Abstract:
:Our ability to detect differentially expressed genes in a microarray experiment can be hampered when the number of biological samples of interest is limited. In this situation, we propose the use of information from self-self hybridizations to acuminate our inference of differential expression. A unified modelling strategy is developed to allow better estimation of the error variance. This principle is similar to the use of a pooled variance estimate in the two-sample t-test. The results from real dataset examples suggest that we can detect more genes that are differentially expressed in the combined models. Our simulation study provides evidence that this method increases sensitivity compared to using the information from comparative hybridizations alone, given the same control for false discovery rate. The largest increase in sensitivity occurs when the amount of information in the comparative hybridization is limited.
journal_name
Comput Biol Chemjournal_title
Computational biology and chemistryauthors
Gusnanto A,Tom B,Burns P,Macaulay I,Thijssen-Timmer DC,Tijssen MR,Langford C,Watkins N,Ouwehand W,Berzuini C,Dudbridge Fdoi
10.1016/j.compbiolchem.2007.03.005subject
Has Abstractpub_date
2007-06-01 00:00:00pages
178-85issue
3eissn
1476-9271issn
1476-928Xpii
S1476-9271(07)00053-9journal_volume
31pub_type
杂志文章abstract::Secondary structure motifs in nucleic acid probes generally impair intended hybridization reactions and so efforts to predict and avoid such structures are commonly employed in probe design schemes. Another key facet of probe design that has received much less attention, however, is that secondary structure at targete...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2005.09.002
更新日期:2005-12-01 00:00:00
abstract::A CIS (common insertion site) indicates a genome region that is hit more frequently by retroviral insertions than expected by chance. Such a region is strongly related to cancer gene loci, which leads to the detection of cancer genes. An algorithm for detecting CISs should satisfy the following: (1) it does not requir...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2014.03.001
更新日期:2014-08-01 00:00:00
abstract::We present the mechanism of interaction of Wnt network module, which is responsible for periodic somitogenesis, with p53 regulatory network, which is one of the main regulators of various cellular functions, and switching of various oscillating states by investigating p53-Wnt model. The variation in Nutlin concentrati...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2015.07.014
更新日期:2015-12-01 00:00:00
abstract::Human histone deacetylase 6 (HDAC6) has been shown to play a major role in oncogenic cell transformation via deacetylation of α-tubulin, making it a viable target of anticancer drug design and development. The crystal structure of HDAC6 catalytic domain 2 has been recently made available, providing avenues for structu...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2018.05.004
更新日期:2018-08-01 00:00:00
abstract::Interleukin-1β is a drug target in rheumatoid arthritis and several auto-immune disorders. In this study, a set of 48 compounds with the determined IC50 values were used for QSAR analysis by MOE. The QSAR model was developed by using training set of 41 compounds, based on 12 unique descriptors. Model was validated by ...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2015.06.004
更新日期:2015-10-01 00:00:00
abstract::The electrostatic (ES) energy of each residue was for the first time quantitatively evaluated in a flavin mononucleotide binding protein (FBP). A residue electrostatic energy (RES) was obtained as the sum of the ES energies between atoms in each residue and all other atoms in the FBP dimer using atomic coordinates obt...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2018.01.001
更新日期:2018-02-01 00:00:00
abstract::Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disorder, and its pathogenesis in males and in cases without accompanying lupus nephritis (LN-) is not fully understood. In this study, we identified 90 (82 up- and 8 downregulated) differentially expressed genes (DEGs) common to female LN-, female LN+ a...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2019.107135
更新日期:2019-12-01 00:00:00
abstract::The growth and spread of drug resistance in bacteria have been well established in both mankind and beasts and thus is a serious public health concern. Due to the increasing problem of drug resistance, control of infectious diseases like diarrhea, pneumonia etc. is becoming more difficult. Hence, it is crucial to unde...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2015.07.011
更新日期:2015-10-01 00:00:00
abstract::In this paper, a method for single individual haplotype (SIH) reconstruction using Asexual reproduction optimization (ARO) is proposed. Haplotypes, as a set of genetic variations in each chromosome, contain vital information such as the relationship between human genome and diseases. Finding haplotypes in diploid orga...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2017.12.005
更新日期:2018-02-01 00:00:00
abstract::Diabetes mellitus is clinically characterized by hyperglycemia. Though many studies have been done to understand the mechanism of Type 2 Diabetes (T2D), however, the complete network of diabetes and its associated disorders through polygenic involvement is still under debate. The present study designed to re-analyze p...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2019.01.010
更新日期:2019-04-01 00:00:00
abstract::Programmed cell death or apoptosis plays a vital physiological role in the development and homeostasis. Any discrepancy in apoptosis may trigger testicular and neurodegenerative diseases, ischemic damage, autoimmune disorders and many types of cancer. Tcte3 (T-complex testis expressed 3) is an accessory component of a...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2014.10.005
更新日期:2014-12-01 00:00:00
abstract::The metabolic rearrangements occurring in cancer cells can be effectively investigated with a Systems Biology approach supported by metabolic network modeling. We here present tissue-specific constraint-based core models for three different types of tumors (liver, breast and lung) that serve this purpose. The core mod...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2016.03.002
更新日期:2016-06-01 00:00:00
abstract::Drug-target interaction (DTI) prediction is a challenging step in further drug repositioning, drug discovery and drug design. The advent of high-throughput technologies brings convenience to the development of DTI prediction methods. With the generation of a high number of data sets, many mathematical models and compu...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2017.03.011
更新日期:2017-08-01 00:00:00
abstract::The potential of using sole respirometric CO2 labeling measurement for 13C metabolic flux analysis was investigated by metabolic simulations. For this purpose a model was created, considering all CO2 forming and consuming reactions in the central catabolic and anabolic pathways. To facilitate the interpretation of the...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2005.02.005
更新日期:2005-04-01 00:00:00
abstract::Prefoldin is a molecular chaperone and acts as a nano-actuator in cargo carriage and drug delivery for disease treatment. Investigating the mechanical properties of nano-actuator helps predict its behavior and measure its performance under various environmental conditions, like external forces that are applied. Accord...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2019.107133
更新日期:2019-12-01 00:00:00
abstract::The DNA binding protein, TDP43 is a major protein involved in amyotrophic lateral sclerosis and other neurological disorders such as frontotemporal dementia, Alzheimer disease, etc. In the present study, we have designed possible siRNAs for the glycine rich region of tardbp mutants causing ALS disorder based on a syst...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2016.01.001
更新日期:2016-04-01 00:00:00
abstract::The concept of chaos being radically different from statistical randomness is introduced into chemometrics research. The chaotic system that is deterministic with underlying patterns and inherent ability in searching the space of interest has been employed to improve the performance of chemometric algorithms. In this ...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/s1476-9271(02)00083-x
更新日期:2003-07-01 00:00:00
abstract::Cell type identification from an unknown sample can often be done by comparing its gene expression profile against a gene expression database containing profiles of a large number of cell-types. This type of compendium-based cell-type identification strategy is particularly successful for human and mouse samples becau...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2018.10.003
更新日期:2018-12-01 00:00:00
abstract::Recent advances in high-throughput genome sequencing technologies have enabled the systematic study of various genomes by making whole genome sequencing affordable. Modern sequencers generate a huge number of small sequence fragments called reads, where the read length and the per-base sequencing cost depend on the te...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2017.03.016
更新日期:2017-08-01 00:00:00
abstract::Protein-ligand docking is an essential process that has accelerated drug discovery. How to accurately and effectively optimize the predominant position and orientation of ligands in the binding pocket of a target protein is a major challenge. This paper proposed a novel ligand binding pose search method called FWAVina...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2020.107363
更新日期:2020-10-01 00:00:00
abstract::2-phenyl-benzotriazole xenobiotic compounds (PBTA-4, PBTA-6, PBTA-7 and PBTA-8) that were previously isolated and identified in waters of the Yodo river, in Japan (Nukaya et al., 2001; Ohe et al., 2004; Watanabe et al., 2001) were characterized as powerful pro-mutagens. In order to predict the activation mechanism of ...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2018.04.004
更新日期:2018-06-01 00:00:00
abstract::Feature selection techniques have been used as the workhorse in biomarker discovery applications for a long time. Surprisingly, the stability of feature selection with respect to sampling variations has long been under-considered. It is only until recently that this issue has received more and more attention. In this ...
journal_title:Computational biology and chemistry
pub_type: 杂志文章,评审
doi:10.1016/j.compbiolchem.2010.07.002
更新日期:2010-08-01 00:00:00
abstract::The resistances of matrix protein 2 (M2) protein inhibitors and neuraminidase inhibitors for influenza virus have attracted much attention and there is an urgent need for new drug. The antiviral drugs that selectively act on RNA polymerase are less prone to resistance and possess fewer side effects on the patient. The...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2020.107241
更新日期:2020-04-01 00:00:00
abstract::This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy. ...
journal_title:Computational biology and chemistry
pub_type: 撤回出版物
doi:10.1016/j.compbiolchem.2016.02.010
更新日期:2016-02-17 00:00:00
abstract::Klebsiella pneumoniae is declared as antibiotic resistant by WHO, with the critical urgency of developing novel antimicrobial therapeutics as drug resistance is the second most dangerous threat after terrorism. Besides many attempts still, there is no effective vaccine available against K. pneumoniae. By utilizing all...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2020.107380
更新日期:2020-12-01 00:00:00
abstract::With advances in genomics, transcriptomics, metabolomics and proteomics, and more expansive electronic clinical record monitoring, as well as advances in computation, we have entered the Big Data era in biomedical research. Data gathering is growing rapidly while only a small fraction of this data is converted to usef...
journal_title:Computational biology and chemistry
pub_type: 杂志文章,评审
doi:10.1016/j.compbiolchem.2015.08.005
更新日期:2015-12-01 00:00:00
abstract::Accurately and reliably identifying the actual number of clusters present with a dataset of gene expression profiles, when no additional information on cluster structure is available, is a problem addressed by few algorithms. GeneMCL transforms microarray analysis data into a graph consisting of nodes connected by edg...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2005.07.002
更新日期:2005-10-01 00:00:00
abstract:AIM:An integrated protocol of virtual screening involving molecular docking, pharmacophore probing, and simulations was established to identify small novel molecules targeting crucial residues involved in the variant apoE ε4 to mimic its behavior as apoE2 thereby eliminating the amyloid plaque accumulation and facilita...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2018.12.013
更新日期:2019-04-01 00:00:00
abstract::The single-stranded transfer DNA from the Ti plasmid of the soil bacteria Agrobacterium nonspecifically integrates into the plant chromosome and is inherited at subsequent cell divisions. How it is transferred across host membranes is unknown, but it is believed that VirE2 proteins form a membrane-spanning pore or cha...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2017.01.016
更新日期:2017-06-01 00:00:00
abstract::Polyphenol oxidases (PPOs)/tyrosinases are metal-dependent enzymes and known as important targets for melanogenesis. Although considerable attempts have been conducted to control the melanin-associated diseases by using various inhibitors. However, the exploration of the best anti-melanin inhibitor without side effect...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2017.02.012
更新日期:2017-06-01 00:00:00