In this study, we introduce a novel de Bruijn graph (dBG) based framework for feature
engineering in biological sequential data such as proteins. This framework simplifies feature …

Spider dragline silk is known for its exceptional strength and toughness; hence
understanding the link between its primary sequence and mechanics is crucial. Here, we …

The field of computational biology has experienced a tremendous growth in the past 15
years. In this bibliography, we survey some of the most significant contributions that were …

Background Scientists routinely scan DNA sequences for transcription factor (TF)
bindingsites (TFBSs). Most of the available tools rely on position-specific scoringmatrices …

Background Discovering overrepresented patterns in amino acid sequences is an important
step in protein functional element identification. We adapted and extended NestedMICA, an …

Let S be a set of k strings over an alphabet Σ; each string has a length between ℓ and n. The
Closest Substring Problem (CSSP) is to find a minimal integer d (and a corresponding string …

Although most methods for solving mixed-integer optimization problems compute a single
optimal solution, a diverse set of near-optimal solutions can often lead to improved …

DNA sequence analysis plays an important role in the study of gene regulatory networks.
DNA motif finding has become a key discipline in the post-gene era and gradually become a …

Computational prediction of nucleotide binding specificity for transcription factors remains a
fundamental and largely unsolved problem. Determination of binding positions is a …

Motivation: Identifying regulatory elements in genomic sequences is a key component in
understanding the control of gene expression. Computationally, this problem is often …