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/29053381/adaptive-networkprofiler-for-identifying-cancer-characteristic-specific-gene-regulatory-networks
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
https://www.readbyqxmd.com/read/29035575/hetfhmm-a-novel-approach-to-infer-tumor-heterogeneity-using-factorial-hidden-markov-models
#7
Mohammad S Rahman, Ann E Nicholson, Gholamreza Haffari
Cancer arises from successive rounds of mutations, resulting in tumor cells with different somatic mutations known as clones. Drug responsiveness and therapeutics of cancer depend on the accurate detection of clones in a tumor sample. Recent research has considered inferring clonal composition of a tumor sample using computational models based on short read data of the sample generated using next-generation sequencing (NGS) technology. Short reads (segmented DNA parts of different tumor cells) are noisy; therefore, inferring the clones and their mutations from the data is a difficult and complex problem...
October 16, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29035572/maintaining-and-enhancing-diversity-of-sampled-protein-conformations-in-robotics-inspired-methods
#8
Jayvee R Abella, Mark Moll, Lydia E Kavraki
The ability to efficiently sample structurally diverse protein conformations allows one to gain a high-level view of a protein's energy landscape. Algorithms from robot motion planning have been used for conformational sampling, and several of these algorithms promote diversity by keeping track of "coverage" in conformational space based on the local sampling density. However, large proteins present special challenges. In particular, larger systems require running many concurrent instances of these algorithms, but these algorithms can quickly become memory intensive because they typically keep previously sampled conformations in memory to maintain coverage estimates...
October 16, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29035570/a-median-solver-and-phylogenetic-inference-based-on-double-cut-and-join-sorting
#9
Ruofan Xia, Yu Lin, Jun Zhou, Bing Feng, Jijun Tang
Genome rearrangement is known as one of the main evolutionary mechanisms on the genomic level. Phylogenetic analysis based on rearrangement played a crucial role in biological research in the past decades, especially with the increasing availability of fully sequenced genomes. In general, phylogenetic analysis aims to solve two problems: small parsimony problem (SPP) and big parsimony problem (BPP). Maximum parsimony is a popular approach for SPP and BPP, which relies on iteratively solving an NP-hard problem, the median problem...
October 16, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29028181/unbiased-taxonomic-annotation-of-metagenomic-samples
#10
Bruno Fosso, Graziano Pesole, Francesc Rosselló, Gabriel Valiente
The classification of reads from a metagenomic sample using a reference taxonomy is usually based on first mapping the reads to the reference sequences and then classifying each read at a node under the lowest common ancestor of the candidate sequences in the reference taxonomy with the least classification error. However, this taxonomic annotation can be biased by an imbalanced taxonomy and also by the presence of multiple nodes in the taxonomy with the least classification error for a given read. In this article, we show that the Rand index is a better indicator of classification error than the often used area under the receiver operating characteristic (ROC) curve and F-measure for both balanced and imbalanced reference taxonomies, and we also address the second source of bias by reducing the taxonomic annotation problem for a whole metagenomic sample to a set cover problem, for which a logarithmic approximation can be obtained in linear time and an exact solution can be obtained by integer linear programming...
October 13, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29028179/reconstructing-one-articulated-networks-with-distance-matrices
#11
Kuang-Yu Chang, Yun Cui, Siu-Ming Yiu, Wing-Kai Hon
Given a distance matrix M that represents evolutionary distances between any two species, an edge-weighted phylogenetic network N is said to satisfy M if between any pair of species, there exists a path in N with a length equal to the corresponding entry in M. In this article, we consider a special class of networks called a one-articulated network, which is a proper superset of galled trees. We show that if the distance matrix M is derived from an ultrametric one-articulated network N (i.e., for any species X and Y, the entry [Formula: see text] is equal to the shortest distance between X and Y in N), we can re-construct a network that satisfies M in [Formula: see text] time, where n denotes the number of species; further, the reconstructed network is guaranteed to be the simplest, in a sense that the number of hybrid nodes is minimized...
October 13, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29028176/a-biclique-approach-to-reference-anchored-gene-blocks-and-its-applications-to-genomic-islands
#12
Arnon Benshahar, Vered Chalifa-Caspi, Danny Hermelin, Michal Ziv-Ukelson
We formalize a new problem variant in gene-block discovery, denoted Reference-Anchored Gene Blocks (RAGB), given a query sequence Q of length n, representing the gene array of a DNA element, a window size bound d on the length of a substring of interest in Q, and a set of target gene sequences [Formula: see text]. Our objective is to identify gene blocks in [Formula: see text] that are centered in a subset q of co-localized genes from Q, and contain genomes from [Formula: see text] in which the corresponding orthologs of the genes from q are also co-localized...
October 13, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29028175/the-information-content-of-discrete-functions-and-their-application-in-genetic-data-analysis
#13
Nikita A Sakhanenko, James Kunert-Graf, David J Galas
The complex of central problems in data analysis consists of three components: (1) detecting the dependence of variables using quantitative measures, (2) defining the significance of these dependence measures, and (3) inferring the functional relationships among dependent variables. We have argued previously that an information theory approach allows separation of the detection problem from the inference of functional form problem. We approach here the third component of inferring functional forms based on information encoded in the functions...
October 13, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28953425/shared-nearest-neighbor-clustering-in-a-locality-sensitive-hashing-framework
#14
Sawsan Kanj, Thomas Brüls, Stéphane Gazut
We present a new algorithm to cluster high-dimensional sequence data and its application to the field of metagenomics, which aims at reconstructing individual genomes from a mixture of genomes sampled from an environmental site, without any prior knowledge of reference data (genomes) or the shape of clusters. Such problems typically cannot be solved directly with classical approaches seeking to estimate the density of clusters, for example, using the shared nearest neighbors (SNN) rule, due to the prohibitive size of contemporary sequence datasets...
September 27, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28953416/the-relationship-between-low-frequency-motions-and-community-structure-of-residue-network-in-protein-molecules
#15
Weitao Sun
The global shape of a protein molecule is believed to be dominant in determining low-frequency deformational motions. However, how structure dynamics relies on residue interactions remains largely unknown. The global residue community structure and the local residue interactions are two important coexisting factors imposing significant effects on low-frequency normal modes. In this work, an algorithm for community structure partition is proposed by integrating Miyazawa-Jernigan empirical potential energy as edge weight...
September 27, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28945460/estimation-of-rates-of-reactions-triggered-by-electron-transfer-in-top-down-mass-spectrometry
#16
Michał Aleksander Ciach, Mateusz Krzysztof Łącki, Błażej Miasojedow, Frederik Lermyte, Dirk Valkenborg, Frank Sobott, Anna Gambin
Electron transfer dissociation (ETD) is a versatile technique used in mass spectrometry for the high-throughput characterization of proteins. It consists of several concurrent reactions triggered by the transfer of an electron from its anion source to sample cations. Transferring an electron causes peptide backbone cleavage while leaving labile post-translational modifications intact. The obtained fragmentation spectra provide valuable information for sequence and structure analyses. In this study, we propose a formal mathematical model of the ETD fragmentation process in the form of a system of stochastic differential equations describing its joint dynamics...
September 25, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28891687/the-application-of-the-weighted-k-partite-graph-problem-to-the-multiple-alignment-for-metabolic-pathways
#17
Wenbin Chen, William Hendrix, Matthew Schmidt, Nagiza F Samatova
The problem of aligning multiple metabolic pathways is one of very challenging problems in computational biology. A metabolic pathway consists of three types of entities: reactions, compounds, and enzymes. Based on similarities between enzymes, Tohsato et al. gave an algorithm for aligning multiple metabolic pathways. However, the algorithm given by Tohsato et al. neglects the similarities among reactions, compounds, enzymes, and pathway topology. How to design algorithms for the alignment problem of multiple metabolic pathways based on the similarity of reactions, compounds, and enzymes? It is a difficult computational problem...
September 11, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28891684/a-computational-based-method-for-predicting-drug-target-interactions-by-using-stacked-autoencoder-deep-neural-network
#18
Lei Wang, Zhu-Hong You, Xing Chen, Shi-Xiong Xia, Feng Liu, Xin Yan, Yong Zhou, Ke-Jian Song
Identifying the interaction between drugs and target proteins is an important area of drug research, which provides a broad prospect for low-risk and faster drug development. However, due to the limitations of traditional experiments when revealing drug-protein interactions (DTIs), the screening of targets not only takes a lot of time and money but also has high false-positive and false-negative rates. Therefore, it is imperative to develop effective automatic computational methods to accurately predict DTIs in the postgenome era...
September 11, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28876085/joint-analysis-of-snp-snp-environment-interactions-for-chronic-dialysis-by-an-improved-branch-and-bound-algorithm
#19
Cheng-Hong Yang, Yu-Da Lin, Li-Yeh Chuang, Jin-Bor Chen, Hsueh-Wei Chang
In previous studies, both single-nucleotide polymorphism (SNP)-SNP or gene-gene (G × G) interactions and SNP-environmental factor (G × E) interactions were reported to partially account for "missing" heritability. However, (G × G) × E interactions were less commonly addressed. The purpose of this study was to develop a novel strategy to evaluate possible (G × G) × E interactions in D-loop-based chronic dialysis association. Using values from our previously published data set (704 controls and 193 cases) of 77 D-loop SNPs and 7 environmental factors (coronary heart disease, hypertension, diabetes mellitus, triglyceride, cholesterol, blood thiol, and TBARS levels), we compared the performances of G, G × G, G × E, and (G × G) × E...
September 6, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28846457/beacon-editor-capturing-signal-transduction-pathways-using-the-systems-biology-graphical-notation-activity-flow-language
#20
Haitham Elmarakeby, Mostafa Arefiyan, Elijah Myers, Song Li, Ruth Grene, Lenwood S Heath
The Beacon Editor is a cross-platform desktop application for the creation and modification of signal transduction pathways using the Systems Biology Graphical Notation Activity Flow (SBGN-AF) language. Prompted by biologists' requests for enhancements, the Beacon Editor includes numerous powerful features for the benefit of creation and presentation.
August 28, 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"