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1.
AAPS J ; 24(1): 19, 2022 01 04.
Article in English | MEDLINE | ID: covidwho-1605878

ABSTRACT

Over the past decade, artificial intelligence (AI) and machine learning (ML) have become the breakthrough technology most anticipated to have a transformative effect on pharmaceutical research and development (R&D). This is partially driven by revolutionary advances in computational technology and the parallel dissipation of previous constraints to the collection/processing of large volumes of data. Meanwhile, the cost of bringing new drugs to market and to patients has become prohibitively expensive. Recognizing these headwinds, AI/ML techniques are appealing to the pharmaceutical industry due to their automated nature, predictive capabilities, and the consequent expected increase in efficiency. ML approaches have been used in drug discovery over the past 15-20 years with increasing sophistication. The most recent aspect of drug development where positive disruption from AI/ML is starting to occur, is in clinical trial design, conduct, and analysis. The COVID-19 pandemic may further accelerate utilization of AI/ML in clinical trials due to an increased reliance on digital technology in clinical trial conduct. As we move towards a world where there is a growing integration of AI/ML into R&D, it is critical to get past the related buzz-words and noise. It is equally important to recognize that the scientific method is not obsolete when making inferences about data. Doing so will help in separating hope from hype and lead to informed decision-making on the optimal use of AI/ML in drug development. This manuscript aims to demystify key concepts, present use-cases and finally offer insights and a balanced view on the optimal use of AI/ML methods in R&D.


Subject(s)
Artificial Intelligence , Clinical Trials as Topic , Computational Biology , Drug Development , Machine Learning , Pharmaceutical Research , Research Design , Animals , Artificial Intelligence/trends , Computational Biology/trends , Diffusion of Innovation , Drug Development/trends , Forecasting , Humans , Machine Learning/trends , Pharmaceutical Research/trends , Research Design/trends
2.
OMICS ; 25(11): 681-692, 2021 11.
Article in English | MEDLINE | ID: covidwho-1541502

ABSTRACT

Multiomics study designs have significantly increased understanding of complex biological systems. The multiomics literature is rapidly expanding and so is their heterogeneity. However, the intricacy and fragmentation of omics data are impeding further research. To examine current trends in multiomics field, we reviewed 52 articles from PubMed and Web of Science, which used an integrated omics approach, published between March 2006 and January 2021. From studies, data regarding investigated loci, species, omics type, and phenotype were extracted, curated, and streamlined according to standardized terminology, and summarized in a previously developed graphical summary. Evaluated studies included 21 omics types or applications of omics technology such as genomics, transcriptomics, metabolomics, epigenomics, environmental omics, and pharmacogenomics, species of various phyla including human, mouse, Arabidopsis thaliana, Saccharomyces cerevisiae, and various phenotypes, including cancer and COVID-19. In the analyzed studies, diverse methods, protocols, results, and terminology were used and accordingly, assessment of the studies was challenging. Adoption of standardized multiomics data presentation in the future will further buttress standardization of terminology and reporting of results in systems science. This shall catalyze, we suggest, innovation in both science communication and laboratory medicine by making available scientific knowledge that is easier to grasp, share, and harness toward medical breakthroughs.


Subject(s)
Computational Biology/trends , Genomics/trends , Metabolomics/trends , Proteomics/trends , Animals , COVID-19 , Computer Graphics , Epigenomics/trends , Gene Expression Profiling/trends , Humans , Pharmacogenetics/trends , Publications , SARS-CoV-2 , Terminology as Topic
4.
J Comput Biol ; 28(4): 345, 2021 04.
Article in English | MEDLINE | ID: covidwho-1202117
5.
Adv Drug Deliv Rev ; 172: 249-274, 2021 05.
Article in English | MEDLINE | ID: covidwho-1064699

ABSTRACT

SARS-CoV-2, which causes COVID-19, was first identified in humans in late 2019 and is a coronavirus which is zoonotic in origin. As it spread around the world there has been an unprecedented effort in developing effective vaccines. Computational methods can be used to speed up the long and costly process of vaccine development. Antigen selection, epitope prediction, and toxicity and allergenicity prediction are areas in which computational tools have already been applied as part of reverse vaccinology for SARS-CoV-2 vaccine development. However, there is potential for computational methods to assist further. We review approaches which have been used and highlight additional bioinformatic approaches and PK modelling as in silico methods which may be useful for SARS-CoV-2 vaccine design but remain currently unexplored. As more novel viruses with pandemic potential are expected to arise in future, these techniques are not limited to application to SARS-CoV-2 but also useful to rapidly respond to novel emerging viruses.


Subject(s)
COVID-19 Vaccines/administration & dosage , COVID-19/prevention & control , Computational Biology/methods , Drug Development/methods , SARS-CoV-2/drug effects , Animals , B-Lymphocytes/drug effects , B-Lymphocytes/immunology , COVID-19/genetics , COVID-19/immunology , COVID-19 Vaccines/genetics , COVID-19 Vaccines/immunology , Computational Biology/trends , Drug Development/trends , Epitopes/genetics , Epitopes/immunology , Gene Expression Profiling/methods , Gene Expression Profiling/trends , Humans , SARS-CoV-2/genetics , SARS-CoV-2/metabolism
7.
Nucleic Acids Res ; 49(D1): D18-D28, 2021 01 08.
Article in English | MEDLINE | ID: covidwho-917706

ABSTRACT

The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a suite of database resources to support worldwide research activities in both academia and industry. With the explosive growth of multi-omics data, CNCB-NGDC is continually expanding, updating and enriching its core database resources through big data deposition, integration and translation. In the past year, considerable efforts have been devoted to 2019nCoVR, a newly established resource providing a global landscape of SARS-CoV-2 genomic sequences, variants, and haplotypes, as well as Aging Atlas, BrainBase, GTDB (Glycosyltransferases Database), LncExpDB, and TransCirc (Translation potential for circular RNAs). Meanwhile, a series of resources have been updated and improved, including BioProject, BioSample, GWH (Genome Warehouse), GVM (Genome Variation Map), GEN (Gene Expression Nebulas) as well as several biodiversity and plant resources. Particularly, BIG Search, a scalable, one-stop, cross-database search engine, has been significantly updated by providing easy access to a large number of internal and external biological resources from CNCB-NGDC, our partners, EBI and NCBI. All of these resources along with their services are publicly accessible at https://bigd.big.ac.cn.


Subject(s)
Big Data , Computational Biology/standards , Databases, Genetic , Genomics/statistics & numerical data , SARS-CoV-2/genetics , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19/virology , China , Computational Biology/methods , Computational Biology/organization & administration , Computational Biology/trends , Data Mining/methods , Data Mining/statistics & numerical data , Epidemics , Genetic Variation , Genome, Viral/genetics , Genomics/methods , Genomics/organization & administration , Humans , Internet , Search Engine/methods , Search Engine/statistics & numerical data
8.
Res Synth Methods ; 12(2): 136-147, 2021 Mar.
Article in English | MEDLINE | ID: covidwho-838918

ABSTRACT

We researchers have taken searching for information for granted for far too long. The COVID-19 pandemic shows us the boundaries of academic searching capabilities, both in terms of our know-how and of the systems we have. With hundreds of studies published daily on COVID-19, for example, we struggle to find, stay up-to-date, and synthesize information-all hampering evidence-informed decision making. This COVID-19 information crisis is indicative of the broader problem of information overloaded academic research. To improve our finding capabilities, we urgently need to improve how we search and the systems we use. We respond to Klopfenstein and Dampier (Res Syn Meth. 2020) who commented on our 2020 paper and proposed a way of improving PubMed's and Google Scholar's search functionalities. Our response puts their commentary in a larger frame and suggests how we can improve academic searching altogether. We urge that researchers need to understand that search skills require dedicated education and training. Better and more efficient searching requires an initial understanding of the different goals that define the way searching needs to be conducted. We explain the main types of searching that we academics routinely engage in; distinguishing lookup, exploratory, and systematic searching. These three types must be conducted using different search methods (heuristics) and using search systems with specific capabilities. To improve academic searching, we introduce the "Search Triangle" model emphasizing the importance of matching goals, heuristics, and systems. Further, we suggest an urgently needed agenda toward search literacy as the norm in academic research and fit-for-purpose search systems.


Subject(s)
COVID-19 , Computational Biology/methods , Information Storage and Retrieval/methods , Search Engine , Biomedical Research , Computational Biology/statistics & numerical data , Computational Biology/trends , Humans , Information Storage and Retrieval/statistics & numerical data , Information Storage and Retrieval/trends , Pandemics , PubMed , Publications , Research Personnel , SARS-CoV-2
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