贾鹏｜东北大学｜学者主页

2026

基于强化学习和数字孪生的地基望远镜智能观测研究（特邀）

左勇勇，贾鹏，白泽宇，程杰，程茇峰

《激光与光电子学进展》

2026

MEIsensor: a deep-learning method for mobile element insertion discovery

Yudong Wang, Peng-Yu Zhang, Shijie Wan, Ze-Xin Zhang, Peisen Sun, Tun Xu, Peng Jia, Kai Ye, Xiao-Fei Yang

bioRxiv

DOI

2026

Variant Calling in the Dark Genome: Benchmarking SNV Calls in the Flanks of Structural Variants.

Ningxin Dang, Peng Jia, Jia-Dong Lin, Yu-Tong Xie, Yongyong Kang, Zixuan Li, Kai Ye, Stephen J. Bush

Genomics, Proteomics & Bioinformatics

DOI

2026

Highly accurate ab initio gene annotation with ANNEVO.

Peng-Yu Zhang, Tun Xu, Songbo Wang, Xiao-Fei Yang, Peisen Sun, Peng Jia, Jia-Dong Lin, Bo Wang, Yi-Zhen Zhang, De-Yu Meng, Stephen J. Bush, Ze-Min Ning, Kai Ye

Nature Methods

DOI

2025

Deciphering Complex Interactions Between LTR Retrotransposons and Three Papaver Species Using LTR_Stream

Tun Xu, S. Bush, Yizhuo Che, Huanhuan Zhao, Tingjie Wang, Peng Jia, Songbo Wang, Peisen Sun, Peng-Yu Zhang, Shenghan Gao, Yu Xu, Cheng-Yao Wang, Ningxin Dang, Yong E. Zhang, Xiao-Fei Yang, Kai Ye

bioRxiv

DOI

2025

Long and Accurate: How HiFi Sequencing is Transforming Genomics

Bo Wang, Peng Jia, Shenghan Gao, Huanhuan Zhao, Gaoyang Zheng, Linfeng Xu, Kai Ye

Genomics, Proteomics & Bioinformatics

DOI

2025

STMiner: Gene-centric spatial transcriptomics for deciphering tumor tissues

Peisen Sun, Stephen J. Bush, Songbo Wang, Peng Jia, Mingxuan Li, Tun Xu, Peng-Yu Zhang, Xiao-Fei Yang, Cheng-Yao Wang, Linfeng Xu, Tingjie Wang, Kai Ye

Cell Genomics

DOI

2025

A Telomere-to-telomere Diploid Reference Genome and Centromere Structure of the Chinese Quartet

Bo Wang, Peng Jia, S. Bush, Xia Wang, Yi Yang, Yu Zhang, Shijie Wan, Xiao-Fei Yang, Peng-Yu Zhang, Yuan-Ting Zheng, Le-Ming Shi, Lian-Hua Dong, Kai Ye

bioRxiv

DOI

2024

A Study on the Decoupling Effect Between Economic Development Level and Carbon Dioxide Emissions: An Empirical Analysis Based on Mineral Resource-Based Cities in Southwest China

Runjia Yang, Xinyue Fan, Jia Peng, Jiaqi Cao, Liang Li, Tingting Feng

Sustainability，Vol. 16, No. 22

DOI

2024

De novo and somatic structural variant discovery with SVision-pro

Songbo Wang, Jia-Dong Lin, Peng Jia, Tun Xu, Xiujuan Li, Yuezhuangnan Liu, Dan Xu, Stephen J. Bush, De-Yu Meng, Kai Ye

Nature Biotechnology

DOI

2023

The Impact of the Green Economy on Carbon Emission Intensity: Comparisons, Challenges, and Mitigating Strategies

Jia Peng, Xianli Hu, Xinyue Fan, Kai Wang, Hao Gong

Sustainability，Vol. 15, No. 14

DOI

2023

基于深度学习模型的船舶碳排放时空预测研究

栾建霖，冯胤伟，李海江，王新建，贾鹏，匡海波

《科研管理》，Vol. 44, No. 3

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2023

一体化运营模式下中国区域港群效率研究

贾鹏，马奇飞，邬桐，陆圣斓，匡海波

《科研管理》，Vol. 44, No. 4

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2023

MSIsensor-RNA: Microsatellite Instability Detection for Bulk and Single-cell Gene Expression Data

Peng Jia, Xuan-Hao Yang, Xiao-Fei Yang, Tingjie Wang, Yu Xu, Kai Ye

bioRxiv

DOI

2023

Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance

Luyao Ren, X. Duan, Lian-Hua Dong, Rui Zhang, Jingcheng Yang, Yuechen Gao, R. Peng, Wanwan Hou, Yaqing Liu, Jing-Jing Li, Ying Yu, Nai-Xin Zhang, J. Shang, Fan Liang, De-Peng Wang, Hui Chen, Lele Sun, Ling-Tong Hao, Andreas Scherer, J. Nordlund, Wenming Xiao, Joshua Xu, W. Tong, Xin Hu, Peng Jia, Kai Ye, Jin-Ming Li, Li Jin, H. Hong, Jing Wang, Shao-Hua Fan, Xiang Fang, Yuan-Ting Zheng, Le-Ming Shi

Genome Biology

DOI

2023

Comparison and benchmark of structural variants detected from long read and long-read assembly

Jia-Dong Lin, Peng Jia, Songbo Wang, W. Kosters, Kai Ye

Briefings Bioinform.

DOI

2023

Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet

Peng Jia, Lian-Hua Dong, Xiao-Fei Yang, Bo Wang, Stephen J. Bush, Tingjie Wang, Jia-Dong Lin, Songbo Wang, Xi-Xi Zhao, Tun Xu, Yizhuo Che, Ningxin Dang, Luyao Ren, Yu-Jing Zhang, Xia Wang, Fan Liang, Yang Wang, Jue Ruan, Han Xia, Yuan-Ting Zheng, Le-Ming Shi, Yi-Jing Lv, Jing Wang, Kai Ye

Genome Biology

DOI

2023

Pindel-TD: A Tandem Duplication Detector Based on A Pattern Growth Approach

Xiao-Fei Yang, Gaoyang Zheng, Peng Jia, Songbo Wang, Kai Ye

bioRxiv

DOI

2022

新型需求响应公交发车时刻和票价优化

贺韵竹，贾鹏，李海江，曹羽歌

《系统工程理论与实践》，Vol. 42, No. 4

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2022

考虑CO

薛凯丽，贾鹏，匡海波

《运筹与管理》，Vol. 31, No. 7

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2022

D2 Plot, a Matrix of DNA Density and Distance to Periphery, Reveals Functional Genome Regions

Yizhuo Che, Xiao-Fei Yang, Peng Jia, Tingjie Wang, Dan Xu, Tianxu Guo, Kai Ye

Advancement of science

DOI

2022

SVision: A deep learning approach to resolve complex structural variants

Jia-Dong Lin, Songbo Wang, P. Audano, Deyu Meng, Jacob I. Flores, W. Kosters, Xiao-Fei Yang, Peng Jia, T. Marschall, C. Beck, Kai Ye

Nature Methods

DOI

2022

Comparison and benchmark of long-read based structural variant detection strategies

Jia-Dong Lin, Peng Jia, Songbo Wang, Kai Ye

bioRxiv

DOI

2022

Haplotype-resolved Chinese male genome assembly based on high-fidelity sequencing

Xiao-Fei Yang, Xi-Xi Zhao, Shoufang Qu, Peng Jia, Bo Wang, Sheng-Han Gao, Tun Xu, Wen-Xin Zhang, Jie Huang, Kai Ye

Fundamental Research

DOI

2022

High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads

Bo Wang, Xiaofei Yang, Yanyan Jia, Yu Xu, Peng Jia, Ningxin Dang, Songbo Wang, Tun Xu, Xixi Zhao, Shenghan Gao, Quanbin Dong, Kai Ye

Genomics,Proteomics & Bioinformatics

2021

Analysis of vehicle skidding potential on horizontal curves

Jia Peng, L. Chu, Tangjie Wang, T. F. Fwa

Accident Analysis And Prevention，Vol. 152

DOI

2021

Three chromosome-scale Papaver genomes reveal punctuated patchwork evolution of the morphinan and noscapine biosynthesis pathway

Xiao-Fei Yang, Sheng-Han Gao, Li Guo, Bo Wang, Yanyan Jia, Jian Zhou, Yizhuo Che, Peng Jia, Jia-Dong Lin, Tun Xu, Jian-Yong Sun, Kai Ye

Nature Communications

DOI

2021

Long read sequencing reveals sequential complex rearrangements driven by 1 Hepatitis B virus integration 2 3

Songbo Wang, Jia-Dong Lin, Xiao-Fei Yang, Zi-Hang Li, Tun Xu, Peng Jia, Tingjie, Wang, Bo Wang, Liang-Shuo Hu, Kai Ye

2020

中国省域综合交通运输效率及空间关联性研究

贾鹏，胡燕，袁爽，匡海波

《科研管理》，Vol. 41, No. 9

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2020

Transportation, germs, culture: a dynamic graph model of COVID-19 outbreak

Xiao-Fei Yang, Tun Xu, Peng Jia, Han Xia, Li Guo, Lei Zhang, Kai Ye

Quant. Biol.

DOI

2020

MSIsensor-pro: Fast, Accurate, and Matched-normal-sample-free Detection of Microsatellite Instability

Peng Jia, Xiaofei Yang, Li Guo, Bowen Liu, Jiadong Lin, Hao Liang, Jianyong Sun, Chengsheng Zhang, Kai Ye

Genomics,Proteomics & Bioinformatics

2019

全国空港客货运格局的时空演化及驱动机制研究

贾鹏，胡燕，匡海波

《系统工程理论与实践》，No. 5

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2019

MEpurity: estimating tumor purity using DNA methylation data

Bowen Liu, Xiao-Fei Yang, Tingjie Wang, Jia-Dong Lin, Yongyong Kang, Peng Jia, Kai Ye

Bioinform.

DOI

2018

基于生态位选择的港口企业价值链分工策略

韩兵，张鹏飞，匡海波，贾鹏

《系统工程理论与实践》，Vol. 38, No. 4

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2018

基于BSC的物流服务供应链绩效指标可拓优度评价

贾鹏，董洁

《统计与决策》，No. 3

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2017

基于港城分离的中国港口供给侧改革研究

匡海波，邓顺江，贾鹏，刘天寿，汤霞

《科研管理》，Vol. 38, No. 4

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2013

基于陆域和空域运输系统的空港可达性评价方法研究

贾鹏，刘瑞菊，杨忠振

《经济地理》，Vol. 33, No. 6

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贾鹏

精选作品

期刊论文

基于强化学习和数字孪生的地基望远镜智能观测研究（特邀）

MEIsensor: a deep-learning method for mobile element insertion discovery

Variant Calling in the Dark Genome: Benchmarking SNV Calls in the Flanks of Structural Variants.

Highly accurate ab initio gene annotation with ANNEVO.

Deciphering Complex Interactions Between LTR Retrotransposons and Three Papaver Species Using LTR_Stream

Long and Accurate: How HiFi Sequencing is Transforming Genomics

STMiner: Gene-centric spatial transcriptomics for deciphering tumor tissues

A Telomere-to-telomere Diploid Reference Genome and Centromere Structure of the Chinese Quartet

A Study on the Decoupling Effect Between Economic Development Level and Carbon Dioxide Emissions: An Empirical Analysis Based on Mineral Resource-Based Cities in Southwest China

De novo and somatic structural variant discovery with SVision-pro

The Impact of the Green Economy on Carbon Emission Intensity: Comparisons, Challenges, and Mitigating Strategies

基于深度学习模型的船舶碳排放时空预测研究

一体化运营模式下中国区域港群效率研究

MSIsensor-RNA: Microsatellite Instability Detection for Bulk and Single-cell Gene Expression Data

Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance

Comparison and benchmark of structural variants detected from long read and long-read assembly

Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet

Pindel-TD: A Tandem Duplication Detector Based on A Pattern Growth Approach

新型需求响应公交发车时刻和票价优化

考虑CO

D2 Plot, a Matrix of DNA Density and Distance to Periphery, Reveals Functional Genome Regions

SVision: A deep learning approach to resolve complex structural variants

Comparison and benchmark of long-read based structural variant detection strategies

Haplotype-resolved Chinese male genome assembly based on high-fidelity sequencing

High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads

Analysis of vehicle skidding potential on horizontal curves

Three chromosome-scale Papaver genomes reveal punctuated patchwork evolution of the morphinan and noscapine biosynthesis pathway

Long read sequencing reveals sequential complex rearrangements driven by 1 Hepatitis B virus integration 2 3

中国省域综合交通运输效率及空间关联性研究

Transportation, germs, culture: a dynamic graph model of COVID-19 outbreak

MSIsensor-pro: Fast, Accurate, and Matched-normal-sample-free Detection of Microsatellite Instability

全国空港客货运格局的时空演化及驱动机制研究

MEpurity: estimating tumor purity using DNA methylation data

基于生态位选择的港口企业价值链分工策略

基于BSC的物流服务供应链绩效指标可拓优度评价

基于港城分离的中国港口供给侧改革研究

基于陆域和空域运输系统的空港可达性评价方法研究