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/28056190/flexible-modeling-of-genetic-effects-on-function-valued-traits
#1
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
#2
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/28045556/generalized-hultman-numbers-and-cycle-structures-of-breakpoint-graphs
#3
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...
January 3, 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
#4
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
#5
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/27983874/a-more-practical-algorithm-for-the-rooted-triplet-distance
#6
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...
December 16, 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
#7
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
#8
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/27936925/comparing-an-atomic-model-or-structure-to-a-corresponding-cryo-electron-microscopy-image-at-the-central-axis-of-a-helix
#9
Stephanie Zeil, Julio Kovacs, Willy Wriggers, Jing He
Three-dimensional density maps of biological specimens from cryo-electron microscopy (cryo-EM) can be interpreted in the form of atomic models that are modeled into the density, or they can be compared to known atomic structures. When the central axis of a helix is detectable in a cryo-EM density map, it is possible to quantify the agreement between this central axis and a central axis calculated from the atomic model or structure. We propose a novel arc-length association method to compare the two axes reliably...
December 12, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27901606/protein-folding-prediction-in-a-cubic-lattice-in-hydrophobic-polar-model
#10
Nicola Yanev, Metodi Traykov, Peter Milanov, Borislav Yurukov
The tertiary structure of the proteins determines their functions. Therefore, the predicting of protein's tertiary structure, based on the primary amino acid sequence from long time, is the most important and challenging subject in biochemistry, molecular biology, and biophysics. One of the most popular protein structure prediction methods, called Hydrophobic-Polar (HP) model, is based on the observation that in polar environment hydrophobic amino acids are in the core of the molecule-in contact between them and more polar amino acids are in contact with the polar environment...
November 30, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27901586/long-single-molecule-reads-can-resolve-the-complexity-of-the-influenza-virus-composed-of-rare-closely-related-mutant-variants
#11
Alexander Artyomenko, Nicholas C Wu, Serghei Mangul, Eleazar Eskin, Ren Sun, Alex Zelikovsky
As a result of a high rate of mutations and recombination events, an RNA-virus exists as a heterogeneous "swarm" of mutant variants. The long read length offered by single-molecule sequencing technologies allows each mutant variant to be sequenced in a single pass. However, high error rate limits the ability to reconstruct heterogeneous viral population composed of rare, related mutant variants. In this article, we present two single-nucleotide variants (2SNV), a method able to tolerate the high error rate of the single-molecule protocol and reconstruct mutant variants...
November 30, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27892712/variability-in-metagenomic-count-data-and-its-influence-on-the-identification-of-differentially-abundant-genes
#12
Viktor Jonsson, Tobias Österlund, Olle Nerman, Erik Kristiansson
Metagenomics is the study of microorganisms in environmental and clinical samples using high-throughput sequencing of random fragments of their DNA. Since metagenomics does not require any prior culturing of isolates, entire microbial communities can be studied directly in their natural state. In metagenomics, the abundance of genes is quantified by sorting and counting the DNA fragments. The resulting count data are high-dimensional and affected by high levels of technical and biological noise that make the statistical analysis challenging...
November 28, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27892695/defining-low-dimensional-projections-to-guide-protein-conformational-sampling
#13
Anastasia Novinskaya, Didier Devaurs, Mark Moll, Lydia E Kavraki
Exploring the conformational space of proteins is critical to characterize their functions. Numerous methods have been proposed to sample a protein's conformational space, including techniques developed in the field of robotics and known as sampling-based motion-planning algorithms (or sampling-based planners). However, these algorithms suffer from the curse of dimensionality when applied to large proteins. Many sampling-based planners attempt to mitigate this issue by keeping track of sampling density to guide conformational sampling toward unexplored regions of the conformational space...
November 28, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27892693/a-graph-approach-to-mining-biological-patterns-in-the-binding-interfaces
#14
Wen Cheng, Changhui Yan
Protein-RNA interactions play important roles in the biological systems. Searching for regular patterns in the Protein-RNA binding interfaces is important for understanding how protein and RNA recognize each other and bind to form a complex. Herein, we present a graph-mining method for discovering biological patterns in the protein-RNA interfaces. We represented known protein-RNA interfaces using graphs and then discovered graph patterns enriched in the interfaces. Comparison of the discovered graph patterns with UniProt annotations showed that the graph patterns had a significant overlap with residue sites that had been proven crucial for the RNA binding by experimental methods...
November 28, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27870559/combinatorial-methods-for-epistasis-and-dominance
#15
Serge Sverdlov, Elizabeth Thompson
We develop computational tools for the analysis of nonlinear genotype-phenotype relationships with epistasis among multiple loci or dominance interactions among multiple alleles within the same locus. Theory distinguishes between separable traits, with removable epistasis, and traits with essential epistasis. Separable traits can be transformed to a natural scale where additive methods apply. The methods we present solve for the natural scale, exactly when possible and approximately when not. Through graph methods, our methods allow for enumeration, counting, or sampling of distinct trait architectures satisfying constraints from the separability theory...
November 21, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27835030/a-mad-bayes-algorithm-for-state-space-inference-and-clustering-with-application-to-querying-large-collections-of-chip-seq-data-sets
#16
Chandler Zuo, Kailei Chen, Sündüz Keleş
Current analytic approaches for querying large collections of chromatin immunoprecipitation followed by sequencing (ChIP-seq) data from multiple cell types rely on individual analysis of each data set (i.e., peak calling) independently. This approach discards the fact that functional elements are frequently shared among related cell types and leads to overestimation of the extent of divergence between different ChIP-seq samples. Methods geared toward multisample investigations have limited applicability in settings that aim to integrate 100s to 1000s of ChIP-seq data sets for query loci (e...
November 11, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27828710/improving-bloom-filter-performance-on-sequence-data-using-k-mer-bloom-filters
#17
David Pellow, Darya Filippova, Carl Kingsford
Using a sequence's k-mer content rather than the full sequence directly has enabled significant performance improvements in several sequencing applications, such as metagenomic species identification, estimation of transcript abundances, and alignment-free comparison of sequencing data. As k-mer sets often reach hundreds of millions of elements, traditional data structures are often impractical for k-mer set storage, and Bloom filters (BFs) and their variants are used instead. BFs reduce the memory footprint required to store millions of k-mers while allowing for fast set containment queries, at the cost of a low false positive rate (FPR)...
November 9, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27788022/on-computing-breakpoint-distances-for-genomes-with-duplicate-genes
#18
Mingfu Shao, Bernard M E Moret
A fundamental problem in comparative genomics is to compute the distance between two genomes in terms of its higher level organization (given by genes or syntenic blocks). For two genomes without duplicate genes, we can easily define (and almost always efficiently compute) a variety of distance measures, but the problem is NP-hard under most models when genomes contain duplicate genes. To tackle duplicate genes, three formulations (exemplar, maximum matching, and any matching) have been proposed, all of which aim to build a matching between homologous genes so as to minimize some distance measure...
October 27, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28051901/influential-mutations-in-the-smad4-trimer-complex-can-be-detected-from-disruptions-of-electrostatic-complementarity
#19
Bridget E Nolan, Emily Levenson, Brian Y Chen
This article examines three techniques for rapidly assessing the electrostatic contribution of individual amino acids to the stability of protein-protein complexes. Whereas the energetic minimization of modeled oligomers may yield more accurate complexes, we examined the possibility that simple modeling may be sufficient to identify amino acids that add to or detract from electrostatic complementarity. The three methods evaluated were (a) the elimination of entire side chains (e.g., glycine scanning), (b) the elimination of the electrostatic contribution from the atoms of a side chain, called nullification, and (c) side chain structure prediction using SCWRL4...
January 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28051900/preface-selected-articles-from-2015-computational-structural-bioinformatics-workshop
#20
Jing He, Nurit Haspel, Brian Chen
No abstract text is available yet for this article.
January 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"