Critical limitations of prognostic signatures based on risk scores summarized from gene expression levels: a case study for resected stage I non-small-cell lung cancer.

abstract：:In order to reach precision medicine and improve patients' quality of life, machine learning is increasingly used in medicine. Brain disorders are often complex and heterogeneous, and several modalities such as demographic, clinical, imaging, genetics and environmental data have been studied to improve their understan...

journal_title：Briefings in bioinformatics

authors： Burgos N,Bottani S,Faouzi J,Thibeau-Sutre E,Colliot O

更新日期：2020-12-15 00:00:00

abstract：:Synonymous mutations do not change the encoded amino acids but may alter the structure or function of an mRNA in ways that impact gene function. Advances in next generation sequencing technologies have detected numerous synonymous mutations in the human genome. Several computational models have been proposed to predic...

journal_title：Briefings in bioinformatics

authors： Cheng N,Li M,Zhao L,Zhang B,Yang Y,Zheng CH,Xia J

更新日期：2020-05-21 00:00:00

abstract：:Relative changes in mRNA as well as protein levels induced by sublethal doses of antibiotics on bacteria are measured and results visualised in the context of metabolic pathway diagrams. The mRNA levels present at a given time point after the addition of the antibiotic are measured using microarrays from Affymetrix. A...

journal_title：Briefings in bioinformatics

authors： Wolf D,Gray CP,de Saizieu A

更新日期：2000-09-01 00:00:00

abstract：:In the business and healthcare sectors data warehousing has provided effective solutions for information usage and knowledge discovery from databases. However, data warehousing applications in the biological research and development (R&D) sector are lagging far behind. The fuzziness and complexity of biological data r...

journal_title：Briefings in bioinformatics

authors： Schönbach C,Kowalski-Saunders P,Brusic V

更新日期：2000-05-01 00:00:00

abstract：BACKGROUND:Whole genome sequencing (WGS) is increasingly used for Mycobacterium tuberculosis (Mtb) research. Countries with the highest tuberculosis (TB) burden face important challenges to integrate WGS into surveillance and research. METHODS:We assessed the global status of Mtb WGS and developed a 3-week training co...

journal_title：Briefings in bioinformatics

authors： Rivière E,Heupink TH,Ismail N,Dippenaar A,Clarke C,Abebe G,Heusden P,Warren R,Meehan CJ,Van Rie A

更新日期：2020-10-03 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：:Understanding the functioning of biological systems depends on tackling complexity spanning spatial scales from genome to organ to whole organism. The basic unit of life, the cell, acts to co-ordinate information received across these scales and processes the myriad of signals to produce an integrated cellular respons...

journal_title：Briefings in bioinformatics

authors： Walker DC,Southgate J

更新日期：2009-07-01 00:00:00

abstract：:The cell-free DNA (cfDNA) methylation profile in liquid biopsy has been utilized to diagnose early-stage disease and estimate therapy response. However, typical clinical procedures are capable of purifying only very small amounts of cfDNA. Whole-genome bisulfite sequencing (WGBS) is the gold standard for measuring DNA...

journal_title：Briefings in bioinformatics

authors： Yin Y,Li J,Li J,Lee M,Zhao S,Guo L,Li J,Zhang M,Huang Y,Li XN,Deng Z,Sun D

更新日期：2020-12-15 00:00:00

abstract：:Effective drug discovery contributes to the treatment of numerous diseases but is limited by high costs and long cycles. The Quantitative Structure-Activity Relationship (QSAR) method was introduced to evaluate the activity of a large number of compounds virtually, reducing the time and labor costs required for chemic...

journal_title：Briefings in bioinformatics

authors： Wang YL,Wang F,Shi XX,Jia CY,Wu FX,Hao GF,Yang GF

更新日期：2020-11-03 00:00:00

abstract：:The products of multi-exon genes are a mixture of alternatively spliced isoforms, from which the translated proteins can have similar, different or even opposing functions. It is therefore essential to differentiate and annotate functions for individual isoforms. Computational approaches provide an efficient complemen...

journal_title：Briefings in bioinformatics

authors： Li HD,Omenn GS,Guan Y

更新日期：2016-11-01 00:00:00

abstract：:P53 is the 'guardian of the genome' and is responsible for regulating cell cycle and apoptosis. The genomic p53 binding regions, where activating transcriptional factors and cofactors like p300 simultaneously bind, are called 'p53-dependent enhancers', which play an important role in tumorigenesis. Current experimenta...

journal_title：Briefings in bioinformatics

authors： Niu X,Deng K,Liu L,Yang K,Hu X

更新日期：2020-05-11 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：:This Briefing reviews the widely used, currently active, up-to-date databases derived from the worldwide Protein Data Bank (PDB) to facilitate browsing, finding and exploring its entries. These databases contain visualization and analysis tools tailored to specific kinds of molecules and interactions, often including ...

journal_title：Briefings in bioinformatics

authors： Abriata LA

更新日期：2017-07-01 00:00:00

abstract：:Transposable elements (TEs) are an important source of human genetic variation with demonstrable effects on phenotype. Recently, a number of computational methods for the detection of polymorphic TE (polyTE) insertion sites from next-generation sequence data have been developed. The use of such tools will become incre...

journal_title：Briefings in bioinformatics

authors： Rishishwar L,Mariño-Ramírez L,Jordan IK

更新日期：2017-11-01 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：: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：: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：: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：: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：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：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：:The explosion in genomic sequence available in public databases has resulted in an unprecedented opportunity for computational whole genome analyses. A number of promising comparative-based approaches have been developed for gene finding, regulatory element discovery and other purposes, and it is clear that these tool...

journal_title：Briefings in bioinformatics

authors： Dubchak I,Pachter L

更新日期：2002-03-01 00:00:00

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：:Research into genome assembly algorithms has experienced a resurgence due to new challenges created by the development of next generation sequencing technologies. Several genome assemblers have been published in recent years specifically targeted at the new sequence data; however, the ever-changing technological lands...

journal_title：Briefings in bioinformatics

authors： Pop M

更新日期：2009-07-01 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：: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：: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：:Functional annotation of protein sequence with high accuracy has become one of the most important issues in modern biomedical studies, and computational approaches of significantly accelerated analysis process and enhanced accuracy are greatly desired. Although a variety of methods have been developed to elevate prote...

journal_title：Briefings in bioinformatics

authors： Hong J,Luo Y,Zhang Y,Ying J,Xue W,Xie T,Tao L,Zhu F

更新日期：2020-07-15 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