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).

• Inference of RNA polymerase II transcription dynamics from chromatin immunoprecipitation time course data.

  PMID 24830797 · PMC4022483 · PLoS computational biology · 2014 · 8 claims · 8 setups

  Has reproduction · 75

  A convolved Gaussian process model of pol-II occupancy across gene segments captures the transcription wave and yields estimates of transcription speed and promoter-proximal pol-II activity.

  mcf7 promoter gene signals pol-ii clustering transcription

• Predicting FOX gene candidates for oxic nitrogen fixation using multi-omic machine learning and comparative bioinformatics.

  PMID 41764348 · PMC13056922 · Scientific reports · 2026 · 8 claims · 6 setups

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  Random Forest, XGBoost, and logistic regression classifiers can meaningfully differentiate literature-validated FOX genes from conserved non-essential genes, with Random Forest achieving the best ROC-AUC (~0.80)

  anabaena diazotrophic gene-level trained bulk quantitative transcription-start-site-derived

• Genome-wide analysis of the H3K4 histone demethylase RBP2 reveals a transcriptional program controlling differentiation.

  PMID 18722178 · PMC3003864 · Molecular cell · 2008 · 7 claims · 8 setups

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  RBP2 target promoters separate into two functionally distinct classes: differentiation-independent genes (mitochondrial function, RNA/DNA metabolism) and differentiation-dependent genes (cell cycle)

  u937 saos-2 chip-chip chip-on-chip gene

• GeneSpeed Beta Cell: an online genomics data repository and analysis resource tailored for the islet cell biologist.

  PMID 18795106 · PMC2532782 · Experimental diabetes research · 2008 · 6 claims · 4 setups

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  GeneSpeed Beta Cell is an online genomics data repository allowing simultaneous multiexperiment viewing and multidimensional (Boolean intersection/union) querying of pancreas- and islet-relevant datasets, integrated with GeneSpeed's domain-based gene categorization.

  embryonic pancreatic panel pituitary affymetrix

• Size-Modulated Mesoderm-Endoderm Divergence and Myocardial Cavitation in Micropatterned Cardioids.

  PMID 41837870 · PMC13248853 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 6 setups

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  Micropatterned cardioids generated from hiPSCs co-develop mesoderm-heart and endoderm-foregut/liver lineages, including a previously unreported non-neural ectoderm population.

  hipsc-derived crispr-engineered micropatterned scrna-seq whole-mount clearing single-cell

• A new family of giardial cysteine-rich non-VSP protein genes and a novel cyst protein.

  PMID 17183673 · PMC1762436 · PloS one · 2006 · 8 claims · 7 setups

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  HCNCp is a novel invariant (non-variant) cyst protein belonging to a new family of high-cysteine membrane proteins (HCMp) abundant in the Giardia genome

  giardia serial northern western

• Promoting human promoters.

  PMID 16760901 · PMC1681504 · Molecular systems biology · 2006 · 8 claims · 5 setups

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  A computational protocol using MARS on known sequence motifs can quantify transcription factor effects on human gene expression despite noise and data size challenges

  gene liver cycle genes computational expression time-course

• Strategies for folding of affinity tagged proteins using GroEL and osmolytes.

  PMID 19082872 · PMC3693453 · Journal of structural and functional genomics · 2009 · 8 claims · 8 setups

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  GroEL/osmolyte mixtures can be used to refold difficult-to-fold chimeric affinity-tagged proteins by exploiting intrinsic chaperonin binding.

  coli sds-page glutathione pepck-gst sds-page maldi-tof native

• Segmented filamentous bacteria are worldwide human gut commensals.

  PMID 41786702 · PMC13153320 · Nature communications · 2026 · 8 claims · 8 setups

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  Identification and morphological/genomic characterization of a novel human SFB species, Anisomitus miae (Human-SFB-ML), from Malian/Gambian/Kenyan fecal samples, displaying SFB-specific morphology including the attachment tip structure

  fecal sfb human-sfb-ml publicly pacbio maximum gram

• 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

• Multimodal epigenetic and enhancer network remodeling shape the transcriptional landscape of human beige adipocytes.

  PMID 41501500 · PMC12881478 · Communications biology · 2026 · 8 claims · 8 setups

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  The white adipocyte transcriptional program is tightly linked to promoter-level modulation of H3K27ac and chromatin accessibility.

  adipose asc-derived white ascs bulk atac-seq chip-seq

• Harnessing the HGP of public health.

  PMID 15176090 · PMC1241998 · Environmental health perspectives · 2004 · 8 claims · 7 setups

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  The tombusvirus p19 protein selectively recognizes and sequesters short (21-22 nucleotide) silencing siRNAs, discriminating them from longer siRNAs by measuring siRNA length via tryptophan-mediated end-stacking interactions

  carnation cirv blood rice x-ray site-directed mass

• The transcription factor EHF promotes the maturation and immunosuppression of conventional dendritic cells.

  PMID 41730908 · PMC13039115 · Nature communications · 2026 · 8 claims · 8 setups

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  EHF orchestrates an immunosuppressive maturation program in cDC1s and cDC2s downstream of TLR7/8/9 sensing of self-nucleic acids

  ehf facs-sorted dss-induced lethal cd4+