Jeffrey Townsend

Professor of Biostatistics and Ecology & Evolutionary Biology

New Haven, CT

About

Jeffrey Townsend is a Professor of Organismic and Evolutionary Biology at Yale University. He received his Ph.D. from Harvard University in 2002 and his Sc.B. from Brown University in 1994. He has been a teacher at St. Ann's School and an Assistant Professor at the University of Connecticut. He is currently the Elihu Professor of Biostatistics at Yale University.

Education

Harvard University

Ph.D., Organismic and Evolutionary Biology / May, 2002

Cambridge, Massachusetts, United States of America

Brown University

Sc.B., Biology / May, 1994

Providence, Rhode Island, United States of America

Experience

Yale University

Professor / July, 2018Present

Elihu Professor of Biostatistics / July, 2018Present

Elihu Associate Professor of Biostatistics / July, 2017June, 2018

Associate Professor / July, 2013June, 2018

Associate Professor / July, 2013June, 2017

Assistant Professor / July, 2006June, 2013

University of Connecticut

Assistant Professor / August, 2004May, 2006

St. Ann's School

Teacher / September, 1994June, 1997

Publications

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

Nature / Oct 01, 2015

Prum, R. O., Berv, J. S., Dornburg, A., Field, D. J., Townsend, J. P., Lemmon, E. M., & Lemmon, A. R. (2015). A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature, 526(7574), 569–573. https://doi.org/10.1038/nature15697

Horizontal gene transfer, genome innovation and evolution

Nature Reviews Microbiology / Aug 01, 2005

Gogarten, J. P., & Townsend, J. P. (2005). Horizontal gene transfer, genome innovation and evolution. Nature Reviews Microbiology, 3(9), 679–687. https://doi.org/10.1038/nrmicro1204

The Ascomycota Tree of Life: A Phylum-wide Phylogeny Clarifies the Origin and Evolution of Fundamental Reproductive and Ecological Traits

Systematic Biology / Apr 01, 2009

Schoch, C. L., Sung, G.-H., López-Giráldez, F., Townsend, J. P., Miadlikowska, J., Hofstetter, V., Robbertse, B., Matheny, P. B., Kauff, F., Wang, Z., Gueidan, C., Andrie, R. M., Trippe, K., Ciufetti, L. M., Wynns, A., Fraker, E., Hodkinson, B. P., Bonito, G., Groenewald, J. Z., … Spatafora, J. W. (2009). The Ascomycota Tree of Life: A Phylum-wide Phylogeny Clarifies the Origin and Evolution of Fundamental Reproductive and Ecological Traits. Systematic Biology, 58(2), 224–239. https://doi.org/10.1093/sysbio/syp020

Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi

Philosophical Transactions of the Royal Society B: Biological Sciences / Oct 06, 2006

Taylor, J. W., Turner, E., Townsend, J. P., Dettman, J. R., & Jacobson, D. (2006). Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi. Philosophical Transactions of the Royal Society B: Biological Sciences, 361(1475), 1947–1963. https://doi.org/10.1098/rstb.2006.1923

Strategies for containing Ebola in West Africa

Science / Nov 21, 2014

Pandey, A., Atkins, K. E., Medlock, J., Wenzel, N., Townsend, J. P., Childs, J. E., Nyenswah, T. G., Ndeffo-Mbah, M. L., & Galvani, A. P. (2014). Strategies for containing Ebola in West Africa. Science, 346(6212), 991–995. https://doi.org/10.1126/science.1260612

Profiling Phylogenetic Informativeness

Systematic Biology / Apr 01, 2007

Townsend, J. P. (2007). Profiling Phylogenetic Informativeness. Systematic Biology, 56(2), 222–231. https://doi.org/10.1080/10635150701311362

Phylogenetic and phylogenomic overview of the Polyporales

Mycologia / Nov 01, 2013

Binder, M., Justo, A., Riley, R., Salamov, A., Lopez-Giraldez, F., Sjökvist, E., Copeland, A., Foster, B., Sun, H., Larsson, E., Larsson, K.-H., Townsend, J., Grigoriev, I. V., & Hibbett, D. S. (2013). Phylogenetic and phylogenomic overview of the Polyporales. Mycologia, 105(6), 1350–1373. https://doi.org/10.3852/13-003

The durability of immunity against reinfection by SARS-CoV-2: a comparative evolutionary study

The Lancet Microbe / Dec 01, 2021

Townsend, J. P., Hassler, H. B., Wang, Z., Miura, S., Singh, J., Kumar, S., Ruddle, N. H., Galvani, A. P., & Dornburg, A. (2021). The durability of immunity against reinfection by SARS-CoV-2: a comparative evolutionary study. The Lancet Microbe, 2(12), e666–e675. https://doi.org/10.1016/s2666-5247(21)00219-6

Multifactorial experimental design and the transitivity of ratios with spotted DNA microarrays

BMC Genomics / Oct 02, 2003

Townsend, J. P. (2003). Multifactorial experimental design and the transitivity of ratios with spotted DNA microarrays. BMC Genomics, 4(1). https://doi.org/10.1186/1471-2164-4-41

Gene expression profiling of mouse postnatal cerebellar development using cDNA microarrays

Gene / May 01, 2004

Lim, C. R., Fukakusa, A., & Matsubara, K. (2004). Gene expression profiling of mouse postnatal cerebellar development using cDNA microarrays. Gene, 333, 3–13. https://doi.org/10.1016/j.gene.2004.02.026

Horizontal Acquisition of Divergent Chromosomal DNA in Bacteria: Effects of Mutator Phenotypes

Genetics / May 01, 2003

Townsend, J. P., Nielsen, K. M., Fisher, D. S., & Hartl, D. L. (2003). Horizontal Acquisition of Divergent Chromosomal DNA in Bacteria: Effects of Mutator Phenotypes. Genetics, 164(1), 13–21. https://doi.org/10.1093/genetics/164.1.13

Potential effectiveness of long-acting injectable pre-exposure prophylaxis for HIV prevention in men who have sex with men: a modelling study

The Lancet HIV / Sep 01, 2018

Marshall, B. D. L., Goedel, W. C., King, M. R. F., Singleton, A., Durham, D. P., Chan, P. A., Townsend, J. P., & Galvani, A. P. (2018). Potential effectiveness of long-acting injectable pre-exposure prophylaxis for HIV prevention in men who have sex with men: a modelling study. The Lancet HIV, 5(9), e498–e505. https://doi.org/10.1016/s2352-3018(18)30097-3

Estimation of Neutral Mutation Rates and Quantification of Somatic Variant Selection Using cancereffectsizeR

Cancer Research / Dec 05, 2022

Mandell, J. D., Cannataro, V. L., & Townsend, J. P. (2022). Estimation of Neutral Mutation Rates and Quantification of Somatic Variant Selection Using cancereffectsizeR. Cancer Research, 83(4), 500–505. https://doi.org/10.1158/0008-5472.can-22-1508

Infection by SARS‐CoV‐2 with alternate frequencies of mRNA vaccine boosting

Journal of Medical Virology / Jan 18, 2023

Townsend, J. P., Hassler, H. B., & Dornburg, A. (2023). Infection by SARS‐CoV‐2 with alternate frequencies of mRNA vaccine boosting. Journal of Medical Virology, 95(2). Portico. https://doi.org/10.1002/jmv.28461

Jot: guiding journal selection with suitability metrics

Journal of the Medical Library Association / Dec 08, 2022

Gaffney, S. G., & Townsend, J. P. (2022). Jot: guiding journal selection with suitability metrics. Journal of the Medical Library Association, 110(3), 376–380. https://doi.org/10.5195/jmla.2022.1499

In Response to “De Novo KRAS G12C-Mutant SCLC: A Case Report”

JTO Clinical and Research Reports / Dec 01, 2022

Moore, M., Zhuo, Y., Mandell, J. D., Gaffney, S. G., & Townsend, J. P. (2022). In Response to “De Novo KRAS G12C-Mutant SCLC: A Case Report.” JTO Clinical and Research Reports, 3(12), 100418. https://doi.org/10.1016/j.jtocrr.2022.100418

Not only mutations but also tumorigenesis can be substantially attributed to DNA damage from reactive oxygen species in RUNX1::RUNX1T1-fusion-positive acute myeloid leukemia

Leukemia / Nov 11, 2022

Mandell, J. D., Fisk, J. N., Cyrenne, E., Xu, M. L., Cannataro, V. L., & Townsend, J. P. (2022). Not only mutations but also tumorigenesis can be substantially attributed to DNA damage from reactive oxygen species in RUNX1::RUNX1T1-fusion-positive acute myeloid leukemia. Leukemia, 36(12), 2931–2933. https://doi.org/10.1038/s41375-022-01752-5

The durability of natural infection and vaccine-induced immunity against future infection by SARS-CoV-2

Proceedings of the National Academy of Sciences / Jul 15, 2022

Townsend, J. P., Hassler, H. B., Sah, P., Galvani, A. P., & Dornburg, A. (2022). The durability of natural infection and vaccine-induced immunity against future infection by SARS-CoV-2. Proceedings of the National Academy of Sciences, 119(31). https://doi.org/10.1073/pnas.2204336119

Cancer Relevance of Human Genes

JNCI: Journal of the National Cancer Institute / Apr 13, 2022

Qing, T., Mohsen, H., Cannataro, V. L., Marczyk, M., Rozenblit, M., Foldi, J., Murray, M., Townsend, J. P., Kluger, Y., Gerstein, M., & Pusztai, L. (2022). Cancer Relevance of Human Genes. JNCI: Journal of the National Cancer Institute, 114(7), 988–995. https://doi.org/10.1093/jnci/djac068

Secondary Metabolism Gene Clusters Exhibit Increasingly Dynamic and Differential Expression during Asexual Growth, Conidiation, and Sexual Development in Neurospora crassa

mSystems / Jun 28, 2022

Wang, Z., Lopez-Giraldez, F., Slot, J., Yarden, O., Trail, F., & Townsend, J. P. (2022). Secondary Metabolism Gene Clusters Exhibit Increasingly Dynamic and Differential Expression during Asexual Growth, Conidiation, and Sexual Development in Neurospora crassa. MSystems, 7(3). https://doi.org/10.1128/msystems.00232-22

Transcriptional Divergence Underpinning Sexual Development in the Fungal Class Sordariomycetes

mBio / Jun 28, 2022

Kim, W., Wang, Z., Kim, H., Pham, K., Tu, Y., Townsend, J. P., & Trail, F. (2022). Transcriptional Divergence Underpinning Sexual Development in the Fungal Class Sordariomycetes. MBio, 13(3). https://doi.org/10.1128/mbio.01100-22

A phylogenetic approach to study the evolution of somatic mutational processes in cancer

Communications Biology / Jun 22, 2022

Miura, S., Vu, T., Choi, J., Townsend, J. P., Karim, S., & Kumar, S. (2022). A phylogenetic approach to study the evolution of somatic mutational processes in cancer. Communications Biology, 5(1). https://doi.org/10.1038/s42003-022-03560-0

Attribution of Cancer Origins to Endogenous, Exogenous, and Preventable Mutational Processes

Molecular Biology and Evolution / Apr 26, 2022

Cannataro, V. L., Mandell, J. D., & Townsend, J. P. (2022). Attribution of Cancer Origins to Endogenous, Exogenous, and Preventable Mutational Processes. Molecular Biology and Evolution, 39(5). https://doi.org/10.1093/molbev/msac084

Quarantine and testing strategies to ameliorate transmission due to travel during the COVID-19 pandemic: a modelling study

The Lancet Regional Health - Europe / Mar 01, 2022

Wells, C. R., Pandey, A., Fitzpatrick, M. C., Crystal, W. S., Singer, B. H., Moghadas, S. M., Galvani, A. P., & Townsend, J. P. (2022). Quarantine and testing strategies to ameliorate transmission due to travel during the COVID-19 pandemic: a modelling study. The Lancet Regional Health - Europe, 14, 100304. https://doi.org/10.1016/j.lanepe.2021.100304

Premetastatic shifts of endogenous and exogenous mutational processes support consolidative therapy in EGFR-driven lung adenocarcinoma

Cancer Letters / Feb 01, 2022

Fisk, J. N., Mahal, A. R., Dornburg, A., Gaffney, S. G., Aneja, S., Contessa, J. N., Rimm, D., Yu, J. B., & Townsend, J. P. (2022). Premetastatic shifts of endogenous and exogenous mutational processes support consolidative therapy in EGFR-driven lung adenocarcinoma. Cancer Letters, 526, 346–351. https://doi.org/10.1016/j.canlet.2021.11.011

Projecting the seasonality of endemic COVID-19

Jan 28, 2022

Townsend, J. P., Lamb, A. D., Hassler, H. B., Sah, P., Nishio, A. A., Nguyen, C., Tew, A. D., Galvani, A. P., & Dornburg, A. (2022). Projecting the seasonality of endemic COVID-19. https://doi.org/10.1101/2022.01.26.22269905

Pairwise and higher-order epistatic effects among somatic cancer mutations across oncogenesis

Jan 22, 2022

Alfaro-Murillo, J. A., & Townsend, J. P. (2022). Pairwise and higher-order epistatic effects among somatic cancer mutations across oncogenesis. https://doi.org/10.1101/2022.01.20.477132

Environmental and sex-specific molecular signatures of glioma causation

Neuro-Oncology / May 04, 2021

Claus, E. B., Cannataro, V. L., Gaffney, S. G., & Townsend, J. P. (2021). Environmental and sex-specific molecular signatures of glioma causation. Neuro-Oncology, 24(1), 29–36. https://doi.org/10.1093/neuonc/noab103

The Prognostic Value of an RT-PCR Test for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Is Contingent on Timing across Disease Time Course in addition to Assay Sensitivity

The Journal of Molecular Diagnostics / Jan 01, 2022

Townsend, J. P., & Wells, C. R. (2022). The Prognostic Value of an RT-PCR Test for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Is Contingent on Timing across Disease Time Course in addition to Assay Sensitivity. The Journal of Molecular Diagnostics, 24(1), 101–103. https://doi.org/10.1016/j.jmoldx.2021.10.002

Heavy mutagenesis by tobacco leads to lung adenocarcinoma tumors with KRAS G12 mutations other than G12D, leading KRAS G12D tumors—on average—to exhibit a lower mutation burden

Lung Cancer / Apr 01, 2022

Tan, C., Mandell, J. D., Dasari, K., Cannataro, V. L., Alfaro-Murillo, J. A., & Townsend, J. P. (2022). Heavy mutagenesis by tobacco leads to lung adenocarcinoma tumors with KRAS G12 mutations other than G12D, leading KRAS G12D tumors—on average—to exhibit a lower mutation burden. Lung Cancer, 166, 265–269. https://doi.org/10.1016/j.lungcan.2021.10.008

Sequencing and Analysis of the Entire Genome of the Mycoparasitic Bioeffector Fungus Trichoderma asperelloides Strain T 203 (Hypocreales)

Microbiology Resource Announcements / Feb 17, 2022

Gortikov, M., Wang, Z., Steindorff, A. S., Grigoriev, I. V., Druzhinina, I. S., Townsend, J. P., & Yarden, O. (2022). Sequencing and Analysis of the Entire Genome of the Mycoparasitic Bioeffector Fungus Trichoderma asperelloides Strain T 203 (Hypocreales). Microbiology Resource Announcements, 11(2). https://doi.org/10.1128/mra.00995-21

The somatic molecular evolution of cancer: Mutation, selection, and epistasis

Progress in Biophysics and Molecular Biology / Oct 01, 2021

Dasari, K., Somarelli, J. A., Kumar, S., & Townsend, J. P. (2021). The somatic molecular evolution of cancer: Mutation, selection, and epistasis. Progress in Biophysics and Molecular Biology, 165, 56–65. https://doi.org/10.1016/j.pbiomolbio.2021.08.003

Chemsearch: collaborative compound libraries with structure-aware browsing

Bioinformatics Advances / Jan 01, 2021

Gaffney, S. G., Smaga, S., Schepartz, A., & Townsend, J. P. (2021). Chemsearch: collaborative compound libraries with structure-aware browsing. Bioinformatics Advances, 1(1). https://doi.org/10.1093/bioadv/vbab008

Mechanistic basis of post-treatment control of SIV after anti-α4β7 antibody therapy

PLOS Computational Biology / Jun 09, 2021

Wells, C. R., Cao, Y., Durham, D. P., Byrareddy, S. N., Ansari, A. A., Ruddle, N. H., Townsend, J. P., Galvani, A. P., & Perelson, A. S. (2021). Mechanistic basis of post-treatment control of SIV after anti-α4β7 antibody therapy. PLOS Computational Biology, 17(6), e1009031. https://doi.org/10.1371/journal.pcbi.1009031

Clinically relevant shifts in endogenous and exogenous mutational processes proximate to metastasis support local consolidative treatment in EGFR-driven non-small cell lung cancer

May 04, 2021

Fisk, J. N., Mahal, A. R., Dornburg, A., Gaffney, S. G., Aneja, S., Contessa, J. N., Rimm, D., Yu, J. B., & Townsend, J. P. (2021). Clinically relevant shifts in endogenous and exogenous mutational processes proximate to metastasis support local consolidative treatment in EGFR-driven non-small cell lung cancer. https://doi.org/10.1101/2021.05.04.21256425

Quarantine and testing strategies to ameliorate transmission due to travel during the COVID-19 pandemic: a modelling study

Apr 26, 2021

Wells, C. R., Pandey, A., Fitzpatrick, M. C., Crystal, W. S., Singer, B. H., Moghadas, S. M., Galvani, A. P., & Townsend, J. P. (2021). Quarantine and testing strategies to ameliorate transmission due to travel during the COVID-19 pandemic: a modelling study. https://doi.org/10.1101/2021.04.25.21256082

Optimal COVID-19 quarantine and testing strategies

Nature Communications / Jan 07, 2021

Wells, C. R., Townsend, J. P., Pandey, A., Moghadas, S. M., Krieger, G., Singer, B., McDonald, R. H., Fitzpatrick, M. C., & Galvani, A. P. (2021). Optimal COVID-19 quarantine and testing strategies. Nature Communications, 12(1). https://doi.org/10.1038/s41467-020-20742-8

Cancer relevance of human genes

Feb 06, 2021

Qing, T., Mohsen, H., Cannataro, V. L., Marczyk, M., Rozenblit, M., Foldi, J., Murray, M. F., Townsend, J. P., Kluger, Y., Gerstein, M., & Pusztai, L. (2021). Cancer relevance of human genes. https://doi.org/10.1101/2021.02.04.429823

Comparative analyses of FDA EUA-approved rapid antigen tests and RT-PCR for COVID-19 quarantine and surveillance-based isolation

Aug 26, 2021

Wells, C. R., Pandey, A., Moghadas, S. M., Singer, B. H., Krieger, G., Heron, R. J. L., Turner, D. E., Abshire, J. P., Phillips, K. M., Michael Donoghue, A., Galvani, A. P., & Townsend, J. P. (2021). Comparative analyses of FDA EUA-approved rapid antigen tests and RT-PCR for COVID-19 quarantine and surveillance-based isolation. https://doi.org/10.1101/2021.08.23.21262499

Identifying modules of cooperating cancer drivers

Molecular Systems Biology / Mar 01, 2021

Klein, M. I., Cannataro, V. L., Townsend, J. P., Newman, S., Stern, D. F., & Zhao, H. (2021). Identifying modules of cooperating cancer drivers. Molecular Systems Biology, 17(3). Portico. https://doi.org/10.15252/msb.20209810

Comparative Genomics within and across Bilaterians Illuminates the Evolutionary History of ALK and LTK Proto-Oncogene Origination and Diversification

Genome Biology and Evolution / Nov 16, 2020

Dornburg, A., Wang, Z., Wang, J., Mo, E. S., López-Giráldez, F., & Townsend, J. P. (2020). Comparative Genomics within and across Bilaterians Illuminates the Evolutionary History of ALK and LTK Proto-Oncogene Origination and Diversification. Genome Biology and Evolution, 13(1). https://doi.org/10.1093/gbe/evaa228

Attribution of Cancer Origins to Endogenous, Exogenous, and Actionable Mutational Processes

Oct 25, 2020

Cannataro, V. L., Mandell, J. D., & Townsend, J. P. (2020). Attribution of Cancer Origins to Endogenous, Exogenous, and Actionable Mutational Processes. https://doi.org/10.1101/2020.10.24.352989

Unmatched Level of Molecular Convergence among Deeply Divergent Complex Multicellular Fungi

Molecular Biology and Evolution / Mar 19, 2020

Merényi, Z., Prasanna, A. N., Wang, Z., Kovács, K., Hegedüs, B., Bálint, B., Papp, B., Townsend, J. P., & Nagy, L. G. (2020). Unmatched Level of Molecular Convergence among Deeply Divergent Complex Multicellular Fungi. Molecular Biology and Evolution, 37(8), 2228–2240. https://doi.org/10.1093/molbev/msaa077

Non-Coding Mutations in Urothelial Bladder Cancer: Biological and Clinical Relevance and Potential Utility as Biomarkers

Bladder Cancer / Jun 11, 2020

Yang, A., Cross, C. N., & Townsend, J. P. (2020). Non-Coding Mutations in Urothelial Bladder Cancer: Biological and Clinical Relevance and Potential Utility as Biomarkers. Bladder Cancer, 6(2), 211–213. https://doi.org/10.3233/blc-200278

Germline variant burden in cancer genes correlates with age at diagnosis and somatic mutation burden

Nature Communications / May 15, 2020

Qing, T., Mohsen, H., Marczyk, M., Ye, Y., O’Meara, T., Zhao, H., Townsend, J. P., Gerstein, M., Hatzis, C., Kluger, Y., & Pusztai, L. (2020). Germline variant burden in cancer genes correlates with age at diagnosis and somatic mutation burden. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-16293-7

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 / Feb 01, 2020

Lu, L., Gaffney, S. G., Cannataro, V. L., & Townsend, J. (2020). 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. https://doi.org/10.1016/j.oraloncology.2019.104554

Re: Ming-Jun Shi, Xiang-Yu Meng, Philippe Lamy, et al. APOBEC-mediated Mutagenesis as a Likely Cause of FGFR3 S249C Mutation Over-representation in Bladder Cancer. Eur Urol 2019;76:9–13

European Urology / Jan 01, 2020

Yang, A., Cannataro, V. L., & Townsend, J. P. (2020). Re: Ming-Jun Shi, Xiang-Yu Meng, Philippe Lamy, et al. APOBEC-mediated Mutagenesis as a Likely Cause of FGFR3 S249C Mutation Over-representation in Bladder Cancer. Eur Urol 2019;76:9–13. European Urology, 77(1), e24–e25. https://doi.org/10.1016/j.eururo.2019.08.018

Dogs and pigs are transport hosts of Necator americanus : Molecular evidence for a zoonotic mechanism of human hookworm transmission in Ghana

Zoonoses and Public Health / Jun 11, 2020

Boyko, R. H., Marie Harrison, L., Humphries, D., Galvani, A. P., Townsend, J. P., Otchere, J., Wilson, M. D., & Cappello, M. (2020). Dogs and pigs are transport hosts of Necator americanus  : Molecular evidence for a zoonotic mechanism of human hookworm transmission in Ghana. Zoonoses and Public Health, 67(5), 474–483. Portico. https://doi.org/10.1111/zph.12708

Identifying Modules of Cooperating Cancer Drivers

Jun 29, 2020

Klein, M. I., Cannataro, V. L., Townsend, J. P., Newman, S., Stern, D. F., & Zhao, H. (2020). Identifying Modules of Cooperating Cancer Drivers. https://doi.org/10.1101/2020.06.29.168229

Implementation of Syringe Services Programs to Prevent Rapid Human Immunodeficiency Virus Transmission in Rural Counties in the United States: A Modeling Study

Clinical Infectious Diseases / May 30, 2019

Goedel, W. C., King, M. R. F., Lurie, M. N., Galea, S., Townsend, J. P., Galvani, A. P., Friedman, S. R., & Marshall, B. D. L. (2019). Implementation of Syringe Services Programs to Prevent Rapid Human Immunodeficiency Virus Transmission in Rural Counties in the United States: A Modeling Study. Clinical Infectious Diseases, 70(6), 1096–1102. https://doi.org/10.1093/cid/ciz321

Inferring Tumor Proliferative Organization from Phylogenetic Tree Measures in a Computational Model

Systematic Biology / Oct 29, 2019

Scott, J. G., Maini, P. K., Anderson, A. R. A., & Fletcher, A. G. (2019). Inferring Tumor Proliferative Organization from Phylogenetic Tree Measures in a Computational Model. Systematic Biology, 69(4), 623–637. https://doi.org/10.1093/sysbio/syz070

Molecular Biology and Evolution of Cancer: From Discovery to Action

Molecular Biology and Evolution / Oct 23, 2019

Somarelli, J. A., Gardner, H., Cannataro, V. L., Gunady, E. F., Boddy, A. M., Johnson, N. A., Fisk, J. N., Gaffney, S. G., Chuang, J. H., Li, S., Ciccarelli, F. D., Panchenko, A. R., Megquier, K., Kumar, S., Dornburg, A., DeGregori, J., & Townsend, J. P. (2019). Molecular Biology and Evolution of Cancer: From Discovery to Action. Molecular Biology and Evolution, 37(2), 320–326. https://doi.org/10.1093/molbev/msz242

Optimal COVID-19 quarantine and testing strategies

Oct 28, 2020

Wells, C. R., Townsend, J. P., Pandey, A., Moghadas, S. M., Krieger, G., Singer, B., McDonald, R. H., Fitzpatrick, M. C., & Galvani, A. P. (2020). Optimal COVID-19 quarantine and testing strategies. https://doi.org/10.1101/2020.10.27.20211631

Integrative Activity of Mating Loci, Environmentally Responsive Genes, and Secondary Metabolism Pathways during Sexual Development of Chaetomium globosum

mBio / Dec 24, 2019

Wang, Z., López-Giráldez, F., Wang, J., Trail, F., & Townsend, J. P. (2019). Integrative Activity of Mating Loci, Environmentally Responsive Genes, and Secondary Metabolism Pathways during Sexual Development of Chaetomium globosum. MBio, 10(6). https://doi.org/10.1128/mbio.02119-19

A multigene phylogeny toward a new phylogenetic classification of Leotiomycetes

IMA Fungus / Jun 07, 2019

Johnston, P. R., Quijada, L., Smith, C. A., Baral, H.-O., Hosoya, T., Baschien, C., Pärtel, K., Zhuang, W.-Y., Haelewaters, D., Park, D., Carl, S., López-Giráldez, F., Wang, Z., & Townsend, J. P. (2019). A multigene phylogeny toward a new phylogenetic classification of Leotiomycetes. IMA Fungus, 10(1). https://doi.org/10.1186/s43008-019-0002-x

Modelling microbial infection to address global health challenges

Nature Microbiology / Sep 20, 2019

Fitzpatrick, M. C., Bauch, C. T., Townsend, J. P., & Galvani, A. P. (2019). Modelling microbial infection to address global health challenges. Nature Microbiology, 4(10), 1612–1619. https://doi.org/10.1038/s41564-019-0565-8

GEM-NET: Lessons in Multi-Institution Teamwork Using Collaboration Software

ACS Central Science / Jul 12, 2019

Gaffney, S. G., Ad, O., Smaga, S., Schepartz, A., & Townsend, J. P. (2019). GEM-NET: Lessons in Multi-Institution Teamwork Using Collaboration Software. ACS Central Science, 5(7), 1159–1169. https://doi.org/10.1021/acscentsci.9b00111

The landscape of novel and complementary targets for immunotherapy: an analysis of gene expression in the tumor microenvironment

Oncotarget / Jul 16, 2019

Gaffney, S. G., Perry, E. B., Chen, P.-M., Greenstein, A., Kaech, S. M., & Townsend, J. P. (2019). The landscape of novel and complementary targets for immunotherapy: an analysis of gene expression in the tumor microenvironment. Oncotarget, 10(44), 4532–4545. https://doi.org/10.18632/oncotarget.27027

Comparative Genomics and Transcriptomics During Sexual Development Gives Insight Into the Life History of the Cosmopolitan Fungus Fusarium neocosmosporiellum

Frontiers in Microbiology / Jun 07, 2019

Kim, W., Cavinder, B., Proctor, R. H., O’Donnell, K., Townsend, J. P., & Trail, F. (2019). Comparative Genomics and Transcriptomics During Sexual Development Gives Insight Into the Life History of the Cosmopolitan Fungus Fusarium neocosmosporiellum. Frontiers in Microbiology, 10. https://doi.org/10.3389/fmicb.2019.01247

Combined Aurora Kinase A (AURKA) and WEE1 Inhibition Demonstrates Synergistic Antitumor Effect in Squamous Cell Carcinoma of the Head and Neck

Clinical Cancer Research / Jun 01, 2019

Lee, J. W., Parameswaran, J., Sandoval-Schaefer, T., Eoh, K. J., Yang, D., Zhu, F., Mehra, R., Sharma, R., Gaffney, S. G., Perry, E. B., Townsend, J. P., Serebriiskii, I. G., Golemis, E. A., Issaeva, N., Yarbrough, W. G., Koo, J. S., & Burtness, B. (2019). Combined Aurora Kinase A (AURKA) and WEE1 Inhibition Demonstrates Synergistic Antitumor Effect in Squamous Cell Carcinoma of the Head and Neck. Clinical Cancer Research, 25(11), 3430–3442. https://doi.org/10.1158/1078-0432.ccr-18-0440

APOBEC-induced mutations and their cancer effect size in head and neck squamous cell carcinoma

Oncogene / Jan 15, 2019

Cannataro, V. L., Gaffney, S. G., Sasaki, T., Issaeva, N., Grewal, N. K. S., Grandis, J. R., Yarbrough, W. G., Burtness, B., Anderson, K. S., & Townsend, J. P. (2019). APOBEC-induced mutations and their cancer effect size in head and neck squamous cell carcinoma. Oncogene, 38(18), 3475–3487. https://doi.org/10.1038/s41388-018-0657-6

Metabolism and Development during Conidial Germination in Response to a Carbon-Nitrogen-Rich Synthetic or a Natural Source of Nutrition in Neurospora crassa

mBio / Apr 30, 2019

Wang, Z., Miguel-Rojas, C., Lopez-Giraldez, F., Yarden, O., Trail, F., & Townsend, J. P. (2019). Metabolism and Development during Conidial Germination in Response to a Carbon-Nitrogen-Rich Synthetic or a Natural Source of Nutrition in Neurospora crassa. MBio, 10(2). https://doi.org/10.1128/mbio.00192-19

Wagging the long tail of drivers of prostate cancer

PLOS Genetics / Jan 17, 2019

Cannataro, V. L., & Townsend, J. P. (2019). Wagging the long tail of drivers of prostate cancer. PLOS Genetics, 15(1), e1007820. https://doi.org/10.1371/journal.pgen.1007820

Optimal Rates for Phylogenetic Inference and Experimental Design in the Era of Genome-Scale Data Sets

Systematic Biology / Jun 25, 2018

Dornburg, A., Su, Z., & Townsend, J. P. (2018). Optimal Rates for Phylogenetic Inference and Experimental Design in the Era of Genome-Scale Data Sets. Systematic Biology, 68(1), 145–156. https://doi.org/10.1093/sysbio/syy047

Evolutionary analyses guide selection of model systems to investigate proto-oncogene function in ALK and LTK

Oct 07, 2019

Wang, Z., Dornburg, A., Wang, J., Mo, E. S., Lopez-Giraldez, F., & Townsend, J. P. (2019). Evolutionary analyses guide selection of model systems to investigate proto-oncogene function in ALK and LTK. https://doi.org/10.1101/795468

Identifying Combinations of Cancer Drivers in Individual Patients

Jun 19, 2019

Klein, M. I., Cannataro, V. L., Townsend, J. P., Stern, D. F., & Zhao, H. (2019). Identifying Combinations of Cancer Drivers in Individual Patients. https://doi.org/10.1101/674234

Modeling Approaches Toward Understanding Infectious Disease Transmission

Immunoepidemiology / Jan 01, 2019

Skrip, L. A., & Townsend, J. P. (2019). Modeling Approaches Toward Understanding Infectious Disease Transmission. Immunoepidemiology, 227–243. https://doi.org/10.1007/978-3-030-25553-4_14

Unmatched level of molecular convergence among deeply divergent complex multicellular fungi

Feb 14, 2019

Merényi, Z., Prasanna, A. N., Zheng, W., Kovács, K., Hegedüs, B., Bálint, B., Papp, B., Townsend, J. P., & Nagy, L. G. (2019). Unmatched level of molecular convergence among deeply divergent complex multicellular fungi. https://doi.org/10.1101/549758

Somatic evolutionary timings of driver mutations

BMC Cancer / Jan 18, 2018

Gomez, K., Miura, S., Huuki, L. A., Spell, B. S., Townsend, J. P., & Kumar, S. (2018). Somatic evolutionary timings of driver mutations. BMC Cancer, 18(1). https://doi.org/10.1186/s12885-017-3977-y

Effect Sizes of Somatic Mutations in Cancer

JNCI: Journal of the National Cancer Institute / Oct 26, 2018

Cannataro, V. L., Gaffney, S. G., & Townsend, J. P. (2018). Effect Sizes of Somatic Mutations in Cancer. JNCI: Journal of the National Cancer Institute, 110(11), 1171–1177. https://doi.org/10.1093/jnci/djy168

The critical importance of retention in HIV prevention

The Lancet HIV / Sep 01, 2018

Golub, S. A., & Enemchukwu, C. U. (2018). The critical importance of retention in HIV prevention. The Lancet HIV, 5(9), e475–e476. https://doi.org/10.1016/s2352-3018(18)30130-9

Using evolutionary genomics, transcriptomics, and systems biology to reveal gene networks underlying fungal development

Fungal Biology Reviews / Sep 01, 2018

Wang, Z., Gudibanda, A., Ugwuowo, U., Trail, F., & Townsend, J. P. (2018). Using evolutionary genomics, transcriptomics, and systems biology to reveal gene networks underlying fungal development. Fungal Biology Reviews, 32(4), 249–264. https://doi.org/10.1016/j.fbr.2018.02.001

Developmental Dynamics of Long Noncoding RNA Expression during Sexual Fruiting Body Formation in Fusarium graminearum

mBio / Sep 05, 2018

Kim, W., Miguel-Rojas, C., Wang, J., Townsend, J. P., & Trail, F. (2018). Developmental Dynamics of Long Noncoding RNA Expression during Sexual Fruiting Body Formation in Fusarium graminearum. MBio, 9(4). https://doi.org/10.1128/mbio.01292-18

Genomic Comparison Among Global Isolates of L. interrogans Serovars Copenhageni and Icterohaemorrhagiae Identified Natural Genetic Variation Caused by an Indel

Frontiers in Cellular and Infection Microbiology / Jun 19, 2018

Santos, L. A., Adhikarla, H., Yan, X., Wang, Z., Fouts, D. E., Vinetz, J. M., Alcantara, L. C. J., Hartskeerl, R. A., Goris, M. G. A., Picardeau, M., Reis, M. G., Townsend, J. P., Zhao, H., Ko, A. I., & Wunder, E. A. (2018). Genomic Comparison Among Global Isolates of L. interrogans Serovars Copenhageni and Icterohaemorrhagiae Identified Natural Genetic Variation Caused by an Indel. Frontiers in Cellular and Infection Microbiology, 8. https://doi.org/10.3389/fcimb.2018.00193

Neutral Theory and the Somatic Evolution of Cancer

Molecular Biology and Evolution / Apr 19, 2018

Cannataro, V. L., & Townsend, J. P. (2018). Neutral Theory and the Somatic Evolution of Cancer. Molecular Biology and Evolution, 35(6), 1308–1315. https://doi.org/10.1093/molbev/msy079

Heterogeneity and mutation in KRAS and associated oncogenes: evaluating the potential for the evolution of resistance to targeting of KRAS G12C

Oncogene / Feb 16, 2018

Cannataro, V. L., Gaffney, S. G., Stender, C., Zhao, Z.-M., Philips, M., Greenstein, A. E., & Townsend, J. P. (2018). Heterogeneity and mutation in KRAS and associated oncogenes: evaluating the potential for the evolution of resistance to targeting of KRAS G12C. Oncogene, 37(18), 2444–2455. https://doi.org/10.1038/s41388-017-0105-z

Analysis of mutation, selection, and epistasis: an informed approach to cancer clinical trials

Oncotarget / Apr 27, 2018

Wilkins, J. F., Cannataro, V. L., Shuch, B., & Townsend, J. P. (2018). Analysis of mutation, selection, and epistasis: an informed approach to cancer clinical trials. Oncotarget, 9(32), 22243–22253. https://doi.org/10.18632/oncotarget.25155

CDKN2A Copy Number Loss Is an Independent Prognostic Factor in HPV-Negative Head and Neck Squamous Cell Carcinoma

Frontiers in Oncology / Apr 04, 2018

Chen, W. S., Bindra, R. S., Mo, A., Hayman, T., Husain, Z., Contessa, J. N., Gaffney, S. G., Townsend, J. P., & Yu, J. B. (2018). CDKN2A Copy Number Loss Is an Independent Prognostic Factor in HPV-Negative Head and Neck Squamous Cell Carcinoma. Frontiers in Oncology, 8. https://doi.org/10.3389/fonc.2018.00095

Lvr, a Signaling System That Controls Global Gene Regulation and Virulence in Pathogenic Leptospira

Frontiers in Cellular and Infection Microbiology / Feb 23, 2018

Adhikarla, H., Wunder, E. A., Mechaly, A. E., Mehta, S., Wang, Z., Santos, L., Bisht, V., Diggle, P., Murray, G., Adler, B., Lopez, F., Townsend, J. P., Groisman, E., Picardeau, M., Buschiazzo, A., & Ko, A. I. (2018). Lvr, a Signaling System That Controls Global Gene Regulation and Virulence in Pathogenic Leptospira. Frontiers in Cellular and Infection Microbiology, 8. https://doi.org/10.3389/fcimb.2018.00045

Sexual stage-induced long noncoding RNAs in the filamentous fungus Fusarium graminearum

Feb 23, 2018

Kim, W., Miguel-Rojas, C., Wang, J., Townsend, J. P., & Trail, F. (2018). Sexual stage-induced long noncoding RNAs in the filamentous fungus Fusarium graminearum. https://doi.org/10.1101/270298

Light sensing by opsins and fungal ecology: NOP‐1 modulates entry into sexual reproduction in response to environmental cues

Molecular Ecology / Dec 12, 2017

Wang, Z., Wang, J., Li, N., Li, J., Trail, F., Dunlap, J. C., & Townsend, J. P. (2017). Light sensing by opsins and fungal ecology: NOP‐1 modulates entry into sexual reproduction in response to environmental cues. Molecular Ecology, 27(1), 216–232. Portico. https://doi.org/10.1111/mec.14425

Neutral Theory and the Somatic Evolution of Cancer

Molecular Biology and Evolution / May 14, 2018

Neutral Theory and the Somatic Evolution of Cancer. (2018). Molecular Biology and Evolution, 35(6), 1561–1561. https://doi.org/10.1093/molbev/msy100

Primary hepatic neuroendocrine carcinoma: report of two cases and literature review

BMC Clinical Pathology / Mar 01, 2018

Zhao, Z.-M., Wang, J., Ugwuowo, U. C., Wang, L., & Townsend, J. P. (2018). Primary hepatic neuroendocrine carcinoma: report of two cases and literature review. BMC Clinical Pathology, 18(1). https://doi.org/10.1186/s12907-018-0070-7

The Cancer Tree

Scientific American / Mar 20, 2018

Townsend, J. P. (2018). The Cancer Tree. Scientific American, 318(4), 34–41. https://doi.org/10.1038/scientificamerican0418-34

Detection of Regional Variation in Selection Intensity within Protein-Coding Genes Using DNA Sequence Polymorphism and Divergence

Molecular Biology and Evolution / Jul 28, 2017

Zhao, Z.-M., Campbell, M. C., Li, N., Lee, D. S. W., Zhang, Z., & Townsend, J. P. (2017). Detection of Regional Variation in Selection Intensity within Protein-Coding Genes Using DNA Sequence Polymorphism and Divergence. Molecular Biology and Evolution, 34(11), 3006–3022. https://doi.org/10.1093/molbev/msx213

The Moran coalescent in a discrete one-dimensional spatial model

Sep 05, 2017

Shpak, M., Lu, J., & Townsend, J. P. (2017). The Moran coalescent in a discrete one-dimensional spatial model. https://doi.org/10.1101/184705

Distributions of Mutational Effects and the Estimation of Directional Selection in Divergent Lineages of Arabidopsis thaliana

Genetics / Aug 01, 2017

Park, B., Rutter, M. T., Fenster, C. B., Symonds, V. V., Ungerer, M. C., & Townsend, J. P. (2017). Distributions of Mutational Effects and the Estimation of Directional Selection in Divergent Lineages of Arabidopsis thaliana. Genetics, 206(4), 2105–2117. https://doi.org/10.1534/genetics.116.199190

The ancestral levels of transcription and the evolution of sexual phenotypes in filamentous fungi

PLOS Genetics / Jul 13, 2017

Trail, F., Wang, Z., Stefanko, K., Cubba, C., & Townsend, J. P. (2017). The ancestral levels of transcription and the evolution of sexual phenotypes in filamentous fungi. PLOS Genetics, 13(7), e1006867. https://doi.org/10.1371/journal.pgen.1006867

The likelihood of heterogeneity or additional mutation in KRAS or associated oncogenes to compromise targeting of oncogenic KRAS G12C

Jun 13, 2017

Cannataro, V. L., Gaffney, S. G., Stender, C., Zhao, Z.-M., Philips, M., Greenstein, A. E., & Townsend, J. P. (2017). The likelihood of heterogeneity or additional mutation in KRAS or associated oncogenes to compromise targeting of oncogenic KRAS G12C. https://doi.org/10.1101/149724

New insights on the sister lineage of percomorph fishes with an anchored hybrid enrichment dataset

Molecular Phylogenetics and Evolution / May 01, 2017

Dornburg, A., Townsend, J. P., Brooks, W., Spriggs, E., Eytan, R. I., Moore, J. A., Wainwright, P. C., Lemmon, A., Lemmon, E. M., & Near, T. J. (2017). New insights on the sister lineage of percomorph fishes with an anchored hybrid enrichment dataset. Molecular Phylogenetics and Evolution, 110, 27–38. https://doi.org/10.1016/j.ympev.2017.02.017

PhyloOncology: Understanding cancer through phylogenetic analysis

Biochimica et Biophysica Acta (BBA) - Reviews on Cancer / Apr 01, 2017

Somarelli, J. A., Ware, K. E., Kostadinov, R., Robinson, J. M., Amri, H., Abu-Asab, M., Fourie, N., Diogo, R., Swofford, D., & Townsend, J. P. (2017). PhyloOncology: Understanding cancer through phylogenetic analysis. Biochimica et Biophysica Acta (BBA) - Reviews on Cancer, 1867(2), 101–108. https://doi.org/10.1016/j.bbcan.2016.10.006

Mutation profiles in early-stage lung squamous cell carcinoma with clinical follow-up and correlation with markers of immune function

Annals of Oncology / Jan 01, 2017

Choi, M., Kadara, H., Zhang, J., Parra, E. R., Rodriguez-Canales, J., Gaffney, S. G., Zhao, Z., Behrens, C., Fujimoto, J., Chow, C., Kim, K., Kalhor, N., Moran, C., Rimm, D., Swisher, S., Gibbons, D. L., Heymach, J., Kaftan, E., Townsend, J. P., … Wistuba, I. I. (2017). Mutation profiles in early-stage lung squamous cell carcinoma with clinical follow-up and correlation with markers of immune function. Annals of Oncology, 28(1), 83–89. https://doi.org/10.1093/annonc/mdw437

Whole-exome sequencing and immune profiling of early-stage lung adenocarcinoma with fully annotated clinical follow-up

Annals of Oncology / Jan 01, 2017

Kadara, H., Choi, M., Zhang, J., Parra, E. R., Rodriguez-Canales, J., Gaffney, S. G., Zhao, Z., Behrens, C., Fujimoto, J., Chow, C., Yoo, Y., Kalhor, N., Moran, C., Rimm, D., Swisher, S., Gibbons, D. L., Heymach, J., Kaftan, E., Townsend, J. P., … Herbst, R. S. (2017). Whole-exome sequencing and immune profiling of early-stage lung adenocarcinoma with fully annotated clinical follow-up. Annals of Oncology, 28(1), 75–82. https://doi.org/10.1093/annonc/mdw436

A working model of the deep relationships of diverse modern human genetic lineages outside of Africa

Molecular Biology and Evolution / Jan 10, 2017

Lipson, M., & Reich, D. (2017). A working model of the deep relationships of diverse modern human genetic lineages outside of Africa. Molecular Biology and Evolution, msw293. https://doi.org/10.1093/molbev/msw293

Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big Data

Fungal Phylogenetics and Phylogenomics / Jan 01, 2017

Dornburg, A., Townsend, J. P., & Wang, Z. (2017). Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big Data. Advances in Genetics, 1–47. https://doi.org/10.1016/bs.adgen.2017.09.007

Oncogenes without a neighboring tumor-suppressor gene are more prone to amplification

Molecular Biology and Evolution / Jan 12, 2017

Wu, W. K. K., Li, X., Wang, X., Dai, R. Z. W., Cheng, A. S. L., Wang, M. H. T., Kwong, T., Chow, T. C., Yu, J., Chan, M. T. V., & Wong, S. H. (2017). Oncogenes without a neighboring tumor-suppressor gene are more prone to amplification. Molecular Biology and Evolution, msw295. https://doi.org/10.1093/molbev/msw295

Preface

Fungal Phylogenetics and Phylogenomics / Jan 01, 2017

Townsend, J. P., & Wang, Z. (2017). Preface. Advances in Genetics, xi–xii. https://doi.org/10.1016/s0065-2660(17)30059-7

Climatic and evolutionary drivers of phase shifts in the plague epidemics of colonial India

Proceedings of the National Academy of Sciences / Oct 24, 2016

Lewnard, J. A., & Townsend, J. P. (2016). Climatic and evolutionary drivers of phase shifts in the plague epidemics of colonial India. Proceedings of the National Academy of Sciences, 113(51), 14601–14608. https://doi.org/10.1073/pnas.1604985113

One Health approach to cost-effective rabies control in India

Proceedings of the National Academy of Sciences / Dec 19, 2016

Fitzpatrick, M. C., Shah, H. A., Pandey, A., Bilinski, A. M., Kakkar, M., Clark, A. D., Townsend, J. P., Abbas, S. S., & Galvani, A. P. (2016). One Health approach to cost-effective rabies control in India. Proceedings of the National Academy of Sciences, 113(51), 14574–14581. https://doi.org/10.1073/pnas.1604975113

PhyInformR: phylogenetic experimental design and phylogenomic data exploration in R

BMC Evolutionary Biology / Dec 01, 2016

Dornburg, A., Fisk, J. N., Tamagnan, J., & Townsend, J. P. (2016). PhyInformR: phylogenetic experimental design and phylogenomic data exploration in R. BMC Evolutionary Biology, 16(1). https://doi.org/10.1186/s12862-016-0837-3

Vaccination strategies against respiratory syncytial virus

Proceedings of the National Academy of Sciences / Oct 31, 2016

Yamin, D., Jones, F. K., DeVincenzo, J. P., Gertler, S., Kobiler, O., Townsend, J. P., & Galvani, A. P. (2016). Vaccination strategies against respiratory syncytial virus. Proceedings of the National Academy of Sciences, 113(46), 13239–13244. https://doi.org/10.1073/pnas.1522597113

PathScore: a web tool for identifying altered pathways in cancer data

Bioinformatics / Aug 08, 2016

Gaffney, S. G., & Townsend, J. P. (2016). PathScore: a web tool for identifying altered pathways in cancer data. Bioinformatics, 32(23), 3688–3690. https://doi.org/10.1093/bioinformatics/btw512

Cost-Effectiveness of Pertussis Vaccination During Pregnancy in the United States

American Journal of Epidemiology / May 13, 2016

Atkins, K. E., Fitzpatrick, M. C., Galvani, A. P., & Townsend, J. P. (2016). Cost-Effectiveness of Pertussis Vaccination During Pregnancy in the United States. American Journal of Epidemiology, 183(12), 1159–1170. https://doi.org/10.1093/aje/kwv347

Cost-effectiveness of next-generation vaccines: The case of pertussis

Vaccine / Jun 01, 2016

Fitzpatrick, M. C., Wenzel, N. S., Scarpino, S. V., Althouse, B. M., Atkins, K. E., Galvani, A. P., & Townsend, J. P. (2016). Cost-effectiveness of next-generation vaccines: The case of pertussis. Vaccine, 34(29), 3405–3411. https://doi.org/10.1016/j.vaccine.2016.04.010

The Fast-Evolving phy-2 Gene Modulates Sexual Development in Response to Light in the Model Fungus Neurospora crassa

mBio / May 04, 2016

Wang, Z., Li, N., Li, J., Dunlap, J. C., Trail, F., & Townsend, J. P. (2016). The Fast-Evolving phy-2 Gene Modulates Sexual Development in Response to Light in the Model Fungus Neurospora crassa. MBio, 7(2). https://doi.org/10.1128/mbio.02148-15

Retrospective Analysis of the 2014–2015 Ebola Epidemic in Liberia

The American Journal of Tropical Medicine and Hygiene / Apr 06, 2016

Atkins, K. E., Nyenswah, T. G., Galvani, A. P., Bawo, L., Yamin, D., Altice, F. L., Fallah, M., Medlock, J., Skrip, L., Wenzel, N. S., Ndeffo-Mbah, M. L., Pandey, A., & Townsend, J. (2016). Retrospective Analysis of the 2014–2015 Ebola Epidemic in Liberia. The American Journal of Tropical Medicine and Hygiene, 94(4), 833–839. https://doi.org/10.4269/ajtmh.15-0328

Quantifying Transmission ofClostridium difficilewithin and outside Healthcare Settings

Emerging Infectious Diseases / Apr 01, 2016

Durham, D. P., Olsen, M. A., Dubberke, E. R., Galvani, A. P., & Townsend, J. P. (2016). Quantifying Transmission ofClostridium difficilewithin and outside Healthcare Settings. Emerging Infectious Diseases, 22(4), 608–616. https://doi.org/10.3201/eid2204.150455

Determinants of Human African Trypanosomiasis Elimination via Paratransgenesis

PLOS Neglected Tropical Diseases / Mar 08, 2016

Gilbert, J. A., Medlock, J., Townsend, J. P., Aksoy, S., Ndeffo Mbah, M., & Galvani, A. P. (2016). Determinants of Human African Trypanosomiasis Elimination via Paratransgenesis. PLOS Neglected Tropical Diseases, 10(3), e0004465. https://doi.org/10.1371/journal.pntd.0004465

Early and multiple origins of metastatic lineages within primary tumors

Proceedings of the National Academy of Sciences / Feb 08, 2016

Zhao, Z.-M., Zhao, B., Bai, Y., Iamarino, A., Gaffney, S. G., Schlessinger, J., Lifton, R. P., Rimm, D. L., & Townsend, J. P. (2016). Early and multiple origins of metastatic lineages within primary tumors. Proceedings of the National Academy of Sciences, 113(8), 2140–2145. https://doi.org/10.1073/pnas.1525677113

The Impact of Enhanced Screening and Treatment on Hepatitis C in the United States

Clinical Infectious Diseases / Nov 30, 2015

Durham, D. P., Skrip, L. A., Bruce, R. D., Vilarinho, S., Elbasha, E. H., Galvani, A. P., & Townsend, J. P. (2015). The Impact of Enhanced Screening and Treatment on Hepatitis C in the United States. Clinical Infectious Diseases, 62(3), 298–304. https://doi.org/10.1093/cid/civ894

Optimizing age of cytomegalovirus screening and vaccination to avert congenital disease in the US

Vaccine / Jan 01, 2016

Alfaro-Murillo, J. A., Townsend, J. P., & Galvani, A. P. (2016). Optimizing age of cytomegalovirus screening and vaccination to avert congenital disease in the US. Vaccine, 34(2), 225–229. https://doi.org/10.1016/j.vaccine.2015.11.039

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

Nature / Jun 01, 2016

Prum, R. O., Berv, J. S., Dornburg, A., Field, D. J., Townsend, J. P., Lemmon, E. M., & Lemmon, A. R. (2016). A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature, 534(7607), S7–S8. https://doi.org/10.1038/nature19417

Future Perspectives and Challenges of Fungal Systematics in the Age of Big Data

Biology of Microfungi / Jan 01, 2016

Wang, Z., Nilsson, R. H., James, T. Y., Dai, Y., & Townsend, J. P. (2016). Future Perspectives and Challenges of Fungal Systematics in the Age of Big Data. Fungal Biology, 25–46. https://doi.org/10.1007/978-3-319-29137-6_3

Genomic and Gene-Expression Comparisons among Phage-Resistant Type-IV Pilus Mutants of Pseudomonas syringae pathovar phaseolicola

PLOS ONE / Dec 15, 2015

Sistrom, M., Park, D., O’Brien, H. E., Wang, Z., Guttman, D. S., Townsend, J. P., & Turner, P. E. (2015). Genomic and Gene-Expression Comparisons among Phage-Resistant Type-IV Pilus Mutants of Pseudomonas syringae pathovar phaseolicola. PLOS ONE, 10(12), e0144514. https://doi.org/10.1371/journal.pone.0144514

Quantitative analyses and modelling to support achievement of the 2020 goals for nine neglected tropical diseases

Parasites & Vectors / Dec 01, 2015

Hollingsworth, T. D., Adams, E. R., Anderson, R. M., Atkins, K., Bartsch, S., Basáñez, M.-G., Behrend, M., Blok, D. J., Chapman, L. A. C., Coffeng, L., Courtenay, O., Crump, R. E., de Vlas, S. J., Dobson, A., Dyson, L., Farkas, H., Galvani, A. P., Gambhir, M., … Zoueva, A. (2015). Quantitative analyses and modelling to support achievement of the 2020 goals for nine neglected tropical diseases. Parasites & Vectors, 8(1). https://doi.org/10.1186/s13071-015-1235-1

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 / May 14, 2015

Su, Z., & Townsend, J. P. (2015). 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(1). https://doi.org/10.1186/s12862-015-0364-7

Impact of bed capacity on spatiotemporal shifts in Ebola transmission

Proceedings of the National Academy of Sciences / Oct 30, 2015

Townsend, J. P., Skrip, L. A., & Galvani, A. P. (2015). Impact of bed capacity on spatiotemporal shifts in Ebola transmission. Proceedings of the National Academy of Sciences, 112(46), 14125–14126. https://doi.org/10.1073/pnas.1518484112

Inferring the Origin of Metastases from Cancer Phylogenies

Cancer Research / Sep 30, 2015

Hong, W. S., Shpak, M., & Townsend, J. P. (2015). Inferring the Origin of Metastases from Cancer Phylogenies. Cancer Research, 75(19), 4021–4025. https://doi.org/10.1158/0008-5472.can-15-1889

Gene Expression Evolves under a House-of-Cards Model of Stabilizing Selection

Molecular Biology and Evolution / Apr 20, 2015

Hodgins-Davis, A., Rice, D. P., & Townsend, J. P. (2015). Gene Expression Evolves under a House-of-Cards Model of Stabilizing Selection. Molecular Biology and Evolution, 32(8), 2130–2140. https://doi.org/10.1093/molbev/msv094

Solving the ecological puzzle of mycorrhizal associations using data from annotated collections and environmental samples - an example of saddle fungi

Environmental Microbiology Reports / Jul 01, 2015

Hwang, J., Zhao, Q., Yang, Z. L., Wang, Z., & Townsend, J. P. (2015). Solving the ecological puzzle of mycorrhizal associations using data from annotated collections and environmental samples - an example of saddle fungi. Environmental Microbiology Reports, 7(4), 658–667. https://doi.org/10.1111/1758-2229.12303

Harnessing Case Isolation and Ring Vaccination to Control Ebola

PLOS Neglected Tropical Diseases / May 29, 2015

Wells, C., Yamin, D., Ndeffo-Mbah, M. L., Wenzel, N., Gaffney, S. G., Townsend, J. P., Meyers, L. A., Fallah, M., Nyenswah, T. G., Altice, F. L., Atkins, K. E., & Galvani, A. P. (2015). Harnessing Case Isolation and Ring Vaccination to Control Ebola. PLOS Neglected Tropical Diseases, 9(5), e0003794. https://doi.org/10.1371/journal.pntd.0003794

Integrating Community-Based Interventions to Reverse the Convergent TB/HIV Epidemics in Rural South Africa

PLOS ONE / May 04, 2015

Gilbert, J. A., Long, E. F., Brooks, R. P., Friedland, G. H., Moll, A. P., Townsend, J. P., Galvani, A. P., & Shenoi, S. V. (2015). Integrating Community-Based Interventions to Reverse the Convergent TB/HIV Epidemics in Rural South Africa. PLOS ONE, 10(5), e0126267. https://doi.org/10.1371/journal.pone.0126267

Epidemiological and Viral Genomic Sequence Analysis of the 2014 Ebola Outbreak Reveals Clustered Transmission

Clinical Infectious Diseases / Dec 15, 2014

Scarpino, S. V., Iamarino, A., Wells, C., Yamin, D., Ndeffo-Mbah, M., Wenzel, N. S., Fox, S. J., Nyenswah, T., Altice, F. L., Galvani, A. P., Meyers, L. A., & Townsend, J. P. (2014). Epidemiological and Viral Genomic Sequence Analysis of the 2014 Ebola Outbreak Reveals Clustered Transmission. Clinical Infectious Diseases, 60(7), 1079–1082. https://doi.org/10.1093/cid/ciu1131

Under-reporting and case fatality estimates for emerging epidemics

BMJ / Mar 16, 2015

Atkins, K. E., Wenzel, N. S., Ndeffo-Mbah, M., Altice, F. L., Townsend, J. P., & Galvani, A. P. (2015). Under-reporting and case fatality estimates for emerging epidemics. BMJ, 350(mar16 3), h1115–h1115. https://doi.org/10.1136/bmj.h1115

Neural Gene Expression Profiles and Androgen Levels Underlie Alternative Reproductive Tactics in the Ocellated Wrasse,Symphodus ocellatus

Ethology / Oct 28, 2014

Stiver, K. A., Harris, R. M., Townsend, J. P., Hofmann, H. A., & Alonzo, S. H. (2014). Neural Gene Expression Profiles and Androgen Levels Underlie Alternative Reproductive Tactics in the Ocellated Wrasse,Symphodus ocellatus. Ethology, 121(2), 152–167. https://doi.org/10.1111/eth.12324

H-CLAP: hierarchical clustering within a linear array with an application in genetics

Statistical Applications in Genetics and Molecular Biology / Jan 01, 2015

Ghosh, S., & Townsend, J. P. (2015). H-CLAP: hierarchical clustering within a linear array with an application in genetics. Statistical Applications in Genetics and Molecular Biology, 14(2). https://doi.org/10.1515/sagmb-2013-0076

Correction: Harnessing Case Isolation and Ring Vaccination to Control Ebola

PLOS Neglected Tropical Diseases / Jun 24, 2015

Wells, C., Yamin, D., Ndeffo-Mbah, M. L., Wenzel, N., Gaffney, S. G., Townsend, J. P., Meyers, L. A., Fallah, M., Nyenswah, T. G., Altice, F. L., Atkins, K. E., & Galvani, A. P. (2015). Correction: Harnessing Case Isolation and Ring Vaccination to Control Ebola. PLOS Neglected Tropical Diseases, 9(6), e0003888. https://doi.org/10.1371/journal.pntd.0003888

Phylogenetic informativeness reconciles ray-finned fish molecular divergence times

BMC Evolutionary Biology / Aug 08, 2014

Dornburg, A., Townsend, J. P., Friedman, M., & Near, T. J. (2014). Phylogenetic informativeness reconciles ray-finned fish molecular divergence times. BMC Evolutionary Biology, 14(1). https://doi.org/10.1186/s12862-014-0169-0

The peopling of the African continent and the diaspora into the new world

Current Opinion in Genetics & Development / Dec 01, 2014

Campbell, M. C., Hirbo, J. B., Townsend, J. P., & Tishkoff, S. A. (2014). The peopling of the African continent and the diaspora into the new world. Current Opinion in Genetics & Development, 29, 120–132. https://doi.org/10.1016/j.gde.2014.09.003

Gene Expression Differences among Three Neurospora Species Reveal Genes Required for Sexual Reproduction in Neurospora crassa

PLoS ONE / Oct 20, 2014

Lehr, N. A., Wang, Z., Li, N., Hewitt, D. A., López-Giráldez, F., Trail, F., & Townsend, J. P. (2014). Gene Expression Differences among Three Neurospora Species Reveal Genes Required for Sexual Reproduction in Neurospora crassa. PLoS ONE, 9(10), e110398. https://doi.org/10.1371/journal.pone.0110398

Genome-Wide Characterization of Light-Regulated Genes inNeurospora crassa

G3 Genes|Genomes|Genetics / Sep 01, 2014

Wu, C., Yang, F., Smith, K. M., Peterson, M., Dekhang, R., Zhang, Y., Zucker, J., Bredeweg, E. L., Mallappa, C., Zhou, X., Lyubetskaya, A., Townsend, J. P., Galagan, J. E., Freitag, M., Dunlap, J. C., Bell-Pedersen, D., & Sachs, M. S. (2014). Genome-Wide Characterization of Light-Regulated Genes inNeurospora crassa. G3 Genes|Genomes|Genetics, 4(9), 1731–1745. https://doi.org/10.1534/g3.114.012617

Cellular Superspreaders: An Epidemiological Perspective on HIV Infection inside the Body

PLoS Pathogens / May 08, 2014

Talbert-Slagle, K., Atkins, K. E., Yan, K.-K., Khurana, E., Gerstein, M., Bradley, E. H., Berg, D., Galvani, A. P., & Townsend, J. P. (2014). Cellular Superspreaders: An Epidemiological Perspective on HIV Infection inside the Body. PLoS Pathogens, 10(5), e1004092. https://doi.org/10.1371/journal.ppat.1004092

The impact of incorporating molecular evolutionary model into predictions of phylogenetic signal and noise

Frontiers in Ecology and Evolution / Apr 16, 2014

Su, Z., Wang, Z., López-Giráldez, F., & Townsend, J. P. (2014). The impact of incorporating molecular evolutionary model into predictions of phylogenetic signal and noise. Frontiers in Ecology and Evolution, 2. https://doi.org/10.3389/fevo.2014.00011

Probabilistic uncertainty analysis of epidemiological modeling to guide public health intervention policy

Epidemics / Mar 01, 2014

Gilbert, J. A., Meyers, L. A., Galvani, A. P., & Townsend, J. P. (2014). Probabilistic uncertainty analysis of epidemiological modeling to guide public health intervention policy. Epidemics, 6, 37–45. https://doi.org/10.1016/j.epidem.2013.11.002

Global Gene Expression and Focused Knockout Analysis Reveals Genes Associated with Fungal Fruiting Body Development in Neurospora crassa

Eukaryotic Cell / Jan 01, 2014

Wang, Z., Lopez-Giraldez, F., Lehr, N., Farré, M., Common, R., Trail, F., & Townsend, J. P. (2014). Global Gene Expression and Focused Knockout Analysis Reveals Genes Associated with Fungal Fruiting Body Development in Neurospora crassa. Eukaryotic Cell, 13(1), 154–169. https://doi.org/10.1128/ec.00248-13

Detecting rare gene transfer events in bacterial populations

Frontiers in Microbiology / Jan 01, 2014

Nielsen, K. M., Bøhn, T., & Townsend, J. P. (2014). Detecting rare gene transfer events in bacterial populations. Frontiers in Microbiology, 4. https://doi.org/10.3389/fmicb.2013.00415

Optimized primers and other critical conditions for efficient fusion PCR to generate knockout vectors in filamentous fungi.

Fungal Genetics Reports / Dec 01, 2013

Harrison, N., Cavinder, B., Townsend, J. P., & Trail, F. (2013). Optimized primers and other critical conditions for efficient fusion PCR to generate knockout vectors in filamentous fungi. Fungal Genetics Reports, 60(1), 1–10. https://doi.org/10.4148/1941-4765.1006

Sex-linked transcriptional divergence in the hermaphrodite fungusNeurospora tetrasperma

Proceedings of the Royal Society B: Biological Sciences / Aug 07, 2013

Samils, N., Gioti, A., Karlsson, M., Sun, Y., Kasuga, T., Bastiaans, E., Wang, Z., Li, N., Townsend, J. P., & Johannesson, H. (2013). Sex-linked transcriptional divergence in the hermaphrodite fungusNeurospora tetrasperma. Proceedings of the Royal Society B: Biological Sciences, 280(1764), 20130862. https://doi.org/10.1098/rspb.2013.0862

Epidemiological mechanisms of genetic resistance to kuru

Journal of The Royal Society Interface / Aug 06, 2013

Atkins, K. E., Townsend, J. P., Medlock, J., & Galvani, A. P. (2013). Epidemiological mechanisms of genetic resistance to kuru. Journal of The Royal Society Interface, 10(85), 20130331. https://doi.org/10.1098/rsif.2013.0331

Potential Cost-Effectiveness of Schistosomiasis Treatment for Reducing HIV Transmission in Africa – The Case of Zimbabwean Women

PLoS Neglected Tropical Diseases / Aug 01, 2013

Ndeffo Mbah, M. L., Poolman, E. M., Atkins, K. E., Orenstein, E. W., Meyers, L. A., Townsend, J. P., & Galvani, A. P. (2013). Potential Cost-Effectiveness of Schistosomiasis Treatment for Reducing HIV Transmission in Africa – The Case of Zimbabwean Women. PLoS Neglected Tropical Diseases, 7(8), e2346. https://doi.org/10.1371/journal.pntd.0002346

AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification

Bioinformatics / Jun 03, 2013

Dai, L., Tian, M., Wu, J., Xiao, J., Wang, X., Townsend, J. P., & Zhang, Z. (2013). AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification. Bioinformatics, 29(14), 1837–1839. https://doi.org/10.1093/bioinformatics/btt284

Optimal targeting of seasonal influenza vaccination toward younger ages is robust to parameter uncertainty

Vaccine / Jun 01, 2013

Ndeffo Mbah, M. L., Medlock, J., Meyers, L. A., Galvani, A. P., & Townsend, J. P. (2013). Optimal targeting of seasonal influenza vaccination toward younger ages is robust to parameter uncertainty. Vaccine, 31(30), 3079–3089. https://doi.org/10.1016/j.vaccine.2013.04.052

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 / Apr 15, 2013

Ndeffo Mbah, M. L., Kjetland, E. F., Atkins, K. E., Poolman, E. M., Orenstein, E. W., Meyers, L. A., Townsend, J. P., & Galvani, A. P. (2013). 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, 110(19), 7952–7957. https://doi.org/10.1073/pnas.1221396110

Yeast response to LA virus indicates coadapted global gene expression during mycoviral infection

FEMS Yeast Research / Jan 02, 2013

McBride, R. C., Boucher, N., Park, D. S., Turner, P. E., & Townsend, J. P. (2013). Yeast response to LA virus indicates coadapted global gene expression during mycoviral infection. FEMS Yeast Research, 13(2), 162–179. https://doi.org/10.1111/1567-1364.12019

Response to: The relative utility of sequence divergence and phylogenetic informativeness profiling in phylogenetic study design

Molecular Phylogenetics and Evolution / Jan 01, 2013

Moeller, A. H., & Townsend, J. P. (2013). Response to: The relative utility of sequence divergence and phylogenetic informativeness profiling in phylogenetic study design. Molecular Phylogenetics and Evolution, 66(1), 436. https://doi.org/10.1016/j.ympev.2012.09.035

Evaluating Phylogenetic Informativeness as a Predictor of Phylogenetic Signal for Metazoan, Fungal, and Mammalian Phylogenomic Data Sets

BioMed Research International / Jan 01, 2013

López-Giráldez, F., Moeller, A. H., & Townsend, J. P. (2013). Evaluating Phylogenetic Informativeness as a Predictor of Phylogenetic Signal for Metazoan, Fungal, and Mammalian Phylogenomic Data Sets. BioMed Research International, 2013, 1–14. https://doi.org/10.1155/2013/621604

Controlling Antimicrobial Resistance through Targeted, Vaccine-Induced Replacement of Strains

PLoS ONE / Dec 05, 2012

Tekle, Y. I., Nielsen, K. M., Liu, J., Pettigrew, M. M., Meyers, L. A., Galvani, A. P., & Townsend, J. P. (2012). Controlling Antimicrobial Resistance through Targeted, Vaccine-Induced Replacement of Strains. PLoS ONE, 7(12), e50688. https://doi.org/10.1371/journal.pone.0050688

Reevaluation of Epidemiological Data Demonstrates That It Is Consistent With Cross-Immunity Among Human Papillomavirus Types

Journal of Infectious Diseases / Aug 07, 2012

Durham, D. P., Poolman, E. M., Ibuka, Y., Townsend, J. P., & Galvani, A. P. (2012). Reevaluation of Epidemiological Data Demonstrates That It Is Consistent With Cross-Immunity Among Human Papillomavirus Types. Journal of Infectious Diseases, 206(8), 1291–1298. https://doi.org/10.1093/infdis/jis494

Phylogenetic Signal and Noise: Predicting the Power of a Data Set to Resolve Phylogeny

Systematic Biology / Mar 03, 2012

Townsend, J. P., Su, Z., & Tekle, Y. I. (2012). Phylogenetic Signal and Noise: Predicting the Power of a Data Set to Resolve Phylogeny. Systematic Biology, 61(5), 835. https://doi.org/10.1093/sysbio/sys036

The influence of altruism on influenza vaccination decisions

Journal of The Royal Society Interface / Apr 11, 2012

Shim, E., Chapman, G. B., Townsend, J. P., & Galvani, A. P. (2012). The influence of altruism on influenza vaccination decisions. Journal of The Royal Society Interface, 9(74), 2234–2243. https://doi.org/10.1098/rsif.2012.0115

Potential for Rabies Control through Dog Vaccination in Wildlife-Abundant Communities of Tanzania

PLoS Neglected Tropical Diseases / Aug 21, 2012

Fitzpatrick, M. C., Hampson, K., Cleaveland, S., Meyers, L. A., Townsend, J. P., & Galvani, A. P. (2012). Potential for Rabies Control through Dog Vaccination in Wildlife-Abundant Communities of Tanzania. PLoS Neglected Tropical Diseases, 6(8), e1796. https://doi.org/10.1371/journal.pntd.0001796

Resampling QTL Effects in the QTL Sign Test Leads to Incongruous Sensitivity to Variance in Effect Size

G3 Genes|Genomes|Genetics / Aug 01, 2012

Rice, D. P., & Townsend, J. P. (2012). Resampling QTL Effects in the QTL Sign Test Leads to Incongruous Sensitivity to Variance in Effect Size. G3 Genes|Genomes|Genetics, 2(8), 905–911. https://doi.org/10.1534/g3.112.003228

Transcriptome analyses during fruiting body formation in Fusarium graminearum and Fusarium verticillioides reflect species life history and ecology

Fungal Genetics and Biology / Aug 01, 2012

Sikhakolli, U. R., López-Giráldez, F., Li, N., Common, R., Townsend, J. P., & Trail, F. (2012). Transcriptome analyses during fruiting body formation in Fusarium graminearum and Fusarium verticillioides reflect species life history and ecology. Fungal Genetics and Biology, 49(8), 663–673. https://doi.org/10.1016/j.fgb.2012.05.009

Sex-specific gene expression during asexual development of Neurospora crassa

Fungal Genetics and Biology / Jul 01, 2012

Wang, Z., Kin, K., López-Giráldez, F., Johannesson, H., & Townsend, J. P. (2012). Sex-specific gene expression during asexual development of Neurospora crassa. Fungal Genetics and Biology, 49(7), 533–543. https://doi.org/10.1016/j.fgb.2012.05.004

RBE controls microRNA164 expression to effect floral organogenesis

Development / Jun 15, 2012

Huang, T., López-Giráldez, F., Townsend, J. P., & Irish, V. F. (2012). RBE controls microRNA164 expression to effect floral organogenesis. Development, 139(12), 2161–2169. https://doi.org/10.1242/dev.075069

Differential impact of nutrition on developmental and metabolic gene expression during fruiting body development in Neurospora crassa

Fungal Genetics and Biology / May 01, 2012

Wang, Z., Lehr, N., Trail, F., & Townsend, J. P. (2012). Differential impact of nutrition on developmental and metabolic gene expression during fruiting body development in Neurospora crassa. Fungal Genetics and Biology, 49(5), 405–413. https://doi.org/10.1016/j.fgb.2012.03.004

A Test for Selection Employing Quantitative Trait Locus and Mutation Accumulation Data

Genetics / Apr 01, 2012

Rice, D. P., & Townsend, J. P. (2012). A Test for Selection Employing Quantitative Trait Locus and Mutation Accumulation Data. Genetics, 190(4), 1533–1545. https://doi.org/10.1534/genetics.111.137075

Abundant Gene-by-Environment Interactions in Gene Expression Reaction Norms to Copper within Saccharomyces cerevisiae

Genome Biology and Evolution / Jan 01, 2012

Hodgins-Davis, A., Adomas, A. B., Warringer, J., & Townsend, J. P. (2012). Abundant Gene-by-Environment Interactions in Gene Expression Reaction Norms to Copper within Saccharomyces cerevisiae. Genome Biology and Evolution, 4(11), 1061–1079. https://doi.org/10.1093/gbe/evs084

Analyses of expressed sequence tags in Neurosporareveal rapid evolution of genes associated with the early stages of sexual reproduction in fungi

BMC Evolutionary Biology / Nov 27, 2012

Nygren, K., Wallberg, A., Samils, N., Stajich, J. E., Townsend, J. P., Karlsson, M., & Johannesson, H. (2012). Analyses of expressed sequence tags in Neurosporareveal rapid evolution of genes associated with the early stages of sexual reproduction in fungi. BMC Evolutionary Biology, 12(1). https://doi.org/10.1186/1471-2148-12-229

Assessing the Probability of Detection of Horizontal Gene Transfer Events in Bacterial Populations

Frontiers in Microbiology / Jan 01, 2012

Townsend, J. P., Bøhn, T., & Nielsen, K. M. (2012). Assessing the Probability of Detection of Horizontal Gene Transfer Events in Bacterial Populations. Frontiers in Microbiology, 3. https://doi.org/10.3389/fmicb.2012.00027

Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance

BMC Bioinformatics / Mar 22, 2012

Zhang, Z., Li, J., Cui, P., Ding, F., Li, A., Townsend, J. P., & Yu, J. (2012). Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance. BMC Bioinformatics, 13(1). https://doi.org/10.1186/1471-2105-13-43

PhyDesign: an online application for profiling phylogenetic informativeness

BMC Evolutionary Biology / May 31, 2011

López-Giráldez, F., & Townsend, J. P. (2011). PhyDesign: an online application for profiling phylogenetic informativeness. BMC Evolutionary Biology, 11(1). https://doi.org/10.1186/1471-2148-11-152

Data Integration in Bioinformatics: Current Efforts and Challenges

Bioinformatics - Trends and Methodologies / Nov 02, 2011

Zhang, Z., B., V., Yu, J., Cheung, K.-H., & P., J. (2011). Data Integration in Bioinformatics: Current Efforts and Challenges. Bioinformatics - Trends and Methodologies. https://doi.org/10.5772/21654

Phylogenetic informativeness profiling of 12 genes for 28 vertebrate taxa without divergence dates

Molecular Phylogenetics and Evolution / Aug 01, 2011

Moeller, A. H., & Townsend, J. P. (2011). Phylogenetic informativeness profiling of 12 genes for 28 vertebrate taxa without divergence dates. Molecular Phylogenetics and Evolution, 60(2), 271–272. https://doi.org/10.1016/j.ympev.2011.04.023

SIR2 and other genes are abundantly expressed in long-lived natural segregants for replicative aging of the budding yeast Saccharomyces cerevisiae

FEMS Yeast Research / Mar 01, 2011

Guo, Z., Adomas, A. B., Jackson, E. D., Qin, H., & Townsend, J. P. (2011). 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(4), 345–355. https://doi.org/10.1111/j.1567-1364.2011.00723.x

Taxon Sampling and the Optimal Rates of Evolution for Phylogenetic Inference

Systematic Biology / Feb 08, 2011

Townsend, J. P., & Leuenberger, C. (2011). Taxon Sampling and the Optimal Rates of Evolution for Phylogenetic Inference. Systematic Biology, 60(3), 358–365. https://doi.org/10.1093/sysbio/syq097

Tasting Soil Fungal Diversity with Earth Tongues: Phylogenetic Test of SATé Alignments for Environmental ITS Data

PLoS ONE / Apr 21, 2011

Wang, Z., Nilsson, R. H., Lopez-Giraldez, F., Zhuang, W., Dai, Y., Johnston, P. R., & Townsend, J. P. (2011). Tasting Soil Fungal Diversity with Earth Tongues: Phylogenetic Test of SATé Alignments for Environmental ITS Data. PLoS ONE, 6(4), e19039. https://doi.org/10.1371/journal.pone.0019039

Retrospective evidence for a biological cost of vancomycin resistance determinants in the absence of glycopeptide selective pressures

Journal of Antimicrobial Chemotherapy / Jan 07, 2011

Johnsen, P. J., Townsend, J. P., Bohn, T., Simonsen, G. S., Sundsfjord, A., & Nielsen, K. M. (2011). Retrospective evidence for a biological cost of vancomycin resistance determinants in the absence of glycopeptide selective pressures. Journal of Antimicrobial Chemotherapy, 66(3), 608–610. https://doi.org/10.1093/jac/dkq512

Getting the Most Out of Your Fungal Microarray Data: Two Cost- and Time-Effective Methods

Methods in Molecular Biology / Jan 01, 2011

Mathioni, S. M., Beló, A., Townsend, J. P., & Donofrio, N. M. (2011). Getting the Most Out of Your Fungal Microarray Data: Two Cost- and Time-Effective Methods. Fungal Genomics, 61–77. https://doi.org/10.1007/978-1-61779-040-9_5

Northern species of earth tongue genus Thuemenidium revisited, considering morphology, ecology and molecular phylogeny

Mycologia / Sep 01, 2010

Ohenoja, E., Wang, Z., Townsend, J. P., Mitchel, D., & Voitk, A. (2010). Northern species of earth tongue genus Thuemenidium revisited, considering morphology, ecology and molecular phylogeny. Mycologia, 102(5), 1089–1095. https://doi.org/10.3852/09-317

LOX: inferring Level Of eXpression from diverse methods of census sequencing

Bioinformatics / Jun 10, 2010

Zhang, Z., López-Giráldez, F., & Townsend, J. P. (2010). LOX: inferring Level Of eXpression from diverse methods of census sequencing. Bioinformatics, 26(15), 1918–1919. https://doi.org/10.1093/bioinformatics/btq303

Optimal Selection of Gene and Ingroup Taxon Sampling for Resolving Phylogenetic Relationships

Systematic Biology / May 19, 2010

Townsend, J. P., & Lopez-Giraldez, F. (2010). Optimal Selection of Gene and Ingroup Taxon Sampling for Resolving Phylogenetic Relationships. Systematic Biology, 59(4), 446–457. https://doi.org/10.1093/sysbio/syq025

Identification of new molecular markers for assembling the eukaryotic tree of life

Molecular Phylogenetics and Evolution / Jun 01, 2010

Tekle, Y. I., Grant, J. R., Kovner, A. M., Townsend, J. P., & Katz, L. A. (2010). Identification of new molecular markers for assembling the eukaryotic tree of life. Molecular Phylogenetics and Evolution, 55(3), 1177–1182. https://doi.org/10.1016/j.ympev.2010.03.010

The filamentous fungal gene expression database (FFGED)

Fungal Genetics and Biology / Mar 01, 2010

Zhang, Z., & Townsend, J. P. (2010). The filamentous fungal gene expression database (FFGED). Fungal Genetics and Biology, 47(3), 199–204. https://doi.org/10.1016/j.fgb.2009.12.001

Multi-targeted priming for genome-wide gene expression assays

BMC Genomics / Aug 17, 2010

Adomas, A. B., Lopez-Giraldez, F., Clark, T. A., Wang, Z., & Townsend, J. P. (2010). Multi-targeted priming for genome-wide gene expression assays. BMC Genomics, 11(1). https://doi.org/10.1186/1471-2164-11-477

Evolving gene expression: from G to E to G×E

Trends in Ecology & Evolution / Dec 01, 2009

Hodgins-Davis, A., & Townsend, J. P. (2009). Evolving gene expression: from G to E to G×E. Trends in Ecology & Evolution, 24(12), 649–658. https://doi.org/10.1016/j.tree.2009.06.011

<I>Geoglossomycetes</I> cl. nov., <I>Geoglossales</I> ord. nov. and taxa above class rank in the <I>Ascomycota</I> Tree of Life

Persoonia - Molecular Phylogeny and Evolution of Fungi / Jun 30, 2009

Schoch, C. L., Wang, Z., Townsend, J. P., & Spatafora, J. W. (2009). &lt;I&gt;Geoglossomycetes&lt;/I&gt; cl. nov., &lt;I&gt;Geoglossales&lt;/I&gt; ord. nov. and taxa above class rank in the &lt;I&gt;Ascomycota&lt;/I&gt; Tree of Life. Persoonia - Molecular Phylogeny and Evolution of Fungi, 22(1), 129–138. https://doi.org/10.3767/003158509x461486

Maximum-Likelihood Model Averaging To Profile Clustering of Site Types across Discrete Linear Sequences

PLoS Computational Biology / Jun 26, 2009

Zhang, Z., & Townsend, J. P. (2009). Maximum-Likelihood Model Averaging To Profile Clustering of Site Types across Discrete Linear Sequences. PLoS Computational Biology, 5(6), e1000421. https://doi.org/10.1371/journal.pcbi.1000421

Factors affecting the reversal of antimicrobial-drug resistance

The Lancet Infectious Diseases / Jun 01, 2009

Johnsen, P. J., Townsend, J. P., Bøhn, T., Simonsen, G. S., Sundsfjord, A., & Nielsen, K. M. (2009). Factors affecting the reversal of antimicrobial-drug resistance. The Lancet Infectious Diseases, 9(6), 357–364. https://doi.org/10.1016/s1473-3099(09)70105-7

Evolution of Reproductive Morphology in Leaf Endophytes

PLoS ONE / Jan 22, 2009

Wang, Z., Johnston, P. R., Yang, Z. L., & Townsend, J. P. (2009). Evolution of Reproductive Morphology in Leaf Endophytes. PLoS ONE, 4(1), e4246. https://doi.org/10.1371/journal.pone.0004246

Measuring Transcription Factor–Binding Site Turnover: A Maximum Likelihood Approach Using Phylogenies

Genome Biology and Evolution / Jan 01, 2009

Otto, W., Stadler, P. F., López-Giraldéz, F., Townsend, J. P., Lynch, V. J., & Wagner, G. P. (2009). Measuring Transcription Factor–Binding Site Turnover: A Maximum Likelihood Approach Using Phylogenies. Genome Biology and Evolution, 1, 85–98. https://doi.org/10.1093/gbe/evp010

Article Commentary: Snapshots of Tree Space

Evolutionary Bioinformatics / Jan 01, 2009

Wang, Z., López-Giréidez, F., & Townsend, J. P. (2009). Article Commentary: Snapshots of Tree Space. Evolutionary Bioinformatics, 5, EBO.S3416. https://doi.org/10.4137/ebo.s3416

RNA extraction, probe preparation, and competitive hybridization for transcriptional profiling using Neurospora crassa long-oligomer DNA microarrays

Fungal Genetics Reports / Dec 01, 2008

Clark, T. A., Guilmette, J. M., Renstrom, D., & Townsend, J. P. (2008). RNA extraction, probe preparation, and competitive hybridization for transcriptional profiling using Neurospora crassa long-oligomer DNA microarrays. Fungal Genetics Reports, 55(1), 18–28. https://doi.org/10.4148/1941-4765.1086

The Phylogenetic Informativeness of Nucleotide and Amino Acid Sequences for Reconstructing the Vertebrate Tree

Journal of Molecular Evolution / Aug 12, 2008

Townsend, J. P., López-Giráldez, F., & Friedman, R. (2008). The Phylogenetic Informativeness of Nucleotide and Amino Acid Sequences for Reconstructing the Vertebrate Tree. Journal of Molecular Evolution, 67(5), 437–447. https://doi.org/10.1007/s00239-008-9142-0

Bringing Web 2.0 to bioinformatics

Briefings in Bioinformatics / Oct 08, 2008

Zhang, Z., Cheung, K.-H., & Townsend, J. P. (2008). Bringing Web 2.0 to bioinformatics. Briefings in Bioinformatics, 10(1), 1–10. https://doi.org/10.1093/bib/bbn041

HCLS 2.0/3.0: Health care and life sciences data mashup using Web 2.0/3.0

Journal of Biomedical Informatics / Oct 01, 2008

Cheung, K.-H., Yip, K. Y., Townsend, J. P., & Scotch, M. (2008). HCLS 2.0/3.0: Health care and life sciences data mashup using Web 2.0/3.0. Journal of Biomedical Informatics, 41(5), 694–705. https://doi.org/10.1016/j.jbi.2008.04.001

Sleuthing the difference a nucleotide can make

Molecular Ecology / Jun 01, 2008

TOWNSEND, J. P. (2008). Sleuthing the difference a nucleotide can make. Molecular Ecology, 17(12), 2793–2795. https://doi.org/10.1111/j.1365-294x.2008.03824.x

Quantifying variation in gene expression

Molecular Ecology / Jul 01, 2007

CLARK, T. A., & TOWNSEND, J. P. (2007). Quantifying variation in gene expression. Molecular Ecology, 16(13), 2613–2616. https://doi.org/10.1111/j.1365-294x.2007.03354.x

Enabling a Community to Dissect an Organism: Overview of the Neurospora Functional Genomics Project

Fungal Genomics / Jan 01, 2007

Dunlap, J. C., Borkovich, K. A., Henn, M. R., Turner, G. E., Sachs, M. S., Glass, N. L., McCluskey, K., Plamann, M., Galagan, J. E., Birren, B. W., Weiss, R. L., Townsend, J. P., Loros, J. J., Nelson, M. A., Lambreghts, R., Colot, H. V., Park, G., Collopy, P., Ringelberg, C., … Xu, J. (2007). Enabling a Community to Dissect an Organism: Overview of the Neurospora Functional Genomics Project. Advances in Genetics, 49–96. https://doi.org/10.1016/s0065-2660(06)57002-6

Phase-specific gene expression underlying morphological adaptations of the dimorphic human pathogenic fungus, Coccidioides posadasii

Fungal Genetics and Biology / Aug 01, 2006

Johannesson, H., Kasuga, T., Schaller, R. A., Good, B., Gardner, M. J., Townsend, J. P., Cole, G. T., & Taylor, J. W. (2006). Phase-specific gene expression underlying morphological adaptations of the dimorphic human pathogenic fungus, Coccidioides posadasii. Fungal Genetics and Biology, 43(8), 545–559. https://doi.org/10.1016/j.fgb.2006.02.003

Population structure and gene evolution inSaccharomyces cerevisiae

FEMS Yeast Research / Aug 01, 2006

Aa, E., Townsend, J. P., Adams, R. I., Nielsen, K. M., & Taylor, J. W. (2006). Population structure and gene evolution inSaccharomyces cerevisiae. FEMS Yeast Research, 6(5), 702–715. https://doi.org/10.1111/j.1567-1364.2006.00059.x

Ecological and evolutionary genomics of Saccharomyces cerevisiae

Molecular Ecology / Feb 23, 2006

LANDRY, C. R., TOWNSEND, J. P., HARTL, D. L., & CAVALIERI, D. (2006). Ecological and evolutionary genomics of Saccharomyces cerevisiae. Molecular Ecology, 15(3), 575–591. https://doi.org/10.1111/j.1365-294x.2006.02778.x

Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination

Nucleic Acids Research / Nov 27, 2005

Kasuga, T. (2005). Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination. Nucleic Acids Research, 33(20), 6469–6485. https://doi.org/10.1093/nar/gki953

Concerted Evolution in the Repeats of an Immunomodulating Cell Surface Protein, SOWgp, of the Human Pathogenic Fungi Coccidioides immitis and C. posadasii

Genetics / Sep 01, 2005

Johannesson, H., Townsend, J. P., Hung, C.-Y., Cole, G. T., & Taylor, J. W. (2005). Concerted Evolution in the Repeats of an Immunomodulating Cell Surface Protein, SOWgp, of the Human Pathogenic Fungi Coccidioides immitis and C. posadasii. Genetics, 171(1), 109–117. https://doi.org/10.1534/genetics.105.040923

A Bayesian method for analysing spotted microarray data

Briefings in Bioinformatics / Jan 01, 2005

Meiklejohn, C. D., & Townsend, J. P. (2005). A Bayesian method for analysing spotted microarray data. Briefings in Bioinformatics, 6(4), 318–330. https://doi.org/10.1093/bib/6.4.318

Designing Experiments Using Spotted Microarrays to Detect Gene Regulation Differences Within and Among Species

Methods in Enzymology / Jan 01, 2005

Townsend, J. P., & Taylor, J. W. (2005). Designing Experiments Using Spotted Microarrays to Detect Gene Regulation Differences Within and Among Species. Molecular Evolution: Producing the Biochemical Data, 597–617. https://doi.org/10.1016/s0076-6879(05)95031-3

Monitoring and modeling horizontal gene transfer

Nature Biotechnology / Aug 31, 2004

Nielsen, K. M., & Townsend, J. P. (2004). Monitoring and modeling horizontal gene transfer. Nature Biotechnology, 22(9), 1110–1114. https://doi.org/10.1038/nbt1006

Mitochondrial genome size variation in New World and Old World populations of Drosophila melanogaster

Heredity / May 12, 2004

Townsend, J. P., & Rand, D. M. (2004). Mitochondrial genome size variation in New World and Old World populations of Drosophila melanogaster. Heredity, 93(1), 98–103. https://doi.org/10.1038/sj.hdy.6800484

Monitoring horizontal gene transfer

Nature Biotechnology / Nov 01, 2004

Davison, J. (2004). Monitoring horizontal gene transfer. Nature Biotechnology, 22(11), 1349–1349. https://doi.org/10.1038/nbt1104-1349a

Population Genetic Variation in Genome-Wide Gene Expression

Molecular Biology and Evolution / Apr 25, 2003

Townsend, J. P. (2003). Population Genetic Variation in Genome-Wide Gene Expression. Molecular Biology and Evolution, 20(6), 955–963. https://doi.org/10.1093/molbev/msg106

Pathway Processor: A Tool for Integrating Whole-Genome Expression Results into Metabolic Networks

Genome Research / Jul 01, 2002

Grosu, P., Townsend, J. P., Hartl, D. L., & Cavalieri, D. (2002). <tt>Pathway Processor</tt>: A Tool for Integrating Whole-Genome Expression Results into Metabolic Networks. Genome Research, 12(7), 1121–1126. https://doi.org/10.1101/gr.226602

Manifold anomalies in gene expression in a vineyard isolate of Saccharomyces cerevisiae revealed by DNA microarray analysis

Proceedings of the National Academy of Sciences / Oct 17, 2000

Cavalieri, D., Townsend, J. P., & Hartl, D. L. (2000). Manifold anomalies in gene expression in a vineyard isolate of Saccharomyces cerevisiae revealed by DNA microarray analysis. Proceedings of the National Academy of Sciences, 97(22), 12369–12374. https://doi.org/10.1073/pnas.210395297

Solvent Accessibility and Purifying Selection Within Proteins of Escherichia coli and Salmonella enterica

Molecular Biology and Evolution / Feb 01, 2000

Bustamante, C. D., Townsend, J. P., & Hartl, D. L. (2000). Solvent Accessibility and Purifying Selection Within Proteins of Escherichia coli and Salmonella enterica. Molecular Biology and Evolution, 17(2), 301–308. https://doi.org/10.1093/oxfordjournals.molbev.a026310

Gene expression profiling in evolutionary genetics

The Evolution of Population Biology / Jan 15, 2004

Hartl, D. L., Meiklejohn, C. D., Castillo-Davis, C. I., Cavalieri, D., Ranz, J. M., & Townsend, J. P. (2004). Gene expression profiling in evolutionary genetics. The Evolution of Population Biology, 74–93. https://doi.org/10.1017/cbo9780511542619.007

Radiation-Specific Clinical Data Should Be Included in Existing Large-Scale Genomic Datasets

International Journal of Radiation Oncology*Biology*Physics / May 01, 2017

Chen, W. S., Townsend, J. P., & Yu, J. B. (2017). Radiation-Specific Clinical Data Should Be Included in Existing Large-Scale Genomic Datasets. International Journal of Radiation Oncology*Biology*Physics, 98(1), 8–10. https://doi.org/10.1016/j.ijrobp.2017.01.023

Links & Social Media

Research Interests

Evolutionary Genomics
Multidisciplinary
General Immunology and Microbiology
Microbiology
Infectious Diseases
General Agricultural and Biological Sciences
Genetics
Cell Biology
Ecology, Evolution, Behavior and Systematics
General Biochemistry, Genetics and Molecular Biology
Molecular Biology
Physiology
General Medicine
Biomedical Engineering
Molecular Medicine
Applied Microbiology and Biotechnology
Bioengineering
Biotechnology
Biochemistry
Biomaterials
Biophysics
General Engineering
General Physics and Astronomy
General Chemistry
Oncology
Hematology
Genetics (clinical)
Health Informatics
Computer Science Applications
Virology
Microbiology (medical)
Agricultural and Biological Sciences (miscellaneous)
Parasitology
Developmental Biology
Cancer Research
Information Systems
Pharmacology (medical)
Pharmacology
Public Health, Environmental and Occupational Health
Epidemiology
Applied Mathematics
Structural Biology
General Earth and Planetary Sciences
General Environmental Science
Immunology and Allergy
Immunology
Computational Mathematics
Computational Theory and Mathematics
Statistics and Probability
Animal Science and Zoology
Histology
Pathology and Forensic Medicine
Library and Information Sciences
Pulmonary and Respiratory Medicine
Modeling and Simulation
Medicine (miscellaneous)
Health Policy
Internal Medicine
Neurology (clinical)
Immunology and Microbiology (miscellaneous)
Cellular and Molecular Neuroscience
Ecology
Urology
Oral Surgery
General Veterinary
General Chemical Engineering
Radiology, Nuclear Medicine and imaging
Radiation
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