Machine Learning and Its Applications to Biology

Overview

Journal PLoS Comput Biol

Specialty Biology

Date 2007 Jul 3

PMID 17604446

Citations 210

Authors

Adi L Tarca

Vincent J Carey

Xue-Wen Chen

Roberto Romero

Sorin Draghici

Affiliations

Soon will be listed here.

Citing Articles

Innovative perspectives on the discovery of small molecule antibiotics.

Cardona S, Rahman A, Novomisky Nechcoff J NPJ Antimicrob Resist. 2025; 3(1):19.

PMID: 40082593 PMC: 11906701. DOI: 10.1038/s44259-025-00089-0.

EnSCAN: ENsemble Scoring for prioritizing CAusative variaNts across multiplatform GWASs for late-onset alzheimer's disease.

Erdogan O, Iyigun C, Aydin Son Y BioData Min. 2025; 18(1):20.

PMID: 40038746 PMC: 11881353. DOI: 10.1186/s13040-025-00436-x.

Machine Learning Descriptors for CO Capture Materials.

Orhan I, Zhao Y, Babarao R, Thornton A, Le T Molecules. 2025; 30(3).

PMID: 39942754 PMC: 11820763. DOI: 10.3390/molecules30030650.

Predicting the seasonal dynamics of Dalbulus maidis (Hemiptera: Cicadellidae) in corn using artificial neural networks.

Carmo D, Paes J, Santos A, Dos Santos J, Filho M, Soares J Neotrop Entomol. 2024; 54(1):1.

PMID: 39638906 DOI: 10.1007/s13744-024-01212-y.

Clinical, genomic, and proteomic perspectives in the analysis of comorbid conditions in type 2 diabetes mellitus: a retrospective study.

Villikudathil A, Mc Guigan D, English A Acta Diabetol. 2024; .

PMID: 39508856 DOI: 10.1007/s00592-024-02383-1.

References

Weston J, Leslie C, Ie E, Zhou D, Elisseeff A, Noble W . Semi-supervised protein classification using cluster kernels. Bioinformatics. 2005; 21(15):3241-7. DOI: 10.1093/bioinformatics/bti497. View

Alizadeh A, Eisen M, Davis R, Ma C, Lossos I, Rosenwald A . Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 2000; 403(6769):503-11. DOI: 10.1038/35000501. View

Zhu J, Zhang M . Cluster, function and promoter: analysis of yeast expression array. Pac Symp Biocomput. 2000; :479-90. View

Tarca A, Cooke J, Mackay J . A robust neural networks approach for spatial and intensity-dependent normalization of cDNA microarray data. Bioinformatics. 2005; 21(11):2674-83. DOI: 10.1093/bioinformatics/bti397. View

Perou C, Jeffrey S, van de Rijn M, Rees C, Eisen M, Ross D . Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Proc Natl Acad Sci U S A. 1999; 96(16):9212-7. PMC: 17759. DOI: 10.1073/pnas.96.16.9212. View

Rosenblatt F . The perceptron: a probabilistic model for information storage and organization in the brain. Psychol Rev. 1958; 65(6):386-408. DOI: 10.1037/h0042519. View

Michiels S, Koscielny S, Hill C . Prediction of cancer outcome with microarrays: a multiple random validation strategy. Lancet. 2005; 365(9458):488-92. DOI: 10.1016/S0140-6736(05)17866-0. View

Stormo G, Schneider T, Gold L, Ehrenfeucht A . Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli. Nucleic Acids Res. 1982; 10(9):2997-3011. PMC: 320670. DOI: 10.1093/nar/10.9.2997. View

Ross D, Scherf U, Eisen M, Perou C, Rees C, Spellman P . Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet. 2000; 24(3):227-35. DOI: 10.1038/73432. View

10.

Chiaretti S, Li X, Gentleman R, Vitale A, Vignetti M, Mandelli F . Gene expression profile of adult T-cell acute lymphocytic leukemia identifies distinct subsets of patients with different response to therapy and survival. Blood. 2003; 103(7):2771-8. DOI: 10.1182/blood-2003-09-3243. View

11.

Guo Y, Hastie T, Tibshirani R . Regularized linear discriminant analysis and its application in microarrays. Biostatistics. 2006; 8(1):86-100. DOI: 10.1093/biostatistics/kxj035. View

12.

Rost B, Sander C . Combining evolutionary information and neural networks to predict protein secondary structure. Proteins. 1994; 19(1):55-72. DOI: 10.1002/prot.340190108. View

13.

Jirapech-Umpai T, Aitken S . Feature selection and classification for microarray data analysis: evolutionary methods for identifying predictive genes. BMC Bioinformatics. 2005; 6:148. PMC: 1181625. DOI: 10.1186/1471-2105-6-148. View

14.

Golub T, Slonim D, Tamayo P, Huard C, Gaasenbeek M, Mesirov J . Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science. 1999; 286(5439):531-7. DOI: 10.1126/science.286.5439.531. View

15.

Fukushima K . Neocognitron: a self organizing neural network model for a mechanism of pattern recognition unaffected by shift in position. Biol Cybern. 1980; 36(4):193-202. DOI: 10.1007/BF00344251. View

16.

Aach J, Rindone W, Church G . Systematic management and analysis of yeast gene expression data. Genome Res. 2000; 10(4):431-45. DOI: 10.1101/gr.10.4.431. View

17.

Alon U, Barkai N, Notterman D, Gish K, Ybarra S, Mack D . Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc Natl Acad Sci U S A. 1999; 96(12):6745-50. PMC: 21986. DOI: 10.1073/pnas.96.12.6745. View