Genomes and Genes
Summary: Computer-based representation of physical systems and phenomena such as chemical processes.
- Bordbar A, Monk J, King Z, Palsson B. Constraint-based models predict metabolic and associated cellular functions. Nat Rev Genet. 2014;15:107-20 pubmed publisher..As reviewed here, these recent successes have tangible implications in the fields of microbial evolution, interaction networks, genetic engineering and drug discovery. ..
- Smith J, Sturrock H, Olives C, Solomon A, Brooker S. Comparing the performance of cluster random sampling and integrated threshold mapping for targeting trachoma control, using computer simulation. PLoS Negl Trop Dis. 2013;7:e2389 pubmed publisher..In addition to strengthening the evidence base around choice of trachoma survey methodologies, this study illustrates the use of a simulated approach in addressing operational research questions for trachoma but also other NTDs. ..
- Arenas M, Dos Santos H, Posada D, Bastolla U. Protein evolution along phylogenetic histories under structurally constrained substitution models. Bioinformatics. 2013;29:3020-8 pubmed publisher..Therefore, we conclude that evolutionary models that consider protein stability and realistic evolutionary histories constitute a better approximation of the real evolutionary process. ..
- Ypma R, van Ballegooijen W, Wallinga J. Relating phylogenetic trees to transmission trees of infectious disease outbreaks. Genetics. 2013;195:1055-62 pubmed publisher..The approach unifies existing methods in the emerging field of phylodynamics with transmission tree reconstruction methods that are used in infectious disease epidemiology. ..
- Linke R, Leichtle A, Sheikh F, Schmidt C, Frenzel H, Graefe H, et al. Assessment of skills using a virtual reality temporal bone surgery simulator. Acta Otorhinolaryngol Ital. 2013;33:273-81 pubmed
- Zenke F, Hennequin G, Gerstner W. Synaptic plasticity in neural networks needs homeostasis with a fast rate detector. PLoS Comput Biol. 2013;9:e1003330 pubmed publisher..Our results strongly suggest the existence of a homeostatic regulatory mechanism that reacts to firing rate changes on the order of seconds to minutes. ..
- Takeyasu Y, Oka K, Miyake J, Kataoka T, Moritomo H, Murase T. Preoperative, computer simulation-based, three-dimensional corrective osteotomy for cubitus varus deformity with use of a custom-designed surgical device. J Bone Joint Surg Am. 2013;95:e173 pubmed publisher..guide system involving a custom-made surgical template designed on the basis of a three-dimensional computer simulation incorporating computed tomography (CT) data...
- Welter M, Rieger H. Interstitial fluid flow and drug delivery in vascularized tumors: a computational model. PLoS ONE. 2013;8:e70395 pubmed publisher..Finally we discuss various strategies to increase drug exposure time of tumor cells. ..
- Bencurova P, Baloun J, Musilova K, Radova L, Tichy B, Pail M, et al. MicroRNA and mesial temporal lobe epilepsy with hippocampal sclerosis: Whole miRNome profiling of human hippocampus. Epilepsia. 2017;58:1782-1793 pubmed publisher..These observations further encourage the potential of microRNA-based biomarkers or therapies. ..
- Huang Z, Lee D, Yoon S. Quantitative intracellular flux modeling and applications in biotherapeutic development and production using CHO cell cultures. Biotechnol Bioeng. 2017;114:2717-2728 pubmed publisher..Improved cell culture system understanding will enable robust developments in cell line and bioprocess engineering thus accelerating consistent process quality control in biopharmaceutical manufacturing. ..
- Benichoux V, Brown A, Anbuhl K, Tollin D. Representation of Multidimensional Stimuli: Quantifying the Most Informative Stimulus Dimension from Neural Responses. J Neurosci. 2017;37:7332-7346 pubmed publisher..We apply this method to the problem of the representation of sound source location in the face of changes in sound source level by neurons of the auditory midbrain. ..
- McAndrew T, Guseva E, Bagrow J. Reply & Supply: Efficient crowdsourcing when workers do more than answer questions. PLoS ONE. 2017;12:e0182662 pubmed publisher..Experiments and simulations demonstrate that these algorithms can efficiently explore an unbounded set of questions without losing confidence in crowd answers. ..
- Li Z, Xin Y, Cui X, Liu X, Wang L, Zhang W, et al. Optimization to the Phellinus experimental environment based on classification forecasting method. PLoS ONE. 2017;12:e0185444 pubmed publisher..GA is used to find the best culture conditions. The forecast accuracy rate more than 90% and the yield we got have a slight increase than the real yield. ..
- Moran K, Fairchild G, Generous N, Hickmann K, Osthus D, Priedhorsky R, et al. Epidemic Forecasting is Messier Than Weather Forecasting: The Role of Human Behavior and Internet Data Streams in Epidemic Forecast. J Infect Dis. 2016;214:S404-S408 pubmed publisher..We conclude that some of the fundamental differences between these 2 fields, such as human behavior, make disease forecasting more challenging than weather forecasting. ..
- Becker A, Grenfell B. tsiR: An R package for time-series Susceptible-Infected-Recovered models of epidemics. PLoS ONE. 2017;12:e0185528 pubmed publisher..Also included in tsiR are a number of diagnostic tools to assess the fit of the TSIR model. This package should be useful for researchers analyzing incidence data for fully-immunizing infectious diseases...
- Vieira E Oliveira T, Kemmoku D, da Silva J, Noritomi P, Passeri L. Finite Element Evaluation of Stable Fixation in Combined Mandibular Fractures. J Oral Maxillofac Surg. 2017;75:2399-2410 pubmed publisher..However, the combination of perpendicular plates in symphyseal fixation and a trapezoidal plate in condylar fixation showed an altered stress distribution. ..
- Jin Q, Grama I, Liu Q. Optimal Weights Mixed Filter for removing mixture of Gaussian and impulse noises. PLoS ONE. 2017;12:e0179051 pubmed publisher..Our simulation results show that the proposed filter is effective for mixed noises, as well as for single impulse noise and for single Gaussian noise. ..
- Blanco N, Foxman B, Malani A, Zhang M, Walk S, Rickard A, et al. An in silico evaluation of treatment regimens for recurrent Clostridium difficile infection. PLoS ONE. 2017;12:e0182815 pubmed publisher..However, the effectiveness of treatment varied by ribotype. Current CDI vancomycin regimen for treating recurrent cases should be studied further to better balance associated risks and benefits. ..
- Joiner W, Sing G, Smith M. Temporal specificity of the initial adaptive response in motor adaptation. PLoS Comput Biol. 2017;13:e1005438 pubmed publisher..This insight has direct implications for the development of computational models of early-stage motor adaptation and the evolution of this adaptive response with continued training. ..
- Sun R, Mendez D. An application of the Continuous Opinions and Discrete Actions (CODA) model to adolescent smoking initiation. PLoS ONE. 2017;12:e0186163 pubmed publisher..As a result, peer influence from social networks plays a big role in the smoking initiation process and should be an important driver in policy formulation...
- Matlak D, Szczurek E. Epistasis in genomic and survival data of cancer patients. PLoS Comput Biol. 2017;13:e1005626 pubmed publisher..With the ability to detect not only pairwise but twelve different types of triple epistasis, applicability of SurvLRT goes beyond cancer therapy, to the level of characterization of shapes of fitness landscapes. ..
- Haynes K, Abdali N, Jhawar V, Zgurskaya H, Parks J, Green A, et al. Identification and Structure-Activity Relationships of Novel Compounds that Potentiate the Activities of Antibiotics in Escherichia coli. J Med Chem. 2017;60:6205-6219 pubmed publisher..coli cells including the ability to penetrate the outer membrane, improved inhibition of efflux relative to 1, and potentiation of the activity of novobiocin and erythromycin. ..
- Schütt H, Wichmann F. An image-computable psychophysical spatial vision model. J Vis. 2017;17:12 pubmed publisher..In addition, it may serve as a building block for models of higher level processing...
- Rogers J, Fishberg A, Youngs N, Wu Y. Reconciliation feasibility in the presence of gene duplication, loss, and coalescence with multiple individuals per species. BMC Bioinformatics. 2017;18:292 pubmed publisher..Going forward, we believe that this model represents a first step towards understanding reconciliations in duplication-loss-coalescence models with multiple samples per species. ..
- Kinsler G, Sinai S, Lee N, Nowak M. Prebiotic selection for motifs in a model of template-free elongation of polymers within compartments. PLoS ONE. 2017;12:e0180208 pubmed publisher..We show that under this system of biased monomer addition, even without template-directed self-replication, genetic motifs can emerge, compete, cooperate, and ultimately survive within the population. ..
- Jin W, Penington C, McCue S, Simpson M. A computational modelling framework to quantify the effects of passaging cell lines. PLoS ONE. 2017;12:e0181941 pubmed publisher..Furthermore, our modelling also suggests some avenues for further experimental examination that could be used to validate or refine our simulation results. ..
- Ajmal M, Mir A, Wahid S, Khor C, Foo J, Siddiqi S, et al. Identification and in silico characterization of a novel p.P208PfsX1 mutation in V-ATPase a3 subunit associated with autosomal recessive osteopetrosis in a Pakistani family. BMC Med Genet. 2017;18:148 pubmed publisher..Moreover, our findings should help in genetic counseling and provide further insight into the disease pathogenesis and potential targeted therapy. ..
- Beuter A. The use of neurocomputational models as alternatives to animal models in the development of electrical brain stimulation treatments. Altern Lab Anim. 2017;45:91-99 pubmed
- Winkler T, Justice A, Cupples L, Kronenberg F, Kutalik Z, Heid I. Approaches to detect genetic effects that differ between two strata in genome-wide meta-analyses: Recommendations based on a systematic evaluation. PLoS ONE. 2017;12:e0181038 pubmed publisher..Our recommendations provide tangible guidelines for future GWAMAs that aim at identifying between-strata differences. A better understanding of such effects will help pinpoint the underlying mechanisms. ..
- Wang R, Shen Y, Tino P, Welchman A, Kourtzi Z. Learning predictive statistics from temporal sequences: Dynamics and strategies. J Vis. 2017;17:1 pubmed publisher..Our findings provide evidence for alternate routes to learning of behaviorally relevant statistics that facilitate our ability to predict future events in variable environments...
- Kreif N, Tran L, Grieve R, Destavola B, Tasker R, Petersen M. Estimating the comparative effectiveness of feeding interventions in the paediatric intensive care unit: a demonstration of longitudinal targeted maximum likelihood estimation. Am J Epidemiol. 2017;: pubmed publisher..TMLE offers a flexible estimation approach, hence we provide a practical guidance in implementation to encourage its wider uptake...
- Kajla S, Mukhopadhyay A, Pradhan A. Development of transgenic Brassica juncea lines for reduced seed sinapine content by perturbing phenylpropanoid pathway genes. PLoS ONE. 2017;12:e0182747 pubmed publisher..8% to 67.2%; the line with maximum reduction had sinapine content of 3.79 mg/g of DSW. The study also revealed that RNAi method was more efficient than the other two methods used in this study. ..
- Negi S, Singh H, Mukhopadhyay A. Gut bacterial peptides with autoimmunity potential as environmental trigger for late onset complex diseases: In-silico study. PLoS ONE. 2017;12:e0180518 pubmed publisher..This dataset provides us with gut bacterial autoimmune candidates which can be studied for their clinical significance in late onset diseases. ..
- Merk B, Litskevich D, Bankhead M, Taylor R. An innovative way of thinking nuclear waste management - Neutron physics of a reactor directly operating on SNF. PLoS ONE. 2017;12:e0180703 pubmed publisher..In addition, this nuclear system provides enhanced resistance against misuse of Pu and a significantly reduced fuel cycle. However, the new system requires a demand driven rethinking of the separation process to be efficient. ..
- Tian Y, Kubatko L. Rooting phylogenetic trees under the coalescent model using site pattern probabilities. BMC Evol Biol. 2017;17:263 pubmed publisher..The method will benefit numerous evolutionary studies that require rooting a phylogenetic tree without having to specify outgroups. ..
- Takayasu L, Suda W, Watanabe E, Fukuda S, Takanashi K, Ohno H, et al. A 3-dimensional mathematical model of microbial proliferation that generates the characteristic cumulative relative abundance distributions in gut microbiomes. PLoS ONE. 2017;12:e0180863 pubmed publisher..Our model indicated that the CRAD may be determined by the ratio of emerging to pre-existing species during non-uniform spatially competitive proliferation, independent of species composition. ..
- Li J, Zeng W, Zhang Y, Ko A, Li C, Zhu H, et al. Ancient DNA reveals genetic connections between early Di-Qiang and Han Chinese. BMC Evol Biol. 2017;17:239 pubmed publisher..Mogou harbors the earliest genetically identifiable Di-Qiang, ancestral to the Taojiazhai, and up to ~33% paternal and ~70% of its maternal haplogroups could be found in present-day Northern Han Chinese. ..
- Hacker W, Li S, Elcock A. Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome. Nucleic Acids Res. 2017;45:7541-7554 pubmed publisher..We anticipate that the models will prove useful in exploring other static and dynamic features of the bacterial chromosome. ..
- Wahid A, Khan D, Hussain I. Robust Adaptive Lasso method for parameter's estimation and variable selection in high-dimensional sparse models. PLoS ONE. 2017;12:e0183518 pubmed publisher..We also discuss the model selection oracle property and the asymptotic normality of the RAL. Simulations findings and real data examples also demonstrate the better performance of the proposed penalized regression approach. ..
- Bogdańska M, Bodnar M, Piotrowska M, Murek M, Schucht P, Beck J, et al. A mathematical model describes the malignant transformation of low grade gliomas: Prognostic implications. PLoS ONE. 2017;12:e0179999 pubmed publisher..We discuss the relationship between patient prognosis and model parameters. We approximate tumour radius and velocity before malignant transformation as well as estimate the onset of this process. ..
- Ahn J, Bang J, Kim W, Lee S. Formic acid as a secondary substrate for succinic acid production by metabolically engineered Mannheimia succiniciproducens. Biotechnol Bioeng. 2017;114:2837-2847 pubmed publisher..08?g/L/h, respectively, using sucrose and FA as dual carbon sources. The strategy employed here will be similarly applicable in developing microorganisms to utilize FA and to produce valuable chemicals and materials from FA...
- Lin L, Chuang H. Analyzing the locomotory gaitprint of Caenorhabditis elegans on the basis of empirical mode decomposition. PLoS ONE. 2017;12:e0181469 pubmed publisher..The overall classification accuracy of the gaitprint analyses of all the strains reached nearly 89%. The method can also be extended to classify some motor neuron-related locomotory defects of C. elegans in the same fashion. ..
- Shahmohammadi Beni M, Hau T, Krstic D, Nikezic D, Yu K. Monte Carlo studies on neutron interactions in radiobiological experiments. PLoS ONE. 2017;12:e0181281 pubmed publisher..Such results would be useful for deciphering the reasons behind discrepancies among existing results in the literature. ..
- Ruan S, Stormo G. Inherent limitations of probabilistic models for protein-DNA binding specificity. PLoS Comput Biol. 2017;13:e1005638 pubmed publisher..Generally probabilistic models are reasonably good approximations, but new high-throughput methods allow for biophysical models with increased accuracy that should be used whenever possible. ..
- Liang B, Zhao J, Wang X. A three-microRNA signature as a diagnostic and prognostic marker in clear cell renal cancer: An In Silico analysis. PLoS ONE. 2017;12:e0180660 pubmed publisher..In conclusion, the three-miRNA signature could be used as a diagnostic and prognostic biomarker in KIRC, and therefore, may help to provide significant clinical implication for the treatment of KIRC. ..
- Rennó Costa C, Tort A. Place and Grid Cells in a Loop: Implications for Memory Function and Spatial Coding. J Neurosci. 2017;37:8062-8076 pubmed publisher..The proposed model accounts for differences in how place and grid cells represent different environments and provides a new interpretation in which place and grid cells mutually interact to form a coupled code for space. ..
- Nakanishi S, Soares L, Biazi L, Nascimento V, Costa A, Rocha G, et al. Fermentation strategy for second generation ethanol production from sugarcane bagasse hydrolyzate by Spathaspora passalidarum and Scheffersomyces stipitis. Biotechnol Bioeng. 2017;114:2211-2221 pubmed publisher..stipitis fermentation. The strategy proposed in this work can be considered as a promising strategy in the production of second generation ethanol. Biotechnol. Bioeng. 2017;114: 2211-2221. © 2017 Wiley Periodicals, Inc. ..
- Gorfine M, Berndt S, Chang Claude J, Hoffmeister M, Le Marchand L, Potter J, et al. Heritability Estimation using a Regularized Regression Approach (HERRA): Applicable to continuous, dichotomous or age-at-onset outcome. PLoS ONE. 2017;12:e0181269 pubmed publisher..068 (SE = 0.017), 0.072 (SE = 0.021) and 0.110 (SE = 5.19 x 10-3). HERRA yields over 50% increase in heritability estimate compared to GCTA or LDAK. ..
- Tilahun G, Makinde O, Malonza D. Modelling and Optimal Control of Typhoid Fever Disease with Cost-Effective Strategies. Comput Math Methods Med. 2017;2017:2324518 pubmed publisher..Numerical results for the typhoid outbreak dynamics and its optimal control revealed that a combination of prevention and treatment is the best cost-effective strategy to eradicate the disease...
- Bells S, Lefebvre J, Prescott S, Dockstader C, Bouffet E, Skocic J, et al. Changes in White Matter Microstructure Impact Cognition by Disrupting the Ability of Neural Assemblies to Synchronize. J Neurosci. 2017;37:8227-8238 pubmed publisher..Together, our human imaging data and computer simulations show a fundamental connection between WM microstructure and neural synchronization that is critical for cognitive processing. ..
- Wu J, Jia Q, Wu S, Zeng H, Sun Y, Wang C, et al. The crystal structure of the Pyrococcus abyssi mono-functional methyltransferase PaTrm5b. Biochem Biophys Res Commun. 2017;493:240-245 pubmed publisher..This study expands our understanding on the methylation mechanism of the Trm5 enzymes and wyosine hypermodification. ..