Dr. ANUP KUMAR HALDER, PhD
Assistant Professor,
Department of Computer Science & Engineering,
Email: ahalder[at] iiitk.ac.in | Contact Number: 08518-289100 - 141(E)
Academic Qualifications
· Ph.D. (Engineering) in Computer Science and Engineering, Jadavpur University, Kolkata, India· M.E. in Computer Science and Engineering, Jadavpur University, Kolkata, India
· B.Tech in Computer Science and Engineering, WBUT, West Bengal, India
Areas of Interest
·
Computational Genomics
·
Biomolecular Interaction
Prediction and Network Biology
·
Deep Learning for Chromatin
Organization
·
Large Language Models (LLMs)
for Biological Sequences
·
Biclustering
·
Drug Repurposing
Professional / Teaching Experience
· Assistant Professor, IIITDM Kurnool (Dec 2025 – Present)
· Assistant Professor, IIIT Raichur (Nov 2024 – Dec 2025)
· Assistant Professor Research, Centre of New Technologies (CeNT), University of Warsaw (April 2024 – Nov 2025)
· Assistant Professor Research, Faculty of Mathematics and Information Sciences, Warsaw University of Technology (April 2022–March 2024)
Publication Profile
· Google Scholar: https://scholar.google.co.in/citations?user=J2v1BgsAAAAJ&hl=en
· Scopus: https://www.scopus.com/authid/detail.uri?authorId=57198352475
· ORCID : https://orcid.org/0000-0003-4825-1901
· Vidwan-ID : 672810
Courses Handled
· Machine Learning,
· Data Structures,
· Soft Computing,
· Bioinformatics,
· Artificial Intelligence
· Fundamentals of Artificial Intelligence
· Database management
Publications:
International Journals:
1. Chakraborty, T., Paul, D., Halsana, A. A., Halder, A. K., Basu, S., Chakraborti, T., DensePPI-2: a bio-inspired update for sequence-based PPI prediction leveraging mutation rates, Briefings in Bioinformatics, Volume 26, Issue 4, July 2025, bbaf394, https://doi.org/10.1093/bib/bbaf394
2. Patua, R., Halder, A. K., Dasgupta, S., Chatterjee, P., Nasipuri, M., Basu, S., PCPredG: Protein Complex Prediction Using Graphlet Features, IEEE Transactions on Computational Biology and Bioinformatics, vol. 22, no. 3, pp. 997–1008, May–June 2025, doi: 10.1109/TCBBIO.2025.3540117
3. Halder, A. K., Bandyopadhyay, S. S., Jedrzejewski, W., Basu, S., Sroka, J., FuzzyPPI: Large-Scale Interaction of Human Proteome at Fuzzy Semantic Space, IEEE Transactions on Big Data, 2024, pp. 1–12, doi: 10.1109/TBDATA.2024.3375149
4. Fichna, J. P., Chiliński, M., Halder, A. K., Cięszczyk, P., Plewczynski, D., Żekanowski, C., Janik, P., Structural Variants and Implicated Processes Associated with Familial Tourette Syndrome, International Journal of Molecular Sciences, 25(11), 5758, 2024, https://doi.org/10.3390/ijms25115758
5. Halder, A. K., Agarwal, A., Jodkowska, K., Plewczynski, D., A systematic analysis of different bioinformatics pipelines for genomic data and its impact on deep learning models for chromatin loop prediction, Briefings in Functional Genomics, 2024, elae009, doi: 10.1093/bfgp/elae009
6. Wiśniewski, M., Babirye, P., Musubika, C., Papakonstantinou, E., Kirimunda, S., Łaźniewski, M., Szczepińska, T., Joloba, M. L., Eliopoulos, E., Bongcam-Rudloff, E., Vlachakis, D., Halder, A. K., Plewczynski, D., Wayengera, M., Use of in silico approaches, synthesis and profiling of Pan-filovirus GP-1, 2 preprotein specific antibodies, Briefings in Functional Genomics, 2024, elae012, doi: 10.1093/bfgp/elae012
7. Sriwastava, B. K., Halder, A. K., Chakraborti, T., Basu, S., RUBic: Rapid Unsupervised Biclustering, BMC Bioinformatics, 2023, doi: 10.1186/s12859-023-05534-3
8.
Halsana,
A. A., Chakroborty, T., Halder, A. K.,
Basu, S., DensePPI: A Novel Image-Based Deep Learning Method for Prediction of
Protein–Protein Interactions, IEEE
Transactions on Nanobioscience, 22(4), 2023, pp. 904–911, doi:
10.1109/TNB.2023.3251192
9. Bandyopadhyay, S. S., Halder, A. K., Saha, S., Chatterjee, P., Nasipuri, M., Basu, S., Assessment of GO-Based Protein Interaction Affinities in the Large-Scale Human–Coronavirus Family Interactome, Vaccines, 11(3), 2023, p. 549, doi: 10.3390/vaccines11030549
10. Halder, A. K., Bandyopadhyay, S. S., Chatterjee, P., Nasipuri, M., Plewczynski, D., Basu, S., 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, pp. 531–542, doi: 10.1109/TCBB.2020.3004970
11. Saha, S., Halder, A. K., Bandyopadhyay, S. S., Chatterjee, P., Nasipuri, M., Bose, D., Basu, S., Drug repurposing for COVID-19 using computational screening: Is Fostamatinib/R406 a potential candidate?, Methods, 203, 2022, pp. 564–574, doi: 10.1016/j.ymeth.2021.08.007
12. Saha, S., Halder, A. K., Bandyopadhyay, S. S., Chatterjee, P., Nasipuri, M., Basu, S., Computational modeling of human-nCoV protein-protein interaction network, Methods, 203, 2022, pp. 488–497, doi: 10.1016/j.ymeth.2021.12.003
13. Saha, S., Chatterjee, P., Halder, A. K., Nasipuri, M., Basu, S., Plewczynski, D., ML-DTD: Machine Learning-Based Drug Target Discovery for the Potential Treatment of COVID-19, Vaccines, 10(10), 2022, doi: 10.3390/vaccines10101643
14. Banik, A., Podder, S., Saha, S., Chatterjee, P., Halder, A. K., Nasipuri, M., Basu, S., Plewczynski, D., Rule-Based Pruning and In Silico Identification of Essential Proteins in Yeast PPIN, Cells, 11(17), 2022, doi: 10.3390/cells11172648
15. Sengupta, K., Saha, S., Halder, A. K., Chatterjee, P., Nasipuri, M., Basu, S., Plewczynski, D., PFP-GO: Integrating protein sequence, domain, and protein-protein interaction information for protein function prediction using ranked GO terms, Frontiers in Genetics, 13, 2022, doi: 10.3389/fgene.2022.969915
16. Zaręba-Kozioł, M., Bartkowiak-Kaczmarek, A., Roszkowska, M., Bijata, K., Figiel, I., Halder, A. K., Kamińska, P., Müller, F. E., Basu, S., Zhang, W., Ponimaskin, E., Włodarczyk, J., S-palmitoylation of synaptic proteins as a novel mechanism underlying sex-dependent differences in neuronal plasticity, International Journal of Molecular Sciences, 22(12), 2021, doi: 10.3390/ijms22126253
17. Bandyopadhyay, S. S., Halder, A. K., Zaręba-Kozioł, M., Bartkowiak-Kaczmarek, A., Dutta, A., Chatterjee, P., Nasipuri, M., Wójtowicz, T., Włodarczyk, J., Basu, S., Rfcm-palm: In-silico prediction of s-palmitoylation sites in the synaptic proteins for male/female mouse data, International Journal of Molecular Sciences, 22(18), 2021, doi: 10.3390/ijms22189901
18. Halder, A. K., Denkiewicz, M., Sengupta, K., Basu, S., Plewczynski, D., Aggregated network centrality shows non-random structure of genomic and proteomic networks, Methods, 181–182, 2020, pp. 5–14, doi: 10.1016/j.ymeth.2019.11.006
19. Halder, A. K., Chatterjee, P., Nasipuri, M., Plewczynski, D., Basu, S., 3gClust: Human Protein Cluster Analysis, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 16(6), 2019, pp. 1773–1784, doi: 10.1109/TCBB.2018.2840996
20. Basu, S., Karuppiah, M., Nasipuri, M., Halder, A. K., Radhakrishnan, N., Bio-inspired cryptosystem with DNA cryptography and neural networks, Journal of Systems Architecture, 94, 2019, pp. 24–31, doi: 10.1016/j.sysarc.2019.02.005
21. Halder, A. K., Dutta, P., Kundu, M., Basu, S., Nasipuri, M., 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, pp. 381–391, doi: 10.1093/bfgp/elx026
22. Dutta, P., Halder, A. K., Basu, S., Kundu, M., A survey on Ebola genome and current trends in computational research on the Ebola virus, Briefings in Functional Genomics, 17(6), 2018, pp. 374–380, doi: 10.1093/bfgp/elx020
International Conferences:
1. Chakraborty, T., Das, A., Bandyopadhyay, S. S., Halder, A. K., Wlodarczyk, J., Basu, S., Prediction of S-Palmitoylation Sites in the Male/Female Mouse Using the Protein Language Model, International Conference on Frontiers in Computing and Systems, Springer Nature Singapore, 2023, pp. 439–447.
2. Paul, D., Patua, R., Saha, S., Halder, A. K., Basu, S., GSPPI: GraphSAGE-Based Prediction of Protein–Protein Interactions Using Graphlet Features, International Conference on Data, Electronics and Computing, Springer Nature Singapore, 2023, pp. 101–112.
3. Halder, A. K., Agarwal, A., Korsak, S., Jodkowska, K., Plewczynski, D., ccLoopER: Deep Prediction of CTCF and Cohesin Mediated Chromatin Looping Using DNA Transformer Model, Pattern Recognition and Machine Intelligence, Springer Nature Switzerland, 2023, pp. 871–878. ISBN: 978-3-031-45170-6. doi: 10.1007/978-3-031-45170-6_91.
4. Chakraborty, T., Das, A., Bandyopadhyay, S. S., Halder, A. K., Wlodarczyk, J., Basu, S., Prediction of S-Palmitoylation Sites in the Male/Female Mouse Using the Protein Language Model, International Conference on Frontiers in Computing and Systems, Springer, 2023, pp. 439–447. doi: 10.1007/978-981-97-2611-0_30.
5. Halsana, A. A., Chakroborty, T., Halder, A. K., Basu, S., DeConPPI: Deep Consensus-Based Prediction of Protein–Protein Interactions, Proceedings of International Conference on Frontiers in Computing and Systems (COMSYS 2022), Springer, Singapore, 2023, pp. 485–493. ISBN: 978-981-99-2680-0. doi: 10.1007/978-981-99-2680-0_42.
6. Bandyopadhyay, S. S., Halder, A. K., Sengupta, K., Chatterjee, P., Nasipuri, M., Plewczynski, D., Basu, S., Multi-level Feature-Based Subcellular Location Prediction of Apoptosis Proteins, International Conference on Data, Electronics and Computing, Springer, 2022, pp. 241–249. doi: 10.1007/978-981-99-1509-5_22.
7. Bandyopadhyay, S. S., Halder, A. K., Chatterjee, P., Sroka, J., Nasipuri, M., Basu, S., Analysis of Large-Scale Human Protein Sequences Using an Efficient Spark-Based DBSCAN Algorithm, Advances in Intelligent Systems and Computing, Vol. 1255, Springer, 2021, pp. 601–609. ISBN: 978-981-15-7833-5. doi: 10.1007/978-981-15-7834-2_56.
8. Halder, A. K., Dutta, P., Kundu, M., Nasipuri, M., Basu, S., Prediction of Thyroid Cancer Genes Using an Ensemble of Post Translational Modification, Semantic and Structural Similarity Based Clustering Results, International Conference on Pattern Recognition and Machine Intelligence, Springer, 2017, pp. 418–423. doi: 10.1007/978-3-319-69900-4_53.
9. Bandyopadhyay, S. S., Halder, A. K., Chatterjee, P., Nasipuri, M., Basu, S., HdK-means: Hadoop Based Parallel K-means Clustering for Big Data, IEEE CALCON 2017 – Proceedings, 2017, pp. 452–456. ISBN: 978-1-5386-3746-3. doi: 10.1109/CALCON.2017.8280774.
Workshop Organized
· One-Week Online FDP on "Advanced Computational Methods in Genomics and Drug Discovery: Bridging AI and Biomedical Science" funded by AICTE and ATAL
Accolades
· Visvesvaraya PhD Fellowship (2015-2020) (UAN: VISPHD-MEITY-1413), , Govt. of India (Dec., 2015 – Nov., 2020)
· Visiting PhD Scholar, Centre of New Technologies (CeNT), University of Warsaw, Poland. (April, 2018 – Sept., 2018)
· UGC-NET 2014
· GATE 2011, 2012