Anup Kumar Halder

Assistant Professor

Computer Science & Engineering Department

Introduction

I am currently an Assistant Professor at IIIT Raichur, joining the institute in November 2024. Prior to joining IIIT Raichur, I served as a Research Assistant Professor at the Laboratory of Functional and Structural Genomics, University of Warsaw, and the Faculty of Mathematics and Information Science, Warsaw University of Technology, Poland. I hold a Ph.D. in Engineering from Jadavpur University, awarded under the prestigious Visvesvaraya Ph.D. Fellowship. My research emphasizes the application of machine learning and deep learning techniques to biological data analysis, with a particular focus on 3D genomics and proteomics. The decoding of complex biological networks, advancing personalized medicine, and drug-repurposing are key focuses of my research efforts.

Research Interests

  • 3D Genomics and Proteomics
  • Bio-LLM
  • Biological Complex Network Analysis
  • Multimodal Dynamic Learning


Contact

Mail
ahalder[at]iiitr.ac.in

Telephone Number
-

Room No.

Website
Google Scholar

Education

Ph.D. in Engineering, Jadavpur University

Research Area: Artificial Intelligence and Machine Learning, Computational Biology
Thesis Supervisor: Prof. Subhadip Basu

M.E. in Computer Science and Engineering, Jadavpur University

B.Tech. in Computer Science and Engineering, West Bengal University of Technology

Experience

Research Experience

Research Assistant Professor (April 2024 - November 2024)

Laboratory of Functional and Structural Genomics, CeNT, University of Warsaw, Poland.

Research Assistant Professor (Jan 2022 - March 2024)

Faculty of Mathematics and Information Sciences, Warsaw University of Technology, Poland.

Visiting Scholar (April 2018 - Sept. 2018)

Centre of New Technologies (CeNT), University of Warsaw, Poland.

Visvesvaraya PhD Fellow (2015 - 2020)

Jadavpur University, Kolkata, India.

Teaching Experience

Assistant Professor (April 2021 - Dec. 2021)

University of Engineering and Management, Kolkata, India.

Guest Lecturer (July 2016 - Dec. 2017)

Dept. of Computer Science and Engineering, Jadavpur University, Kolkata, India.

Assistant Professor (Feb. 2015 - Dec. 2015)

Batanagar Institute of Engineering, Management and Science, Kolkata, India.

Guest Lecturer (July 2014 - Jan. 2014)

Dept. of Computer Science and Engineering, Aliah University, Kolkata, India.

List of Publications

Journals

  1. T. Chakraborty, D. Paul, A. A. Halsana, A. K. Halder, S. Basu, and T. Chakraborti. “DensePPI-2: a bio-inspired update for sequence-based PPI prediction leveraging mutation rates”. Briefings in Bioinformatics, 26(4), 2025. (IF: 7.7)
  2. R. Patua, A. K. Halder*, S. Dasgupta, P. Chatterjee, M. Nasipuri, and S. Basu. “PCPredG: Protein Complex Prediction Using Graphlet Features”. IEEE Transactions on Computational Biology and Bioinformatics, 2025.
  3. A. K. Halder, S. S. Bandyopadhyay, W. Jedrzejewski, S. Basu, and J. Sroka. “FuzzyPPI: Large-Scale Interaction of Human Proteome at Fuzzy Semantic Space”. IEEE Transactions on Big Data, 2024. (IF: 7.2)
  4. A. K. Halder, A. Agarwal, K. Jodkowska, and D. Plewczynski. “A systematic analyses of different bioinformatics pipelines for genomic data and its impact on deep learning models for chromatin loop prediction”. Briefings in Functional Genomics, 2024. (IF: 4.0)
  5. M. Wiśniewski, P. Babirye, C. Musubika, E. Papakonstantinou, S. Kirimunda, M. Łaźniewski, T. Szczepińska, M. L. Joloba, E. Eliopoulos, E. Bongcam-Rudloff, D. Vlachakis, A. K. Halder†, D. Plewczynski, and M. Wayengera. “Use of in silico approaches, synthesis and profiling of Pan-filovirus GP-1,2 preprotein specific antibodies”. Briefings in Functional Genomics, 2024. (IF: 4.0)
  6. J. P. Fichna, M. Chilinski, A. K. Halder, P. Cikeszczyk, D. Plewczynski, C. Zekanowski, and P. Janik. “Structural Variants and Implicated Processes Associated with Familial Tourette Syndrome”. International Journal of Molecular Sciences, 25(11), 2024.
  7. B. K. Sriwastava, A. K. Halder*, T. Chakraborti, and S. Basu. “RUBic: Rapid Unsupervised Biclustering”. BMC Bioinformatics, 2023. (IF: 3.0)
  8. A. A. Halsana, T. Chakroborty, A. K. Halder, and S. Basu. “DensePPI: A Novel Image-Based Deep Learning Method for Prediction of Protein-Protein Interactions”. IEEE Transactions on Nanobioscience, 22(4), 2023. (IF: 3.9)
  9. M. Chiliński, A. K. Halder, and D. Plewczynski. “Prediction of chromatin looping using deep hybrid learning (DHL)”. Quantitative Biology, 11(2), 2023. (IF: 3.1)
  10. S. S. Bandyopadhyay, A. K. Halder, S. Saha, P. Chatterjee, M. Nasipuri, and S. Basu. “Assessment of GO-Based Protein Interaction Affinities in the Large-Scale Human–Coronavirus Family Interactome”. Vaccines, 11(3), 2023. (IF: 7.8)
  11. A. K. Halder, S. S. Bandyopadhyay, P. Chatterjee, M. Nasipuri, D. Plewczynski, and S. Basu. “JUPPI: A Multi-Level Feature Based Method for PPI Prediction and a Refined Strategy for Performance Assessment”. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 19(1), 2022. (IF: 4.5)
  12. S. Saha, A. K. Halder*, S. S. Bandyopadhyay, P. Chatterjee, M. Nasipuri, D. Bose, and S. Basu. “Drug repurposing for COVID-19 using computational screening: Is Fostamatinib/R406 a potential candidate?”. Methods, 203, 2022. (IF: 4.8)
  13. S. Saha, A. K. Halder*, S. S. Bandyopadhyay, P. Chatterjee, M. Nasipuri, and S. Basu. “Computational modeling of human-nCoV protein-protein interaction network”. Methods, 203, 2022. (IF: 4.8)
  14. S. Saha, P. Chatterjee, A. K. Halder, M. Nasipuri, S. Basu, and D. Plewczynski. “ML-DTD: Machine Learning-Based Drug Target Discovery for the Potential Treatment of COVID-19”. Vaccines, 10(10), 2022. (IF: 7.8)
  15. A. Banik, S. Podder, S. Saha, P. Chatterjee, A. K. Halder, M. Nasipuri, S. Basu, and D. Plewczynski. “Rule-Based Pruning and In Silico Identification of Essential Proteins in Yeast PPIN”. Cells, 11(17), 2022. (IF: 6.0)
  16. K. Sengupta, S. Saha, A. K. Halder, P. Chatterjee, M. Nasipuri, S. Basu, and D. Plewczynski. “PFP-GO: Integrating protein sequence, domain and protein-protein interaction information for protein function prediction using ranked GO terms”. Frontiers in Genetics, 13, 2022. (IF: 3.7)
  17. M. Zaręba-Kozioł, A. Bartkowiak-Kaczmarek, M. Roszkowska, K. Bijata, I. Figiel, A. K. Halder, et al. “S-palmitoylation of synaptic proteins as a novel mechanism underlying sex-dependent differences in neuronal plasticity”. International Journal of Molecular Sciences, 22(12), 2021. (IF: 5.6)
  18. S. S. Bandyopadhyay, A. K. Halder, M. Zaręba-Kozioł, A. Bartkowiak-Kaczmarek, A. Dutta, P. Chatterjee, et al. “Rfcm-palm: In-silico prediction of s-palmitoylation sites in synaptic proteins”. International Journal of Molecular Sciences, 22(18), 2021. (IF: 5.6)
  19. A. K. Halder, M. Denkiewicz, K. Sengupta, S. Basu, and D. Plewczynski. “Aggregated network centrality shows non-random structure of genomic and proteomic networks”. Methods, 181–182, 2020. (IF: 4.8)
  20. A. K. Halder, P. Chatterjee, M. Nasipuri, D. Plewczynski, and S. Basu. “3gClust: Human Protein Cluster Analysis”. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 16(6), 2019. (IF: 4.5)
  21. S. Basu, M. Karuppiah, M. Nasipuri, A. K. Halder, and N. Radhakrishnan. “Bio-inspired cryptosystem with DNA cryptography and neural networks”. Journal of Systems Architecture, 94, 2019. (IF: 4.5)
  22. A. K. Halder, P. Dutta, M. Kundu, S. Basu, and M. Nasipuri. “Review of computational methods for virus-host protein interaction prediction: A case study on novel Ebola-human interactions”. Briefings in Functional Genomics, 17(6), 2018. (IF: 4.0)
  23. P. Dutta, A. K. Halder, S. Basu, and M. Kundu. “A survey on Ebola genome and current trends in computational research on the Ebola virus”. Briefings in Functional Genomics, 17(6), 2018. (IF: 4.0)

Conferences

  1. A. K. Halder, A. Agarwal, S. Korsak, K. Jodkowska, and D. Plewczynski. “ccLoopER: Deep Prediction of CTCF and cohesin Mediated Chromatin looping Using DNA Transformer Model”. Pattern Recognition and Machine Intelligence. Springer, 2023.
  2. T. Chakraborty, A. Das, S. S. Bandyopadhyay, A. K. Halder, J. Wlodarczyk, and S. Basu. “Prediction of S-Palmitoylation Sites in the Male/Female Mouse Using the Protein Language Model”. Frontiers in Computing and Systems. Springer, 2023.
  3. A. A. Halsana, T. Chakroborty, A. K. Halder, and S. Basu. “DeConPPI: Deep Consensus-Based Prediction of Protein-Protein Interactions”. Proceedings of International Conference on Frontiers in Computing and Systems. Springer, 2023.
  4. S. S. Bandyopadhyay, A. K. Halder, K. Sengupta, P. Chatterjee, M. Nasipuri, D. Plewczynski, and S. Basu. “Multi-level Feature-Based Subcellular Location Prediction of Apoptosis Proteins”. International Conference on Data, Electronics and Computing. Springer, 2022.
  5. S. S. Bandyopadhyay, A. K. Halder, P. Chatterjee, J. Sroka, M. Nasipuri, and S. Basu. “Analysis of Large-Scale Human Protein Sequences Using an Efficient Spark-Based DBSCAN Algorithm”. Advances in Intelligent Systems and Computing, 1255, 2021.
  6. A. K. Halder, P. Dutta, M. Kundu, M. Nasipuri, and S. Basu. “Prediction of thyroid cancer genes using an ensemble of post translational modification, semantic and structural similarity based clustering results”. Pattern Recognition and Machine Intelligence. Springer, 2017.
  7. S. S. Bandyopadhyay, A. K. Halder, P. Chatterjee, M. Nasipuri, and S. Basu. “HdK-means: Hadoop based parallel K-means clustering for big data”. IEEE CALCON 2017 - Proceedings, 2018.

* shared first authorship, † corresponding author.