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).

• Positive natural selection in the evolution of human metapneumovirus attachment glycoprotein.

  PMID 17931731 · PMC7114232 · Virus research · 2008 · 7 claims · 5 setups

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  8 amino acid sites in the extracellular domain of hMPV lineage 1a show a higher rate of nonsynonymous than synonymous substitutions (posterior probability >0.95), indicating positive selection.

  unique hmpv sequence neighbor-joining codon

• Hepatitis B virus genotypes circulating in Brazil: molecular characterization of genotype F isolates.

  PMID 18036224 · PMC2231365 · BMC microbiology · 2007 · 8 claims · 4 setups

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  Genotypes A, D, and F co-circulate in each of the five Brazilian geographic regions, with no other genotypes identified among 303 isolates

  serum hbv pcr-rflp nucleotide phylogenetic

• Segmented filamentous bacteria are worldwide human gut commensals.

  PMID 41786702 · PMC13153320 · Nature communications · 2026 · 8 claims · 8 setups

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  Identification and morphological/genomic characterization of a novel human SFB species, Anisomitus miae (Human-SFB-ML), from Malian/Gambian/Kenyan fecal samples, displaying SFB-specific morphology including the attachment tip structure

  fecal sfb human-sfb-ml publicly pacbio maximum gram

• Evidence for positive selection in putative virulence factors within the Paracoccidioides brasiliensis species complex.

  PMID 18820744 · PMC2553485 · PLoS neglected tropical diseases · 2008 · 8 claims · 8 setups

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  Positive selection has played an important role in the molecular evolution of putative virulence factors of P. brasiliensis

  brasiliensis gp43 ratio codon-based mutational

• The role of the humoral immune response in the molecular evolution of the envelope C2, V3 and C3 regions in chronically HIV-2 infected patients.

  PMID 18778482 · PMC2563025 · Retrovirology · 2008 · 8 claims · 7 setups

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  Intra-host nucleotide diversity of the HIV-2 C2V3C3 region increases over the course of chronic infection in most patients

  pbmcs clonal env deduced nested maximum-likelihood positive

• Candidate target genes for loss of heterozygosity on human chromosome 17q21.

  PMID 15187990 · PMC2409524 · British journal of cancer · 2004 · 8 claims · 5 setups

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  JUP (plakoglobin) is the only identified gene physically located between the D17S746 and D17S846 markers that define the smallest common region of LOH on chromosome 17q21

  genomic normal breast p1-phage nucleotide rt-pcr cold

• Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs.

  PMID 23536903 · PMC3607606 · PloS one · 2013 · 8 claims · 9 setups

  Has reproduction · 45

  Bubbleparse detects sequence variants directly from NGS reads without a reference genome, using the coloured de Bruijn graph implementation of Cortex plus a new depth-first bubble-finding module.

  arabidopsis bubbleparse escherichia col-0 reference-free alignment-based sequence

• The evolution of human influenza A viruses from 1999 to 2006: a complete genome study.

  PMID 18325125 · PMC2311284 · Virology journal · 2008 · 8 claims · 6 setups

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  H3N2 was the prevalent influenza A strain in Denmark from 1999 to 2006, except the 2000–2001 season when H1N1 dominated

  danish representative h3n2 influenza phylogenetic complete haemagglutination

• 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

• Human stool contains a previously unrecognized diversity of novel astroviruses.

  PMID 19814825 · PMC2765957 · Virology journal · 2009 · 8 claims · 8 setups

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  Human stool contains a previously unrecognized diversity of astroviruses beyond the classic 8 serotypes and AstV-MLB1/AstV-VA1

  stool consensus-pcr-positive negative one consensus specific sanger

• Identification of recombinant human papillomavirus type 16 variants.

  PMID 19758676 · PMC2769496 · Virology · 2009 · 8 claims · 5 setups

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  Concurrent infection with 8 HPV16 variants (1 prototype/European, 6 recombinant clones, plus later African-2) was detected in a single woman via PCR-based cloning and sequencing

  cervical pcr-based recombinant-specific direct

• 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

• Four genomic islands that mark post-1995 pandemic Vibrio parahaemolyticus isolates.

  PMID 16672049 · PMC1464126 · BMC genomics · 2006 · 8 claims · 7 setups

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  Seven genomic islands (VPaI-1 to VPaI-7, 10-81 kb) were identified in V. parahaemolyticus RIMD2210633 by aberrant GC content, presence of integrases/transposases, flanking direct repeats, and absence from related Vibrionaceae genomes.

  parahaemolyticus vulnificus clinical ecori-digested bioinformatic comparative pcr

• Appearance of E1: A226V mutant Chikungunya virus in Coastal Karnataka, India during 2008 outbreak.

  PMID 19857273 · PMC2774687 · Virology journal · 2009 · 7 claims · 5 setups

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  E1:A226V mutant CHIKV was present and continued to circulate in the 2008 Coastal Karnataka outbreak

  blood serum mosquito partial rt-pcr igm virus

• Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G.

  PMID 15269786 · PMC479043 · PLoS biology · 2004 · 7 claims · 6 setups

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  APOBEC3G has been under strong, recurrent positive selection throughout primate evolution (~33 million years)

  apobec3g pairwise human-chimpanzee apobec1 pcr phylogenetic sliding

• Genome wide identification of recessive cancer genes by combinatorial mutation analysis.

  PMID 18846217 · PMC2557123 · PloS one · 2008 · 7 claims · 4 setups

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  A combinatorial mutation analysis identified 154 candidate recessive cancer genes (pRecessiveCancer<1.5x10-7, FDR=0.39)

  refseq tp53 tumor 154-gene est paired array

• Detection of BRAF mutations in the tumour and serum of patients enrolled in the AZD6244 (ARRY-142886) advanced melanoma phase II study.

  PMID 19861964 · PMC2778539 · British journal of cancer · 2009 · 7 claims · 8 setups

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  BRAF mutations can be detected in serum cfDNA of advanced melanoma patients using an ARMS allele-specific PCR assay

  serum-derived tumour serum ht29 arms sanger topo

• Integration of bioinformatic tools for the detection of SARS-CoV-2 co-infection cases.

  PMID 41609640 · PMC12856159 · Microbial genomics · 2026 · 8 claims · 8 setups

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  Sample PH-RITM-1395 represents a Delta–Omicron co-infection, confirmed by convergent evidence from Nextclade, bammix, Freyja, VirStrain, AAF analysis and amplicon sorting rather than contamination

  consensus aligned raw bam nextclade nucleotide strain-level

• Overlapping gene mutations of hepatitis B virus in a chronic hepatitis B patient with hepatitis B surface antigen loss during lamivudine therapy.

  PMID 15953865 · PMC2782199 · Journal of Korean medical science · 2005 · 7 claims · 5 setups

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  Serum HBsAg became negative after 36 months of lamivudine therapy while HBeAg and HBV DNA remained positive

  serum hbv serologic hbv pcr

• Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960.

  PMID 18833279 · PMC3682493 · Nature · 2008 · 7 claims · 8 setups

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  Recovered and characterized HIV-1 sequences (DRC60) from a 1960 Bouin's-fixed paraffin-embedded lymph node biopsy from Léopoldville, Belgian Congo

  archival hiv-1-positive cdna concatenated rt-pcr quantitative pcr