Benchmarking computational tools for polymorphic transposable element detection.

abstract：BACKGROUND:The most frequently mutated gene pairs in pancreatic adenocarcinoma (PAAD) are KRAS and TP53, and our goal is to illustrate the multiomics and molecular dynamics landscapes of KRAS/TP53 mutation and also to obtain prospective novel drugs for KRAS- and TP53-mutated PAAD patients. Moreover, we also made an att...

journal_title：Briefings in bioinformatics

authors： Kaushik AC,Wang YJ,Wang X,Wei DQ

更新日期：2020-07-31 00:00:00

abstract：:While the number of sequenced genes is increasing dramatically, the number of different protein structural families is expected to be more limited. Changes in enzymatic activity or protein interactions can dramatically modify the role of homologous proteins in different organisms or mutants. However, experimental data...

journal_title：Briefings in bioinformatics

authors： Chatonnet A,Cousin X,Robinson A

更新日期：2001-03-01 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：: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：MOTIVATION:The functional changes of the genes, RNAs and proteins will eventually be reflected in the metabolic level. Increasing number of researchers have researched mechanism, biomarkers and targeted drugs by metabolites. However, compared with our knowledge about genes, RNAs, and proteins, we still know few about d...

journal_title：Briefings in bioinformatics

authors： Zhao T,Hu Y,Cheng L

更新日期：2020-10-13 00:00:00

abstract：:RNA structures are widely distributed across all life forms. The global conformation of these structures is defined by a variety of constituent structural units such as helices, hairpin loops, kissing-loop motifs and pseudoknots, which often behave in a modular way. Their ubiquitous distribution is associated with a v...

journal_title：Briefings in bioinformatics

authors： Gupta A,Bansal M

更新日期：2020-07-15 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：MOTIVATION:Computational methods accelerate drug discovery and play an important role in biomedicine, such as molecular property prediction and compound-protein interaction (CPI) identification. A key challenge is to learn useful molecular representation. In the early years, molecular properties are mainly calculated b...

journal_title：Briefings in bioinformatics

authors： Li P,Li Y,Hsieh CY,Zhang S,Liu X,Liu H,Song S,Yao X

更新日期：2020-11-04 00:00:00

abstract：:In recent years, high-throughput genomic technologies like chromatin immunoprecipitation sequencing (ChIp-seq) and transcriptome sequencing (RNA-seq) have been becoming both more refined and less expensive, making them more accessible. Many circular RNAs (circRNAs) that originate from back-spliced exons have been iden...

journal_title：Briefings in bioinformatics

authors： Tang Z,Li X,Zhao J,Qian F,Feng C,Li Y,Zhang J,Jiang Y,Yang Y,Wang Q,Li C

更新日期：2019-11-27 00:00:00

abstract：:The so-called 'omics' approaches used in modern biology aim at massively characterizing the molecular repertories of living systems at different levels. Metabolomics is one of the last additions to the 'omics' family and it deals with the characterization of the set of metabolites in a given biological system. As meta...

journal_title：Briefings in bioinformatics

authors： Chagoyen M,Pazos F

更新日期：2013-11-01 00:00:00

abstract：:DNA methylation plays an essential role in cancer. Differential variability (DV) in cancer was recently observed that contributes to cancer heterogeneity and has been shown to be crucial in detecting epigenetic field defects, DNA methylation alterations happening early in carcinogenesis. As neighboring CpG sites are h...

journal_title：Briefings in bioinformatics

authors： Wang Y,Teschendorff AE,Widschwendter M,Wang S

更新日期：2019-01-18 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：: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：: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：:One of the most complex and computationally intensive tasks of genome sequence analysis is genome assembly. Even today, few centres have the resources, in both software and hardware, to assemble a genome from the thousands or millions of individual sequences generated in a whole-genome shotgun sequencing project. With...

journal_title：Briefings in bioinformatics

authors： Pop M,Phillippy A,Delcher AL,Salzberg SL

更新日期：2004-09-01 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：: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：:microRNAs (miRNAs) are small endogenous non-coding RNAs that function as the universal specificity factors in post-transcriptional gene silencing. Discovering miRNAs, identifying their targets and further inferring miRNA functions have been a critical strategy for understanding normal biological processes of miRNAs an...

journal_title：Briefings in bioinformatics

authors： Liu B,Li J,Cairns MJ

更新日期：2014-01-01 00:00:00

abstract：:The residence of spliceosomal introns within protein-coding genes can fluctuate over time, with genes gaining, losing or conserving introns in a complex process that is not entirely understood. One approach for studying intron evolution is to compare introns with respect to position and type within closely related gen...

journal_title：Briefings in bioinformatics

authors： Wilkerson MD,Ru Y,Brendel VP

更新日期：2009-11-01 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：:Glycosylation of proteins is involved in immune defense, cell-cell adhesion, cellular recognition and pathogen binding and is one of the most common and complex post-translational modifications. Science is still struggling to assign detailed mechanisms and functions to this form of conjugation. Even the structural ana...

journal_title：Briefings in bioinformatics

authors： Dallas DC,Martin WF,Hua S,German JB

更新日期：2013-05-01 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：:The structural description of peptide ligands bound to G protein-coupled receptors (GPCRs) is important for the discovery of new drugs and deeper understanding of the molecular mechanisms of life. Here we describe a three-stage protocol for the molecular docking of peptides to GPCRs using a set of different programs: ...

journal_title：Briefings in bioinformatics

authors： Badaczewska-Dawid AE,Kmiecik S,Koliński M

更新日期：2020-06-10 00:00:00

abstract：:Cell-penetrating peptides (CPPs) facilitate the delivery of therapeutically relevant molecules, including DNA, proteins and oligonucleotides, into cells both in vitro and in vivo. This unique ability explores the possibility of CPPs as therapeutic delivery and its potential applications in clinical therapy. Over the l...

journal_title：Briefings in bioinformatics

authors： Su R,Hu J,Zou Q,Manavalan B,Wei L

更新日期：2020-03-23 00:00:00

abstract：:As a group of important plant species in agriculture and biology, polyploids have been increasingly studied in terms of their genome structure and organization. There are two types of polyploids, allopolyploids and autopolyploids, each resulting from a different genetic origin, which undergo meiotic divisions of a dis...

journal_title：Briefings in bioinformatics

authors： Xu F,Tong C,Lyu Y,Bo W,Pang X,Wu R

更新日期：2015-01-01 00:00:00

abstract：:Fibrosis is a key component in the pathogenic mechanism of a variety of diseases. These diseases involving fibrosis may share common mechanisms and therapeutic targets, and therefore common intervention strategies and medicines may be applicable for these diseases. For this reason, deliberately introducing anti-fibros...

journal_title：Briefings in bioinformatics

authors： Wu D,Gao W,Li X,Tian C,Jiao N,Fang S,Xiao J,Xu Z,Zhu L,Zhang G,Zhu R

更新日期：2020-06-22 00:00:00

abstract：:If the completion of the first draft of the human genome represents the coming of age of bioinformatics, then the emergence of bioinformatics as a university degree subject represents its establishment. In this paper bioinformatics as a subject for formal study is discussed, rather than as a subject for research, and ...

journal_title：Briefings in bioinformatics

authors： Counsell D

更新日期：2003-03-01 00:00:00

abstract：:Molecular interrogation of a biological sample through DNA sequencing, RNA and microRNA profiling, proteomics and other assays, has the potential to provide a systems level approach to predicting treatment response and disease progression, and to developing precision therapies. Large publicly funded projects have gene...

journal_title：Briefings in bioinformatics

authors： Kannan L,Ramos M,Re A,El-Hachem N,Safikhani Z,Gendoo DM,Davis S,Gomez-Cabrero D,Castelo R,Hansen KD,Carey VJ,Morgan M,Culhane AC,Haibe-Kains B,Waldron L

更新日期：2016-07-01 00:00:00

abstract：:Scoring functions (SFs) based on complex machine learning (ML) algorithms have gradually emerged as a promising alternative to overcome the weaknesses of classical SFs. However, extensive efforts have been devoted to the development of SFs based on new protein-ligand interaction representations and advanced alternativ...

journal_title：Briefings in bioinformatics

authors： Xiong GL,Ye WL,Shen C,Lu AP,Hou TJ,Cao DS

更新日期：2020-06-04 00:00:00