| Year |
Citation |
Score |
| 2023 |
Townsend JP, Hassler HB, Lamb AD, Sah P, Alvarez Nishio A, Nguyen C, Tew AD, Galvani AP, Dornburg A. Seasonality of endemic COVID-19. Mbio. e0142623. PMID 37937979 DOI: 10.1128/mbio.01426-23 |
0.57 |
|
| 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 |
0.432 |
|
| 2023 |
Townsend JP, Hassler HB, Emu B, Dornburg A. Infection with alternate frequencies of SARS-CoV-2 vaccine boosting for patients undergoing antineoplastic cancer treatments. Journal of the National Cancer Institute. PMID 37599438 DOI: 10.1093/jnci/djad158 |
0.571 |
|
| 2023 |
Townsend JP, Hassler HB, Dornburg A. Infection by SARS-CoV-2 with alternate frequencies of mRNA vaccine boosting. Journal of Medical Virology. PMID 36602045 DOI: 10.1002/jmv.28461 |
0.565 |
|
| 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 |
0.634 |
|
| 2022 |
Townsend JP, Hassler HB, Sah P, Galvani AP, Dornburg A. The durability of natural infection and vaccine-induced immunity against future infection by SARS-CoV-2. Proceedings of the National Academy of Sciences of the United States of America. 119: e2204336119. PMID 35858382 DOI: 10.1073/pnas.2204336119 |
0.568 |
|
| 2021 |
Fisk JN, Mahal AR, Dornburg A, Gaffney SG, Aneja S, Contessa JN, Rimm D, Yu JB, Townsend JP. Premetastatic shifts of endogenous and exogenous mutational processes support consolidative therapy in EGFR-driven lung adenocarcinoma. Cancer Letters. PMID 34780851 DOI: 10.1016/j.canlet.2021.11.011 |
0.582 |
|
| 2021 |
Townsend JP, Hassler HB, Wang Z, Miura S, Singh J, Kumar S, Ruddle NH, Galvani AP, Dornburg A. The durability of immunity against reinfection by SARS-CoV-2: a comparative evolutionary study. The Lancet. Microbe. PMID 34632431 DOI: 10.1016/S2666-5247(21)00219-6 |
0.568 |
|
| 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 |
0.64 |
|
| 2020 |
Qing T, Mohsen H, Marczyk M, Ye Y, O'Meara T, Zhao H, Townsend JP, Gerstein M, Hatzis C, Kluger Y, Pusztai L. Germline variant burden in cancer genes correlates with age at diagnosis and somatic mutation burden. Nature Communications. 11: 2438. PMID 32415133 DOI: 10.1038/S41467-020-16293-7 |
0.307 |
|
| 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 |
0.368 |
|
| 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 |
0.376 |
|
| 2019 |
Somarelli JA, Gardner H, Cannataro VL, Gunady EF, Boddy AM, Johnson NA, Fisk JN, Gaffney SG, Chuang JH, Li S, Ciccarelli FD, Panchenko AR, Megquier K, Kumar S, Dornburg A, ... ... Townsend JP, et al. Molecular biology and evolution of cancer: from discovery to action. Molecular Biology and Evolution. PMID 31642480 DOI: 10.1093/Molbev/Msz242 |
0.624 |
|
| 2019 |
Gaffney SG, Perry EB, Chen PM, Greenstein A, Kaech SM, Townsend JP. The landscape of novel and complementary targets for immunotherapy: an analysis of gene expression in the tumor microenvironment. Oncotarget. 10: 4532-4545. PMID 31360302 DOI: 10.18632/Oncotarget.27027 |
0.312 |
|
| 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 |
0.386 |
|
| 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 |
0.34 |
|
| 2019 |
Cannataro VL, Gaffney SG, Sasaki T, Issaeva N, Grewal NKS, Grandis JR, Yarbrough WG, Burtness B, Anderson KS, Townsend JP. APOBEC-induced mutations and their cancer effect size in head and neck squamous cell carcinoma. Oncogene. PMID 30647454 DOI: 10.1038/S41388-018-0657-6 |
0.301 |
|
| 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 |
0.359 |
|
| 2018 |
Cannataro VL, Gaffney SG, Townsend JP. Effect Sizes of Somatic Mutations in Cancer. Journal of the National Cancer Institute. PMID 30365005 DOI: 10.1093/Jnci/Djy168 |
0.329 |
|
| 2018 |
Santos LA, Adhikarla H, Yan X, Wang Z, Fouts DE, Vinetz JM, Alcantara LCJ, Hartskeerl RA, Goris MGA, Picardeau M, Reis MG, Townsend JP, Zhao H, Ko AI, Wunder EA. Genomic Comparison Among Global Isolates of Serovars Copenhageni and Icterohaemorrhagiae Identified Natural Genetic Variation Caused by an Indel. Frontiers in Cellular and Infection Microbiology. 8: 193. PMID 29971217 DOI: 10.3389/Fcimb.2018.00193 |
0.334 |
|
| 2018 |
Dornburg A, Su Z, Townsend JP. Optimal rates for phylogenetic inference and experimental design in the era of genome-scale datasets. Systematic Biology. PMID 29939341 DOI: 10.7490/F1000Research.1116969.1 |
0.627 |
|
| 2018 |
Wilkins JF, Cannataro VL, Shuch B, Townsend JP. Analysis of mutation, selection, and epistasis: an informed approach to cancer clinical trials. Oncotarget. 9: 22243-22253. PMID 29854275 DOI: 10.18632/Oncotarget.25155 |
0.31 |
|
| 2018 |
Cannataro VL, Townsend JP. Neutral theory and the somatic evolution of cancer. Molecular Biology and Evolution. PMID 29684198 DOI: 10.1093/Molbev/Msy079 |
0.303 |
|
| 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 |
0.347 |
|
| 2018 |
Townsend JP. The Cancer Tree. Scientific American. 318: 34-41. PMID 29557973 DOI: 10.1038/Scientificamerican0418-34 |
0.314 |
|
| 2018 |
Cannataro VL, Gaffney SG, Stender C, Zhao ZM, Philips M, Greenstein AE, Townsend JP. Heterogeneity and mutation in KRAS and associated oncogenes: evaluating the potential for the evolution of resistance to targeting of KRAS G12C. Oncogene. PMID 29453361 DOI: 10.1038/S41388-017-0105-Z |
0.302 |
|
| 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 |
0.39 |
|
| 2017 |
Dornburg A, Townsend JP, Wang Z. Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big Data. Advances in Genetics. 100: 1-47. PMID 29153398 DOI: 10.1016/Bs.Adgen.2017.09.007 |
0.651 |
|
| 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 |
0.309 |
|
| 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 |
0.513 |
|
| 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 |
0.392 |
|
| 2017 |
Dornburg A, Townsend JP, Brooks W, Spriggs E, Eytan RI, Moore JA, Wainwright PC, Lemmon A, Lemmon EM, Near TJ. New Insights on the Sister Lineage of Percomorph Fishes with an Anchored Hybrid Enrichment Dataset. Molecular Phylogenetics and Evolution. PMID 28254474 DOI: 10.1016/J.Ympev.2017.02.017 |
0.646 |
|
| 2017 |
Choi M, Kadara H, Zhang J, Parra ER, Rodriguez-Canales J, Gaffney SG, Zhao Z, Behrens C, Fujimoto J, Chow C, Kim K, Kalhor N, Moran C, Rimm D, Swisher S, ... ... Townsend JP, et al. Mutation profiles in early-stage lung squamous cell carcinoma with clinical follow-up and correlation with markers of immune function. Annals of Oncology : Official Journal of the European Society For Medical Oncology. 28: 83-89. PMID 28177435 DOI: 10.1093/Annonc/Mdw437 |
0.304 |
|
| 2016 |
Dornburg A, Fisk JN, Tamagnan J, Townsend JP. PhyInformR: phylogenetic experimental design and phylogenomic data exploration in R. Bmc Evolutionary Biology. 16: 262. PMID 27905871 DOI: 10.1186/S12862-016-0837-3 |
0.633 |
|
| 2016 |
Somarelli JA, Ware KE, Kostadinov R, Robinson JM, Amri H, Abu-Asab M, Fourie N, Diogo R, Swofford D, Townsend JP. PhyloOncology: Understanding cancer through phylogenetic analysis. Biochimica Et Biophysica Acta. PMID 27810337 DOI: 10.1016/J.Bbcan.2016.10.006 |
0.319 |
|
| 2016 |
Lewnard JA, Townsend JP. Climatic and evolutionary drivers of phase shifts in the plague epidemics of colonial India. Proceedings of the National Academy of Sciences of the United States of America. PMID 27791071 DOI: 10.1073/Pnas.1604985113 |
0.303 |
|
| 2016 |
Gaffney SG, Townsend JP. PathScore: a web tool for identifying altered pathways in cancer data. Bioinformatics (Oxford, England). PMID 27503224 DOI: 10.1093/Bioinformatics/Btw512 |
0.319 |
|
| 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 |
0.31 |
|
| 2016 |
Zhao ZM, Zhao B, Bai Y, Iamarino A, Gaffney SG, Schlessinger J, Lifton RP, Rimm DL, Townsend JP. Early and multiple origins of metastatic lineages within primary tumors. Proceedings of the National Academy of Sciences of the United States of America. PMID 26858460 DOI: 10.1073/Pnas.1525677113 |
0.322 |
|
| 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 |
0.341 |
|
| 2015 |
Prum RO, Berv JS, Dornburg A, Field DJ, Townsend JP, Lemmon EM, Lemmon AR. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature. 526: 569-73. PMID 26444237 DOI: 10.1038/Nature15697 |
0.648 |
|
| 2015 |
Hong WS, Shpak M, Townsend JP. Inferring the Origin of Metastases from Cancer Phylogenies. Cancer Research. 75: 4021-5. PMID 26260528 DOI: 10.1158/0008-5472.Can-15-1889 |
0.302 |
|
| 2015 |
Hwang J, Zhao Q, Yang ZL, Wang Z, Townsend JP. Solving the ecological puzzle of mycorrhizal associations using data from annotated collections and environmental samples - an example of saddle fungi. Environmental Microbiology Reports. 7: 658-67. PMID 26033481 DOI: 10.1111/1758-2229.12303 |
0.346 |
|
| 2015 |
Su Z, Townsend JP. Utility of characters evolving at diverse rates of evolution to resolve quartet trees with unequal branch lengths: analytical predictions of long-branch effects. Bmc Evolutionary Biology. 15: 86. PMID 25968460 DOI: 10.1186/S12862-015-0364-7 |
0.32 |
|
| 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 |
0.408 |
|
| 2015 |
Scarpino SV, Iamarino A, Wells C, Yamin D, Ndeffo-Mbah M, Wenzel NS, Fox SJ, Nyenswah T, Altice FL, Galvani AP, Meyers LA, Townsend JP. Epidemiological and viral genomic sequence analysis of the 2014 ebola outbreak reveals clustered transmission. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. 60: 1079-82. PMID 25516185 DOI: 10.1093/Cid/Ciu1131 |
0.313 |
|
| 2014 |
Campbell MC, Hirbo JB, Townsend JP, Tishkoff SA. The peopling of the African continent and the diaspora into the new world. Current Opinion in Genetics & Development. 29: 120-32. PMID 25461616 DOI: 10.1016/J.Gde.2014.09.003 |
0.311 |
|
| 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 |
0.376 |
|
| 2014 |
Dornburg A, Townsend JP, Friedman M, Near TJ. Phylogenetic informativeness reconciles ray-finned fish molecular divergence times. Bmc Evolutionary Biology. 14: 169. PMID 25103329 DOI: 10.1186/S12862-014-0169-0 |
0.631 |
|
| 2014 |
Nielsen KM, Bøhn T, Townsend JP. Detecting rare gene transfer events in bacterial populations. Frontiers in Microbiology. 4: 415. PMID 24432015 DOI: 10.3389/Fmicb.2013.00415 |
0.325 |
|
| 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 |
0.364 |
|
| 2014 |
Su Z, Wang Z, López-Giráldez F, Townsend JP. The impact of incorporating molecular evolutionary model into predictions of phylogenetic signal and noise Frontiers in Ecology and Evolution. 2. DOI: 10.3389/Fevo.2014.00011 |
0.31 |
|
| 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 |
0.306 |
|
| 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 |
0.392 |
|
| 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 |
0.381 |
|
| 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 |
0.343 |
|
| 2013 |
Dai L, Tian M, Wu J, Xiao J, Wang X, Townsend JP, Zhang Z. AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification. Bioinformatics (Oxford, England). 29: 1837-9. PMID 23732274 DOI: 10.1093/Bioinformatics/Btt284 |
0.407 |
|
| 2013 |
Moeller AH, Townsend JP. Response to: The relative utility of sequence divergence and phylogenetic informativeness profiling in phylogenetic study design. Molecular Phylogenetics and Evolution. 66: 436. PMID 23063589 DOI: 10.1016/J.Ympev.2012.09.035 |
0.303 |
|
| 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 |
0.39 |
|
| 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 |
0.364 |
|
| 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 |
0.322 |
|
| 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 |
0.332 |
|
| 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 |
0.323 |
|
| 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 |
0.575 |
|
| 2012 |
Townsend JP, Su Z, Tekle YI. Phylogenetic signal and noise: predicting the power of a data set to resolve phylogeny. Systematic Biology. 61: 835-49. PMID 22389443 DOI: 10.1093/Sysbio/Sys036 |
0.333 |
|
| 2012 |
Townsend JP, Bøhn T, Nielsen KM. Assessing the probability of detection of horizontal gene transfer events in bacterial populations. Frontiers in Microbiology. 3: 27. PMID 22363321 DOI: 10.3389/Fmicb.2012.00027 |
0.329 |
|
| 2012 |
Rice DP, Townsend JP. A test for selection employing quantitative trait locus and mutation accumulation data. Genetics. 190: 1533-45. PMID 22298701 DOI: 10.1534/Genetics.111.137075 |
0.317 |
|
| 2011 |
López-Giráldez F, Townsend JP. PhyDesign: an online application for profiling phylogenetic informativeness. Bmc Evolutionary Biology. 11: 152. PMID 21627831 DOI: 10.1186/1471-2148-11-152 |
0.357 |
|
| 2011 |
Mathioni SM, Beló A, Townsend JP, Donofrio NM. Getting the most out of your fungal microarray data: two cost- and time-effective methods. Methods in Molecular Biology (Clifton, N.J.). 722: 61-77. PMID 21590413 DOI: 10.1007/978-1-61779-040-9_5 |
0.323 |
|
| 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 |
0.339 |
|
| 2011 |
Wang Z, Nilsson RH, Lopez-Giraldez F, Zhuang WY, Dai YC, Johnston PR, Townsend JP. Tasting soil fungal diversity with earth tongues: phylogenetic test of SATé alignments for environmental ITS data. Plos One. 6: e19039. PMID 21533038 DOI: 10.1371/Journal.Pone.0019039 |
0.342 |
|
| 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 |
0.341 |
|
| 2010 |
Townsend JP, Lopez-Giraldez F. Optimal selection of gene and ingroup taxon sampling for resolving phylogenetic relationships. Systematic Biology. 59: 446-57. PMID 20547780 DOI: 10.1093/Sysbio/Syq025 |
0.362 |
|
| 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 |
0.522 |
|
| 2010 |
Tekle YI, Grant JR, Kovner AM, Townsend JP, Katz LA. Identification of new molecular markers for assembling the eukaryotic tree of life. Molecular Phylogenetics and Evolution. 55: 1177-82. PMID 20302952 DOI: 10.1016/J.Ympev.2010.03.010 |
0.326 |
|
| 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 |
0.496 |
|
| 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 |
0.374 |
|
| 2009 |
Otto W, Stadler PF, López-Giraldéz F, Townsend JP, Lynch VJ, Wagner GP. Measuring transcription factor-binding site turnover: a maximum likelihood approach using phylogenies. Genome Biology and Evolution. 1: 85-98. PMID 20333180 DOI: 10.1093/Gbe/Evp010 |
0.342 |
|
| 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 |
0.366 |
|
| 2009 |
Zhang Z, Townsend JP. Maximum-likelihood model averaging to profile clustering of site types across discrete linear sequences. Plos Computational Biology. 5: e1000421. PMID 19557160 DOI: 10.1371/Journal.Pcbi.1000421 |
0.445 |
|
| 2009 |
Zhang Z, Cheung KH, Townsend JP. Bringing Web 2.0 to bioinformatics. Briefings in Bioinformatics. 10: 1-10. PMID 18842678 DOI: 10.1093/Bib/Bbn041 |
0.45 |
|
| 2008 |
Townsend JP, López-Giráldez F, Friedman R. The phylogenetic informativeness of nucleotide and amino acid sequences for reconstructing the vertebrate tree. Journal of Molecular Evolution. 67: 437-47. PMID 18696029 DOI: 10.1007/S00239-008-9142-0 |
0.352 |
|
| 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 |
0.37 |
|
| 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 |
0.33 |
|
| 2007 |
Townsend JP. Profiling phylogenetic informativeness. Systematic Biology. 56: 222-31. PMID 17464879 DOI: 10.1080/10635150701311362 |
0.353 |
|
| 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 |
0.357 |
|
| 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 |
0.361 |
|
| 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 |
0.344 |
|
| 2006 |
Landry CR, Townsend JP, Hartl DL, Cavalieri D. Ecological and evolutionary genomics of Saccharomyces cerevisiae. Molecular Ecology. 15: 575-91. PMID 16499686 DOI: 10.1111/J.1365-294X.2006.02778.X |
0.661 |
|
| 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 |
0.721 |
|
| 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 |
0.371 |
|
| 2005 |
Gogarten JP, Townsend JP. Horizontal gene transfer, genome innovation and evolution. Nature Reviews. Microbiology. 3: 679-87. PMID 16138096 DOI: 10.1038/Nrmicro1204 |
0.371 |
|
| 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 |
0.349 |
|
| 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 |
0.361 |
|
| 2004 |
Nielsen KM, Townsend JP. Monitoring and modeling horizontal gene transfer. Nature Biotechnology. 22: 1110-4. PMID 15340481 DOI: 10.1038/Nbt1006 |
0.309 |
|
| 2004 |
Townsend JP, Rand DM. Mitochondrial genome size variation in New World and Old World populations of Drosophila melanogaster. Heredity. 93: 98-103. PMID 15138453 DOI: 10.1038/Sj.Hdy.6800484 |
0.326 |
|
| 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 |
0.339 |
|
| 2003 |
Townsend JP, Nielsen KM, Fisher DS, Hartl DL. Horizontal acquisition of divergent chromosomal DNA in bacteria: effects of mutator phenotypes. Genetics. 164: 13-21. PMID 12750317 DOI: 10.7490/F1000Research.1096391.1 |
0.5 |
|
| 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 |
0.56 |
|
| 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 |
0.545 |
|
| 2002 |
Grosu P, Townsend JP, Hartl DL, Cavalieri D. Pathway Processor: a tool for integrating whole-genome expression results into metabolic networks. Genome Research. 12: 1121-6. PMID 12097350 DOI: 10.1101/Gr.226602 |
0.505 |
|
| 2000 |
Townsend JP, Hartl DL. The kinetics of transposable element autoregulation. Genetica. 108: 229-37. PMID 11294609 DOI: 10.1023/A:1004172703790 |
0.468 |
|
| 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 |
0.552 |
|
| 2000 |
Bustamante CD, Townsend JP, Hartl DL. Solvent accessibility and purifying selection within proteins of Escherichia coli and Salmonella enterica. Molecular Biology and Evolution. 17: 301-8. PMID 10677853 DOI: 10.1093/Oxfordjournals.Molbev.A026310 |
0.572 |
|
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