H. Yu, M. L, J. Sandhu, G. Sun, J.C. Schnable, W. Xie, B. Yu, J.P. Mower, Chi Zhang*. Pervasive misannotation of microexons that are evolutionarily conserved and crucial for gene function in plants. Nature Communications (2022); 13, 820. (featured in Editors' Highlights) [PDF]

L. Han, C.P Jara, O. Wang, S. Thibivilliers, R.K. Woycicki, M.A. Carlson, W.H. Velander, E.P. Araujo, M. Libault, Chi Zhang*, Y. Lei*. Isolating and Cryo-Preserving Pig Skin Cells for Single Cell RNA Sequencing Study. PLoS One (2022); 17(2):e0263869. [PDF]

R. Song, Z. Wang; H. Wang, H. Zhang, X. Wang, H. Nguyen, D. Holding, B. Yu, T. Clemente, S. Jia, Chi Zhang*. InMut-Finder: a software tool for insertion identification in mutagenesis using Nanopore long reads. BMC Genomics (2021); 22, 908. [PDF]

Li, M., Yu, H., Liu, K., Yang, W., Zhou, B., Gan, L., Chi Zhang, Yu, B. Serrate-Associated Protein 1, a splicing-related protein, promotes miRNA biogenesis in Arabidopsis. New Phytologist (2021); 32, 1959-1973. [PDF]

H. Bacher, F. Zhu, T. Gao, K. Liu, B.K. Dhatt, T. Awada, Chi Zhang, A. Distelfeld, H. Yu, Z. Peleg, H. Walia. Wild emmer introgressions alter root-to-shoot growth dynamics in response to water stress. Plant Physiology (2021); 87(3), 1149-1162. [PDF]

Di Liu, Xinyan Xu, Junmiao Wen, Chi Zhang*, Min Fan*. Identification of a EML4-ALK exon 19 fusion variant in lung adenocarcinoma and alectinib resistance. Lung Cancer (2021); 160, 32-35. [PDF]

N. Zhao, F. Wang, S.Ahmed, K. Liu, Chi Zhang, S. Cathcart, D.J Dimaio, Michael Punsoni, B. Guan, P. Zhou, S. Wang, S.K Batra, T. Bronich, T.K Hei, C. Lin, C. Zhang. Androgen receptor, although not a specific marker for, is a novel target to suppress glioma stem cells as a therapeutic strategy for glioblastoma. Frontiers in Oncology, section Cancer Molecular Targets and Therapeutics (2021); 11, 1696. [PDF]

J. Sandhu, L. Irvin, K. Liu, P. Staswick, Chi Zhang, H. Walia. Endoplasmic reticulum stress pathway mediates the early heat stress response of developing rice seeds. Plant, Cell & Environment (2021); 44(8), 2604– 2624. [PDF]

M.J. Baine, J. Burr, L. Zima, Q. Du§, C. Zhang, G. Rux, Chi Zhang, D. Zheng. The potential use of radiomics with pre-radiation therapy MR imaging in predicting risk of pseudoprogression in glioblastoma patients. Journal of Imaging (2021); 7(2), 17. [PDF]

Y. Shi, E. Wahle, Q. Du, L. Krajewski, X. Liang, S. Zhou, Chi Zhang*, M. Baine*, D. Zheng*. Associations between Statin/Omega3 usage and MRI-based radiomics signatures in prostate cancer. Diagnostics (2021);11(1):85. [PDF]

H. Yu, Q. Du, M. Compbell, B. Yu, H. Walia, Chi Zhang*. Genome-Wide Discovery of Natural Variation in Pre-mRNA Splicing and Prioritizing Causal Alternative Splicing to Salt Stress Response in Rice. New Phytologist (2021); 230: 1273-1287. [PDF]
bioconductor link: http://bioconductor.org/packages/release/bioc/html/vasp.html
github link: https://github.com/yuhuihui2011/vasp

Wang, Z; Kang, J; Casas-Mollano, J; Dou, Y; Jia, S; Zhang, Chi; Cerutti, H. MLK4-mediated Phosphorylation of Histone H3 at Threonine 3 (H3T3ph) Promoted Flowering by Transcriptional silencing of FLC in Arabidopsis thaliana. The Plant Journal (2020) (Accepted) [PDF]

L. Wei, M. Fitzgerald, J. Graham1, N. Hutson, Chi Zhang, Z. Huang, Q. Hu, F. Zhan, J. Xie, J. Zhang, S. Liu, E. Remenyik, E. Gellen, O. Colegio, S. Christensen, H. Lin, M. Bax, J. Xu1, W.J. Huss, B.A. Foster, G. Paragh. Ultra-deep sequencing differentiates patterns of skin clonal mutations associated with sun-exposure status and skin cancer burden. Science Advances (2021); 7(1): eabd7703. [PDF]

M. Abdelmoteleb, Chi Zhang, B. Furey, M. Kozubal, H. Griffiths, M. Champeaud, R.E. Goodman. Evaluating potential risks of food allergy of novel food sources based on comparison of proteins predicted from genomes and compared to www.AllergenOnline.org. Food and Chemical Toxicology (2021); 147:111888. [PDF]

A. Lingel, H. Lin, Y. Gavriel, E. Weaver, P. Polepole, V. Lopez, Y. Lei, T.M Petro, B. Solomon, Chi Zhang, L. Zhang. Amyloid precursor protein is a restriction factor that protects against Zika virus infection in mammalian brains. J. Biol. Chem. (2020); jbc.RA120.015165. doi:10.1074/jbc.RA120.015165. [PDF]

S. Li, M. Li, K. Liu, H. Zhang, S. Zhang, C. Zhang, B. Yu. MAC5, an RNA-binding protein, protects pri-miRNAs from SERRATE-dependent exoribonuclease activities. Proc Natl Acad Sci USA (2020) doi: 10.1073/pnas.2008283117. [PDF]

S. Jia, A. Yobi, M. Naldrett, S. Alvarez, R. Angelovici, Chi Zhang, D. Holding. Deletion of maize RDM4 disrupts endosperm maturation, vegetative growth and the transcriptomic response to cold stress. Journal of Experimental Botany (2020) eraa325. [PDF]

S. Liang, Chi Zhang. Prediction of immunogenicity for humanized and full human therapeutic antibodies. PLoS ONE (2020); 15(8): e0238150. [PDF]

M.T. Campbell, Q. Du, K. Liu, S. Sharma, Chi Zhang, H. Walia. Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa). BMC Genomics (2020); volume 21, Article number: 394. [PDF]

G. Moisseyev, K. Park, A. Cui, D. Freitas, D. Rajagopal, A.R. Konda, M. Martin-Olenski, M. Mcham, K. Liu, Q. Du, J. C. Schnable, E.N. Moriyama, E. B. Cahoon, Chi Zhang. RGPDB: Database of root-associated genes and promoters in maize, soybean, and sorghum. DATABASE (2020); baaa038. [PDF]

P. Paul, B.K. Dhatt, M. Miller, J. Folsom, Z. Wang, I Krassovskaya, K. Liu, J. Sandhu, H. Yu, Chi Zhang, T Obata, P. Staswick, H. Walia. MADS78 and 79 are essential regulators of early seed development in rice. Plant Physiology (2019); 182 (2) 933-948; DOI: 10.1104/pp.19.00917. [PDF]

Matthew Moran, Xiao Cheng, Mohamed Sham Shihabudeen Haider Ali, Nishikant Wase, Nghi Nguyen, Weilong Yang, Chi Zhang, Concetta DiRusso, and Xinghui Sun. Transcriptome analysis-identified long noncoding RNA CRNDE in maintaining endothelial cell proliferation, migration, and tube formation. Scientific Report (2019) [Paper #SREP-19-26647B]. [PDF]

J. Li, Y. Lai, Chi Zhang, Q. Zhang. TGCnA: Temporal Gene Coexpression Network Analysis Using A Low-rank plus Sparse Framework. Journal of Applied Statistics (2019); DOI: 10.1080/02664763.2019.1667311. [PDF]

Q. Du, M. Campbell, H. Yu, K. Liu, H. Walia, Q. Zhang, Chi Zhang. Network-based feature selection reveals substructures of gene modules responding to salt stress in rice. Plant Direct (2019);3(8):e00154. [PDF]

Q. Du, M. Baine, K. Bavitz, J. McAllister, X. Liang, H. Yu, J. Ryckman, L. Yu, H. Jiang, S. Zhou, Chi Zhang, D. Zheng. Radiomic feature stability across 4D respiratory phases and its impact on lung tumor prognosis prediction. PloS One 14 (5);e0216480. [PDF]

S. Li, S. Jia, L. Hou, H. Nguyen, S. Sato, D. Holding, E.B. Cahoon, Chi Zhang, T. Clemente, B. Yu. Mapping of transgenic alleles in plants using a Nanopore-based sequencing strategy. Journal of Experimental Botany (2019); 70(15):3825-3833. [PDF]

H. Lin, Q. Li, Q. Du, O. Wang, Z. Wang, L. Akert, M.A. Carlson, Chi Zhang, A. Subramanian, C. Zhang, M. Lunning, M. Li, Y. Lei. Integrated generation of induced pluripotent stem cells in a low-cost device. Biomaterials (2019); 189:23-36. [PDF]

H. Lin, Q. Du, Q. Li, O. Wang, Z. Wang, C. Elowsky, K. Liu, Chi Zhang, S. Chung, B. Duan. Y. Lei. Manufacturing human pluripotent stem cell derived endothelial cells in scalable and cell-friendly microenvironments. Biomater. Sci. (2019); 7(1):373-388. [PDF]

H. Lin, Q. Du, Q. Li, O. Wang, Z. Wang, K. Liu, L. Akert, Chi Zhang, S. Chung, B. Duan, Y. Lei. Differentiating human pluripotent stem cells into vascular smooth muscle cells in three dimensional thermoreversible hydrogels. Biomater. Sci. (2019); 7(1):347-361. [PDF]

H. Lin, X. Qiu, Q. Du, Q. Li, O. Wang, L. Akert, Z. Wang, D. Anderson, K. Liu, L. Gu, Chi Zhang, Y. Lei. Engineered Microenvironment for Manufacturing Human Pluripotent Stem Cell-Derived Vascular Smooth Muscle Cells. Stem Cell Reports (2019); 12(1):84-97. [PDF]

R.K. Ramamurthy, Q. Xiang, E. Hsieh, K. Liu§, Chi Zhang, B.M. Waters. New aspects of iron–copper crosstalk uncovered by transcriptomic characterization of Col-0 and the copper uptake mutant spl7 in Arabidopsis thaliana. Metallomics (2018); 10:1824-1840. [PDF]

S. Jia, K. Morton, Chi Zhang, D. Holding. An exome-seq based tool for mapping and identification of causal genes in maize deletion mutants. Genomics, Proteomics and Bioinformatics (2018); 16(6): 439-450. [PDF]

H. Lin, Q. Du, Q. Li, O. Wang, Z. Wang, K. Liu, C. Elowsky, Chi Zhang, Y. Lei. Hydrogel-Based Bioprocess for Scalable Manufacturing of Human Pluripotent Stem Cell-Derived Neural Stem Cells. ACS Applied Materials and Interfaces (2018); 10(35):29238-29250. [PDF]

D. Baral, B. Dvorak, D. Admiraal, S. Jia, Chi Zhang, X. Li. Tracking the Sources of Antibiotic Resistance Genes in an Urban Stream during Wet Weather using Shotgun Metagenomic Analyses. Environmental Science and Technology (2018) 52(16):9033-9044. [PDF]

H. Lin, Q. Du, Q. Li, O. Wang, Z. Wang, N. Sahu, C. Elowsky, K. Liu, Chi Zhang, S. Chung, B. Duan, Y Lei. A Scalable and Efficient Bioprocess for Manufacturing Human Pluripotent Stem Cell-Derived Endothelial Cells. Stem Cell Reports (2018);11(2):454-469. [PDF]

A. Li, S. Jia§, A. Yobi, Z. Ge, S. Sato, Chi Zhang, R. Angelovici, T. Clemente, DR Holding. Editing of an alpha-kafirin gene family increases digestibility and protein quality in sorghum. Plant Physiology (2018); pii: pp.00200.2018. [PDF]

L. Virlouvet., T.J. Avenson, Q. Du, Chi Zhang, N. Liu, T.J. Avenson, M. Fromm, Z. Avramova, S.E. Russo. Dehydration stress memory: Gene networks linked to physiological responses during repeated stresses of Zea mays. Frontier in Plant Science (2018); Volume 9, Article number 1058. [PDF]

S. Zhang, S. Li, K. Liu, M. Li, L. Zeng, Chi Zhang, B. Yu. MAC3A and MAC3B, two core subunits of the MOS4-associated complex, positively impact miRNA biogenesis. The Plant Cell (2018); 30(2):481-494. [PDF]

S. Li, R. Xu. A. Li, K. Liu, L. Gu, M. Li, H. Zhang, Y. Zhang, S. Zhuang, Q. Wang, G. Gao, N. Li, Chi Zhang, Y. Li, B. Yu. SMA1, a homolog of the splicing factor Prp28, has a multifaceted role in miRNA biogenesis in Arabidopsis. Nucleic Acid Research (2018); 46(17):9148-9159. [PDF]

S. Li, K. Liu, B. Zhou, M. Li, S. Zhang, L. Zeng, Chi Zhang, B. Yu. MAC3A and MAC3B, two core subunits of the MOS4-associated complex, positively impact miRNA biogenesis. The Plant Cell (2018); 30(2):481-494. [PDF]

Q. Zhu, L. Yan, Q. Liu, Chi Zhang, Q. Hu, L. Preus, A.I. Clay, K. Onel, D.O. Stram, L. Pooler, X. Sheng, C.A. Haiman, X. Zhu, S.R. Spellman, M. Pasquini, P.L. McCarthy, S. Liu, T. Hahn, L.E. Sucheston-Campbell. Exomechip Analyses Identify Genes affecting mortality after HLA-Matched Unrelated Donor Blood and Marrow Transplantation. Blood (2018); 131(22):2490-2499, doi:blood-2017-11-817973. [PDF]

S. Zhang, Y. Dou, S. li, G. Ren, D. Chevalier, Chi Zhang, B. Yu. DAWDLE interacts with the DICER-LIKE proteins to mediate small RNA biogenesis. Plant Physiology (2018); PP.00354, doi: 10.1104/pp.18.00354. [PDF]

H. Lin, Q. Li, O. Wang, J. Rauch, B. Harm, H. J. Viljoen, Chi Zhang, E. Van Wyk, C. Zhang, Y. Lei. Automated expansion of primary human T cells in scalable and cell-friendly hydrogel microtubes for adoptive immunotherapy. Adv. Healthcare Mater. (2018) Article ID: 1701297, DOI: 10.1002/adhm.201701297. [PDF]

Q. Du, Chi Zhang, X. Zhu, X. Liang, C. Zhang, V. Verma, K. Follet, S. Wang, Q. Fan, R. Ma, S. Zhou, D. Zheng. Application of statistical and computational methodology to predict brainstem dosimetry for trigeminal neuralgia stereotactic radiosurgery. Medical Physics (2018); 45:1822-1831. [PDF]

Q. Li, H. Lin, J. Rauch, L.P. Deleyrolle, B.A. Reynolds, H.J. Viljoen, Chi Zhang, L. Gu, E. Van Wyk, Y. Lei. Scalable Culturing of Primary Human Glioblastoma Tumor-Initiating Cells with a Cell-Friendly Culture System. Science Report (2018); 8:3531. [PDF]

Q. Li, H. Lin, Q. Du, K. Liu, O. Wang, C. Evans, H. Christian, Chi Zhang, Y. Lei. Scalable and Physiologically Relevant Microenvironments for Human Pluripotent Stem Cell Expansion and Differentiation. Biofabrication (2018); 10(2):025006. [PDF]

K.E. Unvert, F.A. Kovacs, Chi Zhang, R.A. Hellmann-Whitaker, K.N. Arndt. Evolution of Leucyl-tRNA Synthetase Through Eukaryotic Speciation. AJUR (2017); 14(3):69-83. [PDF]

M.T. Campbell, N. Bandillo, F.R. Shiblawi, S. Sharma, K. Liu, Q. Du, A.J. Schmitz, Chi Zhang, A. Very, A.J. Lorenz, H. Walia. Allelic variants of OsHKT1 underlie the divergence between Indica and Japonica subspecies of rice (Oryza sativa) for root sodium content. Plos Genetics (2017); 13(6): e1006823. [PDF]

M.T. Campbell, Q. Du, K. Liu, B. Berger, Chi Zhang, H. Walia. A comprehensive image-based phenomics analysis reveals the complex genetic architecture of shoot growth dynamics in rice (Oryza sativa). The Plant Genome (2017); Vol. 10 No. 2; doi:10.3835/plantgenome2016.07.0064. [PDF]

M. Gelli, A.R. Konda, K. Liu, Chi Zhang, T.E. Clemente, D.R. Holding, I.M. Dweikat. Validation of QTL mapping and transcriptome profiling for identification of candidate genes associated with nitrogen stress tolerance in sorghum. BMC Plant Biology (2017); 17:123. [PDF]

S. Li, K. Liu, S. Zhang, X. Wang, K. Rogers, G. Ren, Chi Zhang, B. Yu. STV1, a ribosomal protein, binds primary microRNA transcripts to promote their interaction with the processing complex in Arabidopsis. Proc Natl Acad Sci USA (2017); 114(6):1424-1429. [PDF]

Y. Dou, S. Li, W. Yang, K. Liu, Q. Du, G. Ren, B. Yu, Chi Zhang. Genome-wide discovery of circular RNAs in Arabidopsis Thaliana. Current Genomics (2017); 18(4):360-365. DOI:10.2174/1389202918666170307161124. [PDF]

H. Wang, Y. Dou, Chi Zhang, B. Yu, Y. Liu, T. Heng-Moss, G. Lu, M. Wachholtz, J. Bradshaw, P. Twigg, G Sarath. Insect and plant-derived miRNAs in greenbug (Schizaphis graminum) and yellow sugarcane aphid (Sipha flava) revealed by deep sequencing. Genes (2016); 599:68-7. [PDF]

K. Carlson, Chi Zhang, L. Harshman. A dataset for assessing temporal changes in gene expression during the aging process of adult Drosophila melanogaster. Data in Brief (2016) 7:1652-1657. [PDF]

S. Jia, A. Li, K. Morton, P. Avoles-Kianian, S.F F. Kianian, Chi Zhang, D. Holding. A Population of Deletion Mutants and an Integrated Mapping and Exome-seq Pipeline for Gene Discovery in Maize. G3 (2016); g3.116.030528; doi:10.1534/g3.116.030528. [PDF]

C. Chen, K. Begcy, K. Liu, J. Folsom, Z. Wang, Chi Zhang, H. Walia. Molecular characterization of rice endosperm development under heat stress identifies OsMADS87 as a determinant of seed size and thermal sensitivity. Plant Physiology (2016); (accepted). [PDF]

C. Chen, K. Begcy, K. Liu, J. Folsom, Z. Wang, Chi Zhang, H. Walia. Heat stress yields a unique MADS box transcription factor in determining seed size and thermal sensitivity. Plant Physiology (2016); 171(1):606-22. [PDF]

M. Gelli, S. Mitchell, K. Liu, T. Clemente, D. Weeks, Chi Zhang, D. Holding, I. Dweikat. Mapping QTLs and association of differentially expressed gene transcripts for multiple agronomic traits under different nitrogen levels in sorghum. BMC Plant Biology (2016); 16(1):16. [PDF]

K. Morton, S. Jia, Chi Zhang, D. Holding. Proteomic profiling of maize opaque endosperm mutants reveals selective accumulation of lysine-enriched proteins. Journal of Experimental Botany (2015); doi:10.1093/jxb/erv532. [PDF]

Z. Wang, J.A. Casas-Mollano, J. Xu, J. M. Riethoven, C. Zhang, H. Cerutti. Osmotic stress induces phosphorylation of histone H3 at threonine 3 in pericentromeric regions of Arabidopsis thaliana. Proc Natl Acad Sci USA (2015); 112(27):8487-8492, 10.1073/pnas.1423325112. [PDF]

Y. Dou, X. Guo, L. Yuan, D.R. Holding, C. Zhang. Differential Expression Analysis in RNA-Seq by a Naive Bayes Classifier with Local Normalization. BioMed Research International (2015) Article ID 789516, doi:10.1155/2015/789516. [PDF]

K. A. Carlson, K. Gardner, A. Pashaj, D.J. Carlson, F. Yu, J.D. Eudy, C. Zhang, L.G. Harshman. Genome-Wide Gene Expression in relation to Age in Large Laboratory Cohorts of Drosophila melanogaster. Genetics Research International (2015); vol. 2015, Article ID 835624, 19 pages. [PDF]

X. Wang, S. Zhang, Y. Dou, C. Zhang, X. Chen, B. Yu, G. Ren. Synergistic and Independent Actions of Multiple Terminal Nucleotidyl Transferases in the 3' Tailing of Small RNAs in Arabidopsis. PLoS Geneti cs (2015); 11(4): e1005091. [PDF]

M.T. Campbell, C.A. Proctor, Y. Dou, A.J. Schmitz, P. Phansak, G.R. Kruger, C. Zhang, H. Walia. Genetic and Molecular Characterization of Submergence Response Identifies Subtol6 as a Major Submergence Tolerance Locus in Maize. PLoS One (2015);10(3): e0120385. [PDF]

W. Lu, F. Ma, A. Churbanov, Y. Wan, Y. Li, G. Kang, Z. Yuan, D. Wang, C. Zhang, J. Xu, M. Lewis, Q. Li. Virus-Host Mucosal Interactions During Early SIV Rectal Transmission. Virology (2014); 464-465C:406-414. [PDF]

A. Block, T. Toruno, C. Elowsky, C. Zhang, J. Steinbrenner, J. Beynon, J. Alfano. The Pseudomonas syringae type III effector HopD1 suppresses effector-triggered immunity, localizes to the endoplasmic reticulum, and targets the Arabidopsis transcription factor NTL9. New Phytologist (2014); 201(4):1358-1370. [PDF]

Y. Dou, B. Yao, C. Zhang. PhosphoSVM: Prediction of phosphorylation sites by integrating various protein sequence attributes with a support vector machine. Amino Acids (2014); DOI: 10.1007/s00726-014-1711-5. [PDF]

M. Gelli, Y. Duo, A.R. Konda, C. Zhang, D. Holding, I. Dweikat. Identification of differentially expressed genes between sorghum genotypes with contrasting nitrogen stress tolerance by genome-wide transcriptional profiling. BMC Genomics (2014); 15:179. [PDF]

X. Liu, T. Lu, Y. Dou, B. Yu, C. Zhang. Identification of RNA Silencing Components in Soybean and Sorghum. BMC Bioinformatics (2014); 15:4. [PDF]

T. Lu, Z. Zhang, C. Zhang. Glycosyl rotation and distortion by key residues in Endocellulase Cel6A from Theromobifida fusca. Glycobiology (2013); 24(3):247-51. [PDF]

G. Li, J. Froehlich, C. Elowsky, J. Msanne, A. Ostosh, C. Zhang, T. Awada, J. Alfano. Distinct Pseudomonas type III effectors utilize a cleavable transit peptide to target chloroplasts. The Plant Journal (2014); 77(2):310-321. [PDF]

L. Yuan, Y. Dou, S.F. Kianian, C. Zhang, D.R. Holding. Deletion mutagenesis identifies a haploinsufficient role for gamma-zein in opaque-2 endosperm modification. Plant Physiology (2013); 164(1):119-130. [PDF]

S. Liang, C. Zhang, Y. Zhou. LEAP: Highly accurate prediction of protein loop conformations by integrating coarse-grained sampling and optimized energy scores with all-atom refinement of backbone and side chains. Journal of Computational Chemistry (2013); 35(4): 335-341. [PDF]

T. Lu, Y. Dou, C. Zhang. Fuzzy clustering of CPP family in plants with evolution and interaction analyses. BMC Bioinformatics (2013); 14(Suppl 13):S10. [PDF]

S. Liang, D. Zheng, D.M. Standley, H. Guo, C. Zhang. A novel function prediction approach using protein overlap networks. BMC Systems Biology (2013); 7:16. [PDF]

B. Yao, D. Zheng, S. Liang, C. Zhang. Conformational B-cell epitope prediction on antigen protein structures: a review of current algorithms and comparison with common binding site prediction methods. PLoS ONE (2013); 8(4):e62249. [PDF]

T. Lu, B. Yao, C. Zhang. DFVF: database of fungal virulence factors. DATABASE (2012); 2012:bas032. [PDF] [Database]

B. Yao, L. Zhang, S. Liang, C. Zhang. SVMTriP: A method to predict antigenic epitopes using support vector machine to integrate tri-peptide similarity and propensity. PLoS ONE (2012); 7(9):e45152. [PDF] [Server and Data]

M. Xie, G. Ren, C. Zhang, B. Yu. The DNA and RNA binding protein FACTOR of DNA METHYLATION 1 requires XH domain-mediated complex formation for its function in RNA-directed DNA methylation. The Plant J (2012); 72:491-500. [PDF]

G. Ren, M. Xie, Y. Dou, S. Zhang, C. Zhang, B. Yu. Regulation of miRNA abundance by RNA binding protein TOUGH in Arabidopsis. Proc Natl Acad Sci USA (2012); 109(31):12817-12821. [PDF]

S. Liang, C. Zhang, J. Sarmiento, D. Standley. Protein loop modeling with optimized backbone potential functions. Journal of Chemical Theory and Computation (2012); 8(5):1820-1827. [PDF]

T. Lu, Y. Yang, B. Yao, S. Liu, Y. Zhou, C. Zhang. Template-based structure prediction and classification of Transcription Factors in Arabidopsis Thaliana. Protein Science (2012); 21(6):828-838. [PDF] [Database]

Y. Dou, J. Wang, J. Yang, C. Zhang. L1pred: a sequence-based prediction tool for catalytic residues in enzymes with the L1-logreg classifier. PLoS ONE (2012); 7(4):e35666.[PDF] [supplementary materials]

X. Guo, K.J. Ronhovde, L. Yuan, B. Yao, M.P. Soundararajan, T. Elthon, C. Zhang, D. Holding. Increased glycolytic flux though pyrophosphate dependent fructose 6 phosphate 1-phosphotransferase accompanies endosperm modification in Quality Protein Maize. Plant Physicolgy (2012); 158(2):917-929. [PDF]

S. Liang, D. Zheng, C. Zhang, D.M. Standley. Fast and accurate prediction of protein side-chain conformations. Bioinformatics (2011) 27(20):2913-4. [PDF]

S. Liang, C. Zhang, D.M. Standley. Protein loop selection using orientation dependent force fields derived by parameter optimization. Proteins, 79(7), 2260-2267 (2011) [PDF]

S. Liang, D. Zheng, D.M. Standley, B. Yao, M. Zacharias and C. Zhang. EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results. BMC Bioinformatics 11, 381 (2010) [PDF] EPSVR Server EPMeta Server

S. Liang, D. Zheng, C. Zhang and M. Zacharias. Prediction of Antigenic Epitopes on Protein Surfaces by Consensus Scoring. BMC Bioinformatics 10, 302 (2009) [PDF] Server

S. Liang, S. Liu, C. Zhang and Y. Zhou. A simple reference state makes a significant improvement in near-native selections from structurally refined docking decoys. Proteins 69, 244--253 (2007) [PDF] Server [On the Cover]

S. Liu, C. Zhang, S. Liang, and Y. Zhou. Fold Recognition by Concurrent Use of Solvent Accessibility and Residue Depth. Proteins, 68, 636--645, (2007) [PDF] Server [On the Cover]

S. Liang, C. Zhang, S. Liu and Y. Zhou. Protein binding site prediction with an empirical scoring function. Nucl. Acids Res.34, 3698-3707 (2006). [PINUP Server] [PDF]

C. Zhang, S. Liu and Y. Zhou. MC²: Identifying high-quality protein-interaction modules by clique merging. J. Proteome Res. 5, 801--807 (2006). [MC² Server] [PDF]

Z. Xu, Chi Zhang, S. Liu, Yaoqi Zhou. QBES: Predicting real values of solvent accessibility from sequences by efficient, constrained energy optimization. Proteins, 63, 961-966 (2006).

S. Liu, C. Zhang, Y. Zhou. Uneven size distribution of mammalian genes in the number of tissues expressed and in the number of co-expressed genes. Human Molec. Genetics, 15, 1313--1318 (2006) [Cover Article]. Abstract. [PDF]

Y. Zhou, H. Zhou, C. Zhang, S. Liu. What is a desirable statistical energy function for proteins and how can it be obtained? Cell Biochem. Biophys. 46(2), 165-74 (2006) [Review].

B. P. Pandey, C. Zhang, X. Yuan, J. Zi and Y. Zhou. Protein flexibility prediction by an all-atom mean-field statistical theory. Protein Science, 14, 1772--1777 (2005). [PDF]

H. Zhou, C. Zhang, S. Liu, Y. Zhou. Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis, and comparative analysis of domain combinations. Nucl. Acids Res. (Server issue) 33, W193--W197 (2005). [PDF]

C. Zhang, S. Liu, Y. Zhou. Docking prediction using biological information, ZDOCK sampling technique and clustering guided by the DFIRE statistical energy function. Proteins (Special CAPRI issue) 60, 314--318 (2005) [Invited, Peer-reviewed Conference Paper]. [PDF]

C. Zhang, S. Liu, Q. Zhu, and Y. Zhou, ``A knowledge-based energy function for protein-ligand, protein-protein and protein-DNA complexes'', J. Med. Chem. 48, 2325-2335 (2005). [PDF] [DDNA Server]

S. Liu, C. Zhang, and Y. Zhou, ``Domain Graph of Arabidopsis thaliana Proteome by comparative analysis'', J. Proteome Res. 4, 435-444 (2005). [PDF] [DOGMA Server/Database]

C. Zhang, S. Liu, H. Zhou, Y. Zhou. The dependence of all-atom statistical potentials on training structural database. Biophys. J. 86, 3349-3358 (2004). [PDF]

Yaoqi Zhou, H. Zhou, Chi Zhang, S. Liu. Toward a Physical Energy Function for Intra- and Inter-protein Interactions by Combining Structural Knowledge with Physical Principles. Biophysical Journal, 86, 306A-307A Part 2 Suppl., (2004).

C. Zhang, S. Liu, H. Zhou, Y. Zhou. An accurate residue-level pair potential of mean force for folding and binding based on the distance-scaled ideal-gas reference state. Protein Sci. 13, 400-411 (2004). [PDF]

C. Zhang, S. Liu, Y. Zhou. Accurate and efficient loop selections using DFIRE-based all-atom statistical potential. Protein Sci. 13, 391-399 (2004). [PDF] [Supplement Materials] [ Server]

S. Liu, C. Zhang, H. Zhou, Y. Zhou. A physical reference state unifies the structure-derived potential of mean force for protein folding and binding. Proteins 56, 93-101 (2004). [PDF] [ Server]

Y. Zhou, C. Zhang, G. Stell, J. Wang. Temperature dependence of the distribution of the first passage time: Results from all-atom discontinuous molecular dynamics simulations of the second beta-hairpin fragment of protein G. J. Am. Chem. Soc., 125, 6300-6305 (2003). [ Subject Area:Folding kinetics] [PDF]

Susan Gardner, V. Bernard, Ulf-G. Meissner, Chi Zhang. Radiative Neutron-Decay in Effective Field Theory. Journal of Research of the NIST, 110, 411-414 (2005).

V. Bernard, Susan Gardner, Ulf-G. Meissner, Chi Zhang. Radiative Neutron-decay in Effective Field Theory. [hep-ph/0403241] Physics Letters B, 593, 105-114 (2004).

Susan Gardner and Chi Zhang. Sharpening Low-Energy, Standard-Model Tests via Correlation Coefficients in Neutron Beta-Decay. Phys. Rev. Lett., 86, 5666 (2001).

D. Manivannan and Chi Zhang, Performance of Communication-Induced Checkpointing Algorithms, International Journal of Computer Systems Science and Engineering, 18(3), 129-136 (2003).