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

Gaffney SG, Ad O, Smaga S, Schepartz A, Townsend JP.

ACS Cent Sci. 2019 Jul 24;5(7):1159-1169. doi: 10.1021/acscentsci.9b00111. Epub 2019 Jul 12.


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

Gaffney SG, Perry EB, Chen PM, Greenstein A, Kaech SM, Townsend JP.

Oncotarget. 2019 Jul 16;10(44):4532-4545. doi: 10.18632/oncotarget.27027. eCollection 2019 Jul 16.


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

Kim W, Cavinder B, Proctor RH, O'Donnell K, Townsend JP, Trail F.

Front Microbiol. 2019 Jun 7;10:1247. doi: 10.3389/fmicb.2019.01247. eCollection 2019.


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

Goedel WC, King MRF, Lurie MN, Galea S, Townsend JP, Galvani AP, Friedman SR, Marshall BDL.

Clin Infect Dis. 2019 May 30. pii: ciz321. doi: 10.1093/cid/ciz321. [Epub ahead of print]


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

Wang Z, Miguel-Rojas C, Lopez-Giraldez F, Yarden O, Trail F, Townsend JP.

MBio. 2019 Mar 26;10(2). pii: e00192-19. doi: 10.1128/mBio.00192-19.


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

Lee 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.

Clin Cancer Res. 2019 Jun 1;25(11):3430-3442. doi: 10.1158/1078-0432.CCR-18-0440. Epub 2019 Feb 12.


Wagging the long tail of drivers of prostate cancer.

Cannataro VL, Townsend JP.

PLoS Genet. 2019 Jan 17;15(1):e1007820. doi: 10.1371/journal.pgen.1007820. eCollection 2019 Jan. No abstract available.


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

Cannataro VL, Gaffney SG, Sasaki T, Issaeva N, Grewal NKS, Grandis JR, Yarbrough WG, Burtness B, Anderson KS, Townsend JP.

Oncogene. 2019 May;38(18):3475-3487. doi: 10.1038/s41388-018-0657-6. Epub 2019 Jan 15.


Increased surfactant protein-D levels in the airways of preterm neonates with sepsis indicated responses to infectious challenges.

Mackay RA, Townsend JP, Calvert J, Anthony M, Wilkinson AR, Postle AD, Clark HW, Todd DA.

Acta Paediatr. 2019 May;108(5):870-876. doi: 10.1111/apa.14630. Epub 2019 Jan 8.


Effect Sizes of Somatic Mutations in Cancer.

Cannataro VL, Gaffney SG, Townsend JP.

J Natl Cancer Inst. 2018 Nov 1;110(11):1171-1177. doi: 10.1093/jnci/djy168.


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

Kim W, Miguel-Rojas C, Wang J, Townsend JP, Trail F.

MBio. 2018 Aug 14;9(4). pii: e01292-18. doi: 10.1128/mBio.01292-18.


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

Santos 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 Jr.

Front Cell Infect Microbiol. 2018 Jun 19;8:193. doi: 10.3389/fcimb.2018.00193. eCollection 2018.


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

Dornburg A, Su Z, Townsend JP.

Syst Biol. 2019 Jan 1;68(1):145-156. doi: 10.1093/sysbio/syy047.


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

Marshall BDL, Goedel WC, King MRF, Singleton A, Durham DP, Chan PA, Townsend JP, Galvani AP.

Lancet HIV. 2018 Sep;5(9):e498-e505. doi: 10.1016/S2352-3018(18)30097-3. Epub 2018 Jun 13.


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

Wilkins JF, Cannataro VL, Shuch B, Townsend JP.

Oncotarget. 2018 Apr 27;9(32):22243-22253. doi: 10.18632/oncotarget.25155. eCollection 2018 Apr 27.


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.

Ann Oncol. 2018 Apr 1;29(4):1072. doi: 10.1093/annonc/mdx062. No abstract available.


Neutral Theory and the Somatic Evolution of Cancer.

Cannataro VL, Townsend JP.

Mol Biol Evol. 2018 Jun 1;35(6):1308-1315. doi: 10.1093/molbev/msy079. Erratum in: Mol Biol Evol. 2018 Jun 1;35(6):1561.


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

Chen WS, Bindra RS, Mo A, Hayman T, Husain Z, Contessa JN, Gaffney SG, Townsend JP, Yu JB.

Front Oncol. 2018 Apr 4;8:95. doi: 10.3389/fonc.2018.00095. eCollection 2018.


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

Adhikarla H, Wunder EA Jr, Mechaly AE, Mehta S, Wang Z, Santos L, Bisht V, Diggle P, Murray G, Adler B, Lopez F, Townsend JP, Groisman E, Picardeau M, Buschiazzo A, Ko AI.

Front Cell Infect Microbiol. 2018 Feb 23;8:45. doi: 10.3389/fcimb.2018.00045. eCollection 2018.


QMCPACK: an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids.

Kim J, Baczewski AT, Beaudet TD, Benali A, Bennett MC, Berrill MA, Blunt NS, Borda EJL, Casula M, Ceperley DM, Chiesa S, Clark BK, Clay RC, Delaney KT, Dewing M, Esler KP, Hao H, Heinonen O, Kent PRC, Krogel JT, Kylänpää I, Li YW, Lopez MG, Luo Y, Malone FD, Martin RM, Mathuriya A, McMinis J, Melton CA, Mitas L, Morales MA, Neuscamman E, Parker WD, Pineda Flores SD, Romero NA, Rubenstein BM, Shea JAR, Shin H, Shulenburger L, Tillack AF, Townsend JP, Tubman NM, Van Der Goetz B, Vincent JE, Yang DC, Yang Y, Zhang S, Zhao L.

J Phys Condens Matter. 2018 May 16;30(19):195901. doi: 10.1088/1361-648X/aab9c3. Epub 2018 Mar 27.


The Cancer Tree.

Townsend JP.

Sci Am. 2018 Mar 20;318(4):34-41. doi: 10.1038/scientificamerican0418-34. No abstract available.


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

Zhao ZM, Wang J, Ugwuowo UC, Wang L, Townsend JP.

BMC Clin Pathol. 2018 Mar 1;18:3. doi: 10.1186/s12907-018-0070-7. eCollection 2018.


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

Cannataro VL, Gaffney SG, Stender C, Zhao ZM, Philips M, Greenstein AE, Townsend JP.

Oncogene. 2018 May;37(18):2444-2455. doi: 10.1038/s41388-017-0105-z. Epub 2018 Feb 16.


Somatic evolutionary timings of driver mutations.

Gomez K, Miura S, Huuki LA, Spell BS, Townsend JP, Kumar S.

BMC Cancer. 2018 Jan 18;18(1):85. doi: 10.1186/s12885-017-3977-y.



Townsend JP, Wang Z.

Adv Genet. 2017;100:xi-xii. doi: 10.1016/S0065-2660(17)30059-7. No abstract available.


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

Dornburg A, Townsend JP, Wang Z.

Adv Genet. 2017;100:1-47. doi: 10.1016/bs.adgen.2017.09.007. Epub 2017 Nov 6.


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

Wang Z, Wang J, Li N, Li J, Trail F, Dunlap JC, Townsend JP.

Mol Ecol. 2018 Jan;27(1):216-232. doi: 10.1111/mec.14425. Epub 2017 Dec 12.


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.

Mol Biol Evol. 2017 Nov 1;34(11):3006-3022. doi: 10.1093/molbev/msx213.


Eye patches: Protein assembly of index-gradient squid lenses.

Cai J, Townsend JP, Dodson TC, Heiney PA, Sweeney AM.

Science. 2017 Aug 11;357(6351):564-569. doi: 10.1126/science.aal2674.


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

Trail F, Wang Z, Stefanko K, Cubba C, Townsend JP.

PLoS Genet. 2017 Jul 13;13(7):e1006867. doi: 10.1371/journal.pgen.1006867. eCollection 2017 Jul.


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

Chen WS, Townsend JP, Yu JB.

Int J Radiat Oncol Biol Phys. 2017 May 1;98(1):8-10. doi: 10.1016/j.ijrobp.2017.01.023. Epub 2017 Jan 16. No abstract available.


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

Park B, Rutter MT, Fenster CB, Symonds VV, Ungerer MC, Townsend JP.

Genetics. 2017 Aug;206(4):2105-2117. doi: 10.1534/genetics.116.199190. Epub 2017 May 26.


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

Dornburg A, Townsend JP, Brooks W, Spriggs E, Eytan RI, Moore JA, Wainwright PC, Lemmon A, Lemmon EM, Near TJ.

Mol Phylogenet Evol. 2017 May;110:27-38. doi: 10.1016/j.ympev.2017.02.017. Epub 2017 Feb 27.


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, 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.

Ann Oncol. 2017 Jan 1;28(1):83-89. doi: 10.1093/annonc/mdw437.


One Health approach to cost-effective rabies control in India.

Fitzpatrick MC, Shah HA, Pandey A, Bilinski AM, Kakkar M, Clark AD, Townsend JP, Abbas SS, Galvani AP.

Proc Natl Acad Sci U S A. 2016 Dec 20;113(51):14574-14581. doi: 10.1073/pnas.1604975113.


PhyInformR: phylogenetic experimental design and phylogenomic data exploration in R.

Dornburg A, Fisk JN, Tamagnan J, Townsend JP.

BMC Evol Biol. 2016 Dec 1;16(1):262.


PhyloOncology: Understanding cancer through phylogenetic analysis.

Somarelli JA, Ware KE, Kostadinov R, Robinson JM, Amri H, Abu-Asab M, Fourie N, Diogo R, Swofford D, Townsend JP.

Biochim Biophys Acta Rev Cancer. 2017 Apr;1867(2):101-108. doi: 10.1016/j.bbcan.2016.10.006. Epub 2016 Oct 31. Review.


Vaccination strategies against respiratory syncytial virus.

Yamin D, Jones FK, DeVincenzo JP, Gertler S, Kobiler O, Townsend JP, Galvani AP.

Proc Natl Acad Sci U S A. 2016 Nov 15;113(46):13239-13244. Epub 2016 Oct 31.


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

Lewnard JA, Townsend JP.

Proc Natl Acad Sci U S A. 2016 Dec 20;113(51):14601-14608. doi: 10.1073/pnas.1604985113. Epub 2016 Oct 24.


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.

Ann Oncol. 2017 Jan 1;28(1):75-82. doi: 10.1093/annonc/mdw436. Erratum in: Ann Oncol. 2018 Apr 1;29(4):1072.


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

Gaffney SG, Townsend JP.

Bioinformatics. 2016 Dec 1;32(23):3688-3690. Epub 2016 Aug 8.


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

Atkins KE, Fitzpatrick MC, Galvani AP, Townsend JP.

Am J Epidemiol. 2016 Jun 15;183(12):1159-70. doi: 10.1093/aje/kwv347. Epub 2016 May 13.


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

Fitzpatrick MC, Wenzel NS, Scarpino SV, Althouse BM, Atkins KE, Galvani AP, Townsend JP.

Vaccine. 2016 Jun 17;34(29):3405-11. doi: 10.1016/j.vaccine.2016.04.010. Epub 2016 Apr 14.


Quantifying Transmission of Clostridium difficile within and outside Healthcare Settings.

Durham DP, Olsen MA, Dubberke ER, Galvani AP, Townsend JP.

Emerg Infect Dis. 2016 Apr;22(4):608-16. doi: 10.3201/eid2204.150455.


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

Wang Z, Li N, Li J, Dunlap JC, Trail F, Townsend JP.

MBio. 2016 Mar 8;7(2):e02148. doi: 10.1128/mBio.02148-15.


Determinants of Human African Trypanosomiasis Elimination via Paratransgenesis.

Gilbert JA, Medlock J, Townsend JP, Aksoy S, Ndeffo Mbah M, Galvani AP.

PLoS Negl Trop Dis. 2016 Mar 8;10(3):e0004465. doi: 10.1371/journal.pntd.0004465. eCollection 2016 Mar.


Crystal Structure of a Complex of Surfactant Protein D (SP-D) and Haemophilus influenzae Lipopolysaccharide Reveals Shielding of Core Structures in SP-D-Resistant Strains.

Clark HW, Mackay RM, Deadman ME, Hood DW, Madsen J, Moxon ER, Townsend JP, Reid KBM, Ahmed A, Shaw AJ, Greenhough TJ, Shrive AK.

Infect Immun. 2016 Apr 22;84(5):1585-1592. doi: 10.1128/IAI.01239-15. Print 2016 May.


Early and multiple origins of metastatic lineages within primary tumors.

Zhao ZM, Zhao B, Bai Y, Iamarino A, Gaffney SG, Schlessinger J, Lifton RP, Rimm DL, Townsend JP.

Proc Natl Acad Sci U S A. 2016 Feb 23;113(8):2140-5. doi: 10.1073/pnas.1525677113. Epub 2016 Feb 8.


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

Sistrom M, Park D, O'Brien HE, Wang Z, Guttman DS, Townsend JP, Turner PE.

PLoS One. 2015 Dec 15;10(12):e0144514. doi: 10.1371/journal.pone.0144514. eCollection 2015.

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