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).

• Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye.

  PMID 30010758 · PMC6065499 · GigaScience · 2018 · 8 claims · 6 setups

  Has reproduction · 91

  A draft genome (Ogye_1.1) was assembled using a hybrid de novo method combining high-depth Illumina short reads (376.6X) and low-depth PacBio long reads (9.7X)

  yeonsan ogye_1.1 locus tissues whole-genome genome structural

• Combining comparative genomics with de novo motif discovery to identify human transcription factor DNA-binding motifs.

  PMID 17217514 · PMC1780116 · BMC bioinformatics · 2006 · 6 claims · 4 setups

  Full-text index only

  A novel method combining 8-species comparative genomics with de novo motif discovery identifies human TF DNA-binding motifs overrepresented and conserved in upstream regions of co-regulated genes

  muscle-specific novo comparative

• Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.

  PMID 16925842 · PMC1810557 · Genome biology · 2006 · 8 claims · 4 setups

  Full-text index only

  MARS, an extension of the Twinscan algorithm, uses multiple pairwise informant genomes to predict human alternatively spliced transcripts de novo without expressed sequence information.

  genome tissues novo pairwise rt-pcr

• Using ESTs to improve the accuracy of de novo gene prediction.

  PMID 16817966 · PMC1534067 · BMC bioinformatics · 2006 · 8 claims · 8 setups

  Full-text index only

  TWINSCAN_EST combines EST alignments with TWINSCAN via a trainable 'ESTseq' representation and improves exact gene structure prediction accuracy on the whole C. elegans genome

  elegans genome chromosome novo gene partial

• An Asilomar moment.

  PMID 12372138 · PMC244904 · Genome biology · 2002 · 7 claims · 3 setups

  Full-text index only

  The current push to restrict genomics/pathogen research funding and publication due to bioterrorism fears parallels the 1975 Asilomar Conference response to recombinant DNA risks.

  mousepox chicken poliovirus gene targeted novo

• Pairagon+N-SCAN_EST: a model-based gene annotation pipeline.

  PMID 16925839 · PMC1810554 · Genome biology · 2006 · 7 claims · 5 setups

  Full-text index only

  Pairagon+N-SCAN_EST, using only native alignments, was as accurate as ENSEMBL and ExoGean in the EGASP mRNA/EST evidence assessment

  encode genome cdna-to-genome novo comparative