A multiobjective approach to the genetic code adaptability problem.

abstract：BACKGROUND:Protein sequence motifs are by definition short fragments of conserved amino acids, often associated with a specific function. Accordingly protein sequence profiles derived from multiple sequence alignments provide an alternative description of functional motifs characterizing families of related sequences. ...

journal_title：BMC bioinformatics

authors： Hummel J,Keshvari N,Weckwerth W,Selbig J

更新日期：2005-06-29 00:00:00

abstract：BACKGROUND:Supervised learning and many stochastic methods for predicting protein-protein interactions require both negative and positive interactions in the training data set. Unlike positive interactions, negative interactions cannot be readily obtained from interaction data, so these must be generated. In protein-pr...

journal_title：BMC bioinformatics

authors： Kim J,Huang DS,Han K

更新日期：2009-01-30 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:Protein-structure alignment is a fundamental tool to study protein function, evolution and model building. In the last decade several methods for structure alignment were introduced, but most of them ignore that structurally similar proteins can share the same spatial arrangement of secondary structure eleme...

journal_title：BMC bioinformatics

authors： Kolbeck B,May P,Schmidt-Goenner T,Steinke T,Knapp EW

更新日期：2006-11-21 00:00:00

abstract：BACKGROUND:Continuous enzyme kinetic assays are often used in high-throughput applications, as they allow rapid acquisition of large amounts of kinetic data and increased confidence compared to discontinuous assays. However, data analysis is often rate-limiting in high-throughput enzyme assays, as manual inspection and...

journal_title：BMC bioinformatics

authors： Olp MD,Kalous KS,Smith BC

更新日期：2020-05-14 00:00:00

abstract：BACKGROUND:For the development of genome assembly tools, some comprehensive and efficiently computable validation measures are required to assess the quality of the assembly. The mostly used N50 measure summarizes the assembly results by the length of the scaffold (or contig) overlapping the midpoint of the length-orde...

journal_title：BMC bioinformatics

authors： Mäkinen V,Salmela L,Ylinen J

更新日期：2012-10-03 00:00:00

abstract：BACKGROUND:Microarray technology allows the analysis of genomic aberrations at an ever increasing resolution, making functional interpretation of these vast amounts of data the main bottleneck in routine implementation of high resolution array platforms, and emphasising the need for a centralised and easy to use CNV da...

journal_title：BMC bioinformatics

authors： Vandeweyer G,Reyniers E,Wuyts W,Rooms L,Kooy RF

更新日期：2011-01-05 00:00:00

abstract：BACKGROUND:High-throughput experiments, such as with DNA microarrays, typically result in hundreds of genes potentially relevant to the process under study, rendering the interpretation of these experiments problematic. Here, we propose and evaluate an approach to find functional associations between large numbers of g...

journal_title：BMC bioinformatics

authors： Jelier R,Jenster G,Dorssers LC,Wouters BJ,Hendriksen PJ,Mons B,Delwel R,Kors JA

更新日期：2007-01-18 00:00:00

abstract：BACKGROUND:The imputation of genotypes increases the power of genome-wide association studies. However, the imputation quality should be assessed in each particular case. Nevertheless, not all imputation softwares control the error of output, e.g., the last release of fastPHASE program (1.4.8) lacks such an option. In ...

journal_title：BMC bioinformatics

authors： Khvorykh GV,Khrunin AV

更新日期：2020-07-24 00:00:00

abstract：BACKGROUND:X-converting enzyme (XCE) involved in nervous control of respiration, is a member of the M13 family of zinc peptidases, for which no natural substrate has been identified yet. In contrast, it's well characterized homologue endothelin-converting enzyme-1 (ECE-1) showed broad substrate specificity and acts as ...

journal_title：BMC bioinformatics

authors： Ul-Haq Z,Iqbal S,Moin ST

更新日期：2012-11-01 00:00:00

abstract：:Following last year's computational vaccinology workshop in Shanghai, China, the third ISV Pre-conference Computational Vaccinology Workshop (ICoVax 2013) was held in Barcelona, Spain. ICoVax 2013 provided an international platform for the attendees to showcase their research and discuss problems and solutions in the ...

journal_title：BMC bioinformatics

authors： De Groot AS,De Groot P,He Y

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:Patient records contain valuable information regarding explanation of diagnosis, progression of disease, prescription and/or effectiveness of treatment, and more. Automatic recognition of clinically important concepts and the identification of relationships between those concepts in patient records are preli...

journal_title：BMC bioinformatics

authors： Islamaj Doğan R,Névéol A,Lu Z

更新日期：2011-06-09 00:00:00

abstract：BACKGROUND:Accurate somatic mutation-calling is essential for insightful mutation analyses in cancer studies. Several mutation-callers are publicly available and more are likely to appear. Nonetheless, mutation-calling is still challenging and there is unlikely to be one established caller that systematically outperfor...

journal_title：BMC bioinformatics

authors： Kim SY,Jacob L,Speed TP

更新日期：2014-05-21 00:00:00

abstract：BACKGROUND:Metabolome analysis with GC/MS has meanwhile been established as one of the "omics" techniques. Compound identification is done by comparison of the MS data with compound libraries. Mass spectral libraries in the field of metabolomics ought to connect the relevant mass traces of the metabolites to other rele...

journal_title：BMC bioinformatics

authors： Thielen B,Heinen S,Schomburg D

更新日期：2009-07-22 00:00:00

abstract：BACKGROUND:T-cells are key players in regulating a specific immune response. Activation of cytotoxic T-cells requires recognition of specific peptides bound to Major Histocompatibility Complex (MHC) class I molecules. MHC-peptide complexes are potential tools for diagnosis and treatment of pathogens and cancer, as well...

journal_title：BMC bioinformatics

authors： Dönnes P,Elofsson A

更新日期：2002-09-11 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:Phylogenetic profiles record the occurrence of homologs of genes across fully sequenced organisms. Proteins with similar profiles are typically components of protein complexes or metabolic pathways. Various existing methods measure similarity between two profiles and, hence, the likelihood that the two prote...

journal_title：BMC bioinformatics

authors： Cokus S,Mizutani S,Pellegrini M

更新日期：2007-05-22 00:00:00

abstract：BACKGROUND:Estimation of individual ancestry from genetic data is useful for the analysis of disease association studies, understanding human population history and interpreting personal genomic variation. New, computationally efficient methods are needed for ancestry inference that can effectively utilize existing inf...

journal_title：BMC bioinformatics

authors： Bansal V,Libiger O

更新日期：2015-01-16 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:Quadruplexes are specific structure motifs occurring, e.g., in telomeres and transcriptional regulatory regions. Recent discoveries confirmed their importance in biomedicine and led to an intensified examination of their properties. So far, the study of these motifs has focused mainly on the sequence and the...

journal_title：BMC bioinformatics

authors： Zok T,Popenda M,Szachniuk M

更新日期：2020-01-31 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:Numerous tools have been developed to predict the fitness effects (i.e., neutral, deleterious, or beneficial) of genetic variants on corresponding proteins. However, prediction in terms of whether a variant causes the variant bearing protein to lose the original function or gain new function is also needed f...

journal_title：BMC bioinformatics

authors： Liu M,Watson LT,Zhang L

更新日期：2015-10-30 00:00:00

abstract：BACKGROUND:With the growing availability of full-text articles online, scientists and other consumers of the life sciences literature now have the ability to go beyond searching bibliographic records (title, abstract, metadata) to directly access full-text content. Motivated by this emerging trend, I posed the followin...

journal_title：BMC bioinformatics

authors： Lin J

更新日期：2009-02-03 00:00:00

abstract：BACKGROUND:The abundant data available for protein interaction networks have not yet been fully understood. New types of analyses are needed to reveal organizational principles of these networks to investigate the details of functional and regulatory clusters of proteins. RESULTS:In the present work, individual cluste...

journal_title：BMC bioinformatics

authors： Sen TZ,Kloczkowski A,Jernigan RL

更新日期：2006-07-24 00:00:00

abstract：BACKGROUND:Adapter trimming is a prerequisite step for analyzing next-generation sequencing (NGS) data when the reads are longer than the target DNA/RNA fragments. Although typically used in small RNA sequencing, adapter trimming is also used widely in other applications, such as genome DNA sequencing and transcriptome...

journal_title：BMC bioinformatics

authors： Jiang H,Lei R,Ding SW,Zhu S

更新日期：2014-06-12 00:00:00

abstract：BACKGROUND:Pseudouridylation is the most prevalent type of posttranscriptional modification in various stable RNAs of all organisms, which significantly affects many cellular processes that are regulated by RNA. Thus, accurate identification of pseudouridine (Ψ) sites in RNA will be of great benefit for understanding t...

journal_title：BMC bioinformatics

authors： He J,Fang T,Zhang Z,Huang B,Zhu X,Xiong Y

更新日期：2018-08-29 00:00:00

abstract：BACKGROUND:Protein-protein interaction (PPI) plays essential roles in cellular functions. The cost, time and other limitations associated with the current experimental methods have motivated the development of computational methods for predicting PPIs. As protein interactions generally occur via domains instead of the ...

journal_title：BMC bioinformatics

authors： González AJ,Liao L

更新日期：2010-10-29 00:00:00

abstract：BACKGROUND:We introduce a novel method, called PuFFIN, that takes advantage of paired-end short reads to build genome-wide nucleosome maps with larger numbers of detected nucleosomes and higher accuracy than existing tools. In contrast to other approaches that require users to optimize several parameters according to t...

journal_title：BMC bioinformatics

authors： Polishko A,Bunnik EM,Le Roch KG,Lonardi S

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:Transposable elements (TEs) are DNA sequences able to mobilize themselves and to increase their copy-number in the host genome. In the past, they have been considered mainly selfish DNA without evident functions. Nevertheless, currently they are believed to have been extensively involved in the evolution of ...

journal_title：BMC bioinformatics

authors： Spirito G,Mangoni D,Sanges R,Gustincich S

更新日期：2019-11-22 00:00:00

abstract：BACKGROUND:Dihydrouridine (D) is a modified base found in conserved positions in the D-loop of tRNA in Bacteria, Eukaryota, and some Archaea. Despite the abundant occurrence of D, little is known about its biochemical roles in mediating tRNA function. It is assumed that D may destabilize the structure of tRNA and thus ...

journal_title：BMC bioinformatics

authors： Kasprzak JM,Czerwoniec A,Bujnicki JM

更新日期：2012-06-28 00:00:00