 · 8 claims · 6 setups

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Intramolecular pairs of oppositely oriented Alu elements within the same pre-mRNA form dsRNA foldback structures that are major substrates for A-to-I RNA editing

huge brain pre-mrna greater genomic rt-pcr quantitative
Computational analysis of splicing errors and mutations in human transcripts.

PMID 18194514 · PMC2234086 · BMC genomics · 2008 · 8 claims · 4 setups

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Retained introns are significantly shorter than constitutively spliced introns

refseq genes intron exon computational splice prediction
Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

PMID 17576681 · PMC1934990 · Nucleic acids research · 2007 · 8 claims · 4 setups

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Cryptic 5'ss are best predicted by computational algorithms that accommodate nucleotide dependencies (e.g., Markov model, maximum entropy, maximum dependence decomposition) rather than by weight-matrix models

disease mammalian compiled literature minigene computational
Relationship between the extent of chromosomal losses and the pattern of CpG methylation in gastric carcinomas.

PMID 16224153 · PMC2779276 · Journal of Korean medical science · 2005 · 7 claims · 4 setups

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High-level-loss (LOH-H) tumors show a tendency toward unmethylation in Maspin, CAGE, MAGE-A2, and RABGEF1 genes

microdissected same bisulfite-modified pcr microsatellite methylation-specific bisulfite
SeqDoC: rapid SNP and mutation detection by direct comparison of DNA sequence chromatograms.

PMID 15927052 · PMC1156871 · BMC bioinformatics · 2005 · 8 claims · 6 setups

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SeqDoC generates a subtracted difference trace between a reference and test chromatogram that highlights single base changes

melanocortin same paired test chromatogram tracediff weak
In silico promoters: modelling of cis-regulatory context facilitates target predictio.

PMID 18505473 · PMC3823354 · Journal of cellular and molecular medicine · 2009 · 8 claims · 8 setups

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An integrated 'profiling of transcriptional targets' (PTT) strategy by Freebern et al. identified IGF-1 as a co-modulator of immune cell function genes in mitogen/drug-activated T cells.

serca2 rantes genes podocyte-associated literature-based promoter cross-referenced
CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features.

PMID 19922652 · PMC3091324 · Genome biology · 2009 · 8 claims · 8 setups

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CTCF binding sites can be classified into three occupancy-based classes (LowOc, MedOc, HighOc) based on similarity to the CTCF PWM motif

cd4+ hela imr90 embryonic chip-seq computational gene
Identification of RNA-Binding Protein Targets with HyperTRIBE in Saccharomyces cerevisiae.

PMID 37240377 · PMC10218906 · International journal of molecular sciences · 2023 · 7 claims · 8 setups

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HyperTRIBE was successfully established in S. cerevisiae by fusing an RBP to the hyper-active catalytic domain of human ADAR2 (E488Q), marking target transcripts with A-to-G editing events detectable by high-throughput sequencing

cerevisiae khd1 wild-type bfr1-heterozygous hypertribe western meme
Genetic variation of SARS coronavirus in Beijing Hospital.

PMID 15200810 · PMC3323231 · Emerging infectious diseases · 2004 · 8 claims · 4 setups

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113 sequence variations at 9 recurrent variant sites were identified in 29 full-length S-gene sequences compared to the BJ01 reference strain

clinical extracted rna-derived cloned nested screening direct
A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome.

PMID 16670430 · PMC1456330 · Nucleic acids research · 2006 · 8 claims · 7 setups

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Highly-degenerate RE1 sites are significantly enriched in promoters of validated and putative REST target genes compared to control promoters

orthologous randomized high-score promoters pssm-based comparative motif
ABS: a database of Annotated regulatory Binding Sites from orthologous promoters.

PMID 16381947 · PMC1347478 · Nucleic acids research · 2006 · 7 claims · 6 setups

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ABS is a public database of experimentally identified TF binding sites conserved in orthologous vertebrate gene promoters, manually curated from the literature.

orthologous literature sequence pairwise
Predicting preferential DNA vector insertion sites: implications for functional genomics and gene therapy.

PMID 18047689 · PMC2106846 · Genome biology · 2007 · 8 claims · 6 setups

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Vector insertion site preferences differ substantially between viral vectors and transposons, affecting both oncogenic risk in gene therapy and utility for functional genomics

hela liver gene peripheral retroviral transposon hydrodynamic
Comparative genomic study reveals a transition from TA richness in invertebrates to GC richness in vertebrates at CpG flanking sites: an indication for context-dependent mutagenicity of methylated CpG sites.

PMID 19329065 · PMC5054122 · Genomics, proteomics & bioinformatics · 2008 · 8 claims · 8 setups

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Nucleotide preference at CpG flanking sites transitions from 5' T (invertebrates) to 5' A (vertebrates) at the invertebrate-vertebrate boundary

genomes same pufferfish elegans nucleotide genome-wide kruskal-wallis
Worldwide distribution of NAT2 diversity: implications for NAT2 evolutionary history.

PMID 18304320 · PMC2292740 · BMC genetics · 2008 · 8 claims · 8 setups

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NAT2 coding region sequence variation in the Mandenka and other sub-Saharan African populations is consistent with selective neutrality and constant population size.

mandenka worldwide hapmap nat2 full snp analysis
Acetylation goes global: the emergence of acetylation biology.

PMID 19920250 · PMC2812806 · Science signaling · 2009 · 8 claims · 4 setups

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Whole-proteome acetylome mapping (via SILAC-coupled high-resolution MS) shows the acetylome approaches the size and complexity of the phosphoproteome, indicating acetylation is a widespread regulatory modification rather than a niche one.

proteome proteome-wide liver anti-acetyllysine silac-based silac-coupled
Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.

PMID 19906316 · PMC2784480 · BMC genomics · 2009 · 8 claims · 7 setups

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Intronic single-block ESTs with poly(A/T) tails reveal previously unidentified novel transcript variants missed by existing databases.

genome poly est cdna est blast cdna
Quantitative phosphoproteomics by mass spectrometry: past, present, and future.

PMID 18846511 · PMC2701620 · Proteomics · 2008 · 8 claims · 6 setups

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Selective enrichment of phosphopeptides (antiphosphotyrosine IP, IMAC, TiO2/MOAC, SCX, chemical tagging) is required to detect substoichiometric, transient phosphorylation events by MS

adipocytes jurkat mammary specified antiphosphotyrosine phosphospecific comparative
Application of alternative de novo motif recognition models for analysis of structural heterogeneity of transcription factor binding sites: a case study of FOXA2 binding sites.

PMID 34547062 · PMC8408018 · Vavilovskii zhurnal genetiki i selektsii · 2021 · 6 claims · 7 setups

Has reproduction · 62

Combining four de novo models (PWM, diPWM, BaMM, InMoDe) significantly increases the fraction of recognized peaks versus PWM alone (by 26.3%).

hg38 foxa2 pwm whole-genome chip-seq pwm dipwm
The EH1 motif in metazoan transcription factors.

PMID 16309560 · PMC1310626 · BMC genomics · 2005 · 8 claims · 5 setups

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There is a statistically significant association between EH1hox motif HMM score and transcription factor function across human, Drosophila and C. elegans proteomes.

homeobox-containing forkhead-containing complete combined meme hmm logistic

Experiments

Importance sampling for the infinite sites model.

Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome.

Computational analysis of splicing errors and mutations in human transcripts.

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Relationship between the extent of chromosomal losses and the pattern of CpG methylation in gastric carcinomas.

SeqDoC: rapid SNP and mutation detection by direct comparison of DNA sequence chromatograms.

In silico promoters: modelling of cis-regulatory context facilitates target predictio.

CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features.

Identification of RNA-Binding Protein Targets with HyperTRIBE in Saccharomyces cerevisiae.

Genetic variation of SARS coronavirus in Beijing Hospital.

A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome.

ABS: a database of Annotated regulatory Binding Sites from orthologous promoters.

Predicting preferential DNA vector insertion sites: implications for functional genomics and gene therapy.

Comparative genomic study reveals a transition from TA richness in invertebrates to GC richness in vertebrates at CpG flanking sites: an indication for context-dependent mutagenicity of methylated CpG sites.

Worldwide distribution of NAT2 diversity: implications for NAT2 evolutionary history.

Acetylation goes global: the emergence of acetylation biology.

Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.

Quantitative phosphoproteomics by mass spectrometry: past, present, and future.

Application of alternative de novo motif recognition models for analysis of structural heterogeneity of transcription factor binding sites: a case study of FOXA2 binding sites.

The EH1 motif in metazoan transcription factors.