40 results on '"Aleksandar Radovanovic"'
Search Results
2. DES-Amyloidoses 'Amyloidoses through the looking-glass': A knowledgebase developed for exploring and linking information related to human amyloid-related diseases
- Author
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Vladan P. Bajic, Adil Salhi, Katja Lakota, Aleksandar Radovanovic, Rozaimi Razali, Lada Zivkovic, Biljana Spremo-Potparevic, Mahmut Uludag, Faroug Tifratene, Olaa Motwalli, Benoit Marchand, Vladimir B. Bajic, Takashi Gojobori, Esma R. Isenovic, and Magbubah Essack
- Subjects
Medicine ,Science - Abstract
More than 30 types of amyloids are linked to close to 50 diseases in humans, the most prominent being Alzheimer’s disease (AD). AD is brain-related local amyloidosis, while another amyloidosis, such as AA amyloidosis, tends to be more systemic. Therefore, we need to know more about the biological entities’ influencing these amyloidosis processes. However, there is currently no support system developed specifically to handle this extraordinarily complex and demanding task. To acquire a systematic view of amyloidosis and how this may be relevant to the brain and other organs, we needed a means to explore "amyloid network systems" that may underly processes that leads to an amyloid-related disease. In this regard, we developed the DES-Amyloidoses knowledgebase (KB) to obtain fast and relevant information regarding the biological network related to amyloid proteins/peptides and amyloid-related diseases. This KB contains information obtained through text and data mining of available scientific literature and other public repositories. The information compiled into the DES-Amyloidoses system based on 19 topic-specific dictionaries resulted in 796,409 associations between terms from these dictionaries. Users can explore this information through various options, including enriched concepts, enriched pairs, and semantic similarity. We show the usefulness of the KB using an example focused on inflammasome-amyloid associations. To our knowledge, this is the only KB dedicated to human amyloid-related diseases derived primarily through literature text mining and complemented by data mining that provides a novel way of exploring information relevant to amyloidoses.
- Published
- 2022
3. DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species
- Author
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Adil Salhi, Sónia Negrão, Magbubah Essack, Mitchell J. L. Morton, Salim Bougouffa, Rozaimi Razali, Aleksandar Radovanovic, Benoit Marchand, Maxat Kulmanov, Robert Hoehndorf, Mark Tester, and Vladimir B. Bajic
- Subjects
Medicine ,Science - Abstract
Abstract Tomato is the most economically important horticultural crop used as a model to study plant biology and particularly fruit development. Knowledge obtained from tomato research initiated improvements in tomato and, being transferrable to other such economically important crops, has led to a surge of tomato-related research and published literature. We developed DES-TOMATO knowledgebase (KB) for exploration of information related to tomato. Information exploration is enabled through terms from 26 dictionaries and combination of these terms. To illustrate the utility of DES-TOMATO, we provide several examples how one can efficiently use this KB to retrieve known or potentially novel information. DES-TOMATO is free for academic and nonprofit users and can be accessed at http://cbrc.kaust.edu.sa/des_tomato/, using any of the mainstream web browsers, including Firefox, Safari and Chrome.
- Published
- 2017
- Full Text
- View/download PDF
4. Information exploration system for sickle cell disease and repurposing of hydroxyfasudil.
- Author
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Magbubah Essack, Aleksandar Radovanovic, and Vladimir B Bajic
- Subjects
Medicine ,Science - Abstract
BACKGROUND: Sickle cell disease (SCD) is a fatal monogenic disorder with no effective cure and thus high rates of morbidity and sequelae. Efforts toward discovery of disease modifying drugs and curative strategies can be augmented by leveraging the plethora of information contained in available biomedical literature. To facilitate research in this direction we have developed a resource, Dragon Exploration System for Sickle Cell Disease (DESSCD) (http://cbrc.kaust.edu.sa/desscd/) that aims to promote the easy exploration of SCD-related data. DESCRIPTION: The Dragon Exploration System (DES), developed based on text mining and complemented by data mining, processed 419,612 MEDLINE abstracts retrieved from a PubMed query using SCD-related keywords. The processed SCD-related data has been made available via the DESSCD web query interface that enables: a/information retrieval using specified concepts, keywords and phrases, and b/the generation of inferred association networks and hypotheses. The usefulness of the system is demonstrated by: a/reproducing a known scientific fact, the "Sickle_Cell_Anemia-Hydroxyurea" association, and b/generating novel and plausible "Sickle_Cell_Anemia-Hydroxyfasudil" hypothesis. A PCT patent (PCT/US12/55042) has been filed for the latter drug repurposing for SCD treatment. CONCLUSION: We developed the DESSCD resource dedicated to exploration of text-mined and data-mined information about SCD. No similar SCD-related resource exists. Thus, we anticipate that DESSCD will serve as a valuable tool for physicians and researchers interested in SCD.
- Published
- 2013
- Full Text
- View/download PDF
5. IBDDB: a manually curated and text-mining-enhanced database of genes involved in inflammatory bowel disease.
- Author
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Farhat Khan, Aleksandar Radovanovic, Takashi Gojobori, and Mandeep Kaur
- Published
- 2021
- Full Text
- View/download PDF
6. bTSSfinder: a novel tool for the prediction of promoters in cyanobacteria and Escherichia coli.
- Author
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Ilham A. Shahmuradov, Rozaimi Mohamad Razali, Salim Bougouffa, Aleksandar Radovanovic, and Vladimir B. Bajic
- Published
- 2017
- Full Text
- View/download PDF
7. DESM: portal for microbial knowledge exploration systems.
- Author
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Adil Salhi, Magbubah Essack, Aleksandar Radovanovic, Benoit Marchand, Salim Bougouffa, André Antunes 0001, Marta Filipa Simões, Feras F. Lafi, Olaa A. Motwalli, Ameerah Bokhari, Tariq Malas, Soha Al Amoudi, Ghofran Othum, Intikhab Alam, Katsuhiko Mineta, Xin Gao 0001, Robert Hoehndorf, John A. C. Archer, Takashi Gojobori, and Vladimir B. Bajic
- Published
- 2016
- Full Text
- View/download PDF
8. Re-infection with a different SARS-CoV-2 clade and prolonged viral shedding in a hematopoietic stem cell transplantation patient
- Author
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Amani H. Yamani, Abeer N. Alshukairi, Ashraf Dada, Ahmed A. Aljohaney, Intikhab Alam, Muhammad Yasir, Husam A. Bahaudden, Ahmed M. Tolah, Tagreed L. Alsubhi, Takashi Gojobori, Esam I. Azhar, Ahmed M. Hassan, Mohammed F. Saeedi, Sherif A. El-Kafrawy, Norah A. Othman, Naif I. AlJohani, Jaffar A. Al-Tawfiq, Aleksandar Radovanovic, Alimuddin Zumla, and Thamir A. Alandijany
- Subjects
Microbiology (medical) ,Whole genome sequencing ,2019-20 coronavirus outbreak ,SARS-CoV-2 ,business.industry ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,medicine.medical_treatment ,COVID-19 ,Infectious and parasitic diseases ,RC109-216 ,General Medicine ,Hematopoietic stem cell transplantation ,Re-infection ,medicine.disease ,Virology ,Lymphoma ,Prolonged viral shedding ,Infectious Diseases ,Hematological stem cell transplant ,Medicine ,Viral shedding ,business ,Clade ,Immunocompromised ,Re infection - Abstract
Immunocompromised patients who have a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection pose many clinical and public health challenges. We describe the case of a hematopoietic stem cell transplantation patient with lymphoma who had a protracted illness requiring three consecutive hospital admissions. Whole genome sequencing confirmed two different SARS-CoV-2 clades. Clinical management issues and the unanswered questions arising from this case are discussed.
- Published
- 2021
9. DDPC: Dragon Database of Genes associated with Prostate Cancer.
- Author
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Monique Maqungo, Mandeep Kaur, Samuel K. Kwofie, Aleksandar Radovanovic, Ulf Schaefer, Sebastian Schmeier, Ekow Oppon, Alan Christoffels, and Vladimir B. Bajic
- Published
- 2011
- Full Text
- View/download PDF
10. Database for exploration of functional context of genes implicated in ovarian cancer.
- Author
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Mandeep Kaur, Aleksandar Radovanovic, Magbubah Essack, Ulf Schaefer, Monique Maqungo, Tracey Kibler, Sebastian Schmeier, Alan Christoffels, Kothandaraman Narasimhan, Mahesh Choolani, and Vladimir B. Bajic
- Published
- 2009
- Full Text
- View/download PDF
11. DES-Amyloidoses 'Amyloidoses through thelooking-glass': A knowledgebase developedfor exploring and linking information relatedto human amyloid-related diseases
- Author
-
Vladan P. Bajic, Adil Salhi, Katja Lakota, Aleksandar Radovanovic, Rozaimi Razali, Lada Zivkovic, Biljana Spremo-Potparevic, Mahmut Uludag, Faroug Tifratene, Olaa Motwalli, Benoit Marchand, Vladimir B. Bajic, Takashi Gojobori, Esma R. Isenovic, and Magbubah Essack
- Subjects
Amyloid ,Serum Amyloid A Protein ,Multidisciplinary ,Alzheimer Disease ,Knowledge Bases ,Humans ,Amyloidosis - Abstract
More than 30 types of amyloids are linked to close to 50 diseases in humans, the most prominent being Alzheimer’s disease (AD). AD is brain-related local amyloidosis, while another amyloidosis, such as AA amyloidosis, tends to be more systemic. Therefore, we need to know more about the biological entities’ influencing these amyloidosis processes. However, there is currently no support system developed specifically to handle this extraordinarily complex and demanding task. To acquire a systematic view of amyloidosis and how this may be relevant to the brain and other organs, we needed a means to explore "amyloid network systems" that may underly processes that leads to an amyloid-related disease. In this regard, we developed the DES-Amyloidoses knowledgebase (KB) to obtain fast and relevant information regarding the biological network related to amyloid proteins/peptides and amyloid-related diseases. This KB contains information obtained through text and data mining of available scientific literature and other public repositories. The information compiled into the DES-Amyloidoses system based on 19 topic-specific dictionaries resulted in 796,409 associations between terms from these dictionaries. Users can explore this information through various options, including enriched concepts, enriched pairs, and semantic similarity. We show the usefulness of the KB using an example focused on inflammasome-amyloid associations. To our knowledge, this is the only KB dedicated to human amyloid-related diseases derived primarily through literature text mining and complemented by data mining that provides a novel way of exploring information relevant to amyloidoses.
- Published
- 2022
12. DENdb: database of integrated human enhancers.
- Author
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Haitham Ashoor, Dimitrios Kleftogiannis, Aleksandar Radovanovic, and Vladimir B. Bajic
- Published
- 2015
- Full Text
- View/download PDF
13. DEOP: a database on osmoprotectants and associated pathways.
- Author
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Salim Bougouffa, Aleksandar Radovanovic, Magbubah Essack, and Vladimir B. Bajic
- Published
- 2014
- Full Text
- View/download PDF
14. CovMT: an interactive SARS-CoV-2 mutation tracker, with a focus on critical variants
- Author
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Mohammed Alarawi, Intikhab Alam, Aleksandar Radovanovic, Takashi Gojobori, Allan Anthony Kamau, Roberto Incitti, and Esam I. Azhar
- Subjects
Focus (computing) ,2019-20 coronavirus outbreak ,Coronavirus disease 2019 (COVID-19) ,SARS-CoV-2 ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Computational biology ,Biology ,Corrections ,Infectious Diseases ,Mutation (genetic algorithm) ,Mutation ,Spike Glycoprotein, Coronavirus ,Correspondence ,Humans - Published
- 2021
- Full Text
- View/download PDF
15. IBDDB: a manually curated and text-mining-enhanced database of genes involved in inflammatory bowel disease
- Author
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Aleksandar Radovanovic, Takashi Gojobori, Mandeep Kaur, and Farhat Khan
- Subjects
PubMed ,Databases, Factual ,Computer science ,media_common.quotation_subject ,Knowledge Bases ,MEDLINE ,Disease ,computer.software_genre ,Inflammatory bowel disease ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,0302 clinical medicine ,Text mining ,Reading (process) ,medicine ,Data Mining ,Humans ,030304 developmental biology ,media_common ,0303 health sciences ,Database ,business.industry ,medicine.disease ,File format ,Inflammatory Bowel Diseases ,Database Tool ,AcademicSubjects/SCI00960 ,030211 gastroenterology & hepatology ,General Agricultural and Biological Sciences ,business ,computer ,Information Systems - Abstract
To date, research on inflammatory bowel disease (IBD, encompassing Crohn’s disease and ulcerative colitis), a chronic complex disorder, has generated a large amount of data scattered across published literature (1 06 333) listed in PubMed on 14 October 2020, and no dedicated database currently exists that catalogues information on genes associated with IBD. We aimed to manually curate 289 genes that are experimentally validated to be linked with IBD and its known phenotypes. Furthermore, we have developed an integrated platform providing information about different aspects of these genes by incorporating several resources and an extensive text-mined knowledgebase. The curated IBD database (IBDDB) allows the selective display of collated 34 subject-specific concepts (listed as columns) exportable through a user-friendly IBDDB portal. The information embedded in concepts was acquired via text-mining of PubMed (manually cleaned and curated), accompanied by data-mining from varied resources. The user can also explore different biomedical entities and their co-occurrence with other entities (about one million) from 11 curated dictionaries in the indexed PubMed records. This functionality permits the user to generate and cross-examine a new hypothesis that is otherwise not easy to comprehend by just reading the published abstracts and papers. Users can download required information using various file formats and can display information in the form of networks. To our knowledge, no curated database of IBD-related genes is available so far. IBDDB is free for academic users and can be accessed at https://www.cbrc.kaust.edu.sa/ibd/.
- Published
- 2021
16. An interactive COVID-19 virus Mutation Tracker (CovMT) with a particular focus on critical mutations in the Receptor Binding Domain (RBD) region of the Spike protein
- Author
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Muhammed Alarawi, Roberto Incitti, Takashi Gojobori, Allan Anthony Kamau, Intikhab Alam, Aleksandar Radovanovic, and Esam I. Azhar
- Subjects
World Wide Web ,2019-20 coronavirus outbreak ,Focus (computing) ,Coronavirus disease 2019 (COVID-19) ,Computer science ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Mutation (genetic algorithm) ,Spike Protein ,Domain (software engineering) - Abstract
Almost one year has passed since the appearance of SARS-CoV-2, causing the COVID-19 pandemic. The number of confirmed SARS-Cov-2 cases worldwide has now reached ∼92 million, with 2 million reported deaths (https://covid19.who.int). Nearly 400,000 SARS-Cov-2 genomes were sequenced from COVID-19 samples and added to public resources such as GISAID (https://gisaid.org). With the vaccines becoming available or entering trials (https://covid19.trackvaccines.org), it is vital to keep track of mutations in the genome of SARS-CoV-2, especially in the Spike protein’s Receptor Binding Domain (RBD) region, which could have a potential impact on disease severity and treatment strategies.1–3 In the wake of a recent increase in cases with a potentially more infective RBD mutation (N501Y) in the United Kingdom, countries worldwide are concerned about the spread of this or similar variants. Impressive sampling and timely increase in sequencing efforts related to COVID-19 in the United Kingdom (UK) helped detect and monitor the spread of the new N501Y variant. Similar sequencing efforts are needed in other countries for timely tracking of this or different variants. To track geographic sequencing efforts and mutations, with a particular focus on RBD region of the Spike protein, we present our daily updated COVID-19 virus Mutation Tracker system, see https://www.cbrc.kaust.edu.sa/covmt.
- Published
- 2021
17. DES-Mutation: System for Exploring Links of Mutations and Diseases
- Author
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Christophe Van Neste, Ameerah Bokhari, Faroug Tifratene, Rozaimi Mohamad Razali, Yu Li, Magbubah Essack, Adil Salhi, Mahmut Uludag, Aleksandar Radovanovic, Arwa Bin Raies, Vasiliki Kordopati, Vladimir B. Bajic, and Ahdab AlSaieedi
- Subjects
0301 basic medicine ,BETA-THALASSEMIA ,DATABASE ,Knowledge Bases ,HUMAN PHENOTYPE ,BIOMEDICAL LITERATURE ,lcsh:Medicine ,Context (language use) ,Disease ,Computational biology ,Biology ,medicine.disease_cause ,GENOME ANNOTATION ,Article ,03 medical and health sciences ,chemistry.chemical_compound ,GENETIC-VARIANTS ,SEQUENCE VARIATION ,Medicine and Health Sciences ,IRON OVERLOAD ,medicine ,Humans ,lcsh:Science ,TEXT-MINING TOOL ,Organism ,Mutation ,Multidisciplinary ,lcsh:R ,Genetic Diseases, Inborn ,Biology and Life Sciences ,Genome project ,Phenotype ,ALZHEIMERS-DISEASE ,030104 developmental biology ,chemistry ,Human genome ,lcsh:Q ,DNA ,Software - Abstract
During cellular division DNA replicates and this process is the basis for passing genetic information to the next generation. However, the DNA copy process sometimes produces a copy that is not perfect, that is, one with mutations. The collection of all such mutations in the DNA copy of an organism makes it unique and determines the organism’s phenotype. However, mutations are often the cause of diseases. Thus, it is useful to have the capability to explore links between mutations and disease. We approached this problem by analyzing a vast amount of published information linking mutations to disease states. Based on such information, we developed the DES-Mutation knowledgebase which allows for exploration of not only mutation-disease links, but also links between mutations and concepts from 27 topic-specific dictionaries such as human genes/proteins, toxins, pathogens, etc. This allows for a more detailed insight into mutation-disease links and context. On a sample of 600 mutation-disease associations predicted and curated, our system achieves precision of 72.83%. To demonstrate the utility of DES-Mutation, we provide case studies related to known or potentially novel information involving disease mutations. To our knowledge, this is the first mutation-disease knowledgebase dedicated to the exploration of this topic through text-mining and data-mining of different mutation types and their associations with terms from multiple thematic dictionaries.
- Published
- 2018
18. DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species
- Author
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Mark Tester, Sónia Negrão, Adil Salhi, Benoit Marchand, Magbubah Essack, Salim Bougouffa, Mitchell J. L. Morton, Rozaimi Mohamad Razali, Maxat Kulmanov, Vladimir B. Bajic, Aleksandar Radovanovic, and Robert Hoehndorf
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0301 basic medicine ,Multidisciplinary ,Computer science ,Knowledge Bases ,Science ,Fruit development ,Information Storage and Retrieval ,Genes, Plant ,Plant biology ,Article ,Semantics ,World Wide Web ,Crop ,03 medical and health sciences ,Knowledge exploration ,030104 developmental biology ,Solanum lycopersicum ,Medicine ,Genetic Association Studies ,Simulation - Abstract
Tomato is the most economically important horticultural crop used as a model to study plant biology and particularly fruit development. Knowledge obtained from tomato research initiated improvements in tomato and, being transferrable to other such economically important crops, has led to a surge of tomato-related research and published literature. We developed DES-TOMATO knowledgebase (KB) for exploration of information related to tomato. Information exploration is enabled through terms from 26 dictionaries and combination of these terms. To illustrate the utility of DES-TOMATO, we provide several examples how one can efficiently use this KB to retrieve known or potentially novel information. DES-TOMATO is free for academic and nonprofit users and can be accessed at http://cbrc.kaust.edu.sa/des_tomato/, using any of the mainstream web browsers, including Firefox, Safari and Chrome.
- Published
- 2017
19. Queen Victoria's Diamond Jubilee as a global spectacle and projection of late Victorian imperialism
- Author
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D Aleksandar Radovanovic
- Subjects
Diamond jubilee ,Projection (mathematics) ,media_common.quotation_subject ,Spectacle ,Art history ,Art ,Queen (playing card) ,media_common - Published
- 2017
20. Correction to Lancet Infect Dis 2021; published online Feb 8. https://doi.org/10.1016/S1473-3099(21)00078-5
- Author
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Aleksandar Radovanovic
- Subjects
Infectious Diseases - Published
- 2021
21. Dragon exploration system on marine sponge compounds interactions.
- Author
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Sunil Sagar, Mandeep Kaur, Aleksandar Radovanovic, and Vladimir B. Bajic
- Published
- 2013
- Full Text
- View/download PDF
22. DESM: portal for microbial knowledge exploration systems
- Author
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Takashi Gojobori, Ghofran Othum, Katsuhiko Mineta, Feras F. Lafi, Tariq Malas, Benoit Marchand, Aleksandar Radovanovic, Marta Filipa Simões, Magbubah Essack, André Antunes, Salim Bougouffa, Soha Al Amoudi, John A.C. Archer, Intikhab Allam, Robert Hoehndorf, Adil Salhi, Ameerah Bokhari, Xin Gao, Olaa Amin Motwalli, and Vladimir B. Bajic
- Subjects
0301 basic medicine ,Databases, Factual ,Knowledge Bases ,030106 microbiology ,Antitubercular Agents ,Dictionaries as Topic ,Biology ,03 medical and health sciences ,Industrial Microbiology ,Controlled vocabulary ,Genetics ,Database Issue ,Data Mining ,Humans ,Internet ,Bacteria ,business.industry ,Entrez Gene ,Drug Repositioning ,Fungi ,Industrial microbiology ,Data science ,Archaea ,Variety (cybernetics) ,Biotechnology ,Knowledge exploration ,Vocabulary, Controlled ,Viruses ,The Internet ,User interface ,business - Abstract
Microorganisms produce an enormous variety of chemical compounds. It is of general interest for microbiology and biotechnology researchers to have means to explore information about molecular and genetic basis of functioning of different microorganisms and their ability for bioproduction. To enable such exploration, we compiled 45 topic-specific knowledgebases (KBs) accessible through DESM portal (www.cbrc.kaust.edu.sa/desm). The KBs contain information derived through text-mining of PubMed information and complemented by information data-mined from various other resources (e.g. ChEBI, Entrez Gene, GO, KOBAS, KEGG, UniPathways, BioGrid). All PubMed records were indexed using 4,538,278 concepts from 29 dictionaries, with 1 638 986 records utilized in KBs. Concepts used are normalized whenever possible. Most of the KBs focus on a particular type of microbial activity, such as production of biocatalysts or nutraceuticals. Others are focused on specific categories of microorganisms, e.g. streptomyces or cyanobacteria. KBs are all structured in a uniform manner and have a standardized user interface. Information exploration is enabled through various searches. Users can explore statistically most significant concepts or pairs of concepts, generate hypotheses, create interactive networks of associated concepts and export results. We believe DESM will be a useful complement to the existing resources to benefit microbiology and biotechnology research.
- Published
- 2015
23. DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining
- Author
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Sebastian Schmeier, Lina Ma, Benoit Marchand, Zhang Zhang, Vladimir B. Bajic, Vladan Bajic, Adil Salhi, Tanvir Alam, Magbubah Essack, and Aleksandar Radovanovic
- Subjects
0301 basic medicine ,data-mining ,Knowledge Bases ,Dictionaries as Topic ,Scientific literature ,Computational biology ,Biology ,Bioinformatics ,Noncoding RNA ,03 medical and health sciences ,Broad spectrum ,0302 clinical medicine ,Alzheimer Disease ,literature-mining ,1-(5-Isoquinolinesulfonyl)-2-Methylpiperazine ,Data Mining ,Humans ,long noncoding RNA ,Molecular Biology ,microRNA ,text-mining ,Cell Biology ,bioinformatics ,Non-coding RNA ,information integration ,Long non-coding RNA ,3. Good health ,knowledgebase ,MicroRNAs ,Gene Ontology ,030104 developmental biology ,Disease Progression ,RNA, Long Noncoding ,Human genome ,Alzheimer disease ,Relevant information ,Software ,030217 neurology & neurosurgery ,Research Paper ,Information integration - Abstract
Noncoding RNAs (ncRNAs), particularly microRNAs (miRNAs) and long ncRNAs (lncRNAs), are important players in diseases and emerge as novel drug targets. Thus, unraveling the relationships between ncRNAs and other biomedical entities in cells are critical for better understanding ncRNA roles that may eventually help develop their use in medicine. To support ncRNA research and facilitate retrieval of relevant information regarding miRNAs and lncRNAs from the plethora of published ncRNA-related research, we developed DES-ncRNA (www.cbrc.kaust.edu.sa/des_ncrna). DES-ncRNA is a knowledgebase containing text- and data-mined information from public scientific literature and other public resources. Exploration of mined information is enabled through terms and pairs of terms from 19 topic-specific dictionaries including, for example, antibiotics, toxins, drugs, enzymes, mutations, pathways, human genes and proteins, drug indications and side effects, mutations, diseases, etc. DES-ncRNA contains approximately 878,000 associations of terms from these dictionaries of which 36,222 (5,373) are with regards to miRNAs (lncRNAs). We provide several ways to explore information regarding ncRNAs to users including controlled generation of association networks as well as hypotheses generation. We show an example how DES-ncRNA can aid research on Alzheimer disease and suggest potential therapeutic role for Fasudil. DES-ncRNA is a powerful tool that can be used on its own or as a complement to the existing resources, to support research in human ncRNA. To our knowledge, this is the only knowledgebase dedicated to human miRNAs and lncRNAs derived primarily through literature-mining enabling exploration of a broad spectrum of associated biomedical entities, not paralleled by any other resource.
- Published
- 2017
24. Review of the three-years work of catheterization laboratory in General hospital Valjevo
- Author
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Biljana Rakić, Ivica Obradović, Branislav Pavlović, Aleksandar Radovanovic, Milan Nikolić, Slavica Vulović, A Milan Nedeljeković, Irena Matić, Marko Stanković, and Dušan Ružičić
- Subjects
Nursing ,Work (electrical) ,business.industry ,Medicine ,Medical emergency ,General hospital ,business ,medicine.disease - Published
- 2013
25. bTSSfinder: a novel tool for the prediction of promoters in cyanobacteria and Escherichia coli
- Author
-
Aleksandar Radovanovic, Salim Bougouffa, Ilham A. Shahmuradov, Rozaimi Mohamad Razali, and Vladimir B. Bajic
- Subjects
0301 basic medicine ,Statistics and Probability ,Cyanobacteria ,Transcriptional Activation ,Transcription, Genetic ,030106 microbiology ,Sigma Factor ,Bacterial genome size ,Computational biology ,medicine.disease_cause ,Biochemistry ,03 medical and health sciences ,Sigma factor ,medicine ,Escherichia coli ,Promoter Regions, Genetic ,Molecular Biology ,Supplementary data ,Physics ,Transcription initiation site ,biology ,business.industry ,Sigma ,Promoter ,DNA-Directed RNA Polymerases ,biology.organism_classification ,Original Papers ,Computer Science Applications ,Biotechnology ,Computational Mathematics ,030104 developmental biology ,Computational Theory and Mathematics ,Transcription Initiation Site ,business ,Sequence Analysis ,Genome, Bacterial ,Software - Abstract
Motivation The computational search for promoters in prokaryotes remains an attractive problem in bioinformatics. Despite the attention it has received for many years, the problem has not been addressed satisfactorily. In any bacterial genome, the transcription start site is chosen mostly by the sigma (σ) factor proteins, which control the gene activation. The majority of published bacterial promoter prediction tools target σ70 promoters in Escherichia coli. Moreover, no σ-specific classification of promoters is available for prokaryotes other than for E. coli. Results Here, we introduce bTSSfinder, a novel tool that predicts putative promoters for five classes of σ factors in Cyanobacteria (σA, σC, σH, σG and σF) and for five classes of sigma factors in E. coli (σ70, σ38, σ32, σ28 and σ24). Comparing to currently available tools, bTSSfinder achieves higher accuracy (MCC = 0.86, F1-score = 0.93) compared to the next best tool with MCC = 0.59, F1-score = 0.79) and covers multiple classes of promoters. Availability and Implementation bTSSfinder is available standalone and online at http://www.cbrc.kaust.edu.sa/btssfinder. Supplementary information Supplementary data are available at Bioinformatics online.
- Published
- 2016
26. War brought home: Post-traumatic stress disorder in the post-Vietnam America through the documentary form of Emily Mann‘s play still life
- Author
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Aleksandar Radovanovic
- Subjects
media_common.quotation_subject ,Post-Traumatic Stress Disorder ,The Vietnam War ,Emily Mann ,Context (language use) ,Gender studies ,Criminology ,Racism ,Dehumanization ,Psyche ,Spanish Civil War ,Vietnam War ,State (polity) ,“Theatre of Testimony” ,General Earth and Planetary Sciences ,lcsh:Criminal law and procedure ,The My Lai Massacre ,Ideology ,Sociology ,lcsh:K5000-5582 ,General Environmental Science ,media_common - Abstract
The collective moral dilemma that the United States society plunged into during the Vietnam War was intensified by the problem of Post-Traumatic Stress Disorder, which assumed undreamed- of proportions among returnees from the front. In her play Still Life, Emily Mann uses the example of a war veteran in order to examine PTSD not only in the context of war brutality which scars the warrior’s psyche, but also in the light of malign social circumstances which contribute to the development of the illness. The play suggests that the spread of PTSD was rooted not only in the technological advancement which enhanced the destructive potential of weaponry, but also in the state ideology which manifested itself in dehumanization of the enemy, shifting the burning issue of racism to the frontline, and enlistment policy based on class and racial discrimination. Traumatic experiences of the play‘s protagonists create an image of America in which boot camp for Vietnam was not limited to Parris Island, but pervaded the society through family and institutional dysfunction. Their confessions trace the war on its way back home, as a place from which it has sprung and is still being waged in, finding its victims both in veterans and people in their immediate surroundings. The playwright employs “Theatre of Testimony” in order to dramatize and simultaneously document her findings, which is why this paper deals in equal measure with her dramatic method and the way the content of the play interacts with the Vietnam heritage.
- Published
- 2012
27. DESTAF: A database of text-mined associations for reproductive toxins potentially affecting human fertility
- Author
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Allan Anthony Kamau, Mandeep Kaur, Aleksandar Radovanovic, Alan Christoffels, Sunil Sagar, Vladimir B. Bajic, Sundararajan Vijayaraghava Seshadri, Ulf Schaefer, and Adam Dawe
- Subjects
Male ,Human fertility ,Databases, Factual ,Reproductive toxicology ,Interface (Java) ,Computer science ,Toxicology ,computer.software_genre ,Risk Assessment ,Field (computer science) ,User-Computer Interface ,Resource (project management) ,Risk Factors ,Software Design ,Databases, Genetic ,Cluster Analysis ,Data Mining ,Humans ,Database ,Reproduction ,Rapid assessment ,Systems Integration ,Fertility ,Gene Expression Regulation ,Developmental toxicology ,Female ,computer - Abstract
The Dragon Exploration System for Toxicants and Fertility (DESTAF) is a publicly available resource which enables researchers to efficiently explore both known and potentially novel information and associations in the field of reproductive toxicology. To create DESTAF we used data from the literature (including over 10 500 PubMed abstracts), several publicly available biomedical repositories, and specialized, curated dictionaries. DESTAF has an interface designed to facilitate rapid assessment of the key associations between relevant concepts, allowing for a more in-depth exploration of information based on different gene/protein-, enzyme/metabolite-, toxin/chemical-, disease- or anatomically centric perspectives. As a special feature, DESTAF allows for the creation and initial testing of potentially new association hypotheses that suggest links between biological entities identified through the database. DESTAF, along with a PDF manual, can be found at http://cbrc.kaust.edu.sa/destaf . It is free to academic and non-commercial users and will be updated quarterly.
- Published
- 2012
28. DDPC: Dragon Database of Genes associated with Prostate Cancer
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Alan Christoffels, Ulf Schaefer, Aleksandar Radovanovic, Mandeep Kaur, Ekow Oppon, Vladimir B. Bajic, Monique Maqungo, Sebastian Schmeier, and Samuel K. Kwofie
- Subjects
Male ,Regulation of gene expression ,Database ,Knowledge Bases ,Gene regulatory network ,Prostatic Neoplasms ,Promoter ,Articles ,Biology ,medicine.disease ,computer.software_genre ,Bioinformatics ,DNA binding site ,Prostate cancer ,Databases, Genetic ,Genetics ,medicine ,Data Mining ,Humans ,computer ,DrugBank ,Transcription factor ,Gene ,Genes, Neoplasm - Abstract
Prostate cancer (PC) is one of the most commonly diagnosed cancers in men. PC is relatively difficult to diagnose due to a lack of clear early symptoms. Extensive research of PC has led to the availability of a large amount of data on PC. Several hundred genes are implicated in different stages of PC, which may help in developing diagnostic methods or even cures. In spite of this accumulated information, effective diagnostics and treatments remain evasive. We have developed Dragon Database of Genes associated with Prostate Cancer (DDPC) as an integrated knowledgebase of genes experimentally verified as implicated in PC. DDPC is distinctive from other databases in that (i) it provides pre-compiled biomedical text-mining information on PC, which otherwise require tedious computational analyses, (ii) it integrates data on molecular interactions, pathways, gene ontologies, gene regulation at molecular level, predicted transcription factor binding sites on promoters of PC implicated genes and transcription factors that correspond to these binding sites and (iii) it contains DrugBank data on drugs associated with PC. We believe this resource will serve as a source of useful information for research on PC. DDPC is freely accessible for academic and non-profit users via http://apps.sanbi.ac.za/ddpc/ and http://cbrc.kaust.edu.sa/ddpc/.
- Published
- 2010
29. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line
- Author
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Albin Sandelin, Takashi Gojobori, Timo Lassmann, Hiroshi Asahara, Claes Wahlestedt, Lukasz Huminiecki, Georges St. Laurent, Yoshinari Ando, Takehiro Hashimoto, Denis C. Bauer, Ariel S. Schwartz, Pär G. Engström, Michael Rehli, Hiromi Nishiyori, Katharine M. Irvine, Andreas Lennartsson, Susanne Heinzel, Yoichi Takenaka, Ole Winther, Nicole Cloonan, Megumi Hashimoto, Winston Hide, Takuma Sano, Boris Lenhard, Michiel J. L. de Hoon, Sarah A. Teichmann, Timothy Ravasi, Naoko Imamoto, Ryoko Ishihara, Syuhei Kimura, Mariko Hatakeyama, Yusuke Inoue, Joe Chiba, Shizu Takeda, Linda Wu, Julian Gough, John Quackenbush, Miho Sera, Yasumasa Kimura, Vladimir B. Bajic, Frank Brombacher, Kazumi Yamaguchi, Toshitsugu Okayama, David Fredman, Hideya Kawaji, Colin A. Semple, Ryan J. Taft, Cas Simons, Ko Fujimori, Masaaki Furuno, Andrew Waterhouse, Ajit Kumar, Jesper Tegnér, Tsugumi Kawashima, Nikolai Petrovsky, J. Lynn Fink, Michihira Tagami, Jun Otomo, Etsuko Miyamoto-Sato, Shiro Fukuda, Cameron Ross MacPherson, Shintaro Katayama, Erika Bulger, Toshio Kojima, Alistair R. R. Forrest, Anders Jacobsen, Yasushi Okazaki, Rohan D. Teasdale, Chikatoshi Kai, Johan Björkegren, Takahiro Suzuki, Carsten O. Daub, Christian Schönbach, Miki Kojima, Sebastian Schmeier, Alistair M. Chalk, Hiroaki Kitano, Sanne Nygaard, Kazuhiko Nakabayashi, Kai Tan, Yasuhiro Tomaru, Noriko Ninomiya, Piotr J. Balwierz, Marina Lizio, Altuna Akalin, Maki Asada, Norihiro Maeda, Satoshi Inoue, Takahiro Arakawa, Shohei Noma, Adam Dawe, Michael Hörnquist, Mika Gustafsson, Stuart Meier, Sei Miyamoto, Ryuichiro Kimura, Takeshi Konno, Kate Schroder, Christine A. Wells, Kazunori Waki, Christopher G. Maher, Nicolas Bertin, Ai Kaiho, Chihiro Ogawa, Shinji Kondo, Mika Nakano, Sean M. Grimmond, Matthew J. Sweet, Jun Yasuda, Aleksandar Radovanovic, Valerio Orlando, Yukari Takahashi, Mihaela Zavolan, Jessica Severin, Markus C. Kerr, Anders Krogh, Hiroshi Yanagawa, Hisashi Miura, John S. Mattick, Eivind Valen, Josée Dostie, Magbubah Essack, Monique Maqungo, Haruka Okuda-Yabukami, Oliver Hofmann, Anthony G Beckhouse, Rintaro Saito, Yutaka Nakachi, Yuki Hasegawa, Masanori Suzuki, Mitsuyoshi Murata, Harukazu Suzuki, Nicholas Matigian, Takao Iwayanagi, Hisashi Koga, Jun Kawai, Hideo Matsuda, Charles Plessy, Mikhail Pachkov, Kengo Imamura, Morten Lindow, Yayoi Kitazume, Erik Arner, Kazuho Ikeo, Yoshihide Hayashizaki, Timothy L. Bailey, Geoffrey J. Faulkner, Martin S. Taylor, Mutsumi Kanamori-Katayama, Mandeep Kaur, Christophe Simon, Piero Carninci, Atsutaka Kubosaki, Chika Kawazu, Katsuhiko Shirahige, Adele Kruger, Jessica C. Mar, Kayoko Murakami, David A. Hume, and Erik van Nimwegen
- Subjects
Transcription, Genetic ,Cellular differentiation ,Molecular Sequence Data ,Gene regulatory network ,Biology ,Bioinformatics ,Article ,Cell Line ,03 medical and health sciences ,0302 clinical medicine ,Transcription (biology) ,Serum response factor ,Genetics ,Humans ,Gene Regulatory Networks ,RNA, Small Interfering ,Promoter Regions, Genetic ,Transcription factor ,030304 developmental biology ,Cell Proliferation ,Oligonucleotide Array Sequence Analysis ,0303 health sciences ,Base Sequence ,Models, Genetic ,Gene Expression Profiling ,Pioneer factor ,Myeloid leukemia ,Cell Differentiation ,Cell biology ,Gene expression profiling ,Leukemia, Myeloid ,030220 oncology & carcinogenesis - Abstract
Using deep sequencing (deepCAGE), the FANTOM4 study measured the genome-wide dynamics of transcription-start-site usage in the human monocytic cell line THP-1 throughout a time course of growth arrest and differentiation. Modeling the expression dynamics in terms of predicted cis-regulatory sites, we identified the key transcription regulators, their time-dependent activities and target genes. Systematic siRNA knockdown of 52 transcription factors confirmed the roles of individual factors in the regulatory network. Our results indicate that cellular states are constrained by complex networks involving both positive and negative regulatory interactions among substantial numbers of transcription factors and that no single transcription factor is both necessary and sufficient to drive the differentiation process.
- Published
- 2009
- Full Text
- View/download PDF
30. Database for exploration of functional context of genes implicated in ovarian cancer
- Author
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Kothandaraman Narasimhan, Tracey Kibler, Magbubah Essack, Vladimir B. Bajic, Sebastian Schmeier, Aleksandar Radovanovic, Mandeep Kaur, Monique Maqungo, Ulf Schaefer, Alan Christoffels, and Mahesh Choolani
- Subjects
Sequence analysis ,Gene regulatory network ,Context (language use) ,Disease ,Biology ,Bioinformatics ,computer.software_genre ,Databases, Genetic ,Genetics ,medicine ,Humans ,Gene Regulatory Networks ,Promoter Regions, Genetic ,Gene ,Ovarian Neoplasms ,Binding Sites ,Database ,Articles ,medicine.disease ,Gynecological cancer ,Identification (biology) ,Female ,Ovarian cancer ,computer ,Genes, Neoplasm ,Transcription Factors - Abstract
Ovarian cancer (OC) is becoming the most common gynecological cancer in developed countries and the most lethal gynecological malignancy. It is also the fifth leading cause of all cancer-related deaths in women. The identification of diagnostic biomarkers and development of early detection techniques for OC largely depends on the understanding of the complex functionality and regulation of genes involved in this disease. Unfortunately, information about these OC genes is scattered throughout the literature and various databases making extraction of relevant functional information a complex task. To reduce this problem, we have developed a database dedicated to OC genes to support exploration of functional characterization and analysis of biological processes related to OC. The database contains general information about OC genes, enriched with the results of transcription regulation sequence analysis and with relevant text mining to provide insights into associations of the OC genes with other genes, metabolites, pathways and nuclear proteins. Overall, it enables exploration of relevant information for OC genes from multiple angles, making it a unique resource for OC and will serve as a useful complement to the existing public resources for those interested in OC genetics. Access is free for academic and non-profit users and database can be accessed at http://apps.sanbi.ac.za/ddoc/.
- Published
- 2008
31. DENdb: database of integrated human enhancers
- Author
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Dimitrios Kleftogiannis, Vladimir B. Bajic, Haitham Ashoor, and Aleksandar Radovanovic
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Regulation of gene expression ,Genetics ,Database ,Enhancer RNAs ,Biology ,computer.software_genre ,Response Elements ,General Biochemistry, Genetics and Molecular Biology ,Chromatin ,chemistry.chemical_compound ,chemistry ,Regulatory sequence ,Humans ,Original Article ,Nucleotide Motifs ,General Agricultural and Biological Sciences ,Enhancer ,Databases, Nucleic Acid ,computer ,Transcription factor ,Gene ,DNA ,Information Systems ,Transcription Factors - Abstract
Enhancers are cis-acting DNA regulatory regions that play a key role in distal control of transcriptional activities. Identification of enhancers, coupled with a comprehensive functional analysis of their properties, could improve our understanding of complex gene transcription mechanisms and gene regulation processes in general. We developed DENdb, a centralized on-line repository of predicted enhancers derived from multiple human cell-lines. DENdb integrates enhancers predicted by five different methods generating an enriched catalogue of putative enhancers for each of the analysed cell-lines. DENdb provides information about the overlap of enhancers with DNase I hypersensitive regions, ChIP-seq regions of a number of transcription factors and transcription factor binding motifs, means to explore enhancer interactions with DNA using several chromatin interaction assays and enhancer neighbouring genes. DENdb is designed as a relational database that facilitates fast and efficient searching, browsing and visualization of information. Database URL: http://www.cbrc.kaust.edu.sa/dendb/.
- Published
- 2015
32. Using the internet in networking of synchronized phasor measurement units
- Author
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Aleksandar Radovanovic
- Subjects
Engineering ,business.industry ,Phasor ,Energy Engineering and Power Technology ,Phasor measurement unit ,law.invention ,Client–server model ,Units of measurement ,law ,Embedded system ,Internet Protocol ,Global Positioning System ,Systems design ,The Internet ,Electrical and Electronic Engineering ,business ,Computer network - Abstract
This paper describes the design and implementation of an experimental phasor measurement unit (PMU) network. The PMUs synchronically measures current and voltage phasors at key system buses in real time. They are synchronised using time transmission from the Global Positioning System (GPS) satellites. The measurements are transmitted either via dedicated links between specified sites, or over a switched link that is established for the purpose of the communication. At the communication and functional level, we implemented TCP/IP protocols as a flexible way of accessing and controlling the PMUs. Use of the Internet technology and client–server concept gives the ability to add any number of PMUs to the network and give access to any number of users at any location.
- Published
- 2001
33. Exploration of miRNA families for hypotheses generation
- Author
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Vladimir B. Bajic, John A.C. Archer, Aleksandar Radovanovic, and Timothy K. K. Kamanu
- Subjects
Genetics ,Web browser ,Multidisciplinary ,Computational Biology ,Genomics ,Computational biology ,Biology ,Plants ,Web Browser ,Article ,MicroRNAs ,Species Specificity ,Multigene Family ,microRNA ,Animals ,Humans ,Genomic imprinting ,Gene ,Function (biology) - Abstract
Technological improvements have resulted in increased discovery of new microRNAs (miRNAs) and refinement and enrichment of existing miRNA families. miRNA families are important because they suggest a common sequence or structure configuration in sets of genes that hint to a shared function. Exploratory tools to enhance investigation of characteristics of miRNA families and the functions of family-specific miRNA genes are lacking. We have developed, miRNAVISA, a user-friendly web-based tool that allows customized interrogation and comparisons of miRNA families for hypotheses generation, and comparison of per-species chromosomal distribution of miRNA genes in different families. This study illustrates hypothesis generation using miRNAVISA in seven species. Our results unveil a subclass of miRNAs that may be regulated by genomic imprinting, and also suggest that some miRNA families may be species-specific, as well as chromosome- and/or strand-specific.
- Published
- 2013
- Full Text
- View/download PDF
34. Dragon exploratory system on hepatitis C virus (DESHCV)
- Author
-
Monique Maqungo, Aleksandar Radovanovic, Samuel K. Kwofie, Vijayaraghava Seshadri Sundararajan, Vladimir B. Bajic, and Alan Christoffels
- Subjects
Microbiology (medical) ,Proteomics ,PubMed ,Hepatitis C virus ,Software Validation ,MEDLINE ,Scientific literature ,Hepacivirus ,Biology ,Bioinformatics ,medicine.disease_cause ,Microbiology ,Antiviral Agents ,World Wide Web ,User-Computer Interface ,Viral Proteins ,Resource (project management) ,Knowledge extraction ,Computer Systems ,Genetics ,medicine ,Data Mining ,Humans ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Internet ,business.industry ,Infectious Diseases ,Knowledge base ,Database Management Systems ,The Internet ,Web resource ,business - Abstract
Even though hepatitis C virus (HCV) cDNA was characterized about 20 years ago, there is insufficient understanding of the molecular etiology underlying HCV infections. Current global rates of infection and its increasingly chronic character are causes of concern for health policy experts. Vast amount of data accumulated from biochemical, genomic, proteomic, and other biological analyses allows for novel insights into the HCV viral structure, life cycle and functions of its proteins. Biomedical text-mining is a useful approach for analyzing the increasing corpus of published scientific literature on HCV. We report here the first comprehensive HCV customized biomedical text-mining based online web resource, dragon exploratory system on hepatitis C virus (DESHCV), a biomedical text-mining and relationship exploring knowledge base was developed by exploring literature on HCV. The pre-compiled dictionaries existing in the dragon exploratory system (DES) were enriched with biomedical concepts pertaining to HCV proteins, their name variants and symbols to make it suitable for targeted information exploration and knowledge extraction as focused on HCV. A list of 32,895 abstracts retrieved via PubMed database using specific keywords searches related to HCV were processed based on concept recognition of terms from several dictionaries. The web query interface enables retrieval of information using specified concepts, keywords and phrases, generating text-derived association networks and hypotheses, which could be tested to identify potentially novel relationship between different concepts. Such an approach could also augment efforts in the search for diagnostic or even therapeutic targets. DESHCV thus represents online literature-based discovery resource freely accessible for academic and non-profit users via http://apps.sanbi.ac.za/DESHCV/ and its mirror site http://cbrc.kaust.edu.sa/deshcv/.
- Published
- 2010
35. DDEC: Dragon database of genes implicated in esophageal cancer
- Author
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Sebastian Schmeier, Mandeep Kaur, Sundararajan Vijayaraghava Seshadri, Magbubah Essack, Ulf Schaefer, Aleksandar Radovanovic, Vladimir B. Bajic, and Alan Christoffels
- Subjects
Male ,Cancer Research ,Esophageal Neoplasms ,Information Storage and Retrieval ,Disease ,computer.software_genre ,Bioinformatics ,lcsh:RC254-282 ,Database ,User-Computer Interface ,Surgical oncology ,Databases, Genetic ,Genetics ,medicine ,Humans ,Databases, Protein ,Survival rate ,Gene ,Ovarian Neoplasms ,Models, Genetic ,business.industry ,Gene Expression Profiling ,Cancer ,Esophageal cancer ,lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,medicine.disease ,Gene Expression Regulation, Neoplastic ,Gene expression profiling ,Treatment Outcome ,Oncology ,Database Management Systems ,Female ,Ovarian cancer ,business ,computer ,Software - Abstract
Background Esophageal cancer ranks eighth in order of cancer occurrence. Its lethality primarily stems from inability to detect the disease during the early organ-confined stage and the lack of effective therapies for advanced-stage disease. Moreover, the understanding of molecular processes involved in esophageal cancer is not complete, hampering the development of efficient diagnostics and therapy. Efforts made by the scientific community to improve the survival rate of esophageal cancer have resulted in a wealth of scattered information that is difficult to find and not easily amendable to data-mining. To reduce this gap and to complement available cancer related bioinformatic resources, we have developed a comprehensive database (Dragon Database of Genes Implicated in Esophageal Cancer) with esophageal cancer related information, as an integrated knowledge database aimed at representing a gateway to esophageal cancer related data. Description Manually curated 529 genes differentially expressed in EC are contained in the database. We extracted and analyzed the promoter regions of these genes and complemented gene-related information with transcription factors that potentially control them. We further, precompiled text-mined and data-mined reports about each of these genes to allow for easy exploration of information about associations of EC-implicated genes with other human genes and proteins, metabolites and enzymes, toxins, chemicals with pharmacological effects, disease concepts and human anatomy. The resulting database, DDEC, has a useful feature to display potential associations that are rarely reported and thus difficult to identify. Moreover, DDEC enables inspection of potentially new 'association hypotheses' generated based on the precompiled reports. Conclusion We hope that this resource will serve as a useful complement to the existing public resources and as a good starting point for researchers and physicians interested in EC genetics. DDEC is freely accessible to academic and non-profit users at http://apps.sanbi.ac.za/ddec/. DDEC will be updated twice a year.
- Published
- 2009
36. DDESC: Dragon database for exploration of sodium channels in human
- Author
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Sunil Sagar, Mandeep Kaur, Sundararajan Vijayaraghava Seshadri, Adam Dawe, Aleksandar Radovanovic, Alan Christoffels, Vladimir B. Bajic, and Ulf Schaefer
- Subjects
Genetics ,Mutation ,lcsh:QH426-470 ,lcsh:Biotechnology ,Long QT syndrome ,Sodium channel ,Biology ,medicine.disease ,medicine.disease_cause ,Sodium Channels ,Database ,lcsh:Genetics ,Epilepsy ,Channelopathy ,lcsh:TP248.13-248.65 ,Databases, Genetic ,medicine ,Humans ,Integral membrane protein ,Software ,Ion channel ,Biotechnology ,Brugada syndrome - Abstract
Background Sodium channels are heteromultimeric, integral membrane proteins that belong to a superfamily of ion channels. The mutations in genes encoding for sodium channel proteins have been linked with several inherited genetic disorders such as febrile epilepsy, Brugada syndrome, ventricular fibrillation, long QT syndrome, or channelopathy associated insensitivity to pain. In spite of these significant effects that sodium channel proteins/genes could have on human health, there is no publicly available resource focused on sodium channels that would support exploration of the sodium channel related information. Results We report here Dragon Database for Exploration of Sodium Channels in Human (DDESC), which provides comprehensive information related to sodium channels regarding different entities, such as "genes and proteins", "metabolites and enzymes", "toxins", "chemicals with pharmacological effects", "disease concepts", "human anatomy", "pathways and pathway reactions" and their potential links. DDESC is compiled based on text- and data-mining. It allows users to explore potential associations between different entities related to sodium channels in human, as well as to automatically generate novel hypotheses. Conclusion DDESC is first publicly available resource where the information related to sodium channels in human can be explored at different levels. This database is freely accessible for academic and non-profit users via the worldwide web http://apps.sanbi.ac.za/ddesc.
- Published
- 2008
37. Information Exploration System for Sickle Cell Disease and Repurposing of Hydroxyfasudil
- Author
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Vladimir B. Bajic, Magbubah Essack, and Aleksandar Radovanovic
- Subjects
PubMed ,Text Mining ,MEDLINE ,lcsh:Medicine ,Information Storage and Retrieval ,Biological Data Management ,Anemia, Sickle Cell ,Disease ,Bioinformatics ,Databases ,Text mining ,Autosomal Recessive ,Antisickling Agents ,1-(5-Isoquinolinesulfonyl)-2-Methylpiperazine ,Databases, Genetic ,Genetics ,Data Mining ,Humans ,Hydroxyurea ,Medicine ,lcsh:Science ,Biology ,Repurposing ,Clinical Genetics ,Sickle Cell Disease ,Multidisciplinary ,Information retrieval ,Web search query ,business.industry ,lcsh:R ,Information processing ,Computational Biology ,Human Genetics ,Hematology ,Hemoglobinopathies ,Drug development ,Computer Science ,lcsh:Q ,Information Technology ,business ,Software ,Research Article ,Medical literature - Abstract
Background Sickle cell disease (SCD) is a fatal monogenic disorder with no effective cure and thus high rates of morbidity and sequelae. Efforts toward discovery of disease modifying drugs and curative strategies can be augmented by leveraging the plethora of information contained in available biomedical literature. To facilitate research in this direction we have developed a resource, Dragon Exploration System for Sickle Cell Disease (DESSCD) (http://cbrc.kaust.edu.sa/desscd/) that aims to promote the easy exploration of SCD-related data. Description The Dragon Exploration System (DES), developed based on text mining and complemented by data mining, processed 419,612 MEDLINE abstracts retrieved from a PubMed query using SCD-related keywords. The processed SCD-related data has been made available via the DESSCD web query interface that enables: a/information retrieval using specified concepts, keywords and phrases, and b/the generation of inferred association networks and hypotheses. The usefulness of the system is demonstrated by: a/reproducing a known scientific fact, the “Sickle_Cell_Anemia–Hydroxyurea” association, and b/generating novel and plausible “Sickle_Cell_Anemia–Hydroxyfasudil” hypothesis. A PCT patent (PCT/US12/55042) has been filed for the latter drug repurposing for SCD treatment. Conclusion We developed the DESSCD resource dedicated to exploration of text-mined and data-mined information about SCD. No similar SCD-related resource exists. Thus, we anticipate that DESSCD will serve as a valuable tool for physicians and researchers interested in SCD.
- Published
- 2013
38. Dragon exploration system on marine sponge compounds interactions
- Author
-
Mandeep Kaur, Aleksandar Radovanovic, Sunil Sagar, and Vladimir B. Bajic
- Subjects
Natural products ,business.industry ,Drug discovery ,Chemical data ,Biology ,Library and Information Sciences ,Sponge compounds interactions ,Data science ,Computer Graphics and Computer-Aided Design ,Text-mining ,Field (computer science) ,Computer Science Applications ,Database ,Information integration ,Knowledge base ,Lead (geology) ,Resource (project management) ,Web resource ,Physical and Theoretical Chemistry ,business - Abstract
Background Natural products are considered a rich source of new chemical structures that may lead to the therapeutic agents in all major disease areas. About 50% of the drugs introduced in the market in the last 20 years were natural products/derivatives or natural products mimics, which clearly shows the influence of natural products in drug discovery. Results In an effort to further support the research in this field, we have developed an integrative knowledge base on Marine Sponge Compounds Interactions (Dragon Exploration System on Marine Sponge Compounds Interactions - DESMSCI) as a web resource. This knowledge base provides information about the associations of the sponge compounds with different biological concepts such as human genes or proteins, diseases, as well as pathways, based on the literature information available in PubMed and information deposited in several other databases. As such, DESMSCI is aimed as a research support resource for problems on the utilization of marine sponge compounds. DESMSCI allows visualization of relationships between different chemical compounds and biological concepts through textual and tabular views, graphs and relational networks. In addition, DESMSCI has built in hypotheses discovery module that generates potentially new/interesting associations among different biomedical concepts. We also present a case study derived from the hypotheses generated by DESMSCI which provides a possible novel mode of action for variolins in Alzheimer’s disease. Conclusion DESMSCI is the first publicly available (http://www.cbrc.kaust.edu.sa/desmsci) comprehensive resource where users can explore information, compiled by text- and data-mining approaches, on biological and chemical data related to sponge compounds.
- Published
- 2013
39. An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man
- Author
-
Yayoi Kitazume, Oliver Hofmann, Trey Ideker, Erik van Nimwegen, Carsten O. Daub, Harukazu Suzuki, David A. Hume, Chikatoshi Kai, Jung Hoon Han, Hideya Kawaji, Aleksandar Radovanovic, Kengo Imamura, Shiro Fukuda, Rohan D. Teasdale, Kai Tan, Timo Lassmann, Shintaro Katayama, Piero Carninci, Kayoko Murakami, Julian Gough, Carlo Vittorio Cannistraci, Mandeep Kaur, Boris Lenhard, Mutsumi Kanamori-Katayama, Atsutaka Kubosaki, Jesper Tegnér, Ariel S. Schwartz, Chihiro Ogawa, Jun Kawai, Vladimir B. Bajic, Michihira Tagami, Winston Hide, Takehiro Hashimoto, Altuna Akalin, Sean M. Grimmond, Nicolas Bertin, Sebastian Schmeier, Yoshihide Hayashizaki, Takahiro Arakawa, Sarah A. Teichmann, Timothy Ravasi, Cameron Ross MacPherson, Atanas Kamburov, Alistair R. R. Forrest, Noriko Ninomiya, and Ryoko Ishihara
- Subjects
0106 biological sciences ,Cellular differentiation ,Gene regulatory network ,Computational biology ,Biology ,Cell fate determination ,01 natural sciences ,Article ,Monocytes ,General Biochemistry, Genetics and Molecular Biology ,Protein–protein interaction ,Evolution, Molecular ,Mice ,03 medical and health sciences ,0302 clinical medicine ,Gene expression ,Transcriptional regulation ,Animals ,Humans ,Gene Regulatory Networks ,Smad3 Protein ,Transcription factor ,GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries) ,030304 developmental biology ,Genetics ,Regulation of gene expression ,0303 health sciences ,Biochemistry, Genetics and Molecular Biology(all) ,Cell Differentiation ,DNA ,Gene Expression Regulation ,Organ Specificity ,030220 oncology & carcinogenesis ,Trans-Activators ,Transcription Factors ,010606 plant biology & botany - Abstract
Combinatorial interactions among transcription factors are critical to directing tissue-specific gene expression. To build a global atlas of these combinations, we have screened for physical interactions among the majority of human and mouse DNA-binding transcription factors (TFs). The complete networks contain 762 human and 877 mouse interactions. Analysis of the networks reveals that highly connected TFs are broadly expressed across tissues, and that roughly half of the measured interactions are conserved between mouse and human. The data highlight the importance of TF combinations for determining cell fate, and they lead to the identification of a SMAD3/FLI1 complex expressed during development of immunity. The availability of large TF combinatorial networks in both human and mouse will provide many opportunities to study gene regulation, tissue differentiation, and mammalian evolution.
- Published
- 2010
40. Oskar Vajld na Divlјem zapadu: karikatura, feminiziranost i keltski primitivizam
- Author
-
Aleksandar Radovanović
- Subjects
Oskar Vajld ,esteticizam ,Divlјi zapad ,feminiziranost ,viktorijanska karikatura ,anglo-irski odnosi ,Anthropology ,GN1-890 - Abstract
Ovaj rad vraća se u 1882. godinu kako bi razmotrio američku predavačku turneju Oskara Vajlda u kontekstu savremenog opažanja feminiziranosti i anglosaksonskog pogleda na keltsku drugost. Uzimajući u obzir specifične kulturne okolnosti Sjedinjenih Država, anglo-američkih i anglo-irskih odnosa, rad se fokusira na tadašnje karikature Oskara Vajlda kao odraz rodnih i rasnih predrasuda koje je pobuđivala njegova feminizirana i kulturno divergentna pojava. Kao scenografska pozadina Vajldovih predavanja pomalјa se britanska percepcija Sjedinjenih Država kao egzotičnog kulturnog podneblјa čiji primitivizam budi romantičnu fascinaciju Engleza, ali čiji privredni zamajac i rastući politički uticaj ulivaju zebnju u perspektivu imperijalnog poretka i status Britanije kao globalnog lidera. Vajld nije u Nјujork stigao kao Irac, već kao kulturni izaslanik Engleske. Uživlјavajući se u ulogu estetskog prosvetitelјa koji materijalistički nastrojenom američkom društvu obznanjuje moderne tendencije u engleskoj umetnosti, Vajld je svojim nastupima implicitno potvrđivao kulturni primat matice. Feminiziranost ekscentričnog predavača delom je bila prihvaćena kao umetnička poza i manifestacija evropejske sofisticiranosti, ali ujedno je bila tumačena i kao simptom degeneracije koja podriva njegovu muževnost, pa i kao obeležje keltske nazadnosti koja onemogućava integraciju sa anglosaksonskom rasom.
- Published
- 2018
- Full Text
- View/download PDF
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