The KC Lab Publication Page

2017  
Chapman CH*, Adami C, Wilke CO, KC DB
The evolution of logic circuits for the purpose of protein contact map prediction
PeerJ 5:e3139 https://doi.org/10.7717/peerj.3139, 2017.
[Article]
2016  
Ismail H*, Jones A*, JH Kim, Newman RH, KC DB
RF-Phos: A novel general phosphorylation site prediction tool based on Random Forest
BioMed Research International, 2016, 3281590.
[Article]
Ismail H*, Newman RH, KC DB
RF-Hydroxysite: a random forest based predictor for hydroxylation sites
Molecular Biosystems, 12(8):2427-35, 2016
Article] [Server]
KC DB
Recent advances in sequence-based protein structure prediction
Briefings in Bioinformatics, 2016, In Press.
[Article]
Jha A*, Flurchick KM, Bidash M, KC DB
Parallel-SymD: A parallel approach to detect internal symmetry in protein domains
BioMed Research International, 2016, 4628592.
[Article]
Jiang Y, …., Chapman CH, KC DB,…., Predrag Radivojac
An expanded evaluation of protein function prediction methods show an improvement in accuracy
Genome Biology 17:184, 2016.
[Article]
Amini H*, Shahbazi A, Bikdash M, KC DB, Yuan W, Hashemisohi A*, Wang L
Numerical and experimental investigation of hydrodynamics and light transfer in open raceway ponds at various algal cell concentrations and medium depths
Chemical Engineering Science 156, 11-23, 2016.
[C]Hudson, T, Harrison, S, KC DB, Prins J, Muganda PM
Differential expression of human cytomegalovirus microRNA in triple-negative breast cancer tumors
In Proceedings of the 107th Annual Meeting , April 16-20, 2016; New Orleans, LA, AACR; DOI: 10.1158/1538-7445, Published 15 July 2016.
[C]Chapman SD, Adami C, Wilke CO, KC DB
The evolution of logic circuits for the purpose of protein contact map prediction
25th International Joint Conference on Artificial Intelligence IJCAI-16 BOOM Workshop 07/09/2016 July 9, 2016, New York, USA. Article
2015  
Ismail H*, Saigo H., KC DB
Improved Classification of Nuclear Receptors with Random Forest
IEEE ACM Transactions on Bioinformatics and Computational Biology To appear.
Khan IK, Wei Q, Chapman S*, KC DB, Kihara D
PFP and ESG protein function prediction methods in 2014: Effects of database updates and ensemble approaches
Giga Science , 4:43, 2015.
[C]Ismail H*, Jones A*, Kim J, Newman R, KC DB
RF-Phos: Random Forest Based prediction for phosphorylation sites
2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2015), Nov 9-12, 2015, Washington DC. Article
[C]Ismail H*, Jones A*, Kim J, Newman R, KC DB
Phosphorylation site prediction using random forest
5th IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), , October 15-17, Fl, USA. Article
[C]Ismail H*, Saigo H., KC DB
Improved Classification of Nuclear Receptors with Random Forest
26th annual GIW and 14th annual InCOB, GIW/INCOB 2015, , Sep 9-11, 2015, Odaiba, Tokyo, Japan. Article
2014  
Yu Y*, Megri AC, Flurchick KM, KC DB
The improvement of Computational Perfromance of the zonal model POMA using parallel techniques
American Journal of Engineering and Applied Sciences , 7(1), 185-193, 2014.
Tai CH, Paul R, KC DB, Schilling J, Lee BK
SymD webserver: a platform for detecting internally symmetric protein structures
Nucleic Acids Res , 42(W1):W296-W300, 2014 .
[C] Kordmahalleh MM*, Sefidmazgi MG*, Homaifar A, KC DB, Guiseppi-Elie A
Time-series forecasting with evolvable partially connected artificial neural network
Proceeding of Genetic and Evolution Computation Conference, GECCO14 , Pages 79-80, 2014. Article
[C] Chapman S*, Harrison S, Bikdash M, KC DB
The bustle of bioinformatics: Cloudy with a Chance for Big Data
3rd ASE Cyber Security Conferences, CA, USA, May 27-31, 2014, Pages 1-7. Article
2013  
KC DB
Structure-based methods for computational protein functional site prediction
Computational Structural Biotechnology Journal, 8:e201308005, 2013. PMID: 24688745.
[C] Kordmahalleh MK*, Homaifar A, KC DB
Hierarchical Multi-label Gene Function Prediction using Adaptive Mutation in Crowding Niching
13th IEEE International Conference on Bioinformatics and Bioengineering (BIBE 2013), 1-6, Chania, Greece, 10-13 November, 2013. Article
[C] Swanson B*, Harrison. S, KC DB, Muganda P
Comparative analysis of bioinformatic tools for the detection of viral DNA sequences in tumor cells
Proceedings of the Sixth AACR Conference: The Science of Cancer Health Disparities; Dec 6–9, 2013; Atlanta, GA. Philadelphia (PA): AACR Cancer Epidemiol Biomarkers Prev 2014;23(11 Suppl):Abstract nr C04. doi:10.1158/1538-7755.DISP13-C04, Article
<2013^  
KC DB, Livesay DR
Topology improves phylogenetic motif functional site predictions
IEEE/ACM Transactions on Computational Biology and Bioinformatics , 8:226-233, 2011.
KC DB
Improving Consensus Structure by Eliminating Averaging Artifacts, BMC Structural Biology
BMC Structural Biology, 9:12, 2009.
KC DB, Livesay DR
Improving position specific predictions of protein functional sites using phylogenetic motifs
Bioinformatics, 24:2308-2316, 2008.
Brown JB, KC DB, Tomita E., Akutsu T
Multiple methods for protein side chain packing using maximum weight cliques
Genome Informatics, 17-1, 3-12, 2006
Akutsu T, Hayashida M, KC DB, Tomita E, Suzuki J, Horimoto K
Protein Threading by Dynamic Programming and Clique Based Approaches
IEICE Transactions on Fundamentals of Electronics, Communication and Computer Science, E89-A, 1215-1222, 2006.
KC DB, Tomita E, Suzuki J, Horimoto K, Akutsu T.
Protein Threading With Profiles and Distance Constraints Using Clique Based Algorithms
Journal of Bioinformatics and Computational Biology , 4:19-42, 2006.
KC DB, Moesa HA, Akutsu T
Efficient Determination of Cluster Boundaries for Analysis of Gene Expression Profile Data Using Hierarchical Clustering and Wavelet Transform
Genome Informatics ,16(1): 132-141, 2005.
KC DB, Tomita E, Suzuki J. Akutsu T
Protein side-chain packing problem: A maximum common edge-weight clique algorithmic approach,
Journal of Bioinformatics and Computational Biology , 3(1): 103-126, 2005.
KC DB, Akutsu T, Tomita E, Seki T., Fujiyama A.
Point Matching Under Non-uniform Distortions and Protein Side Chain Packing Based on an Efficient Clique Algorithm
Genome Informatics, 13: 143-152, 2002.
* : Denotes student author ^ : Denotes selected publication only [C]: Conference Papers/Abstracts