Dapeng Zhang, Ph.D.
Associate Professor
Biology
Courses Taught
Bioinformatics I, Principles of Genetics, Biological Conflicts, Bioinformatics Colloquium
Education
Ph.D., University of Ottawa
Research Interests
We are interested in using Bioinformatics, Genomics, Evolutionary Theory, and Machine Learning techniques to address various biological and health-related questions, including:
- Molecular mechanisms underlying biological conflicts, such as host-pathogen interactions, genetic conflicts, cell-cell interactions, and diseases in humans, animals, and plants. The focused systems include polymorphic toxin/effector systems, DNA modification systems, bacterial anti-phage effector systems, and eukaryotic immune systems.
- Diversification mechanisms of biomolecules, including DNA, RNA, and proteins.
- Antibiotic resistance and machine learning-based predictions.
- Protein domain classification and function prediction.
- Development of novel bioinformatics and machine learning methods, as well as specialized databases.
Labs and Facilities
See Zhang's .
Publications and Media Placements
Tan Y, Aravind L, Zhang D. Genomic underpinnings of Cytoplasmic Incompatibility: CIF gene neighborhood diversification through lateral transfers and recombination in Wolbachia. Genome Biology and Evolution, 2024, 16(8):evae171.
Tan Y, Scornet AL, Yap YF, Zhang D. Machine learning-based classification reveals distinct clusters of non-coding genomic allelic variations associated with Erm-mediated antibiotic resistance. mSystems, 2024, 9(7):e0043024.
Zhao Q, Bertolli S, Park Y, Tan Y, Cutler KJ, Srinivas P, Asfahl KL, Garcia CF, Gallagher L, Li Y, Wang Y, Coleman-Derr D, DiMaio F, Zhang D, Peterson B, Veesler D, Mougous JD. Streptomyces umbrella toxin particles block hyphal growth of competing specie. Nature, 2024, 629: 165–173
Shields K, Ranava D, Tan Y, Zhang D, Yap MF. Epitranscriptional m6A modification of rRNA negatively impacts translation and host colonization in Staphylococcus aureus. PLoS Pathogens, 2024, 20 (1), e1011968.
Li H, Schneider T, Tan Y, Zhang D. Ribonuclease T2 represents a distinct circularly permutated version of the BECR RNases. Protein Science, 2023, 32(1):e4531​.
Li H, Tan Y, Zhang D*. Genomic discovery and structural dissection of a novel polymorphic toxin system
in gram-positive bacteria. Computational and Structural Biotechnology Journal, 2022, 20:4517-4531.
Schneider T, Tan Y, Li H, Fisher J, Zhang D*. Photoglobin, a distinct family of non-heme binding globins, defines a potential
photosensor in prokaryotic signal transduction systems. Computational and Structural Biotechnology Journal, 2022, 20: 261-273.
Tan Y, Wang C, Schneider T, Li H, de Souza RF, Tang X, Swisher Grimm K, Hsieh TF,
Wang X, Li X, Zhang D* Comparative phylogenomic analysis reveals evolutionary genomic changes and novel
toxin families in endophytic Liberibacter pathogens. Microbiology Spectrum, 2021, 9 (2), e00509-21.
Tan Y, Schneider T, Shukla P, Chandrasekharan M, Aravind L, Zhang D*. Unification and extensive diversification of M/ORF3-related ion channel proteins in coronaviruses and other nidoviruses. Virus Evolution, 2021, 7(1): veab014.
Lin Z, Wang X, Wang J, Tan Y, Tang X, Werren J, Zhang D, Wang X. Comparative analysis revealed expansion of mitochondrial DNA control region containing unusually high G-C tandem repeat arrays in Nasonia vitripennis. International Journal of Biological Macromolecules, 2021, 166: 1246-1257.
Tan Y, Schneider T, Leong M, Aravind L, Zhang D* Novel Immunoglobulin Domain Proteins Provide Insights into Evolution and Pathogenesis of SARS-CoV-2-Related Viruses. mBio, 2020, 11(3):e00760-20.
Zhang C, Hung Y, Rim HJ, Zhang D, Frost JM, Shin H, Jang H, Liu F, Xiao W, Iyer LM, Aravind L, Zhang X, Fischer RL, Huh JH, ​Hsieh TF. The Catalytic Core of DEMETER Guides Active DNA Demethylation in Arabidopsis. PNAS. 2019, 116(35):17563-17571.​
Kostyniuk DJ, Zhang D, Martyniuk CJ, Marandel L, Gilmour KM, Mennigen J. Social status regulates the hepatic miRNAome in rainbow trout: Implications for posttranscriptional regulation of metabolic pathways. Plos ONE. 2019, 14(6):e0217978.
Makarova KS, Wolf YI, Karamycheva S, Zhang D, Aravind L, Koonin EV. Antimicrobial peptides, polymorphic toxins and self-nonself recognition systems in archaea: an untapped armory for inter-microbial conflicts. mBio. 10 (3), e00715-19.
Zeng Li, Zhang D (co-first), McLoughlin HS, Zalon AJ, Basappa J, Aravind L, Paulson HL. Loss of the Spinocerebellar Ataxia type 3 disease protein ATXN3 alters transcription of multiple signal transduction pathways. Plos ONE. 2018, 13(9): e0204438.
Wang Y, Liu J, Jin X, Zhang D, Li D, Hao F, Feng Y, Gu S, Meng F, Tian M, Zheng Y, Xin L, Zhang X, Han X, Aravind L, Wei M. O-GlcNAcylation destabilizes the active tetrameric PKM2 to promote the Warburg effect. PNAS. 2017, 114(52):13732-13737.
Li J, Bonkowski MS, Moniot S, Zhang D, Hubbard BP, Ling AJ, Rajman LA, Qin B, Lou Z, Gorbunova V, Aravind L, Steegborn C, Sinclair DA. A conserved NAD+ binding pocket that regulates protein-protein interactions during aging. Science. 2017, 355(6331):1312-1317.
Zhang D, Burroughs AM, Vidal ND, Iyer LM, Aravind L. Transposons to toxins: the provenance, architecture and diversification of a widespread class of eukaryotic effectors. Nucleic Acids Research. 2016, 44(8):3513-3533.
Iyer LM, Zhang D, Aravind L. Adenine methylation in eukaryotes: Apprehending the complex evolutionary history and functional potential of an epigenetic modification. BioEssays. 2016, 38(1):27-40.
Burroughs AM, Zhang D, Schäffer DE, Iyer LM, Aravind L. Comparative genomic analyses reveal a vast, novel network of nucleotide-centric systems in biological conflicts, immunity and signaling. Nucleic Acids Research. 2015, 43(22):10633-10654.
Aravind L, Zhang D, de Souza RF, Anand S, Iyer LM. The natural history of ADP-ribosyltransferases. Current Topics in Microbiology and Immunology. 2015, 384: 3-32.
Aravind L, Burroughs AM, Zhang D, Iyer LM. Protein and DNA modifications: evolutionary imprints of bacterial biochemical diversification and geochemistry on the provenance of eukaryotic epigenetics. Cold Spring Harbor Perspectives in Biology. 2014, 6(7):a016063.
Zhang D, Iyer LM, Burroughs AM, Aravind L. Resilience of biochemical activity in protein domains in the face of structural divergence. Current Opinion in Structural Biology. 2014, 26:92-103
Pusapati GV1, Hughes CE1, Dorn KV1, Zhang D (co-first), Sugianto P, Aravind L, Rohatgi R. EFCAB7 and IQCE regulate hedgehog signaling by tethering the EVC-EVC2 complex to the base of primary cilia. Developmental Cell. 2014, 28(5):483-496.
Iyer LM1, Zhang D (co-first), de Souza RF, Pukkila PJ, Rao A, Aravind L. Lineage-specific expansions of TET/JBP genes and a new class of DNA transposons shape fungal genomic and epigenetic landscapes. PNAS. 2014, 111(5):1676-1683.
Iyer LM, Zhang D, Burroughs AM, Aravind L. Computational identification of novel biochemical systems involved in oxidation, glycosylation and other complex modifications of bases in DNA. Nucleic Acids Research. 2013, 41(16):7635-7655.
Zhang D, Iyer LM, He F, Aravind L. Discovery of Novel DENN Proteins: Implications for the Evolution of Eukaryotic Intracellular Membrane Structures and Human Disease. Frontiers in Genetics: Bioinformatics and Computational Biology. 2012, 3:283.
Zhang D, Xi Y, Coccimiglio ML, Mennigen JA, Jonz MG, Ekker M, Trudeau VL. Functional prediction and physiological characterization of a novel short trans-membrane protein 1 as a subunit of mitochondrial respiratory complexes. Physiological Genomics. 2012, 44(23):1133-1140.
Zhang D, Aravind L. Novel transglutaminase-like peptidase and C2 domains elucidate the structure, biogenesis and evolution of the ciliary compartment. Cell Cycle. 2012, 1(20):3861-3875.
Zhang D, Iyer LM, Aravind L. Bacterial GRAS domain proteins throw new light on gibberellic acid response mechanisms. Bioinformatics. 2012, 28(19):2407-2411.
Zhang D, de Souza RF, Anantharaman V, Iyer LM, Aravind L. Polymorphic toxin systems: Comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Biology Direct. 2012, 7:18.
Iyer LM, Zhang D, Rogozin IB, Aravind L. Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. Nucleic Acids Research. 2011, 39(22):9473-9497.
Zhang D, Iyer LM, Aravind L. A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems. Nucleic Acids Research. 2011, 39(11):4532-4552.
Zhang D, Aravind L. Identification of novel families and classification of the C2 domain superfamily elucidate the origin and evolution of membrane targeting activities in eukaryotes. Gene. 2010, 469(1-2):18-30.
Zhang D, Xiong H, Mennigen JA, Popesku JT, Marlatt VL, Martyniuk CJ, Crump K, Cossins AR, Xia X, Trudeau VL. Defining global neuroendocrine gene expression patterns associated with reproductive seasonality in fish. PLoS One. 2009, 4(6):e5816.
Xiong H, Zhang D, Martyniuk CJ, Trudeau VL, Xia X. Using generalized procrustes analysis (GPA) for normalization of cDNA microarray data. BMC Bioinformatics. 2008, 9:25.
Zhang D, Xiong H, Shan J, Xia X, Trudeau VL. Functional insight into Maelstrom in the germline piRNA pathway: A unique domain homologous to the DnaQ-H 3'-5' exonuclease, its lineage-specific expansion/loss and evolutionarily active site switch. Biology Direct. 2008, 3:48.