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Chen R. A Historic Retrospective on the Early Bioinformatics Research in China. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:897-899. [PMID: 37923291 PMCID: PMC10928369 DOI: 10.1016/j.gpb.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 10/28/2023] [Accepted: 10/28/2023] [Indexed: 11/07/2023]
Affiliation(s)
- Runsheng Chen
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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2
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A Bibliometric Analysis of Mexican Bioinformatics: A Portrait of Actors, Structure, and Dynamics. BIOLOGY 2022; 11:biology11010131. [PMID: 35053129 PMCID: PMC8772911 DOI: 10.3390/biology11010131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/24/2021] [Accepted: 12/25/2021] [Indexed: 11/17/2022]
Abstract
Bioinformatics is a very important informatics tool for health and biological sciences, focusing on biological data management. The objective of this work was to perform a bibliometric analysis regarding the development of Mexican bioinformatics. An exhaustive revision of the literature associated with Mexican bioinformatics in a period of 25-years was performed. Bibliometric tools, such as performance analysis and science mapping were included in the analysis. We identified the main actors as well as the structure and dynamics of Mexican bioinformatics. Some of the main findings were as follows: the thematic structure in the field is defined by the research lines of outstanding authors; the outstanding collaborations of Mexican institutions with foreign countries and institutions are influenced by the geographic proximity and binational agreements, as well as philanthropic and academic programs that promote collaborations, and there is an inclination for health issues promoted by public health financing and philanthropic organizations. It is identified that publications had an explosion since 2012, we consider that this growth may be influenced by the democratization of data, derived from the mass sequencing of biological molecules stored in public databases.
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Bioinformatics in Mexico: A diagnostic from the academic perspective and recommendations for a public policy. PLoS One 2020; 15:e0243531. [PMID: 33320879 PMCID: PMC7737905 DOI: 10.1371/journal.pone.0243531] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 11/24/2020] [Indexed: 11/19/2022] Open
Abstract
In this work, we present a diagnostic analysis of strengths, weaknesses, opportunities and threats (SWOT) of the current state of Bioinformatics in Mexico. We conducted semi-structured interviews among researchers and academics with key expertise in this field, identified by bibliometric analyses and qualitative sampling techniques. Additionally, an online survey was conducted reaching a higher number of respondents. Among the relevant findings of our study, the lack of specialized human resources and technological infrastructure stood out, along with deficiencies in the number and quality of academic programs, scarce public investment and a weak relationship between public and private institutions. However, there are great opportunities for developing a national Bioinformatics to support different economic sectors. In our opinion, this work could be useful to favor a comprehensive network among Mexican researchers, in order to lay the foundations of a national strategy towards a well designed public policy.
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Chasapi A, Aivaliotis M, Angelis L, Chanalaris A, Iliopoulos I, Kappas I, Karapiperis C, Kyrpides NC, Pafilis E, Panteris E, Topalis P, Tsiamis G, Vizirianakis IS, Vlassi M, Promponas VJ, Ouzounis CA. Establishment of computational biology in Greece and Cyprus: Past, present, and future. PLoS Comput Biol 2019; 15:e1007532. [PMID: 31856214 PMCID: PMC6922331 DOI: 10.1371/journal.pcbi.1007532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Anastasia Chasapi
- Biological Computation & Process Lab, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica, Greece
| | - Michalis Aivaliotis
- School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessalonica, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece
| | - Lefteris Angelis
- School of Informatics, Aristotle University of Thessaloniki, Thessalonica, Greece
| | - Anastasios Chanalaris
- Botnar Research Centre, NDORMS, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Ioannis Iliopoulos
- Division of Basic Sciences, School of Medicine, University of Crete, Heraklion, Greece
| | - Ilias Kappas
- School of Biology, Aristotle University of Thessaloniki, Thessalonica, Greece
| | - Christos Karapiperis
- School of Informatics, Aristotle University of Thessaloniki, Thessalonica, Greece
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America
| | - Evangelos Pafilis
- Institute of Marine Biology Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
| | - Eleftherios Panteris
- First Psychiatric Clinic, Papageorgiou General Hospital, Aristotle University of Thessaloniki, Thessalonica, Greece
| | - Pantelis Topalis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece
| | - George Tsiamis
- Department of Environmental Engineering, School of Engineering, University of Patras, Patras, Greece
| | - Ioannis S. Vizirianakis
- Department of Pharmacology, School of Pharmacy, Aristotle University of Thessaloniki, Thessalonica, Greece
| | - Metaxia Vlassi
- Institute of Biosciences & Applications, National Centre for Scientific Research Demokritos, Athens, Greece
| | - Vasilis J. Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
- * E-mail: (VJP); (CAO)
| | - Christos A. Ouzounis
- Biological Computation & Process Lab, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica, Greece
- * E-mail: (VJP); (CAO)
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Guerfali FZ, Laouini D, Boudabous A, Tekaia F. Designing and running an advanced Bioinformatics and genome analyses course in Tunisia. PLoS Comput Biol 2019; 15:e1006373. [PMID: 30689625 PMCID: PMC6349305 DOI: 10.1371/journal.pcbi.1006373] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Genome data, with underlying new knowledge, are accumulating at exponential rate thanks to ever-improving sequencing technologies and the parallel development of dedicated efficient Bioinformatics methods and tools. Advanced Education in Bioinformatics and Genome Analyses is to a large extent not accessible to students in developing countries where endeavors to set up Bioinformatics courses concern most often only basic levels. Here, we report a pioneering pilot experience concerning the design and implementation, from scratch, of a three-months advanced and extensive course in Bioinformatics and Genome Analyses in the Institut Pasteur de Tunis. Most significantly the outcome of the course was upgrading the participants’ skills in Bioinformatics and Genome Analyses to recognized international standards. Here we detail the different steps involved in the implementation of this course as well as the topics covered in the program. The description of this pilot experience might be helpful for the implementation of other similar educational projects, notably in developing countries, aiming to go beyond basics and providing young researchers with high-level skills.
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Affiliation(s)
- Fatma Z. Guerfali
- Université Tunis El Manar, Tunis, Tunisia
- Institut Pasteur de Tunis, LR11IPT02, Laboratory of Transmission, Control and Immunobiology of Infections (LTCII), Tunis-Belvédère, Tunisia
| | - Dhafer Laouini
- Université Tunis El Manar, Tunis, Tunisia
- Institut Pasteur de Tunis, LR11IPT02, Laboratory of Transmission, Control and Immunobiology of Infections (LTCII), Tunis-Belvédère, Tunisia
| | - Abdellatif Boudabous
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire Microorganisme et Biomolécules Actives, Campus Universitaire Farhat Heched, El Manar, Tunis, Tunisia
| | - Fredj Tekaia
- Institut Pasteur Paris, 28 rue du Dr Roux, 75724 Paris cedex 15, France
- * E-mail:
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Yang B, Rousseau R, Wang X, Huang S. How important is scientific software in bioinformatics research? A comparative study between international and Chinese research communities. J Assoc Inf Sci Technol 2018. [DOI: 10.1002/asi.24031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Bo Yang
- Department of Information Management; Nanjing Agricultural University; Nanjing 210095 China
- Research Center for Correlation of Domain Knowledge; Nanjing Agricultural University; Nanjing 210095 China
| | - Ronald Rousseau
- KU Leuven, Facultair Onderzoekscentrum ECOOM, Naamsestraat 61; Leuven B-3000 Belgium
- University of Antwerp (UA), Faculty of Social sciences, Middelheimlaan 1; B-2020 Antwerp Belgium
| | - Xue Wang
- Department of Information Management; Nanjing Agricultural University; Nanjing 210095 China
| | - Shuiqing Huang
- Department of Information Management; Nanjing Agricultural University; Nanjing 210095 China
- Research Center for Correlation of Domain Knowledge; Nanjing Agricultural University; Nanjing 210095 China
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Bioinformaticians wrestling with the big biomedical data. J Genet Genomics 2017; 44:223-225. [DOI: 10.1016/j.jgg.2017.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 05/01/2017] [Indexed: 12/14/2022]
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GSA and BIGD: Filling the Gap of Bioinformatics Resource and Service in China<sup/>. GENOMICS PROTEOMICS & BIOINFORMATICS 2017; 15:11-13. [PMID: 28235641 PMCID: PMC5339405 DOI: 10.1016/j.gpb.2017.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 02/10/2017] [Indexed: 12/22/2022]
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Salter B, Zhou Y, Datta S, Salter C. Bioinformatics and the Politics of Innovation in the Life Sciences: Science and the State in the United Kingdom, China, and India. SCIENCE, TECHNOLOGY & HUMAN VALUES 2016; 41:793-826. [PMID: 27546935 PMCID: PMC4982557 DOI: 10.1177/0162243916631022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The governments of China, India, and the United Kingdom are unanimous in their belief that bioinformatics should supply the link between basic life sciences research and its translation into health benefits for the population and the economy. Yet at the same time, as ambitious states vying for position in the future global bioeconomy they differ considerably in the strategies adopted in pursuit of this goal. At the heart of these differences lies the interaction between epistemic change within the scientific community itself and the apparatus of the state. Drawing on desk-based research and thirty-two interviews with scientists and policy makers in the three countries, this article analyzes the politics that shape this interaction. From this analysis emerges an understanding of the variable capacities of different kinds of states and political systems to work with science in harnessing the potential of new epistemic territories in global life sciences innovation.
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Affiliation(s)
- Brian Salter
- Department of Political Economy, King’s College London, London, UK
| | - Yinhua Zhou
- Department of Political Economy, King’s College London, London, UK
| | - Saheli Datta
- Department of Political Economy, King’s College London, London, UK
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Zhu W, Zhu Y, Yang X. Information engineering infrastructure for life sciences and its implementation in China. SCIENCE CHINA. LIFE SCIENCES 2013; 56:220-227. [PMID: 23526387 DOI: 10.1007/s11427-013-4440-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 12/31/2012] [Indexed: 06/02/2023]
Abstract
Biological data, represented by the data from omics platforms, are accumulating exponentially. As some other data-intensive scientific disciplines such as high-energy physics, climatology, meteorology, geology, geography and environmental sciences, modern life sciences have entered the information-rich era, the era of the 4th paradigm. The creation of Chinese information engineering infrastructure for pan-omics studies (CIEIPOS) has been long overdue as part of national scientific infrastructure, in accelerating the further development of Chinese life sciences, and translating rich data into knowledge and medical applications. By gathering facts of current status of international and Chinese bioinformatics communities in collecting, managing and utilizing biological data, the essay stresses the significance and urgency to create a 'data hub' in CIEIPOS, discusses challenges and possible solutions to integrate, query and visualize these data. Another important component of CIEIPOS, which is not part of traditional biological data centers such as NCBI and EBI, is omics informatics. Mass spectroscopy platform was taken as an example to illustrate the complexity of omics informatics. Its heavy dependency on computational power is highlighted. The demand for such power in omics studies is argued as the fundamental function to meet for CIEIPOS. Implementation outlook of CIEIPOS in hardware and network is discussed.
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Affiliation(s)
- Weimin Zhu
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing 100730, China.
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Li Q, Li X, Li C, Chen L, Song J, Tang Y, Xu X. A network-based multi-target computational estimation scheme for anticoagulant activities of compounds. PLoS One 2011; 6:e14774. [PMID: 21445339 PMCID: PMC3062543 DOI: 10.1371/journal.pone.0014774] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Accepted: 02/19/2011] [Indexed: 12/26/2022] Open
Abstract
Background Traditional virtual screening method pays more attention on predicted binding affinity between drug molecule and target related to a certain disease instead of phenotypic data of drug molecule against disease system, as is often less effective on discovery of the drug which is used to treat many types of complex diseases. Virtual screening against a complex disease by general network estimation has become feasible with the development of network biology and system biology. More effective methods of computational estimation for the whole efficacy of a compound in a complex disease system are needed, given the distinct weightiness of the different target in a biological process and the standpoint that partial inhibition of several targets can be more efficient than the complete inhibition of a single target. Methodology We developed a novel approach by integrating the affinity predictions from multi-target docking studies with biological network efficiency analysis to estimate the anticoagulant activities of compounds. From results of network efficiency calculation for human clotting cascade, factor Xa and thrombin were identified as the two most fragile enzymes, while the catalytic reaction mediated by complex IXa:VIIIa and the formation of the complex VIIIa:IXa were recognized as the two most fragile biological matter in the human clotting cascade system. Furthermore, the method which combined network efficiency with molecular docking scores was applied to estimate the anticoagulant activities of a serial of argatroban intermediates and eight natural products respectively. The better correlation (r = 0.671) between the experimental data and the decrease of the network deficiency suggests that the approach could be a promising computational systems biology tool to aid identification of anticoagulant activities of compounds in drug discovery. Conclusions This article proposes a network-based multi-target computational estimation method for anticoagulant activities of compounds by combining network efficiency analysis with scoring function from molecular docking.
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Affiliation(s)
- Qian Li
- Beijing National Laboratory for Molecular Sciences, State Key Lab of Rare Earth Material Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing, People's Republic of China
- Beijing National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xudong Li
- Beijing National Laboratory for Molecular Sciences, State Key Lab of Rare Earth Material Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing, People's Republic of China
| | - Canghai Li
- Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, People's Republic of China
| | - Lirong Chen
- Beijing National Laboratory for Molecular Sciences, State Key Lab of Rare Earth Material Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing, People's Republic of China
- * E-mail: (LC); (YT); (XX)
| | - Jun Song
- Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, People's Republic of China
| | - Yalin Tang
- Beijing National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing, People's Republic of China
- * E-mail: (LC); (YT); (XX)
| | - Xiaojie Xu
- Beijing National Laboratory for Molecular Sciences, State Key Lab of Rare Earth Material Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing, People's Republic of China
- * E-mail: (LC); (YT); (XX)
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