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 22nd
Louisiana Biomedical Research Network (LBRN) Annual Meeting, USA,
2024 [Poster],
Won
2nd 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 22nd
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].
- 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.
- 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, 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 19th 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 19th Annual Meeting, Louisiana, USA, 2021 [Poster].
2020
- [J1] Manish Bhattà, Avdesh Mishraà, Md Wasi Ul
Kabirà,
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 7th 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 7th 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 7th 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 7th
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 7th 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 7th Annual Conference on Computational
Biology and Bioinformatics,
Louisiana, USA, 2019 [Poster]. Won the 2nd
best poster prize.
- Bhupenda Acharya, Md Tamjidul Hoque, “Analysis
of Mental Impairment in HIV-Perinatally Infected Children using Machine
Learning Prediction Model,” The 7th
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 7th 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 8th 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
6th 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 6th 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 6th 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 6th 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 6th 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
6th 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 6th 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
6th 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
6th 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
5th 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 5th 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,” 61st 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,” 61st 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,”
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,” 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,” 4th 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] 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, 6th
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.