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).

• TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes.

  PMID 34197621 · PMC8464036 · Nucleic acids research · 2021 · 8 claims · 8 setups

  Has reproduction · 60

  TRAPID 2.0 is a web application performing global characterization of de novo transcriptomes via structural, functional, and taxonomic annotation in an initial processing phase, followed by an exploratory phase of downstream analyses.

  mmetsp query putative ciliate taxonomic similarity non-coding

• Diversity of the parB and repA genes of the Burkholderia cepacia complex and their utility for rapid identification of Burkholderia cenocepacia.

  PMID 18328098 · PMC2324101 · BMC microbiology · 2008 · 8 claims · 7 setups

  Full-text index only

  repA sequences show distinct clustering of B. cenocepacia relative to other Bcc species, enabling design of a species-specific multiplex PCR

  burkholderia six bcc panel pcr phylogenetic multilocus

• Large-Scale Phylogenomics of the Lactobacillus casei Group Highlights Taxonomic Inconsistencies and Reveals Novel Clade-Associated Features.

  PMID 28845461 · PMC5566788 · mSystems · 2017 · 8 claims · 8 setups

  Has reproduction · 94

  The L. casei group resolves into three distinct clades (A, B, C) supported by phylogeny, GC content, ANI, and TETRA, and many strains are misclassified relative to their nearest type strain.

  casei orthogroups unclassified selected whole-genome comparative pairwise

• How can developing countries harness biotechnology to improve health?

  PMID 18053180 · PMC2238767 · BMC public health · 2007 · 8 claims · 2 setups

  Full-text index only

  Five Executive Courses on Genomics and Public Health Policy were held in five developing-world regions (Africa, India, Eastern Mediterranean, Latin America/Caribbean, Western Pacific/Southeast Asia) to generate recommendations on harnessing biotechnology for health.

  developing-world course structured participant

• RotaC: a web-based tool for the complete genome classification of group A rotaviruses.

  PMID 19930627 · PMC2785824 · BMC microbiology · 2009 · 7 claims · 4 setups

  Full-text index only

  RotaC is a freely available web-based tool for complete genome classification of group A rotaviruses across all 11 gene segments.

  group rotavirus neighbor-joining profile pairwise

• Species-Wide Phylogenomics of the Staphylococcus aureus Agr Operon Revealed Convergent Evolution of Frameshift Mutations.

  PMID 35044202 · PMC8768832 · Microbiology spectrum · 2022 · 8 claims · 7 setups

  Has reproduction · 79

  AgrVATE, a novel kmer-based BLASTn and in silico PCR/Snippy pipeline, enables fast, standardized agr group typing and frameshift/null mutation detection from genome assemblies

  aureus complete extracted agr kmer-based sheep mash

• ABO exon and intron analysis in individuals with the AweakB phenotype reveals a novel O1v-A2 hybrid allele that causes four missense mutations in the A transferase.

  PMID 14617382 · PMC305365 · BMC genetics · 2003 · 8 claims · 7 setups

  Full-text index only

  A novel O1v-A2 hybrid allele, containing four missense mutations, causes the A weak B phenotype in five individuals of African descent

  genomic red computational abo sequencing blood

• Microbial metagenomics.

  PMID 16207365 · PMC1257460 · Genome biology · 2005 · 8 claims · 8 setups

  Full-text index only

  Metagenomic sequencing of the human GI tract reveals microbial community composition (e.g., Actinobacteria and Archaea prominence) differing from prior culture-based estimates dominated by Firmicutes and Bacteroides

  gastrointestinal acid ocean group metagenomic shotgun comparative

• Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling.

  PMID 19901961 · PMC2820592 · Oncogene · 2010 · 8 claims · 6 setups

  Full-text index only

  Unsupervised gene expression clustering identifies 3 reproducible molecular subtypes of LMS (Group I/muscle-enriched, Group II, Group III)

  lms independent soft gene array immunohistochemistry

• Opportunities and challenges in synthetic oligosaccharide and glycoconjugate research.

  PMID 20161474 · PMC2794050 · Nature chemistry · 2009 · 8 claims · 7 setups

  Full-text index only

  A parallel combinatorial one-pot multi-step protecting-group procedure (Lewis acid catalyzed, up to seven steps) can transform tetra-O-TMS glucopyranosides into differentially protected monosaccharide building blocks without intermittent work-up/purification

  library database oligovalent b-cells glycan bioinformatics one-pot

• Global genetic diversity of human metapneumovirus fusion gene.

  PMID 15207075 · PMC3323143 · Emerging infectious diseases · 2004 · 8 claims · 6 setups

  Full-text index only

  Phylogenetic analysis of the HMPV F gene identifies two main groups (A and B, 93%-96% amino acid identity) further divided into four subgroups (A1, A2, B1, B2)

  hmpv llc-mk2 clinical rt-pcr sequence phylogenetic

• FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq.

  PMID 23768108 · PMC3691734 · BMC bioinformatics · 2013 · 8 claims · 8 setups

  Has reproduction · 65

  FusionQ is a novel tool that detects gene fusions, constructs chimerical transcript structures, and estimates their abundances from paired-end RNA-Seq data.

  simulated four rna-seq randomly simulated paired-end read-mappability

• Phylogeography of mtDNA haplogroup R7 in the Indian peninsula.

  PMID 18680585 · PMC2529308 · BMC evolutionary biology · 2008 · 8 claims · 7 setups

  Full-text index only

  R7a1, a recently derived sub-branch of haplogroup R7, is particularly frequent among Munda-speaking tribal groups

  mtdnas haplogroup genetic geographic complete hvs-i reduced-median

• An accurate method for identifying recent recombinants from unaligned sequences.

  PMID 35025988 · PMC8963311 · Bioinformatics (Oxford, England) · 2022 · 8 claims · 4 setups

  Has reproduction · 84

  A novel algorithm combining the JHMM (Zilversmit et al. 2013) mosaic representation with a distance-based triple comparison can identify recombinant sequences and their parents from unaligned, gene-length sequences without a reference panel.

  simulated dblα coalescent comparative recombinant

• Paroxysmal exercise-induced dyskinesia and epilepsy is due to mutations in SLC2A1, encoding the glucose transporter GLUT1.

  PMID 18577546 · PMC2442425 · Brain : a journal of neurology · 2008 · 8 claims · 8 setups

  Full-text index only

  Co-occurring PED and epilepsy can be caused by autosomal dominant heterozygous mutations in SLC2A1, encoding the glucose transporter GLUT1

  family genomic xenopus patients genome-wide pcr glucose

• Reconstructing Indian population history.

  PMID 19779445 · PMC2842210 · Nature · 2009 · 8 claims · 8 setups

  Full-text index only

  Most Indian populations descend from a mixture of two ancient, genetically divergent populations: ANI (close to Middle Easterners, Central Asians, Europeans) and ASI (as distinct from ANI and East Asians as those are from each other).

  indian pairs gujarati genome-wide principal fst-based

• MtSNPscore: a combined evidence approach for assessing cumulative impact of mitochondrial variations in disease.

  PMID 19758471 · PMC2745589 · BMC bioinformatics · 2009 · 8 claims · 5 setups

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  MtSNPscore, a weighted scoring pipeline combining literature evidence, in silico predictions, and case/control frequency, can prioritize likely pathogenic mtDNA variations

  sporadic mitochondrial reported ataxia mitochondrial functional compensatory

• Human methylome variation across Infinium 450K data on the Gene Expression Omnibus.

  PMID 33937763 · PMC8061458 · NAR genomics and bioinformatics · 2021 · 8 claims · 6 setups

  Has reproduction · 88

  Approximately two-thirds of compiled HM450K samples are from blood, one-quarter from brain, and roughly one-third from cancer patients.

  hm450k seven annotated illumina beadarray model-based