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).

• Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.

  PMID 18515841 · PMC2447758 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  Babelomics is a web suite offering both conventional functional enrichment methods and more advanced gene set analysis (GSA) methods, a combination offered by only one other tool (FuncAssociate) among competitors.

  user-supplied ranked gene fasta-formatted functional gene novo

• A biomedically enriched collection of 7000 human ORF clones.

  PMID 18231609 · PMC2211400 · PloS one · 2008 · 8 claims · 4 setups

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  Produced and made available over 7000 fully sequence-verified plasmid ORF clones representing over 3400 unique human genes, in both closed (stop codon) and fusion (no stop codon) formats.

  genes mgc plasmid literature pcr sequence

• Opportunities and challenges in synthetic oligosaccharide and glycoconjugate research.

  PMID 20161474 · PMC2794050 · Nature chemistry · 2009 · 8 claims · 7 setups

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  A parallel combinatorial one-pot multi-step protecting-group procedure (Lewis acid catalyzed, up to seven steps) can transform tetra-O-TMS glucopyranosides into differentially protected monosaccharide building blocks without intermittent work-up/purification

  library database oligovalent b-cells glycan bioinformatics one-pot

• Searching for new clues about the molecular cause of endomyocardial fibrosis by way of in silico proteomics and analytical chemistry.

  PMID 19823676 · PMC2757908 · PloS one · 2009 · 8 claims · 4 setups

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  Cross-reactivity of antibodies against C-terminal sequences of ribosomal P proteins from several animals, plants and protozoa with heart tissue may mediate EMF similarly to how T. cruzi C-termini mediate Chaga's disease

  tcp0 tcp2β blast-p phylogenetic structure

• High-throughput crystallography for structural genomics.

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

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  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

• Modification-specific proteomics: strategies for characterization of post-translational modifications using enrichment techniques.

  PMID 19743430 · PMC2892724 · Proteomics · 2009 · 8 claims · 8 setups

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  Lack of efficient enrichment procedures for PTM peptides is a major bottleneck in PTM proteomic research

  cytosolic cellular unspecified yeast immunoaffinity azide chemical

• Microbial community dynamics over large spatial and environmental gradients in a subtropical ocean basin.

  PMID 41568968 · PMC12915303 · Applied and environmental microbiology · 2026 · 8 claims · 7 setups

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  Cluster analysis of 18S (and similarly 16S) community data revealed three clusters corresponding to depth zones: photic zone, deep chlorophyll maximum (DCM), and aphotic zone

  seawater sterivex-filtered extracted log-transformed metabarcoding hydrographic extraction

• Chemically guided single-cell transcriptomics reveals sulfotransferase-mediated scaffold remodeling in securinine biosynthesis.

  PMID 41577683 · PMC12929733 · Nature communications · 2026 · 8 claims · 8 setups

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  FsMS is a ketoreductase that reduces premenisdaurilide to menisdaurilide

  suffruticosa synthetic nicotiana pacbio single-cell d2o

• Signatures of Innovation and Selection in the Extremotolerant Yeast Kluyveromyces marxianus.

  PMID 41874284 · PMC13011806 · Genome biology and evolution · 2026 · 8 claims · 9 setups

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  K. marxianus shows a unique stress-resistance syndrome (heat, ethanol, caffeine, propidium iodide, MMS) relative to other Kluyveromyces species

  kluyveromyces marxianus one-to-one liquid heat-shock stress

• Multi-omics analysis of interspecies interactions in a soil Streptomyces community provides functional insights into siderophore ecology.

  PMID 41942569 · PMC13061897 · Scientific reports · 2026 · 8 claims · 7 setups

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  Strain A shows pronounced phenotypic growth stimulation (increased colony area, aerial hyphae) when co-cultured with strains B, C, and D, strongest with strain C

  environmental agar streptomyces genomes pairwise untargeted rna-seq

• An Asilomar moment.

  PMID 12372138 · PMC244904 · Genome biology · 2002 · 7 claims · 3 setups

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  The current push to restrict genomics/pathogen research funding and publication due to bioterrorism fears parallels the 1975 Asilomar Conference response to recombinant DNA risks.

  mousepox chicken poliovirus gene targeted novo

• The lords of the genomes.

  PMID 15461811 · PMC545592 · Genome biology · 2004 · 8 claims · 8 setups

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  Functionally active clusters of transcription-factor binding sites are evolutionarily conserved between Drosophila species, whereas inactive clusters are not, even when sequence identity alone cannot distinguish them

  drosophila cdna-derived saccharomyces acid reporter-gene enhancer chromatin

• KEGG for linking genomes to life and the environment.

  PMID 18077471 · PMC2238879 · Nucleic acids research · 2008 · 8 claims · 4 setups

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  KEGG provides a reference knowledge base for linking genomes to life via PATHWAY mapping and to the environment via BRITE mapping.

  protein-coding newly microarray kegg sequence computational glycan

• CYCLONET--an integrated database on cell cycle regulation and carcinogenesis.

  PMID 17202170 · PMC1899094 · Nucleic acids research · 2007 · 7 claims · 4 setups

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  Cyclonet is a web-based integrated database combining 'omics' and chemoinformatics data on mammalian cell cycle regulation in normal and pathological (cancer) states, built on a systems biology approach.

  breast commercial vertebrate genes cdna activity computational

• The evolution of sexual signaling is linked to odorant receptor tuning in perfume-collecting orchid bees.

  PMID 31932598 · PMC6957680 · Nature communications · 2020 · 8 claims · 6 setups

  Has reproduction · 93

  E. dilemma and E. viridissima are genetically distinct lineages despite low genome-wide differentiation

  dilemma orchid males bees snp gas whole-genome

• Exploring microproteins from various model organisms using the mip-mining database.

  PMID 37919660 · PMC10623795 · BMC genomics · 2023 · 5 claims · 4 setups

  Has reproduction · 85

  Mip-mining is a database of 336 curated RNA-seq datasets from 8626 samples across nine species, built specifically to explore microprotein functions under stress and disease conditions

  nine cerevisiae thaliana bulk transcriptome growth

• Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma.

  PMID 31784732 · PMC6886578 · Nature genetics · 2019 · 8 claims · 8 setups

  Has reproduction · 58

  SOX8 is a previously unrecognized core regulatory TF in FP-RMS, co-localizing with other CR TFs at SEs and essential for tumor cell growth

  rms rh4 h3k27ac pooled chip-seq

• RNA modifications detection by comparative Nanopore direct RNA sequencing.

  PMID 34893601 · PMC8664944 · Nature communications · 2021 · 7 claims · 5 setups

  Has reproduction · 50

  Nanocompore is a model-free comparative method that uses a 2-component Gaussian mixture model (GMM) and univariate statistical tests on signal intensity/dwell time to detect RNA modifications in Nanopore direct RNA sequencing data without needing a training set

  simulated synthetic escherichia saccharomyces nanopore computational

• Identification of Proteins Deregulated by Platinum-Based Chemotherapy as Novel Biomarkers and Therapeutic Targets in Non-Small Cell Lung Cancer.

  PMID 33777753 · PMC7991912 · Frontiers in oncology · 2021 · 7 claims · 8 setups

  Has reproduction · 81

  Cisplatin exposure induces significant deregulation of protein expression networks in NSCLC cells

  h460 nsclc swath-ms western machine

• The nuclear pore complex.

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

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  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