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).

• Quantification of local morphodynamics and local GTPase activity by edge evolution tracking.

  PMID 19008941 · PMC2573959 · PLoS computational biology · 2008 · 7 claims · 2 setups

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  Edge evolution tracking (EET) is an algorithm that quantifies the relationship between local morphological changes and local fluorescence intensities around a cell edge using time-lapse images.

  fret computational

• Large-scale structural analysis of the core promoter in mammalian and plant genomes.

  PMID 16049029 · PMC1181242 · Nucleic acids research · 2005 · 8 claims · 7 setups

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  DNA encodes at least two independent levels of functional information: protein/TF-binding sequence information and physical/structural properties of the molecule itself.

  core-promoter arabidopsis rice computational adaptive linear

• In silico whole-genome screening for cancer-related single-nucleotide polymorphisms located in human mRNA untranslated regions.

  PMID 17201911 · PMC1774567 · BMC genomics · 2007 · 8 claims · 5 setups

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  A computational EST-based pipeline can identify UTR-SNPs that are statistically over-represented in cancerous versus normal tissue libraries

  est acute 100-nt whole-genome est-based pcr-based secondary

• C-terminal mutants of apolipoprotein L-I efficiently kill both Trypanosoma brucei brucei and Trypanosoma brucei rhodesiense.

  PMID 19997494 · PMC2778949 · PLoS pathogens · 2009 · 8 claims · 8 setups

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  The C-terminal helix of apoL1 is entirely responsible for its interaction with SRA

  coli brucei computational papio bacterial trypanolytic nickel-bead

• SECIS elements in the coding regions of selenoprotein transcripts are functional in higher eukaryotes.

  PMID 17169995 · PMC1802603 · Nucleic acids research · 2007 · 8 claims · 5 setups

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  SECIS elements located within coding regions of selenoprotein mRNAs support functional Sec insertion in mammalian cells

  viral hek293 hepatoma tblastn computational western

• Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

  PMID 17576681 · PMC1934990 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  Cryptic 5'ss are best predicted by computational algorithms that accommodate nucleotide dependencies (e.g., Markov model, maximum entropy, maximum dependence decomposition) rather than by weight-matrix models

  disease mammalian compiled literature minigene computational

• Altered spin state equilibrium in the T309V mutant of cytochrome P450 2D6: a spectroscopic and computational study.

  PMID 17318599 · PMC1915625 · Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2007 · 7 claims · 7 setups

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  The T309V mutation shifts the CYP2D6 heme spin equilibrium toward the six-coordinate low-spin (6cLS) state, decreasing the five-coordinate high-spin (5cHS) fraction relative to wild type.

  recombinant cyp2d6 computational resonance uv-vis sds-page

• The SARS-CoV-2 subgenome landscape and its novel regulatory features.

  PMID 33713597 · PMC7927579 · Molecular cell · 2021 · 8 claims · 6 setups

  Has reproduction · 84

  Template switching in SARS-CoV-2 can occur bidirectionally, generating diverse subgenomes through successive template-switching events

  vero caco-2 sars-cov-2 ngs nanopore northern

• Reduced secretion of fibulin 5 in age-related macular degeneration and cutis laxa.

  PMID 16652333 · PMC1828612 · Human mutation · 2006 · 7 claims · 6 setups

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  FBLN5 missense mutations are associated with ARMD in a European (UK/Dutch) cohort, confirming prior US findings

  armd dutch fibulin pef6-ssflag mutation computational site-directed

• Screening for microsatellite instability identifies frequent 3'-untranslated region mutation of the RB1-inducible coiled-coil 1 gene in colon tumors.

  PMID 19888451 · PMC2766054 · PloS one · 2009 · 7 claims · 4 setups

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  Somatic mutation frequency (%MSI) of 3'UTR microsatellites in MSI-H colorectal tumors correlates significantly with microsatellite length (r=0.86, p=7.2×10−13), following an exponential growth model.

  msi-h computational rb1cc1 normal pcr nonlinear real-time

• Structural genomics: a new era for pharmaceutical research.

  PMID 11864367 · PMC139010 · Genome biology · 2002 · 8 claims · 6 setups

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  Automation of crystal mounting, diffraction data collection, and structure determination/refinement is a critical factor enabling large-scale structural genomics projects.

  proteins target hiv x-ray thermal initio

• The flexible pocketome engine for structural chemogenomics.

  PMID 19727619 · PMC2975493 · Methods in molecular biology (Clifton, N.J.) · 2009 · 8 claims · 8 setups

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  A comprehensive structural Pocketome combined with ensemble docking enables de novo, structure-based prediction of ligand binding poses and activities for new proteins and new chemical scaffolds.

  pdb bacteriorhodopsin enr asn automated virtual energy-based

• Comparisons of substitution, insertion and deletion probes for resequencing and mutational analysis using oligonucleotide microarrays.

  PMID 15722479 · PMC549431 · Nucleic acids research · 2005 · 7 claims · 4 setups

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  Two base deletion probes display the highest average hybridization specificity, followed by single base substitution, single base deletion, and single base insertion probes.

  atm hybridized probe oligonucleotide transcription microarray

• Crystal structure of the HSV-1 Fc receptor bound to Fc reveals a mechanism for antibody bipolar bridging.

  PMID 16646632 · PMC1450327 · PLoS biology · 2006 · 8 claims · 5 setups

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  The C-terminal domain of the gE ectodomain (CgE) is the minimal Fc-binding domain of gE-gI

  recombinant selenomethionine-substituted ge-gi models surface x-ray computational

• Hyb: a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data.

  PMID 24211736 · PMC3969109 · Methods (San Diego, Calif.) · 2014 · 8 claims · 6 setups

  Has reproduction · 71

  The 'hyb' pipeline detects, calls, folds and annotates chimeric reads from CLASH high-throughput sequencing data.

  ago1 test clash multiplexed clash benchmarking demultiplexing

• Effects of two common polymorphisms in the 3' untranslated regions of estrogen receptor beta on mRNA stability and translatability.

  PMID 19754929 · PMC2759954 · BMC genetics · 2009 · 8 claims · 4 setups

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  Breast tumor heterozygotes show a significant difference in relative mRNA levels between the two alleles of rs4986938

  breast hek293 erβ1 allelic luciferase stability