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Kim J, Baczewski AT, Beaudet TD, Benali A, Bennett MC, Berrill MA, Blunt NS, Borda EJL, Casula M, Ceperley DM, Chiesa S, Clark BK, Clay RC, Delaney KT, Dewing M, Esler KP, Hao H, Heinonen O, Kent PRC, Krogel JT, Kylänpää I, Li YW, Lopez MG, Luo Y, Malone FD, Martin RM, Mathuriya A, McMinis J, Melton CA, Mitas L, Morales MA, Neuscamman E, Parker WD, Pineda Flores SD, Romero NA, Rubenstein BM, Shea JAR, Shin H, Shulenburger L, Tillack AF, Townsend JP, Tubman NM, Van Der Goetz B, Vincent JE, Yang DC, Yang Y, Zhang S, Zhao L: QMCPACK: an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids. J Phys Condens Matter. 2018 May 16; 2018 Mar 27. PMID: 29582782

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. 2018 May; 2018 Feb 16. PMID: 29453361

Cannataro VL, Townsend JP: Neutral theory and the somatic evolution of cancer. Mol Biol Evol. 2018 Apr 19; 2018 Apr 19. PMID: 29684198

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. Front Oncol. 2018; 2018 Apr 4. PMID: 29670856

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, Gibbons DL, Heymach J, Kaftan E, Townsend JP, Lynch TJ, Schlessinger J, Lee J, Lifton RP, Wistuba II, Herbst RS: Whole-exome sequencing and immune profiling of early-stage lung adenocarcinoma with fully annotated clinical follow-up. Ann Oncol. 2018 Apr 1. PMID: 29688333

Townsend JP: The Cancer Tree. Sci Am. 2018 Mar 20. PMID: 29557973

Zhao ZM, Wang J, Ugwuowo UC, Wang L, Townsend JP: Primary hepatic neuroendocrine carcinoma: report of two cases and literature review. BMC Clin Pathol. 2018; 2018 Mar 1. PMID: 29507528

Adhikarla H, Wunder EA Jr., 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, Ko AI: Lvr, a Signaling System That Controls Global Gene Regulation and Virulence in Pathogenic Leptospira. Front Cell Infect Microbiol. 2018; 2018 Feb 23. PMID: 29600195

Gomez K, Miura S, Huuki LA, Spell BS, Townsend JP, Kumar S: Somatic evolutionary timings of driver mutations. BMC Cancer. 2018 Jan 18; 2018 Jan 18. PMID: 29347918

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. Mol Ecol. 2018 Jan; 2017 Dec 12. PMID: 29134709

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. Mol Biol Evol. 2017 Nov 1. PMID: 28962009

Cai J, Townsend JP, Dodson TC, Heiney PA, Sweeney AM: Eye patches: Protein assembly of index-gradient squid lenses. Science. 2017 Aug 11. PMID: 28798124

Park B, Rutter MT, Fenster CB, Symonds VV, Ungerer MC, Townsend JP: Distributions of Mutational Effects and the Estimation of Directional Selection in Divergent Lineages of Arabidopsis thaliana. Genetics. 2017 Aug; 2017 May 26. PMID: 28550014

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 Genet. 2017 Jul; 2017 Jul 13. PMID: 28704372

Chen WS, Townsend JP, Yu JB: Radiation-Specific Clinical Data Should Be Included in Existing Large-Scale Genomic Datasets. Int J Radiat Oncol Biol Phys. 2017 May 1; 2017 Jan 16. PMID: 28587055

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. Mol Phylogenet Evol. 2017 May; 2017 Feb 27. PMID: 28254474

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. Biochim Biophys Acta. 2017 Apr; 2016 Oct 31. PMID: 27810337

Townsend JP, Wang Z: Preface. Adv Genet. 2017. PMID: 29153406

Dornburg A, Townsend JP, Wang Z: Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big Data. Adv Genet. 2017; 2017 Nov 6. PMID: 29153398

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, Gibbons DL, Heymach J, Kaftan E, Townsend JP, Lynch TJ, Schlessinger J, Lee J, Lifton RP, Herbst RS, Wistuba II: Mutation profiles in early-stage lung squamous cell carcinoma with clinical follow-up and correlation with markers of immune function. Ann Oncol. 2017 Jan 1. PMID: 28177435

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, Gibbons DL, Heymach J, Kaftan E, Townsend JP, Lynch TJ, Schlessinger J, Lee J, Lifton RP, Wistuba II, Herbst RS: Whole-exome sequencing and immune profiling of early-stage lung adenocarcinoma with fully annotated clinical follow-up. Ann Oncol. 2017 Jan 1. PMID: 27687306

Fitzpatrick MC, Shah HA, Pandey A, Bilinski AM, Kakkar M, Clark AD, Townsend JP, Abbas SS, Galvani AP: One Health approach to cost-effective rabies control in India. Proc Natl Acad Sci U S A. 2016 Dec 20. PMID: 27994161

Lewnard JA, Townsend JP: Climatic and evolutionary drivers of phase shifts in the plague epidemics of colonial India. Proc Natl Acad Sci U S A. 2016 Dec 20; 2016 Oct 24. PMID: 27791071

Gaffney SG, Townsend JP: PathScore: a web tool for identifying altered pathways in cancer data. Bioinformatics. 2016 Dec 1; 2016 Aug 8. PMID: 27503224

Dornburg A, Fisk JN, Tamagnan J, Townsend JP: PhyInformR: phylogenetic experimental design and phylogenomic data exploration in R. BMC Evol Biol. 2016 Dec 1; 2016 Dec 1. PMID: 27905871

Yamin D, Jones FK, DeVincenzo JP, Gertler S, Kobiler O, Townsend JP, Galvani AP: Vaccination strategies against respiratory syncytial virus. Proc Natl Acad Sci U S A. 2016 Nov 15; 2016 Oct 31. PMID: 27799521

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. 2016 Jun 17; 2016 Apr 14. PMID: 27087151

Atkins KE, Fitzpatrick MC, Galvani AP, Townsend JP: Cost-Effectiveness of Pertussis Vaccination During Pregnancy in the United States. Am J Epidemiol. 2016 Jun 15; 2016 May 13. PMID: 27188951

Durham DP, Olsen MA, Dubberke ER, Galvani AP, Townsend JP: Quantifying Transmission of Clostridium difficile within and outside Healthcare Settings. Emerg Infect Dis. 2016 Apr. PMID: 26982504

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. 2016 Mar 8; 2016 Mar 8. PMID: 26956589

Gilbert JA, Medlock J, Townsend JP, Aksoy S, Ndeffo Mbah M, Galvani AP: Determinants of Human African Trypanosomiasis Elimination via Paratransgenesis. PLoS Negl Trop Dis. 2016 Mar; 2016 Mar 8. PMID: 26954675

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. Proc Natl Acad Sci U S A. 2016 Feb 23; 2016 Feb 8. PMID: 26858460

Durham DP, Skrip LA, Bruce RD, Vilarinho S, Elbasha EH, Galvani AP, Townsend JP: The Impact of Enhanced Screening and Treatment on Hepatitis C in the United States. Clin Infect Dis. 2016 Feb 1; 2015 Nov 30. PMID: 26628566

Alfaro-Murillo JA, Townsend JP, Galvani AP: Optimizing age of cytomegalovirus screening and vaccination to avert congenital disease in the US. Vaccine. 2016 Jan 4; 2015 Nov 27. PMID: 26631416

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. 2015; 2015 Dec 15. PMID: 26670219

Townsend JP, Skrip LA, Galvani AP: Impact of bed capacity on spatiotemporal shifts in Ebola transmission. Proc Natl Acad Sci U S A. 2015 Nov 17; 2015 Oct 30. PMID: 26518509

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. 2015 Oct 22; 2015 Oct 7. PMID: 26444237

Hong WS, Shpak M, Townsend JP: Inferring the Origin of Metastases from Cancer Phylogenies. Cancer Res. 2015 Oct 1; 2015 Aug 10. PMID: 26260528

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. Environ Microbiol Rep. 2015 Aug; 2015 Jul 1. PMID: 26033481

Hodgins-Davis A, Rice DP, Townsend JP: Gene Expression Evolves under a House-of-Cards Model of Stabilizing Selection. Mol Biol Evol. 2015 Aug; 2015 Apr 20. PMID: 25901014

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 Negl Trop Dis. 2015 Jun; 2015 Jun 24. PMID: 26107520

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 Negl Trop Dis. 2015 May; 2015 May 29. PMID: 26024528

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 Evol Biol. 2015 May 14; 2015 May 14. PMID: 25968460

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. 2015; 2015 May 4. PMID: 25938501

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. Clin Infect Dis. 2015 Apr 1; 2014 Dec 15. PMID: 25516185

Ghosh S, Townsend JP: H-CLAP: hierarchical clustering within a linear array with an application in genetics. Stat Appl Genet Mol Biol. 2015 Apr. PMID: 25803088

Atkins KE, Wenzel NS, Ndeffo-Mbah M, Altice FL, Townsend JP, Galvani AP: Under-reporting and case fatality estimates for emerging epidemics. BMJ. 2015 Mar 16; 2015 Mar 16. PMID: 25779635

Campbell MC, Hirbo JB, Townsend JP, Tishkoff SA: The peopling of the African continent and the diaspora into the new world. Curr Opin Genet Dev. 2014 Dec. PMID: 25461616

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. 2014 Nov 21; 2014 Oct 30. PMID: 25414312

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. 2014; 2014 Oct 20. PMID: 25329823

Dornburg A, Townsend JP, Friedman M, Near TJ: Phylogenetic informativeness reconciles ray-finned fish molecular divergence times. BMC Evol Biol. 2014 Aug 8; 2014 Aug 8. PMID: 25103329

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, Bell-Pedersen D, Sachs MS: Genome-wide characterization of light-regulated genes in Neurospora crassa. G3 (Bethesda). 2014 Jul 21; 2014 Jul 21. PMID: 25053707

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 Pathog. 2014 May; 2014 May 8. PMID: 24811311

Gilbert JA, Meyers LA, Galvani AP, Townsend JP: Probabilistic uncertainty analysis of epidemiological modeling to guide public health intervention policy. Epidemics. 2014 Mar; 2013 Nov 19. PMID: 24593920

Nielsen KM, Bøhn T, Townsend JP: Detecting rare gene transfer events in bacterial populations. Front Microbiol. 2014 Jan 7; 2014 Jan 7. PMID: 24432015

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. Eukaryot Cell. 2014 Jan; 2013 Nov 15. PMID: 24243796

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 Negl Trop Dis. 2013; 2013 Aug 1. PMID: 23936578

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. 2013 Jul 15; 2013 Jun 3. PMID: 23732274

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. 2013 Jun 26; 2013 May 16. PMID: 23684837

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. Proc Biol Sci. 2013 Aug 7; 2013 Jun 19. PMID: 23782882

Atkins KE, Townsend JP, Medlock J, Galvani AP: Epidemiological mechanisms of genetic resistance to kuru. J R Soc Interface. 2013 Aug 6; 2013 Jun 5. PMID: 23740487

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. Proc Natl Acad Sci U S A. 2013 May 7; 2013 Apr 15. PMID: 23589884

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 Res. 2013 Mar; 2013 Jan 2. PMID: 23122216

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 Res Int. 2013; 2013 Jun 26. PMID: 23878813

Moeller AH, Townsend JP: Response to: The relative utility of sequence divergence and phylogenetic informativeness profiling in phylogenetic study design. Mol Phylogenet Evol. 2013 Jan; 2012 Oct 9. PMID: 23063589

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 Evol Biol. 2012 Nov 27; 2012 Nov 27. PMID: 23186325

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. J Infect Dis. 2012 Oct; 2012 Aug 7. PMID: 22872732

Townsend JP, Su Z, Tekle YI: Phylogenetic signal and noise: predicting the power of a data set to resolve phylogeny. Syst Biol. 2012 Oct; 2012 Mar 3. PMID: 22389443

Shim E, Chapman GB, Townsend JP, Galvani AP: The influence of altruism on influenza vaccination decisions. J R Soc Interface. 2012 Sep 7; 2012 Apr 11. PMID: 22496100

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 Genet Biol. 2012 Aug; 2012 Jun 15. PMID: 22705880

Rice DP, Townsend JP: Resampling QTL effects in the QTL sign test leads to incongruous sensitivity to variance in effect size. G3 (Bethesda). 2012 Aug; 2012 Aug 1. PMID: 22908039

Wang Z, Kin K, López-Giráldez F, Johannesson H, Townsend JP: Sex-specific gene expression during asexual development of Neurospora crassa. Fungal Genet Biol. 2012 Jul; 2012 May 22. PMID: 22626843

Huang T, López-Giráldez F, Townsend JP, Irish VF: RBE controls microRNA164 expression to effect floral organogenesis. Development. 2012 Jun; 2012 May 9. PMID: 22573623

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 Genet Biol. 2012 May; 2012 Mar 26. PMID: 22469835

Rice DP, Townsend JP: A test for selection employing quantitative trait locus and mutation accumulation data. Genetics. 2012 Apr; 2012 Jan 31. PMID: 22298701

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. 2012 Mar 22; 2012 Mar 22. PMID: 22435713

Townsend JP, Bøhn T, Nielsen KM: Assessing the probability of detection of horizontal gene transfer events in bacterial populations. Front Microbiol. 2012; 2012 Feb 20. PMID: 22363321

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 Biol Evol. 2012. PMID: 23019066

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 Negl Trop Dis. 2012; 2012 Aug 21. PMID: 22928056

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. 2012; 2012 Dec 5. PMID: 23227198

Moeller AH, Townsend JP: Phylogenetic informativeness profiling of 12 genes for 28 vertebrate taxa without divergence dates. Mol Phylogenet Evol. 2011 Aug; 2011 May 1. PMID: 21558010

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 Res. 2011 Jun; 2011 Mar 1. PMID: 21306556

López-Giráldez F, Townsend JP: PhyDesign: an online application for profiling phylogenetic informativeness. BMC Evol Biol. 2011 May 31; 2011 May 31. PMID: 21627831

Townsend JP, Leuenberger C: Taxon sampling and the optimal rates of evolution for phylogenetic inference. Syst Biol. 2011 May; 2011 Feb 8. PMID: 21303824

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. 2011 Apr 21; 2011 Apr 21. PMID: 21533038

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. J Antimicrob Chemother. 2011 Mar; 2011 Jan 7. PMID: 21217128

Mathioni SM, Beló A, Townsend JP, Donofrio NM: Getting the most out of your fungal microarray data: two cost- and time-effective methods. Methods Mol Biol. 2011. PMID: 21590413

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. 2010 Sep-Oct. PMID: 20943508

Adomas AB, Lopez-Giraldez F, Clark TA, Wang Z, Townsend JP: Multi-targeted priming for genome-wide gene expression assays. BMC Genomics. 2010 Aug 17; 2010 Aug 17. PMID: 20716356

Zhang Z, López-Giráldez F, Townsend JP: LOX: inferring Level Of eXpression from diverse methods of census sequencing. Bioinformatics. 2010 Aug 1; 2010 Jun 10. PMID: 20538728

Townsend JP, Lopez-Giraldez F: Optimal selection of gene and ingroup taxon sampling for resolving phylogenetic relationships. Syst Biol. 2010 Jul; 2010 May 19. PMID: 20547780

Tekle YI, Grant JR, Kovner AM, Townsend JP, Katz LA: Identification of new molecular markers for assembling the eukaryotic tree of life. Mol Phylogenet Evol. 2010 Jun; 2010 Mar 17. PMID: 20302952

Zhang Z, Townsend JP: The filamentous fungal gene expression database (FFGED). Fungal Genet Biol. 2010 Mar; 2009 Dec 16. PMID: 20025988

Hodgins-Davis A, Townsend JP: Evolving gene expression: from G to E to GxE. Trends Ecol Evol. 2009 Dec; 2009 Aug 21. PMID: 19699549

Johnsen PJ, Townsend JP, Bøhn T, Simonsen GS, Sundsfjord A, Nielsen KM: Factors affecting the reversal of antimicrobial-drug resistance. Lancet Infect Dis. 2009 Jun. PMID: 19467475

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. 2009 Jun; 2009 Jun 5. PMID: 19915689

Zhang Z, Townsend JP: Maximum-likelihood model averaging to profile clustering of site types across discrete linear sequences. PLoS Comput Biol. 2009 Jun; 2009 Jun 26. PMID: 19557160

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 Biol Evol. 2009 May 25; 2009 May 25. PMID: 20333180

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, Fraker E, Hodkinson BP, Bonito G, Groenewald JZ, Arzanlou M, de Hoog GS, Crous PW, Hewitt D, Pfister DH, Peterson K, Gryzenhout M, Wingfield MJ, Aptroot A, Suh SO, Blackwell M, Hillis DM, Griffith GW, Castlebury LA, Rossman AY, Lumbsch HT, Lücking R, Büdel B, Rauhut A, Diederich P, Ertz D, Geiser DM, Hosaka K, Inderbitzin P, Kohlmeyer J, Volkmann-Kohlmeyer B, Mostert L, O'Donnell K, Sipman H, Rogers JD, Shoemaker RA, Sugiyama J, Summerbell RC, Untereiner W, Johnston PR, Stenroos S, Zuccaro A, Dyer PS, Crittenden PD, Cole MS, Hansen K, Trappe JM, Yahr R, Lutzoni F, Spatafora JW: The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits. Syst Biol. 2009 Apr; 2009 Jun 4. PMID: 20525580

Zhang Z, Cheung KH, Townsend JP: Bringing Web 2.0 to bioinformatics. Brief Bioinform. 2009 Jan; 2008 Oct 8. PMID: 18842678

Wang Z, Johnston PR, Yang ZL, Townsend JP: Evolution of reproductive morphology in leaf endophytes. PLoS One. 2009; 2009 Jan 22. PMID: 19158947

Townsend JP, López-Giráldez F, Friedman R: The phylogenetic informativeness of nucleotide and amino acid sequences for reconstructing the vertebrate tree. J Mol Evol. 2008 Nov; 2008 Aug 12. PMID: 18696029

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. J Biomed Inform. 2008 Oct; 2008 Apr 11. PMID: 18487092

Townsend JP: Sleuthing the difference a nucleotide can make. Mol Ecol. 2008 Jun. PMID: 18565029

Clark TA, Townsend JP: Quantifying variation in gene expression. Mol Ecol. 2007 Jul. PMID: 17594433

Townsend JP: Profiling phylogenetic informativeness. Syst Biol. 2007 Apr. PMID: 17464879

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, Colot HV, Park G, Collopy P, Ringelberg C, Crew C, Litvinkova L, DeCaprio D, Hood HM, Curilla S, Shi M, Crawford M, Koerhsen M, Montgomery P, Larson L, Pearson M, Kasuga T, Tian C, Baştürkmen M, Altamirano L, Xu J: Enabling a community to dissect an organism: overview of the Neurospora functional genomics project. Adv Genet. 2007. PMID: 17352902

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. Philos Trans R Soc Lond B Biol Sci. 2006 Nov 29. PMID: 17062413

Aa E, Townsend JP, Adams RI, Nielsen KM, Taylor JW: Population structure and gene evolution in Saccharomyces cerevisiae. FEMS Yeast Res. 2006 Aug. PMID: 16879422

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 Genet Biol. 2006 Aug; 2006 May 12. PMID: 16697669

Landry CR, Townsend JP, Hartl DL, Cavalieri D: Ecological and evolutionary genomics of Saccharomyces cerevisiae. Mol Ecol. 2006 Mar. PMID: 16499686

Meiklejohn CD, Townsend JP: A Bayesian method for analysing spotted microarray data. Brief Bioinform. 2005 Dec. PMID: 16420731

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 Res. 2005; 2005 Nov 14. PMID: 16287898

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. 2005 Sep; 2005 Jun 18. PMID: 15965255

Gogarten JP, Townsend JP: Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol. 2005 Sep. PMID: 16138096

Townsend JP, Taylor JW: Designing experiments using spotted microarrays to detect gene regulation differences within and among species. Methods Enzymol. 2005. PMID: 15865986

Townsend JP: Multifactorial experimental design and the transitivity of ratios with spotted DNA microarrays. BMC Genomics. 2003 Oct 2; 2003 Oct 2. PMID: 14525623

Townsend JP, Cavalieri D, Hartl DL: Population genetic variation in genome-wide gene expression. Mol Biol Evol. 2003 Jun; 2003 Apr 25. PMID: 12716989

Townsend JP, Nielsen KM, Fisher DS, Hartl DL: Horizontal acquisition of divergent chromosomal DNA in bacteria: effects of mutator phenotypes. Genetics. 2003 May. PMID: 12750317