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The rapid increase in available protein structure datasets requires new techniques for fast, yet, effective analysis of protein 3D structures. In this work, we propose a structure-based signature for protein families, suitable for rapid analysis of multidomain domain protein structures. Our method is alignment-free, using protein strings as the basic representation. A key novelty is the two-stage...
UniProtKB has collected more than 88 million protein sequences by July 2017. Less than 0.2% of these proteins, however, have added experimental GO annotations. To reduce this huge gap, automatic protein function prediction (AFP) becomes increasingly important. Results on CAFA (the Critical Assessment of protein Function Annotation algorithms) benchmark demonstrates that sequence homology based methods...
A large number of long non-coding RNAs (lncRNAs) have been identified over the past decades. Accumulating evidence proves that lncRNAs play key roles in various biological processes. However, the majority of the lncRNAs have not been functionally characterized. The annotation of lncRNA functions has become an area of focus in the fields of biology and bioinformatics. In this paper, we develop a global...
Co-evolution exists ubiquitously in biological systems. At the molecular level, interacting proteins, such as ligands and their receptors and components in protein complexes, co-evolve to maintain their structural and functional interactions. Many proteins contain multiple functional domains interacting with different partners, making co-evolution of interacting domains occur more prominently. Multiple...
Proteins from the same family have similar functions. Hence, it is important to discover from a protein family conserved sequence patterns with variations to unveil the functionality of a functional domain. Aligned Pattern Clusters (APCs) are knowledge-rich representations comparing with probabilistic models. If significant aligned residue associations (ARAs) were discovered in APCs, they could reveal...
Recent advances in sequencing allow the study of all identified human genes (≈ 22,000 protein encoding genes), which have differential expression between tissues. However, current knowledge on gene interactions lags behind, especially when one of the elements encodes a mitochondrial protein (≈ 1500). Mitochondrial proteins are encoded either by mitochondrial DNA (mtDNA; 13 proteins) or by nuclear...
We have developed a fast, scalable, and purely geometric structure search combining techniques from information retrieval and big data with a novel approach to encoding sequences of torsion angles. Along the way, we introduce a new torsion angle plot without breaks in continuity while still maintaining traditional torsion angle ranges, to assist in identifying separable regions of torsion angles....
Identification of the conserved non-coding sequences (CNSs) for plants is a challenging problem because the plants have small CNSs compared to animals. The existing alignment based methods are neither efficient nor sensitive to smaller CNSs when the number of species is large. In this paper, we propose an alignment-free approach that can process any number sequences simultaneously. Our approach uses...
T cells play a critical role in the adaptive immune response. They perform their function by recognizing infected cells presenting peptides on a specialized complex known as the MHC. The recognition process involves binding of the peptide-loaded MHC to the T cell receptor (TCR), a surface molecule comprised of an alpha and a beta chain. A large body of evidence suggests that T cells can respond to...
Identifying the interactions between proteins and Long non-coding RNAs (lncRNAs) can provide valuable clues for understanding the mechanisms and physiological functions of lncRNAs. In this work, we propose a computational method, PLIPCOM, which can accurately detect protein-lncRNA interactions by integrating two groups of network features. Low dimensional diffusion characteristics and HeteSim features...
Hi-C technique is an important tool for the study of 3D genome organization. In the past few years, we have seen an explosion of Hi-C data in a variety of cell/tissue types. While these publicly available data presents an unprecedented opportunity to interrogate chromosomal architecture, how to quantitatively compare Hi-C data from different tissues and identify tissue-specific chromatin interactions...
In this paper, we computationally predicted the interactions between HIV-1 and human proteins, based on the hypothesis that proteins with similar interface architecture share similar interaction partners. Evolution – aware protein structural alignment method UniAlign was used to calculate the similarity between two protein interface architectures. Using experimentally verified HIV-1, human protein-protein...
MicroRNAs regulate virtually the whole gene network in human body and have been implicated in most physiological and pathological conditions including cancers. Understanding the precise mechanisms of microRNA-mRNA interaction is fundamentally important to elucidate the important roles of miRNA in regulating various cellular and disease developmental stages. Numerous computational methods have been...
In eukaryotes, protein ubiquitylation is an important type of post-translation modification, in which the ubiquitin conjugates to a substrate protein. To have a better insight of the mechanisms underlying ubiquitylation, a key step is to identify protein ubiquitylation sites. Many existing computational methods are based on feature engineering, which may lead to biased and incomplete features. Deep...
The recognized significance of rumen microbiome has inspired efforts to examine the composition of rumen microbial communities in a large scale. One of the key research areas is to infer association and dependencies between members of rumen microbial communities through correlation analysis. However, it has been found that due to the compositional nature of data, simply applying correlation-based...
The alignment of protein-protein interaction (PPI) networks is an effective approach to uncover the functionally conserved sub-structure between networks. A wealth of approaches have been developed for global PPI network alignment in recent years. However, due to the computational intractability caused by its NP-completeness, global PPI network alignment remains challenging in finding large conserved...
The spread of antibiotic resistance is a growing problem known to be caused by antibiotic usage itself. This problem can be analyzed at different levels. Antibiotic administration policies and practices affect the societal system, which is made by human individuals and by their relations. Individuals developing resistance interact with each other and with the environment while receiving antibiotic...
Improvements in melanoma diagnosis, treatment and prognosis are urgently warranted, given that it causes 3 out of 4 skin cancer deaths. A large amount of genomic and molecular data indicate that alterations occur at multiple scales in different stages of melanoma. Metabolic rewiring is a characteristic feature of progressive cancers that facilitates sustenance of tumors, and caters to the changing...
Cancer of the pancreas is a highly lethal disease and has an extremely poor prognosis. Mathematical modelling and computer simulations have been proposed as important tool to predictor initiation and progression of cancer diseases, which are very important in cancer study. Among these studies, it is widely assumed that the gene mutation rate is unchanged, which is not realistic based on recently biological...
Recently, microRNAs were found to have potential as both diagnostic biomarkers and therapeutic targets for lung cancer, especially in identifying early-stage cancer. However, a miRNA biomarker derived from the standard normal v.s tumor differential expression analysis is not robust, as its functional interactions with messenger-RNA targets may change between different lung cancer subtypes. Furthermore,...
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