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List of works by Jeffrey P. Townsend

A Bayesian method for analysing spotted microarray data.

scientific article

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

scientific article

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

scientific article published in Nature

A multigene phylogeny toward a new phylogenetic classification of Leotiomycetes

scientific article published on 07 June 2019

A test for selection employing quantitative trait locus and mutation accumulation data.

scientific article

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

scientific article published on 15 January 2019

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

scientific article published on 27 November 2012

Abundant gene-by-environment interactions in gene expression reaction norms to copper within Saccharomyces cerevisiae

scientific article

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

scientific article

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

scientific article

Assessing the probability of detection of horizontal gene transfer events in bacterial populations.

scientific article published on 20 February 2012

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

scientific article

Bringing Web 2.0 to bioinformatics

scientific article (publication date: 2009)

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

scientific article published on 4 April 2018

Cellular superspreaders: an epidemiological perspective on HIV infection inside the body

scientific article (publication date: May 2014)

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

scientific article published on 24 October 2016

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

scientific article published on 12 February 2019

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

scientific article published on 7 June 2019

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

scholarly article

Concerted evolution in the repeats of an immunomodulating cell surface protein, SOWgp, of the human pathogenic fungi Coccidioides immitis and C. posadasii

scientific article

Controlling antimicrobial resistance through targeted, vaccine-induced replacement of strains

scientific article

Correction: Harnessing Case Isolation and Ring Vaccination to Control Ebola

scientific article published on 24 June 2015

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

scientific article published on 13 May 2016

Cost-effectiveness of a community-based intervention for reducing the transmission of Schistosoma haematobium and HIV in Africa

scientific article published on 15 April 2013

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

scientific article published on 14 April 2016

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

article

Detecting rare gene transfer events in bacterial populations

scientific article

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

scientific article

Determinants of Human African Trypanosomiasis Elimination via Paratransgenesis

scientific article

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

scientific article published on 14 August 2018

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

scientific article

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

scientific article published on 26 May 2017

Early and multiple origins of metastatic lineages within primary tumors

scientific article published on 8 February 2016

Ecological and evolutionary genomics of Saccharomyces cerevisiae

scientific article

Effect Sizes of Somatic Mutations in Cancer

Effect sizes of somatic mutations in cancer

Epidemiological and viral genomic sequence analysis of the 2014 ebola outbreak reveals clustered transmission

scientific article

Epidemiological mechanisms of genetic resistance to kuru

scientific article

Evaluating phylogenetic informativeness as a predictor of phylogenetic signal for metazoan, fungal, and mammalian phylogenomic data sets

scientific article

Evolution of reproductive morphology in leaf endophytes

scientific article

Evolving gene expression: from G to E to GxE.

scientific article

Factors affecting the reversal of antimicrobial-drug resistance.

scientific article published on June 2009

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

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

scientific article published on 12 July 2019

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

scientific article published on 20 April 2015

Gene expression differences among three Neurospora species reveal genes required for sexual reproduction in Neurospora crassa

scientific article

Gene expression profiling in evolutionary genetics

article

Genome-wide characterization of light-regulated genes in Neurospora crassa.

scientific article

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

scientific article published on 19 June 2018

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

scientific article published on 15 December 2015

Genomic and gene-expression comparisons among phage-resistant type-IV pilus mutants of Pseudomonas syringae pathovar phaseolicola

article

Geoglossomycetes cl. nov., Geoglossales ord. nov. and taxa above class rank in the Ascomycota Tree of Life. ⬇️

scientific article

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

scientific article published on 15 May 2020

Getting the most out of your fungal microarray data: two cost- and time-effective methods.

scientific article

Global gene expression and focused knockout analysis reveals genes associated with fungal fruiting body development in Neurospora crassa

scientific article

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

scientific article published on April 2015

Harnessing case isolation and ring vaccination to control Ebola

scientific article published on 29 May 2015

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

scientific article published on 16 February 2018

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

scientific article published on 17 March 2010

Impact of bed capacity on spatiotemporal shifts in Ebola transmission

scientific article

Inferring the Origin of Metastases from Cancer Phylogenies

scientific article published on 10 August 2015

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

scientific article

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

scientific article published on 10 December 2019

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

scientific article

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

scientific article published on 13 November 2017

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

scientific article

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

scientific article published on 23 February 2018

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

scientific article

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

scientific article

Maximum-likelihood model averaging to profile clustering of site types across discrete linear sequences

scientific article

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

scientific article published on 09 June 2021

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

scientific article published in 2019

Modelling microbial infection to address global health challenges

scientific article published on 20 September 2019

Monitoring and modeling horizontal gene transfer

scientific article published in September 2004

Multi-targeted priming for genome-wide gene expression assays

scientific article

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

scientific article published in January 2017

Neutral Theory and the Somatic Evolution of Cancer

scientific article published on 01 June 2018

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

scientific article

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

scientific article published on 11 June 2020

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

scientific article

One Health approach to cost-effective rabies control in India

scientific article

Optimal COVID-19 quarantine and testing strategies

scientific article published on 08 November 2020

Optimal COVID-19 quarantine and testing strategies

scientific article published on 07 January 2021

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

scientific article published on 01 January 2019

Optimal selection of gene and ingroup taxon sampling for resolving phylogenetic relationships

scientific article published on 19 May 2010

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

scientific article published on 16 May 2013

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

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

scientific article published on 27 November 2015

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

Pathway Processor: a tool for integrating whole-genome expression results into metabolic networks

scientific article published on July 2002

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

scientific article

PhyDesign: an online application for profiling phylogenetic informativeness

scientific article

PhyInformR: phylogenetic experimental design and phylogenomic data exploration in R

scientific article

PhyloOncology: Understanding cancer through phylogenetic analysis.

scientific article

Phylogenetic and phylogenomic overview of the Polyporales

scientific article (publication date: 11 August 2013)

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

scientific article published in May 2011

Phylogenetic informativeness reconciles ray-finned fish molecular divergence times

scientific article

Phylogenetic signal and noise: predicting the power of a data set to resolve phylogeny

scientific article

Population genetic variation in genome-wide gene expression

scientific article

Population structure and gene evolution in Saccharomyces cerevisiae

scientific article

Potential cost-effectiveness of schistosomiasis treatment for reducing HIV transmission in Africa--the case of Zimbabwean women

scientific article (publication date: 2013)

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

article

Potential for rabies control through dog vaccination in wildlife-abundant communities of Tanzania

scientific article

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

scientific article

Profiling phylogenetic informativeness

scientific article published in April 2007

Quantifying Transmission of Clostridium difficile within and outside Healthcare Settings

scientific article published on April 2016

Quantifying variation in gene expression

scientific article published in July 2007

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

scientific article published on 9 December 2015

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

RBE controls microRNA164 expression to effect floral organogenesis.

scientific article published on 9 May 2012

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

scientific article

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

scientific article published on 30 August 2019

Reevaluation of epidemiological data demonstrates that it is consistent with cross-immunity among human papillomavirus types

scientific article

Resampling QTL effects in the QTL sign test leads to incongruous sensitivity to variance in effect size.

scientific article

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

scientific article published on 9 October 2012

Retrospective Analysis of the 2014-2015 Ebola Epidemic in Liberia

scientific article published on 29 February 2016

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

scientific article published on 01 March 2011

Sex-linked transcriptional divergence in the hermaphrodite fungus Neurospora tetrasperma.

scientific article published on 19 June 2013

Sex-specific gene expression during asexual development of Neurospora crassa

scientific article

Sexual stage-induced long noncoding RNAs in the filamentous fungusFusarium graminearum

Sleuthing the difference a nucleotide can make

scientific article published in June 2008

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

scientific article

Somatic evolutionary timings of driver mutations.

scientific article published on 18 January 2018

Strategies for containing Ebola in West Africa

scientific article

Tasting soil fungal diversity with earth tongues: phylogenetic test of SATé alignments for environmental ITS data

scientific article

Taxon sampling and the optimal rates of evolution for phylogenetic inference.

scientific article published on 8 February 2011

The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits

scientific article

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

scientific article published on 8 March 2016

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

scientific article

The Moran coalescent in a discrete one-dimensional spatial model

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

scientific article published on 13 July 2017

The filamentous fungal gene expression database (FFGED)

scientific article

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

article

The influence of altruism on influenza vaccination decisions

scientific article

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

scientific article published on 16 July 2019

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

scholarly article published 13 June 2017

The phylogenetic informativeness of nucleotide and amino acid sequences for reconstructing the vertebrate tree

scientific article published on 12 August 2008

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

scientific article published on 15 June 2012

Transfer RNA methyltransferase gene NSUN2 mRNA expression modifies the effect of T cell activation score on patient survival in head and neck squamous carcinoma

scientific article published on 27 December 2019

Under-reporting and case fatality estimates for emerging epidemics

scientific article

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

scientific article published in 2018

Utility of characters evolving at diverse rates of evolution to resolve quartet trees with unequal branch lengths: analytical predictions of long-branch effects

scientific article published on 14 May 2015

Vaccination strategies against respiratory syncytial virus

scientific article published on 31 October 2016

Wagging the long tail of drivers of prostate cancer

scientific article published on 17 January 2019

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

scientific article published on 29 September 2016

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

scientific article published on January 2, 2013

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