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).

• Proteomic analysis of nipple aspirate fluid from women with early-stage breast cancer using isotope-coded affinity tags and tandem mass spectrometry reveals differential expression of vitamin D binding protein.

  PMID 16542425 · PMC1431555 · BMC cancer · 2006 · 8 claims · 5 setups

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  ICAT tandem MS can identify and quantify differences in specific protein expression between NAF from tumor-bearing and disease-free breasts

  paired icat-labeled spectra naf icat sds-page liquid

• The selection of software and database for metagenomics sequence analysis impacts the outcome of microbial profiling and pathogen detection.

  PMID 37027361 · PMC10081788 · PloS one · 2023 · 7 claims · 7 setups

  Has reproduction · 86

  Obtaining an accurate species-level microbial profile using current direct-read metagenomics profiling software is still a challenging task.

  simulated kidney biological extracted shotgun taxonomic pathogen

• Genomic and proteomic profiling I: leiomyomas in African Americans and Caucasians.

  PMID 17716379 · PMC2063502 · Reproductive biology and endocrinology : RB&E · 2007 · 7 claims · 6 setups

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  268 genes (177 over-expressed, 91 under-expressed) are differentially expressed in leiomyomas of African Americans compared to Caucasians (P<0.01, 2-fold cutoff)

  paired same excised paraffin-embedded microarray realtime 2d-page

• Epidemiology of doublet/multiplet mutations in lung cancers: evidence that a subset arises by chronocoordinate events.

  PMID 19005564 · PMC2579325 · PloS one · 2008 · 8 claims · 7 setups

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  Doublet mutations are significantly more frequent in EGFR (6.0%) and TP53 (2.3%) in human lung cancer than spontaneous doublets in mouse lacI (0.7%), about 8-fold and 3-fold higher respectively.

  egfr tp53 laci lung literature comparative statistical

• Proteomic comparison of two-dimensional gel electrophoresis profiles from human lung squamous carcinoma and normal bronchial epithelial tissues.

  PMID 15626334 · PMC5172349 · Genomics, proteomics & bioinformatics · 2003 · 8 claims · 5 setups

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  Well-resolved, reproducible 2-DE profiles of human lung squamous carcinoma and normal bronchial epithelial tissues were obtained under optimized conditions (0.75-mg protein load, TCA precipitation)

  lung scanned excised peptide 2-d 2-de maldi-tof-ms

• Genome-wide signatures of convergent evolution in echolocating mammals.

  PMID 24005325 · PMC3836225 · Nature · 2013 · 8 claims · 8 setups

  Has reproduction

  Genome-wide convergent sequence evolution between echolocating lineages is not rare but widespread and continuously distributed, with signatures consistent with convergence in nearly 200 loci out of 2,326 examined.

  four raw orthologous mammalian whole-genome novo homology-based

• Proteomic analysis of differentially expressed proteins in hepatitis B virus-related hepatocellular carcinoma tissues.

  PMID 19715608 · PMC2743659 · Journal of experimental & clinical cancer research : CR · 2009 · 8 claims · 5 setups

  Full-text index only

  17 differentially expressed proteins were identified between HBV-related HCC tissue and adjacent non-tumorous liver tissue by 2-DE/MALDI-TOF-MS

  hcc excised pmf extract 2-de maldi-tof-ms database

• Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression.

  PMID 23951250 · PMC3741199 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 67

  Cryosectioning single blastoderm-stage D. melanogaster embryos along the A–P axis and sequencing mRNA from each slice yields reliable genome-wide spatial expression patterns.

  single methanol-fixed reads slice mrna-seq light-microscopy read

• Comparative transcriptome analysis of tomato (Solanum lycopersicum) in response to exogenous abscisic acid.

  PMID 24289302 · PMC4046761 · BMC genomics · 2013 · 8 claims · 7 setups

  Has reproduction · 63

  Exogenous ABA alters the expression of a majority (54.73%) of expressed tomato leaf transcripts, with 2,787 significantly differentially expressed genes, predominantly up-regulated.

  tomato assembled illumina read functional

• Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues.

  PMID 16188928 · PMC4631381 · Bioinformatics (Oxford, England) · 2005 · 7 claims · 4 setups

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  Genes upregulated in squamous cell lung cancer are highly connected (well-connected) nodes in the protein interactome

  squamous ophid degs oligonucleotide interaction connectivity

• Finding disease candidate genes by liquid association.

  PMID 17915034 · PMC2246280 · Genome biology · 2007 · 7 claims · 6 setups

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  LA can detect functionally associated genes that are not directly co-expressed by identifying a mediating gene Z whose expression level changes the correlation between X and Y.

  nci_cdna gnf_2002 finnish gnf_2004 liquid transmission correlation

• A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

  PMID 25202605 · PMC4103609 · Applications in plant sciences · 2014 · 8 claims · 8 setups

  Has reproduction · 87

  A custom sequence capture probe set (9678 baits targeting 1061 orthologous genes) was designed to enrich COS loci across the Compositae.

  compositae same species helianthus targeted genome genomic

• The EH1 motif in metazoan transcription factors.

  PMID 16309560 · PMC1310626 · BMC genomics · 2005 · 8 claims · 5 setups

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  There is a statistically significant association between EH1hox motif HMM score and transcription factor function across human, Drosophila and C. elegans proteomes.

  homeobox-containing forkhead-containing complete combined meme hmm logistic

• DFAST and DAGA: web-based integrated genome annotation tools and resources.

  PMID 27867804 · PMC5107635 · Bioscience of microbiota, food and health · 2016 · 8 claims · 7 setups

  Has reproduction · 89

  DFAST is a web-based bacterial genome annotation and DDBJ submission pipeline with integrated CheckM quality assessment and ANI taxonomic assessment.

  lactobacillus genomes representative raw genome ortholog average

• Involvement of N4BP2L1, PLEKHA4, and BEGAIN genes in breast cancer and muscle cell development.

  PMID 38859961 · PMC11163233 · Frontiers in cell and developmental biology · 2024 · 8 claims · 8 setups

  Has reproduction · 73

  N4BP2L1, PLEKHA4, and BEGAIN, normally highly expressed in breast myoepithelial and smooth muscle cells, are significantly downregulated in breast tumor tissue of a 50-patient cohort

  breast paired embryonic hesc-derived bulk rt-qpcr immunofluorescence

• A genome-wide survey of segmental duplications that mediate common human genetic variation of chromosomal architecture.

  PMID 15588494 · PMC3525102 · Human genomics · 2004 · 8 claims · 5 setups

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  PSD-mediated genomic architecture analogous to the 8p23/4p16 inversion regions is not unique to those loci but recurs genome-wide.

  genomic genome extracted pairwise online genome-wide

• Distinctive pattern of sequence polymorphism in the NS3 protein of hepatitis C virus type 1b reflects conflicting evolutionary pressures.

  PMID 18632963 · PMC2577380 · The Journal of general virology · 2008 · 7 claims · 6 setups

  Full-text index only

  NS3 shows less evidence of purifying selection acting on its CTL epitopes than the other 9 HCV proteins, while outside the CTL epitopes NS3 is more conserved than the other proteins.

  complete hcv-1b sequence nonsynonymous comparative neighbor-joining maximum

• Viral Diagnostics in Plants Using Next Generation Sequencing: Computational Analysis in Practice.

  PMID 29123534 · PMC5662881 · Frontiers in plant science · 2017 · 8 claims · 8 setups

  Has reproduction · 100

  NGS/RNA-seq enables unbiased, hypothesis-free detection of multiple known and emergent plant viruses, unlike RT-PCR which only detects one or a few known viruses per test.

  garlic pepper pear grapevine rna-seq mrna-seq transcriptome

• Genomic Description of 'Candidatus Abyssubacteria,' a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes.

  PMID 30210471 · PMC6121073 · Frontiers in microbiology · 2018 · 8 claims · 7 setups

  Has reproduction · 91

  SURF_5 and SURF_17 are the first full genomes of a novel bacterial lineage, 'Candidatus Abyssubacteria,' within the candidate phylum Hydrogenedentes

  deep co-assembled surf_17 surf_5 whole-genome novo 16s

• Pharmaco-proteomic study of hydroxyurea-induced modifications in the sickle red blood cell membrane proteome.

  PMID 18849548 · PMC4260454 · Experimental biology and medicine (Maywood, N.J.) · 2008 · 6 claims · 6 setups

  Full-text index only

  50 μM HU treatment of SS RBC membranes causes statistically significant changes in a discrete set of membrane proteins, distinct from HbF induction.

  sickle rbc excised 2d-dige tandem immunoblot