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Bioinformatics & Computational Biology

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https://www.readbyqxmd.com/read/28735540/the-n%C3%A2-%C3%AF-interaction
#1
Robert W Newberry, Ronald T Raines
The carbonyl group holds a prominent position in chemistry and biology not only because it allows diverse transformations but also because it supports key intermolecular interactions, including hydrogen bonding. More recently, carbonyl groups have been found to interact with a variety of nucleophiles, including other carbonyl groups, in what we have termed an n→π* interaction. In an n→π* interaction, a nucleophile donates lone-pair (n) electron density into the empty π* orbital of a nearby carbonyl group...
July 23, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28735000/application-of-pharmacometrics-and-quantitative-systems-pharmacology-to-cancer-therapy-the-example-of-luminal-a-breast-cancer
#2
REVIEW
Brett Fleisher, Kayla Andrews, Ashley A Brown, Sihem Ait-Oudhia
Breast cancer (BC) is the most common cancer in women, and the second most frequent cause of cancer-related deaths in women worldwide. It is a heterogeneous disease composed of multiple subtypes with distinct morphologies and clinical implications. Quantitative systems pharmacology (QSP) is an emerging discipline bridging systems biology with pharmacokinetics (PK) and pharmacodynamics (PD) leveraging the systematic understanding of drugs' efficacy and toxicity. Despite numerous challenges in applying computational methodologies for QSP and mechanism-based PK/PD models to biological, physiological, and pharmacological data, bridging these disciplines has the potential to enhance our understanding of complex disease systems such as BC...
July 19, 2017: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
https://www.readbyqxmd.com/read/28713548/2017-iscb-accomplishment-by-a-senior-scientist-award-pavel-pevzner
#3
EDITORIAL
Christiana N Fogg, Diane E Kovats, Bonnie Berger
The International Society for Computational Biology ( ISCB) recognizes an established scientist each year with the Accomplishment by a Senior Scientist Award for significant contributions he or she has made to the field. This award honors scientists who have contributed to the advancement of computational biology and bioinformatics through their research, service, and education work. Pavel Pevzner, PhD, Ronald R. Taylor Professor of Computer Science and Director of the NIH Center for Computational Mass Spectrometry at University of California, San Diego, has been selected as the winner of the 2017 Accomplishment by a Senior Scientist Award...
2017: F1000Research
https://www.readbyqxmd.com/read/28705239/nap-the-network-analysis-profiler-a-web-tool-for-easier-topological-analysis-and-comparison-of-medium-scale-biological-networks
#4
Theodosios Theodosiou, Georgios Efstathiou, Nikolas Papanikolaou, Nikos C Kyrpides, Pantelis G Bagos, Ioannis Iliopoulos, Georgios A Pavlopoulos
OBJECTIVE: Nowadays, due to the technological advances of high-throughput techniques, Systems Biology has seen a tremendous growth of data generation. With network analysis, looking at biological systems at a higher level in order to better understand a system, its topology and the relationships between its components is of a great importance. Gene expression, signal transduction, protein/chemical interactions, biomedical literature co-occurrences, are few of the examples captured in biological network representations where nodes represent certain bioentities and edges represent the connections between them...
July 14, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28686599/flux-balance-analysis-predicts-warburg-like-effects-of-mouse-hepatocyte-deficient-in-mir-122a
#5
Hua-Qing Wu, Mei-Ling Cheng, Jin-Mei Lai, Hsuan-Hui Wu, Meng-Chun Chen, Wen-Huan Liu, Wu-Hsiung Wu, Peter Mu-Hsin Chang, Chi-Ying F Huang, Ann-Ping Tsou, Ming-Shi Shiao, Feng-Sheng Wang
The liver is a vital organ involving in various major metabolic functions in human body. MicroRNA-122 (miR-122) plays an important role in the regulation of liver metabolism, but its intrinsic physiological functions require further clarification. This study integrated the genome-scale metabolic model of hepatocytes and mouse experimental data with germline deletion of Mir122a (Mir122a-/-) to infer Warburg-like effects. Elevated expression of MiR-122a target genes in Mir122a-/-mice, especially those encoding for metabolic enzymes, was applied to analyze the flux distributions of the genome-scale metabolic model in normal and deficient states...
July 7, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28682786/application-of-computational-methods-in-planaria-research-a-current-update
#6
Shyamasree Ghosh
Planaria is a member of the Phylum Platyhelminthes including flatworms. Planarians possess the unique ability of regeneration from adult stem cells or neoblasts and finds importance as a model organism for regeneration and developmental studies. Although research is being actively carried out globally through conventional methods to understand the process of regeneration from neoblasts, biology of development, neurobiology and immunology of Planaria, there are many thought provoking questions related to stem cell plasticity, and uniqueness of regenerative potential in Planarians amongst other members of Phylum Platyhelminthes...
July 6, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28673016/falcon-a-toolbox-for-the-fast-contextualisation-of-logical-networks
#7
Sébastien De Landtsheer, Panuwat Trairatphisan, Philippe Lucarelli, Thomas Sauter
Motivation: Mathematical modelling of regulatory networks allows for the discovery of knowledge at the system level. However, existing modelling tools are often computation-heavy and do not offer intuitive ways to explore the model, to test hypotheses or to interpret the results biologically. Results: We have developed a computational approach to contextualise logical models of regulatory networks with biological measurements based on a probabilistic description of rule-based interactions between the different molecules...
June 29, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28669847/a-review-on-multiple-sequence-alignment-from-the-perspective-of-genetic-algorithm
#8
REVIEW
Biswanath Chowdhury, Gautam Garai
Sequence alignment is an active research area in the field of bioinformatics. It is also a crucial task as it guides many other tasks like phylogenetic analysis, function, and/or structure prediction of biological macromolecules like DNA, RNA, and Protein. Proteins are the building blocks of every living organism. Although protein alignment problem has been studied for several decades, unfortunately, every available method produces alignment results differently for a single alignment problem. Multiple sequence alignment is characterized as a very high computational complex problem...
June 29, 2017: Genomics
https://www.readbyqxmd.com/read/28669348/the-structural-bioinformatics-analysis-of-biophenolic-lignan-estrogen-receptor-interaction
#9
Farzaneh Mohamadyar-Toupkanlou, Mina Esfandiari, Mahshid Sadat Kashef-Saberi, Mahboubeh Kabiri Renani, Masoud Soleimani
BACKGROUND: Plant lignans have proven efficacious in blocking estrogen receptors of breast cancer cells. However, available studies have mostly dealt with anti-cancer effects of groups of lignans in certain foods or plants and the effects of specific lignans, especially from a molecular interaction viewpoint, has been rarely addressed in the literature. OBJECTIVE: We aimed to computationally predict the binding ability and binding strength of pinoresinol, matairesinol, lariciresinol and secoisolariciresinol as potent ligands of estrogen receptor alpha (ER-α), in order to study these lignans as drugs...
June 23, 2017: Current Cancer Drug Targets
https://www.readbyqxmd.com/read/28666141/computational-design-of-peptide-ligands-to-target-the-intermolecular-interaction-between-viral-envelope-protein-and-pediatric-receptor
#10
Darong Xu, Hongliang Bian, Jinlan Cai, Daocheng Bao, Qing Jin, Min Zhu, Cuifeng Zhang, Tingting Tao
The recognition and binding of viral envelope protein to pediatric receptor subverts the membrane-trafficking apparatus to mediate virion export in young children. Here, we described a successful computational design of peptide ligands to target the intermolecular interaction between the virus large envelope protein (LHB) and adaptin receptor (ADT). Based on the crystal structure of ADT in complex with an oligopeptide segment corresponding to the core binding site of LHB, a sequence-specific amino acid preference profile was determined systematically for the ADT-binding peptides using structural bioinformatics approach...
June 17, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28646874/cmsa-a-heterogeneous-cpu-gpu-computing-system-for-multiple-similar-rna-dna-sequence-alignment
#11
Xi Chen, Chen Wang, Shanjiang Tang, Ce Yu, Quan Zou
BACKGROUND: The multiple sequence alignment (MSA) is a classic and powerful technique for sequence analysis in bioinformatics. With the rapid growth of biological datasets, MSA parallelization becomes necessary to keep its running time in an acceptable level. Although there are a lot of work on MSA problems, their approaches are either insufficient or contain some implicit assumptions that limit the generality of usage. First, the information of users' sequences, including the sizes of datasets and the lengths of sequences, can be of arbitrary values and are generally unknown before submitted, which are unfortunately ignored by previous work...
June 24, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28644851/comorbidities-in-the-diseasome-are-more-apparent-than-real-what-bayesian-filtering-reveals-about-the-comorbidities-of-depression
#12
Peter Marx, Peter Antal, Bence Bolgar, Gyorgy Bagdy, Bill Deakin, Gabriella Juhasz
Comorbidity patterns have become a major source of information to explore shared mechanisms of pathogenesis between disorders. In hypothesis-free exploration of comorbid conditions, disease-disease networks are usually identified by pairwise methods. However, interpretation of the results is hindered by several confounders. In particular a very large number of pairwise associations can arise indirectly through other comorbidity associations and they increase exponentially with the increasing breadth of the investigated diseases...
June 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28631251/regulation-of-cardiac-myocyte-cell-death-and-differentiation-by-myocardin
#13
REVIEW
Joseph W Gordon
Myocardin is a cardiac- and smooth muscle-enriched transcriptional co-activator that was originally described as an interacting partner of the serum response factor. Shortly after myocardin's discovery, a wealth of published literature described the role of myocardin as a regulator of smooth muscle differentiation and phenotype modulation, while gene-targeting studies confirmed the essential role of myocardin in vascular development. More recently, myocardin has been implicated as an important regulator of cardiac myocyte differentiation in studies demonstrating direct programming of fibroblasts towards the cardiac lineage...
June 19, 2017: Molecular and Cellular Biochemistry
https://www.readbyqxmd.com/read/28625714/proteomic-analysis-of-seminal-plasma-from-locally-adapted-curraleiro-p%C3%A3-duro-bulls-bos-taurus-identifying-biomarkers-involved-in-sperm-physiology-in-endangered-animals-for-conservation-of-biodiversity
#14
E B Menezes, R V de Oliveira, M F van Tilburg, E A Barbosa, N V Nascimento, A L M C S Velho, F B Moreno, R A Moreira, A C O Monteiro-Moreira, G M C Carvalho, A F Ramos, E Memili, A A Moura
The present study was aimed at evaluating the seminal plasma proteins and sperm parameters of Curraleiro Pé-Duro bulls. Semen was collected from 10 bulls by electroejaculation, and sperm parameters were evaluated in fresh and frozen-thawed semen. Seminal plasma proteins were analyzed by 2-D SDS-PAGE and mass spectrophotometry. Tools in computational biology were used to generate bioinformatic knowledge and evaluate gene ontology, protein-protein interactions, phylogenetic trees and multiple sequence alignments...
May 29, 2017: Animal Reproduction Science
https://www.readbyqxmd.com/read/28625502/a-computable-phenotype-improves-cohort-ascertainment-in-a-pediatric-pulmonary-hypertension-registry
#15
Alon Geva, Jessica L Gronsbell, Tianxi Cai, Tianrun Cai, Shawn N Murphy, Jessica C Lyons, Michelle M Heinz, Marc D Natter, Nandan Patibandla, Jonathan Bickel, Mary P Mullen, Kenneth D Mandl
OBJECTIVES: To compare registry and electronic health record (EHR) data mining approaches for cohort ascertainment in patients with pediatric pulmonary hypertension (PH) in an effort to overcome some of the limitations of registry enrollment alone in identifying patients with particular disease phenotypes. STUDY DESIGN: This study was a single-center retrospective analysis of EHR and registry data at Boston Children's Hospital. The local Informatics for Integrating Biology and the Bedside (i2b2) data warehouse was queried for billing codes, prescriptions, and narrative data related to pediatric PH...
June 15, 2017: Journal of Pediatrics
https://www.readbyqxmd.com/read/28617229/analyzing-the-field-of-bioinformatics-with-the-multi-faceted-topic-modeling-technique
#16
Go Eun Heo, Keun Young Kang, Min Song, Jeong-Hoon Lee
BACKGROUND: Bioinformatics is an interdisciplinary field at the intersection of molecular biology and computing technology. To characterize the field as convergent domain, researchers have used bibliometrics, augmented with text-mining techniques for content analysis. In previous studies, Latent Dirichlet Allocation (LDA) was the most representative topic modeling technique for identifying topic structure of subject areas. However, as opposed to revealing the topic structure in relation to metadata such as authors, publication date, and journals, LDA only displays the simple topic structure...
May 31, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28609295/clubber-removing-the-bioinformatics-bottleneck-in-big-data-analyses
#17
Maximilian Miller, Chengsheng Zhu, Yana Bromberg
With the advent of modern day high-throughput technologies, the bottleneck in biological discovery has shifted from the cost of doing experiments to that of analyzing results. clubber is our automated cluster-load balancing system developed for optimizing these "big data" analyses. Its plug-and-play framework encourages re-use of existing solutions for bioinformatics problems. clubber's goals are to reduce computation times and to facilitate use of cluster computing. The first goal is achieved by automating the balance of parallel submissions across available high performance computing (HPC) resources...
June 13, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28609292/knowledge-discovery-in-biological-databases-for-revealing-candidate-genes-linked-to-complex-phenotypes
#18
Keywan Hassani-Pak, Christopher Rawlings
Genetics and "omics" studies designed to uncover genotype to phenotype relationships often identify large numbers of potential candidate genes, among which the causal genes are hidden. Scientists generally lack the time and technical expertise to review all relevant information available from the literature, from key model species and from a potentially wide range of related biological databases in a variety of data formats with variable quality and coverage. Computational tools are needed for the integration and evaluation of heterogeneous information in order to prioritise candidate genes and components of interaction networks that, if perturbed through potential interventions, have a positive impact on the biological outcome in the whole organism without producing negative side effects...
June 13, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28582565/isambard-an-open-source-computational-environment-for-biomolecular-analysis-modelling-and-design
#19
Christopher W Wood, Jack W Heal, Andrew R Thomson, Gail J Bartlett, Amaurys A Ibarra, R Leo Brady, Richard B Sessions, Derek N Woolfson
Motivation: The rational design of biomolecules is becoming a reality. However, further computational tools are needed to facilitate and accelerate this, and to make it accessible to more users. Results: Here we introduce ISAMBARD, a tool for structural analysis, model building and rational design of biomolecules. ISAMBARD is open-source, modular, computationally scalable and intuitive to use. These features allow non-experts to explore biomolecular design in silico ...
June 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28575140/optimizing-drug-development-in-oncology-by-clinical-trial-simulation-why-and-how
#20
Jocelyn Gal, Gérard Milano, Jean-Marc Ferrero, Esma Saâda-Bouzid, Julien Viotti, Sylvie Chabaud, Paul Gougis, Christophe Le Tourneau, Renaud Schiappa, Agnes Paquet, Emmanuel Chamorey
In therapeutic research, the safety and efficacy of pharmaceutical products are necessarily tested on humans via clinical trials after an extensive and expensive preclinical development period. Methodologies such as computer modeling and clinical trial simulation (CTS) might represent a valuable option to reduce animal and human assays. The relevance of these methods is well recognized in pharmacokinetics and pharmacodynamics from the preclinical phase to postmarketing. However, they are barely used and are poorly regarded for drug approval, despite Food and Drug Administration and European Medicines Agency recommendations...
May 29, 2017: Briefings in Bioinformatics
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