journal
MENU ▼
Read by QxMD icon Read
search

Journal of Computational Biology: a Journal of Computational Molecular Cell Biology

journal
https://www.readbyqxmd.com/read/29185807/icon-mic-implementing-a-cpu-mic-collaboration-parallel-framework-for-icon-on-tianhe-2-supercomputer
#1
Zihao Wang, Yu Chen, Jingrong Zhang, Lun Li, Xiaohua Wan, Zhiyong Liu, Fei Sun, Fa Zhang
Electron tomography (ET) is an important technique for studying the three-dimensional structures of the biological ultrastructure. Recently, ET has reached sub-nanometer resolution for investigating the native and conformational dynamics of macromolecular complexes by combining with the sub-tomogram averaging approach. Due to the limited sampling angles, ET reconstruction typically suffers from the "missing wedge" problem. Using a validation procedure, iterative compressed-sensing optimized nonuniform fast Fourier transform (NUFFT) reconstruction (ICON) demonstrates its power in restoring validated missing information for a low-signal-to-noise ratio biological ET dataset...
November 29, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29185805/an-optimized-method-for-bayesian-connectivity-change-point-model
#2
Xiuchun Xiao, Bing Liu, Jing Zhang, Xueli Xiao, Yi Pan
The brain undergoes functional dynamic changes at all times. Investigating functional dynamics has been recently verified to be helpful for detecting psychological conditions and powerful for analyzing disease-related abnormalities of the brain. This article aims to detect functional dynamics. Specifically, we focus on how to effectively distinguish corresponding functional connectivity and change points from functional magnetic resonance imaging (fMRI) data. By combining Bayesian connectivity change point model (BCCPM), a modified genetic algorithm (GA) is presented to optimize the evolutionary procedure toward the most probable distributions of real change points in fMRI...
November 29, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29185804/theory-of-morphogenesis
#3
Andrey Minarsky, Nadya Morozova, Robert Penner, Christophe Soulé
A model of morphogenesis is proposed based on seven explicit postulates. The mathematical import and biological significance of the postulates are explored and discussed.
November 29, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29185792/metres-an-efficient-database-for-genomic-applications
#4
Jordi Vilaplana, Rui Alves, Francesc Solsona, Jordi Mateo, Ivan Teixidó, Marc Pifarré
MetReS (Metabolic Reconstruction Server) is a genomic database that is shared between two software applications that address important biological problems. Biblio-MetReS is a data-mining tool that enables the reconstruction of molecular networks based on automated text-mining analysis of published scientific literature. Homol-MetReS allows functional (re)annotation of proteomes, to properly identify both the individual proteins involved in the processes of interest and their function. The main goal of this work was to identify the areas where the performance of the MetReS database performance could be improved and to test whether this improvement would scale to larger datasets and more complex types of analysis...
November 29, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29172679/in-silico-approach-to-investigate-the-structural-and-functional-attributes-of-familial-hypercholesterolemia-variants-reported-in-the-saudi-population
#5
Fatima A Morad, Omran M Rashidi, Saida S Sadath, Faisal A Al-Allaf, Mohammad Athar, Mohamed N Alama, Sherif E Edris, Nabeel S Bondagji, Noor A Shaik, Babajan Banaganapalli, Zuhier Awan
Familial hypercholesterolemia (FH) is a metabolic disorder that leads primarily to premature cardiovascular diseases, the main cause of mortality in Saudi Arabia (SA). FH is underreported and underdiagnosed in SA with statistical evidence of high expected prevalence in such a consanguineous community. Lacking knowledge of which and how these alterations are actually impacting lipid metabolism is one of the main reasons why FH is insufficiently diagnosed in the region. The aim of this study was to develop a fast prediction approach using an integrated bioinformatics method for future screening of the potential causative variants from national registries...
November 27, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29172668/symmetrical-parameterization-of-rigid-body-transformations-for-biomolecular-structures
#6
Jin Seob Kim, Gregory S Chirikjian
Assessing preferred relative rigid body position and orientation is important in the description of biomolecular structures (such as proteins) and their interactions. In this article, we extend and apply the "symmetrical parameterization," which we recently introduced in the kinematics community, to address problems in structural biology. We also review parameterization methods that are widely used in structural biology to describe relative rigid body motions (in particular, orientations) as a basis for comparison...
November 27, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29140728/sample-based-models-of-protein-energy-landscapes-and-slow-structural-rearrangements
#7
Tatiana Maximova, Zijing Zhang, Daniel B Carr, Erion Plaku, Amarda Shehu
Proteins often undergo slow structural rearrangements that involve several angstroms and surpass the nanosecond timescale. These spatiotemporal scales challenge physics-based simulations and open the way to sample-based models of structural dynamics. This article improves an understanding of current capabilities and limitations of sample-based models of dynamics. Borrowing from widely used concepts in evolutionary computation, this article introduces two conflicting aspects of sampling capability and quantifies them via statistical (and graphical) analysis tools...
November 15, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29140718/pem-fitter-a-coarse-grained-method-to-validate-protein-candidate-models
#8
Kamal Al Nasr, Christopher Jones, Feras Yousef, Ruba Jebril
The volumetric images produced by Cryo-Electron Microscopy (cryo-EM) technique are used to model macromolecular assemblies and machines. De novo protein modeling uses these images to computationally model the structure of the molecules. Many candidate conformations are usually generated during the intermediate step. Conventionally, each of these candidates is evaluated by time-consuming approaches such as potential energy. We introduce an initial version of a geometrical screening method that uses the skeleton of the cryo-EM images to evaluate candidate structures...
November 15, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29116822/multiple-sequence-alignment-based-on-a-suffix-tree-and-center-star-strategy-a-linear-method-for-multiple-nucleotide-sequence-alignment-on-spark-parallel-framework
#9
Wenhe Su, Xiangke Liao, Yutong Lu, Quan Zou, Shaoliang Peng
Multiple sequence alignment (MSA) is an essential prerequisite and dominant method to deduce the biological facts from a set of molecular biological sequences. It refers to a series of algorithmic solutions for the alignment of evolutionarily related sequences while taking into account evolutionary events such as mutations, insertions, deletions, and rearrangements under certain conditions. These methods can be applied to DNA, RNA, or protein sequences. In this work, we take advantage of a center-star strategy to reduce the MSA problem to pairwise alignments, and we use a suffix tree to match identical substrings between two pairwise sequences...
November 8, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29116820/gsmc-combining-parallel-gibbs-sampling-with-maximal-cliques-for-hunting-dna-motif
#10
Chao Pei, Shu-Lin Wang, Jianwen Fang, Wei Zhang
Regulatory elements are responsible for regulating gene transcription. Therefore, identification of these elements is a tremendous challenge in the field of gene expression. Transcription factors (TFs) play a key role in gene regulation by binding to target promoter sequences. A set of conserved sequence patterns with a highly similar structure that is bound by a TF is called a motif. Motif discovery has been a difficult problem over the past decades. Meanwhile, it is a foundation stone in meeting this challenge...
November 8, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29099245/an-exhaustive-scan-method-for-snp-main-effects-and-snp%C3%A2-%C3%A3-%C3%A2-snp-interactions-over-highly-homozygous-genomes
#11
Shin-Fu Tsai, Chih-Wei Tung, Chen-An Tsai, Chen-Tuo Liao
Genome-wide association studies (GWAS) have been a powerful tool for exploring potential relationships between single-nucleotide polymorphisms (SNPs) and biological traits. For screening out important genetic variants, it is desired to perform an exhaustive scan over a whole genome. However, this is usually a challenging and daunting task in computation, due mainly to the large number of SNPs in GWAS. In this article, we propose a computationally effective algorithm for highly homozygous genomes. Pseudo standard error (PSE) is known to be a highly efficient and robust estimator for the standard deviation of a quantitative trait...
November 3, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29099235/a-multiscale-algorithm-for-spatiotemporal-modeling-of-multivalent-protein-protein-interaction
#12
M D Shahinuzzaman, Dipak Barua
This article introduces a multiscale framework for spatiotemporal modeling of protein-protein interaction. Cellular protein molecules represent multivalent species that contain modular features, such as binding domains and phosphorylation motifs. The binding and transformations of these features occur at a small time and spatial scale. On the other hand, space and time involved in protein diffusion, colocalization, and formation of complexes could be relatively large. Here, we present an agent-based framework integrated with a multiscale Brownian Dynamics (BD) simulation algorithm...
November 3, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29083930/convolutional-neural-network-for-histopathological-analysis-of-osteosarcoma
#13
Rashika Mishra, Ovidiu Daescu, Patrick Leavey, Dinesh Rakheja, Anita Sengupta
Pathologists often deal with high complexity and sometimes disagreement over osteosarcoma tumor classification due to cellular heterogeneity in the dataset. Segmentation and classification of histology tissue in H&E stained tumor image datasets is a challenging task because of intra-class variations, inter-class similarity, crowded context, and noisy data. In recent years, deep learning approaches have led to encouraging results in breast cancer and prostate cancer analysis. In this article, we propose convolutional neural network (CNN) as a tool to improve efficiency and accuracy of osteosarcoma tumor classification into tumor classes (viable tumor, necrosis) versus nontumor...
October 30, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29058464/prediction-of-central-nervous-system-side-effects-through-drug-permeability-to-blood-brain-barrier-and-recommendation-algorithm
#14
Jun Fan, Jing Yang, Zhenran Jiang
Drug side effects are one of the public health concerns. Using powerful machine-learning methods to predict potential side effects before the drugs reach the clinical stages is of great importance to reduce time consumption and protect the security of patients. Recently, researchers have proved that the central nervous system (CNS) side effects of a drug are closely related to its permeability to the blood-brain barrier (BBB). Inspired by this, we proposed an extended neighborhood-based recommendation method to predict CNS side effects using drug permeability to the BBB and other known features of drug...
October 23, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29053381/adaptive-networkprofiler-for-identifying-cancer-characteristic-specific-gene-regulatory-networks
#15
Heewon Park, Teppei Shimamura, Seiya Imoto, Satoru Miyano
There is currently much discussion about sample (patient)-specific gene regulatory network identification, since the efficiently constructed sample-specific gene networks lead to effective personalized cancer therapy. Although statistical approaches have been proposed for inferring gene regulatory networks, the methods cannot reveal sample-specific characteristics because the existing methods, such as an L1-type regularization, provide averaged results for all samples. Thus, we cannot reveal sample-specific characteristics in transcriptional regulatory networks...
October 20, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29048940/a-cpgcluster-teaching-learning-based-optimization-for-prediction-of-cpg-islands-in-the-human-genome
#16
Cheng-Hong Yang, Yi-Cheng Chiang, Li-Yeh Chuang, Yu-Da Lin
Many CpG island detection methods have been proposed based on sliding window and clustering technology, but the accuracy of these methods is proportional to the time required. Therefore, an accurate and rapid method for identifying CpG islands remains an important challenge in the complete human genome. We propose a hybrid method CpGTLBO to detect the CpG islands in the human genome. The method uses the clustering approach and the teaching-learning-based optimization (TLBO) algorithm. The clustering approach is used to detect CpG island candidates, and it can effectively reduce the huge volume of unnecessary DNA fragments...
October 19, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29039688/melc-genomics-a-framework-for-de-novo-genome-assembly
#17
Evaldo Bezerra Costa
The development of next-generation sequencing platforms increased substantially the capacity of data generation. In addition, in the past years, the costs for whole genome sequencing have been reduced that made it easier to access this technology. As a result, the storage and analysis of the data generated became a challenge, ushering in the development of bioinformatic tools, such as programs and programming languages, able to store, process, and analyze this huge amount of information. In this article, we present MELC genomics, a framework for genome assembly in a simple and fast workflow...
October 17, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29035581/gene-expression-as-a-dosimeter-in-irradiated-drosophila-melanogaster
#18
Samana Shrestha, Adam Vanasse, Leon N Cooper, Michael P Antosh
Biological indicators would be of use in radiation dosimetry in situations where an exposed person is not wearing a dosimeter, or when physical dosimeters are insufficient to estimate the risk caused by the radiation exposure. In this work, we investigate the use of gene expression as a dosimeter. Gene expression analysis was done on 15,222 genes of Drosophila melanogaster (fruit flies) at days 2, 10, and 20 postirradiation, with X-ray exposures of 10, 1000, 5000, 10,000, and 20,000 roentgens. Several genes were identified, which could serve as a biodosimeter in an irradiated D...
October 16, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29035580/mutation-sensitivity-maps-identifying-residue-substitutions-that-impact-protein-structure-via-a-rigidity-analysis-in-silico-mutation-approach
#19
Michael Siderius, Filip Jagodzinski
Understanding how an amino acid substitution affects a protein's structure can aid in the design of pharmaceutical drugs that aim at countering diseases caused by protein mutants. Unfortunately, performing even a few amino acid substitutions in vitro is both time and cost prohibitive, whereas an exhaustive analysis that involves systematically mutating all amino acids in the physical protein is infeasible. Computational methods have been developed to predict the effects of mutations, but even many of them are computationally intensive or are else dependent on homology or experimental data that may not be available for the protein being studied...
October 16, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29035579/beta-barrel-detection-for-medium-resolution-cryo-electron-microscopy-density-maps-using-genetic-algorithms-and-ray-tracing
#20
Albert Ng, Dong Si
Cryo-electron microscopy (cryo-EM) is a technique that produces three-dimensional density maps of large protein complexes. This allows for the study of the structure of these proteins. Identifying the secondary structures within proteins is vital to understanding the overall structure and function of the protein. The [Formula: see text]-barrel is one such secondary structure, commonly found in lipocalins and membrane proteins. In this article, we present a novel approach that utilizes genetic algorithms, kd-trees, and ray tracing to automatically detect and extract [Formula: see text]-barrels from cryo-EM density maps...
October 16, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
journal
journal
31979
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"