Protein-DNA docking with a coarse-grained force field.

abstract：:Advances of high-throughput technologies have rapidly produced more and more data from DNAs and RNAs to proteins, especially large volumes of genome-scale data. However, connection of the genomic information to cellular functions and biological behaviours relies on the development of effective approaches at higher sys...

journal_title：BMC bioinformatics

authors： Yang JY,Dunker A,Liu JS,Qin X,Arabnia HR,Yang W,Niemierko A,Chen Z,Luo Z,Wang L,Liu Y,Xu D,Deng Y,Tong W,Yang M

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:Human immunology studies often rely on the isolation and quantification of cell populations from an input sample based on flow cytometry and related techniques. Such techniques classify cells into populations based on the detection of a pattern of markers. The description of the cell populations targeted in ...

journal_title：BMC bioinformatics

authors： Overton JA,Vita R,Dunn P,Burel JG,Bukhari SAC,Cheung KH,Kleinstein SH,Diehl AD,Peters B

更新日期：2019-04-25 00:00:00

abstract：BACKGROUND:Although metatranscriptomics-the study of diverse microbial population activity based on RNA-seq data-is rapidly growing in popularity, there are limited options for biologists to analyze this type of data. Current approaches for processing metatranscriptomes rely on restricted databases and a dedicated comp...

journal_title：BMC bioinformatics

authors： Westreich ST,Korf I,Mills DA,Lemay DG

更新日期：2016-09-29 00:00:00

abstract：BACKGROUND:The advance of next generation sequencing enables higher throughput with lower price, and as the basic of high-throughput sequencing data analysis, variant calling is widely used in disease research, clinical treatment and medicine research. However, current mainstream variant caller tools have a serious pro...

journal_title：BMC bioinformatics

authors： Xiao A,Wu Z,Dong S

更新日期：2019-02-14 00:00:00

abstract：BACKGROUND:Protein function prediction is an important problem in the post-genomic era. Recent advances in experimental biology have enabled the production of vast amounts of protein-protein interaction (PPI) data. Thus, using PPI data to functionally annotate proteins has been extensively studied. However, most existi...

journal_title：BMC bioinformatics

authors： Xiong W,Liu H,Guan J,Zhou S

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:One very important functional domain of proteins is the protein-protein interacting region (PPIR), which forms the binding interface between interacting polypeptide chains. Post-translational modifications (PTMs) that occur in the PPIR can either interfere with or facilitate the interaction between proteins....

journal_title：BMC bioinformatics

authors： Saethang T,Payne DM,Avihingsanon Y,Pisitkun T

更新日期：2016-08-17 00:00:00

abstract：BACKGROUND:Temporal gene expression profiles characterize the time-dynamics of expression of specific genes and are increasingly collected in current gene expression experiments. In the analysis of experiments where gene expression is obtained over the life cycle, it is of interest to relate temporal patterns of gene e...

journal_title：BMC bioinformatics

authors： Müller HG,Chiou JM,Leng X

更新日期：2008-01-28 00:00:00

abstract：BACKGROUND:Copy number alterations (CNAs), due to their large impact on the genome, have been an important contributing factor to oncogenesis and metastasis. Detecting genomic alterations from the shallow-sequencing data of a low-purity tumor sample remains a challenging task. RESULTS:We introduce Accucopy, a method t...

journal_title：BMC bioinformatics

authors： Fan X,Luo G,Huang YS

更新日期：2021-01-15 00:00:00

abstract：BACKGROUND:Extant genomes share regions where genes have the same order and orientation, which are thought to arise from the conservation of an ancestral order of genes during evolution. Such regions of so-called conserved synteny, or synteny blocks, must be precisely identified and quantified, as a prerequisite to bet...

journal_title：BMC bioinformatics

authors： Lucas JM,Muffato M,Roest Crollius H

更新日期：2014-08-08 00:00:00

abstract：BACKGROUND:The ability to detect nuclei in embryos is essential for studying the development of multicellular organisms. A system of automated nuclear detection has already been tested on a set of four-dimensional (4D) Nomarski differential interference contrast (DIC) microscope images of Caenorhabditis elegans embryos...

journal_title：BMC bioinformatics

authors： Hamahashi S,Onami S,Kitano H

更新日期：2005-05-24 00:00:00

abstract：BACKGROUND:In current comparative proteomics studies, the large number of images generated by 2D gels is currently compared using spot matching algorithms. Unfortunately, differences in gel migration and sample variability make efficient spot alignment very difficult to obtain, and, as consequence most of the software ...

journal_title：BMC bioinformatics

authors： Pérès S,Molina L,Salvetat N,Granier C,Molina F

更新日期：2008-10-28 00:00:00

abstract：BACKGROUND:Protein quality assessment (QA) useful for ranking and selecting protein models has long been viewed as one of the major challenges for protein tertiary structure prediction. Especially, estimating the quality of a single protein model, which is important for selecting a few good models out of a large model ...

journal_title：BMC bioinformatics

authors： Cao R,Bhattacharya D,Hou J,Cheng J

更新日期：2016-12-05 00:00:00

abstract：BACKGROUND:In addition to single-locus (main) effects of disease variants, there is a growing consensus that gene-gene and gene-environment interactions may play important roles in disease etiology. However, for the very large numbers of genetic markers currently in use, it has proven difficult to develop suitable and ...

journal_title：BMC bioinformatics

authors： Long Q,Zhang Q,Ott J

更新日期：2009-01-30 00:00:00

abstract：BACKGROUND:Techniques for reconstruction of biological networks which are based on perturbation experiments often predict direct interactions between nodes that do not exist. Transitive reduction removes such relations if they can be explained by an indirect path of influences. The existing algorithms for transitive re...

journal_title：BMC bioinformatics

authors： Bošnački D,Odenbrett MR,Wijs A,Ligtenberg W,Hilbers P

更新日期：2012-10-30 00:00:00

abstract：BACKGROUND:Many models have been proposed to detect copy number alterations in chromosomal copy number profiles, but it is usually not obvious to decide which is most effective for a given data set. Furthermore, most methods have a smoothing parameter that determines the number of breakpoints and must be chosen using v...

journal_title：BMC bioinformatics

authors： Hocking TD,Schleiermacher G,Janoueix-Lerosey I,Boeva V,Cappo J,Delattre O,Bach F,Vert JP

更新日期：2013-05-22 00:00:00

abstract：BACKGROUND:Integrative network methods are commonly used for interpretation of high-throughput experimental biological data: transcriptomics, proteomics, metabolomics and others. One of the common approaches is finding a connected subnetwork of a global interaction network that best encompasses significant individual c...

journal_title：BMC bioinformatics

authors： Alexeev N,Isomurodov J,Sukhov V,Korotkevich G,Sergushichev A

更新日期：2020-11-18 00:00:00

abstract：BACKGROUND:Protein aggregation is a significant problem in the biopharmaceutical industry (protein drug stability) and is associated medically with over 40 human diseases. Although a number of computational models have been developed for predicting aggregation propensity and identifying aggregation-prone regions in pro...

journal_title：BMC bioinformatics

authors： Fang Y,Gao S,Tai D,Middaugh CR,Fang J

更新日期：2013-10-28 00:00:00

abstract：BACKGROUND:Amino acids in proteins are not used equally. Some of the differences in the amino acid composition of proteins are between species (mainly due to nucleotide composition and lifestyle) and some are between proteins from the same species (related to protein function, expression or subcellular localization, fo...

journal_title：BMC bioinformatics

authors： Pasamontes A,Garcia-Vallve S

更新日期：2006-05-18 00:00:00

abstract：BACKGROUND:G-protein-coupled receptors (GPCRs) play a key role in diverse physiological processes and are the targets of almost two-thirds of the marketed drugs. The 3 D structures of GPCRs are largely unavailable; however, a large number of GPCR primary sequences are known. To facilitate the identification and charact...

journal_title：BMC bioinformatics

authors： Peng ZL,Yang JY,Chen X

更新日期：2010-08-09 00:00:00

abstract：BACKGROUND:Molecular data, e.g. arising from microarray technology, is often used for predicting survival probabilities of patients. For multivariate risk prediction models on such high-dimensional data, there are established techniques that combine parameter estimation and variable selection. One big challenge is to i...

journal_title：BMC bioinformatics

authors： Sariyar M,Hoffmann I,Binder H

更新日期：2014-02-26 00:00:00

abstract：BACKGROUND:Searching for similar compounds in a database is the most important process for in-silico drug screening. Since a query compound is an important starting point for the new drug, a query holder, who is afraid of the query being monitored by the database server, usually downloads all the records in the databas...

journal_title：BMC bioinformatics

authors： Shimizu K,Nuida K,Arai H,Mitsunari S,Attrapadung N,Hamada M,Tsuda K,Hirokawa T,Sakuma J,Hanaoka G,Asai K

更新日期：2015-01-01 00:00:00

abstract：BACKGROUND:Ensemble predictors such as the random forest are known to have superior accuracy but their black-box predictions are difficult to interpret. In contrast, a generalized linear model (GLM) is very interpretable especially when forward feature selection is used to construct the model. However, forward feature ...

journal_title：BMC bioinformatics

authors： Song L,Langfelder P,Horvath S

更新日期：2013-01-16 00:00:00

abstract：:Selected reaction monitoring (SRM)-based proteomics approaches enable highly sensitive and reproducible assays for profiling of thousands of peptides in one experiment. The development of such assays involves the determination of retention time, detectability and fragmentation properties of peptides, followed by an op...

journal_title：BMC bioinformatics

authors： Nahnsen S,Kohlbacher O

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:Novel sequence motifs detection is becoming increasingly essential in computational biology. However, the high computational cost greatly constrains the efficiency of most motif discovery algorithms. RESULTS:In this paper, we accelerate MEME algorithm targeted on Intel Many Integrated Core (MIC) Architectur...

journal_title：BMC bioinformatics

authors： Peng S,Cheng M,Huang K,Cui Y,Zhang Z,Guo R,Zhang X,Yang S,Liao X,Lu Y,Zou Q,Shi B

更新日期：2018-08-13 00:00:00

abstract：BACKGROUND:GmrSD is a modification-dependent restriction endonuclease that specifically targets and cleaves glucosylated hydroxymethylcytosine (glc-HMC) modified DNA. It is encoded either as two separate single-domain GmrS and GmrD proteins or as a single protein carrying both domains. Previous studies suggested that G...

journal_title：BMC bioinformatics

authors： Machnicka MA,Kaminska KH,Dunin-Horkawicz S,Bujnicki JM

更新日期：2015-10-23 00:00:00

abstract：BACKGROUND:The Cell Ontology (CL) is an ontology for the representation of in vivo cell types. As biological ontologies such as the CL grow in complexity, they become increasingly difficult to use and maintain. By making the information in the ontology computable, we can use automated reasoners to detect errors and ass...

journal_title：BMC bioinformatics

authors： Meehan TF,Masci AM,Abdulla A,Cowell LG,Blake JA,Mungall CJ,Diehl AD

更新日期：2011-01-05 00:00:00

abstract：BACKGROUND:Chemical named entities represent an important facet of biomedical text. RESULTS:We have developed a system to use character-based n-grams, Maximum Entropy Markov Models and rescoring to recognise chemical names and other such entities, and to make confidence estimates for the extracted entities. An adjusta...

journal_title：BMC bioinformatics

authors： Corbett P,Copestake A

更新日期：2008-11-19 00:00:00

abstract：BACKGROUND:Proteins are dynamic molecules with motions ranging from picoseconds to longer than seconds. Many protein functions, however, appear to occur on the micro to millisecond timescale and therefore there has been intense research of the importance of these motions in catalysis and molecular interactions. Nuclear...

journal_title：BMC bioinformatics

authors： Bieri M,Gooley PR

更新日期：2011-10-27 00:00:00

abstract：BACKGROUND:Graph theory provides a computational framework for modeling a variety of datasets including those emerging from genomics, proteomics, and chemical genetics. Networks of genes, proteins, small molecules, or other objects of study can be represented as graphs of nodes (vertices) and interactions (edges) that ...

journal_title：BMC bioinformatics

authors： Forman JJ,Clemons PA,Schreiber SL,Haggarty SJ

更新日期：2005-10-19 00:00:00

abstract：BACKGROUNDS:Next-Generation Sequencing (NGS) is now widely used in biomedical research for various applications. Processing of NGS data requires multiple programs and customization of the processing pipelines according to the data platforms. However, rapid progress of the NGS applications and processing methods urgentl...

journal_title：BMC bioinformatics

authors： Joo T,Choi JH,Lee JH,Park SE,Jeon Y,Jung SH,Woo HG

更新日期：2019-02-20 00:00:00