Irinotecan and vandetanib create synergies for treatment of pancreatic cancer patients with concomitant TP53 and KRAS mutations.

abstract：:The presence of different transcripts of a gene across samples can be analysed by whole-transcriptome microarrays. Reproducing results from published microarray data represents a challenge owing to the vast amounts of data and the large variety of preprocessing and filtering steps used before the actual analysis is ca...

journal_title：Briefings in bioinformatics

authors： Rodrigo-Domingo M,Waagepetersen R,Bødker JS,Falgreen S,Kjeldsen MK,Johnsen HE,Dybkær K,Bøgsted M

更新日期：2014-07-01 00:00:00

abstract：:Integrated modelling of biological systems is challenged by composing components with sufficient kinetic data and components with insufficient kinetic data or components built only using experts' experience and knowledge. Fuzzy continuous Petri nets (FCPNs) combine continuous Petri nets with fuzzy inference systems, a...

journal_title：Briefings in bioinformatics

authors： Liu F,Sun W,Heiner M,Gilbert D

更新日期：2021-01-18 00:00:00

abstract：:Correlated reaction sets (Co-Sets) are mathematically defined modules in biochemical reaction networks which facilitate the study of biological processes by decomposing complex reaction networks into conceptually simple units. According to the degree of association, Co-Sets can be classified into three types: perfect,...

journal_title：Briefings in bioinformatics

authors： Xi Y,Chen YP,Qian C,Wang F

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：:Daily work in molecular biology presently depends on a large number of computational tools. An in-depth, large-scale study of that 'ecosystem' of Web tools, its characteristics, interconnectivity, patterns of usage/citation, temporal evolution and rate of decay is crucial for understanding the forces that shape it and...

journal_title：Briefings in bioinformatics

authors： Pazos F,Chagoyen M

更新日期：2019-07-19 00:00:00

abstract：:Dissecting the genetic mechanism underlying a complex disease hinges on discovering gene-environment interactions (GXE). However, detecting GXE is a challenging problem especially when the genetic variants under study are rare. Haplotype-based tests have several advantages over the so-called collapsing tests for detec...

journal_title：Briefings in bioinformatics

authors： Papachristou C,Biswas S

更新日期：2020-05-21 00:00:00

abstract：:The use of microarray technology to measure gene expression on a genome-wide scale has been well established for more than a decade. Methods to process and analyse the vast quantity of expression data generated by a typical microarray experiment are similarly well-established. The Affymetrix Exon 1.0 ST array is a rel...

journal_title：Briefings in bioinformatics

authors： Lockstone HE

更新日期：2011-11-01 00:00:00

abstract：:Access to gene expression data has become increasingly common in recent years; however, analysis has become more difficult as it is often desirable to integrate data from different platforms. Probe mapping across microarray platforms is the first and most crucial step for data integration. In this article, we systemat...

journal_title：Briefings in bioinformatics

authors： Allen JD,Wang S,Chen M,Girard L,Minna JD,Xie Y,Xiao G

更新日期：2012-09-01 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：: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：: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：: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：:Precision medicine promises to revolutionize treatment, shifting therapeutic approaches from the classical one-size-fits-all to those more tailored to the patient's individual genomic profile, lifestyle and environmental exposures. Yet, to advance precision medicine's main objective-ensuring the optimum diagnosis, tre...

journal_title：Briefings in bioinformatics

authors： Gutiérrez-Sacristán A,De Niz C,Kothari C,Kong SW,Mandl KD,Avillach P

更新日期：2021-01-18 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：: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：OBJECTIVE:Development of novel informatics methods focused on improving pregnancy outcomes remains an active area of research. The purpose of this study is to systematically review the ways that artificial intelligence (AI) and machine learning (ML), including deep learning (DL), methodologies can inform patient care d...

journal_title：Briefings in bioinformatics

authors： Davidson L,Boland MR

更新日期：2021-01-06 00:00:00

abstract：:Exchanging and sharing scientific results are essential for researchers in the field of computational modelling. BioModels.net defines agreed-upon standards for model curation. A fundamental one, MIRIAM (Minimum Information Requested in the Annotation of Models), standardises the annotation and curation process of qua...

journal_title：Briefings in bioinformatics

authors： Li C,Courtot M,Le Novère N,Laibe C

更新日期：2010-05-01 00:00:00

abstract：:Prognostic tests using expression profiles of several dozen genes help provide treatment choices for prostate cancer (PCa). However, these tests require improvement to meet the clinical need for resolving overtreatment, which continues to be a pervasive problem in PCa management. Genomic selection (GS) methodology, wh...

journal_title：Briefings in bioinformatics

authors： Li R,Wang S,Cui Y,Qu H,Chater JM,Zhang L,Wei J,Wang M,Xu Y,Yu L,Lu J,Feng Y,Zhou R,Huang Y,Ma R,Zhu J,Zhong W,Jia Z

更新日期：2020-09-08 00:00:00

abstract：:Computational biology is essential in the process of translating biological knowledge into clinical practice, as well as in the understanding of biological phenomena based on the resources and technologies originating from the clinical environment. One such key contribution of computational biology is the discovery of...

journal_title：Briefings in bioinformatics

authors： Azuaje F,Devaux Y,Wagner D

更新日期：2009-07-01 00:00:00

abstract：:The prevalence of dropout events is a serious problem for single-cell Hi-C (scHiC) data due to insufficient sequencing depth and data coverage, which brings difficulties in downstream studies such as clustering and structural analysis. Complicating things further is the fact that dropouts are confounded with structura...

journal_title：Briefings in bioinformatics

authors： Han C,Xie Q,Lin S

更新日期：2020-11-17 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：: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：: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：:DNA-binding hot spot residues of proteins are dominant and fundamental interface residues that contribute most of the binding free energy of protein-DNA interfaces. As experimental methods for identifying hot spots are expensive and time consuming, computational approaches are urgently required in predicting hot spots...

journal_title：Briefings in bioinformatics

authors： Zhang S,Zhao L,Zheng CH,Xia J

更新日期：2020-05-21 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 iteratively reweighted least square (IRLS) method is mostly identical to maximum likelihood (ML) method in terms of parameter estimation and power of quantitative trait locus (QTL) detection. But the IRLS is greatly superior to ML in terms of computing speed and the robustness of parameter estimation. In conjuncti...

journal_title：Briefings in bioinformatics

authors： Liu Y,Yang T,Li H,Yang R

更新日期：2014-01-01 00:00:00

abstract：:Accurately identifying the interactions between genomic factors and the response of cancer drugs plays important roles in drug discovery, drug repositioning and cancer treatment. A number of studies revealed that interactions between genes and drugs were 'many-genes-to-many drugs' interactions, i.e. common modules, op...

journal_title：Briefings in bioinformatics

authors： Huang J,Chen J,Zhang B,Zhu L,Cai H

更新日期：2020-06-26 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：: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：:Moonlighting proteins provide more options for cells to execute multiple functions without increasing the genome and transcriptome complexity. Although there have long been calls for computational methods for the prediction of moonlighting proteins, no method has been designed for determining moonlighting long noncodi...

journal_title：Briefings in bioinformatics

authors： Liu X,Xu Y,Wang R,Liu S,Wang J,Luo Y,Leung KS,Cheng L

更新日期：2021-01-18 00:00:00