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).

• RNA modifications detection by comparative Nanopore direct RNA sequencing.

  PMID 34893601 · PMC8664944 · Nature communications · 2021 · 7 claims · 5 setups

  Has reproduction · 50

  Nanocompore is a model-free comparative method that uses a 2-component Gaussian mixture model (GMM) and univariate statistical tests on signal intensity/dwell time to detect RNA modifications in Nanopore direct RNA sequencing data without needing a training set

  simulated synthetic escherichia saccharomyces nanopore computational

• Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing.

  PMID 34244540 · PMC8270970 · Scientific reports · 2021 · 8 claims · 5 setups

  Has reproduction · 50

  BoHV-1 infection causes substantial up- and down-regulation of host gene networks, including antiviral response and viral transcription/translation-associated genes

  bovine direct amplified synthetic

• Identification of herpesvirus transcripts from genomic regions around the replication origins.

  PMID 37773348 · PMC10541914 · Scientific reports · 2023 · 8 claims · 8 setups

  Has reproduction · 59

  Herpesviruses display distinct patterns of transcriptional overlaps near or at the replication origins (Oris)

  nine same vzv prv direct cage-seq qrt-pcr

• Non-cross-linking gold nanoparticle aggregation as a detection method for single-base substitutions.

  PMID 15640441 · PMC546178 · Nucleic acids research · 2005 · 8 claims · 7 setups

  Full-text index only

  NCL aggregation of DNA-modified gold nanoparticles shows extraordinary selectivity against terminal mismatches at the free ends of surface-bound duplexes

  probe-modified probe-gnp synthetic four uv-vis ssdna pcr

• Rapid identification of PAX2/5/8 direct downstream targets in the otic vesicle by combinatorial use of bioinformatics tools.

  PMID 18828907 · PMC2760872 · Genome biology · 2008 · 8 claims · 8 setups

  Full-text index only

  A combinatorial bioinformatics pipeline (evolutionary double filtering comparative genomics, GXD/ZFIN database queries, MEDLINE text mining) can rapidly and specifically identify PAX2/5/8 direct downstream targets in the otic vesicle

  genome candidate gxd medline evolutionary gene expression

• Population diversity and antibody selective pressure to Plasmodium falciparum MSP1 block2 locus in an African malaria-endemic setting.

  PMID 19832989 · PMC2770483 · BMC microbiology · 2009 · 8 claims · 5 setups

  Full-text index only

  The relative proportion of the three Pfmsp1 block2 allelic families (K1, Mad20, RO33) in Dielmo showed no significant temporal fluctuation over a 10-year period (1990-99).

  plasmodium dielmo semi-nested direct cross-sectional

• Enhancer RNAs stimulate Pol II pause release by harnessing multivalent interactions to NELF.

  PMID 35508485 · PMC9068813 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 55

  eRNAs longer than 200 nucleotides that contain unpaired guanosines make multiple, allosteric contacts with NELF subunits -A and -E to trigger efficient NELF release

  cortical transcribed reconstituted erna-bound gro-seq exo-seq shape-map

• Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions.

  PMID 17880677 · PMC2375035 · Genome biology · 2007 · 7 claims · 8 setups

  Full-text index only

  Combining pairs of omics evidence types into two-dimensional 'evidence landscapes' allows regions to be identified that specifically and purely predict either physical or metabolic protein interactions

  saccharomyces correlated chip-chip gene