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).

• Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML database--Xindice.

  PMID 16403238 · PMC1351203 · BMC bioinformatics · 2006 · 8 claims · 4 setups

  Full-text index only

  No NPC proteome database existed prior to this work despite availability of other cancer proteome databases

  nasopharyngeal excised subset monoisotopic 2-de maldi-tof q-tof

• A hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples.

  PMID 18194558 · PMC2248205 · BMC genetics · 2008 · 8 claims · 5 setups

  Full-text index only

  A hierarchical/modular approach integrating quality control, LD, physical distance, and gene ontology identifies authentic associations among those found by statistical tests in pooled DNA GWAS

  pooled sickle centenarian snp pooled gene

• A genome-wide association study of social and non-social autistic-like traits in the general population using pooled DNA, 500 K SNP microarrays and both community and diagnosed autism replication samples.

  PMID 20012890 · PMC2797846 · Behavior genetics · 2010 · 6 claims · 4 setups

  Full-text index only

  SNP Microarrays and Pooling (SNP-MaP) is a valid economical method for genome-wide screening of quantitative trait extremes using pooled DNA on microarrays

  teds diagnosed ceph snp individual transmission

• Quantitative analysis of age specific variation in the abundance of human female parotid salivary proteins.

  PMID 19764810 · PMC2834885 · Journal of proteome research · 2009 · 7 claims · 5 setups

  Full-text index only

  Protein expression in human female parotid saliva is age-dependent, with distinct protein sets differentially abundant between young and older healthy women

  pooled hcic trypsin-digested normalized hydrophobic sds-page mudpit

• CRISPR/Cas9 Screens Reveal Multiple Layers of B cell CD40 Regulation.

  PMID 31365872 · PMC6684324 · Cell reports · 2019 · 8 claims · 8 setups

  Has reproduction

  Genome-wide CRISPR/Cas9 screens in CD40L-stimulated Daudi B cells identify known CD40/NF-κB pathway components plus many novel positive and negative CD40 regulators.

  daudi celf1 genome-wide flow immunoblot

• From tides to nucleotides: Genomic signatures of adaptation to environmental heterogeneity in barnacles.

  PMID 33960035 · PMC9292448 · Molecular ecology · 2021 · 7 claims · 6 setups

  Has reproduction · 59

  382 (over 383) genomic regions contain SNPs that are consistently zonated across all surveyed intertidal habitats spanning the North Atlantic.

  semibalanus individual rocky barnacles pool-seq sanger temperature

• Synaptic proteins linked to HIV-1 infection and immunoproteasome induction: proteomic analysis of human synaptosomes.

  PMID 19693676 · PMC2824116 · Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology · 2010 · 8 claims · 7 setups

  Full-text index only

  Proteomic screening of human synaptosomes identifies a set of proteins differentially expressed in HIV/AIDS brain

  frontal excised synaptosome paraffin-embedded 2d-page maldi-tof western

• Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS).

  PMID 17601345 · PMC1929076 · BMC genomics · 2007 · 8 claims · 8 setups

  Full-text index only

  MPSS detected 10,279 UniGene clusters, representing 7,475 known genes, in human hepatocytes

  hepatocytes promoters genes hepatocyte mpss rt-pcr hierarchical

• Population genomics of human gene expression.

  PMID 17873874 · PMC2683249 · Nature genetics · 2007 · 8 claims · 8 setups

  Full-text index only

  Gene expression levels in lymphoblastoid cell lines are a heritable trait

  ebv-transformed ceu lymphoblastoid unrelated genome-wide custom cis-eqtl

• SNP@Evolution: a hierarchical database of positive selection on the human genome.

  PMID 19732458 · PMC2755008 · BMC evolutionary biology · 2009 · 7 claims · 6 setups

  Full-text index only

  SNP@Evolution is a hierarchical database integrating HET, FST, and iHS from HapMap Phase II and III to identify genome-wide positive selection signals

  hapmap autosomes simulated sliding snp sliding haplotype-based

• Macrophages on the run: Exercise balances macrophage polarization for improved health.

  PMID 39476967 · PMC11585839 · Molecular metabolism · 2024 · 8 claims · 7 setups

  Has reproduction · 81

  Immediate/acute exercise triggers an M1 (pro-inflammatory) macrophage polarization surge.

  gene affymetrix pooled muscle meta-analysis stepminer gene

• The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.

  PMID 24068976 · PMC3778014 · PLoS genetics · 2013 · 8 claims · 8 setups

  Has reproduction · 76

  The 50 Mb P. confluens genome with 13,369 predicted protein-coding genes is more characteristic of higher filamentous ascomycetes than of the large, repeat-rich Tuber melanosporum genome, showing that the truffle's expanded genome is not typical of the Pezizales.

  pyronema confluens fungal whole-genome k-mer rna-seq

• ddRAD-seq reveals the genetic structure and detects signals of selection in Italian brown trout.

  PMID 35100964 · PMC8805291 · Genetics, selection, evolution : GSE · 2022 · 7 claims · 8 setups

  Has reproduction · 87

  Italian brown trout populations are genetically differentiated but show strong admixture introduced by stocking, especially with the Atlantic lineage.

  salmo brown subset five ddrad-seq read population

• Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.

  PMID 25122667 · PMC4232532 · G3 (Bethesda, Md.) · 2014 · 8 claims · 8 setups

  Has reproduction · 50

  330,995 SNPs were identified in transcribed regions between B. rapa genotypes R500 and IMB211, at an average frequency of one SNP per 200 bases.

  brassica r500 rapa genomic bulk reference-based snp

• Quantitative serum proteomics using dual stable isotope coding and nano LC-MS/MSMS.

  PMID 19817497 · PMC4684172 · Journal of proteome research · 2009 · 7 claims · 6 setups

  Full-text index only

  DSIC labeling achieves high efficiency: 100% for Cysteine (acrylamide) and 98% for Lysine (succinic anhydride)

  standard dsic-labeled immunodepleted serum labeling quantitative in-solution

• Proteomic analysis of Alzheimer's disease cerebrospinal fluid from neuropathologically diagnosed subjects.

  PMID 19689240 · PMC2832860 · Current Alzheimer research · 2009 · 8 claims · 6 setups

  Full-text index only

  2D DIGE analysis of postmortem V-CSF pools identified 21-22 protein spots that significantly differ among neuropathologically-diagnosed AD, non-demented controls (NDC), and non-AD dementia (non-ADD) groups

  postmortem trypsin-digested individual subjects difference mass micro