Items where Author is "Lyons, J."

Yang, Y. and Heffernan, R. and Paliwal, K. and Lyons, J. and Dehzangi, A. and Sharma, Alokanand and Wang, J. and Sattar, A. and Zhou, Y. (2017) SPIDER2: a package to predict secondary structure, accessible surface area, and main - chain torsional angles by deep neural networks. In: Prediction of Protein Secondary Structure. Methods in Molecular Biology. Humana Press, New York, pp. 55-63. ISBN 9781493964048

Lyons, J. and Paliwal, K.K. and Dehzangi, A. and Heffernan, R. and Tsunoda, T. and Sharma, Alokanand (2016) Protein fold recognition using HMM–HMM alignment and dynamic programming. Journal of Theoretical Biology, 393 . pp. 67-74. ISSN 0022-5193

Heffernan, R. and Dehzangi, Abdollah and Lyons, J. and Paliwal, K.K. and Sharma, Alokanand and Wang, J. and Sattar, A. and Zhou, Y. and Yang, Y. (2016) Highly Accurate Sequence-based Prediction of Half-Sphere Exposures of Amino Acid Residues in Proteins. Bioinformatics, 32 (6). pp. 843-849. ISSN 1367-4803

Sharma, Alokanand and Sharma, Ronesh and Dehzangi, A. and Lyons, J. and Paliwal, K.K. and Tsunoda, T. (2015) Importance of Dimensionality Reduction in Protein Fold Recognition. [Conference Proceedings]

Lyons, J. and Dehzangi, A. and Heffernan, R. and Yang, Yuedong and Zhou, Y. and Sharma, Alokanand and Paliwal, K.K. (2015) Advancing the accuracy of protein fold recognition by utilizing profiles from hidden Markov models. IEEE Transactions on Nanobioscience, 14 (7). pp. 761-772. ISSN 1536-1241

Saini, Harsh and Raicar, Gaurav and Sharma, Alokanand and Lal, Sunil P. and Dehzangi, A. and Lyons, J. and Paliwal, K.K. and Imoto, S. and Miyano, S. (2015) 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, 380 . pp. 291-298. ISSN 0022-5193

Dehzangi, A. and Sohrabi, S. and Heffernan, R. and Sharma, Alokanand and Lyons, J. and Paliwal, K.K. and Sattar, A. (2015) Gram - positive and gram - negative subcellular localization using rotation forest and physicochemical-based features. BMC Bioinformatics, 16 (S1). pp. 1-12. ISSN 1471-2105

Dehzangi, A. and Heffernan, R. and Sharma, Alokanand and Lyons, J. and Paliwal, K.K. and Sattar, A. (2015) Gram-positive and Gram-negative protein subcellular localization by incorporating evolutionary-based descriptors into Chou׳ s general PseAAC. Journal of Theoretical Biology, 364 . pp. 284-294. ISSN 0022-5193

Heffernan, R. and Dehzangi, A. and Lyons, J. and Paliwal, K.K. and Sharma, Alokanand and Wang, J. and Sattar, A. and Zhou, Y. and Yang, Y. (2015) Highly accurate sequence - based prediction of half - sphere exposures of amino acid residues in proteins. Bioinformatics, 14 . pp. 1-7. ISSN 1367-4803

Heffernan, R. and Paliwal, K.K. and Lyons, J. and Dehzangi, A. and Sharma, Alokanand and Wang, J. and Sattar, A. and Yang, Y. and Zhou, Y. (2015) Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning. Scientific Reports, 5 (11476). pp. 1-11. ISSN NA

Sharma, Ronesh and Dehzangi, A. and Lyons, J. and Paliwal, K.K. and Tsunoda, T. and Sharma, Alokanand (2015) Predict gram - positive and gram - negative subcellular localization via incorporating evolutionary information and physicochemical features into Chou’s general PseAAC. IEEE Transactions on NanoBioscience, 14 (8). pp. 915-926. ISSN 1536-1241

Dehzangi, A. and Sharma, Alokanand and Lyons, J. and Paliwal, K.K. and Sattar, A. (2015) A mixture of physicochemical and evolutionary–based feature extraction approaches for protein fold recognition. International Journal of Data Mining and Bioinformatics, 11 (1). pp. 115-138. ISSN 1748-5673

Paliwal, K.K. and Sharma, Alokanand and Lyons, J. and Dehzangi, A. (2014) Improving protein fold recognition using the amalgamation of evolutionary-based and structural-based information. BMC Bioinformatics, 15 (16). pp. 1-9. ISSN 1471-2105

Saini, Harsh and Raicar, Gaurav and Lal, Sunil P. and Dehzangi, A. and Lyons, J. and Paliwal, K.K. and Imoto, S. and Miyano, S. and Sharma, Alokanand (2014) Genetic algorithm for an optimized weighted voting scheme incorporating k-separated bigram transition probabilities to improve protein fold recognition. [Conference Proceedings]

Dehzangi, A. and Paliwal, K.K. and Lyons, J. and Sharma, Alokanand and Sattar, A. (2014) A segmentation - based method to extract structural and evolutionary features for protein fold recognition. IEEE-ACM Transactions on Computational Biology and Bioinformatics, PP (99). pp. 1-11. ISSN 1557-9964

Paliwal, K.K. and Sharma, Alokanand and Lyons, J. and Dehzangi, A. (2014) A tri - gram based feature extraction technique using linear probabilities of position specific scoring matrix for protein fold recognition. IEEE Transactions on Nanobioscience, 13 (1). pp. 44-50. ISSN 1536-1241

Sharma, Alokanand and Lyons, J. and Dehzangi, A. and Imoto, S. and Miyano, S. and Nakai, K and Patil, A (2014) Evaluation of sequence features from intrinsically disordered regions for the estimation of protein function. PLos One, 9 (2). pp. 1-7. ISSN 1932-6203

Dehzangi, A. and Paliwal, K.K. and Lyons, J. and Sharma, Alokanand and Sattar, A. (2014) Proposing a highly accurate protein structural class predictor using segmentation - based features. BMC Genomics, 15 (1). pp. 1-13. ISSN 1471-2164

Lyons, J. and Biswas, S.N. and Sharma, Alokanand and Dehzangi, A. and Paliwal, K.K. (2014) Protein fold recognition by alignment of amino acid residues using kernelized dynamic time warping. Journal of Theoretical Biology, 354 . pp. 137-145. ISSN 0022-5193

Saini, Harsh and Raicar, Gaurav and Sharma, Alokanand and Lal, Sunil P. and Dehzangi, A. and Ananthanarayanan, Rajeshkannan and Lyons, J. and Biswas, N. and Paliwal, K.K. (2014) Protein structural class prediction via k - separated bigrams using position specific scoring matrix. Journal of Advanced Computational Intelligence and Intelligent Informatics, 18 (4). pp. 474-479. ISSN 1343-0130

Dehzangi, A. and Paliwal, K.K. and Sharma, Alokanand and Lyons, J. and Sattar, A. (2013) Protein fold recognition using an overlapping segmentation approach and a mixture of feature extraction models. In: Lecture Notes in Bioinformatics. Lecture Notes in Computer Science, 8272 . Springer International Publishing, Switzerland, pp. 32-43. ISBN Print 9783319036793 Online 9783319036809

Dehzangi, A. and Paliwal, K.K. and Lyons, J. and Sharma, Alokanand and Sattar, A. (2013) Enhancing protein fold prediction accuracy using evolutionary and structural features. In: Lecture Notes in Computer Science. Lecture Notes in Computer Science, 7986 . Springer Berlin Heidelberg, Switzerland, pp. 196-207. ISBN Print 9783642391583 Online 9783642391590

Dehzangi, A. and Paliwal, K.K. and Lyons, J. and Sharma, Alokanand and Sattar, A. (2013) Exploring potential discriminatory information embedded in PSSM to enhance protein structural class prediction accuracy. In: Lecture Notes in Bioinformatics. Lecture Notes in Computer Science, 7986 . Springer Berlin Heidelberg, Switzerland , pp. 208-219. ISBN Print 9783642391583 Online 9783642391590