A survey of software tools for microRNA discovery and characterization using RNA-seq.

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：:Regulation of proteolysis plays a critical role in a myriad of important cellular processes. The key to better understanding the mechanisms that control this process is to identify the specific substrates that each protease targets. To address this, we have developed iProt-Sub, a powerful bioinformatics tool for the a...

journal_title：Briefings in bioinformatics

authors： Song J,Wang Y,Li F,Akutsu T,Rawlings ND,Webb GI,Chou KC

更新日期：2019-03-25 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：: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：:Patients with spinal muscular atrophy (SMA) are susceptible to the respiratory infections and might be at a heightened risk of poor clinical outcomes upon contracting coronavirus disease 2019 (COVID-19). In the face of the COVID-19 pandemic, the potential associations of SMA with the susceptibility to and prognosticat...

journal_title：Briefings in bioinformatics

authors： Li Z,Li X,Shen J,Tan H,Rong T,Lin Y,Feng E,Chen Z,Jiao Y,Liu G,Zhang L,Vai Chan MT,Kei Wu WK

更新日期：2020-11-14 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：:Lipidomics, the systematic study of the lipid composition of a cell or tissue, is an invaluable complement to knowledge gained by genomics and proteomics research. Mass spectrometry provides a means to detect hundreds of lipids in parallel, and this includes low abundance species of lipids. Nevertheless, frequently oc...

journal_title：Briefings in bioinformatics

authors： Hartler J,Tharakan R,Köfeler HC,Graham DR,Thallinger GG

更新日期：2013-05-01 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：:SARS-CoV-2 is an intensively investigated virus from the order Nidovirales (Coronaviridae family) that causes COVID-19 disease in humans. Through enormous scientific effort, thousands of viral strains have been sequenced to date, thereby creating a strong background for deep bioinformatics studies of the SARS-CoV-2 ge...

journal_title：Briefings in bioinformatics

authors： Goswami P,Bartas M,Lexa M,Bohálová N,Volná A,Červeň J,Červeňová V,Pečinka P,Špunda V,Fojta M,Brázda V

更新日期：2020-12-21 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：: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：:Atomic charges play a very important role in drug-target recognition. However, computation of atomic charges with high-level quantum mechanics (QM) calculations is very time-consuming. A number of machine learning (ML)-based atomic charge prediction methods have been proposed to speed up the calculation of high-accura...

journal_title：Briefings in bioinformatics

authors： Wang J,Cao D,Tang C,Xu L,He Q,Yang B,Chen X,Sun H,Hou T

更新日期：2020-08-25 00:00:00

abstract：:CyanoPATH is a database that curates and analyzes the common genomic functional repertoire for cyanobacteria harmful algal blooms (CyanoHABs) in eutrophic waters. Based on the literature of empirical studies and genome/protein databases, it summarizes four types of information: common biological functions (pathways) d...

journal_title：Briefings in bioinformatics

authors： Du W,Li G,Ho N,Jenkins L,Hockaday D,Tan J,Cao H

更新日期：2020-12-16 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：: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：: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：: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：:With the increasing recognition of its role in trait and disease development, it is crucial to account for genetic imprinting to illustrate the genetic architecture of complex traits. Genetic mapping can be innovated to test and estimate effects of genetic imprinting in a segregating population derived from experiment...

journal_title：Briefings in bioinformatics

authors： Sun L,Zhu X,Bo W,Xu F,Cheng T,Zhang Q,Wu R

更新日期：2015-05-01 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：:Since the 1st discovery of transcriptional enhancers in 1981, their textbook definition has remained largely unchanged in the past 37 years. With the emergence of high-throughput assays and genome editing, which are switching the paradigm from bottom-up discovery and testing of individual enhancers to top-down profili...

journal_title：Briefings in bioinformatics

authors： Ho EY,Cao Q,Gu M,Chan RW,Wu Q,Gerstein M,Yip KY

更新日期：2020-05-21 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：: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：:Success in precision medicine depends on accessing high-quality genetic and molecular data from large, well-annotated patient cohorts that couple biological samples to comprehensive clinical data, which in conjunction can lead to effective therapies. From such a scenario emerges the need for a new professional profile...

journal_title：Briefings in bioinformatics

authors： Gómez-López G,Dopazo J,Cigudosa JC,Valencia A,Al-Shahrour F

更新日期：2019-05-21 00:00:00

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：: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：:Drug-drug interactions (DDIs) constitute an important concern in drug development and postmarketing pharmacovigilance. They are considered the cause of many adverse drug effects exposing patients to higher risks and increasing public health system costs. Methods to follow-up and discover possible DDIs causing harm to ...

journal_title：Briefings in bioinformatics

authors： Vilar S,Friedman C,Hripcsak G

更新日期：2018-09-28 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

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：:We introduce the Beta Workbench (BWB), a scalable tool built on top of the newly defined BlenX language to model, simulate and analyse biological systems. We show the features and the incremental modelling process supported by the BWB on a running example based on the mitogen-activated kinase pathway. Finally, we prov...

journal_title：Briefings in bioinformatics

authors： Dematté L,Priami C,Romanel A

更新日期：2008-09-01 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