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 159

System / cell line: predicted ✕ Assay: site ✕ Clear

Phosphorylation states of cell cycle and DNA repair proteins can be altered by the nsSNPs.

PMID 16111488 · PMC1208866 · BMC cancer · 2005 · 8 claims · 4 setups

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15 of 89 nsSNPs (16.9%) studied were predicted to abolish or create phosphorylation sites in 14 of 32 proteins (44.0%)

orthologues repair case-control phosphorylation cross-species database
Prediction and assessment of splicing alterations: implications for clinical testing.

PMID 18951448 · PMC2832470 · Human mutation · 2008 · 8 claims · 5 setups

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Bioinformatic prediction alone is insufficient; in vitro analysis is needed to confirm or establish splicing aberrations for clinical variant classification

brca1 lymphocytes mammalian large bioinformatic cycloheximide mini-gene
TC-hunter: identification of the insertion site of a transgenic gene within the host genome.

PMID 35184734 · PMC8859905 · BMC genomics · 2022 · 7 claims · 4 setups

Has reproduction · 69

TC-hunter is an open-source Nextflow pipeline that identifies transgene insertion sites using chimeric reads and discordant read pairs from NGS data.

ppm1d-transgenic genome genome read touchdown-pcr
oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets.

PMID 22973536 · PMC3429929 · G3 (Bethesda, Md.) · 2012 · 8 claims · 6 setups

Has reproduction · 49

oPOSSUM-3 is a web-accessible system that identifies over-represented TFBS and TFBS families in DNA sequences of co-expressed genes or in sequences from high-throughput methods such as ChIP-Seq.

hg19 large-scale gene-based jaspar tfbs sequence-based anchored
MODBASE: a database of annotated comparative protein structure models and associated resources.

PMID 16381869 · PMC1347422 · Nucleic acids research · 2006 · 8 claims · 7 setups

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MODBASE is a database of automatically calculated comparative protein structure models covering all UniProt sequences matchable to a known structure

uniprot non-redundant complexes saccharomyces comparative pairwise domain-domain
Rubinstein-Taybi Syndrome: spectrum of CREBBP mutations in Italian patients.

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

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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
Identification and characterisation of the angiotensin converting enzyme-3 (ACE3) gene: a novel mammalian homologue of ACE.

PMID 17597519 · PMC1925091 · BMC genomics · 2007 · 7 claims · 7 setups

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A novel single-domain ACE-like gene, ACE3, exists in mouse, rat, cow, dog and human genomes, located on the same chromosome downstream of ACE.

dog predicted ace3 panel blast sequence homology
targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis.

PMID 19099550 · PMC2651862 · BMC systems biology · 2008 · 8 claims · 8 setups

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A comprehensive in silico target identification pipeline (targetTB) integrating interactome, reactome, essentiality, sequence and structural analyses can identify high-confidence drug targets for Mtb

tuberculosis mtb protein-protein flux transposon
SNP@Promoter: a database of human SNPs (single nucleotide polymorphisms) within the putative promoter regions.

PMID 18315851 · PMC2259403 · BMC bioinformatics · 2008 · 8 claims · 4 setups

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SNP@Promoter is a database of human SNPs within putative promoter regions and predicted transcription factor binding sites

genome predicted target computational snp evolutionary
CTCFBSDB: a CTCF-binding site database for characterization of vertebrate genomic insulators.

PMID 17981843 · PMC2238977 · Nucleic acids research · 2008 · 7 claims · 8 setups

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CTCF is the only identified trans-acting factor in vertebrates that confers enhancer-blocking insulator activity

ohlsson ren zhao tissues chip-chip massive motif
The distribution of SNPs in human gene regulatory regions.

PMID 16209714 · PMC1260019 · BMC genomics · 2005 · 8 claims · 6 setups

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SNPs occur with higher density closer to the transcriptional start site within gene promoter regions than in further upstream regions

gene mammalian promoter experimentally genome-wide computational binding
NetworKIN: a resource for exploring cellular phosphorylation networks.

PMID 17981841 · PMC2238868 · Nucleic acids research · 2008 · 8 claims · 4 setups

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NetworKIN integrates consensus substrate motifs with probabilistic network context modelling to predict cellular kinase-substrate relations.

phosphoproteome kinome interactome 53bp1 consensus blastp probabilistic
MODBASE, a database of annotated comparative protein structure models and associated resources.

PMID 18948282 · PMC2686492 · Nucleic acids research · 2009 · 8 claims · 8 setups

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MODBASE contains 5,152,695 reliable comparative protein structure models for 1,593,209 unique protein sequences.

sequences chains template chain comparative pairwise ligand
Computational identification of transcriptional regulatory elements in DNA sequence.

PMID 16855295 · PMC1524905 · Nucleic acids research · 2006 · 8 claims · 3 setups

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Weight matrix (PWM/PSSM) models of TF binding sites are grounded in biophysical theory of protein-DNA interactions, with position weights corresponding to log-odds contributions to binding free energy

saccharomyces generic pwm-based pwm
Transcriptome-wide analyses of piRNA binding sites suggest distinct mechanisms regulate piRNA binding and silencing in C. elegans.

PMID 36737102 · PMC10158993 · RNA (New York, N.Y.) · 2023 · 8 claims · 7 setups

Has reproduction · 88

C. elegans piRNAs preferentially bind the coding regions (CDS) of target mRNAs in vivo, rather than 3' UTRs.

elegans clash bioinformatic iclip
Mutation analysis of the MSMB gene in familial prostate cancer.

PMID 19997100 · PMC2816656 · British journal of cancer · 2010 · 8 claims · 5 setups

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No deleterious mutations were found in the MSMB coding region in 192 familial prostate cancer cases

germline blood 161-nt genotype sanger taqman transcription
Genome-wide survey of allele-specific splicing in humans.

PMID 18518984 · PMC2427040 · BMC genomics · 2008 · 8 claims · 5 setups

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A genome-wide computational scan identified 30,977 SNPs located within predicted splicing regulatory sequences (donor sites, acceptor sites, branch points, and ESEs)

genome cdna hapmap computational est exon
Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

PMID 17452356 · PMC1904267 · Nucleic acids research · 2007 · 8 claims · 7 setups

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PASE (Prediction of Alternative Signaling Exons) is a computational algorithm combining Markov splice-site models, a Bayesian classifier, species conservation, and Scansite motif scoring to identify novel alternative cassette exons involved in cell signaling.

elegans pooled pcr known semi-nested cloning initio
Dissecting microregulation of a master regulatory network.

PMID 18294391 · PMC2289817 · BMC genomics · 2008 · 8 claims · 6 setups

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143 human miRNAs (termed p53-miRs) each contain at least one putative p53 binding site within 10 kb flanking sequence and are predicted to target at least one known gene

genome mirnas mirna-target predicted p53 mirna cross-referencing
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

Experiments

Phosphorylation states of cell cycle and DNA repair proteins can be altered by the nsSNPs.

Prediction and assessment of splicing alterations: implications for clinical testing.

TC-hunter: identification of the insertion site of a transgenic gene within the host genome.

oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets.

MODBASE: a database of annotated comparative protein structure models and associated resources.

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

Identification and characterisation of the angiotensin converting enzyme-3 (ACE3) gene: a novel mammalian homologue of ACE.

targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis.

SNP@Promoter: a database of human SNPs (single nucleotide polymorphisms) within the putative promoter regions.

CTCFBSDB: a CTCF-binding site database for characterization of vertebrate genomic insulators.

The distribution of SNPs in human gene regulatory regions.

NetworKIN: a resource for exploring cellular phosphorylation networks.

MODBASE, a database of annotated comparative protein structure models and associated resources.

Computational identification of transcriptional regulatory elements in DNA sequence.

Transcriptome-wide analyses of piRNA binding sites suggest distinct mechanisms regulate piRNA binding and silencing in C. elegans.

Mutation analysis of the MSMB gene in familial prostate cancer.

Genome-wide survey of allele-specific splicing in humans.

Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

Dissecting microregulation of a master regulatory network.

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