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).

• SNAP predicts effect of mutations on protein function.

  PMID 18757876 · PMC2562009 · Bioinformatics (Oxford, England) · 2008 · 8 claims · 3 setups

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  SNAP is a publicly available web-server implementation predicting functional effects (neutral/non-neutral) of single amino acid substitutions.

  mutant insulin neural alanine mutation

• Application of genomics to toxicology research.

  PMID 12634120 · PMC1241273 · Environmental health perspectives · 2002 · 8 claims · 3 setups

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  Toxic chemical exposures alter gene expression, producing a diagnostic transcriptional 'fingerprint' that can be matched against known toxicants to classify untested chemicals' toxic potential.

  yeast rodents rodent microarray proposed cross-species

• Helicobacter pylori: after the genomes, back to biology.

  PMID 12668641 · PMC2193897 · The Journal of experimental medicine · 2003 · 8 claims · 5 setups

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  STM screening of 960 H. pylori mutants in gerbils identifies genes required for in vivo colonization

  helicobacter diffuse signature-tagged genome yeast

• SNAP: predict effect of non-synonymous polymorphisms on function.

  PMID 17526529 · PMC1920242 · Nucleic acids research · 2007 · 7 claims · 8 setups

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  SNAP, a neural network-based method using sequence-derived information, predicts whether a non-synonymous SNP is neutral or non-neutral for protein function

  combined escherichia bacteriophage hiv-1 neural benchmark comparative

• Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning.

  PMID 19756158 · PMC2742196 · PLoS computational biology · 2009 · 8 claims · 4 setups

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  MIP active learning is a novel active learning method that preferentially seeks informative Positive (functionally active) examples rather than only maximizing classifier accuracy.

  engineered p53 computational yeast-based regional homology

• The protein-phosphatome of the human malaria parasite Plasmodium falciparum.

  PMID 18793411 · PMC2559854 · BMC genomics · 2008 · 8 claims · 8 setups

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  P. falciparum possesses 27 putative protein phosphatase sequences across the four major PP families (PPP, PPM, PTP, NIF), plus 7 additional sequences predicted to dephosphorylate non-protein substrates, totaling 34.

  sapiens ppp-domain metallophosphatase pf14_0142 hmm sequence neighbour-net

• The Li2 mutation results in reduced subgenome expression bias in elongating fibers of allotetraploid cotton (Gossypium hirsutum L.).

  PMID 24598808 · PMC3944810 · PloS one · 2014 · 8 claims · 7 setups

  Has reproduction · 58

  The Li2 mutation significantly reduces subgenome (homeolog) expression bias in the elongating fiber transcriptome.

  developing rna-seq expressed subgenome-biased paired-end rna-seq rt-qpcr

• Multiple K-ras mutations in hyperplasia and carcinoma in cases of human pancreatic carcinoma.

  PMID 10543256 · PMC5926143 · Japanese journal of cancer research : Gann · 1999 · 7 claims · 6 setups

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  K-ras codon 12 mutations are present in the majority of solid-type (85%) and ductectatic-type (73%) pancreatic carcinomas.

  pancreatic mucous microdissected extracted k-ras histopathological microdissection

• Crunching the bio-numbers.

  PMID 14664241 · PMC1316909 · Environmental health perspectives · 2003 · 8 claims · 6 setups

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  The eTag Assay System rapidly identifies genes and related proteins without complex sample preparation or follow-up bioinformatics, unlike microarrays

  blood model brain lung etag sirna addl

• Iterative class discovery and feature selection using Minimal Spanning Trees.

  PMID 15355552 · PMC520744 · BMC bioinformatics · 2004 · 7 claims · 5 setups

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  Iterating between MST-based clustering and t-statistic feature selection removes noise genes step-wise while sharpening the sample clustering

  simulated breast acute diffuse synthetic cdna microarray

• MitoP2: the mitochondrial proteome database--now including mouse data.

  PMID 16381964 · PMC1347489 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  MitoP2 is a database integrating manually annotated mitochondrial reference proteins, functions, and disease associations for yeast, human, and mouse, with cross-species orthologue mapping

  saccharomyces yeast heart liver genome-wide single transcriptome

• Prediction by graph theoretic measures of structural effects in proteins arising from non-synonymous single nucleotide polymorphisms.

  PMID 18654622 · PMC2447880 · PLoS computational biology · 2008 · 8 claims · 5 setups

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  Bongo identifies mutations causing local and global structural effects with a remarkably low false positive rate

  p53 1bpi mutations disease-associated graph correlation structural

• 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

• Medical sequencing of candidate genes for nonsyndromic cleft lip and palate.

  PMID 16327884 · PMC1298935 · PLoS genetics · 2005 · 8 claims · 8 setups

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  Point mutations in FOXE1, GLI2, JAG2, LHX8, MSX1, MSX2, SATB2, SKI, SPRY2, and TBX10 may be rare causes of isolated CL/P

  family additional unrelated mutant direct linkage targeted

• Expression genomics in breast cancer research: microarrays at the crossroads of biology and medicine.

  PMID 17397520 · PMC1868923 · Breast cancer research : BCR · 2007 · 8 claims · 8 setups

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  Genome-wide expression microarray studies reveal transcriptional networks/signatures that explain breast cancer biological and clinical heterogeneity

  breast early-stage diffuse dlbcl gene

• What makes species unique? The contribution of proteins with obscure features.

  PMID 16859532 · PMC1779552 · Genome biology · 2006 · 7 claims · 8 setups

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  POFs constitute 18-38% (average 26%) of a typical eukaryotic proteome

  eukaryotic animal cerevisiae homo hmmpfam blast tblastn

• DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.

  PMID 18987736 · PMC2603574 · Nature · 2008 · 8 claims · 8 setups

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  Whole genome sequencing can identify unbiased, novel somatic mutations in a cytogenetically normal AML genome that would not have been found by candidate-gene resequencing.

  aml tumor novo additional genome snp comparative

• Human synthetic lethal inference as potential anti-cancer target gene detection.

  PMID 20015360 · PMC2804737 · BMC systems biology · 2009 · 7 claims · 8 setups

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  Targeting the synthetic lethal partner of a gene mutated in cancer selectively damages tumor cells while sparing healthy cells, offering a rationale for anti-cancer drug design

  saccharomyces sapiens ihsln genes database phylogenetic gene

• Mutation spectrum of homogentisic acid oxidase (HGD) in alkaptonuria.

  PMID 19862842 · PMC2830005 · Human mutation · 2009 · 8 claims · 6 setups

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  Mutations in HGD, which encodes homogentisate dioxygenase, cause AKU by blocking conversion of homogentisic acid to maleylacetoacetic acid in the tyrosine catabolic pathway

  aku hgd recombinant hgd missense splice

• The changing face of genomics.

  PMID 15128443 · PMC416465 · Genome biology · 2004 · 8 claims · 8 setups

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  Genome-wide ChIP-chip mapping of ~200 yeast transcriptional regulators across environmental conditions reveals general principles of promoter architecture and regulatory response types

  yeast drosophila zebrafish elegans chip-chip comparative insertional