Jeffrey Townsend, PhD
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Research Summary
1. BIOINFORMATIC TOOLS FOR CANCER GENETICS AND EPIDEMIOLOGY
Whole-exome sequencing has created tremendous potential for revealing the genetic basis and underlying molecular mechanisms of many forms of cancer. However, somatic mutations occur at a significant frequency within tumors of most cancer types, and identification of the mutations that are on the causative trajectory from normal tissue to cancerous tissue is challenging. We are making algorithmic advances to estimate the cancer effects of somatic amino-acid replacement mutations appearing within mutated genes, and applying phyologenetic approaches to reveal the temporal evolution of cancer from tumorigenesis to resection as well as in response to therapeutic intervention.
2. BIOSTATISTICAL ANALYSIS FOR NONLINEAR MATHEMATICAL MODELS OF THE EPIDEMIOLOGY OF DISEASE
I am developing probabilistic statistical methodologies for the mathematical modeling of disease emergence and spread. For diverse reasons, data for estimation of epidemiological parameters is often sparse. Evaluating a model with the “best point estimate” of sparse data may convey a misleading certitude to policy makers basing decisions on deterministic models of disease outbreak, spread, and persistence. Conversely, policy makers who are aware that models are parameterized with limited data may be dismissive of deterministic predictions that yet have significant validity. We address these issues by probabilistic sensitivity analysis of parameters and full uncertainty analysis of outcomes of interest.
Extensive Research Description
1. TOOLS FOR CANCER GENETICS AND EPIDEMIOLOGY
Whole-exome sequencing has created tremendous potential for revealing the genetic basis and underlying molecular mechanisms of many forms of cancer. However, somatic mutations occur at a significant frequency within tumors of most cancer types, and identification of the mutations that are on the causative trajectory from normal tissue to cancerous tissue is challenging. We are making algorithmic advances in clustering across discrete linear sequences to enact two powerful approaches to this identification. First, we are applying maximum likelihood approaches that we have developed for model-averaged clustering in discrete linear sequences to somatic amino acid replacement mutations appearing within mutated genes. Because amino acids of proteins that are functionally important are locally clustered in domains, mutations in multiple tumors that are functionally important to the development of cancer cluster in the linear sequence of relevant genes, allowing inference of relevance and function even in cases without three-dimensional protein structure. These clustering analyses have the power to demonstrate, for instance, cross-cancer consistency in the functional importance of the DNA binding domain of tumor suppressor p53, whether in a cancer with extensive exome data (ovarian serous adenocarcinoma) or in a cancer with much less extensive exome data (e.g. rectal adenocarcinoma).
Second, we are applying evolutionary theory to the problem of identification of the genetic architecture of underlying cancer development. The path from normal to cancerous tissue is navigated by an evolutionary process. Tools from evolutionary theory have the potential to parse those mutations that are selected within cells on the path to cancer from those mutations that arise incidentally during the somatic evolution of cancer. The theory we are applying makes use of differences in expectation for synonymous and replacement mutations. Synonymous mutations are expected to have no functional impact; thus they yield a proxy expectation for the “incidental” mutations, whereas carcinogenic replacement mutations will spread within tumors more frequently and are clustered within gene sequence. Our theory also employs human population polymorphism data, which most evolutionary biologists believe can be largely assumed to be neutral. This data facilitates calibration of the probable impact of replacement changes to sequence conservation by eliminating the confounding variable of the degree of purifying selection, which decreases the number of mutations observed in some genes and allows others to accumulate many mutations with little impact.
We are extending this approach to estimating selection intensity on mutations along the trajectory toward cancer, revealing the level of selection within tumors for replacement mutations compared to synonymous mutations. This evolutionary analysis is ideal for detecting the history of selection on sites within genes during the evolution of cancer from exome sequencing data. These sites, particularly when representing gain-of-function mutations, will help identify candidate loci for pharmacological intervention. This approach will be applied to identify targets for pharmacological intervention and design “personal genomics” drugs appropriate for the genetics of individual cancers in individual patients. As a component of that project, we are constructing an “active-experiment” cancer exome database to facilitate further bioinformatics investigation of cancer exome data.
2. BIOSTATISTICAL ANALYSIS FOR NONLINEAR MATHEMATICAL MODELS OF THE EPIDEMIOLOGY OF DISEASE
I am developing probabilistic statistical methodologies for the mathematical modeling of disease emergence and spread. Robustness of models has usually been assessed by techniques that explore the relative impact and importance of parameters upon the mathematical behavior of the function and the mathematical predictions of the model. For diverse reasons including the difficulty or cost of acquisition, restrictions due to privacy, and urgency of analysis in the case of outbreaks, data for estimation of epidemiological parameters is often sparse. Evaluating a model with the “best point estimate” of sparse data may convey a misleading certitude to policy makers basing decisions on deterministic models of disease outbreak, spread, and persistence. Conversely, policy makers who are aware that models are parameterized with limited data may be dismissive of deterministic predictions that yet have significant validity. These issues may be most straightforwardly addressed by probabilistic sensitivity analysis of parameters and full uncertainty analysis of outcomes of interest. These analyses amount to accommodating the uncertainty of parameters directly into an analysis by probabilistically resampling data or likely distributions of parameters to calculate a probabilistic distribution of outcomes.
For instance, one of the most common modeling approaches for evaluating interventions is based on differential equation models of disease such as the standard Susceptible-Infected-Recovered (SIR) model. In the SIR model and other more complex constructions, a closed-form solution can often be calculated for the basic reproductive number, R0, the average number of secondary infections that would follow upon a primary infection in a naïve host population. In a population where there is preexisting immunity due to either vaccination or previous infection, the effective reproductive number, Re, is defined as the average number of secondary infections following a primary infection in a population that is not completely naïve.
is of particular interest in public health because interventions that bring its value below 1 are predicted to eradicate the disease. This deterministic threshold of is proposed as the basis for policy decisions regarding the level of interventions that should be implemented. However, the best estimates for the parameters that are needed for the closed-form solution of are inevitably inexact. To address this point, sensitivity analyses are frequently performed to evaluate models and explore the relationship between model parameters and outcomes. In such deterministic sensitivity analyses, one or more parameters are perturbed and the corresponding effects on outcomes are examined. The perturbation can be done either by evaluating the effect of arbitrarily small changes in parameter values (e.g. ± 1%) or by evaluating the effects across a range of values defined by plausible probability density functions. Because the values of other parameters are held fixed at best point estimates, these strategies do not account for interaction effects in non-linear dynamic models, and do not assess global uncertainty in outcome. Uncertainty analysis has been recommended for many fields of mathematical modeling, including medical decision making, as an optimal approach to presenting models. In the case of dynamic transmission modeling, however, authoritative best practices have not included uncertainty analyses. Modeling guidelines recommend probabilistic sensitivity analysis, in which both global parameter uncertainty and output uncertainty are addressed, as the best practice method for uncertainty analysis. Yet that ideal has not been extended to dynamic transmission models, for which its implementation has been challenging.
We are developing methods for global probabilistic sensitivity analysis that allow the contribution of each parameter to model outcomes to be investigated while also taking into account the uncertainty of other model parameters. Uncertainty in parameter values can be accounted for by sampling randomly from empirical data or from probability density functions fit to empirical data. Depending on the instance, such sampling techniques include bootstrapping, Monte Carlo sampling, and Latin hypercube sampling. The model output generated from parameter samples can then be analyzed using linear (e.g. partial correlation coefficients), monotonic (e.g. partial rank correlation coefficients) and non-monotonic statistical tests (e.g. sensitivity index) to determine the contribution of each parameter to the variation in output values. Indeed, for a global sensitivity analysis to yield probabilities associated with outcomes that are of greatest utility to policy makers, probabilistic analyses of parameter uncertainty must be carried through to the model outcomes. For example, the probability of eradication of an epidemic is sensitive to both levels of vaccination and treatment. Moreover, a policy based on the analysis of data should take into consideration not only the best estimate of necessary action, but also the uncertainty around that outcome estimate. The former policy advice, indicating an exact cline of treatment and vaccination that should put into abeyance an influenza epidemic, is very different and can be misleading compared to the probabilistic statement, which gives a policymaker a predictive probability that a particular policy of treatment and vaccination will put into abeyance an influenza epidemic. Similar approaches applied with a next-generation matrix to rabies vaccination in Tanzania were able to demonstrate that WHO goals in two districts of 70% vaccination coverage of dogs had more than enough probability to control rabies, if only the process to achieve those not impractical goals could be mustered.
A public health decision maker would find most useful the assignment of the probability of eradication to each level of treatment, so that they may precisely weigh the cost of intervention against the potential for failure. These probabilistic outcome distributions also feed forward extremely fluidly with cost-effectiveness estimation, a field which has embraced uncertainty analysis but which has until our recent work not incorporated uncertainty from nonlinear infectious disease models into calculations.
We have many projects ongoing in the lab, covering topics summarized below, including many we have already published on and many that we have not. In particular, we have a lot of projects on the somatic evolution of cancer that are not yet in publications.
Coauthors
Research Interests
Algorithms; Bacteria; Bacterial Infections and Mycoses; Beer; Bread; Cell Transformation, Neoplastic; Coccidioidomycosis; Computing Methodologies; Biological Evolution; Fungi; Genetic Engineering; Microbiological Phenomena; Models, Genetic; Models, Theoretical; Mycoses; Neoplasm Metastasis; Neoplasms; Phylogeny; Viruses; Wine; Models, Statistical; Likelihood Functions; Logistic Models; Polymerase Chain Reaction; Sequence Analysis, DNA; Nonlinear Dynamics; Molecular Epidemiology; Gene Transfer Techniques; Crops, Agricultural; Evolution, Molecular; Nature; Sequence Analysis, Protein; Gene Expression Profiling; Public Health Informatics; Microarray Analysis; Genetic Speciation; Host-Pathogen Interactions; Genetic Phenomena; Mathematical Concepts; Organisms; Phenomena and Processes
Public Health Interests
Antimicrobial Resistance; Bioinformatics; Cancer; Evolution; Genetics, Genomics, Epigenetics; Health Policy; Hepatitis; HIV/AIDS; Infectious Diseases; Influenza; Metabolism; Microbial Ecology; Modeling; Vaccines; Zoonotic Diseases; Pollution; Tick-borne Diseases; COVID-19
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Selected Publications
- Quarantine and serial testing for variants of SARS-CoV-2 with benefits of vaccination and boosting on consequent control of COVID-19Wells CR, Pandey A, Gokcebel S, Krieger G, Donoghue AM, Singer BH, Moghadas SM, Galvani AP, Townsend JP. Quarantine and serial testing for variants of SARS-CoV-2 with benefits of vaccination and boosting on consequent control of COVID-19. PNAS Nexus 2022, 1: pgac100. PMID: 35909795, PMCID: PMC9335027, DOI: 10.1093/pnasnexus/pgac100.
- Testing for COVID-19 is Much More Effective When Performed Immediately Prior to Social MixingWells CR, Gokcebel S, Pandey A, Galvani AP, Townsend JP. Testing for COVID-19 is Much More Effective When Performed Immediately Prior to Social Mixing. International Journal Of Public Health 2022, 67: 1604659. PMID: 35967267, PMCID: PMC9363582, DOI: 10.3389/ijph.2022.1604659.
- The durability of natural infection and vaccine-induced immunity against future infection by SARS-CoV-2Townsend JP, Hassler HB, Sah P, Galvani AP, Dornburg A. The durability of natural infection and vaccine-induced immunity against future infection by SARS-CoV-2. Proceedings Of The National Academy Of Sciences Of The United States Of America 2022, 119: e2204336119. PMID: 35858382, PMCID: PMC9351502, DOI: 10.1073/pnas.2204336119.
- Comparative analyses of eighteen rapid antigen tests and RT-PCR for COVID-19 quarantine and surveillance-based isolationWells CR, Pandey A, Moghadas SM, Singer BH, Krieger G, Heron RJL, Turner DE, Abshire JP, Phillips KM, Michael Donoghue A, Galvani AP, Townsend JP. Comparative analyses of eighteen rapid antigen tests and RT-PCR for COVID-19 quarantine and surveillance-based isolation. Communications Medicine 2022, 2: 84. PMID: 35822105, PMCID: PMC9271059, DOI: 10.1038/s43856-022-00147-y.
- APOBEC mutagenesis and selection for NFE2L2 contribute to the origin of lung squamous-cell carcinomaCannataro VL, Kudalkar S, Dasari K, Gaffney SG, Lazowski HM, Jackson LK, Yildiz I, Das RK, Rothberg B, Anderson KS, Townsend JP. APOBEC mutagenesis and selection for NFE2L2 contribute to the origin of lung squamous-cell carcinoma. Lung Cancer 2022, 171: 34-41. PMID: 35872531, PMCID: PMC10126952, DOI: 10.1016/j.lungcan.2022.07.004.
- Attribution of Cancer Origins to Endogenous, Exogenous, and Preventable Mutational ProcessesCannataro VL, Mandell JD, Townsend JP. Attribution of Cancer Origins to Endogenous, Exogenous, and Preventable Mutational Processes. Molecular Biology And Evolution 2022, 39: msac084. PMID: 35580068, PMCID: PMC9113445, DOI: 10.1093/molbev/msac084.
- Quarantine and testing strategies to ameliorate transmission due to travel during the COVID-19 pandemic: a modelling studyWells CR, Pandey A, Fitzpatrick MC, Crystal WS, Singer BH, Moghadas SM, Galvani AP, Townsend JP. Quarantine and testing strategies to ameliorate transmission due to travel during the COVID-19 pandemic: a modelling study. The Lancet Regional Health - Europe 2022, 14: 100304. PMID: 35036981, PMCID: PMC8743228, DOI: 10.1016/j.lanepe.2021.100304.
- 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 SensitivityTownsend JP, Wells CR. 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. Journal Of Molecular Diagnostics 2021, 24: 101-103. PMID: 34974875, PMCID: PMC8717055, DOI: 10.1016/j.jmoldx.2021.10.002.
- Quarantine and testing strategies to ameliorate transmission due to travel during the COVID-19 pandemic: a modelling study.Wells CR, Pandey A, Fitzpatrick MC, Crystal WS, Singer BH, Moghadas SM, Galvani AP, Townsend JP. Quarantine and testing strategies to ameliorate transmission due to travel during the COVID-19 pandemic: a modelling study. MedRxiv : The Preprint Server For Health Sciences 2021 PMID: 34729563, PMCID: PMC8562544, DOI: 10.1101/2021.04.25.21256082.
- Premetastatic shifts of endogenous and exogenous mutational processes support consolidative therapy in EGFR-driven lung adenocarcinomaFisk JN, Mahal AR, Dornburg A, Gaffney SG, Aneja S, Contessa JN, Rimm D, Yu JB, Townsend JP. Premetastatic shifts of endogenous and exogenous mutational processes support consolidative therapy in EGFR-driven lung adenocarcinoma. Cancer Letters 2021, 526: 346-351. PMID: 34780851, PMCID: PMC8702484, DOI: 10.1016/j.canlet.2021.11.011.
- 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 burdenTan C, Mandell JD, Dasari K, Cannataro VL, Alfaro-Murillo JA, Townsend JP. 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 2021, 166: 265-269. PMID: 34736794, DOI: 10.1016/j.lungcan.2021.10.008.
- The durability of immunity against reinfection by SARS-CoV-2: a comparative evolutionary studyTownsend JP, Hassler HB, Wang Z, Miura S, Singh J, Kumar S, Ruddle NH, Galvani AP, Dornburg A. The durability of immunity against reinfection by SARS-CoV-2: a comparative evolutionary study. The Lancet Microbe 2021, 2: e666-e675. PMID: 34632431, PMCID: PMC8486316, DOI: 10.1016/s2666-5247(21)00219-6.
- Environmental and sex-specific molecular signatures of glioma causationClaus EB, Cannataro VL, Gaffney SG, Townsend JP. Environmental and sex-specific molecular signatures of glioma causation. Neuro-Oncology 2021, 24: noab103-. PMID: 33942853, PMCID: PMC8730771, DOI: 10.1093/neuonc/noab103.
- Optimal COVID-19 quarantine and testing strategiesWells CR, Townsend JP, Pandey A, Moghadas SM, Krieger G, Singer B, McDonald RH, Fitzpatrick MC, Galvani AP. Optimal COVID-19 quarantine and testing strategies. Nature Communications 2021, 12: 356. PMID: 33414470, PMCID: PMC7788536, DOI: 10.1038/s41467-020-20742-8.
- GEM-NET: Lessons in Multi-Institution Teamwork Using Collaboration SoftwareGaffney SG, Ad O, Smaga S, Schepartz A, Townsend JP. GEM-NET: Lessons in Multi-Institution Teamwork Using Collaboration Software. ACS Central Science 2019, 5: 1159-1169. PMID: 31404233, PMCID: PMC6661976, DOI: 10.1021/acscentsci.9b00111.
- The landscape of novel and complementary targets for immunotherapy: an analysis of gene expression in the tumor microenvironmentGaffney SG, Perry EB, Chen PM, Greenstein A, Kaech SM, Townsend JP. The landscape of novel and complementary targets for immunotherapy: an analysis of gene expression in the tumor microenvironment. Oncotarget 2019, 10: 4532-4545. PMID: 31360302, PMCID: PMC6642048, DOI: 10.18632/oncotarget.27027.
- Molecular biology and evolution of cancer: from discovery to actionSomarelli JA, Gardner H, Cannataro VL, Gunady EF, Boddy AM, Johnson NA, Fisk JN, Gaffney SG, Chuang JH, Li S, Ciccarelli FD, Panchenko AR, Megquier K, Kumar S, Dornburg A, DeGregori J, Townsend JP. Molecular biology and evolution of cancer: from discovery to action. Molecular Biology And Evolution 2019, 37: 320-326. PMID: 31642480, PMCID: PMC6993850, DOI: 10.1093/molbev/msz242.
- Jot: guiding journal selection with suitability metricsGaffney S, Townsend J. Jot: guiding journal selection with suitability metrics. Journal Of The Medical Library Association 2022, 110: 376-380. PMID: 36589304, PMCID: PMC9782573, DOI: 10.5195/jmla.2022.1499.
- Estimation of neutral mutation rates and quantification of somatic variant selection using canceffectsizeRMandell J, Cannataro V, Townsend J. Estimation of neutral mutation rates and quantification of somatic variant selection using canceffectsizeR. Cancer Research 2022, 83: 500-505. PMID: 36469362, PMCID: PMC9929515, DOI: 10.1158/0008-5472.can-22-1508.
- Infection by SARS‐CoV‐2 with alternate frequencies of mRNA vaccine boostingTownsend J, Hassler H, Dornburg A. Infection by SARS‐CoV‐2 with alternate frequencies of mRNA vaccine boosting. Journal Of Medical Virology 2023, 95: e28461. PMID: 36602045, DOI: 10.1002/jmv.28461.
- The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomicsWang Z, Kim W, Wang Y, Yakubovich E, Dong C, Trail F, Townsend J, Yarden O. The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomics. Frontiers In Fungal Biology 2023, 4: 1214537. DOI: 10.3389/ffunb.2023.1214537.
- Abstract 126: Extreme selection constrains ability of EGFR-driven lung adenocarcinoma to diversify in response to erlotinib therapyFisk J, Gaffney S, Politi K, Gettinger S, de Miguel F, Townsend J. Abstract 126: Extreme selection constrains ability of EGFR-driven lung adenocarcinoma to diversify in response to erlotinib therapy. Cancer Research 2023, 83: 126-126. DOI: 10.1158/1538-7445.am2023-126.
- Comparative Transcriptomics of Fusarium graminearum and Magnaporthe oryzae Spore Germination Leading up To InfectionMiguel-Rojas C, Cavinder B, Townsend J, Trail F. Comparative Transcriptomics of Fusarium graminearum and Magnaporthe oryzae Spore Germination Leading up To Infection. MBio 2023, 14: e02442-22. PMID: 36598191, PMCID: PMC9973345, DOI: 10.1128/mbio.02442-22.
- Chapter 5 Measurement and meaning in gene expression evolutionDiaz R, Wang Z, Townsend J. Chapter 5 Measurement and meaning in gene expression evolution. 2023, 111-129. DOI: 10.1016/b978-0-323-91810-7.00008-x.
- Not only mutations but also tumorigenesis can be substantially attributed to DNA damage from reactive oxygen species in RUNX1::RUNX1T1-fusion-positive acute myeloid leukemiaMandell J, Fisk J, Cyrenne E, Xu M, Cannataro V, Townsend J. 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 2022, 36: 2931-2933. PMID: 36369483, PMCID: PMC9712081, DOI: 10.1038/s41375-022-01752-5.
- Placing human gene families into their evolutionary contextDornburg A, Mallik R, Wang Z, Bernal M, Thompson B, Bruford E, Nebert D, Vasiliou V, Yohe L, Yoder J, Townsend J. Placing human gene families into their evolutionary context. Human Genomics 2022, 16: 56. PMID: 36369063, PMCID: PMC9652883, DOI: 10.1186/s40246-022-00429-5.
- In Response to “De Novo KRAS G12C-Mutant SCLC: A Case Report”Moore M, Zhuo Y, Mandell J, Gaffney S, Townsend J. In Response to “De Novo KRAS G12C-Mutant SCLC: A Case Report”. JTO Clinical And Research Reports 2022, 3: 100418. PMID: 36590382, PMCID: PMC9797388, DOI: 10.1016/j.jtocrr.2022.100418.
- Clone Phylogenetics Reveals Metastatic Tumor Migrations, Maps, and ModelsChroni A, Miura S, Hamilton L, Vu T, Gaffney SG, Aly V, Karim S, Sanderford M, Townsend JP, Kumar S. Clone Phylogenetics Reveals Metastatic Tumor Migrations, Maps, and Models. Cancers 2022, 14: 4326. PMID: 36077861, PMCID: PMC9454754, DOI: 10.3390/cancers14174326.
- Differential Expression of Cell Wall Remodeling Genes Is Part of the Dynamic Phase-Specific Transcriptional Program of Conidial Germination of Trichoderma asperelloidesGortikov M, Yakubovich E, Wang Z, López-Giráldez F, Tu Y, Townsend JP, Yarden O. Differential Expression of Cell Wall Remodeling Genes Is Part of the Dynamic Phase-Specific Transcriptional Program of Conidial Germination of Trichoderma asperelloides. Journal Of Fungi 2022, 8: 854. PMID: 36012842, PMCID: PMC9410309, DOI: 10.3390/jof8080854.
- Comparative analyses of eighteen rapid antigen tests and RT-PCR for COVID-19 quarantine and surveillance-based isolation.Wells C, Pandey A, Moghadas S, Singer B, Krieger G, Heron R, Turner D, Abshire J, Phillips K, Michael Donoghue A, Galvani A, Townsend J. Comparative analyses of eighteen rapid antigen tests and RT-PCR for COVID-19 quarantine and surveillance-based isolation. Communications Medicine 2022, 2: 84. PMID: 36380232, DOI: 10.1038/s43856-022-00147-y.
- A phylogenetic approach to study the evolution of somatic mutational processes in cancerMiura S, Vu T, Choi J, Townsend JP, Karim S, Kumar S. A phylogenetic approach to study the evolution of somatic mutational processes in cancer. Communications Biology 2022, 5: 617. PMID: 35732905, PMCID: PMC9217972, DOI: 10.1038/s42003-022-03560-0.
- Secondary Metabolism Gene Clusters Exhibit Increasingly Dynamic and Differential Expression during Asexual Growth, Conidiation, and Sexual Development in Neurospora crassaWang Z, Lopez-Giraldez F, Slot J, Yarden O, Trail F, Townsend JP. Secondary Metabolism Gene Clusters Exhibit Increasingly Dynamic and Differential Expression during Asexual Growth, Conidiation, and Sexual Development in Neurospora crassa. MSystems 2022, 7: e00232-22. PMID: 35638725, PMCID: PMC9239088, DOI: 10.1128/msystems.00232-22.
- Transcriptional Divergence Underpinning Sexual Development in the Fungal Class SordariomycetesKim W, Wang Z, Kim H, Pham K, Tu Y, Townsend JP, Trail F. Transcriptional Divergence Underpinning Sexual Development in the Fungal Class Sordariomycetes. MBio 2022, 13: e01100-22. PMID: 35638737, PMCID: PMC9239162, DOI: 10.1128/mbio.01100-22.
- Cancer Relevance of Human Genes.Qing T, Mohsen H, Cannataro VL, Marczyk M, Rozenblit M, Foldi J, Murray M, Townsend J, Kluger Y, Gerstein M, Pusztai L. Cancer Relevance of Human Genes. Journal Of The National Cancer Institute 2022, 114: 988-995. PMID: 35417011, PMCID: PMC9275765, DOI: 10.1093/jnci/djac068.
- Sequencing and Analysis of the Entire Genome of the Mycoparasitic Bioeffector Fungus Trichoderma asperelloides Strain T 203 (Hypocreales)Gortikov M, Wang Z, Steindorff AS, Grigoriev IV, Druzhinina IS, Townsend JP, Yarden O. Sequencing and Analysis of the Entire Genome of the Mycoparasitic Bioeffector Fungus Trichoderma asperelloides Strain T 203 (Hypocreales). Microbiology Resource Announcements 2022, 11: e00995-21. PMID: 35175124, PMCID: PMC8852338, DOI: 10.1128/mra.00995-21.
- The somatic molecular evolution of cancer: Mutation, selection, and epistasisDasari K, Somarelli JA, Kumar S, Townsend JP. The somatic molecular evolution of cancer: Mutation, selection, and epistasis. Progress In Biophysics And Molecular Biology 2021, 165: 56-65. PMID: 34364910, PMCID: PMC8819680, DOI: 10.1016/j.pbiomolbio.2021.08.003.
- Chemsearch: collaborative compound libraries with structure-aware browsingGaffney S, Smaga S, Schepartz A, Townsend J. Chemsearch: collaborative compound libraries with structure-aware browsing. Bioinformatics Advances 2021, 1: vbab008. PMID: 36700113, PMCID: PMC9710581, DOI: 10.1093/bioadv/vbab008.
- Mechanistic basis of post-treatment control of SIV after anti-α4β7 antibody therapyWells CR, Cao Y, Durham DP, Byrareddy SN, Ansari AA, Ruddle NH, Townsend JP, Galvani AP, Perelson AS. Mechanistic basis of post-treatment control of SIV after anti-α4β7 antibody therapy. PLOS Computational Biology 2021, 17: e1009031. PMID: 34106916, PMCID: PMC8189501, DOI: 10.1371/journal.pcbi.1009031.
- Chemsearch: collaborative compound libraries with structure-aware browsingGaffney S, Smaga S, Schepartz A, Townsend J. Chemsearch: collaborative compound libraries with structure-aware browsing. Bioinformatics Advances 2021, 1: vbab008. DOI: 10.1093/bioadv/vbab008.
- The GUL-1 Protein Binds Multiple RNAs Involved in Cell Wall Remodeling and Affects the MAK-1 Pathway in Neurospora crassaHerold I, Zolti A, Garduño-Rosales M, Wang Z, López-Giráldez F, Mouriño-Pérez R, Townsend J, Ulitsky I, Yarden O. The GUL-1 Protein Binds Multiple RNAs Involved in Cell Wall Remodeling and Affects the MAK-1 Pathway in Neurospora crassa. Frontiers In Fungal Biology 2021, 2: 672696. DOI: 10.3389/ffunb.2021.672696.
- Identifying modules of cooperating cancer driversKlein MI, Cannataro VL, Townsend JP, Newman S, Stern DF, Zhao H. Identifying modules of cooperating cancer drivers. Molecular Systems Biology 2021, 17: e9810. PMID: 33769711, PMCID: PMC7995435, DOI: 10.15252/msb.20209810.
- 85. The Impact of Carbapenem-Sparing Interventions on the Evolution of Resistance in Pseudomonas aeruginosa in the USATownsend J, Pandey A, Tang A, Chen Y, Foster E, Nathwani D, Merchant S, Sarpong E, Fitzpatrick M, Galvani A. 85. The Impact of Carbapenem-Sparing Interventions on the Evolution of Resistance in Pseudomonas aeruginosa in the USA. Open Forum Infectious Diseases 2020, 7: s59-s60. PMCID: PMC7777285, DOI: 10.1093/ofid/ofaa439.130.
- Comparative genomics within and across Bilaterians illuminates the evolutionary history of ALK and LTK proto-oncogene origination and diversificationDornburg A, Wang Z, Wang J, Mo ES, Lopez-Giraldez F, Townsend JP. Comparative genomics within and across Bilaterians illuminates the evolutionary history of ALK and LTK proto-oncogene origination and diversification. Genome Biology And Evolution 2020, 13: evaa228-. PMID: 33196781, PMCID: PMC7851593, DOI: 10.1093/gbe/evaa228.
- Getting quantitative on the effects of somatic mutation on cancerTownsend JP. Getting quantitative on the effects of somatic mutation on cancer. Oncoscience 2020, 7: 83-84. PMID: 33457449, PMCID: PMC7781488, DOI: 10.18632/oncoscience.521.
- Dogs and pigs are transport hosts of Necator americanus: Molecular evidence for a zoonotic mechanism of human hookworm transmission in GhanaBoyko RH, Harrison L, Humphries D, Galvani AP, Townsend JP, Otchere J, Wilson MD, Cappello M. 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 2020, 67: 474-483. PMID: 32529782, DOI: 10.1111/zph.12708.
- Non-Coding Mutations in Urothelial Bladder Cancer: Biological and Clinical Relevance and Potential Utility as BiomarkersYang A, Cross CN, Townsend JP. Non-Coding Mutations in Urothelial Bladder Cancer: Biological and Clinical Relevance and Potential Utility as Biomarkers. Bladder Cancer 2020, 6: 211-213. PMID: 32793790, PMCID: PMC7390591, DOI: 10.3233/blc-200278.
- Germline variant burden in cancer genes correlates with age at diagnosis and somatic mutation burdenQing T, Mohsen H, Marczyk M, Ye Y, O’Meara T, Zhao H, Townsend JP, Gerstein M, Hatzis C, Kluger Y, Pusztai L. Germline variant burden in cancer genes correlates with age at diagnosis and somatic mutation burden. Nature Communications 2020, 11: 2438. PMID: 32415133, PMCID: PMC7228928, DOI: 10.1038/s41467-020-16293-7.
- Unmatched level of molecular convergence among deeply divergent complex multicellular fungiMerényi Z, Prasanna AN, Wang Z, Kovács K, Hegedüs B, Bálint B, Papp B, Townsend JP, Nagy LG. Unmatched level of molecular convergence among deeply divergent complex multicellular fungi. Molecular Biology And Evolution 2020, 37: 2228-2240. PMID: 32191325, PMCID: PMC7403615, DOI: 10.1093/molbev/msaa077.
- Transfer RNA methyltransferase gene NSUN2 mRNA expression modifies the effect of T cell activation score on patient survival in head and neck squamous carcinomaLu L, Gaffney SG, Cannataro VL, Townsend J. Transfer RNA methyltransferase gene NSUN2 mRNA expression modifies the effect of T cell activation score on patient survival in head and neck squamous carcinoma. Oral Oncology 2019, 101: 104554. PMID: 31887619, PMCID: PMC7273869, DOI: 10.1016/j.oraloncology.2019.104554.
- Integrative Activity of Mating Loci, Environmentally Responsive Genes, and Secondary Metabolism Pathways during Sexual Development of Chaetomium globosumWang Z, López-Giráldez F, Wang J, Trail F, Townsend JP. Integrative Activity of Mating Loci, Environmentally Responsive Genes, and Secondary Metabolism Pathways during Sexual Development of Chaetomium globosum. MBio 2019, 10: e02119-19. PMID: 31822585, PMCID: PMC6904875, DOI: 10.1128/mbio.02119-19.
- EPID-26. SEX-SPECIFIC GLIOMA MOLECULAR SIGNATURESClaus E, Cannataro V, Gaffney S, Townsend J. EPID-26. SEX-SPECIFIC GLIOMA MOLECULAR SIGNATURES. Neuro-Oncology 2019, 21: vi80-vi80. PMCID: PMC6846890, DOI: 10.1093/neuonc/noz175.326.
- Modeling Approaches Toward Understanding Infectious Disease TransmissionSkrip L, Townsend J. Modeling Approaches Toward Understanding Infectious Disease Transmission. 2019, 227-243. PMCID: PMC7121152, DOI: 10.1007/978-3-030-25553-4_14.
- Modelling microbial infection to address global health challengesFitzpatrick MC, Bauch CT, Townsend JP, Galvani AP. Modelling microbial infection to address global health challenges. Nature Microbiology 2019, 4: 1612-1619. PMID: 31541212, PMCID: PMC6800015, DOI: 10.1038/s41564-019-0565-8.
- 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;76:9–13Yang A, Cannataro VL, Townsend JP. 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 2019, 77: e24-e25. PMID: 31474441, PMCID: PMC7017921, DOI: 10.1016/j.eururo.2019.08.018.
- A multigene phylogeny toward a new phylogenetic classification of LeotiomycetesJohnston PR, Quijada L, Smith CA, Baral HO, Hosoya T, Baschien C, Pärtel K, Zhuang WY, Haelewaters D, Park D, Carl S, López-Giráldez F, Wang Z, Townsend JP. A multigene phylogeny toward a new phylogenetic classification of Leotiomycetes. IMA Fungus 2019, 10: 1. PMID: 32647610, PMCID: PMC7325659, DOI: 10.1186/s43008-019-0002-x.
- Comparative Genomics and Transcriptomics During Sexual Development Gives Insight Into the Life History of the Cosmopolitan Fungus Fusarium neocosmosporiellumKim W, Cavinder B, Proctor RH, O’Donnell K, Townsend JP, Trail F. Comparative Genomics and Transcriptomics During Sexual Development Gives Insight Into the Life History of the Cosmopolitan Fungus Fusarium neocosmosporiellum. Frontiers In Microbiology 2019, 10: 1247. PMID: 31231336, PMCID: PMC6568001, DOI: 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 NeckLee JW, Parameswaran J, Sandoval-Schaefer T, Eoh KJ, Yang DH, Zhu F, Mehra R, Sharma R, Gaffney SG, Perry EB, Townsend JP, Serebriiskii IG, Golemis EA, Issaeva N, Yarbrough WG, Koo JS, Burtness B. Combined Aurora Kinase A (AURKA) and WEE1 Inhibition Demonstrates Synergistic Antitumor Effect in Squamous Cell Carcinoma of the Head and Neck. Clinical Cancer Research 2019, 25: 3430-3442. PMID: 30755439, PMCID: PMC6548643, DOI: 10.1158/1078-0432.ccr-18-0440.
- Implementation of Syringe Services Programs to Prevent Rapid Human Immunodeficiency Virus Transmission in Rural Counties in the United States: A Modeling StudyGoedel WC, King MRF, Lurie MN, Galea S, Townsend JP, Galvani AP, Friedman SR, Marshall BDL. 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 2019, 70: 1096-1102. PMID: 31143944, PMCID: PMC7319062, DOI: 10.1093/cid/ciz321.
- Metabolism and Development during Conidial Germination in Response to a Carbon-Nitrogen-Rich Synthetic or a Natural Source of Nutrition in Neurospora crassaWang Z, Miguel-Rojas C, Lopez-Giraldez F, Yarden O, Trail F, Townsend JP. Metabolism and Development during Conidial Germination in Response to a Carbon-Nitrogen-Rich Synthetic or a Natural Source of Nutrition in Neurospora crassa. MBio 2019, 10: e00192-19. PMID: 30914504, PMCID: PMC6437048, DOI: 10.1128/mbio.00192-19.
- Wagging the long tail of drivers of prostate cancerCannataro VL, Townsend JP. Wagging the long tail of drivers of prostate cancer. PLOS Genetics 2019, 15: e1007820. PMID: 30653503, PMCID: PMC6336235, DOI: 10.1371/journal.pgen.1007820.
- APOBEC-induced mutations and their cancer effect size in head and neck squamous cell carcinomaCannataro VL, Gaffney SG, Sasaki T, Issaeva N, Grewal NKS, Grandis JR, Yarbrough WG, Burtness B, Anderson KS, Townsend JP. APOBEC-induced mutations and their cancer effect size in head and neck squamous cell carcinoma. Oncogene 2019, 38: 3475-3487. PMID: 30647454, PMCID: PMC6499643, DOI: 10.1038/s41388-018-0657-6.
- Effect Sizes of Somatic Mutations in CancerCannataro VL, Gaffney SG, Townsend JP. Effect Sizes of Somatic Mutations in Cancer. Journal Of The National Cancer Institute 2018, 110: 1171-1177. PMID: 30365005, PMCID: PMC6235682, DOI: 10.1093/jnci/djy168.
- Using evolutionary genomics, transcriptomics, and systems biology to reveal gene networks underlying fungal developmentWang Z, Gudibanda A, Ugwuowo U, Trail F, Townsend J. Using evolutionary genomics, transcriptomics, and systems biology to reveal gene networks underlying fungal development. Fungal Biology Reviews 2018, 32: 249-264. DOI: 10.1016/j.fbr.2018.02.001.
- Developmental Dynamics of Long Noncoding RNA Expression during Sexual Fruiting Body Formation in Fusarium graminearumKim W, Miguel-Rojas C, Wang J, Townsend JP, Trail F. Developmental Dynamics of Long Noncoding RNA Expression during Sexual Fruiting Body Formation in Fusarium graminearum. MBio 2018, 9: e01292-18. PMID: 30108170, PMCID: PMC6094484, DOI: 10.1128/mbio.01292-18.
- Optimal Rates for Phylogenetic Inference and Experimental Design in the Era of Genome-Scale Data SetsDornburg A, Su Z, Townsend JP. Optimal Rates for Phylogenetic Inference and Experimental Design in the Era of Genome-Scale Data Sets. Systematic Biology 2018, 68: 145-156. PMID: 29939341, DOI: 10.1093/sysbio/syy047.
- Genomic Comparison Among Global Isolates of L. interrogans Serovars Copenhageni and Icterohaemorrhagiae Identified Natural Genetic Variation Caused by an IndelSantos LA, Adhikarla H, Yan X, Wang Z, Fouts DE, Vinetz JM, Alcantara LCJ, Hartskeerl RA, Goris MGA, Picardeau M, Reis MG, Townsend JP, Zhao H, Ko AI, Wunder EA. Genomic Comparison Among Global Isolates of L. interrogans Serovars Copenhageni and Icterohaemorrhagiae Identified Natural Genetic Variation Caused by an Indel. Frontiers In Cellular And Infection Microbiology 2018, 8: 193. PMID: 29971217, PMCID: PMC6018220, DOI: 10.3389/fcimb.2018.00193.
- Potential effectiveness of long-acting injectable pre-exposure prophylaxis for HIV prevention in men who have sex with men: a modelling studyMarshall BDL, Goedel WC, King MRF, Singleton A, Durham DP, Chan PA, Townsend JP, Galvani AP. 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 2018, 5: e498-e505. PMID: 29908917, PMCID: PMC6138558, DOI: 10.1016/s2352-3018(18)30097-3.
- Analysis of mutation, selection, and epistasis: an informed approach to cancer clinical trialsWilkins JF, Cannataro VL, Shuch B, Townsend JP. Analysis of mutation, selection, and epistasis: an informed approach to cancer clinical trials. Oncotarget 2018, 9: 22243-22253. PMID: 29854275, PMCID: PMC5976461, DOI: 10.18632/oncotarget.25155.
- Neutral Theory and the Somatic Evolution of CancerCannataro VL, Townsend JP. Neutral Theory and the Somatic Evolution of Cancer. Molecular Biology And Evolution 2018, 35: 1308-1315. PMID: 29684198, PMCID: PMC5967571, DOI: 10.1093/molbev/msy079.
- CDKN2A Copy Number Loss Is an Independent Prognostic Factor in HPV-Negative Head and Neck Squamous Cell CarcinomaChen WS, Bindra RS, Mo A, Hayman T, Husain Z, Contessa JN, Gaffney SG, Townsend JP, Yu JB. CDKN2A Copy Number Loss Is an Independent Prognostic Factor in HPV-Negative Head and Neck Squamous Cell Carcinoma. Frontiers In Oncology 2018, 8: 95. PMID: 29670856, PMCID: PMC5893829, DOI: 10.3389/fonc.2018.00095.
- Whole-exome sequencing and immune profiling of early-stage lung adenocarcinoma with fully annotated clinical follow-upKadara H, Choi M, Zhang J, Parra ER, Rodriguez-Canales J, Gaffney SG, Zhao Z, Behrens C, Fujimoto J, Chow C, Yoo Y, Kalhor N, Moran C, Rimm D, Swisher S, Gibbons DL, Heymach J, Kaftan E, Townsend JP, Lynch TJ, Schlessinger J, Lee J, Lifton RP, Wistuba II, Herbst RS. Whole-exome sequencing and immune profiling of early-stage lung adenocarcinoma with fully annotated clinical follow-up. Annals Of Oncology 2018, 29: 1072. PMID: 29688333, PMCID: PMC6887935, DOI: 10.1093/annonc/mdx062.
- The Cancer TreeTownsend JP. The Cancer Tree. Scientific American 2018, 318: 34-41. PMID: 29557973, DOI: 10.1038/scientificamerican0418-34.
- Primary hepatic neuroendocrine carcinoma: report of two cases and literature reviewZhao ZM, Wang J, Ugwuowo UC, Wang L, Townsend JP. Primary hepatic neuroendocrine carcinoma: report of two cases and literature review. BMC Clinical Pathology 2018, 18: 3. PMID: 29507528, PMCID: PMC5831736, DOI: 10.1186/s12907-018-0070-7.
- Lvr, a Signaling System That Controls Global Gene Regulation and Virulence in Pathogenic LeptospiraAdhikarla H, Wunder EA, Mechaly AE, Mehta S, Wang Z, Santos L, Bisht V, Diggle P, Murray G, Adler B, Lopez F, Townsend JP, Groisman E, Picardeau M, Buschiazzo A, Ko AI. Lvr, a Signaling System That Controls Global Gene Regulation and Virulence in Pathogenic Leptospira. Frontiers In Cellular And Infection Microbiology 2018, 8: 45. PMID: 29600195, PMCID: PMC5863495, DOI: 10.3389/fcimb.2018.00045.
- Heterogeneity and mutation in KRAS and associated oncogenes: evaluating the potential for the evolution of resistance to targeting of KRAS G12CCannataro VL, Gaffney SG, Stender C, Zhao ZM, Philips M, Greenstein AE, Townsend JP. Heterogeneity and mutation in KRAS and associated oncogenes: evaluating the potential for the evolution of resistance to targeting of KRAS G12C. Oncogene 2018, 37: 2444-2455. PMID: 29453361, DOI: 10.1038/s41388-017-0105-z.
- Somatic evolutionary timings of driver mutationsGomez K, Miura S, Huuki LA, Spell BS, Townsend JP, Kumar S. Somatic evolutionary timings of driver mutations. BMC Cancer 2018, 18: 85. PMID: 29347918, PMCID: PMC5774140, DOI: 10.1186/s12885-017-3977-y.
- Light sensing by opsins and fungal ecology: NOP‐1 modulates entry into sexual reproduction in response to environmental cuesWang Z, Wang J, Li N, Li J, Trail F, Dunlap JC, Townsend JP. Light sensing by opsins and fungal ecology: NOP‐1 modulates entry into sexual reproduction in response to environmental cues. Molecular Ecology 2017, 27: 216-232. PMID: 29134709, PMCID: PMC5797489, DOI: 10.1111/mec.14425.
- Chapter One Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big DataDornburg A, Townsend JP, Wang Z. Chapter One Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big Data. 2017, 100: 1-47. PMID: 29153398, DOI: 10.1016/bs.adgen.2017.09.007.
- The Likelihood of Heterogeneity or Additional Mutation to Compromise Targeting of KRAS G12CCannataro V, Gaffney S, Stender C, Zhao Z, Philips M, Greenstein A, Townsend J. The Likelihood of Heterogeneity or Additional Mutation to Compromise Targeting of KRAS G12C. Journal Of Thoracic Oncology 2017, 12: s1538. DOI: 10.1016/j.jtho.2017.06.029.
- Effect Sizes of Somatic Mutations in Lung Cancer: Identifying New Targets and Prioritizing Old OnesCannataro V, Brumberg K, Gaffney S, Townsend J. Effect Sizes of Somatic Mutations in Lung Cancer: Identifying New Targets and Prioritizing Old Ones. Journal Of Thoracic Oncology 2017, 12: s1542-s1543. DOI: 10.1016/j.jtho.2017.06.047.
- Distributions of Mutational Effects and the Estimation of Directional Selection in Divergent Lineages of Arabidopsis thalianaPark B, Rutter MT, Fenster CB, Symonds VV, Ungerer MC, Townsend JP. Distributions of Mutational Effects and the Estimation of Directional Selection in Divergent Lineages of Arabidopsis thaliana. Genetics 2017, 206: 2105-2117. PMID: 28550014, PMCID: PMC5560809, DOI: 10.1534/genetics.116.199190.
- Detection of Regional Variation in Selection Intensity within Protein-Coding Genes Using DNA Sequence Polymorphism and Divergence.Zhao ZM, Campbell MC, Li N, Lee DSW, Zhang Z, Townsend JP. Detection of Regional Variation in Selection Intensity within Protein-Coding Genes Using DNA Sequence Polymorphism and Divergence. Molecular Biology And Evolution 2017, 34: 3006-3022. PMID: 28962009, PMCID: PMC5850860, DOI: 10.1093/molbev/msx213.
- The ancestral levels of transcription and the evolution of sexual phenotypes in filamentous fungiTrail F, Wang Z, Stefanko K, Cubba C, Townsend JP. The ancestral levels of transcription and the evolution of sexual phenotypes in filamentous fungi. PLOS Genetics 2017, 13: e1006867. PMID: 28704372, PMCID: PMC5509106, DOI: 10.1371/journal.pgen.1006867.
- CDKN2A copy number loss in HPV- and HPV+ head and neck cancer to indicate poor prognosis: An integrated genomic and clinical TCGA analysis.Chen W, Bindra R, Mo A, Hayman T, Husain Z, Contessa J, Gaffney S, Townsend J, Yu J. CDKN2A copy number loss in HPV- and HPV+ head and neck cancer to indicate poor prognosis: An integrated genomic and clinical TCGA analysis. Journal Of Clinical Oncology 2017, 35: 6060-6060. DOI: 10.1200/jco.2017.35.15_suppl.6060.
- P12.06 Significantly Mutated Genes for Radiation-Associated MeningiomaClaus E, Greenhalgh S, Gaffney S, Bilguvar K, Calvocoressi L, Lu L, Al-Mefty O, Zhao Z, Townsend J. P12.06 Significantly Mutated Genes for Radiation-Associated Meningioma. Neuro-Oncology 2017, 19: iii96-iii96. PMCID: PMC5464023, DOI: 10.1093/neuonc/nox036.364.
- New insights on the sister lineage of percomorph fishes with an anchored hybrid enrichment datasetDornburg A, Townsend JP, Brooks W, Spriggs E, Eytan RI, Moore JA, Wainwright PC, Lemmon A, Lemmon EM, Near TJ. New insights on the sister lineage of percomorph fishes with an anchored hybrid enrichment dataset. Molecular Phylogenetics And Evolution 2017, 110: 27-38. PMID: 28254474, DOI: 10.1016/j.ympev.2017.02.017.
- Radiation-Specific Clinical Data Should Be Included in Existing Large-Scale Genomic DatasetsChen WS, Townsend JP, Yu JB. Radiation-Specific Clinical Data Should Be Included in Existing Large-Scale Genomic Datasets. International Journal Of Radiation Oncology • Biology • Physics 2017, 98: 8-10. PMID: 28587055, DOI: 10.1016/j.ijrobp.2017.01.023.
- Whole-exome sequencing and immune profiling of early-stage lung adenocarcinoma with fully annotated clinical follow-up.Kadara H, Choi M, Zhang J, Parra ER, Rodriguez-Canales J, Gaffney SG, Zhao Z, Behrens C, Fujimoto J, Chow C, Yoo Y, Kalhor N, Moran C, Rimm D, Swisher S, Gibbons DL, Heymach J, Kaftan E, Townsend JP, Lynch TJ, Schlessinger J, Lee J, Lifton RP, Wistuba II, Herbst RS. Whole-exome sequencing and immune profiling of early-stage lung adenocarcinoma with fully annotated clinical follow-up. Annals Of Oncology : Official Journal Of The European Society For Medical Oncology / ESMO 2017, 28: 75-82. PMID: 31792518, DOI: 10.1093/annonc/mdw436.
- MA16.02 Mutational Landscape of TKI Naïve and Resistant EGFR Mutant Lung AdenocarcinomasHastings K, Choi J, Wurtz A, Walther Z, Cai G, Oliva I, Zhao Z, Gaffney S, Iamarino A, Zhao S, Bi M, Goldberg S, Chiang A, Liu Z, Townsend J, Schlessinger J, Lifton R, Herbst R, Gettinger S, Politi K. MA16.02 Mutational Landscape of TKI Naïve and Resistant EGFR Mutant Lung Adenocarcinomas. Journal Of Thoracic Oncology 2017, 12: s435. DOI: 10.1016/j.jtho.2016.11.507.
- PrefaceTownsend JP, Wang Z. Preface. 2017, 100: xi-xii. PMID: 29153406, DOI: 10.1016/s0065-2660(17)30059-7.
- Whole-exome sequencing and immune profiling of early-stage lung adenocarcinoma with fully annotated clinical follow-upKadara H, Choi M, Zhang J, Parra ER, Rodriguez-Canales J, Gaffney SG, Zhao Z, Behrens C, Fujimoto J, Chow C, Yoo Y, Kalhor N, Moran C, Rimm D, Swisher S, Gibbons DL, Heymach J, Kaftan E, Townsend JP, Lynch TJ, Schlessinger J, Lee J, Lifton RP, Wistuba II, Herbst RS. Whole-exome sequencing and immune profiling of early-stage lung adenocarcinoma with fully annotated clinical follow-up. Annals Of Oncology 2017, 28: 75-82. PMID: 27687306, PMCID: PMC5982809, DOI: 10.1093/annonc/mdw436.
- Mutation profiles in early-stage lung squamous cell carcinoma with clinical follow-up and correlation with markers of immune functionChoi M, Kadara H, Zhang J, Parra ER, Rodriguez-Canales J, Gaffney SG, Zhao Z, Behrens C, Fujimoto J, Chow C, Kim K, Kalhor N, Moran C, Rimm D, Swisher S, Gibbons DL, Heymach J, Kaftan E, Townsend JP, Lynch TJ, Schlessinger J, Lee J, Lifton RP, Herbst RS, Wistuba II. Mutation profiles in early-stage lung squamous cell carcinoma with clinical follow-up and correlation with markers of immune function. Annals Of Oncology 2017, 28: 83-89. PMID: 28177435, PMCID: PMC6246501, DOI: 10.1093/annonc/mdw437.
- One Health approach to cost-effective rabies control in IndiaFitzpatrick MC, Shah HA, Pandey A, Bilinski AM, Kakkar M, Clark AD, Townsend JP, Abbas SS, Galvani AP. One Health approach to cost-effective rabies control in India. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: 14574-14581. PMID: 27994161, PMCID: PMC5187709, DOI: 10.1073/pnas.1604975113.
- PhyInformR: phylogenetic experimental design and phylogenomic data exploration in RDornburg A, Fisk JN, Tamagnan J, Townsend JP. PhyInformR: phylogenetic experimental design and phylogenomic data exploration in R. BMC Ecology And Evolution 2016, 16: 262. PMID: 27905871, PMCID: PMC5134231, DOI: 10.1186/s12862-016-0837-3.
- Vaccination strategies against respiratory syncytial virusYamin D, Jones FK, DeVincenzo JP, Gertler S, Kobiler O, Townsend JP, Galvani AP. Vaccination strategies against respiratory syncytial virus. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: 13239-13244. PMID: 27799521, PMCID: PMC5135296, DOI: 10.1073/pnas.1522597113.
- PhyloOncology: Understanding cancer through phylogenetic analysisSomarelli JA, Ware KE, Kostadinov R, Robinson JM, Amri H, Abu-Asab M, Fourie N, Diogo R, Swofford D, Townsend JP. PhyloOncology: Understanding cancer through phylogenetic analysis. Biochimica Et Biophysica Acta (BBA) - Reviews On Cancer 2016, 1867: 101-108. PMID: 27810337, PMCID: PMC9583457, DOI: 10.1016/j.bbcan.2016.10.006.
- Climatic and evolutionary drivers of phase shifts in the plague epidemics of colonial IndiaLewnard JA, Townsend JP. Climatic and evolutionary drivers of phase shifts in the plague epidemics of colonial India. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: 14601-14608. PMID: 27791071, PMCID: PMC5187705, DOI: 10.1073/pnas.1604985113.
- Mutation profiles in early-stage lung squamous cell carcinoma with clinical follow-up and correlation with markers of immune function.Choi M, Kadara H, Zhang J, Cuentas EP, Canales JR, Gaffney SG, Zhao Z, Behrens C, Fujimoto J, Chow C, Kim K, Kalhor N, Moran C, Rimm D, Swisher S, Gibbons DL, Heymach J, Kaftan E, Townsend JP, Lynch TJ, Schlessinger J, Lee JJ, Lifton RP, Herbst RS, Wistuba II. Mutation profiles in early-stage lung squamous cell carcinoma with clinical follow-up and correlation with markers of immune function. Annals Of Oncology : Official Journal Of The European Society For Medical Oncology / ESMO 2016 PMID: 27687303, DOI: 10.1093/annonc/mdw437.
- PathScore: a web tool for identifying altered pathways in cancer data.Gaffney SG, Townsend JP. PathScore: a web tool for identifying altered pathways in cancer data. Bioinformatics 2016, 32: 3688-3690. PMID: 27503224, DOI: 10.1093/bioinformatics/btw512.
- Abstract 142: Mutation and immune profiles in early-stage lung squamous cell carcinomaChoi M, Kadara H, Zhang J, Parra Cuentas E, Rodriguez Canales J, Gaffney S, Zhao Z, Behrens C, Fujimoto J, Chow C, Kalhor N, Moran C, Rimm D, Swisher S, Gibbons D, Heymach J, Kaftan E, Townsend J, Lynch T, Schlessinger J, Lee J, Lifton R, Herbst R, Wistuba I. Abstract 142: Mutation and immune profiles in early-stage lung squamous cell carcinoma. Cancer Research 2016, 76: 142-142. DOI: 10.1158/1538-7445.am2016-142.
- Abstract 89: Whole-exome sequencing and immune profiling of early-stage lung adenocarcinomaKadara H, Choi M, Zhang J, Parra Cuentas E, Rodriguez Canales J, Gaffney S, Zhao Z, Behrens C, Fujimoto J, Chow C, Kalhor N, Moran C, Rimm D, Swisher S, Gibbons D, Heymach J, Kaftan E, Townsend J, Lynch T, Schlessinger J, Lee J, Lifton R, Wistuba I, Herbst R. Abstract 89: Whole-exome sequencing and immune profiling of early-stage lung adenocarcinoma. Cancer Research 2016, 76: 89-89. DOI: 10.1158/1538-7445.am2016-89.
- A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencingPrum R, Berv J, Dornburg A, Field D, Townsend J, Lemmon E, Lemmon A. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature 2016, 534: s7-s8. DOI: 10.1038/nature19417.
- Cost-Effectiveness of Pertussis Vaccination During Pregnancy in the United States.Atkins KE, Fitzpatrick MC, Galvani AP, Townsend JP. Cost-Effectiveness of Pertussis Vaccination During Pregnancy in the United States. American Journal Of Epidemiology 2016, 183: 1159-70. PMID: 27188951, PMCID: PMC4908210, DOI: 10.1093/aje/kwv347.
- Cost-effectiveness of next-generation vaccines: The case of pertussisFitzpatrick MC, Wenzel NS, Scarpino SV, Althouse BM, Atkins KE, Galvani AP, Townsend JP. Cost-effectiveness of next-generation vaccines: The case of pertussis. Vaccine 2016, 34: 3405-3411. PMID: 27087151, DOI: 10.1016/j.vaccine.2016.04.010.
- Quantifying Transmission of Clostridium difficile within and outside Healthcare SettingsDurham DP, Olsen MA, Dubberke ER, Galvani AP, Townsend JP. Quantifying Transmission of Clostridium difficile within and outside Healthcare Settings. Emerging Infectious Diseases 2016, 22: 608-616. PMID: 26982504, PMCID: PMC4806959, DOI: 10.3201/eid2204.150455.
- Determinants of Human African Trypanosomiasis Elimination via ParatransgenesisGilbert JA, Medlock J, Townsend JP, Aksoy S, Mbah M, Galvani AP. Determinants of Human African Trypanosomiasis Elimination via Paratransgenesis. PLOS Neglected Tropical Diseases 2016, 10: e0004465. PMID: 26954675, PMCID: PMC4783105, DOI: 10.1371/journal.pntd.0004465.
- The Fast-Evolving phy-2 Gene Modulates Sexual Development in Response to Light in the Model Fungus Neurospora crassaWang Z, Li N, Li J, Dunlap JC, Trail F, Townsend JP. The Fast-Evolving phy-2 Gene Modulates Sexual Development in Response to Light in the Model Fungus Neurospora crassa. MBio 2016, 7: e02148-15. PMID: 26956589, PMCID: PMC4810495, DOI: 10.1128/mbio.02148-15.
- Retrospective Analysis of the 2014-2015 Ebola Epidemic in Liberia.Atkins KE, Pandey A, Wenzel NS, Skrip L, Yamin D, Nyenswah TG, Fallah M, Bawo L, Medlock J, Altice FL, Townsend J, Ndeffo-Mbah ML, Galvani AP. Retrospective Analysis of the 2014-2015 Ebola Epidemic in Liberia. American Journal Of Tropical Medicine And Hygiene 2016, 94: 833-9. PMID: 26928839, PMCID: PMC4824226, DOI: 10.4269/ajtmh.15-0328.
- Early and multiple origins of metastatic lineages within primary tumorsZhao ZM, Zhao B, Bai Y, Iamarino A, Gaffney SG, Schlessinger J, Lifton RP, Rimm DL, Townsend JP. Early and multiple origins of metastatic lineages within primary tumors. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: 2140-2145. PMID: 26858460, PMCID: PMC4776530, DOI: 10.1073/pnas.1525677113.
- Future Perspectives and Challenges of Fungal Systematics in the Age of Big DataWang Z, Nilsson R, James T, Dai Y, Townsend J. Future Perspectives and Challenges of Fungal Systematics in the Age of Big Data. 2016, 25-46. DOI: 10.1007/978-3-319-29137-6_3.
- Genomic and Gene-Expression Comparisons among Phage-Resistant Type-IV Pilus Mutants of Pseudomonas syringae pathovar phaseolicolaSistrom M, Park D, O’Brien H, Wang Z, Guttman DS, Townsend JP, Turner PE. Genomic and Gene-Expression Comparisons among Phage-Resistant Type-IV Pilus Mutants of Pseudomonas syringae pathovar phaseolicola. PLOS ONE 2015, 10: e0144514. PMID: 26670219, PMCID: PMC4687649, DOI: 10.1371/journal.pone.0144514.
- Quantitative analyses and modelling to support achievement of the 2020 goals for nine neglected tropical diseasesHollingsworth TD, Adams ER, Anderson RM, Atkins K, Bartsch S, Basáñez MG, Behrend M, Blok DJ, Chapman LA, Coffeng L, Courtenay O, Crump RE, de Vlas SJ, Dobson A, Dyson L, Farkas H, Galvani AP, Gambhir M, Gurarie D, Irvine MA, Jervis S, Keeling MJ, Kelly-Hope L, King C, Lee BY, Le Rutte EA, Lietman TM, Ndeffo-Mbah M, Medley GF, Michael E, Pandey A, Peterson JK, Pinsent A, Porco TC, Richardus JH, Reimer L, Rock KS, Singh BK, Stolk W, Swaminathan S, Torr SJ, Townsend J, Truscott J, Walker M, Zoueva A, NTD Modelling Consortium. Quantitative analyses and modelling to support achievement of the 2020 goals for nine neglected tropical diseases. Parasites & Vectors 2015, 8: 630. PMID: 26652272, PMCID: PMC4674954, DOI: 10.1186/s13071-015-1235-1.
- The Impact of Enhanced Screening and Treatment on Hepatitis C in the United StatesDurham DP, Skrip LA, Bruce RD, Vilarinho S, Elbasha EH, Galvani AP, Townsend JP. The Impact of Enhanced Screening and Treatment on Hepatitis C in the United States. Clinical Infectious Diseases 2015, 62: 298-304. PMID: 26628566, PMCID: PMC4706637, DOI: 10.1093/cid/civ894.
- Optimizing age of cytomegalovirus screening and vaccination to avert congenital disease in the USAlfaro-Murillo JA, Townsend JP, Galvani AP. Optimizing age of cytomegalovirus screening and vaccination to avert congenital disease in the US. Vaccine 2015, 34: 225-229. PMID: 26631416, DOI: 10.1016/j.vaccine.2015.11.039.
- Impact of bed capacity on spatiotemporal shifts in Ebola transmissionTownsend JP, Skrip LA, Galvani AP. Impact of bed capacity on spatiotemporal shifts in Ebola transmission. Proceedings Of The National Academy Of Sciences Of The United States Of America 2015, 112: 14125-14126. PMID: 26518509, PMCID: PMC4655579, DOI: 10.1073/pnas.1518484112.
- A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencingPrum RO, Berv JS, Dornburg A, Field DJ, Townsend JP, Lemmon EM, Lemmon AR. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature 2015, 526: 569-573. PMID: 26444237, DOI: 10.1038/nature15697.
- Inferring the Origin of Metastases from Cancer PhylogeniesHong WS, Shpak M, Townsend JP. Inferring the Origin of Metastases from Cancer Phylogenies. Cancer Research 2015, 75: 4021-4025. PMID: 26260528, PMCID: PMC4833389, DOI: 10.1158/0008-5472.can-15-1889.
- Mapping Disease Transmission Risk: Enriching Models Using Biogeography and Ecology - Volume 21, Number 8—August 2015 - Emerging Infectious Diseases journal - CDCTownsend J. Mapping Disease Transmission Risk: Enriching Models Using Biogeography and Ecology - Volume 21, Number 8—August 2015 - Emerging Infectious Diseases journal - CDC. Emerging Infectious Diseases 2015, 21: 1489-1489. PMCID: PMC4517721, DOI: 10.3201/eid2108.150665.
- Ecology of saddle fungiHwang J, Zhao Q, Yang ZL, Wang Z, Townsend JP. Ecology of saddle fungi. Environmental Microbiology Reports 2015, 7: 658-667. PMID: 26033481, DOI: 10.1111/1758-2229.12303.
- Correction: Harnessing Case Isolation and Ring Vaccination to Control EbolaWells C, Yamin D, Ndeffo-Mbah ML, Wenzel N, Gaffney SG, Townsend JP, Meyers LA, Fallah M, Nyenswah TG, Altice FL, Atkins KE, Galvani AP. Correction: Harnessing Case Isolation and Ring Vaccination to Control Ebola. PLOS Neglected Tropical Diseases 2015, 9: e0003888. PMID: 26107520, PMCID: PMC4481340, DOI: 10.1371/journal.pntd.0003888.
- Harnessing Case Isolation and Ring Vaccination to Control EbolaWells C, Yamin D, Ndeffo-Mbah ML, Wenzel N, Gaffney SG, Townsend JP, Meyers LA, Fallah M, Nyenswah TG, Altice FL, Atkins KE, Galvani AP. Harnessing Case Isolation and Ring Vaccination to Control Ebola. PLOS Neglected Tropical Diseases 2015, 9: e0003794. PMID: 26024528, PMCID: PMC4449200, DOI: 10.1371/journal.pntd.0003794.
- Utility of characters evolving at diverse rates of evolution to resolve quartet trees with unequal branch lengths: analytical predictions of long-branch effectsSu Z, Townsend JP. Utility of characters evolving at diverse rates of evolution to resolve quartet trees with unequal branch lengths: analytical predictions of long-branch effects. BMC Ecology And Evolution 2015, 15: 86. PMID: 25968460, PMCID: PMC4429678, DOI: 10.1186/s12862-015-0364-7.
- Integrating Community-Based Interventions to Reverse the Convergent TB/HIV Epidemics in Rural South AfricaGilbert JA, Long EF, Brooks RP, Friedland GH, Moll AP, Townsend JP, Galvani AP, Shenoi SV. Integrating Community-Based Interventions to Reverse the Convergent TB/HIV Epidemics in Rural South Africa. PLOS ONE 2015, 10: e0126267. PMID: 25938501, PMCID: PMC4418809, DOI: 10.1371/journal.pone.0126267.
- Gene Expression Evolves under a House-of-Cards Model of Stabilizing SelectionHodgins-Davis A, Rice DP, Townsend JP. Gene Expression Evolves under a House-of-Cards Model of Stabilizing Selection. Molecular Biology And Evolution 2015, 32: 2130-2140. PMID: 25901014, PMCID: PMC4592357, DOI: 10.1093/molbev/msv094.
- H-CLAP: hierarchical clustering within a linear array with an application in geneticsGhosh S, Townsend JP. H-CLAP: hierarchical clustering within a linear array with an application in genetics. Statistical Applications In Genetics And Molecular Biology 2015, 14: 125-141. PMID: 25803088, DOI: 10.1515/sagmb-2013-0076.
- Under-reporting and case fatality estimates for emerging epidemicsAtkins KE, Wenzel NS, Ndeffo-Mbah M, Altice FL, Townsend JP, Galvani AP. Under-reporting and case fatality estimates for emerging epidemics. The BMJ 2015, 350: h1115. PMID: 25779635, PMCID: PMC4707560, DOI: 10.1136/bmj.h1115.
- Epidemiological and Viral Genomic Sequence Analysis of the 2014 Ebola Outbreak Reveals Clustered TransmissionScarpino SV, Iamarino A, Wells C, Yamin D, Ndeffo-Mbah M, Wenzel NS, Fox SJ, Nyenswah T, Altice FL, Galvani AP, Meyers LA, Townsend JP. Epidemiological and Viral Genomic Sequence Analysis of the 2014 Ebola Outbreak Reveals Clustered Transmission. Clinical Infectious Diseases 2014, 60: 1079-1082. PMID: 25516185, PMCID: PMC4375398, DOI: 10.1093/cid/ciu1131.
- The peopling of the African continent and the diaspora into the new worldCampbell MC, Hirbo JB, Townsend JP, Tishkoff SA. The peopling of the African continent and the diaspora into the new world. Current Opinion In Genetics & Development 2014, 29: 120-132. PMID: 25461616, PMCID: PMC4308437, DOI: 10.1016/j.gde.2014.09.003.
- Strategies for containing Ebola in West AfricaPandey A, Atkins KE, Medlock J, Wenzel N, Townsend JP, Childs JE, Nyenswah TG, Ndeffo-Mbah ML, Galvani AP. Strategies for containing Ebola in West Africa. Science 2014, 346: 991-995. PMID: 25414312, PMCID: PMC4316831, DOI: 10.1126/science.1260612.
- Neural Gene Expression Profiles and Androgen Levels Underlie Alternative Reproductive Tactics in the Ocellated Wrasse, Symphodus ocellatusStiver K, Harris R, Townsend J, Hofmann H, Alonzo S. Neural Gene Expression Profiles and Androgen Levels Underlie Alternative Reproductive Tactics in the Ocellated Wrasse, Symphodus ocellatus. Ethology 2014, 121: 152-167. DOI: 10.1111/eth.12324.
- Gene Expression Differences among Three Neurospora Species Reveal Genes Required for Sexual Reproduction in Neurospora crassaLehr NA, Wang Z, Li N, Hewitt DA, López-Giráldez F, Trail F, Townsend JP. Gene Expression Differences among Three Neurospora Species Reveal Genes Required for Sexual Reproduction in Neurospora crassa. PLOS ONE 2014, 9: e110398. PMID: 25329823, PMCID: PMC4203796, DOI: 10.1371/journal.pone.0110398.
- Genome-Wide Characterization of Light-Regulated Genes in Neurospora crassaWu C, Yang F, Smith KM, Peterson M, Dekhang R, Zhang Y, Zucker J, Bredeweg EL, Mallappa C, Zhou X, Lyubetskaya A, Townsend JP, Galagan JE, Freitag M, Dunlap JC, Bell-Pedersen D, Sachs MS. Genome-Wide Characterization of Light-Regulated Genes in Neurospora crassa. G3: Genes, Genomes, Genetics 2014, 4: 1731-1745. PMID: 25053707, PMCID: PMC4169166, DOI: 10.1534/g3.114.012617.
- Phylogenetic informativeness reconciles ray-finned fish molecular divergence timesDornburg A, Townsend JP, Friedman M, Near TJ. Phylogenetic informativeness reconciles ray-finned fish molecular divergence times. BMC Ecology And Evolution 2014, 14: 169. PMID: 25103329, PMCID: PMC4236503, DOI: 10.1186/s12862-014-0169-0.
- GENETIC CHANGES IN RADIATION-ASSOCIATED MENINGIOMAClaus E, Calvocoressi L, Greenhalgh S, Walsh K, Schildkraut J, Bondy M, Wiemels J, Wrensch M, Al-Mefty O, Townsend J. GENETIC CHANGES IN RADIATION-ASSOCIATED MENINGIOMA. Neuro-Oncology 2014, 16: iii1-iii1. PMCID: PMC4144484, DOI: 10.1093/neuonc/nou206.2.
- Cellular Superspreaders: An Epidemiological Perspective on HIV Infection inside the BodyTalbert-Slagle K, Atkins KE, Yan KK, Khurana E, Gerstein M, Bradley EH, Berg D, Galvani AP, Townsend JP. Cellular Superspreaders: An Epidemiological Perspective on HIV Infection inside the Body. PLOS Pathogens 2014, 10: e1004092. PMID: 24811311, PMCID: PMC4014458, DOI: 10.1371/journal.ppat.1004092.
- The impact of incorporating molecular evolutionary model into predictions of phylogenetic signal and noiseSu Z, Wang Z, López-Giráldez F, Townsend J. The impact of incorporating molecular evolutionary model into predictions of phylogenetic signal and noise. Frontiers In Ecology And Evolution 2014, 2: 11. DOI: 10.3389/fevo.2014.00011.
- Detecting rare gene transfer events in bacterial populationsNielsen KM, Bøhn T, Townsend JP. Detecting rare gene transfer events in bacterial populations. Frontiers In Microbiology 2014, 4: 415. PMID: 24432015, PMCID: PMC3882822, DOI: 10.3389/fmicb.2013.00415.
- Optimized primers and other critical conditions for efficient fusion PCR to generate knockout vectors in filamentous fungi.Harrison N, Cavinder B, Townsend J, Trail F. Optimized primers and other critical conditions for efficient fusion PCR to generate knockout vectors in filamentous fungi. Fungal Genetics Reports 2013, 60: 1-10. DOI: 10.4148/1941-4765.1006.
- Probabilistic uncertainty analysis of epidemiological modeling to guide public health intervention policyGilbert JA, Meyers LA, Galvani AP, Townsend JP. Probabilistic uncertainty analysis of epidemiological modeling to guide public health intervention policy. Epidemics 2013, 6: 37-45. PMID: 24593920, PMCID: PMC4316830, DOI: 10.1016/j.epidem.2013.11.002.
- Global Gene Expression and Focused Knockout Analysis Reveals Genes Associated with Fungal Fruiting Body Development in Neurospora crassaWang Z, Lopez-Giraldez F, Lehr N, Farré M, Common R, Trail F, Townsend JP. Global Gene Expression and Focused Knockout Analysis Reveals Genes Associated with Fungal Fruiting Body Development in Neurospora crassa. MSphere 2013, 13: 154-169. PMID: 24243796, PMCID: PMC3910948, DOI: 10.1128/ec.00248-13.
- Phylogenetic and phylogenomic overview of the PolyporalesBinder M, Justo A, Riley R, Salamov A, Lopez-Giraldez F, Sjökvist E, Copeland A, Foster B, Sun H, Larsson E, Larsson KH, Townsend J, Grigoriev IV, Hibbett DS. Phylogenetic and phylogenomic overview of the Polyporales. Mycologia 2013, 105: 1350-1373. PMID: 23935031, DOI: 10.3852/13-003.
- Sex-linked transcriptional divergence in the hermaphrodite fungus Neurospora tetraspermaSamils N, Gioti A, Karlsson M, Sun Y, Kasuga T, Bastiaans E, Wang Z, Li N, Townsend JP, Johannesson H. Sex-linked transcriptional divergence in the hermaphrodite fungus Neurospora tetrasperma. Proceedings Of The Royal Society B 2013, 280: 20130862. PMID: 23782882, PMCID: PMC3712418, DOI: 10.1098/rspb.2013.0862.
- Epidemiological mechanisms of genetic resistance to kuruAtkins KE, Townsend JP, Medlock J, Galvani AP. Epidemiological mechanisms of genetic resistance to kuru. Journal Of The Royal Society Interface 2013, 10: 20130331. PMID: 23740487, PMCID: PMC4043168, DOI: 10.1098/rsif.2013.0331.
- Potential Cost-Effectiveness of Schistosomiasis Treatment for Reducing HIV Transmission in Africa – The Case of Zimbabwean WomenMbah M, Poolman EM, Atkins KE, Orenstein EW, Meyers LA, Townsend JP, Galvani AP. Potential Cost-Effectiveness of Schistosomiasis Treatment for Reducing HIV Transmission in Africa – The Case of Zimbabwean Women. PLOS Neglected Tropical Diseases 2013, 7: e2346. PMID: 23936578, PMCID: PMC3731236, DOI: 10.1371/journal.pntd.0002346.
- Evaluating Phylogenetic Informativeness as a Predictor of Phylogenetic Signal for Metazoan, Fungal, and Mammalian Phylogenomic Data SetsLópez-Giráldez F, Moeller AH, Townsend JP. Evaluating Phylogenetic Informativeness as a Predictor of Phylogenetic Signal for Metazoan, Fungal, and Mammalian Phylogenomic Data Sets. BioMed Research International 2013, 2013: 621604. PMID: 23878813, PMCID: PMC3708382, DOI: 10.1155/2013/621604.
- AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantificationDai L, Tian M, Wu J, Xiao J, Wang X, Townsend JP, Zhang Z. AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification. Bioinformatics 2013, 29: 1837-1839. PMID: 23732274, PMCID: PMC3702255, DOI: 10.1093/bioinformatics/btt284.
- Optimal targeting of seasonal influenza vaccination toward younger ages is robust to parameter uncertaintyMbah M, Medlock J, Meyers LA, Galvani AP, Townsend JP. Optimal targeting of seasonal influenza vaccination toward younger ages is robust to parameter uncertainty. Vaccine 2013, 31: 3079-3089. PMID: 23684837, PMCID: PMC3764605, DOI: 10.1016/j.vaccine.2013.04.052.
- Cost-effectiveness of a community-based intervention for reducing the transmission of Schistosoma haematobium and HIV in AfricaMbah M, Kjetland EF, Atkins KE, Poolman EM, Orenstein EW, Meyers LA, Townsend JP, Galvani AP. Cost-effectiveness of a community-based intervention for reducing the transmission of Schistosoma haematobium and HIV in Africa. Proceedings Of The National Academy Of Sciences Of The United States Of America 2013, 110: 7952-7957. PMID: 23589884, PMCID: PMC3651507, DOI: 10.1073/pnas.1221396110.
- Yeast response to LA virus indicates coadapted global gene expression during mycoviral infectionMcBride RC, Boucher N, Park DS, Turner PE, Townsend JP. Yeast response to LA virus indicates coadapted global gene expression during mycoviral infection. FEMS Yeast Research 2013, 13: 162-179. PMID: 23122216, DOI: 10.1111/1567-1364.12019.
- Controlling Antimicrobial Resistance through Targeted, Vaccine-Induced Replacement of StrainsTekle YI, Nielsen KM, Liu J, Pettigrew MM, Meyers LA, Galvani AP, Townsend JP. Controlling Antimicrobial Resistance through Targeted, Vaccine-Induced Replacement of Strains. PLOS ONE 2012, 7: e50688. PMID: 23227198, PMCID: PMC3515573, DOI: 10.1371/journal.pone.0050688.
- Abundant Gene-by-Environment Interactions in Gene Expression Reaction Norms to Copper within Saccharomyces cerevisiaeHodgins-Davis A, Adomas A, Warringer J, Townsend J. Abundant Gene-by-Environment Interactions in Gene Expression Reaction Norms to Copper within Saccharomyces cerevisiae. Genome Biology And Evolution 2012, 4: 1188-1188. PMCID: PMC3514958, DOI: 10.1093/gbe/evs105.
- Analyses of expressed sequence tags in Neurosporareveal rapid evolution of genes associated with the early stages of sexual reproduction in fungiNygren K, Wallberg A, Samils N, Stajich JE, Townsend JP, Karlsson M, Johannesson H. Analyses of expressed sequence tags in Neurosporareveal rapid evolution of genes associated with the early stages of sexual reproduction in fungi. BMC Ecology And Evolution 2012, 12: 229. PMID: 23186325, PMCID: PMC3571971, DOI: 10.1186/1471-2148-12-229.
- Response to: The relative utility of sequence divergence and phylogenetic informativeness profiling in phylogenetic study designMoeller AH, Townsend JP. Response to: The relative utility of sequence divergence and phylogenetic informativeness profiling in phylogenetic study design. Molecular Phylogenetics And Evolution 2012, 66: 436. PMID: 23063589, DOI: 10.1016/j.ympev.2012.09.035.
- Potential for Rabies Control through Dog Vaccination in Wildlife-Abundant Communities of TanzaniaFitzpatrick MC, Hampson K, Cleaveland S, Meyers LA, Townsend JP, Galvani AP. Potential for Rabies Control through Dog Vaccination in Wildlife-Abundant Communities of Tanzania. PLOS Neglected Tropical Diseases 2012, 6: e1796. PMID: 22928056, PMCID: PMC3424251, DOI: 10.1371/journal.pntd.0001796.
- Reevaluation of Epidemiological Data Demonstrates That It Is Consistent With Cross-Immunity Among Human Papillomavirus TypesDurham DP, Poolman EM, Ibuka Y, Townsend JP, Galvani AP. Reevaluation of Epidemiological Data Demonstrates That It Is Consistent With Cross-Immunity Among Human Papillomavirus Types. The Journal Of Infectious Diseases 2012, 206: 1291-1298. PMID: 22872732, PMCID: PMC3448971, DOI: 10.1093/infdis/jis494.
- Resampling QTL Effects in the QTL Sign Test Leads to Incongruous Sensitivity to Variance in Effect SizeRice DP, Townsend JP. Resampling QTL Effects in the QTL Sign Test Leads to Incongruous Sensitivity to Variance in Effect Size. G3: Genes, Genomes, Genetics 2012, 2: 905-911. PMID: 22908039, PMCID: PMC3411246, DOI: 10.1534/g3.112.003228.
- Transcriptome analyses during fruiting body formation in Fusarium graminearum and Fusarium verticillioides reflect species life history and ecologySikhakolli UR, López-Giráldez F, Li N, Common R, Townsend JP, Trail F. Transcriptome analyses during fruiting body formation in Fusarium graminearum and Fusarium verticillioides reflect species life history and ecology. Fungal Genetics And Biology 2012, 49: 663-673. PMID: 22705880, DOI: 10.1016/j.fgb.2012.05.009.
- Sex-specific gene expression during asexual development of Neurospora crassaWang Z, Kin K, López-Giráldez F, Johannesson H, Townsend JP. Sex-specific gene expression during asexual development of Neurospora crassa. Fungal Genetics And Biology 2012, 49: 533-543. PMID: 22626843, PMCID: PMC3397379, DOI: 10.1016/j.fgb.2012.05.004.
- RBE controls microRNA164 expression to effect floral organogenesisHuang T, López-Giráldez F, Townsend JP, Irish VF. RBE controls microRNA164 expression to effect floral organogenesis. Development 2012, 139: 2161-2169. PMID: 22573623, DOI: 10.1242/dev.075069.
- The influence of altruism on influenza vaccination decisionsShim E, Chapman GB, Townsend JP, Galvani AP. The influence of altruism on influenza vaccination decisions. Journal Of The Royal Society Interface 2012, 9: 2234-2243. PMID: 22496100, PMCID: PMC3405754, DOI: 10.1098/rsif.2012.0115.
- A Test for Selection Employing Quantitative Trait Locus and Mutation Accumulation DataRice DP, Townsend JP. A Test for Selection Employing Quantitative Trait Locus and Mutation Accumulation Data. Genetics 2012, 190: 1533-1545. PMID: 22298701, PMCID: PMC3316662, DOI: 10.1534/genetics.111.137075.
- Differential impact of nutrition on developmental and metabolic gene expression during fruiting body development in Neurospora crassaWang Z, Lehr N, Trail F, Townsend JP. Differential impact of nutrition on developmental and metabolic gene expression during fruiting body development in Neurospora crassa. Fungal Genetics And Biology 2012, 49: 405-413. PMID: 22469835, PMCID: PMC3397380, DOI: 10.1016/j.fgb.2012.03.004.
- Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significanceZhang Z, Li J, Cui P, Ding F, Li A, Townsend JP, Yu J. Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance. BMC Bioinformatics 2012, 13: 43. PMID: 22435713, PMCID: PMC3368730, DOI: 10.1186/1471-2105-13-43.
- Phylogenetic Signal and Noise: Predicting the Power of a Data Set to Resolve PhylogenyTownsend JP, Su Z, Tekle YI. Phylogenetic Signal and Noise: Predicting the Power of a Data Set to Resolve Phylogeny. Systematic Biology 2012, 61: 835-849. PMID: 22389443, DOI: 10.1093/sysbio/sys036.
- Assessing the Probability of Detection of Horizontal Gene Transfer Events in Bacterial PopulationsTownsend JP, Bøhn T, Nielsen KM. Assessing the Probability of Detection of Horizontal Gene Transfer Events in Bacterial Populations. Frontiers In Microbiology 2012, 3: 27. PMID: 22363321, PMCID: PMC3282476, DOI: 10.3389/fmicb.2012.00027.
- Abundant Gene-by-Environment Interactions in Gene Expression Reaction Norms to Copper within Saccharomyces cerevisiaeHodgins-Davis A, Adomas AB, Warringer J, Townsend JP. Abundant Gene-by-Environment Interactions in Gene Expression Reaction Norms to Copper within Saccharomyces cerevisiae. Genome Biology And Evolution 2012, 4: 1061-1079. PMID: 23019066, PMCID: PMC3514956, DOI: 10.1093/gbe/evs084.
- Data Integration in Bioinformatics: Current Efforts and ChallengesZhang Z, Bajic V, Yu J, Cheung K, Townsend J. Data Integration in Bioinformatics: Current Efforts and Challenges. 2011 DOI: 10.5772/21654.
- PhyDesign: an online application for profiling phylogenetic informativenessLópez-Giráldez F, Townsend JP. PhyDesign: an online application for profiling phylogenetic informativeness. BMC Ecology And Evolution 2011, 11: 152. PMID: 21627831, PMCID: PMC3124428, DOI: 10.1186/1471-2148-11-152.
- Phylogenetic informativeness profiling of 12 genes for 28 vertebrate taxa without divergence datesMoeller AH, Townsend JP. Phylogenetic informativeness profiling of 12 genes for 28 vertebrate taxa without divergence dates. Molecular Phylogenetics And Evolution 2011, 60: 271-272. PMID: 21558010, DOI: 10.1016/j.ympev.2011.04.023.
- Getting the Most Out of Your Fungal Microarray Data: Two Cost- and Time-Effective MethodsMathioni SM, Beló A, Townsend JP, Donofrio NM. Getting the Most Out of Your Fungal Microarray Data: Two Cost- and Time-Effective Methods. 2011, 722: 61-77. PMID: 21590413, DOI: 10.1007/978-1-61779-040-9_5.
- Tasting Soil Fungal Diversity with Earth Tongues: Phylogenetic Test of SATé Alignments for Environmental ITS DataWang Z, Nilsson RH, Lopez-Giraldez F, Zhuang WY, Dai YC, Johnston PR, Townsend JP. Tasting Soil Fungal Diversity with Earth Tongues: Phylogenetic Test of SATé Alignments for Environmental ITS Data. PLOS ONE 2011, 6: e19039. PMID: 21533038, PMCID: PMC3080880, DOI: 10.1371/journal.pone.0019039.
- SIR2 and other genes are abundantly expressed in long‐lived natural segregants for replicative aging of the budding yeast Saccharomyces cerevisiaeGuo Z, Adomas AB, Jackson ED, Qin H, Townsend JP. SIR2 and other genes are abundantly expressed in long‐lived natural segregants for replicative aging of the budding yeast Saccharomyces cerevisiae. FEMS Yeast Research 2011, 11: 345-355. PMID: 21306556, DOI: 10.1111/j.1567-1364.2011.00723.x.
- Taxon Sampling and the Optimal Rates of Evolution for Phylogenetic InferenceTownsend JP, Leuenberger C. Taxon Sampling and the Optimal Rates of Evolution for Phylogenetic Inference. Systematic Biology 2011, 60: 358-365. PMID: 21303824, DOI: 10.1093/sysbio/syq097.
- Retrospective evidence for a biological cost of vancomycin resistance determinants in the absence of glycopeptide selective pressuresJohnsen P, Townsend J, Bøhn T, Simonsen G, Sundsfjord A, Nielsen K. Retrospective evidence for a biological cost of vancomycin resistance determinants in the absence of glycopeptide selective pressures. Journal Of Antimicrobial Chemotherapy 2011, 66: 608-610. PMID: 21217128, PMCID: PMC3037156, DOI: 10.1093/jac/dkq512.
- Northern species of earth tongue genus Thuemenidium revisited, considering morphology, ecology and molecular phylogenyOhenoja E, Wang Z, Townsend JP, Mitchel D, Voitk A. Northern species of earth tongue genus Thuemenidium revisited, considering morphology, ecology and molecular phylogeny. Mycologia 2010, 102: 1089-1095. PMID: 20943508, DOI: 10.3852/09-317.
- Multi-targeted priming for genome-wide gene expression assaysAdomas AB, Lopez-Giraldez F, Clark TA, Wang Z, Townsend JP. Multi-targeted priming for genome-wide gene expression assays. BMC Genomics 2010, 11: 477. PMID: 20716356, PMCID: PMC3091673, DOI: 10.1186/1471-2164-11-477.
- LOX: inferring Level Of eXpression from diverse methods of census sequencingZhang Z, López-Giráldez F, Townsend JP. LOX: inferring Level Of eXpression from diverse methods of census sequencing. Bioinformatics 2010, 26: 1918-1919. PMID: 20538728, PMCID: PMC2905554, DOI: 10.1093/bioinformatics/btq303.
- Optimal Selection of Gene and Ingroup Taxon Sampling for Resolving Phylogenetic RelationshipsTownsend JP, Lopez-Giraldez F. Optimal Selection of Gene and Ingroup Taxon Sampling for Resolving Phylogenetic Relationships. Systematic Biology 2010, 59: 446-457. PMID: 20547780, DOI: 10.1093/sysbio/syq025.
- Identification of new molecular markers for assembling the eukaryotic tree of lifeTekle YI, Grant JR, Kovner AM, Townsend JP, Katz LA. Identification of new molecular markers for assembling the eukaryotic tree of life. Molecular Phylogenetics And Evolution 2010, 55: 1177-1182. PMID: 20302952, DOI: 10.1016/j.ympev.2010.03.010.
- The filamentous fungal gene expression database (FFGED)Zhang Z, Townsend JP. The filamentous fungal gene expression database (FFGED). Fungal Genetics And Biology 2009, 47: 199-204. PMID: 20025988, PMCID: PMC2822089, DOI: 10.1016/j.fgb.2009.12.001.
- Evolving gene expression: from G to E to G×EHodgins-Davis A, Townsend JP. Evolving gene expression: from G to E to G×E. Trends In Ecology & Evolution 2009, 24: 649-658. PMID: 19699549, PMCID: PMC2805859, DOI: 10.1016/j.tree.2009.06.011.
- Maximum-Likelihood Model Averaging To Profile Clustering of Site Types across Discrete Linear SequencesZhang Z, Townsend JP. Maximum-Likelihood Model Averaging To Profile Clustering of Site Types across Discrete Linear Sequences. PLOS Computational Biology 2009, 5: e1000421. PMID: 19557160, PMCID: PMC2695770, DOI: 10.1371/journal.pcbi.1000421.
- Geoglossomycetes cl. nov., Geoglossales ord. nov. and taxa above class rank in the Ascomycota Tree of LifeSchoch CL, Wang Z, Townsend JP, Spatafora JW. Geoglossomycetes cl. nov., Geoglossales ord. nov. and taxa above class rank in the Ascomycota Tree of Life. Persoonia 2009, 22: 129-138. PMID: 19915689, PMCID: PMC2776753, DOI: 10.3767/003158509x461486.
- Factors affecting the reversal of antimicrobial-drug resistanceJohnsen PJ, Townsend JP, Bøhn T, Simonsen GS, Sundsfjord A, Nielsen KM. Factors affecting the reversal of antimicrobial-drug resistance. The Lancet Infectious Diseases 2009, 9: 357-364. PMID: 19467475, DOI: 10.1016/s1473-3099(09)70105-7.
- The Ascomycota Tree of Life: A Phylum-wide Phylogeny Clarifies the Origin and Evolution of Fundamental Reproductive and Ecological TraitsSchoch CL, Sung GH, López-Giráldez F, Townsend JP, Miadlikowska J, Hofstetter V, Robbertse B, Matheny PB, Kauff F, Wang Z, Gueidan C, Andrie RM, Trippe K, Ciufetti LM, Wynns A, Fraker E, Hodkinson BP, Bonito G, Groenewald JZ, Arzanlou, de Hoog GS, Crous PW, Hewitt D, Pfister DH, Peterson K, Gryzenhout M, Wingfield MJ, Aptroot A, Suh SO, Blackwell M, Hillis DM, Griffith GW, Castlebury LA, Rossman AY, Lumbsch HT, Lücking R, Büdel B, Rauhut A, Diederich P, Ertz D, Geiser DM, Hosaka K, Inderbitzin P, Kohlmeyer J, Volkmann-Kohlmeyer B, Mostert L, O'Donnell K, Sipman H, Rogers JD, Shoemaker RA, Sugiyama J, Summerbell RC, Untereiner W, Johnston PR, Stenroos S, Zuccaro A, Dyer PS, Crittenden PD, Cole MS, Hansen K, Trappe JM, Yahr R, Lutzoni F, Spatafora JW. The Ascomycota Tree of Life: A Phylum-wide Phylogeny Clarifies the Origin and Evolution of Fundamental Reproductive and Ecological Traits. Systematic Biology 2009, 58: 224-239. PMID: 20525580, DOI: 10.1093/sysbio/syp020.
- Evolution of Reproductive Morphology in Leaf EndophytesWang Z, Johnston PR, Yang ZL, Townsend JP. Evolution of Reproductive Morphology in Leaf Endophytes. PLOS ONE 2009, 4: e4246. PMID: 19158947, PMCID: PMC2617777, DOI: 10.1371/journal.pone.0004246.
- Article Commentary: Snapshots of Tree SpaceWang Z, López-Giréidez F, Townsend J. Article Commentary: Snapshots of Tree Space. Evolutionary Bioinformatics 2009, 5: ebo.s3416. DOI: 10.4137/ebo.s3416.
- Measuring Transcription Factor–Binding Site Turnover: A Maximum Likelihood Approach Using PhylogeniesOtto W, Stadler PF, López-Giraldéz F, Townsend JP, Lynch VJ, Wagner GP. Measuring Transcription Factor–Binding Site Turnover: A Maximum Likelihood Approach Using Phylogenies. Genome Biology And Evolution 2009, 1: 85-98. PMID: 20333180, PMCID: PMC2817405, DOI: 10.1093/gbe/evp010.
- RNA extraction, probe preparation, and competitive hybridization for transcriptional profiling using Neurospora crassa long-oligomer DNA microarraysClark T, Guilmette J, Renstrom D, Townsend J. RNA extraction, probe preparation, and competitive hybridization for transcriptional profiling using Neurospora crassa long-oligomer DNA microarrays. Fungal Genetics Reports 2008, 55: 18-28. DOI: 10.4148/1941-4765.1086.
- Bringing Web 2.0 to bioinformaticsZhang Z, Cheung KH, Townsend JP. Bringing Web 2.0 to bioinformatics. Briefings In Bioinformatics 2008, 10: 1-10. PMID: 18842678, PMCID: PMC2638627, DOI: 10.1093/bib/bbn041.
- The Phylogenetic Informativeness of Nucleotide and Amino Acid Sequences for Reconstructing the Vertebrate TreeTownsend JP, López-Giráldez F, Friedman R. The Phylogenetic Informativeness of Nucleotide and Amino Acid Sequences for Reconstructing the Vertebrate Tree. Journal Of Molecular Evolution 2008, 67: 437-447. PMID: 18696029, DOI: 10.1007/s00239-008-9142-0.
- Sleuthing the difference a nucleotide can makeTownsend JP. Sleuthing the difference a nucleotide can make. Molecular Ecology 2008, 17: 2793-2795. PMID: 18565029, DOI: 10.1111/j.1365-294x.2008.03824.x.
- HCLS 2.0/3.0: Health care and life sciences data mashup using Web 2.0/3.0Cheung KH, Yip KY, Townsend JP, Scotch M. HCLS 2.0/3.0: Health care and life sciences data mashup using Web 2.0/3.0. Journal Of Biomedical Informatics 2008, 41: 694-705. PMID: 18487092, PMCID: PMC2933816, DOI: 10.1016/j.jbi.2008.04.001.
- Quantifying variation in gene expressionCLARK TA, TOWNSEND JP. Quantifying variation in gene expression. Molecular Ecology 2007, 16: 2613-2616. PMID: 17594433, DOI: 10.1111/j.1365-294x.2007.03354.x.
- Profiling Phylogenetic InformativenessTownsend JP, Naylor G. Profiling Phylogenetic Informativeness. Systematic Biology 2007, 56: 222-231. PMID: 17464879, DOI: 10.1080/10635150701311362.
- Enabling a Community to Dissect an Organism: Overview of the Neurospora Functional Genomics ProjectDunlap JC, Borkovich KA, Henn MR, Turner GE, Sachs MS, Glass NL, McCluskey K, Plamann M, Galagan JE, Birren BW, Weiss RL, Townsend JP, Loros JJ, Nelson MA, Lambreghts R, Colot HV, Park G, Collopy P, Ringelberg C, Crew C, Litvinkova L, DeCaprio D, Hood HM, Curilla S, Shi M, Crawford M, Koerhsen M, Montgomery P, Larson L, Pearson M, Kasuga T, Tian C, Baştürkmen M, Altamirano L, Xu J. Enabling a Community to Dissect an Organism: Overview of the Neurospora Functional Genomics Project. 2007, 57: 49-96. PMID: 17352902, PMCID: PMC3673015, DOI: 10.1016/s0065-2660(06)57002-6.
- Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom FungiTaylor JW, Turner E, Townsend JP, Dettman JR, Jacobson D. Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi. Philosophical Transactions Of The Royal Society B Biological Sciences 2006, 361: 1947-1963. PMID: 17062413, PMCID: PMC1764934, DOI: 10.1098/rstb.2006.1923.
- Phase-specific gene expression underlying morphological adaptations of the dimorphic human pathogenic fungus, Coccidioides posadasiiJohannesson H, Kasuga T, Schaller RA, Good B, Gardner MJ, Townsend JP, Cole GT, Taylor JW. Phase-specific gene expression underlying morphological adaptations of the dimorphic human pathogenic fungus, Coccidioides posadasii. Fungal Genetics And Biology 2006, 43: 545-559. PMID: 16697669, DOI: 10.1016/j.fgb.2006.02.003.
- Population structure and gene evolution in Saccharomyces cerevisiaeAa E, Townsend JP, Adams RI, Nielsen KM, Taylor JW. Population structure and gene evolution in Saccharomyces cerevisiae. FEMS Yeast Research 2006, 6: 702-715. PMID: 16879422, DOI: 10.1111/j.1567-1364.2006.00059.x.
- Ecological and evolutionary genomics of Saccharomyces cerevisiaeLANDRY CR, TOWNSEND JP, HARTL DL, CAVALIERI D. Ecological and evolutionary genomics of Saccharomyces cerevisiae. Molecular Ecology 2006, 15: 575-591. PMID: 16499686, DOI: 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 germinationKasuga T, Townsend JP, Tian C, Gilbert LB, Mannhaupt G, Taylor JW, Glass NL. Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination. Nucleic Acids Research 2005, 33: 6469-6485. PMID: 16287898, PMCID: PMC1283539, DOI: 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. posadasiiJohannesson H, Townsend JP, Hung CY, Cole GT, Taylor JW. Concerted Evolution in the Repeats of an Immunomodulating Cell Surface Protein, SOWgp, of the Human Pathogenic Fungi Coccidioides immitis and C. posadasii. Genetics 2005, 171: 109-117. PMID: 15965255, PMCID: PMC1456504, DOI: 10.1534/genetics.105.040923.
- Horizontal gene transfer, genome innovation and evolutionGogarten JP, Townsend JP. Horizontal gene transfer, genome innovation and evolution. Nature Reviews Microbiology 2005, 3: 679-687. PMID: 16138096, DOI: 10.1038/nrmicro1204.
- Designing Experiments Using Spotted Microarrays to Detect Gene Regulation Differences Within and Among SpeciesTownsend JP, Taylor JW. Designing Experiments Using Spotted Microarrays to Detect Gene Regulation Differences Within and Among Species. 2005, 395: 597-617. PMID: 15865986, DOI: 10.1016/s0076-6879(05)95031-3.
- A Bayesian method for analysing spotted microarray dataMeiklejohn CD, Townsend JP. A Bayesian method for analysing spotted microarray data. Briefings In Bioinformatics 2005, 6: 318-330. PMID: 16420731, DOI: 10.1093/bib/6.4.318.
- Monitoring and modeling horizontal gene transferNielsen KM, Townsend JP. Monitoring and modeling horizontal gene transfer. Nature Biotechnology 2004, 22: 1110-1114. PMID: 15340481, DOI: 10.1038/nbt1006.
- Mitochondrial genome size variation in New World and Old World populations of Drosophila melanogasterTownsend JP, Rand DM. Mitochondrial genome size variation in New World and Old World populations of Drosophila melanogaster. Heredity 2004, 93: 98-103. PMID: 15138453, DOI: 10.1038/sj.hdy.6800484.
- Resolution of large and small differences in gene expression using models for the Bayesian analysis of gene expression levels and spotted DNA microarraysTownsend JP. Resolution of large and small differences in gene expression using models for the Bayesian analysis of gene expression levels and spotted DNA microarrays. BMC Bioinformatics 2004, 5: 54. PMID: 15128431, PMCID: PMC420235, DOI: 10.1186/1471-2105-5-54.
- Gene expression profiling in evolutionary geneticsHartl D, Meiklejohn C, Castillo-Davis C, Cavalieri D, Ranz J, Townsend J. Gene expression profiling in evolutionary genetics. 2004, 74-93. DOI: 10.1017/cbo9780511542619.007.
- Multifactorial experimental design and the transitivity of ratios with spotted DNA microarraysTownsend JP. Multifactorial experimental design and the transitivity of ratios with spotted DNA microarrays. BMC Genomics 2003, 4: 41. PMID: 14525623, PMCID: PMC239860, DOI: 10.1186/1471-2164-4-41.
- Horizontal acquisition of divergent chromosomal DNA in bacteria: effects of mutator phenotypes.Townsend JP, Nielsen KM, Fisher DS, Hartl DL. Horizontal acquisition of divergent chromosomal DNA in bacteria: effects of mutator phenotypes. Genetics 2003, 164: 13-21. PMID: 12750317, PMCID: PMC1462543, DOI: 10.1093/genetics/164.1.13.
- Population Genetic Variation in Genome-Wide Gene ExpressionTownsend JP, Cavalieri D, Hartl DL. Population Genetic Variation in Genome-Wide Gene Expression. Molecular Biology And Evolution 2003, 20: 955-963. PMID: 12716989, DOI: 10.1093/molbev/msg106.
- Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatmentsTownsend JP, Hartl DL. Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments. Genome Biology 2002, 3: research0071.1. PMID: 12537560, PMCID: PMC151173, DOI: 10.1186/gb-2002-3-12-research0071.
- Pathway Processor: A Tool for Integrating Whole-Genome Expression Results into Metabolic NetworksGrosu P, Townsend JP, Hartl DL, Cavalieri D. Pathway Processor: A Tool for Integrating Whole-Genome Expression Results into Metabolic Networks. Genome Research 2002, 12: 1121-1126. PMID: 12097350, PMCID: PMC186628, DOI: 10.1101/gr.226602.
- Manifold anomalies in gene expression in a vineyard isolate of Saccharomyces cerevisiae revealed by DNA microarray analysisCavalieri D, Townsend J, Hartl D. Manifold anomalies in gene expression in a vineyard isolate of Saccharomyces cerevisiae revealed by DNA microarray analysis. Proceedings Of The National Academy Of Sciences Of The United States Of America 2000, 97: 12369-12374. PMID: 11035792, PMCID: PMC17348, DOI: 10.1073/pnas.210395297.
- Solvent Accessibility and Purifying Selection Within Proteins of Escherichia coli and Salmonella entericaBustamante CD, Townsend JP, Hartl DL. Solvent Accessibility and Purifying Selection Within Proteins of Escherichia coli and Salmonella enterica. Molecular Biology And Evolution 2000, 17: 301-308. PMID: 10677853, DOI: 10.1093/oxfordjournals.molbev.a026310.
- The Kinetics of Transposable Element AutoregulationTownsend J, Hartl D. The Kinetics of Transposable Element Autoregulation. Genetica 2000, 108: 229. PMID: 11294609, DOI: 10.1023/a:1004172703790.