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).

• Novel integrative genomics strategies to identify genes for complex traits.

  PMID 16886998 · PMC2367618 · Animal genetics · 2006 · 8 claims · 7 setups

  Full-text index only

  Forward genetics is restricted to genes harboring mutations, systematically missing network genes that causally influence disease without themselves being mutated.

  bxd mice bxh alox5 qtl knockout linkage

• Paired-end mapping reveals extensive structural variation in the human genome.

  PMID 17901297 · PMC2674581 · Science (New York, N.Y.) · 2007 · 8 claims · 8 setups

  Full-text index only

  Paired-end mapping (PEM) combining 3-kb fragment paired-end capture, massive 454 sequencing, and computational mapping detects SVs ~3 kb or larger with an average breakpoint resolution of 644 bp

  genomic na15510 stretched reference paired-end pcr array

• siRNA screen of the human signaling proteome identifies the PtdIns(3,4,5)P3-mTOR signaling pathway as a primary regulator of transferrin uptake.

  PMID 17640392 · PMC2323231 · Genome biology · 2007 · 8 claims · 8 setups

  Full-text index only

  The PtdIns(3,4,5)P3-mTOR signaling pathway is a primary positive regulator of transferrin uptake.

  hela sirna secondary synthetic

• QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data.

  PMID 17341461 · PMC1874617 · Nucleic acids research · 2007 · 8 claims · 7 setups

  Full-text index only

  QuantiSNP (OB-HMM) provides probabilistic quantification of copy number states and significantly improves accuracy of segmental aneuploidy identification and breakpoint mapping relative to existing tools (BeadStudio/Illumina)

  genomic same pseudo-normal artificially snp fish molecular

• Integrative microRNA and proteomic approaches identify novel osteoarthritis genes and their collaborative metabolic and inflammatory networks.

  PMID 19011694 · PMC2582945 · PloS one · 2008 · 8 claims · 8 setups

  Full-text index only

  A 16-microRNA signature (9 up, 7 down) distinguishes osteoarthritic from normal cartilage.

  patient-derived normal integrated taqman qrt-pcr northern

• Biomarker discovery in neurodegenerative diseases: a proteomic approach.

  PMID 18938247 · PMC2939006 · Neurobiology of disease · 2009 · 6 claims · 8 setups

  Full-text index only

  Proteomic profiling of CSF and plasma can identify candidate protein biomarkers that distinguish AD patients from controls with high sensitivity and specificity

  csf plasma brain 2-dge lc-ms seldi-tof-ms

• Uprobe 2008: an online resource for universal overgo hybridization-based probe retrieval and design.

  PMID 18515352 · PMC2447791 · Nucleic acids research · 2008 · 7 claims · 7 setups

  Full-text index only

  Uprobe provides new predesigned whole-genome universal overgo probe sets for screening marsupial, rodent, and carnivore BAC libraries.

  wallaby squirrel deer clouded overgo bac comparative

• Prediction-based approaches to characterize bidirectional promoters in the mammalian genome.

  PMID 18366609 · PMC2386062 · BMC genomics · 2008 · 8 claims · 7 setups

  Full-text index only

  The mapping algorithm identified 5,647 candidate bidirectional promoter regions in the mouse genome, similar in number to those previously found in human.

  genome seven genes computational cage comparative

• Identification of ERGIC-53 as an intracellular transport receptor of alpha1-antitrypsin.

  PMID 18283111 · PMC2265576 · The Journal of cell biology · 2008 · 8 claims · 6 setups

  Full-text index only

  α1-antitrypsin is a novel ERGIC-53 cargo protein identified via a YFP protein-fragment complementation assay (PCA) cDNA library screen

  cos-1 hela hepg2 ergic-53 yfp sirna [35s]methionine

• Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes.

  PMID 18187510 · PMC2275096 · Nucleic acids research · 2008 · 8 claims · 6 setups

  Full-text index only

  G-richness downstream of the TSS is strand-biased, concentrated on the nontemplate strand, with a peak at +200 to +300 bp

  refseq chicken random genome-wide quadparser regulatory

• Metagenomic study of the oral microbiota by Illumina high-throughput sequencing.

  PMID 19796657 · PMC3568755 · Journal of microbiological methods · 2009 · 8 claims · 6 setups

  Full-text index only

  The 16S rRNA V5 hypervariable region, amplified as a short ~82-base segment, provides reliable taxonomic identification of oral bacteria against public databases like HOMD.

  pooled 16s sequenced topo 16s primer taxonomic

• Discovery and identification of potential biomarkers of papillary thyroid carcinoma.

  PMID 19785722 · PMC2761863 · Molecular cancer · 2009 · 8 claims · 7 setups

  Full-text index only

  A 3-peak (m/z 9190, 6631, 8697 Da) SVM classification model discriminates PTC from non-cancer controls with high sensitivity and specificity

  serum hplc-purified trypsin-digested crude seldi-tof-ms solid-phase maldi-tof-ms

• The promise and reality of personal genomics.

  PMID 19723346 · PMC2768970 · Genome biology · 2009 · 7 claims · 6 setups

  Full-text index only

  Despite being the most complete and accurate individually sequenced human genome to date, AK1 sequencing still misses a substantial fraction of variants, showing sequencing technology remains far from complete/reliable.

  ak1 six whole-genome copy-number genotyping-based

• Local combinational variables: an approach used in DNA-binding helix-turn-helix motif prediction with sequence information.

  PMID 19651875 · PMC2761287 · Nucleic acids research · 2009 · 8 claims · 7 setups

  Full-text index only

  The LCV approach predicts HTH motifs with 93.29% accuracy, 93.93% sensitivity and 92.66% specificity using only primary sequence information

  quintessentialset-88 hth same newly lcs svm traditional

• pmid-42094231

  PMID 42094231 · PMC13139922 · 7 claims · 6 setups

  Full-text index only

  No genes were significantly differentially expressed in nasal epithelium between participants with and without widespread radiologic BE (FDR<0.1)

  nasal bronchial bulk gene cell-type

• Prevalence of H63D, S65C and C282Y hereditary hemochromatosis gene mutations in Slovenian population by an improved high-throughput genotyping assay.

  PMID 18036208 · PMC2253505 · BMC medical genetics · 2007 · 7 claims · 3 setups

  Full-text index only

  Improved short, non-overlapping TaqMan MGB probes accurately and simultaneously discriminate the H63D, S65C and C282Y HFE polymorphisms without cross-interference between the closely spaced codon 63/65 SNPs.

  genomic real-time rflp sequencing

• EpiToolKit--a web server for computational immunomics.

  PMID 18440979 · PMC2447732 · Nucleic acids research · 2008 · 7 claims · 3 setups

  Full-text index only

  EpiToolKit is a web server integrating five MHC class I and two MHC class II epitope prediction methods in a unified, user-friendly interface.

  randomly novel minor mhc polymorphic

• Prediction of candidate primary immunodeficiency disease genes using a support vector machine learning approach.

  PMID 19801557 · PMC2780952 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2009 · 6 claims · 3 setups

  Full-text index only

  An SVM trained on 69 binary features of known PID genes can accurately classify PID vs non-PID genes and predict novel candidate PID genes

  genome training svm support leave-one-out sensitivity

• Prognostic biomarker discovery in pancreatic cancer through hybrid ensemble feature selection and multi-omics data.

  PMID 41957754 · PMC13188360 · BioData mining · 2026 · 8 claims · 2 setups

  Has reproduction · 92

  hEFS integrates data subsampling with multiple (nine) survival prediction models, combining embedded and wrapper-based feature selection strategies

  pancreatic pdac multi-omics gene

• Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts.

  PMID 19835606 · PMC2784330 · Genome biology · 2009 · 7 claims · 2 setups

  Full-text index only

  Hybrid selection of cDNA dramatically increases the specificity of sequencing reads mapping to targeted cancer-related transcripts.

  k-562 targeted sanger