The Birth of Bio-data Science: Trends, Expectations, and Applications

Overview

Journal Genomics Proteomics Bioinformatics

Specialty Biology

Date 2020 May 20

PMID 32428604

Citations 4

Authors

Wilson Wen Bin Goh

Limsoon Wong

Affiliations

Soon will be listed here.

Citing Articles

Thinking points for effective batch correction on biomedical data.

Hui H, Kong W, Goh W Brief Bioinform. 2024; 25(6).

PMID: 39397427 PMC: 11471903. DOI: 10.1093/bib/bbae515.

In silico medicine and -omics strategies in nephrology: contributions and relevance to the diagnosis and prevention of chronic kidney disease.

Checa-Ros A, Locascio A, Steib N, Okojie O, Malte-Weier T, Bermudez V Kidney Res Clin Pract. 2024; 44(1):49-57.

PMID: 39034863 PMC: 11838848. DOI: 10.23876/j.krcp.23.334.

A Multidisciplinary Hyper-Modeling Scheme in Personalized In Silico Oncology: Coupling Cell Kinetics with Metabolism, Signaling Networks, and Biomechanics as Plug-In Component Models of a Cancer Digital Twin.

Kolokotroni E, Abler D, Ghosh A, Tzamali E, Grogan J, Georgiadi E J Pers Med. 2024; 14(5).

PMID: 38793058 PMC: 11122096. DOI: 10.3390/jpm14050475.

Geniac: Automatic Configuration GENerator and Installer for nextflow pipelines.

Allain F, Romejon J, La Rosa P, Jarlier F, Servant N, Hupe P Open Res Eur. 2023; 1:76.

PMID: 37645091 PMC: 10445886. DOI: 10.12688/openreseurope.13861.2.

DTFLOW: Inference and Visualization of Single-cell Pseudotime Trajectory Using Diffusion Propagation.

Wei J, Zhou T, Zhang X, Tian T Genomics Proteomics Bioinformatics. 2021; 19(2):306-318.

PMID: 33662626 PMC: 8602766. DOI: 10.1016/j.gpb.2020.08.003.

References

Stephens Z, Lee S, Faghri F, Campbell R, Zhai C, Efron M . Big Data: Astronomical or Genomical?. PLoS Biol. 2015; 13(7):e1002195. PMC: 4494865. DOI: 10.1371/journal.pbio.1002195. View

Vizcaino J, Cote R, Csordas A, Dianes J, Fabregat A, Foster J . The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res. 2012; 41(Database issue):D1063-9. PMC: 3531176. DOI: 10.1093/nar/gks1262. View

Irizarry R, Hobbs B, Collin F, Beazer-Barclay Y, Antonellis K, Scherf U . Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003; 4(2):249-64. DOI: 10.1093/biostatistics/4.2.249. View

Goh W, Wong L . Protein complex-based analysis is resistant to the obfuscating consequences of batch effects --- a case study in clinical proteomics. BMC Genomics. 2017; 18(Suppl 2):142. PMC: 5374662. DOI: 10.1186/s12864-017-3490-3. View

Goh W, Wong L . Advancing Clinical Proteomics via Analysis Based on Biological Complexes: A Tale of Five Paradigms. J Proteome Res. 2016; 15(9):3167-79. DOI: 10.1021/acs.jproteome.6b00402. View

Legrain P, Aebersold R, Archakov A, Bairoch A, Bala K, Beretta L . The human proteome project: current state and future direction. Mol Cell Proteomics. 2011; 10(7):M111.009993. PMC: 3134076. DOI: 10.1074/mcp.M111.009993. View

Goh W, Wong L . Dealing with Confounders in Omics Analysis. Trends Biotechnol. 2018; 36(5):488-498. DOI: 10.1016/j.tibtech.2018.01.013. View

Goh W, Wong L . Turning straw into gold: building robustness into gene signature inference. Drug Discov Today. 2018; 24(1):31-36. DOI: 10.1016/j.drudis.2018.08.002. View

Goh W, Sze C . AI Paradigms for Teaching Biotechnology. Trends Biotechnol. 2018; 37(1):1-5. DOI: 10.1016/j.tibtech.2018.09.009. View

10.

Eraslan G, Avsec Z, Gagneur J, Theis F . Deep learning: new computational modelling techniques for genomics. Nat Rev Genet. 2019; 20(7):389-403. DOI: 10.1038/s41576-019-0122-6. View

11.

Gao J, Liu Y, DSouza R, Barabasi A . Target control of complex networks. Nat Commun. 2014; 5:5415. PMC: 4243219. DOI: 10.1038/ncomms6415. View

12.

Gessulat S, Schmidt T, Zolg D, Samaras P, Schnatbaum K, Zerweck J . Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning. Nat Methods. 2019; 16(6):509-518. DOI: 10.1038/s41592-019-0426-7. View

13.

Goh W, Wong L . Integrating Networks and Proteomics: Moving Forward. Trends Biotechnol. 2016; 34(12):951-959. DOI: 10.1016/j.tibtech.2016.05.015. View

14.

Goh W, Wong L . Design principles for clinical network-based proteomics. Drug Discov Today. 2016; 21(7):1130-8. DOI: 10.1016/j.drudis.2016.05.013. View

15.

Amunts K, Ebell C, Muller J, Telefont M, Knoll A, Lippert T . The Human Brain Project: Creating a European Research Infrastructure to Decode the Human Brain. Neuron. 2016; 92(3):574-581. DOI: 10.1016/j.neuron.2016.10.046. View

16.

Canisius S, Martens J, Wessels L . A novel independence test for somatic alterations in cancer shows that biology drives mutual exclusivity but chance explains most co-occurrence. Genome Biol. 2016; 17(1):261. PMC: 5162102. DOI: 10.1186/s13059-016-1114-x. View

17.

Strasser B . Collecting, comparing, and computing sequences: the making of Margaret O. Dayhoff's Atlas of Protein Sequence and Structure, 1954-1965. J Hist Biol. 2010; 43(4):623-60. DOI: 10.1007/s10739-009-9221-0. View

18.

Ioannidis J . Why most published research findings are false. PLoS Med. 2005; 2(8):e124. PMC: 1182327. DOI: 10.1371/journal.pmed.0020124. View

19.

Goh W, Wong L . Evaluating feature-selection stability in next-generation proteomics. J Bioinform Comput Biol. 2016; 14(5):1650029. DOI: 10.1142/S0219720016500293. View

20.

Navale V, Bourne P . Cloud computing applications for biomedical science: A perspective. PLoS Comput Biol. 2018; 14(6):e1006144. PMC: 6002019. DOI: 10.1371/journal.pcbi.1006144. View