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Interdisciplinary Sciences, Computational Life Sciences

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https://www.readbyqxmd.com/read/28432608/fpgasw-accelerating-large-scale-smith-waterman-sequence-alignment-application-with-backtracking-on-fpga-linear-systolic-array
#1
Xia Fei, Zou Dan, Lu Lina, Man Xin, Zhang Chunlei
The Smith-Waterman (SW) algorithm based on dynamic programming is a well-known classical method for high precision sequence matching and has become the gold standard to evaluate sequence alignment software. In this paper, we propose fine-grained parallelized SW algorithms using affine gap penalty and implement a parallel computing structures to accelerating the SW with backtracking on FPGA platform. We analysis the dynamic parallel computing features of anti-diagonal elements and storage expansion problem resulting from backtracking stage, and propose a series of optimization strategies to eliminate data dependency, reduce storage requirements, and overlap memory access latency...
April 21, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28405889/asymptotic-expansion-method-with-respect-to-small-parameter-for-ternary-diffusion-models
#2
Marek Danielewski, Henryk Leszczyński, Anna Szafrańska
Ternary diffusion models lead to strongly coupled systems of PDEs. We choose the smallest diffusion coefficient as a small parameter in a power series expansion whose components fulfill relatively simple equations. Although this series is divergent, one can use its finite sums to derive feasible numerical approximations, e.g. finite difference methods (FDMs).
April 12, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28391494/metrical-consistency-nmf-for-predicting-gene-phenotype-associations
#3
Shuai Han, Hong Cai, Dan Che, Yaogong Zhang, Yalou Huang, Maoqiang Xie
Discovering gene-phenotype associations is significant to understand the disease mechanisms. Nonnegative matrix factorization (NMF) has been widely used in computational biology for its good performance and interpretability. In this paper, we proposed a novel metrical consistency NMF (MCNMF) method for candidate gene prioritization. The MCNMF method assume that phenotype similarities, calculated from various independent ways, should be consistent in case that the associations between genes and phenotypes are completely known...
April 8, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28391493/computational-comparison-and-visualization-of-viruses-in-the-perspective-of-clinical-information
#4
António M Lopes, J A Tenreiro Machado, Alexandra M Galhano
This paper addresses the visualization of complex information using multidimensional scaling (MDS). MDS is a technique adopted for processing data with multiple features scattered in high-dimensional spaces. For illustrating the proposed techniques, the case of viral diseases is considered. The study evaluates the characteristics of 21 viruses in the perspective of clinical information. Several new schemes are proposed for improving the visualization of the MDS charts. The results follow standard clinical practice, proving that the method represents a valuable tool to study a large number of viruses...
April 8, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28374118/structural-insight-into-the-mechanism-of-dibenzo-a-l-pyrene-and-benzo-a-pyrene-mediated-cell-proliferation-using-molecular-docking-simulations
#5
M Kalim A Khan, Salman Akhtar, Jamal M Arif
In the proposed work, we have explicated the mechanism of dibenzo[a,l]pyrene (DBP) and benzo[a]pyrene (BP) modulated cell proliferation by assessing the plausible binding with CASPASES, BAX, Bcl-2, MDM2, p53, p21, p16, CylinD1-CDK4 complex, CylinE1-CDK2 complex, H-Ras, K-Ras, BRCA1, and BRCA2 through exploiting the inherent potential of AutoDock Tools 4.0. In silico findings revealed that potent carcinogenic metabolites of DBP (e.g., (-)-anti-DBPDE and (+)-syn-DBPDE) and BP (e.g., (+)-anti-BPDE) exhibited better binding interactions to Caspase-9 than Caspase-8 and Caspase-3...
April 3, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28374117/virtual-screening-for-potential-inhibitors-of-ctx-m-15-protein-of-klebsiella-pneumoniae
#6
Tayebeh Farhadi, Atefeh Fakharian, Roman S Ovchinnikov
The Gram-negative bacterium Klebsiella pneumoniae, responsible for a wide variety of nosocomial infections in immuno-deficient patients, involves the respiratory, urinary and gastrointestinal tract infections and septicemia. Extended spectrum β-lactamases (ESBL) belong to β-lactamases capable of conferring antibiotic resistance in Gram-negative bacteria. CTX-M-15, a prevalent ESBL reported from Enterobacteriaceae including K. pneumoniae, was selected as a potent anti-bacterial target. To identify the novel drug-like compounds, structure-based screening procedure was employed against downloaded drug-like compounds from ZINC database...
April 3, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28361256/computational-approaches-and-related-tools-to-identify-micrornas-in-a-species-a-bird-s-eye-view
#7
REVIEW
Anjana Rajendiran, Aniruddha Chatterjee, Archana Pan
MicroRNAs (miRNAs) are a family of non-coding RNAs that play a central role in fine-tuning gene expression regulation. Over the past decade, identification and annotation of miRNAs have become a major focus in epigenomics research. However, detection and characterization of miRNA are challenging due to its small size (~22 nucleotide-long) and susceptibility to degradation. The difficulties involved in experimental prediction and characterization of miRNA coding genes have led to the development of in silico-based approaches...
March 30, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28352971/ir-spectra-of-different-o2-content-hemoglobin-from-computational-study-promising-detector-of-hemoglobin-variant-in-medical-diagnosis
#8
Su-Qin Zhou, Tu-Nan Chen, Guang-Fu Ji, En-Ren Wang
IR spectra of heme and different O2-content hemoglobin were studied by the quantum computation method at the molecule level. IR spectra of heme and different O2-content hemoglobin were quantificationally characterized from 0 to 100 THz. The IR spectra of oxy-heme and de-oxy-heme are obviously different at the frequency regions of 9.08-9.48, 38.38-39.78, 50.46-50.82, and 89.04-91.00 THz. At 24.72 THz, there exists the absorption peak for oxy-heme, whereas there is not the absorption peak for de-oxy-heme. Whether the heme contains Fe-O-O bond or not has the great influence on its IR spectra and vibration intensities of functional groups in the mid-infrared area...
March 28, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28349439/egfr-gene-regulation-in-colorectal-cancer-cells-by-garlic-phytocompounds-with-special-emphasis-on-s-allyl-l-cysteine-sulfoxide
#9
Nabarun Roy, P A Nazeem, T D Babu, P S Abida, Arunaksharan Narayanankutty, Ravisankar Valsalan, P A Valsala, Achuthan C Raghavamenon
Colorectal cancer is one among the most common cancers in the world and a major cause of cancer related deaths. Similar to other cancers, colorectal carcinogenesis is often associated with over expression of genes related to cell growth and proliferation, especially Epidermal Growth Factor Receptor (EGFR). There is an increasing attention towards the plant derived compounds in prevention of colorectal carcinogenesis by downregulating EGFR. Among plants, garlic (Allium sativum L.) is emerging with anticancer properties by virtue of its organosulfur compounds...
March 27, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28290051/construction-of-a-comprehensive-protein-protein-interaction-map-for-vitiligo-disease-to-identify-key-regulatory-elements-a-systemic-approach
#10
Anvita Gupta Malhotra, Mohit Jha, Sudha Singh, Khushhali M Pandey
Vitiligo is an idiopathic disorder characterized by depigmented patches on the skin due to progressive loss of melanocytes. Several genetic, immunological, and pathophysiological investigations have established vitiligo as a polygenetic disorder with multifactorial etiology. However, no definite model explaining the interplay between these causative factors has been established hitherto. Therefore, we studied the disorder at the system level to identify the key proteins involved by exploring their molecular connectivity in terms of topological parameters...
March 13, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28283929/molecular-docking-studies-to-explore-potential-binding-pockets-and-inhibitors-for-chikungunya-virus-envelope-glycoproteins
#11
Phuong T V Nguyen, Haibo Yu, Paul A Keller
The chikungunya virus (CHIKV) envelope glycoproteins are considered important potential targets for anti-CHIKV drug discovery due to their crucial roles in virus attachment and virus entry. In this study, using two available crystal structures of the immature and mature forms of envelope glycoproteins, virtual screenings based on blind dockings and focused dockings were carried out to identify potential binding pockets and hit compounds for the virus. The chemical library database of compounds, NCI Diversity Set II, was used in these docking studies...
March 11, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28271460/structural-evaluation-and-binding-mode-analysis-of-ccl19-and-ccr7-proteins-identification-of-novel-leads-for-rheumatic-and-autoimmune-diseases-an-insilico-study
#12
Santhi Prada Vellanki, Ramasree Dulapalli, Bhargavi Kondagari, Navaneetha Nambigari, Rajender Vadija, Vishwanath Ramatenki, Rama Krishna Dumpati, Uma Vuruputuri
The Human Chemokine (C-C motif) ligand 19 (CCL19) protein plays a major role in rheumatic and autoimmune diseases. The 3D models of the CCL19 and its receptor CCR7 are generated using homology modeling and are validated using standard computational protocols. Disulfide bridges identified in 3D model of CCL19 protein give extra stability to the overall protein structure. The active site region of protein CCL19, containing N-terminal amino acid residues (Gly22 to Leu31), is predicted using in silico techniques...
March 7, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28247172/an-algorithm-for-sequencing-by-hybridization-based-on-an-alternating-dna-chip
#13
Marcin Radom, Piotr Formanowicz
Sequencing by hybridization allows the reconstruction of the DNA string of a given length from smaller fragments. These fragments are obtained in the hybridization experiment in which the DNA hybridizes to a DNA chip. In a classical approach, the chip consists of all oligonucleotides of a given length, with only one type of oligonucleotide for each probe of the chip. In this paper, we propose an algorithm solving the non-classical case of SBH, where the chip probes consist set of oligonucleotides described by some specific pattern...
February 28, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28217823/novel-insight-from-computational-virtual-screening-depict-the-binding-potential-of-selected-phytotherapeutics-against-probable-drug-targets-of-clostridium-difficile
#14
Suman Kamath, Sinosh Skariyachan
This study explores computational screening and molecular docking approaches to screen novel herbal therapeutics against probable drug targets of Clostridium difficile. The essential genes were predicted by comparative genome analysis of C. difficile and best homologous organisms using BLAST search at database of essential genes (DEG). The functions of these genes in various metabolic pathways were predicted and some of these genes were considered as potential targets. Three major proteins were selected as putative targets, namely permease IIC component, ABC transporter and histidine kinase...
February 20, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28194576/design-synthesis-and-antibacterial-activities-of-novel-heterocyclic-arylsulphonamide-derivatives
#15
Anuradha Singh, Ritika Srivastava, Ramendra K Singh
Design, synthesis, and antibacterial activities of a series of arylsulphonamide derivatives as probable peptide deformylase (PDF) inhibitors have been discussed. Compounds have been designed following Lipinski's rule and after docking into the active site of PDF protein (PDB code: 1G2A) synthesized later on. Furthermore, to assess their antibacterial activity, screening of the compound was done in vitro conditions against Gram-positive and Gram-negative bacterial strains. In silico, studies revealed these compounds as potential antibacterial agents and this fact was also supported by their prominent scoring functions...
February 13, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28303531/comprehensive-analysis-of-mile-gene-expression-data-set-advances-discovery-of-leukaemia-type-and-subtype-biomarkers
#16
Wojciech Labaj, Anna Papiez, Andrzej Polanski, Joanna Polanska
Large collections of data in studies on cancer such as leukaemia provoke the necessity of applying tailored analysis algorithms to ensure supreme information extraction. In this work, a custom-fit pipeline is demonstrated for thorough investigation of the voluminous MILE gene expression data set. Three analyses are accomplished, each for gaining a deeper understanding of the processes underlying leukaemia types and subtypes. First, the main disease groups are tested for differential expression against the healthy control as in a standard case-control study...
March 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28281239/an-agent-based-clustering-approach-for-gene-selection-in-gene-expression-microarray
#17
Juan Ramos, José A Castellanos-Garzón, Alfonso González-Briones, Juan F de Paz, Juan M Corchado
Gene selection is a major research area in microarray analysis, which seeks to discover differentially expressed genes for a particular target annotation. Such genes also often called informative genes are able to differentiate tissue samples belonging to different classes of the studied disease. Despite the fact that there is a wide number of proposals, the complexity imposed by this problem remains a challenge today. This research proposes a gene selection approach by means of a clustering-based multi-agent system...
March 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28255832/analysing-algorithms-and-data-sources-for-the-tissue-specific-reconstruction-of-liver-healthy-and-cancer-cells
#18
Jorge Ferreira, Sara Correia, Miguel Rocha
Genome-Scale Metabolic Models (GSMMs), mathematical representations of the cell metabolism in different organisms including humans, are resourceful tools to simulate metabolic phenotypes and understand associated diseases, such as obesity, diabetes and cancer. In the last years, different algorithms have been developed to generate tissue-specific metabolic models that simulate different phenotypes for distinct cell types. Hepatocyte cells are one of the main sites of metabolic conversions, mainly due to their diverse physiological functions...
March 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28238112/development-of-a-framework-for-metabolic-pathway-analysis-driven-strain-optimization-methods
#19
Vitor Vieira, Paulo Maia, Isabel Rocha, Miguel Rocha
Genome-scale metabolic models (GSMMs) have become important assets for rational design of compound overproduction using microbial cell factories. Most computational strain optimization methods (CSOM) using GSMMs, while useful in metabolic engineering, rely on the definition of questionable cell objectives, leading to some bias. Metabolic pathway analysis approaches do not require an objective function. Though their use brings immediate advantages, it has mostly been restricted to small scale models due to computational demands...
March 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/27878456/an-improved-protein-surface-extraction-method-using-rotating-cylinder-probe
#20
Kalpana Singh, Tapobrata Lahiri
For extraction of information on binding sites of a protein, the commonly known geometry-based methods utilize the corresponding PDB file to extract its surface as a first step. Finally, the surface is used to find the binding site atoms. As shown in this paper work, since none of the mostly used surface extraction methods can retrieve a sizeable percentage of the binding site atoms, the scope of development of a better method remains. In this direction, this paper presents a new benchmarking criteria based on utilization of binding site information to compare performance of these surface extraction methods...
March 2017: Interdisciplinary Sciences, Computational Life Sciences
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