keyword
MENU ▼
Read by QxMD icon Read
search

computers in biology and medicine

keyword
https://www.readbyqxmd.com/read/29159991/journey-to-the-centre-of-the-cell-virtual-reality-immersion-into-scientific-data
#1
REVIEW
Angus P R Johnston, James Rae, Nicholas Ariotti, Benjamin Bailey, Andrew Lija, Robyn Webb, Charles Ferguson, Sheryl Maher, Thomas P Davis, Richard I Webb, John McGhee, Robert G Parton
Visualization of scientific data is crucial not only for scientific discovery but also to communicate science and medicine to both experts and a general audience. Until recently, we have been limited to visualizing the three-dimensional (3D) world of biology in 2 dimensions. Renderings of 3D cells are still traditionally displayed using two-dimensional (2D) media, such as on a computer screen or paper. However, the advent of consumer grade virtual reality (VR) headsets such as Oculus Rift and HTC Vive means it is now possible to visualize and interact with scientific data in a 3D virtual world...
November 21, 2017: Traffic
https://www.readbyqxmd.com/read/29156742/prmda-personalized-recommendation-based-mirna-disease-association-prediction
#2
Zhu-Hong You, Luo-Pin Wang, Xing Chen, Shanwen Zhang, Xiao-Fang Li, Gui-Ying Yan, Zheng-Wei Li
Recently, researchers have been increasingly focusing on microRNAs (miRNAs) with accumulating evidence indicating that miRNAs serve as a vital role in various biological processes and dysfunctions of miRNAs are closely related with human complex diseases. Predicting potential associations between miRNAs and diseases is attached considerable significance in the domains of biology, medicine, and bioinformatics. In this study, we developed a computational model of Personalized Recommendation-based MiRNA-Disease Association prediction (PRMDA) to predict potential related miRNA for all diseases by implementing personalized recommendation-based algorithm based on integrated similarity for diseases and miRNAs...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29153398/maximizing-power-in-phylogenetics-and-phylogenomics-a-perspective-illuminated-by-fungal-big-data
#3
Alex Dornburg, Jeffrey P Townsend, Zheng Wang
Since its original inception over 150 years ago by Darwin, we have made tremendous progress toward the reconstruction of the Tree of Life. In particular, the transition from analyzing datasets comprised of small numbers of loci to those comprised of hundreds of loci, if not entire genomes, has aided in resolving some of the most vexing of evolutionary problems while giving us a new perspective on biodiversity. Correspondingly, phylogenetic trees have taken a central role in fields that span ecology, conservation, and medicine...
2017: Advances in Genetics
https://www.readbyqxmd.com/read/29151574/machine-learning-meets-complex-networks-via-coalescent-embedding-in-the-hyperbolic-space
#4
Alessandro Muscoloni, Josephine Maria Thomas, Sara Ciucci, Ginestra Bianconi, Carlo Vittorio Cannistraci
Physicists recently observed that realistic complex networks emerge as discrete samples from a continuous hyperbolic geometry enclosed in a circle: the radius represents the node centrality and the angular displacement between two nodes resembles their topological proximity. The hyperbolic circle aims to become a universal space of representation and analysis of many real networks. Yet, inferring the angular coordinates to map a real network back to its latent geometry remains a challenging inverse problem...
November 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/29149552/predicting-nano-bio-interactions-by-integrating-nanoparticle-libraries-and-quantitative-nanostructure-activity-relationship-modeling
#5
Wenyi Wang, Alexander Sedykh, Hainan Sun, Linlin Zhao, Daniel P Russo, Hongyu Zhou, Bing Yan, Hao Zhu
The discovery of biocompatible or bioactive nanoparticles for medicinal applications is an expensive and time-consuming process that may be significantly facilitated by incorporating more rational approaches combining both experimental and computational methods. However, it is currently hindered by two limitations: 1) the lack of high quality comprehensive data for computational modeling, and 2) the lack of an effective modeling method for the complex nanomaterial structures. In this study, we tackled both issues by first synthesizing a large library of nanoparticles and obtained comprehensive data on their characterizations and bioactivities...
November 17, 2017: ACS Nano
https://www.readbyqxmd.com/read/29148257/multiscale-memory-and-bioelectric-error-correction-in-the-cytoplasm-cytoskeleton-membrane-system
#6
REVIEW
Chris Fields, Michael Levin
A fundamental aspect of life is the modification of anatomy, physiology, and behavior in the face of changing conditions. This is especially illustrated by the adaptive regulation of growth and form that underlies the ability of most organisms-from single cells to complex large metazoa-to develop, remodel, and regenerate to specific anatomical patterns. What is the relationship of the genome and other cellular components to the robust computations that underlie this remarkable pattern homeostasis? Here we examine the role of constraints defined at the cellular level, especially endogenous bioelectricity, in generating and propagating biological information...
November 17, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/29131507/the-disruptive-effect-of-lysozyme-on-the-bacterial-cell-wall-explored-by-an-in-silico-structural-outlook
#7
Emiliano D Primo, Lisandro H Otero, Francisco Ruiz, Sebastián Klinke, Walter Giordano
The bacterial cell wall, a structural unit of peptidoglycan polymer comprised of glycan strands consisting of a repeating disaccharide motif [N-acetylglucosamine (NAG) and N-acetylmuramylpentapeptide (NAM pentapeptide)], encases bacteria and provides structural integrity and protection. Lysozymes are enzymes that break down the bacterial cell wall and disrupt the bacterial life cycle by cleaving the linkage between the NAG and NAM carbohydrates. Lab exercises focused on the effects of lysozyme on the bacterial cell wall are frequently incorporated in biochemistry classes designed for undergraduate students in diverse fields as biology, microbiology, chemistry, agronomy, medicine, and veterinary medicine...
November 13, 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/29118436/combining-membrane-proteomics-and-computational-three-way-pathway-analysis-revealed-signalling-pathways-preferentially-regulated-in-human-ipscs-and-human-escs
#8
Wei-Sheng Tien, Pei-Mien Chen, Ching-Yu Chuang, Shook-Mun Lui, Hung-Chih Kuo, Yu-Ju Chen, Kun-Pin Wu
Owing to the clinical potential of human induced pluripotent stem cells (hiPSCs) in regenerative medicine, a thorough examination of the similarities and differences between hiPSCs and human embryonic stem cells (hESCs) has become indispensable. Moreover, as the important roles of membrane proteins in biological signalling, functional analyses of membrane proteome are therefore promising. In this study, a pathway analysis by the bioinformatics tool GSEA was first performed to identify significant pathways associated with the three comparative membrane proteomics experiments: hiPSCs versus precursor human foreskin fibroblasts (HFF), hESCs versus precursor HFF, and hiPSCs versus hESCs...
November 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29100113/precise-confidence-intervals-of-regression-based-reference-limits-method-comparisons-and-sample-size-requirements
#9
Gwowen Shieh
Covariate-dependent reference limits have been extensively applied in biology and medicine for determining the substantial magnitude and relative importance of quantitative measurements. Confidence interval and sample size procedures are available for studying regression-based reference limits. However, the existing popular methods employ different technical simplifications and are applicable only in certain limited situations. This paper describes exact confidence intervals of regression-based reference limits and compares the exact approach with the approximate methods under a wide range of model configurations...
October 20, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/29098954/guidelines-for-genome-scale-analysis-of-biological-rhythms
#10
Michael E Hughes, Katherine C Abruzzi, Ravi Allada, Ron Anafi, Alaaddin Bulak Arpat, Gad Asher, Pierre Baldi, Charissa de Bekker, Deborah Bell-Pedersen, Justin Blau, Steve Brown, M Fernanda Ceriani, Zheng Chen, Joanna C Chiu, Juergen Cox, Alexander M Crowell, Jason P DeBruyne, Derk-Jan Dijk, Luciano DiTacchio, Francis J Doyle, Giles E Duffield, Jay C Dunlap, Kristin Eckel-Mahan, Karyn A Esser, Garret A FitzGerald, Daniel B Forger, Lauren J Francey, Ying-Hui Fu, Frédéric Gachon, David Gatfield, Paul de Goede, Susan S Golden, Carla Green, John Harer, Stacey Harmer, Jeff Haspel, Michael H Hastings, Hanspeter Herzel, Erik D Herzog, Christy Hoffmann, Christian Hong, Jacob J Hughey, Jennifer M Hurley, Horacio O de la Iglesia, Carl Johnson, Steve A Kay, Nobuya Koike, Karl Kornacker, Achim Kramer, Katja Lamia, Tanya Leise, Scott A Lewis, Jiajia Li, Xiaodong Li, Andrew C Liu, Jennifer J Loros, Tami A Martino, Jerome S Menet, Martha Merrow, Andrew J Millar, Todd Mockler, Felix Naef, Emi Nagoshi, Michael N Nitabach, Maria Olmedo, Dmitri A Nusinow, Louis J Ptáček, David Rand, Akhilesh B Reddy, Maria S Robles, Till Roenneberg, Michael Rosbash, Marc D Ruben, Samuel S C Rund, Aziz Sancar, Paolo Sassone-Corsi, Amita Sehgal, Scott Sherrill-Mix, Debra J Skene, Kai-Florian Storch, Joseph S Takahashi, Hiroki R Ueda, Han Wang, Charles Weitz, Pål O Westermark, Herman Wijnen, Ying Xu, Gang Wu, Seung-Hee Yoo, Michael Young, Eric Erquan Zhang, Tomasz Zielinski, John B Hogenesch
Genome biology approaches have made enormous contributions to our understanding of biological rhythms, particularly in identifying outputs of the clock, including RNAs, proteins, and metabolites, whose abundance oscillates throughout the day. These methods hold significant promise for future discovery, particularly when combined with computational modeling. However, genome-scale experiments are costly and laborious, yielding "big data" that are conceptually and statistically difficult to analyze. There is no obvious consensus regarding design or analysis...
October 2017: Journal of Biological Rhythms
https://www.readbyqxmd.com/read/29077790/precision-medicine-needs-pioneering-clinical-bioinformaticians
#11
Gonzalo Gómez-López, Joaquín Dopazo, Juan C Cigudosa, Alfonso Valencia, Fátima Al-Shahrour
Success in precision medicine depends on accessing high-quality genetic and molecular data from large, well-annotated patient cohorts that couple biological samples to comprehensive clinical data, which in conjunction can lead to effective therapies. From such a scenario emerges the need for a new professional profile, an expert bioinformatician with training in clinical areas who can make sense of multi-omics data to improve therapeutic interventions in patients, and the design of optimized basket trials. In this review, we first describe the main policies and international initiatives that focus on precision medicine...
October 25, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29073909/genotype-driven-identification-of-a-molecular-network-predictive-of-advanced-coronary-calcium-in-clinseq%C3%A2-and-framingham-heart-study-cohorts
#12
Cihan Oguz, Shurjo K Sen, Adam R Davis, Yi-Ping Fu, Christopher J O'Donnell, Gary H Gibbons
BACKGROUND: One goal of personalized medicine is leveraging the emerging tools of data science to guide medical decision-making. Achieving this using disparate data sources is most daunting for polygenic traits. To this end, we employed random forests (RFs) and neural networks (NNs) for predictive modeling of coronary artery calcium (CAC), which is an intermediate endo-phenotype of coronary artery disease (CAD). METHODS: Model inputs were derived from advanced cases in the ClinSeq®; discovery cohort (n=16) and the FHS replication cohort (n=36) from 89 (th) -99 (th) CAC score percentile range, and age-matched controls (ClinSeq®; n=16, FHS n=36) with no detectable CAC (all subjects were Caucasian males)...
October 26, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29065841/synthesis-cytotoxicity-evaluation-molecular-docking-and-utility-of-novel-chalcones-as-precursors-for-heterocycles-incorporating-pyrazole-moiety
#13
Sobhi M Gomha, Magda A Abdallah, Ikhlass M Abbas, Mariam S H Kazem
BACKGROUND: Chalcones, 2-pyrazolines and thiazoles have been reported to possess various pharmacological activities. OBJECTIVES: Synthesis of new chalcones and utilizing them as a building block for constructing a series of thiazole derivatives and evaluate some of them as anticancer agents. METHODS: The new compounds were synthesized via stirring at room temperature or thermal heating. Cytotoxic evaluation of the new synthesized compounds was tested using the method of Skehan et al...
October 20, 2017: Medicinal Chemistry
https://www.readbyqxmd.com/read/29062170/diseases-and-molecular-diagnostics-a-step-closer-to-precision-medicine
#14
EDITORIAL
Shailendra Dwivedi, Purvi Purohit, Radhieka Misra, Puneet Pareek, Apul Goel, Sanjay Khattri, Kamlesh Kumar Pant, Sanjeev Misra, Praveen Sharma
The current advent of molecular technologies together with a multidisciplinary interplay of several fields led to the development of genomics, which concentrates on the detection of pathogenic events at the genome level. The structural and functional genomics approaches have now pinpointed the technical challenge in the exploration of disease-related genes and the recognition of their structural alterations or elucidation of gene function. Various promising technologies and diagnostic applications of structural genomics are currently preparing a large database of disease-genes, genetic alterations etc...
October 2017: Indian Journal of Clinical Biochemistry: IJCB
https://www.readbyqxmd.com/read/29059639/-complexity-of-the-phenomenon-of-life-the-challenge-for-medicine
#15
Mieczysław Chorąży
The human organism presents a complex biological system that has hierarchical organization. The lowest, basal hierarchical level is composed of chemical molecules. The system's structure as "the whole" is maintained by complex interactions of its parts (molecules). New forms and functions, not present in molecules themselves emerge from their orchestrated and coordinated interaction, creating the novel "whole". The "whole" is not a simple summation of its parts. Therefore, on the basis of reductionist analysis and solely on the list of component elements of biological systems it is not possible to predict the future form and function of the "whole"...
2017: Wiadomości Lekarskie: Organ Polskiego Towarzystwa Lekarskiego
https://www.readbyqxmd.com/read/29042301/towards-a-first-implementation-of-the-wlimes-approach-in-living-system-studies-advancing-the-diagnostics-and-therapy-in-personalized-medicine
#16
Plamen L Simeonov
The goal of this paper is to advance an extensible theory of living systems using an approach to biomathematics and biocomputation that suitably addresses self-organized, self-referential and anticipatory systems with multi-temporal multi-agents. Our first step is to provide foundations for modelling of emergent and evolving dynamic multi-level organic complexes and their sustentative processes in artificial and natural life systems. Main applications are in life sciences, medicine, ecology and astrobiology, as well as robotics, industrial automation, man-machine interface and creative design...
October 16, 2017: Bio Systems
https://www.readbyqxmd.com/read/29039067/in-silico-system-pharmacology-for-the-potential-bioactive-ingredients-contained-in-xingnaojing-injection-and-its-material-basis-for-sepsis-treatment
#17
Shi-Tang Ma, Cheng-Tao Feng, You-Xi Xiong, Xiao-Lin Zhang, Cheng-Gui Miao, Hao Yu
OBJECTIVE: To elucidate the action mechanism of Xingnaojing Injection (, XNJI) for sepsis, and to target screen the potential bioactive ingredients. METHODS: An integrated protocol that combines in silico target screen (molecular docking) and database mapping was employed to find the potential inhibitors from XNJI for the sepsis-related targets and to establish the compound-target (C-T) interaction network. The XNJI's bioactive components database was investigated and the sepsis-associated targets were comprehensively constructed; the 3D structure of adenosine receptor A2a and 5-lipoxygenase proteins were established and evaluated with homology modeling method; system network pharmacology for sepsis treatment was studied between the bioactive ingredients and the sepsis targets using computational biology methods to distinguish inhibitors from non inhibitors for the selected sepsis-related targets and C-T network construction...
October 17, 2017: Chinese Journal of Integrative Medicine
https://www.readbyqxmd.com/read/29033394/diagnostic-biomarkers-for-lung-cancer-prevention
#18
Roberto Gasparri, Rosalia Romano, Giulia Sedda, Alessandro Borri, Francesco Petrella, Domenico Galetta, Monica Casiraghi, Lorenzo Spaggiari
Lung cancer is the leading cause of death for neoplasm. The lung cancer mortality is frequently associated with late diagnosis, therefore an early diagnosis is a key factor to significantly improve overall survival in high risk populations of asymptomatic patients. Conventional cancer screenings (low-dose computed tomography or chest x-ray) today offers early detection but are invasive and expensive. Up to date these studies evaluated the solid and topographic cancer structure and morphology. Today the concept of tumor has been remodeled and it has been defined as a disease that has its own genetic, biological and metabolic identity and on this new awareness we should base the new screening methods...
October 16, 2017: Journal of Breath Research
https://www.readbyqxmd.com/read/29026602/re-phrasing-the-question-a-simple-tool-for-evaluation-of-adherence-to-therapy-in-patients-with-inflammatory-bowel-disease
#19
T Engel, B Ungar, G Ben-Haim, N Levhar, R Eliakim, S Ben-Horin
BACKGROUND: Non-adherence to medication in patients with inflammatory bowel disease (IBD) is a challenging problem which is often overlooked or under-estimated by the physician or denied by the patient. We aimed to examine if re-phrasing the wording of the question used by the physician could help in revealing more patients who are non-adherent, and for whom appropriate counseling may be instituted. METHODS: A cross-sectional questionnaire-based study of IBD patients treated in a tertiary center was conducted...
October 2017: United European Gastroenterology Journal
https://www.readbyqxmd.com/read/29025326/onco-proteogenomics-multi-omics-level-data-integration-for-accurate-phenotype-prediction
#20
Lampros Dimitrakopoulos, Ioannis Prassas, Eleftherios P Diamandis, George S Charames
The overall goal of translational oncology is to identify molecular alterations indicative of cancer or of responsiveness to specific therapeutic regimens. While next-generation sequencing has played a pioneering role in this quest, the latest advances in proteomic technologies promise to provide a holistic approach to the further elucidation of tumor biology. Genetic information may be written in DNA and flow from DNA to RNA to protein, according to the central dogma of molecular biology, but the observed phenotype is dictated predominantly by the DNA protein coding region-derived proteotype...
October 12, 2017: Critical Reviews in Clinical Laboratory Sciences
keyword
keyword
118962
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"