Publications

* indicates the corresponding author. ^§ indicates undergraduate student author. ^à indicates equal authorship.

[J1] => Peer-reviewed journal publication. [C1] => Peer-reviewed conference paper. [B1] => Peer-reviewed book chapter.

2024

• [J1] Md Wasi Ul Kabir, Md Tamjidul Hoque*, “DisPredict3.0: Prediction of Intrinsically Disordered Regions/Proteins Using Protein Language Model,” in Applied Mathematics and Computation, Elsevier, 2024 [Published].

• [J1] Md Wasi Ul Kabir, Duaa Mohammad Alawad, Pujan Pokhrel, Md Tamjidul Hoque*, “DRBpred: A Sequence-based Machine Learning Method to effectively predict DNA and RNA Binding Residues,” in Computers in Biology and Medicine, Elsevier, 2024 [Published].

• Duaa Alawad, Ataur Katebi, Md Tamjidul Hoque*, “EnsembleRegNet: Leveraging Ensemble Encoder-Decoder and Multiple-Layer Perceptron Bagging for Predicting Gene Regulatory Networks from Single-Cell RNA-Seq Data,” in 22^nd Louisiana Biomedical Research Network (LBRN) Annual Meeting, USA, 2024 [Poster], Won 2^nd best poster prize.

• Md Wasi Ul Kabir, Md Tamjidul Hoque*, “Predicting and Representing the Structure of an Unstructured Protein through an Ensemble of Low-Energy Conformations,” in 22^nd Louisiana Biomedical Research Network (LBRN) Annual Meeting, USA, 2024 [Poster].

2023

• [J1] Alessio Del Conte, Adel Bouhraoua, Mahta Mehdiabadi, Damiano Clementel, Alexander Miguel Monzon, CAID Predictors: Md Tamjidul Hoque, Md Wasi Ul Kabir, et al., Silvio C E Tosatto, Damiano Piovesan, “CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins,” in Nucleic Acids Research, Oxford Academic Journal, 2023 [Published].

• [J1] Duaa Mohammad Alawad, Ataur Katebi, Md Wasi Ul Kabir, Md Tamjidul Hoque*, “AGRN: Accurate Gene Regulatory Network inference using ensemble machine learning methods,” in Oxford Bioinformatics Advances Journal, 2023 [Published].

• [J1] Manisha Panta, Md Tamjidul Hoque*, Kendall N. Niles, Joe Tom, Mahdi Abdelguerfi, Maik Flanagin, “Deep Learning Approach for Accurate Segmentation of Sand Boils in Levee Systems,” IEEE Access Journal, 2023 [Published].

• [J1] Md Wasi Ul Kabir, Duaa Mohammad Alawad, Avdesh Mishra, Md Tamjidul Hoque*, “TAFPred: Torsion Angle Fluctuations Prediction from Protein Sequences,” in Biology/MDPI Journal, 2023 [Published].

• [J1] Rasha Riyadh Alshawi, Md Tamjidul Hoque*, Maik Flanagin, “A Depth-Wise Separable U-Net Architecture with Multiscale Filters to Detect Sinkholes,” Remote Sensing Journal, in Special Issue “Machine Learning and GeoAI for Remote Sensing Environmental Monitoring,” 2023 [Published].

• [J1] Manisha Panta, Md Tamjidul Hoque*, Mahdi Abdelguerfi, Maik Flanagin, “IterLUNet: Deep Learning Architecture for Pixel-Wise Crack Detection in Levee Systems,” IEEE Access Journal, 2023 [Published].

• [J1] Yashwanth Karthik Kumar Mamidi Tarun Karthik Kumar Mamidi, Md Wasi Ul Kabir, Jiande Wu, Md Tamjidul Hoque*, Chindo Hicks*, “PCa-Clf: A Classifier of Prostate Cancer Patients into Patients with Indolent and Aggressive Tumors Using Machine Learning,” in MAKE/MDPI Journal, 2023 [Published].

• [C1] Md Wasi Ul Kabir, Duaa Mohammad Alawad, Avdesh Mushra, Md Tamjidul Hoque*, “Prediction of Phi and Psi Angle Fluctuations from Protein Sequences,” in IEEE CIBCB 2023 conference, The Netherlands [Accepted].

• Duaa Mohammad Alawad, Ataur Katebi, Md Tamjidul Hoque*, “EGRC: Efficient Gene Regulatory Network inference using graph convolution network,” at InnovateUNO 2023 [Poster]. 

• Duaa Mohammad Alawad, Ataur Katebi, Md Wasi UI Kabir, Md Tamjidul Hoque*, “Accurate inferring Gene Regulatory Network-based ensemble machine learning methods,” at InnovateUNO 2023 [Poster]. 

• Amrit Rajbhandari, Md Wasi UI Kabir, Md Tamjidul Hoque*, “Identifying Disordered Proteins using AlphaFold2 and ESMFold,” at InnovateUNO 2023 [Poster].

• Md Wasi UI Kabir, Marco Tabora^§, Md Tamjidul Hoque*, “Intrinsically Disordered Protein Prediction using Pretrained Language Model,” at InnovateUNO 2023 [Poster].

• Md Wasi UI Kabir, Michael Carbone, Avdesh Mishra, Md Tamjidul Hoque*, “Prediction of Conformational Ensembles of Disordered Proteins,” at InnovateUNO 2023 [Poster].

• Steven Bordelon, Ben Samuel, Md Tamjidul Hoque, “Utilizing the OpenCV Machine Learning Library to Remove Commercials from the Streaming Experience,” at InnovateUNO 2023 [Abstract][Video].

• Advanced Technology seminar presentation (01 PM - 4:30 PM): Md Tamjidul Hoque, “A Review of Today’s Deep Machine Learning and Artificial Intelligence” at OCEANS 2023 conference.

2022

• [J1] Daniel T. Murphy, Elias Ioup, Md Tamjidul Hoque*, Mahdi Abdelguerfi, “Residual Learning for Marine Mammal Classification,” IEEE Access Journal, 2022 [Published].

• [J1] Simon Lailvaux*, Avdesh Mishra, Pooja Pun^§, Md Wasi Ul Kabir, Robbie Wilson, Anthony Herrel, Md Tamjidul Hoque*, “Machine learning accurately predicts the multivariate performance phenotype from morphology in lizards,” PLOS One, 2022 [Published].

• [J1] Pujan Pokhrel, Elias Ioup, Julian Simeonov, Md Tamjidul Hoque*, Mahdi Abdelguerfi, “A Transformer-Based Regression Scheme for Forecasting Significant Wave Heights in Oceans,” IEEE Journal of Oceanic Engineering, 2022 [Published].

• [J1] Nicholas Moran, Ben Stringer, Bruce Lin, Md Tamjidul Hoque*, “Machine Learning Model Selection for Predicting Bathymetry,” Deep-Sea Research Part I Journal, Elsevier, 2022 [Published].

• [J1] Austin Schmidt, Md Wasi Ul Kabir, Md Tamjidul Hoque*, “Machine Learning based Restaurant Sales Forecasting,” Machine Learning and Knowledge Extraction (MAKE) journal, MDPI, 2022 [Published].

• [C1] Daniel Murphy, Elias Ioup, Christopher Michael, Md Tamjidul Hoque*, Mahdi Abdelguerfi, “Multi-Channel Residual Learning for Marine Mammal Vocalization Classification,” in IEEE IGARSS 2022 conference [Published].

• [C1] Manisha Panta, Md Tamjidul Hoque*, Mahdi Abdelguerfi, Maik Flanagin, “Pixel-Level Crack Detection in Levee Systems: A Comparative Study,” in IEEE IGARSS 2022 conference [Published][Presentation].

• Md Wasi Ul Kabir, Md Tamjidul Hoque*, “Dispredict3.0: Intrinsically Disordered Protein prediction enhanced with Protein Language Model,” 9th Annual LA Conference on Computational Biology and Bioinformatics, Louisiana, USA, 2022 [Poster].

• Aasish Rijal^§, Md Wasi Ul Kabir, Md Tamjidul Hoque*, Thomas Soniat, “A Machine Learning Approach for Oyster Disease Prediction,” 9th Annual LA Conference on Computational Biology and Bioinformatics, Louisiana, USA, 2022 [Presentation and Poster] [pptx].

• Nayan Howladar, Md Wasi Ul Kabir, Tamjidul Hoque*, “Protein-Protein Interaction Prediction from Language of Biological Coding,” 9th Annual LA Conference on Computational Biology and Bioinformatics, Louisiana, USA, 2022 [Poster].

• Krishna Shah, Duaa Alawad, Md Wasi Ul Kabir, Md Tamjidul Hoque*, “Using Language-based Features for ncRNA-protein Interaction Prediction,” 9th Annual LA Conference on Computational Biology and Bioinformatics, Louisiana, USA, 2022 [Poster], Won 2nd best poster prize in Graduate Student Category.

• Duaa Alawad, Ataur Katebi, Md Tamjidul Hoque*, “Inferring Gene Regulatory Network using Graph Transformer Self-Attention Network,” 9th Annual LA Conference on Computational Biology and Bioinformatics, Louisiana, USA, 2022 [Poster].

2021

• [J1] Aditi Kuchi, Manisha Panta, Md Tamjidul Hoque*, Mahdi Abdelguerfi, Maik C. Flanagin, “A Machine Learning Approach to Detecting Cracks in Levees and Floodwalls,” Remote Sensing Applications: Society and Environment, Elsevier, 2021 [Published].

• [J1] Manisha Panta, Avdesh Misha, Md Tamjidul Hoque*, and Joel Atallah*, “ClassifyTE: A stacking based prediction of hierarchical classification of transposable elements,” Oxford Bioinformatics, 2021 [Published] [Tech. paper].

• [J1] Avdesh Mishra, Reecha Khanal^§, Md Wasi Ul Kabir, and Md Tamjidul Hoque*, “AIRBP: Accurate Identification of RNA-binding Proteins Using Machine Learning Techniques,” Artificial Intelligence In Medicine, Elsevier [Published] [Tech. paper].

• [J1] Marco Necci, Damiano Piovesan, CAID Predictors: Md Tamjidul Hoque, et al., DisProt Curators, Silvio C.E. Tosatto, “Critical Assessment of Protein Intrinsic Disorder Prediction,” Nature Method [Published] [Tech. paper].

• [J1] Avdesh Mishra, Md Wasi Ul Kabir, Md Tamjidul Hoque*, “diSBPred: A Machine Learning based Approach for Disulfide Bond Prediction,” Computational Biology and Chemistry Journal, Elsevier [Published].

• Duaa Alawad, Md Wasi Ul Kabir, Krishna Shah, Nayan Howladar, Muhammad Farooq, Sofiane Benkara, Amrit Rajbhandari, Dang Pham, Joshua Pierre, Md Tamjidul Hoque*, “Gene-Protein Regulatory Network,” at InnovateUNO 2021.

• Duaa Alawad, Md Wasi Ul Kabir, Md Tamjidul Hoque*, “Inferring gene regulatory network using Ensemble Machine Learning Algorithms,” at InnovateUNO 2021.

• Md Wasi Ul Kabir, Aasish Rijal^§, Thomas Soniat, Md Tamjidul Hoque*, “A Machine Learning Approach for Oyster Disease Prediction,” at InnovateUNO 2021.

• Nayan Howladar, Md Wasi Ul Kabir, Md Tamjidul Hoque*, “Protein-Protein Interaction Prediction Tool using Hybrid Feature Extraction and Self-Attention,” at InnovateUNO 2021.

• Hoang Nguyen^§, Md Wasi Ul Kabir, Md Tamjidul Hoque*, “Prediction of Intrinsically Disordered Protein Regions using Machine Learning Methods,” at InnovateUNO 2021.

• Dang Pham, Md Wasi Ul Kabir, Md Tamjidul Hoque*, “Feature preprocessing in object recognition,” Video Presentation at InnovateUNO 2021.

• Amrit Rajbhandari, Md Wasi Ul Kabir, Duaa Alawad, Md Tamjidul Hoque*, “Disordered RNA, DNA, and Protein Binding Regions Prediction using Machine Learning Methods,” Video Presesntation at InnovateUNO 2021.

• Aasish Rijal^§, Md Wasi Ul Kabir, Md Tamjidul Hoque*, “An Effective Machine Learning Method to Predict Residues of DNA- and RNA-Binding Protein,” at InnovateUNO 2021.

• Krishna Shah, Md Wasi Ul Kabir, Duaa Alawad, Md Tamjidul Hoque*, “RNA-Protein Network Analysis Using Machine Learning Methods and SCENIC Protocol,” Video Presentation at InnovateUNO 2021.

• Md Wasi Ul Kabir, Duaa Alawad, Krishna Shah, Nayan Howladar, Muhammad Farooq, Sofiane Benkara, Amrit Rajbhandari, Dang Pham, Joshua Pierre, Md Tamjidul Hoque*, “AI-based Integrated Approach for Gene Protein Regulatory Network,” Technical-Paper@University of New Orleans, 2021, Louisiana, USA, 2021 [Tech-paper].

• Md Wasi Ul Kabir, Aasish Rijal^§ and Md Tamjidul Hoque*, “A Sequence-based Machine Learning Method to effectively predict DNA and RNA Binding Residues,” 8th Annual Louisiana Biomedical Research Network Conference on Computational Biology and Bioinformatics, 2021, Louisiana, USA, 2021 [Presentation-Talk] [Poster], Won the 1^st best poster prize [Announcement].

• Md Wasi Ul Kabir, Hoang Dai Nguyen^§ and Md Tamjidul Hoque*, “Machine Learning-based Effective Prediction of Protein Disordered Regions,” 8th Annual Louisiana Biomedical Research Network Conference on Computational Biology and Bioinformatics, 2021, Louisiana, USA, 2021 [Poster].
• Duaa Mohammad Alawad and Md Tamjidul Hoque*, “Reconstructing Gene Regulatory Network for the Differentiation of Hematopoietic Stem Cells,” 8th Annual Louisiana Biomedical Research Network Conference on Computational Biology and Bioinformatics, 2021, Louisiana, USA, 2021 [Poster].

• Md Wasi Ul Kabir and Md Tamjidul Hoque*, “An Improved Machine Learning Method to Predict the Backbone Torsion Angle Fluctuations from a Protein Sequence,” LBRN 19^th Annual Meeting, Louisiana, USA, 2021[Poster].

• Duaa Mohammad Alawad and Md Tamjidul Hoque*, “Reconstructing gene regulatory network for the differentiation of hematopoietic stem cells,” LBRN 19^th Annual Meeting, Louisiana, USA, 2021 [Poster].

2020

• [J1] Manish Bhatt^à, Avdesh Mishra^à, Md Wasi Ul Kabir^à, Elizabeth Ruth Blankenship, Rishav Rajendra^§, Md Tamjidul Hoque*, Irfan Ahmed, “Hierarchy-based File Fragment Classification,” Machine Learning and Knowledge Extraction (MAKE) journal, MDPI, 2020 [Published].

• [J1] Duaa Mohammad Alawad, Avdesh Mishra, and Md Tamjidul Hoque*, “AIBH: Accurate Identification of Brain Hemorrhage using Genetic Algorithm based Feature Selection and Stacking,” Machine Learning and Knowledge Extraction (MAKE) journal, MDPI, 2020 [Published].

• [C1] Aditi Sharma Kuchi, Md Tamjidul Hoque*, Mahdi Abdelguerfi, and Maik Flanagin, “Levee-Crack Detection from Satellite or Drone Imagery Using Machine Learning Approaches,” in IEEE IGARSS 2020 conference [Published].

• [C1] Astha Sharma, Md Tamjidul Hoque*, Elias Loup, Mahdi Abdelguerfi, “Flight Data of Airplane for Wind Forecasting,” in IEEE IGARSS 2020 conference [Published].

• [C1] Pujan Pokhrel, Elias Ioup, Md Tamjidul Hoque*, Mahdi Abdelguerfi, Julian Simeonov, “Forecasting Rogue Waves In Oceanic Waters,” IEEE International Conference on Machine Learning and Applications (ICMLA), Miami, Florida, December 2020 [Published].

• [C1] Rishav Rajendra^§, Christopher Michael, Elias Ioup, Md Tamjidul Hoque*, Mahdi Abdelguerfi, “Online Feature Selection for Semantic Segmentation,” The 9th International Conference on Data Analytics, Nice – France, 2020 [Published] [Presentation].

• Austin Schmidt, Md Tamjidul Hoque, “Forecasting Restaurant Sales with Machine Learning,” at InnovateUNO [abstract, Oral Presentation].

• Md Wasi Ul Kabir, Md Tamjidul Hoque, “An Efficient Method to Predict the Backbone Torsion Angle Fluctuations from a Protein Sequence,” at InnovateUNO [abstract, Oral Presentation].

• Nanda Das^§, Md Wasi Ul Kabir, Pujan Pokhrel^§, Md Tamjidul Hoque, “Prediction of DNA-Binding Residues of a Protein Sequence using a Stacked Machine Learning Method,” at InnovateUNO [abstract, Oral Presentation].

• Sofiane Benkara, Md Tamjidul Hoque, “Autonomous navigation in dynamic environments,” at InnovateUNO [abstract, Oral Presentation].

• Duaa Alawad, Md Tamjidul Hoque, “New Circuit Generates Distinct Dynamical Behaviors by Combining a Toggle Switch and a Repressilator,” at InnovateUNO [abstract, Oral Presentation].

2019

• [J1] Suraj G Gattani, Avdesh Mishra, Md Tamjidul Hoque*, “StackCBPred: A Stacking based Prediction of Protein-Carbohydrate Binding Sites from Sequence,” Carbohydrate Research, Elsevier Journal, 2019 [Published].

• [J1] Aditi Sharma Kuchi, Md Tamjidul Hoque*, Mahdi Abdelguerfi, and Maik Flanagin, “Machine Learning Applications in Detecting Sand Boils from Images,” Array, Elsevier Journal, 2019 [Published].

• [J1] Corey Maryan, Md Tamjidul Hoque*, Christopher Michael, Elias Ioup, Mahdi Abdelguerfi, “Machine Learning Applications in Detecting Rip Channels from Images,” Applied Soft Computing, Elsevier Journal, 2019 [Published].

• [C1] Manisha Panta, Avdesh Mishra, Md Tamjidul Hoque*, Joel Atallah*, “Machine Learning based Prediction of Hierarchical Classification of Transposable Elements,” accepted for presentation at BIOKDD 2019 conference [Paper].

• [C1] Adesh Mishra, Md Tamjidul Hoque*, “3DIGARS-PSP: A Novel Statistical Energy Function and Effective Conformational Search Strategy based ab initio Protein Structure Prediction,” in ICCIT 2019 conference [Published].

• [C1] Simon Lailvaux, Avdesh Mishra, Md Tamjidul Hoque, Robbie Wilson, “A machine learning approach to predicting the multivariate performance phenotype,” Annual Meeting of the Society-for-Integrative-and-Comparative-Biology (SICB), Tampa FL, Jan 03-07, 2019. CARY: OXFORD UNIV PRESS INC., 2019 [Presentation/Abstract].

• [B1] Michael Flot, Avdesh Mishra, Aditi Sharma Kuchi, Md Tamjidul Hoque*, “StackSSSPred: A Stacking-Based Prediction of Supersecondary Structure from Sequence,” Book Chapter (Chapter 5, pp 101-122), in: Kister A. (eds) Protein Supersecondary Structures. Methods in Molecular Biology, vol 1958. Humana Press, New York, NY, 2019 [Published].

• Pooja Pun^§, Avdesh Mishra, Simon Lailvaux, Md Tamjidul Hoque*, “A Machine Learning Approach to Functional Morphology and Performance Prediction,” The 7^th Annual Conference on Computational Biology and Bioinformatics, Louisiana, USA, 2019 [Poster].

• Avdesh Mishra, Reecha Khanal^§, Md Tamjidul Hoque*, “Accurate Identification of RNA-binding Proteins (AIRBP) Using Machine Learning Techniques,” The 7^th Annual Conference on Computational Biology and Bioinformatics, Louisiana, USA, 2019 [Poster].

• Manisha Panta, Avdesh Mishra, Md Tamjidul Hoque*, Joel Atallah, “Prediction of Hierarchical Classification of Transposable Elements using Machine Learning Techniques,” The 7^th Annual Conference on Computational Biology and Bioinformatics, Louisiana, USA, 2019 [Presentation]. 

• Avdesh Mishra, Md Tamjidul Hoque*, “Three-Dimensional Ideal Gas Reference State based Energy Function for Flexible Proteins,” The 7^th Annual Conference on Computational Biology and Bioinformatics, Louisiana, USA, 2019 [Poster].  

• Pujan Pokhrel^§, Avdesh Mishra, Md Tamjidul Hoque*, “Prediction of DNA Binding Residues from Sequences using Machine Learning Techniques,” The 7^th Annual Conference on Computational Biology and Bioinformatics, Louisiana, USA, 2019 [Poster]. 

• Duaa Alawad, Avdesh Mishra, Md Tamjidul Hoque*, “Effective Brain Hemorrhage Diagnosis from Image Using Machine Learning Approach,” The 7^th Annual Conference on Computational Biology and Bioinformatics, Louisiana, USA, 2019 [Poster]. Won the 2^nd best poster prize.

• Bhupenda Acharya, Md Tamjidul Hoque, “Analysis of Mental Impairment in HIV-Perinatally Infected Children using Machine Learning Prediction Model,” The 7^th Annual Conference on Computational Biology and Bioinformatics, Louisiana, USA, 2019 [Poster].

• Sumaiya Iqbal, Avdesh Mishra, Yashwanth Mamidi, Md Tamjidul Hoque*, “A Genetic Algorithm with Adaptive and Memory-Assisted Local Operators,” The 7^th Annual Conference on Computational Biology and Bioinformatics, Louisiana, USA, 2019 [Poster].

• Reecha Khanal^§, Avdesh Mishra, Md Tamjidul Hoque*, “Effective Prediction of RNA-Binding Proteins Using Machine Learning Techniques,” The 8^th annual University of Louisiana System (ULS) Academic Summit, Louisiana, USA, 2019 [Presentation]. 

2018

• [J1] Avdesh Mishra, Pujan Pokhrel^§, Md Tamjidul Hoque*, “StackDPPred: A Stacking based Prediction of DNA-binding Protein from Sequence,” in Oxford Bioinformatics Journal, 2018 [Published].

• [J1] Sumaiya Iqbal, Md Tamjidul Hoque*, “PBRpredict-Suite: A Suite of Models to Predict Peptide Recognition Domain Residues from Protein Sequence,” in Oxford Bioinformatics Journal, 2018 [Published].

• [J1] Devin Joseph Frey, Avdesh Mishra, Md Tamjidul Hoque*, Mahdi Abdelguerfi, Thomas Soniat, “A Machine Learning Approach to Determine Oyster Vessel Behavior,” Machine Learning and Knowledge Extraction (MAKE) journal, MDPI, 2018, [Published].

• [J1] Sumit Tarafder^§, Md Toukir Ahmed^§, Sumaiya Iqbal, Md Tamjidul Hoque, M Sohel Rahman, “RBSURFpred: Modeling Protein Accessible Surface Area in Real and Binary Space using Regularized and Optimized Regression,” published in Journal of Theoretical Biology, Elsevier, Vol. 441, 14 March 2018, pp. 44-57.

• [J1] Chaitanya Anne, Avdesh Mishra, Md Tamjidul Hoque*, Shengru Tu, “Multiclass Patent Document Classification,” Artificial Intelligence Research Journal, 2018 [Published].

• [C1] Samin Rastgoufard, Sumaiya Iqbal, Md Tamjidul Hoque, Dimitrios Charalampidis, “Genetic Algorithm Variant based Effective Solutions for Economic Dispatch Problems,” in TPEC 2018 (The 2018 IEEE Texas Power and Energy Conference), USA, [Code_Data, readme], [Published].

• Avdesh Mishra, Reecha Khanal^§, Md Tamjidul Hoque*, “Prediction of RNA-binding Protein using Machine Learning Technique,” The 6^th Annual Conference on Computational Biology and Bioinformatics, Louisiana, USA, 2018 [Presentation][Poster].

• Avdesh Mishra, Manisha Panta, Md Tamjidul Hoque*, Joel Atallah, “Prediction of Hierarchical Classification of Transposable Elements using Machine Learning Approach,” The 6^th Annual Conference on Computational Biology and Bioinformatics, Louisiana, USA, 2018 [Presentation][Poster].

• Avdesh Mishra, Md Tamjidul Hoque*, “A Machine Learning based Approach for Disulfide Bond Prediction,” The 6^th Annual Conference on Computational Biology and Bioinformatics, Louisiana, USA, 2018 [Poster].

• Md Kauser Ahmed, Avdesh Mishra, Md Tamjidul Hoque*, “TAFPred: An Efficient Torsion Angular Fluctuation Predictor of a Protein from its sequence,” The 6^th Annual Conference on Computational Biology and Bioinformatics, Louisiana, USA, 2018 [Poster].

• Pujan Pokhrel^§, Avdesh Mishra, Md Tamjidul Hoque*, “StackDPPred: A Stacking based Prediction of DNA Binding Proteins from Sequences,” The 6^th Annual Conference on Computational Biology and Bioinformatics, Louisiana, USA, 2018 [Poster].

• Duaa Alawad, Avdesh Mishra, Md Tamjidul Hoque*, “Effective Brain Hemorrhage Diagnosis from Image Using Machine Learning Approach,” The 6^th Annual Conference on Computational Biology and Bioinformatics, Louisiana, USA, 2018 [Poster].

• Lijing Cui, Avdesh Mishra, Joel Andrepont^§, Md Tamjidul Hoque*, “Sequence-Based Prediction of Protein Carbohydrate Binding Sites Using Machine Learning Techniques,” The 6^th Annual Conference on Computational Biology and Bioinformatics, Louisiana, USA, 2018 [Poster].

• Michael Flot, Avdesh Mishra, Md Tamjidul Hoque*, “Prediction of Protein Secondary Structure from Sequence using Machine Learning Approach,” The 6^th Annual Conference on Computational Biology and Bioinformatics, Louisiana, USA, 2018 [Poster].

• Suraj Gattani, Avdesh Mishra, Md Tamjidul Hoque*, “Sequence and Structure based Protein Peptide Binding Residue Prediction,” The 6^th Annual Conference on Computational Biology and Bioinformatics, Louisiana, USA, 2018 [Poster].

2017

• [J1] Md Tamjidul Hoque*, Sumaiya Iqbal, “Genetic Algorithm based Improved Sampling for Protein Structure Prediction,” International Journal of Bio-Inspired Computation, International Journal of Bio-Inspired Computation, Vol. 9, Issue 3, 2017 pp. 129 – 141 [Published]

• [J1] Sumaiya Iqbal, Md Tamjidul Hoque*, “hGRGA: A Scalable Genetic Algorithm using Homologous Gene Schema Replacement,” in Journal: Swarm and Evolutionary Computation, Elsevier, Volume 34, June 2017, Pages 33-49 [Published].

• [J1] Avdesh Mishra, Md Tamjidul Hoque*, “Three-Dimensional Ideal Gas Reference State based Energy Function,” Current Bioinformatics, Bentham Journal, Volume 12, 6 Issues, pp. 171 – 180, 2017 [Published].

• [J1] Kenneth R. Walsh, Md Tamjidul Hoque, Kim H. Williams, “Human Machine Learning Symbiosis,” Journal of Learning in Higher Education, vol. 13, 1, p55-62, 2017 [Published].

• Sumaiya Iqbal, Md Tamjidul Hoque*, “Prediction of Peptide-Binding Residues of Receptor Proteins in a Complex,” The 5^th Annual Conference on Computational Biology and Bioinformatics, Louisiana, USA, 2017 [Presentation].

• Avdesh Mishra, Md Tamjidul Hoque*, “Improved Protein Structure Prediction using Advanced Scoring Function and Effective Sampling,” The 5^th Annual Conference on Computational Biology and Bioinformatics, Louisiana, USA, 2017 [Presentation].

• Avdesh Mishra, Md Tamjidul Hoque*, “Next Generation Evolutionary Sampling and Energy Function Guided Ab Initio Protein Structure Prediction,” 61^st Annual Meeting of the Biophysical Society, New Orleans, USA, 2017 [Poster] [Abstract].

• Sumaiya Iqbal, Md Tamjidul Hoque*, “A Study of Disorder-to-Order Transition by Characterizing the Binding Partners using a Statistical Potential,” 61^st Annual Meeting of the Biophysical Society, New Orleans, USA, 2017 [Poster] [Abstract].

2016

• [J1] 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, Volume 37, Issue 12, Pages 1119–1124, 2016 [Published].

• [J1] 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, Volume: 20, Issue: 4, pp. 627-644, Aug. 2016 [Published].

• [J1] Sumaiya Iqbal, Md Tamjidul Hoque*, “Estimation of Position Specific Energy as a Feature of Protein Residues from Sequence alone for Structural Classification,” PLOS One Journal [Published].

• [J1] 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,” Computational Biology and Chemistry Journal, Elsevier, Volume 61, April 2016, Pages 162-177 [Published].

• [J1] Avdesh Mishra, Sumaiya Iqbal, Md Tamjidul Hoque*, “Discriminate Protein Decoys from Native by using a Scoring Function based on Ubiquitous Phi and Psi Angles Computed for All Atom,” Journal of Theoretical Biology, Volume 398, pp.112-121, 2016 [Published].

• [J1] Nasrul Islam, Sumaiya Iqbal, Ataur R Katebi, Md Tamjidul Hoque*, “A Balanced Secondary Structure Predictor,” Journal of Theoretical Biology, Volume 389, 21 January 2016, Pages 60-71 [Published].

• [C1] Kenneth R. Walsh, Md Tamjidul Hoque, Kim H. Williams, “Human Machine Learning Symbiosis,” International Conference on Learning and Administration in Higher Education, TN, USA, 2016.

• [C1] Sumaiya Iqbal, Md Tamjidul Hoque*, “A Homologous Gene Replacement based Genetic Algorithm,” GECCO, 2016 [Paper] [Poster].

• [C1] Sumaiya Iqbal, Md Tamjidul Hoque*, “Estimation of Free Energy Contribution of Protein Residues as Feature for Structure Prediction from Sequence,” CCBC/GLBIO 2016.

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

2015

• [J1] Sumaiya Iqbal, Md Tamjidul Hoque*, “DisPredict: A Predictor of Disordered Protein using Optimized RBF Kernel,” PLOS One Journal [Published].

• [J1] Sumaiya Iqbal, Avdesh Mishra, Md Tamjidul Hoque*, “Improved Prediction of Accessible Surface Area Results in Efficient Energy Function Application,” Journal of Theoretical Biology, Volume 380, 7 September 2015, Pages 380-391 [Published].

2014

• [J1] 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,” Advances in Bioinformatics Journal [Published].

• [C1] Sumaiya Iqbal, Md Nasrul Islam, Md Tamjidul Hoque*, “Improved Protein Disorder Predictor by Smoothing Output,” 17th International Conference on Computer and Information Technology (ICCIT), 2014 [Published].

• [C1] 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.

2013

• [J1] 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.

• [J1] 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 [Published].

• [J1] 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 [Published].

• [C1] 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.

• [C1] 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.

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

2012

• [C1] 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

• [C1] 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

• [C1] Trent Higgs, Bela Stantic, Md Tamjidul Hoque and Abdul Sattar, “Refining Genetic Algorithm Twin Removal for High-Resolution Protein Structure Prediction,” IEEE CEC 2012.

• [C1] Trent Higgs, Bela Stantic, Md Tamjidul Hoque and Abdul Sattar, “Applying Feature-Based Resampling to Protein Structure Prediction,” BiCoB, 2012 [PDF].

• [C1] Trent Higgs, Bela Stantic, Md Tamjidul Hoque and Abdul Sattar, “Benefits of Genetic Algorithm Feature-Based Resampling for Protein Structure Prediction”, Bioinformatics, 2012.

2011

• [J1] 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 [Published].

2010

• [J1] 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.

• [J1] 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.

• [C1] Trent Higgs, Bela Stantic, Md Tamjidul Hoque and Abdul Sattar, Genetic Algorithm Feature-Based Resampling for Protein Structure Prediction,” in WCCI/IEEE CEC, 2010.

• [C1] M A Rashid, Md Tamjidul Hoque and Abdul Sattar, “Association Rules Mining Based Diseases Correlation Prediction,” in Medinfo2010.

• [C1] Trent Higgs, Bela Stantic and Md Tamjidul Hoque, Mutation operator and its Effects on protein Structure Prediction in Genetic Algorithms,” in Medinfo2010.

2009

• [J1] 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.

• [C1] 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.

• [B1] 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.

2008

• [C1] Md Tamjidul Hoque*, M. Chetty, A Lewis, A Sattar “DFS based partial pathways in GA for protein structure prediction,” PRIB 2008.

• [C1] Trent Higgs, Bela Stantic and Md Tamjidul Hoque, Hydrophobic-Hydrophilic Forces and their Effects on Protein Structural Similarity, LNBI/PRIB 2008.

• [C1] 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.

• [C1] 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.

2007

• [C1] 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.

• [C1] Md Tamjidul Hoque*, M. Chetty, L. S. Dooley, “Generalized schemata theorem incorporating twin removal for protein structure predictions,” PRIB 2007.

• [B1] 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.

2006

• [C1] 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.

• [C1] 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.

• [C1] 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.

• [C1] 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

• [J1] 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.

• [C1] 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.

• [C1] 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.

• [C1] 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.

2004

• [C1] 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.

• [C1] 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

• [C1] Md Tamjidul Hoque* and M. Kaykobad, Quantitative Approaches for Bangla Spell Checker, 6^th International Conference on Computer and Information Technology (ICCIT), 2003.

2002

• [C1] Md Tamjidul Hoque* and M. Kaykobad, Coding System for Bangla Spell Checker, 5th International Conference on Computer and Information Technology (ICCIT), 2002.

• [C1] 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.

2000

• [C1] Md Tamjidul Hoque* and Ahmed Tareq, Development of Software Tool for Generating Coverability Tree in Petri Nets, IASTD, 2000.

1997

• [C1] 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.