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).

• Increased constraints on MC4R during primate and human evolution.

  PMID 19011902 · PMC9947067 · Human genetics · 2009 · 6 claims · 7 setups

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  There is a significant paucity of genetic diversity at MC4R in humans but not in chimpanzees.

  hgdp-ceph germans central additional dhplc direct coding

• 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

• Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics.

  PMID 17203985 · PMC2664920 · Journal of proteome research · 2007 · 8 claims · 4 setups

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  An information-theoretic log-likelihood scoring method can predict experimentally observed missed cleavage sites from amino acid sequence alone with up to 90% accuracy.

  pepseeker local known swissprot tandem peptide pmf

• 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

• Recurrent RNA edits in human preimplantation potentially enhance maternal mRNA clearance.

  PMID 36543858 · PMC9772385 · Communications biology · 2022 · 8 claims · 7 setups

  Has reproduction · 100

  Compiled the largest human embryonic A-to-I editome to date from 2071 RNA-seq transcriptomes and identified thousands of per-stage Recurrent Embryonic Edits (REEs, present in ≥50% of samples per stage)

  preimplantation single uniparental embryos rna-seq paired gene

• Identification and functional implications of pseudouridine RNA modification on small noncoding RNAs in the mammalian pathogen Trypanosoma brucei.

  PMID 35714765 · PMC9283944 · The Journal of biological chemistry · 2022 · 8 claims · 4 setups

  Has reproduction · 80

  Genome-wide Ψ mapping using HydraPsiSeq and small RNA Ψ-seq identifies Ψ sites on snoRNA, 7SL RNA, vtRNA, SL RNA, and tRNA in T. brucei

  brucei hydrapsiseq small primer

• Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini.

  PMID 18722006 · PMC2566540 · Cell · 2008 · 7 claims · 8 setups

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  A subtiligase-based N-terminal biotinylation and enrichment method enables global identification and sequencing of protease cleavage sites in complex mixtures

  jurkat computational immunoblotting structural protein-protein

• Target identification for repurposed drugs active against SARS-CoV-2 via high-throughput inverse docking.

  PMID 34825285 · PMC8616721 · Journal of computer-aided molecular design · 2022 · 8 claims · 6 setups

  Has reproduction · 63

  Combining Vinardo, Ledock, and Korp-PL scoring functions (via averaged Z-scores) improves correct target identification over any single scoring function.

  curated repurposed glycosylated interior inverse molecular exploratory

• Comparative genomics of cyclin-dependent kinases suggest co-evolution of the RNAP II C-terminal domain and CTD-directed CDKs.

  PMID 15380029 · PMC521075 · BMC genomics · 2004 · 8 claims · 6 setups

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  Cell-cycle related CDKs (orthologs of CDK1-6) are present in all sampled eukaryotic organisms, including the most ancestral protists.

  animals cdk encephalitozoon pfmrk comparative bayesian distance

• Computer identification of snoRNA genes using a Mammalian Orthologous Intron Database.

  PMID 16093549 · PMC1184218 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  Created the Mammalian Orthologous Intron Database (MOID) containing orthologous introns of human, mouse and rat identified via conserved reading-frame position

  introns ribosomal rrna comparative orthologous pairwise

• Identification of herpesvirus transcripts from genomic regions around the replication origins.

  PMID 37773348 · PMC10541914 · Scientific reports · 2023 · 8 claims · 8 setups

  Has reproduction · 59

  Herpesviruses display distinct patterns of transcriptional overlaps near or at the replication origins (Oris)

  nine same vzv prv direct cage-seq qrt-pcr

• Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family example.

  PMID 15752422 · PMC555591 · BMC evolutionary biology · 2005 · 8 claims · 8 setups

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  A previously unidentified fourth human SULT1A gene (SULT1A4) exists on chromosome 16 and is transcriptionally active

  genome chimpanzee sult1a3 est blast-like comparative pairwise

• The identification and characterization of a novel protein, c19orf10, in the synovium.

  PMID 17362502 · PMC1906808 · Arthritis research & therapy · 2007 · 8 claims · 8 setups

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  c19orf10 is a novel protein produced in significant amounts by fibroblast-like synoviocytes (FLSs), identified via proteomic analysis

  fibroblast-like coli balb chicken two-dimensional recombinant monoclonal

• Network inference and network response identification: moving genome-scale data to the next level of biological discovery.

  PMID 20174676 · PMC3087299 · Molecular bioSystems · 2010 · 8 claims · 8 setups

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  Cellular response to a signal is assumed to involve only specific TRN modules (conditionally active subnetworks) rather than the entire network, providing quantitative tractability

  yeast specified normal coli chip-on-chip chip-sequencing correlation-based

• 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

• Identification of a novel functional deletion variant in the 5'-UTR of the DJ-1 gene.

  PMID 19825160 · PMC2767350 · BMC medical genetics · 2009 · 8 claims · 6 setups

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  A novel 16 bp deletion variant (g.-6_+10del) was identified in the DJ-1 5'-UTR, spanning the transcription start site, 93 bp downstream of a known Sp1 site.

  genomic hek293 m17 south sscp dual-luciferase pcr-rflp

• In vivo phosphoproteome of human skeletal muscle revealed by phosphopeptide enrichment and HPLC-ESI-MS/MS.

  PMID 19764811 · PMC2783959 · Journal of proteome research · 2009 · 8 claims · 6 setups

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  This is the first large-scale in vivo phosphoproteomic study of human skeletal muscle

  vastus skeletal spectra identified phosphopeptide in-solution strong

• Mass spectrometry group has mass appeal.

  PMID 15598607 · PMC1247668 · Environmental health perspectives · 2004 · 7 claims · 4 setups

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  Mass spectrometry can identify proteins and their post-translational modifications with high specificity and sensitivity, making it central to toxicoproteomics.

  sf9 experimental general mass proteomics combined

• PRIDE: a public repository of protein and peptide identifications for the proteomics community.

  PMID 16381953 · PMC1347500 · Nucleic acids research · 2006 · 8 claims · 6 setups

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  PRIDE is a PSI-compliant public repository for protein and peptide identifications, associated post-translational modifications, and supporting mass spectra from the scientific literature.

  plasma platelet jurkat specified peptide peptide-centric mass

• 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