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https://www.readbyqxmd.com/read/28430854/dynamic-modeling-and-network-approaches-for-omics-time-course-data-overview-of-computational-approaches-and-applications
#1
Yulan Liang, Arpad Kelemen
Inferring networks and dynamics of genes, proteins, cells and other biological entities from high-throughput biological omics data is a central and challenging issue in computational and systems biology. This is essential for understanding the complexity of human health, disease susceptibility and pathogenesis for Predictive, Preventive, Personalized and Participatory (P4) system and precision medicine. The delineation of the possible interactions of all genes/proteins in a genome/proteome is a task for which conventional experimental techniques are ill suited...
April 18, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28426839/medical-history-in-the-hellenic-journal-of-nuclear-medicine
#2
EDITORIAL
Andreas Otte, Byeong Cheol Ahn
The Hellenic Journal of Nuclear Medicine is about to celebrate its 20th anniversary end of 2017. On board of the editorial team since 2003, this journal has influenced me like a good friend over the many past years. From time to time, the journal has published interesting and valuable historical notes. They show that nuclear medicine has a history and that medicine is its basis. They also teach us today, and some of the ancient perspectives and approaches are still valid. The reader of HJNM may be interested in these historical contributions, as they are timeless...
January 2017: Hellenic Journal of Nuclear Medicine
https://www.readbyqxmd.com/read/28426095/models-of-global-gene-expression-define-major-domains-of-cell-type-and-tissue-identity
#3
Andrew P Hutchins, Zhongzhou Yang, Yuhao Li, Fangfang He, Xiuling Fu, Xiaoshan Wang, Dongwei Li, Kairong Liu, Jiangping He, Yong Wang, Jiekai Chen, Miguel A Esteban, Duanqing Pei
The current classification of cells in an organism is largely based on their anatomic and developmental origin. Cells types and tissues are traditionally classified into those that arise from the three embryonic germ layers, the ectoderm, mesoderm and endoderm, but this model does not take into account the organization of cell type-specific patterns of gene expression. Here, we present computational models for cell type and tissue specification derived from a collection of 921 RNA-sequencing samples from 272 distinct mouse cell types or tissues...
March 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28405621/lipidfinder-a-computational-workflow-for-discovery-of-lipids-identifies-eicosanoid-phosphoinositides-in-platelets
#4
Anne O'Connor, Christopher J Brasher, David A Slatter, Sven W Meckelmann, Jade I Hawksworth, Stuart M Allen, Valerie B O'Donnell
Accurate and high-quality curation of lipidomic datasets generated from plasma, cells, or tissues is becoming essential for cell biology investigations and biomarker discovery for personalized medicine. However, a major challenge lies in removing artifacts otherwise mistakenly interpreted as real lipids from large mass spectrometry files (>60 K features), while retaining genuine ions in the dataset. This requires powerful informatics tools; however, available workflows have not been tailored specifically for lipidomics, particularly discovery research...
April 6, 2017: JCI Insight
https://www.readbyqxmd.com/read/28398502/pygold-a-python-based-api-for-docking-based-virtual-screening-workflow-generation
#5
Hitesh Patel, Tobias Brinkjost, Oliver Koch
Motivation: Molecular docking is one of the successful approaches in structure based discovery and development of bioactive molecules in chemical biology and medicinal chemistry. Due to the huge amount of computational time that is still required, docking is often the last step in a virtual screening approach. Such screenings are set as workflows spanned over many steps, each aiming at different filtering task. These workflows can be automatized in large parts using python based toolkits except for docking using the docking software GOLD...
April 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28387809/the-anatomy-of-phenotype-ontologies-principles-properties-and-applications
#6
Georgios V Gkoutos, Paul N Schofield, Robert Hoehndorf
The past decade has seen an explosion in the collection of genotype data in domains as diverse as medicine, ecology, livestock and plant breeding. Along with this comes the challenge of dealing with the related phenotype data, which is not only large but also highly multidimensional. Computational analysis of phenotypes has therefore become critical for our ability to understand the biological meaning of genomic data in the biological sciences. At the heart of computational phenotype analysis are the phenotype ontologies...
April 6, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28381613/direct-determination-of-diploid-genome-sequences
#7
Neil I Weisenfeld, Vijay Kumar, Preyas Shah, Deanna M Church, David B Jaffe
Determining the genome sequence of an organism is challenging, yet fundamental to understanding its biology. Over the past decade, thousands of human genomes have been sequenced, contributing deeply to biomedical research. In the vast majority of cases, these have been analyzed by aligning sequence reads to a single reference genome, biasing the resulting analyses, and in general, failing to capture sequences novel to a given genome. Some de novo assemblies have been constructed free of reference bias, but nearly all were constructed by merging homologous loci into single "consensus" sequences, generally absent from nature...
April 5, 2017: Genome Research
https://www.readbyqxmd.com/read/28361683/comparative-network-stratification-analysis-for-identifying-functional-interpretable-network-biomarkers
#8
Chuanchao Zhang, Juan Liu, Qianqian Shi, Tao Zeng, Luonan Chen
BACKGROUND: A major challenge of bioinformatics in the era of precision medicine is to identify the molecular biomarkers for complex diseases. It is a general expectation that these biomarkers or signatures have not only strong discrimination ability, but also readable interpretations in a biological sense. Generally, the conventional expression-based or network-based methods mainly capture differential genes or differential networks as biomarkers, however, such biomarkers only focus on phenotypic discrimination and usually have less biological or functional interpretation...
March 14, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28359959/designing-new-surfactant-peptides-for-binding-to-carbon-nanotubes-via-computational-approaches
#9
Alireza Mansouri, Karim Mahnam
The non-covalent interaction between single-walled carbon nanotube and surfactant peptides makes them soluble in biological media to be used in nano-medicine, drug delivery and gene therapy. Pervious study has shown that two important parameters in binding peptides into nanotubes are hydrophobic effect and the number of aromatic amino acids. Ten surfactant peptides with the length of eight residue, including Lys, Trp, Tyr, Phe and Val, were designed to investigate the important parameters in binding peptides to a (6, 6) carbon nanotube...
March 14, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28348175/omics-and-exercise-global-approaches-for-mapping-exercise-biological-networks
#10
Nolan J Hoffman
The application of global "-omics" technologies to exercise has introduced new opportunities to map the complexity and interconnectedness of biological networks underlying the tissue-specific responses and systemic health benefits of exercise. This review will introduce major research tracks and recent advancements in this emerging field, as well as critical gaps in understanding the orchestration of molecular exercise dynamics that will benefit from unbiased omics investigations. Furthermore, significant research hurdles that need to be overcome to effectively fill these gaps related to data collection, computation, interpretation, and integration across omics applications will be discussed...
March 27, 2017: Cold Spring Harbor Perspectives in Medicine
https://www.readbyqxmd.com/read/28346484/a-neighborhood-wide-association-study-nwas-example-of-prostate-cancer-aggressiveness
#11
Shannon M Lynch, Nandita Mitra, Michelle Ross, Craig Newcomb, Karl Dailey, Tara Jackson, Charnita M Zeigler-Johnson, Harold Riethman, Charles C Branas, Timothy R Rebbeck
PURPOSE: Cancer results from complex interactions of multiple variables at the biologic, individual, and social levels. Compared to other levels, social effects that occur geospatially in neighborhoods are not as well-studied, and empiric methods to assess these effects are limited. We propose a novel Neighborhood-Wide Association Study(NWAS), analogous to genome-wide association studies(GWAS), that utilizes high-dimensional computing approaches from biology to comprehensively and empirically identify neighborhood factors associated with disease...
2017: PloS One
https://www.readbyqxmd.com/read/28346087/pubchem-bioassay
#12
Yanli Wang, Tiejun Cheng, Stephen H Bryant
High-throughput screening (HTS) is now routinely conducted for drug discovery by both pharmaceutical companies and screening centers at academic institutions and universities. Rapid advance in assay development, robot automation, and computer technology has led to the generation of terabytes of data in screening laboratories. Despite the technology development toward HTS productivity, fewer efforts were devoted to HTS data integration and sharing. As a result, the huge amount of HTS data was rarely made available to the public...
January 1, 2017: SLAS Discovery
https://www.readbyqxmd.com/read/28334396/quantifying-circular-rna-expression-from-rna-seq-data-using-model-based-framework
#13
Musheng Li, Xueying Xie, Jing Zhou, Mengying Sheng, Xiaofeng Yin, Eun-A Ko, Tong Zhou, Wanjun Gu
Motivation: Circular RNAs (circRNAs) are a class of non-coding RNAs that are widely expressed in various cell lines and tissues of many organisms. Although the exact function of many circRNAs is largely unknown, the cell type- and tissue-specific circRNA expression has implicated their crucial functions in many biological processes. Hence, the quantification of circRNA expression from high-throughput RNA-seq data is becoming important to ascertain. Although many model-based methods have been developed to quantify linear RNA expression from RNA-seq data, these methods are not applicable to circRNA quantification...
March 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28302551/role-of-structural-bioinformatics-in-drug-discovery-by-computational-snp-analysis-a-proposed-protocol-for-analyzing-variation-at-the-protein-level
#14
REVIEW
David K Brown, Özlem Tastan Bishop
With the completion of the human genome project at the beginning of the 21st century, the biological sciences entered an unprecedented age of data generation, and made its first steps toward an era of personalized medicine. This abundance of sequence data has led to the proliferation of numerous sequence-based techniques for associating variation with disease, such as genome-wide association studies and candidate gene association studies. However, these statistical methods do not provide an understanding of the functional effects of variation...
March 13, 2017: Global Heart
https://www.readbyqxmd.com/read/28297627/clinical-and-technical-aspects-of-genomic-diagnostics-for-precision-oncology
#15
Yuri Sheikine, Frank C Kuo, Neal I Lindeman
The emergence of precision medicine has been predicated on significant recent advances in diagnostic technology, particularly the advent of next-generation sequencing (NGS). Although the chemical technology underlying NGS is complex, and the computational biology expertise required to build systems to facilely interpret the results is highly specialized, the variables involved in designing and deploying a genomic testing program for cancer can be readily understood and applied by understanding several basic considerations...
March 20, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28287035/biological-basis-of-radiation-protection-needs-rejuvenation
#16
Tatjana Paunesku, Benjamin Haley, Antone Brooks, Gayle E Woloschak
PURPOSE: Human beings encounter radiation in many different situations - from proximity to radioactive waste sites to participation in medical procedures using X-rays etc. Limits for radiation exposures are legally regulated; however, current radiation protection policy does not explicitly acknowledge that biological, cellular and molecular effects of low doses and low dose rates of radiation differ from effects induced by medium and high dose radiation exposures. Recent technical developments in biology and medicine, from single cell techniques to big data computational research, have enabled new approaches for study of biology of low doses of radiation...
March 13, 2017: International Journal of Radiation Biology
https://www.readbyqxmd.com/read/28279612/estimating-preferences-for-modes-of-drug-administration-the-case-of-us-healthcare-professionals
#17
Ebenezer K Tetteh, Steve Morris, Nigel Titchener-Hooker
BACKGROUND: There are hidden drug administration costs that arise from a mismatch between end-user preferences and how manufacturers choose to formulate their drug products for delivery to patients. The corollary of this is: there are "intangible benefits" from considering end-user preferences in manufacturing patient-friendly medicines. It is important then to have some idea of what pharmaceutical manufacturers should consider in making patient-friendly medicines and of the magnitude of the indirect benefits from doing so...
February 16, 2017: Research in Social & Administrative Pharmacy: RSAP
https://www.readbyqxmd.com/read/28259529/novel-pyrrolopyrimidines-as-mps1-ttk-kinase-inhibitors-for-breast-cancer
#18
Yasuro Sugimoto, Dwitiya B Sawant, Harold A Fisk, Liguang Mao, Chenglong Li, Somsundaram Chettiar, Pui-Kai Li, Michael V Darby, Robert W Brueggemeier
New targeted therapy approaches for certain subtypes of breast cancer, such as triple-negative breast cancers and other aggressive phenotypes, are desired. High levels of the mitotic checkpoint kinase Mps1/TTK have correlated with high histologic grade in breast cancer, suggesting a potential new therapeutic target for aggressive breast cancers (BC). Novel small molecules targeting Mps1 were designed by computer assisted docking analyses, and several candidate compounds were synthesized. These compounds were evaluated in anti-proliferative assays of a panel of 15 breast cancer cell lines and further examined for their ability to inhibit a variety of Mps1-dependent biological functions...
April 1, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28256516/swissadme-a-free-web-tool-to-evaluate-pharmacokinetics-drug-likeness-and-medicinal-chemistry-friendliness-of-small-molecules
#19
Antoine Daina, Olivier Michielin, Vincent Zoete
To be effective as a drug, a potent molecule must reach its target in the body in sufficient concentration, and stay there in a bioactive form long enough for the expected biologic events to occur. Drug development involves assessment of absorption, distribution, metabolism and excretion (ADME) increasingly earlier in the discovery process, at a stage when considered compounds are numerous but access to the physical samples is limited. In that context, computer models constitute valid alternatives to experiments...
March 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28255315/in-silico-designing-of-a-new-cysteine-analogue-of-hirudin-variant-3-for-site-specific-pegylation
#20
Seyed Mehdi Sajjadi, Hamzeh Rahimi, Saeed Mohammadi, Mohammad Faranoush, Hasan Mirzahoseini, Gholamreza Toogeh
Hirudin is an anticoagulant agent of the salivary glands of the medicinal leech. Recombinant hirudin (r-Hir) displays certain drawbacks including bleeding and immunogenicity. To solve these problems, cysteine-specific PEGylation has been proposed as a successful technique. However, proper selection of the appropriate cysteine residue for substitution is a critical step. This study has, for the first time, used a computational approach aimed at identifying a single potential PEGylation site for replacement by cysteine residue in the hirudin variant 3 (HV3)...
February 2017: Research in Pharmaceutical Sciences
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