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IEEE/ACM Transactions on Computational Biology and Bioinformatics
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Date Reviewed
Regularized non-negative matrix factorization for identifying differentially expressed genes and clustering samples: a survey
Liu J., Wang D., Gao Y., Zheng C., Xu Y., Yu J. IEEE/ACM Transactions on Computational Biology and Bioinformatics 15(3): 974-987, 2018. Type: Article
This paper surveys the application of non-negative matrix factorization (NMF), a well-known dimensionality reduction technique in bioinformatics “for identifying differentially expressed genes and clustering samples.̶...
Apr 5 2019
Prediction of HIV drug resistance by combining sequence and structural properties
Khalid Z., Sezerman O. IEEE/ACM Transactions on Computational Biology and Bioinformatics 15(3): 966-973, 2018. Type: Article
Human immunodeficiency virus infection and acquired immune deficiency syndrome (HIV/AIDS) has been one of the deadliest diseases for the past three decades. Treatment is challenging even today....
Nov 7 2018
Attention recognition in EEG-based affective learning research using CFS+KNN algorithm
Hu B., Li X., Sun S., Ratcliffe M. IEEE/ACM Transactions on Computational Biology and Bioinformatics 15(1): 38-45, 2018. Type: Article
Probably the core of this paper is the usage of “correlation-based feature selection (CFS) plus a
k
-nearest neighbors (KNN) data mining algorithm.” The authors compare it with some other machine l...
Jun 21 2018
Private data analytics on biomedical sensing data via distributed computation
Gong Y., Fang Y., Guo Y. IEEE/ACM Transactions on Computational Biology and Bioinformatics 13(3): 431-444, 2016. Type: Article
Predictive model training systems actually lack positive samples such as biomedical data from healthy people due to data privacy preservation issues that mHealth users face. This paper therefore presents a novel approach that preserves...
Jun 2 2017
Reconstruction of gene regulatory networks based on repairing sparse low-rank matrices
Chang Y., Dobbe R., Bhushan P., Gray J., Tomlin C. IEEE/ACM Transactions on Computational Biology and Bioinformatics 13(4): 767-777, 2016. Type: Article
The reconstruction of gene regulatory networks (GRN) is a complex problem that merits attention due to the need to organize time series gene expression data into meaningful structures. Data-driven techniques allow large datasets to be ...
Feb 1 2017
Multiple kernel fuzzy SVM-based data fusion for improving peptide identification
Jian L., Xia Z., Niu X., Liang X., Samir P., Link A. IEEE/ACM Transactions on Computational Biology and Bioinformatics 13(4): 804-809, 2016. Type: Article
This paper proposes a fuzzy support vector machine (SVM)-based data fusion technique that aims to distinguish true or false peptide-spectrum matchings (PSM) from integrated SEQUEST scores. The proposed system, MFS, has comparable perfo...
Jan 19 2017
A new efficient algorithm for the all sorting reversals problem with no bad components
Wang B. IEEE/ACM Transactions on Computational Biology and Bioinformatics 13(4): 599-609, 2016. Type: Article
The paradigm of Wang’s paper is computational biology, more specifically genome rearrangement. The genome rearrangement problem simply means changing one genome sequence to another in the shortest possible way....
Jan 17 2017
Aligning and clustering patterns to reveal the protein functionality of sequences
Wong A., Lee E. IEEE/ACM Transactions on Computational Biology and Bioinformatics 11(3): 548-560, 2014. Type: Article
Protein sequence analysis is a technique for discovering the structures and functions of proteins in living organisms using functions like comparison of sequences, identification of intrinsic features, sequence differences and variatio...
Nov 10 2014
Designing logical rules to model the response of biomolecular networks with complex interactions: an application to cancer modeling
Guziolowski C., Blachon S., Baumuratova T., Stoll G., Radulescu O., Siegel A. IEEE/ACM Transactions on Computational Biology and Bioinformatics 8(5): 1223-1234, 2011. Type: Article
The presence of factors external to genes makes genetic expression variable. Guziolowski and others propose a way to model a biomolecular network through the use of logical rules imposed onto a network of some known interactions. They ...
Jan 5 2012
Model composition for macromolecular regulatory networks
Randhawa R., Shaffer C., Tyson J. IEEE/ACM Transactions on Computational Biology and Bioinformatics 7(2): 278-287, 2010. Type: Article
Deterministic and stochastic mathematical models of macromolecular processes along regulatory networks provide great insights on the physiological properties of cells. An appropriate way to deal with the challenges of mathematical mode...
Apr 7 2011
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