Publications

2025

  1. phenodp.jpg
    PhenoDP: leveraging deep learning for phenotype-based case reporting, disease ranking, and symptom recommendation
    Baole Wen, Sheng Shi, Yi Long, Yanan Dang, and Weidong Tian
    Genome Medicine, 2025
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    Association of human-specific expanded short tandem repeats with neuron-specific regulatory features
    Qiming Liu and Weidong Tian
    Science Advances, 2025
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2024

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    ReCIDE: robust estimation of cell type proportions by integrating single-reference-based deconvolutions
    Minghan Li, Yuqing Su, Yanbo Gao, and Weidong Tian
    Briefings in Bioinformatics, 2024
  2. MGA loss-of-function variants cause premature ovarian insufficiency
    Shuyan Tang, Ting Guo, Chengcheng Song, Lingbo Wang, Jun Zhang, Aleksandar Rajkovic, Xiaoqi Lin, Shiling Chen, Yujun Liu, Weidong Tian, and 1 more author
    The Journal of Clinical Investigation, 2024

2023

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    AtacAnnoR: a reference-based annotation tool for single cell ATAC-seq data
    Lejin Tian, Yunxiao Xie, Zhaobin Xie, Jasmine Tian, and Weidong Tian
    Briefings in Bioinformatics, 2023
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  2. Single-cell RNA-seq reveals developmental deficiencies in both the placentation and the decidualization in women with late-onset preeclampsia
    J. Yang, L. Gong, Q. Liu, H. Zhao, Z. Wang, X. Li, W. Tian, and Q. Zhou
    Front Immunol, 2023
    DOI
  3. Kinase-independent role of mTOR and on-/off-target effects of an mTOR kinase inhibitor
    C. Fan, M. Wunderlich, X. Cai, Z. Yan, F. Zhang, A.K. Davis, L. Xu, F. Guo, Q.R. Lu, M. Azam, and 2 more authors
    Leukemia, 2023
    Epub 2023 Aug 2.PMID: 37532788
    DOI

2022

  1. Deconvolution of a Large Cohort of Placental Microarray Data Reveals Clinically Distinct Subtypes of Preeclampsia
    Tian Yao, Qiming Liu, and Weidong Tian
    Frontiers in Bioengineering and Biotechnology, 2022
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    PhenoBERT: a combined deep learning method for automated recognition of human phenotype ontology
    Yuhao Feng, Lei Qi, and Weidong Tian
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2022
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  3. Large-scale prediction of key dynamic interacting proteins in multiple cancers
    Jifeng Zhang, Xiao Wang, Zhicheng Ji, and Weidong Tian
    International journal of biological macromolecules, 2022
  4. MUC1 triggers lineage plasticity of Her2 positive mammary tumors
    Zhi Pang, Xinran Dong, Huayun Deng, Chengzhi Wang, Xiaodong Liao, Chunhua Liao, Yahui Liao, Weidong Tian, Jinke Cheng, Guoqiang Chen, and 1 more author
    Oncogene, 2022
  5. Large-scale prediction of key dynamic interacting proteins in multiple cancers Int J Biol Macromol
    J. Zhang, X. Wang, Z. Ji, and Tian W#
    2022
    DOI
  6. Deconvolution of a Large Cohort of Placental Microarray Data Reveals Clinically Distinct Subtypes of Preeclampsia
    T. Yao, Q. Liu, and Tian W#
    Front Bioeng Biotechnol. Jul, 2022
    DOI
  7. scMAGIC: accurately annotating single cells using two rounds of reference-based classification
    Y. Zhang, F. Zhang, Z. Wang, S. Wu, and Tian W#
    Nucleic Acids Research, 2022
    DOI
  8. PhenoBERT: a combined deep learning method for automated recognition of human phenotype ontology
    Y. Feng, L. Qi, and W. Tian
    IEEE/ACM Trans Comput Biol Bioinform, 2022
    DOI
  9. MUC1 triggers lineage plasticity of Her2 positive mammary tumors
    Z. Pang, X. Dong, H. Deng, C. Wang, X. Liao, C. Liao, Y. Liao, W. Tian, J. Cheng, G. Chen, and 2 more authors
    Oncogene, 2022
    DOI
  10. Single‐cell transcriptomics reveals pathogenic dysregulation of previously unrecognised chondral stem/progenitor cells in children with microtia
    J. Ma, Y. Zhang, Z. Yan, P. Wu, C. Li, R. Yang, X. Lu, X. Chen, Fu He, Ma D.# Y, and 2 more authors
    Clin Transl Med, 2022
    DOI

2021

  1. CRMarker: A manually curated comprehensive resource of cancer RNA markers
    Zhang J#, Yan S, Li R, Wang G, Kang S, Wang Y, Hou W, Wang C, and Tian W#
    Int J Biol Macromol, 2021
    DOI
  2. Adaptive responses to mTOR gene targeting in hematopoietic stem cells reveal a proliferative mechanism evasive to mTOR inhibition
    C. Fan, C. Zhao, F. Zhang, M. Kesarwani, Z. Tu, X. Cai, A.K. Davis, L. Xu, C.L. Hochstetler, X. Chen, and 6 more authors
    Proc Natl Acad Sci U S A, 2021
    PMID: 33443202; PMCID: PMC7817152.
    DOI

2020

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    Identification of DNA methylation patterns and biomarkers for clear-cell renal cell carcinoma by multi-omics data analysis
    Pengfei Liu and Weidong Tian
    PeerJ, 2020
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  2. Global synthesis of effects of plant species diversity on trophic groups and interactions
    N.F. Wan, X.R. Zheng, L.W. Fu, L.P. Kiær, Z. Zhang, R. Chaplin-Kramer, M. Dainese, J. Tan, S.Y. Qiu, Y.Q. Hu, and 7 more authors
    Nat Plants, 2020
    Epub 2020 May 4.
    DOI
  3. Unsupervised Inference of Developmental Directions for Single Cells Using VECTOR
    F. Zhang, X. Li, and W.# Tian
    Cell Reports, 2020
    PMID: 32846127
    DOI
  4. Identification of DNA methylation patterns and biomarkers for clear-cell renal cell carcinoma by multi-omics data analysis
    P. Liu and W.# Tian
    Peer J, 2020
    DOI
  5. Network Properties of Cancer Prognostic Gene Signatures in the Human Protein Interactome
    Zhang J#, Yan S, Jiang C, Ji Z, Wang C, and Tian W#
    Genes, 2020
    DOI
  6. qMGR: A new approach for quantifying mitochondrial genome rearrangement
    Zhang J#, Kan X, Miao G, Hu S, Sun Q, and Tian W#
    Mitochondrion, 2020
    DOI

2019

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    PhenoPro: a novel toolkit for assisting in the diagnosis of Mendelian disease
    Zixiu Li, Feng Zhang, Yukai Wang, Yue Qiu, Yang Wu, Yulan Lu, Lin Yang, William J Qu, Huijun Wang, Wenhao Zhou, and 1 more author
    Bioinformatics, 2019
    DOI
  2. zhang2019novel.webp
    A novel approach to remove the batch effect of single-cell data
    Feng Zhang, Yu Wu, and Weidong Tian
    Cell discovery, 2019
    DOI HTML
  3. Single-Cell Transcriptomics in Medulloblastoma Reveals Tumor-Initiating Progenitors and Oncogenic Cascades during Tumorigenesis and Relapse
    L. Zhang, X. He, X. Liu, F. Zhang, L.F. Huang, A.S. Potter, L. Xu, W. Zhou, T. Zheng, Z. Luo, and 23 more authors
    Cancer Cell, 2019
    pii: S1535-6108(19)30336-8.
    DOI
  4. Evolution and Comprehensive Analysis of DNaseI Hypersensitive Sites in Brain-Related Genes Regulatory Regions of Primates
    Y. Lu, X. Wang, H. Yu, J. Li, Z. Jiang, B. Chen, Y. Lu, C. Han, W. Wang, Y. Ouyang, and 4 more authors
    Frontiers in Genetics, 2019
    eCollection 2019. (PMID: 30930929
    DOI

2018

  1. Increasing plant diversity with border crops reduces insecticide use and increases crop yield in urban agriculture
    N.F. Wan, Y.M. Cai, Y.J. Shen, X.Y. Ji, X.W. Wu, X.R. Zheng, W. Cheng, J. Li, Y.P. Jiang, X. Chen, and 9 more authors
    Elife, 2018
    pii: e35103.
    DOI

2017

  1. Dynamic Editome of Zebrafish under Aminoglycosides Treatment and Its Potential Involvement in Ototoxicity
    S. Yan, Y. Lu, L. He, X. Zhao, L. Wu, H. Zhu, M. Jiang, Y. Su, W. Cao, W.# Tian, and 1 more author
    Front Pharmacol. Nov, 2017
    eCollection 2017. (PMID: 29213239
    DOI
  2. SPRINT: an SNP-free toolkit for identifying RNA editing sites
    F. Zhang, Y. Lu, S. Yan, Q. Xing, and Tian W#
    Bioinformatics, 2017
    PMID: 29036410
    DOI
  3. Whole genome sequencing identifies a novel ALMS1 gene mutation in two Chinese siblings with Alström syndrome
    L. Yang, Z. Li, M. Mei, X. Fan, G. Zhan, H. Wang, G. Huang, M. Wang, W. Tian, and W. Zhou
    BMC Med Genet. Jul, 2017
    PMID: 28724398
  4. GenePANDA-a novel network-based gene prioritizing tool for complex diseases
    T. Yin, S. Chen, X. Wu, and Tian W#
    Scientific Reports, 2017
    PMID: 28252032
  5. Regulation of mRNA splicing by MeCP2 via epigenetic modifications in the brain
    T.L. Cheng, J. Chen, H. Wan, B. Tang, W. Tian, L. Liao, and Z. Qiu
    Scientific Reports, 2017
    PMID: 28211484

2016

  1. China’s community-based strategy of universal preconception care in rural areas at a population level using a novel risk classification system for stratifying couples preconception health status
    Q. Zhou, S. Zhang, Q. Wang, H. Shen, W. Tian, J. Chen, G. Acharya, and X. Li
    BMC Health Serv Res, 2016
    PMID: 28031048
  2. Cellulose synthesis genes CESA6 and CSI1 are important for salt stress tolerance in Arabidopsis
    S.S. Zhang, L. Sun, X. Dong, S.J. Lu, W. Tian, and J.X. Liu
    J Integrative Plant Biology, 2016
    PMID: 26503768
  3. Prediction of Candiyear Drugs for Treating Pancreatic Cancer by Using a Combined Approach
    Y. Ma, J. Hu, N. Zhang, X. Dong, Y. Li, B. Yang, W.# Tian, and X.# Wang
    PloS one, 2016
    PMID: 26910401
  4. An expanded evaluation of protein function prediction methods shows an improvement in accuracy
    Y. Jiang, T.R. Oron, W.T. Clark, A.R. Bankapur, D. D’Andrea, R. Lepore, C.S. Funk, I. Kahanda, K.M. Verspoor, A. Ben-Hur, and 109 more authors
    M. J, 2016
    PMID: 27604469
  5. Explaining the disease phenotype of intergenic SNP through predicted long range regulation
    J. Chen and W.# Tian
    Nucleic acids research, 2016
    PMID: 27280978
  6. Genome-Wide Identification of Regulatory Sequences Undergoing Accelerated Evolution in the Human Genome
    X. Dong, X. Wang, F. Zhang, and W.# Tian
    Molecular Biology and Evolution, 2016
    PMID: 27401230
  7. GoFDR: A sequence alignment based method for predicting protein functions
    Q. Gong, W. Ning, and W.# Tian
    Methods, 2016
    PMID: 26277418
  8. LEGO: a novel method for gene set over-representation analysis by incorporating network-based gene weights
    X. Dong, Y. Hao, X. Wang, and W.# Tian
    Scientific Reports, 2016
    PMID: 26750448
  9. GSA-Lightning: ultra-fast permutation-based gene set analysis
    B.H. Chang and W.# Tian
    Bioinformatics, 2016
    PMID: 27296982

2015

  1. Positive selection on D-lactate dehydrogenases of Lactobacillus delbrueckii subspecies bulgaricus
    J. Zhang, G. Gong, X. Wang, H. Zhang, and W.# Tian
    IET Systems Biology, 2015
    PMID: 26243834
  2. Prediction of Metabolic Gene Biomarkers for Neurodegenerative Disease by an Integrated Network-Based Approach
    Q. Ni, X. Su, J. Chen, and W.# Tian
    BioMed research international, 2015
    PMID: 26064912
  3. Solute Carrier Family 26 Member a2 (slc26a2) Regulates Otic Development and Hair Cell Survival in Zebrafish
    F. Liu, W. Xia, J. Hu, Y. Wang, F. Yang, S. Sun, J. Zhang, N. Jiang, H. Wang, and W. Tian
    PloS one, 2015
    PMID: 26375458

2014

  1. microRNA expression profiling of heart tissue during fetal development
    J. Zhou, X. Dong, Q. Zhou, H. Wang, Y. Qian, W. Tian, D. Ma, and X. Li
    International journal of molecular medicine, 2014
    PMID: 24604530
  2. Short-term and continuing stresses differentially interplay with multiple hormones to regulate plant survival and growth
    C. Yang, J. Liu, X. Dong, Z. Cai, W. Tian, and X. Wang
    Molecular plant, 2014
    PMID: 24499771
  3. The effect of multiple single nucleotide polymorphisms in the folic acid pathway genes on homocysteine metabolism
    S. Liang, Y. Zhou, H. Wang, Y. Qian, D. Ma, W. Tian, V. Persaud-Sharma, C. Yu, Y. Ren, and S. Zhou
    BioMed research international, 2014
    PMID: 24524080

2013

  1. Support vector machine: classifying and predicting mutagenicity of complex mixtures based on pollution profiles
    W. Zheng, D. Tian, X. Wang, W. Tian, H. Zhang, S. Jiang, G. He, Y. Zheng, and W. Qu
    Toxicology, 2013
    PMID: 23395826
  2. Revealing of Mycobacterium marinum transcriptome by RNA-seq
    S. Wang, X. Dong, Y. Zhu, C. Wang, G. Sun, T. Luo, W. Tian, H. Zheng, and Q. Gao
    PloS one, 2013
    PMID: 24098731
  3. A large-scale evaluation of computational protein function prediction
    P. Radivojac, W.T. Clark, T.R. Oron, A.M. Schnoes, T. Wittkop, A. Sokolov, K. Graim, C. Funk, K. Verspoor, A. Ben-Hur, and 61 more authors
    Nature methods, 2013
    PMID: 23353650
  4. Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome
    Y. Lu, Y. Zhou, and W.# Tian
    Nucleic acids research, 2013
    PMID: 24003029
  5. Integration of cancer gene co-expression network and metabolic network to uncover potential cancer drug targets
    J. Chen, M. Ma, N. Shen, J.J. Xi, and W.# Tian
    Journal of proteome research, 2013
    PMID: 23590569
  6. Functional-network-based gene set analysis using gene-ontology
    B. Chang, R. Kustra, and W.# Tian
    PloS one, 2013
    PMID: 23418449

2012

  1. Epigenetic features are significantly associated with alternative splicing
    Y. Zhou, Y. Lu, and W.# Tian
    BMC genomics, 2012
    PMID: 22455468
  2. Pollution trees: identifying similarities among complex pollutant mixtures in water and correlating them to mutagenicity
    W. Zheng, X. Wang, D. Tian, H. Zhang, W. Tian, M.E. Andersen, Y. Zheng, X. Sun, S. Jiang, and Z. Cao
    Environmental science & technology, 2012
    PMID: 22680987
  3. Dynamic population changes in Mycobacterium tuberculosis during acquisition and fixation of drug resistance in patients
    J Infect Dis, 2012
    Epub 2012 Sep 14.
    DOI
  4. Virion protein 16 induces demethylation of DNA integrated within chromatin in a novel mammalian cell model
    L. Yang, H. Wang, X. Luo, P. Mao, W. Tian, Y. Shi, G. Huang, J. Zhang, and D. Ma
    Acta biochimica et biophysica Sinica, 2012
    PMID: 22120152
  5. SAP–a sequence mapping and analyzing program for long sequence reads alignment and accurate variants discovery
    Z. Sun and W.# Tian
    PloS one, 2012
    PMID: 22880129
  6. An iterative network partition algorithm for accurate identification of dense network modules
    S. Sun, X. Dong, Y. Fu, and W.# Tian
    Nucleic acids research, 2012
    PMID: 22121225
  7. 3rd et al
    G. Sun, T. Luo, C. Yang, X. Dong, J. Li, Y. Zhu, H. Zheng, W. Tian, S. Wang, and C.E. Barry
    The Journal of infectious diseases, 2012
    PMID: 22984115
  8. Molecular mechanisms and function prediction of long noncoding RNA
    H. Ma, Y. Hao, X. Dong, Q. Gong, J. Chen, J. Zhang, and W.# Tian
    The Scientific World Journal, 2012
    PMCID: PMC3540756
  9. Identification of novel candiyear maternal serum protein markers for Down syndrome by integrated proteomic and bioinformatic analysis
    Y. Kang, X. Dong, Q. Zhou, Y. Zhang, Y. Cheng, R. Hu, C. Su, H. Jin, X. Liu, D. Ma, and 2 more authors
    Prenatal diagnosis, 2012
    PMID: 22430729
  10. A network-based gene-weighting approach for pathway analysis
    Z. Fang, W.# Tian, and H.# Ji
    Cell research, 2012
    PMID: 21894192

2011

  1. Comparative genomics study of polyhydroxyalkanoates (PHA) and ectoine relevant genes from Halomonas sp. TD01 revealed extensive horizontal gene transfer events and co-evolutionary relationships
    L. Cai, D. Tan, G. Aibaidula, X.R. Dong, J.C. Chen, W.D.# Tian, and G.Q.# Chen
    Microbial cell factories, 2011
    PMID: 22040376

2010

  1. Lung adenocarcinoma from East Asian never-smokers is a disease largely defined by targetable oncogenic mutant kinases
    Y. Sun, Y. Ren, Z. Fang, C. Li, R. Fang, B. Gao, X. Han, W. Tian, W. Pao, and H. Chen
    Journal of clinical oncology : official journal of the American Society of Clinical Oncology, 2010
    PMID: 20855837
  2. FuncBase: a resource for quantitative gene function annotation
    J.E. Beaver, M. Tasan, F.D. Gibbons, W. Tian, T.R. Hughes, and F.P. Roth
    Bioinformatics, 2010
    PMCID: 2894510

2008

  1. Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function
    W. Tian, L.V. Zhang, M. Tasan, F.D. Gibbons, O.D. King, J. Park, Z. Wunderlich, J.M. Cherry, and F.P. Roth
    Genome biology, 2008
    PMCID: 2447541
  2. An en masse phenotype and function prediction system for Mus musculus
    M. Tasan, W. Tian, D.P. Hill, F.D. Gibbons, J.A. Blake, and F.P. Roth
    Genome biology, 2008
    PMCID: 2447542
  3. Isoform discovery by targeted cloning, ’deep-well’ pooling and parallel sequencing
    K. Salehi-Ashtiani, X. Yang, A. Derti, W. Tian, T. Hao, C. Lin, K. Makowski, L. Shen, R.R. Murray, and D. Szeto
    Nature methods, 2008
    PMCID: 2743938

2006

  1. High precision multi-genome scale reannotation of enzyme function by EFICAz
    A.K. Arakaki, W. Tian, and J. Skolnick
    BMC genomics, 2006
    PMCID: 1764738

2004

  1. EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference
    W. Tian, A.K. Arakaki, and J. Skolnick
    Nucleic acids research, 2004
    PMCID: 535665

2003

  1. How well is enzyme function conserved as a function of pairwise sequence identity?
    W. Tian and J. Skolnick
    Journal of molecular biology, 2003
    PMID: 14568541) (Faculty of 1000 Biology

2000

  1. Production of polyesters consisting of medium chain length 3-hydroxyalkanoic acids by Pseudomonas mendocina 0806 from various carbon sources
    W. Tian, K. Hong, G.Q. Chen, Q. Wu, R.Q. Zhang, and W. Huang
    Antonie van Leeuwenhoek, 2000
    PMID: 10696875

1999

  1. A rapid method for detecting bacterial polyhydroxyalkanoates in intact cells by Fourier transform infrared spectroscopy
    K. Hong, Sun S, Tian W, Chen GQ, and Huang W
    Appl Microbiol Biotechnol, 1999
    DOI:
    DOI

1998

  1. Production of novel polyhydroxyalkanoates by Pseudomonas stutzeri 1317 from glucose and soybean oil
    W.N. He, W. Tian, G. Zhang, G.Q. Chen, and Z.M. Zhang
    FEMS Microbiol Lett, 1998
    DOI:
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