Select Publications
- Tracing the evolution of single-cell cancer 3D genomes: an atlas for cancer gene discovery.Liu M, Jin S, Agabiti SS, Jensen TB, Yang T, Radda JSD, Ruiz CF, Baldissera G, Rajaei M, Townsend JP, Muzumdar MD, Wang S. bioRxiv. 2024 Sep 9; 2024 Sep 9. PMID: 37546882.
- Genomic Landscape of Osteosarcoma of Bone in an Older-Aged Patient Population and Analysis of Possible Etiologies Based on Molecular Signature.Kaseb H, Tan C, Townsend JP, Costa J, Laskin WB. Genet Test Mol Biomarkers. 2024 Sep; 2024 Jul 25. PMID: 39052504.
- Varying the intensity of cystoscopic surveillance for high-risk non-muscle-invasive bladder cancer.Su ZT, Florissi IS, Mahon KM, Li T, Rezaee ME, Singla N, Patel SH, Townsend JP, Kates MR. BJU Int. 2024 Aug 29; 2024 Aug 29. PMID: 39210627.
- Corrigendum: The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomics.Wang Z, Kim W, Wang YW, Yakubovich E, Dong C, Trail F, Townsend JP, Yarden O. Front Fungal Biol. 2024; 2024 Aug 20. PMID: 39228963.
- Perioperative Modified FOLFIRINOX for Resectable Pancreatic Cancer: A Nonrandomized Controlled Trial.Cecchini M, Salem RR, Robert M, Czerniak S, Blaha O, Zelterman D, Rajaei M, Townsend JP, Cai G, Chowdhury S, Yugawa D, Tseng R, Mejia Arbelaez C, Jiao J, Shroyer K, Thumar J, Kortmansky J, Zaheer W, Fischbach N, Persico J, Stein S, Khan SA, Cha C, Billingsley KG, Kunstman JW, Johung KL, Wiess C, Muzumdar MD, Spickard E, Aushev VN, Laliotis G, Jurdi A, Liu MC, Escobar-Hoyos L, Lacy J. JAMA Oncol. 2024 Aug 1. PMID: 38900452.
- Sufficient COVID-19 quarantine and testing on international travelers to forestall cross-border transmission after China's removal of the zero-COVID policy in early 2023.Bojja D, Zuo S, Townsend JP. Int J Infect Dis. 2024 Aug; 2024 May 14. PMID: 38750721.
- Rare Drivers at Low Prevalence with High Cancer Effects in T-Cell and B-Cell Pediatric Acute Lymphoblastic Leukemia.Mandell JD, Diviti S, Xu M, Townsend JP. Int J Mol Sci. 2024 Jun 15; 2024 Jun 15. PMID: 38928295.
- Novel non-invasive molecular signatures for oral cavity cancer, by whole transcriptome and small non-coding RNA sequencing analyses: Predicted association with PI3K/AKT/mTOR pathway.Vageli DP, Doukas PG, Townsend JP, Pickering C, Judson BL. Cancer Med. 2024 Jun. PMID: 38819439.
- Seasonality of endemic COVID-19.Townsend JP, Hassler HB, Lamb AD, Sah P, Alvarez Nishio A, Nguyen C, Tew AD, Galvani AP, Dornburg A. mBio. 2023 Dec 19; 2023 Nov 8. PMID: 37937979.
- Infection with alternate frequencies of SARS-CoV-2 vaccine boosting for patients undergoing antineoplastic cancer treatments.Townsend JP, Hassler HB, Emu B, Dornburg A. J Natl Cancer Inst. 2023 Dec 6. PMID: 37599438.
- Pairwise and higher-order epistatic effects among somatic cancer mutations across oncogenesis.Alfaro-Murillo JA, Townsend JP. Math Biosci. 2023 Dec; 2023 Nov 22. PMID: 37996064.
- Lineage-specific genes are clustered with HET-domain genes and respond to environmental and genetic manipulations regulating reproduction in Neurospora.Wang Z, Wang YW, Kasuga T, Lopez-Giraldez F, Zhang Y, Zhang Z, Wang Y, Dong C, Sil A, Trail F, Yarden O, Townsend JP. PLoS Genet. 2023 Nov; 2023 Nov 7. PMID: 37934795.
- Origins of lineage-specific elements via gene duplication, relocation, and regional rearrangement in Neurospora crassa.Wang Z, Wang YW, Kasuga T, Hassler H, Lopez-Giraldez F, Dong C, Yarden O, Townsend JP. Mol Ecol. 2023 Oct 16; 2023 Oct 16. PMID: 37843462.
- The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomics.Wang Z, Kim W, Wang YW, Yakubovich E, Dong C, Trail F, Townsend JP, Yarden O. Front Fungal Biol. 2023; 2023 Jun 30. PMID: 37746130.
- Comparative Transcriptomics of Fusarium graminearum and Magnaporthe oryzae Spore Germination Leading up To Infection.Miguel-Rojas C, Cavinder B, Townsend JP, Trail F. mBio. 2023 Feb 28; 2023 Jan 4. PMID: 36598191.
- Estimation of Neutral Mutation Rates and Quantification of Somatic Variant Selection Using cancereffectsizeR.Mandell JD, Cannataro VL, Townsend JP. Cancer Res. 2023 Feb 15. PMID: 36469362.
- Quantifying the feeding behavior and trophic impact of a widespread oceanic ctenophore.Potter B, Corrales-Ugalde M, Townsend JP, Colin SP, Sutherland KR, Costello JH, Collins R, Gemmell BJ. Sci Rep. 2023 Feb 9; 2023 Feb 9. PMID: 36759558.
- Infection by SARS-CoV-2 with alternate frequencies of mRNA vaccine boosting.Townsend JP, Hassler HB, Dornburg A. J Med Virol. 2023 Feb. PMID: 36602045.
- In Response to "De Novo KRAS G12C-Mutant SCLC: A Case Report".Moore M, Zhuo Y, Mandell JD, Gaffney SG, Townsend JP. JTO Clin Res Rep. 2022 Dec; 2022 Sep 27. PMID: 36590382.
- 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.Mandell JD, Fisk JN, Cyrenne E, Xu ML, Cannataro VL, Townsend JP. Leukemia. 2022 Dec; 2022 Nov 11. PMID: 36369483.
- Placing human gene families into their evolutionary context.Dornburg A, Mallik R, Wang Z, Bernal MA, Thompson B, Bruford EA, Nebert DW, Vasiliou V, Yohe LR, Yoder JA, Townsend JP. Hum Genomics. 2022 Nov 11; 2022 Nov 11. PMID: 36369063.
- Clone Phylogenetics Reveals Metastatic Tumor Migrations, Maps, and Models.Chroni A, Miura S, Hamilton L, Vu T, Gaffney SG, Aly V, Karim S, Sanderford M, Townsend JP, Kumar S. Cancers (Basel). 2022 Sep 4; 2022 Sep 4. PMID: 36077861.
- APOBEC mutagenesis and selection for NFE2L2 contribute to the origin of lung squamous-cell carcinoma.Cannataro VL, Kudalkar S, Dasari K, Gaffney SG, Lazowski HM, Jackson LK, Yildiz I, Das RK, Gould Rothberg BE, Anderson KS, Townsend JP. Lung Cancer. 2022 Sep; 2022 Jul 9. PMID: 35872531.
- Differential Expression of Cell Wall Remodeling Genes Is Part of the Dynamic Phase-Specific Transcriptional Program of Conidial Germination of Trichoderma asperelloides.Gortikov M, Yakubovich E, Wang Z, López-Giráldez F, Tu Y, Townsend JP, Yarden O. J Fungi (Basel). 2022 Aug 15; 2022 Aug 15. PMID: 36012842.
- The durability of natural infection and vaccine-induced immunity against future infection by SARS-CoV-2.Townsend JP, Hassler HB, Sah P, Galvani AP, Dornburg A. Proc Natl Acad Sci U S A. 2022 Aug 2; 2022 Jul 15. PMID: 35858382.
- Testing for COVID-19 is Much More Effective When Performed Immediately Prior to Social Mixing.Wells CR, Gokcebel S, Pandey A, Galvani AP, Townsend JP. Int J Public Health. 2022; 2022 Jul 27. PMID: 35967267.
- Quarantine and serial testing for variants of SARS-CoV-2 with benefits of vaccination and boosting on consequent control of COVID-19.Wells CR, Pandey A, Gokcebel S, Krieger G, Donoghue AM, Singer BH, Moghadas SM, Galvani AP, Townsend JP. PNAS Nexus. 2022 Jul; 2022 Jul 27. PMID: 35909795.
- Cancer Relevance of Human Genes.Qing T, Mohsen H, Cannataro VL, Marczyk M, Rozenblit M, Foldi J, Murray M, Townsend JP, Kluger Y, Gerstein M, Pusztai L. J Natl Cancer Inst. 2022 Jul 11. PMID: 35417011.
- Comparative analyses of eighteen rapid antigen tests and RT-PCR for COVID-19 quarantine and surveillance-based isolation.Wells CR, Pandey A, Moghadas SM, Singer BH, Krieger G, Heron RJL, Turner DE, Abshire JP, Phillips KM, Michael Donoghue A, Galvani AP, Townsend JP. Commun Med (Lond). 2022; 2022 Jul 9. PMID: 35822105.
- Jot: guiding journal selection with suitability metrics.Gaffney SG, Townsend JP. J Med Libr Assoc. 2022 Jul 1. PMID: 36589304.
- Transcriptional Divergence Underpinning Sexual Development in the Fungal Class Sordariomycetes.Kim W, Wang Z, Kim H, Pham K, Tu Y, Townsend JP, Trail F. mBio. 2022 Jun 28; 2022 May 31. PMID: 35638737.
- Secondary Metabolism Gene Clusters Exhibit Increasingly Dynamic and Differential Expression during Asexual Growth, Conidiation, and Sexual Development in Neurospora crassa.Wang Z, Lopez-Giraldez F, Slot J, Yarden O, Trail F, Townsend JP. mSystems. 2022 Jun 28; 2022 May 31. PMID: 35638725.
- A phylogenetic approach to study the evolution of somatic mutational processes in cancer.Miura S, Vu T, Choi J, Townsend JP, Karim S, Kumar S. Commun Biol. 2022 Jun 22; 2022 Jun 22. PMID: 35732905.
- Attribution of Cancer Origins to Endogenous, Exogenous, and Preventable Mutational Processes.Cannataro VL, Mandell JD, Townsend JP. Mol Biol Evol. 2022 May 3. PMID: 35580068.
- 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.Tan C, Mandell JD, Dasari K, Cannataro VL, Alfaro-Murillo JA, Townsend JP. Lung Cancer. 2022 Apr; 2021 Oct 28. PMID: 34736794.
- 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. Lancet Reg Health Eur. 2022 Mar; 2022 Jan 10. PMID: 35036981.
- Chiropteran chatter in Chautauqua, NY (USA): Using acoustic sampling and geographic information systems to create a baseline bat habitat dataset.Townsend JP, Renschler CS, Aldstadt J. Sci Total Environ. 2022 Mar 1; 2021 Dec 13. PMID: 34915009.
- 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. Microbiol Resour Announc. 2022 Feb 17; 2022 Feb 17. PMID: 35175124.
- Premetastatic shifts of endogenous and exogenous mutational processes support consolidative therapy in EGFR-driven lung adenocarcinoma.Fisk JN, Mahal AR, Dornburg A, Gaffney SG, Aneja S, Contessa JN, Rimm D, Yu JB, Townsend JP. Cancer Lett. 2022 Feb 1; 2021 Nov 12. PMID: 34780851.
- Environmental and sex-specific molecular signatures of glioma causation.Claus EB, Cannataro VL, Gaffney SG, Townsend JP. Neuro Oncol. 2022 Jan 5. PMID: 33942853.
- 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.Townsend JP, Wells CR. J Mol Diagn. 2022 Jan. PMID: 34974875.
- 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. medRxiv. 2021 Dec 17; 2021 Dec 17. PMID: 34729563.
- TIAMMAt: Leveraging Biodiversity to Revise Protein Domain Models, Evidence from Innate Immunity.Tassia MG, David KT, Townsend JP, Halanych KM. Mol Biol Evol. 2021 Dec 9. PMID: 34459919.
- The durability of immunity against reinfection by SARS-CoV-2: a comparative evolutionary study.Townsend JP, Hassler HB, Wang Z, Miura S, Singh J, Kumar S, Ruddle NH, Galvani AP, Dornburg A. Lancet Microbe. 2021 Dec; 2021 Oct 1. PMID: 34632431.
- The somatic molecular evolution of cancer: Mutation, selection, and epistasis.Dasari K, Somarelli JA, Kumar S, Townsend JP. Prog Biophys Mol Biol. 2021 Oct; 2021 Aug 6. PMID: 34364910.
- Chemsearch: collaborative compound libraries with structure-aware browsing.Gaffney SG, Smaga S, Schepartz A, Townsend JP. Bioinform Adv. 2021; 2021 Jul 16. PMID: 36700113.
- Cool your jets: biological jet propulsion in marine invertebrates.Gemmell BJ, Dabiri JO, Colin SP, Costello JH, Townsend JP, Sutherland KR. J Exp Biol. 2021 Jun 15; 2021 Jun 17. PMID: 34137893.
- Mechanistic basis of post-treatment control of SIV after anti-α4β7 antibody therapy.Wells CR, Cao Y, Durham DP, Byrareddy SN, Ansari AA, Ruddle NH, Townsend JP, Galvani AP, Perelson AS. PLoS Comput Biol. 2021 Jun; 2021 Jun 9. PMID: 34106916.
- The GUL-1 Protein Binds Multiple RNAs Involved in Cell Wall Remodeling and Affects the MAK-1 Pathway in Neurospora crassa.Herold I, Zolti A, Garduño-Rosales M, Wang Z, López-Giráldez F, Mouriño-Pérez RR, Townsend JP, Ulitsky I, Yarden O. Front Fungal Biol. 2021; 2021 Apr 16. PMID: 37744127.
- Developing Biohybrid Robotic Jellyfish (Aurelia aurita) for Free-swimming Tests in the Laboratory and in the Field.Xu NW, Townsend JP, Costello JH, Colin SP, Gemmell BJ, Dabiri JO. Bio Protoc. 2021 Apr 5; 2021 Apr 5. PMID: 33889668.
- Identifying modules of cooperating cancer drivers.Klein MI, Cannataro VL, Townsend JP, Newman S, Stern DF, Zhao H. Mol Syst Biol. 2021 Mar. PMID: 33769711.
- Melting and density of MgSiO(3) determined by shock compression of bridgmanite to 1254GPa.Fei Y, Seagle CT, Townsend JP, McCoy CA, Boujibar A, Driscoll P, Shulenburger L, Furnish MD. Nat Commun. 2021 Feb 9; 2021 Feb 9. PMID: 33563984.
- Optimal COVID-19 quarantine and testing strategies.Wells CR, Townsend JP, Pandey A, Moghadas SM, Krieger G, Singer B, McDonald RH, Fitzpatrick MC, Galvani AP. Nat Commun. 2021 Jan 7; 2021 Jan 7. PMID: 33414470.
- Comparative Genomics within and across Bilaterians Illuminates the Evolutionary History of ALK and LTK Proto-Oncogene Origination and Diversification.Dornburg A, Wang Z, Wang J, Mo ES, López-Giráldez F, Townsend JP. Genome Biol Evol. 2021 Jan 7. PMID: 33196781.
- Postnatal adaptations of phosphatidylcholine metabolism in extremely preterm infants: implications for choline and PUFA metabolism.Goss KCW, Goss VM, Townsend JP, Koster G, Clark HW, Postle AD. Am J Clin Nutr. 2020 Dec 10. PMID: 32778895.
- Optimal COVID-19 quarantine and testing strategies.Wells CR, Townsend JP, Pandey A, Moghadas SM, Krieger G, Singer B, McDonald RH, Fitzpatrick MC, Galvani AP. medRxiv. 2020 Nov 30; 2020 Nov 30. PMID: 33173923.
- Field Testing of Biohybrid Robotic Jellyfish to Demonstrate Enhanced Swimming Speeds.Xu NW, Townsend JP, Costello JH, Colin SP, Gemmell BJ, Dabiri JO. Biomimetics (Basel). 2020 Nov 21; 2020 Nov 21. PMID: 33233340.
- Getting quantitative on the effects of somatic mutation on cancer.Townsend JP. Oncoscience. 2020 Nov; 2020 Oct 27. PMID: 33457449.
- Dogs and pigs are transport hosts of Necator americanus: Molecular evidence for a zoonotic mechanism of human hookworm transmission in Ghana.Boyko RH, Marie Harrison L, Humphries D, Galvani AP, Townsend JP, Otchere J, Wilson MD, Cappello M. Zoonoses Public Health. 2020 Aug; 2020 Jun 11. PMID: 32529782.
- Unmatched Level of Molecular Convergence among Deeply Divergent Complex Multicellular Fungi.Merényi Z, Prasanna AN, Wang Z, Kovács K, Hegedüs B, Bálint B, Papp B, Townsend JP, Nagy LG. Mol Biol Evol. 2020 Aug 1. PMID: 32191325.
- Non-Coding Mutations in Urothelial Bladder Cancer: Biological and Clinical Relevance and Potential Utility as Biomarkers.Yang A, Cross CN, Townsend JP. Bladder Cancer. 2020 Jun 11; 2020 Jun 11. PMID: 32793790.
- Ink Release and Swimming Behavior in the Oceanic Ctenophore Eurhamphaea vexilligera.Townsend JP, Gemmell BJ, Sutherland KR, Colin SP, Costello JH. Biol Bull. 2020 Jun; 2020 Jun 8. PMID: 32597720.
- Germline variant burden in cancer genes correlates with age at diagnosis and somatic mutation burden.Qing T, Mohsen H, Marczyk M, Ye Y, O'Meara T, Zhao H, Townsend JP, Gerstein M, Hatzis C, Kluger Y, Pusztai L. Nat Commun. 2020 May 15; 2020 May 15. PMID: 32415133.
- 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. 2020 Mar 3. PMID: 31143944.
- Molecular Biology and Evolution of Cancer: From Discovery to Action.Somarelli 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. Mol Biol Evol. 2020 Feb 1. PMID: 31642480.
- 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.Yang A, Cannataro VL, Townsend JP. Eur Urol. 2020 Jan; 2019 Aug 30. PMID: 31474441.
- Integrative Activity of Mating Loci, Environmentally Responsive Genes, and Secondary Metabolism Pathways during Sexual Development of Chaetomium globosum.Wang Z, López-Giráldez F, Wang J, Trail F, Townsend JP. mBio. 2019 Dec 10; 2019 Dec 10. PMID: 31822585.
- Modelling microbial infection to address global health challenges.Fitzpatrick MC, Bauch CT, Townsend JP, Galvani AP. Nat Microbiol. 2019 Oct; 2019 Sep 20. PMID: 31541212.
- 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; 2019 Jul 12. PMID: 31404233.
- 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; 2019 Jul 16. PMID: 31360302.
- A multigene phylogeny toward a new phylogenetic classification of Leotiomycetes.Johnston 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. IMA Fungus. 2019; 2019 Jun 7. PMID: 32647610.
- 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; 2019 Jun 7. PMID: 31231336.
- 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; 2019 Feb 12. PMID: 30755439.
- 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; 2019 Jan 15. PMID: 30647454.
- 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; 2019 Jan 8. PMID: 30375054.
- 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; 2019 Mar 26. PMID: 30914504.
- Catecholic Compounds in Ctenophore Colloblast and Nerve Net Proteins Suggest a Structural Role for DOPA-Like Molecules in an Early-Diverging Animal Lineage.Townsend JP, Sweeney AM. Biol Bull. 2019 Feb; 2018 Dec 10. PMID: 30707604.
- Wagging the long tail of drivers of prostate cancer.Cannataro VL, Townsend JP. PLoS Genet. 2019 Jan; 2019 Jan 17. PMID: 30653503.
- 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. PMID: 29939341.
- Effect Sizes of Somatic Mutations in Cancer.Cannataro VL, Gaffney SG, Townsend JP. J Natl Cancer Inst. 2018 Nov 1. PMID: 30365005.
- 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; 2018 Jun 13. PMID: 29908917.
- 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; 2018 Aug 14. PMID: 30108170.
- 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; 2018 Jun 19. PMID: 29971217.
- Neutral Theory and the Somatic Evolution of Cancer.Cannataro VL, Townsend JP. Mol Biol Evol. 2018 Jun 1. PMID: 29684198.
- 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; 2018 Mar 27. PMID: 29582782.
- 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; 2018 Feb 16. PMID: 29453361.
- 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; 2018 Apr 27. PMID: 29854275.
- Evidence for Extending Anomalous Miocene Volcanism at the Edge of the East Antarctic Craton.Licht KJ, Groth T, Townsend JP, Hennessy AJ, Hemming SR, Flood TP, Studinger M. Geophys Res Lett. 2018 Apr 16; 2018 Mar 26. PMID: 33122867.
- 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; 2018 Apr 4. PMID: 29670856.
- 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. PMID: 29688333.
- The Cancer Tree.Townsend JP. Sci Am. 2018 Mar 20. PMID: 29557973.
- 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; 2018 Mar 1. PMID: 29507528.
- 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; 2018 Feb 23. PMID: 29600195.
- Somatic evolutionary timings of driver mutations.Gomez K, Miura S, Huuki LA, Spell BS, Townsend JP, Kumar S. BMC Cancer. 2018 Jan 18; 2018 Jan 18. PMID: 29347918.
- 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; 2017 Dec 12. PMID: 29134709.
- 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. PMID: 28962009.
- Eye patches: Protein assembly of index-gradient squid lenses.Cai J, Townsend JP, Dodson TC, Heiney PA, Sweeney AM. Science. 2017 Aug 11. PMID: 28798124.
- 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; 2017 May 26. PMID: 28550014.
- 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; 2017 Jul 13. PMID: 28704372.
- 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; 2017 Jan 16. PMID: 28587055.