Jeffrey P. Townsend, Ph.D. - Publications

Affiliations: 
Harvard University, Cambridge, MA, United States 
Area:
evolutionary biology, molecular genetics

122 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Claus EB, Cannataro VL, Gaffney SG, Townsend JP. Environmental and sex-specific molecular signatures of glioma causation. Neuro-Oncology. PMID 33942853 DOI: 10.1093/neuonc/noab103  0.36
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  0.56
2019 Lu L, Gaffney SG, Cannataro VL, Townsend J. Transfer RNA methyltransferase gene NSUN2 mRNA expression modifies the effect of T cell activation score on patient survival in head and neck squamous carcinoma. Oral Oncology. 101: 104554. PMID 31887619 DOI: 10.1016/J.Oraloncology.2019.104554  0.36
2019 Gaffney SG, Ad O, Smaga S, Schepartz A, Townsend JP. GEM-NET: Lessons in Multi-Institution Teamwork Using Collaboration Software. Acs Central Science. 5: 1159-1169. PMID 31404233 DOI: 10.1021/Acscentsci.9B00111  0.36
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  0.36
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  0.56
2019 Lee JW, Parameswaran J, Sandoval-Schaefer T, Eoh KJ, Yang DH, Zhu F, Mehra R, Sharma R, Gaffney SG, Perry EB, Townsend JP, Serebriiskii IG, Golemis EA, Issaeva N, Yarbrough WG, et al. Combined Aurora kinase A (AURKA) and WEE1 inhibition demonstrates synergistic antitumor effect in squamous cell carcinoma of the head and neck. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 30755439 DOI: 10.1158/1078-0432.Ccr-18-0440  0.36
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  0.36
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  0.36
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  0.56
2018 Kadara H, Choi M, Zhang J, Parra ER, Rodriguez-Canales J, Gaffney SG, Zhao Z, Behrens C, Fujimoto J, Chow C, Yoo Y, Kalhor N, Moran C, Rimm D, Swisher S, ... ... Townsend JP, et al. Whole-exome sequencing and immune profiling of early-stage lung adenocarcinoma with fully annotated clinical follow-up. Annals of Oncology : Official Journal of the European Society For Medical Oncology. 29: 1072. PMID 29688333 DOI: 10.1093/Annonc/Mdx062  0.36
2018 Chen WS, Bindra RS, Mo A, Hayman T, Husain Z, Contessa JN, Gaffney SG, Townsend JP, Yu JB. CDKN2A Copy Number Loss Is an Independent Prognostic Factor in HPV-Negative Head and Neck Squamous Cell Carcinoma. Frontiers in Oncology. 8: 95. PMID 29670856 DOI: 10.3389/Fonc.2018.00095  0.8
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  0.56
2017 Townsend JP, Wang Z. Preface. Advances in Genetics. 100: xi-xii. PMID 29153406 DOI: 10.1016/S0065-2660(17)30059-7  0.56
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  0.8
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  1
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  0.56
2017 Chen WS, Townsend JP, Yu JB. Radiation-Specific Clinical Data Should Be Included in Existing Large-Scale Genomic Datasets. International Journal of Radiation Oncology, Biology, Physics. 98: 8-10. PMID 28587055 DOI: 10.1016/J.Ijrobp.2017.01.023  0.8
2017 Kadara H, Choi M, Zhang J, Parra ER, Rodriguez-Canales J, Gaffney SG, Zhao Z, Behrens C, Fujimoto J, Chow C, Yoo Y, Kalhor N, Moran C, Rimm D, Swisher S, ... ... Townsend JP, et al. Whole-exome sequencing and immune profiling of early-stage lung adenocarcinoma with fully annotated clinical follow-up. Annals of Oncology : Official Journal of the European Society For Medical Oncology. PMID 28368511 DOI: 10.1093/annonc/mdx062  0.36
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  0.36
2016 Kadara H, Choi M, Zhang J, Cuentas EP, Canales JR, Gaffney SG, Zhao Z, Behrens C, Fujimoto J, Chow C, Yoo Y, Kalhor N, Moran C, Rimm D, Swisher S, ... ... Townsend JP, et al. Whole-exome sequencing and immune profiling of early-stage lung adenocarcinoma with fully annotated clinical follow-up. Annals of Oncology : Official Journal of the European Society For Medical Oncology. PMID 27687306 DOI: 10.1093/Annonc/Mdw436  0.36
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  0.36
2016 Fitzpatrick MC, Wenzel NS, Scarpino SV, Althouse BM, Atkins KE, Galvani AP, Townsend JP. Cost-effectiveness of next-generation vaccines: The case of pertussis. Vaccine. PMID 27087151 DOI: 10.1016/J.Vaccine.2016.04.010  1
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  1
2016 Gilbert JA, Medlock J, Townsend JP, Aksoy S, Ndeffo Mbah M, Galvani AP. Determinants of Human African Trypanosomiasis Elimination via Paratransgenesis. Plos Neglected Tropical Diseases. 10: e0004465. PMID 26954675 DOI: 10.1371/Journal.Pntd.0004465  1
2016 Atkins KE, Pandey A, Wenzel NS, Skrip L, Yamin D, Nyenswah TG, Fallah M, Bawo L, Medlock J, Altice FL, Townsend J, Ndeffo-Mbah ML, Galvani AP. Retrospective Analysis of the 2014-2015 Ebola Epidemic in Liberia. The American Journal of Tropical Medicine and Hygiene. PMID 26928839 DOI: 10.4269/Ajtmh.15-0328  1
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  0.36
2016 Kadara H, Choi M, Zhang J, Cuentas EP, Canales JR, Gaffney S, Zhao Z, Behrens C, Fujimoto J, Chow C, Kalhor N, Moran C, Rimm D, Swisher SG, Gibbons DL, ... ... Townsend J, et al. Abstract 89: Whole-exome sequencing and immune profiling of early-stage lung adenocarcinoma Cancer Research. 76: 89-89. DOI: 10.1158/1538-7445.Am2016-89  0.36
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  0.36
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  1
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  1
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  1
2015 Wells C, Yamin D, Ndeffo-Mbah ML, Wenzel N, Gaffney SG, Townsend JP, Meyers LA, Fallah M, Nyenswah TG, Altice FL, Atkins KE, Galvani AP. Correction: Harnessing Case Isolation and Ring Vaccination to Control Ebola. Plos Neglected Tropical Diseases. 9: e0003888. PMID 26107520 DOI: 10.1371/Journal.Pntd.0003888  0.36
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  1
2015 Wells C, Yamin D, Ndeffo-Mbah ML, Wenzel N, Gaffney SG, Townsend JP, Meyers LA, Fallah M, Nyenswah TG, Altice FL, Atkins KE, Galvani AP. Harnessing case isolation and ring vaccination to control ebola. Plos Neglected Tropical Diseases. 9: e0003794. PMID 26024528 DOI: 10.1371/Journal.Pntd.0003794  1
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  1
2015 Gilbert JA, Long EF, Brooks RP, Friedland GH, Moll AP, Townsend JP, Galvani AP, Shenoi SV. Integrating Community-Based Interventions to Reverse the Convergent TB/HIV Epidemics in Rural South Africa. Plos One. 10: e0126267. PMID 25938501 DOI: 10.1371/Journal.Pone.0126267  1
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  1
2015 Ghosh S, Townsend JP. H-CLAP: hierarchical clustering within a linear array with an application in genetics. Statistical Applications in Genetics and Molecular Biology. 14: 125-41. PMID 25803088 DOI: 10.1515/Sagmb-2013-0076  1
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  1
2015 Stiver KA, Harris RM, Townsend JP, Hofmann HA, Alonzo SH. Neural Gene Expression Profiles and Androgen Levels Underlie Alternative Reproductive Tactics in the Ocellated Wrasse, Symphodus ocellatus Ethology. 121: 152-167. DOI: 10.1111/Eth.12324  1
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  1
2014 Pandey A, Atkins KE, Medlock J, Wenzel N, Townsend JP, Childs JE, Nyenswah TG, Ndeffo-Mbah ML, Galvani AP. Strategies for containing Ebola in West Africa. Science (New York, N.Y.). 346: 991-5. PMID 25414312 DOI: 10.1126/Science.1260612  1
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  1
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  1
2014 Wu C, Yang F, Smith KM, Peterson M, Dekhang R, Zhang Y, Zucker J, Bredeweg EL, Mallappa C, Zhou X, Lyubetskaya A, Townsend JP, Galagan JE, Freitag M, Dunlap JC, et al. Genome-wide characterization of light-regulated genes in Neurospora crassa. G3 (Bethesda, Md.). 4: 1731-45. PMID 25053707 DOI: 10.1534/G3.114.012617  1
2014 Talbert-Slagle K, Atkins KE, Yan KK, Khurana E, Gerstein M, Bradley EH, Berg D, Galvani AP, Townsend JP. Cellular superspreaders: an epidemiological perspective on HIV infection inside the body. Plos Pathogens. 10: e1004092. PMID 24811311 DOI: 10.1371/Journal.Ppat.1004092  1
2014 Gilbert JA, Meyers LA, Galvani AP, Townsend JP. Probabilistic uncertainty analysis of epidemiological modeling to guide public health intervention policy. Epidemics. 6: 37-45. PMID 24593920 DOI: 10.1016/J.Epidem.2013.11.002  1
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  1
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  1
2014 Su Z, Lopez-Giraldez F, Tekle Y, Leuenberger C, Townsend J. Phylogenetic experimental design F1000research. 5. DOI: 10.7490/F1000Research.1096505.1  0.6
2013 Ndeffo Mbah ML, Poolman EM, Atkins KE, Orenstein EW, Meyers LA, Townsend JP, Galvani AP. Potential cost-effectiveness of schistosomiasis treatment for reducing HIV transmission in Africa--the case of Zimbabwean women. Plos Neglected Tropical Diseases. 7: e2346. PMID 23936578 DOI: 10.1371/Journal.Pntd.0002346  1
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  1
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  1
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  1
2013 Atkins KE, Townsend JP, Medlock J, Galvani AP. Epidemiological mechanisms of genetic resistance to kuru. Journal of the Royal Society, Interface / the Royal Society. 10: 20130331. PMID 23740487 DOI: 10.1098/Rsif.2013.0331  1
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  1
2013 Ndeffo Mbah ML, Medlock J, Meyers LA, Galvani AP, Townsend JP. Optimal targeting of seasonal influenza vaccination toward younger ages is robust to parameter uncertainty. Vaccine. 31: 3079-89. PMID 23684837 DOI: 10.1016/J.Vaccine.2013.04.052  1
2013 Ndeffo Mbah ML, Kjetland EF, Atkins KE, Poolman EM, Orenstein EW, Meyers LA, Townsend JP, Galvani AP. Cost-effectiveness of a community-based intervention for reducing the transmission of Schistosoma haematobium and HIV in Africa. Proceedings of the National Academy of Sciences of the United States of America. 110: 7952-7. PMID 23589884 DOI: 10.1073/Pnas.1221396110  1
2013 McBride RC, Boucher N, Park DS, Turner PE, Townsend JP. Yeast response to LA virus indicates coadapted global gene expression during mycoviral infection. Fems Yeast Research. 13: 162-79. PMID 23122216 DOI: 10.1111/1567-1364.12019  1
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  1
2012 Tekle YI, Nielsen KM, Liu J, Pettigrew MM, Meyers LA, Galvani AP, Townsend JP. Controlling antimicrobial resistance through targeted, vaccine-induced replacement of strains. Plos One. 7: e50688. PMID 23227198 DOI: 10.1371/Journal.Pone.0050688  1
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  1
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  1
2012 Fitzpatrick MC, Hampson K, Cleaveland S, Meyers LA, Townsend JP, Galvani AP. Potential for rabies control through dog vaccination in wildlife-abundant communities of Tanzania. Plos Neglected Tropical Diseases. 6: e1796. PMID 22928056 DOI: 10.1371/Journal.Pntd.0001796  1
2012 Rice DP, Townsend JP. Resampling QTL effects in the QTL sign test leads to incongruous sensitivity to variance in effect size. G3 (Bethesda, Md.). 2: 905-11. PMID 22908039 DOI: 10.1534/G3.112.003228  1
2012 Durham DP, Poolman EM, Ibuka Y, Townsend JP, Galvani AP. Reevaluation of epidemiological data demonstrates that it is consistent with cross-immunity among human papillomavirus types. The Journal of Infectious Diseases. 206: 1291-8. PMID 22872732 DOI: 10.1093/Infdis/Jis494  1
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  1
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  1
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  1
2012 Shim E, Chapman GB, Townsend JP, Galvani AP. The influence of altruism on influenza vaccination decisions. Journal of the Royal Society, Interface / the Royal Society. 9: 2234-43. PMID 22496100 DOI: 10.1098/Rsif.2012.0115  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2011 Townsend JP, Leuenberger C. Taxon sampling and the optimal rates of evolution for phylogenetic inference. Systematic Biology. 60: 358-65. PMID 21303824 DOI: 10.1093/Sysbio/Syq097  1
2011 Johnsen PJ, Townsend JP, Bøhn T, Simonsen GS, Sundsfjord A, Nielsen KM. Retrospective evidence for a biological cost of vancomycin resistance determinants in the absence of glycopeptide selective pressures. The Journal of Antimicrobial Chemotherapy. 66: 608-10. PMID 21217128 DOI: 10.1093/Jac/Dkq512  1
2010 Ohenoja E, Wang Z, Townsend JP, Mitchel D, Voitk A. Northern species of earth tongue genus Thuemenidium revisited, considering morphology, ecology and molecular phylogeny. Mycologia. 102: 1089-95. PMID 20943508 DOI: 10.3852/09-317  1
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  1
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  1
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  1
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  1
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  1
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  1
2009 Schoch CL, Wang Z, Townsend JP, Spatafora JW. Geoglossomycetes cl. nov., Geoglossales ord. nov. and taxa above class rank in the Ascomycota Tree of Life. Persoonia. 22: 129-38. PMID 19915689 DOI: 10.3767/003158509X461486  1
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  1
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  1
2009 Johnsen PJ, Townsend JP, Bøhn T, Simonsen GS, Sundsfjord A, Nielsen KM. Factors affecting the reversal of antimicrobial-drug resistance. The Lancet. Infectious Diseases. 9: 357-64. PMID 19467475 DOI: 10.1016/S1473-3099(09)70105-7  1
2009 Wang Z, Johnston PR, Yang ZL, Townsend JP. Evolution of reproductive morphology in leaf endophytes. Plos One. 4: e4246. PMID 19158947 DOI: 10.1371/Journal.Pone.0004246  1
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  1
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  1
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  1
2008 Cheung KH, Yip KY, Townsend JP, Scotch M. HCLS 2.0/3.0: health care and life sciences data mashup using Web 2.0/3.0. Journal of Biomedical Informatics. 41: 694-705. PMID 18487092 DOI: 10.1016/J.Jbi.2008.04.001  1
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  1
2007 Townsend JP. Profiling phylogenetic informativeness. Systematic Biology. 56: 222-31. PMID 17464879 DOI: 10.1080/10635150701311362  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2005 Gogarten JP, Townsend JP. Horizontal gene transfer, genome innovation and evolution. Nature Reviews. Microbiology. 3: 679-87. PMID 16138096 DOI: 10.1038/Nrmicro1204  1
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  1
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  1
2004 Davison J, Heinemann JA, Traavik T, Nielsen KM, Townsend J. Monitoring horizontal gene transfer [3] (multiple letters) Nature Biotechnology. 22: 1349-1350. PMID 15529149  1
2004 Nielsen KM, Townsend JP. Monitoring and modeling horizontal gene transfer. Nature Biotechnology. 22: 1110-4. PMID 15340481 DOI: 10.1038/Nbt1006  1
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  1
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  1
2003 Townsend JP. Multifactorial experimental design and the transitivity of ratios with spotted DNA microarrays. Bmc Genomics. 4: 41. PMID 14525623 DOI: 10.1186/1471-2164-4-41  1
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  1
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  1
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  1
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  1
2000 Townsend JP, Hartl DL. The kinetics of transposable element autoregulation. Genetica. 108: 229-37. PMID 11294609 DOI: 10.1023/A:1004172703790  1
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  1
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  1
Show low-probability matches.