NOXclass: prediction of protein-protein interaction types.

abstract：BACKGROUND:High-throughput sequencing can identify numerous potential genomic targets for microbial strain typing, but identification of the most informative combinations requires the use of computational screening tools. This paper describes novel software-- Automated Selection of Typing Target Subsets (AuSeTTS)--that...

journal_title：BMC bioinformatics

authors： O'Sullivan MV,Sintchenko V,Gilbert GL

更新日期：2013-05-01 00:00:00

abstract：BACKGROUND:Nearly all cellular processes involve proteins structurally rearranging to accommodate molecular partners. The energy landscape underscores the inherent nature of proteins as dynamic molecules interconverting between structures with varying energies. In principle, reconstructing a protein's energy landscape ...

journal_title：BMC bioinformatics

authors： Morris D,Maximova T,Plaku E,Shehu A

更新日期：2019-06-06 00:00:00

abstract：BACKGROUND:Protein-protein interactions (PPIs) play crucial roles in the execution of various cellular processes and form the basis of biological mechanisms. Although large amount of PPIs data for different species has been generated by high-throughput experimental techniques, current PPI pairs obtained with experiment...

journal_title：BMC bioinformatics

authors： You ZH,Lei YK,Zhu L,Xia J,Wang B

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:We introduce the decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information (ProCKSI). ProCKSI integrates various protein similarity measures through an easy to use interface that allows the comparison of multiple proteins simultaneously. It employs the Universal Simila...

journal_title：BMC bioinformatics

authors： Barthel D,Hirst JD,Błazewicz J,Burke EK,Krasnogor N

更新日期：2007-10-26 00:00:00

abstract：BACKGROUND:One of the most important goals of the mathematical modeling of gene regulatory networks is to alter their behavior toward desirable phenotypes. Therapeutic techniques are derived for intervention in terms of stationary control policies. In large networks, it becomes computationally burdensome to derive an o...

journal_title：BMC bioinformatics

authors： Ghaffari N,Ivanov I,Qian X,Dougherty ER

更新日期：2011-10-18 00:00:00

abstract：BACKGROUND:An increasing number of bioinformatics methods are considering the phylogenetic relationships between biological sequences. Implementing new methodologies using the maximum likelihood phylogenetic framework can be a time consuming task. RESULTS:The bioinformatics library libcov is a collection of C++ classe...

journal_title：BMC bioinformatics

authors： Butt D,Roger AJ,Blouin C

更新日期：2005-06-06 00:00:00

abstract：BACKGROUND:Improvements in protein sequence annotation and an increase in the number of annotated protein databases has fueled development of an increasing number of software tools to predict secreted proteins. Six software programs capable of high throughput and employing a wide range of prediction methods, SignalP 3....

journal_title：BMC bioinformatics

authors： Klee EW,Ellis LB

更新日期：2005-10-14 00:00:00

abstract：:Many different approaches have been developed to model and simulate gene regulatory networks. We proposed the following categories for gene regulatory network models: network parts lists, network topology models, network control logic models, and dynamic models. Here we will describe some examples for each of these ca...

journal_title：BMC bioinformatics

authors： Schlitt T,Brazma A

更新日期：2007-09-27 00:00:00

abstract：BACKGROUND:Parsimony and maximum likelihood methods of phylogenetic tree estimation and parsimony methods for genome rearrangements are central to the study of genome evolution yet to date they have largely been pursued in isolation. RESULTS:We present a data structure called a history graph that offers a practical ba...

journal_title：BMC bioinformatics

authors： Paten B,Zerbino DR,Hickey G,Haussler D

更新日期：2014-06-19 00:00:00

abstract：BACKGROUND:Current malaria diagnosis relies primarily on microscopic examination of Giemsa-stained thick and thin blood films. This method requires vigorously trained technicians to efficiently detect and classify the malaria parasite species such as Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) for an appropria...

journal_title：BMC bioinformatics

authors： Kaewkamnerd S,Uthaipibull C,Intarapanich A,Pannarut M,Chaotheing S,Tongsima S

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:Normalization is the process of removing non-biological sources of variation between array experiments. Recent investigations of data in gene expression databases for varying organisms and tissues have shown that the majority of expressed genes exhibit a power-law distribution with an exponent close to -1 (i...

journal_title：BMC bioinformatics

authors： Lu T,Costello CM,Croucher PJ,Häsler R,Deuschl G,Schreiber S

更新日期：2005-02-23 00:00:00

abstract：BACKGROUND:The advent of RNA interference techniques enables the selective silencing of biologically interesting genes in an efficient way. In combination with DNA microarray technology this enables researchers to gain insights into signaling pathways by observing downstream effects of individual knock-downs on gene ex...

journal_title：BMC bioinformatics

authors： Froehlich H,Fellmann M,Sueltmann H,Poustka A,Beissbarth T

更新日期：2007-10-15 00:00:00

abstract：BACKGROUND:High-throughput sequencing has rapidly become an essential part of precision cancer medicine. But validating results obtained from analyzing and interpreting genomic data remains a rate-limiting factor. The gold standard, of course, remains manual validation by expert panels, which is not without its weaknes...

journal_title：BMC bioinformatics

authors： Bian X,Zhu B,Wang M,Hu Y,Chen Q,Nguyen C,Hicks B,Meerzaman D

更新日期：2018-11-19 00:00:00

abstract：BACKGROUND:The application of high-throughput sequencing in a broad range of quantitative genomic assays (e.g., DNA-seq, ChIP-seq) has created a high demand for the analysis of large-scale read-count data. Typically, the genome is divided into tiling windows and windowed read-count data is generated for the entire geno...

journal_title：BMC bioinformatics

authors： Wang W,Sun W,Wang W,Szatkiewicz J

更新日期：2018-03-01 00:00:00

abstract：BACKGROUND:Correctly identifying genomic regions enriched with histone modifications and transcription factors is key to understanding their regulatory and developmental roles. Conceptually, these regions are divided into two categories, narrow peaks and broad domains, and different algorithms are used to identify each...

journal_title：BMC bioinformatics

authors： Starmer J,Magnuson T

更新日期：2016-03-24 00:00:00

abstract：BACKGROUND:T-cell epitopes that promiscuously bind to multiple alleles of a human leukocyte antigen (HLA) supertype are prime targets for development of vaccines and immunotherapies because they are relevant to a large proportion of the human population. The presence of clusters of promiscuous T-cell epitopes, immunolo...

journal_title：BMC bioinformatics

authors： Zhang GL,Khan AM,Srinivasan KN,Heiny A,Lee K,Kwoh CK,August JT,Brusic V

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:HH-suite is a widely used open source software suite for sensitive sequence similarity searches and protein fold recognition. It is based on pairwise alignment of profile Hidden Markov models (HMMs), which represent multiple sequence alignments of homologous proteins. RESULTS:We developed a single-instructi...

journal_title：BMC bioinformatics

authors： Steinegger M,Meier M,Mirdita M,Vöhringer H,Haunsberger SJ,Söding J

更新日期：2019-09-14 00:00:00

abstract：BACKGROUND:Single nucleotide polymorphisms (SNPs) are the most frequent type of sequence variation between individuals, and represent a promising tool for finding genetic determinants of complex diseases and understanding the differences in drug response. In this regard, it is of particular interest to study the effect...

journal_title：BMC bioinformatics

authors： Bauer-Mehren A,Furlong LI,Rautschka M,Sanz F

更新日期：2009-08-27 00:00:00

abstract：BACKGROUND:A common feature of microarray experiments is the occurrence of missing gene expression data. These missing values occur for a variety of reasons, in particular, because of the filtering of poor quality spots and the removal of undefined values when a logarithmic transformation is applied to negative backgro...

journal_title：BMC bioinformatics

authors： Tom BD,Gilks WR,Brooke-Powell ET,Ajioka JW

更新日期：2005-09-26 00:00:00

abstract：BACKGROUND:Detailed information on DNA-binding transcription factors (the key players in the regulation of gene expression) and on transcriptional regulatory interactions of microorganisms deduced from literature-derived knowledge, computer predictions and global DNA microarray hybridization experiments, has opened the...

journal_title：BMC bioinformatics

authors： Baumbach J

更新日期：2007-11-06 00:00:00

abstract：BACKGROUND:The Distributed Annotation System (DAS) allows merging of DNA sequence annotations from multiple sources and provides a single annotation view. A straightforward way to establish a DAS annotation server is to use the "Lightweight DAS" server (LDAS). Onto this type of server, annotations can be uploaded as fl...

journal_title：BMC bioinformatics

authors： Negre V,Grunau C

更新日期：2004-05-07 00:00:00

abstract：BACKGROUND:For many types of analyses, data about gene structure and locations of non-coding regions of genes are required. Although a vast amount of genomic sequence data is available, precise annotation of genes is lacking behind. Finding the corresponding gene of a given protein sequence by means of conventional too...

journal_title：BMC bioinformatics

authors： Keller O,Odronitz F,Stanke M,Kollmar M,Waack S

更新日期：2008-06-13 00:00:00

abstract：BACKGROUND:Mouse xenografts from (patient-derived) tumors (PDX) or tumor cell lines are widely used as models to study various biological and preclinical aspects of cancer. However, analyses of their RNA and DNA profiles are challenging, because they comprise reads not only from the grafted human cancer but also from t...

journal_title：BMC bioinformatics

authors： Kluin RJC,Kemper K,Kuilman T,de Ruiter JR,Iyer V,Forment JV,Cornelissen-Steijger P,de Rink I,Ter Brugge P,Song JY,Klarenbeek S,McDermott U,Jonkers J,Velds A,Adams DJ,Peeper DS,Krijgsman O

更新日期：2018-10-04 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNAs) are small ~22 nucleotide non-coding RNAs that function as post-transcriptional regulators of messenger RNA (mRNA) through base-pairing to 6-8 nucleotide long target sites, usually located within the mRNA 3' untranslated region. A common approach to validate and probe microRNA-mRNA interact...

journal_title：BMC bioinformatics

authors： Ryan BC,Werner TS,Howard PL,Chow RL

更新日期：2016-04-27 00:00:00

abstract：BACKGROUND:A new method for the prediction of protein structural classes is constructed based on Rough Sets algorithm, which is a rule-based data mining method. Amino acid compositions and 8 physicochemical properties data are used as conditional attributes for the construction of decision system. After reducing the de...

journal_title：BMC bioinformatics

authors： Cao Y,Liu S,Zhang L,Qin J,Wang J,Tang K

更新日期：2006-01-14 00:00:00

abstract：BACKGROUND:The nucleosome is the fundamental packing unit of DNAs in eukaryotic cells. Its detailed positioning on the genome is closely related to chromosome functions. Increasing evidence has shown that genomic DNA sequence itself is highly predictive of nucleosome positioning genome-wide. Therefore a fast software t...

journal_title：BMC bioinformatics

authors： Xi L,Fondufe-Mittendorf Y,Xia L,Flatow J,Widom J,Wang JP

更新日期：2010-06-24 00:00:00

abstract：BACKGROUND:A survey of presences and absences of specific species across multiple biogeographic units (or bioregions) are used in a broad area of biological studies from ecology to microbiology. Using binary presence-absence data, we evaluate species co-occurrences that help elucidate relationships among organisms and ...

journal_title：BMC bioinformatics

authors： Chung NC,Miasojedow B,Startek M,Gambin A

更新日期：2019-12-24 00:00:00

abstract：BACKGROUND:Contact-guided protein structure prediction methods are becoming more and more successful because of the latest advances in residue-residue contact prediction. To support contact-driven structure prediction, effective tools that can quickly build tertiary structural models of good quality from predicted cont...

journal_title：BMC bioinformatics

authors： Adhikari B,Cheng J

更新日期：2018-01-25 00:00:00

abstract：BACKGROUND:Cancer is a complex disease which is characterized by the accumulation of genetic alterations during the patient's lifetime. With the development of the next-generation sequencing technology, multiple omics data, such as cancer genomic, epigenomic and transcriptomic data etc., can be measured from each indiv...

journal_title：BMC bioinformatics

authors： Wei PJ,Zhang D,Xia J,Zheng CH

更新日期：2016-12-23 00:00:00

abstract：BACKGROUND:Horizontal gene transfer, i.e. the acquisition of genetic material from nonparent organism, is considered an important force driving species evolution. Many cases of horizontal gene transfer from prokaryotes to eukaryotes have been registered, but no transfer mechanism has been deciphered so far, although vi...

journal_title：BMC bioinformatics

authors： Daugavet MA,Shabelnikov SV,Podgornaya OI

更新日期：2020-07-24 00:00:00