百晓学者学者目录

韩仁敏

教授，山东大学

精选作品

期刊论文

2026

Benchmarking deep learning methods for C α atom prediction in cryo-EM density maps

Tian Zhang, Z Liu, Yiqing Ma, Chenjie Feng, Renmin Han

Bioinformatics

DOI

2026

A variational framework with composite sparse regularization for cryo-electron tomography reconstruction

Chenyun Yu, Zihe Xu, Qiong Zeng, Xiaohua Wan, Haythem El-Messiry, Fa Zhang, Renmin Han

Bioinformatics

DOI

2026

Optimized L1-norm smoothing gradient improves electron tomography’s tilt series alignment with both localized and virtual fiducial markers

Xinyan Li, Zihe Xu, Shengkai Guo, Chenjie Feng, Renmin Han

Ultramicroscopy

DOI

2026

vEMRec: High‐Resolution Volume Electron Microscopy Reconstruction Based on Structure‐Preserving and High‐Fidelity 3D Alignment

Zhenbang Zhang, Hongjia Li, Zhongjun Yang, Zhi-Qiang Xu, Duan-Chen Sun, Xin Gao, Fa Zhang, Renmin Han

Advancement of science

DOI

2025

从数据到机制：医数交叉驱动肿瘤精准诊疗的研究现状与展望

孙端辰，韩仁敏，马成林，段贸腾，王斐，刘丙强

《中国科学基金》

DOI

2025

CryoAlign2: efficient global and local Cryo-EM map retrieval based on parallel-accelerated local spatial structural features

Zhe Liu, Bin-Tao He, Tian Zhang, Chen-Jie Feng, Fa Zhang, Zhongjun Yang, Renmin Han

Bioinform.

DOI

2025

Robust projection parameter calibration in cryo-ET with L1-norm optimization.

Sheng-Kai Guo, Zihe Xu, Xinyan Li, Zhidong Yang, Chen-Jie Feng, Renmin Han

Ultramicroscopy

DOI

2025

Adaptive Gaussian representation for differentiable cryo-electron tomography reconstruction.

Chi Zhang, Zhidong Yang, Renmin Han, Fa Zhang, Jie-Qing Feng

Journal of Structural Biology

DOI

2025

TiltRec: an ultra-fast and open-source toolkit for cryo-electron tomographic reconstruction

Yanxin Jiao, Hongjia Li, Yang Xue, Guoliang Yang, Lei Qi, Fa Zhang, Dawei Zang, Renmin Han

Bioinform.

DOI

2024

vEMstitch: an algorithm for fully automatic image stitching of volume electron microscopy

Bin-Tao He, Yan Zhang, Zhenbang Zhang, Yi-Ran Cheng, Fa Zhang, Fei Sun, Renmin Han

GigaScience

DOI

2024

Accurate global and local 3D alignment of cryo-EM density maps using local spatial structural features

Bin-Tao He, Fa Zhang, Chen-Jie Feng, Jian-Yi Yang, Xin Gao, Renmin Han

Nature Communications

DOI

2024

Accurate Prediction of Protein Structural Flexibility by Deep Learning Integrating Intricate Atomic Structures and Cryo-EM Density Information

Xintao Song, Lei Bao, Chen-Jie Feng, Qiang Huang, Fa Zhang, Xin Gao, Renmin Han

Nature Communications

DOI

2024

Markerauto2: A fast and robust fully automatic fiducial marker-based tilt series alignment software for electron tomography.

Zihe Xu, Hongjia Li, Xiao-Hua Wan, Jose-Jesus Fernández, Fei Sun, Fa Zhang, Renmin Han

Structure

DOI

2024

Improved Denoising of Cryo-Electron Microscopy Micrographs with Simulation-Aware Pretraining

Zhidong Yang, Hongjia Li, Dawei Zang, Renmin Han, Fa Zhang

J. Comput. Biol.

DOI

2024

FP-Zernike: An Open-source Structural Database Construction Toolkit for Fast Structure Retrieval

Jun-Hai Qi, Chen-Jie Feng, Yulin Shi, Jian-Yi Yang, Fa Zhang, Guo-Jun Li, Renmin Han

Genomics, Proteomics & Bioinformatics

DOI

2024

UPicker: a semi-supervised particle picking transformer method for cryo-EM micrographs

Chi Zhang, Yi-Ran Cheng, Kaiwen Feng, Fa Zhang, Renmin Han, Jie-Qing Feng

Briefings Bioinform.

DOI

2024

Serial Section Microscopy Image Inpainting Guided by Axial Optical Flow

Yi-Ran Cheng, Bin-Tao He, Fa Zhang, Renmin Han

ACM Multimedia

DOI

2023

CryoAlign: feature-based method for global and local 3D alignment of EM density maps

Bin-Tao He, Fa Zhang, Chen-Jie Feng, Jian-Yi Yang, Xin Gao, Renmin Han

arXiv.org

DOI

2023

Self-supervised noise modeling and sparsity guided electron tomography volumetric image denoising.

Zhidong Yang, Dawei Zang, Hongjia Li, Zhao Zhang, Fa Zhang, Renmin Han

Ultramicroscopy

DOI

2023

MarkerDetector: A method for robust fiducial marker detection in electron micrographs using wavelet-based template.

Gaoxin Hou, Zhidong Yang, Dawei Zang, Jose-Jesus Fernández, Fa Zhang, Renmin Han

Journal of Structural Biology

DOI

2023

SaID: Simulation-Aware Image Denoising Pre-trained Model for Cryo-EM Micrographs

Zhidong Yang, Hongjia Li, Dawei Zang, Renmin Han, Fa Zhang

International Symposium on Bioinformatics Research and Applications

DOI

2023

trRosettaRNA: automated prediction of RNA 3D structure with transformer network

Wen-Kai Wang, Chen-Jie Feng, Renmin Han, Ziyi Wang, Lisha Ye, Zongyang Du, Hong Wei, Fa Zhang, Zhenling Peng, Jian-Yi Yang

Nature Communications

DOI

2022

SimCP-NS: similarity-based copy paste for semi-supervised 3D EM neuron segmentation

Tingting Zhang, Wenjia Meng, Xueshi Yu, Gang Pan, Renmin Han

Bioinformatics

DOI

2022

Neighborhood-aware Geometric Encoding Network for Point Cloud Registration

Lifa Zhu, Hai-Ning Guan, Changwei Lin, Renmin Han

arXiv.org

2022

Protein structure prediction in the deep learning era.

Zhenling Peng, Wen-Kai Wang, Renmin Han, Fa Zhang, Jian-Yi Yang

Current Opinion in Structural Biology

DOI

2022

A hybrid unsupervised approach for accurate short read clustering and barcoded sample demultiplexing in nanopore sequencing

Renmin Han, Jun-Hai Qi, Yang Xue, Xiujuan Sun, Fa Zhang, Xin Gao, Guo-Jun Li

bioRxiv

DOI

2022

Correction of image distortion in large-field ssEM stitching by an unsupervised intermediate-space solving network

Bintao He, Y. Zhang, Fa Zhang, Renmin Han

Bioinform.

DOI

2021

A Hybrid Frequency-Spatial Domain Model for Sparse Image Reconstruction in Scanning Transmission Electron Microscopy

Bintao He, Fa Zhang, Huan-Shui Zhang, Renmin Han

IEEE International Conference on Computer Vision

DOI

2021

Macromolecules Structural Classification with a 3D Dilated Dense Network in Cryo-electron Tomography

Shan Gao, Renmin Han, Xiangrui Zeng, Zhi-Yong Liu, Min Xu, Fa Zhang

IEEE/ACM Transactions on Computational Biology & Bioinformatics

DOI

2021

Self-Supervised Cryo-Electron Tomography Volumetric Image Restoration from Single Noisy Volume with Sparsity Constraint

Zhidong Yang, Fa Zhang, Renmin Han

IEEE International Conference on Computer Vision

DOI

2021

ARBic: an all-round biclustering algorithm for analyzing gene expression data

Xiangyu Liu, Ting Yu, Xiaoyu Zhao, Chao-Yi Long, Renmin Han, Z. Su, Guojun Li

NAR Genomics and Bioinformatics

DOI

2021

Robust and ultrafast fiducial marker correspondence in electron tomography by a two-stage algorithm considering local constraints

Renmin Han, Guojun Li, Xin Gao

Bioinform.

DOI

2021

Structure of the full-length human Pannexin1 channel and insights into its role in pyroptosis

Sensen Zhang, B. Yuan, J. Lam, Jun Zhou, Xuan Zhou, G. Ramos-Mandujano, Xueyuan Tian, Yang Liu, Renmin Han, Yu Li, Xin Gao, Mo Li, Mao-Jun Yang

Cell Discovery

DOI

2021

TransRef enables accurate transcriptome assembly by redefining accurate neo-splicing graphs

Ting Yu, Renmin Han, Z. Fang, Zeng-Chao Mu, Hongyu Zheng, Juntao Liu

Briefings Bioinform.

DOI

2020

Compressed sensing improved iterative reconstruction-reprojection algorithm for electron tomography

Lun Li, Renmin Han, Zhao-Tian Zhang, Tiande Guo, Zhi-Yong Liu, Fa Zhang

BMC Bioinformatics

DOI

2020

Dilated-DenseNet For Macromolecule Classification In Cryo-electron Tomography

Shan Gao, Renmin Han, Xiangrui Zeng, Xuefeng Cui, Zhi-Yong Liu, Min Xu, Fa Zhang

International Symposium on Bioinformatics Research and Applications

DOI

2019

A novel constrained reconstruction model towards high-resolution subtomogram averaging

Renmin Han, Lun Li, Peng Yang, Fa Zhang, Xin Gao

Bioinform.

DOI

2019

Accurate Targeted Sequencing at Anywhere and Realtime

Xin Gao, Mo Li, Sheng Wang, Renmin Han, Samhan M. Alsolami, C. Bi, Dong Luo, Xuan Zhou

2019

A joint method for marker-free alignment of tilt series in electron tomography

Renmin Han, Zhipeng Bao, Xiangrui Zeng, T. Niu, Fa Zhang, Min Xu, Xin Gao

Bioinform.

DOI

2019

PureseqTM: efficient and accurate prediction of transmembrane topology from amino acid sequence only

Qing Wang, Chongming Ni, Zhen Li, Xiu-Feng Li, Renmin Han, Feng Zhao, Jin-Bo Xu, Xin Gao, Sheng Wang

bioRxiv

DOI

2019

PIXER: an automated particle-selection method based on segmentation using a deep neural network

Jingrong Zhang, Zihao Wang, Yu Chen, Renmin Han, Zhi-Yong Liu, Fei Sun, Fa Zhang

BMC Bioinformatics

DOI

2018

An accurate and rapid continuous wavelet dynamic time warping algorithm for end‐to‐end mapping in ultra‐long nanopore sequencing

Renmin Han, Yu Li, Xin Gao, Sheng Wang

Bioinform.

DOI

2018

Searching and mapping genomic subsequences in nanopore raw signals through novel dynamic time warping algorithms

Renmin Han, Sheng Wang, Xin Gao

2018

Novel algorithms for efficient subsequence searching and mapping in nanopore raw signals towards targeted sequencing

Renmin Han, Sheng Wang, Xin Gao

bioRxiv

DOI

2018

Fiducial marker detection via deep learning approach for electron tomography

Yu Hao, Renmin Han, Xiao-Hua Wan, Fa Zhang, Shiwei Sun

IEEE International Conference on Bioinformatics and Biomedicine

DOI

2018

AuTom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction

Renmin Han, Xiao-Hua Wan, Lun Li, A. Lawrence, Peng Yang, Yu Li, Sheng Wang, Fei Sun, Zhi-Yong Liu, Xin Gao, Fa Zhang

Bioinform.

DOI

2017

DeepSimulator: a deep simulator for Nanopore sequencing

Yu Li, Renmin Han, C. Bi, Mo Li, Sheng Wang, Xin Gao

bioRxiv

DOI

2017

A fast fiducial marker tracking model for fully automatic alignment in electron tomography

Renmin Han, Fa Zhang, Xin Gao

Bioinform.

DOI

2017

AuTom: A novel automatic platform for electron tomography reconstruction.

Renmin Han, Xiao-Hua Wan, Zihao Wang, Yu Hao, Jingrong Zhang, Yu Chen, Xin Gao, Zhi-Yong Liu, Fei Ren, Fei Sun, Fa Zhang

Journal of Structural Biology

DOI

2016

Live cell single molecule-guided Bayesian localization super resolution microscopy

Fan Xu, Ming-Shu Zhang, Wenting He, Renmin Han, Fudong Xue, Zhi-Yong Liu, Fa Zhang, J. Lippincott-Schwartz, Ping-Yong Xu

Cell Research

DOI

2015

Drift correction for single-molecule imaging by molecular constraint field, a distance minimum metric

Renmin Han, Liansan Wang, Fan Xu, Yong-Deng Zhang, Ming-Shu Zhang, Zhi-Yong Liu, Fei Ren, Fa Zhang

BMC Biophysics

DOI

2014

A marker-free automatic alignment method based on scale-invariant features.

Renmin Han, Fa Zhang, Xiao-Hua Wan, José-Jesús Fernández, Fei Sun, Zhi-Yong Liu

Journal of Structural Biology

DOI

2013

Iterative Methods in Large Field Electron Microscope Tomography

Xiao-Hua Wan, Sébastien Phan, A. Lawrence, Fa Zhang, Renmin Han, Zhi-Yong Liu, Mark Ellisman

SIAM Journal on Scientific Computing

DOI

A Supervised Multi-task Framework for Joint Cryo-ET Restoration Enabled by Generative Physical Simulation

Xin-Sheng Wang, Zhidong Yang, Xiao-Hua Wan, Renmin Han, Shuai Tang, Hao Dong, Fa Zhang, Bin Hu

会议论文

2021

Noise-Transfer2Clean: Denoising cryo-EM images based on noise modeling and transfer

李鸿佳，Hui Zhang，Xiaohua Wan，Zhidong Yang，Chengmin Li，Jintao Li，Renmin Han，Ping Zhu，Fa Zhang

《第七届全国冷冻电子显微学与结构生物学专题研讨会》

DOI

2015

A novel fully automatic scheme for fiducial marker-based alignment in electron tomography.

Renmin Han, Liansan Wang, Zhi-Yong Liu, Fei Sun, Fa Zhang

Journal of Structural Biology

DOI

2013

A Marker Free Automatic Alignment Method Based on SIFT

Renmin Han, Fa Zhang, Zhiyong Liu

《第一届国际暨第十三次中国生物物理学术大会摘要集——S1冷冻电镜与结构生物学》

预印本

2026

CryoDiff: An uncertainty-aware diffusion model for Cryo-EM map enhancement

Bocheng Wen, Bintao He, Yiran Cheng, Shaozhen Zhou, Fa Zhang, Renmin Han

bioRxiv (Cold Spring Harbor Laboratory)

DOI

2025

Resolving compositional and conformational heterogeneity in cryo-EM with deformable 3D Gaussian representations

Bintao He, Yiran Cheng, Hongjia Li, Xiang Gao, Xin Gao, Fa Zhang, Renmin Han

arXiv preprint

2018

DLBI: Deep learning guided Bayesian inference for structure reconstruction of super-resolution fluorescence microscopy

Yu Li, Fan Xu, Fa Zhang, Pingyong Xu, Mingshu Zhang, Ming Fan, Lihua Li, Xin Gao, Renmin Han

arXiv preprint

DOI

研究方向

生物信息 医学图像处理 高性能计算 机器学习 逆问题求解

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