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).

• HGA: de novo genome assembly method for bacterial genomes using high coverage short sequencing reads.

  PMID 26945881 · PMC4779561 · BMC genomics · 2016 · 8 claims · 7 setups

  Has reproduction · 58

  HGA leads to significant improvement in assembly quality (N50 and corrected N50) for all 7 evaluated GAGE-B bacterial datasets using most of the 8 evaluated assemblers

  bacillus mycobacterium rhodobacter vibrio novo contigs-combining re-assembly

• A genomics-based approach to biodefence preparedness.

  PMID 14708013 · PMC7097618 · Nature reviews. Genetics · 2004 · 7 claims · 8 setups

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  Genome sequence data are now available for essentially all 25-30 principal human bacterial pathogens, including most CDC category A-C bioterror agents

  bacillus brucella neisseria gastric comparative transcriptome two-dimensional

• Heteropolymeric triplex-based genomic assay to detect pathogens or single-nucleotide polymorphisms in human genomic samples.

  PMID 17375191 · PMC1810429 · PloS one · 2007 · 7 claims · 6 setups

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  The Genomic Assay can detect 100 copies of Bacillus globigii genomic dsDNA, including in the presence of human genomic dsDNA background, without PCR amplification

  bacillus drosophila genomic triplex

• Biodefense versus bioterrorism.

  PMID 18771576 · PMC2575524 · Genome biology · 2008 · 5 claims · 4 setups

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  Whole-genome sequencing and comparative genomics of the attack strain were used to trace the anthrax letters to a specific laboratory flask

  bacillus ancestral cultures anthrax whole-genome comparative colony

• Rise of the machines.

  PMID 18670625 · PMC2467494 · PLoS genetics · 2008 · 8 claims · 4 setups

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  New short-read sequencing platforms (Illumina Genome Analyzer, 454 FLX, ABI SOLiD) enable rapid, scalable whole-genome resequencing that was previously restricted to dedicated sequencing centers using Sanger methods.

  bacillus independent subtilis whole-genome read

• The role of genomics in the identification, prediction, and prevention of biological threats.

  PMID 19855827 · PMC2757898 · PLoS biology · 2009 · 8 claims · 5 setups

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  Genomics should be used proactively, not just reactively, to build biopreparedness against biological threats

  bacillus escherichia sars pandemic whole-genome pangenomic low-resolution

• Sequencing of 16S rRNA gene: a rapid tool for identification of Bacillus anthracis.

  PMID 12396926 · PMC2730316 · Emerging infectious diseases · 2002 · 7 claims · 4 setups

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  All 86 B. anthracis isolates tested share an identical 16S rRNA gene sequence, designated 16S type 6

  bacillus clinical additional 16s nested comparative

• An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data.

  PMID 17984082 · PMC2239001 · Nucleic acids research · 2008 · 8 claims · 7 setups

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  The Biodefense Proteomics Resource Center (RC) is a public cyberinfrastructure that stores, integrates, and disseminates experimental data from seven Proteomics Research Centers (PRCs) on biodefense pathogens and host interactions

  brucella toxoplasma bacillus homo label-free mass genomic

• Differential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure.

  PMID 35869080 · PMC9307511 · Nature communications · 2022 · 7 claims · 4 setups

  Has reproduction · 80

  DiffScan is a computational framework combining a Normalization module and a Scan module to identify SVRs at nucleotide resolution from SP data.

  transcripts platforms bacillus multi-subcellular simulated negative benchmark

• Evaluating native-like structures of RNA-protein complexes through the deep learning method.

  PMID 36828844 · PMC9958188 · Nature communications · 2023 · 8 claims · 7 setups

  Has reproduction · 67

  DRPScore identifies native-like RNA-protein structures with higher success rates than ITScore-PR, DARS-RNP, and 3dRPC across bound and unbound testing sets.

  bound-bound unbound-bound unbound-unbound bacillus structure interface secondary

• ORFer--retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files.

  PMID 12493080 · PMC139979 · BMC bioinformatics · 2002 · 6 claims · 6 setups

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  ORFer retrieves protein and nucleic acid sequences and annotations from NCBI GenBank using the XML sequence format

  sequences parsed bacillus anopheles large-scale sequence orf

• Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets.

  PMID 19779614 · PMC2745575 · PloS one · 2009 · 8 claims · 8 setups

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  A protein-centric data integration approach (Master Protein Directory) enables integration and mining of heterogeneous pathogen-host omics data across multiple research centers

  macrophage hela vaccinia bacillus gene protein-protein comparative

• Microbial genomics: from sequence to function.

  PMID 10998380 · PMC2627950 · Emerging infectious diseases · 2000 · 8 claims · 4 setups

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  Whole-genome shotgun sequencing (sequencing and assembly of random genome fragments), first demonstrated with Haemophilus influenzae in 1995, is now the method of choice for sequencing most genomes, including the human genome.

  yeast bacteria microbial high-throughput microarray ribosomal

• Microbial metagenomics.

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

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  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

• Defining the proteome.

  PMID 16356278 · PMC1414090 · Genome biology · 2005 · 8 claims · 8 setups

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  Integration of multi-omics data is an important step toward a systems-biology approach to the proteome

  brain chicken bacillus yeast proteome proteomics two-dimensional

• Diet and DNA.

  PMID 15174456 · PMC1315985 · Environmental health perspectives · 2004 · 8 claims · 8 setups

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  The tombusvirus CIRV p19 protein selectively binds short (21-22 nt) silencing siRNAs, using tryptophan residues Trp39 and Trp42 as molecular 'calipers' that stack with the ends of the siRNA duplex

  cirv blood rice smokers x-ray site-directed mass

• Versatile and open software for comparing large genomes.

  PMID 14759262 · PMC395750 · Genome biology · 2004 · 8 claims · 8 setups

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  MUMmer 3.0 efficiently handles comparisons of large eukaryotic genomes at varying evolutionary distances

  escherichia chromosome drosophila anopheles suffix-tree whole-genome protein-level

• Harnessing the HGP of public health.

  PMID 15176090 · PMC1241998 · Environmental health perspectives · 2004 · 8 claims · 7 setups

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  The tombusvirus p19 protein selectively recognizes and sequesters short (21-22 nucleotide) silencing siRNAs, discriminating them from longer siRNAs by measuring siRNA length via tryptophan-mediated end-stacking interactions

  carnation cirv blood rice x-ray site-directed mass

• International sequencing consortium.

  PMID 15174459 · PMC1315987 · Environmental health perspectives · 2004 · 8 claims · 6 setups

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  The p19 viral silencing-suppressor protein selectively recognizes short (21-22 nt) silencing siRNAs by measuring duplex length, using tryptophan residues (Trp39, Trp42) as molecular calipers that stack against the siRNA end base pairs.

  cirv blood sampled rice x-ray site-directed mass