Network alignment (NA) aims to find similar (conserved) regions between networks. Until recently, existing methods were limited to aligning static networks. However, real-world systems, including biological ones, are dynamic. Hence, we had introduced ...

Mathematical models of cellular processes can systematically predict the phenotypes of novel combinations of multi-gene mutations. Searching for informative predictions and prioritizing them for experimental validation is challenging since the number of ...

Selecting a non-redundant representative subset of sequences is a common step in many bioinformatics workflows, such as the creation of non-redundant training sets for sequence and structural models or selection of "operational taxonomic units" from ...

Even a single amino acid substitution in a protein can be the cause of a debilitating disease. Experimentally studying the effects of all possible multiple mutations in a protein is infeasible since it requires a combinatorial number of mutants to be ...

Molecular dynamics (MD) simulation is a powerful technique for sampling the conformational landscape of natively folded proteins (NFPs) and structurally dynamic intrinsically disordered proteins (IDPs). NFPs and IDPs can be viewed as nonlinear dynamical ...

Research in the field of HIV transmission has yet to provide a vaccine for this imponderable virus. Though progress has been made to extend the life of those chronically infected, a solution to the transmission of the disease remains elusive. Previous ...

The adaptive immune system is a defense system against repeated infection. In order to trigger the immune response, antigen peptides from the infecting agent must first be recognized by the Major Histocompatibility Complex (MHC) proteins. Identifying ...

Cryo-electron microscopy (cryo-EM) has become a major technique for protein structure determination. Many atomic structures have been derived from cryo-EM density maps of about 3Å resolution. Side-chain conformations are well determined in density maps ...

Protein-peptide binding interactions play an important role in cellular regulation and are functionally important in many diseases. If no prior knowledge of the location of a binding site is available, prediction may be needed as a starting point for ...

Protein surface shape plays an essential role in various function of proteins. In order to efficiently investigate protein function and evolutionary history, we introduce a global protein surface shape representation called EMNets. EMNets provides an ...

Cryo-electron microscopy (cryo-EM) is an emerging biophysical technique for structural determination of protein complexes. However, accurate detection of secondary structures is still challenging when cryo-EM density maps are at medium resolutions (5-10 ...

Significant efforts are devoted to resolving biologically-active structures in wet and dry laboratories. In particular, due to hardware and algorithmic innovations, computational methods can now obtain thousands of structures that populate the structure ...

Due to the central role that tertiary structure plays in determining protein function, resolving protein tertiary structures is an integral research thrust in both wet and dry laboratories. Dry laboratories have primarily focused on small- to medium-...

The rapid accumulation of protein structures presents a unique set of challenges and opportunities in the analysis, comparison, modeling, and prediction of macromolecular structures and their interactions. This workshop brought together researchers with ...

\sectionBackground Amyotrophic lateral sclerosis (ALS), is a neurodegenerative disease that primarily effects motor neurons in both brain and spinal cord \citezarei2015comprehensive. Several independent studies conformed the deposition of TAR DNA-...

Schizophrenia and autism are examples of polygenic diseases caused by a multitude of genetic variants. Recently, both diseases have been associated with disrupted neuron motility and migration patterns, suggesting that aberrant cell motility is a ...

Understanding sensitivity is an important step to study system robustness and adaptability. In this work, we model and investigate intra-cellular networks via discrete modeling approach, which assigns a set of discrete values and a deterministic update ...

The inference of gene networks from large-scale human genomic data is challenging due to the difficulty in identifying correct regulators for each gene in a high-dimensional search space. We present a Bayesian approach integrating external data sources ...

Abstract Objective. As Genome-Wide Association Studies (GWAS) have been increasingly used with data from various populations, it has been observed that data from different populations reveal different sets of Single Nucleotide Polymorphisms (SNPs) that ...