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).

• Plant Soft Rot Development and Regulation from the Viewpoint of Transcriptomic Profiling.

  PMID 32927917 · PMC7570247 · Plants (Basel, Switzerland) · 2020 · 8 claims · 6 setups

  Has reproduction

  Pba infection of tobacco causes large-scale differential gene expression (8636 DEGs), reflecting profound host physiological reprogramming.

  tobacco potato whole-genome bulk qpcr rna-seq

• Application of proteomics methods for pathogen discovery.

  PMID 19751767 · PMC7119679 · Journal of virological methods · 2010 · 8 claims · 6 setups

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  Proteomic techniques can detect and characterize unknown infectious agents in cell culture without prior knowledge of the pathogen

  hlf sequences synthetic conventional 2d-dige gelc-ms

• Genomic transcriptional profiling identifies a candidate blood biomarker signature for the diagnosis of septicemic melioidosis.

  PMID 19903332 · PMC3091321 · Genome biology · 2009 · 6 claims · 5 setups

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  A candidate 37-transcript diagnostic signature distinguishes septicemic melioidosis from sepsis caused by other organisms with 100% accuracy in the training set and 78%/80% accuracy in two independent validation sets

  blood whole-genome unsupervised class

• eVITTA: a web-based visualization and inference toolbox for transcriptome analysis.

  PMID 34019643 · PMC8218201 · Nucleic acids research · 2021 · 8 claims · 5 setups

  Has reproduction · 82

  eVITTA is a web-based toolbox with three modules (easyGEO, easyGSEA, easyVizR) that analyze, interpret, and compare transcriptome data from published NCBI GEO studies or new experiments

  nasopharyngeal elegans bulk microarray

• Application of functional genomics to the chimeric mouse model of HCV infection: optimization of microarray protocols and genomics analysis.

  PMID 16725047 · PMC1482685 · Virology journal · 2006 · 6 claims · 4 setups

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  Mouse liver mRNA cross-hybridizes to corresponding human gene probes on the Agilent Human 22K oligonucleotide microarray

  liver genomic hcv-infected agilent two-color semi-quantitative real-time

• Systems biology and the host response to viral infection.

  PMID 18066032 · PMC7097743 · Nature biotechnology · 2007 · 8 claims · 8 setups

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  Systems biology integration of 'omics data (transcriptomics, proteomics, genomics) with computational modeling is needed to fully understand virus-host interactions and identify novel antiviral targets

  lung cd4 rhesus kshv microarray quantitative genomic

• Emergence of recombinant forms of HIV: dynamics and scaling.

  PMID 17967052 · PMC2041978 · PLoS computational biology · 2007 · 7 claims · 5 setups

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  A detailed mathematical model incorporating multiple cell infections and recombination quantitatively captures experimental observations of recombinant HIV emergence dynamics in vitro

  cd4+ scid-hu splenocytes computational single-round replication-competent proviral

• Proteomic analyses associate cystatin B with restricted HIV-1 replication in placental macrophages.

  PMID 18951626 · PMC3867668 · Placenta · 2008 · 6 claims · 6 setups

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  Placental macrophages support significantly lower HIV-1 replication than monocyte-derived macrophages

  placental mdm hiv-1 seldi-tof sds-page

• HIV replication enhances production of free fatty acids, low density lipoproteins and many key proteins involved in lipid metabolism: a proteomics study.

  PMID 18714345 · PMC2500163 · PloS one · 2008 · 7 claims · 4 setups

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  HIV infection of a human T-cell line differentially regulates 18 proteins involved in lipid metabolism.

  t-cell identified gel maldi-tof bioinformatics

• Proteomic characterization of HIV-modulated membrane receptors, kinases and signaling proteins involved in novel angiogenic pathways.

  PMID 19712456 · PMC2754444 · Journal of translational medicine · 2009 · 7 claims · 5 setups

  Full-text index only

  31 HIV-modulated cellular proteins were identified as functionally associated with signaling events involved in angiogenesis

  rh9 hiv-infected identified subtractive mass enzyme-linked

• Adaptive learning embedding features to improve the predictive performance of SARS-CoV-2 phosphorylation sites.

  PMID 37847658 · PMC10628388 · Bioinformatics (Oxford, England) · 2023 · 7 claims · 3 setups

  Has reproduction · 67

  PSPred-ALE, a deep learning predictor using a self-adaptive learning embedding algorithm, automatically extracts contextual sequence features and identifies SARS-CoV-2 phosphorylation sites without feature engineering.

  lung peptide same bulk deep traditional

• Profiling Selective Packaging of Host RNA and Viral RNA Modification in SARS-CoV-2 Viral Preparations.

  PMID 35186917 · PMC8851031 · Frontiers in cell and developmental biology · 2022 · 8 claims · 3 setups

  Has reproduction · 56

  SARS-CoV-2 viral preparations show selective enrichment of specific host tRNAs, tRNA fragments, and SRP RNA compared to uninfected VeroE6 cells

  veroe6 cell-free small large trna

• Spatially clustered loci with multiple enhancers are frequent targets of HIV-1 integration.

  PMID 31492853 · PMC6731298 · Nature communications · 2019 · 8 claims · 7 setups

  Has reproduction · 77

  HIV-1 recurrently integrates into genes that are proximal to super-enhancer (SE) genomic elements in both patients and in vitro T cell cultures.

  activated cd4+ cd3 uninfected hiv-1 chip-seq rna-seq

• 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

• Proteomic analyses of monocyte-derived macrophages infected with human immunodeficiency virus type 1 primary isolates from Hispanic women with and without cognitive impairment.

  PMID 19115125 · PMC2947716 · Journal of neurovirology · 2009 · 7 claims · 5 setups

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  HIV-1 isolates from CI patients induce a distinct macrophage proteome signature compared to isolates from NC patients and SF162

  monocyte-derived mdm mdms western p24 seldi-tof sds-page

• Protein isoaspartate methyltransferase prevents apoptosis induced by oxidative stress in endothelial cells: role of Bcl-Xl deamidation and methylation.

  PMID 18806875 · PMC2532751 · PloS one · 2008 · 8 claims · 8 setups

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  PCMT overexpression protects porcine aortic endothelial cells (PAEC) from H2O2-induced apoptosis, raising the threshold H2O2 concentration required to trigger cell death.

  porcine paec umbilical huvec methyltransferase sds-page fragmentation

• Sequence variation of PfEMP1-DBLalpha in association with rosette formation in Plasmodium falciparum isolates causing severe and uncomplicated malaria.

  PMID 19650937 · PMC3224928 · Malaria journal · 2009 · 8 claims · 5 setups

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  Sequence group 1 (mainly from uncomplicated malaria) is significantly different in distribution from sequence group 3 (mainly from severe malaria)

  falciparum falciparum-infected pcr-amplified non-identical static rosette rt-pcr

• Gene Set Enrichment Analysis Reveals Individual Variability in Host Responses in Tuberculosis Patients.

  PMID 34421903 · PMC8375662 · Frontiers in immunology · 2021 · 8 claims · 8 setups

  Has reproduction · 71

  TB patients show substantial individual variability in the intensity of hallmark IFN responses, as well as in complement system, metabolic, and other pathway responses.

  blood cynomolgus external gene differential principal

• Post-translational generation of constitutively active cores from larger phosphatases in the malaria parasite, Plasmodium falciparum: implications for proteomics.

  PMID 15230980 · PMC459218 · BMC molecular biology · 2004 · 8 claims · 8 setups

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  P. falciparum produces full-length PfCnA/PfCnB (calcineurin) and PP7 as well as proteolytically processed catalytic cores in vivo, likely as intermediates of a degradation pathway

  falciparum coli native falciparum-infected rt-pcr recombinant peptide