Note: The copyrights for these publications are held by the journals in which they were originally published. Please act accordingly.

2016

  • Kenneth R. Walsh, Md Tamjidul Hoque, Kim H. Williams, “Human Machine Learning Symbiosis”, Accepted in International Conference on Learning and Administration in Higher Education, TN, USA, 2016.

  • Sumaiya Iqbal, Md Tamjidul Hoque, “A Homologous Gene Replacement based Genetic Algorithm”, Accepted in GECCO, 2016.

  • Sumaiya Iqbal, Denson Smith, Md Tamjidul Hoque, “Accurate Identification of disordered protein residues using deep neural network”, Accepted in 4th Annual LA Conference on Computational Biology and Bioinformatics, 2016, Oral, Poster.

  • Avdesh Mishra, Sumaiya Iqbal, Md Tamjidul Hoque, “An Eclectic Energy Function to Discriminate Native from Decoys”, Accepted in 4th Annual LA Conference on Computational Biology and Bioinformatics, 2016, Oral, Poster.

  • Denson Smith, Sumaiya Iqbal, Md Tamjidul Hoque, “A Hybrid Evolutionary Feature Selection Method for Microarray Data”, Accepted in 4th Annual LA Conference on Computational Biology and Bioinformatics, 2016, Oral, Poster.

  • Avdesh Mishra, Sumaiya Iqbal and Md Tamjidul Hoque, “Discriminate Protein Decoys from Native by using a Scoring Function based on Ubiquitous Phi and Psi Angles Computed for All Atom”, in Journal of Theoretical Biology (online).

  • Sumaiya Iqbal and Md Tamjidul Hoque, “Estimation of Free Energy Contribution of Protein Residues as Feature for Structure Prediction from Sequence”, Accepted in CCBC/GLBIO 2016.

  • Mahmood A. Rashid, Sumaiya Iqbal, Firas Khatib, Md Tamjidul Hoque, Abdul Sattar, “Guided macro-mutation in a graded energy based genetic algorithm for protein structure prediction”, in Computational Biology and Chemistry Journal, Elsevier (published).

2015

  • Md Tamjidul Hoque, Yuedong Yang, Avdesh Mishra, Yaoqi Zhou, “sDFIRE: Sequence‐specific statistical energy function for protein structure prediction by decoy selections”, Journal of Computational Chemistry, Wiley (published).

  • Mahmood A. Rashid, Firas Khatib, Md Tamjidul Hoque, Abdul Sattar, “An Enhanced Genetic Algorithm for Ab initio Protein Structure Prediction”, IEEE Transactions on Evolutionary Computation, DOI: 10.1109/TEVC.2015.2505317.

  • Nasrul Islam, Sumaiya Iqbal, Ataur R Katebi, Md Tamjidul Hoque, “A Balanced Secondary Structure Predictor”, Journal of Theoretical Biology, doi: 10.1016/j.jtbi.2015.10.015 (published).

  • Sumaiya Iqbal, Md Tamjidul Hoque, “DisPredict: A Predictor of Disordered Protein using Optimized RBF Kernel”, PLOS One Journal (published).

  • Avdesh Mishra, Md Tamjidul Hoque, “Three-Dimensional Ideal Gas Reference State based Energy Function”, Current Bioinformatics, Bentham Journal (Accepted).

  • Sumaiya Iqbal, Avdesh Mishra, Md Tamjidul Hoque, “Improved Prediction of Accessible Surface Area Results in Efficient Energy Function Application”, Journal of Theoretical Biology, doi: 10.1016/j.jtbi.2015.06.012 (published).

2014

  • Sumaiya Iqbal, Md Nasrul Islam, Md Tamjidul Hoque, “Improved Protein Disorder Predictor by Smoothing Output”, ICCIT 2014.

  • Mahmood A. Rashid, Md. Masbaul Alam, M.A.Hakim Newton, Md Tamjidul Hoque, Abdul Sattar “Amino Acids Pattern-Biased Spiral Search for Protein Structure Prediction”, PRICAI-2014.

  • Mahmood A. Rashid, Md Tamjidul Hoque, M.A.Hakim Newton, Abdul Sattar and Swakkhar Shatabda, “A parallel framework for multi-point spiral search in ab initio protein structure prediction,” Journal: Advances in Bioinformatics (online)

2013

  • Md Tamjidul Hoque, Louisa Windus, Carrie Lovitt, Vicky M Avery, “PCaAnalyser: A 2D-Image Analysis Based Module for Effective Determination of Prostate Cancer Progression in 3D Culture”, Journal: PLOS One (published). For the source code of PCaAnalyser with examples and instructions, click here.

  • Md Tamjidul Hoque, “Genetic Algorithm for Ab Initio Protein Structure Prediction”, ISBN-10: 3659419427, ISBN-13: 978-3659419423, July 2013.

  • Mahmood Abdur Rashid, M.A.Hakim Newton, Md Tamjidul Hoque and Abdul Sattar, “Mixing energy models in genetic algorithms for on-lattice protein structure prediction”, Journal of BioMed Research International (online).

  • Mahmood Abdur Rashid, M.A.Hakim Newton, Md Tamjidul Hoque and Abdul Sattar, “Collaborative Parallel Local Search for Simplified Protein Structure Prediction”, 2013 12th IEEE International Conference on Trust, Security and Privacy in Computing and Communications.

  • Mahmood Abdur Rashid, M.A.Hakim Newton, Md Tamjidul Hoque and Abdul Sattar, “A Local Search Embedded Genetic Algorithm for Simplified Protein Structure Prediction”, IEEE CEC 2013.

  • Mahmood Abdur Rashid, M.A.Hakim Newton, Md Tamjidul Hoque, Swakkhar Shatabda, Duc-Nghia Pham and Abdul Sattar,” Spiral search: a Hydrophobic-Core Directed Local Search for Simplified PSP on 3D FCC Lattice”, BMC Bioinformatics, 2013

  • Liu S, Wu Y, Lin T, Abel R, Redmann JP, Summa CM, Jaber V, Lim NM and Mobley DL “ Lead Optimization Mapper: Automatic free energy calculations for lead optimization “ J Comput Aided Mol Des 2013 Sep;27(9):755-70 doi: 10.1007/s10822-013-9678-y (PDF Format)

2012

  • Mahmood A Rashid, Md Tamjidul Hoque, M.A.Hakim Newton, Duc Nghia Pham and Abdul Sattar, “A New Genetic Algorithm for Simplified Protein Structure Prediction”, AI, 2012

  • Mahmood A Rashid, Swakkhar Shatabda, M.A.Hakim Newton, Md Tamjidul Hoque, Duc Nghia Pham and Abdul Sattar, “Random-Walk: A Stagnation Recovery Technique for Simplified Protein Structure Prediction”, ACM-BCB, 2012

  • Trent Higgs, Bela Stantic, Md Tamjidul Hoque and Abdul Sattar, “Refining Genetic Algorithm Twin Removal for High-Resolution Protein Structure Prediction”, IEEE CEC 2012.

  • Trent Higgs, Bela Stantic, Md Tamjidul Hoque and Abdul Sattar, “Applying Feature-Based Resampling to Protein Structure Prediction”, BiCoB, 2012 (paper).

  • Trent Higgs, Bela Stantic, Md Tamjidul Hoque and Abdul Sattar, “Benefits of Genetic Algorithm Feature-Based Resampling for Protein Structure Prediction”, Bioinformatics, 2012.

  • Craig RB, Summa CM, Corti M, and Pincus SH “ Anti-HIV Double Variable Domain Immunoglobulins Binding Both gp41 and gp120 for Targeted Delivery of Immunoconjugates “ PLoS ONE 7(10) : e46778. doi:10.1371/journal.pone.0046778 (2012) (PDF Format)

2011

  • Md Tamjidul Hoque, M. Chetty, Andrew Lewis, Abdul Sattar, “Twin Removal in Genetic Algorithms for Protein Structure Prediction using Low Resolution Model.” IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), Jan-Mar: 2011, Vol 8, no. 1, pp.234-245.

2010

  • Md Tamjidul Hoque, M. Chetty, Andrew Lewis, and Abdul Sattar, Vicky M Avery, DFS Generated Pathways in GA Crossover for Protein Structure Prediction, NeuroComputing, Elsevier, 73:2308-2316, 2010.

  • Md Tamjidul Hoque and Vicky Avery, Novel Strategies to Speed-up Query Response. Research Journal of Information Technology (RJIT), Vol 2, Issue 1, Pp. 11-20, 2010.

  • Trent Higgs, Bela Stantic, Md Tamjidul Hoque and Abdul Sattar, Genetic Algorithm Feature-Based Resampling for Protein Structure Prediction,” in WCCI/IEEE CEC, 2010.

  • M A Rashid, Md Tamjidul Hoque and Abdul Sattar, “Association Rules Mining Based Diseases Correlation Prediction”, in Medinfo2010.

  • Trent Higgs, Bela Stantic and Md Tamjidul Hoque, Mutation operator and its Effects on protein Structure Prediction in Genetic Algorithms,” in Medinfo2010.

  • Garay J, D’Angelo J, Park YK, Summa CM, Aiken ML, Morales E, Badizadegan K, Fiebiger E, and Dickinson BL “ Crosstalk Between PKA and Epac Regulates the Phenotypic Maturation and Function of Human Dendritic Cells “ Journal of Immunology 2010 (185) 3227-3238 (PDF Format)

2009

  • Md Tamjidul Hoque, M. Chetty, Abdul Sattar, Extended HP Model for Protein Structure Prediction.” Journal of Computational Biology (JCB), Vol. 16, Number 1, Pp. 85-103, 2009.

  • Md Tamjidul Hoque, M. Chetty, Abdul Sattar, Genetic Algorithm in Ab Initio Protein Structure Prediction using Low Resolution Model: A Review,” Biomedical Data and Applications, pringer-Verlag,series in Studies in Computational Intelligence (SCI) series, 2009.

  • Gregory A. Fechner, Anthony R. Carroll, Md Tamjidul Hoque, Vicky M. Avery, The use of high content analysis to determine the chemotherapeutic potential of marine and plant natural products, Society for Biomolecular Sciences (SBS) conference, 2009.

2008

  • Md Tamjidul Hoque, M. Chetty, A Lewis, A Sattar “DFS based partial pathways in GA for protein structure prediction”, PRIB 2008.

  • Trent Higgs, Bela Stantic and Md Tamjidul Hoque, Hydrophobic-Hydrophilic Forces and their Effects on Protein Structural Similarity, LNBI/PRIB 2008.

  • T. Higgs, B. Stantic, Tamjidul Hoque, Hydrophobic-hydrophilic patterns and their effects on the protein folding prediction process, International Conference on Genome Informatics’, Gold Coast, Australia, 2008.

  • Trent Higgs, Bela Stantic, Md Tamjidul Hoque, Optimal Length of Fragments for use in Protein Structure Prediction. Advances in Computer Science and Technology (ACST), Langkawi, Malaysia, 2008.

  • Zhao Z, Fu B, Alanis FJ, and Summa CM “ Feedback Algorithm and Web-Server for Protein Structure Alignment “ Journal of Computational Biology 2008 (15) 505-524 (PDF Format)

  • Chopra G, Summa CM, and Levitt M “ Solvent Dramatically Affects Protein Structure Refinement “ Proceedings of the National Academy of Sciences USA 2008 (105) 20239-20244 (PDF Format) Supporting Materials (PDF Format)

2007

  • Md Tamjidul Hoque, M. Chetty, Abdul Sattar, Protein Folding Prediction in 3D FCC HP Lattice Model Using Genetic Algorithm.” Bioinformatics special session, IEEE Congress on Evolutionary Computation (CEC), Singapore, 2007.

  • Md Tamjidul Hoque, M. Chetty, L. S. Dooley, Significance of Hybrid Evolutionary Computation for Ab Inito Protein Folding Prediction, Hybrid Evolutionary Algorithms (Volume 75), Springer-Verlag, Berlin,series in the SCI, pages 241-268, 2007.

  • Md Tamjidul Hoque, M. Chetty, L. S. Dooley, “Generalized schemata theorem incorporating twin removal for protein structure predictions”, PRIB 2007.

  • Summa CM and Levitt M “ Near Native Structure Refinement Using in vacuo Energy Minimization “ Proceedings of the National Academy of Sciences USA 2007 (104) 3177-3182 (PDF Format)

2006

  • Md Tamjidul Hoque and Muhammad Towhidul Hoque, New Strategies to Speed-Up Query Response Significantly, 9th International Conference on Computer and Information Technology (ICCIT), 2006.

  • Md Tamjidul Hoque, M. Chetty, L. S. Dooley, Non-Isomorphic Coding in Lattice Model and its Impact for Protein Folding Prediction Using Genetic Algorithm, IEEE Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2006.

  • Md Tamjidul Hoque, M. Chetty, L. S. Dooley, A Guided Genetic Algorithm for Protein Folding Prediction Using 3D Hydrophobic-Hydrophilic Model, special session, in WCCI / IEEE Congress on Evolutionary Computation, 2006.

  • Md Tamjidul Hoque, M. Chetty, L. S. Dooley, A Hybrid Genetic Algorithm for 2D FCC Hydrophobic-Hydrophilic Lattice Model to Predict Protein Folding, AI 2006 (19th ACS Australian Joint Conference on Artificial Intelligence), 2006, LNAI.

2005

  • Md Tamjidul Hoque, M. Chetty, L. S. Dooley, Fast computation of the fitness function for protein folding prediction in a 2D hydrophilic-hydrophobic model, Journal published in the special issue of the International Journal of Simulation Systems, Science and Technology, 2005.

  • Md Tamjidul Hoque, M. Chetty, L. S. Dooley, Efficient Computation of Fitness Function by Pruning in Hydrophobic-Hydrophilic Model, in the 6th International Symposium on Biological and Medical Data Analysis (ISBMDA) LNBI, 2005.

  • Md Tamjidul Hoque and Muhammad Towhidul Hoque, Development of Software Tool for Safety Checking by Generating Coverability Tree Using Petri Nets, 8th International Conference on Computer and Information Technology (ICCIT), 2005.

  • Md Tamjidul Hoque, M. Chetty, L. S. Dooley, A New Guided Genetic Algorithm for 2D Hydrophobic-Hydrophilic Model to Predict Protein Folding, IEEE Congress on Evolutionary Computation (CEC), pp. 259-266, ISBN 0-7803-9364-3, Edinburgh, 2005.

  • Summa CM, DeGrado WF, and Levitt M “ An Atomic Environment Potential for use in Protein Structure Prediction “ Journal of Molecular Biology 2005 (352) 986-1001 (PDF Format)

2004

  • Md Tamjidul Hoque, M. Chetty, L. S. Dooley, An Efficient Algorithm for Computing the Fitness Function of a Hydrophobic-Hydrophilic Model, 4th International Conference on Hybrid Intelligent Systems (HIS 2004), pp. 285-290, Japan, 2004.

  • Md Tamjidul Hoque, M. Chetty, L. S. Dooley, Partially Computed Fitness Function Based Genetic Algorithm for Hydrophobic-Hydrophilic Model, 4th International Conference on Hybrid Intelligent Systems (HIS 2004), pp. 285-290, Japan, 2004.

2003

  • Md Tamjidul Hoque and M. Kaykobad, Quantitative Approaches for Bangla Spell Checker, 6th International Conference on Computer and Information Technology (ICCIT), 2003.

  • Slovic AM, Summa CM, Lear JD, DeGrado WF, “ Computational Design of a Water-Soluble Analog of Phospholamban, “ Protein Science 2003 (12) 337-348 (PDF Format)

2002

  • Md Tamjidul Hoque and M. Kaykobad, Coding System for Bangla Spell Checker, 5th International Conference on Computer and Information Technology (ICCIT), 2002.

  • Md Tamjidul Hoque and M. Kaykobad, Use of Phonetic Similarity Property for Bangla Spell Checker, 5th International Conference on Computer and Information Technology (ICCIT), 2002.

  • ” Computational Methods and their Applications for de novo Functional Protein Design and Memebrane Protein Solubilization, “ my dissertation from The University of Pennsylvania with William F. DeGrado (bzip2’d PDF Format 18.5M)

  • Summa CM, Rosenblatt M, Hong JK, Lear, JD, DeGrado WF, “ Computational de novo Design, and Characterization of an A2B2 Diiiron Protein, “ Journal of Molecular Biology 2002 (321) 923-938 (PDF Format)

  • North B, Summa CM, Ghirlanda G, and DeGrado WF, “ Dn-Symmetrical Tertiary Templates for the Design of Tubular Proteins, “ Journal of Molecular Biology 2001 (311) 1081-1090 (PDF Format)

2000

  • Md Tamjidul Hoque and Ahmed Tareq, Development of Software Tool for Generating Coverability Tree in Petri Nets, IASTD, 2000.

  • Lombardi A, Summa CM, Geremia S, et. al., “ Retrostructural Analysis of Metalloproteins: Application to the design of a minimal model of diiron proteins, “ Proceedings of the National Academy of Sciences USA 2000 (97) 6298-305 (PDF Format)

1999

  • Summa CM, Lombardi A, Lewis M, DeGrado WF, “ Tertiary Templates for the Design of Diiron Proteins, “ Current Opinion in Structural Biology 1999 (9) 500-508. (PDF Format)

  • DeGrado WF, Summa CM, Pavone V, Nastri F, Lombardi A, “ De Novo Design and Structural Characterization of Proteins and Metalloproteins, “ Annual Review of Biochemistry 1999 (68) 779-819 (PDF Format)

1997

  • Md Tamjidul Hoque and Muhammad Masroor Ali, Noise Removal Algorithm from Images by using Breadth First Search Strategy, National Conference on Computer and Information Sys., (NCCIS), 1997.

Meeting Posters and Abstracts

  • Summa CM and Levitt M, “Using a Knowledge-Based Potential for Energy Refinement of Near-Native Protein Structure Models, “ CASP7 Meeting - Asilomar, CA November 2006 (Poster and Invited Talk)

  • Summa CM and Levitt M, “ Using a Knowledge-Based Potential for Energy Refinement of Near-Native Protein Structure Models, “ Protein Society Meeting (August 2006)

  • Raschke T, Summa CM, Kolodny R, and Levitt M, “Ab initio structure prediction of target proteins in CASP5,” CASP5 Meeting - Asilomar, CA 2002

  • Ghirlanda G, Summa CM, Pasternak A, Getahun Z, Lahr S, Rosenblatt MM, Lombardi A, DeGrado WF, “ A Parametric Approach for Understanding and Designing Metalloproteins “ Abstracts of Papers of the American Chemical Society 2001 (211) U699-U700

  • Summa CM and DeGrado WF, “ A Multi-body Atomic Potential Function for use in Automated de novo Protein Design “ Protein Society Meeting (1996)