张学工｜清华大学｜学者主页

2026

Cross-dataset annotation harmonization for cell-type hierarchy construction

Tian-Hong Zhou, Yi-Xin Chen, Ying-Tao Zhu, Jin-Meng Jia, Xuegong Zhang, Lei Wei

Bioinform.

DOI

2026

How different AI models understand cells differently

Yu-Bo Zhao, Duo-Zhi Sun, Minsheng Hao, Yifan Xiong, Chen Li, Tieliang Gong, Lei Wei, Xuegong Zhang

bioRxiv

DOI

2026

A generic reference defined by consensus peaks for single-cell ATAC-seq data analysis

Qiuchen Meng, Xin-Ze Wu, Wenchang Chen, Yu-Bo Zhao, Chen Li, Zheng Wei, Xiaocheng Zeng, Jiaqi Li, Xi Xi, Sijie Chen, Catherine Zhang, Sheng-Quan Chen, Jiaqi Li, Xiao-Wo Wang, R. Jiang, Lei Wei, Xuegong Zhang

Nature Communications

DOI

2026

Forecasting cell state futures from static snapshots

Er-Pai Luo, Haoxiang Gao, Haiyang Bian, Shuguang Peng, Ya-Ru Li, Chen Li, Minsheng Hao, Mo Chen, Yuli She, Lei Wei, Kai Liu, Xuegong Zhang

bioRxiv

DOI

2026

Tokenizing single-cell transcriptomes as a native language for large language models

Chu-Xi Xiao, Yuang Ding, Haiyang Bian, Yi-Xin Chen, Lei Wei, Xuegong Zhang

bioRxiv

DOI

2026

Unified multimodal learning enables generalized cellular response prediction to diverse perturbations

Chen Li, Lei Wei, Xuegong Zhang

bioRxiv

DOI

2026

Identifying fate-determining transcription factors with single-cell omics.

Xi Xi, Chen Li, Lei Wei, Xuegong Zhang

Trends in Genetics

DOI

2025

Quantifying Early-Stage Lung Adenocarcinoma Progression with a Radiomic Trajectory

Zhen-Bin Qiu, Jiaqi Li, Shihua Dou, Qiuchen Meng, Meng-Min Wang, Hong-Ji Li, Chao Zhang, Hongsheng Xie, Ben-Yuan Jiang, Jun-Tao Lin, Jia-Tao Zhang, Fang-Ping Xu, Jin-Hai Yan, Lei Wei, Yi-Long Wu, Haibo Wang, Lin Yang, Xuegong Zhang, Wen-Zhao Zhong

Npj Digital Medicine，Vol. 8, No. 10

DOI

2025

A phenotype-based AI pipeline outperforms human experts in differentially diagnosing rare diseases using EHRs

Xiaohao Mao, Yu Huang, Ye Jin, Lun Wang, Xuanzhong Chen, Honghong Liu, Xinglin Yang, Haopeng Xu, Xiaodong Luan, Ying Xiao, Siqin Feng, Jiahao Zhu, Xuegong Zhang, Rui Jiang, Shuyang Zhang, Ting Chen

Npj Digital Medicine，Vol. 8, No. 10

DOI

2025

DeepSeek与医学大语言模型：技术创新与医疗服务模式重构

闾海荣，江瑞，张学工，王存库

《医学信息学杂志》

2025

Multi-modal Diffusion Model with Dual-Cross-Attention for Multi-Omics Data Generation and Translation

Er-Pai Luo, Lei Wei, Minsheng Hao, Xuegong Zhang, Qiao Liu

bioRxiv

DOI

2025

Computational methods and data resources for predicting tumor neoantigens

Xiaofei Zhao, Lei Wei, Xuegong Zhang

Briefings Bioinform.

DOI

2025

Benchmarking AI Models for In Silico Gene Perturbation of Cells

Chen Li, Haoxiang Gao, Yuli She, Haiyang Bian, Qinglin Chen, Kai Liu, Lei Wei, Xuegong Zhang

bioRxiv

DOI

2025

GeST: Towards Building A Generative Pretrained Transformer for Learning Cellular Spatial Context

Minsheng Hao, Nan Yan, Haiyang Bian, Yi-Xin Chen, Jin Gu, Lei Wei, Xuegong Zhang

bioRxiv

DOI

2025

hECA v2.0: an AI-ready ensemble cell atlas of single-cell RNA and ATAC sequencing data

Xi Xi, Yi-Xin Chen, Xin-Ze Wu, Minsheng Hao, Jiaqi Li, Haiyang Bian, Qiuchen Meng, Fan-Hong Li, Chen Li, Chu-Xi Xiao, Xiaomin Dong, Renke You, Yifan Xiong, Peng Yang, Zijing Gao, Xue-Jian Cui, Yan Pan, Zhen Li, Wenrui Li, Zhuo-Feng Li, Xiao-Yang Chen, Yan Cui, Hai-Rong Lv, Rui Jiang, Lei Wei, Xuegong Zhang

Scientific Data

DOI

2025

TFcomb identifies transcription factor combinations for cellular reprogramming based on single-cell multiomics data

Chen Li, Sijie Chen, Yi-Xin Chen, Haiyang Bian, Minsheng Hao, Lei Wei, Xuegong Zhang

Genome Research

DOI

2025

scRecover: Discriminating True and False Zeros in Single‐Cell RNA‐Seq Data for Imputation

Zhun Miao, Xinyi Lin, Jiaqi Li, Joshua W. K. Ho, Qiuchen Meng, Xuegong Zhang

Statistics in Medicine

DOI

2025

Biomedical data and AI

Hao Xu, Shibo Zhou, Zefeng Zhu, Vincenzo Vitelli, Liangyi Chen, Zi-Wei Dai, Ning Yang, Luhua Lai, Sheng-Yong Yang, S. Ovchinnikov, Zhuoran Qiao, Sirui Liu, Chen Song, Jianfeng Pei, Han Wen, Jian-Feng Feng, Yao-Yao Zhang, Zhengwei Xie, Yang-Yu Liu, Zhi-Yuan Li, Fu-Lai Jin, Hao Li, Mohammad Lotfollahi, Xuegong Zhang, Ge Yang, Shi-Hua Zhang, Ge Gao, Pu-Lin Li, Qi Liu, J. Han

Science China Life Sciences

DOI

2025

A mechanism-informed deep neural network enables prioritization of regulators that drive cell state transitions

Xi Xi, Jiaqi Li, Jin-Meng Jia, Qiuchen Meng, Chen Li, Xiao-Wo Wang, Lei Wei, Xuegong Zhang

Nature Communications

DOI

2025

SpatialZoomer: multi-scale feature analysis of spatial transcriptomics

Xin-Qi Li, Yuhan Fan, Yue Han, Wenbo Guo, Jingmin Huang, Nan Yan, Ze-Yu Chen, Yanhong Wu, Yuxin Miao, Lin Hou, Xuegong Zhang, Ze-Yu Chen, Jin Gu

bioRxiv

DOI

2025

uHAF: a unified hierarchical annotation framework for cell type standardization and harmonization

Haiyang Bian, Yinxin Chen, Lei Wei, Xuegong Zhang

Bioinform.

DOI

2025

uniLIVER: a human liver cell atlas for data-driven cellular state mapping

Yanhong Wu, Yuhan Fan, Yuxin Miao, Yuman Li, Guifang Du, Zeyu Chen, Jinmei Diao, Yu-Ann Chen, Mingli Ye, Renke You, Amin Chen, Yixin Chen, Wenrui Li, Wenbo Guo, Jiahong Dong, Xuegong Zhang, Yunfang Wang, Jin Gu

Journal of Genetics and Genomics

2025

Benchmarking AI scientists for omics data–driven biological discovery

Er-Pai Luo, Jin-Meng Jia, Yifan Xiong, Xiang-Yue Li, Xiaobo Guo, Baoqi Yu, Minsheng Hao, Lei Wei, Xuegong Zhang

Bioinformatics

DOI

2025

A unified single-cell atlas of human lung provides insights into pulmonary diseases

Fanjie Wu, Wen-Hao Cai, Hai Tang, Shikang Zheng, Haiyue Zhang, Yi-Xin Chen, Yutong Han, Dingli Zhou, Ruihan Wang, Ming-Li Ye, Renke You, Amin Chen, Jiaqi Li, Xuegong Zhang, Wei-Zhong Li

EBioMedicine

DOI

2025

NeoGuider: neoepitope prediction using advanced feature engineering

Xiaofei Zhao, Lei Wei, Zhen Xie, Xuegong Zhang

Genome Medicine

DOI

2024

A brain cell atlas integrating single-cell transcriptomes across human brain regions

Xinyue Chen, Yin Huang, Liang-Feng Huang, Ziliang Huang, Zhao-Zhe Hao, Lahong Xu, Nana Xu, Zhi Li, Y. Mou, Ming-Li Ye, Renke You, Xuegong Zhang, Sheng Liu, Zhi-Chao Miao

Nature Medicine

DOI

2024

Systematic analysis on the horse-shoe-like effect in PCA plots of scRNA-seq data

Najeebullah Shah, Qiuchen Meng, Ziheng Zou, Xuegong Zhang

Bioinformatics Advances

DOI

2024

Current opinions on large cellular models

Minsheng Hao, Lei Wei, Fan Yang, Jian-Hua Yao, C. Theodoris, Bo Wang, Xin Li, Ge Yang, Xuegong Zhang

Quant. Biol.

DOI

2024

A transformer-based weakly supervised computational pathology method for clinical-grade diagnosis and molecular marker discovery of gliomas

Rui Jiang, Xiaoxu Yin, Pengshuai Yang, Lin-Yeh Cheng, Juan Hu, Jiao Yang, Ying Wang, Xiaodan Fu, Li Shang, Li-Ling Li, Wei Lin, Hua-Jun Zhou, Fu-Feng Chen, Xuegong Zhang, Zhongliang Hu, Hai-Rong Lv

Nature Machine Intelligence

DOI

2024

NeoHunter: Flexible software for systematically detecting neoantigens from sequencing data

Tianxing Ma, Zetong Zhao, Haochen Li, Lei Wei, Xuegong Zhang

Quant. Biol.

DOI

2024

General-purpose pre-trained large cellular models for single-cell transcriptomics

Haiyang Bian, Yi-Xin Chen, Er-Pai Luo, Xin-Ze Wu, Minsheng Hao, Lei Wei, Xuegong Zhang

National Science Review

DOI

2024

scDirect: key transcription factor identification for directing cell state transitions based on single-cell multi-omics data

Chen Li, Sijie Chen, Yi-Xin Chen, Haiyang Bian, Minsheng Hao, Lei Wei, Xuegong Zhang

bioRxiv

DOI

2024

HCCDB v2.0: Decompose Expression Variations by Single-cell RNA-seq and Spatial Transcriptomics in HCC

Ziming Jiang, Yanhong Wu, Yuxin Miao, Kaige Deng, Fan Yang, Shuhuan Xu, Yu-Peng Wang, Renke You, Lei Zhang, Yuhan Fan, Wenbo Guo, Qiu-Yu Lian, Lei Chen, Xuegong Zhang, Yongchang Zheng, Jin Gu

Genomics, Proteomics & Bioinformatics

DOI

2024

A universal single-cell transcriptomics atlas of human lung decodes multiple pulmonary diseases

Fanjie Wu, Wen-Hao Cai, Hai Tang, Shikang Zheng, Haiyue Zhang, Yi-Xin Chen, Yutong Han, Dingli Zhou, Ruihan Wang, Ming-Li Ye, Renke You, Amin Chen, Jiaqi Li, Xuegong Zhang, Wei-Zhong Li

bioRxiv

DOI

2024

Hierarchical Interpretation of Out-of-Distribution Cells Using Bottlenecked Transformer

Qifei Wang, He Zhu, Yi-Wen Hu, Yan-Jie Chen, Yuwei Wang, Xuegong Zhang, J. Zou, M. Kellis, Yue Li, Dianbo Liu, Lan Jiang

bioRxiv

DOI

2024

scStateDynamics: deciphering the drug-responsive tumor cell state dynamics by modeling single-cell level expression changes

Wenbo Guo, Xin-Qi Li, Dongfang Wang, Nan Yan, Qi-Fan Hu, Fan Yang, Xuegong Zhang, Jian-Hua Yao, Jin Gu

Genome Biology

DOI

2024

Single-cell transcriptomic analysis reveals tumor cell heterogeneity and immune microenvironment features of pituitary neuroendocrine tumors

Nan Yan, Weiyan Xie, Dongfang Wang, Qiu-yue Fang, Jing Guo, Yiyuan Chen, Xin-Qi Li, L. Gong, Jia-lin Wang, Wenbo Guo, Xuegong Zhang, Ya-Zhuo Zhang, Jin Gu, Chu-Zhong Li

Genome Medicine

DOI

2024

scTML: a pan-cancer single-cell landscape of multiple mutation types

Haochen Li, Tianxing Ma, Zetong Zhao, Yi-Xin Chen, Xi Xi, Xiaofei Zhao, Xiao-Xiang Zhou, Yibo Gao, Lei Wei, Xuegong Zhang

Nucleic Acids Research

DOI

2024

Toward mastering the cell language by learning to generate

Yi-Xin Chen, Haiyang Bian, Lei Wei, Jin-Meng Jia, Xiaomin Dong, Yu-Zhuo Li, Yu-Bo Zhao, Xin-Ze Wu, Chen Li, Er-Pai Luo, Chu-Xi Xiao, Minsheng Hao, Xuegong Zhang

bioRxiv

DOI

2024

STEM enables mapping of single-cell and spatial transcriptomics data with transfer learning

Minsheng Hao, Er-Pai Luo, Yi-Xin Chen, Yanhong Wu, Chen Li, Sijie Chen, Haoxiang Gao, Haiyang Bian, Jin Gu, Lei Wei, Xuegong Zhang

Communications Biology

DOI

2024

QueST: Querying Functional and Structural Niches on Spatial Transcriptomics Data via Contrastive Subgraph Embedding

Mo Chen, Minsheng Hao, Xuegong Zhang, Lei Wei

arXiv.org

DOI

2024

scDiffusion: conditional generation of high-quality single-cell data using diffusion model

Er-Pai Luo, Minsheng Hao, Lei Wei, Xuegong Zhang

Bioinform.

DOI

2024

scMulan: A Multitask Generative Pre-Trained Language Model for Single-Cell Analysis

Haiyang Bian, Yixin Chen, Xiaomin Dong, Chen Li, Minsheng Hao, Sijie Chen, Jinyi Hu, Maosong Sun, Lei Wei, Xuegong Zhang

Annual International Conference on Research in Computational Molecular Biology

DOI

2023

The spatial and single-cell analysis reveals remodeled immune microenvironment induced by synthetic oncolytic adenovirus treatment.

Gan Liu, Qi-Fan Hu, Shuguang Peng, Hui Ning, Jia-Jia Mai, Xi Chen, Minzhen Tao, Qiang Liu, Huiya Huang, Yun Jiang, Yan-Hua Ding, Xuegong Zhang, Jin Gu, Zhen Xie

Cancer Letters

DOI

2023

Benchmarking multi-omics integration algorithms across single-cell RNA and ATAC data

Chu-Xi Xiao, Yi-Xin Chen, Qiuchen Meng, Lei Wei, Xuegong Zhang

bioRxiv

DOI

2023

scDecouple: decoupling cellular response from infected proportion bias in scCRISPR-seq

Qiuchen Meng, Lei Wei, K. Ma, Ming Shi, Xin-Yi Lin, J. Ho, Yin-Qing Li, Xuegong Zhang

bioRxiv

DOI

2023

Latent feature extraction with a prior-based self-attention framework for spatial transcriptomics

Zhen Li, Xiao-Yang Chen, Xuegong Zhang, Rui Jiang, Shengquan Chen

Genome Research

DOI

2023

Consensus peaks of chromatin accessibility in the human genome

Qiuchen Meng, Xin-Ze Wu, Chen Li, Jiaqi Li, Xi Xi, Shengquan Chen, Rui Jiang, Lei Wei, Xuegong Zhang

2023

NeuronMotif: Deciphering cis-regulatory codes by layer-wise demixing of deep neural networks

Zheng Wei, Kui Hua, Lei Wei, Shining Ma, Rui Jiang, Xuegong Zhang, Yanda Li, Wing Hong Wong, Xiaowo Wang

Proceedings of the National Academy of Sciences of the United States of America

DOI

2023

Decoding functional cell–cell communication events by multi-view graph learning on spatial transcriptomics

Haochen Li, Tianxing Ma, Minsheng Hao, Wenbo Guo, Jin Gu, Lei Wei, Xuegong Zhang

bioRxiv

DOI

2022

数基生命系统——用控制和系统的观点对生命的数字化建模

张学工，王颖，汪小我，江瑞，古槿

《厦门大学学报(自然科学版)》

2022

Yanda Li: A never-stopping pioneer, investigator and founder

Xuegong Zhang, Jin Gu

Quant. Biol.

DOI

2022

Multifaceted Spatial and Functional Zonation of Cardiac Cells in Adult Human Heart.

Liang Chen, Kui Hua, Ningning Zhang, Jingyu Wang, J. Meng, Zhenliang Hu, Haoxiang Gao, Fan-Hong Li, Yang Chen, Jie Ren, Liyang Liu, Qi-Ming Zhou, Jin Gu, Jiangping Song, Xuegong Zhang, Sheng-Shou Hu

Circulation

DOI

2022

Learning Spatially-Aware Representations of Transcriptomic Data via Transfer Learning

Minsheng Hao, Lei Wei, Xuegong Zhang

2022

Inferring Intercellular Communication and Intracellular Regulations From Single-Cell or Spatial Transcriptomics Data: A Systematic Survey and Benchmarking

Jiaxin Luo, Lulu Yan, Lei Wei, Minghua Deng, Xuegong Zhang, Xiaoqiang Sun

Social Science Research Network

DOI

2022

Protocol for using GRPath to identify putative gene regulation paths in complex human diseases

Xi Xi, Haochen Li, Lei Wei, Xuegong Zhang

STAR Protocols

DOI

2022

Protocol for profiling cell-centric assembled single-cell human transcriptome data in hECA

Yi-Xin Chen, Minsheng Hao, Haoxiang Gao, Jiaqi Li, Sijie Chen, Fan-Hong Li, Lei Wei, Xuegong Zhang

STAR Protocols

DOI

2022

Unfolding the genotype-to-phenotype black box of cardiovascular diseases through cross-scale modeling

Xi Xi, Haochen Li, Shengquan Chen, Ting-Ting Lv, Tianxing Ma, Rui Jiang, Ping Zhang, Wing Hong Wong, Xuegong Zhang

iScience

DOI

2021

模式识别模式识别与机器学习

张学工

《清华大学出版社》

2021

加速生命科学与智能科技融合，助力大健康技术创新与产业升级

董家鸿，高家红，张学工，宋尔卫，贺福初

《科技导报》

2021

ARIC: Accurate and robust inference of cell type proportions from bulk gene expression or DNA methylation data

Wei Zhang, Hanwen Xu, Rong Qiao, Bixi Zhong, Xiang-Lin Zhang, Jin Gu, Xuegong Zhang, Lei Wei, Xiaowo Wang

bioRxiv

DOI

2018

人类智能的基因调控机理

张学工，江瑞，汪小我

《高科技与产业化》

2018

Single cell transcriptomes reveal characteristics of miRNA in gene expression noise reduction

Tao Hu, Lei Wei, Shuailin Li, Tianrun Cheng, Xuegong Zhang, Xiaowo Wang

bioRxiv

DOI

2015

基于分子标记的宏基因组16S rRNA基因高变区选择策略

张军毅，朱冰川，徐超，丁啸，李俊锋，张学工，陆祖宏

《应用生态学报》

2013

高通量测序技术在临床医学中的应用进展

刘莉扬，张学工

《医学综述》

2013

Research in Computational Molecular Biology: 17th Annual International Conference, RECOMB 2013, Beijing, China, April 7-10, 2013. Proceedings

Minghua Deng, Rui Jiang, Feng-Zhu Sun, Xuegong Zhang

2010

新一代高通量RNA测序数据的处理与分析

王曦，汪小我，王立坤，冯智星，张学工

《生物化学与生物物理进展》

2010

模式识别 = Pattern recognition

张学工

《清华大学出版社》

2010

基础医学科研进展信息聚合平台构建

郝志勇，庄永龙，张学工

《医学信息学杂志》

2009

DNA甲基化的生物信息学研究进展

凡时财，张学工

《生物化学与生物物理进展》

2008

转录因子结合位点的计算分析方法

李婷婷，蒋博，汪小我，张学工

《生物物理学报》

2008

脊椎动物中微小RNA进化模式研究

汪小我，张学工，李衍达

《中国科学:生命科学》

2005

MicroRNA identification based on sequence and structure alignment

Xiaowo Wang, Jing Zhang, Fei Li, Jin Gu, Tao He, Xuegong Zhang, Yanda Li

Bioinform.

DOI

2004

多巴胺通路的基因与精神分裂症风险的多位点关联研究

孙向青，贾彦彬，张学工，许琪，沈岩，李衍达

《中国科学:生命科学》

2004

PCA-FA:Applying Supervised Learning to Analyze Gene Expression Data

翁时锋，张长水，张学工

Tsinghua Science and Technology

2004

非线性降维在高维医学数据处理中的应用

翁时锋，张长水，张学工

《清华大学学报(自然科学版)》

精选作品

期刊论文

模式识别

Cross-dataset annotation harmonization for cell-type hierarchy construction

How different AI models understand cells differently

A generic reference defined by consensus peaks for single-cell ATAC-seq data analysis

Forecasting cell state futures from static snapshots

Tokenizing single-cell transcriptomes as a native language for large language models

Unified multimodal learning enables generalized cellular response prediction to diverse perturbations

Identifying fate-determining transcription factors with single-cell omics.

Quantifying Early-Stage Lung Adenocarcinoma Progression with a Radiomic Trajectory

A phenotype-based AI pipeline outperforms human experts in differentially diagnosing rare diseases using EHRs

DeepSeek与医学大语言模型：技术创新与医疗服务模式重构

Multi-modal Diffusion Model with Dual-Cross-Attention for Multi-Omics Data Generation and Translation

Computational methods and data resources for predicting tumor neoantigens

Benchmarking AI Models for In Silico Gene Perturbation of Cells

GeST: Towards Building A Generative Pretrained Transformer for Learning Cellular Spatial Context

hECA v2.0: an AI-ready ensemble cell atlas of single-cell RNA and ATAC sequencing data

TFcomb identifies transcription factor combinations for cellular reprogramming based on single-cell multiomics data

scRecover: Discriminating True and False Zeros in Single‐Cell RNA‐Seq Data for Imputation

Biomedical data and AI

A mechanism-informed deep neural network enables prioritization of regulators that drive cell state transitions

SpatialZoomer: multi-scale feature analysis of spatial transcriptomics

uHAF: a unified hierarchical annotation framework for cell type standardization and harmonization

uniLIVER: a human liver cell atlas for data-driven cellular state mapping

Benchmarking AI scientists for omics data–driven biological discovery

A unified single-cell atlas of human lung provides insights into pulmonary diseases

NeoGuider: neoepitope prediction using advanced feature engineering

A brain cell atlas integrating single-cell transcriptomes across human brain regions

Systematic analysis on the horse-shoe-like effect in PCA plots of scRNA-seq data

Current opinions on large cellular models

A transformer-based weakly supervised computational pathology method for clinical-grade diagnosis and molecular marker discovery of gliomas

NeoHunter: Flexible software for systematically detecting neoantigens from sequencing data

General-purpose pre-trained large cellular models for single-cell transcriptomics

scDirect: key transcription factor identification for directing cell state transitions based on single-cell multi-omics data

HCCDB v2.0: Decompose Expression Variations by Single-cell RNA-seq and Spatial Transcriptomics in HCC

A universal single-cell transcriptomics atlas of human lung decodes multiple pulmonary diseases

Hierarchical Interpretation of Out-of-Distribution Cells Using Bottlenecked Transformer

scStateDynamics: deciphering the drug-responsive tumor cell state dynamics by modeling single-cell level expression changes

Single-cell transcriptomic analysis reveals tumor cell heterogeneity and immune microenvironment features of pituitary neuroendocrine tumors

scTML: a pan-cancer single-cell landscape of multiple mutation types

Toward mastering the cell language by learning to generate

STEM enables mapping of single-cell and spatial transcriptomics data with transfer learning

QueST: Querying Functional and Structural Niches on Spatial Transcriptomics Data via Contrastive Subgraph Embedding

scDiffusion: conditional generation of high-quality single-cell data using diffusion model

scMulan: A Multitask Generative Pre-Trained Language Model for Single-Cell Analysis

The spatial and single-cell analysis reveals remodeled immune microenvironment induced by synthetic oncolytic adenovirus treatment.

Benchmarking multi-omics integration algorithms across single-cell RNA and ATAC data

scDecouple: decoupling cellular response from infected proportion bias in scCRISPR-seq

Latent feature extraction with a prior-based self-attention framework for spatial transcriptomics

Consensus peaks of chromatin accessibility in the human genome

NeuronMotif: Deciphering cis-regulatory codes by layer-wise demixing of deep neural networks

Decoding functional cell–cell communication events by multi-view graph learning on spatial transcriptomics

数基生命系统——用控制和系统的观点对生命的数字化建模

Yanda Li: A never-stopping pioneer, investigator and founder

Multifaceted Spatial and Functional Zonation of Cardiac Cells in Adult Human Heart.

Learning Spatially-Aware Representations of Transcriptomic Data via Transfer Learning

Inferring Intercellular Communication and Intracellular Regulations From Single-Cell or Spatial Transcriptomics Data: A Systematic Survey and Benchmarking

Protocol for using GRPath to identify putative gene regulation paths in complex human diseases

Protocol for profiling cell-centric assembled single-cell human transcriptome data in hECA

Unfolding the genotype-to-phenotype black box of cardiovascular diseases through cross-scale modeling

模式识别 模式识别与机器学习

加速生命科学与智能科技融合，助力大健康技术创新与产业升级

ARIC: Accurate and robust inference of cell type proportions from bulk gene expression or DNA methylation data

人类智能的基因调控机理

Single cell transcriptomes reveal characteristics of miRNA in gene expression noise reduction

基于分子标记的宏基因组16S rRNA基因高变区选择策略

高通量测序技术在临床医学中的应用进展

Research in Computational Molecular Biology: 17th Annual International Conference, RECOMB 2013, Beijing, China, April 7-10, 2013. Proceedings

新一代高通量RNA测序数据的处理与分析

模式识别 = Pattern recognition

基础医学科研进展信息聚合平台构建

DNA甲基化的生物信息学研究进展

转录因子结合位点的计算分析方法

脊椎动物中微小RNA进化模式研究

MicroRNA identification based on sequence and structure alignment

多巴胺通路的基因与精神分裂症风险的多位点关联研究

PCA-FA:Applying Supervised Learning to Analyze Gene Expression Data

非线性降维在高维医学数据处理中的应用

会议论文

模式识别模式识别与机器学习