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Bioinformatics & Computational Biology

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https://www.readbyqxmd.com/read/27914045/achievements-and-challenges-in-computational-protein-design
#1
Ilan Samish
Computational protein design (CPD), a yet evolving field, includes computer-aided engineering for partial or full de novo designs of proteins of interest. Designs are defined by a requested structure, function, or working environment. This chapter describes the birth and maturation of the field by presenting 101 CPD examples in a chronological order emphasizing achievements and pending challenges. Integrating these aspects presents the plethora of CPD approaches with the hope of providing a "CPD 101". These reflect on the broader structural bioinformatics and computational biophysics field and include: (1) integration of knowledge-based and energy-based methods, (2) hierarchical designated approach towards local, regional, and global motifs and the integration of high- and low-resolution design schemes that fit each such region, (3) systematic differential approaches towards different protein regions, (4) identification of key hot-spot residues and the relative effect of remote regions, (5) assessment of shape-complementarity, electrostatics and solvation effects, (6) integration of thermal plasticity and functional dynamics, (7) negative design, (8) systematic integration of experimental approaches, (9) objective cross-assessment of methods, and (10) successful ranking of potential designs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27909575/a-step-by-step-workflow-for-low-level-analysis-of-single-cell-rna-seq-data
#2
Aaron T L Lun, Davis J McCarthy, John C Marioni
Single-cell RNA sequencing (scRNA-seq) is widely used to profile the transcriptome of individual cells. This provides biological resolution that cannot be matched by bulk RNA sequencing, at the cost of increased technical noise and data complexity. The differences between scRNA-seq and bulk RNA-seq data mean that the analysis of the former cannot be performed by recycling bioinformatics pipelines for the latter. Rather, dedicated single-cell methods are required at various steps to exploit the cellular resolution while accounting for technical noise...
2016: F1000Research
https://www.readbyqxmd.com/read/27893735/computational-discovery-of-putative-leads-for-drug-repositioning-through-drug-target-interaction-prediction
#3
Edgar D Coelho, Joel P Arrais, José Luís Oliveira
De novo experimental drug discovery is an expensive and time-consuming task. It requires the identification of drug-target interactions (DTIs) towards targets of biological interest, either to inhibit or enhance a specific molecular function. Dedicated computational models for protein simulation and DTI prediction are crucial for speed and to reduce the costs associated with DTI identification. In this paper we present a computational pipeline that enables the discovery of putative leads for drug repositioning that can be applied to any microbial proteome, as long as the interactome of interest is at least partially known...
November 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27893399/enumerating-substituted-benzene-isomers-of-tree-like-chemical-graphs
#4
Jinghui Li, Hiroshi Nagamochi, Tatsuya Akutsu
Enumeration of chemical structures is useful for drug design, which is one of the main targets of computational biology and bioinformatics. A chemical graph G with no other cycles than benzene rings is called tree-like, and becomes a tree T possibly with multiple edges if we contract each benzene ring into a single virtual atom of valence 6. All tree-like chemical graphs with a given tree representation T are called the substituted benzene isomers of T. When we replace each virtual atom in T with a benzene ring to obtain a substituted benzene isomer, distinct isomers of T are caused by the difference in arrangements of atom groups around a benzene ring...
November 15, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/27887974/perusal-of-parasitic-nematode-omics-in-the-post-genomic-era
#5
Jonathan D Stoltzfus, Adeiye A Pilgrim, De'Broski R Herbert
The advent of high-throughput, next-generation sequencing methods combined with advances in computational biology and bioinformatics have greatly accelerated discovery within biomedical research. This "post-genomics" era has ushered in powerful approaches allowing one to quantify RNA transcript and protein abundance for every gene in the genome - often for multiple conditions. Herein, we chronicle how the post-genomics era has advanced our overall understanding of parasitic nematodes through transcriptomics and proteomics and highlight some of the important advances made in each major nematode clade...
November 22, 2016: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/27882067/bioinformatic-identification-of-rare-codon-clusters-rccs-in-hbv-genome-and-evaluation-of-rccs-in-proteins-structure-of-hepatitis-b-virus
#6
Mojtaba Mortazavi, Mohammad Zarenezhad, Saeid Gholamzadeh, Seyed Moayed Alavian, Mohammad Ghorbani, Reza Dehghani, Abdorrasoul Malekpour, Mohammadhasan Meshkibaf, Ali Fakhrzad
BACKGROUND: Hepatitis B virus (HBV) as an infectious disease that has nine genotypes (A - I) and a 'putative' genotype J. OBJECTIVES: The aim of this study was to identify the rare codon clusters (RCC) in the HBV genome and to evaluate these RCCs in the HBV proteins structure. METHODS: For detection of protein family accession numbers (Pfam) in HBV proteins, the UniProt database and Pfam search tool were used. Protein family accession numbers is a comprehensive and accurate collection of protein domains and families...
October 2016: Hepatitis Monthly
https://www.readbyqxmd.com/read/27863463/the-chip-seq-tools-and-web-server-a-resource-for-analyzing-chip-seq-and-other-types-of-genomic-data
#7
Giovanna Ambrosini, René Dreos, Sunil Kumar, Philipp Bucher
BACKGROUND: ChIP-seq and related high-throughput chromatin profilig assays generate ever increasing volumes of highly valuable biological data. To make sense out of it, biologists need versatile, efficient and user-friendly tools for access, visualization and itegrative analysis of such data. RESULTS: Here we present the ChIP-Seq command line tools and web server, implementing basic algorithms for ChIP-seq data analysis starting with a read alignment file. The tools are optimized for memory-efficiency and speed thus allowing for processing of large data volumes on inexpensive hardware...
November 18, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27843944/systematic-identification-and-bioinformatic-analysis-of-micrornas-in-response-to-infections-of-coxsackievirus-a16-and-enterovirus-71
#8
Zheng Zhu, Yuhua Qi, Huan Fan, Lunbiao Cui, Zhiyang Shi
Hand, foot, and mouth disease (HFMD), mainly caused by coxsackievirus A16 (CVA16) and enterovirus 71 (EV71) infections, remains a serious public health issue with thousands of newly diagnostic cases each year since 2008 in China. The mechanisms underlying viral infection, however, are elusive to date. In the present study, we systematically investigated the host cellular microRNA (miRNA) expression patterns in response to CVA16 and EV71 infections. Through microarray examination, 27 miRNAs (15 upregulated and 12 downregulated) were found to be coassociated with the replication process of two viruses, while the expression levels of 15 and 5 miRNAs were significantly changed in CVA16- and EV71-infected cells, respectively...
2016: BioMed Research International
https://www.readbyqxmd.com/read/27843486/efficient-regularized-regression-with-l0-penalty-for-variable-selection-and-network-construction
#9
Zhenqiu Liu, Gang Li
Variable selections for regression with high-dimensional big data have found many applications in bioinformatics and computational biology. One appealing approach is the L0 regularized regression which penalizes the number of nonzero features in the model directly. However, it is well known that L0 optimization is NP-hard and computationally challenging. In this paper, we propose efficient EM (L0EM) and dual L0EM (DL0EM) algorithms that directly approximate the L0 optimization problem. While L0EM is efficient with large sample size, DL0EM is efficient with high-dimensional (n ≪ m) data...
2016: Computational and Mathematical Methods in Medicine
https://www.readbyqxmd.com/read/27829232/circular-rnas-and-their-associations-with-breast-cancer-subtypes
#10
Asha A Nair, Nifang Niu, Xiaojia Tang, Kevin J Thompson, Liewei Wang, Jean-Pierre Kocher, Subbaya Subramanian, Krishna R Kalari
Circular RNAs (circRNAs) are highly stable forms of non-coding RNAs with diverse biological functions. They are implicated in modulation of gene expression thus affecting various cellular and disease processes. Based on existing bioinformatics approaches, we developed a comprehensive workflow called Circ-Seq to identify and report expressed circRNAs. Circ-Seq also provides informative genomic annotation along circRNA fused junctions thus allowing prioritization of circRNA candidates. We applied Circ-Seq first to RNA-sequence data from breast cancer cell lines and validated one of the large circRNAs identified...
November 5, 2016: Oncotarget
https://www.readbyqxmd.com/read/27812935/computational-methods-for-annotation-transfers-from-sequence
#11
Domenico Cozzetto, David T Jones
Surveys of public sequence resources show that experimentally supported functional information is still completely missing for a considerable fraction of known proteins and is clearly incomplete for an even larger portion. Bioinformatics methods have long made use of very diverse data sources alone or in combination to predict protein function, with the understanding that different data types help elucidate complementary biological roles. This chapter focuses on methods accepting amino acid sequences as input and producing GO term assignments directly as outputs; the relevant biological and computational concepts are presented along with the advantages and limitations of individual approaches...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27801297/path2enet-generation-of-human-pathway-derived-networks-in-an-expression-specific-context
#12
Conrad Droste, Javier De Las Rivas
BACKGROUND: Biological pathways are subsets of the complex biomolecular wiring that occur in living cells. They are usually rationalized and depicted in cartoon maps or charts to show them in a friendly visible way. Despite these efforts to present biological pathways, the current progress of bioinformatics indicates that translation of pathways in networks can be a very useful approach to achieve a computer-based view of the complex processes and interactions that occurr in a living system...
October 25, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27797764/rednemo-topology-based-ppi-network-reconstruction-via-repeated-diffusion-with-neighborhood-modifications
#13
Ferhat Alkan, Cesim Erten
MOTIVATION: Analysis of protein-protein interaction (PPI) networks provides invaluable insight into several systems biology problems. High-throughput experimental techniques together with computational methods provide large-scale PPI networks. However a major issue with these networks is their erroneous nature; they contain false-positive interactions and usually many more false-negatives. Recently several computational methods have been proposed for network reconstruction based on topology, where given an input PPI network the goal is to reconstruct the network by identifying false positives/negatives as correctly as possible...
October 22, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27794042/the-rcsb-protein-data-bank-integrative-view-of-protein-gene-and-3d-structural-information
#14
Peter W Rose, Andreas Prlić, Ali Altunkaya, Chunxiao Bi, Anthony R Bradley, Cole H Christie, Luigi Di Costanzo, Jose M Duarte, Shuchismita Dutta, Zukang Feng, Rachel Kramer Green, David S Goodsell, Brian Hudson, Tara Kalro, Robert Lowe, Ezra Peisach, Christopher Randle, Alexander S Rose, Chenghua Shao, Yi-Ping Tao, Yana Valasatava, Maria Voigt, John D Westbrook, Jesse Woo, Huangwang Yang, Jasmine Y Young, Christine Zardecki, Helen M Berman, Stephen K Burley
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, http://rcsb.org), the US data center for the global PDB archive, makes PDB data freely available to all users, from structural biologists to computational biologists and beyond. New tools and resources have been added to the RCSB PDB web portal in support of a 'Structural View of Biology.' Recent developments have improved the User experience, including the high-speed NGL Viewer that provides 3D molecular visualization in any web browser, improved support for data file download and enhanced organization of website pages for query, reporting and individual structure exploration...
October 27, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27793083/mevolib-v1-0-the-first-molecular-evolution-library-for-python
#15
Jorge Álvarez-Jarreta, Eduardo Ruiz-Pesini
BACKGROUND: Molecular evolution studies involve many different hard computational problems solved, in most cases, with heuristic algorithms that provide a nearly optimal solution. Hence, diverse software tools exist for the different stages involved in a molecular evolution workflow. RESULTS: We present MEvoLib, the first molecular evolution library for Python, providing a framework to work with different tools and methods involved in the common tasks of molecular evolution workflows...
October 28, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27784624/multiple-sequence-alignment-using-multi-objective-based-bacterial-foraging-optimization-algorithm
#16
R Ranjani Rani, D Ramyachitra
Multiple sequence alignment (MSA) is a widespread approach in computational biology and bioinformatics. MSA deals with how the sequences of nucleotides and amino acids are sequenced with possible alignment and minimum number of gaps between them, which directs to the functional, evolutionary and structural relationships among the sequences. Still the computation of MSA is a challenging task to provide an efficient accuracy and statistically significant results of alignments. In this work, the Bacterial Foraging Optimization Algorithm was employed to align the biological sequences which resulted in a non-dominated optimal solution...
October 23, 2016: Bio Systems
https://www.readbyqxmd.com/read/27778110/surface-proteome-mining-for-identification-of-potential-vaccine-candidates-against-campylobacter-jejuni-an-in-silico-approach
#17
Kusum Mehla, Jayashree Ramana
Campylobacter jejuni remains a major cause of human gastroenteritis with estimated annual incidence rate of 450 million infections worldwide. C. jejuni is a major burden to public health in both socioeconomically developing and industrialized nations. Virulence determinants involved in C. jejuni pathogenesis are multifactorial in nature and not yet fully understood. Despite the completion of the first C. jejuni genome project in 2000, there are currently no vaccines in the market against this pathogen. Traditional vaccinology approach is an arduous and time extensive task...
October 24, 2016: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27777973/systems-biology-analysis-reveals-role-of-mdm2-in-diabetic-nephropathy
#18
Rintaro Saito, Anaïs Rocanin-Arjo, Young-Hyun You, Manjula Darshi, Benjamin Van Espen, Satoshi Miyamoto, Jessica Pham, Minya Pu, Simone Romoli, Loki Natarajan, Wenjun Ju, Matthias Kretzler, Robert Nelson, Keiichiro Ono, Dana Thomasova, Shrikant R Mulay, Trey Ideker, Vivette D'Agati, Ergin Beyret, Juan Carlos Izpisua Belmonte, Hans Joachim Anders, Kumar Sharma
To derive new insights in diabetic complications, we integrated publicly available human protein-protein interaction (PPI) networks with global metabolic networks using metabolomic data from patients with diabetic nephropathy. We focused on the participating proteins in the network that were computationally predicted to connect the urine metabolites. MDM2 had the highest significant number of PPI connections. As validation, significant downregulation of MDM2 gene expression was found in both glomerular and tubulointerstitial compartments of kidney biopsy tissue from 2 independent cohorts of patients with diabetic nephropathy...
October 20, 2016: JCI Insight
https://www.readbyqxmd.com/read/27769991/computational-pan-genomics-status-promises-and-challenges
#19
(no author information available yet)
Many disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case of Homo sapiens, the number of sequenced genomes will approach hundreds of thousands in the next few years. Simply scaling up established bioinformatics pipelines will not be sufficient for leveraging the full potential of such rich genomic data sets. Instead, novel, qualitatively different computational methods and paradigms are needed...
October 21, 2016: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/27766933/proceedings-of-the-2016-midsouth-computational-biology-and-bioinformatics-society-mcbios-conference
#20
Jonathan D Wren, Inimary Toby, Huxiao Hong, Bindu Nanduri, Rakesh Kaundal, Mikhail G Dozmorov, Shraddha Thakkar
No abstract text is available yet for this article.
October 6, 2016: BMC Bioinformatics
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