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).

• Nature of protein family signatures: insights from singular value analysis of position-specific scoring matrices.

  PMID 18398479 · PMC2276316 · PloS one · 2008 · 8 claims · 6 setups

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  The first singular component of a PSSM acts to disfavor substitutions, penalizing potentially functionally important residues at conserved sites more severely.

  representative pfam pdb right psi-blast hidden singular

• Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

  PMID 17576681 · PMC1934990 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  Cryptic 5'ss are best predicted by computational algorithms that accommodate nucleotide dependencies (e.g., Markov model, maximum entropy, maximum dependence decomposition) rather than by weight-matrix models

  disease mammalian compiled literature minigene computational

• Large-scale discovery of insertion hotspots and preferential integration sites of human transposed elements.

  PMID 20008508 · PMC2836564 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  Most TEs insert within specific 'hotspots' along the targeted TE rather than uniformly.

  genome sequences unique nested chi-square position-specific

• Prodepth: predict residue depth by support vector regression approach from protein sequences only.

  PMID 19759917 · PMC2742725 · PloS one · 2009 · 8 claims · 8 setups

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  Residue depth can be reliably predicted solely from protein primary sequence using support vector regression on sequence-derived features.

  structure sequences sequence residue dssp psi-blast