Functional relevance of dynamic properties of Dimeric NADP-dependent Isocitrate Dehydrogenases.

abstract：BACKGROUND:Cancer progression is caused by the sequential accumulation of mutations, but not all orders of accumulation are equally likely. When the fixation of some mutations depends on the presence of previous ones, identifying restrictions in the order of accumulation of mutations can lead to the discovery of therap...

journal_title：BMC bioinformatics

authors： Diaz-Uriarte R

更新日期：2015-02-12 00:00:00

abstract：BACKGROUND:PacBio sequencing platform offers longer read lengths than the second-generation sequencing technologies. It has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes. Due to its extremely wide range of application areas, fast sequencing simulation syste...

journal_title：BMC bioinformatics

authors： Wei ZG,Zhang SW

更新日期：2018-05-22 00:00:00

abstract：BACKGROUND:The search for enriched features has become widely used to characterize a set of genes or proteins. A key aspect of this technique is its ability to identify correlations amongst heterogeneous data such as Gene Ontology annotations, gene expression data and genome location of genes. Despite the rapid growth ...

journal_title：BMC bioinformatics

authors： Barriot R,Sherman DJ,Dutour I

更新日期：2007-09-11 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:Differential co-expression (DCX) signifies change in degree of co-expression of a set of genes among different biological conditions. It has been used to identify differential co-expression networks or interactomes. Many algorithms have been developed for single-factor differential co-expression analysis and...

journal_title：BMC bioinformatics

authors： Liany H,Rajapakse JC,Karuturi RKM

更新日期：2017-12-28 00:00:00

abstract：BACKGROUND:Comprehensive two-dimensional gas chromatography coupled with mass spectrometry (GC × GC-MS) is a powerful technique which has gained increasing attention over the last two decades. The GC × GC-MS provides much increased separation capacity, chemical selectivity and sensitivity for complex sample analysis an...

journal_title：BMC bioinformatics

authors： Kim S,Koo I,Fang A,Zhang X

更新日期：2011-06-15 00:00:00

abstract：BACKGROUND:Extensive studies have been carried out on Caenorhabditis elegans as a model organism to elucidate mechanisms of aging and the effects of perturbing known aging-related genes on lifespan and behavior. This research has generated large amounts of experimental data that is increasingly difficult to integrate a...

journal_title：BMC bioinformatics

authors： Callahan A,Cifuentes JJ,Dumontier M

更新日期：2015-02-07 00:00:00

abstract：BACKGROUND:Microarray experiments enable simultaneous measurement of the expression levels of virtually all transcripts present in cells, thereby providing a 'molecular picture' of the cell state. On the other hand, the genomic responses to a pharmacological or hormonal stimulus are dynamic molecular processes, where t...

journal_title：BMC bioinformatics

authors： Mutarelli M,Cicatiello L,Ferraro L,Grober OM,Ravo M,Facchiano AM,Angelini C,Weisz A

更新日期：2008-03-26 00:00:00

abstract：BACKGROUND:Eukaryotic whole genome sequences are accumulating at an impressive rate. Effective methods for comparing multiple whole eukaryotic genomes on a large scale are needed. Most attempted solutions involve the production of large scale alignments, and many of these require a high stringency pre-screen for putati...

journal_title：BMC bioinformatics

authors： Stuart GW,Berry MW

更新日期：2004-12-17 00:00:00

abstract：BACKGROUND:Inferring gene regulatory networks (GRNs) from gene expression data remains a challenge in system biology. In past decade, numerous methods have been developed for the inference of GRNs. It remains a challenge due to the fact that the data is noisy and high dimensional, and there exists a large number of pot...

journal_title：BMC bioinformatics

authors： Che D,Guo S,Jiang Q,Chen L

更新日期：2020-07-14 00:00:00

abstract：BACKGROUND:The number of protein structures from structural genomics centers dramatically increases in the Protein Data Bank (PDB). Many of these structures are functionally unannotated because they have no sequence similarity to proteins of known function. However, it is possible to successfully infer function using o...

journal_title：BMC bioinformatics

authors： von Grotthuss M,Plewczynski D,Ginalski K,Rychlewski L,Shakhnovich EI

更新日期：2006-02-06 00:00:00

abstract：BACKGROUND:The UNO/RIC Nanopore Detector provides a new way to study the binding and conformational changes of individual antibodies. Many critical questions regarding antibody function are still unresolved, questions that can be approached in a new way with the nanopore detector. RESULTS:We present evidence that diff...

journal_title：BMC bioinformatics

authors： Winters-Hilt S,Morales E,Amin I,Stoyanov A

更新日期：2007-11-01 00:00:00

abstract：BACKGROUND:The sequencing of many genomes and tiling arrays consisting of millions of DNA segments spanning entire genomes have made high-resolution copy number analysis possible. Microarray-based comparative genomic hybridization (array CGH) has enabled the high-resolution detection of DNA copy number aberrations. Whi...

journal_title：BMC bioinformatics

authors： Skvortsov D,Abdueva D,Stitzer ME,Finkel SE,Tavaré S

更新日期：2007-06-14 00:00:00

abstract：BACKGROUND:Routine application of gene expression microarray technology is rapidly producing large amounts of data that necessitate new approaches of analysis. The analysis of a specific microarray experiment profits enormously from cross-comparing to other experiments. This process is generally performed by numerical ...

journal_title：BMC bioinformatics

authors： Finocchiaro G,Mancuso F,Muller H

更新日期：2005-12-01 00:00:00

abstract：BACKGROUND:One of the greatest challenges in Metabolic Engineering is to develop quantitative models and algorithms to identify a set of genetic manipulations that will result in a microbial strain with a desirable metabolic phenotype which typically means having a high yield/productivity. This challenge is not only du...

journal_title：BMC bioinformatics

authors： Rocha M,Maia P,Mendes R,Pinto JP,Ferreira EC,Nielsen J,Patil KR,Rocha I

更新日期：2008-11-27 00:00:00

abstract：BACKGROUND:Deep mutational scanning is a technique to estimate the impacts of mutations on a gene by using deep sequencing to count mutations in a library of variants before and after imposing a functional selection. The impacts of mutations must be inferred from changes in their counts after selection. RESULTS:I desc...

journal_title：BMC bioinformatics

authors： Bloom JD

更新日期：2015-05-20 00:00:00

abstract：BACKGROUND:Protein solvent accessibility prediction is a pivotal intermediate step towards modeling protein tertiary structures directly from one-dimensional sequences. It also plays an important part in identifying protein folds and domains. Although some methods have been presented to the protein solvent accessibilit...

journal_title：BMC bioinformatics

authors： Fan C,Liu D,Huang R,Chen Z,Deng L

更新日期：2016-01-11 00:00:00

abstract：BACKGROUND:Activation of naïve B lymphocytes by extracellular ligands, e.g. antigen, lipopolysaccharide (LPS) and CD40 ligand, induces a combination of common and ligand-specific phenotypic changes through complex signal transduction pathways. For example, although all three of these ligands induce proliferation, only ...

journal_title：BMC bioinformatics

authors： Lee JA,Sinkovits RS,Mock D,Rab EL,Cai J,Yang P,Saunders B,Hsueh RC,Choi S,Subramaniam S,Scheuermann RH,Alliance for Cellular Signaling.

更新日期：2006-05-02 00:00:00

abstract：BACKGROUND:Ontologies are widely used to represent knowledge in biomedicine. Systematic approaches for detecting errors and disagreements are needed for large ontologies with hundreds or thousands of terms and semantic relationships. A recent approach of defining terms using logical definitions is now increasingly bein...

journal_title：BMC bioinformatics

authors： Köhler S,Bauer S,Mungall CJ,Carletti G,Smith CL,Schofield P,Gkoutos GV,Robinson PN

更新日期：2011-10-27 00:00:00

abstract：BACKGROUND:This paper presents a novel approach for Generative Anatomy Modeling Language (GAML). This approach automatically detects the geometric partitions in 3D anatomy that in turn speeds up integrated non-linear optimization model in GAML for 3D anatomy modeling with constraints (e.g. joints). This integrated non-...

journal_title：BMC bioinformatics

authors： Demirel D,Cetinsaya B,Halic T,Kockara S,Ahmadi S

更新日期：2019-03-14 00:00:00

abstract：BACKGROUND:Enzyme active sites can be connected to the exterior environment by one or more channels passing through the protein. Despite our current knowledge of enzyme structure and function, surprisingly little is known about how often channels are present or about any structural features such channels may have in co...

journal_title：BMC bioinformatics

authors： Pravda L,Berka K,Svobodová Vařeková R,Sehnal D,Banáš P,Laskowski RA,Koča J,Otyepka M

更新日期：2014-11-18 00:00:00

abstract：BACKGROUND:Genome-wide expression quantitative trait loci (eQTL) studies have emerged as a powerful tool to understand the genetic basis of gene expression and complex traits. The traditional eQTL methods focus on testing the associations between individual single-nucleotide polymorphisms (SNPs) and gene expression tra...

journal_title：BMC bioinformatics

authors： Cheng W,Shi Y,Zhang X,Wang W

更新日期：2015-01-16 00:00:00

abstract：BACKGROUND:Understanding the community structure of microbes is typically accomplished by sequencing 16S ribosomal RNA (16S rRNA) genes. These community data can be represented by constructing a phylogenetic tree and comparing it with other samples using statistical methods. However, owing to high computational complex...

journal_title：BMC bioinformatics

authors： Mori H,Maruyama F,Kurokawa K

更新日期：2010-06-18 00:00:00

abstract：BACKGROUND:Complex networks are studied across many fields of science and are particularly important to understand biological processes. Motifs in networks are small connected sub-graphs that occur significantly in higher frequencies than in random networks. They have recently gathered much attention as a useful concep...

journal_title：BMC bioinformatics

authors： Kashani ZR,Ahrabian H,Elahi E,Nowzari-Dalini A,Ansari ES,Asadi S,Mohammadi S,Schreiber F,Masoudi-Nejad A

更新日期：2009-10-04 00:00:00

abstract：BACKGROUND:The identification of a consensus RNA motif often consists in finding a conserved secondary structure with minimum free energy in an ensemble of aligned sequences. However, an alignment is often difficult to obtain without prior structural information. Thus the need for tools to automate this process. RESUL...

journal_title：BMC bioinformatics

authors： Anwar M,Nguyen T,Turcotte M

更新日期：2006-05-05 00:00:00

abstract：BACKGROUND:Non-coding RNAs gain more attention as their diverse roles in many cellular processes are discovered. At the same time, the need for efficient computational prediction of ncRNAs increases with the pace of sequencing technology. Existing tools are based on various approaches and techniques, but none of them p...

journal_title：BMC bioinformatics

authors： Raasch P,Schmitz U,Patenge N,Vera J,Kreikemeyer B,Wolkenhauer O

更新日期：2010-09-29 00:00:00

abstract：BACKGROUND:In binary high-throughput screening projects where the goal is the identification of low-frequency events, beyond the obvious issue of efficiency, false positives and false negatives are a major concern. Pooling constitutes a natural solution: it reduces the number of tests, while providing critical duplicat...

journal_title：BMC bioinformatics

authors： Thierry-Mieg N

更新日期：2006-01-19 00:00:00

abstract：BACKGROUND:The PathoLogic program constructs Pathway/Genome databases by using a genome's annotation to predict the set of metabolic pathways present in an organism. PathoLogic determines the set of reactions composing those pathways from the enzymes annotated in the organism's genome. Most annotation efforts fail to a...

journal_title：BMC bioinformatics

authors： Green ML,Karp PD

更新日期：2004-06-09 00:00:00

abstract：BACKGROUND:One of the major challenges in biology is the correct identification of promoter regions. Computational methods based on motif searching have been the traditional approach taken. Recent studies have shown that DNA structural properties, such as curvature, stacking energy, and stress-induced duplex destabiliz...

journal_title：BMC bioinformatics

authors： Bland C,Newsome AS,Markovets AA

更新日期：2010-10-07 00:00:00

abstract：BACKGROUND:Protein sequence profile-profile alignment is an important approach to recognizing remote homologs and generating accurate pairwise alignments. It plays an important role in protein sequence database search, protein structure prediction, protein function prediction, and phylogenetic analysis. RESULTS:In thi...

journal_title：BMC bioinformatics

authors： Deng X,Cheng J

更新日期：2014-07-25 00:00:00