Publications

@article{abir2026cfmgp,
  title   = {CFM-GP: Unified Conditional Flow Matching to Learn Gene Perturbation Across Cell Types},
  author  = {Abir, Abrar Rahman and Dip, Sajib Acharjee and Zhang, Liqing},
  journal = {NAR Genomics and Bioinformatics},
  volume  = {8},
  number  = {3},
  pages   = {lqag087},
  year    = {2026},
  doi     = {10.1093/nargab/lqag087}
}

@article{haghani2026crossspecies,
  title   = {Cross-species plant single-cell analysis: community challenges and shared solutions},
  author  = {Haghani, Maryam and Chau, Tran N. and Alajoleen, Razan and Chen, Chia-Yu and Dip, Sajib Acharjee and Gurung, Vandana and Hsu, Che-Wei and Kittivorawong, Chadinthon and Kundu, Sanchari and Li, Xiaohui and Luo, Juncheng and Salehin, Mohammad and Simenc, Mathew and Yun, Jie and Bargmann, Bastiaan O. R. and Li, Song},
  journal = {Journal of Experimental Botany},
  pages   = {erag218},
  year    = {2026},
  doi     = {10.1093/jxb/erag218}
}

@article{dip2026llmagents,
  title   = {Large Language Model Agents for Biological Intelligence Across Genomics, Proteomics, Spatial Biology, and Biomedicine},
  author  = {Dip, Sajib Acharjee and Mallick, Dipanwita and Shuvo, Uddip Acharjee and Soumma, Shovito Barua and Rafsani, Fazle and Paul, Bikash Kumar and Moumi, Nazifa Ahmed and Ahmed, Shafayat and Zhang, Liqing},
  journal = {Briefings in Bioinformatics},
  volume  = {27},
  number  = {2},
  pages   = {bbag110},
  year    = {2026},
  doi     = {10.1093/bib/bbag110}
}

@article{abir2025uncotad,
  title   = {UnCOT-AD: Unpaired Cross-Omics Translation Enables Multi-Omics Integration for Alzheimer's Disease Prediction},
  author  = {Abir, Abrar Rahman and Dip, Sajib Acharjee and Zhang, Liqing},
  journal = {Briefings in Bioinformatics},
  volume  = {26},
  number  = {4},
  pages   = {bbaf438},
  year    = {2025},
  doi     = {10.1093/bib/bbaf438}
}

@inproceedings{dip2026llm4cell,
  title     = {LLM4Cell: Taxonomy and Evaluation of LLM and Agentic Models for Single-Cell Biology},
  author    = {Dip, Sajib Acharjee and Zafor, Adrika and Paul, Bikash Kumar and Shuvo, Uddip Acharjee and Emon, Muhit Islam and Wang, Xuan and Zhang, Liqing},
  booktitle = {Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers)},
  pages     = {41913--41954},
  year      = {2026},
  publisher = {Association for Computational Linguistics},
  doi       = {10.18653/v1/2026.acl-long.1942}
}

@inproceedings{dip2026stableshift,
  author    = {Dip, Sajib Acharjee and Zhang, Liqing},
  title     = {Stable-Shift: Predicting Transcriptional Responses of Unseen Gene Perturbations Using Graph Neural Networks with Biological Priors},
  booktitle = {Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics},
  year      = {2026},
  articleno = {101},
  numpages  = {6},
  doi       = {10.1145/3807503.3820871}
}

@inproceedings{dip2026patch,
  author    = {Dip, Sajib Acharjee and Zhang, Liqing},
  title     = {Patch-Level Tissue Context Improves Learning from Frozen Pathology Foundation Model Embeddings},
  booktitle = {Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics},
  year      = {2026},
  articleno = {72},
  numpages  = {6},
  doi       = {10.1145/3807503.3820870}
}

@inproceedings{zafor2026oncomark,
  title     = {OncoMark: A Two-Stage Gated Framework for Cancer Hallmark Detection from Biomedical Text},
  author    = {Zafor, Adrika and Dip, Sajib Acharjee and Zhang, Liqing},
  booktitle = {The International FLAIRS Conference Proceedings},
  volume    = {39},
  number    = {1},
  year      = {2026},
  doi       = {10.32473/flairs.39.1.141834}
}

@inproceedings{nath2025leukemia,
  title     = {Subtype-Specific Biomarker Discovery in Leukemia: Bridging Expression Profiling and Machine Learning},
  author    = {Nath, Anik Dev and Amin, Md Al and Dip, Sajib Acharjee and Jerin, Mahjebin and Paul, Bikash Kumar and Bhuiyan, Touhid},
  booktitle = {2025 IEEE International Women in Engineering (WIE) Conference on Electrical and Computer Engineering (WIECON-ECE)},
  pages     = {1126--1131},
  year      = {2025},
  publisher = {IEEE},
  doi       = {10.1109/wiecon-ece69386.2025.11526172}
}

@inproceedings{kawsar2025hmpv,
  title     = {Integrated Multi-Omics Network Pharmacology Uncovers Novel Biomarkers and Therapeutic Candidates in Human Metapneumovirus Infection},
  author    = {Kawsar, Md and Shareen, Dilruba and Dip, Sajib Acharjee and Sarker, Ram Prosad and Paul, Bikash Kumar and Bhuiyan, Touhid},
  booktitle = {2025 IEEE International Women in Engineering (WIE) Conference on Electrical and Computer Engineering (WIECON-ECE)},
  pages     = {1061--1066},
  year      = {2025},
  publisher = {IEEE},
  doi       = {10.1109/wiecon-ece69386.2025.11526543}
}

@inproceedings{shuvo2024chatgpt,
  title     = {Assessing ChatGPT's Code Generation Capabilities with Short vs Long Context Programming Problems},
  author    = {Shuvo, Uddip Acharjee and Dip, Sajib Acharjee and Vaskar, Nirvar Roy and Islam, A. B. M. Alim Al},
  booktitle = {Proceedings of the 11th International Conference on Networking, Systems, and Security},
  pages     = {32--40},
  year      = {2024},
  publisher = {ACM},
  doi       = {10.1145/3704522.3704535}
}

@article{dip2024equitable,
  title   = {Equitable Skin Disease Prediction Using Transfer Learning and Domain Adaptation},
  author  = {Dip, Sajib Acharjee and Ibn Arif, Kazi Hasan and Shuvo, Uddip Acharjee and Khan, Ishtiaque Ahmed and Meng, Na},
  journal = {Proceedings of the AAAI Symposium Series},
  volume  = {4},
  number  = {1},
  pages   = {259--266},
  year    = {2024},
  doi     = {10.1609/aaaiss.v4i1.31800}
}

@article{dip2024deepage,
  title     = {DeepAge: Harnessing Deep Neural Network for Epigenetic Age Estimation From DNA Methylation Data of Human Blood Samples},
  author    = {Dip, Sajib Acharjee and Ma, Da and Zhang, Liqing},
  journal   = {Proceedings of the AAAI Symposium Series},
  volume    = {4},
  number    = {1},
  pages     = {267--274},
  year      = {2024},
  doi       = {10.1609/aaaiss.v4i1.31801}
}

@inproceedings{dip2024patholm,
  title     = {PathoLM: Identifying Pathogenicity from the DNA Sequence Through the Genome Foundation Model},
  author    = {Dip, Sajib Acharjee and Shuvo, Uddip Acharjee and Chau, Tran and Song, Haoqiu and Choi, Petra and Wang, Xuan and Zhang, Liqing},
  booktitle = {Proceedings of the 19th Machine Learning in Computational Biology Meeting},
  series    = {Proceedings of Machine Learning Research},
  volume    = {261},
  pages     = {153--161},
  year      = {2024},
  publisher = {PMLR}
}

@incollection{uddin2025cryoet,
  title     = {Feature Detection in Cryo-Electron Tomography Image Analysis},
  author    = {Uddin, Mostofa Rafid and Dip, Sajib Acharjee and Jha, Rajat Aayush and Zeng, Xiangrui and Xu, Min},
  booktitle = {Cryo-electron Tomography},
  pages     = {173--215},
  year      = {2025},
  publisher = {Elsevier},
  doi       = {10.1016/b978-0-443-18829-9.00008-6}
}

@misc{dip2026thinkagain,
  title     = {Think Again or Think Longer? Selective Verification for Budget-Aware Reasoning},
  author    = {Dip, Sajib Acharjee and Zhou, Dawei and Zhang, Liqing},
  year      = {2026},
  publisher = {arXiv},
  doi       = {10.48550/arXiv.2606.19808}
}

@misc{noshin2026bensyc,
  title     = {BenSyc: Benchmarking Conversational Sycophancy and Human Alignment in LLMs for Bengali Contexts},
  author    = {Noshin, Kazi and Dip, Sajib Acharjee and Prangon, Ranat Das and Tamim, Fardin Hassan and Ahmed, Syed Ishtiaque and Zhang, Liqing and Sultana, Sharifa},
  year      = {2026},
  publisher = {arXiv},
  doi       = {10.48550/arXiv.2606.10061}
}

@misc{dip2026plantmarkerbench,
  title     = {PlantMarkerBench: A Multi-Species Benchmark for Evidence-Grounded Plant Marker Reasoning},
  author    = {Dip, Sajib Acharjee and Li, Song and Zhang, Liqing},
  year      = {2026},
  publisher = {arXiv},
  doi       = {10.48550/arXiv.2605.10032}
}

@misc{dip2025nicheagent,
  title     = {NicheAgent: LLM-Guided Zero-Shot Niche Identification for Spatial Transcriptomics},
  author    = {Dip, Sajib Acharjee and Zhang, Liqing},
  year      = {2025},
  publisher = {bioRxiv},
  doi       = {10.64898/2025.12.09.693287}
}

@inproceedings{dip2025protfunagent,
  title     = {ProtFunAgent: Agentic LLM Cascades for Low-Resource Protein Function Gap-Filling via Homology RAG and Ontology-Constrained Decoding},
  author    = {Dip, Sajib Acharjee and Choy, John and Zhang, Liqing},
  booktitle = {NeurIPS 2025 Workshop},
  year      = {2025}
}

@misc{dip2025lightweight,
  title     = {Can Lightweight LLM Agents Improve Spatial Transcriptomics Annotation?},
  author    = {Dip, Sajib Acharjee and Zhang, Liqing},
  year      = {2025},
  publisher = {bioRxiv},
  doi       = {10.1101/2025.11.08.687410}
}

@misc{dip2025moxgate,
  title     = {MoXGATE: Modality-aware Cross-Attention for Multi-Omic Gastrointestinal Cancer Sub-type Classification},
  author    = {Dip, Sajib Acharjee and Shuvo, Uddip Acharjee and Mallick, Dipanwita and Abir, Abrar Rahman and Zhang, Liqing},
  year      = {2025},
  publisher = {arXiv},
  doi       = {10.48550/arXiv.2506.06980}
}

@inproceedings{dip2025wcyclegan,
  title     = {Wasserstein CycleGAN for Single-Cell RNA-seq Data Generation Using Cross-Modality Translation},
  author    = {Dip, Sajib Acharjee and Chau, Tran and Li, Song and Zhang, Liqing},
  booktitle = {ICLR 2025 Workshop on Machine Learning for Genomics Explorations (MLGenX)},
  year      = {2025}
}

@misc{arif2025paint,
  title     = {PAINT: Paying Attention to INformed Tokens to Mitigate Hallucination in Large Vision-Language Model},
  author    = {Arif, Kazi Hasan Ibn and Dip, Sajib Acharjee and Hussain, Khizar and Zhang, Liqing and Thomas, Chris},
  year      = {2025},
  publisher = {arXiv},
  doi       = {10.48550/arXiv.2501.12206}
}

@misc{bi2024aibiomedicine,
  title     = {AI for Biomedicine in the Era of Large Language Models},
  author    = {Bi, Zhenyu and Dip, Sajib Acharjee and Hajialigol, Daniel and Kommu, Sindhura and Liu, Hanwen and Lu, Meng and Wang, Xuan},
  year      = {2024},
  publisher = {arXiv},
  doi       = {10.48550/arXiv.2403.15673}
}

@article{arko2025mito,
  title     = {Mitochondrial-Targeted Therapies in Ischemic Cardiomyopathy: A Systematic Review of Preclinical and Clinical Evidence (2000-2025)},
  author    = {Arko, Soumyadipto Biswas and Saha, Utsow and Dip, Sajib Acharjee},
  journal   = {Circulation},
  volume    = {152},
  number    = {Suppl 3},
  pages     = {4368251},
  year      = {2025},
  doi       = {10.1161/circ.152.suppl_3.4368251}
}