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).

• System-based proteomic analysis of the interferon response in human liver cells.

  PMID 15287976 · PMC507879 · Genome biology · 2004 · 7 claims · 4 setups

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  ICAT-based quantitative proteomics identified 1,364 proteins in Huh7 cells at <5% false-positive rate, with 54 induced and 24 repressed >2-fold by IFN treatment

  huh7 computational icat gene interaction

• A quantitative proteomics analysis of subcellular proteome localization and changes induced by DNA damage.

  PMID 20026476 · PMC2849709 · Molecular & cellular proteomics : MCP · 2010 · 6 claims · 5 setups

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  A SILAC-based 'spatial proteomics' method can quantitatively measure the relative subcellular distribution of thousands of proteins across cytoplasm, nucleus, and nucleolus.

  hct116 silac silac-based immunofluorescence

• Extent of laminin-5 assembly and secretion effect junctional epidermolysis bullosa phenotype.

  PMID 9547338 · PMC2212220 · The Journal of experimental medicine · 1998 · 6 claims · 6 setups

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  The most severe (Herlitz) form of JEB correlates best with mutations causing premature termination codons (PTCs), not with mutation location in a particular protein domain

  keratinocytes keratinocyte genomic pcr biosynthetic northern pcr

• Identification of androgen-coregulated protein networks from the microsomes of human prostate cancer cells.

  PMID 14709176 · PMC395736 · Genome biology · 2003 · 8 claims · 5 setups

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  Distinct cellular processes are coregulated by androgen while others are essentially unaffected in LNCaP cells

  lncap computational icat western hypergeometric

• A mouse to human search for plasma proteome changes associated with pancreatic tumor development.

  PMID 18547137 · PMC2504036 · PLoS medicine · 2008 · 7 claims · 8 setups

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  GEM models combined with in-depth proteomic analysis provide a useful strategy to identify candidate cancer markers applicable to human disease with potential for early detection

  plasma immunodepleted pancreatic shotgun two-dimensional immunodepletion

• Integrated proteomic analysis of human cancer cells and plasma from tumor bearing mice for ovarian cancer biomarker discovery.

  PMID 19936259 · PMC2775948 · PloS one · 2009 · 8 claims · 8 setups

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  Integrated proteomic analysis of a cancer mouse model and human cancer cell populations provides an effective approach to identify potential circulating protein biomarkers.

  k-ras ovarian lists tumor quantitative pathway immunoblot

• Quantitative serum proteomics using dual stable isotope coding and nano LC-MS/MSMS.

  PMID 19817497 · PMC4684172 · Journal of proteome research · 2009 · 7 claims · 6 setups

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  DSIC labeling achieves high efficiency: 100% for Cysteine (acrylamide) and 98% for Lysine (succinic anhydride)

  standard dsic-labeled immunodepleted serum labeling quantitative in-solution

• Integrated algorithms for high-throughput examination of covalently labeled biomolecules by structural mass spectrometry.

  PMID 19788317 · PMC2764328 · Analytical chemistry · 2009 · 7 claims · 4 setups

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  ProtMapMS automates data format conversion, mass spectrum interpretation, peptide detection/verification, modification site confirmation, and quantification of peptide oxidation extent from covalent labeling MS data

  insulin oxidative enzymatic computational

• ConNIS and labeling instability: New statistical methods for improving the detection of essential genes in TraDIS libraries.

  PMID 41790830 · PMC12991369 · PLoS computational biology · 2026 · 8 claims · 3 setups

  Has reproduction · 83

  ConNIS provides an analytic solution for the probability of observing the longest insertion-free sequence within a gene given its length and number of insertion sites under non-essentiality.

  simulated four real simulation semi-synthetic real-world

• Proteomic analysis of ovarian cancer cells reveals dynamic processes of protein secretion and shedding of extra-cellular domains.

  PMID 18560578 · PMC2409963 · PloS one · 2008 · 8 claims · 6 setups

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  Ovarian cancer cells exhibit extensive shedding of extra-cellular domains from cell surface proteins into the extracellular milieu.

  ovcar3 analysis lc-ms cell-surface silac

• Empirical Bayes analysis of quantitative proteomics experiments.

  PMID 19829701 · PMC2759080 · PloS one · 2009 · 8 claims · 4 setups

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  Developed a new empirical Bayes framework that models log2 SILAC protein ratios and is robust to non-Gaussian tails and data sparsity, unlike Gaussian mixture models or Efron's original spline-based approach

  hela predicted computational silac utr gaussian

• iTRAQ-based proteomics profiling reveals increased metabolic activity and cellular cross-talk in angiogenic compared with invasive glioblastoma phenotype.

  PMID 19674965 · PMC2773724 · Molecular & cellular proteomics : MCP · 2009 · 6 claims · 5 setups

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  Serial transplantation of human GBM xenografts in nude rats converts an initially highly infiltrative, non-angiogenic phenotype into a highly angiogenic phenotype over 4-6 generations.

  membrane-enriched xenograft homogenate quantified itraq western bradford

• Comparisons of substitution, insertion and deletion probes for resequencing and mutational analysis using oligonucleotide microarrays.

  PMID 15722479 · PMC549431 · Nucleic acids research · 2005 · 7 claims · 4 setups

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  Two base deletion probes display the highest average hybridization specificity, followed by single base substitution, single base deletion, and single base insertion probes.

  atm hybridized probe oligonucleotide transcription microarray

• Systems biology and the host response to viral infection.

  PMID 18066032 · PMC7097743 · Nature biotechnology · 2007 · 8 claims · 8 setups

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  Systems biology integration of 'omics data (transcriptomics, proteomics, genomics) with computational modeling is needed to fully understand virus-host interactions and identify novel antiviral targets

  lung cd4 rhesus kshv microarray quantitative genomic

• 'Unknown' proteins and 'orphan' enzymes: the missing half of the engineering parts list--and how to find it.

  PMID 20001958 · PMC3022307 · The Biochemical journal · 2009 · 8 claims · 8 setups

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  Comparative genomics is the single most effective strategy for predicting functions of unknown proteins and finding genes for orphan enzymes

  lactococcus lactis arabidopsis coli gene recombinant enzyme

• Neonatal salivary analysis reveals global developmental gene expression changes in the premature infant.

  PMID 19959617 · PMC2853178 · Clinical chemistry · 2010 · 7 claims · 6 setups

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  Salivary genomic microarray analysis reveals global developmental gene expression changes in premature infants over postnatal age

  saliva amplified extracted differentially genome quality extraction

• Stable isotope labeling tandem mass spectrometry (SILT): integration with peptide identification and extension to data-dependent scans.

  PMID 18774841 · PMC2707264 · Journal of proteome research · 2008 · 8 claims · 5 setups

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  Using MS/MS ion intensities with stable isotope labeling (SILT) decreases the effects of contamination from unrelated co-eluting compounds compared to precursor ion intensity methods.

  astrocytes hepg2 app695δnl labeled nano-lc sds-page immunoprecipitation

• Getting started in computational immunology.

  PMID 18769677 · PMC2518523 · PLoS computational biology · 2008 · 8 claims · 7 setups

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  Affinity maturation is driven by cycles of somatic hypermutation and affinity-dependent selection acting on B cell Ig receptors.

  splenic lymphocytes lymph secondary flow microdissection intravital

• Diagnostic proteomics: serum proteomic patterns for the detection of early stage cancers.

  PMID 15258335 · PMC3851082 · Disease markers · 2003 · 8 claims · 8 setups

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  Proteomic pattern analysis of serum mass spectra, without identifying the underlying proteins, can distinguish cancer patients from healthy controls with high sensitivity and specificity.

  serum frozen ig-depleted clinical seldi-tof maldi lc-ms

• Widespread mono- and oligoadenylation direct small noncoding RNA maturation versus degradation fates.

  PMID 41350938 · PMC12811392 · The EMBO journal · 2026 · 7 claims · 3 setups

  Has reproduction · 78

  Newly transcribed human sncRNAs undergo widespread post-transcriptional adenylation in two distinct forms: transient oligoadenylation and stable monoadenylation.

  hek global nascent differential