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

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

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

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

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

Systematic Biology / Apr 01, 2007

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

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 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

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 / 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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 / 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Schoch, C. L., Wang, Z., Townsend, J. P., & Spatafora, J. W. (2009). <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, 22(1), 129–138. https://doi.org/10.3767/003158509x461486

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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