Abstract：
:Using wavelet packet decomposition, the energy coefficients in the fifth level of viral protein sequences were achieved to predict interspecies transmission. Since avian-origin influenza viruses could have high sequence similarities with human-origin avian influenza virus and could have the phenotype of interspecies transmission, viral data should be filtered to prevent the misconduct of feature selection and false performance of predicting models. Considering the balance of data size, the empirical cut-off value 97% was used to screen avian-origin influenza virus with high sequence similarity. The excellent performances of cross validation show that the SVM model has the best capability of predicting transmission and evaluating the contribution of five amino acid factors. The robust model was finally used to evaluate the filtered data of avian-origin virus and the results confirmed that double check for ambiguous phenotype of avian-origin virus with high sequence similarity was necessary and part of them have the ability to across species barriers.
journal_name
Comput Biol Chemjournal_title
Computational biology and chemistryauthors
Qiang X,Kou Zdoi
10.1016/j.compbiolchem.2018.11.029subject
Has Abstractpub_date
2019-02-01 00:00:00pages
455-459eissn
1476-9271issn
1476-928Xpii
S1476-9271(18)30793-Xjournal_volume
78pub_type
杂志文章abstract：:Protein function prediction is a crucial task in the post-genomics era due to their diverse irreplaceable roles in a biological system. Traditional methods involved cost-intensive and time-consuming molecular biology techniques but they proved to be ineffective after the outburst of sequencing data through the advent ...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2019.107147
更新日期：2019-12-01 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
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journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2013.01.002
更新日期：2013-06-01 00:00:00
abstract：:Polymerase chain reaction (PCR) is an important diagnostic tool for the amplification of DNA. The PCR process can be treated as a problem in biochemical engineering. This study focuses on the development of a mathematical model of the polymerase chain reaction. The PCR process consists of three steps: denaturation of ...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2004.03.001
更新日期：2004-07-01 00:00:00
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 str...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2007.03.005
更新日期：2007-06-01 00:00:00
abstract：BACKGROUND:Breast cancer remains the most lethal type of cancer for women. A significant proportion of breast cancer cases are characterised by overexpression of the human epidermal growth factor receptor 2 protein (HER2). These cancers are commonly treated by Herceptin (Trastuzumab), but resistance to drug treatment f...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
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更新日期：2019-06-01 00:00:00
abstract：:Annular structures have been observed experimentally in aggregates of polyglutamine-containing proteins and other proteins associated with diseases of the brain. Here we report the observation of annular structures in molecular-level simulations of large systems of model polyglutamine peptides. A system of 24 polyglut...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2006.01.003
更新日期：2006-06-01 00:00:00
abstract：:The vibrational wavenumbers of optimized molecular structure of 1-phenylcyclopentane carboxylic acid (1PCPCA) molecule have been calculated by quantum chemical theory and compared with experimental results. The density functional theory (DFT) approach is followed using the method B3LYP and 6-311++G(d,p) basis set. Usi...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2019.05.011
更新日期：2019-10-01 00:00:00
abstract：:Janus kinase 1 and 3 are non-receptor protein tyrosine kinases, involved in the regulation of various cytokines implicated in the pathogenesis of autoimmune and inflammatory disease conditions. Thus, they serve as therapeutic targets for the designing of multi-targeted agents for the treatment of inflammatory-mediated...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2018.07.009
更新日期：2018-10-01 00:00:00
abstract：:The eukaryotic chaperonin, CCT (Chaperonin Containing TCP1 or TriC-TCP-1 Ring Complex) has been subjected to physical and genetic analyses in S. cerevisiae which can be extrapolated to human CCT (hCCT), owing to its structural and functional similarities with yeast CCT (yCCT). Studies on hCCT and its interactome acqui...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2016.09.002
更新日期：2016-10-01 00:00:00
abstract：:Germline stem cells (GSCs) are known to transmit genetic information from parents to offspring. These GSCs can undergo reprogramming to transform themselves into pluripotent stem cells, called as Multipotent adult Germline stem cells (maGSCs). The mechanism of the reprogramming of GSCs to maGSCs is elusive. To investi...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2018.08.001
更新日期：2018-10-01 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：:Recoding events occur in competition with standard readout of the transcript, and are site-specific. Recoding is the reprogramming of mRNA translation by localized alterations in the standard translational rules. Frame-shifting is one class of recoding and defined as protein translations that start not at the first, b...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2009.04.002
更新日期：2009-06-01 00:00:00
abstract：:MADS-box family transcription factors play key roles in various developmental processes in plants. Here, we identified 108 MADS-box genes in the genome of chrysanthemum (Chrysanthemum nankingense). We classified these genes based on their phylogenetic relationships with MADS-box genes in Arabidopsis thaliana and lettu...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2020.107424
更新日期：2020-12-05 00:00:00
abstract：:The present study is focused on a series of newly synthesized 1-aryl-3-ethyl-3-methylsuccinimide derivatives, as potential anticonvulsants. The retention behavior of eleven succinimide derivatives was determined by using reversed phase high performance liquid chromatography (RP-HPLC) and reversed phase high performanc...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2019.107161
更新日期：2020-02-01 00:00:00
abstract：:A computational inestigation on the difference in colors of two plants 'Peony' and 'Morning glory' by the same pigment 'Peonidin' has been performed by means of absorption characteristics. Peonidin imparts purple color to the flowers in Peony and blue to that in Morning glory. TDDFT tool in Gaussian 09 software packag...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2018.07.015
更新日期：2018-10-01 00:00:00
abstract：:Triticum aestivum L. known as common wheat is one of the most important cereal crops feeding a large and growing population. Various environmental stress factors including drought, high salinity and heat etc. adversely affect wheat production in a significant manner. Dehydration-responsive element-binding (DREB1A) fac...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2016.07.008
更新日期：2016-10-01 00:00:00
abstract：BACKGROUND:Recent studies have indicated that microRNA (miRNA) may play an oncogenic or tumor suppressor role in human cancer. To study the regulatory role of miRNAs in tumorigenesis, an integrated platform has been set up to provide a user friendly interface for query. The main advantage of the present platform is tha...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2013.02.001
更新日期：2013-06-01 00:00:00
abstract：:Often the quantitative data coming from proteomics and metabolomics studies have irregular distribution with a spike. None of the wide used methods for human QTL mapping are applicable to such traits. Researchers have to reduce the sample, excluding the spike, and analyze only continuous measurements. In this study, w...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2011.11.004
更新日期：2012-02-01 00:00:00
abstract：:The shortest common supersequence (SCS) problem is a classical NP-hard problem, which is normally solved by heuristic algorithms. One important heuristic that is inspired by the process of chemical reactions in nature is the chemical reaction optimization (CRO) and its algorithm known as CRO_SCS. In this paper we prop...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2020.107327
更新日期：2020-10-01 00:00:00
abstract：:MicroRNAs (miRNAs) are small (19-25 base long), non-coding RNAs that regulate post-transcriptional gene expression by cleaving targeted mRNAs in several eukaryotes. The miRNAs play vital roles in multiple biological and metabolic processes, including developmental timing, signal transduction, cell maintenance and diff...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2017.08.005
更新日期：2017-10-01 00:00:00
abstract：:The identification of isatin sulfonamide as a potent small molecule inhibitor of caspase-3 had fuelled the synthesis and characterization of the numerous sulfonamide class of inhibitors to optimize for potency. Recent works that relied on the ligand-based approaches have successfully shown the regions of optimizations...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2017.08.006
更新日期：2017-12-01 00:00:00
abstract：:MicroRNAs (miRNAs) have been implicated in complex vertebrate developmental and pathological systems as a versatile class of molecules involved in the regulation of various biological processes and molecular pathways. To elucidate the role of miRNAs in human somatic cells, an understanding of the molecular framework r...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2009.09.003
更新日期：2009-12-01 00:00:00
abstract：:The induced pluripotent cells (iPSCs) are derived from somatic cells by reprogramming their genetic profiles. Such a process requires coordinated dynamic expression of hundreds of genes and proteins. As both deterministic and stochastic elements control the reprogramming process, it is not easy to have a way to reflec...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2011.05.002
更新日期：2011-08-10 00:00:00
abstract：:Successful prediction of protein domain boundaries provides valuable information not only for the computational structure prediction of multi-domain proteins but also for the experimental structure determination. In this work, a novel index at the profile level is presented, namely, the profile domain linker propensit...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2006.01.001
更新日期：2006-04-01 00:00:00
abstract：:Nicotinamidase is a key enzyme for the salvage pathway catalyzing the first step for the conversion of nicotinamide (NAm) to nicotinic acid (NA) required for the synthesis of Nicotinamide Adenine Dinucleotide (NAD+) in the subsequent steps. Leishmania protozoan parasites are NAD+ auxotrophs and need precursors (nicoti...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2019.107150
更新日期：2019-12-01 00:00:00
abstract：:Detection of protein complexes is very important to understand the principles of cellular organization and function. Recently, large protein-protein interactions (PPIs) networks have become available using high-throughput experimental techniques. These networks make it possible to develop computational methods for pro...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2015.07.012
更新日期：2015-10-01 00:00:00
abstract：:Many Traditional Chinese Medicines (TCMs) are effective to relieve complicated diseases such as type II diabetes mellitus (T2DM). In this work, molecular docking and network analysis were employed to elucidate the action mechanism of a medical composition which had clinical efficacy for T2DM. We found that multiple ac...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2011.07.003
更新日期：2011-10-12 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：:Ecology is said by many to suffer for want of a central theory, such as Newton's laws of motion provide for classical mechanics or Schroedinger's wave equation provides for quantum physics. From among a plurality of contending laws to govern ecosystem behavior, the principle of increasing ascendency shows some early p...
journal_title：Computational biology and chemistry
pub_type： 杂志文章,评审
doi：10.1016/s1476-9271(03)00050-1
更新日期：2003-12-01 00:00:00
