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).

• Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks.

  PMID 19638617 · PMC2889494 · Science signaling · 2009 · 8 claims · 6 setups

  Full-text index only

  Pathway reconstruction can be modeled as a prize-collecting Steiner tree problem, balancing penalties for excluding terminal nodes against costs for including edges, controlled by a parameter β.

  saccharomyces phosphoproteomic expression curated

• A proteomics grade electron transfer dissociation-enabled hybrid linear ion trap-orbitrap mass spectrometer.

  PMID 18613715 · PMC2601597 · Journal of proteome research · 2008 · 8 claims · 5 setups

  Full-text index only

  A NCI source coupled via an added octopole and the c-trap to a QLT-orbitrap enables fast, efficient ETD reagent anion injection (4-8 ms)

  saccharomyces histone glioblastoma fluoranthene lc-ms etd anion

• 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

• Proteomics data repositories.

  PMID 19795424 · PMC2908408 · Proteomics · 2009 · 5 claims · 5 setups

  Full-text index only

  The YRC Public Data Repository (YRC PDR) provides a single unified interface disseminating multi-technology proteomics data (mass spectrometry, yeast two-hybrid, fluorescence microscopy, structure prediction) linked to protein annotations from many source databases.

  multi-organism yeast proteomes cerevisiae tandem yeast fluorescence

• Filtering high-throughput protein-protein interaction data using a combination of genomic features.

  PMID 15833142 · PMC1127019 · BMC bioinformatics · 2005 · 8 claims · 8 setups

  Full-text index only

  A combination of three genomic features (interacting Pfam domains, GO annotations, sequence homology) using naive Bayesian networks predicts true protein-protein interactions with high sensitivity and good specificity.

  saccharomyces bank caenorhabditis homo yeast mass naive

• InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale.

  PMID 17868464 · PMC2375030 · Genome biology · 2007 · 8 claims · 8 setups

  Full-text index only

  InSite predicts protein-pair-specific binding motifs ('Motif M on protein A binds to protein B') by integrating heterogeneous PPI and motif-motif interaction evidence within a Bayesian network trained by EM

  saccharomyces homo bank computational yeast tandem

• Identification of mitochondrial disease genes through integrative analysis of multiple datasets.

  PMID 18930150 · PMC2774125 · Methods (San Diego, Calif.) · 2008 · 8 claims · 8 setups

  Full-text index only

  Data integration of multiple functional genomics datasets effectively predicts mitochondrial gene function and prioritizes candidate mitochondrial disease genes.

  saccharomyces higher yeast mitochondria genome-wide rnai gene

• From single cells to whole organisms.

  PMID 16420683 · PMC1414103 · Genome biology · 2005 · 8 claims · 8 setups

  Full-text index only

  The genetic-interaction map in S. cerevisiae is roughly four times as complex as the protein-protein interaction map, and genetic interactions do not overlap with physical interactions but instead predict functional neighborhoods

  saccharomyces caenorhabditis mammalian cylindromatosis automated interference rnai

• The PeptideAtlas project.

  PMID 16381952 · PMC1347403 · Nucleic acids research · 2006 · 8 claims · 5 setups

  Full-text index only

  PeptideAtlas provides an automated repository that identifies peptides by MS/MS, statistically validates identifications, and maps them to eukaryotic genomes to enable data exchange and integration with genomic data.

  plasma drosophila yeast tandem sequence

• Disome-seq reveals widespread ribosome collisions that promote cotranslational protein folding.

  PMID 33402206 · PMC7784341 · Genome biology · 2021 · 8 claims · 8 setups

  Has reproduction · 74

  Disome-seq sequences mRNA fragments protected by two stacked (collided) ribosomes, detecting ribosome collisions at codon resolution.

  saccharomyces yeast disome-seq monosome-seq mrna-seq

• Comparing protein abundance and mRNA expression levels on a genomic scale.

  PMID 12952525 · PMC193646 · Genome biology · 2003 · 8 claims · 8 setups

  Full-text index only

  Correlations between mRNA expression and protein abundance are generally poor or limited across most studies reviewed, including in yeast and human cancers

  yeast laser-dissected serum myeloid two-dimensional seldi-tof isotope-coded

• Microbial genomics: from sequence to function.

  PMID 10998380 · PMC2627950 · Emerging infectious diseases · 2000 · 8 claims · 4 setups

  Full-text index only

  Whole-genome shotgun sequencing (sequencing and assembly of random genome fragments), first demonstrated with Haemophilus influenzae in 1995, is now the method of choice for sequencing most genomes, including the human genome.

  yeast bacteria microbial high-throughput microarray ribosomal

• Putting proteins in one place.

  PMID 12790144 · PMC1316915 · Environmental health perspectives · 2003 · 8 claims · 7 setups

  Full-text index only

  Rapamycin inhibits TOR, causing the silencing protein Sir3 to detach from chromatin at stress-response genes, triggering a coordinated multigene stress response that halts cancer cell proliferation

  saccharomyces yeast vascular skin chemical chromatin microarray

• High-throughput crystallography for structural genomics.

  PMID 19765976 · PMC2764548 · Current opinion in structural biology · 2009 · 8 claims · 8 setups

  Full-text index only

  SG programs use genomic sequence data to select structurally novel protein targets, avoiding proteins with known structural homologues

  recombinant recalcitrant hundred family hydrogen situ site-directed

• The nuclear pore complex.

  PMID 11574060 · PMC138961 · Genome biology · 2001 · 8 claims · 8 setups

  Full-text index only

  NPC structure is broadly conserved across eukaryotes but differs substantially in size and architecture between yeast and vertebrates

  xenopus saccharomyces yeast caenorhabditis cryo-electron proteomic protein-a

• A map of human protein interactions derived from co-expression of human mRNAs and their orthologs.

  PMID 18414481 · PMC2387231 · Molecular systems biology · 2008 · 8 claims · 6 setups

  Full-text index only

  Comparing human mRNA co-expression with co-expression of orthologous gene pairs in five other organisms identifies proteins that physically associate

  genes hela proteins worm co-expression quantitative functional

• Proteomic view of mitochondrial function.

  PMID 18331620 · PMC2374722 · Genome biology · 2008 · 8 claims · 8 setups

  Full-text index only

  Most modulators of basal mitochondrial function identified in the Drosophila RNAi screen are located outside the mitochondrion, since only 17 of 152 hits had a clear mitochondrial function.

  drosophila saccharomyces caenorhabditis yeast genome-wide phenotypic morphology

• The integrated world of functional genomics.

  PMID 12537543 · PMC151279 · Genome biology · 2003 · 8 claims · 8 setups

  Full-text index only

  Integrating chromatin immunoprecipitation (promoter-binding) data with expression data reveals the yeast cell-cycle transcriptional regulatory network, including network motifs such as autoregulation, multi-component loops, and feedforward loops.

  cerevisiae sequenced elegans drosophila chromatin integration comparative

• Expansion of the human mitochondrial proteome by intra- and inter-compartmental protein duplication.

  PMID 19930686 · PMC3091328 · Genome biology · 2009 · 8 claims · 6 setups

  Full-text index only

  The human mitochondrial proteome expanded via two prevailing gene duplication modes: intra-mitochondrial and inter-compartmental duplication

  cerevisiae mitocarta mitochondrial tissues comparative subcellular gene

• Whither genomics?

  PMID 11104516 · PMC138820 · Genome biology · 2000 · 8 claims · 8 setups

  Full-text index only

  Genomics is both a science (understanding genome structure/evolution) and a tool (learning gene function) that collects comprehensive data on all genes, in contrast to genetics which studies a few genes controlling a phenotype

  mammalian budding yeast general expression genome-wide synthetic