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Towards predictive virtual embryos with genomics and AI

published in Nature Methods

Natalie Cao, Yifan Lu, Xiaojie Qiu+.

The Virtual Embryo Challenge: Generative Modeling of Embryogenesis Across Space, Scale and Time

accepted to the NeurIPS 2026 Competition Track

Jiayuan Ding, Yifan Lu, Qingquan Zhang, Zehua Zeng, Weize Xu, Nic Fishman, You He, Siyu He, Le Song, Eric Xing, James Zou, Emily Fox, Marinka Zitnik, Neil Chi, Xiaojie Qiu+.

Tabula: A Tabular Self-Supervised Foundation Model for Single-Cell Transcriptomics

published at NeurIPS 2025

Jiayuan Ding, Jianhui Lin, Shiyu Jiang, Yixin Wang, Ziyang Miao, Zhaoyu Fang, Jiliang Tang+, Min Li+, Xiaojie Qiu+.

Geometric Generative Modeling with Noise-Conditioned Graph Networks

published at ICML 2025

Peter Pao-Huang, Mitchell Black, Xiaojie Qiu+.

Storm: Incorporating transient stochastic dynamics to infer the RNA velocity with metabolic labeling information

Qiangwei Peng, Xiaojie Qiu+, Tiejun Li+

Spatiotemporal modeling of molecular holograms

published in Cell and also highlighted in Nature and Nature Methods

Xiaojie Qiu*+, Daniel Y Zhu*, Yifan Lu*, Jiajun Yao*, Zehua Jing*, Kyung Hoi Min*, Mengnan Cheng*, Hailin Pan, Lulu Zuo, Samuel King, Qi Fang, Huiwen Zheng, Mingyue Wang, Shuai Wang, Qingquan Zhang, Sichao Yu, Sha Liao, Chao Liu, Xinchao Wu, Yiwei Lai, Shijie Hao, Zhewei Zhang, Liang Wu, Yong Zhang, Mei Li, Zhencheng Tu, Jinpei Lin, Zhuoxuan Yang, Yuxiang Li, Ying Gu, David Ellison, Yuancheng Ryan Lu, Qinan Hu, Yuhui Hu, Ao Chen, Longqi Liu, Jonathan S Weissman, Jiayi Ma+, Xun Xu+, Shiping Liu+, Yinqi Bai+

Spatiotemporally resolved transcriptomics reveals the subcellular RNA kinetic landscape

Jingyi Ren*, Haowen Zhou*, Hu Zeng*, Connie Kangni Wang, Jiahao Huang, Xiaojie Qiu, Xin Sui, Qiang Li, Xunwei Wu, Zuwan Lin, Jennifer A Lo, Kamal Maher, Yichun He, Xin Tang, Judson Lam, Hongyu Chen, Brian Li, David E Fisher, Jia Liu, Xiao Wang+.

Massively parallel base editing to map variant effects in human hematopoiesis

Jorge D Martin-Rufino, Nicole Castano, Michael Pang, Emanuelle I Grody, Samantha Joubran, Alexis Caulier, Lara Wahlster, Tongqing Li, Xiaojie Qiu, Anna Maria Riera-Escandell, Gregory A Newby, Aziz Al’Khafaji, Santosh Chaudhary, Susan Black, Chen Weng, Glen Munson, David R Liu, Marcin W Wlodarski, Kacie Sims, Jamie H Oakley, Ross M Fasano, Ramnik J Xavier, Eric S Lander, Daryl E Klein, Vijay G Sankaran+.

Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays

published in Cell and selected as cover story

Ao Chen*, Sha Liao*, Mengnan Cheng*, Kailong Ma*, Liang Wu*, Yiwei Lai*, Xiaojie Qiu*, Jin Yang, Jiangshan Xu, Shijie Hao, Xin Wang, Huifang Lu, Xi Chen, Xing Liu, Xin Huang, Zhao Li, Yan Hong, Yujia Jiang, Jian Peng, Shuai Liu, Mengzhe Shen, Chuanyu Liu, Quanshui Li, Yue Yuan, Xiaoyu Wei, Huiwen Zheng, Weimin Feng, Zhifeng Wang, Yang Liu, Zhaohui Wang, Yunzhi Yang, Haitao Xiang, Lei Han, Baoming Qin, Pengcheng Guo, Guangyao Lai, Pura Muñoz-Cánoves, Patrick H Maxwell, Jean Paul Thiery, Qing-Feng Wu, Fuxiang Zhao, Bichao Chen, Mei Li, Xi Dai, Shuai Wang, Haoyan Kuang, Junhou Hui, Liqun Wang, Ji-Feng Fei, Ou Wang, Xiaofeng Wei, Haorong Lu, Bo Wang, Shiping Liu, Ying Gu, Ming Ni, Wenwei Zhang, Feng Mu, Ye Yin, Huanming Yang, Michael Lisby, Richard J Cornall, Jan Mulder, Mathias Uhlén, Miguel A Esteban+, Yuxiang Li+, Longqi Liu+, Xun Xu+, Jian Wang+.

Mapping transcriptomic vector fields of single cells

Xiaojie Qiu*+, Yan Zhang*, Jorge D Martin-Rufino, Chen Weng, Shayan Hosseinzadeh, Dian Yang, Angela N Pogson, Marco Y Hein, Kyung Hoi Joseph Min, Li Wang, Emanuelle I Grody, Matthew J Shurtleff, Ruoshi Yuan, Song Xu, Yian Ma, Joseph M Replogle, Eric S Lander, Spyros Darmanis, Ivet Bahar, Vijay G Sankaran, Jianhua Xing+, Jonathan S Weissman+.

Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution

Dian Yang*, Matthew G Jones*, Santiago Naranjo, William M Rideout, Kyung Hoi Joseph Min, Raymond Ho, Wei Wu, Joseph M Replogle, Jennifer L Page, Jeffrey J Quinn, Felix Horns, Xiaojie Qiu, Michael Z Chen, William A Freed-Pastor, Christopher S McGinnis, David M Patterson, Zev J Gartner, Eric D Chow, Trever G Bivona, Michelle M Chan, Nir Yosef+, Tyler Jacks+, Jonathan S Weissman+.

Massively parallel and time-resolved RNA sequencing in single cells with scNT-seq

Qi Qiu*, Peng Hu*, Xiaojie Qiu, Kiya W Govek, Pablo G Cámara, Hao Wu+.

Inferring causal gene regulatory networks from coupled single-cell expression dynamics using scribe

Xiaojie Qiu*, Arman Rahimzamani*, Li Wang, Bingcheng Ren, Qi Mao, Timothy Durham, José L McFaline-Figueroa, Lauren Saunders, Cole Trapnell+, Sreeram Kannan+.

A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition

José L McFaline-Figueroa, Andrew J Hill, Xiaojie Qiu, Dana Jackson, Jay Shendure, Cole Trapnell+.

The single-cell transcriptional landscape of mammalian organogenesis

Junyue Cao*, Malte Spielmann*, Xiaojie Qiu, Xingfan Huang, Daniel M Ibrahim, Andrew J Hill, Fan Zhang, Stefan Mundlos, Lena Christiansen, Frank J Steemers, Cole Trapnell+, Jay Shendure+.

The cis-regulatory dynamics of embryonic development at single-cell resolution

Darren A Cusanovich*, James P Reddington*, David A Garfield*, Riza M Daza, Delasa Aghamirzaie, Raquel Marco-Ferreres, Hannah A Pliner, Lena Christiansen, Xiaojie Qiu, Frank J Steemers, Cole Trapnell, Jay Shendure+, Eileen EM Furlong+.

Single-cell mRNA quantification and differential analysis with Census

Xiaojie Qiu, Andrew Hill, Jonathan Packer, Dejun Lin, Yi-An Ma, Cole Trapnell+.

Reversed graph embedding resolves complex single-cell trajectories

Xiaojie Qiu, Qi Mao, Ying Tang, Li Wang, Raghav Chawla, Hannah A Pliner, Cole Trapnell+.

Comprehensive single-cell transcriptional profiling of a multicellular organism

Junyue Cao*, Jonathan S Packer*, Vijay Ramani, Darren A Cusanovich, Chau Huynh, Riza Daza, Xiaojie Qiu, Choli Lee, Scott N Furlan, Frank J Steemers, Andrew Adey, Robert H Waterston+, Cole Trapnell+, Jay Shendure+.

Bio-Babel: autonomous cross-language reconstruction of agent-ready computational biology ecosystems

Nianping Liu*, Xuanzhi Chen*, Miao Cui, Xiaoying Liao, Xiaoke Song, Sairam Pantham, Weize Xu, Xiaojie Qiu+.

The Landscape of Single-Cell Foundation Models: Design Principles, Applications, and Open Challenges

Shiyu Jiang, Zhaoyu Fang, Yujie Zhang, Xuting Zhang, Jérémie Kalfon, Weixu Wang, Xi Fu, Aakash Patel, Syed Rizvi, Yuancheng Ryan Lu, Siyu He, Yixin Wang, Kejun Ying, Peter Pao-Huang, Yifan Lu, Weize Xu, Mengchen Wang, Ziyang Miao, Jianhui Lin, Zitong Jerry Wang, Wei Ouyang, Tianlong Chen, Guoxian Yu, Min Li, Jiayi Ma, Fei Wang, Yuying Xie, Jiliang Tang, Raul Rabadan, David van Dijk, Pengtao Xie, Peng He, Emily B Fox, Le Song, Fabian J Theis, Eric Xing, Christina V Theodoris, Xiaojie Qiu+, Jiayuan Ding+.

Predictive single cell foundation model for gene regulation and aging with privacy-preserving tabular learning

Jiayuan Ding, Jianhui Lin, Ziyang Miao, Nils Mechtel, Shiyu Jiang, Yixin Wang, Zhaoyu Fang, Jorge D Martin-Rufino, Chen Weng, Reuben Saunders, Weize Xu, Jonathan S Weissman, Min Li, Jiliang Tang, Wei Ouyang, Yuancheng Ryan Lu+, Xiaojie Qiu+.

Generative Modeling of Mouse Embryogenesis for Fate and Disease Prediction

Yimin Fan, Xinyuan Liu, Yixuan Wang, Zehua Zeng, Lei Li, Xiaojie Qiu+, Yu Li+.

Generative Modeling with Flux Matching

Peter Pao-Huang, Xiaojie Qiu, Stefano Ermon.

PantheonOS: an evolvable multi-agent framework for automatic genomics discovery

Weize Xu, Erwin Poussi, Quan Zhong, Zehua Zeng, Christopher Zou, Xuehai Wang, Yifan Lu, Miao Cui, Daiji Okamura, Cinlong Huang, Jiayuan Ding, Zhe Zhao, Yuheng Yang, Xinhai Pan, Varshini Vijay, Naoki Konno, Nianping Liu, Lei Li, X Rosa Ma, Stephanie D Conley, Colin Kern, William R Goodyer, Bogdan Bintu, Quan Zhu, Neil C Chi, Jiang He, Lorenz Rognoni, Xiuwei Zhang, Jun Wu, David Ellison, Marlene Rabinovitch, Jesse M Engreitz, Xiaojie Qiu+.

MERFISH+, a large-scale, multi-omics spatial technology resolves the molecular holograms of the 3D human developing heart

Colin Kern, Qingquan Zhang, Yifan Lu, Jacqueline Eschbach, Zehua Zeng, Elie N Farah, Chu-Yi Tai, Kaifu Yang, Ignatius Jenie, Fenyong Yao, Zoey Zhao, Qixuan Ma, Carlos Garcia Padilla, Alexander Monell, Siavash Moghadami, Fugui Zhu, Bin Li, Angie Hou, Grant Tucker, David Ellison, Neil C Chi+, Xiaojie Qiu+, Quan Zhu+, Bogdan Bintu+.

Toward a privacy-preserving predictive foundation model of single-cell transcriptomics with federated learning and tabular modeling

Jiayuan Ding, Jianhui Lin, Shiyu Jiang, Yixin Wang, Ziyang Miao, Zhaoyu Fang, Jiliang Tang+, Min Li+, Xiaojie Qiu+.

Graph-Dynamo: Learning stochastic cellular state transition dynamics from single cell data

Yan Zhang*, Xiaojie Qiu*, Jonathan S Weissman, Ivet Bahar, Jianhua Xing+.

Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq

Sara Sunshine, Andreas S Puschnik, Joseph M Replogle, Matthew T Laurie, Jamin Liu, Beth Shoshana Zha, James K Nuñez, Janie R Byrum, Aidan H McMorrow, Matthew B Frieman, Juliane Winkler, Xiaojie Qiu, Oren S Rosenberg, Manuel D Leonetti, Chun Jimmie Ye, Jonathan S Weissman+, Joseph L DeRisi+, Marco Y Hein+

Single-cell Stereo-seq reveals induced progenitor cells involved in axolotl brain regeneration

Xiaoyu Wei*, Sulei Fu*, Hanbo Li*, Yang Liu*, Shuai Wang*, Weimin Feng*, Yunzhi Yang*, Xiawei Liu, Yan-Yun Zeng, Mengnan Cheng, Yiwei Lai, Xiaojie Qiu, Liang Wu, Nannan Zhang, Yujia Jiang, Jiangshan Xu, Xiaoshan Su, Cheng Peng, Lei Han, Wilson Pak-Kin Lou, Chuanyu Liu, Yue Yuan, Kailong Ma, Tao Yang, Xiangyu Pan, Shang Gao, Ao Chen, Miguel A Esteban, Huanming Yang, Jian Wang, Guangyi Fan, Longqi Liu, Liang Chen+, Xun Xu+, Ji-Feng Fei+, Ying Gu+.

Inferring gene regulation from stochastic transcriptional variation across single cells at steady state

Anika Gupta*, Jorge D Martin-Rufino*, Thouis R Jones, Vidya Subramanian, Xiaojie Qiu, Emanuelle I Grody, Alex Bloemendal, Chen Weng, Sheng-Yong Niu, Kyung Hoi Min, Arnav Mehta, Kaite Zhang, Layla Siraj, Aziz Al'Khafaji, Vijay G Sankaran, Soumya Raychaudhuri, Brian Cleary, Sharon Grossman, Eric S Lander+.

Thyroid hormone regulates distinct paths to maturation in pigment cell lineages

Lauren M Saunders, Abhishek K Mishra, Andrew J Aman, Victor M Lewis, Matthew B Toomey, Jonathan S Packer, Xiaojie Qiu, Jose L McFaline-Figueroa, Joseph C Corbo, Cole Trapnell+, David M Parichy+.

Aligning single-cell developmental and reprogramming trajectories identifies molecular determinants of myogenic reprogramming outcome

Davide Cacchiarelli, Xiaojie Qiu, Sanjay Srivatsan, Anna Manfredi, Michael Ziller, Eliah Overbey, Antonio Grimaldi, Jonna Grimsby, Prapti Pokharel, Kenneth J Livak, Shuqiang Li, Alexander Meissner, Tarjei S Mikkelsen, John L Rinn, Cole Trapnell+.

Cicero predicts cis-regulatory DNA interactions from single-cell chromatin accessibility data

Hannah A Pliner, Jonathan S Packer, José L McFaline-Figueroa, Darren A Cusanovich, Riza M Daza, Delasa Aghamirzaie, Sanjay Srivatsan, Xiaojie Qiu, Dana Jackson, Anna Minkina, Andrew C Adey, Frank J Steemers, Jay Shendure+, Cole Trapnell+.

Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis

Naresh K Hanchate, Kunio Kondoh, Zhonghua Lu, Donghui Kuang, Xiaolan Ye, Xiaojie Qiu, Lior Pachter, Cole Trapnell+, Linda B Buck+.

From understanding the development landscape of the canonical fate-switch pair to constructing a dynamic landscape for two-step neural differentiation

Xiaojie Qiu*, Shanshan Ding*, Tieliu Shi+.

A transcriptional dynamic network during Arabidopsis thaliana pollen development

Jigang Wang, Xiaojie Qiu*, Yuhua Li, Youping Deng, Tieliu Shi+.

HCCNet: an integrated network database of hepatocellular carcinoma

Bing He, Xiaojie Qiu, Peng Li, Lishan Wang, Qi Lv, Tieliu Shi+.