2016 International Conference on Bioinformatics and Systems Biology (BSB)最新文献_第4页

Monitoring deforestation using acoustic signals 利用声信号监测森林砍伐

2016 International Conference on Bioinformatics and Systems Biology (BSB) Pub Date : 2016-03-04 DOI: 10.1109/BSB.2016.7552133

Gajendra Sharma, Manish Kumar, S. Verma

引用次数: 0

In silico interaction studies of first dual inhibitor against BACE-1/GSK-3β 首个抗BACE-1/GSK-3β双抑制剂的硅相互作用研究

2016 International Conference on Bioinformatics and Systems Biology (BSB) Pub Date : 2016-03-04 DOI: 10.1109/BSB.2016.7552161

Akhil Kumar, Gaurava Srivastava, Ashok Sharma

引用次数: 0

Discovery of cancer linked biomarker genes through common subcluster mining 通过共同亚簇挖掘发现癌症相关生物标志物基因

2016 International Conference on Bioinformatics and Systems Biology (BSB) Pub Date : 2016-03-04 DOI: 10.1109/BSB.2016.7552153

Arnab Sadhu, B. Bhattacharyya

引用次数: 4

Glucose concentration varies logarithmically under both glycemic conditions in a computationally reconstructed human energy pool network (HEPNet) 在计算重建的人体能量池网络(HEPNet)中，葡萄糖浓度在两种血糖条件下呈对数变化。

2016 International Conference on Bioinformatics and Systems Biology (BSB) Pub Date : 2016-03-04 DOI: 10.1109/BSB.2016.7552162

A. Sengupta, P. Narad

{"title":"Glucose concentration varies logarithmically under both glycemic conditions in a computationally reconstructed human energy pool network (HEPNet)","authors":"A. Sengupta, P. Narad","doi":"10.1109/BSB.2016.7552162","DOIUrl":"https://doi.org/10.1109/BSB.2016.7552162","url":null,"abstract":"The developing method of network medicine offers a stage to investigate efficiently not only the molecular complexity of a certain disease but additionally recognizes the ailment modules and the interconnectivity of the pathways. Hyper and hypo glycemia are one of the major diseases faced today in the western world. The level of glucose in the blood is controlled by insulin and glucagon henceforth a homeostasis is maintained. To solve this problem we present a formulated hypothesis where the basis revolves around the central idea of energy conservation and the energy currencies in a cell. Further we reconstructed a Human Energy Pool Network (HEPNet) with 4 compartments, 173 metabolic reactions and 158 metabolites; analyzed and characterized from various resources under a range of conditions into a kinetic model backbone. Ordinary differential equations generated through the network inferred that the glucose concentration is dependent on several factors but varies as a logarithmic function. Time course simulations were carried out and flux balance analysis validated the findings that ATP flux is dependent on 7 reactions with glucose playing a major role referred to as the Glucose component which varies logarithmically in a flux based ordinary differential equation. This glucose component denotes the change of flux behavior in the hypoglycemic and hyperglycemic condition.","PeriodicalId":363820,"journal":{"name":"2016 International Conference on Bioinformatics and Systems Biology (BSB)","volume":"469 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"117009472","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification of human proteins vulnerable to multiple organisms 鉴定易受多种生物影响的人类蛋白质

2016 International Conference on Bioinformatics and Systems Biology (BSB) Pub Date : 2016-03-04 DOI: 10.1109/BSB.2016.7552164

S. Chatterjee, B. Sanjeev

{"title":"Identification of human proteins vulnerable to multiple organisms","authors":"S. Chatterjee, B. Sanjeev","doi":"10.1109/BSB.2016.7552164","DOIUrl":"https://doi.org/10.1109/BSB.2016.7552164","url":null,"abstract":"While most studies emphasize on certain aspects of Pathogen-Host Interactions (PHI), such as the preferential attachment of bacteria or virus to its human receptor homolog, studies have attempted to methodically classify interactions among pathogenic proteins and their host proteins. Here we have analyzed 182 pathogens from The Pathogen-Host Interaction Search Tool (PHISTO) [1] and could identify the proteins/protein coding genes that act on both virus and bacteria. Importantly there were few proteins viz. P53 (Tumor protein p53), NFKB1 (Nuclear factor of kappa light polypeptide gene enhancer in B-cells 1), GBLP (Guanine nucleotide-binding protein subunit beta-2-like-1), TOX4 (TOX high mobility group box family member 4), PDIA1 (Protein disulfide-isomerase precursor), MHY9 (Myosin 9), RAC1 (Ras-related C3 botulinum toxin substrate 1), CCAR2 (Cell cycle and apoptosis regulator protein 2) and ILF3 (Interleukin enhancer binding factor 3) that were more susceptible to both bacterial and viral pathogens. Identification of such important interacting proteins (IIPs) can elicit significant insights for better understanding the molecular mechanisms of such pathogens that interact with the human host.","PeriodicalId":363820,"journal":{"name":"2016 International Conference on Bioinformatics and Systems Biology (BSB)","volume":"27 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127975381","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome analysis of Rhizobium species using codon usage bias tools 利用密码子使用偏差工具对根瘤菌进行基因组分析

2016 International Conference on Bioinformatics and Systems Biology (BSB) Pub Date : 2016-03-04 DOI: 10.1109/BSB.2016.7552158

N. Rai, D. Mishra, Sanjeev Kumar, A. Rai, K. K. Chaturvedi, S. B. Lal, Anil Kumar, M. Farooqi, P. G. Majumdar, S. Archak

{"title":"Genome analysis of Rhizobium species using codon usage bias tools","authors":"N. Rai, D. Mishra, Sanjeev Kumar, A. Rai, K. K. Chaturvedi, S. B. Lal, Anil Kumar, M. Farooqi, P. G. Majumdar, S. Archak","doi":"10.1109/BSB.2016.7552158","DOIUrl":"https://doi.org/10.1109/BSB.2016.7552158","url":null,"abstract":"Bacteria from genus Rhizobium have ability to fix atmospheric nitrogen in symbiosis with leguminous plants resulting in formation of root nodules. They act as an alternate source of nitrogenous fertilizers. The study of codon usage patterns of Rhizobium species is gaining increasing attention over the times. In the present study three strains of Rhizobium namely Sinorhizobium meliloti 1021, Bradyrhizobium japonicum USDA110 and Rhizobium tropici CIAT899 whose complete genome sequence are available were retrieved from NCBI for the analysis of codon usage. The overall codon usage analysis showed that codons ending with G and C are preferred more in the rhizobium genome than codon ending with A and T. ENc plot revealed that compositional constraints along with translational selection are the major cause of codon usage bias. Correspondence analysis (COA) showed that the variation in codon usage is accounted mainly by the first two axes. From the Pearson correlation analysis significant correlation was identified among the first axis of COA and Codon adaptation index (CAI) and other factors of codon usage bias. 17 optimal codons were identified that were shared among these three strains.","PeriodicalId":363820,"journal":{"name":"2016 International Conference on Bioinformatics and Systems Biology (BSB)","volume":"24 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131626736","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

In silico identification of novel virulent protein of phytophthora infestans related to late blight disease 晚疫病相关病原菌新型毒力蛋白的计算机鉴定

2016 International Conference on Bioinformatics and Systems Biology (BSB) Pub Date : 2016-03-04 DOI: 10.1109/BSB.2016.7552145

R. Tripathi, Pawan Sharma, P. Chakraborty, P. Varadwaj

{"title":"In silico identification of novel virulent protein of phytophthora infestans related to late blight disease","authors":"R. Tripathi, Pawan Sharma, P. Chakraborty, P. Varadwaj","doi":"10.1109/BSB.2016.7552145","DOIUrl":"https://doi.org/10.1109/BSB.2016.7552145","url":null,"abstract":"Phytophthora infestans (Mont.) de Bary, oomycetes model organism is a destructive pathogen having a broad host range within Solanaceae family resulting in devastating economic losses every year. It causes late blight of Solanum tuberosum (potato) and S. lycopersicum (tomato). Current studies of the host-pathogen system emphasize on gene expression pattern of the Solanaceae members neglecting pathogen gene expression. In this paper the molecular properties of virulent proteins were investigated and classified on the basis of their functional, biophysical and biochemical properties. Bio-computational investigations and statistical analysis of the protein sequences was done. IpiO (ACU56995.1) one of the known virulent protein responsible for the disease, showed its similarity with HSF-type DNA-binding (EEY62722.1) non-virulent protein. Molecular modeling of the non-virulent protein was done. Modeled structure provided substantial parameters under Ramachandran plot, stereo-chemical aspects of the model was evaluated using RAMPAGE web server. Comparative genomic approach, and at a more basic level characterizations of P. infestans virulent proteins as well as understanding the perturbations they facilitate in plants will greatly enhance one's understanding of P. infestans virulence and host specificity.","PeriodicalId":363820,"journal":{"name":"2016 International Conference on Bioinformatics and Systems Biology (BSB)","volume":"2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134572883","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evolutionary divergence and comparative homology modeling analysis of LpxC enzyme from human pathogenic bacteria 人致病菌LpxC酶的进化分化及比较同源性建模分析

2016 International Conference on Bioinformatics and Systems Biology (BSB) Pub Date : 2016-03-04 DOI: 10.1109/BSB.2016.7552129

Ayon Pal, A. K. Bothra, U. Mandal, Subhasis Mukhopadhyay

{"title":"Evolutionary divergence and comparative homology modeling analysis of LpxC enzyme from human pathogenic bacteria","authors":"Ayon Pal, A. K. Bothra, U. Mandal, Subhasis Mukhopadhyay","doi":"10.1109/BSB.2016.7552129","DOIUrl":"https://doi.org/10.1109/BSB.2016.7552129","url":null,"abstract":"Multidrug defiant organisms result in severe mortality and stand as a big challenge worldwide. The gram negative bacilli (GNB) in particular is a massive cause of concern with high levels of resistance due to novel mechanisms. This study deals with thorough analysis of the phylogeny, evolutionary divergence and protein tertiary structure analysis of an important drug target, the bacterial metallo-amidase enzyme LpxC. The LpxC enzyme exists universally in all the gram-negative bacteria and catalyzes the first committed step of Lipid A biosynthesis. Evolutionary divergence study revealed the lpxC gene to be under strong degree of purifying selection in many highly pathogenic bacterial species. Homology modeling of the LpxC enzyme from different human pathogenic bacteria was carried out along with critical model evaluation and structural alignment analysis. Investigation of clefts on the LpxC protein surface demonstrated the presence of specific residues within the substrate-binding cleft. Preference for different secondary structural elements within the major cleft was also noticed in the LpxC enzyme from the sixteen selected pathogenic bacterial species.","PeriodicalId":363820,"journal":{"name":"2016 International Conference on Bioinformatics and Systems Biology (BSB)","volume":"13 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132668398","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

In-silico based designing of inhibitors against thevirulence and filamentation of Candida albicans, a common human pathogen 白色念珠菌是一种常见的人类病原体

2016 International Conference on Bioinformatics and Systems Biology (BSB) Pub Date : 2016-03-04 DOI: 10.1109/BSB.2016.7552118

Sonal Mishra, K. Misra

引用次数: 1

Deciphering the structural community from the Deulajhari hot spring using the next-generation sequencing 利用新一代测序技术破译Deulajhari温泉的结构群落

2016 International Conference on Bioinformatics and Systems Biology (BSB) Pub Date : 2016-03-04 DOI: 10.1109/BSB.2016.7552144

Archana Singh, Mahendra Gaur, E. Subudhi

{"title":"Deciphering the structural community from the Deulajhari hot spring using the next-generation sequencing","authors":"Archana Singh, Mahendra Gaur, E. Subudhi","doi":"10.1109/BSB.2016.7552144","DOIUrl":"https://doi.org/10.1109/BSB.2016.7552144","url":null,"abstract":"Deciphering the microbial diversity of the Deulajhari thermal springs is the major goal of our study. In our study the taxonomic description of the bacterial community structure was deduced from the 1.52 Gb metagenomics sequence size from the Deulajhari hot spring located in the Angul district of Odisha. Covered with the dense foliage, it has a high temperature, i.e. 69°C and alkaline pH i.e. 8.09. Various physiochemical parameter analysis of the sediment like; electro conductivity (0.025dSm-1), total organic carbon content (0.356%), nitrogen (125 kg/ha), phosphorus (7.88 kg/ha) and potassium (169.34 kg/ha) were done. Sediment sample of the Deulajhari hot spring was further processed for the 16S rRNA V3-V4 region by the amplicon metagenome sequencing from community DNA. Approximately 88.12% of the total microbial diversity was represented by the Proteobacteria followed by Bacteroidetes 10.76%, Firmicutes 0.35%, Spirochetes 0.18%, Thermi 0.13% and chloroflexi 0.11% at the phylum level. Thus through the metagenomics sequencing of the Deulajhari hot spring using IIllumina platform, we represent the complete microbial community structure present there in respective of their allocation, profusion and diverse coexisting microbiota.","PeriodicalId":363820,"journal":{"name":"2016 International Conference on Bioinformatics and Systems Biology (BSB)","volume":"27 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115446182","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0