田卫东｜复旦大学｜学者主页

2026

Evaluating deconvolution methods using real bulk RNA-expression data for robust prognostic insights across cancer types

Minghan Li, Yuqing Su, Yi Tang, Yuehfan Lee, Weidong Tian

Genome Biology

DOI

2026

scReGAT: Leveraging Knowledge of Regulatory Interactions to Predict Long-range Gene Regulation at Single-cell Resolution.

Baole Wen, Yanan Dang, Yu Zhang, Yi Long, Weidong Tian

Genomics, Proteomics & Bioinformatics

DOI

2025

Identifying candidate genes for spermatogenic failure and predicting ICSI outcomes using single-cell RNA sequencing and protein-protein interaction networks.

Liu Liu, Shao-yi Huang, Feng Jiang, Guoqing Liang, Xiaobin Zhu, Hong Zhu, Weidong Tian

Human Reproduction

DOI

2025

Association of human-specific expanded short tandem repeats with neuron-specific regulatory features

Qiming Liu, Weidong Tian

Science Advances

DOI

2025

PhenoDP: leveraging deep learning for phenotype-based case reporting, disease ranking, and symptom recommendation

Baole Wen, Shengmin Shi, Yi Long, Yanan Dang, Weidong Tian

Genome Medicine

DOI

2025

SCRIPT: Predicting Single‐Cell Long‐Range Cis‐Regulation Based on Pretrained Graph Attention Networks

Yu Zhang, Baole Wen, Yi-Feng Jiao, Yu-Chen Liu, Xin Guo, Yushuai Wu, Ji-Yang Li, Li-Mei Han, Ying-Hui Xu, Xin Gao, Yuan Qi, Yuan Cheng, Ying He, Weidong Tian

bioRxiv

DOI

2024

ReCIDE: robust estimation of cell type proportions by integrating single-reference-based deconvolutions

Minghan Li, Yuqing Su, Yan-Bo Gao, Weidong Tian

Briefings Bioinform.

DOI

2023

AtacAnnoR: a reference-based annotation tool for single cell ATAC-seq data

Lejin Tian, Yunxiao Xie, Zhaobin Xie, Jasmine Tian, Weidong Tian

Briefings in Bioinformatics

DOI

2023

Single-cell RNA-seq reveals developmental deficiencies in both the placentation and the decidualization in women with late-onset preeclampsia

Jing Han Yang, Lili Gong, Qiming Liu, Huanqiang Zhao, Zekun Wang, Xiaotian Li, Weidong Tian, Qiongjie Zhou

Frontiers in Immunology

DOI

2022

PhenoBERT: A Combined Deep Learning Method for Automated Recognition of Human Phenotype Ontology

Yuhao Feng, Lei Qi, Weidong Tian

IEEE/ACM Transactions on Computational Biology & Bioinformatics

DOI

2022

Large-scale prediction of key dynamic interacting proteins in multiple cancers

Jifeng Zhang, Xiao Wang, Zhicheng Ji, Weidong Tian

International Journal of Biological Macromolecules

DOI

2022

Deconvolution of a Large Cohort of Placental Microarray Data Reveals Clinically Distinct Subtypes of Preeclampsia

Tian Yao, Qiming Liu, Weidong Tian

Frontiers in Bioengineering and Biotechnology

DOI

2022

Single‐cell transcriptomics reveals pathogenic dysregulation of previously unrecognised chondral stem/progenitor cells in children with microtia

Jing Ma, Yu Zhang, Zijun Yan, Peixuan Wu, Chenlong Li, Run Yang, Xinyu Lu, Xin Chen, Aijuan He, Yaoyao Fu, Duan Ma, Weidong Tian, Tianyu Zhang

Clinical and Translational Medicine

DOI

2021

CRMarker: A manually curated comprehensive resource of cancer RNA markers.

Ji-Feng Zhang, Shou-Bao Yan, Ruoyu Li, Gang Wang, S-I Kang, Ying Wang, Wenmin Hou, Chenrun Wang, Weidong Tian

International Journal of Biological Macromolecules

DOI

2021

scMAGIC: accurately annotating single cells using two rounds of reference-based classification

Yu Zhang, Feng Zhang, Zekun Wang, Siyi Wu, Weidong Tian

Nucleic Acids Research

DOI

2020

Identification of DNA methylation patterns and biomarkers for clear-cell renal cell carcinoma by multi-omics data analysis

Pengfei Liu, Weidong Tian

PeerJ

DOI

2020

qMGR: a new approach for quantifying mitochondrial genome rearrangement.

Ji-Feng Zhang, Xian-Zhao Kan, Guopen Miao, Shun-Jie Hu, Qi Sun, Weidong Tian

Mitochondrion (Amsterdam. Print)

DOI

2020

Network Properties of Cancer Prognostic Gene Signatures in the Human Protein Interactome

Ji-Feng Zhang, Shou-Bao Yan, Chen Jiang, Zhi-Cheng Ji, Chenrun Wang, Weidong Tian

Genes

DOI

2020

Unsupervised Inference of Developmental Directions for Single Cells Using VECTOR.

Feng Zhang, Xiaoying Li, Weidong Tian

Cell Reports

DOI

2019

PhenoPro: a novel toolkit for assisting in the diagnosis of Mendelian disease

Zixiu Li, Feng Zhang, Yu-Kai Wang, Yue Qiu, Yang Wu, Yu-Lan Lu, Lin Yang, William J Qu, Hui-Jun Wang, Wen-Hao Zhou, Weidong Tian

Bioinform.

DOI

2019

Evolution and Comprehensive Analysis of DNaseI Hypersensitive Sites in Regulatory Regions of Primate Brain-Related Genes

Yue-Er Lu, Xiao Wang, Hang Yu, Jianlin Li, Zhiqiang Jiang, Bang-Wei Chen, Yue-Qi Lu, Wei Wang, Chongyin Han, Ying Ouyang, Li-Zhen Huang, Chun-Bo Chen, Weidong Tian, Fei Ling

Frontiers in Genetics

DOI

2019

A novel approach to remove the batch effect of single-cell data

Feng Zhang, Yu Wu, Weidong Tian

Cell Discovery

DOI

2019

Single-Cell Transcriptomics in Medulloblastoma Reveals Tumor-Initiating Progenitors and Oncogenic Cascades during Tumorigenesis and Relapse

Liguo Zhang, Xuelian He, Xuezhao Liu, Feng Zhang, Lei Frank Huang, Andrew Potter, Lingli Xu, Wenhao Zhou, Tao Zheng, Zaili Luo, Kalen Berry, Allison K. Pribnow, Stephanie M. C. Smith, Christine E. Fuller, Blaise V. Jones, Maryam Fouladi, Rachid Drissi, Zeng-jie Yang, William Clay Gustafson, Marc Remke, Scott L. Pomeroy, Emily J. Girard, James M. Olson, A. Sorana Morrissy, Maria Claudia Vladoiu, Jiao Zhang, Weidong Tian, Mei Xin, Michael D. Taylor, S. Steven Potter, Martine F. Roussel, William A. Weiss, Qing Richard Lu

Cancer Cell

DOI

2018

阿尔茨海默症靶基因及其药物的预测研究

侯吉，李小林，田卫东

《复旦学报(自然科学版)》

2018

基于GenePANDA算法的精神分裂症药物靶基因预测

孙慧，田卫东

《复旦学报(自然科学版)》

2017

一种基于基因组甲基化探针的肺腺癌诊断模型

窦亚光，田卫东

《复旦学报(自然科学版)》

2017

Regulation of mRNA splicing by MeCP2 via epigenetic modifications in the brain

Tian-Lin Cheng, Jingqi Chen, Huida Wan, B. Tang, Weidong Tian, L. Liao, Z. Qiu

Scientific Reports

DOI

2017

Whole genome sequencing identifies a novel ALMS1 gene mutation in two Chinese siblings with Alström syndrome

Lin Yang, Zixiu Li, Mei Mei, Xiao-Mei Fan, Guo-dong Zhan, Hui-Jun Wang, Guo-Ying Huang, Ming-Bang Wang, Weidong Tian, Wen-Hao Zhou

BMC Medical Genetics

DOI

2017

GenePANDA—a novel network-based gene prioritizing tool for complex diseases

Tian-Shu Yin, Shu Chen, Xiaohui Wu, Weidong Tian

Scientific Reports

DOI

2017

SPRINT: an SNP-free toolkit for identifying RNA editing sites

Feng Zhang, Yu-Lan Lu, Sijia Yan, Q. Xing, Weidong Tian

Bioinform.

DOI

2017

Dynamic Editome of Zebrafish under Aminoglycosides Treatment and Its Potential Involvement in Ototoxicity

Sijia Yan, Yu-Lan Lu, Lin He, Xin-Zhi Zhao, Li-Hua Wu, Huizhong Zhu, Meng-Lin Jiang, Yu Su, Wei-Ya Cao, Weidong Tian, Q. Xing

Frontiers in Pharmacology

DOI

2016

用基因互作网络识别胰腺导管腺癌基因生物标记

王新格，田卫东

《复旦学报(自然科学版)》

2016

Genome-Wide Identification of Regulatory Sequences Undergoing Accelerated Evolution in the Human Genome

Xin-Ran Dong, Xiao Wang, Feng Zhang, Weidong Tian

Molecular biology and evolution

DOI

2016

Prediction of Candidate Drugs for Treating Pancreatic Cancer by Using a Combined Approach

Yan-Fen Ma, Jian Hu, Ning Zhang, Xin-Ran Dong, Y. Li, Bo Yang, Weidong Tian, Xiaoqin Wang

PLoS ONE

DOI

2016

GoFDR: A sequence alignment based method for predicting protein functions.

Qingtian Gong, W. Ning, Weidong Tian

Methods

DOI

2016

GSA-Lightning: ultra-fast permutation-based gene set analysis

B. Chang, Weidong Tian

Bioinform.

DOI

2016

Progress in Gene Functional Enrichment Analysis

Q. Ni, Weidong Tian, Hui Sun, Xiao Wang, Tian-Shu Yin, Ya-Jie Dou, Boyi Li, Xi-Lin Jiang

DOI

2016

Explaining the disease phenotype of intergenic SNP through predicted long range regulation

Jingqi Chen, Weidong Tian

Nucleic Acids Research

DOI

2016

LEGO: a novel method for gene set over-representation analysis by incorporating network-based gene weights

Xin-Ran Dong, Yun Hao, Xiao Wang, Weidong Tian

Scientific Reports

DOI

2016

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Yuxiang Jiang, Tal Ronnen Oron, Wyatt Travis Clark, Asma Bankapur, Daniel D’Andrea, Rosalba Lepore, Christopher S. Funk, Indika Kahanda, Karin M. Verspoor, Asa Ben‐Hur, Da Chen Emily Koo, Duncan Penfold-Brown, Dennis E. Shasha, Noah Youngs, Richard Bonneau, Alexandra Lin, Sayed Mohammad Ebrahim Sahraeian, Pier Luigi Martelli, Giuseppe Profiti, Rita Casadio, Renzhi Cao, Zhaolong Zhong, Jianlin Jack Cheng, Adrian Altenhoff, Nives Škunca, Christophe Dessimoz, Tunca Doğan, Kai Hakala, Suwisa Kaewphan, Farrokh Mehryary, Tapio Salakoski, Filip Ginter, Hai Fang, Ben Smithers, Matt E. Oates, Julian Gough, Petri Törönen, Patrik Koskinen, Liisa Holm, Ching-Tai Chen, Wen−Lian Hsu, Kevin Bryson, Domenico Cozzetto, Federico Minneci, David T. Jones, Samuel Chapman, Dukka B. KC, Ishita Khan, Daisuke Kihara, Dan Ofer, Nadav Rappoport, Amos Stern, Elena Cibrián–Uhalte, Paul Denny, Rebecca E. Foulger, Reija Hieta, Duncan Legge, Ruth C. Lovering, Michele Magrane, Anna N. Melidoni, Prudence Mutowo, Klemens Pichler, Aleksandra Shypitsyna, Biao Li, Pooya Zakeri, Sarah ElShal, Léon-Charles Tranchevent, Sayoni Das, Natalie L. Dawson, David Lee, Jonathan Gill Lees, Ian Sillitoe, Prajwal Bhat, Tamás Nepusz, Alfonso E. Romero, Rajkumar Sasidharan, Haixuan Yang, Alberto Paccanaro, Jesse A Gillis, Adriana Estela Sedeño-Cortés, Paul Pavlidis, Shou Feng, Juan Miguel Cejuela, Tatyana Goldberg, Tobias Hamp, Lothar Richter, Asaf A. Salamov, Toni Gabaldón, Marina Marcet‐Houben, Fran Supek, Qingtian Gong, Wei Ning, Yuanpeng Zhou, Weidong Tian, Marco Falda, Paolo Fontana, Enrico Lavezzo, Stefano Toppo, Carlo Ferrari, Manuel Giollo

Genome biology

DOI

2015

Prediction of Metabolic Gene Biomarkers for Neurodegenerative Disease by an Integrated Network-Based Approach

Q. Ni, Xianming Su, Jingqi Chen, Weidong Tian

BioMed Research International

DOI

2015

Solute Carrier Family 26 Member a2 (slc26a2) Regulates Otic Development and Hair Cell Survival in Zebrafish

Fei Liu, Wen-Jun Xia, Jiong-Jiong Hu, Yingzhi Wang, Fan Yang, Shaoyang Sun, Jin Zhang, Nan Jiang, Hui-Jun Wang, Weidong Tian, Xu Wang, Duan Ma

PLoS ONE

DOI

2014

microRNA expression profiling of heart tissue during fetal development.

Jizi Zhou, Xin-Ran Dong, Qiong-Jie Zhou, Hui-Jun Wang, Yan-Yan Qian, Weidong Tian, Duan Ma, Xiao-Tian Li

International Journal of Molecular Medicine

DOI

2013

精神分裂症相关基因的预测——基于大规模数据的整合分析

梁燕，史艺宾，田卫东

《复旦学报(自然科学版)》

2013

Integration of cancer gene co-expression network and metabolic network to uncover potential cancer drug targets.

Jingqi Chen, Ming Ma, Ning Shen, J. Xi, Weidong Tian

Journal of Proteome Research

DOI

2013

A large-scale evaluation of computational protein function prediction

P. Radivojac, W. Clark, Tal Ronnen-Oron, A. Schnoes, T. Wittkop, Artem Sokolov, Kiley S. Graim, Christopher S. Funk, Karin M. Verspoor, Asa Ben-Hur, G. Pandey, Jeffrey M. Yunes, A. Talwalkar, Susanna Repo, Michael L Souza, D. Piovesan, R. Casadio, Z. Wang, Jian-Lin Cheng, Hai Fang, J. Gough, Patrik Koskinen, P. Törönen, Jussi Nokso-Koivisto, Liisa Holm, D. Cozzetto, D. W. Buchan, Kevin Bryson, David T. Jones, Bhakti Limaye, Harshal Inamdar, Avik Datta, Sunitha Manjari, Rajendra R. Joshi, Meghana Chitale, D. Kihara, A. M. Lisewski, S. Erdin, E. Venner, O. Lichtarge, R. Rentzsch, Hai-Xuan Yang, A. Romero, Prajwal Bhat, Alberto Paccanaro, T. Hamp, R. Kassner, Stefan Seemayer, Esmeralda Vicedo, Christian Schaefer, Dominik Achten, Florian Auer, A. Böhm, T. Braun, Maximilian Hecht, Mark Heron, Peter Hönigschmid, T. Hopf, Stefanie Kaufmann, M. Kiening, D. Krompass, C. Landerer, Yannick Mahlich, Manfred Roos, Jari Björne, Tapio Salakoski, Andrew Wong, H. Shatkay, Fanny Gatzmann, Ingolf Sommer, M. Wass, M. Sternberg, N. Skunca, F. Supek, Matko Bosnjak, P. Panov, S. Džeroski, T. Šmuc, Yiannis Kourmpetis, A. V. van Dijk, C. T. ter Braak, Yuanpeng Zhou, Qingtian Gong, Xin-Ran Dong, Weidong Tian, M. Falda, P. Fontana, E. Lavezzo, B. Di Camillo, S. Toppo, Liang Lan, Nemanja Djuric, Yuhong Guo, S. Vucetic, A. Bairoch, M. Linial, P. Babbitt, S. Brenner, C. Orengo, B. Rost, S. Mooney, I. Friedberg

Nature Methods

DOI

2013

Functional-Network-Based Gene Set Analysis Using Gene-Ontology

B. Chang, R. Kustra, Weidong Tian

PLoS ONE

DOI

2013

Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome

Yu-Lan Lu, Yuanpeng Zhou, Weidong Tian

Nucleic Acids Research

DOI

2013

Computational Systems Biology

Xing-Ming Zhao, Weidong Tian, Rui Jiang, Jun Wan

TheScientificWorldJournal

DOI

2012

TF-coEx:一种基于基因共表达网络的转录因子功能预测新方法

陈靖祺，柳靓婧，田卫东

《复旦学报(自然科学版)》

2012

A Resource of Quantitative Functional Annotation for Homo sapiens Genes

M. Taşan, H. Drabkin, John E. Beaver, Nian-Chua Hon, Julie Dunham, Weidong Tian, J. Blake, Frederick P. Roth

G3: Genes, Genomes, Genetics

DOI

2012

Molecular Mechanisms and Function Prediction of Long Noncoding RNA

Han-Dong Ma, Yun Hao, Xin-Ran Dong, Qingtian Gong, Jingqi Chen, Ji-Feng Zhang, Weidong Tian

TheScientificWorldJournal

DOI

2012

SAP—A Sequence Mapping and Analyzing Program for Long Sequence Reads Alignment and Accurate Variants Discovery

Zheng Sun, Weidong Tian

PLoS ONE

DOI

2012

Virion protein 16 induces demethylation of DNA integrated within chromatin in a novel mammalian cell model.

Lu Yang, Hui-Jun Wang, Xin Luo, Peng Mao, Weidong Tian, Y. Shi, Guo-Ying Huang, Jin Zhang, Duan Ma

Acta Biochimica et Biophysica Sinica

DOI

2012

Epigenetic features are significantly associated with alternative splicing

Yuanpeng Zhou, Yu-Lan Lu, Weidong Tian

BMC Genomics

DOI

2012

Identification of novel candidate maternal serum protein markers for Down syndrome by integrated proteomic and bioinformatic analysis

Yuan Kang, Xin-Ran Dong, Qiong-Jie Zhou, Ying Zhang, Yan Cheng, R. Hu, C. Su, Hong Jin, Xiaohui Liu, Duan Ma, Weidong Tian, Xiao-Tian Li

Prenatal Diagnosis

DOI

2011

An iterative network partition algorithm for accurate identification of dense network modules

S. Sun, Xin-Ran Dong, Yao Fu, Weidong Tian

Nucleic Acids Research

DOI

2011

Predicting Gene Function Using Omics Data: From Data Preparation to Data Integration

Weidong Tian, Xin-Ran Dong, Yuanpeng Zhou, Ren Ren

DOI

2010

FuncBase : a resource for quantitative gene function annotation

John E. Beaver, M. Taşan, Francis D. Gibbons, Weidong Tian, Timothy R. Hughes, Frederick P. Roth

Bioinform.

DOI

2008

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence

L. Peña-Castillo, M. Taşan, Chad L. Myers, Hyunju Lee, T. Joshi, Chao Zhang, Y. Guan, M. Leone, A. Pagnani, W. Kim, Chase Krumpelman, Weidong Tian, Guillaume Obozinski, Yan-Jun Qi, S. Mostafavi, G. Lin, G. Berriz, Francis D. Gibbons, Gert R. G. Lanckriet, Jian Qiu, Charles E. Grant, Zafer Barutçuoglu, D. Hill, David Warde-Farley, Chris Grouios, Debajyoti Ray, J. Blake, Minghua Deng, Michael I. Jordan, William Stafford Noble, Q. Morris, J. Klein-Seetharaman, Z. Bar-joseph, Ting Chen, Feng-Zhu Sun, O. Troyanskaya, E. Marcotte, Dong Xu, T. Hughes, Frederick P. Roth

Genome Biology

DOI

2008

Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function

Weidong Tian, Lan V. Zhang, M. Taşan, Francis D. Gibbons, O. King, Julie Park, Zeba Wunderlich, J. Cherry, Frederick P. Roth

Genome Biology

DOI

2008

An en masse phenotype and function prediction system for Mus musculus

M. Taşan, Weidong Tian, D. Hill, Francis D. Gibbons, J. Blake, Frederick P. Roth

Genome Biology

DOI

2008

Isoform discovery by targeted cloning, 'deep-well' pooling and parallel sequencing

K. Salehi-Ashtiani, Xin-Ping Yang, A. Derti, Weidong Tian, T. Hao, Chen-Wei Lin, K. Makowski, Lei Shen, Ryan R. Murray, David Szeto, Nadeem A. Tusneem, Douglas R. Smith, M. Cusick, D. Hill, Frederick P. Roth, M. Vidal

Nature Methods

DOI

2006

High precision multi-genome scale reannotation of enzyme function by EFICAz

Adrián K. Arakaki, Weidong Tian, J. Skolnick

BMC Genomics

DOI

2004

EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference.

Weidong Tian, Adrián K. Arakaki, J. Skolnick

Nucleic Acids Research

DOI

2003

How well is enzyme function conserved as a function of pairwise sequence identity?

Weidong Tian, J. Skolnick

Journal of Molecular Biology

DOI

精选作品

期刊论文

Evaluating deconvolution methods using real bulk RNA-expression data for robust prognostic insights across cancer types

scReGAT: Leveraging Knowledge of Regulatory Interactions to Predict Long-range Gene Regulation at Single-cell Resolution.

Identifying candidate genes for spermatogenic failure and predicting ICSI outcomes using single-cell RNA sequencing and protein-protein interaction networks.

Association of human-specific expanded short tandem repeats with neuron-specific regulatory features

PhenoDP: leveraging deep learning for phenotype-based case reporting, disease ranking, and symptom recommendation

SCRIPT: Predicting Single‐Cell Long‐Range Cis‐Regulation Based on Pretrained Graph Attention Networks

ReCIDE: robust estimation of cell type proportions by integrating single-reference-based deconvolutions

AtacAnnoR: a reference-based annotation tool for single cell ATAC-seq data

Single-cell RNA-seq reveals developmental deficiencies in both the placentation and the decidualization in women with late-onset preeclampsia

PhenoBERT: A Combined Deep Learning Method for Automated Recognition of Human Phenotype Ontology

Large-scale prediction of key dynamic interacting proteins in multiple cancers

Deconvolution of a Large Cohort of Placental Microarray Data Reveals Clinically Distinct Subtypes of Preeclampsia

Single‐cell transcriptomics reveals pathogenic dysregulation of previously unrecognised chondral stem/progenitor cells in children with microtia

CRMarker: A manually curated comprehensive resource of cancer RNA markers.

scMAGIC: accurately annotating single cells using two rounds of reference-based classification

Identification of DNA methylation patterns and biomarkers for clear-cell renal cell carcinoma by multi-omics data analysis

qMGR: a new approach for quantifying mitochondrial genome rearrangement.

Network Properties of Cancer Prognostic Gene Signatures in the Human Protein Interactome

Unsupervised Inference of Developmental Directions for Single Cells Using VECTOR.

PhenoPro: a novel toolkit for assisting in the diagnosis of Mendelian disease

Evolution and Comprehensive Analysis of DNaseI Hypersensitive Sites in Regulatory Regions of Primate Brain-Related Genes

A novel approach to remove the batch effect of single-cell data

Single-Cell Transcriptomics in Medulloblastoma Reveals Tumor-Initiating Progenitors and Oncogenic Cascades during Tumorigenesis and Relapse

阿尔茨海默症靶基因及其药物的预测研究

基于GenePANDA算法的精神分裂症药物靶基因预测

一种基于基因组甲基化探针的肺腺癌诊断模型

Regulation of mRNA splicing by MeCP2 via epigenetic modifications in the brain

Whole genome sequencing identifies a novel ALMS1 gene mutation in two Chinese siblings with Alström syndrome

GenePANDA—a novel network-based gene prioritizing tool for complex diseases

SPRINT: an SNP-free toolkit for identifying RNA editing sites

Dynamic Editome of Zebrafish under Aminoglycosides Treatment and Its Potential Involvement in Ototoxicity

用基因互作网络识别胰腺导管腺癌基因生物标记

Genome-Wide Identification of Regulatory Sequences Undergoing Accelerated Evolution in the Human Genome

Prediction of Candidate Drugs for Treating Pancreatic Cancer by Using a Combined Approach

GoFDR: A sequence alignment based method for predicting protein functions.

GSA-Lightning: ultra-fast permutation-based gene set analysis

Progress in Gene Functional Enrichment Analysis

Explaining the disease phenotype of intergenic SNP through predicted long range regulation

LEGO: a novel method for gene set over-representation analysis by incorporating network-based gene weights

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Prediction of Metabolic Gene Biomarkers for Neurodegenerative Disease by an Integrated Network-Based Approach

Solute Carrier Family 26 Member a2 (slc26a2) Regulates Otic Development and Hair Cell Survival in Zebrafish

microRNA expression profiling of heart tissue during fetal development.

精神分裂症相关基因的预测——基于大规模数据的整合分析

Integration of cancer gene co-expression network and metabolic network to uncover potential cancer drug targets.

A large-scale evaluation of computational protein function prediction

Functional-Network-Based Gene Set Analysis Using Gene-Ontology

Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome

Computational Systems Biology

TF-coEx:一种基于基因共表达网络的转录因子功能预测新方法

A Resource of Quantitative Functional Annotation for Homo sapiens Genes

Molecular Mechanisms and Function Prediction of Long Noncoding RNA

SAP—A Sequence Mapping and Analyzing Program for Long Sequence Reads Alignment and Accurate Variants Discovery

Virion protein 16 induces demethylation of DNA integrated within chromatin in a novel mammalian cell model.

Epigenetic features are significantly associated with alternative splicing

Identification of novel candidate maternal serum protein markers for Down syndrome by integrated proteomic and bioinformatic analysis

An iterative network partition algorithm for accurate identification of dense network modules

Predicting Gene Function Using Omics Data: From Data Preparation to Data Integration

FuncBase : a resource for quantitative gene function annotation

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence

Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function

An en masse phenotype and function prediction system for Mus musculus

Isoform discovery by targeted cloning, 'deep-well' pooling and parallel sequencing

High precision multi-genome scale reannotation of enzyme function by EFICAz

EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference.

How well is enzyme function conserved as a function of pairwise sequence identity?

会议论文

Evolution of DNaseI Hypersensitive Sites in Brain-Related Genes Regulatory Regions of Primates

MicroRNA Expression Profiles and Target Genes in Chinese Patients with Non-syndromic Isolated Cleft Palate

Changes of IncRNAs and related genes in minor and majorβ-thalassemia

研究方向