TY  - JOUR
AU  - Bajić, Vladan P.
AU  - Salhi, Adil
AU  - Lakota, Katja
AU  - Radovanović, Aleksandar
AU  - Razali, Rozaimi
AU  - Živković, Lada
AU  - Spremo-Potparević, Biljana
AU  - Uludag, Mahmut
AU  - Tifratene, Faroug
AU  - Motwalli, Olaa
AU  - Marchand, Benoit
AU  - Bajić, Vladimir
AU  - Gojobori, Takashi
AU  - Isenović, Esma R.
AU  - Essack, Magbubah
PY  - 2022
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/10387
AB  - More than 30 types of amyloids are linked to close to 50 diseases in humans, the most prom- inent 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 net- work 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 rele- vant information regarding the biological network related to amyloid proteins/peptides and amyloid-related diseases. This KB contains information obtained through text and data min- ing 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 infor- mation 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.
T2  - PLoS ONE
T1  - DES-Amyloidoses “Amyloidoses through thelooking-glass”: A knowledgebase developedfor exploring and linking information relatedto human amyloid-related diseases
VL  - 17
IS  - 7
DO  - 10.1371/journal.pone.0271737
ER  - 

@article{
author = "Bajić, Vladan P. and Salhi, Adil and Lakota, Katja and Radovanović, Aleksandar and Razali, Rozaimi and Živković, Lada and Spremo-Potparević, Biljana and Uludag, Mahmut and Tifratene, Faroug and Motwalli, Olaa and Marchand, Benoit and Bajić, Vladimir and Gojobori, Takashi and Isenović, Esma R. and Essack, Magbubah",
year = "2022",
abstract = "More than 30 types of amyloids are linked to close to 50 diseases in humans, the most prom- inent 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 net- work 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 rele- vant information regarding the biological network related to amyloid proteins/peptides and amyloid-related diseases. This KB contains information obtained through text and data min- ing 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 infor- mation 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.",
journal = "PLoS ONE",
title = "DES-Amyloidoses “Amyloidoses through thelooking-glass”: A knowledgebase developedfor exploring and linking information relatedto human amyloid-related diseases",
volume = "17",
number = "7",
doi = "10.1371/journal.pone.0271737"
}

Bajić, V. P., Salhi, A., Lakota, K., Radovanović, A., Razali, R., Živković, L., Spremo-Potparević, B., Uludag, M., Tifratene, F., Motwalli, O., Marchand, B., Bajić, V., Gojobori, T., Isenović, E. R.,& Essack, M.. (2022). DES-Amyloidoses “Amyloidoses through thelooking-glass”: A knowledgebase developedfor exploring and linking information relatedto human amyloid-related diseases. in PLoS ONE, 17(7).
https://doi.org/10.1371/journal.pone.0271737

Bajić VP, Salhi A, Lakota K, Radovanović A, Razali R, Živković L, Spremo-Potparević B, Uludag M, Tifratene F, Motwalli O, Marchand B, Bajić V, Gojobori T, Isenović ER, Essack M. DES-Amyloidoses “Amyloidoses through thelooking-glass”: A knowledgebase developedfor exploring and linking information relatedto human amyloid-related diseases. in PLoS ONE. 2022;17(7).
doi:10.1371/journal.pone.0271737 .

Bajić, Vladan P., Salhi, Adil, Lakota, Katja, Radovanović, Aleksandar, Razali, Rozaimi, Živković, Lada, Spremo-Potparević, Biljana, Uludag, Mahmut, Tifratene, Faroug, Motwalli, Olaa, Marchand, Benoit, Bajić, Vladimir, Gojobori, Takashi, Isenović, Esma R., Essack, Magbubah, "DES-Amyloidoses “Amyloidoses through thelooking-glass”: A knowledgebase developedfor exploring and linking information relatedto human amyloid-related diseases" in PLoS ONE, 17, no. 7 (2022),
https://doi.org/10.1371/journal.pone.0271737 . .

TY  - JOUR
AU  - Gluvić, Zoran
AU  - Obradović, Milan M.
AU  - Sudar-Milovanović, Emina
AU  - Zafirović, Sonja
AU  - Radak, Đorđe J.
AU  - Essack, Magbubah
AU  - Bajić, Vladimir B.
AU  - Gojobori, Takashi
AU  - Isenović, Esma R.
PY  - 2020
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/8474
AB  - Hypothyroidism is a common endocrine disorder that predominantly occurs in females. It is associated with an increased risk of cardiovascular diseases (CVD), but the molecular mechanism is not known. Disturbance in lipid metabolism, the regulation of oxidative stress, and inflammation characterize the progression of subclinical hypothyroidism. The initiation and progression of endothelial dysfunction also exhibit these changes, which is the initial step in developing CVD. Animal and human studies highlight the critical role of nitric oxide (NO) as a reliable biomarker for cardiovascular risk in subclinical and clinical hypothyroidism. In this review, we summarize the recent literature findings associated with NO production by the thyroid hormones in both physiological and pathophysiological conditions. We also discuss the levothyroxine treatment effect on serum NO levels in hypothyroid patients. © 2020 The Authors
T2  - Biomedicine and Pharmacotherapy
T1  - Regulation of nitric oxide production in hypothyroidism
VL  - 124
SP  - 109881
DO  - 10.1016/j.biopha.2020.109881
ER  - 

@article{
author = "Gluvić, Zoran and Obradović, Milan M. and Sudar-Milovanović, Emina and Zafirović, Sonja and Radak, Đorđe J. and Essack, Magbubah and Bajić, Vladimir B. and Gojobori, Takashi and Isenović, Esma R.",
year = "2020",
abstract = "Hypothyroidism is a common endocrine disorder that predominantly occurs in females. It is associated with an increased risk of cardiovascular diseases (CVD), but the molecular mechanism is not known. Disturbance in lipid metabolism, the regulation of oxidative stress, and inflammation characterize the progression of subclinical hypothyroidism. The initiation and progression of endothelial dysfunction also exhibit these changes, which is the initial step in developing CVD. Animal and human studies highlight the critical role of nitric oxide (NO) as a reliable biomarker for cardiovascular risk in subclinical and clinical hypothyroidism. In this review, we summarize the recent literature findings associated with NO production by the thyroid hormones in both physiological and pathophysiological conditions. We also discuss the levothyroxine treatment effect on serum NO levels in hypothyroid patients. © 2020 The Authors",
journal = "Biomedicine and Pharmacotherapy",
title = "Regulation of nitric oxide production in hypothyroidism",
volume = "124",
pages = "109881",
doi = "10.1016/j.biopha.2020.109881"
}

Gluvić, Z., Obradović, M. M., Sudar-Milovanović, E., Zafirović, S., Radak, Đ. J., Essack, M., Bajić, V. B., Gojobori, T.,& Isenović, E. R.. (2020). Regulation of nitric oxide production in hypothyroidism. in Biomedicine and Pharmacotherapy, 124, 109881.
https://doi.org/10.1016/j.biopha.2020.109881

Gluvić Z, Obradović MM, Sudar-Milovanović E, Zafirović S, Radak ĐJ, Essack M, Bajić VB, Gojobori T, Isenović ER. Regulation of nitric oxide production in hypothyroidism. in Biomedicine and Pharmacotherapy. 2020;124:109881.
doi:10.1016/j.biopha.2020.109881 .

Gluvić, Zoran, Obradović, Milan M., Sudar-Milovanović, Emina, Zafirović, Sonja, Radak, Đorđe J., Essack, Magbubah, Bajić, Vladimir B., Gojobori, Takashi, Isenović, Esma R., "Regulation of nitric oxide production in hypothyroidism" in Biomedicine and Pharmacotherapy, 124 (2020):109881,
https://doi.org/10.1016/j.biopha.2020.109881 . .

TY  - JOUR
AU  - Bajić, Vladan P.
AU  - Essack, Magbubah
AU  - Živković, Lada
AU  - Stewart, Alan J.
AU  - Zafirović, Sonja
AU  - Bajić, Vladimir B.
AU  - Gojobori, Takashi
AU  - Isenović, Esma R.
AU  - Spremo-Potparević, Biljana
PY  - 2020
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/8825
AB  - Alzheimer’s disease (AD) is a neurodegenerative disease that affects millions of individuals worldwide and can occur relatively early or later in life. It is well known that genetic components, such as the amyloid precursor protein gene on chromosome 21, are fundamental in early-onset AD (EOAD). To date, however, only the apolipoprotein E4 (ApoE4) gene has been proved to be a genetic risk factor for late-onset AD (LOAD). In recent years, despite the hypothesis that many additional unidentified genes are likely to play a role in AD development, it is surprising that additional gene polymorphisms associated with LOAD have failed to come to light. In this review, we examine the role of X chromosome epigenetics and, based upon GWAS studies, the PCDHX11 gene. Furthermore, we explore other genetic risk factors of AD that involve X-chromosome epigenetics. © Copyright © 2020 Bajic, Essack, Zivkovic, Stewart, Zafirovic, Bajic, Gojobori, Isenovic and Spremo-Potparevic.
T2  - Frontiers in Genetics
T1  - The X Files: “The Mystery of X Chromosome Instability in Alzheimer’s Disease”
VL  - 10
DO  - 10.3389/fgene.2019.01368
ER  - 

@article{
author = "Bajić, Vladan P. and Essack, Magbubah and Živković, Lada and Stewart, Alan J. and Zafirović, Sonja and Bajić, Vladimir B. and Gojobori, Takashi and Isenović, Esma R. and Spremo-Potparević, Biljana",
year = "2020",
abstract = "Alzheimer’s disease (AD) is a neurodegenerative disease that affects millions of individuals worldwide and can occur relatively early or later in life. It is well known that genetic components, such as the amyloid precursor protein gene on chromosome 21, are fundamental in early-onset AD (EOAD). To date, however, only the apolipoprotein E4 (ApoE4) gene has been proved to be a genetic risk factor for late-onset AD (LOAD). In recent years, despite the hypothesis that many additional unidentified genes are likely to play a role in AD development, it is surprising that additional gene polymorphisms associated with LOAD have failed to come to light. In this review, we examine the role of X chromosome epigenetics and, based upon GWAS studies, the PCDHX11 gene. Furthermore, we explore other genetic risk factors of AD that involve X-chromosome epigenetics. © Copyright © 2020 Bajic, Essack, Zivkovic, Stewart, Zafirovic, Bajic, Gojobori, Isenovic and Spremo-Potparevic.",
journal = "Frontiers in Genetics",
title = "The X Files: “The Mystery of X Chromosome Instability in Alzheimer’s Disease”",
volume = "10",
doi = "10.3389/fgene.2019.01368"
}

Bajić, V. P., Essack, M., Živković, L., Stewart, A. J., Zafirović, S., Bajić, V. B., Gojobori, T., Isenović, E. R.,& Spremo-Potparević, B.. (2020). The X Files: “The Mystery of X Chromosome Instability in Alzheimer’s Disease”. in Frontiers in Genetics, 10.
https://doi.org/10.3389/fgene.2019.01368

Bajić VP, Essack M, Živković L, Stewart AJ, Zafirović S, Bajić VB, Gojobori T, Isenović ER, Spremo-Potparević B. The X Files: “The Mystery of X Chromosome Instability in Alzheimer’s Disease”. in Frontiers in Genetics. 2020;10.
doi:10.3389/fgene.2019.01368 .

Bajić, Vladan P., Essack, Magbubah, Živković, Lada, Stewart, Alan J., Zafirović, Sonja, Bajić, Vladimir B., Gojobori, Takashi, Isenović, Esma R., Spremo-Potparević, Biljana, "The X Files: “The Mystery of X Chromosome Instability in Alzheimer’s Disease”" in Frontiers in Genetics, 10 (2020),
https://doi.org/10.3389/fgene.2019.01368 . .

TY  - JOUR
AU  - Zarić, Božidarka
AU  - Radovanović, Jelena N.
AU  - Gluvić, Zoran
AU  - Stewart, Alan J.
AU  - Essack, Magbubah
AU  - Motwalli, Olaa
AU  - Gojobori, Takashi
AU  - Isenović, Esma R.
PY  - 2020
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/9681
AB  - Cardiovascular disease is the leading global health concern and responsible for more deaths worldwide than any other type of disorder. Atherosclerosis is a chronic inflammatory disease in the arterial wall, which underpins several types of cardiovascular disease. It has emerged that a strong relationship exists between alterations in amino acid (AA) metabolism and the development of atherosclerosis. Recent studies have reported positive correlations between levels of branched-chain amino acids (BCAAs) such as leucine, valine, and isoleucine in plasma and the occurrence of metabolic disturbances. Elevated serum levels of BCAAs indicate a high cardiometabolic risk. Thus, BCAAs may also impact atherosclerosis prevention and offer a novel therapeutic strategy for specific individuals at risk of coronary events. The metabolism of AAs, such as L-arginine, homoarginine, and L-tryptophan, is recognized as a critical regulator of vascular homeostasis. Dietary intake of homoarginine, taurine, and glycine can improve atherosclerosis by endothelium remodeling. Available data also suggest that the regulation of AA metabolism by indoleamine 2,3-dioxygenase (IDO) and arginases 1 and 2 are mediated through various immunological signals and that immunosuppressive AA metabolizing enzymes are promising therapeutic targets against atherosclerosis. Further clinical studies and basic studies that make use of animal models are required. Here we review recent data examining links between AA metabolism and the development of atherosclerosis.
T2  - Frontiers in Immunology
T1  - Atherosclerosis Linked to Aberrant Amino Acid Metabolism and Immunosuppressive Amino Acid Catabolizing Enzymes
VL  - 11
SP  - 2341
DO  - 10.3389/fimmu.2020.551758
ER  - 

@article{
author = "Zarić, Božidarka and Radovanović, Jelena N. and Gluvić, Zoran and Stewart, Alan J. and Essack, Magbubah and Motwalli, Olaa and Gojobori, Takashi and Isenović, Esma R.",
year = "2020",
abstract = "Cardiovascular disease is the leading global health concern and responsible for more deaths worldwide than any other type of disorder. Atherosclerosis is a chronic inflammatory disease in the arterial wall, which underpins several types of cardiovascular disease. It has emerged that a strong relationship exists between alterations in amino acid (AA) metabolism and the development of atherosclerosis. Recent studies have reported positive correlations between levels of branched-chain amino acids (BCAAs) such as leucine, valine, and isoleucine in plasma and the occurrence of metabolic disturbances. Elevated serum levels of BCAAs indicate a high cardiometabolic risk. Thus, BCAAs may also impact atherosclerosis prevention and offer a novel therapeutic strategy for specific individuals at risk of coronary events. The metabolism of AAs, such as L-arginine, homoarginine, and L-tryptophan, is recognized as a critical regulator of vascular homeostasis. Dietary intake of homoarginine, taurine, and glycine can improve atherosclerosis by endothelium remodeling. Available data also suggest that the regulation of AA metabolism by indoleamine 2,3-dioxygenase (IDO) and arginases 1 and 2 are mediated through various immunological signals and that immunosuppressive AA metabolizing enzymes are promising therapeutic targets against atherosclerosis. Further clinical studies and basic studies that make use of animal models are required. Here we review recent data examining links between AA metabolism and the development of atherosclerosis.",
journal = "Frontiers in Immunology",
title = "Atherosclerosis Linked to Aberrant Amino Acid Metabolism and Immunosuppressive Amino Acid Catabolizing Enzymes",
volume = "11",
pages = "2341",
doi = "10.3389/fimmu.2020.551758"
}

Zarić, B., Radovanović, J. N., Gluvić, Z., Stewart, A. J., Essack, M., Motwalli, O., Gojobori, T.,& Isenović, E. R.. (2020). Atherosclerosis Linked to Aberrant Amino Acid Metabolism and Immunosuppressive Amino Acid Catabolizing Enzymes. in Frontiers in Immunology, 11, 2341.
https://doi.org/10.3389/fimmu.2020.551758

Zarić B, Radovanović JN, Gluvić Z, Stewart AJ, Essack M, Motwalli O, Gojobori T, Isenović ER. Atherosclerosis Linked to Aberrant Amino Acid Metabolism and Immunosuppressive Amino Acid Catabolizing Enzymes. in Frontiers in Immunology. 2020;11:2341.
doi:10.3389/fimmu.2020.551758 .

Zarić, Božidarka, Radovanović, Jelena N., Gluvić, Zoran, Stewart, Alan J., Essack, Magbubah, Motwalli, Olaa, Gojobori, Takashi, Isenović, Esma R., "Atherosclerosis Linked to Aberrant Amino Acid Metabolism and Immunosuppressive Amino Acid Catabolizing Enzymes" in Frontiers in Immunology, 11 (2020):2341,
https://doi.org/10.3389/fimmu.2020.551758 . .

TY  - JOUR
AU  - Essack, Magbubah
AU  - Salhi, Adil
AU  - Van Neste, Christophe
AU  - Raies, Arwa Bin
AU  - Tifratene, Faroug
AU  - Uludag, Mahmut
AU  - Hungler, Arnaud
AU  - Zarić, Božidarka
AU  - Zafirović, Sonja
AU  - Gojobori, Takashi
AU  - Isenović, Esma R.
AU  - Bajić, Vladan P.
PY  - 2020
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/8945
AB  - Normal cellular physiology and biochemical processes require undamaged RNA molecules. However, RNAs are frequently subjected to oxidative damage. Overproduction of reactive oxygen species (ROS) leads to RNA oxidation and disturbs redox (oxidation-reduction reaction) homeostasis. When oxidation damage affects RNA carrying protein-coding information, this may result in the synthesis of aberrant proteins as well as a lower efficiency of translation. Both of these, as well as imbalanced redox homeostasis, may lead to numerous human diseases. The number of studies on the effects of RNA oxidative damage in mammals is increasing by year due to the understanding that this oxidation fundamentally leads to numerous human diseases. To enable researchers in this field to explore information relevant to RNA oxidation and effects on human diseases, we developed DES-ROD, an online knowledgebase that contains processed information from 298,603 relevant documents that consist of PubMed abstracts and PubMed Central full-text articles. The system utilizes concepts/terms from 38 curated thematic dictionaries mapped to the analyzed documents. Researchers can explore enriched concepts, as well as enriched pairs of putatively associated concepts. In this way, one can explore mutual relationships between any combinations of two concepts from used dictionaries. Dictionaries cover a wide range of biomedical topics, such as human genes and proteins, pathways, Gene Ontology categories, mutations, noncoding RNAs, enzymes, toxins, metabolites, and diseases. This makes insights into different facets of the effects of RNA oxidation and the control of this process possible. The usefulness of the DES-ROD system is demonstrated by case studies on some known information, as well as potentially novel information involving RNA oxidation and diseases. DES-ROD is the first knowledgebase based on text and data mining that focused on the exploration of RNA oxidation and human diseases.
T2  - Oxidative Medicine and Cellular Longevity
T1  - DES-ROD: Exploring Literature to Develop New Links between RNA Oxidation and Human Diseases
VL  - 2020
SP  - 5904315
DO  - 10.1155/2020/5904315
ER  - 

@article{
author = "Essack, Magbubah and Salhi, Adil and Van Neste, Christophe and Raies, Arwa Bin and Tifratene, Faroug and Uludag, Mahmut and Hungler, Arnaud and Zarić, Božidarka and Zafirović, Sonja and Gojobori, Takashi and Isenović, Esma R. and Bajić, Vladan P.",
year = "2020",
abstract = "Normal cellular physiology and biochemical processes require undamaged RNA molecules. However, RNAs are frequently subjected to oxidative damage. Overproduction of reactive oxygen species (ROS) leads to RNA oxidation and disturbs redox (oxidation-reduction reaction) homeostasis. When oxidation damage affects RNA carrying protein-coding information, this may result in the synthesis of aberrant proteins as well as a lower efficiency of translation. Both of these, as well as imbalanced redox homeostasis, may lead to numerous human diseases. The number of studies on the effects of RNA oxidative damage in mammals is increasing by year due to the understanding that this oxidation fundamentally leads to numerous human diseases. To enable researchers in this field to explore information relevant to RNA oxidation and effects on human diseases, we developed DES-ROD, an online knowledgebase that contains processed information from 298,603 relevant documents that consist of PubMed abstracts and PubMed Central full-text articles. The system utilizes concepts/terms from 38 curated thematic dictionaries mapped to the analyzed documents. Researchers can explore enriched concepts, as well as enriched pairs of putatively associated concepts. In this way, one can explore mutual relationships between any combinations of two concepts from used dictionaries. Dictionaries cover a wide range of biomedical topics, such as human genes and proteins, pathways, Gene Ontology categories, mutations, noncoding RNAs, enzymes, toxins, metabolites, and diseases. This makes insights into different facets of the effects of RNA oxidation and the control of this process possible. The usefulness of the DES-ROD system is demonstrated by case studies on some known information, as well as potentially novel information involving RNA oxidation and diseases. DES-ROD is the first knowledgebase based on text and data mining that focused on the exploration of RNA oxidation and human diseases.",
journal = "Oxidative Medicine and Cellular Longevity",
title = "DES-ROD: Exploring Literature to Develop New Links between RNA Oxidation and Human Diseases",
volume = "2020",
pages = "5904315",
doi = "10.1155/2020/5904315"
}

Essack, M., Salhi, A., Van Neste, C., Raies, A. B., Tifratene, F., Uludag, M., Hungler, A., Zarić, B., Zafirović, S., Gojobori, T., Isenović, E. R.,& Bajić, V. P.. (2020). DES-ROD: Exploring Literature to Develop New Links between RNA Oxidation and Human Diseases. in Oxidative Medicine and Cellular Longevity, 2020, 5904315.
https://doi.org/10.1155/2020/5904315

Essack M, Salhi A, Van Neste C, Raies AB, Tifratene F, Uludag M, Hungler A, Zarić B, Zafirović S, Gojobori T, Isenović ER, Bajić VP. DES-ROD: Exploring Literature to Develop New Links between RNA Oxidation and Human Diseases. in Oxidative Medicine and Cellular Longevity. 2020;2020:5904315.
doi:10.1155/2020/5904315 .

Essack, Magbubah, Salhi, Adil, Van Neste, Christophe, Raies, Arwa Bin, Tifratene, Faroug, Uludag, Mahmut, Hungler, Arnaud, Zarić, Božidarka, Zafirović, Sonja, Gojobori, Takashi, Isenović, Esma R., Bajić, Vladan P., "DES-ROD: Exploring Literature to Develop New Links between RNA Oxidation and Human Diseases" in Oxidative Medicine and Cellular Longevity, 2020 (2020):5904315,
https://doi.org/10.1155/2020/5904315 . .