BCB

Given a signaling network, the target combination identification problem aims to predict efficacious and safe target combinations for treatment of a disease. State-of-the-art in silico methods use Monte Carlo simulated annealing (mcsa) to modify a ...

Cytosine methylation is a DNA modification that has great impact on the regulation of gene expression and important implications for the biology and health of several living beings, including humans. Bisulfite conversion followed by next generation ...

The regulatory mechanism of recombination is one of the most fundamental problems in genomics, with wide applications in genome wide association studies (GWAS), birth-defect diseases, molecular evolution, cancer research, etc. Recombination events ...

We present ARMiCoRe, a novel approach to a classical bioinformatics problem, viz. multiple sequence alignment (MSA) of gene and protein sequences. Aligning multiple biological sequences is a key step in elucidating evolutionary relationships, annotating ...

Proteins and many other biologically relevant molecules are flexible, and the flexibility of a given molecule is one of its important characteristics. In particular, the degree of global and local flexibility of proteins is an important characteristic ...

Modeling large-scale protein motions, such as those involved in folding and binding interactions, is crucial to better understanding not only how proteins move and interact with other molecules but also how proteins misfold, thus causing many ...

Genome-Wide Association Studies (GWAS) in the past have focused on single-marker associations with traits of interest, which may fail to detect combination effects of Single-Nucleotide Polymorphisms (SNPs) or genes with weak individual effects, ...

Interactions between proteins and small-molecule chemicals modulate many protein functions and biological processes, and identifying these interactions is a crucial step in modern drug discovery. Supervised learning methods for predicting protein-...

Analysis of molecular interaction networks is pervasive in systems biology. This research relies almost entirely on graphs for modeling interactions. However, edges in graphs cannot represent multi-way interactions among molecules, which occur very ...

Functional site prediction is an important problem in the structural genomics era where we have a large number of experimentally determined protein structures with unknown function. The functional sites provide useful insights into protein function. In ...

Simultaneously sequencing multiple clones using second generation sequencers can speed up many essential clone-based sequencing methods. However, in applications such as fosmid clone sequencing and full-length cDNA sequencing it is important to create ...

Detecting and quantifying the timing and the genetic contributions of parental populations to a hybrid population is an important but challenging problem in reconstructing evolutionary histories from genetic variation data. With the advent of high ...

Images form a significant and useful source of information in published biomedical articles, which is still under-utilized in biomedical document classification and retrieval. Much current work on biomedical image retrieval and classification employs ...

Numerous methods exist for inferring the ancestry mosaic of an admixed individual based on its genotypes and those of its ancestors. These methods rely on bialleic SNPs obtained from genotype calling algorithms, which classify each marker as belonging ...

While traditional work on anaphora resolution has focused on resolving anaphors in newspaper and newswire articles, the surge of interest in biomedical natural language processing in recent years has stimulated work on anaphora resolution in biomedical ...

Identifying functional modules and understanding their organization in biological networks is of great importance. Recently, module identification by block modeling has demonstrated its advantages over the existing algorithms only considering ...

A central challenge in ab-initio protein structure prediction is the selection of low-resolution decoy conformations whose subsequent refinement leads to high-resolution near-native conformations. Successful selection strategies are tightly coupled with ...

Fragment-based descriptions of protein structures have been successfully used in fast comparison methods for protein structures mining and classification. These descriptions reduce the dimensionality problem and allow the application of sequence ...

ChIP-chip and ChIP-seq are techniques for the isolation and identification of the binding sites of DNA-associated proteins along the genome. Both techniques produce genome-wide location data. The geometric arrangements of these binding sites can provide ...

Nature possesses a secret formula for the energy as a function of the structure of a protein. In protein design, approximations are made to both the structural representation of the molecule and to the form of the energy equation, such that the ...

We have designed and implemented an efficient tool for short read alignment that is sensitive to a given set of SNP. In particular, it returns alignments that permit mismatches at these SNPs. We then make use of it to develop a method for detecting SNPs,...

Electron tomography is a promising technology for imaging ultrastructures at nanoscale resolutions. However, image and quantitative analyses are often hindered by high levels of noise, staining heterogeneity, and material damage either as a result of ...

Pseudogenes are dysfunctional DNA sequences that share sequence similarities with functional genes. Accurate identification of pseudogenes is important to understand biological and evolutionary histories of genomes and genes. Most existing pseudogene ...

The fine-scale stochastic behavior of genetic regulatory networks is often modeled using stochastic master equations. The inherently high computational complexity of the stochastic master equation simulation presents a challenge in its application to ...

Genome Wide Association Studies (GWAS) comprehensively compare common genetic variants in affected and control populations to identify variants that are potentially associated with diseases. In recent years, GWAS successfully identified susceptible ...

Protein function prediction is one of the fundamental issues in the post-genomic era. Multi-label learning is widely used for predicting functions of proteins. Most multi-label learning methods assume that the proteins with annotation do not have any ...

Detecting Electrocardiogram (ECG) abnormalities is the process of identifying irregular cardiac activities which may lead to severe heart damage or even sudden death. Due to the rapid development of cyberphysic systems and health informatics, embedding ...

We propose a framework for studying visual morphological patterns across histopathological whole-slide images (WSIs). Image representation is an important component of computer-aided decision support systems for histopathological cancer diagnosis. Such ...

A range of experimental results indicate that the cell nucleus is highly organized, with many chromosomes forming relatively stable associations. An interesting prospect is that elements of this chromosomal organization may exist to facilitate ...

We propose a similarity measure based on the multivariate hypergeometric distribution for the pairwise comparison of images and data vectors. The formulation and performance of the proposed measure are compared with other similarity measures using ...

Algorithms for protein structure comparison employ diverse and effective representations of molecular shape. However, they do not generally represent the shape of the electrostatic potential field, except at the molecular surface. This approach neglects ...

Functional module detection in Protein-Protein Interaction (PPI) networks is essential to understanding the organization, evolution and interaction of the cellular systems. In recent years, most of the researches have focused on detecting the functional ...

The study of the molecular control of organ growth requires the establishment of the causal relationship between gene expression and cell behaviors. Specifically, we seek to understand this relationship at the shoot apical meristem (SAM) of model plant ...

We develop novel single-GPU parallel algorithms for syntenic alignment using CUDA. Our algorithms can be used to determine the optimal alignment score as well as the actual optimal alignment for a single pair of sequences. Experimental results show that ...

Finding informative genes for prostate cancer has always been an important topic in cancer study. With the widespread use of genomic analysis and microarray experiments, a large number of genes can be analyzed efficiently to find the informative ones ...

Genome-wide profiling of DNA-binding proteins using ChIP-Seq has emerged as an alternative to ChIP-chip methods. Due to the large amounts of data produced by next generation sequencing, ChIP-Seq offers many advantages, such as much higher resolution, ...

Ontology term recognition is a key task of ontology-based text mining. Previous approaches of statistical analysis and syntactic pattern matching have such limitations that they do not consider relations between words and that their handcrafted patterns ...

The regulatory mechanism of meiotic recombination hotspots is a fundamental problem in biology, with broad impacts on areas ranging from disease study to evolution. Recently, many genomic and epigenomic features have been associated with recombination ...

Stochastic effect in cellular systems has been a hot topic in systems biology. Stochastic modeling and simulation methods are important tools to study stochastic effect. Given the low efficiency of stochastic simulation algorithms, the hybrid method, ...

Genome-wide association studies (GWAS) analyze genetic variation (SNPs) across the entire human genome, searching for SNPs that are associated with certain phenotypes, most often diseases, such as breast cancer. In GWAS, we seek a ranking of SNPs in ...

Understanding protein and RNA biomolecular folding and assembly processes have important applications because misfolding is associated with diseases like Alzheimer's and Parkinson's. However, simulating biologically relevant biomolecules on timescales ...

The recent advance in next generation sequencing (NGS) techniques has enabled the direct analysis of the genetic information within a whole microbial community, bypassing the culturing individual microbial species in the lab. One can profile the marker ...

Network propagation algorithms have proved useful for the analysis of high-dimensional genomic data. One limitation is that the current formulation only allows network propagation on positively weighted graphs. In this paper, we explore two signed ...

Protein structure prediction is one of the most challenging problems in computational biology. Given a protein's amino acid sequence, a simplified version of the problem is to find an on-lattice self-avoiding walk that minimizes the interaction energy ...

One of the most widely-used methods to date for recognizing protein sequences that are evolutionarily related, termed homologs, has been profile hidden Markov models. For the cases where positive training data for these methods is sparse, Kumar and ...

As prevalence and awareness of osteoporosis increase and treatments of proven efficacy become available, the demand for management of patients with the disease will also rise. It calls for innovative research on understanding of osteoporosis and ...

Massively parallel whole transcriptome sequencing, commonly referred to as RNA-Seq, has become the technology of choice for performing gene expression profiling. However, reconstruction of full-length novel transcripts from RNA-Seq data remains ...

The rapidly diminishing cost of genome sequencing is driving renewed interest in large scale genome sequencing programs such as Genome 10K (G10K). Despite renewed interest the assembly of large genomes from short reads is still an extremely resource ...

Large-scale genomic pairwise aligners usually start with a seeding procedure, which scans two sequences to obtain base matches (called hits) that follow a certain pattern (called a seed). The seed pattern and size determine the sensitivity and ...

With the growing development and application of genetic data availability, it provides new possibilities in establishing the genealogical relationships of individual organisms such as sibling reconstruction, parentage inference, and inheritance ...

Existing ontology-based knowledge representations systems have achieved considerable success in semantic querying on large biomedical text corpora over keyword-based systems. However, their query expressivity is limited due to the lack of cross-ontology ...

Proteins are dynamic molecules, and understanding how they flex and bend provides fundamental insights to their functions. Methods such as molecular dynamics are computationally expensive, and can simulate protein motions on limited timescales. Rigidity ...

Recently we have developed a new algorithm, PROVEAN (<u>Pro</u>tein <u>V</u>ariation <u>E</u>ffect <u>An</u>alyzer), for predicting the functional effect of protein sequence variations, including single amino acid substitutions and small insertions and ...

DNA methylation, a well-studied mechanism of epigenetic regulation, plays important roles in cancer. Increased levels of global DNA methylation is observed in primary solid tumors including endometrial carcinomas and is generally associated with ...

Identifying protective antigens from bacterial pathogens is important for developing vaccines. Most computational methods for predicting protein antigenicity rely on sequence similarity between a query protein sequence and at least one known antigen. ...

Gene regulatory networks model dependencies between genes, and thus they potentially explain normal cell physiology, as well as pathological phenotypes. Because high-throughput technologies for measuring gene expression provide increasingly complete and ...

DNA sequences are denoted mostly in raw text format, where 2-bit compressed representations are preferred either to gain space or perform some processing fast via computers intrinsic bitwise operations, e.g., search applications. Studies aiming to ...

While microarrays have been successfully used by the researchers to analyze gene expression levels, cutting edge high throughput sequencing technologies now made it possible to go one step further. Recent studies show that absolute expression levels are ...

IgE antibodies bound to cell-surface receptors, FceRI, crosslink through the binding of antigens on the cell surface. This formation of aggregates is what simulates mast cells and basophils in order to initiate an allergic response. Experimental studies ...

Genome-wide expression quantitative trait loci (eQTL) studies have emerged as a powerful tool to understand the genetic basis of gene expression and complex traits. The traditional eQTL methods focus on testing the associations between individual single-...

As biological pathway databases continually increase in size and availability, efficient tools and techniques to query these databases are needed to mine useful biological information. A plethora of existing techniques already allow for exact or ...

Array-based oligonucleotide synthesis technologies provide access to thousands of custom-designed sequence variants at low cost. Large-scale synthesis and high-throughput assays have become valuable experimental tools to study in detail the interplay ...

Cryo-electron Microscopy (cryoEM) is an advanced imaging technique that produces volume maps at different resolutions. This technique is capable of visualizing large molecular complexes such as viruses and ribosomes. At the medium resolutions, such as 5 ...

Recent advances in high throughput data collection and imaging technologies have resulted in the availability of diverse biomedical datasets that capture complementary information pertaining to the biological processes in an organism. Biomarkers that ...

One of the used techniques to address protein structure investigation is to look for recurrent fragments (also called substructures or spatial motifs), then use these spatial motifs as patterns to characterize the proteins under consideration. An ...

Current clinical judgment in bladder cancer (BC) relies primarily on pathological stage and grade. We investigated whether a molecular classification of tumor cell differentiation, based on a developmental biology approach, can provide additional ...

Over the past few years, massively parallel DNA sequencing platforms have become widely available, reducing the cost of DNA sequencing by over five orders of magnitude. We used two of these methods to reveal the genome sequence of a highly abundant ...

The transcriptional activity of nuclear factor (NF)-κB is primarily regulated by interaction with inhibitory IκB proteins. The primary role of IκB protein is masking the nuclear localization signal of NF-κB, preventing its translocation to the nucleus. ...

Bromodomain-containing protein 4 (BRD4) is a positive regulatory component of P-TEFb complex, which is composed of CDK9 and Cyclin T1/2. P-TEFb complex promotes elongation by phosphorylating serine 2 of the Pol II carboxyl-terminal domain (CTD), which ...

Interleukin-1 receptor-associated kinases (IRAKs) are important in TIR-mediated signal transduction. Although IRAK proteins are structurally similar, recent biochemical studies have shown that each IRAK member plays a non-redundant role in TLR/IL-1R ...

The prediction of particular types of protein-protein interactions (PPIs) based on knowledge of their interacting domains is a problem that has drawn the attention of researchers in the past few years. We focus on the prediction and analysis of obligate ...

The ability to locate in silico, in a protein structure, the active site, the binding site or the initiation site of conformational changes is important for understanding the functional mechanisms and is a prerequisite for the rational prediction of ...

A protein making up living organisms is synthesized as a one-dimensional array of amino acids based on the information stored in a gene, in which each amino acid of 20 types is encoded by a triplet of four types of bases called a codon. Considering that ...

Analysis of large particle or molecular simulation data is integral part of the basic-science research community. It often involves computing functions such as point-to-point interactions of particles. Spatial distance histogram (SDH) is one such vital ...

Computational Systems Modeling could play a significant role in improving and speeding up of the drug development process. By the incorporation of cellular modeling into a High Information Content Drug Screening platform the information content of the ...

Acute lymphoblastic leukemia (ALL) is the most common pediatric cancer and the leading cause of cancer-related death among children. Advances in the understanding of the pathobiology of ALL have led to risk-targeted treatment regimes and increased ...

Nuclear Localization Signals (NLS) are the most direct evidence for nuclear localization of proteins. Despite a couple of NLS prediction methods have been developed, the prediction performance is far from being satisfactory. In this study we proposed a ...

Analysis of microarray data with several treatments is an important problem in gene expression studies. We previously introduced a method that employs directed graphs to represent gene response to pairs of treatments. In our method, genes sharing the ...

The massive datasets generated by next-generation sequencing (NGS) studies present major challenges for data management and analysis. In our ongoing pediatric oncogenomics study, we have sequenced over 120 childhood acute lymphoblastic (ALL) quartets (...

The tremendous demand on computer memory and computing time for prediction of complex secondary structures limits the applicability of most RNA secondary structure prediction programs available to short RNA sequences. We propose to approach this problem ...

We present, https://drugsite.msi.umn.edu, a centralized database and an associated application suite that supports searching for complex substructures in macromolecules from the Protein Data Bank (PDB) [2] and user uploaded structures, storing and ...

In this paper, we applied a regularized multinomial logistic regression (RMLR) for multicolor fluorescence in-situ hybridization (M-FISH) image analysis, in order to better classify chromosomes. The RMLR integrates complementary information from multi-...

Robust and accurate detection of copy number variations (CNVs) from next-generation sequencing (NGS) data is challenging. Because of the high fluctuation of read depth signal, most existing methods, which use only one data sample, yield high false ...

The canonical genetic code is almost universal and is present in most complex organisms. A question that has intrigued researchers is why exactly this code was chosen instead of another one. Many researchers believe that the genetic code is a product of ...

Complex diseases are commonly caused by a combination of genetic alterations in several genes, which lead to abnormal propagation of signals along biological pathways. Assuming that DNA alterations can modulate, through biological pathways, ...

The progress in understanding of molecular mechanisms underlying common heritable disorders (e.g. autism, schizophrenia, diabetes) depends on the availability of new bioinformatics approaches for identification of their characteristic genetic variations ...

Many works have been done to identify functional modules in Protein-Protein Interaction (PPI) networks but the results are far from satisfaction. One main reason is that the PPI data generated from high-throughput experiments is noisy and incomplete. ...

In this paper, we use structural bioinformatics tools to the macromolecular modeling of protein tertiary structure SCI1 Nicotiana tabacum L

Current design tools cannot accurately predict the adsorption of proteins in microfluidic devices that handle biological liquids. A continuum model was developed to predict the transport of hard-sphere particles in a liquid and the adsorption of the ...

New technology has resulted in high-throughput screens for pairwise genetic interactions in yeast and other model organisms. For each pair in a collection of non-essential genes, an epistasis score is obtained, representing how much sicker (or healthier)...

Analysis of gene expression data from studies to assess patterns of gene expression to multiple treatments is usually challenging due to the inadequacy of sample size. We introduce an approach of representing gene expression response to multiple ...

In this paper, we briefly compare the performance of gene finding methods which are based on hidden Markov models (HMMs) and digital signal processing (DSP). We apply the methods to three benchmark datasets consisting of sequences from various species (...

Glycosylphosphatidylinositol (GPI) anchored proteins are involved in many biological processes and are of medical importance. The identification and analysis of the entire collection of free and protein linked GPIs within an organism (i.e., GPIomics) ...