The KC Lab Publication Page

2018  
Ismail H*, Saigo, H, KC DB
RF-NR: Random Forest based approach for improved classification of Nuclear Receptors
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2018, in Press.
MacCarthy E, Perry D, KC DB
Advances in proteins super-secondary structure prediction and application to protein structure prediction
Methods in Molecular Biology: Protein Supersecondary Structure (Springer), Editor: Kister A, 2018, in Press.
Albarakati H, McConnell EW, Hicks LM, Poole LB, Newman RH, KC DB
SVM-SulfoSite: A support vector machine based predictor for sulfenylations sites
Scientific Reports, 8 , Article Number:11288, 2018.
[ Article]
Amini H, Wang LJ, Hasemisohi A, Shahbazi A, Bikdash M, KC DB, Yuan WQ
An integrated growth kinetics and computational fluid dynamics model for the analysis of algal productivity in open raceway ponds
Computers and Electronics in Agriculture , 145, 363-372, 2018.
[ Article ]
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]
KC DB
Recent advances in sequence-based protein structure prediction
Briefings in Bioinformatics , 1:18(6):1021-1032, 2017.
White C*, Ismail H*, Saigo, H, KC DB
CNN-BLPred: A Convolutional Neural Network based predictor for Beta-lactamases (BL) and their classes
BMC Bioinformatics, 18(suppl 16):577, 2017.
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, 3281590, 2016.
[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]
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  
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