My current H-index is 31 (my Google Scholar page)
Representative Articles:
2022
59) 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.
58) 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.
57) 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.
2021
56) 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.
55) Zhao Y, He W, Li W, Zhao Z, Wang Q, Hou Y, Tan Y, Zhang D. Acidic pH irreversibly activates the signaling enzyme SARM1. FEBS Journal, 2021, doi: 10.1111/febs.16104.
54) 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.
53) Hicksa K, Tan Y, Cao W, Hathcock T. Boothe D, Kennis R, Zhang D, Wang X, and White A. Genomic and in vitro pharmacodynamic analysis of rifampicin resistance at clinically relevant concentrations in multidrug-resistant canine Staphylococcus pseudintermedius isolates. Veterinary Dermatology , 2021, 32 (3), 219-e67.
52) 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.
2020
51) Sur S, Nakanishi H, Steele R, Zhang D, Varvares M, Ray R. Long non-coding RNA ELDR enhances oral cancer growth by promoting ILF3-cyclin E1 signaling. EMBO Reports, 2020, 21 (12), e51042.
50) Cao W, Hicks K, White A, Hathcock T, Kennis R, Boothe D, Zhang D, Wang X. Draft Genome Assemblies of Two Staphylococcus pseudintermedius Strains Isolated from Canine Skin Biopsy Specimens. Microbiology Resource Announcements, 2020, 9(22):e00369-20.
49) 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.
2019
48) Kostyniuk DJ, Marandel L, Jubouri M, Dias K, Panserat S, Zhang D, de Souza RF, Martyniuk CJ, Mennigen JA. Profiling the rainbow trout hepatic miRNAome under diet-induced hyperglycemia. Physiological Genomics. 2019, 51(9):411-431.
47) 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. Proceedings of the National Academy of Sciences of the United States of America. 2019, 116(35):17563-17571.
46) 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.
45) 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.
2018
44) 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.
2017
43) 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. Proceedings of the National Academy of Sciences of the United States of America. 2017, 114(52):13732-13737.
42) Burroughs AM, Kaur G, Zhang D, Aravind L. Novel clades of the hu/ihf superfamily point to unexpected roles in the eukaryotic centrosome, chromosome partitioning, and biological conflicts. Cell Cycle. 2017, 16(11):1093-1103.
41) 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.
2016
40) 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.
39) Iyer LM, Zhang D, Aravind L. Adenine methylation in eukaryotic DNA: apprehending the complex evolutionary history and functional potential of an epigenetic modification. BioEssays. 2016, 38(1):27-40.
38) Mennigen JA, Zhang D. MicroTrout: A comprehensive, genome-wide miRNA target prediction framework for rainbow trout, Onchorynchus mykiss. Comparative Biochemistry and Physiology - Part D: Genomics & Proteomics. 2016, 20: 19–26.
37) Venables MJ, Navarro-Martín L, Basak A, Baum BR, Zhang D, Trudeau VL. Characterization of multiple nestin isoforms in the goldfish brain. Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics. 2016, 19:8-17.
36) He F, Jones JM, Figueroa-Romero C, Zhang D, Feldman EF, Meisler MH, Callaghan BC, Todd PK. Screening for novel hexanucleotide repeat expansions at ALS- and FTD-associated loci. Neurology: Genetics. 2016, 2(3): e71.
2015
35) Burroughs AM, Zhang D, Iyer LM, Schaeffer D, 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.
34) Burroughs AM, Zhang D, Aravind L. The eukaryotic translation initiation regulator CDC123 defines a divergent clade of ATP-grasp enzymes with a predicted role in novel protein modifications. Biology Direct. 2015, 10(1):21.
33) Xi Y, Honeywell C, Zhang D, Schwartzentruber J, Beaulieu CL, Tetreault M, Hartley T, Majewski J, Aravind L, Care4Rare Canada Consortium, Gollob M, Boycott KM, Gow RM. Whole exome sequencing identifies the TNNI3K gene as a cause of familial conduction system disease and congenital junctional ectopic tachycardia. International Journal of Cardiology. 2015, 185:114-116.
32) Aravind L, Zhang D, Iyer LM. The TET/JBP family of nucleic base-modifying 2-oxoglutarate and iron-dependent dioxygenases. 2-Oxoglutarate-Dependent Oxygenases. 2015, 3 (12): 289-308.
31) 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.
2014
30) Iyer LM, 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. Proceedings of the National Academy of Sciences of the United States of America. 2014, 111(5):1676-1683.
29) 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, 26C:92-103.
28) Pusapati G, Hughes CE, Dorn KV, 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.
27) 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.
2013
26) 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.
25) Lado WE, Zhang D, Mennigen JA, Zamora JM, Popesku JT, Lewis JE, Trudeau VL. Rapid modulation of gene expression profiles in the forebrain of male goldfish following exposure to waterborne sex pheromones. General and Comparative Endocrinology. 2013, 192:204-213.
2012
24) Zhang D, Iyer LM, He F, Aravind L. Discovery of novel DENN proteins: implications for dynamics and evolution of eukaryotic intracellular membrane structures and human disease. Frontiers in Genetics: Bioinformatics and Computational Biology. 2012, 3:283.
23) Zhang D, Xi Y,Coccimiglio ML, Mennigen JA, Jonz M, 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.
22) Zhang D, Aravind L. Novel transglutaminase-like peptidase and C2 domains elucidate the structure, biogenesis and evolution of the ciliary compartment. Cell Cycle. 2012, 3861-3875.
21) Zhang D, Iyer LM, Aravind L. Bacterial GRAS domain proteins throw new light on gibberellic acid response mechanisms. Bioinformatics. 2012, 28(19): 2407-2411.
20) Aravind L, Anantharaman V, Zhang D, de Souza RF, Iyer LM. Gene flow and biological conflict systems in the origin and evolution of eukaryotes. Frontier in Cellular and Infection Microbiology. 2012, 2:89.
19) 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.
2011
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.
17) 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.
2010
16) 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.
15) Anantharaman V, Zhang D, Aravind L. OST-HTH: a novel predicted RNA-binding domain. Biology Direct. 2010, 5:13.
14) Zhao E, Grey CL, Zhang D, Mennigen JA, Basak A, Chang JP, Trudeau VL. Secretoneurin (SN) is a paracrine factor from lactotrophs stimulating gonadotropin release in the goldfish pituitary. American Journal of Physiology - Regulatory, Integrative and Comparative Physiology. 2010, 299(5):R1290-1297.
13) Zhang D, Duarte-Guterman P, Langlois VS, Trudeau VL. Temporal expression and steroidal regulation of piRNA pathway genes (mael, piwi, vasa) during Silurana (Xenopus) tropicalis embryogenesis. Comparative Biochemistry and Physiology - Part C: Toxicology & Pharmacology. 2010, 152(2): 202-206.
12) Langlois VS, Zhang D, Cooke G, Trudeau VL. Evolution of steroid 5-alpha-reductases and comparison of their function with 5-beta-reductase. General and Comparative Endocrinology. 2010, 166(3): 489-497.
2009
11) Zhang D, Xiong H, Mennigen JA, Popesku JT, Marlatt VL, Martyniuk CJ, Crump K, Xia X, Cossins AR, Trudeau VL. Defining neuroendocrine gene expression patterns associated with reproductive seasonality in fish. PLoS ONE. 2009, 4(6): e5816.
10) Zhang D. Homology between DUF784, DUF1278 domains and the plant prolamin superfamily typifies evolutionary changes of disulfide bonding patterns. Cell Cycle. 2009, 8(20): 3428-3430.
9) Zhang D, Popesku JT, Martyniuk CJ, Xiong H, Duarte-Guterman P, Yao L, Xia X, Trudeau VL. Profiling neuroendocrine gene expression changes following fadrozole-induced estrogen decline in the female goldfish. Physiological Genomics. 2009, 38: 351-361.
8) Zhao E, Zhang D, Basak A, Trudeau VL. New insights into granin-derived peptides: evolution and endocrine roles. General and Comparative Endocrinology. 2009, 164(2-3): 161-174.
2008
7) 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.
6) Popesku JT, Martyniuk CJ, Mennigen JA, Xiong H, Zhang D, Xia X, Cossins AR, Trudeau VL. The goldfish (Carassius auratus) as a model for neuroendocrine signaling. Molecular and Cellular Endocrinology. 2008, 293(1-2):43-56.
5) Xiong H, Zhang D, Martyniuk CJ, Trudeau VL, Xia X. Using generalized Procrustes analysis for normalization of cDNA microarray data. BMC Bioinformatics. 2008, 9:25.
4) Zhang D, Trudeau VL. The XS domain of a plant specific SGS3 protein adopts a unique RNA recognition motif (RRM) fold. Cell Cycle.2008, 7(14):2268-2270.
3) Marlatt VL, Martyniuk CJ, Zhang D, Xiong H, Watt J, Xia X, Moon T, Trudeau VL. Auto-regulation of estrogen receptor subtypes and gene expression profiling of 17beta-estradiol action in the neuroendocrine axis of male goldfish. Molecular and Cellular Endocrinology. 2008, 283(1-2):38-48.
2006
2) Zhang D, Martyniuk CJ, Trudeau VL. SANTA domain: a novel conserved protein module in Eukaryota with potential involvement in chromatin regulation. Bioinformatics. 2006, 22 (20):2459-2462.
1) Zhang D, Trudeau VL. Integration of membrane and nuclear estrogen receptor signaling. Comparative Biochemistry and Physiology - Part A: Molecular & Integrative Physiology. 2006, 144 (3):306-315.
Representative Articles:
- 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.
- 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.
- 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.
- 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 (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. Proceedings of the National Academy of Sciences of the United States of America. 2014, 111(5):1676-1683.
- 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, 26C:92-103.
- 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, 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.
- Zhang D, Iyer LM, He F, Aravind L. Discovery of novel DENN proteins: implications for dynamics and evolution of eukaryotic intracellular membrane structures and human disease. Frontiers in Genetics: Bioinformatics and Computational Biology. 2012, 3:283.
- 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, Xiong H, Mennigen JA, Popesku JT, Marlatt VL, Martyniuk CJ, Crump K, Xia X, Cossins AR, Trudeau VL. Defining neuroendocrine gene expression patterns associated with reproductive seasonality in fish. PLoS ONE. 2009, 4(6): e5816.
2022
59) 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.
58) 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.
57) 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.
2021
56) 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.
55) Zhao Y, He W, Li W, Zhao Z, Wang Q, Hou Y, Tan Y, Zhang D. Acidic pH irreversibly activates the signaling enzyme SARM1. FEBS Journal, 2021, doi: 10.1111/febs.16104.
54) 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.
- BioRxiv version: Unification of the M/ORF3-related proteins points to a diversified role for ion conductance in pathogenesis of coronaviruses and other nidoviruses. bioRxiv. 2020 November 11;2020.11.10.377366. doi: 10.1101/2020.11.10.377366.
53) Hicksa K, Tan Y, Cao W, Hathcock T. Boothe D, Kennis R, Zhang D, Wang X, and White A. Genomic and in vitro pharmacodynamic analysis of rifampicin resistance at clinically relevant concentrations in multidrug-resistant canine Staphylococcus pseudintermedius isolates. Veterinary Dermatology , 2021, 32 (3), 219-e67.
52) 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.
2020
51) Sur S, Nakanishi H, Steele R, Zhang D, Varvares M, Ray R. Long non-coding RNA ELDR enhances oral cancer growth by promoting ILF3-cyclin E1 signaling. EMBO Reports, 2020, 21 (12), e51042.
50) Cao W, Hicks K, White A, Hathcock T, Kennis R, Boothe D, Zhang D, Wang X. Draft Genome Assemblies of Two Staphylococcus pseudintermedius Strains Isolated from Canine Skin Biopsy Specimens. Microbiology Resource Announcements, 2020, 9(22):e00369-20.
49) 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.
- BioRxiv version: Novel Immunoglobulin Domain Proteins Provide Insights into Evolution and Pathogenesis Mechanisms of SARS-Related Coronaviruses. bioRxiv . 2020 Mar 7;2020.03.04.977736. doi: 10.1101/2020.03.04.977736.
2019
48) Kostyniuk DJ, Marandel L, Jubouri M, Dias K, Panserat S, Zhang D, de Souza RF, Martyniuk CJ, Mennigen JA. Profiling the rainbow trout hepatic miRNAome under diet-induced hyperglycemia. Physiological Genomics. 2019, 51(9):411-431.
47) 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. Proceedings of the National Academy of Sciences of the United States of America. 2019, 116(35):17563-17571.
46) 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.
45) 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.
2018
44) 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.
2017
43) 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. Proceedings of the National Academy of Sciences of the United States of America. 2017, 114(52):13732-13737.
42) Burroughs AM, Kaur G, Zhang D, Aravind L. Novel clades of the hu/ihf superfamily point to unexpected roles in the eukaryotic centrosome, chromosome partitioning, and biological conflicts. Cell Cycle. 2017, 16(11):1093-1103.
41) 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.
- Over 150 news highlights (Altmetric)
- Over 90 citations
2016
40) 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.
39) Iyer LM, Zhang D, Aravind L. Adenine methylation in eukaryotic DNA: apprehending the complex evolutionary history and functional potential of an epigenetic modification. BioEssays. 2016, 38(1):27-40.
- Over 75 citations
38) Mennigen JA, Zhang D. MicroTrout: A comprehensive, genome-wide miRNA target prediction framework for rainbow trout, Onchorynchus mykiss. Comparative Biochemistry and Physiology - Part D: Genomics & Proteomics. 2016, 20: 19–26.
37) Venables MJ, Navarro-Martín L, Basak A, Baum BR, Zhang D, Trudeau VL. Characterization of multiple nestin isoforms in the goldfish brain. Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics. 2016, 19:8-17.
36) He F, Jones JM, Figueroa-Romero C, Zhang D, Feldman EF, Meisler MH, Callaghan BC, Todd PK. Screening for novel hexanucleotide repeat expansions at ALS- and FTD-associated loci. Neurology: Genetics. 2016, 2(3): e71.
2015
35) Burroughs AM, Zhang D, Iyer LM, Schaeffer D, 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.
- Over 75 citations
34) Burroughs AM, Zhang D, Aravind L. The eukaryotic translation initiation regulator CDC123 defines a divergent clade of ATP-grasp enzymes with a predicted role in novel protein modifications. Biology Direct. 2015, 10(1):21.
33) Xi Y, Honeywell C, Zhang D, Schwartzentruber J, Beaulieu CL, Tetreault M, Hartley T, Majewski J, Aravind L, Care4Rare Canada Consortium, Gollob M, Boycott KM, Gow RM. Whole exome sequencing identifies the TNNI3K gene as a cause of familial conduction system disease and congenital junctional ectopic tachycardia. International Journal of Cardiology. 2015, 185:114-116.
32) Aravind L, Zhang D, Iyer LM. The TET/JBP family of nucleic base-modifying 2-oxoglutarate and iron-dependent dioxygenases. 2-Oxoglutarate-Dependent Oxygenases. 2015, 3 (12): 289-308.
31) 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.
2014
30) Iyer LM, 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. Proceedings of the National Academy of Sciences of the United States of America. 2014, 111(5):1676-1683.
29) 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, 26C:92-103.
28) Pusapati G, Hughes CE, Dorn KV, 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.
- Over 50 citations
27) 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.
- Featured as cover article
2013
26) 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.
- NAR featured article
- Over 60 citations
25) Lado WE, Zhang D, Mennigen JA, Zamora JM, Popesku JT, Lewis JE, Trudeau VL. Rapid modulation of gene expression profiles in the forebrain of male goldfish following exposure to waterborne sex pheromones. General and Comparative Endocrinology. 2013, 192:204-213.
2012
24) Zhang D, Iyer LM, He F, Aravind L. Discovery of novel DENN proteins: implications for dynamics and evolution of eukaryotic intracellular membrane structures and human disease. Frontiers in Genetics: Bioinformatics and Computational Biology. 2012, 3:283.
- News Highlights on Alzheimer Research Forum and Birt-Hogg-Dubé Syndrome Foundation
- Over 210 citations
23) Zhang D, Xi Y,Coccimiglio ML, Mennigen JA, Jonz M, 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.
22) Zhang D, Aravind L. Novel transglutaminase-like peptidase and C2 domains elucidate the structure, biogenesis and evolution of the ciliary compartment. Cell Cycle. 2012, 3861-3875.
21) Zhang D, Iyer LM, Aravind L. Bacterial GRAS domain proteins throw new light on gibberellic acid response mechanisms. Bioinformatics. 2012, 28(19): 2407-2411.
- Over 50 citations
20) Aravind L, Anantharaman V, Zhang D, de Souza RF, Iyer LM. Gene flow and biological conflict systems in the origin and evolution of eukaryotes. Frontier in Cellular and Infection Microbiology. 2012, 2:89.
19) 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.
- Featured as the No. 28 most accessed article all the time in the journal
- A monograph of 76 pages, reporting over 150 novel toxin domains and over 90 novel immunity protein families involved in species conflict and host-pathogen interactions
- Over 275 citations
2011
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.
- NAR featured article and top accessed article
- Over 100 citations
17) 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.
- NAR featured article and top accessed article
- Over 120 citations
2010
16) 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.
- Highly accessed
- Over 80 citations
15) Anantharaman V, Zhang D, Aravind L. OST-HTH: a novel predicted RNA-binding domain. Biology Direct. 2010, 5:13.
14) Zhao E, Grey CL, Zhang D, Mennigen JA, Basak A, Chang JP, Trudeau VL. Secretoneurin (SN) is a paracrine factor from lactotrophs stimulating gonadotropin release in the goldfish pituitary. American Journal of Physiology - Regulatory, Integrative and Comparative Physiology. 2010, 299(5):R1290-1297.
13) Zhang D, Duarte-Guterman P, Langlois VS, Trudeau VL. Temporal expression and steroidal regulation of piRNA pathway genes (mael, piwi, vasa) during Silurana (Xenopus) tropicalis embryogenesis. Comparative Biochemistry and Physiology - Part C: Toxicology & Pharmacology. 2010, 152(2): 202-206.
12) Langlois VS, Zhang D, Cooke G, Trudeau VL. Evolution of steroid 5-alpha-reductases and comparison of their function with 5-beta-reductase. General and Comparative Endocrinology. 2010, 166(3): 489-497.
2009
11) Zhang D, Xiong H, Mennigen JA, Popesku JT, Marlatt VL, Martyniuk CJ, Crump K, Xia X, Cossins AR, Trudeau VL. Defining neuroendocrine gene expression patterns associated with reproductive seasonality in fish. PLoS ONE. 2009, 4(6): e5816.
- Over 40 citations
10) Zhang D. Homology between DUF784, DUF1278 domains and the plant prolamin superfamily typifies evolutionary changes of disulfide bonding patterns. Cell Cycle. 2009, 8(20): 3428-3430.
9) Zhang D, Popesku JT, Martyniuk CJ, Xiong H, Duarte-Guterman P, Yao L, Xia X, Trudeau VL. Profiling neuroendocrine gene expression changes following fadrozole-induced estrogen decline in the female goldfish. Physiological Genomics. 2009, 38: 351-361.
8) Zhao E, Zhang D, Basak A, Trudeau VL. New insights into granin-derived peptides: evolution and endocrine roles. General and Comparative Endocrinology. 2009, 164(2-3): 161-174.
- Featured as cover article
2008
7) 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.
- Over 40 citations
6) Popesku JT, Martyniuk CJ, Mennigen JA, Xiong H, Zhang D, Xia X, Cossins AR, Trudeau VL. The goldfish (Carassius auratus) as a model for neuroendocrine signaling. Molecular and Cellular Endocrinology. 2008, 293(1-2):43-56.
5) Xiong H, Zhang D, Martyniuk CJ, Trudeau VL, Xia X. Using generalized Procrustes analysis for normalization of cDNA microarray data. BMC Bioinformatics. 2008, 9:25.
- Highly accessed
- Over 40 citations
4) Zhang D, Trudeau VL. The XS domain of a plant specific SGS3 protein adopts a unique RNA recognition motif (RRM) fold. Cell Cycle.2008, 7(14):2268-2270.
- Faculty of 1000 Biology
3) Marlatt VL, Martyniuk CJ, Zhang D, Xiong H, Watt J, Xia X, Moon T, Trudeau VL. Auto-regulation of estrogen receptor subtypes and gene expression profiling of 17beta-estradiol action in the neuroendocrine axis of male goldfish. Molecular and Cellular Endocrinology. 2008, 283(1-2):38-48.
- Over 110 citations
2006
2) Zhang D, Martyniuk CJ, Trudeau VL. SANTA domain: a novel conserved protein module in Eukaryota with potential involvement in chromatin regulation. Bioinformatics. 2006, 22 (20):2459-2462.
1) Zhang D, Trudeau VL. Integration of membrane and nuclear estrogen receptor signaling. Comparative Biochemistry and Physiology - Part A: Molecular & Integrative Physiology. 2006, 144 (3):306-315.
- Top accessed for 5 years
- Over 110 citations
