Teaching the bioinformatics of signaling networks: an integrated approach to facilitate multi-disciplinary learning.

abstract：:Understanding the interconnections of microbial pathogenicity phenomena, such as biofilm formation, quorum sensing and antimicrobial resistance, is a tremendous open challenge for biomedical research. Progress made by wet-lab researchers and bioinformaticians in understanding the underlying regulatory phenomena has be...

journal_title：Briefings in bioinformatics

authors： Castelhano Santos N,Pereira MO,Lourenço A

更新日期：2015-01-01 00:00:00

abstract：:Researchers have long been presented with the challenge imposed by the role of genetic heterogeneity in drug response. For many years, Pharmacogenomics and pharmacomicrobiomics has been investigating the influence of an individual's genetic background to drug response and disposition. More recently, the human gut micr...

journal_title：Briefings in bioinformatics

authors： Hassan R,Allali I,Agamah FE,Elsheikh SSM,Thomford NE,Dandara C,Chimusa ER

更新日期：2020-12-01 00:00:00

abstract：:Mass spectrometry (MS)-based proteomics has undergone rapid advancements in recent years, creating challenging problems for bioinformatics. We focus on four aspects where bioinformatics plays a crucial role (and proteomics is needed for clinical application): peptide-spectra matching (PSM) based on the new data-indepe...

journal_title：Briefings in bioinformatics

authors： Goh WWB,Wong L

更新日期：2019-01-18 00:00:00

abstract：:Programs for RNA mutational analysis that are structure-based and rely on secondary structure prediction have been developed and expanded in the past several years. They can be used for a variety of purposes, such as in suggesting point mutations that will alter RNA virus replication or translation initiation, investi...

journal_title：Briefings in bioinformatics

authors： Barash D,Churkin A

更新日期：2011-03-01 00:00:00

abstract：:Protein phosphorylation is a reversible and ubiquitous post-translational modification that primarily occurs at serine, threonine and tyrosine residues and regulates a variety of biological processes. In this paper, we first briefly summarized the current progresses in computational prediction of eukaryotic protein ph...

journal_title：Briefings in bioinformatics

authors： Cao M,Chen G,Yu J,Shi S

更新日期：2020-03-23 00:00:00

abstract：:Gene expression profiling holds great potential as a new approach to histological diagnosis and precision medicine of cancers of unknown primary (CUP). Batch effects and different data types greatly decrease the predictive performance of biomarker-based algorithms, and few methods have been widely applied to identify ...

journal_title：Briefings in bioinformatics

authors： Shen Y,Chu Q,Yin X,He Y,Bai P,Wang Y,Fang W,Timko MP,Fan L,Jiang W

更新日期：2020-04-08 00:00:00

abstract：:Many bioinformatics problems, such as sequence alignment, gene prediction, phylogenetic tree estimation and RNA secondary structure prediction, are often affected by the 'uncertainty' of a solution, that is, the probability of the solution is extremely small. This situation arises for estimation problems on high-dimen...

journal_title：Briefings in bioinformatics

authors： Hamada M

更新日期：2014-09-01 00:00:00

abstract：:Phase separation is an important mechanism that mediates the spatial distribution of proteins in different cellular compartments. While phase-separated proteins share certain sequence characteristics, including intrinsically disordered regions (IDRs) and prion-like domains, such characteristics are insufficient for ma...

journal_title：Briefings in bioinformatics

authors： Yu C,Shen B,You K,Huang Q,Shi M,Wu C,Chen Y,Zhang C,Li T

更新日期：2020-09-02 00:00:00

abstract：:Biologists very often use enrichment methods based on statistical hypothesis tests to identify gene properties that are significantly over-represented in a given set of genes of interest, by comparison with a 'background' set of genes. These enrichment methods, although based on rigorous statistical foundations, are n...

journal_title：Briefings in bioinformatics

authors： Fabris F,Palmer D,de Magalhães JP,Freitas AA

更新日期：2020-05-21 00:00:00

abstract：:Short tandem repeats are highly polymorphic and associated with a wide range of phenotypic variation, some of which cause neurodegenerative disease in humans. With advances in high-throughput sequencing technologies, there are novel opportunities to study genetic variation. While available sequencing technologies and ...

journal_title：Briefings in bioinformatics

authors： Cao MD,Balasubramanian S,Bodén M

更新日期：2015-03-01 00:00:00

abstract：:It is easy for today's students and researchers to believe that modern bioinformatics emerged recently to assist next-generation sequencing data analysis. However, the very beginnings of bioinformatics occurred more than 50 years ago, when desktop computers were still a hypothesis and DNA could not yet be sequenced. T...

journal_title：Briefings in bioinformatics

authors： Gauthier J,Vincent AT,Charette SJ,Derome N

更新日期：2019-11-27 00:00:00

abstract：:Aberrant DNA methylation is a fundamental characterization of epigenetics for carcinogenesis. Abnormality of DNA methylation-related functional elements (DMFEs) may lead to dysfunction of regulatory genes in the progression of cancers, contributing to prognosis of many cancers. There is an urgent need to construct a t...

journal_title：Briefings in bioinformatics

authors： Zhang C,Zhao N,Zhang X,Xiao J,Li J,Lv D,Zhou W,Li Y,Xu J,Li X

更新日期：2020-08-11 00:00:00

abstract：:Gene expression data have played an essential role in many biomedical studies. When the number of genes is large and sample size is limited, there is a 'lack of information' problem, leading to low-quality findings. To tackle this problem, both horizontal and vertical data integrations have been developed, where verti...

journal_title：Briefings in bioinformatics

authors： Wu M,Yi H,Ma S

更新日期：2020-08-14 00:00:00

abstract：:Genomic data hold salient information about the characteristics of a living organism. Throughout the past decade, pinnacle developments have given us more accurate and inexpensive methods to retrieve genome sequences of humans. However, with the advancement of genomic research, there is a growing privacy concern regar...

journal_title：Briefings in bioinformatics

authors： Aziz MMA,Sadat MN,Alhadidi D,Wang S,Jiang X,Brown CL,Mohammed N

更新日期：2019-05-21 00:00:00

abstract：:In drug development, preclinical safety and pharmacokinetics assessments of candidate drugs to ensure the safety profile are a must. While in vivo and in vitro tests are traditionally used, experimental determinations have disadvantages, as they are usually time-consuming and costly. In silico predictions of these pre...

journal_title：Briefings in bioinformatics

authors： Hsiao Y,Su BH,Tseng YJ

更新日期：2020-08-07 00:00:00

abstract：:Circular RNA (circRNA) is a group of RNA family generated by RNA circularization, which was discovered ubiquitously across different species and tissues. However, there is no global view of tissue specificity for circRNAs to date. Here we performed the comprehensive analysis to characterize the features of human and m...

journal_title：Briefings in bioinformatics

authors： Xia S,Feng J,Lei L,Hu J,Xia L,Wang J,Xiang Y,Liu L,Zhong S,Han L,He C

更新日期：2017-11-01 00:00:00

abstract：:The formation of phenotypic traits, such as biomass production, tumor volume and viral abundance, undergoes a complex process in which interactions between genes and developmental stimuli take place at each level of biological organization from cells to organisms. Traditional studies emphasize the impact of genes by d...

journal_title：Briefings in bioinformatics

authors： Wang Z,Wang Y,Wang N,Wang J,Wang Z,Vallejos CE,Wu R

更新日期：2014-01-01 00:00:00

abstract：:Biological knowledge can be inferred from three major levels of information: molecules, organisms and ecologies. Bioinformatics is an established field that has made significant advances in the development of systems and techniques to organize contemporary molecular data; biodiversity informatics is an emerging discip...

journal_title：Briefings in bioinformatics

authors： Sarkar IN

更新日期：2007-09-01 00:00:00

abstract：:For many complex diseases, an earlier and more reliable diagnosis is considered a key prerequisite for developing more effective therapies to prevent or delay disease progression. Classical statistical learning approaches for specimen classification using omics data, however, often cannot provide diagnostic models wit...

journal_title：Briefings in bioinformatics

authors： Glaab E

更新日期：2016-05-01 00:00:00

abstract：:Small noncoding RNAs (sRNA/sncRNAs) are generated from different genomic loci and play important roles in biological processes, such as cell proliferation and the regulation of gene expression. Next-generation sequencing (NGS) has provided an unprecedented opportunity to discover and quantify diverse kinds of sncRNA, ...

journal_title：Briefings in bioinformatics

authors： Liu Q,Ding C,Lang X,Guo G,Chen J,Su X

更新日期：2021-01-18 00:00:00

abstract：:A proliferation of chemical, reaction and enzyme databases, new computational methods and software tools for data-driven rational biosynthesis design have emerged in recent years. With the coming of the era of big data, particularly in the bio-medical field, data-driven rational biosynthesis design could potentially b...

journal_title：Briefings in bioinformatics

authors： Chen F,Yuan L,Ding S,Tian Y,Hu QN

更新日期：2020-07-15 00:00:00

abstract：:Computational detection methods have been widely used in studies on the biogenesis and the function of circular RNAs (circRNAs). However, all of the existing tools showed disadvantages on certain aspects of circRNA detection. Here, we propose an improved multithreading detection tool, CIRI2, which used an adapted maxi...

journal_title：Briefings in bioinformatics

authors： Gao Y,Zhang J,Zhao F

更新日期：2018-09-28 00:00:00

abstract：:The modelling of biological systems is accompanied with epistemic uncertainties that range from structural uncertainty to parametric uncertainty due to such limitations as insufficient understanding of the underlying mechanism and incomplete measurement data of a system. Fuzzy logic approaches such as fuzzy Petri nets...

journal_title：Briefings in bioinformatics

authors： Liu F,Heiner M,Gilbert D

更新日期：2018-12-27 00:00:00

abstract：:A number of supervised machine learning models have recently been introduced for the prediction of drug-target interactions based on chemical structure and genomic sequence information. Although these models could offer improved means for many network pharmacology applications, such as repositioning of drugs for new t...

journal_title：Briefings in bioinformatics

authors： Pahikkala T,Airola A,Pietilä S,Shakyawar S,Szwajda A,Tang J,Aittokallio T

更新日期：2015-03-01 00:00:00

abstract：:Effectively representing Medical Subject Headings (MeSH) headings (terms) such as disease and drug as discriminative vectors could greatly improve the performance of downstream computational prediction models. However, these terms are often abstract and difficult to quantify. In this paper, we converted the MeSH tree ...

journal_title：Briefings in bioinformatics

authors： Guo ZH,You ZH,Huang DS,Yi HC,Zheng K,Chen ZH,Wang YB

更新日期：2020-03-31 00:00:00

abstract：:Exploring protein-ligand interactions is a subject of immense interest, as it provides deeper insights into molecular recognition, mechanism of interaction and subsequent functions. Predicting an accurate model for a protein-ligand interaction is a challenging task. Molecular docking is a computational method used for...

journal_title：Briefings in bioinformatics

authors： Mohammad T,Mathur Y,Hassan MI

更新日期：2020-10-26 00:00:00

abstract：:An initiative to increase biopharmaceutical research productivity by capturing, sharing and computationally integrating proprietary scientific discoveries with public knowledge is described. This initiative involves both organisational process change and multiple interoperating software systems. The software component...

journal_title：Briefings in bioinformatics

authors： Ficenec D,Osborne M,Pradines J,Richards D,Felciano R,Cho RJ,Chen RO,Liefeld T,Owen J,Ruttenberg A,Reich C,Horvath J,Clark T

更新日期：2003-09-01 00:00:00

abstract：:Atomic charges play a very important role in drug-target recognition. However, computation of atomic charges with high-level quantum mechanics (QM) calculations is very time-consuming. A number of machine learning (ML)-based atomic charge prediction methods have been proposed to speed up the calculation of high-accura...

journal_title：Briefings in bioinformatics

authors： Wang J,Cao D,Tang C,Xu L,He Q,Yang B,Chen X,Sun H,Hou T

更新日期：2020-08-25 00:00:00

abstract：: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 anima...

journal_title：Briefings in bioinformatics

authors： Gal J,Milano G,Ferrero JM,Saâda-Bouzid E,Viotti J,Chabaud S,Gougis P,Le Tourneau C,Schiappa R,Paquet A,Chamorey E

更新日期：2018-11-27 00:00:00

abstract：:Information Integrator is an extension to IBM's relational database DB2, which uses data federation to provide benefits to molecular biology researchers through two unique capabilities: increased flexibility in combining data from disparate sources, and SQL access to non-SQL data, easing the task of automating data an...

journal_title：Briefings in bioinformatics

authors： Arenson AD

更新日期：2003-12-01 00:00:00