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).

• Prediction of candidate primary immunodeficiency disease genes using a support vector machine learning approach.

  PMID 19801557 · PMC2780952 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2009 · 6 claims · 3 setups

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  An SVM trained on 69 binary features of known PID genes can accurately classify PID vs non-PID genes and predict novel candidate PID genes

  genome training svm support leave-one-out sensitivity

• "Reverse ecology" and the power of population genomics.

  PMID 18752601 · PMC2626434 · Evolution; international journal of organic evolution · 2008 · 8 claims · 7 setups

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  Population genomic data can be used to rapidly identify genes targeted by adaptive natural selection, an approach termed 'reverse ecology'.

  cerevisiae melanogaster sapiens simulans likelihood mcdonald-kreitman mkprf

• The UCSC Genome Browser Database: update 2009.

  PMID 18996895 · PMC2686463 · Nucleic acids research · 2009 · 8 claims · 6 setups

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  The UCSC Genome Browser Database (GBD) is a publicly available, integrated collection of genome assembly sequences and annotations across many organisms, including extensive comparative-genomic resources.

  chimp vertebrate mrnas genome genome-wide multiz blat

• A genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genome stability.

  PMID 19647519 · PMC2772893 · Molecular cell · 2009 · 8 claims · 6 setups

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  A genome-wide siRNA screen in HeLa cells using γH2AX as a readout identifies genes whose knockdown elevates DNA damage/genome instability

  hela candidate screen genome-wide propidium sirna

• Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta.

  PMID 18294402 · PMC2287170 · BMC genomics · 2008 · 8 claims · 6 setups

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  Constructed full-length-enriched cDNA libraries and determined 85,721 EST sequences and 9407 full-insert sequences from cynomolgus macaque brain (7 regions), testis, and liver

  cynomolgus 3-year-old macaque est full-insert oligonucleotide

• Comparison between short-term stress and long-term adaptive responses reveal common paths to molecular adaptation.

  PMID 35243257 · PMC8873613 · iScience · 2022 · 8 claims · 7 setups

  Has reproduction · 59

  Short-term stress and long-term adaptations share common metabolic pathways

  great embryonic gef mapk1 bulk gene transcription

• An "omics" approach to uropathogenic Escherichia coli vaccinology.

  PMID 19758805 · PMC2770165 · Trends in microbiology · 2009 · 8 claims · 8 setups

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  An 'omics'-based screening strategy integrating genomic, proteomic, and metabolomic data can identify PASivE UPEC proteins as vaccine candidates

  upec vaccination comparative two-dimensional

• In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age.

  PMID 32898168 · PMC7478592 · PLoS biology · 2020 · 8 claims · 6 setups

  Has reproduction · 89

  SARS-CoV-2 infection induces a strong interferon-mediated antiviral response in the nasopharynx, up-regulating antiviral factors (OAS1-3, IFIT1-3, MX2, RSAD2, HERC5) and Th1 chemokines CXCL9/10/11, while down-regulating ribosomal protein transcripts.

  nasopharyngeal airway patient-matched swab shotgun bulk rt-pcr

• A comparative study of techniques for differential expression analysis on RNA-Seq data.

  PMID 25119138 · PMC4132098 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 58

  edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives.

  brain neurospheres lymphoblastoid simulation single-end paired-end rna-seq

• A functional map of NFkappaB signaling identifies novel modulators and multiple system controls.

  PMID 17553156 · PMC2394752 · Genome biology · 2007 · 8 claims · 6 setups

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  154 positive and 88 negative modulators of NFκB signaling were identified from genomic screens

  hek-293t tissues gain-of-function loss-of-function glucocorticoid

• Prioritization of candidate cancer genes--an aid to oncogenomic studies.

  PMID 18710882 · PMC2566894 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  Computational classifiers using combinations of protein conservation, gene structure, protein domains, protein interactions, and regulatory data can distinguish known cancer genes (CD/CR) from unlabelled human genes

  genes cancer interpro interactome averaged cross-validation domain

• Human PAML browser: a database of positive selection on human genes using phylogenetic methods.

  PMID 17962310 · PMC2238824 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  The Human PAML Browser is a web-accessible database of codeml-based positive selection test results for 13,721 human genes with orthologs in UCSC multispecies alignments.

  same genes orangutan codeml gene sequence

• Evidence for positive selection in putative virulence factors within the Paracoccidioides brasiliensis species complex.

  PMID 18820744 · PMC2553485 · PLoS neglected tropical diseases · 2008 · 8 claims · 8 setups

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  Positive selection has played an important role in the molecular evolution of putative virulence factors of P. brasiliensis

  brasiliensis gp43 ratio codon-based mutational

• Commonality of functional annotation: a method for prioritization of candidate genes from genome-wide linkage studies.

  PMID 18263617 · PMC2275105 · Nucleic acids research · 2008 · 8 claims · 7 setups

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  Genes correlated with a common complex trait are more likely to share GO functional annotations than genes not correlated with that trait

  genes candidate simulated alzheimer's genome-wide term null-hypothesis

• POCUS: mining genomic sequence annotation to predict disease genes.

  PMID 14611661 · PMC329128 · Genome biology · 2003 · 8 claims · 6 setups

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  Genes predisposing to the same disease tend to share functional annotation IDs (GO/InterPro) more than expected by chance

  omim genome disease comparative pocus expression-id

• Microarray analysis: genome-scale hypothesis scanning.

  PMID 14551912 · PMC212694 · PLoS biology · 2003 · 8 claims · 5 setups

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  Microarrays can be used to both test and generate hypotheses, not merely to fish for candidate genes.

  drosophila yeast diffuse breast microarray integrated gene

• SNPdetector: a software tool for sensitive and accurate SNP detection.

  PMID 16261194 · PMC1274293 · PLoS computational biology · 2005 · 7 claims · 7 setups

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  SNPdetector, which models human visual inspection of sequencing traces, achieves low false positive and false negative rates in automated SNP and mutation detection

  inbred unrelated zebra same pcr manual comparative

• A genome-wide survey demonstrates widespread non-linear mRNA in expressed sequences from multiple species.

  PMID 16237125 · PMC1258171 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  A genome-wide computational survey identifies 245 genes in mammals (264 across six species) that produce RREO events in expressed sequences

  expressed representative random genes computational orf statistical

• Speeding disease gene discovery by sequence based candidate prioritization.

  PMID 15766383 · PMC1274252 · BMC bioinformatics · 2005 · 7 claims · 8 setups

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  Disease genes (OMIM) differ significantly from non-disease genes in sequence-based features including gene/cDNA/protein size, exon number, homolog conservation, secretion signal, 3' UTR length, CpG islands, and distance to nearest gene.

  ensembl training same hgmd comparative machine tenfold

• Adaptive history of single copy genes highly expressed in the term human placenta.

  PMID 18848617 · PMC2759754 · Genomics · 2009 · 8 claims · 6 setups

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  222 single copy eutherian genes are highly expressed (>=3x median) in the term human placenta

  term single same lists microarray comparative site