Publications

Preprints

2025

1. Preprint

   SpaTRACE: Spatiotemporal recurrent auto-encoder for reconstructing signaling and regulatory networks from spatiotemporal transcriptomics data

   Hongliang Zhou^* ,  Hao Chen^*† ,  Zoe Rudnick ,  Sarah I Baalbaki ,  Young Je Lee ,  and  Jose Lugo-Martinez^†

   2025

   Bib

   @preprint{zhou2025spatrace,
     title = {SpaTRACE: Spatiotemporal recurrent auto-encoder for reconstructing signaling and regulatory networks from spatiotemporal transcriptomics data},
     author = {Zhou<sup>*</sup>, Hongliang and Chen<sup>*</sup><sup>†</sup>, Hao and Rudnick, Zoe and Baalbaki, Sarah I and Lee, Young Je and Lugo-Martinez<sup>†</sup>, Jose},
     journal = {bioRxiv},
     pages = {2025--11},
     year = {2025},
     publisher = {Cold Spring Harbor Laboratory}
   }

Peer reviewed articles

2026

1. IEEE VIS

   Loom: Multi-Region Analysis of Spatial Transcriptomics with Local Neighborhoods and Global Trajectories

   S. Zhao ,  M.N. Nipu ,  H. Fathollahian ,  H. Chen ,  A. Salahudeen ,  O. Karginova ,  and  G.E. Marai

   In IEEE Trans. of Vis. and Comp. Graphics , 2026

   Bib

   @inproceedings{zhao2026loom,
     title = {Loom: Multi-Region Analysis of Spatial Transcriptomics with Local Neighborhoods and Global Trajectories},
     author = {Zhao, S. and Nipu, M.N. and Fathollahian, H. and Chen, H. and Salahudeen, A. and Karginova, O. and Marai, G.E.},
     booktitle = {IEEE Trans. of Vis. and Comp. Graphics},
     volume = {},
     pages = {},
     year = {2026},
     organization = {IEEE}
   }

2025

1. Genome Res.

   A unified analysis of atlas single cell data

   Hao Chen ,  Nam D Nguyen ,  Matthew Ruffalo ,  and  Ziv Bar-Joseph

   Genome Research, 2025
2. STAR Protocols

   Protocol to recover single cell expression profiles from spatial transcriptomics in cluster computing

   Young Je Lee^* ,  Hao Chen^* ,  and  Jose Lugo-Martinez

   STAR Protocols, 2025

2024

1. Cell Rep. Methods

   Recovering single-cell expression profiles from spatial transcriptomics with scResolve

   Hao Chen ,  Young Je Lee ,  Jose A Ovando-Ricardez ,  Lorena Rosas ,  Mauricio Rojas ,  Ana L Mora ,  Ziv Bar-Joseph ,  and  Jose Lugo-Martinez

   Cell Reports Methods, 2024
2. Genome Research

   Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences

   Chencheng Xu ,  Suying Bao ,  Ye Wang ,  Wenxing Li ,  Hao Chen ,  Yufeng Shen ,  Tao Jiang ,  and  Chaolin Zhang

   Genome Research, 2024
3. Nature Commun.

   Drug target prediction through deep learning functional representation of gene signatures

   Hao Chen^† ,  Frederick King ,  Bin Zhou ,  Yu Wang ,  Carter Canedy ,  Joel Hayashi ,  Yong Zhong ,  Max Chang ,  Lars Pache ,  Julian Wong ,  Yong Jia ,  John Joslin ,  Tao Jiang ,  Christopher Benner ,  Sumit K Chanda ,  and  Yingyao Zhou^†

   Nature Communications, 2024

   Bib

   @article{zhou2023drug,
     title = {Drug target prediction through deep learning functional representation of gene signatures},
     author = {Chen<sup>†</sup>, Hao and King, Frederick and Zhou, Bin and Wang, Yu and Canedy, Carter and Hayashi, Joel and Zhong, Yong and Chang, Max and Pache, Lars and Wong, Julian and Jia, Yong and Joslin, John and Jiang, Tao and Benner, Christopher and Chanda, Sumit K and Zhou<sup>†</sup>, Yingyao},
     journal = {Nature Communications},
     volume = {15},
     number = {1},
     pages = {1853},
     year = {2024}
   }

2023

1. BIBM

   Isoform Function Prediction Based on Heterogeneous Graph Attention Networks

   Kuo Guo ,  Yifan Li ,  Hao Chen ,  Hong-Bin Shen ,  and  Yang Yang

   In the proceedings of IEEE International Conference on Bioinformatics and Biomedicine (BIBM) , 2023

   Bib

   @inproceedings{10386048,
     author = {Guo, Kuo and Li, Yifan and Chen, Hao and Shen, Hong-Bin and Yang, Yang},
     booktitle = {the proceedings of IEEE International Conference on Bioinformatics and Biomedicine (BIBM)},
     title = {Isoform Function Prediction Based on Heterogeneous Graph Attention Networks},
     year = {2023},
     volume = {},
     number = {},
     pages = {522-527},
     doi = {10.1109/BIBM58861.2023.10386048}
   }

2. Nature Methods

   SCS: cell segmentation for high-resolution spatial transcriptomics

   Hao Chen ,  Dongshunyi Li ,  and  Ziv Bar-Joseph

   Nature Methods, 2023

   Bib

   @article{chen2023cell,
     title = {SCS: cell segmentation for high-resolution spatial transcriptomics},
     author = {Chen, Hao and Li, Dongshunyi and Bar-Joseph, Ziv},
     journal = {Nature Methods},
     volume = {20},
     pages = {1237–1243},
     year = {2023},
     organization = {Springer Nature}
   }

3. RECOMB

   Cell segmentation for high-resolution spatial transcriptomics

   Hao Chen ,  Dongshunyi Li ,  and  Ziv Bar-Joseph

   In proceedings of 27th Annual International Conference on Research in Computational Molecular Biology (RECOMB) , 2023

   Bib

   @inproceedings{chen2023celm,
     title = {Cell segmentation for high-resolution spatial transcriptomics},
     author = {Chen, Hao and Li, Dongshunyi and Bar-Joseph, Ziv},
     booktitle = {proceedings of 27th Annual International Conference on Research in Computational Molecular Biology (RECOMB)},
     volume = {13976},
     pages = {251},
     year = {2023},
     organization = {Springer Nature}
   }

4. Nature Aging

   Spatial mapping of cellular senescence: emerging challenges and opportunities

   Aditi U Gurkar ,  Akos A Gerencser ,  Ana L Mora ,  Andrew C Nelson ,  Anru R Zhang ,  Anthony B Lagnado ,  Archibald Enninful ,  Christopher Benz ,  David Furman ,  Delphine Beaulieu ,  Diana Jurk ,  Elizabeth L Thompson ,  Fei Wu ,  Fernanda Rodriguez ,  Grant Barthel ,  Hao Chen ,  Hemali Phatnani ,  Indra Heckenbach ,  Jeffrey H Chuang ,  Jeremy Horrell ,  Joana Petrescu ,  Jonathan K Alder ,  Jun Hee Lee ,  Laura J Niedernhofer ,  Manoj Kumar ,  Melanie Königshoff ,  Marta Bueno ,  Miiko Sokka ,  Morten Scheibye-Knudsen ,  Nicola Neretti ,  Oliver Eickelberg ,  Peter D Adams ,  Qianjiang Hu ,  Quan Zhu ,  Rebecca A Porritt ,  Runze Dong ,  Samuel Peters ,  Stella Victorelli ,  Thomas Pengo ,  Timur Khaliullin ,  Vidyani Suryadevara ,  Xiaonan Fu ,  Ziv Bar-Joseph ,  Zhicheng Ji ,  and  João F Passos

   Nature Aging, 2023

   Bib

   @article{gurkar2023spatial,
     title = {Spatial mapping of cellular senescence: emerging challenges and opportunities},
     author = {Gurkar, Aditi U and Gerencser, Akos A and Mora, Ana L and Nelson, Andrew C and Zhang, Anru R and Lagnado, Anthony B and Enninful, Archibald and Benz, Christopher and Furman, David and Beaulieu, Delphine and Jurk, Diana and Thompson, Elizabeth L and Wu, Fei and Rodriguez, Fernanda and Barthel, Grant and Chen, Hao and Phatnani, Hemali and Heckenbach, Indra and Chuang, Jeffrey H and Horrell, Jeremy and Petrescu, Joana and Alder, Jonathan K and Lee, Jun Hee and Niedernhofer, Laura J and Kumar, Manoj and Königshoff, Melanie and Bueno, Marta and Sokka, Miiko and Scheibye-Knudsen, Morten and Neretti, Nicola and Eickelberg, Oliver and Adams, Peter D and Hu, Qianjiang and Zhu, Quan and Porritt, Rebecca A and Dong, Runze and Peters, Samuel and Victorelli, Stella and Pengo, Thomas and Khaliullin, Timur and Suryadevara, Vidyani and Fu, Xiaonan and Bar-Joseph, Ziv and Ji, Zhicheng and Passos, João F},
     journal = {Nature Aging},
     volume = {3},
     number = {7},
     pages = {776--790},
     year = {2023},
     publisher = {Nature Publishing Group US New York}
   }

2022

1. Nature Aging

   NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health

   SenNet Consortium

   Nature Aging, 2022

   Bib

   @article{sennet2022nih,
     title = {NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health},
     author = {Consortium, SenNet},
     journal = {Nature Aging},
     volume = {2},
     number = {12},
     pages = {1090--1100},
     year = {2022},
     publisher = {Nature Publishing Group US New York}
   }

2. Curr. Genom.

   A Global Analysis of Alternative Splicing of Dichocarpum Medicinal Plants, Ranunculales

   Da-Cheng Hao^* ,  Hao Chen^* ,  Pei-Gen Xiao ,  and  Tao Jiang

   Current Genomics, 2022

   Bib

   @article{hao2022global,
     title = {A Global Analysis of Alternative Splicing of Dichocarpum Medicinal Plants, Ranunculales},
     author = {Hao<sup>*</sup>, Da-Cheng and Chen<sup>*</sup>, Hao and Xiao, Pei-Gen and Jiang, Tao},
     journal = {Current Genomics},
     volume = {23},
     number = {3},
     pages = {207},
     year = {2022},
     publisher = {Bentham Science Publishers}
   }

2021

1. NAR G&B

   Finer: enhancing the prediction of tissue-specific functions of isoforms by refining isoform interaction networks

   Hao Chen ,  Dipan Shaw ,  Dongbo Bu ,  and  Tao Jiang

   NAR Genomics and Bioinformatics, 2021

   Bib

   @article{chen2021finer,
     title = {Finer: enhancing the prediction of tissue-specific functions of isoforms by refining isoform interaction networks},
     author = {Chen, Hao and Shaw, Dipan and Bu, Dongbo and Jiang, Tao},
     journal = {NAR Genomics and Bioinformatics},
     volume = {3},
     number = {2},
     pages = {lqab057},
     year = {2021},
     publisher = {Oxford University Press}
   }

2. BMC Bioinform.

   DeepLPI: a multimodal deep learning method for predicting the interactions between lncRNAs and protein isoforms

   Dipan Shaw ,  Hao Chen ,  Minzhu Xie ,  and  Tao Jiang

   BMC Bioinformatics, 2021

   Bib

   @article{shaw2021deeplpi,
     title = {DeepLPI: a multimodal deep learning method for predicting the interactions between lncRNAs and protein isoforms},
     author = {Shaw, Dipan and Chen, Hao and Xie, Minzhu and Jiang, Tao},
     journal = {BMC Bioinformatics},
     volume = {22},
     number = {1},
     pages = {1--22},
     year = {2021},
     publisher = {BioMed Central}
   }

2019

1. ISMB/ECCB

   DIFFUSE: predicting isoform functions from sequences and expression profiles via deep learning

   Hao Chen ,  Dipan Shaw ,  Jianyang Zeng ,  Dongbo Bu ,  and  Tao Jiang

   Bioinformatics; Also in proceedings of the 27th Annual International Conference on Intelligent Systems for Molecular Biology and 17th European Conference on Computational Biology (ISMB/ECCB), 2019

   Bib

   @article{chen2019diffuse,
     title = {DIFFUSE: predicting isoform functions from sequences and expression profiles via deep learning},
     author = {Chen, Hao and Shaw, Dipan and Zeng, Jianyang and Bu, Dongbo and Jiang, Tao},
     journal = {Bioinformatics; Also in proceedings of the 27th Annual International Conference on Intelligent Systems for Molecular Biology and 17th European Conference on Computational Biology (ISMB/ECCB)},
     volume = {35},
     number = {14},
     pages = {i284--i294},
     year = {2019},
     publisher = {Oxford University Press}
   }

2018

1. Bioinformatics

   DeepIsoFun: a deep domain adaptation approach to predict isoform functions

   Dipan Shaw ,  Hao Chen ,  and  Tao Jiang

   Bioinformatics, 2018

   Bib

   @article{shaw2018deepisofun,
     title = {DeepIsoFun: a deep domain adaptation approach to predict isoform functions},
     author = {Shaw, Dipan and Chen, Hao and Jiang, Tao},
     journal = {Bioinformatics},
     volume = {35},
     number = {15},
     pages = {2535--2544},
     year = {2018},
     publisher = {Oxford University Press}
   }