2026
2025
2024
2023
2022
2021
2020
2019
2018
2017
2016
2015
2026
10.05
Publication: Resolving cell–cell interaction networks and their molecular logic in complex tissues was published in Nature Methods!
Title:Resolving cell–cell interaction networks and their molecular logic in complex tissues
Authors:Lei Tang*, Kang Tian*, Xiaolei Fu*, Yingjia Xu*, Jincheng Wu, Jinsong Zhang, Xi-Wen Wang, Chunxiang Ye, Qiong Wu, Wei Wu, Changjiang Feng#, Qiangfeng Cliff Zhang#
Link:Nature Methods
2026
10.02
Publication: DeCoRE: A computational method to resolve RNA structural heterogeneity from RNA structure probing data by direct RNA sequencing was published in Science Advances!
Title:DeCoRE: A computational method to resolve RNA structural heterogeneity from RNA structure probing data by direct RNA sequencing
Authors:Yong Huang*, Jinsong Zhang*, Lei Sun#, Qiangfeng Cliff Zhang#
Link:Science Advances
2026
09.16
Congrats: Muzhi Dai passed the PhD thesis defense
Event:Muzhi Dai passed the PhD thesis defense
Venue:Room E403, Biomedical Building, THU
2026
06.03
Congrats: Pengfei Wang passed the PhD thesis defense
Event:Pengfei Wang passed the PhD thesis defense
Venue:Room E109, Biomedical Building, THU
2026
04.11
Publication: CryoNet.Refine: A One-step Diffusion Model for Rapid Refinement of Structural Models with Cryo-EM Density Map Restraints was accepted by ICLR 2026!
Title:CryoNet.Refine: A One-step Diffusion Model for Rapid Refinement of Structural Models with Cryo-EM Density Map Restraints
Authors:Fuyao Huang*, Xiaozhu Yu*, Kui Xu#, and Qiangfeng Cliff Zhang#
Link:ICLR 2026
2026
02.24
Publication: CryoLVM: Self-supervised Learning from Cryo-EM Density Maps with Large Vision Models was accepted by ICLR 2026!
Title:CryoLVM: Self-supervised Learning from Cryo-EM Density Maps with Large Vision Models
Authors:Weining Fu*, Kai Shu*, Kui Xu#, and Qiangfeng Cliff Zhang#
Link:ICLR 2026
2025
11.21
Congrats: Zhang Lab 10th Anniversary Symposium & Reunion
Title:ZhangLab 10th Anniversary Symposium & Reunion
Time:21–22 Nov 2025
Venue:Beijing Ruilinwan Hot Spring Hotel
Participants:41 members (14 alumni, 27 current)
Highlights:Reunion dinner; Scientific symposium; Happy Hour; Hot spring social.
2025
09.19
Seminar: Systems vaccinology drives the analysis and application of vaccine immune response mechanisms
Title:Systems vaccinology drives the analysis and application of vaccine immune response mechanisms
Speaker:Dr. Zijie Zhang
Venue:Room E403, Biomedical Building, THU
2025
06.06
Congrats: The First National Conference on Artificial Intelligence Biology was grandly convened
Title:The First National Conference on Artificial Intelligence Biology was grandly convened
Address:Lin'an Hangzhou
Link:Live Picture
2025
04.17
Seminar: We invited Dr. Yaoqi Zhou from Shenzhen Bay Laboratory to talk about Challenges of RNA Language Large Models and Structure Prediction
Title:Challenges of RNA Language Large Models and Structure Prediction
Speaker:Dr. Yaoqi Zhou
Venue:Room E109, Biomedical Building, THU
2024
10.19
Congrats: Prof. Zhang was awarded the "2024 Scientific Explorer Prize" for his work in the intelligent prediction of RNA three-dimensional structures and small molecule intervention!
Event:Prof. Zhang was awarded the "2024 Scientific Explorer Prize" for his work in the intelligent prediction of RNA three-dimensional structures and small molecule intervention!
Time:19 Oct 2024
Link:Xplorer Prize
2024
09.06
Congrats: Huang Yong passed the PhD thesis defense
Event:Huang Yong passed the PhD thesis defense
Venue:Room E403, Biomedical Building, THU
2024
5.31
Publication: Our paper on tissue module discovery in single-cell-resolution spatial transcriptomics data was accepted by Cell Systems!
Title:Tissue module discovery in single-cell-resolution spatial transcriptomics data via cell-cell interaction-aware cell embedding
Authors:Y. Li, J. Zhang, et al.
Time:31 May 2024
Link:Cell Systems
2024
05.23
Congrats: Li Yuzhe passed the PhD thesis defense
Event:Li Yuzhe passed the PhD thesis defense
Venue:Block B, Biomedical Building, THU
2024
05.23
Congrats: Tian Kang passed the PhD thesis defense
Event:Tian Kang passed the PhD thesis defense
Venue:Block B, Biomedical Building, THU
2024
3.26
Publication: Our paper on mapping of the influenza A virus genome RNA structure and interactions was accepted by Cell Reports!
Title:Mapping of the influenza A virus genome RNA structure and interactions reveals essential elements of viral replication
Authors:R. Yang, M. Pan, J. Guo, Y. Huang, et al.
Time:26 Mar 2024
Link:Cell Reports
2024
1.9
Publication: Our paper on identification of functionally conserved lncRNA was accepted by Nature Genetics!
Title:Computational prediction and experimental validation identify functionally conserved lncRNAs from zebrafish to human
Authors:W. Huang, T. Xiong, Y. Zhao, et al.
Time:9 Jan 2024
Link:Nature Genetics
2023
12.21
Congrats: Yang Rui passed the PhD thesis defense
Event:Yang Rui passed the PhD thesis defense
Venue:Room 143, Bioscience Building, THU
2022
11.17
Congrats: Our paper on predicting dynamic cellular protein–RNA interactions won the annual outstanding paper award of Cell Research!
Title:Predicting dynamic cellular protein–RNA interactions by deep learning using in vivo RNA structures
Authors:Lei Sun, Kui Xu, Wenze Huang, Yucheng T. Yang et al.
Link:Cell Research
2022
8.17
Congrats: Prof. Zhang won the CSBMB-Promega Award for Biochemistry!
Event:Prof. Zhang won the CSBMB-Promega Award for Biochemistry!
Time:17 Aug 2022
2021
11.17
Publication: Our paper on missing RNA structure profiles imputation was accepted by Nature Machine Intelligence!
Title:A deep learning method for recovering missing signals in transcriptome-wide RNA structure profiles from probing experiments
Authors:J. Gong, K. Xu, et al.
Time:17 Nov 2021
2021
11.4
Publication: Our paper on viral RNA–host protein interactomes was accepted by Cell Research!
Title:Comparison of viral RNA–host protein interactomes across pathogenic RNA viruses informs rapid antiviral drug discovery for SARS-CoV-2
Authors:S. Zhang, W. Huang, et al.
Time:4 Nov 2021
Link:Cell Research
2021
11.1
Publication: Our paper on chromatin-remodeling enzyme Smarca5 was accepted by eLife!
Title:The chromatin-remodeling enzyme Smarca5 regulates erythrocyte aggregation via Keap1-Nrf2 signaling
Authors:Y. Ding, Y. Li, et al.
Time:1 Nov 2021
Link:eLife
2021
9.12
Congrats: Huang Wenze passed the PhD thesis defense
Event:Huang Wenze passed the PhD thesis defense
Venue:Room 325, Bioscience Building, THU
2021
6.30
Publication: Our paper on RNA structure probing review was accepted by Nature Chemical Biology!
Title:RNA structure probing uncovers RNA structure-dependent biological functions
Authors:X. Wang, C. Liu, et al.
Time:30 June 2021
2021
6.7
Publication: Our paper on icSHAPE-MaP of Dicer targeted RNAs was accepted by Nature Communications!
Title:RNA structure probing reveals the structural basis of Dicer binding and cleavage
Authors:Q. Luo, J. Zhang, P. Li, et al.
Time:07 June 2021
2021
5.23
Congrats: Li Pan, Xu Kui and Zhang Jinsong passed the PhD thesis defense
Event:Li Pan, Xu Kui and Zhang Jinsong passed the PhD thesis defense
Venue:Room E109, Biomedical Building, THU
2021
5.17
Seminar: We invited Dr. Marco MARCIA from EMBL Grenoble to talk about how RNA 3D structure determines MEG3 function
Title:The multiple dimensions of lncRNAs - How 3D structure determines MEG3 function
Speaker:Marco MARCIA, PhD
Time:3:30-4:30 pm, May 17th (Monday), 2021
Zoom ID:982 4074 1662
2021
5.12
Lei Sun won Outstanding Postdoctoral Fellow of Tsinghua University!
Direction:RNA secondary structure
Link:Tsinghua Postdoct
2021
2.23
Publication: Our paper on Predicting dynamic cellular protein–RNA interactions was accepted by Cell Research!
Title:Predicting dynamic cellular protein–RNA interactions by deep learning using in vivo RNA structures
Authors:Lei Sun, Kui Xu, Wenze Huang, Yucheng T. Yang et al.
Time:23 Feb 2020
Link:Cell Research
2021
2.9
Publication: Our paper on structural characterization of the SARS-CoV-2 RNA genome was accepted by Cell!
Title:In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugs
Authors:Lei Sun,Pan Li,Xiaohui Ju,Jian Rao,Wenze Huang et al.
Time:9 Feb 2021
Link:Cell
2021
1.10
Lei Xiong won the Outstanding Graduates of Beijing!
Direction:Single Cell
2020
9.14
Congrats: Gong Jing, Piao Meiling and Xiong Lei passed the PhD thesis defense
Event:Xiong Lei,Piao Meiling and Gong jing passed the PhD thesis defense
Venue:Room E109, Biomedical Building, THU
2020
5.18
Publication: Our paper on RNA structural dynamics regulation of early embryogenesis was accepted by Genome Biology!
Title:RNA structural dynamics regulate early embryogenesis through controlling transcriptome fate and function
Authors:Boyang Shi, Jinsong Zhang, Jian Heng, Jing Gong et al.
Time:18 May 2020
Link:Genome Biology
2020
2.17
Congrats: SCALE method is selected as "Top Ten Advances in Bioinformatics in China" in 2019
Title:SCALE method for single-cell ATAC-seq analysis via latent feature extraction
Authors:L. Xiong, K. Xu, K. Tian, et al.
Time:17 February 2020
2020
2.15
Congrats: SCALE method is selected as "Top Ten Algorithms and Tools for Bioinformatics in China" in 2019
Title:SCALE method for single-cell ATAC-seq analysis via latent feature extraction
Authors:L. Xiong, K. Xu, K. Tian, et al.
Time:15 February 2020
2020
2.3
Publication: Our paper on Keth-seq for transcriptome-wide RNA structure was accepted by Nature chemical biology!
Title:Keth-seq for transcriptome-wide RNA structure mapping
Authors:X. Weng, J. Gong, Y. Chen, T. Wu et al.
Time:03 February 2020
2019
12.30
Congrats: Lei Xiong won the 2019 Advanced Innovation Center Structure Biology outstanding scholarship
Project:SCALE method for single-cell ATAC-seq analysis via latent feature extraction
Direction:Single Cell
Amount:RMB 20,000
2019
12.30
Congrats: Pan Li won the 2019 Advanced Innovation Center Structure Biology outstanding scholarship
Project:Integrative Analysis of Zika Virus Genome RNA Structure Reveals Critical Determinants of Viral Infectivity
Direction:RNA secondary structure
Amount:RMB 20,000
2019
11.15
Seminar: We invited Dr. William J. Greenleaf from Stanford University to talk about a single cell framework for multi-omic analysis
Title:A single cell framework for multi-omic analysis of disease identifies malignant regulatory signatures
Speaker:William J. Greenleaf, PhD
Time:13:30-15:00 pm, Nov. 15th (Friday), 2019
Venue:ZhengYutong Lecture Hall(郑裕彤讲堂)
2019
10.8
Publication: Our paper on single-cell ATAC-seq analysis was accepted by Nature Communications!
Title:SCALE method for single-cell ATAC-seq analysis via latent feature extraction
Authors:L. Xiong, K. Xu, K. Tian, et al.
Time:08 October 2019
2019
8.23
Congrats: Sun lei passed the PhD thesis defense
Event:Ph.D. student Sun lei completed his doctoral diploma and is about to receive his Ph.D.
Venue:Room 425, New Life Science Building, THU
2019
8.23
Seminar: We invited Dr. Yaël Fregier from University of Artois to talk about Transfer learning for GANs
Title:Transfer learning for GANs
Speaker:Yaël Fregier, PhD
Time:16:00-17:00pm, Aug. 23th (Friday), 2019
Venue:Room 407, New Life Science Building, THU
2019
8.12
Seminar: We invited Dr. Eric Miska from University of Cambridge to talk about RNA structure and chemical modification
Title:RNA:from structure and chemical modification to new functions
Speaker:Eric Miska, PhD
Time:11:00-12:00pm, Aug. 12th (Monday), 2019
Venue:Room 143, New Life Science Building, THU
2019
8.5
Seminar: We invited Dr. Chuan He from HHMI to talk about RNA methylation and chromatin structure
Title:Studies of RNA methylation and chromatin structure
Speaker:Chuan He, PhD
Time:14:30-16:00am, Aug. 5th (Monday), 2019
Venue:Room B323, Medical Science Building, THU
2019
7.3
Seminar: We invited Dr. Zhang Chaolin from Columbia University to talk about RNA in neurodevelopment
Title:An RNA-centric view of neurodevelopment: From single nucleotide resolution maps to functions
Speaker:Chaolin Zhang, PhD
Time:16:00-18:00, July 3rd, 2019
Venue:Room B323, Medical Building, THU
2019
5.17
Seminar: We invited Dr. Yi Xing from University of Pennsylvania to talk about alternative isoform variation
Title:Alternative isoform variation in cancer transcriptomes
Speaker:Xing yi, PhD
Time:14:00-15:00, May 17th, 2019
Venue:Room 143, New Biology Building, THU
2019
2.7
Publication: Our paper on RNA structures across cellular compartments was accepted by Nature Structure & molecular biology!
Title:RNA structure maps across mammalian cellular compartments
Authors:L. Sun, F. M. Fazal, P. Li et al.
Time:07 February 2019
2019
2.2
PhD student Kui Xu attends the 33rd AAAI Conference on Artificial Intelligence (AAAI 2019) for spotlight presentation at Hawaii, USA
Date:Jan. 27th, 2019 – Feb. 2nd, 2019
Attendee:Kui Xu
Link:AAAI-19
2018
12.1
Congrats: Qian Xingyang won the 2018 Advanced Innovation Center Structure Biology innovation scholarship
Project:Functional and structural analysis of conserved secondary structural elements of lncRNA
Direction:RNA secondary structure
Amount:RMB 30,000
2018
11.30
Seminar: We invited Dr. Anindya Dutta from University of Virginia to talk about tRNA-Derived fragments and long noncoding RNAs
Title:tRFs and long noncoding RNAs, with a short digression on HPV induced cell transformation
Speaker:Anindya Dutta MD, PhD
Time:11:00-12:00am, Nov. 30th (Friday), 2018
Venue:Room 143, New Biology Building, THU
2018
11.21
Publication: Our paper on ZIKV RNA structures was accepted by Cell Host & Microbe and online today!
Title:Integrative Analysis of Zika Virus Genome RNA Structure Reveals Critical Determinants of Viral Infectivity
Authors:P. Li, Y. Wei, M. Mei, L. Tang et al.
Time:21 November 2018
Link:Cell Host & Microbe
2018
11.17
Publication: Our review on lncRNA structure and interaction was accepted by Trends in Biochemical Sciences and online today!
Title:Revealing lncRNA Structures and Interactions by Sequencing-Based Approaches
Authors:X. Qian, J. Zhao, P.Y. Yeung et al.
Time:17 November 2018
2018
11.8
Seminar: We invited Dr. Xingqi Chen from Karolinska Institute to talk about ATAC-seq
Title:Joint single-cell DNA accessibility and protein eptiope profiling reveals environmental regulation of epigenomic heterogeneit
Speaker:Xingqi Chen, PhD
Time:2:00-3:00 pm, Nov. 8th (Thursday), 2018
Venue:Room 143, New Biology Building, THU
2018
11.1
Publication: Our paper on molecular structure estimation from Cryo-EM density volumes was accepted by The 33rd AAAI Conference on Artificial Intelligence (AAAI)!
Title:A²-Net: Molecular Structure Estimation From Cryo-EM Density Volumes
Authors:Kui Xu et al.
Time:1 November 2018
Link:AAAI-19
2018
10.23
Seminar: We invited Dr. Shuo Gu from NIH to talk about miRNA processing
Title:Structural differences between pri-miRNA paralogs promotes alternative Drosha cleavage and expands target repertories
Speaker:Shuo Gu, PhD
Time:1:30-3:00 pm, Oct. 23th (Tuesday), 2018
Venue:Room 143, New Biology Building, THU
2018
8.22
Seminar: We invited Dr. Ye Grace Chen from Yale University to talk about circular RNA in immunity
Title:Circular RNA immunity
Speaker:Ye Grace Chen, PhD
Time:10:00-11:00 am, Aug. 22nd (Wednesday), 2018
Venue:Room 143, New Biology Building, THU
2018
8.7
Our RNA-RNA interactions review paper was accepted by Quantitative Biology and online today !
Title:Advances and challenges towards the study of RNA-RNA interactions in a transcriptome-wide scale
Authors:J. Gong, Y. Ju et al.
Time:07 August 2018
Link:Quantitative Biology
2018
7.17
Seminar: We invited Dr. Xiang-Jun Lu from Columbia University to talk about illuminating the 3D structure of RNA with 3DNA-DSSR
Title:Illuminating the 3D structure of RNA with 3DNA-DSSR
Speaker:Xiang-Jun Lu
Time:2:00-3:00 pm, June. 27th (Wednesday), 2018
Venue:Room 143, New Biology Building, THU
2018
7.6
Seminar: We invited Dr. Yinghao Wu from Albert Einstein College to talk about membrane receptors
Title:Understand binding kinetics of membrane receptors and their functional roles in cell adhesion and signaling by multi-scale modeling
Speaker:Yinghao Wu, PhD
Time:2:00-3:00pm, July. 6th (Friday), 2018
Venue:Room B416, Medical Science Building, THU
2018
1.8
Seminar: We invited Dr. Yanlei Diao from University of Massachusetts Amherst to talk about big and fast data analysis for genomics
Title:Big and fast data analysis for genomics
Speaker:Yanlei Diao
Time:10:00-11:00 am, Jan. 8th (Monday), 2018
Venue:Room 143, New Biology Building, THU
2017
12.21
Congrats: Xu Kui won the 2017 Advanced Innovation Center Structure Biology innovation scholarship
Project:Application of virtual reality technology in structural biology
Direction:Computational structural biology, graphic images, machine learning
Amount:RMB 30,000
2017
12.21
Congrats: Piao Meiling won the 2017 Advanced Innovation Center Structure Biology innovation scholarship
Project:Probing RNA structurome in mouse early embryos by smartSHAPE, a new low-input RNA secondary structure probing technique
Direction:RNA secondary structure
Amount:RMB 30,000
2017
11.6
Seminar: We invited Dr. Mark A. Kay from Stanford University to talk about a functional tRNA
Title:A tRNA derived small RNA regulates ribosome biogenesis and is a target for cancer therapy
Speaker:Mark A. Kay MD, PhD
Time:10:00-11:00 am, Nov. 6th (Monday), 2017
Venue:Room 143, New Biology Building, THU
2017
10.18
Seminar: We invited Dr. Huang Huang from Stanford University to talk about single cell analysis of antigen-specific T cell response
Title:Single cell analysis of antigen-specific T cell response against Mycobacterium tuberculosis
Speaker:Huang Huang, PhD
Time:10:00-11:00 am, Oct. 18th (Wednesday), 2017
Venue:Room 143, New Biology Building, THU
2017
10.12
Publication: Our review on RNA structure probing was accepted by GPB and online today!
Title:NA Regulations and Functions Decoded by Transcriptome-wide RNA Structure Probing
Authors:M. Piao et al.
Time:12 October 2017
2017
10.4
Publication: Our paper on RNA-RNA interaction database RISE was accepted by NAR and online today!
Title:RISE: a database of RNA interactome from sequencing experiments
Authors:J. Gong, D. Shao et al.
Time:4 October 2017
2016
10.19
Seminar: We invited Dr. Huafeng Xu from UCSF to talk about protein evolution
Title:Protein evolution under a computational microscope
Speaker:Huafeng Xu, PhD
Time:2:00-3:00 pm, Oct. 19th (Wednesday), 2016
Venue:Room 143, New Biology Building, THU
2016
8.13
Seminar: We invited Dr. Michael Snyder from Stanford University to talk about autism spectrum disorders
Title:Building integrative frameworks to study autism spectrum disorders
Speaker:Michael Snyder, PhD
Time:10:30-11:30 pm, Aug. 8th (Thursday), 2016
Venue:Room 143, New Biology Building, THU
2016
5.31
Seminar: We invited Dr. Ido Golding from Baylor College of Medicine to talk about kinetics of gene regulation
Title:Deciphering the stochastic kinetics of gene regulation
Speaker:Ido Golding, PhD
Time:10:00-11:30 am, May. 31st (Tuesday), 2016
Venue:Room 143, New Biology Building, THU
2016
5.9
Seminar: We invited Dr. Luonan Chen from Shanghai Institutes for Biological Sciences to talk about early-signals for critical transition
Title:Detecting early-signals for critical transition during complex biological processes by dynamical network biomarkers
Speaker:Luonan Chen, PhD
Time:10:00-11:30 am, May. 9th (Monday), 2016
Venue:Room B321, Medical Science Building, THU
2016
3.24
Seminar: We invited Dr. Yi Xing from University of Pennsylvania to talk about transcriptome isoform complexity
Title:Elucidate transcriptome isoform complexity using massive RNA-seq data
Speaker:Yi Xing, PhD
Time:10:00-11:00 am, Mar. 24th (Thursday), 2016
Venue:Room 143, New Biology Building, THU
2015
12.25
Seminar: We invited Dr. Wei Wang from UCSD to talk about epigenomics in development
Title:Epigenomics in development
Speaker:Wei Wang, PhD
Time:2:00-3:00 pm, Dec. 25th (Friday), 2015
Venue:Room 143, New Biology Building, THU
2015
11.16
Seminar: We invited Dr. Mark A. Kay from Stanford University to talk about novel nucleic acid vector approaches
Title:Novel nucleic acid vector approaches for delivering genes and non-coding RNAs
Speaker:Mark A. Kay MD, PhD
Time:9:30-10:30am, Nov. 16th (Monday), 2015
Venue:Room 143, New Biology Building, THU
2015
7.15
Seminar: We invited Dr. Yaoqi Zhou from Institute for Glycomics to talk about personalized medicine
Title:迈向个性化医疗：生物信息学和分子生物学的结合
Speaker:周耀旗 博士
Time:10:30-11:30am, July. 15th (Wednesday), 2015
Venue:Room B323, Medical Science Building, THU
2015
5.23
Welcome: Sun Lei joined the lab!
Time:May 23rd, 2015
Position:PhD Student
Field:RNA Structure probing and functional analysis
2015
3.31
Welcome: Xu Kui joined the lab!
Time:Mar. 31st, 2015
Position:PhD Student
Field:Machine learning, 3D image modeling
2015
2.28
Welcome: Wei Wendi joined the lab!
Time:Feb. 28th, 2015
Position:Lab manager
Field:Financial reimbursement, staff reception, …
