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).

• Assessing individual differences in genome-wide gene expression in human whole blood: reliability over four hours and stability over 10 months.

  PMID 19653838 · PMC3819565 · Twin research and human genetics : the official journal of the International Society for Twin Studies · 2009 · 8 claims · 5 setups

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  A subset of probesets (3,414) shows 4-hour test-retest reliability exceeding r=0.70 for detecting individual differences in gene expression.

  blood edta reliably genome-wide twin sub-type

• AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome.

  PMID 16925833 · PMC1810548 · Genome biology · 2006 · 8 claims · 5 setups

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  AUGUSTUS predicted significantly more genes correctly than any other ab initio program in EGASP

  genome human-mouse genes initio comparative extrinsic

• ECgene: genome annotation for alternative splicing.

  PMID 15608289 · PMC540072 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  ECgene combines genome-based EST clustering with a graph-theoretic transcript assembly procedure to predict gene models including alternative splicing events.

  brca2 rgs17 organs cdna genomic genome transcript

• ChimerDB 2.0--a knowledgebase for fusion genes updated.

  PMID 19906715 · PMC2808913 · Nucleic acids research · 2010 · 8 claims · 4 setups

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  ChimerDB 2.0 is an updated knowledgebase integrating fusion transcripts from GenBank transcriptome analysis with Sanger CGP, OMIM, PubMed, and Mitelman's database data.

  genbank sra pubmed transcript-to-genome ngs literature

• Integrative analysis of the human cis-antisense gene pairs, miRNAs and their transcription regulation patterns.

  PMID 19906709 · PMC2811022 · Nucleic acids research · 2010 · 8 claims · 5 setups

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  A genome-wide catalog of up to ~9000 overlapping antisense loci (23,782 non-redundant SAT pairs, clustered into 8894) was compiled and stored in the USAGP database

  genome affymetrix antisense mirna computational microarray sage

• A Deeper Insight into Evolutionary Patterns and Phylogenetic History of ASFV Epidemics in Sardinia (Italy) through Extensive Genomic Sequencing.

  PMID 34696424 · PMC8539718 · Viruses · 2021 · 7 claims · 8 setups

  Has reproduction · 76

  58 new whole genomes of Sardinian ASFV isolates were sequenced, the largest ASFV whole-genome sequencing effort to date

  asfv b602l porcine sardinian whole-genome sanger haemoadsorption

• Coverage of whole proteome by structural genomics observed through protein homology modeling database.

  PMID 17146617 · PMC1769342 · Journal of structural and functional genomics · 2006 · 8 claims · 7 setups

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  FAMSBASE, a homology-modeling database of whole-genome ORFs, currently covers about 50% of predicted ORFs (368,724 of 734,193) across 276 genomes with modeled 3D structures.

  orfs predicted modeled representative homology transmembrane intrinsic

• BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.

  PMID 17202167 · PMC1899097 · Nucleic acids research · 2007 · 7 claims · 6 setups

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  BRENDA is the largest publicly available enzyme information system worldwide, manually curated from primary literature and covering all identified enzymes regardless of source.

  pubmed randomly enzyme full text-mining manual transmembrane

• CRISPRbuilder-TB: "CRISPR-builder for tuberculosis". Exhaustive reconstruction of the CRISPR locus in mycobacterium tuberculosis complex using SRA.

  PMID 33667225 · PMC7968741 · PLoS computational biology · 2021 · 8 claims · 7 setups

  Has reproduction · 97

  CRISPRbuilder-TB is a new pipeline that reconstructs MTC CRISPR-Cas loci directly from short SRA reads without requiring genome assembly

  simulated wgs reference same novo blast-based k-mer

• Coffee, caffeine-related genes, and Parkinson's disease: a case-control study.

  PMID 18759349 · PMC4554698 · Movement disorders : official journal of the Movement Disorder Society · 2008 · 8 claims · 5 setups

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  Coffee drinking (ever/never or by cups/day) was not associated with PD susceptibility

  blood-derived subjects matched genomic snp structured conditional

• Tri-nucleotide threading for parallel amplification of minute amounts of genomic DNA.

  PMID 16582098 · PMC1421508 · Nucleic acids research · 2006 · 6 claims · 5 setups

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  TnT enables parallel amplification of 75 SNPs from sub-nanogram amounts of genomic DNA

  genomic dbsnp tnt duplex bioinformatic

• A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

  PMID 19923232 · PMC2817484 · Nucleic acids research · 2010 · 8 claims · 7 setups

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  A Perl-based pipeline that BLASTs/BLATs Illumina probe sequences against genomes and transcript databases (RefSeq, UCSC Known Genes, UniGene/GenBank, Ensembl) can classify probes by quality grade (Perfect/Good/Bad/No match) and is applicable across 8 BeadArray platforms and other array types

  maqc hepatocytes japanese illeum microarray dasl sequence