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).
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PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes.
PMID 17202160 · PMC1899096 · Nucleic acids research · 2007 · 7 claims · 5 setups
PolyA_DB 2 catalogs poly(A) sites for genes in human, mouse, rat, chicken and zebrafish, identified by aligning cDNA/ESTs with genome sequences
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Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.
PMID 19906316 · PMC2784480 · BMC genomics · 2009 · 8 claims · 7 setups
Intronic single-block ESTs with poly(A/T) tails reveal previously unidentified novel transcript variants missed by existing databases.
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Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3'-end of genes.
PMID 18757892 · PMC2553571 · Nucleic acids research · 2008 · 8 claims · 6 setups
3'-most (L type) poly(A) sites are more conserved than upstream F/M type sites, while intronic (C/H type) sites are the least conserved
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Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species.
PMID 16849434 · PMC1524920 · Nucleic acids research · 2006 · 8 claims · 7 setups
A fast integrative in silico pipeline combining UniGene mRNA/EST mapping to GoldenPath genomes with CDS, poly(A) signal, poly(A) tail and splicing site evidence can reliably identify cis-NATs genome-wide across multiple species
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Association of poly-purine/poly-pyrimidine sequences with meiotic recombination hot spots.
PMID 16846522 · PMC1543642 · BMC genomics · 2006 · 7 claims · 6 setups
PPT frequency is significantly elevated in yeast meiotic recombination hot spots compared with cold spots
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Has reproduction · 66
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
S. stercoralis possesses homologs of nearly all C. elegans dauer genes, but with significant differences in protein structure, developmental regulation, and gene family expansion.
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A macaque's-eye view of human insertions and deletions: differences in mechanisms.
PMID 17941704 · PMC1976337 · PLoS computational biology · 2007 · 7 claims · 4 setups
Insertion and deletion rates are differentially associated with replication- versus recombination-related genomic features, indicating the two mutation types are driven in part by distinct mechanisms
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Has reproduction · 77
Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling.
PMID 24888378 · PMC4070569 · BMC genomics · 2014 · 8 claims · 8 setups
Ribo-Zero-Seq removes rRNA with efficiency comparable to poly(A)-based mRNA-Seq in both FF and FFPE RNA, whereas DSN-Seq leaves significantly more rRNA and shows greater variation.
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Has reproduction · 67
A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome.
PMID 25009556 · PMC4070175 · Frontiers in genetics · 2014 · 8 claims · 8 setups
Multiple k-mer (MK) assemblies are more complete than single k-mer (SK) assemblies, showing higher reads-mapped-back-to-transcripts (RMBT) and higher CEGMA complete-gene percentages for all three tools.
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Endonuclease-independent insertion provides an alternative pathway for L1 retrotransposition in the human genome.
PMID 17517773 · PMC1920257 · Nucleic acids research · 2007 · 8 claims · 5 setups
An endonuclease-independent pathway (NCLI) for L1 insertion has been active in recent human genome evolution
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Has reproduction · 75
Roar: detecting alternative polyadenylation with standard mRNA sequencing libraries.
PMID 27756200 · PMC5069797 · BMC bioinformatics · 2016 · 8 claims · 5 setups
Roar, a method using PRE/POST read counts around annotated APA sites to compute an m/M ratio and a ratio-of-ratios (roar) statistic, detects differential 3'UTR shortening/lengthening from standard RNA-seq libraries.
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Has reproduction · 86
RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.
PMID 22199257 · PMC3315322 · Nucleic acids research · 2012 · 8 claims · 7 setups
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.
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Retropseudogenes derived from the human Ro/SS-A autoantigen-associated hY RNAs.
PMID 15817567 · PMC1074747 · Nucleic acids research · 2005 · 8 claims · 8 setups
966 pseudogenes derived from the four human Y (hY) RNAs were characterized in the human genome
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Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes.
PMID 15809229 · PMC1074396 · Nucleic acids research · 2005 · 8 claims · 6 setups
Comparative gene finding (SGP2) between human and chicken, followed by RT-PCR verification, adds at most ~0.2% new genes to the multi-exonic human gene catalog
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Identifying related L1 retrotransposons by analyzing 3' transduced sequences.
PMID 12734010 · PMC156586 · Genome biology · 2003 · 8 claims · 6 setups
L1 elements with transduction-derived 3' sequence (L1-TDs) can be computationally identified using RepeatMasker/TSDfinder and grouped into families sharing a common progenitor via BLAST comparison of downstream sequences.