AI LAB

Publications


2018

[1] Uddin, R., Sharma, A., Farid, D., Rahman, M., Dehzangi, A., Shatabda, S., EvoStruct-Sub: an accurate gram-positive protein subcellular localization predictor using evolutionary and structural features, Journal of Theoretical Biology, vol. 443, pp. 138-146, 2018 Paper.pdf.

[2] Sharma, R., Bayarjargal, M., Tsunoda, T., Patil, A. and Sharma, A., MoRFPred-plus: Computational Identification of MoRFs in Protein Sequence using physicochemical properties and HMM profiles, Journal of Theoretical Biology, vol. 437, pp. 9-16, 2018. Paper.pdf Download package https://github.com/roneshsharma/MoRFpred-plus/wiki/MoRFpred-plus:-Download

[3] Sharma, R., Raicar, G., Tsunoda, T., Patil, A., and Sharma, A., OPAL: prediction of MoRF regions in intrinsically disordered protein sequence, Bioinformatics, vol. 34, no. 11, pp. 1850-1858, 2018. Suppl.zip, Webserver http://www.alok-ai-lab.com/tools/opal/, Download packages: Matlab, Octave

[4] Dehzangi, A, Lopez, Y., Lal, S.P., Taherzadeh, G., Sattar, A., Tsunoda, T., Sharma, A., Improving succinylation prediction accuracy by incorporating the secondary structure via helix, strand and coil, and evolutionary infomration from profile bigrams, PLoS ONE, 13(2):e0191900, 2018 Paper.pdf

[5] López, Y.*, Sharma, A*, Dehzangi, A., Lal, S.P., Taherzadeh, G., Sattar, A., Tsunoda, T., Success: evolutionary and structural properties of amino acids prove effective for succinylation site prediction, BMC Genomics, 19(Suppl 1):923, 2018. Paper.pdf Download https://github.com/YosvanyLopez/Success

[6] Kumar,S., Sharma, A., A new parameter tuning approach for enhanced motor imagery EEG signal classification, Medical & Biological Engineering & Computing, 2018. Paper.pdf Download https://github.com/ShiuKumar/TFPO-CSP

[7] Lopez, Y, Kamola PJ, Sharma R, Shigemizu D, Tsunoda T, Sharma A, Computational Pipelines and Workflows in Bioinformatics, Enclyclopedia of Bioinformatics and Computational Biology, ISBN 9780128114148, Elsevier, 2018, Download/View BookChapter.pdf


2017

[1] Shatabda, S., Saha, S., Sharma, A., Dehzangi, A., iPHLoc-ES: Identification of Bacteriophage Protein Locations using Evolutionary and Structural Features, Journal of Theoretical Biology, vol. 435, pp. 229-237, 2017

[2] Kumar, S., Mamun, K., Sharma, A. CSP-TSM: optimizing the performance of Riemannian tangent space mapping using common spatial pattern for MI-BCI, Computers in Biology and Medicine, vol. 91, pp. 231-242, 2017

[3] ‘Community assessment of cancer drug combination screens identifies strategies for synergy prediction’ (to appear in Nature Biotechnology)

[4] Sharma, A., Boroevich, K.A., Shigemizu, D., Kamatani, Y., Kubo, M., Tsunoda, T., Hierarchical maximum likelihood clustering approach, IEEE Transactions on Bio-Medical Engineering, vol. 64, issue 1, pp. 112-122, 2017. Download package http://emu.src.riken.jp/HML/

[5] López, Y., Dehzangi, A., Lal, S.P., Taherzadeh, G., Michaelson, J., Sattar, A., Tsunoda, T., Sharma, A., SucStruct: prediction of succinylated lysine residues by using structural properties of amino acids, Analytical Biochemistry, vol. 527, pp. 24-32, 2017. Download https://github.com/YosvanyLopez/SucStruct

[6] Dehzangi, A., López, Y., Lal, S.P., Taherzadeh, G., Mchaelson, J., Sattar, A., Tsunoda, T., Sharma, A. PSSM-Suc: accurately predicting succinylation using position specific scoring matrix into bigram for feature extraction, Journal of Theoretical Biology, 425, pp. 97-102, 2017. Download https://github.com/YosvanyLopez/SucEvol

[7] Sharma, A., Kamola, P.J., Tsunoda, T., 2D-EM clustering approach for high-dimensional data through folding feature vectors, BMC Bioinformatics, vol. 18, Suppl 16, pp. 547, 2017. Download package http://emu.src.riken.jp/2D-EM/

[8] Sharma, A., López, Y., Tsunoda, T., Divisive hierarchical maximum likelihood clustering, BMC Bioinformatics, vol. 18, Suppl 16, pp. 546, 2017. Download: http://emu.src.riken.jp/DRAGON/

[9] Kumar, S., Sharma, A., Tsunoda, T., An improved discriminative filter bank selection approach for motor imagery EEG signal classification using mutual information, BMC Bioinformatics, vol. 18, Suppl 16, pp. 545, 2017.

[10] Zaman, R., Chowdhury, S., Rashid, M., Sharma, A., Dehzangi, A., Shatabda, S., HMMBinder: DNA-binding protein prediction using HMM profile based features, BioMed Research International, vol. 2017, Article ID 4590609, 2017.

[11] Y. Yang, R. Heffernan, K. Paliwal, J. Lyons, A. Dehzangi, A. Sharma, J. Wang, A. Sattar, Y. Zhou, SPIDER2: A Package to Predict Secondary S tructure, Accessible Surface Area, and Main-Chain Torsional Angles by Deep Neural Networks, Book Title: Prediction of Protein Secondary Structure, Series Title: Methods Molecular Biology, vol. 1484, ISSN:978-1-4939-6404-8., 2017.


2016

[1] Lyons, J., Paliwal, K.K., Dehzangi, A., Heffernan, R., Tsunoda, T., Sharma, A., Protein fold recognition using HMM-HMM alignment and dynamic programming, Journal of Theoretical Biology, vol. 393, pp. 67-74, 2016.

[2] Raicar, G., Saini, H., Dehzangi, A., Lal, S., Sharma, A., Improving protein fold recognition and structural class prediction accuracies using physicochemical properties of amino acids, Journal of Theoretical Biology, vol. 402, pp. 117-128, 2016.

[3] Saini, H., Raicar, G., Lal, S., Dehzangi, A., Imoto, S., Sharma, A., Protein fold recognition using genetic algorithm optimized voting scheme and profile bigram, Journal of Software, vol. 11, issue 8, pp. 756-767, 2016.

[4] Mamun, K., Sharma, A., Hoque, A.S.M., Szecsi, T., Patient condition monitoring modular hospital robot, Journal of Software, vol. 11, no. 8, pp. 768-786, 2016.

[5] Heffernan, R, Dehzangi, A., Lyons, J., Paliwal, K.K., Sharma, A., Wang, J., Sattar, A., Zhou, Y., Yang, Y., Highly Accurate Sequence-based Prediction of Half-Sphere Exposures of Amino Acid Residues in Proteins, Bioinformatics, vol. 32, no. 6, pp. 843-849, 2016. Download http://sparks-lab.org/

[6] Sharma, A., Shigemizu, D., Boroevich, K.A., López, Y., Kamatani, Y., Kubo, M., Tsunoda, T., Stepwise iterative maximum likelihood clustering approach, BMC Bioinformatics, 17(319),1-14, 2016. Download package http://emu.src.riken.jp/SIML/

[7] Sharma, R., Kumar, S., Tsunoda, T., Patil, A., Sharma, A., Predicting MoRFs in protein sequences using HMM profiles, INCOB 2016, BMC Bioinformatics, Suppl. 15, 2016.

[8] Saini, H., Lal, S., Naidu, V.V., Pickering, V.W., Singh, G., Tsunoda, T., Sharma, A., Gene masking - a technique to improve accuracy for cancer classification with high dimensionality in microarray data, INCOB 2016, BMC Medical Genomics, Suppl. 6, 2016.

[9] Kumar, S., Sharma, R., Sharma, A., Tsunoda, T., Decimation Filter with Common Spatial Pattern and Fishers Discriminant Analysis for Motor Imagery Classification, IEEE World Congress on Computational Intelligence, IJCNN, 24-29 July, Vancouver, Canada, pp. 2090-2095, 2016.

[10] Kumar, S., Sharma, A., Mamun, K., Tsunoda, T., A deep learning approach for motor imagery EEG signal classification, IEEE APWC, 2016.

[11] López, Y., Sharma, A., Tsunoda, T., Survey of highly mutated transcription factor binding sites in human cancers, INCOB 2016, Sep 21-23, Singapore (Poster).

[12] Kumar, R., Lal, S.P., Sharma, A., Detecting denial of service attacks in the cloud, 14th Int. Conf. on Pervasive Intelligence and Computing, 2nd Intl Conf on Big Data Intelligence and Computing and Cyber Science and Technology Congress(DASC/PiCom/DataCom/CyberSciTech), 2016 IEEE 14th Intl C, 309-316, 2016.


2015

[1] Sharma, A. Paliwal, K.K., A Deterministic Approach to Regularized Linear Discriminant Analysis, Neurocomputing, vol. 151, pp. 207-214, 2015.

[2] Dehzangi, A., Sharma, A., Lyons, J., Paliwal, K.K., Sattar, A., A mixture of physicochemical and evolutionary-based feature extraction approached for protein fold recognition, International Journal of Data Mining and Bioinformatics, vol. 11, no. 1, pp. 115-138, 2015.

[3] Heffernan, R. Paliwal, K.K., Lyons, J., Dehzangi, A., Sharma, A., Wang, J. Sattar, A., Yang, Y., Zhou, Y., Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning, Scientific Reports, Nature Publishing Group, vol. 5, article no. 11476, pp. 1-11, 2015. Online Server http://sparks-lab.org/

[4] Saini, H., Raicar, G., Sharma, A., Lal, S., Dehzangi, A., Lyons, J., Paliwal, K.K., Imoto, S., Miyano, S., Probabilistic expression of spatially varied amino acid dimers into general form of Chou’s pseudo amino acid composition for protein fold recognition, Journal of Theoretical Biology, vol. 380, no. 7, pp. 291-298, 2015.

[5] Dehzangi, A., Sohrabi, S., Lyons, J., Sharma, A., Paliwal, K.K., Sattar, A., Gram-positive and gram-negative subcellular localization using rotation forest and physicochemical-based features, BMC Bioinformatics, vol. 16, issue Suppl 4:S1, pp. 1-8, 2015.

[6] Dehzangi, A., Heffernan, R., Sharma, A., Lyons, J., Paliwal, K.K., Sattar, A., Gram-positive and Gram-negative Protein Subcellular Localization by Incorporating Evolutionary-based Descriptors into Chou's General PseAAC, Journal of Theoretical Biology, vol. 364, pp. 284-294, 2015.

[7] Lyons, J., Dehzangi, A., Heffernan, R., Yang, Y., Zhou, Y., Sharma, A., Paliwal, K.K., Advancing the accuracy of protein fold recognition by utilizing profile of hidden Markov models, IEEE Transactions on NanoBioscience, vol 14, issue 7, pp. 761-772, 2015.

[8] Saini, H., Raicar, G., Dehzangi, A., Lal, S., Sharma, A., Subcellular localization for Gram Positive and Gram Negative Bacterial Proteins using Linear Interpolation Smoothing Model, Journal of Theoretical Biology, vol. 386, pp 25-33, 2015.

[9] Sharma, A., Paliwal, K.K., Linear discriminant analysis for the small sample size problem: an overview, International Journal of Machine Learning and Cybernetics, vol. 6, issue 3, pp. 443-454, 2015.

[10] Sharma, R, Dehzangi, A, Lyons, J., Paliwal, KK, Tsunoda, T, Sharma, A., Predict Gram-positive and Gram-negative subcellular localization via incorporating evolutionary information and physicochemical features into Chou’s general PseAAC, IEEE Transactions on NanoBioscience, vol. 14, issue 8, pp. 915-926, 2015.

[11] Sharma, A., Sharma, R., Paliwal, K.K., Dehzangi, A., Lyons, J., Tsunoda, T., Importance of Dimensionality Reduction in Protein Fold Recognition, IEEE Asia-Pacific World Congress on Computer Science and Engineering, pp. 1-6, 2-4 Dec, 2015.

[12] Kumar, S., Sharma, A., Mamun, KA, Tsunoda, T, Application of Cepstrum Analysis and Linear Predictive Coding for Motor Imaginary Task Classification, IEEE Asia-Pacific World Congress on Computer Science and Engineering, pp. 1-6, 2-4 Dec, 2015.


For older papers please see Google Scholar or email.