Office: 309 S.R. Collins Engr. Bldg.
Phone: (936) 261-9878
Email: mhshuvo@pvamu.edu

I am a tenure-track Assistant Professor in the Department of Computer Science at Prairie View A&M University. My primary research interests include:

> Computational Biology
> Machine Learning
> Data Analytics
> Artificial Intelligence

My current research lies at the intersection of structural biology, machine learning, and data science. Broadly, I am developing data-driven computational methods for macromolecules to understand their structures and functions by leveraging cutting-edge Artificial Intelligence techniques.

I have been honored with multiple fellowship awards including the Pratt Fellowship Award, 2023 at Virginia Tech. Additionally, I received the 1st place prize in the Young Scientist Excellence Award competition at MCBIOS, 2022

Prior to joining PVAMU, I obtained my Ph.D. in Computer Science from Virginia Tech in 2023 under the supervision of Dr. Debswapna Bhattacharya.

I am open to collaboration and actively pursuing collaborative opportunities to broaden my interdisciplinary research capabilities, particularly in the realm of Computational Biology, Artificial Intelligence, and applied machine learning.

Google Scholar  

ADVISING

Graduate Students

  1. Danario Edgar
  2. Damario Johnson [Co-advised with Dr. Yang and Dr. Perkins]
  3. Joshua Gado [Co-advised with Dr. Yang and Dr. Perkins]
  4. Ms. Shamalle Payton

Undergraduate Students

  1. Jafin Khan

FORMER ADVISEES

Graduate Students

  1. Segun Samuel Akinwa
  2. Sheriff Adepoju
Undergraduate Students

  1. Sowande Crews
  2. Jalloni Adam Edward Gibson
  3. Francisco Ele Ekang Mofuman
  4. Diego Javier Hatem
TEACHING

Courses I frequently teach

    COMP 5690: Masters Thesis
    CINS 5306: Data Structures and Algorithms
    COMP 4323: Network Security
    COMP 4207: Senior Design
    CINS 4100: Ethics and Social Issues in Computing
    COMP 3322: Software Engineering
    COMP 3305: Analysis of Algorithms
    COMP 2310: Discrete Structures
    COMP 1337 & 1122: Computer Science II

NEWS

10/22/2025 Hosted Dr. Rahmatullah Roche for a research talk at CCSB@PVAMU | Watch
10/17/2025 Elected as a Faculty Advisory Council member for the College of Engineering at PVAMU
10/08/2025 Presented our research works at CCSB@PVAMU
09/10/2025 Awarded the RISE Undergraduate Research Grant by Research & Innovation Division at PVAMU
08/06/2025 Attended Quantum Security and Machine Learning Workshop at the University of Tennessee at Chattanooga
07/28/2025 Our EquiPNAS article is amongst the most-cited recent articles in Nucleic Acids Research
07/18/2025 Served as a Data Science PFx Instructor at the Atlanta University Center Consortium
07/18/2025 Attended the AI-assisted Cybersecurity Workshop at Tennessee Tech University
05/30/2025 Contributed to the GET-PHIT Summer 2025 bootcamp | Snapshot
04/22/2025 Awarded $5,000 in Google Cloud research resources
02/19/2025 Presented our research works at CCSB@PVAMU | Watch
01/02/2025 Our EquiRank paper is published in Computational and Structural Biotechnology Journal
12/18/2024 Attended GenAI Faculty Summit organized by Google. Snapshot
10/12/2024 Presented our EquiRank work at ICIBM 2024, held at Rice University
09/15/2024 Awarded FEP award by the Roy G. Perry College of Engineering at PVAMU
08/31/2024 Organized Machine Learning workshop jointly with Dr. Wang, sponsored by Google's TEC
08/23/2024 Our EquiRank work has been accepted to ICIBM 2024
07/19/2024 Served as a Data Science PFx Instructor at the Atlanta University Center Consortium
04/09/2024 Selected as 1 of the 20 Researchers for the Research Affinity Cohort (RAC) program of the National Data Science Alliance (NDSA)
04/05/2024 Presented research work on Faculty Research Day at PVAMU R&I Week, 2024
04/02/2024 Graduate student Sheriff Adepoju presented a poster at PVAMU R&I Week, 2024
03/12/2024 Awarded the Google TEC Impact Fund, led jointly with Dr. Wang
01/28/2024 Our EquiPNAS paper is published in NAR
01/02/2024 I joined the Department of Computer Science at Prairie View A&M University as an Assistant Professor
12/05/2023 Successfully defended Ph.D. dissertation. Acknowledgment
11/10/2023 Accepted a tenure-track Assistant Professor position in the Computer Science department at Prairie View A&M University
10/25/2023 Passed the CS@VT Research Defense
09/17/2023 Our EquiPNAS preprint is available at bioRxiv
08/31/2023 Our EquiPPIS paper has been accepted for publication in PLOS Computational Biology and available here
07/25/2023 Awarded the Pratt Fellowship at VT
06/19/2023 Served as a subreviewer
06/02/2023 Our PIQLE paper has been accepted by Bioinformatics Advances and available here
05/09/2023 Passed the CS@VT PhD preliminary exam
03/28/2023 Our book chapter on homology modeling is published and available here
03/17/2023 Our iQDeep paper has been accepted for publication in JMB
02/15/2023 Our PIQLE paper is available at bioRxiv
12/17/2022 Our EquiPPIS paper is available at bioRxiv
11/22/2022 The CASP15 abstract has been published and is available here
11/16/2022 Our book chapter on homology modeling has been accepted for publication to Springer Nature
8/19/2022 Participated in the 15th Critical Assessment of Protein Structure Prediction experiments (CASP15)
07/31/2022 Our iQDeep web server is released for beta testing
07/12/2022 Our rrQNet paper is published in PROTEINS
06/20/2022 Our DeepRefiner abstract has been accepted for the ACM-BCB 2022 Highlights Track
04/27/2022 Won first place in Young Scientist Excellence Award competition at MCBIOS 2022
04/08/2022 Selected as one of the finalists for Young Scientist Excellence Award at MCBIOS 2022
11/15/2021 Passed the CS@VT PhD qualifier process
8/30/2021 The CASP-COVID experiment paper is published in PROTEINS
8/11/2021 Moved to Virginia. Snapshot
6/10/2021 Served as a subreviewer at BIOKDD 2021
5/17/2021 Our DeepRefiner paper is published in Nucleic Acids Research
4/21/2021 Our DeepRefiner paper is accepted by Nucleic Acids Research
4/21/2021 Our review paper is accepted by Frontiers
12/20/2020 Our DeepRefiner webserver is publicly released
7/16/2020 Presented the poster for our aceepted QDeep method at ISMB 2020. Presentation
7/13/2020 Our QDeep paper is published in ISMB 2020 special issue of Bioinformatics
6/12/2020 Received ISMB 2020 fellowship award
6/6/2020 Our QDeep paper is accepted by ISMB 2020
5/18/2020 Participated 14th Critical Assessment of Protein Structure Prediction challenge (CASP14)
3/13/2020 Participated CASP_Commons (COVID-19, 2020)
5/30/2020 Our method QDeep is accepted for a poster presentation at ISMB 2020 as part of the 3DSIG COSI
1/13/2020 Our SPECS paper is accepted by PLOS ONE
5/1/2018 Participated 13th Critical Assessment of Protein Structure Prediction challenge (CASP13)

RESEARCH

Protein Structure Quality

Protein Structure Quality Assessment

Deep learning for error estimation, structure scoring, and refinement

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Molecular Interactions

Protein–Protein & Protein–Nucleic Acid Interactions

Equivariant graph neural networks for binding site prediction, interface identification, and interface accuracy estimation

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Geometric Deep Learning

Large Language Models (LLMs)

Protein Language Models (pLMs) for molecular embeddings

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Protein Homology Modeling

Protein Homology Modeling

Threading, template-based modeling, and contact-assisted threading for accurate protein structure prediction

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COVID-19 Modelling

COVID-19 Modelling

CASP_Commons:Community-wide SARS-2-CoV structure modeling initiative

Read more
Applied Machine Learning

Applied Machine Learning

AI applications in intelligent transportation and sustainable materials discovery

Read more

PUBLICATIONS


    2025
  • Md Hossain Shuvo, Debswapna Bhattacharya.
    EquiRank: improved protein-protein interface quality estimation using protein-language-model-informed equivariant graph neural networks
    International Conference on Intelligent Biology and Medicine, 2024
    Computational and Structural Biotechnology Journal, Volume 27, 160 - 170, 2025
    PDF | GitHub
    2024
  • Rahmatullah Roche, Bernard Moussad, Md Hossain Shuvo, Sumit Tarafder, Debswapna Bhattacharya.
    EquiPNAS: improved protein–nucleic acid binding site prediction using protein-language-model-informed equivariant deep graph neural networks
    Nucleic Acids Research, gkae039, 2024
    PDF | GitHub
    2023
  • Md Hossain Shuvo, Mohimenul Karim, Rahmatullah Roche, Debswapna Bhattacharya.
    PIQLE: protein-protein interface quality estimation by deep graph learning of multimeric interaction geometries
    Bioinformatics Advances, vbad070, 2023
    PDF | GitHub
  • Md Hossain Shuvo, Mohimenul Karim, Debswapna Bhattacharya.
    iQDeep: an integrated web server for protein scoring using multiscale deep learning models
    Journal of Molecular Biology, 168057, 2023
    PDF | Server
  • Rahmatullah Roche, Bernard Moussad, Md Hossain Shuvo, Debswapna Bhattacharya.
    E(3) equivariant graph neural networks for robust and accurate protein–protein interaction site prediction
    PLOS Computational Biology, e1011435
    PDF | GitHub
  • Sutanu Bhattacharya, Rahmatullah Roche, Md Hossain Shuvo, Bernard Moussad, Debswapna Bhattacharya.
    Contact-Assisted Threading in Low-Homology Protein Modeling
    Methods in Molecular Biology book series, vol. 2627, 2023
    PDF
    2022
  • Rahmatullah Roche, Sutanu Bhattacharya, Md Hossain Shuvo, Debswapna Bhattacharya.
    rrQNet: Protein contact map quality estimation by deep evolutionary reconciliation
    Proteins: Structure, Function, and Bioinformatics, (2022).
    PDF | GitHub
    2021
  • Andriy Kryshtafovych,..., Md Hossain Shuvo., ...,
    Modeling SARS-CoV2 proteins in the CASP-commons experiment
    Proteins: Structure, Function, and Bioinformatics, (2021).
    PDF
  • Md Hossain Shuvo, Muhammad Gulfam, Debswapna Bhattacharya.
    DeepRefiner: high-accuracy protein structure refinement by deep network calibration
    Nucleic Acids Research, Web Server Issue, gkab361 (2021).
    Selected for Highlight Talk at 13th ACM-BCB conference
    PDF | Server
  • Sutanu Bhattacharya, Rahmatullah Roche, Md Hossain Shuvo, Debswapna Bhattacharya.
    Recent Advances in Protein Homology Detection Propelled by Inter-Residue Interaction Map Threading of protein structural models
    Frontiers in Molecular Biosciences, 8: 643752 (2021).
    PDF | In memoriam of Cyrus Chothia
    2020
  • Md Hossain Shuvo, Sutanu Bhattacharya, Debswapna Bhattacharya.
    QDeep: distance-based protein model quality estimation by residue-level ensemble error classifications using stacked deep residual neural networks
    ISMB Proceedings (2020), Bioinformatics, 36(S1): i285-i291 (2020).
    PDF | GitHub
  • Rahul Alapati, Md Hossain Shuvo, Debswapna Bhattacharya.
    SPECS: Integration of side-chain orientation and global distance-based measures for improved evaluation of protein structural models
    PLOS ONE, 15(2): e0228245 (2020).
    PDF | GitHub | Server

ACADEMICS


    EDUCATION
  • Ph.D. in Computer Science
    Virginia Tech
    Dec 2023
  • M.Sc. in Computer Science
    Alabama A&M University
    July 2017
  • B.Sc. in Computer Science and Engineering
    Bangladesh University of Business and Technology
    July 2014
    AWARDS & HONORS
  • Awarded FEP award by the Roy G. Perry College of Engineering at PVAMU
    September 15, 2024
  • Awarded Google TEC Equity Collective Fund
    March 12, 2024
  • Awarded the Pratt Fellowship at Virginia Tech
    July 25, 2023
  • DeepRefiner has been accepted for the ACM-BCB 2022 Highlights Track
    August 7-10, 2022
  • Awarded 1st place prize in Young Scientist Excellence Award competition at 18th annual MCBIOS Conference, 2022
    April 27, 2022
  • Awarded conference fellowship for MCBIOS 2022
    April 25-27, 2022
  • Awarded conference fellowship for ISMB 2020
    July 13-16, 2020
  • Awarded 2nd place prize at AAMU STEM Day-2016
    April 14, 2016
  • Awarded travel fellowship for IEEE SoutheastCon 2016
    March 30 - April 3, 2016
    POSTERS AND PRESENTATIONS
  • M. H. Shuvo, S. Bhattacharya, D. Bhattacharya, "QDeep: distance-based protein model quality estimation by residue-level ensemble error classifications using stacked deep residual neural networks", ISMB 2020
    Slide | Presentation
    ACADEMIC EXPERIENCES
  • Assistant Professor
    Prairie View A&M University
    Jan 2024 - Present

    1. COMP 3305: Analysis of Algorithms
    2. COMP 3322: Software Engineering
    3. COMP 1337: Computer Science II
    4. COMP 1122: Computer Science Lab II

    Show details
  • Graduate Research Assistant
    Virginia Tech
    Aug 2021 - Dec 2023

    Graduate Research Assistant:
    Under the supervision of Dr. Debswapna Bhattacharya
    VTech: Aug 2021 - Dec 2023
    AU: Jan 2018 - Jul 2021
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  • Graduate Teaching and Research Assistant
    Auburn University
    Jan 2018 - Jul 2021

    Graduate Research Assistant:
    Under the supervision of Dr. Debswapna Bhattacharya (Jan 2018 - Jul 2021)
    Graduate Teaching Assistant:
    >COMP1210: Fundamentals of Computing I: Fall 2018, Spring 2019, Fall 2019, Spring 2020
    >COMP 5970/6970: Computational Biology
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  • Graduate Assistant
    Alabama Agricultural and Mechanical University
    Aug 2015 - Jul 2017
  • Lecturer, Dept. of Stat, Math & Com
    Dhaka Commerce College
    Jan 2015 - Aug 2015
  • Lecturer, Dept. of ICT
    Dhaka Cambrian College
    Aug 2014 - Dec 2014