Position-weight matrices (PWMs) are broadly used to locate transcription factor binding sites in DNA sequences. The majority of existing PWMs provide a low level of both sensitivity and specificity. We present a new computational algorithm, a modification of the Staden-Bucher approach, that improves the PWM. We applied the proposed technique on the PWM of the GC-box, binding site for Sp1. The c...

We prove an asymptotic estimate for the number of m×n non-negative integer matrices (contingency tables) with prescribed row and column sums and, more generally, for the number of integer feasible flows in a network. Similarly, we estimate the volume of the polytope of m × n non-negative real matrices with prescribed row and column sums. Our estimates are solutions of convex optimization proble...

Let ∆1, . . . ,∆K be d × n matrices. We define the row product of these matrices as a d × n matrix, whose rows are entry-wise products of rows of ∆1, . . . ,∆K . This construction arises in certain computer science problems. We study the question, to which extent the spectral and geometric properties of the row product of independent random matrices resemble those properties for a d × n matrix ...