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Bioinformatics & Computational Biology

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https://www.readbyqxmd.com/read/28934129/a-comprehensive-survey-of-the-roles-of-highly-disordered-proteins-in-type-2-diabetes
#1
Zhihua Du, Vladimir N Uversky
Type 2 diabetes mellitus (T2DM) is a chronic and progressive disease that is strongly associated with hyperglycemia (high blood sugar) related to either insulin resistance or insufficient insulin production. Among the various molecular events and players implicated in the manifestation and development of diabetes mellitus, proteins play several important roles. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database has information on 34 human proteins experimentally shown to be related to the T2DM pathogenesis...
September 21, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28917669/knowledge-driven-computational-modeling-in-alzheimer-s-research-current-state-and-future-trends
#2
Hugo Geerts, Martin Hofmann-Apitius, Thomas J Anastasio
Neurodegenerative diseases such as Alzheimer's disease (AD) follow a slowly progressing dysfunctional trajectory, with a large presymptomatic component and many comorbidities. Using preclinical models and large-scale omics studies ranging from genetics to imaging, a large number of processes that might be involved in AD pathology at different stages and levels have been identified. The sheer number of putative hypotheses makes it almost impossible to estimate their contribution to the clinical outcome and to develop a comprehensive view on the pathological processes driving the clinical phenotype...
September 14, 2017: Alzheimer's & Dementia: the Journal of the Alzheimer's Association
https://www.readbyqxmd.com/read/28892296/tailored-approaches-in-drug-development-and-diagnostics-from-molecular-design-to-biological-model-systems
#3
REVIEW
Cecilia Sahlgren, Annika Meinander, Hongbo Zhang, Fang Cheng, Maren Preis, Chunlin Xu, Tiina A Salminen, Diana Toivola, Daniel Abankwa, Ari Rosling, Didem Şen Karaman, Outi M H Salo-Ahen, Ronald Österbacka, John E Eriksson, Stefan Willför, Ion Petre, Jouko Peltonen, Reko Leino, Mark Johnson, Jessica Rosenholm, Niklas Sandler
Approaches to increase the efficiency in developing drugs and diagnostics tools, including new drug delivery and diagnostic technologies, are needed for improved diagnosis and treatment of major diseases and health problems such as cancer, inflammatory diseases, chronic wounds, and antibiotic resistance. Development within several areas of research ranging from computational sciences, material sciences, bioengineering to biomedical sciences and bioimaging is needed to realize innovative drug development and diagnostic (DDD) approaches...
September 11, 2017: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/28890129/bioinformatics-approaches-to-predict-target-genes-from-transcription-factor-binding-data
#4
REVIEW
Alexandra Essebier, Marnie Lamprecht, Michael Piper, Mikael Boden
Transcription factors regulate gene expression and play an essential role in development by maintaining proliferative states, driving cellular differentiation and determining cell fate. Transcription factors are capable of regulating multiple genes over potentially long distances making target gene identification challenging. Currently available experimental approaches to detect distal interactions have multiple weaknesses that have motivated the development of computational approaches. Although an improvement over experimental approaches, existing computational approaches are still limited in their application, with different weaknesses depending on the approach...
September 7, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28882000/integrative-deep-models-for-alternative-splicing
#5
Anupama Jha, Matthew R Gazzara, Yoseph Barash
Motivation: Advancements in sequencing technologies have highlighted the role of alternative splicing (AS) in increasing transcriptome complexity. This role of AS, combined with the relation of aberrant splicing to malignant states, motivated two streams of research, experimental and computational. The first involves a myriad of techniques such as RNA-Seq and CLIP-Seq to identify splicing regulators and their putative targets. The second involves probabilistic models, also known as splicing codes, which infer regulatory mechanisms and predict splicing outcome directly from genomic sequence...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28881998/systematic-identification-of-feature-combinations-for-predicting-drug-response-with-bayesian-multi-view-multi-task-linear-regression
#6
Muhammad Ammad-Ud-Din, Suleiman A Khan, Krister Wennerberg, Tero Aittokallio
Motivation: A prime challenge in precision cancer medicine is to identify genomic and molecular features that are predictive of drug treatment responses in cancer cells. Although there are several computational models for accurate drug response prediction, these often lack the ability to infer which feature combinations are the most predictive, particularly for high-dimensional molecular datasets. As increasing amounts of diverse genome-wide data sources are becoming available, there is a need to build new computational models that can effectively combine these data sources and identify maximally predictive feature combinations...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28881987/efficient-simulation-of-intrinsic-extrinsic-and-external-noise-in-biochemical-systems
#7
Dennis Pischel, Kai Sundmacher, Robert J Flassig
Motivation: Biological cells operate in a noisy regime influenced by intrinsic, extrinsic and external noise, which leads to large differences of individual cell states. Stochastic effects must be taken into account to characterize biochemical kinetics accurately. Since the exact solution of the chemical master equation, which governs the underlying stochastic process, cannot be derived for most biochemical systems, approximate methods are used to obtain a solution. Results: In this study, a method to efficiently simulate the various sources of noise simultaneously is proposed and benchmarked on several examples...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28881981/titer-predicting-translation-initiation-sites-by-deep-learning
#8
Sai Zhang, Hailin Hu, Tao Jiang, Lei Zhang, Jianyang Zeng
Motivation: Translation initiation is a key step in the regulation of gene expression. In addition to the annotated translation initiation sites (TISs), the translation process may also start at multiple alternative TISs (including both AUG and non-AUG codons), which makes it challenging to predict TISs and study the underlying regulatory mechanisms. Meanwhile, the advent of several high-throughput sequencing techniques for profiling initiating ribosomes at single-nucleotide resolution, e...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28881980/alignment-of-dynamic-networks
#9
V Vijayan, D Critchlow, T Milenkovic
Motivation: Network alignment (NA) aims to find a node mapping that conserves similar regions between compared networks. NA is applicable to many fields, including computational biology, where NA can guide the transfer of biological knowledge from well- to poorly-studied species across aligned network regions. Existing NA methods can only align static networks. However, most complex real-world systems evolve over time and should thus be modeled as dynamic networks. We hypothesize that aligning dynamic network representations of evolving systems will produce superior alignments compared to aligning the systems' static network representations, as is currently done...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28861131/unique-down-to-our-microbes-assessment-of-an-inquiry-based-metagenomics-activity
#10
Thomas B Lentz, Laura E Ott, Sabrina D Robertson, Sarah C Windsor, Joshua B Kelley, Michael S Wollenberg, Robert R Dunn, Carlos C Goller
Metagenomics is an important method for studying microbial life. However, undergraduate exposure to metagenomics is hindered by associated software, computing demands, and dataset access. In this inquiry-based activity designed for introductory life science majors and nonmajors, students perform an investigation of the bacterial communities inhabiting the human belly button and associated metagenomics data collected through a citizen science project and visualized using an open-access bioinformatics tool. The activity is designed for attainment of the following student learning outcomes: defining terms associated with metagenomics analyses, describing the biological impact of the microbiota on human health, formulating a hypothesis, analyzing and interpreting metagenomics data to compare microbiota, evaluating a specific hypothesis, and synthesizing a conceptual model as to why bacterial populations vary...
2017: Journal of Microbiology & Biology Education: JMBE
https://www.readbyqxmd.com/read/28859346/data-science-priorities-for-a-university-hospital-based-institute-of-infectious-diseases-a-viewpoint
#11
Alain-Jacques Valleron
Automation of laboratory tests, bioinformatic analysis of biological sequences, and professional data management are used routinely in a modern university hospital-based infectious diseases institute. This dates back to at least the 1980s. However, the scientific methods of this 21st century are changing with the increased power and speed of computers, with the "big data" revolution having already happened in genomics and environment, and eventually arriving in medical informatics. The research will be increasingly "data driven," and the powerful machine learning methods whose efficiency is demonstrated in daily life will also revolutionize medical research...
August 15, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/28843296/research-techniques-made-simple-bioinformatics-for-genome-scale-biology
#12
Amy C Foulkes, David S Watson, Christopher E M Griffiths, Richard B Warren, Wolfgang Huber, Michael R Barnes
High-throughput biology presents unique opportunities and challenges for dermatological research. Drawing on a small handful of exemplary studies, we review some of the major lessons of these new technologies. We caution against several common errors and introduce helpful statistical concepts that may be unfamiliar to researchers without experience in bioinformatics. We recommend specific software tools that can aid dermatologists at varying levels of computational literacy, including platforms with command line and graphical user interfaces...
September 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/28839186/an-integrated-bioinformatics-platform-for-investigating-the-human-e3-ubiquitin-ligase-substrate-interaction-network
#13
Yang Li, Ping Xie, Liang Lu, Jian Wang, Lihong Diao, Zhongyang Liu, Feifei Guo, Yangzhige He, Yuan Liu, Qin Huang, Han Liang, Dong Li, Fuchu He
The ubiquitination mediated by ubiquitin activating enzyme (E1), ubiquitin conjugating enzyme (E2), and ubiquitin ligase (E3) cascade is crucial to protein degradation, transcription regulation, and cell signaling in eukaryotic cells. The high specificity of ubiquitination is regulated by the interaction between E3 ubiquitin ligases and their target substrates. Unfortunately, the landscape of human E3-substrate network has not been systematically uncovered. Therefore, there is an urgent need to develop a high-throughput and efficient strategy to identify the E3-substrate interaction...
August 24, 2017: Nature Communications
https://www.readbyqxmd.com/read/28821273/a-practical-guide-to-single-cell-rna-sequencing-for-biomedical-research-and-clinical-applications
#14
REVIEW
Ashraful Haque, Jessica Engel, Sarah A Teichmann, Tapio Lönnberg
RNA sequencing (RNA-seq) is a genomic approach for the detection and quantitative analysis of messenger RNA molecules in a biological sample and is useful for studying cellular responses. RNA-seq has fueled much discovery and innovation in medicine over recent years. For practical reasons, the technique is usually conducted on samples comprising thousands to millions of cells. However, this has hindered direct assessment of the fundamental unit of biology-the cell. Since the first single-cell RNA-sequencing (scRNA-seq) study was published in 2009, many more have been conducted, mostly by specialist laboratories with unique skills in wet-lab single-cell genomics, bioinformatics, and computation...
August 18, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28809010/bioinformatics-resources-for-interpreting-proteomics-mass-spectrometry-data
#15
Iulia M Lazar
Developments in mass spectrometry (MS) instrumentation have supported the advance of a variety of proteomic technologies that have enabled scientists to assess differences between healthy and diseased states. In particular, the ability to identify altered biological processes in a cell has led to the identification of novel drug targets, the development of more effective therapeutic drugs, and the growth of new diagnostic approaches and tools for personalized medicine applications. Nevertheless, large-scale proteomic data generated by modern mass spectrometers are extremely complex and necessitate equally complex bioinformatics tools and computational algorithms for their interpretation...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28794860/minion-analysis-and-reference-consortium-phase-2-data-release-and-analysis-of-r9-0-chemistry
#16
Miten Jain, John R Tyson, Matthew Loose, Camilla L C Ip, David A Eccles, Justin O'Grady, Sunir Malla, Richard M Leggett, Ola Wallerman, Hans J Jansen, Vadim Zalunin, Ewan Birney, Bonnie L Brown, Terrance P Snutch, Hugh E Olsen
BACKGROUND: Long-read sequencing is rapidly evolving and reshaping the suite of opportunities for genomic analysis. For the MinION in particular, as both the platform and chemistry develop, the user community requires reference data to set performance expectations and maximally exploit third-generation sequencing. We performed an analysis of MinION data derived from whole genome sequencing of Escherichiacoli K-12 using the R9.0 chemistry, comparing the results with the older R7.3 chemistry...
2017: F1000Research
https://www.readbyqxmd.com/read/28794828/scalability-and-validation-of-big-data-bioinformatics-software
#17
REVIEW
Andrian Yang, Michael Troup, Joshua W K Ho
This review examines two important aspects that are central to modern big data bioinformatics analysis - software scalability and validity. We argue that not only are the issues of scalability and validation common to all big data bioinformatics analyses, they can be tackled by conceptually related methodological approaches, namely divide-and-conquer (scalability) and multiple executions (validation). Scalability is defined as the ability for a program to scale based on workload. It has always been an important consideration when developing bioinformatics algorithms and programs...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28789971/the-use-of-high-throughput-screening-techniques-to-evaluate-mitochondrial-toxicity
#18
Lauren P Wills
Toxicologists and chemical regulators depend on accurate and effective methods to evaluate and predict the toxicity of thousands of current and future compounds. Robust high-throughput screening (HTS) experiments have the potential to efficiently test large numbers of chemical compounds for effects on biological pathways. HTS assays can be utilized to examine chemical toxicity across multiple mechanisms of action, experimental models, concentrations, and lengths of exposure. Many agricultural, industrial, and pharmaceutical chemicals classified as harmful to human and environmental health exert their effects through the mechanism of mitochondrial toxicity...
August 5, 2017: Toxicology
https://www.readbyqxmd.com/read/28780735/rna-folding-kinetics-using-monte-carlo-and-gillespie-algorithms
#19
Peter Clote, Amir H Bayegan
RNA secondary structure folding kinetics is known to be important for the biological function of certain processes, such as the hok/sok system in E. coli. Although linear algebra provides an exact computational solution of secondary structure folding kinetics with respect to the Turner energy model for tiny ([Formula: see text]20 nt) RNA sequences, the folding kinetics for larger sequences can only be approximated by binning structures into macrostates in a coarse-grained model, or by repeatedly simulating secondary structure folding with either the Monte Carlo algorithm or the Gillespie algorithm...
August 5, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28777078/an-overview-of-comparative-modelling-and-resources-dedicated-to-large-scale-modelling-of-genome-sequences
#20
Su Datt Lam, Sayoni Das, Ian Sillitoe, Christine Orengo
Computational modelling of proteins has been a major catalyst in structural biology. Bioinformatics groups have exploited the repositories of known structures to predict high-quality structural models with high efficiency at low cost. This article provides an overview of comparative modelling, reviews recent developments and describes resources dedicated to large-scale comparative modelling of genome sequences. The value of subclustering protein domain superfamilies to guide the template-selection process is investigated...
August 1, 2017: Acta Crystallographica. Section D, Structural Biology
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