Baojun Wu, Ph D
Education
Ph.D., Developmental immunology, Shandong University, China.
Research interests
Origin and evolution of immune system, mitochondrial genome evolution and fungi genome evolution.
Publications(*Corresponding author; #Contributed equally)
Comparative Genomics and Genome Architecture [9 publications]
Wu B, Cox MP. Characterization of bicistronic transcription in budding yeast. mSystems 6 (2021), e01002-20.
Nguyen DT#, Wu B#, Xiao S#, Hao W. Evolution of a record-setting AT-rich genome: indel mutation, recombination, and substitution bias. Genome Biol Evol 12 (2020), 2344–2354.
Wu B, Hao W. Mitochondrial-encoded endonucleases drive recombination of protein coding genes in yeast. Environ Microbiol 21 (2019), 4233-4240.
Wu B,* and Knudson A. Tracing de novo origin of protein-coding genes in yeast. mBio 9 (2018) e01024-18.
Wu B, Macielog, AI, Hao W. Origin and spread of spliceosomal introns: insights from the fungal clade Zymoseptoria. Genome Biol Evol 9 (2017), 2658–2667.
Xiao S, Nguyen DT, Wu B, Hao, W. Genetic drift and indel mutation in the evolution of yeast mitochondrial genome size. Genome Biol Evol 9 (2017), 3088–3099.
Wu B, Buljic A, Hao W. Extensive horizontal transfer and homologous recombination generate highly chimeric mitochondrial genomes in yeast. Mol Biol Evol 32 (2015), 2559-2570.
Wu B, Hao W. A dynamic mobile DNA family in the yeast mitochondrial genome. G3 5 (2015), 1273-1282.
Wu B, Hao W. Horizontal transfer and gene conversion as an important driving force in shaping the landscape of mitochondrial introns. G3 4 (2014), 605-612.
Genomics on Adaptation [7 publications]
Sabat G, Ahrendt S, Wu B, Gaskell J, Held BW, Toapanta C, Vuong TV, Lipzen A, Zhang J, Schilling JS et al: Proteome of the wood decay fungus Fomitopsis pinicola Is altered by substrate. Microbiol Resour Announc 2022:e0058622.
Wu B., Hao W and Cox, MP. Reconstruction of gene innovation associated with major evolutionary transitions in the kingdom Fungi. BMC Biology 20 (2022), 144.
Min B, Wu B, Gaskell J, Zhang J, Toapanta C, Ahrendt S, Blanchette RA, Master E, Cullen D, Hibbett, DS, Grigoriev IV. RNA-editing in Basidiomycota, revisited. ISME Commun 1 (2021), 70.
Wu B, Cox, MP. Comparative genomics reveals a core gene toolbox for lifestyle transitions in Hypocreales fungi. Environ Microbiol 23 (2021), 3251-3264.
Wu B, Cox, MP. Greater genetic and regulatory plasticity of retained duplicates in Epichloë endophytic fungi. Mol Ecol 28 (2019), 5103-5114.
Wu B#, Xu Z#, Knudson A#, Carlson A, Chen N, Kovaka S, LaButti K, Lipzen A, Pennachio C, Riley R, Schakwitz W, Umezawa K, Ohm RA, Grigoriev IV, Nagy LG, Gibbons J, Hibbett D. Genomics and development of Lentinus tigrinus, a white-rot wood-decaying mushroom with dimorphic fruiting bodies. Genome Biol Evol 10 (2018), 3250–3261.
Wu B, Gaskell J, Held BW, Toapanta C, Vuong T, Ahrendt S, Lipzen A, Zhang J, Schilling JS, Master E, Grigoriev IV, Blanchette RA, Cullen D, Hibbett DS. Substrate-specific differential gene expression and RNA editing in the brown rot fungus Fomitopsis. Appl Environ Microbiol 84 (2018) e00991-18.
Study on Spontaneous Mutation [1 publication]
Nguyen DT, Wu B, Long H, Zhang N, Patterson C, Simpson S, Morris K, Thomas WK, Lynch M, Hao W. Variable spontaneous mutation and loss of heterozygosity among heterozygous genomes in yeast. Mol Biol Evol 37 (2020), 3118–3130.
Evolution of Immune System [10 publications]
Wu B, Gong J, Yuan S, Zhang Y, Wei T. Patterns of evolutionary selection pressure in the immune signaling protein TRAF3IP2 in mammals. Gene 531 (2013), 403-410.
Wu B, Gong J, Liu L, Li T, Wei T, Bai, Z. Evolution of prokaryotic homologues of the eukaryotic SEFIR protein domain. Gene 492 (2012), 160-166.
Liu L, Du X, Wang Z, Wu B, Jin M, Xin B, Wang D, Bai Z. A simplified intrathymic injection technique for mice. Biotech Histochem 87 (2012), 140-147.
Wu B, Xin B, Jin M, Wei T, Bai Z. Comparative and phylogeneticanalyses of three TIR domain-containing adaptors in metazoans: implications for evolution of TLR signaling pathways. Dev Comp Immunol 35 (2011), 764-773.
Wu B, Jin M, Gong J, Du X, Bai Z. Dynamic evolution of CIKS(TRAF3IP2/Act1) in metazoans. Dev Comp Immunol 35 (2011), 1186-1192.
Wu B, Jin M, Zhang Y, Wei T, Bai Z. Evolution of the IL17 receptor family in chordates: a new subfamily IL17REL. Immunogenetics 63 (2011), 835-845.
Wu B, Huan T, Gong J, Zhou P, Bai Z. Domain combination of the vertebrate-like TLR gene family: implications for their origin and evolution. J.Genet 90 (2011), 401-408.
Du X, Bai Z, Zhang J, Liu L, Han Y, Wang Z, Huan T, Wu B. Prolonged survival of human hepatocarcinoma cells in the liver of newborn C57BL/6 mice and resulting cellular xenorejection, especially the activation of hepatic natural killer T cells. Pathobiology 77 (2010), 115-128.
Xiao Y, Wang J, Wu B, Bai Z. Screening of bone fracture healing related genes from differentially gene expression profiles in osteogenic growth peptide-induced rat bone marrow stromal cells. Chinese Journal of osteoporosis 16 (2010), 473-475.
Xiao Y, Wang J, Liu L, Wu B, Bai Z. Establishment of an immunoassay method for Osteogenic Growth Peptide. Chinese Journal of Immunology 25 (2009), 1116-1118.
Oral Presentations
Wu, B. Retained duplication in Epichloë. Lincoln University. 02/2019 Christchurch, NZ.
Wu, B. The Secret of Intron: Origin and Spread. Clark University. 03/2017 Worcester USA.
Wu, B. Evolutionary story of IL17Rs and TLRs signaling pathway. Bio-Techne Corporation. 08/2015 Minneapolis USA.
Poster Presentations
Wu, B and Hao, W. Transposable Elements in the Yeast Mitochondrial Genome. The 23st Annual Conference of the SMBE, 07/2015 Venice.
Wu, B and Hao, W. Horizontal transfer and genome size evolution in yeast mitochondria. The 22st Annual Conference of the SMBE, 06/2014 Puerto Rico.
Wu, B and Hao,W. Homologous Recombination Facilitates Selfish Gene Invasion: Insights from Chimeric Group I Introns. The 21st Annual Conference of the Society for Molecular Biology and Evolution, July 2013 Chicago.
Wu, B., Wei, T. and Bai, Z. Evolution of SEFIR Protein Domain: A Horizontal Gene Transfer from Eukaryotes to Prokaryotes.The 6th International Conference on Bioinformatics and Biomedical Engineering (iCBBE), May 2012 Shanghai.
Reviewer services
Gene, Genome, G3, Molecular Genetics and Genomics, Mycologia, Evolutionary Bioinformatics, Gene reports, Frontiers in Genetics, Frontiers in Immunology, Frontiers in Microbiology, Frontiers in Plant Science, Frontiers in Cellular and Infection Microbiology, Journal of Fungi, Scientific Reports, Plos one and PLOS Computational Biology.
Editorial Appointment
02/2016-present, Editorial Board of Frontiers in Microbiology.
Research experiences
Postdoctoral Fellow at Massey University with Murray Cox/Tim Cooper.
Postdoctoral Fellow at Clark university with Dr. David Hibbett.
Postdoctoral Fellow at Wayne state university with Dr. Weilong Hao.
Contribution to LRRML and TollML databases.
Award
China Baosteel Scholarship (Outstanding Student Award), Baosteel Education Fund, 2011.
Ph.D., Developmental immunology, Shandong University, China.
Research interests
Origin and evolution of immune system, mitochondrial genome evolution and fungi genome evolution.
Publications(*Corresponding author; #Contributed equally)
Comparative Genomics and Genome Architecture [9 publications]
Wu B, Cox MP. Characterization of bicistronic transcription in budding yeast. mSystems 6 (2021), e01002-20.
Nguyen DT#, Wu B#, Xiao S#, Hao W. Evolution of a record-setting AT-rich genome: indel mutation, recombination, and substitution bias. Genome Biol Evol 12 (2020), 2344–2354.
Wu B, Hao W. Mitochondrial-encoded endonucleases drive recombination of protein coding genes in yeast. Environ Microbiol 21 (2019), 4233-4240.
Wu B,* and Knudson A. Tracing de novo origin of protein-coding genes in yeast. mBio 9 (2018) e01024-18.
Wu B, Macielog, AI, Hao W. Origin and spread of spliceosomal introns: insights from the fungal clade Zymoseptoria. Genome Biol Evol 9 (2017), 2658–2667.
Xiao S, Nguyen DT, Wu B, Hao, W. Genetic drift and indel mutation in the evolution of yeast mitochondrial genome size. Genome Biol Evol 9 (2017), 3088–3099.
Wu B, Buljic A, Hao W. Extensive horizontal transfer and homologous recombination generate highly chimeric mitochondrial genomes in yeast. Mol Biol Evol 32 (2015), 2559-2570.
Wu B, Hao W. A dynamic mobile DNA family in the yeast mitochondrial genome. G3 5 (2015), 1273-1282.
Wu B, Hao W. Horizontal transfer and gene conversion as an important driving force in shaping the landscape of mitochondrial introns. G3 4 (2014), 605-612.
Genomics on Adaptation [7 publications]
Sabat G, Ahrendt S, Wu B, Gaskell J, Held BW, Toapanta C, Vuong TV, Lipzen A, Zhang J, Schilling JS et al: Proteome of the wood decay fungus Fomitopsis pinicola Is altered by substrate. Microbiol Resour Announc 2022:e0058622.
Wu B., Hao W and Cox, MP. Reconstruction of gene innovation associated with major evolutionary transitions in the kingdom Fungi. BMC Biology 20 (2022), 144.
Min B, Wu B, Gaskell J, Zhang J, Toapanta C, Ahrendt S, Blanchette RA, Master E, Cullen D, Hibbett, DS, Grigoriev IV. RNA-editing in Basidiomycota, revisited. ISME Commun 1 (2021), 70.
Wu B, Cox, MP. Comparative genomics reveals a core gene toolbox for lifestyle transitions in Hypocreales fungi. Environ Microbiol 23 (2021), 3251-3264.
Wu B, Cox, MP. Greater genetic and regulatory plasticity of retained duplicates in Epichloë endophytic fungi. Mol Ecol 28 (2019), 5103-5114.
Wu B#, Xu Z#, Knudson A#, Carlson A, Chen N, Kovaka S, LaButti K, Lipzen A, Pennachio C, Riley R, Schakwitz W, Umezawa K, Ohm RA, Grigoriev IV, Nagy LG, Gibbons J, Hibbett D. Genomics and development of Lentinus tigrinus, a white-rot wood-decaying mushroom with dimorphic fruiting bodies. Genome Biol Evol 10 (2018), 3250–3261.
Wu B, Gaskell J, Held BW, Toapanta C, Vuong T, Ahrendt S, Lipzen A, Zhang J, Schilling JS, Master E, Grigoriev IV, Blanchette RA, Cullen D, Hibbett DS. Substrate-specific differential gene expression and RNA editing in the brown rot fungus Fomitopsis. Appl Environ Microbiol 84 (2018) e00991-18.
Study on Spontaneous Mutation [1 publication]
Nguyen DT, Wu B, Long H, Zhang N, Patterson C, Simpson S, Morris K, Thomas WK, Lynch M, Hao W. Variable spontaneous mutation and loss of heterozygosity among heterozygous genomes in yeast. Mol Biol Evol 37 (2020), 3118–3130.
Evolution of Immune System [10 publications]
Wu B, Gong J, Yuan S, Zhang Y, Wei T. Patterns of evolutionary selection pressure in the immune signaling protein TRAF3IP2 in mammals. Gene 531 (2013), 403-410.
Wu B, Gong J, Liu L, Li T, Wei T, Bai, Z. Evolution of prokaryotic homologues of the eukaryotic SEFIR protein domain. Gene 492 (2012), 160-166.
Liu L, Du X, Wang Z, Wu B, Jin M, Xin B, Wang D, Bai Z. A simplified intrathymic injection technique for mice. Biotech Histochem 87 (2012), 140-147.
Wu B, Xin B, Jin M, Wei T, Bai Z. Comparative and phylogeneticanalyses of three TIR domain-containing adaptors in metazoans: implications for evolution of TLR signaling pathways. Dev Comp Immunol 35 (2011), 764-773.
Wu B, Jin M, Gong J, Du X, Bai Z. Dynamic evolution of CIKS(TRAF3IP2/Act1) in metazoans. Dev Comp Immunol 35 (2011), 1186-1192.
Wu B, Jin M, Zhang Y, Wei T, Bai Z. Evolution of the IL17 receptor family in chordates: a new subfamily IL17REL. Immunogenetics 63 (2011), 835-845.
Wu B, Huan T, Gong J, Zhou P, Bai Z. Domain combination of the vertebrate-like TLR gene family: implications for their origin and evolution. J.Genet 90 (2011), 401-408.
Du X, Bai Z, Zhang J, Liu L, Han Y, Wang Z, Huan T, Wu B. Prolonged survival of human hepatocarcinoma cells in the liver of newborn C57BL/6 mice and resulting cellular xenorejection, especially the activation of hepatic natural killer T cells. Pathobiology 77 (2010), 115-128.
Xiao Y, Wang J, Wu B, Bai Z. Screening of bone fracture healing related genes from differentially gene expression profiles in osteogenic growth peptide-induced rat bone marrow stromal cells. Chinese Journal of osteoporosis 16 (2010), 473-475.
Xiao Y, Wang J, Liu L, Wu B, Bai Z. Establishment of an immunoassay method for Osteogenic Growth Peptide. Chinese Journal of Immunology 25 (2009), 1116-1118.
Oral Presentations
Wu, B. Retained duplication in Epichloë. Lincoln University. 02/2019 Christchurch, NZ.
Wu, B. The Secret of Intron: Origin and Spread. Clark University. 03/2017 Worcester USA.
Wu, B. Evolutionary story of IL17Rs and TLRs signaling pathway. Bio-Techne Corporation. 08/2015 Minneapolis USA.
Poster Presentations
Wu, B and Hao, W. Transposable Elements in the Yeast Mitochondrial Genome. The 23st Annual Conference of the SMBE, 07/2015 Venice.
Wu, B and Hao, W. Horizontal transfer and genome size evolution in yeast mitochondria. The 22st Annual Conference of the SMBE, 06/2014 Puerto Rico.
Wu, B and Hao,W. Homologous Recombination Facilitates Selfish Gene Invasion: Insights from Chimeric Group I Introns. The 21st Annual Conference of the Society for Molecular Biology and Evolution, July 2013 Chicago.
Wu, B., Wei, T. and Bai, Z. Evolution of SEFIR Protein Domain: A Horizontal Gene Transfer from Eukaryotes to Prokaryotes.The 6th International Conference on Bioinformatics and Biomedical Engineering (iCBBE), May 2012 Shanghai.
Reviewer services
Gene, Genome, G3, Molecular Genetics and Genomics, Mycologia, Evolutionary Bioinformatics, Gene reports, Frontiers in Genetics, Frontiers in Immunology, Frontiers in Microbiology, Frontiers in Plant Science, Frontiers in Cellular and Infection Microbiology, Journal of Fungi, Scientific Reports, Plos one and PLOS Computational Biology.
Editorial Appointment
02/2016-present, Editorial Board of Frontiers in Microbiology.
Research experiences
Postdoctoral Fellow at Massey University with Murray Cox/Tim Cooper.
Postdoctoral Fellow at Clark university with Dr. David Hibbett.
Postdoctoral Fellow at Wayne state university with Dr. Weilong Hao.
Contribution to LRRML and TollML databases.
Award
China Baosteel Scholarship (Outstanding Student Award), Baosteel Education Fund, 2011.