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 due to the inherent complexity of the metabolic and regulatory networks, but also to the lack of appropriate modelling and optimization tools. To this end, Evolutionary Algorithms (EAs) have been proposed for in silico metabolic engineering, for example, to identify sets of gene deletions towards maximization of a desired physiological objective function. In this approach, each mutant strain is evaluated by resorting to the simulation of its phenotype using the Flux-Balance Analysis (FBA) approach, together with the premise that microorganisms have maximized their growth along natural evolution. RESULTS:This work reports on improved EAs, as well as novel Simulated Annealing (SA) algorithms to address the task of in silico metabolic engineering. Both approaches use a variable size set-based representation, thereby allowing the automatic finding of the best number of gene deletions necessary for achieving a given productivity goal. The work presents extensive computational experiments, involving four case studies that consider the production of succinic and lactic acid as the targets, by using S. cerevisiae and E. coli as model organisms. The proposed algorithms are able to reach optimal/near-optimal solutions regarding the production of the desired compounds and presenting low variability among the several runs. CONCLUSION:The results show that the proposed SA and EA both perform well in the optimization task. A comparison between them is favourable to the SA in terms of consistency in obtaining optimal solutions and faster convergence. In both cases, the use of variable size representations allows the automatic discovery of the approximate number of gene deletions, without compromising the optimality of the solutions.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Rocha M,Maia P,Mendes R,Pinto JP,Ferreira EC,Nielsen J,Patil KR,Rocha Idoi
10.1186/1471-2105-9-499subject
Has Abstractpub_date
2008-11-27 00:00:00pages
499issn
1471-2105pii
1471-2105-9-499journal_volume
9pub_type
杂志文章abstract:BACKGROUND:Enrichment analysis is a popular approach to identify pathways or sets of genes which are significantly enriched in the context of differentially expressed genes. The traditional gene set enrichment approach considers a pathway as a simple gene list disregarding any knowledge of gene or protein interactions....
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-015-0751-5
更新日期:2015-10-22 00:00:00
abstract:BACKGROUND:High throughput DNA/RNA sequencing has revolutionized biological and clinical research. Sequencing is widely used, and generates very large amounts of data, mainly due to reduced cost and advanced technologies. Quickly assessing the quality of giga-to-tera base levels of sequencing data has become a routine ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3015-y
更新日期:2019-08-15 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
pub_type: 杂志文章
doi:10.1186/s12859-015-0773-z
更新日期:2015-10-23 00:00:00
abstract:BACKGROUND:The incorporation of biological knowledge can enhance the analysis of biomedical data. We present a novel method that uses a proteomic knowledge base to enhance the performance of a rule-learning algorithm in identifying putative biomarkers of disease from high-dimensional proteomic mass spectral data. In pa...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-S9-S16
更新日期:2009-09-17 00:00:00
abstract:BACKGROUND:Hierarchical Multi-Label Classification is a classification task where the classes to be predicted are hierarchically organized. Each instance can be assigned to classes belonging to more than one path in the hierarchy. This scenario is typically found in protein function prediction, considering that each pr...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-1232-1
更新日期:2016-09-15 00:00:00
abstract:BACKGROUND:Inflammation is a core element of many different, systemic and chronic diseases that usually involve an important autoimmune component. The clinical phase of inflammatory diseases is often the culmination of a long series of pathologic events that started years before. The systemic characteristics and relate...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2413-x
更新日期:2018-11-30 00:00:00
abstract:BACKGROUND:We present a model for tagging gene and protein mentions from text using the probabilistic sequence tagging framework of conditional random fields (CRFs). Conditional random fields model the probability P(t/o) of a tag sequence given an observation sequence directly, and have previously been employed success...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-6-S1-S6
更新日期:2005-01-01 00:00:00
abstract:BACKGROUND:Orthologs inference is the starting point of most comparative genomics studies, and a plethora of methods have been designed in the last decade to address this challenging task. In this paper we focus on the problems of deciding consistency with a species tree (known or not) of a partial set of orthology/par...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-1267-3
更新日期:2016-11-11 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
pub_type: 杂志文章
doi:10.1186/1471-2105-8-S7-S20
更新日期:2007-11-01 00:00:00
abstract:BACKGROUND:Researchers involved in the annotation of large numbers of gene, clone or protein identifiers are usually required to perform a one-by-one conversion for each identifier. When the field of research is one such as microarray experiments, this number may be around 30,000. RESULTS:To help researchers map acces...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-9
更新日期:2007-01-10 00:00:00
abstract:BACKGROUND:The rate of protein structures being deposited in the Protein Data Bank surpasses the capacity to experimentally characterise them and therefore computational methods to analyse these structures have become increasingly important. Identifying the region of the protein most likely to be involved in function i...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-379
更新日期:2009-11-18 00:00:00
abstract:BACKGROUND:Peptidases are proteolytic enzymes responsible for fundamental cellular activities in all organisms. Apparently about 2-5% of the genes encode for peptidases, irrespectively of the organism source. The basic peptidase function is "protein digestion" and this can be potentially dangerous in living organisms w...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-8-S1-S3
更新日期:2007-03-08 00:00:00
abstract:BACKGROUND:Research related to cancer is vast, and continues in earnest in many directions. Due to the complexity of cancer, a better understanding of tumor growth dynamics can be gleaned from a dynamic computational model. We present a comprehensive, fully executable, spatial and temporal 3D computational model of the...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-1168-5
更新日期:2016-08-24 00:00:00
abstract:BACKGROUND:Genomes are subjected to rearrangements that change the orientation and ordering of genes during evolution. The most common rearrangements that occur in uni-chromosomal genomes are inversions (or reversals) to adapt to the changing environment. Since genome rearrangements are rarer than point mutations, gene...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3293-4
更新日期:2019-12-27 00:00:00
abstract:BACKGROUND:While researchers have utilized versions of the Affymetrix human GeneChip for the assessment of expression patterns in non human primate (NHP) samples, there has been no comprehensive sequence analysis study undertaken to demonstrate that the probe sequences designed to detect human transcripts are reliably ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-5-165
更新日期:2004-10-26 00:00:00
abstract:BACKGROUND:Urokinase, its receptor and the integrins are functionally associated and involved in regulation of cell signaling, migration, adhesion and proliferation. No structural information is available on this potential multimolecular complex. However, the tri-dimensional structure of urokinase, urokinase receptor a...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-S2-S8
更新日期:2008-03-26 00:00:00
abstract:BACKGROUND:Network enrichment analysis is a powerful method, which allows to integrate gene enrichment analysis with the information on relationships between genes that is provided by gene networks. Existing tests for network enrichment analysis deal only with undirected networks, they can be computationally slow and a...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-016-1203-6
更新日期:2016-09-05 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
pub_type: 杂志文章
doi:10.1186/s12859-015-0781-z
更新日期:2015-10-30 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
pub_type: 杂志文章
doi:10.1186/1471-2105-12-421
更新日期:2011-10-27 00:00:00
abstract:BACKGROUND:Microsatellite (simple sequence repeat - SSR) and single nucleotide polymorphism (SNP) markers are two types of important genetic markers useful in genetic mapping and genotyping. Often, large-scale genomic research projects require high-throughput computer-assisted primer design. Numerous such web-based or ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-253
更新日期:2008-05-29 00:00:00
abstract:UNLABELLED: BACKGROUND:Acquiring and exploring whole genome sequence information for a species under investigation is now a routine experimental approach. On most genome browsers, typically, only the DNA sequence, EST support, motif search results, and GO annotations are displayed. However, for many species, a growing...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-447
更新日期:2011-11-15 00:00:00
abstract:BACKGROUND:The identification of genes responsible for human inherited diseases is one of the most challenging tasks in human genetics. Recent studies based on phenotype similarity and gene proximity have demonstrated great success in prioritizing candidate genes for human diseases. However, most of these methods rely ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-S1-S11
更新日期:2011-02-15 00:00:00
abstract:BACKGROUND:To further our understanding of immunopeptidomics, improved tools are needed to identify peptides presented by major histocompatibility complex class I (MHC-I). Many existing tools are limited by their reliance upon chemical affinity data, which is less biologically relevant than sampling by mass spectrometr...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-018-2561-z
更新日期:2019-01-05 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
pub_type: 杂志文章
doi:10.1186/1471-2105-6-256
更新日期:2005-10-14 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
pub_type: 杂志文章
doi:10.1186/1471-2105-7-510
更新日期:2006-11-21 00:00:00
abstract:BACKGROUND:Metabolomics experiments using Mass Spectrometry (MS) technology measure the mass to charge ratio (m/z) and intensity of ionised molecules in crude extracts of complex biological samples to generate high dimensional metabolite 'fingerprint' or metabolite 'profile' data. High resolution MS instruments perform...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-10-227
更新日期:2009-07-21 00:00:00
abstract:BACKGROUND:Substitution matrices are key parameters for the alignment of two protein sequences, and consequently for most comparative genomics studies. The composition of biological sequences can vary importantly between species and groups of species, and classical matrices such as those in the BLOSUM series fail to ac...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-12-457
更新日期:2011-11-24 00:00:00
abstract:BACKGROUND:Observed levels of gene expression strongly depend on both activity of DNA binding transcription factors (TFs) and chromatin state through different histone modifications (HMs). In order to recover the functional relationship between local chromatin state, TF binding and observed levels of gene expression, r...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-019-3331-2
更新日期:2020-01-02 00:00:00
abstract:BACKGROUND:Our knowledge of global protein-protein interaction (PPI) networks in complex organisms such as humans is hindered by technical limitations of current methods. RESULTS:On the basis of short co-occurring polypeptide regions, we developed a tool called MP-PIPE capable of predicting a global human PPI network ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/s12859-014-0383-1
更新日期:2014-12-10 00:00:00
abstract:BACKGROUND:Mass spectrometry is an essential analytical technique for high-throughput analysis in proteomics and metabolomics. The development of new separation techniques, precise mass analyzers and experimental protocols is a very active field of research. This leads to more complex experimental setups yielding ever ...
journal_title:BMC bioinformatics
pub_type: 杂志文章
doi:10.1186/1471-2105-9-163
更新日期:2008-03-26 00:00:00