We introduce the notion of a multiprofile and use it for finding subtle motifs in DNA sequences.
Multiprofiles generalize the notion of a profile and allow one to detect subtle consensus …

Background Identification of specific genes and gene expression patterns important for
bacterial survival, transmission and pathogenesis is critically needed to enable development of …

The target-decoy approach (TDA) has done the field of proteomics a great service by filling in
the need to estimate the false discovery rates (FDR) of peptide identifications. While TDA is …

Genomics studies routinely depend on similarity searches based on the strategy of finding
short seed matches (contiguous k bases) which are then extended. The particular choice of …

… Moreover, the left eigenvector u corresponding to λj is positive, and without loss of generality
u’s entries sum to 1. Note that u is also a left eigenvector of A with uA = λu. Similarly, there …

… The p-values of the false PSMs were randomly sampled from a uniform U(0,1) distribution,
whereas the p-values of the true PSMs were generated U(0,1) × 10 –ξ , where ξ ∼ Poisson(a) …

Interpreting the potentially vast number of hypotheses generated by a shotgun proteomics
experiment requires a valid and accurate procedure for assigning statistical confidence …

DNA replication origins are necessary for the duplication of genomes. In addition, plasmid-based
expression systems require DNA replication origins to maintain plasmids efficiently. …

Controlling the false discovery rate (FDR) among discoveries from a tandem mass
spectrometry proteomics experiment using target decoy competition (TDC) controls only the …

… This explains why in practice m i is higher when Q i = U than when Q i = A (Table 1 and
Supplementary Fig. S6). Therefore, this new approach effectively assigns a lower score to an …