Towards a comprehensive picture of the genetic landscape of complex traits.

abstract：:While elementary flux mode (EFM) analysis is now recognized as a cornerstone computational technique for cellular pathway analysis and engineering, EFM application to genome-scale models remains computationally prohibitive. This article provides a review of aspects of EFM computation that elucidates bottlenecks in sca...

journal_title：Briefings in bioinformatics

authors： Ullah E,Yosafshahi M,Hassoun S

更新日期：2020-12-01 00:00:00

abstract：:Despite its central role in the adaptation and microevolution of traits, the genetic architecture of phenotypic plasticity, i.e. multiple phenotypes produced by a single genotype in changing environments, remains elusive. We know little about the genes that underlie the plastic response of traits to the environment, t...

journal_title：Briefings in bioinformatics

authors： Wang Z,Pang X,Lv Y,Xu F,Zhou T,Li X,Feng S,Li J,Li Z,Wu R

更新日期：2013-01-01 00:00:00

abstract：:Protein dynamics is central to all biological processes, including signal transduction, cellular regulation and biological catalysis. Among them, in-depth exploration of ligand-driven protein dynamics contributes to an optimal understanding of protein function, which is particularly relevant to drug discovery. Hence, ...

journal_title：Briefings in bioinformatics

authors： Yang JF,Wang F,Chen YZ,Hao GF,Yang GF

更新日期：2020-12-01 00:00:00

abstract：:Most of the microRNAs (miRNAs) play their regulatory roles through posttranscriptional target decay or translational inhibition. For both plants and animals, these regulatory events were previously considered to take place in cytoplasm, as mature miRNAs were observed to be exported to the cytoplasm for Argonaute (AGO)...

journal_title：Briefings in bioinformatics

authors： Yu D,Tang Z,Shao C,Ma X,Xiang T,Fan Z,Wang H,Meng Y

更新日期：2018-11-27 00:00:00

abstract：:As one of the most important fundamental problems in protein sequence analysis, protein remote homology detection is critical for both theoretical research (protein structure and function studies) and real world applications (drug design). Although several computational predictors have been proposed, their detection p...

journal_title：Briefings in bioinformatics

authors： Liu B,Jiang S,Zou Q

更新日期：2018-11-07 00:00:00

abstract：:Understanding biological complexity demands a combination of high-throughput data and interdisciplinary skills. One way to bring to bear the necessary combination of data types and expertise is by encapsulating domain knowledge in software and composing that software to create a customized data analysis environment. T...

journal_title：Briefings in bioinformatics

authors： Bare JC,Baliga NS

更新日期：2014-07-01 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：:Precision and personalized medicine will be increasingly based on the integration of various type of information, particularly electronic health records and genome sequences. The availability of cheap genome sequencing services and the information interoperability will increase the role of online bioinformatics analys...

journal_title：Briefings in bioinformatics

authors： Bianchi L,Liò P

更新日期：2017-11-01 00:00:00

abstract：:Online sequence repositories are teeming with RNA sequencing (RNA-Seq) data from a wide range of eukaryotes. Although most of these data sets contain large numbers of organelle-derived reads, researchers tend to ignore these data, focusing instead on the nuclear-derived transcripts. Consequently, GenBank contains mass...

journal_title：Briefings in bioinformatics

authors： Smith DR,Sanitá Lima M

更新日期：2017-11-01 00:00:00

abstract：:Since the completion of the Human Genome Project, it has been widely established that most DNA is not transcribed into proteins. These non-protein-coding regions are believed to be moderators within transcriptional and post-transcriptional processes, which play key roles in the onset of diseases. Long non-coding RNAs ...

journal_title：Briefings in bioinformatics

authors： Yotsukura S,duVerle D,Hancock T,Natsume-Kitatani Y,Mamitsuka H

更新日期：2017-01-01 00:00:00

abstract：:Ontologies are now pervasive in biomedicine, where they serve as a means to standardize terminology, to enable access to domain knowledge, to verify data consistency and to facilitate integrative analyses over heterogeneous biomedical data. For this purpose, research on biomedical ontologies applies theories and metho...

journal_title：Briefings in bioinformatics

authors： Hoehndorf R,Dumontier M,Gkoutos GV

更新日期：2013-11-01 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：:Verification in phylogenetics represents an extremely difficult subject. Phylogenetic analysis deals with the reconstruction of evolutionary histories of species, and as long as mankind is not able to travel in time, it will not be possible to verify deep evolutionary histories reconstructed with modern computational ...

journal_title：Briefings in bioinformatics

authors： Stamatakis A,Izquierdo-Carrasco F

更新日期：2011-05-01 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：:Understanding the genetic basis of human traits/diseases and the underlying mechanisms of how these traits/diseases are affected by genetic variations is critical for public health. Current genome-wide functional genomics data uncovered a large number of functional elements in the noncoding regions of human genome, pr...

journal_title：Briefings in bioinformatics

authors： Li MJ,Yan B,Sham PC,Wang J

更新日期：2015-05-01 00:00:00

abstract：:Phylogenomic databases provide orthology predictions for species with fully sequenced genomes. Although the goal seems well-defined, the content of these databases differs greatly. Seven ortholog databases (Ensembl Compara, eggNOG, HOGENOM, InParanoid, OMA, OrthoDB, Panther) were compared on the basis of reference tre...

journal_title：Briefings in bioinformatics

authors： Boeckmann B,Robinson-Rechavi M,Xenarios I,Dessimoz C

更新日期：2011-09-01 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：: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：:Cell lines are widely used as in vitro models of tumorigenesis. However, an increasing number of researchers have found that cell lines differ from their sourced tumour samples after long-term cell culture. The application of unsuitable cell lines in experiments will affect the experimental accuracy and the treatment ...

journal_title：Briefings in bioinformatics

authors： Zhao N,Liu Y,Wei Y,Yan Z,Zhang Q,Wu C,Chang Z,Xu Y

更新日期：2017-05-01 00:00:00

abstract：:Deoxyribonucleic acid replication is one of the most crucial tasks taking place in the cell, and it has to be precisely regulated. This process is initiated in the replication origins (ORIs), and thus it is essential to identify such sites for a deeper understanding of the cellular processes and functions related to t...

journal_title：Briefings in bioinformatics

authors： Manavalan B,Basith S,Shin TH,Lee G

更新日期：2020-11-25 00:00:00

abstract：:Despite The Central Dogma states the destiny of gene as 'DNA makes RNA and RNA makes protein', the nucleic acids not only store and transmit genetic information but also, surprisingly, join in intracellular vital movement as a regulator of gene expression. Bioinformatics has contributed to knowledge for a series of em...

journal_title：Briefings in bioinformatics

authors： Zhang S,Zhou Y,Wang Y,Wang Z,Xiao Q,Zhang Y,Lou Y,Qiu Y,Zhu F

更新日期：2020-04-06 00:00:00

abstract：:Nucleosomes contribute to compacting the genome into the nucleus and regulate the physical access of regulatory proteins to DNA either directly or through the epigenetic modifications of the histone tails. Precise mapping of nucleosome positioning across the genome is, therefore, essential to understanding the genome ...

journal_title：Briefings in bioinformatics

authors： Quintales L,Vázquez E,Antequera F

更新日期：2015-07-01 00:00:00

abstract：:Precision medicine has changed thinking in cancer therapy, highlighting a better understanding of the individual clinical interventions. But what role do the drivers and pathways identified from pan-cancer genome analysis play in the tumor? In this letter, we will highlight the importance of in silico modeling in prec...

journal_title：Briefings in bioinformatics

authors： Kunz M,Jeromin J,Fuchs M,Christoph J,Veronesi G,Flentje M,Nietzer S,Dandekar G,Dandekar T

更新日期：2020-05-21 00:00:00

abstract：:The discipline of bioinformatics has developed rapidly since the complete sequencing of the first genomes in the 1990s. The development of many high-throughput techniques during the last decades has ensured that bioinformatics has grown into a discipline that overlaps with, and is required for, the modern practice of ...

journal_title：Briefings in bioinformatics

authors： Tastan Bishop Ö,Adebiyi EF,Alzohairy AM,Everett D,Ghedira K,Ghouila A,Kumuthini J,Mulder NJ,Panji S,Patterton HG,H3ABioNet Consortium.,H3Africa Consortium.

更新日期：2015-03-01 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：:Computational and mathematical modelling has become a valuable tool for investigating biological systems. Modelling enables prediction of how biological components interact to deliver system-level properties and extrapolation of biological system performance to contexts and experimental conditions where this is unknow...

journal_title：Briefings in bioinformatics

authors： Read MN,Alden K,Timmis J,Andrews PS

更新日期：2018-09-18 00:00:00

abstract：:Accurate inference of orthologous genes is a pre-requisite for most comparative genomics studies, and is also important for functional annotation of new genomes. Identification of orthologous gene sets typically involves phylogenetic tree analysis, heuristic algorithms based on sequence conservation, synteny analysis,...

journal_title：Briefings in bioinformatics

authors： Kristensen DM,Wolf YI,Mushegian AR,Koonin EV

更新日期：2011-09-01 00:00:00

abstract：:Array-based gene expression studies frequently serve to identify genes that are expressed differently under two or more conditions. The actual analysis of the data, however, may be hampered by a number of technical and statistical problems. Possible remedies on the level of computational analysis lie in appropriate pr...

journal_title：Briefings in bioinformatics

authors： Steinhoff C,Vingron M

更新日期：2006-06-01 00:00:00

abstract：:Technical advances such as the development of molecular cloning, Sanger sequencing, PCR and oligonucleotide microarrays are key to our current capacity to sequence, annotate and study complete organismal genomes. Recent years have seen the development of a variety of so-called 'next-generation' sequencing platforms, w...

journal_title：Briefings in bioinformatics

authors： Horner DS,Pavesi G,Castrignanò T,De Meo PD,Liuni S,Sammeth M,Picardi E,Pesole G

更新日期：2010-03-01 00:00:00

abstract：:While leading to millions of people's deaths every year the treatment of viral infectious diseases remains a huge public health challenge.Therefore, an in-depth understanding of human-virus protein-protein interactions (PPIs) as the molecular interface between a virus and its host cell is of paramount importance to ob...

journal_title：Briefings in bioinformatics

authors： Yang X,Lian X,Fu C,Wuchty S,Yang S,Zhang Z

更新日期：2021-01-30 00:00:00