Recursive model for dose-time responses in pharmacological studies.

abstract：BACKGROUND:The human immunodeficiency virus type 1 (HIV-1) aspartic protease is an important enzyme owing to its imperative part in viral development and a causative agent of deadliest disease known as acquired immune deficiency syndrome (AIDS). Development of HIV-1 protease inhibitors can help understand the specifici...

journal_title：BMC bioinformatics

authors： Singh O,Su EC

更新日期：2016-12-23 00:00:00

abstract：BACKGROUND:Time-course microarray experiments are being increasingly used to characterize dynamic biological processes. In these experiments, the goal is to identify genes differentially expressed in time-course data, measured between different biological conditions. These differentially expressed genes can reveal the ...

journal_title：BMC bioinformatics

authors： Jonnalagadda S,Srinivasan R

更新日期：2008-06-06 00:00:00

abstract：BACKGROUND:Supercomputers have become indispensable infrastructures in science and industries. In particular, most state-of-the-art scientific results utilize massively parallel supercomputers ranked in TOP500. However, their use is still limited in the bioinformatics field due to the fundamental fact that the asynchro...

journal_title：BMC bioinformatics

authors： Ito S,Yadome M,Nishiki T,Ishiduki S,Inoue H,Yamaguchi R,Miyano S

更新日期：2019-12-02 00:00:00

abstract：BACKGROUND:Protein-protein interactions (PPIs) play important roles in various cellular processes. However, the low quality of current PPI data detected from high-throughput screening techniques has diminished the potential usefulness of the data. We need to develop a method to address the high data noise and incomplet...

journal_title：BMC bioinformatics

authors： Wu M,Li X,Chua HN,Kwoh CK,Ng SK

更新日期：2010-10-15 00:00:00

abstract：BACKGROUND:Cluster analysis is the most common unsupervised method for finding hidden groups in data. Clustering presents two main challenges: (1) finding the optimal number of clusters, and (2) removing "outliers" among the objects being clustered. Few clustering algorithms currently deal directly with the outlier pro...

journal_title：BMC bioinformatics

authors： Wang M,Abrams ZB,Kornblau SM,Coombes KR

更新日期：2018-01-08 00:00:00

abstract：BACKGROUND:Bovine Viral Diarrhea Virus (BVDV) infection is widespread in cattle worldwide, causing important economic losses. Pathogenesis of the disease caused by BVDV is complex, as each BVDV strain has two biotypes: non-cytopathic (ncp) and cytopathic (cp). BVDV can cause a persistent latent infection and immune sup...

journal_title：BMC bioinformatics

authors： Ammari M,McCarthy FM,Nanduri B,Pinchuk LM

更新日期：2010-10-07 00:00:00

abstract：BACKGROUND:Genes occurring co-localized in multiple genomes can be strong indicators for either functional constraints on the genome organization or remnant ancestral gene order. The computational detection of these patterns, which are usually referred to as gene clusters, has become increasingly sensitive over the pas...

journal_title：BMC bioinformatics

authors： Jahn K,Winter S,Stoye J,Böcker S

更新日期：2013-01-01 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:The third edition of the BioNLP Shared Task was held with the grand theme "knowledge base construction (KB)". The Genia Event (GE) task was re-designed and implemented in light of this theme. For its final report, the participating systems were evaluated from a perspective of annotation. To further explore t...

journal_title：BMC bioinformatics

authors： Kim JD,Kim JJ,Han X,Rebholz-Schuhmann D

更新日期：2015-01-01 00:00:00

abstract：:Shotgun proteomics has recently emerged as a powerful approach to characterizing proteomes in biological samples. Its overall objective is to identify the form and quantity of each protein in a high-throughput manner by coupling liquid chromatography with tandem mass spectrometry. As a consequence of its high throughp...

journal_title：BMC bioinformatics

authors： Li YF,Radivojac P

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:Protein function is closely intertwined with protein structure. Discovery of meaningful structure-function relationships is of utmost importance in protein biochemistry and has led to creation of high-quality, manually curated classification databases, such as the gold-standard SCOP (Structural Classificatio...

journal_title：BMC bioinformatics

authors： Asarnow D,Singh R

更新日期：2014-01-01 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:Systems biology modeling from microarray data requires the most contemporary structural and functional array annotation. However, microarray annotations, especially for non-commercial, non-traditional biomedical model organisms, are often dated. In addition, most microarray analysis tools do not readily acce...

journal_title：BMC bioinformatics

authors： van den Berg BH,Konieczka JH,McCarthy FM,Burgess SC

更新日期：2009-01-23 00:00:00

abstract：BACKGROUND:We previously developed GoMiner, an application that organizes lists of 'interesting' genes (for example, under-and overexpressed genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology. The original version of GoMiner was oriented toward visualization and interp...

journal_title：BMC bioinformatics

authors： Zeeberg BR,Qin H,Narasimhan S,Sunshine M,Cao H,Kane DW,Reimers M,Stephens RM,Bryant D,Burt SK,Elnekave E,Hari DM,Wynn TA,Cunningham-Rundles C,Stewart DM,Nelson D,Weinstein JN

更新日期：2005-07-05 00:00:00

abstract：BACKGROUND:Current microRNA (miRNA) research in progress has engendered rapid accumulation of expression data evolving from microarray experiments. Such experiments are generally performed over different tissues belonging to a specific species of metazoan. For disease diagnosis, microarray probes are also prepared with...

journal_title：BMC bioinformatics

authors： Bandyopadhyay S,Bhattacharyya M

更新日期：2009-05-28 00:00:00

abstract：BACKGROUND:A major goal of the analysis of high-dimensional RNA expression data from tumor tissue is to identify prognostic signatures for discriminating patient subgroups. For this purpose genome-wide identification of bimodally expressed genes from gene array data is relevant because distinguishability of high and lo...

journal_title：BMC bioinformatics

authors： Hellwig B,Hengstler JG,Schmidt M,Gehrmann MC,Schormann W,Rahnenführer J

更新日期：2010-05-25 00:00:00

abstract：BACKGROUND:Integration of heterogeneous data types is a challenging problem, especially in biology, where the number of databases and data types increase rapidly. Amongst the problems that one has to face are integrity, consistency, redundancy, connectivity, expressiveness and updatability. DESCRIPTION:Here we present...

journal_title：BMC bioinformatics

authors： Birkland A,Yona G

更新日期：2006-02-15 00:00:00

abstract：BACKGROUND:A number of software packages are available to generate DNA multiple sequence alignments (MSAs) evolved under continuous-time Markov processes on phylogenetic trees. On the other hand, methods of simulating the DNA MSA directly from the transition matrices do not exist. Moreover, existing software restricts ...

journal_title：BMC bioinformatics

authors： Kedzierska AM,Casanellas M

更新日期：2012-08-28 00:00:00

abstract：BACKGROUND:XHMM is a widely used tool for copy-number variant (CNV) discovery from whole exome sequencing data but can require hours to days to run for large cohorts. A more scalable implementation would reduce the need for specialized computational resources and enable increased exploration of the configuration parame...

journal_title：BMC bioinformatics

authors： Linderman MD,Chia D,Wallace F,Nothaft FA

更新日期：2019-10-11 00:00:00

abstract：BACKGROUND:Reverse transcription followed by real-time PCR is widely used for quantification of specific mRNA, and with the use of double-stranded DNA binding dyes it is becoming a standard for microarray data validation. Despite the kinetic information generated by real-time PCR, most popular analysis methods assume c...

journal_title：BMC bioinformatics

authors： Alvarez MJ,Vila-Ortiz GJ,Salibe MC,Podhajcer OL,Pitossi FJ

更新日期：2007-03-09 00:00:00

abstract：BACKGROUND:Although carbohydrates are the third major class of biological macromolecules, after proteins and DNA, there is neither a comprehensive database for carbohydrate structures nor an established universal structure encoding scheme for computational purposes. Funding for further development of the Complex Carboh...

journal_title：BMC bioinformatics

authors： Ranzinger R,Herget S,Wetter T,von der Lieth CW

更新日期：2008-09-19 00:00:00

abstract：BACKGROUND:When constructing new biomarker or gene signature scores for time-to-event outcomes, the underlying aims are to develop a discrimination model that helps to predict whether patients have a poor or good prognosis and to identify the most influential variables for this task. In practice, this is often done fit...

journal_title：BMC bioinformatics

authors： Mayr A,Hofner B,Schmid M

更新日期：2016-07-22 00:00:00

abstract：BACKGROUND:Multiple sequence alignment (MSA) is a fundamental analysis method used in bioinformatics and many comparative genomic applications. Prior MSA acceleration attempts with reconfigurable computing have only addressed the first stage of progressive alignment and consequently exhibit performance limitations acco...

journal_title：BMC bioinformatics

authors： Lloyd S,Snell QO

更新日期：2011-12-07 00:00:00

abstract：BACKGROUND:Word sense disambiguation (WSD) attempts to solve lexical ambiguities by identifying the correct meaning of a word based on its context. WSD has been demonstrated to be an important step in knowledge-based approaches to automatic summarization. However, the correlation between the accuracy of the WSD methods...

journal_title：BMC bioinformatics

authors： Plaza L,Jimeno-Yepes AJ,Díaz A,Aronson AR

更新日期：2011-08-26 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNA) are regulatory genes that target and repress other RNA molecules via sequence-specific binding. Several biological processes are regulated across many organisms by evolutionarily conserved miRNAs. Plants and invertebrates employ their miRNA in defense against viruses by targeting and degrad...

journal_title：BMC bioinformatics

authors： Carl JW Jr,Trgovcich J,Hannenhalli S

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:It is well known that the search for homologous RNAs is more effective if both sequence and structure information is incorporated into the search. However, current tools for searching with RNA sequence-structure patterns cannot fully handle mutations occurring on both these levels or are simply not fast enou...

journal_title：BMC bioinformatics

authors： Meyer F,Kurtz S,Beckstette M

更新日期：2013-07-17 00:00:00

abstract：BACKGROUND:In protein design, correct use of topology is among the initial and most critical feature. Meticulous selection of backbone topology aids in drastically reducing the structure search space. With ProLego, we present a server application to explore the component aspect of protein structures and provide an intu...

journal_title：BMC bioinformatics

authors： Khan T,Panday SK,Ghosh I

更新日期：2018-05-04 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:PCR has the potential to detect and precisely quantify specific DNA sequences, but it is not yet often used as a fully quantitative method. A number of data collection and processing strategies have been described for the implementation of quantitative PCR. However, they can be experimentally cumbersome, the...

journal_title：BMC bioinformatics

authors： Karlen Y,McNair A,Perseguers S,Mazza C,Mermod N

更新日期：2007-04-20 00:00:00

abstract：BACKGROUND:Machine learning has been utilized to predict cancer drug response from multi-omics data generated from sensitivities of cancer cell lines to different therapeutic compounds. Here, we build machine learning models using gene expression data from patients' primary tumor tissues to predict whether a patient wi...

journal_title：BMC bioinformatics

authors： Clayton EA,Pujol TA,McDonald JF,Qiu P

更新日期：2020-09-30 00:00:00