Filters








16,599 Hits in 6.4 sec

TOWARD DISCOVERING DISEASE-SPECIFIC GENE NETWORKS FROM ONLINE LITERATURE

ZHUO ZHANG, SUISHENG TANG, SEE-KIONG NG
2005 Proceedings of the 3rd Asia-Pacific Bioinformatics Conference  
We compared the gene networks of two complex human CNS diseases extracted by DiseasePathweaver to the corresponding networks from the human-curated KEGG database and found that our system can accurately  ...  Using DiseasePathweaver, a biologist can obtain a global overview of the gene interaction network related to a specific human disease, together with well-documented evidences linking to each gene and its  ...  We have applied DPW to discover a disease-specific interaction network for ALS. The resulting network is shown in Figure 3 .  ... 
doi:10.1142/9781860947322_0016 fatcat:4256eoaygvc4rc6cet4vqes5ci

Systems Biology Approaches for Discovering Biomarkers for Traumatic Brain Injury

Jacob D. Feala, Mohamed Diwan M. AbdulHameed, Chenggang Yu, Bhaskar Dutta, Xueping Yu, Kara Schmid, Jitendra Dave, Frank Tortella, Jaques Reifman
2013 Journal of Neurotrauma  
As an exemplar, we apply network and pathway analysis to a manually compiled list of 32 protein biomarker candidates from the literature, recover known TBI-related mechanisms, and generate hypothetical  ...  One possibility is to apply emerging systems biology strategies to holistically probe and analyze the complex interweaving molecular pathways and networks that mediate the secondary cellular response through  ...  Pathways are often manually curated from the literature into large online compendia (see Table 3 for a list), which can be exploited to link disease-or injury-specific differentially expressed genes  ... 
doi:10.1089/neu.2012.2631 pmid:23510232 pmcid:PMC3700463 fatcat:esd3io3qpjh27ghjpuja5nzyzu

Enriching Human Interactome with Functional Mutations to Detect High-Impact Network Modules Underlying Complex Diseases

Cui, Srinivasan, Korkin
2019 Genes  
However, carving a disease network module from the whole interactome is a difficult task.  ...  Specifically, our approach incorporates and propagates the functional impact of non-synonymous single nucleotide polymorphisms (nsSNPs) on PPIs to implicate the genes that are most likely influenced by  ...  Specifically, we derived the seed genes for network propagation from the GWAS dataset (see Section 2.2 in Methods).  ... 
doi:10.3390/genes10110933 pmid:31731769 pmcid:PMC6895925 fatcat:hlfpixohdvcwxdmm3fvgwgmbfa

Treating Different Diseases With the Same Method—A Traditional Chinese Medicine Concept Analyzed for Its Biological Basis

Xing Zhai, Xi Wang, Li Wang, Linlin Xiu, Weilu Wang, Xiaohan Pang
2020 Frontiers in Pharmacology  
establish a digital dictionary of gene specifically related to individual diseases.  ...  We aim to use big data technology and complex network theory to mine the genes specifically relevant to these TCM syndromes.  ...  A total of 21 sub networks (right of Figure 6 ) were discovered from the gene division of Qi deficiency and blood stasis syndromes of stroke.  ... 
doi:10.3389/fphar.2020.00946 pmid:32670064 pmcid:PMC7332878 fatcat:bep3hmltprbaflv54b7kwbbmj4

Integrative networks illuminate biological factors underlying gene-disease associations [article]

Arjun Krishnan, Jaclyn N Taroni, Casey S Greene
2016 bioRxiv   pre-print
Once constructed, these networks provide the means to identify broad biological patterns underlying genes associated with complex traits and diseases.  ...  Such networks become more valuable as they become more context specific, for example, by capturing how genes work together in a certain tissue or cell type.  ...  identified in sequencing studies or weak associations mined from literature.  ... 
doi:10.1101/062695 fatcat:pqccv76v4zgwlfstlpwcuqqjlu

Integrative Networks Illuminate Biological Factors Underlying Gene–Disease Associations

Arjun Krishnan, Jaclyn N. Taroni, Casey S. Greene
2016 Current Genetic Medicine Reports  
Such networks become more valuable as they become more context specific, for example, by capturing how genes work together in a certain tissue or cell type.  ...  Once constructed, these networks provide the means to identify broad biological patterns underlying genes associated with complex traits and diseases.  ...  identified in sequencing studies or weak associations mined from literature.  ... 
doi:10.1007/s40142-016-0102-5 fatcat:kidqk7ei7bfzxfszk7nmdpo4xi

Chapter 2: Data-Driven View of Disease Biology

Casey S. Greene, Olga G. Troyanskaya, Fran Lewitter, Maricel Kann
2012 PLoS Computational Biology  
Here we discuss approaches that effectively weight and integrate hundreds of heterogeneous datasets to genegene networks that focus on a specific process or disease.  ...  Investigators often use these datasets individually to help elucidate molecular mechanisms of human diseases.  ...  These experiments range from those targeted towards tissue specificity [9] to those targeted towards specific diseases such as cancer [10] .  ... 
doi:10.1371/journal.pcbi.1002816 pmid:23300408 pmcid:PMC3531282 fatcat:mst53agedra3jhlubdoy4otavi

Heterogeneous Network Edge Prediction: A Data Integration Approach to Prioritize Disease-Associated Genes [article]

Daniel S Himmelstein, Sergio E Baranzini
2014 bioRxiv   pre-print
From this network composed of 40,343 nodes and 1,608,168 edges, we extracted features that describe the topology between specific genes and diseases.  ...  First we constructed a network with 18 node types—genes, diseases, tissues, pathophysiologies, and 14 MSigDB (molecular signatures database)collections—and 19 edge types from high-throughput publicly-available  ...  Disease-specific performance tends towards the mean, as disease-specific information has been altered by permutation.  ... 
doi:10.1101/011569 fatcat:uwxh3nidtfh37afyj7s2ipn46m

The Alzheimer's comorbidity phenome: mining from a large patient database and phenome-driven genetics prediction

Chunlei Zheng, Rong Xu
2018 JAMIA Open  
We aim to construct a heterogeneous network that integrates disease comorbidity network (DCN) from FAERS with protein-protein interaction (PPI) to prioritize the AD risk genes using network-based ranking  ...  We built a DCN based on indication data from FAERS using association rule mining. DCN was further integrated with PPI network.  ...  To test the performance of our network, we compared comorbidities of AD from DCN with known comorbidities of AD from literature.  ... 
doi:10.1093/jamiaopen/ooy050 pmid:30944912 pmcid:PMC6434979 fatcat:hcgswvfhzfchze2b7p3tyqlkhi

BioGraph: unsupervised biomedical knowledge discovery via automated hypothesis generation

Anthony ML Liekens, Jeroen De Knijf, Walter Daelemans, Bart Goethals, Peter De Rijk, Jurgen Del-Favero
2011 Genome Biology  
We show that BioGraph can retrospectively confirm recently discovered disease genes and identify potential susceptibility genes, outperforming existing technologies, without requiring prior domain knowledge  ...  The platform offers prioritizations of putative disease genes, supported by functional hypotheses.  ...  Acknowledgements This work was supported by the GOA project 'BioGraph: Text mining on heterogeneous databases: An application to optimized discovery of disease relevant genetic variants' of the University  ... 
doi:10.1186/gb-2011-12-6-r57 pmid:21696594 pmcid:PMC3218845 fatcat:zrc6r2d6djep3bmuu7ghq5swlu

BioMap

Kamal Kumar, Mathew J. Palakal, Snehasis Mukhopadhyay, Mathew J. Stephens, Huian Li
2004 Proceedings of the 2004 ACM symposium on Applied computing - SAC '04  
Knowledge, in this case, is defined as one-to-many and many-to-many relationships among biological entities such as gene, protein, drug, disease, etc.  ...  As data and information space continue to grow exponentially, the need for rapidly surveying the published literature, synthesizing, and discovering the embedded "knowledge" is becoming critical to allow  ...  The relationships thus discovered from the MEDLINE collection will be maintained in a relational database along with the specific links to literature sources, genes and protein sequence databases, popular  ... 
doi:10.1145/967900.967927 dblp:conf/sac/KumarPMSL04 fatcat:2usbpchpzbfadlrhki5ionnqqu

Understanding human metabolic physiology: a genome-to-systems approach

Monica L. Mo, Bernhard Ø. Palsson
2009 Trends in Biotechnology  
Efforts have been initiated towards developing context-specific metabolic networks from high-throughput data [51, 53] , providing the basis for constructing specific, segmented networks from a global  ...  Literature documents specific biochemical details from experiments on the gene product functions, such as reaction mechanism and substrate specificity. Figure 3 . 3 Figure 3.  ... 
doi:10.1016/j.tibtech.2008.09.007 pmid:19010556 fatcat:2dasytln5nagjn72cbuxvdlxxe

Meta-Analysis of Gene Popularity: Less Than Half of Gene Citations Stem from Gene Regulatory Networks

Ionut Sebastian Mihai, Debojyoti Das, Gabija Maršalkaite, Johan Henriksson
2021 Genes  
Here we present a meta-analysis of the reasons why different genes have been studied and to what extent, with a focus on the gene-specific biological features.  ...  The reasons for selecting a gene for further study might vary from historical momentum to funding availability, thus leading to unequal attention distribution among all genes.  ...  It is possible that most genes were first discovered in isolation and only then added to regulatory networks.  ... 
doi:10.3390/genes12020319 pmid:33672419 fatcat:unnlnjicrvaldl2iswz4qchf7a

Target discovery from data mining approaches

Yongliang Yang, S. James Adelstein, Amin I. Kassis
2009 Drug Discovery Today  
network, as long as it is relevant to a specific disease and its progression [4] .  ...  The list of seed genes was then used to construct a disease-specific gene-interaction network mined from the full text articles stored in PubMed Central (PMC), based on the dependency parsing and support  ... 
doi:10.1016/j.drudis.2008.12.005 pmid:19135549 fatcat:plsts2psuvclneuhgd5tlianwi

Target discovery from data mining approaches

Yongliang Yang, S. James Adelstein, Amin I. Kassis
2012 Drug Discovery Today  
network, as long as it is relevant to a specific disease and its progression [4] .  ...  The list of seed genes was then used to construct a disease-specific gene-interaction network mined from the full text articles stored in PubMed Central (PMC), based on the dependency parsing and support  ... 
doi:10.1016/j.drudis.2011.12.006 pmid:22178890 fatcat:c7k3puzntbhcrmzjlw6uvgxhny
« Previous Showing results 1 — 15 out of 16,599 results