PubAg

Main content area

You searched for: Subject "bioinformatics" Remove constraint Subject: "bioinformatics"
Start Over

Search

10,476  Search Results

« Previous | 1 - 20 of 10,476 |
Number of results to display per page

Search Results

1. Cross-linking/mass spectrometry to get a closer view on protein interaction networks

Author:
Iacobucci, Claudio; Götze, Michael; Sinz, Andrea
Source:
Current opinion in biotechnology 2020 v.63 pp. 48-53
ISSN:
0958-1669
Subject:
bioinformatics,   etc   ; crosslinking; mass spectrometry;     Show all 3 Subjects
Abstract:
... Just recently, chemical cross-linking combined with mass spectrometry (XL-MS) has emerged as valuable tool to study protein interaction networks on the system-wide level. The current challenges in XL-MS are to develop robust workflows enabling a comprehensive capture of dynamic biological assemblies in their native environment in a routine manner. In this review, we will highlight both the latest ...
DOI:
10.1016/j.copbio.2019.12.009

2. ERRATUM TO: Application of shotgun metagenomics to smoked salmon experimentally spiked: Comparison between sequencing and microbiological data using different bioinformatic approaches

Author:
De Cesare, Alessandra; Oliveri, Chiara; Lucchi, Alex; Pasquali, Frederique; Pamp, Sünje Johanna; Mordhorst, Hanne; Wylezich, Claudia; Poulsen, Casper; Manfreda, Gerardo
Source:
Italian journal of food safety 2020 v.9 no.1 pp. 8991
ISSN:
2239-7132
Subject:
bioinformatics,   etc   ; metagenomics; smoked salmon;     Show all 3 Subjects
Abstract:
... The authors would like to correct the authorship in this publication, for the below-mentioned reason. ...
DOI:
10.4081/ijfs.2020.8991
PubMed:
32300574
PubMed Central:
PMC7154600

3. Computational parametric analysis of the design of cross-flow turbines under constraints

Author:
Leguizamón, Sebastián; Avellan, François
Source:
Renewable energy 2020 v.159 pp. 300-311
ISSN:
0960-1481
Subject:
bioinformatics,   etc   ; capital; pipes; steel; turbines; water power;     Show all 6 Subjects
Abstract:
... The cross-flow turbine is an attractive technology for small-scale hydropower generation thanks to its low capital cost and relatively high efficiency even under partial discharge operating conditions. It has been proposed that this kind of turbine can be manufactured from standard steel pipe sections given its simple geometry, an alternative that would further decrease the turbine’s capital cost ...
DOI:
10.1016/j.renene.2020.03.187

4. Art and Science of the Cellular Mesoscale

Author:
Goodsell, David S.; Olson, Arthur J.; Forli, Stefano
Source:
Trends in biochemical sciences 2020 v.45 no.6 pp. 472-483
ISSN:
0968-0004
Subject:
bioinformatics,   etc   ; infrastructure; microscopy; models; structural biology;     Show all 5 Subjects
Abstract:
... Experimental information from microscopy, structural biology, and bioinformatics may be integrated to build structural models of entire cells with molecular detail. This integrative modeling is challenging in several ways: the intrinsic complexity of biology results in models with many closely packed and heterogeneous components; the wealth of available experimental data is scattered among multipl ...
DOI:
10.1016/j.tibs.2020.02.010
PubMed:
32413324
PubMed Central:
PMC7230070

5. How to functionalise metal–organic frameworks to enable guest nanocluster embedment

Author:
King, James; Zhang, Linda; Doszczeczko, Szymon; Sambalova, Olga; Luo, Hui; Rohman, Fadli; Phillips, Omotoyosi; Borgschulte, Andreas; Hirscher, Michael; Addicoat, Matthew; Szilágyi, Petra Ágota
Source:
Journal of materials chemistry A 2020 v.8 no.9 pp. 4889-4897
ISSN:
2050-7496
Subject:
bioinformatics,   etc   ; coordination polymers; models; moieties; nanoparticles; prediction;     Show all 6 Subjects
Abstract:
... We report on the development and verification of an enhanced computational model capable of robust predictions and yielding a single descriptor to the successful embedding of guest nanoclusters into the pores of functionalised metal–organic frameworks. Using the predictions of this model, we have been able to embed Pd nanoclusters in the pores of Br-UiO-66 and show that the embedding of Pd nanoclu ...
DOI:
10.1039/c9ta12837a

6. Multi-scale approaches for the simulation of cardiac electrophysiology: I – Sub-cellular and stochastic calcium dynamics from cell to organ

Author:
Colman, Michael A.; Holmes, Maxx; Whittaker, Dominic G.; Jayasinghe, Izzy; Benson, Alan P.
Source:
Methods 2020
ISSN:
1046-2023
Subject:
bioinformatics,   etc   ; arrhythmia; calcium; electrophysiology; heart; models;     Show all 6 Subjects
Abstract:
... Computational models of the heart at multiple spatial scales, from sub-cellular nanodomains to the whole-organ, are a powerful tool for the simulation of cardiac electrophysiology. Application of these models has provided remarkable insight into the normal and pathological functioning of the heart. In these two articles, we present methods for modelling cardiac electrophysiology at all of these sp ...
DOI:
10.1016/j.ymeth.2020.02.011

7. Fused variable screening for massive imbalanced data

Author:
Xie, Jinhan; Hao, Meiling; Liu, Wenxin; Lin, Yuanyuan
Source:
Computational statistics & data analysis 2020 v.141 pp. 94-108
ISSN:
0167-9473
Subject:
bioinformatics,   etc   ; fraud; gene expression; models; screening;     Show all 5 Subjects
Abstract:
... Imbalanced data, in which the data exhibit an unequal or highly-skewed distribution between its classes/categories, are pervasive in many scientific fields, with application range from bioinformatics, text classification, face recognition, fraud detection, etc. Imbalanced data in modern science are often of massive size and high dimensionality, for example, gene expression data for diagnosing rare ...
DOI:
10.1016/j.csda.2019.06.013

8. High-dimensional structure learning of binary pairwise Markov networks: A comparative numerical study

Author:
Pensar, Johan; Xu, Yingying; Puranen, Santeri; Pesonen, Maiju; Kabashima, Yoshiyuki; Corander, Jukka
Source:
Computational statistics & data analysis 2020 v.141 pp. 62-76
ISSN:
0167-9473
Subject:
bioinformatics,   etc   ; data collection; equipment; learning; models; probability;     Show all 6 Subjects
Abstract:
... Learning the undirected graph structure of a Markov network from data is a problem that has received a lot of attention during the last few decades. As a result of the general applicability of the model class, a myriad of methods have been developed in parallel in several research fields. Recently, as the size of the considered systems has increased, the focus of new methods has been shifted towar ...
DOI:
10.1016/j.csda.2019.06.012

9. Using approximate Bayesian computation for estimating parameters in the cue-based retrieval model of sentence processing

Author:
Vasishth, Shravan
Source:
MethodsX 2020 v.7 pp. 100850
ISSN:
2215-0161
Subject:
bioinformatics,   etc   ; Bayesian theory; models; reading; uncertainty;     Show all 5 Subjects
Abstract:
... A commonly used approach to parameter estimation in computational models is the so-called grid search procedure: the entire parameter space is searched in small steps to determine the parameter value that provides the best fit to the observed data. This approach has several disadvantages: first, it can be computationally very expensive; second, one optimal point value of the parameter is reported ...
DOI:
10.1016/j.mex.2020.100850
PubMed:
32300544
PubMed Central:
PMC7152701

10. Correction to: Computationally-assisted discovery and structure elucidation of natural products

Author:
Nugroho, Alfarius Eko; Morita, Hiroshi
Source:
Natural medicines 2019 v.73 no.4 pp. 696
ISSN:
1340-3443
Subject:
bioinformatics,   etc   ; algorithms; chemistry;     Show all 3 Subjects
Abstract:
... The article Computationally-assisted discovery and structure elucidation of natural products, written by Alfarius Eko Nugroho and Hiroshi Morita, was originally published electronically on the publisher’s internet portal (currently SpringerLink) on 15 May 2019 without open access. ...
DOI:
10.1007/s11418-019-01340-5
PubMed:
31254164
PubMed Central:
PMC6713674

11. A simplified model for expedient computational assessment of the novel REEFS wave energy converter power output

Author:
Lopes de Almeida, J.P.P.G.; Abrantes, J.R.C.B.; Bento, J.G.S.E.S.
Source:
Renewable energy 2020 v.157 pp. 43-54
ISSN:
0960-1481
Subject:
bioinformatics,   etc   ; electric power; energy conversion; mathematical models; reefs; water power;     Show all 6 Subjects
Abstract:
... REEFS is a new multipurpose wave energy converter. It produces electric energy and contributes to shore protection. It is a large nearshore submerged device that can originate high waves breaking like the natural reefs do. The device makes use of the wave’s pressure and velocity spatial differentials, to produce electric energy. A laboratorial concept proof based in a small scale physical model (1 ...
DOI:
10.1016/j.renene.2020.04.128

12. Computer simulation of the core-shell microgels synthesis via precipitation polymerization

Author:
Gavrilov, Alexey A.; Rudyak, Vladimir Yu.; Chertovich, Alexander V.
Source:
Journal of colloid and interface science 2020 v.574 pp. 393-398
ISSN:
0021-9797
Subject:
bioinformatics,   etc   ; computer simulation; crosslinking; microgels; models; polymerization; prediction;     Show all 7 Subjects
Abstract:
... In this work we presented a novel computational model of precipitation polymerization allowing one to obtain core-shell microgels via a realistic cross-linking process based on the experimental procedure. We showed that the cross-linker–monomer reactivity ratios r are responsible for the microgel internal structure. Values of r lower than 1 correspond to the case when alternating sequences occur a ...
DOI:
10.1016/j.jcis.2020.04.064

13. Expanding the understanding of the heterogeneous nature of melanoma with bioinformatics and disorder-based proteomics

Author:
Djulbegovic, Mak B.; Uversky, Vladimir N.
Source:
International journal of biological macromolecules 2020 v.150 pp. 1281-1293
ISSN:
0141-8130
Subject:
bioinformatics,   etc   ; drugs; genetic heterogeneity; melanoma; precision medicine; proteins; proteomics; risk;     Show all 8 Subjects
Abstract:
... The past few decades show that incidences of melanoma are on the rise. The risk associated with this disease is an interplay between genetic and host factors and sun exposure. While scientific progress in the treatment of melanoma is remarkable, additional research is needed to improve patient outcomes and to better understand the heterogenous nature of this disease. Fortunately, as the clinical c ...
DOI:
10.1016/j.ijbiomac.2019.10.139

14. Robust optimal design of building cooling sources considering the uncertainty and cross-correlation of demand and source

Author:
Niu, Jide; Tian, Zhe; Yue, Lu
Source:
Applied energy 2020 v.265 pp. 114793
ISSN:
0306-2619
Subject:
bioinformatics,   etc   ; deterministic models; energy; renewable energy sources; risk; uncertainty;     Show all 6 Subjects
Abstract:
... The demand and renewable energy uncertainties introduce significant complexity to the design of renewable cooling sources. Conventional design method may introduce a risk of suboptimal solution due to overlooking the multiple uncertainties. The stochastic programming model is widely used for optimal design of building cooling sources, while it may encounter computational burden when considering a ...
DOI:
10.1016/j.apenergy.2020.114793

15. A simple computational model for MOF-5W absorption and photoluminescence to distinguish MOF-5 from its hydrolysis products

Author:
Rodríguez, Nicolás Artemio; Parra, Rodrigo; San Román, Enrique; Grela, María Alejandra
Source:
Journal of materials science 2020 v.55 no.15 pp. 6588-6597
ISSN:
0022-2461
Subject:
bioinformatics,   etc   ; X-ray diffraction; hydrolysis; ligands; photoluminescence; protonation; spectroscopy;     Show all 7 Subjects
Abstract:
... In the present study, changes in absorptance and emission spectra of MOF-5 after being exposed to water are examined in detail and compared with DFT calculations. The results of the computational studies show the effect of water molecules in the absorptance spectra of MOF-5W, the first hydrolysis product of MOF-5, highlighting the role of the protonation of the ligand on the bandgap of these mater ...
DOI:
10.1007/s10853-020-04442-8

16. A Review of Computational Models for the Flow of Milled Biomass Part I: Discrete-Particle Models

Author:
Xia, Yidong; Stickel, Jonathan J.; Jin, Wencheng; Klinger, Jordan
Source:
ACS sustainable chemistry & engineering 2020 v.8 no.16 pp. 6142-6156
ISSN:
2168-0485
Subject:
bioinformatics,   etc   ; biomass; equipment; mathematical models; mechanics; renewable energy sources;     Show all 6 Subjects
Abstract:
... Biomass is a renewable and sustainable energy resource. Current design of biomass handling and feeding equipment leverage both experiments and numerical modeling. This paper reviews the state-of-the-art discrete element methods (DEM) for the flow of milled biomass (Part I), accompanied by a comprehensive review on continuum-based computational models (Part II). The present review on DEM is primari ...
DOI:
10.1021/acssuschemeng.0c00402

17. A Review of Computational Models for the Flow of Milled Biomass Part II: Continuum-Mechanics Models

Author:
Jin, Wencheng; Stickel, Jonathan J.; Xia, Yidong; Klinger, Jordan
Source:
ACS sustainable chemistry & engineering 2020 v.8 no.16 pp. 6157-6172
ISSN:
2168-0485
Subject:
bioinformatics,   etc   ; biomass; equations; finite element analysis; lignocellulose; materials handling; models;     Show all 7 Subjects
Abstract:
... The design of efficient material-handling systems for milled lignocellulosic biomass is challenging due to their complex particle morphologies and frictional interactions. Computational modeling, including the discrete element method (DEM) and continuum-based finite-element/volume methods, may offer scientific insight and predictive capabilities for the flow of milled biomass in hoppers and feeder ...
DOI:
10.1021/acssuschemeng.0c00412

18. Genetic evolution and codon usage analysis of NKX-2.5 gene governing heart development in some mammals

Author:
Malakar, Arup Kr.; Halder, Binata; Paul, Prosenjit; Deka, Himangshu; Chakraborty, Supriyo
Source:
Genomics 2020 v.112 no.2 pp. 1319-1329
ISSN:
0888-7543
Subject:
bioinformatics,   etc   ; amino acids; codons; heart; mammals; mutation; natural selection;     Show all 7 Subjects
Abstract:
... NKX-2.5 gene is responsible for cardiac development and its targeted disruption apprehends cardiac development at the linear heart tube stage. Bioinformatic analysis was employed to investigate the codon usage pattern and dN/dS of mammalian NKX-2.5 gene. The relative synonymous codon usage analysis revealed variation in codon usage and two synonymous codons namely ATA (Ile) and GTA (Val) were abse ...
DOI:
10.1016/j.ygeno.2019.07.023

19. PattRec: An easy-to-use CNV detection tool optimized for targeted NGS assays with diagnostic purposes

Author:
Roca, Iria; González-Castro, Lorena; Maynou, Joan; Palacios, Lourdes; Fernández, Helena; Couce, Mª Luz; Fernández-Marmiesse, Ana
Source:
Genomics 2020 v.112 no.2 pp. 1245-1256
ISSN:
0888-7543
Subject:
bioinformatics,   etc   ; computer software; databases; high-throughput nucleotide sequencing; human diseases;     Show all 5 Subjects
Abstract:
... Genetic laboratories use custom-commercial targeted next-generation sequencing (tg-NGS) assays to identify disease-causing variants. Although the high coverage achieved with these tests allows for the detection of copy number variants (CNVs), which account for an important proportion of the genetic burden in human diseases, an easy-to-use tool for automatic CNV detection is still lacking. This art ...
DOI:
10.1016/j.ygeno.2019.07.011

20. Report of the 2019 NIST-FDA workshop on standards for next generation sequencing detection of viral adventitious agents in biologics and biomanufacturing

Author:
Cleveland, Megan H.; Anekella, Bharathi; Brewer, Michael; Chin, Pei-Ju; Couch, Heather; Delwart, Eric; Huggett, Jim; Jackson, Scott; Martin, Javier; Monpoeho, Serge; Morrison, Tom; Ng, Siemon H.S.; Ussery, David; Khan, Arifa S.
Source:
Biologicals 2020
ISSN:
1045-1056
Subject:
bioinformatics,   etc   ; high-throughput nucleotide sequencing; manufacturing; product safety; viruses;     Show all 5 Subjects
Abstract:
... Adventitious virus testing assures product safety by demonstrating the absence of viruses that could be unintentionally introduced during the manufacturing process. The capabilities of next-generation sequencing (NGS) for broad virus detection in biologics have been demonstrated by the detection of known and novel viruses that were previously missed using the recommended routine assays for adventi ...
DOI:
10.1016/j.biologicals.2020.02.003