Zheng Wang, PhD
Research Scientist in Biostatistics (Biostatistics); Affiliated Faculty, Yale Institute for Global Health
Research & Publications
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Selected Publications
- The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomicsWang Z, Kim W, Wang Y, Yakubovich E, Dong C, Trail F, Townsend J, Yarden O. The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomics. Frontiers In Fungal Biology 2023, 4: 1214537. DOI: 10.3389/ffunb.2023.1214537.
- Light sensing by opsins and fungal ecology: NOP‐1 modulates entry into sexual reproduction in response to environmental cuesWang Z, Wang J, Li N, Li J, Trail F, Dunlap JC, Townsend JP. Light sensing by opsins and fungal ecology: NOP‐1 modulates entry into sexual reproduction in response to environmental cues. Molecular Ecology 2017, 27: 216-232. PMID: 29134709, PMCID: PMC5797489, DOI: 10.1111/mec.14425.
- Metabolism and Development during Conidial Germination in Response to a Carbon-Nitrogen-Rich Synthetic or a Natural Source of Nutrition in Neurospora crassaWang Z, Miguel-Rojas C, Lopez-Giraldez F, Yarden O, Trail F, Townsend JP. Metabolism and Development during Conidial Germination in Response to a Carbon-Nitrogen-Rich Synthetic or a Natural Source of Nutrition in Neurospora crassa. MBio 2019, 10: e00192-19. PMID: 30914504, PMCID: PMC6437048, DOI: 10.1128/mbio.00192-19.
- A multigene phylogeny toward a new phylogenetic classification of LeotiomycetesJohnston PR, Quijada L, Smith CA, Baral HO, Hosoya T, Baschien C, Pärtel K, Zhuang WY, Haelewaters D, Park D, Carl S, López-Giráldez F, Wang Z, Townsend JP. A multigene phylogeny toward a new phylogenetic classification of Leotiomycetes. IMA Fungus 2019, 10: 1. PMID: 32647610, PMCID: PMC7325659, DOI: 10.1186/s43008-019-0002-x.
- The Fast-Evolving phy-2 Gene Modulates Sexual Development in Response to Light in the Model Fungus Neurospora crassaWang Z, Li N, Li J, Dunlap JC, Trail F, Townsend JP. The Fast-Evolving phy-2 Gene Modulates Sexual Development in Response to Light in the Model Fungus Neurospora crassa. MBio 2016, 7: e02148-15. PMID: 26956589, PMCID: PMC4810495, DOI: 10.1128/mbio.02148-15.
- Chapter One Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big DataDornburg A, Townsend JP, Wang Z. Chapter One Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big Data. 2017, 100: 1-47. PMID: 29153398, DOI: 10.1016/bs.adgen.2017.09.007.
- Sex-specific gene expression during asexual development of Neurospora crassaWang Z, Kin K, López-Giráldez F, Johannesson H, Townsend JP. Sex-specific gene expression during asexual development of Neurospora crassa. Fungal Genetics And Biology 2012, 49: 533-543. PMID: 22626843, PMCID: PMC3397379, DOI: 10.1016/j.fgb.2012.05.004.
- Global Gene Expression and Focused Knockout Analysis Reveals Genes Associated with Fungal Fruiting Body Development in Neurospora crassaWang Z, Lopez-Giraldez F, Lehr N, Farré M, Common R, Trail F, Townsend JP. Global Gene Expression and Focused Knockout Analysis Reveals Genes Associated with Fungal Fruiting Body Development in Neurospora crassa. MSphere 2013, 13: 154-169. PMID: 24243796, PMCID: PMC3910948, DOI: 10.1128/ec.00248-13.
- Toward a phylogenetic classification of the Leotiomycetes based on rDNA dataWang Z, Johnston PR, Takamatsu S, Spatafora JW, Hibbett DS. Toward a phylogenetic classification of the Leotiomycetes based on rDNA data. Mycologia 2006, 98: 1065-1075. PMID: 17486981, DOI: 10.3852/mycologia.98.6.1065.
- Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi).Matheny PB, Wang Z, Binder M, Curtis JM, Lim YW, Nilsson RH, Hughes KW, Hofstetter V, Ammirati JF, Schoch CL, Langer E, Langer G, McLaughlin DJ, Wilson AW, Frøslev T, Ge ZW, Kerrigan RW, Slot JC, Yang ZL, Baroni TJ, Fischer M, Hosaka K, Matsuura K, Seidl MT, Vauras J, Hibbett DS. Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi). Molecular Phylogenetics And Evolution 2007, 43: 430-51. PMID: 17081773, DOI: 10.1016/j.ympev.2006.08.024.
- A higher-level phylogenetic classification of the Fungi.Hibbett DS, Binder M, Bischoff JF, Blackwell M, Cannon PF, Eriksson OE, Huhndorf S, James T, Kirk PM, Lücking R, Thorsten Lumbsch H, Lutzoni F, Matheny PB, McLaughlin DJ, Powell MJ, Redhead S, Schoch CL, Spatafora JW, Stalpers JA, Vilgalys R, Aime MC, Aptroot A, Bauer R, Begerow D, Benny GL, Castlebury LA, Crous PW, Dai YC, Gams W, Geiser DM, Griffith GW, Gueidan C, Hawksworth DL, Hestmark G, Hosaka K, Humber RA, Hyde KD, Ironside JE, Kõljalg U, Kurtzman CP, Larsson KH, Lichtwardt R, Longcore J, Miadlikowska J, Miller A, Moncalvo JM, Mozley-Standridge S, Oberwinkler F, Parmasto E, Reeb V, Rogers JD, Roux C, Ryvarden L, Sampaio JP, Schüssler A, Sugiyama J, Thorn RG, Tibell L, Untereiner WA, Walker C, Wang Z, Weir A, Weiss M, White MM, Winka K, Yao YJ, Zhang N. A higher-level phylogenetic classification of the Fungi. Mycological Research 2007, 111: 509-47. PMID: 17572334, DOI: 10.1016/j.mycres.2007.03.004.
- Evolution of Reproductive Morphology in Leaf EndophytesWang Z, Johnston PR, Yang ZL, Townsend JP. Evolution of Reproductive Morphology in Leaf Endophytes. PLOS ONE 2009, 4: e4246. PMID: 19158947, PMCID: PMC2617777, DOI: 10.1371/journal.pone.0004246.
- Life history and systematics of the aquatic discomycete Mitrula (Helotiales, Ascomycota) based on cultural, morphological, and molecular studiesWang Z, Binder M, Hibbett DS. Life history and systematics of the aquatic discomycete Mitrula (Helotiales, Ascomycota) based on cultural, morphological, and molecular studies. American Journal Of Botany 2005, 92: 1565-1574. PMID: 21646174, DOI: 10.3732/ajb.92.9.1565.
- Evolution of helotialean fungi (Leotiomycetes, Pezizomycotina): A nuclear rDNA phylogenyWang Z, Binder M, Schoch CL, Johnston PR, Spatafora JW, Hibbett DS. Evolution of helotialean fungi (Leotiomycetes, Pezizomycotina): A nuclear rDNA phylogeny. Molecular Phylogenetics And Evolution 2006, 41: 295-312. PMID: 16837216, DOI: 10.1016/j.ympev.2006.05.031.
- Toward a phylogenetic classification of the Leotiomycetes based on rDNA dataWang Z, Johnston P, Takamatsu S, Spatafora J, Hibbett D. Toward a phylogenetic classification of the Leotiomycetes based on rDNA data. Mycologia 2006, 98: 1065-1075. DOI: 10.1080/15572536.2006.11832634.
- A new species of Cudonia based on morphological and molecular dataWang Z, Binder M, Hibbett D. A new species of Cudonia based on morphological and molecular data. Mycologia 2002, 94: 641-650. DOI: 10.1080/15572536.2003.11833192.
- Chapter 5 Measurement and meaning in gene expression evolutionDiaz R, Wang Z, Townsend J. Chapter 5 Measurement and meaning in gene expression evolution. 2023, 111-129. DOI: 10.1016/b978-0-323-91810-7.00008-x.
- Placing human gene families into their evolutionary contextDornburg A, Mallik R, Wang Z, Bernal M, Thompson B, Bruford E, Nebert D, Vasiliou V, Yohe L, Yoder J, Townsend J. Placing human gene families into their evolutionary context. Human Genomics 2022, 16: 56. PMID: 36369063, PMCID: PMC9652883, DOI: 10.1186/s40246-022-00429-5.
- Differential Expression of Cell Wall Remodeling Genes Is Part of the Dynamic Phase-Specific Transcriptional Program of Conidial Germination of Trichoderma asperelloidesGortikov M, Yakubovich E, Wang Z, López-Giráldez F, Tu Y, Townsend JP, Yarden O. Differential Expression of Cell Wall Remodeling Genes Is Part of the Dynamic Phase-Specific Transcriptional Program of Conidial Germination of Trichoderma asperelloides. Journal Of Fungi 2022, 8: 854. PMID: 36012842, PMCID: PMC9410309, DOI: 10.3390/jof8080854.
- Secondary Metabolism Gene Clusters Exhibit Increasingly Dynamic and Differential Expression during Asexual Growth, Conidiation, and Sexual Development in Neurospora crassaWang Z, Lopez-Giraldez F, Slot J, Yarden O, Trail F, Townsend JP. Secondary Metabolism Gene Clusters Exhibit Increasingly Dynamic and Differential Expression during Asexual Growth, Conidiation, and Sexual Development in Neurospora crassa. MSystems 2022, 7: e00232-22. PMID: 35638725, PMCID: PMC9239088, DOI: 10.1128/msystems.00232-22.
- Transcriptional Divergence Underpinning Sexual Development in the Fungal Class SordariomycetesKim W, Wang Z, Kim H, Pham K, Tu Y, Townsend JP, Trail F. Transcriptional Divergence Underpinning Sexual Development in the Fungal Class Sordariomycetes. MBio 2022, 13: e01100-22. PMID: 35638737, PMCID: PMC9239162, DOI: 10.1128/mbio.01100-22.
- Sequencing and Analysis of the Entire Genome of the Mycoparasitic Bioeffector Fungus Trichoderma asperelloides Strain T 203 (Hypocreales)Gortikov M, Wang Z, Steindorff AS, Grigoriev IV, Druzhinina IS, Townsend JP, Yarden O. Sequencing and Analysis of the Entire Genome of the Mycoparasitic Bioeffector Fungus Trichoderma asperelloides Strain T 203 (Hypocreales). Microbiology Resource Announcements 2022, 11: e00995-21. PMID: 35175124, PMCID: PMC8852338, DOI: 10.1128/mra.00995-21.
- The GUL-1 Protein Binds Multiple RNAs Involved in Cell Wall Remodeling and Affects the MAK-1 Pathway in Neurospora crassaHerold I, Zolti A, Garduño-Rosales M, Wang Z, López-Giráldez F, Mouriño-Pérez R, Townsend J, Ulitsky I, Yarden O. The GUL-1 Protein Binds Multiple RNAs Involved in Cell Wall Remodeling and Affects the MAK-1 Pathway in Neurospora crassa. Frontiers In Fungal Biology 2021, 2: 672696. DOI: 10.3389/ffunb.2021.672696.
- Using evolutionary genomics, transcriptomics, and systems biology to reveal gene networks underlying fungal developmentWang Z, Gudibanda A, Ugwuowo U, Trail F, Townsend J. Using evolutionary genomics, transcriptomics, and systems biology to reveal gene networks underlying fungal development. Fungal Biology Reviews 2018, 32: 249-264. DOI: 10.1016/j.fbr.2018.02.001.
- Future Perspectives and Challenges of Fungal Systematics in the Age of Big DataWang Z, Nilsson R, James T, Dai Y, Townsend J. Future Perspectives and Challenges of Fungal Systematics in the Age of Big Data. 2016, 25-46. DOI: 10.1007/978-3-319-29137-6_3.
- 3 Pezizomycotina: Sordariomycetes and LeotiomycetesZhang N, Wang Z. 3 Pezizomycotina: Sordariomycetes and Leotiomycetes. 2015, 57-88. DOI: 10.1007/978-3-662-46011-5_3.
- The impact of incorporating molecular evolutionary model into predictions of phylogenetic signal and noiseSu Z, Wang Z, López-Giráldez F, Townsend J. The impact of incorporating molecular evolutionary model into predictions of phylogenetic signal and noise. Frontiers In Ecology And Evolution 2014, 2: 11. DOI: 10.3389/fevo.2014.00011.
- Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing dataBengtsson‐Palme J, Ryberg M, Hartmann M, Branco S, Wang Z, Godhe A, Wit P, Sánchez‐García M, Ebersberger I, Sousa F, Amend A, Jumpponen A, Unterseher M, Kristiansson E, Abarenkov K, Bertrand Y, Sanli K, Eriksson K, Vik U, Veldre V, Nilsson R. Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods In Ecology And Evolution 2013, 4: 914-919. DOI: 10.1111/2041-210x.12073.
- New species and distinctive geographical divergences of the genus Sparassis (Basidiomycota): evidence from morphological and molecular dataZhao Q, Feng B, Yang Z, Dai Y, Wang Z, Tolgor B. New species and distinctive geographical divergences of the genus Sparassis (Basidiomycota): evidence from morphological and molecular data. Mycological Progress 2012, 12: 445-454. DOI: 10.1007/s11557-012-0853-7.
- A note on the incidence of reverse complementary fungal ITS sequences in the public sequence databases and a software tool for their detection and reorientationNilsson R, Veldre V, Wang Z, Eckart M, Branco S, Hartmann M, Quince C, Godhe A, Bertrand Y, Alfredsson J, Larsson K, Kõljalg U, Abarenkov K. A note on the incidence of reverse complementary fungal ITS sequences in the public sequence databases and a software tool for their detection and reorientation. Mycoscience 2011, 52: 278-282. DOI: 10.1007/s10267-010-0086-z.
- A note on the incidence of reverse complementary fungal ITS sequences in the public sequence databases and a software tool for their detection and reorientationNilsson R, Veldre V, Wang Z, Eckart M, Branco S, Hartmann M, Quince C, Godhe A, Bertrand Y, Alfredsson J, Larsson K, Kõljalg U, Abarenkov K. A note on the incidence of reverse complementary fungal ITS sequences in the public sequence databases and a software tool for their detection and reorientation. Mycoscience 2011, 52: 278-282. DOI: 10.47371/s10267-010-0086-z.
- Article Commentary: Snapshots of Tree SpaceWang Z, López-Giréidez F, Townsend J. Article Commentary: Snapshots of Tree Space. Evolutionary Bioinformatics 2009, 5: ebo.s3416. DOI: 10.4137/ebo.s3416.
- Phylogeny and a new species of Sparassis (Polyporales, Basidiomycota): evidence from mitochondrial atp6, nuclear rDNA and rpb2 genesDai Y, Wang Z, Binder M, Hibbett D. Phylogeny and a new species of Sparassis (Polyporales, Basidiomycota): evidence from mitochondrial atp6, nuclear rDNA and rpb2 genes. Mycologia 2006, 98: 584-592. DOI: 10.1080/15572536.2006.11832661.
- Sparassis cystidiosa sp. nov. from Thailand is described using morphological and molecular dataDesjardin D, Wang Z, Binder M, Hibbett D. Sparassis cystidiosa sp. nov. from Thailand is described using morphological and molecular data. Mycologia 2004, 96: 1010-1014. DOI: 10.1080/15572536.2005.11832901.
- Phylogenetic relationships of Sparassis inferred from nuclear and mitochondrial ribosomal DNA and RNA polymerase sequencesWang Z, Binder M, Dai Y, Hibbett D. Phylogenetic relationships of Sparassis inferred from nuclear and mitochondrial ribosomal DNA and RNA polymerase sequences. Mycologia 2004, 96: 1015-1029. DOI: 10.1080/15572536.2005.11832902.
- Sparassis cystidiosa sp. nov. from Thailand is described using morphological and molecular data.Desjardin DE, Wang Z, Binder M, Hibbett DS. Sparassis cystidiosa sp. nov. from Thailand is described using morphological and molecular data. Mycologia 2004, 96: 1010-4. PMID: 21148922.
- Phylogenetic relationships of Sparassis inferred from nuclear and mitochondrial ribosomal DNA and RNA polymerase sequences.Wang Z, Binder M, Dai YC, Hibbett DS. Phylogenetic relationships of Sparassis inferred from nuclear and mitochondrial ribosomal DNA and RNA polymerase sequences. Mycologia 2004, 96: 1015-29. PMID: 21148923, DOI: 10.2307/3762086.
- Another fossil agaric from Dominican amberHibbett D, Binder M, Wang Z, Goldman Y. Another fossil agaric from Dominican amber. Mycologia 2003, 95: 685-687. DOI: 10.1080/15572536.2004.11833071.