Related papers: DiffPaSS -- High-performance differentiable pairin…
We participated in three of the protein-protein interaction subtasks of the Second BioCreative Challenge: classification of abstracts relevant for protein-protein interaction (IAS), discovery of protein pairs (IPS) and text passages…
Fast, efficient and reliable algorithms for pairwise alignment of protein structures are in ever increasing demand for analyzing the rapidly growing data of protein structures. CLePAPS is a tool developed for this purpose. It distinguishes…
Discovering patterns in data that best describe the differences between classes allows to hypothesize and reason about class-specific mechanisms. In molecular biology, for example, this bears promise of advancing the understanding of…
Sequences of nucleotides (for DNA and RNA) or amino acids (for proteins) are central objects in biology. Among the most important computational problems is that of sequence alignment, i.e. arranging sequences from different organisms in…
Understanding the molecular determinants of specificity in protein-protein interaction is an outstanding challenge of postgenome biology. The availability of large protein databases generated from sequences of hundreds of bacterial genomes…
The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over…
We propose a method for detecting differential gene expression that exploits the correlation between genes. Our proposal averages the univariate scores of each feature with the scores in correlation neighborhoods. In a number of real and…
CLeFAPS, a fast and flexible pairwise structural alignment algorithm based on a rigid-body framework, namely CLePAPS, is proposed. Instead of allowing twists (or bends), the flexible in CLeFAPS means: (a) flexibilization of the algorithm's…
Protein contacts provide key information for the understanding of protein structure and function, and therefore contact prediction from sequences is an important problem. Recent research shows that some correctly predicted long-range…
Correlations between two variables of a high-dimensional system can be indicative of an underlying interaction, but can also result from indirect effects. Inverse Ising inference is a method to distinguish one from the other. Essentially,…
Propensity score matching is a tool for causal inference in non-randomized studies that allows for conditioning on large sets of covariates. The use of propensity scores in the social sciences is currently experiencing a tremendous…
Understanding protein-protein interactions is central to our understanding of almost all complex biological processes. Computational tools exploiting rapidly growing genomic databases to characterize protein-protein interactions are…
Score matching is a vital tool for learning the distribution of data with applications across many areas including diffusion processes, energy based modelling, and graphical model estimation. Despite all these applications, little work…
The analysis of correlations of amino acid occurrences in globular proteins has led to the development of statistical tools that can identify native contacts -- portions of the chains that come to close distance in folded structural…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
Motivation Protein fold recognition is an important problem in structural bioinformatics. Almost all traditional fold recognition methods use sequence (homology) comparison to indirectly predict the fold of a tar get protein based on the…
Numerous cellular functions rely on protein$\unicode{x2013}$protein interactions. Efforts to comprehensively characterize them remain challenged however by the diversity of molecular recognition mechanisms employed within the proteome. Deep…
Background: Coevolution within a protein family is often predicted using statistics that measure the degree of covariation between positions in the protein sequence. Mutual Information is a measure of dependence between two random variables…
Various methods have been developed to analyze the association between organisms and their genomic sequences. Among them, sequence alignment is the most frequently used for comparative analysis of biological genomes. However, the…
Pairwise comparison data arise in many domains with subjective assessment experiments, for example in image and video quality assessment. In these experiments observers are asked to express a preference between two conditions. However, many…