Year |
Citation |
Score |
2023 |
Wang Z, Wang YW, Kasuga T, Lopez-Giraldez F, Zhang Y, Zhang Z, Wang Y, Dong C, Sil A, Trail F, Yarden O, Townsend JP. Lineage-specific genes are clustered with HET-domain genes and respond to environmental and genetic manipulations regulating reproduction in Neurospora. Plos Genetics. 19: e1011019. PMID 37934795 DOI: 10.1371/journal.pgen.1011019 |
0.69 |
|
2023 |
Wang Z, Wang YW, Kasuga T, Hassler H, Lopez-Giraldez F, Dong C, Yarden O, Townsend JP. Origins of lineage-specific elements via gene duplication, relocation, and regional rearrangement in Neurospora crassa. Molecular Ecology. PMID 37843462 DOI: 10.1111/mec.17168 |
0.721 |
|
2023 |
Wang Z, Kim W, Wang YW, Yakubovich E, Dong C, Trail F, Townsend JP, Yarden O. The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomics. Frontiers in Fungal Biology. 4: 1214537. PMID 37746130 DOI: 10.3389/ffunb.2023.1214537 |
0.312 |
|
2023 |
Miguel-Rojas C, Cavinder B, Townsend JP, Trail F. Comparative Transcriptomics of Fusarium graminearum and Magnaporthe oryzae Spore Germination Leading up To Infection. Mbio. e0244222. PMID 36598191 DOI: 10.1128/mbio.02442-22 |
0.31 |
|
2022 |
Dornburg A, Mallik R, Wang Z, Bernal MA, Thompson B, Bruford EA, Nebert DW, Vasiliou V, Yohe LR, Yoder JA, Townsend JP. Placing human gene families into their evolutionary context. Human Genomics. 16: 56. PMID 36369063 DOI: 10.1186/s40246-022-00429-5 |
0.35 |
|
2022 |
Gortikov 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 . Journal of Fungi (Basel, Switzerland). 8. PMID 36012842 DOI: 10.3390/jof8080854 |
0.36 |
|
2022 |
Kim W, Wang Z, Kim H, Pham K, Tu Y, Townsend JP, Trail F. Transcriptional Divergence Underpinning Sexual Development in the Fungal Class Sordariomycetes. Mbio. e0110022. PMID 35638737 DOI: 10.1128/mbio.01100-22 |
0.53 |
|
2022 |
Wang 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. e0023222. PMID 35638725 DOI: 10.1128/msystems.00232-22 |
0.409 |
|
2022 |
Qing T, Mohsen H, Cannataro V, Marczyk M, Rozenblit M, Foldi J, Murray M, Townsend J, Kluger Y, Gerstein M, Pusztai L. Cancer Relevance of Human Genes. Journal of the National Cancer Institute. PMID 35417011 DOI: 10.1093/jnci/djac068 |
0.342 |
|
2020 |
Dornburg A, Wang Z, Wang J, Mo ES, Lopez-Giraldez F, Townsend JP. Comparative genomics within and across Bilaterians illuminates the evolutionary history of ALK and LTK proto-oncogene origination and diversification. Genome Biology and Evolution. PMID 33196781 DOI: 10.1093/gbe/evaa228 |
0.407 |
|
2020 |
Merényi Z, Prasanna AN, Wang Z, Kovács K, Hegedüs B, Bálint B, Papp B, Townsend JP, Nagy LG. Unmatched level of molecular convergence among deeply divergent complex multicellular fungi. Molecular Biology and Evolution. PMID 32191325 DOI: 10.1093/Molbev/Msaa077 |
0.361 |
|
2019 |
Johnston 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 . Ima Fungus. 10: 1. PMID 32647610 DOI: 10.1186/s43008-019-0002-x |
0.383 |
|
2019 |
Wang Z, López-Giráldez F, Wang J, Trail F, Townsend JP. Integrative Activity of Mating Loci, Environmentally Responsive Genes, and Secondary Metabolism Pathways during Sexual Development of Chaetomium globosum. Mbio. 10. PMID 31822585 DOI: 10.1128/Mbio.02119-19 |
0.482 |
|
2019 |
Kim W, Cavinder B, Proctor RH, O'Donnell K, Townsend JP, Trail F. Comparative Genomics and Transcriptomics During Sexual Development Gives Insight Into the Life History of the Cosmopolitan Fungus . Frontiers in Microbiology. 10: 1247. PMID 31231336 DOI: 10.3389/Fmicb.2019.01247 |
0.418 |
|
2019 |
Wang 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 . Mbio. 10. PMID 30914504 DOI: 10.1128/Mbio.00192-19 |
0.375 |
|
2019 |
Claus E, Cannataro V, Gaffney S, Townsend J. EPID-26. SEX-SPECIFIC GLIOMA MOLECULAR SIGNATURES Neuro-Oncology. 21: vi80-vi80. DOI: 10.1093/Neuonc/Noz175.326 |
0.423 |
|
2018 |
Adhikarla H, Wunder EA, Mechaly AE, Mehta S, Wang Z, Santos L, Bisht V, Diggle P, Murray G, Adler B, Lopez F, Townsend JP, Groisman E, Picardeau M, Buschiazzo A, et al. Lvr, a Signaling System That Controls Global Gene Regulation and Virulence in Pathogenic. Frontiers in Cellular and Infection Microbiology. 8: 45. PMID 29600195 DOI: 10.3389/Fcimb.2018.00045 |
0.375 |
|
2018 |
Wang Z, Gudibanda A, Ugwuowo U, Trail F, Townsend JP. Using evolutionary genomics, transcriptomics, and systems biology to reveal gene networks underlying fungal development Fungal Biology Reviews. 32: 249-264. DOI: 10.1016/J.Fbr.2018.02.001 |
0.378 |
|
2017 |
Wang 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. PMID 29134709 DOI: 10.1111/Mec.14425 |
0.315 |
|
2017 |
Zhao ZM, Campbell MC, Li N, Lee DSW, Zhang Z, Townsend JP. Detection of regional variation in selection intensity within protein-coding genes using DNA sequence polymorphism and divergence. Molecular Biology and Evolution. PMID 28962009 DOI: 10.1093/Molbev/Msx213 |
0.301 |
|
2017 |
Trail F, Wang Z, Stefanko K, Cubba C, Townsend JP. The ancestral levels of transcription and the evolution of sexual phenotypes in filamentous fungi. Plos Genetics. 13: e1006867. PMID 28704372 DOI: 10.1371/Journal.Pgen.1006867 |
0.517 |
|
2016 |
Wang 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. 7. PMID 26956589 DOI: 10.1128/Mbio.02148-15 |
0.309 |
|
2016 |
Choi M, Kadara H, Zhang J, Cuentas EP, Canales JR, Gaffney SG, Zhao Z, Behrens C, Fujimoto J, Chow C, Kalhor N, Moran C, Rimm D, Swisher S, Gibbons DL, ... ... Townsend J, et al. Abstract 142: Mutation and immune profiles in early-stage lung squamous cell carcinoma Cancer Research. 76: 142-142. DOI: 10.1158/1538-7445.Am2016-142 |
0.315 |
|
2015 |
Sistrom M, Park D, O'Brien HE, Wang Z, Guttman DS, Townsend JP, Turner PE. Genomic and Gene-Expression Comparisons among Phage-Resistant Type-IV Pilus Mutants of Pseudomonas syringae pathovar phaseolicola. Plos One. 10: e0144514. PMID 26670219 DOI: 10.1371/Journal.Pone.0144514 |
0.37 |
|
2015 |
Hodgins-Davis A, Rice DP, Townsend JP. Gene Expression Evolves under a House-of-Cards Model of Stabilizing Selection. Molecular Biology and Evolution. 32: 2130-40. PMID 25901014 DOI: 10.1093/Molbev/Msv094 |
0.441 |
|
2014 |
Lehr NA, Wang Z, Li N, Hewitt DA, López-Giráldez F, Trail F, Townsend JP. Gene expression differences among three Neurospora species reveal genes required for sexual reproduction in Neurospora crassa. Plos One. 9: e110398. PMID 25329823 DOI: 10.1371/Journal.Pone.0110398 |
0.493 |
|
2014 |
Wang 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. Eukaryotic Cell. 13: 154-69. PMID 24243796 DOI: 10.1128/Ec.00248-13 |
0.48 |
|
2014 |
Johannesson H, Townsend J, Taylor J. Concerted evolution of repeat units within the gene encoding an immunomodulating parasitic cell surface glycoprotein in the human pathogenic fungi Coccidioides immitis and C. posadasii F1000research. 5. DOI: 10.7490/F1000Research.1096506.1 |
0.53 |
|
2014 |
Claus EB, Calvocoressi L, Greenhalgh S, Walsh K, Schildkraut J, Bondy M, Wiemels J, Wrensch M, Al-Mefty O, Townsend J. GENETIC CHANGES IN RADIATION-ASSOCIATED MENINGIOMA Neuro-Oncology. 16: iii1-iii1. DOI: 10.1093/Neuonc/Nou206.2 |
0.308 |
|
2013 |
Binder M, Justo A, Riley R, Salamov A, Lopez-Giraldez F, Sjökvist E, Copeland A, Foster B, Sun H, Larsson E, Larsson KH, Townsend J, Grigoriev IV, Hibbett DS. Phylogenetic and phylogenomic overview of the Polyporales. Mycologia. 105: 1350-73. PMID 23935031 DOI: 10.3852/13-003 |
0.476 |
|
2013 |
López-Giráldez F, Moeller AH, Townsend JP. Evaluating phylogenetic informativeness as a predictor of phylogenetic signal for metazoan, fungal, and mammalian phylogenomic data sets. Biomed Research International. 2013: 621604. PMID 23878813 DOI: 10.1155/2013/621604 |
0.338 |
|
2013 |
Samils N, Gioti A, Karlsson M, Sun Y, Kasuga T, Bastiaans E, Wang Z, Li N, Townsend JP, Johannesson H. Sex-linked transcriptional divergence in the hermaphrodite fungus Neurospora tetrasperma. Proceedings. Biological Sciences / the Royal Society. 280: 20130862. PMID 23782882 DOI: 10.1098/Rspb.2013.0862 |
0.74 |
|
2012 |
Nygren K, Wallberg A, Samils N, Stajich JE, Townsend JP, Karlsson M, Johannesson H. Analyses of expressed sequence tags in Neurospora reveal rapid evolution of genes associated with the early stages of sexual reproduction in fungi. Bmc Evolutionary Biology. 12: 229. PMID 23186325 DOI: 10.1186/1471-2148-12-229 |
0.756 |
|
2012 |
Hodgins-Davis A, Adomas AB, Warringer J, Townsend JP. Abundant gene-by-environment interactions in gene expression reaction norms to copper within Saccharomyces cerevisiae. Genome Biology and Evolution. 4: 1061-79. PMID 23019066 DOI: 10.1093/Gbe/Evs084 |
0.41 |
|
2012 |
Sikhakolli UR, López-Giráldez F, Li N, Common R, Townsend JP, Trail F. Transcriptome analyses during fruiting body formation in Fusarium graminearum and Fusarium verticillioides reflect species life history and ecology. Fungal Genetics and Biology : Fg & B. 49: 663-73. PMID 22705880 DOI: 10.1016/J.Fgb.2012.05.009 |
0.377 |
|
2012 |
Wang Z, Kin K, López-Giráldez F, Johannesson H, Townsend JP. Sex-specific gene expression during asexual development of Neurospora crassa. Fungal Genetics and Biology : Fg & B. 49: 533-43. PMID 22626843 DOI: 10.1016/J.Fgb.2012.05.004 |
0.676 |
|
2012 |
Huang T, López-Giráldez F, Townsend JP, Irish VF. RBE controls microRNA164 expression to effect floral organogenesis. Development (Cambridge, England). 139: 2161-9. PMID 22573623 DOI: 10.1242/Dev.075069 |
0.311 |
|
2012 |
Wang Z, Lehr N, Trail F, Townsend JP. Differential impact of nutrition on developmental and metabolic gene expression during fruiting body development in Neurospora crassa. Fungal Genetics and Biology : Fg & B. 49: 405-13. PMID 22469835 DOI: 10.1016/J.Fgb.2012.03.004 |
0.338 |
|
2012 |
Zhang Z, Li J, Cui P, Ding F, Li A, Townsend JP, Yu J. Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance. Bmc Bioinformatics. 13: 43. PMID 22435713 DOI: 10.1186/1471-2105-13-43 |
0.316 |
|
2011 |
Moeller AH, Townsend JP. Phylogenetic informativeness profiling of 12 genes for 28 vertebrate taxa without divergence dates. Molecular Phylogenetics and Evolution. 60: 271-2. PMID 21558010 DOI: 10.1016/J.Ympev.2011.04.023 |
0.383 |
|
2011 |
Guo Z, Adomas AB, Jackson ED, Qin H, Townsend JP. SIR2 and other genes are abundantly expressed in long-lived natural segregants for replicative aging of the budding yeast Saccharomyces cerevisiae. Fems Yeast Research. 11: 345-55. PMID 21306556 DOI: 10.1111/J.1567-1364.2011.00723.X |
0.375 |
|
2010 |
Adomas AB, Lopez-Giraldez F, Clark TA, Wang Z, Townsend JP. Multi-targeted priming for genome-wide gene expression assays. Bmc Genomics. 11: 477. PMID 20716356 DOI: 10.1186/1471-2164-11-477 |
0.4 |
|
2010 |
Zhang Z, López-Giráldez F, Townsend JP. LOX: inferring Level Of eXpression from diverse methods of census sequencing. Bioinformatics (Oxford, England). 26: 1918-9. PMID 20538728 DOI: 10.1093/Bioinformatics/Btq303 |
0.362 |
|
2010 |
Zhang Z, Townsend JP. The filamentous fungal gene expression database (FFGED). Fungal Genetics and Biology : Fg & B. 47: 199-204. PMID 20025988 DOI: 10.1016/J.Fgb.2009.12.001 |
0.338 |
|
2009 |
Schoch CL, Sung GH, López-Giráldez F, Townsend JP, Miadlikowska J, Hofstetter V, Robbertse B, Matheny PB, Kauff F, Wang Z, Gueidan C, Andrie RM, Trippe K, Ciufetti LM, Wynns A, et al. The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits. Systematic Biology. 58: 224-39. PMID 20525580 DOI: 10.1093/Sysbio/Syp020 |
0.655 |
|
2009 |
Hodgins-Davis A, Townsend JP. Evolving gene expression: from G to E to GxE. Trends in Ecology & Evolution. 24: 649-58. PMID 19699549 DOI: 10.1016/J.Tree.2009.06.011 |
0.433 |
|
2009 |
Townsend JA, Wright DA, Winfrey RJ, Fu F, Maeder ML, Joung JK, Voytas DF. High-frequency modification of plant genes using engineered zinc-finger nucleases. Nature. 459: 442-5. PMID 19404258 DOI: 10.1038/Nature07845 |
0.309 |
|
2008 |
Townsend JP. Sleuthing the difference a nucleotide can make. Molecular Ecology. 17: 2793-5. PMID 18565029 DOI: 10.1111/J.1365-294X.2008.03824.X |
0.413 |
|
2007 |
Clark TA, Townsend JP. Quantifying variation in gene expression. Molecular Ecology. 16: 2613-6. PMID 17594433 DOI: 10.1111/J.1365-294X.2007.03354.X |
0.426 |
|
2007 |
Dunlap JC, Borkovich KA, Henn MR, Turner GE, Sachs MS, Glass NL, McCluskey K, Plamann M, Galagan JE, Birren BW, Weiss RL, Townsend JP, Loros JJ, Nelson MA, Lambreghts R, et al. Enabling a community to dissect an organism: overview of the Neurospora functional genomics project. Advances in Genetics. 57: 49-96. PMID 17352902 DOI: 10.1016/S0065-2660(06)57002-6 |
0.656 |
|
2006 |
Taylor JW, Turner E, Townsend JP, Dettman JR, Jacobson D. Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 361: 1947-63. PMID 17062413 DOI: 10.1098/Rstb.2006.1923 |
0.689 |
|
2006 |
Aa E, Townsend JP, Adams RI, Nielsen KM, Taylor JW. Population structure and gene evolution in Saccharomyces cerevisiae. Fems Yeast Research. 6: 702-15. PMID 16879422 DOI: 10.1111/J.1567-1364.2006.00059.X |
0.498 |
|
2006 |
Johannesson H, Kasuga T, Schaller RA, Good B, Gardner MJ, Townsend JP, Cole GT, Taylor JW. Phase-specific gene expression underlying morphological adaptations of the dimorphic human pathogenic fungus, Coccidioides posadasii. Fungal Genetics and Biology : Fg & B. 43: 545-59. PMID 16697669 DOI: 10.1016/J.Fgb.2006.02.003 |
0.751 |
|
2005 |
Meiklejohn CD, Townsend JP. A Bayesian method for analysing spotted microarray data. Briefings in Bioinformatics. 6: 318-30. PMID 16420731 DOI: 10.1093/Bib/6.4.318 |
0.383 |
|
2005 |
Kasuga T, Townsend JP, Tian C, Gilbert LB, Mannhaupt G, Taylor JW, Glass NL. Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination. Nucleic Acids Research. 33: 6469-85. PMID 16287898 DOI: 10.1093/Nar/Gki953 |
0.705 |
|
2005 |
Gogarten JP, Townsend JP. Horizontal gene transfer, genome innovation and evolution. Nature Reviews. Microbiology. 3: 679-87. PMID 16138096 DOI: 10.1038/Nrmicro1204 |
0.423 |
|
2005 |
Johannesson H, Townsend JP, Hung CY, Cole GT, Taylor JW. Concerted evolution in the repeats of an immunomodulating cell surface protein, SOWgp, of the human pathogenic fungi Coccidioides immitis and C. posadasii. Genetics. 171: 109-17. PMID 15965255 DOI: 10.1534/Genetics.105.040923 |
0.667 |
|
2005 |
Townsend JP, Taylor JW. Designing experiments using spotted microarrays to detect gene regulation differences within and among species. Methods in Enzymology. 395: 597-617. PMID 15865986 DOI: 10.1016/S0076-6879(05)95031-3 |
0.547 |
|
2004 |
Townsend JP. Resolution of large and small differences in gene expression using models for the Bayesian analysis of gene expression levels and spotted DNA microarrays. Bmc Bioinformatics. 5: 54. PMID 15128431 DOI: 10.1186/1471-2105-5-54 |
0.354 |
|
2003 |
Townsend JP, Cavalieri D, Hartl DL. Population genetic variation in genome-wide gene expression. Molecular Biology and Evolution. 20: 955-63. PMID 12716989 DOI: 10.1093/Molbev/Msg106 |
0.436 |
|
2002 |
Townsend JP, Hartl DL. Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments. Genome Biology. 3: RESEARCH0071. PMID 12537560 DOI: 10.1186/Gb-2002-3-12-Research0071 |
0.393 |
|
2000 |
Cavalieri D, Townsend JP, Hartl DL. Manifold anomalies in gene expression in a vineyard isolate of Saccharomyces cerevisiae revealed by DNA microarray analysis. Proceedings of the National Academy of Sciences of the United States of America. 97: 12369-74. PMID 11035792 DOI: 10.1073/Pnas.210395297 |
0.46 |
|
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