Publications

Bold: Ghulam Murtaza; ^* equal contribution. First author on 7 of 15 publications.

Accepted

Doudou Yu, Jürgen Germann, Ghulam Murtaza, Kaitlyn H. Hajdarovic, Kelsey R. Babcock, Shiva Kazempour Dehkordi, Alexander C. Jackson, Ivana Delalle, Miranda E. Orr, Habil Zare, Ritambhara Singh, William S. Noble, Andrei G. Vlassenko, Manu S. Goyal, Ashley E. Webb. HypoAD: volumetric and single-cell analysis reveals changes in the human hypothalamus in aging and Alzheimer's disease. Accepted at Nature

[PDF]

@article{yu2025hypoad,
  title    = {HypoAD: volumetric and single-cell analysis reveals changes in the human hypothalamus in aging and Alzheimer's disease},
  author   = {Yu, Doudou and Germann, J{\"u}rgen and Murtaza, Ghulam and Hajdarovic, Kaitlyn H and Babcock, Kelsey R and Dehkordi, Shiva Kazempour and Jackson, Alexander C and Delalle, Ivana and Orr, Miranda E and Zare, Habil and Singh, Ritambhara and Noble, William S and Vlassenko, Andrei G and Goyal, Manu S and Webb, Ashley E},
  journal  = {bioRxiv},
  year     = {2025},
  publisher= {Cold Spring Harbor Laboratory},
  doi      = {10.1101/2025.10.08.681270}
}

Preprints

Ghulam Murtaza, Shengqi Hang, Xumeng Zhang, Shuhua Xu, Tangqi Fang, Doudou Yu, Anupama Jha, Ritambhara Singh, Sheng Wang, William S. Noble. scWeave: A deep learning model that bidirectionally translates between gene expression and chromatin structure at single cell resolution. bioRxiv, 2026

[PDF]

@article{murtaza2026scweave,
  title    = {scWeave: A deep learning model that bidirectionally translates between gene expression and chromatin structure at single cell resolution},
  author   = {Murtaza, Ghulam and Hang, Shengqi and Zhang, Xumeng and Xu, Shuhua and Fang, Tangqi and Yu, Doudou and Jha, Anupama and Singh, Ritambhara and Wang, Sheng and Noble, William S},
  journal  = {bioRxiv},
  year     = {2026},
  publisher= {Cold Spring Harbor Laboratory},
  doi      = {10.64898/2026.07.13.738265}
}

Justin Wagner, Ayse G. Keskus, Keisuke K. Oshima, … Ghulam Murtaza, et al. A near-complete human pancreatic cancer genome. bioRxiv, 2026

[PDF]

@article{wagner2026pancreatic,
  title    = {A near-complete human pancreatic cancer genome},
  author   = {Wagner, Justin and Keskus, Ayse G and Oshima, Keisuke K and Ranallo-Benavidez, T. Rhyker and McDaniel, Jennifer and Chuang, Shu-Cheng and Sikic, Mile and Lin, Dehui and Paulin, Luis F and English, Adam C and Sedlazeck, Fritz J and Munding, Elizabeth M and Sanborn, J. Zachary and Carroll, Andrew and Chang, Pi-Chuan and Cook, Daniel E and Shafin, Kishwar and de Ligt, Joep and Hassaine, Rayan and Cameron, Daniel and Catreux, Severine and Lee, Yeonghun and Murray, Lisa and Truong, Sean and Brueffer, Christian and Zimin, Aleksey V and Cross, Erin and McGowan, Matthew and Vernich, Michael and Liss, Andrew S and Kocher, Jean-Pierre and Stephens, Zachary and Ahmad, Tanveer and Bryant, Asher and Dwarshuis, Nathan and He, Hua-Jun and He, Zhiyong and Olson, Nathan D and Thibaud-Nissen, Francoise and Antipov, Dmitry and Koren, Sergey and Phillippy, Adam and Rhie, Arang and Wilson, Melissa and Musunuri, Rajeeva Lochan and Narzisi, Giuseppe and Jain, Miten and Wenger, Aaron M and Eacker, Stephen and Sahraeian, Sayed Mohammad Ebrahim and Boutros, Paul C and Patel, Yash and Yamaguchi, Takafumi N and McConnell, Joseph and Borchers, Matthew and Gerton, Jennifer L and Kostos, Paxton and Potapova, Tamara A and Guarracino, Andrea and Jehangir, Maryam and Benjamin, Hila and Mootor, Mohammed Faizal Eeman and Xu, Yuan and Asri, Mobin and Miga, Karen H and Park, Jimin and Paten, Benedict and Luo, Ruibang and Zheng, Zhenxian and Choi, Jae Young and Nguyen, Linh and Vats, Pankaj and Robinson, Dan R and Vo, Josh N and Gao, Shenghan and Murtaza, Ghulam and Stergachis, Andrew B and Ranchalis, Jane and Mason, Christopher E and Cheng, Haoyu and Shiraishi, Yuichi and Sakamoto, Yoshitaka and Dubocanin, Danilo and Barthel, Floris P and Xiao, Chunlin and Logsdon, Glennis A and Kolmogorov, Mikhail and Zook, Justin M},
  journal  = {bioRxiv},
  year     = {2026},
  publisher= {Cold Spring Harbor Laboratory},
  doi      = {10.64898/2026.05.01.722316}
}

Tangqi Fang, Yongkang Li, Xiao Wang, Zhiping Xiao, Shengqi Hang, Ghulam Murtaza, Junwei Yang, Hanwen Xu, Anupama Jha, William S. Noble, Sheng Wang. Evo2HiC: a multimodal foundation model for integrative analysis of genome sequence and architecture. bioRxiv, 2025

[PDF]

@article{fang2025evo2hic,
  title    = {Evo2HiC: a multimodal foundation model for integrative analysis of genome sequence and architecture},
  author   = {Fang, Tangqi and Li, Yongkang and Wang, Xiao and Xiao, Zhiping and Hang, Shengqi and Murtaza, Ghulam and Yang, Junwei and Xu, Hanwen and Jha, Anupama and Noble, William S and Wang, Sheng},
  journal  = {bioRxiv},
  year     = {2025},
  publisher= {Cold Spring Harbor Laboratory},
  doi      = {10.1101/2025.11.18.689171}
}

Shengqi Hang, Xiao Wang, Ghulam Murtaza, Anupama Jha, Bo Wen, Tangqi Fang, Justin Sanders, Sheng Wang, William S. Noble. Puget predicts gene expression across cell types using sequence and 3D chromatin organization data. bioRxiv, 2025

[PDF]

@article{hang2025puget,
  title    = {Puget predicts gene expression across cell types using sequence and 3D chromatin organization data},
  author   = {Hang, Shengqi and Wang, Xiao and Murtaza, Ghulam and Jha, Anupama and Wen, Bo and Fang, Tangqi and Sanders, Justin and Wang, Sheng and Noble, William S},
  journal  = {bioRxiv},
  year     = {2025},
  publisher= {Cold Spring Harbor Laboratory},
  doi      = {10.1101/2025.11.19.689320}
}

In Preparation

Ananthan Nambiar^*, Ghulam Murtaza^*, Doudou Yu^*, William S. Noble, et al. A living benchmark for evaluating transcriptomic aging clocks across scales and species. In preparation

@unpublished{nambiar2026agingclocks,
  title    = {A living benchmark for evaluating transcriptomic aging clocks across scales and species},
  author   = {Nambiar, Ananthan and Murtaza, Ghulam and Yu, Doudou and Noble, William S and others},
  year     = {2026},
  note     = {In preparation}
}

Peer-reviewed

Tassallah Abdullahi, Ioanna Gemou, Nihal V. Nayak, Ghulam Murtaza, Stephen H. Bach, Carsten Eickhoff, Ritambhara Singh. K-Paths: Reasoning over Graph Paths for Drug Repurposing and Drug Interaction Prediction. ACM SIGKDD (KDD) 2025

[Code] [arXiv]

@inproceedings{abdullahi2025kpaths,
  title    = {K-Paths: Reasoning over Graph Paths for Drug Repurposing and Drug Interaction Prediction},
  author   = {Abdullahi, Tassallah and Gemou, Ioanna and Nayak, Nihal V and Murtaza, Ghulam and Bach, Stephen H and Eickhoff, Carsten and Singh, Ritambhara},
  booktitle= {Proceedings of the 31st ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD)},
  year     = {2025},
  doi      = {10.1145/3711896.3737011}
}

Ghulam Murtaza, Justin Wagner, Justin M. Zook, Ritambhara Singh. GrapHiC: An integrative graph-based approach for imputing missing Hi-C reads. IEEE/ACM TCBB 2025

[PDF]

@article{murtaza2024graphic,
  title    = {GrapHiC: An integrative graph-based approach for imputing missing Hi-C reads},
  author   = {Murtaza, Ghulam and Wagner, Justin and Zook, Justin M and Singh, Ritambhara},
  journal  = {IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)},
  year     = {2025},
  volume   = {22},
  number   = {2},
  pages    = {409--419},
  doi      = {10.1109/TCBB.2024.3477909}
}

Winston Li, Ghulam Murtaza, Ritambhara Singh. scContrast: A contrastive learning based approach for encoding single-cell gene expression data. AI4NA, ICLR 2025

[PDF]

@inproceedings{li2025sccontrast,
  title    = {scContrast: A contrastive learning based approach for encoding single-cell gene expression data},
  author   = {Li, Winston and Murtaza, Ghulam and Singh, Ritambhara},
  booktitle= {AI4NA Workshop, ICLR},
  year     = {2025},
  doi      = {10.1101/2025.04.07.647292}
}

Ghulam Murtaza, Byron Butaney, Justin Wagner, Ritambhara Singh. scGrapHiC: Deep learning-based graph deconvolution for Hi-C using single cell gene expression. ISMB 2024 (Finalist for the Ian Lawson Van Toch Best Paper Award)

[PDF]

@inproceedings{murtaza2024scgraphic,
  title    = {scGrapHiC: Deep learning-based graph deconvolution for Hi-C using single cell gene expression},
  author   = {Murtaza, Ghulam and Butaney, Byron and Wagner, Justin and Singh, Ritambhara},
  booktitle= {Bioinformatics (Proceedings of ISMB)},
  year     = {2024}
}

Ghulam Murtaza, Atishay Jain, Madeline Hughes, Justin Wagner, Ritambhara Singh. A Comprehensive Evaluation of Generalizability of Deep Learning-Based Hi-C Resolution Improvement Methods. Genes 2024

@article{murtaza2024comprehensive,
  title    = {A Comprehensive Evaluation of Generalizability of Deep Learning-Based Hi-C Resolution Improvement Methods},
  author   = {Murtaza, Ghulam and Jain, Atishay and Hughes, Madeline and Wagner, Justin and Singh, Ritambhara},
  journal  = {Genes},
  year     = {2024},
  volume   = {15},
  number   = {1},
  pages    = {54},
  doi      = {10.3390/genes15010054}
}

Ghulam Murtaza, Justin Wagner, Justin M. Zook, Ritambhara Singh. GrapHiC: An integrative graph based approach for imputing missing Hi-C reads. BIOKDD 2023

@inproceedings{murtaza2023graphicbiokdd,
  title    = {GrapHiC: An integrative graph based approach for imputing missing Hi-C reads},
  author   = {Murtaza, Ghulam and Wagner, Justin and Zook, Justin M and Singh, Ritambhara},
  booktitle= {BIOKDD},
  year     = {2023}
}

Ghulam Murtaza, Theophilus A. Benson. WebOptProfiler: Providing performance clarity for Mobile Webpage Optimizations. ACM HotMobile 2021

@inproceedings{murtaza2021weboptprofiler,
  title    = {WebOptProfiler: Providing performance clarity for Mobile Webpage Optimizations},
  author   = {Murtaza, Ghulam and Benson, Theophilus A},
  booktitle= {Proceedings of the 22nd International Workshop on Mobile Computing Systems and Applications (HotMobile)},
  year     = {2021},
  doi      = {10.1145/3446382.3449073}
}

Fahad R. Dogar, Ihsan Ayyub Qazi, A. Tariq, Ghulam Murtaza, A. Ahmed, N. Stocking. MissIt: Using Missed Calls for Free, Extremely Low Bit-Rate Communication in Developing Regions. ACM CHI 2020

@inproceedings{dogar2020missit,
  title    = {MissIt: Using Missed Calls for Free, Extremely Low Bit-Rate Communication in Developing Regions},
  author   = {Dogar, Fahad R and Qazi, Ihsan Ayyub and Tariq, A and Murtaza, Ghulam and Ahmed, A and Stocking, N},
  booktitle= {Proceedings of the 2020 CHI Conference on Human Factors in Computing Systems (CHI)},
  year     = {2020},
  doi      = {10.1145/3313831.3376259}
}

Ihsan Ayyub Qazi, Zafar Qazi, Theophilus A. Benson, E. Latif, Abdul Manan, Ghulam Murtaza, A. Tariq. Mobile web browsing under memory pressure. ACM SIGCOMM CCR 2020

@article{qazi2020mobile,
  title    = {Mobile web browsing under memory pressure},
  author   = {Qazi, Ihsan Ayyub and Qazi, Zafar and Benson, Theophilus A and Latif, E and Manan, Abdul and Murtaza, Ghulam and Tariq, A},
  journal  = {ACM SIGCOMM Computer Communication Review},
  year     = {2020},
  volume   = {50},
  number   = {4},
  doi      = {10.1145/3431832.3431837}
}

Ghulam Murtaza, Theophilus A. Benson. WebOpt Profiler: Providing performance clarity for Web Optimizations. ACM CoNEXT Student Workshop 2020

@inproceedings{murtaza2020weboptprofilerconext,
  title    = {WebOpt Profiler: Providing performance clarity for Web Optimizations},
  author   = {Murtaza, Ghulam and Benson, Theophilus A},
  booktitle= {Proceedings of the CoNEXT Student Workshop},
  year     = {2020},
  doi      = {10.1145/3426746.3434050}
}