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).

• Large-scale mutagenesis in p19(ARF)- and p53-deficient mice identifies cancer genes and their collaborative networks.

  PMID 18485879 · PMC2405818 · Cell · 2008 · 8 claims · 8 setups

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  A large-scale retroviral insertional mutagenesis screen identified 10,806 insertion sites implicating over 300 loci in tumorigenesis

  p53 tumor tumors computational retroviral linker-mediated flow

• 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

• Identification and characterization of HLA-A*0301 epitopes in HIV-1 gag proteins using a novel approach.

  PMID 19903485 · PMC2836169 · Journal of immunological methods · 2010 · 7 claims · 7 setups

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  PS mutations V7I and I34L (p17) and K403R (p7) in HIV-1 gag significantly correlate with HLA-A*0301

  hiv-1-infected genomic hiv-1 hla-a*0301 statistical pcr gag

• Spotted-fever group Rickettsia in Dermacentor variabilis, Maryland.

  PMID 15496254 · PMC3320417 · Emerging infectious diseases · 2004 · 8 claims · 6 setups

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  SFG Rickettsia infection prevalence in Maryland D. variabilis was 3.8% (15/392)

  dermacentor tick-derived glta field pcr single sequencing

• The evolutionary dynamics of a rapidly mutating virus within and between hosts: the case of hepatitis C virus.

  PMID 19911046 · PMC2768904 · PLoS computational biology · 2009 · 8 claims · 3 setups

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  The replication rate of the strain that initiates an infection has a strong effect on the fitness of the infection at the between-host level, even though the virus evolves rapidly within the host.

  computational same simulation stochastic parameter-sweep multivariate

• Human genomic diversity, viral genomics and proteomics, as exemplified by human papillomaviruses and H5N1 influenza viruses.

  PMID 19706363 · PMC3525194 · Human genomics · 2009 · 8 claims · 6 setups

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  A novel HPV type (HPV-85) was identified and phylogenetically characterized, showing closest relatedness to HPV-70/39/18/45/59 within the A7 genital HPV group

  novel hpv gene h5n1 whole-genome intrinsic statistical

• 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

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

  rh9 hiv-infected identified subtractive mass enzyme-linked

• Dynamic Gene Attention Focus (DyGAF): Enhancing Biomarker Identification Through Dual-Model Attention Networks.

  PMID 40160891 · PMC11951896 · Bioinformatics and biology insights · 2025 · 6 claims · 5 setups

  Has reproduction · 44

  DyGAF, a dual-model attention neural network (independent Model A + dependent Model B), identifies and ranks genes by significance for COVID-19 biomarker discovery more effectively than differential expression analysis (DEA) and random forest (RF) feature selection

  nasopharyngeal same dygaf-ranked bulk differential random

• Application of ProteinChip array profiling in serum biomarker discovery for patients suffering from severe acute respiratory syndrome.

  PMID 18220240 · PMC7120874 · Methods in molecular biology (Clifton, N.J.) · 2007 · 8 claims · 5 setups

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  SELDI-TOF-MS ProteinChip array profiling of serum can identify differentially expressed protein biomarkers in SARS-CoV infected patients versus controls.

  serum sars seldi-tof-ms ion serial

• Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics.

  PMID 17305421 · PMC1797821 · PLoS computational biology · 2007 · 8 claims · 8 setups

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  The synonymous substitution rate (dS) of HIV env is strongly correlated with disease progression parameters (progression time, CD4+ decline rate, viral load increase rate), unlike the nonsynonymous rate (dN).

  longitudinal backbone env intra-patient relaxed-clock correlation site-to-site

• Conserved positive selection signals in gp41 across multiple subtypes and difference in selection signals detectable in gp41 sequences sampled during acute and chronic HIV-1 subtype C infection.

  PMID 19025632 · PMC2630941 · Virology journal · 2008 · 8 claims · 4 setups

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  Twelve gp41 sites (outside the overlapping rev exon2 reading frame) show positive selection conserved across multiple HIV-1 M subtypes/CRFs, making them candidate targets for broadly protective vaccines.

  gp41 hiv-1 recombination site-specific comparative

• Genomic variability associated with the presence of occult hepatitis B virus in HIV co-infected individuals.

  PMID 19889143 · PMC3032083 · Journal of viral hepatitis · 2010 · 7 claims · 8 setups

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  O-HBV-associated mutations in PreS/S/polymerase regions likely contribute to undetectable HBsAg by interfering with serologic detection, altering antigen secretion, and/or decreasing replicative fitness

  serum hbv full-length o-hbv nested phylogenetic quasispecies

• Genetic variants of Ehrlichia phagocytophila, Rhode Island and Connecticut.

  PMID 11996680 · PMC3369764 · Emerging infectious diseases · 2002 · 7 claims · 6 setups

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  All 50 E. phagocytophila-positive samples from Bridgeport, CT (1996-1998) had 16S rRNA sequences identical to the human agent (EP-ha).

  ixodes white-footed eastern pcr-positive nested sequencing cloning

• Genotypic analysis of two hypervariable human cytomegalovirus genes.

  PMID 18649324 · PMC2658010 · Journal of medical virology · 2008 · 8 claims · 8 setups

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  UL146 sequences from 184 samples fall into the same 14 genotypes (G1-G14) previously defined, with no new genotypes found.

  hcmv clinical pcr ul146 pcr nested molecular