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https://www.readbyqxmd.com/read/28714509/a-comparative-review-of-computational-methods-for-pathway-perturbation-analysis-dynamical-and-topological-perspectives
#1
REVIEW
Q Vanhaelen, A M Aliper, A Zhavoronkov
Stem cells offer great promise within the field of regenerative medicine but despite encouraging results, the large scale use of stem cells for therapeutic applications still faces challenges when it comes to controlling signaling pathway responses with respect to environmental perturbations. This step is critical for the elaboration of stable and reproducible differentiation protocols, and computational modeling can be helpful to overcome these difficulties. This article is a comparative review of the mechanism-based methods used for hypothesis-driven approaches and data-driven methods which are two types of computational approaches commonly used for analysing the dynamics of pathways involved in stem cell regulation...
July 17, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28713546/2017-iscb-overton-prize-christoph-bock
#2
EDITORIAL
Christiana N Fogg, Diane E Kovats, Bonnie Berger
The International Society for Computational Biology (ISCB) each year recognizes the achievements of an early to mid-career scientist with the Overton Prize. This prize honors the untimely death of Dr. G. Christian Overton, an admired computational biologist and founding ISCB Board member. Winners of the Overton Prize are independent investigators who are in the early to middle phases of their careers and are selected because of their significant contributions to computational biology through research, teaching, and service...
2017: F1000Research
https://www.readbyqxmd.com/read/28690664/chinese-herbal-medicine-meets-biological-networks-of-complex-diseases-a-computational-perspective
#3
REVIEW
Shuo Gu, Jianfeng Pei
With the rapid development of cheminformatics, computational biology, and systems biology, great progress has been made recently in the computational research of Chinese herbal medicine with in-depth understanding towards pharmacognosy. This paper summarized these studies in the aspects of computational methods, traditional Chinese medicine (TCM) compound databases, and TCM network pharmacology. Furthermore, we chose arachidonic acid metabolic network as a case study to demonstrate the regulatory function of herbal medicine in the treatment of inflammation at network level...
2017: Evidence-based Complementary and Alternative Medicine: ECAM
https://www.readbyqxmd.com/read/28672838/recent-advances-in-conotoxin-classification-by-using-machine-learning-methods
#4
REVIEW
Fu-Ying Dao, Hui Yang, Zhen-Dong Su, Wuritu Yang, Yun Wu, Ding Hui, Wei Chen, Hua Tang, Hao Lin
Conotoxins are disulfide-rich small peptides, which are invaluable peptides that target ion channel and neuronal receptors. Conotoxins have been demonstrated as potent pharmaceuticals in the treatment of a series of diseases, such as Alzheimer's disease, Parkinson's disease, and epilepsy. In addition, conotoxins are also ideal molecular templates for the development of new drug lead compounds and play important roles in neurobiological research as well. Thus, the accurate identification of conotoxin types will provide key clues for the biological research and clinical medicine...
June 25, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28649444/reverse-engineering-highlights-potential-principles-of-large-gene-regulatory-network-design-and-learning
#5
Clément Carré, André Mas, Gabriel Krouk
Inferring transcriptional gene regulatory networks from transcriptomic datasets is a key challenge of systems biology, with potential impacts ranging from medicine to agronomy. There are several techniques used presently to experimentally assay transcription factors to target relationships, defining important information about real gene regulatory networks connections. These techniques include classical ChIP-seq, yeast one-hybrid, or more recently, DAP-seq or target technologies. These techniques are usually used to validate algorithm predictions...
2017: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/28643930/moving-towards-precision-orthodontics-an-evolving-paradigm-shift-in-the-planning-and-delivery-of-customized-orthodontic-therapy
#6
REVIEW
A H Jheon, S Oberoi, R C Solem, S Kapila
Advances in precision medicine portend similar progress in orthodontics and will be increasingly harnessed to achieve customized treatment approaches and enhance treatment efficiencies. Our goal is to provide a background on emerging advances in computer technologies and biomedicine and highlight their current and likely future applications to precision orthodontics. A review of orthodontically relevant technologies and advances in pertinent biological research was undertaken. Innovations in computer hardware and software, and 3D imaging technologies offer the ability for customized treatment and biomechanical planning that will be more fully realized within the next few decades...
June 2017: Orthodontics & Craniofacial Research
https://www.readbyqxmd.com/read/28643003/recent-developments-in-solution-nuclear-magnetic-resonance-nmr-based-molecular-biology
#7
REVIEW
Joshua J Ziarek, Diego Baptista, Gerhard Wagner
Visualizing post-translational modifications, conformations, and interaction surfaces of protein structures at atomic resolution underpins the development of novel therapeutics to combat disease. As computational resources expand, in silico calculations coupled with experimentally derived structures and functional assays have led to an explosion in structure-based drug design (SBDD) with several compounds in clinical trials. It is increasingly clear that "hidden" transition-state structures along activation trajectories can be harnessed to develop novel classes of allosteric inhibitors...
June 23, 2017: Journal of Molecular Medicine: Official Organ of the "Gesellschaft Deutscher Naturforscher und Ärzte"
https://www.readbyqxmd.com/read/28641555/supervised-machine-learning-methods-applied-to-predict-ligand-binding-affinity
#8
Gabriela Sehnem Heck, Val Oliveira Pintro, Richard Rene Pereira, Mauricio Boff de Ávila, Nayara Maria Bernhardt Levin, Walter Filgueira de Azevedo
BACKGROUND: Calculation of ligand-binding affinity is an open problem in computational medicinal chemistry. The ability to computationally predict affinities has a beneficial impact in the early stages of drug development, since it allows a mathematical model to assess protein-ligand interactions. Due to the availability of structural and binding information, machine learning methods have been applied to generate scoring functions with good predictive power. OBJECTIVE: Our goal here is to review recent developments in the application of machine learning methods to predict ligand- binding affinity...
June 22, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28640705/genomic-analysis-of-childhood-brain-tumors-methods-for-genome-wide-discovery-and-precision-medicine-become-mainstream
#9
Stephen C Mack, Paul A Northcott
Recent breakthroughs in next-generation sequencing technology and complementary genomic platforms have transformed our capacity to interrogate the molecular landscapes of human cancers, including childhood brain tumors. Numerous high-throughput genomic studies have been reported for the major histologic brain tumor entities diagnosed in children, including interrogations at the level of the genome, epigenome, and transcriptome, many of which have yielded essential new insights into disease biology. The nature of these discoveries has been largely platform dependent, exemplifying the usefulness of applying different genomic and computational strategies, or integrative approaches, to address specific biologic and/or clinical questions...
July 20, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28639657/exploring-the-catalytic-mechanism-of-dihydropteroate-synthase-elucidating-the-differences-between-the-substrate-and-inhibitor
#10
Warot Chotpatiwetchkul, Kanokthip Boonyarattanakalin, Duangkamol Gleeson, M Paul Gleeson
Dihydropteroate synthase (DHPS) catalyzes the condensation of 6-hydroxymethyl-7,8-dihydropterin pyrophosphate (DHPPP) with p-aminobenzoic acid (pABA) and is a well validated target for anti-malarial and anti-bacterial drugs. However, in recent years its utility as a therapeutic target has diminished considerably due to multiple mutations. As such, considerable structural biology and medicinal chemistry effort has been expended to understand and overcome this issue. To date no detailed computational analysis of the protein mechanism has been made despite the detailed crystal structures and multiple mechanistic proposals being made...
July 5, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28638442/computational-dynamic-approaches-for-temporal-omics-data-with-applications-to-systems-medicine
#11
REVIEW
Yulan Liang, Arpad Kelemen
Modeling and predicting biological dynamic systems and simultaneously estimating the kinetic structural and functional parameters are extremely important in systems and computational biology. This is key for understanding the complexity of the human health, drug response, disease susceptibility and pathogenesis for systems medicine. Temporal omics data used to measure the dynamic biological systems are essentials to discover complex biological interactions and clinical mechanism and causations. However, the delineation of the possible associations and causalities of genes, proteins, metabolites, cells and other biological entities from high throughput time course omics data is challenging for which conventional experimental techniques are not suited in the big omics era...
2017: BioData Mining
https://www.readbyqxmd.com/read/28630158/computational-studies-of-peptide-induced-membrane-pore-formation
#12
REVIEW
Richard Lipkin, Themis Lazaridis
A variety of peptides induce pores in biological membranes; the most common ones are naturally produced antimicrobial peptides (AMPs), which are small, usually cationic, and defend diverse organisms against biological threats. Because it is not possible to observe these pores directly on a molecular scale, the structure of AMP-induced pores and the exact sequence of steps leading to their formation remain uncertain. Hence, these questions have been investigated via molecular modelling. In this article, we review computational studies of AMP pore formation using all-atom, coarse-grained, and implicit solvent models; evaluate the results obtained and suggest future research directions to further elucidate the pore formation mechanism of AMPs...
August 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28625302/pharmacogenetics-in-obstetric-anesthesia
#13
REVIEW
Ruth Landau, Richard Smiley
The 21st century has been billed as the era of "precision/personalized medicine." Genetic investigation of clinical syndromes may guide therapy as well as reveal previously unknown biological or pharmacological pathways that may result in novel drug therapies. Several clinical issues in obstetrics and obstetric anesthesiology have been targets for genetic investigations. These include evaluation of the genetic effects on preterm labor and the progression of labor, spinal anesthesia-induced hypotension and the response to medications used to treat hypotension, and the effect of gene variants on pain and analgesic responses...
March 2017: Best Practice & Research. Clinical Anaesthesiology
https://www.readbyqxmd.com/read/28620761/medicinal-chemistry-of-%C3%AF-1-receptor-ligands-pharmacophore-models-synthesis-structure-affinity-relationships-and-pharmacological-applications
#14
Frauke Weber, Bernhard Wünsch
In the first part of this chapter, we summarize the various pharmacophore models for σ1 receptor ligands. Common to all of them is a basic amine flanked by two hydrophobic regions, representing the pharmacophoric elements. The development of computer-based models like the 3D homology model is described as well as the first crystal structure of the σ1 receptor. The second part focuses on the synthesis and biological properties of different σ1 receptor ligands, identified as 1-9. Monocyclic piperazines 1 and bicyclic piperazines 2 and 3 were developed as cytotoxic compounds, thus the IC50 values of cell growth and survival inhibition studies are given for all derivatives...
June 16, 2017: Handbook of Experimental Pharmacology
https://www.readbyqxmd.com/read/28620443/pattern-recognition-for-predictive-preventive-and-personalized-medicine-in-cancer
#15
REVIEW
Tingting Cheng, Xianquan Zhan
Predictive, preventive, and personalized medicine (PPPM) is the hot spot and future direction in the field of cancer. Cancer is a complex, whole-body disease that involved multi-factors, multi-processes, and multi-consequences. A series of molecular alterations at different levels of genes (genome), RNAs (transcriptome), proteins (proteome), peptides (peptidome), metabolites (metabolome), and imaging characteristics (radiome) that resulted from exogenous and endogenous carcinogens are involved in tumorigenesis and mutually associate and function in a network system, thus determines the difficulty in the use of a single molecule as biomarker for personalized prediction, prevention, diagnosis, and treatment for cancer...
March 2017: EPMA Journal
https://www.readbyqxmd.com/read/28608962/image-based-computational-fluid-dynamics-in-the-lung-virtual-reality-or-new-clinical-practice
#16
REVIEW
Kelly S Burrowes, Jan De Backer, Haribalan Kumar
The development and implementation of personalized medicine is paramount to improving the efficiency and efficacy of patient care. In the respiratory system, function is largely dictated by the choreographed movement of air and blood to the gas exchange surface. The passage of air begins in the upper airways, either via the mouth or nose, and terminates at the alveolar interface, while blood flows from the heart to the alveoli and back again. Computational fluid dynamics (CFD) is a well-established tool for predicting fluid flows and pressure distributions within complex systems...
June 13, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28608836/evaluation-of-the-antidiabetic-activity-and-chemical-composition-of-geranium-collinum-root-extracts-computational-and-experimental-investigations
#17
Sodik Numonov, Salamet Edirs, Khayrulla Bobakulov, Muhammad Nasimullah Qureshi, Khurshed Bozorov, Farukh Sharopov, William N Setzer, Haiqing Zhao, Maidina Habasi, Mizhgona Sharofova, Haji Akber Aisa
The root of Geranium collinum Steph is known in Tajik traditional medicine for its hepatoprotective, antioxidant, and anti-inflammatory therapeutic effects. The present study was conducted to evaluate of potential antidiabetic, antioxidant activities, total polyphenolic and flavonoid content from the different extracts (aqueous, aqueous-ethanolic) and individual compounds isolated of the root parts of G. collinum. The 50% aqueous-ethanolic extract possesses potent antidiabetic activity, with IC50 values of 0...
June 13, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28605519/cancersubtypes-an-r-bioconductor-package-for-molecular-cancer-subtype-identification-validation-and-visualization
#18
Taosheng Xu, Thuc Duy Le, Lin Liu, Ning Su, Rujing Wang, Bingyu Sun, Antonio Colaprico, Gianluca Bontempi, Jiuyong Li
Summary: Identifying molecular cancer subtypes from multi-omics data is an important step in the personalized medicine. We introduce CancerSubtypes , an R package for identifying cancer subtypes using multi-omics data, including gene expression, miRNA expression and DNA methylation data. CancerSubtypes integrates four main computational methods which are highly cited for cancer subtype identification and provides a standardized framework for data pre-processing, feature selection, and result follow-up analyses, including results computing, biology validation and visualization...
June 12, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28596936/new-bioengineering-breakthroughs-and-enabling-tools-in-regenerative-medicine
#19
REVIEW
Alvaro Mata, Helena S Azevedo, Lorenzo Botto, Nuria Gavara, Lei Su
PURPOSE OF REVIEW: In this review, we provide a general overview of recent bioengineering breakthroughs and enabling tools that are transforming the field of regenerative medicine (RM). We focus on five key areas that are evolving and increasingly interacting including mechanobiology, biomaterials and scaffolds, intracellular delivery strategies, imaging techniques, and computational and mathematical modeling. RECENT FINDINGS: Mechanobiology plays an increasingly important role in tissue regeneration and design of therapies...
2017: Current Stem Cell Reports
https://www.readbyqxmd.com/read/28592660/mechanical-interactions-in-bacterial-colonies-and-the-surfing-probability-of-beneficial-mutations
#20
Fred D Farrell, Matti Gralka, Oskar Hallatschek, Bartlomiej Waclaw
Bacterial conglomerates such as biofilms and microcolonies are ubiquitous in nature and play an important role in industry and medicine. In contrast to well-mixed cultures routinely used in microbial research, bacteria in a microcolony interact mechanically with one another and with the substrate to which they are attached. Here, we use a computer model of a microbial colony of rod-shaped cells to investigate how physical interactions between cells determine their motion in the colony and how this affects biological evolution...
June 2017: Journal of the Royal Society, Interface
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