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

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https://www.readbyqxmd.com/read/28177780/calculating-higher-order-moments-of-phylogenetic-stochastic-mapping-summaries-in-linear-time
#1
Amrit Dhar, Vladimir N Minin
Stochastic mapping is a simulation-based method for probabilistically mapping substitution histories onto phylogenies according to continuous-time Markov models of evolution. This technique can be used to infer properties of the evolutionary process on the phylogeny and, unlike parsimony-based mapping, conditions on the observed data to randomly draw substitution mappings that do not necessarily require the minimum number of events on a tree. Most stochastic mapping applications simulate substitution mappings only to estimate the mean and/or variance of two commonly used mapping summaries: the number of particular types of substitutions (labeled substitution counts) and the time spent in a particular group of states (labeled dwelling times) on the tree...
February 8, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28177752/a-computational-approach-to-studying-protein-folding-problems-considering-the-crucial-role-of-the-intracellular-environment
#2
Pedro P González-Pérez, Daniel J Orta, Irving Peña, Eduardo C Flores, José U Ramírez, Hiram I Beltrán, Salomón J Alas
Intracellular protein folding (PF) is performed in a highly inhomogeneous, crowded, and correlated environment. Due to this inherent complexity, the study and understanding of PF phenomena is a fundamental issue in the field of computational systems biology. In particular, it is important to use a modeled medium that accurately reflects PF in natural systems. In the current study, we present a simulation wherein PF is carried out within an inhomogeneous modeled medium. Simulation resources included a two-dimensional hydrophobic-polar (HP) model, evolutionary algorithms, and the dual site-bond model...
February 8, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28177699/comparing-phylogenetic-trees-by-matching-nodes-using-the-transfer-distance-between-partitions
#3
Damian Bogdanowicz, Krzysztof Giaro
Ability to quantify dissimilarity of different phylogenetic trees describing the relationship between the same group of taxa is required in various types of phylogenetic studies. For example, such metrics are used to assess the quality of phylogeny construction methods, to define optimization criteria in supertree building algorithms, or to find horizontal gene transfer (HGT) events. Among the set of metrics described so far in the literature, the most commonly used seems to be the Robinson-Foulds distance...
February 8, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28177654/phenotype-analysis-method-for-identification-of-gene-functions-involved-in-asymmetric-division-of-caenorhabditis-elegans
#4
Sihai Yang, Xianhua Han, Yukako Tohsato, Koji Kyoda, Shuichi Onami, Ikuko Nishikawa, Yenwei Chen
In gene function analysis, it is arduous to identify gene function individually, and the way to screen out all involved genes according to a particular phenotype or disease usually shows us little information for a specific problem. We present a data-driven analysis system based on wild type (WT) embryos to study the concrete function of each gene associated with certain category of abnormal phenotypes. It can be applied to genes with very few RNAi embryos. Instead of presupposing the particular function of a gene, its function is confirmed by the statistical testing of built models...
February 8, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28177649/evolutionary-relationships-and-taxa-specific-conserved-signature-indels-among-cellulases-of-archaea-bacteria-and-eukarya
#5
Lebin Thomas, Hari Ram, Ved Pal Singh
The cellulases from different cellulolytic organisms have evolutionary relationships, which range from single-celled prokaryotes to the complex eukaryotes of the living world. This in silico analysis revealed the presence of a conserved cellulase domain along with evolutionary relationships among cellulases from several species of Archaea, Bacteria, and Eukarya. The amino acid sequences of cellulases from Archaea and Bacteria showed closer identity with their domain or phylum members that provided insights into convergent and divergent evolution of cellulases from other enzymes with different substrate specificities...
February 8, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28128642/multitask-matrix-completion-for-learning-protein-interactions-across-diseases
#6
Meghana Kshirsagar, Keerthiram Murugesan, Jaime G Carbonell, Judith Klein-Seetharaman
Disease-causing pathogens such as viruses introduce their proteins into the host cells in which they interact with the host's proteins, enabling the virus to replicate inside the host. These interactions between pathogen and host proteins are key to understanding infectious diseases. Often multiple diseases involve phylogenetically related or biologically similar pathogens. Here we present a multitask learning method to jointly model interactions between human proteins and three different but related viruses: Hepatitis C, Ebola virus, and Influenza A...
January 27, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28056190/flexible-modeling-of-genetic-effects-on-function-valued-traits
#7
Nicolo Fusi, Jennifer Listgarten
Genome-wide association studies commonly examine one trait at a time. Occasionally they examine several related traits with the hope of increasing power; in such a setting, the traits are not generally smoothly varying in any way such as time or space. However, for function-valued traits, the trait is often smoothly varying along the axis of interest, such as space or time. For instance, in the case of longitudinal traits such as growth curves, the axis of interest is time; for spatially varying traits such as chromatin accessibility, it would be position along the genome...
January 5, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28056180/clonality-inference-from-single-tumor-samples-using-low-coverage-sequence-data
#8
Nilgun Donmez, Salem Malikic, Alexander W Wyatt, Martin E Gleave, Colin C Collins, S Cenk Sahinalp
Inference of intra-tumor heterogeneity can provide valuable insight into cancer evolution. Somatic mutations detected by sequencing can help estimate the purity of a tumor sample and reconstruct its subclonal composition. Although several methods have been developed to infer intra-tumor heterogeneity, the majority of these tools rely on variant allele frequencies as estimated via ultra-deep sequencing from multiple samples of the same tumor. In practice, obtaining sequencing data from a large number of samples per patient is only feasible in a few cancer types such as liquid tumors, or in rare cases involving solid tumors selected for research...
January 5, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27992255/drosophila-h2a-and-h2a-z-nucleosome-sequences-reveal-different-nucleosome-positioning-sequence-patterns
#9
Doo Yang, Ilya Ioshikhes
Nucleosomes are implicated in transcriptional regulation as well as in packing and stabilizing the DNA. Nucleosome positions affect the transcription by impeding or facilitating the binding of transcription factors. The DNA sequence, especially the periodic occurrences of dinucleotides, is a major factor that affects the nucleosome positioning. We analyzed the Drosophila DNA sequences bound by H2A and H2A.Z nucleosomes. Periodic patterns of dinucleotides (weak-weak/strong-strong or purine-purine/pyrimidine-pyrimidine) were identified as WW/SS and RR/YY nucleosome positioning sequence (NPS) patterns...
December 19, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27992242/a-multiresolution-graphical-representation-for-similarity-relationship-and-multiresolution-clustering-for-biological-sequences
#10
Lianping Yang, Weilin Zhang
How we can describe the similarity relationship between the biological sequences is a basic but important problem in bioinformatics. The first graphical representation method for the similarity relationship rather than for single sequence is proposed in this article, which makes the similarity intuitional. Some properties such as sensitivity and continuity of the similarity are proved theoretically, which indicate that the similarity describer has the advantage of both alignment and alignment-free methods. With the aid of multiresolution analysis tools, we can exhibit the similarity's different profiles, from high resolution to low resolution...
December 19, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27960065/toward-a-better-compression-for-dna-sequences-using-huffman-encoding
#11
Anas Al-Okaily, Badar Almarri, Sultan Al Yami, Chun-Hsi Huang
Due to the significant amount of DNA data that are being generated by next-generation sequencing machines for genomes of lengths ranging from megabases to gigabases, there is an increasing need to compress such data to a less space and a faster transmission. Different implementations of Huffman encoding incorporating the characteristics of DNA sequences prove to better compress DNA data. These implementations center on the concepts of selecting frequent repeats so as to force a skewed Huffman tree, as well as the construction of multiple Huffman trees when encoding...
December 13, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27936934/pathtimex-joint-inference-of-mutually-exclusive-cancer-pathways-and-their-progression-dynamics
#12
Simona Cristea, Jack Kuipers, Niko Beerenwinkel
High-throughput sequencing technologies have facilitated the generation of an unprecedented amount of genomic cancer data, opening the way to a more profound understanding of tumorigenesis. In this endeavor, two fundamental questions have emerged, namely (1) which alterations drive tumor progression and (2) in which order do they occur? Answering these questions is crucial for therapeutic decisions involving targeted agents. Because of interpatient heterogeneity, progression at the level of pathways is more reproducible than progression at the level of single genes...
December 12, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28140675/preface-selected-articles-of-the-second-international-conference-on-algorithms-for-computational-biology-alcob-2015
#13
Adrian-Horia Dediu, Carlos Martín-Vide
No abstract text is available yet for this article.
February 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28045556/generalized-hultman-numbers-and-cycle-structures-of-breakpoint-graphs
#14
Nikita Alexeev, Anna Pologova, Max A Alekseyev
Genome rearrangements can be modeled as k-breaks, which break a genome at k positions and glue the resulting fragments in a new order. In particular, reversals, translocations, fusions, and fissions are modeled as 2-breaks, and transpositions are modeled as 3-breaks. Although k-break rearrangements for [Formula: see text] have not been observed in evolution, they are used in cancer genomics to model chromothripsis, a catastrophic event of multiple breakages happening simultaneously in a genome. It is known that the k-break distance between two genomes (i...
February 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27983874/a-more-practical-algorithm-for-the-rooted-triplet-distance
#15
Jesper Jansson, Ramesh Rajaby
The rooted triplet distance is a measure of the dissimilarity of two phylogenetic trees with identical leaf label sets. An algorithm by Brodal et al. that computes it in [Formula: see text] time and [Formula: see text] space, where n is the number of leaf labels, has recently been implemented in the software package tqDist. In this article, we show that replacing the hierarchical decomposition tree used in Brodal et al.'s algorithm by a centroid paths-based data structure yields an [Formula: see text]-time and [Formula: see text]-space algorithm that, although slower in theory, is faster in practice as well as less memory consuming...
February 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27759426/interaction-based-feature-selection-for-uncovering-cancer-driver-genes-through-copy-number-driven-expression-level
#16
Heewon Park, Atsushi Niida, Seiya Imoto, Satoru Miyano
Driver gene selection is crucial to understand the heterogeneous system of cancer. To identity cancer driver genes, various statistical strategies have been proposed, especially the L1-type regularization methods have drawn a large amount of attention. However, the statistical approaches have been developed purely from algorithmic and statistical point, and the existing studies have applied the statistical approaches to genomic data analysis without consideration of biological knowledge. We consider a statistical strategy incorporating biological knowledge to identify cancer driver gene...
February 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27704866/sorting-by-cuts-joins-and-whole-chromosome-duplications
#17
Ron Zeira, Ron Shamir
Genome rearrangement problems have been extensively studied due to their importance in biology. Most studied models assumed a single copy per gene. However, in reality, duplicated genes are common, most notably in cancer. In this study, we make a step toward handling duplicated genes by considering a model that allows the atomic operations of cut, join, and whole chromosome duplication. Given two linear genomes, [Formula: see text] with one copy per gene and [Formula: see text] with two copies per gene, we give a linear time algorithm for computing a shortest sequence of operations transforming [Formula: see text] into [Formula: see text] such that all intermediate genomes are linear...
February 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27529135/effect-of-protein-repetitiveness-on-protein-protein-interaction-prediction-results-using-support-vector-machines
#18
Jie Zhou
BACKGROUND: There are many computational approaches to predict the protein-protein interactions using support vector machines (SVMs) with high performance. In fact, performance of currently reported methods are significantly over-estimated and affected by the object repetitiveness in the datasets used. OBJECTIVE: To study the effect of object repetitiveness of datasets on predicting results. METHOD: We present novel methods to construct different positive datasets with or without repeating proteins using graph maximum matching in the protein-protein interaction datasets and corresponding series of negative datasets with different proteins repetitiveness are constructed using graph adjacency matrix...
February 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27508455/identification-of-genes-involved-in-breast-cancer-metastasis-by-integrating-protein-protein-interaction-information-with-expression-data
#19
Xin Tian, Mingyuan Xin, Jian Luo, Mingyao Liu, Zhenran Jiang
The selection of relevant genes for breast cancer metastasis is critical for the treatment and prognosis of cancer patients. Although much effort has been devoted to the gene selection procedures by use of different statistical analysis methods or computational techniques, the interpretation of the variables in the resulting survival models has been limited so far. This article proposes a new Random Forest (RF)-based algorithm to identify important variables highly related with breast cancer metastasis, which is based on the important scores of two variable selection algorithms, including the mean decrease Gini (MDG) criteria of Random Forest and the GeneRank algorithm with protein-protein interaction (PPI) information...
February 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27387364/statistically-consistent-k-mer-methods-for-phylogenetic-tree-reconstruction
#20
Elizabeth S Allman, John A Rhodes, Seth Sullivant
Frequencies of k-mers in sequences are sometimes used as a basis for inferring phylogenetic trees without first obtaining a multiple sequence alignment. We show that a standard approach of using the squared Euclidean distance between k-mer vectors to approximate a tree metric can be statistically inconsistent. To remedy this, we derive model-based distance corrections for orthologous sequences without gaps, which lead to consistent tree inference. The identifiability of model parameters from k-mer frequencies is also studied...
February 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
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