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).

• Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster.

  PMID 23284297 · PMC3527207 · PLoS genetics · 2012 · 8 claims · 8 setups

  Has reproduction · 93

  Wolbachia infection status can be accurately predicted in silico from whole-genome shotgun sequence of individual host strains, showing 99% concordance with diagnostic PCR.

  melanogaster dgrp complete wolbachia-infected whole-genome diagnostic coverage-based

• Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells.

  PMID 32596448 · PMC7299619 · Science advances · 2020 · 8 claims · 8 setups

  Has reproduction · 57

  Genome-wide transcriptional bursting kinetics (intrinsic noise, burst size, frequency) can be estimated from allele-specific scRNA-seq of hybrid mESCs

  cast inbred gfp mescs single-cell smfish flow

• Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss).

  PMID 15836796 · PMC1090573 · BMC genomics · 2005 · 8 claims · 7 setups

  Full-text index only

  89 polymorphic microsatellite markers were developed from rainbow trout EST-derived cDNA clones

  normalized rainbow salmonids microsatellite sanger pcr

• A large-scale proteomic analysis of human embryonic stem cells.

  PMID 18162134 · PMC2211323 · BMC genomics · 2007 · 8 claims · 5 setups

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  Two large-scale western blot systems (PowerBlot, Kinexus) identify over 600 proteins expressed in undifferentiated hESCs across 18 functional classes

  bg01 bg03 hescs powerblot kinexus immunofluorescence

• DBD--taxonomically broad transcription factor predictions: new content and functionality.

  PMID 18073188 · PMC2238844 · Nucleic acids research · 2008 · 8 claims · 3 setups

  Full-text index only

  DBD is a database of predicted sequence-specific DNA-binding transcription factors covering over 700 publicly available proteomes, up from 150 in the initial version.

  proteomes eukaryotic genomes hmm-based comparative heatmap

• CASK loss of function differentially regulates neuronal maturation and synaptic function in human induced cortical excitatory neurons.

  PMID 36262316 · PMC9574418 · iScience · 2022 · 7 claims · 8 setups

  Has reproduction · 62

  CASK LOF increases neuronal complexity (neurite overgrowth) in developing/immature human excitatory neurons

  cask ko1 day mature bulk qrt-pcr western

• Differential bone morphology and hypoxia activity in skeletal metastases of ER(+) and ER(-) breast cancer.

  PMID 39572705 · PMC11582807 · Communications biology · 2024 · 8 claims · 8 setups

  Has reproduction · 68

  ER− MDA-MB-231 breast cancer forms more osteolytic bone metastases than ER+ MCF-7 breast cancer

  mcf-7 breast bone tumor-free immunofluorescence co-culture rna-seq

• Genetic Dissection of Tissue-Specific Apolipoprotein E Function for Hypercholesterolemia and Diet-Induced Obesity.

  PMID 26695075 · PMC4687855 · PloS one · 2015 · 8 claims · 8 setups

  Has reproduction

  Hepatocyte apoE is required for normal VLDL production and protects against diet-induced dyslipidemia

  liver plasma pooled real-time western elisa

• Using random walks to identify cancer-associated modules in expression data.

  PMID 24128261 · PMC4015830 · BioData mining · 2013 · 8 claims · 8 setups

  Has reproduction

  Walktrap-GM, a random-walk community detection algorithm adapted with stopping criteria (maximum modularity, maximum size, maximum module score), identifies modules significantly enriched with cancer genes in expression-weighted interaction networks.

  hepatocellular breast sporadic geo gene differential interaction

• Wiggle-predicting functionally flexible regions from primary sequence.

  PMID 16839194 · PMC1500818 · PLoS computational biology · 2006 · 7 claims · 6 setups

  Full-text index only

  A GNM-derived, correlation-weighted 'FF score' can objectively define functionally flexible regions (FFRs) that match experimentally confirmed flexible/functional regions (hinges, recognition loops, catalytic loops).

  hiv bovine calmodulin nonredundant gaussian gnm support

• Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics.

  PMID 18053132 · PMC2254445 · BMC bioinformatics · 2007 · 6 claims · 5 setups

  Full-text index only

  The paired oligo-border kernel (POBK) combined with SVMs predicts peptide adsorption/elution in SAX-SPE and retention time in IP-RP-HPLC more accurately than existing methods.

  peptides peptide sax-spe ip-rp-hplc cross-run

• MLGA--a rapid and cost-efficient assay for gene copy-number analysis.

  PMID 17823203 · PMC2034490 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  MLGA is a novel selector-based technique using multiplex ligation-dependent circularization of genomic DNA fragments for copy-number analysis

  pooled genomic aneuploid dog mlga

• Analyses and comparison of accuracy of different genotype imputation methods.

  PMID 18958166 · PMC2569208 · PloS one · 2008 · 8 claims · 3 setups

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  Stronger LD produces higher imputation accuracy rates for all five methods

  simulated real linux genotype computational

• Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments.

  PMID 36088548 · PMC9487593 · Briefings in bioinformatics · 2022 · 8 claims · 6 setups

  Has reproduction · 94

  Well-established, hierarchically organized pathway annotation systems (e.g. GO, Reactome, KEGG) yield the best overall enrichment performance despite covering much of the human genome only in general terms.

  user-submitted string pubmed protein-coding gene hierarchical text-mining

• Deletion of dinucleotide repeat (Delta 14 allele) in the methylthioadenosine phosphorylase (MTAP) promoter and the allelotype of MTAP promoter in the Japanese population.

  PMID 11985785 · PMC5927014 · Japanese journal of cancer research : Gann · 2002 · 8 claims · 4 setups

  Full-text index only

  DHL-9 lymphoma cells lack detectable MTAP enzyme activity despite possessing an intact (non-deleted) MTAP gene

  dhl-9 genomic lymphoblastoid hela pcr allele-specific luciferase

• Identification and characterization of a novel mammalian Mg2+ transporter with channel-like properties.

  PMID 15804357 · PMC1129089 · BMC genomics · 2005 · 8 claims · 6 setups

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  MagT1 is a novel mammalian Mg2+ transporter with channel-like properties, showing no amino acid sequence identity to other known transporters

  kidney mdct tissues xenopus oligonucleotide northern real-time

• Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets.

  PMID 17598913 · PMC1929078 · BMC genomics · 2007 · 8 claims · 4 setups

  Full-text index only

  Standard Affymetrix expression GeneChips (MOE430, HG-U133) contain probe sets that detect natural antisense transcripts (NATs)

  moe430 pooled organs probe strand-specific microarray

• Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect.

  PMID 18267968 · PMC2367719 · Nucleic acids research · 2008 · 6 claims · 8 setups

  Full-text index only

  The seed arm (guide strand positions 2-8), its complementary passenger-strand sequence, the 5' end of the guide strand, and the 3' overhang of the passenger strand can be simultaneously replaced with DNA without substantial loss of gene-silencing activity.

  cho-k1 e14tg2a recombinant hela dual-luciferase rt-pcr electrophoresis

• SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells.

  PMID 20008100 · PMC2836562 · Nucleic acids research · 2010 · 8 claims · 6 setups

  Full-text index only

  SeqBuster is a versatile web-based and stand-alone bioinformatic toolkit for processing and analyzing large-scale small RNA deep sequencing datasets.

  embryonic hesc small sequence adapter

• Expanding CEP290 mutational spectrum in ciliopathies.

  PMID 19764032 · PMC4340070 · American journal of medical genetics. Part A · 2009 · 7 claims · 4 setups

  Full-text index only

  A large heterozygous genomic deletion spanning the CEP290 C-terminus (exons 42-54) was identified in a JSRD-COR patient previously known to carry only one CEP290 point mutation.

  peripheral genomic quantitative cdna pcr