Abstract：
:We have developed a computational technique refereed to as complex phylogenetic profiling. Our approach combines logic analyses of gene phylogenetic profiles and phenotype data. Logic analysis of phylogenetic profiles identifies sets of proteins whose presence or absence follows certain logic relationships. Our approach identifies phenotype specific logic, i.e. it identifies sets of proteins simultaneously present or absent only in genomes with a given phenotype. For example, for most genomes expressing phenotype A, the presence of protein C presumes the presence of protein B, while for other genomes (not expressing phenotype A) the presence of protein C presumes the absence of protein B. Application of complex phylogenetic profiling to bacterial data and several well studied phenotypes reveals genotype-phenotype associations on the level of fundamental biochemical pathways.
journal_name
Comput Biol Chemjournal_title
Computational biology and chemistryauthors
Antonov AV,Mewes HWdoi
10.1016/j.compbiolchem.2008.07.003subject
Has Abstractpub_date
2008-12-01 00:00:00pages
412-6issue
6eissn
1476-9271issn
1476-928Xpii
S1476-9271(08)00083-2journal_volume
32pub_type
杂志文章abstract：:In this study, the dipeptidyl peptidase-IV (DPP-IV) inhibition activities of a series of novel aminomethyl-piperidones were investigated by molecular docking studies and modeled by quantitative structure-activity relationship (QSAR) methodology. Molecular docking studies were used to find the best conformations of the...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2016.08.003
更新日期：2016-10-01 00:00:00
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journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2015.11.006
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abstract：:Due to their lethal consequences and a relatively high probability of introduction of repair errors and mutations, single and double strand breaks are among the most important and dangerous DNA lesions. However, the mechanisms of their recognition and repair processes are only poorly known at present. This work define...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2005.12.001
更新日期：2006-04-01 00:00:00
abstract：:Genome-wide association analysis involved many single-nucleotide polymorphisms (SNPs) data is challenging mathematically and computationally. Hence, we propose the odds ratio-based discrete binary particle swarm optimization (OR-DBPSO) method that uses the OR as a new quantitative measure of disease risk among many SN...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2008.07.029
更新日期：2009-02-01 00:00:00
abstract：:The Protein Structure Prediction (PSP) problem comprises, among other issues, forecasting the three-dimensional native structure of proteins using only their primary structure information. Most computational studies in this area use synthetic data instead of real biological data. However, the closer to the real-world,...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2019.107192
更新日期：2020-02-01 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
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journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2017.10.007
更新日期：2017-12-01 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
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journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2016.09.003
更新日期：2016-12-01 00:00:00
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journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2003.12.002
更新日期：2004-02-01 00:00:00
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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
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journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2018.11.021
更新日期：2019-02-01 00:00:00
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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
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journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2010.12.005
更新日期：2011-02-01 00:00:00
abstract：:Accurate clustering of cells from single-cell RNA sequencing (scRNA-seq) data is an essential step for biological analysis such as putative cell type identification. However, scRNA-seq data has high dimension and high sparsity, which makes traditional clustering methods less effective to reflect the similarity between...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2020.107415
更新日期：2020-11-18 00:00:00
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journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2020.107407
更新日期：2020-11-05 00:00:00
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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：BACKGROUND:Associating protein complexes to human inherited diseases is critical for better understanding of biological processes and functional mechanisms of the disease. Many protein complexes have been identified and functionally annotated by computational and purification methods so far, however, the particular rol...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2017.04.007
更新日期：2017-08-01 00:00:00
abstract：:The P-type ATPases (P-ATPases) are present in all living cells where they mediate ion transport across membranes on the expense of ATP hydrolysis. Different ions which are transported by these pumps are protons like calcium, sodium, potassium, and heavy metals such as manganese, iron, copper, and zinc. Maintenance of ...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2017.04.006
更新日期：2017-06-01 00:00:00
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journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2008.03.015
更新日期：2008-08-01 00:00:00
abstract：:Caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the COVID-19 pandemic is ongoing, with no proven safe and effective vaccine to date. Further, effective therapeutic agents for COVID-19 are limited, and as a result, the identification of potential small molecule antiviral drugs is of particul...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2020.107408
更新日期：2020-12-01 00:00:00
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journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2018.09.009
更新日期：2018-12-01 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：: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：: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 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：:Nodulation is one of the very important processes of legume plants as it is the initiating event of fixing nitrogen. Although ethylene has essential role in normal plant metabolism but it has also negative impact on plants particularly in nodule formation in legume plants. It is also produced due to a variety of bioti...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2017.02.005
更新日期：2017-06-01 00:00:00
abstract：BACKGROUND:The current availability of public protein-protein interaction (PPI) databases which are usually modelled as PPI networks has led to the rapid development of protein function prediction approaches. The existing network-based prediction approaches mainly focus on the topological similarities between immediate...
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：:Adenosine deaminase (ADA) is an enzyme involved in purine metabolism. ADA converts adenosine to inosine and liberates ammonia. Because of their critical role in the differentiation and maturation of cells, the regulation of ADA activity is considered as a potential therapeutic approach to prevent malignant and inflamm...
journal_title：Computational biology and chemistry
pub_type： 杂志文章
doi：10.1016/j.compbiolchem.2016.08.005
更新日期：2016-10-01 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
