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).

• 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

• The impact of microRNAs on protein output.

  PMID 18668037 · PMC2745094 · Nature · 2008 · 8 claims · 8 setups

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  MicroRNA targeting for protein repression occurs primarily through seed-matched sites (6mer, 7mer-A1, 7mer-m8, 8mer) located in favourable predicted contexts within 3′ UTRs

  hela neutrophils bone mir-223 quantitative blot microarray

• miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes.

  PMID 18029362 · PMC2238982 · Nucleic acids research · 2008 · 8 claims · 6 setups

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  miRNAMap 2.0 is a resource collecting experimentally verified miRNAs and experimentally verified miRNA target genes in human, mouse, rat and other metazoan genomes

  major tissues conserved predicted quantitative bead-based microarray

• A new era for proteomics research?

  PMID 19014405 · PMC2614486 · Genome biology · 2008 · 8 claims · 8 setups

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  Refined mass spectrometry instrumentation and software now make whole-proteome coverage of model organisms in a single experiment conceivable

  proteins lines kinases breast mass silac kinase-specific

• Differential recruitment of pre-mRNA splicing factors to alternatively spliced transcripts in vivo.

  PMID 16231974 · PMC1262628 · PLoS biology · 2005 · 8 claims · 8 setups

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  Distinct combinations of pre-mRNA splicing factors are recruited to sites of alternatively spliced transcripts in intact cells, providing the first in vivo evidence for differential splicing factor association.

  cos-1 cos-7 tau10-1 rt-pcr quantitative rna-fish

• Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells.

  PMID 18084025 · PMC2241897 · Nucleic acids research · 2008 · 5 claims · 7 setups

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  QUMA (quantitative real-time PCR) and AUMA (fingerprinting PCR) methods can quantify and individually identify unmethylated Alu elements on a genomic scale using the methylation-sensitive SmaI site as a surrogate marker

  paired colorectal genome normal quma auma bioinformatic

• Phosphoproteomics by mass spectrometry: insights, implications, applications and limitations.

  PMID 19929607 · PMC2931417 · Expert review of proteomics · 2009 · 8 claims · 8 setups

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  Serine/threonine phosphorylation widely functions to modulate protein-protein interactions (PPIs) across signaling systems

  hela jurkat exposed yeast quantitative antibody-based analog-sensitive

• 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

• Expression and mutation analysis of the discoidin domain receptors 1 and 2 in non-small cell lung carcinoma.

  PMID 17299390 · PMC2360060 · British journal of cancer · 2007 · 8 claims · 6 setups

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  DDR1 is significantly upregulated in NSCLC tumour tissue compared with matched normal lung tissue

  nsclc matched lung quantitative pcr genomic

• Proteomics-based identification of novel factor inhibiting hypoxia-inducible factor (FIH) substrates indicates widespread asparaginyl hydroxylation of ankyrin repeat domain-containing proteins.

  PMID 18936059 · PMC2649815 · Molecular & cellular proteomics : MCP · 2009 · 8 claims · 5 setups

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  DMOG pretreatment acts as a pharmacological 'substrate trap' that stabilizes transient FIH-substrate interactions, enabling their identification by SILAC-based proteomics

  hek293 u2os 293t 293t-expressed co-immunoprecipitation silac-based co-immunoprecipitation-immunoblotting

• From genomes to systems.

  PMID 15535877 · PMC545775 · Genome biology · 2004 · 8 claims · 8 setups

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  Biological networks (protein-gene interactions in the genome, protein-protein interactions in the proteome, biochemical reactions in the metabolome) are scale-free rather than random

  serum trypanosoma alzheimer's complexes gel maldi-ms ft-icr

• Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication.

  PMID 16899447 · PMC1557810 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  The RE1 PSSM identifies functional RE1 binding sites with greater sensitivity and selectivity than the previously used RE1 consensus sequence

  fibroblast hela hek293 set genome-wide electrophoretic rt-pcr

• N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast.

  PMID 36422864 · PMC9731578 · eLife · 2022 · 8 claims · 8 setups

  Has reproduction · 55

  Pho92 specifically binds m6A-modified RNA via its YTH domain, both in vitro and in vivo

  cerevisiae diploid yeast recombinant affinity rt-qpcr chip-seq

• 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

• A search for structurally similar cellular internal ribosome entry sites.

  PMID 17591613 · PMC1950536 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  Cellular IRES are not defined by an overall conserved structure (unlike viral IRES) but instead depend on short RNA motifs and shared trans-acting factors (ITAFs)

  transcribed hek 293t enzymatic chemical structural

• Bayesian prediction of RNA translation from ribosome profiling.

  PMID 28126919 · PMC5389577 · Nucleic acids research · 2017 · 8 claims · 4 setups

  Has reproduction · 62

  Rp-Bp is an unsupervised Bayesian approach that uses a two-component 'high-low-low' mixture model to predict translated ORFs from ribosome profiles

  hek293 ribo-seq ribosome proteomics quantitative

• Phosphoproteomics: new insights into cellular signaling.

  PMID 16168091 · PMC1242200 · Genome biology · 2005 · 8 claims · 8 setups

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  Protein kinases are one of the largest gene families in humans and mice, accounting for 1.7% of the human genome

  yeast hela beta2-adrenergic erk phosphopeptide targeted silac

• Genomic profiling of microRNA and messenger RNA reveals deregulated microRNA expression in prostate cancer.

  PMID 18676839 · PMC2597340 · Cancer research · 2008 · 8 claims · 7 setups

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  MicroRNA processing components (Dicer, DGCR8) and microRNA host genes (MCM7, C9orf5) are significantly up-regulated in prostate tumors versus non-tumor tissue

  prostate subset lncap 22rv1 microrna quantitative western

• Evaluation of the bacterial diversity among and within individual venous leg ulcers using bacterial tag-encoded FLX and titanium amplicon pyrosequencing and metagenomic approaches.

  PMID 19860898 · PMC2773781 · BMC microbiology · 2009 · 7 claims · 5 setups

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  VLU infections are polymicrobial with no single bacterium colonizing the wounds

  individual pooled second btefap quantitative bulk

• Progressive transformation of the HIV-1 reservoir cell profile over two decades of antiviral therapy.

  PMID 36596305 · PMC9839361 · Cell host & microbe · 2023 · 8 claims · 7 setups

  Has reproduction · 80

  After long-term ART, intact HIV-1 proviruses are predominantly integrated in heterochromatin locations, most prominently centromeric satellite/micro-satellite DNA.

  pbmc single cd4 flip-seq mip-seq prip-seq