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).

• Non-EST based prediction of exon skipping and intron retention events using Pfam information.

  PMID 16204458 · PMC1243800 · Nucleic acids research · 2005 · 7 claims · 5 setups

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  A novel ab initio method predicts exon skipping and intron retention events using only Pfam domain annotation, via a Viterbi-like dynamic programming algorithm applied to the Pfam alignment.

  refseq dbest genome pfam initio est comparative

• EGASP: the human ENCODE Genome Annotation Assessment Project.

  PMID 16925836 · PMC1810551 · Genome biology · 2006 · 8 claims · 6 setups

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  Best-performing computational gene prediction methods correctly predict at least one transcript for close to 70% of annotated genes in the ENCODE regions.

  encode computational manual rt-pcr

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

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

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  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

• Screening of dystrophin gene deletions in Egyptian patients with DMD/BMD muscular dystrophies.

  PMID 11381192 · PMC3851408 · Disease markers · 2000 · 6 claims · 5 setups

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  Multiplex PCR screening of 18 dystrophin exons detected deletions in 55% of 100 Egyptian DMD/BMD families

  genomic egyptian same peripheral multiplex clinical electromyography

• RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.

  PMID 22199257 · PMC3315322 · Nucleic acids research · 2012 · 8 claims · 7 setups

  Has reproduction · 86

  RNASEQR is a new RNA-seq mapper/aligner that combines a BWT-based (Bowtie) transcriptomic/genomic alignment with hash-based BLAT local alignment in three sequential steps: transcriptome mapping, novel exon detection, and anchor-and-align novel splice junction identification.

  ccds glioblastoma experimental simulated simulated bulk quality

• Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity.

  PMID 16351747 · PMC1866387 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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  Systematic in silico search identified 5 novel human kinase genes (on chromosomes 1, 11, 13, 15, 16) and 1 pseudogene (chromosome X) absent from KinBase

  genome genomic kinase psi-blast comparative genscan

• Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.

  PMID 16536879 · PMC1479377 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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  ENACE, a cross-species EST-to-genome comparison algorithm, can identify novel cassette-on exons and retained introns for EST-scanty species and distinguish conserved vs lineage-specific exons

  presumably orthologous enace genes cross-species rt-pcr-sequencing nonsynonymous-to-synonymous

• Characterizing natural variation using next-generation sequencing technologies.

  PMID 19801172 · PMC3994700 · Trends in genetics : TIG · 2009 · 8 claims · 8 setups

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  Next-generation sequencing enables complete, genome-wide surveys of genetic variation at unprecedented resolution, overcoming limitations of genotyping panels and microarrays.

  pichia individuals saccharomyces individual whole-genome partial comparative

• Target identification for repurposed drugs active against SARS-CoV-2 via high-throughput inverse docking.

  PMID 34825285 · PMC8616721 · Journal of computer-aided molecular design · 2022 · 8 claims · 6 setups

  Has reproduction · 63

  Combining Vinardo, Ledock, and Korp-PL scoring functions (via averaged Z-scores) improves correct target identification over any single scoring function.

  curated repurposed glycosylated interior inverse molecular exploratory

• RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.

  PMID 23145190 · PMC3493385 · PLoS neglected tropical diseases · 2012 · 8 claims · 8 setups

  Has reproduction · 66

  S. stercoralis possesses homologs of nearly all C. elegans dauer genes, but with significant differences in protein structure, developmental regulation, and gene family expansion.

  strongyloides stercoralis mongolian adapter-ligated polyadenylated novo comparative

• Genome Network and FANTOM3: assessing the complexity of the transcriptome.

  PMID 16683037 · PMC1449904 · PLoS genetics · 2006 · 8 claims · 7 setups

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  63% of the genome is transcribed from at least one strand, versus the earlier belief that only 2% is transcribed into protein-coding mRNA

  fantom3 genome large-scale mammalian cage full-length genome

• Twin peaks: the draft human genome sequence.

  PMID 11276423 · PMC138909 · Genome biology · 2001 · 8 claims · 8 setups

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  The predicted number of human genes (~26,000-40,000) is far lower than the widely assumed ~100,000, though downstream RNA/protein complexity can still generate substantial biological complexity.

  genome genomic genes yeast whole-genome bac computational