Pattern recognition analysis on long noncoding RNAs: a tool for prediction in plants.

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：: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：: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：:Identification of new drug-target interactions (DTIs) is an important but a time-consuming and costly step in drug discovery. In recent years, to mitigate these drawbacks, researchers have sought to identify DTIs using computational approaches. However, most existing methods construct drug networks and target networks...

journal_title：Briefings in bioinformatics

authors： Zhao T,Hu Y,Valsdottir LR,Zang T,Peng J

更新日期：2020-05-04 00:00:00

abstract：:A class-imbalanced classifier is a decision rule to predict the class membership of new samples from an available data set where the class sizes differ considerably. When the class sizes are very different, most standard classification algorithms may favor the larger (majority) class resulting in poor accuracy in the ...

journal_title：Briefings in bioinformatics

authors： Lin WJ,Chen JJ

更新日期：2013-01-01 00:00:00

abstract：:The understanding of complex biological networks often relies on both a dedicated layout and a topology. Currently, there are three major competing layout-aware systems biology formats, but there are no software tools or software libraries supporting all of them. This complicates the management of molecular network la...

journal_title：Briefings in bioinformatics

authors： Hoksza D,Gawron P,Ostaszewski M,Hasenauer J,Schneider R

更新日期：2020-07-15 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：: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：:Numerous studies have shown that copy number variation (CNV) in lncRNA regions play critical roles in the initiation and progression of cancer. However, our knowledge about their functionalities is still limited. Here, we firstly provided a computational method to identify lncRNAs with copy number variation (lncRNAs-C...

journal_title：Briefings in bioinformatics

authors： Xu Y,Wu T,Li F,Dong Q,Wang J,Shang D,Xu Y,Zhang C,Dou Y,Hu C,Yang H,Zheng X,Zhang Y,Wang L,Li X

更新日期：2020-12-01 00:00:00

abstract：MOTIVATION:Over the past decade, the field of next-generation sequencing (NGS) has seen dramatic advances in methods and a decrease in costs. Consequently, a large expansion of data has been generated by NGS, most of which have originated from RNA-sequencing (RNA-seq) experiments. Because mitochondrial genes are expres...

journal_title：Briefings in bioinformatics

authors： Nachtigall PG,Grazziotin FG,Junqueira-de-Azevedo ILM

更新日期：2021-01-30 00:00:00

abstract：:Occurrence and development of cancers are governed by complex networks of interacting intercellular and intracellular signals. The technology of single-cell RNA sequencing (scRNA-seq) provides an unprecedented opportunity for dissecting the interplay between the cancer cells and the associated microenvironment. Here w...

journal_title：Briefings in bioinformatics

authors： Zhang J,Guan M,Wang Q,Zhang J,Zhou T,Sun X

更新日期：2020-05-21 00:00:00

abstract：:Mediation analysis has been a useful tool for investigating the effect of mediators that lie in the path from the independent variable to the outcome. With the increasing dimensionality of mediators such as in (epi)genomics studies, high-dimensional mediation model is needed. In this work, we focus on epigenetic studi...

journal_title：Briefings in bioinformatics

authors： Fang R,Yang H,Gao Y,Cao H,Goode EL,Cui Y

更新日期：2020-07-01 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：: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：UNLABELLED:So-called next-generation sequencing (NGS) has provided the ability to sequence on a massive scale at low cost, enabling biologists to perform powerful experiments and gain insight into biological processes. BamView has been developed to visualize and analyse sequence reads from NGS platforms, which have bee...

journal_title：Briefings in bioinformatics

authors： Carver T,Harris SR,Otto TD,Berriman M,Parkhill J,McQuillan JA

更新日期：2013-03-01 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：:Cells are compartmentalized by numerous membrane-bounded organelles and membraneless organelles (MLOs) to ensure temporal and spatial regulation of various biological processes. A number of MLOs, such as nucleoli, nuclear speckles and stress granules, exist as liquid droplets within the cells and arise from the conden...

journal_title：Briefings in bioinformatics

authors： Hou C,Xie H,Fu Y,Ma Y,Li T

更新日期：2020-10-30 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：:The Gulbenkian Training Programme in Bioinformatics has been offering hands-on training courses in Oeiras, PT for more than a decade. This article is a review of its functional organization and evolution. We aim to share our experience with people considering setting-up similar training facilities elsewhere. More than...

journal_title：Briefings in bioinformatics

authors： Fernandes PL

更新日期：2010-11-01 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：: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：:In clinical cancer treatment, genomic alterations would often affect the response of patients to anticancer drugs. Studies have shown that molecular features of tumors could be biomarkers predictive of sensitivity or resistance to anticancer agents, but the identification of actionable mutations are often constrained ...

journal_title：Briefings in bioinformatics

authors： Yao H,Liang Q,Qian X,Wang J,Sham PC,Li MJ

更新日期：2020-12-01 00:00:00

abstract：:Data from the SEER reports reveal that the occurrence rate of a cancer type generally follows a unimodal distribution over age, peaking at an age that is cancer-type specific and ranges from 30+ through 70+. Previous studies attribute such bell-shaped distributions to the reduced proliferative potential in senior year...

journal_title：Briefings in bioinformatics

authors： Qiu S,An Z,Tan R,He PA,Jing J,Li H,Wu S,Xu Y

更新日期：2020-12-30 00:00:00

abstract：:Phenotypes have gained increased notoriety in the clinical and biological domain owing to their application in numerous areas such as the discovery of disease genes and drug targets, phylogenetics and pharmacogenomics. Phenotypes, defined as observable characteristics of organisms, can be seen as one of the bridges th...

journal_title：Briefings in bioinformatics

authors： Oellrich A,Collier N,Groza T,Rebholz-Schuhmann D,Shah N,Bodenreider O,Boland MR,Georgiev I,Liu H,Livingston K,Luna A,Mallon AM,Manda P,Robinson PN,Rustici G,Simon M,Wang L,Winnenburg R,Dumontier M

更新日期：2016-09-01 00:00:00

abstract：:The contribution of transposable elements (TEs) to genome structure and evolution as well as their impact on genome sequencing, assembly, annotation and alignment has generated increasing interest in developing new methods for their computational analysis. Here we review the diversity of innovative approaches to ident...

journal_title：Briefings in bioinformatics

authors： Bergman CM,Quesneville H

更新日期：2007-11-01 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：:Gene set analysis (GSA) is one of the methods of choice for analyzing the results of current omics studies; however, it has been mainly developed to analyze mRNA (microarray, RNA-Seq) data. The following review includes an update regarding general methods and resources for GSA and then emphasizes GSA methods and tools...

journal_title：Briefings in bioinformatics

authors： Mora A

更新日期：2020-09-25 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：:In view of great difficulties in the pathogenesis analysis of Alzheimer's disease (AD) presently, profiling the modifiable risk factors is crucial for early detection and intervention of AD. However, the causal associations among them have yet to be identified, and the effective integration and application of these da...

journal_title：Briefings in bioinformatics

authors： Wang Z,Meng L,Liu H,Shen L,Ji HF

更新日期：2020-09-21 00:00:00

abstract：:Computational aspects of host-parasite phylogenies form part of a set of general associations between areas and organisms, hosts and parasites, and species and genes. The problem is not new and the commonalities of exploring vicariance biogeography (organisms tracking areas) and host-parasite co-speciation (parasites ...

journal_title：Briefings in bioinformatics

authors： Stevens J

更新日期：2004-12-01 00:00:00