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).

• Sequence analysis of p53 response-elements suggests multiple binding modes of the p53 tetramer to DNA targets.

  PMID 17439973 · PMC1888811 · Nucleic acids research · 2007 · 8 claims · 5 setups

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  p53REs are not simple direct repeats of half-sites; the two half-sites couple to form a higher-order 20-bp full-site palindrome

  compiled genome artificial sequence computational simulated

• NETISCE: a network-based tool for cell fate reprogramming.

  PMID 35725577 · PMC9209484 · NPJ systems biology and applications · 2022 · 8 claims · 4 setups

  Has reproduction · 85

  NETISCE predicts cell fate reprogramming targets in static (GRN/signaling) networks without needing full kinetic parameterization of a dynamical model.

  ascidian pluripotent drosophila signal fvs-finding sfa

• MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data.

  PMID 16381984 · PMC1347458 · Nucleic acids research · 2006 · 8 claims · 5 setups

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  MPromDb is a novel database integrating experimentally supported gene promoters, TSS annotation, cis-regulatory elements, CpG islands, and ChIP-chip data with an integrated visualization interface.

  chip-chip sequence genbank

• ABS: a database of Annotated regulatory Binding Sites from orthologous promoters.

  PMID 16381947 · PMC1347478 · Nucleic acids research · 2006 · 7 claims · 6 setups

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  ABS is a public database of experimentally identified TF binding sites conserved in orthologous vertebrate gene promoters, manually curated from the literature.

  orthologous literature sequence pairwise

• Human Protein Reference Database--2009 update.

  PMID 18988627 · PMC2686490 · Nucleic acids research · 2009 · 8 claims · 8 setups

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  HPRD is a curated database of experimentally derived human protein-protein interactions, post-translational modifications, and tissue expression data

  mastl proteins phosphorylation yeast mass

• Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.

  PMID 17567995 · PMC1891336 · Genome research · 2007 · 7 claims · 3 setups

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  Four different alignment methods show large-scale consistency but substantial differences in small-scale rearrangements, sensitivity, and specificity.

  mammalian aligned constrained sequence evolutionary comparative

• The MAPPER database: a multi-genome catalog of putative transcription factor binding sites.

  PMID 15608292 · PMC540057 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  Built a library of 1134 HMM models (359 matrix-derived, 718 factor-derived, 57 JASPAR-derived), corresponding to 863 distinct TF names, from TRANSFAC and JASPAR binding site data

  genome drosophila transfac b99 profile sequence case-study

• Epistemic uncertainty challenges aging clock reliability in predicting rejuvenation effects.

  PMID 39072888 · PMC11561706 · Aging cell · 2024 · 8 claims · 8 setups

  Has reproduction · 93

  DNA methylation profiles observed across cellular reprogramming are poorly represented in the training data of existing aging clocks, introducing high out-of-distribution/epistemic uncertainty in their age estimates

  males skin liver linear dnam epigenetic

• Cotranscriptional RNA strand exchange underlies the gene regulation mechanism in a purine-sensing transcriptional riboswitch.

  PMID 35348734 · PMC9756952 · Nucleic acids research · 2022 · 7 claims · 6 setups

  Has reproduction · 91

  A nascent intermediate central helix forms in the yxjA riboswitch that is mutually exclusive with both the aptamer's P1 helix and the expression platform's intrinsic terminator hairpin.

  coli yxja refolded flow bulk cotranscriptional

• iCOMIC: a graphical interface-driven bioinformatics pipeline for analyzing cancer omics data.

  PMID 35899080 · PMC9310080 · NAR genomics and bioinformatics · 2022 · 8 claims · 4 setups

  Has reproduction · 58

  iCOMIC provides a GUI-driven, Snakemake-based pipeline integrating multiple tools for DNA-Seq and RNA-Seq analysis with minimal command-line interaction.

  giab monocyte missense somatic germline rna-seq machine

• Oligomeric protein structure networks: insights into protein-protein interactions.

  PMID 16336694 · PMC1326230 · BMC bioinformatics · 2005 · 8 claims · 6 setups

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  Interface amino acid clusters identified at Imin=6% correlate well with residues losing accessible surface area (δASA) upon oligomerization

  non-redundant same known complexes structure hub comparison

• Phosphorylation states of cell cycle and DNA repair proteins can be altered by the nsSNPs.

  PMID 16111488 · PMC1208866 · BMC cancer · 2005 · 8 claims · 4 setups

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  15 of 89 nsSNPs (16.9%) studied were predicted to abolish or create phosphorylation sites in 14 of 32 proteins (44.0%)

  orthologues repair case-control phosphorylation cross-species database

• Association of poly-purine/poly-pyrimidine sequences with meiotic recombination hot spots.

  PMID 16846522 · PMC1543642 · BMC genomics · 2006 · 7 claims · 6 setups

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  PPT frequency is significantly elevated in yeast meiotic recombination hot spots compared with cold spots

  cerevisiae genome chimpanzee hot computational microarray comparative

• Dissecting microregulation of a master regulatory network.

  PMID 18294391 · PMC2289817 · BMC genomics · 2008 · 8 claims · 6 setups

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  143 human miRNAs (termed p53-miRs) each contain at least one putative p53 binding site within 10 kb flanking sequence and are predicted to target at least one known gene

  genome mirnas mirna-target predicted p53 mirna cross-referencing

• MEROPS: the peptidase database.

  PMID 19892822 · PMC2808883 · Nucleic acids research · 2010 · 8 claims · 5 setups

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  MEROPS is a manually curated hierarchical classification of peptidases and protein inhibitors organized into protein species, families, and clans based on sequence and structural homology.

  archaean holotype c-x-c proteins comparative domain substrate

• Magnetization transfer imaging in 'premanifest' Huntington's disease.

  PMID 19823894 · PMC2837878 · Journal of neurology · 2010 · 8 claims · 4 setups

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  MTI parameters (mean MTR and normalized peak height) of whole brain, grey matter and white matter did not differ significantly between premanifest HD carriers and non-carriers

  premanifest magnetization 3d-t1-weighted clinical

• In Silico screening for functional candidates amongst hypothetical proteins.

  PMID 19754976 · PMC2758874 · BMC bioinformatics · 2009 · 7 claims · 6 setups

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  An in silico selection strategy combining subcellular targeting-signal prediction with protein domain identification can enrich for true functional proteins among hypothetical proteins

  hypothetical targetp-selected mitochondria-predicted subcellular domain database

• Widespread allele-specific topological domains in the human genome are not confined to imprinted gene clusters.

  PMID 36869353 · PMC9983196 · Genome biology · 2023 · 8 claims · 5 setups

  Has reproduction · 64

  HiCFlow, a new bioinformatic pipeline, performs de novo haplotype assembly, phasing, and visualization of allele-specific (parental) chromatin conformation directly from Hi-C data without requiring pre-phased haplotypes.

  1-7hb2 gm12878 imr-90 lines region hi-c genome-wide

• Comparative genomics.

  PMID 14624258 · PMC261895 · PLoS biology · 2003 · 8 claims · 7 setups

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  Conserved DNA between species tends to encode shared functional features, while divergent DNA underlies species differences

  caenorhabditis yeast mammalian vertebrate whole-genome comparative interspecies-similarity-informed

• A genome-wide survey of Major Histocompatibility Complex (MHC) genes and their paralogues in zebrafish.

  PMID 16271140 · PMC1309616 · BMC genomics · 2005 · 8 claims · 4 setups

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  149 putative MHC gene loci and their paralogues were identified in the zebrafish genome using sequence similarity searches against the Zv4 draft assembly.

  zebrafish sequence comparative cross-validation