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Items: 1 to 50 of 139

1.

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.

2.

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.

3.

Optimal rates for phylogenetic inference and experimental design in the era of genome-scale datasets.

Dornburg A, Su Z, Townsend JP.

Syst Biol. 2018 Jun 25. doi: 10.1093/sysbio/syy047. [Epub ahead of print]

PMID:
29939341
4.

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 Jun 13. pii: S2352-3018(18)30097-3. doi: 10.1016/S2352-3018(18)30097-3. [Epub ahead of print]

PMID:
29908917
5.

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.

6.

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.

PMID:
29688333
7.

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.

PMID:
29684198
8.

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.

9.

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.

10.

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.

PMID:
29582782
11.

The Cancer Tree.

Townsend JP.

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

PMID:
29557973
12.

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.

13.

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.

PMID:
29453361
14.

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.

15.

Preface.

Townsend JP, Wang Z.

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

PMID:
29153406
16.

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.

PMID:
29153398
17.

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.

PMID:
29134709
18.

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.

PMID:
28962009
19.

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.

20.

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.

21.

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.

PMID:
28587055
22.

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.

23.

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.

PMID:
28254474
24.

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.

PMID:
28177435
25.

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.

26.

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.

27.

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

PMID:
27810337
28.

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.

29.

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.

30.

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.

31.

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.

PMID:
27503224
32.

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.

33.

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.

PMID:
27087151
34.

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.

35.

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.

36.

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.

37.

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.

38.

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.

39.

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.

40.

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

Alfaro-Murillo JA, Townsend JP, Galvani AP.

Vaccine. 2016 Jan 4;34(2):225-229. doi: 10.1016/j.vaccine.2015.11.039. Epub 2015 Nov 27.

PMID:
26631416
41.

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

Durham DP, Skrip LA, Bruce RD, Vilarinho S, Elbasha EH, Galvani AP, Townsend JP.

Clin Infect Dis. 2016 Feb 1;62(3):298-304. doi: 10.1093/cid/civ894. Epub 2015 Nov 30.

42.

Impact of bed capacity on spatiotemporal shifts in Ebola transmission.

Townsend JP, Skrip LA, Galvani AP.

Proc Natl Acad Sci U S A. 2015 Nov 17;112(46):14125-6. doi: 10.1073/pnas.1518484112. Epub 2015 Oct 30. No abstract available.

43.

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

Prum RO, Berv JS, Dornburg A, Field DJ, Townsend JP, Lemmon EM, Lemmon AR.

Nature. 2015 Oct 22;526(7574):569-73. doi: 10.1038/nature15697. Epub 2015 Oct 7.

PMID:
26444237
44.

Inferring the Origin of Metastases from Cancer Phylogenies.

Hong WS, Shpak M, Townsend JP.

Cancer Res. 2015 Oct 1;75(19):4021-5. doi: 10.1158/0008-5472.CAN-15-1889. Epub 2015 Aug 10. Review.

45.

Correction: Harnessing Case Isolation and Ring Vaccination to Control Ebola.

Wells C, Yamin D, Ndeffo-Mbah ML, Wenzel N, Gaffney SG, Townsend JP, Meyers LA, Fallah M, Nyenswah TG, Altice FL, Atkins KE, Galvani AP.

PLoS Negl Trop Dis. 2015 Jun 24;9(6):e0003888. doi: 10.1371/journal.pntd.0003888. eCollection 2015 Jun. No abstract available.

46.

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

Hwang J, Zhao Q, Yang ZL, Wang Z, Townsend JP.

Environ Microbiol Rep. 2015 Aug;7(4):658-67. doi: 10.1111/1758-2229.12303. Epub 2015 Jul 1.

PMID:
26033481
47.

Harnessing case isolation and ring vaccination to control Ebola.

Wells C, Yamin D, Ndeffo-Mbah ML, Wenzel N, Gaffney SG, Townsend JP, Meyers LA, Fallah M, Nyenswah TG, Altice FL, Atkins KE, Galvani AP.

PLoS Negl Trop Dis. 2015 May 29;9(5):e0003794. doi: 10.1371/journal.pntd.0003794. eCollection 2015 May. Erratum in: PLoS Negl Trop Dis. 2015 Jun;9(6):e0003888.

49.

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

Gilbert JA, Long EF, Brooks RP, Friedland GH, Moll AP, Townsend JP, Galvani AP, Shenoi SV.

PLoS One. 2015 May 4;10(5):e0126267. doi: 10.1371/journal.pone.0126267. eCollection 2015.

50.

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

Hodgins-Davis A, Rice DP, Townsend JP.

Mol Biol Evol. 2015 Aug;32(8):2130-40. doi: 10.1093/molbev/msv094. Epub 2015 Apr 20.

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