RSS-Feed abonnieren

DOI: 10.1055/s-0041-1726540
Predictions, Pivots, and a Pandemic: a Review of 2020's Top Translational Bioinformatics Publications

Summary
Objectives: Provide an overview of the emerging themes and notable papers which were published in 2020 in the field of Bioinformatics and Translational Informatics (BTI) for the International Medical Informatics Association Yearbook.
Methods: A team of 16 individuals scanned the literature from the past year. Using a scoring rubric, papers were evaluated on their novelty, importance, and objective quality. 1,224 Medical Subject Headings (MeSH) terms extracted from these papers were used to identify themes and research focuses. The authors then used the scoring results to select notable papers and trends presented in this manuscript.
Results: The search phase identified 263 potential papers and central themes of coronavirus disease 2019 (COVID-19), machine learning, and bioinformatics were examined in greater detail.
Conclusions: When addressing a once in a centruy pandemic, scientists worldwide answered the call, with informaticians playing a critical role. Productivity and innovations reached new heights in both TBI and science, but significant research gaps remain.
Publikationsverlauf
Artikel online veröffentlicht:
03. September 2021
© 2021. IMIA and Thieme. This is an open access article published by Thieme under the terms of the Creative Commons Attribution-NonDerivative-NonCommercial License, permitting copying and reproduction so long as the original work is given appropriate credit. Contents may not be used for commercial purposes, or adapted, remixed, transformed or built upon. (https://creativecommons.org/licenses/by-nc-nd/4.0/)
Georg Thieme Verlag KG
Rüdigerstraße 14, 70469 Stuttgart, Germany
-
References
- 1 Smaï-Tabbone M, Rance B. Contributions from the 2019 Literature on Bioinformatics and Translational Informatics. Yearb Med Inform 2020; (29) 188-92
- 2 Shrock E, Fujimura E, Kula T, Timms RT, Lee IH, Leng Y. et al. Viral epitope profiling of COVID-19 patients reveals cross-reactivity and correlates of severity. Science 2020; 370 6520 eabd4250
- 3 Su Y, Chen D, Yuan D, Lausted C, Choi J, Dai CL. et al. Multi-Omics Resolves a Sharp Disease-State Shift between Mild and Moderate COVID-19. Cell 2020; 183 (06) 1479-95.e20
- 4 Panda PK, Arul MN, Patel P, Verma SK, Luo W, Rubahn HG. et al. Structure-based drug designing and immunoinformatics approach for SARS-CoV-2. Sci Adv 2020; 6 (08) eabb8097
- 5 Romano JD, Bernauer M, McGrath SP, Nagar SD, Freimuth DD. A Decade of Translational Bioinformatics: A Retrospective Analysis of “Year-in-Review” Presentations. AMIA Jt Summits Transl Sci Proc. [Internet]2019 May 6 [cited 2021 March 24];2019;335-44. Available from: http://www.ncbi.nlm.nih.gov/pubmed/31258986
- 6 World Health Organization (WHO). Statement on the second meeting of the International Health Regulations (2005) Emergency Committee regarding the outbreak of novel coronavirus (2019-nCoV), (2020). Available from: https://www.who.int/news/item/30-01-2020-statement-on-the-second-meeting-of-the-international-health-regulations-(2005)-emergency-committee-regarding-the-outbreak-of-novel-coronavirus-(2019-ncov)
- 7 Mullen L, Potter C, Gostin LO, Cicero A, Nuzzo JB. An analysis of International Health Regulations Emergency Committees and Public Health Emergency of International Concern Designations. BMJ Glob Health 2020; 5 (06) e002502
- 8 Dong E, Du H, Gardner L. An interactive web-based dashboard to track COVID-19 in real time. Lancet Infect Dis 2020; 20 (05) 533-4
- 9 Dawood FS, Iuliano AD, Reed C, Meltzer MI, Shay DK, Cheng PY. et al. Estimated global mortality associated with the first 12 months of 2009 pandemic influenza A H1N1 virus circulation: A modelling study. Lancet Infect Dis 2012; 12 (09) 687-95
- 10 International Monetary Fund. World Economic Outlook Update: June 2020 - A Crisis Like No Other, An Uncertain Recovery. World Econ Outlook Reports 2020;20. Available from: https://www.imf.org/en/Publications/WEO/Issues/2020/06/24/WEOUpdateJune2020
- 11 Cutler DM, Summers LH. The COVID-19 Pandemic and the $16 Trillion Virus. JAMA 2020; 324 (15) 1495-6
- 12 Zumbrun J. Coronavirus Slump Is Worst Since Great Depression. Will It Be as Painful?. Wall Str J. 2020 . Available from: https://www.wsj.com/articles/coronavirus-slump-is-worst-since-great-depression-will-it-be-as-painful-11589115601
- 13 Lee JJ, Haupt JP. Scientific globalism during a global crisis: research collaboration and open access publications on COVID-19. High Educ (Dordr) 2020; 24: 1-18
- 14 Institut Pasteur. Whole genome of novel coronavirus, 2019-nCoV, sequenced. ScienceDaily. 2020 . Available from: https://www.sciencedaily.com/releases/2020/01/200131114748.htm
- 15 Zhang Y-Z. Novel 2019 coronavirus genome - SARS-CoV-2 coronavirus - Virological (n.d.) [cited 2021 March 15]. Available from: https://virological.org/t/novel-2019-coronavirus-genome/319
- 16 Vaccine Development. Testing, and Regulation | History of Vaccines, (n.d.) .) [cited 2021 March 14]. Available from: https://www.historyofvaccines.org/content/articles/vaccine-development-testing-and-regulation
- 17 CDC. Pinkbook | Mumps | Epidemiology of Vaccine Preventable Diseases | CDC, (n.d.) [cited 2021 March 14]. Available from: https://www.cdc.gov/vaccines/pubs/pinkbook/mumps.html#vaccines
- 18 Kaur SP, Gupta V. COVID-19 Vaccine: A comprehensive status report. Virus Res 2020; 288: 198114
- 19 Zimmer C, Corum J, Wee S-L. Covid-19 Vaccine Tracker Updates. New York Times [Internet]2021[cited 2021 March 14]. Available from: https://www.nytimes.com/interactive/2020/science/coronavirus-vaccine-tracker.html
- 20 Chen Q, Allot A, Lu Z. LitCovid: An open database of COVID-19 literature. Nucleic Acids Res 2020; 49 (D1) D1534-D1540
- 21 Yong E. How Science Beat the Virus. Atl [Internet] 2020. Available from: https://www.theatlantic.com/magazine/archive/2021/01/science-covid-19-manhattan-project/617262/
- 22 Eisen MB, Akhmanova A, Behrens TE, Weigel D. Publishing in the time of COVID-19. Elife 2020; 9: e57162
- 23 Horbach SPJM. Pandemic publishing: Medical journals strongly speed up their publication process for COVID-19. Quant Sci Stud 2020; 1: 1056-67
- 24 Palayew A, Norgaard O, Safreed-Harmon K, Andersen TH, Rasmussen LN, Lazarus JV. Pandemic publishing poses a new COVID-19 challenge. Nat Hum Behav 2020; 4 (07) 666-9
- 25 EngineeringUK. Young people and Covid-19: How the pandemic has affected careers experiences and aspirations. [Internet]2020 [cited 2021 March 23]. Available from: https://www.voced.edu.au/content/ngv%3A87723
- 26 Retracted coronavirus (COVID-19) papers – Retraction Watch [Internet](n.d.) [cited 2021 March 23]. Available from: https://retractionwatch.com/retracted-coronavirus-covid-19-papers/
- 27 Vlasschaert C, Topf JM, Hiremath S. Proliferation of Papers and Preprints During the Coronavirus Disease 2019 Pandemic: Progress or Problems With Peer Review?. Adv Chronic Kidney Dis 2020; 27 (05) 418-26
- 28 King A. Fast news or fake news?: The advantages and the pitfalls of rapid publication through pre-print servers during a pandemic. EMBO Rep 2020; 21 (06) e50817
- 29 Bendavid E, Mulaney B, Sood N, Shah S, Ling E, Bromley-Dulfano R. et al. COVID-19 antibody seroprevalence in Santa Clara County, California. In J Epidemiol 2021; 50 (02) 410-9
- 30 Gelman A. Concerns with that Stanford study of coronavirus prevalence [Internet]2020. [cited 2021 March 23]. Available from: https://statmodeling.stat.columbia.edu/2020/04/19/fatal-flaws-in-stanford-study-of-coronavirus-prevalence/
- 31 Vogel G. Antibody surveys suggesting vast undercount of coronavirus infections may be unreliable. Science [Internet] 2020;
- 32 Myers KR, Tham WY, Yin Y, Cohodes N, Thursby JG, Thursby MC. et al. Unequal effects of the COVID-19 pandemic on scientists. Nat Hum Behav 2020; 4 (09) 880-3
- 33 Ashdown GW, Dimon M, Fan M, Terán FSR, Witmer K, Gaboriau DCA. et al. A machine learning approach to define antimalarial drug action from heterogeneous cell-based screens. Sci Adv 2020; 6 (39) eaba9338
- 34 Gao Y, Cui Y. Deep transfer learning for reducing health care disparities arising from biomedical data inequality. Nat Commun 2020; 11 (01) 5131
- 35 Ha J, Park C, Park C, Park S. IMIPMF: Inferring miRNA-disease interactions using probabilistic matrix factorization. J Biomed Inform 2020; 102: 103358
- 36 Raket LL, Jaskolowski J, Kinon BJ, Brasen JC, Jönsson L, Wehnert A. et al. Dynamic ElecTronic hEalth reCord deTection (DETECT) of individuals at risk of a first episode of psychosis: a case-control development and validation study, Lancet Digit Health. 2020; 2 (05) e229-e239
- 37 Stokes JM, Yang K, Swanson K, Jin W, Cubillos-Ruiz A, Donghia NM. et al. A deep learning approach to antibiotic discovery. Cell 2020; 180 (04) 688-702
- 38 Vinks AA, Punt NC, Menke F, Kirkendall E, Butler D, Duggan TJ. et al. Electronic Health Record-Embedded Decision Support Platform for Morphine Precision Dosing in Neonates. Clin Pharmacol Ther 2020; 107 (01) 186-94
- 39 Kuang S, Wei Y, Wang L. Expression-based prediction of human essential genes and candidate lncRNAs in cancer cells. Bioinformatics 2021; 37 (03) 396-403
- 40 Tripodi IJ, Callahan TJ, Westfall JT, Meitzer NS, Dowell RD, Hunter LE. Applying knowledge-driven mechanistic inference to toxicogenomics. Toxicol In Vitro 2020; 66: 104877
- 41 Wang Z, Zhou M, Arnold C. Toward heterogeneous information fusion: bipartite graph convolutional networks for in silico drug repurposing. Bioinformatics 2020; ;36(Suppl_1): i525-i533
- 42 Kipf TN, Welling M. Semi-supervised classification with graph convolutional networks. ArXiv Prepr 2016. ArXiv1609.02907
- 43 Liu Q, Hu Z, Jiang R, Zhou M. DeepCDR: a hybrid graph convolutional network for predicting cancer drug response. Bioinformatics 2020; ;36(Suppl_2): i911-i918
- 44 Christian C, Borden BA, Danahey K, Yeo KTJ, van Wijk XMR, Ratain MJ. et al. Pharmacogenomic-Based Decision Support to Predict Adherence to Medications. Clin Pharmacol Ther 2020; 108 (02) 368-76
- 45 Fatima N, Rueda L. iSOM-GSN: an integrative approach for transforming multi-omic data into gene similarity networks via self-organizing maps. Bioinformatics 2020; 36 (15) 4248-54
- 46 Hasan MM, Schaduangrat N, Basith S, Lee G, Shoombuatong W, Manavalan B. HLPpred-Fuse: Improved and robust prediction of hemolytic peptide and its activity by fusing multiple feature representation. Bioinformatics 2020; 36 (11) 3350-6
- 47 Lundberg S, Lee S-I. A Unified Approach to Interpreting Model Predictions. Adv Neural Inf Process Syst 2017-December. [Internet]2017 [cited 2021 April 10]:4766-75. Available from: http://arxiv.org/abs/1705.07874
- 48 Zhang A, Teng L, Alterovitz G. An explainable machine learning platform for pyrazinamide resistance prediction and genetic feature identification of Mycobacterium tuberculosis. J Am Med Inform Assoc 2021; 28 (03) 533-40
- 49 Smedley NF, El-Saden S, Hsu W. Discovering and interpreting transcriptomic drivers of imaging traits using neural networks. Bioinformatics 2020; 36 (11) 3537-48
- 50 Zerka F, Barakat S, Walsh S, Bogowicz M, Leijenaar RTH, Jochems A. et al. Systematic review of privacy-preserving distributed machine learning from federated databases in health care. JCO Clin Cancer Inform 2020; 4: 184-200
- 51 Li R, Duan R, Zhang X, Lumley T, Pendergrass S, Bauer C. et al. Lossless integration of multiple electronic health records for identifying pleiotropy using summary statistics. Nat Commun 2021; 12 (01) 168
- 52 Raisaro JL, Marino F, Troncoso-Pastoriza J, Beau-Lejdstrom R, Bellazzi R, Murphy R. et al. SCOR: A secure international informatics infrastructure to investigate COVID-19. J Am Med Inform Assoc 2020; 27 (11) 1721-6
- 53 Li X, Liu L, Goodall GJ, Schreiber A, Xu T, Li J. et al. A novel single-cell based method for breast cancer prognosis. PLOS Comput Biol 2020; 16 (08) e1008133
- 54 Cao J, Zhou W, Steemers F, Trapnell C, Shendure J. Sci-fate characterizes the dynamics of gene expression in single cells. Nat. Biotechnol 2020; 38 (08) 980-8
- 55 Wang S, Zheng Y, Li J, Yu Y, Zhang W, Song M. et al. Single-Cell Transcriptomic Atlas of Primate Ovarian Aging. Cell 2020; 180 (03) 585-600.e19
- 56 Corces MR, Shcherbina A, Kundu S, Gloudemans MJ, Frésard L, Granja JM. et al. Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer's and Parkinson's diseases. Nat Genet 2020; 52 (11) 1158-68
- 57 Yao DW, O'Connor LJ, Price AL, Gusev A. Quantifying genetic effects on disease mediated by assayed gene expression levels. Nat Genet 2020; 52 (06) 626-33
- 58 Pividori M, Rajagopal PS, Barbeira A, Liang YMelia O, Bastarache L. et al; GTEx. Consortium. PhenomeXcan: Mapping the genome to the phenome through the transcriptome. Sci Adv 2020; 6 (37) eaba2083
- 59 Ramlall V, Thangaraj PM, Meydan C, Foox J, Butler D, Kim J. et al. Immune complement and coagulation dysfunction in adverse outcomes of SARS-CoV-2 infection. Nat Med 2020; 26 (10) 1609-15
- 60 Cortes A, Albers PK, Dendrou CA, Fugger L, McVean G. Identifying cross-disease components of genetic risk across hospital data in the UK Biobank. Nat Genet 2020; 52 (01) 126-34
- 61 Li R, Duan R, Zhang X, Lumley T, Pendergrass S, Bauer C. et al. Lossless integration of multiple electronic health records for identifying pleiotropy using summary statistics. Nat Commun 2021; 12 (01) 168
- 62 Hindorff LA, Bonham VL, Brody LC, Ginoza MEC, Hutter CM, Manolio TA. et al. Prioritizing diversity in human genomics research. Nat Rev Genet 2018; 19 (03) 175-85
- 63 Kelly DE, Hansen MEB, Tishkoff SA. Global variation in gene expression and the value of diverse sampling. Curr Opin Syst Biol 2017; 1: 102-8 doi.
- 64 Popejoy AB, Fullerton SM. Genomics is failing on diversity. Nature 2016; 538 (7624) 161-4
- 65 Martin AR, Kanai M, Kamatani Y, Okada Y, Neale BM, Daly MJ. Clinical use of current polygenic risk scores may exacerbate health disparities. Nat Genet 2019; 51 (04) 584-91
- 66 Mostafavi H, Harpak A, Agarwal I, Conley D, Pritchard JK, Przeworski M. Variable prediction accuracy of polygenic scores within an ancestry group. Elife 2020; 9: e48376
- 67 Craig JE, Han X, Qassim A, Hassall M, Cooke Bailey JN, Kinzy TG. et al. Multitrait analysis of glaucoma identifies new risk loci and enables polygenic prediction of disease susceptibility and progression. Nat Genet 2020; 52 (02) 160-6