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Bioinformatics & Computational Biology

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https://www.readbyqxmd.com/read/28547747/deciphering-common-recognition-principles-of-nucleoside-mono-di-and-tri-phosphates-binding-in-diverse-proteins-via-structural-matching-of-their-binding-sites
#1
Raghu Bhagavat, Narayanaswamy Srinivasan, Nagasuma Chandra
Nucleoside triphosphate (NTP) ligands are of high biological importance and essential for all life forms. A pre-requisite for them to participate in diverse biochemical processes is their recognition by diverse proteins. It is thus of great interest to understand the basis for such recognition in different proteins. Towards this, we have employed a structural bioinformatics approach and analyse structures of 4677 NTP complexes available in PDB. Binding sites were extracted and compared exhaustively by using PocketMatch, a sensitive in-house site comparison algorithm, which resulted in grouping the entire dataset into 27 site-types...
May 25, 2017: Proteins
https://www.readbyqxmd.com/read/28542514/panweb-a-web-interface-for-pan-genomic-analysis
#2
Yan Pantoja, Kenny Pinheiro, Allan Veras, Fabrício Araújo, Ailton Lopes de Sousa, Luis Carlos Guimarães, Artur Silva, Rommel T J Ramos
With increased production of genomic data since the advent of next-generation sequencing (NGS), there has been a need to develop new bioinformatics tools and areas, such as comparative genomics. In comparative genomics, the genetic material of an organism is directly compared to that of another organism to better understand biological species. Moreover, the exponentially growing number of deposited prokaryote genomes has enabled the investigation of several genomic characteristics that are intrinsic to certain species...
2017: PloS One
https://www.readbyqxmd.com/read/28541404/m2align-parallel-multiple-sequence-alignment-with-a-multi-objective-metaheuristic
#3
Cristian Zambrano-Vega, Antonio J Nebro, José García-Nieto, José F Aldana Montes
Motivation: Multiple Sequence Alignment (MSA) is an NP-complete optimization problem found in computational biology, where the time complexity of finding an optimal alignment raises exponentially along with the number of sequences and their lengths. Additionally, to assess the quality of a MSA, a number of objectives can be taken into account, such as maximizing the sum-of-pairs, maximizing the totally conserved columns, minimizing the number of gaps, or maximizing structural information based scores such as STRIKE...
May 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28535296/metasra-normalized-human-sample-specific-metadata-for-the-sequence-read-archive
#4
Matthew N Bernstein, AnHai Doan, Colin N Dewey
Motivation: The NCBI's Sequence Read Archive (SRA) promises great biological insight if one could analyze the data in the aggregate; however, the data remain largely underutilized, in part, due to the poor structure of the metadata associated with each sample. The rules governing submissions to the SRA do not dictate a standardized set of terms that should be used to describe the biological samples from which the sequencing data are derived. As a result, the metadata include many synonyms, spelling variants, and references to outside sources of information...
May 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28533216/a-diverse-community-to-study-communities-integration-of-experiments-and-mathematical-models-to-study-microbial-consortia
#5
Antonella Succurro, Fiona Wanjiku Moejes, Oliver Ebenhöh
The last few years have seen the advancement of high-throughput experimental techniques produce an extraordinary amount of data. Bioinformatics and statistical analyses have become instrumental to interpreting the information coming from e.g. sequencing data, and often motivate further targeted experiments. The broad discipline of "computational biology" spans far beyond the well-established field of bioinformatics, but it is our impression that more theoretical methods like mathematical models are not yet as well integrated in the research studying microbial interactions...
May 22, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28502001/clustering-and-network-analysis-of-reverse-phase-protein-array-data
#6
Adam Byron
Molecular profiling of proteins and phosphoproteins using a reverse phase protein array (RPPA) platform, with a panel of target-specific antibodies, enables the parallel, quantitative proteomic analysis of many biological samples in a microarray format. Hence, RPPA analysis can generate a high volume of multidimensional data that must be effectively interrogated and interpreted. A range of computational techniques for data mining can be applied to detect and explore data structure and to form functional predictions from large datasets...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28499419/across-proteome-modeling-of-dimer-structures-for-the-bottom-up-assembly-of-protein-protein-interaction-networks
#7
Surabhi Maheshwari, Michal Brylinski
BACKGROUND: Deciphering complete networks of interactions between proteins is the key to comprehend cellular regulatory mechanisms. A significant effort has been devoted to expanding the coverage of the proteome-wide interaction space at molecular level. Although a growing body of research shows that protein docking can, in principle, be used to predict biologically relevant interactions, the accuracy of the across-proteome identification of interacting partners and the selection of near-native complex structures still need to be improved...
May 12, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28487426/digitally-barcoding-mycobacterium-tuberculosis-reveals-in-vivo-infection-dynamics-in-the-macaque-model-of-tuberculosis
#8
Constance J Martin, Anthony M Cadena, Vivian W Leung, Philana Ling Lin, Pauline Maiello, Nathan Hicks, Michael R Chase, JoAnne L Flynn, Sarah M Fortune
Infection with Mycobacterium tuberculosis causes a spectrum of outcomes; the majority of individuals contain but do not eliminate the infection, while a small subset present with primary active tuberculosis (TB) disease. This variability in infection outcomes is recapitulated at the granuloma level within each host, such that some sites of infection can be fully cleared while others progress. Understanding the spectrum of TB outcomes requires new tools to deconstruct the mechanisms underlying differences in granuloma fate...
May 9, 2017: MBio
https://www.readbyqxmd.com/read/28481952/identification-of-potential-new-treatment-response-markers-and-therapeutic-targets-using-a-gaussian-process-based-method-in-lapatinib-insensitive-breast-cancer-models
#9
Tapesh Santra, Sandra Roche, Neil Conlon, Norma O'Donovan, John Crown, Robert O'Connor, Walter Kolch
Molecularly targeted therapeutics hold promise of revolutionizing treatments of advanced malignancies. However, a large number of patients do not respond to these treatments. Here, we take a systems biology approach to understand the molecular mechanisms that prevent breast cancer (BC) cells from responding to lapatinib, a dual kinase inhibitor that targets human epidermal growth factor receptor 2 (HER2) and epidermal growth factor receptor (EGFR). To this end, we analysed temporal gene expression profiles of four BC cell lines, two of which respond and the remaining two do not respond to lapatinib...
2017: PloS One
https://www.readbyqxmd.com/read/28469415/current-developments-in-machine-learning-techniques-in-biological-data-mining
#10
EDITORIAL
Gerard G Dumancas, Indra Adrianto, Ghalib Bello, Mikhail Dozmorov
This supplement is intended to focus on the use of machine learning techniques to generate meaningful information on biological data. This supplement under Bioinformatics and Biology Insights aims to provide scientists and researchers working in this rapid and evolving field with online, open-access articles authored by leading international experts in this field. Advances in the field of biology have generated massive opportunities to allow the implementation of modern computational and statistical techniques...
2017: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/28461555/cell-scientist-to-watch-mitchell-guttman
#11
(no author information available yet)
Mitchell received a bachelor's degree in molecular and computational biology and a master's degree in computational biology and bioinformatics from the University of Pennsylvania. He then joined the laboratory of Eric Lander at the Broad Institute of MIT and Harvard and was awarded his PhD in 2012. The same year he was named in the Forbes '30 under 30: science and healthcare' list of rising stars and received an NIH early independence award. Mitchell subsequently moved to the California Institute of Technology as an Assistant Professor to establish his own laboratory...
May 1, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28460068/in-silico-polypharmacology-of-natural-products
#12
Jiansong Fang, Chuang Liu, Qi Wang, Ping Lin, Feixiong Cheng
Natural products with polypharmacological profiles have demonstrated promise as novel therapeutics for various complex diseases, including cancer. Currently, many gaps exist in our knowledge of which compounds interact with which targets, and experimentally testing all possible interactions is infeasible. Recent advances and developments of systems pharmacology and computational (in silico) approaches provide powerful tools for exploring the polypharmacological profiles of natural products. In this review, we introduce recent progresses and advances of computational tools and systems pharmacology approaches for identifying drug targets of natural products by focusing on the development of targeted cancer therapy...
April 27, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28459942/riblast-an-ultrafast-rna-rna-interaction-prediction-system-based-on-a-seed-and-extension-approach
#13
Tsukasa Fukunaga, Michiaki Hamada
Motivation: LncRNAs play important roles in various biological processes. Although more than 58,000 human lncRNA genes have been discovered, most known lncRNAs are still poorly characterised. One approach to understanding the functions of lncRNAs is the detection of the interacting RNA target of each lncRNA. Because experimental detections of comprehensive lncRNA-RNA interactions are difficult, computational prediction of lncRNA-RNA interactions is an indispensable technique. However, the high computational costs of existing RNA-RNA interaction prediction tools prevent their application to largescale lncRNA datasets...
April 28, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28458782/protein-post-translational-modifications-in-silico-prediction-tools-and-molecular-modeling
#14
REVIEW
Martina Audagnotto, Matteo Dal Peraro
Post-translational modifications (PTMs) occur in almost all proteins and play an important role in numerous biological processes by significantly affecting proteins' structure and dynamics. Several computational approaches have been developed to study PTMs (e.g., phosphorylation, sumoylation or palmitoylation) showing the importance of these techniques in predicting modified sites that can be further investigated with experimental approaches. In this review, we summarize some of the available online platforms and their contribution in the study of PTMs...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28453671/wright-fisher-exact-solver-wfes-scalable-analysis-of-population-genetic-models-without-simulation-or-diffusion-theory
#15
Ivan Krukov, Bianca de Sanctis, A P Jason de Koning
Motivation: The simplifying assumptions that are used widely in theoretical population genetics may not always be appropriate for empirical population genetics. General computational approaches that do not require the assumptions of classical theory are therefore quite desirable. One such general approach is provided by the theory of absorbing Markov chains, which can be used to obtain exact results by directly analyzing population genetic Markov models, such as the classic bi-allelic Wright-Fisher model...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453669/image-based-correction-of-continuous-and-discontinuous-non-planar-axial-distortion-in-serial-section-microscopy
#16
Philipp Hanslovsky, John A Bogovic, Stephan Saalfeld
Motivation: Serial section microscopy is an established method for detailed anatomy reconstruction of biological specimen. During the last decade, high resolution electron microscopy (EM) of serial sections has become the de-facto standard for reconstruction of neural connectivity at ever increasing scales (EM connectomics). In serial section microscopy, the axial dimension of the volume is sampled by physically removing thin sections from the embedded specimen and subsequently imaging either the block-face or the section series...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453668/a-mass-graph-based-approach-for-the-identification-of-modified-proteoforms-using-top-down-tandem-mass-spectra
#17
Qiang Kou, Si Wu, Nikola Tolic, Ljiljana Paša-Tolic, Yunlong Liu, Xiaowen Liu
Motivation: Although proteomics has rapidly developed in the past decade, researchers are still in the early stage of exploring the world of complex proteoforms, which are protein products with various primary structure alterations resulting from gene mutations, alternative splicing, post-translational modifications, and other biological processes. Proteoform identification is essential to mapping proteoforms to their biological functions as well as discovering novel proteoforms and new protein functions...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453667/linearity-of-network-proximity-measures-implications-for-set-based-queries-and-significance-testing
#18
Sean Maxwell, Mark R Chance, Mehmet Koyutürk
Motivation: In recent years, various network proximity measures have been proposed to facilitate the use of biomolecular interaction data in a broad range of applications. These applications include functional annotation, disease gene prioritization, comparative analysis of biological systems and prediction of new interactions. In such applications, a major task is the scoring or ranking of the nodes in the network in terms of their proximity to a given set of 'seed' nodes (e.g. a group of proteins that are identified to be associated with a disease, or are deferentially expressed in a certain condition)...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28451967/using-pfp-and-esg-protein-function-prediction-web-servers
#19
Qing Wei, Joshua McGraw, Ishita Khan, Daisuke Kihara
Elucidating biological function of proteins is a fundamental problem in molecular biology and bioinformatics. Conventionally, protein function is annotated based on homology using sequence similarity search tools such as BLAST and FASTA. These methods perform well when obvious homologs exist for a query sequence; however, they will not provide any functional information otherwise. As a result, the functions of many genes in newly sequenced genomes are left unknown, which await functional interpretation. Here, we introduce two webservers for function prediction methods, which effectively use distantly related sequences to improve function annotation coverage and accuracy: Protein Function Prediction (PFP) and Extended Similarity Group (ESG)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28448031/transcriptomic-analysis-of-c-elegans-rna-sequencing-data-through-the-tuxedo-suite-on-the-galaxy-project
#20
Francis R G Amrit, Arjumand Ghazi
Next generation sequencing (NGS) technologies have revolutionized the nature of biological investigation. Of these, RNA Sequencing (RNA-Seq) has emerged as a powerful tool for gene-expression analysis and transcriptome mapping. However, handling RNA-Seq datasets requires sophisticated computational expertise and poses inherent challenges for biology researchers. This bottleneck has been mitigated by the open access Galaxy project that allows users without bioinformatics skills to analyze RNA-Seq data, and the Database for Annotation, Visualization, and Integrated Discovery (DAVID), a Gene Ontology (GO) term analysis suite that helps derive biological meaning from large data sets...
April 8, 2017: Journal of Visualized Experiments: JoVE
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