汪小我｜清华大学｜学者主页

2026

人工智能驱动合成生物学研究

兰晶岗，傅雄飞，汪小我，张先恩

《合成生物学》

2026

Deciphering key factors of active learning performance in biomolecular design

Zhi Yixuan, Qixiu Du, Han Yu, Lei Wei, Xiaowo Wang

Bioinformatics

DOI

2026

Deep learning unlocks sequence-divergent synthetic promoters to empower Streptomyces natural product engineering

Q Zhou, Ye Wang, Jixin Dong, Xiaomin Zhao, Alan J. X. Guo, Xiaowo Wang, Yunzi Luo

Metabolic Engineering

DOI

2025

Foundation models in bioinformatics

Fei Guo, Renchu Guan, Yaohang Li, Qi Liu, Xiaowo Wang, Can Yang, Jianxin Wang

National Science Review

2025

A generic reference defined by consensus peaks for scATAC-seq data analysis

Qiuchen Meng, Xin-Ze Wu, Wenchang Chen, Yu-Bo Zhao, Chen Li, Zheng Wei, Jiaqi Li, Xi Xi, Sijie Chen, Catherine Zhang, Sheng-Quan Chen, Jiaqi Li, Xiaowo Wang, Rui Jiang, Lei Wei, Xuegong Zhang

bioRxiv

DOI

2025

Deconer: An Evaluation Toolkit for Reference-based Deconvolution Methods Using Gene Expression Data

Wei Zhang, Xianglin Zhang, Qiao Liu, Lei Wei, Qiao Xu, Rui Gao, Zhi‐Ping Liu, Xiaowo Wang

Genomics Proteomics & Bioinformatics

DOI

2025

Advancing genetic engineering with active learning: theory, implementations and potential opportunities

Qixiu Du, Haochen Wang, Benben Jiang, Xiaowo Wang

Briefings in Bioinformatics

DOI

2025

De novo design of insulated cis-regulatory elements based on deep learning-predicted fitness landscape

Haochen Wang, Yanhui Xiang, Ziming Liu, Wen Yin, Boyan Li, Long Qian, Xiaowo Wang, Chunbo Lou

Nucleic Acids Research

DOI

2025

esMPRA: an easy-to-use systematic pipeline for MPRA experiment quality control and data analysis

Jiaqi Li, Pengcheng Zhang, Xi Xi, Xiaowo Wang

Bioinformatics

DOI

2025

Simulation-guided pan-cancer analysis identifies a novel regulator of CpG island hypermethylation heterogeneity

Xianglin Zhang, Wei Zhang, Jinyi Zhang, Xiuhong Lyu, Haoran Pan, Tianwei Jia, Ting Wang, Xiaowo Wang, Haiyang Guo

Briefings in Bioinformatics

DOI

2025

Assessment of anemia recovery using peripheral blood smears by deep semi-supervised learning

Qianming Yan, Yingying Zhang, Wei Lei, Xuehui Liu, Xiaowo Wang

Annals of Hematology

DOI

2025

Systematic representation and optimization enable the inverse design of cross-species regulatory sequences in bacteria

Pengcheng Zhang, Qixiu Du, Ye Wang, Lei Wei, Xiaowo Wang

Nature Communications

DOI

2025

Modeling and designing enhancers by introducing and harnessing transcription factor binding units

Jiaqi Li, Pengcheng Zhang, Xi Xi, Liyang Liu, Lei Wei, Xiaowo Wang

Nature Communications

DOI

2024

Artificial intelligence-guided strategies for next-generation biological sequence design

Pengcheng Zhang, Lei Wei, Jiaqi Li, Xiaowo Wang

National Science Review

DOI

2024

Efficient computation by molecular competition networks

Haoxiao Cai, Lei Wei, Xiaoran Zhang, Rong Qiao, Xiaowo Wang

Physical Review Research

DOI

2024

Synthetic promoter design in Escherichia coli based on multinomial diffusion model

Qixiu Du, May Nee Poon, Xiaocheng Zeng, Pengcheng Zhang, Zheng Wei, Haochen Wang, Ye Wang, Lei Wei, Xiaowo Wang

iScience

DOI

2024

Unveil cis-acting combinatorial mRNA motifs by interpreting deep neural network

Xiaocheng Zeng, Wei Zheng, Qixiu Du, Jiaqi Li, Zhen Xie, Xiaowo Wang

Bioinformatics

DOI

2024

GPro: generative AI-empowered toolkit for promoter design

Haochen Wang, Qixiu Du, Ye Wang, Hanwen Xu, Wei Zheng, Xiaowo Wang

Bioinformatics

DOI

2024

DIProT: A deep learning based interactive toolkit for efficient and effective Protein design

Jieling He, Wenxu Wu, Xiaowo Wang

Synthetic and Systems Biotechnology

DOI

2024

Discovering and Overcoming the Bias in Neoantigen Identification by Unified Machine Learning Models

Ziting Zhang, Wenxu Wu, Lei Wei, Xiaowo Wang

Lecture notes in computer science

DOI

2023

Enabling technology and core theory of synthetic biology

Xian-En Zhang, Chenli Liu, Jun-biao Dai, Ying-Jin Yuan, Caixia Gao, Yan Feng, Bian Wu, Ping Wei, Chun You, Xiaowo Wang, Tong Si

Science China Life Sciences

DOI

2023

Building digital life systems for future biology and medicine

Xuegong Zhang, Lei Wei, Rui Jiang, Xiaowo Wang, Jin Gu, Zhen Xie, Hairong Lv

Quantitative Biology

DOI

2023

Deep flanking sequence engineering for efficient promoter design using DeepSEED

Peng-Cheng Zhang, Hao-Chen Wang, Han-Wen Xu, Lei Wei, Liyang Liu, Zhi-Rui Hu, Xiaowo Wang

Nature Communications

DOI

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

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

Highly Regional Genes: graph-based gene selection for single cell RNA-seq data.

Yanhong Wu, Qi-Fan Hu, Shicheng Wang, Changyi Liu, Yiran Shan, Wenbo Guo, Rui Jiang, Xiaowo Wang, Jin Gu

Journal of genetics and genomics = Yi chuan xue bao

DOI

2022

DeSP: a systematic DNA storage error simulation pipeline

Le-Kang Yuan, Zhen Xie, Ye Wang, Xiaowo Wang

BMC Bioinformatics

DOI

2022

YTHDF3 modulates hematopoietic stem cells by recognizing RNA m6A modification on Ccnd1

Xiaofei Zhang, Ting-Ting Cong, Lei Wei, Bixi Zhong, Xiaowo Wang, J. Sun, Shu-Xia Wang, M. Xu, P. Zhu, Hong Jiang, Jianwei Wang

Haematologica

DOI

2022

Evaluating methylation of human ribosomal DNA at each CpG site reveals its utility for cancer detection using cell-free DNA

Xiang-Lin Zhang, Xiao-Dong Jia, Bixi Zhong, Lei Wei, Jia-Qi Li, Wei Zhang, Huan Fang, Yanda Li, Yinying Lu, Xiaowo Wang

Briefings Bioinform.

DOI

2022

Correction to: DeSP: a systematic DNA storage error simulation pipeline

Le-Kang Yuan, Zhen Xie, Ye Wang, Xiaowo Wang

BMC Bioinformatics

DOI

2022

MeConcord: a new metric to quantitatively characterize DNA methylation heterogeneity across reads and CpG sites

Xiang-Lin Zhang, Xiaowo Wang

Bioinform.

DOI

2022

In silico and in vitro protocols for quantifying gene expression noise modulated by microRNAs

Lei Wei, Shuailin Li, Xiaowo Wang

STAR Protocols

DOI

2022

Prognostic Value of Survival-Associated Splicing Factor SNRPA1 Overexpression and its Potential Mechanism in Liver Cancer

Mengying Liu, Yueda Lu, Lei Wei, Xiaowo Wang, Yinying Lu, Xiaodong Jia, Shihui Wang, Wenlin An

Journal of Cancer Science and Clinical Therapeutics

DOI

2021

基于细胞—计算机交互的细胞控制方法

颜钱明，张鹏程，乔榕，古槿，汪小我

《自动化学报》

DOI

2021

生物分子序列的人工智能设计

王也，王昊晨，晏明皓，胡冠华，汪小我

《合成生物学》

2021

Single-cell Transcriptomes Reveal Characteristics of MicroRNAs in Gene Expression Noise Reduction

Tao Hu, Lei Wei, Shuailin Li, Tianrun Cheng, Xue-Gong Zhang, Xiaowo Wang

Genomics, Proteomics & Bioinformatics

DOI

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, Xianglin Zhang, Jin Gu, Xuegong Zhang, Lei Wei, Xiaowo Wang

Briefings in Bioinformatics

DOI

2021

Design of biomolecular sequences by artificial intelligence

Ye Wang, Hao-Chen Wang, Ming-hui Yan, Guan-Hua Hu, Xiaowo Wang

DOI

2021

Characterizing microRNA-mediated modulation of gene expression noise and its effect on synthetic gene circuits.

Lei Wei, Shuailin Li, Peng-Cheng Zhang, Tao Hu, Michael Q. Zhang, Zhen Xie, Xiaowo Wang

Cell Reports

DOI

2021

OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions

Shengquan Chen, Qiao Liu, Xuejian Cui, Zhanying Feng, Chunquan Li, Xiaowo Wang, Xue-Gong Zhang, Yong Wang, Rui Jiang

Nucleic Acids Res.

DOI

2021

DISMIR: Deep learning-based noninvasive cancer detection by integrating DNA sequence and methylation information of individual cell-free DNA reads

Jia-Qi Li, Lei Wei, Xiang-Lin Zhang, Wei Zhang, Hao-Chen Wang, Bixi Zhong, Zhen Xie, Hairong Lv, Xiaowo Wang

Briefings Bioinform.

DOI

2021

hECA: The cell-centric assembly of a cell atlas

Sijie Chen, Yanting Luo, Haoxiang Gao, Fan-Hong Li, Jiaqi Li, Yi-Xin Chen, Renke You, Minsheng Hao, Haiyang Bian, Xi Xi, Wenrui Li, Wei-Yuan Li, M. Ye, Qiuchen Meng, Ziheng Zou, Chen Li, Haochen Li, Yang-Yuan Zhang, Yan-Fei Cui, Lei Wei, Fufeng Chen, Xiaowo Wang, Hairong Lv, Kui Hua, Rui Jiang, Xue-Gong Zhang

bioRxiv

DOI

2021

CellTracker: an automated toolbox for single-cell segmentation and tracking of time-lapse microscopy images

Tao Hu, Shixiong Xu, Lei Wei, Xue-Gong Zhang, Xiaowo Wang

Bioinform.

DOI

2021

PccGEO: prior constraints conditioned genetic elements optimization

Hanwen Xu, Peng-Cheng Zhang, Hao-Chen Wang, Lei Wei, Zhirui Hu, Xiaowo Wang

bioRxiv

DOI

2021

cfDNApipe: a comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data

Wei Zhang, Lei Wei, Jiaqi Huang, Bixi Zhong, Jia-Qi Li, Hanwen Xu, Shuying He, Yu Liu, Ju-Hong Liu, Hairong Lv, Xiaowo Wang

Bioinform.

DOI

2021

Deep Hashing Based Model for Image Similarity Retrieval in DNA Storage

Haoxiao Cai, Ye Wang, Xiaowo Wang

ACM Cloud and Autonomic Computing Conference

DOI

2021

The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence

Xiang-Lin Zhang, Xue-Hui Liu, Zhenhai Du, Lei Wei, Huan Fang, Qiongye Dong, Jing Niu, Yanda Li, Juntao Gao, Michael Q. Zhang, Wei Xie, Xiaowo Wang

Genome Research

DOI

2020

Dynamic transcriptome profiling in DNA damage-induced cellular senescence and transient cell-cycle arrest.

Zhen Zhao, Qiongye Dong, Xue-Hui Liu, Lei Wei, Liyang Liu, Yanda Li, Xiaowo Wang

Genomics

DOI

2020

CRISPR-ERA: A Webserver for Guide RNA Design of Gene Editing and Regulation.

Honglei Liu, Xiaowo Wang

Methods in molecular biology

DOI

2020

Systematic genome-wide querying of coding and non-coding functional elements in E. coli using CRISPRi

Harneet S. Rishi, Esteban Toro, Honglei Liu, Xiaowo Wang, L. Qi, A. Arkin

bioRxiv

DOI

2020

Biochemical constraint compatible address design for fuzzy retrieval of images in DNA Storage

Ye Wang, Shi-Wei Liu, Xiaowo Wang

ACM Cloud and Autonomic Computing Conference

DOI

2020

Aging-induced IL27Ra Signaling Impairs Hematopoietic Stem Cells.

Hanqing He, Panglian Xu, Xiaofei Zhang, Min Liao, Qiongye Dong, Ting-Ting Cong, Baixue Tang, Xiuxiu Yang, Maoqing Ye, Yingjun Chang, Weihua Liu, Xiaowo Wang, Z. Ju, Jianwei Wang

Blood

DOI

2020

Synthetic promoter design in Escherichia coli based on a deep generative network

Ye Wang, Hao-Chen Wang, Lei Wei, Shuailin Li, Liyang Liu, Xiaowo Wang

Nucleic Acids Research

DOI

2019

血浆游离DNA全基因组甲基化测序的实用稳定性评估

方欢，钟碧溪，魏磊，张祥林，张威，汪小我

《生物工程学报》

DOI

2019

Regulation by competition: a hidden layer of gene regulatory network

Lei Wei, Ye Yuan, Tao Hu, Shuailin Li, Tianrun Cheng, Jinzhi Lei, Zhen Xie, Michael Q. Zhang, Xiaowo Wang

Quantitative Biology

DOI

2019

A large-scale CRISPR screen and identification of essential genes in cellular senescence bypass

Xue-Hui Liu, Lei Wei, Qiongye Dong, Liyang Liu, Michael Q. Zhang, Zhen Xie, Xiaowo Wang

Aging

DOI

2019

Long noncoding RNA GSTM3TV2 upregulates LAT2 and OLR1 by competitively sponging let-7 to promote gemcitabine resistance in pancreatic cancer

G. Xiong, Chang Liu, Gang Yang, Meng-Yu Feng, Jian-Wei Xu, Fang-Yu Zhao, L. You, Li Zhou, Lian-Fang Zheng, Ya Hu, Xiaowo Wang, Tai-Ping Zhang, Yu-Pei Zhao

Journal of Hematology & Oncology

DOI

2019

Ribosomal DNA methylation as stable biomarkers for detection of cancer in plasma

Xiang-Lin Zhang, Huan Fang, Wei Zhang, Bixi Zhong, Yanda Li, Xiaowo Wang

bioRxiv

DOI

2018

三维基因组数据分析方法进展

张祥林，方欢，汪小我

《生物化学与生物物理进展》

2018

通过合成基因线路实现细胞分类

胡冠华，王也，魏磊，汪小我

《生命科学》

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

Calorie restriction is the most reasonable anti-ageing intervention: a meta-analysis of survival curves

Yaru Liang, Chang Liu, Maoyang Lu, Qiongye Dong, Zi-Mu Wang, Zhuo-Ran Wang, Wenxiang Xiong, Nan-Nan Zhang, Jiawei Zhou, Qingfei Liu, Xiaowo Wang, Zhao Wang

Scientific Reports

DOI

2018

Regulatory RNA binding proteins contribute to the transcriptome-wide splicing alterations in human cellular senescence

Qiongye Dong, Lei Wei, Michael Q. Zhang, Xiaowo Wang

Aging

DOI

2018

SIP: An Interchangeable Pipeline for scRNA-seq Data Processing

Sijie Chen, Zheng Wei, Yang Chen, Kui Hua, Wei Zhang, Changyi Liu, Haoxiang Gao, Hao Sun, Zhenyi Wang, Qi-Jin Yin, Shengquan Chen, Shaoming Song, Chen Feng, Hai-Rong Lu, Rui Jiang, Xiaowo Wang, Jin Gu, Xue-Gong Zhang

bioRxiv

DOI

2018

esATAC: an easy-to-use systematic pipeline for ATAC-seq data analysis

Zheng Wei, Wei Zhang, Huan Fang, Yanda Li, Xiaowo Wang

Bioinform.

DOI

2017

合成基因线路规模化设计面临的挑战

魏磊，袁野，汪小我

《生物工程学报》

2017

HCSGD: An integrated database of human cellular senescence genes.

Qiongye Dong, Hongqing Han, Xue-Hui Liu, Lei Wei, Wei Zhang, Zhen Zhao, Michael Q. Zhang, Xiaowo Wang

Journal of genetics and genomics = Yi chuan xue bao

DOI

2017

[Challenges in large-scale synthetic gene circuits design].

Lei Wei, Ye Yuan, Xiaowo Wang

Sheng wu gong cheng xue bao = Chinese journal of biotechnology

DOI

2017

Regulation by competing: A hidden layer of gene regulatory networks

Xiaowo Wang

CASE

DOI

2017

DEsingle for detecting three types of differential expression in single-cell RNA-seq data

Zhun Miao, Ke Deng, Xiaowo Wang, Xue-Gong Zhang

bioRxiv

DOI

2017

Allelic reprogramming of 3D chromatin architecture during early mammalian development

Zhenhai Du, Hui Zheng, Bo Huang, Rui Ma, Jing-Yi Wu, Xiang-Lin Zhang, Jing He, Yunlong Xiang, Qiu-Jun Wang, Yuan-Yuan Li, Jing Ma, Xu Zhang, Ke Zhang, Yang Wang, Michael Q. Zhang, Juntao Gao, Jesse R. Dixon, Xiaowo Wang, Jianyang Zeng, Wei Xie

Nature

DOI

2017

Using CRISPR-ERA Webserver for sgRNA Design.

Honglei Liu, Xiaowo Wang, L. Qi

Bio-protocol

DOI

2016

A quantitative understanding of microRNA-mediated competing endogenous RNA regulation

Ye Yuan, Xinying Ren, Zhen Xie, Xiaowo Wang

Quantitative Biology

DOI

2016

Advances in computational ChIA-PET data analysis

Chao He, Guipeng Li, Diekidel M. Nadhir, Yang Chen, Xiaowo Wang, Michael Q. Zhang

Quantitative Biology

DOI

2016

From big biological data to big discovery: The past decade and the future

Xue-Gong Zhang, Rui Jiang, Xiaowo Wang, Jin Gu, Ting Chen

DOI

2016

Plasma microRNA panels to diagnose pancreatic cancer: Results from a multicenter study

Zhe Cao, Chang Liu, Jian-Wei Xu, L. You, Chun-You Wang, W. Lou, Bei Sun, Y. Miao, Xubao Liu, Xiaowo Wang, Tai-Ping Zhang, Yu-Pei Zhao

OncoTarget

DOI

2016

生物大データから知識発見までの10年間の展望と将来展望【JST・京大機械翻訳】

Xue-Gong Zhang, Rui Jiang, Xiaowo Wang, Jin Gu, Ting Chen

2015

抗衰老药物对线虫生存曲线影响的荟萃分析

梁亚茹，刘畅，王卓然，董琼叶，汪小我，王钊

《中国科学:生命科学》

2015

MICC: an R package for identifying chromatin interactions from ChIA-PET data

Chao He, Michael Q. Zhang, Xiaowo Wang

Bioinform.

DOI

2015

CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation

Honglei Liu, Zheng Wei, Antonia A. Dominguez, Yanda Li, Xiaowo Wang, L. Qi

Bioinform.

DOI

2015

Model-guided quantitative analysis of microRNA-mediated regulation on competing endogenous RNAs using a synthetic gene circuit

Ye Yuan, Bing Liu, Peng Xie, Michael Q. Zhang, Yanda Li, Zhen Xie, Xiaowo Wang

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

DOI

2015

Meta-analytic Insights into the Effects of Different Anti-aging Drugs on Survival Curves of Caenorhabditis elegans

Yaru Liang, Chang Liu, Zhuo-Ran Wang, Qiongye Dong, Xiaowo Wang, Zhao Wang

DOI

2014

OP-Synthetic: identification of optimal genetic manipulations for the overproduction of native and non-native metabolites

Honglei Liu, Yanda Li, Xiaowo Wang

Quantitative Biology

DOI

2014

MIROR: a method for cell-type specific microRNA occupancy rate prediction.

Peng Xie, Yu Liu, Yanda Li, Michael Q. Zhang, Xiaowo Wang

Molecular Biosystems

DOI

2014

Nucleosome eviction and multiple co-factor binding predict estrogen-receptor-alpha-associated long-range interactions

Chao He, Xiaowo Wang, Michael Q. Zhang

Nucleic Acids Research

DOI

2013

Basics for Bioinformatics

Xue-Gong Zhang, Xue-Ya Zhou, Xiaowo Wang

DOI

2013

Sequence signatures of genes with accompanying antisense transcripts in Saccharomyces cerevisiae

Yingxue Li, Xue-Ning Liu, Xiaowo Wang, Xue-Gong Zhang

Science China Life Sciences

DOI

2013

CRISPR interference (CRISPRi) for sequence-specific control of gene expression

Matthew H. Larson, Luke A. Gilbert, Xiaowo Wang, W. Lim, J. Weissman, L. Qi

Nature Protocols

DOI

2012

ATRX-mediated chromatin association of histone variant macroH2A1 regulates α-globin expression.

K. Ratnakumar, Luis F. Duarte, G. Leroy, D. Hasson, Daniel Smeets, C. Vardabasso, Clemens Bönisch, Tianying Zeng, B. Xiang, David Y. Zhang, Hai-Tao Li, Xiaowo Wang, S. B. Hake, L. Schermelleh, B. Garcia, E. Bernstein

Genes & Development

DOI

2012

The atypical E2F family member E2F7 couples the p53 and RB pathways during cellular senescence.

O. Aksoy, A. Chicas, Tianying Zeng, Zhen Zhao, M. McCurrach, Xiaowo Wang, S. Lowe

Genes & Development

DOI

2012

Chromatin state and microRNA determine different gene expression dynamics responsive to TNF stimulation

Rui-Juan Li, Weilong Guo, Jin Gu, Michael Q. Zhang, Xiaowo Wang

Genomics

DOI

2012

H3K4 demethylation by Jarid1a and Jarid1b contributes to retinoblastoma-mediated gene silencing during cellular senescence

A. Chicas, A. Kapoor, Xiaowo Wang, O. Aksoy, Adam G. Evertts, Michael Q. Zhang, B. Garcia, E. Bernstein, S. Lowe

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

DOI

2011

Control of the senescence-associated secretory phenotype by NF-κB promotes senescence and enhances chemosensitivity.

Y. Chien, C. Scuoppo, Xiaowo Wang, Xue-Ping Fang, B. Balgley, Jessica E. Bolden, P. Premsrirut, Weijun Luo, A. Chicas, C. S. Lee, S. Kogan, S. Lowe

Genes & Development

DOI

2011

Observations on novel splice junctions from RNA sequencing data.

Likun Wang, Xiaowo Wang, Xi Wang, Yanchun Liang, Xue-Gong Zhang

Biochemical and Biophysical Research Communications - BBRC

DOI

2011

EpiRegNet: Constructing epigenetic regulatory network from high throughput gene expression data for humans

L. Wang, Pan-Wen Wang, Mu-Lin-Jun Li, J. Qin, Xiaowo Wang, Michael Q. Zhang, Jun-Wen Wang

Epigenetics

DOI

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

Identification and characterization of human snoRNA core promoters.

Tingting Li, Xue-Ya Zhou, Xiaowo Wang, Dahai Zhu, Yong Zhang

Genomics

DOI

2010

Dissecting the unique role of the retinoblastoma tumor suppressor during cellular senescence

A. Chicas, Xiaowo Wang, Chao-Lin Zhang, M. McCurrach, Zhen Zhao, Ozlem Mert, R. Dickins, Masashi Narita, Michael Ruogu Zhang, S. Lowe

Cancer Cell

DOI

2010

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

Likun Wang, Zhixing Feng, Xi Wang, Xiaowo Wang, Xue-Gong Zhang

Bioinform.

DOI

2009

High-resolution human core-promoter prediction with CoreBoost_HM.

Xiaowo Wang, Z. Xuan, Xiao-Yue Zhao, Yanda Li, Michael Q. Zhang

Genome Research

DOI

2009

CoreBoost_HMhuman core-promoter prediction with

Xiaowo Wang, Z. Xuan, Xiao-Yue Zhao

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

microRNA相关问题的计算分析

汪小我

《清华大学》

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》

2008

Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse

Tao Peng, Chenghai Xue, Jian-Ning Bi, Tingting Li, Xiaowo Wang, Xue-Gong Zhang, Yanda Li

BMC Genomics

DOI

2008

Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species

Xiaowo Wang, Jin Gu, Michael Q. Zhang, Yanda Li

Bioinform.

DOI

2008

Complicated evolutionary patterns of microRNAs in vertebrates

Xiaowo Wang, Xue-Gong Zhang, Yan-Da Li

Science in China Series C: Life Sciences

DOI

2006

Primary transcripts and expressions of mammal intergenic microRNAs detected by mapping ESTs to their flanking sequences

Jin Gu, T. He, Yunfei Pei, Fei Li, Xiaowo Wang, Jing Zhang, Xue-Gong Zhang, Yanda Li

Mammalian Genome

DOI

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

精选作品

期刊论文

人工智能驱动合成生物学研究

Deciphering key factors of active learning performance in biomolecular design

Deep learning unlocks sequence-divergent synthetic promoters to empower Streptomyces natural product engineering

Foundation models in bioinformatics

A generic reference defined by consensus peaks for scATAC-seq data analysis

Deconer: An Evaluation Toolkit for Reference-based Deconvolution Methods Using Gene Expression Data

Advancing genetic engineering with active learning: theory, implementations and potential opportunities

De novo design of insulated cis-regulatory elements based on deep learning-predicted fitness landscape

esMPRA: an easy-to-use systematic pipeline for MPRA experiment quality control and data analysis

Simulation-guided pan-cancer analysis identifies a novel regulator of CpG island hypermethylation heterogeneity

Assessment of anemia recovery using peripheral blood smears by deep semi-supervised learning

Systematic representation and optimization enable the inverse design of cross-species regulatory sequences in bacteria

Modeling and designing enhancers by introducing and harnessing transcription factor binding units

Artificial intelligence-guided strategies for next-generation biological sequence design

Efficient computation by molecular competition networks

Synthetic promoter design in Escherichia coli based on multinomial diffusion model

Unveil cis-acting combinatorial mRNA motifs by interpreting deep neural network

GPro: generative AI-empowered toolkit for promoter design

DIProT: A deep learning based interactive toolkit for efficient and effective Protein design

Discovering and Overcoming the Bias in Neoantigen Identification by Unified Machine Learning Models

Enabling technology and core theory of synthetic biology

Building digital life systems for future biology and medicine

Deep flanking sequence engineering for efficient promoter design using DeepSEED

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

数基生命系统——用控制和系统的观点对生命的数字化建模

Highly Regional Genes: graph-based gene selection for single cell RNA-seq data.

DeSP: a systematic DNA storage error simulation pipeline

YTHDF3 modulates hematopoietic stem cells by recognizing RNA m6A modification on Ccnd1

Evaluating methylation of human ribosomal DNA at each CpG site reveals its utility for cancer detection using cell-free DNA

Correction to: DeSP: a systematic DNA storage error simulation pipeline

MeConcord: a new metric to quantitatively characterize DNA methylation heterogeneity across reads and CpG sites

In silico and in vitro protocols for quantifying gene expression noise modulated by microRNAs

Prognostic Value of Survival-Associated Splicing Factor SNRPA1 Overexpression and its Potential Mechanism in Liver Cancer

基于细胞—计算机交互的细胞控制方法

生物分子序列的人工智能设计

Single-cell Transcriptomes Reveal Characteristics of MicroRNAs in Gene Expression Noise Reduction

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

Design of biomolecular sequences by artificial intelligence

Characterizing microRNA-mediated modulation of gene expression noise and its effect on synthetic gene circuits.

OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions

DISMIR: Deep learning-based noninvasive cancer detection by integrating DNA sequence and methylation information of individual cell-free DNA reads

hECA: The cell-centric assembly of a cell atlas

CellTracker: an automated toolbox for single-cell segmentation and tracking of time-lapse microscopy images

PccGEO: prior constraints conditioned genetic elements optimization

cfDNApipe: a comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data

Deep Hashing Based Model for Image Similarity Retrieval in DNA Storage

The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence

Dynamic transcriptome profiling in DNA damage-induced cellular senescence and transient cell-cycle arrest.

CRISPR-ERA: A Webserver for Guide RNA Design of Gene Editing and Regulation.

Systematic genome-wide querying of coding and non-coding functional elements in E. coli using CRISPRi

Biochemical constraint compatible address design for fuzzy retrieval of images in DNA Storage

Aging-induced IL27Ra Signaling Impairs Hematopoietic Stem Cells.

Synthetic promoter design in Escherichia coli based on a deep generative network

血浆游离DNA全基因组甲基化测序的实用稳定性评估

Regulation by competition: a hidden layer of gene regulatory network

A large-scale CRISPR screen and identification of essential genes in cellular senescence bypass

Long noncoding RNA GSTM3TV2 upregulates LAT2 and OLR1 by competitively sponging let-7 to promote gemcitabine resistance in pancreatic cancer

Ribosomal DNA methylation as stable biomarkers for detection of cancer in plasma

三维基因组数据分析方法进展

通过合成基因线路实现细胞分类

人类智能的基因调控机理

Calorie restriction is the most reasonable anti-ageing intervention: a meta-analysis of survival curves

Regulatory RNA binding proteins contribute to the transcriptome-wide splicing alterations in human cellular senescence

SIP: An Interchangeable Pipeline for scRNA-seq Data Processing

esATAC: an easy-to-use systematic pipeline for ATAC-seq data analysis

合成基因线路规模化设计面临的挑战

HCSGD: An integrated database of human cellular senescence genes.

[Challenges in large-scale synthetic gene circuits design].

Regulation by competing: A hidden layer of gene regulatory networks

DEsingle for detecting three types of differential expression in single-cell RNA-seq data

Allelic reprogramming of 3D chromatin architecture during early mammalian development

Using CRISPR-ERA Webserver for sgRNA Design.

A quantitative understanding of microRNA-mediated competing endogenous RNA regulation

Advances in computational ChIA-PET data analysis

From big biological data to big discovery: The past decade and the future

Plasma microRNA panels to diagnose pancreatic cancer: Results from a multicenter study

生物大データから知識発見までの10年間の展望と将来展望【JST・京大機械翻訳】

抗衰老药物对线虫生存曲线影响的荟萃分析