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EPIC-CoGe: Managing and Analyzing Genomic Data.

Nelson ADL, Haug-Baltzell AK, Davey S, Gregory BD, Lyons E.

Bioinformatics. 2018 Feb 20. doi: 10.1093/bioinformatics/bty106. [Epub ahead of print]


Digeneans of northern fur seals Callorhinus ursinus (Pinnipedia: Otariidae) from five subpopulations on St. Paul Island, Alaska.

Kuzmina TA, Tkach VV, Spraker TR, Lyons ET, Kudlai O.

Parasitol Res. 2018 Feb 12. doi: 10.1007/s00436-018-5784-z. [Epub ahead of print]


Development of an Outpatient Guideline for Optimal Anticoagulation Bridging in Patients With Durable Mechanical Circulatory Support.

Levesque AA, Rimsans JM, Sylvester KW, Lyons EN, Frankel KA, Coakley LL, Hickey M, Montoya KA, Mehra MR, Givertz MM, Stewart GC, Connors JM.

Crit Pathw Cardiol. 2018 Mar;17(1):32-37. doi: 10.1097/HPC.0000000000000131.


Combination deworming for the control of double-resistant cyathostomin parasites - short and long term consequences.

Scare JA, Lyons ET, Wielgus KM, Nielsen MK.

Vet Parasitol. 2018 Feb 15;251:112-118. doi: 10.1016/j.vetpar.2018.01.010. Epub 2018 Jan 16.


Predictors of enrollment in individual- and couple-based lifestyle intervention trials for cancer survivors.

Cox-Martin E, Song J, Demark-Wahnefried W, Lyons EJ, Basen-Engquist K.

Support Care Cancer. 2018 Feb 8. doi: 10.1007/s00520-018-4084-6. [Epub ahead of print]


Stereotype Threat Effects on Learning From a Cognitively Demanding Mathematics Lesson.

Lyons EM, Simms N, Begolli KN, Richland LE.

Cogn Sci. 2018 Mar;42(2):678-690. doi: 10.1111/cogs.12558. Epub 2017 Dec 1.


Strongyloides westeri worm and egg counts in naturally infected young horses.

Miller FL, Bellaw JL, Lyons ET, Nielsen MK.

Vet Parasitol. 2017 Dec 15;248:1-3. doi: 10.1016/j.vetpar.2017.10.010. Epub 2017 Oct 20.


Veterinarian Nominated Common Conditions of Rabbits and Guinea Pigs Compared with Published Literature.

Robinson NJ, Lyons E, Grindlay D, Brennan ML.

Vet Sci. 2017 Nov 22;4(4). pii: E58. doi: 10.3390/vetsci4040058.


Brief Report: Active Ingredients for Adherence to a Tracker-Based Physical Activity Intervention in Older Adults.

Swartz MC, Lewis ZH, Swartz MD, Martinez E, Lyons EJ.

J Appl Gerontol. 2017 Nov 1:733464817739350. doi: 10.1177/0733464817739350. [Epub ahead of print]


Genome sequence of the progenitor of the wheat D genome Aegilops tauschii.

Luo MC, Gu YQ, Puiu D, Wang H, Twardziok SO, Deal KR, Huo N, Zhu T, Wang L, Wang Y, McGuire PE, Liu S, Long H, Ramasamy RK, Rodriguez JC, Van SL, Yuan L, Wang Z, Xia Z, Xiao L, Anderson OD, Ouyang S, Liang Y, Zimin AV, Pertea G, Qi P, Bennetzen JL, Dai X, Dawson MW, Müller HG, Kugler K, Rivarola-Duarte L, Spannagl M, Mayer KFX, Lu FH, Bevan MW, Leroy P, Li P, You FM, Sun Q, Liu Z, Lyons E, Wicker T, Salzberg SL, Devos KM, Dvořák J.

Nature. 2017 Nov 23;551(7681):498-502. doi: 10.1038/nature24486. Epub 2017 Nov 15.


Large-scale DNA Barcode Library Generation for Biomolecule Identification in High-throughput Screens.

Lyons E, Sheridan P, Tremmel G, Miyano S, Sugano S.

Sci Rep. 2017 Oct 24;7(1):13899. doi: 10.1038/s41598-017-12825-2.


Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments.

Varshney RK, Shi C, Thudi M, Mariac C, Wallace J, Qi P, Zhang H, Zhao Y, Wang X, Rathore A, Srivastava RK, Chitikineni A, Fan G, Bajaj P, Punnuri S, Gupta SK, Wang H, Jiang Y, Couderc M, Katta MAVSK, Paudel DR, Mungra KD, Chen W, Harris-Shultz KR, Garg V, Desai N, Doddamani D, Kane NA, Conner JA, Ghatak A, Chaturvedi P, Subramaniam S, Yadav OP, Berthouly-Salazar C, Hamidou F, Wang J, Liang X, Clotault J, Upadhyaya HD, Cubry P, Rhoné B, Gueye MC, Sunkar R, Dupuy C, Sparvoli F, Cheng S, Mahala RS, Singh B, Yadav RS, Lyons E, Datta SK, Hash CT, Devos KM, Buckler E, Bennetzen JL, Paterson AH, Ozias-Akins P, Grando S, Wang J, Mohapatra T, Weckwerth W, Reif JC, Liu X, Vigouroux Y, Xu X.

Nat Biotechnol. 2017 Oct;35(10):969-976. doi: 10.1038/nbt.3943. Epub 2017 Sep 18.


The feasibility and RE-AIM evaluation of the TAME health pilot study.

Lewis ZH, Ottenbacher KJ, Fisher SR, Jennings K, Brown AF, Swartz MC, Martinez E, Lyons EJ.

Int J Behav Nutr Phys Act. 2017 Aug 14;14(1):106. doi: 10.1186/s12966-017-0560-5.


Physical activity and exercise self-regulation in cancer survivors: A qualitative study.

Tsai E, Robertson MC, Lyons EJ, Swartz MC, Basen-Engquist K.

Psychooncology. 2018 Feb;27(2):563-568. doi: 10.1002/pon.4519. Epub 2017 Sep 29.


Social Media and Mobile Technology for Cancer Prevention and Treatment.

Prochaska JJ, Coughlin SS, Lyons EJ.

Am Soc Clin Oncol Educ Book. 2017;37:128-137. doi: 10.14694/EDBK_173841. Review.


Evolinc: A Tool for the Identification and Evolutionary Comparison of Long Intergenic Non-coding RNAs.

Nelson ADL, Devisetty UK, Palos K, Haug-Baltzell AK, Lyons E, Beilstein MA.

Front Genet. 2017 May 9;8:52. doi: 10.3389/fgene.2017.00052. eCollection 2017.


Wild tobacco genomes reveal the evolution of nicotine biosynthesis.

Xu S, Brockmöller T, Navarro-Quezada A, Kuhl H, Gase K, Ling Z, Zhou W, Kreitzer C, Stanke M, Tang H, Lyons E, Pandey P, Pandey SP, Timmermann B, Gaquerel E, Baldwin IT.

Proc Natl Acad Sci U S A. 2017 Jun 6;114(23):6133-6138. doi: 10.1073/pnas.1700073114. Epub 2017 May 23.


Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms.

Joyce BL, Haug-Baltzell AK, Hulvey JP, McCarthy F, Devisetty UK, Lyons E.

J Vis Exp. 2017 May 9;(123). doi: 10.3791/55009.


A Global View of RNA-Protein Interactions Identifies Post-transcriptional Regulators of Root Hair Cell Fate.

Foley SW, Gosai SJ, Wang D, Selamoglu N, Sollitti AC, Köster T, Steffen A, Lyons E, Daldal F, Garcia BA, Staiger D, Deal RB, Gregory BD.

Dev Cell. 2017 Apr 24;41(2):204-220.e5. doi: 10.1016/j.devcel.2017.03.018.


Effect of Home- and Community-Based Physical Activity Interventions on Physical Function Among Cancer Survivors: A Systematic Review and Meta-Analysis.

Swartz MC, Lewis ZH, Lyons EJ, Jennings K, Middleton A, Deer RR, Arnold D, Dresser K, Ottenbacher KJ, Goodwin JS.

Arch Phys Med Rehabil. 2017 Aug;98(8):1652-1665. doi: 10.1016/j.apmr.2017.03.017. Epub 2017 Apr 17. Review.


SynMap2 and SynMap3D: web-based whole-genome synteny browsers.

Haug-Baltzell A, Stephens SA, Davey S, Scheidegger CE, Lyons E.

Bioinformatics. 2017 Jul 15;33(14):2197-2198. doi: 10.1093/bioinformatics/btx144.


Encysted cyathostomin larvae in foals - progression of stages and the effect of seasonality.

Nielsen MK, Lyons ET.

Vet Parasitol. 2017 Mar 15;236:108-112. doi: 10.1016/j.vetpar.2017.02.013. Epub 2017 Feb 20.


Mobile Health Physical Activity Intervention Preferences in Cancer Survivors: A Qualitative Study.

Robertson MC, Tsai E, Lyons EJ, Srinivasan S, Swartz MC, Baum ML, Basen-Engquist KM.

JMIR Mhealth Uhealth. 2017 Jan 24;5(1):e3. doi: 10.2196/mhealth.6970.


Getting Research on Games for Health Funded.

Baranowski T, Blumberg F, Gao Z, Kato PM, Kok G, Lu AS, Lyons EJ, Morrill BA, Peng W, Prins PJ, Snyder L, Staiano AE, Thompson D.

Games Health J. 2017 Feb;6(1):1-8. doi: 10.1089/g4h.2016.0106. Epub 2016 Dec 27. No abstract available.


Dynamics of Parascaris and Strongylus spp. parasites in untreated juvenile horses.

Fabiani JV, Lyons ET, Nielsen MK.

Vet Parasitol. 2016 Oct 30;230:62-66. doi: 10.1016/j.vetpar.2016.11.002. Epub 2016 Nov 7.


Bringing your tools to CyVerse Discovery Environment using Docker.

Devisetty UK, Kennedy K, Sarando P, Merchant N, Lyons E.

F1000Res. 2016 Jun 21;5:1442. eCollection 2016.


FractBias: a graphical tool for assessing fractionation bias following polyploidy.

Joyce BL, Haug-Baltzell A, Davey S, Bomhoff M, Schnable JC, Lyons E.

Bioinformatics. 2017 Feb 15;33(4):552-554. doi: 10.1093/bioinformatics/btw666.


Cannabinoid receptor interacting protein suppresses agonist-driven CB1 receptor internalization and regulates receptor replenishment in an agonist-biased manner.

Blume LC, Leone-Kabler S, Luessen DJ, Marrs GS, Lyons E, Bass CE, Chen R, Selley DE, Howlett AC.

J Neurochem. 2016 Nov;139(3):396-407. doi: 10.1111/jnc.13767. Epub 2016 Sep 26.


A Genomic Analysis of Factors Driving lincRNA Diversification: Lessons from Plants.

Nelson AD, Forsythe ES, Devisetty UK, Clausen DS, Haug-Batzell AK, Meldrum AM, Frank MR, Lyons E, Beilstein MA.

G3 (Bethesda). 2016 Sep 8;6(9):2881-91. doi: 10.1534/g3.116.030338.


A Novel Treatment Protects Chlorella at Commercial Scale from the Predatory Bacterium Vampirovibrio chlorellavorus.

Ganuza E, Sellers CE, Bennett BW, Lyons EM, Carney LT.

Front Microbiol. 2016 Jun 20;7:848. doi: 10.3389/fmicb.2016.00848. eCollection 2016.


An Exploration of Comfort and Discomfort Amongst Children and Young People with Intellectual Disabilities Who Depend on Postural Management Equipment.

Lyons EA, Jones DE, Swallow VM, Chandler C.

J Appl Res Intellect Disabil. 2017 Jul;30(4):727-742. doi: 10.1111/jar.12267. Epub 2016 Jun 13.


Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida.

Bombarely A, Moser M, Amrad A, Bao M, Bapaume L, Barry CS, Bliek M, Boersma MR, Borghi L, Bruggmann R, Bucher M, D'Agostino N, Davies K, Druege U, Dudareva N, Egea-Cortines M, Delledonne M, Fernandez-Pozo N, Franken P, Grandont L, Heslop-Harrison JS, Hintzsche J, Johns M, Koes R, Lv X, Lyons E, Malla D, Martinoia E, Mattson NS, Morel P, Mueller LA, Muhlemann J, Nouri E, Passeri V, Pezzotti M, Qi Q, Reinhardt D, Rich M, Richert-Pöggeler KR, Robbins TP, Schatz MC, Schranz ME, Schuurink RC, Schwarzacher T, Spelt K, Tang H, Urbanus SL, Vandenbussche M, Vijverberg K, Villarino GH, Warner RM, Weiss J, Yue Z, Zethof J, Quattrocchio F, Sims TL, Kuhlemeier C.

Nat Plants. 2016 May 27;2(6):16074. doi: 10.1038/nplants.2016.74.


The genome of black raspberry (Rubus occidentalis).

VanBuren R, Bryant D, Bushakra JM, Vining KJ, Edger PP, Rowley ER, Priest HD, Michael TP, Lyons E, Filichkin SA, Dossett M, Finn CE, Bassil NV, Mockler TC.

Plant J. 2016 Sep;87(6):535-47. doi: 10.1111/tpj.13215. Epub 2016 Jul 20.


Testing Activity Monitors' Effect on Health: Study Protocol for a Randomized Controlled Trial Among Older Primary Care Patients.

Lewis ZH, Ottenbacher KJ, Fisher SR, Jennings K, Brown AF, Swartz MC, Lyons EJ.

JMIR Res Protoc. 2016 Apr 29;5(2):e59. doi: 10.2196/resprot.5454.


Psychometric Analysis of the Three-Factor Eating Questionnaire-R18V2 in Adolescent and Young Adult-Aged Central Nervous System Tumor Survivors.

Swartz MC, Basen-Engquist KM, Markham C, Lyons EJ, Cox M, Chandra J, Ater JL, Askins MA, Scheurer ME, Lupo PJ, Hill R, Murray J, Chan W, Swank PR.

J Adolesc Young Adult Oncol. 2016 Sep;5(3):278-85. doi: 10.1089/jayao.2015.0058. Epub 2016 Apr 4.


Testing the effects of narrative and play on physical activity among breast cancer survivors using mobile apps: study protocol for a randomized controlled trial.

Lyons EJ, Baranowski T, Basen-Engquist KM, Lewis ZH, Swartz MC, Jennings K, Volpi E.

BMC Cancer. 2016 Mar 9;16:202. doi: 10.1186/s12885-016-2244-y.


Interest in Health Behavior Intervention Delivery Modalities Among Cancer Survivors: A Cross-Sectional Study.

Martin EC, Basen-Engquist K, Cox MG, Lyons EJ, Carmack CL, Blalock JA, Demark-Wahnefried W.

JMIR Cancer. 2016 Feb 11;2(1):e1. doi: 10.2196/cancer.5247.


What's the Point?: A Review of Reward Systems Implemented in Gamification Interventions.

Lewis ZH, Swartz MC, Lyons EJ.

Games Health J. 2016 Apr;5(2):93-9. doi: 10.1089/g4h.2015.0078. Epub 2016 Jan 26. Review.


Relevance of in vitro agar based screens to characterize the anti-fungal activities of bacterial endophyte communities.

Shehata HR, Lyons EM, Jordan KS, Raizada MN.

BMC Microbiol. 2016 Jan 16;16:8. doi: 10.1186/s12866-016-0623-9.


Stigma and self-esteem across societies: avoiding blanket psychological responses to gay men experiencing homophobia.

Zervoulis K, Lyons E, Dinos S.

BJPsych Bull. 2015 Aug;39(4):167-73. doi: 10.1192/pb.bp.114.048421.


The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences.

Merchant N, Lyons E, Goff S, Vaughn M, Ware D, Micklos D, Antin P.

PLoS Biol. 2016 Jan 11;14(1):e1002342. doi: 10.1371/journal.pbio.1002342. eCollection 2016 Jan.


Bacterial endophytes from wild and ancient maize are able to suppress the fungal pathogen Sclerotinia homoeocarpa.

Shehata HR, Lyons EM, Jordan KS, Raizada MN.

J Appl Microbiol. 2016 Mar;120(3):756-69. doi: 10.1111/jam.13050.


SynFind: Compiling Syntenic Regions across Any Set of Genomes on Demand.

Tang H, Bomhoff MD, Briones E, Zhang L, Schnable JC, Lyons E.

Genome Biol Evol. 2015 Nov 11;7(12):3286-98. doi: 10.1093/gbe/evv219.


Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum.

VanBuren R, Bryant D, Edger PP, Tang H, Burgess D, Challabathula D, Spittle K, Hall R, Gu J, Lyons E, Freeling M, Bartels D, Ten Hallers B, Hastie A, Michael TP, Mockler TC.

Nature. 2015 Nov 26;527(7579):508-11. doi: 10.1038/nature15714. Epub 2015 Nov 11.


Tailoring Sponsor-Payer Engagement to Facilitate Effective and Fair Patient Access.

Purchase JL, Lyons EJ, Singh S.

Value Health. 2015 Nov;18(7):A555. doi: 10.1016/j.jval.2015.09.1793. Epub 2015 Oct 20. No abstract available.


The pineapple genome and the evolution of CAM photosynthesis.

Ming R, VanBuren R, Wai CM, Tang H, Schatz MC, Bowers JE, Lyons E, Wang ML, Chen J, Biggers E, Zhang J, Huang L, Zhang L, Miao W, Zhang J, Ye Z, Miao C, Lin Z, Wang H, Zhou H, Yim WC, Priest HD, Zheng C, Woodhouse M, Edger PP, Guyot R, Guo HB, Guo H, Zheng G, Singh R, Sharma A, Min X, Zheng Y, Lee H, Gurtowski J, Sedlazeck FJ, Harkess A, McKain MR, Liao Z, Fang J, Liu J, Zhang X, Zhang Q, Hu W, Qin Y, Wang K, Chen LY, Shirley N, Lin YR, Liu LY, Hernandez AG, Wright CL, Bulone V, Tuskan GA, Heath K, Zee F, Moore PH, Sunkar R, Leebens-Mack JH, Mockler T, Bennetzen JL, Freeling M, Sankoff D, Paterson AH, Zhu X, Yang X, Smith JA, Cushman JC, Paull RE, Yu Q.

Nat Genet. 2015 Dec;47(12):1435-42. doi: 10.1038/ng.3435. Epub 2015 Nov 2.


Identification of dopamine receptors across the extant avian family tree and analysis with other clades uncovers a polyploid expansion among vertebrates.

Haug-Baltzell A, Jarvis ED, McCarthy FM, Lyons E.

Front Neurosci. 2015 Oct 7;9:361. doi: 10.3389/fnins.2015.00361. eCollection 2015.


Biphasic appearance of corticated and decorticated ascarid egg shedding in untreated horse foals.

Donoghue EM, Lyons ET, Bellaw JL, Nielsen MK.

Vet Parasitol. 2015 Nov 30;214(1-2):114-7. doi: 10.1016/j.vetpar.2015.09.003. Epub 2015 Sep 11.


Cultivating Engagement and Enjoyment in Exergames Using Feedback, Challenge, and Rewards.

Lyons EJ.

Games Health J. 2015 Feb;4(1):12-8. doi: 10.1089/g4h.2014.0072. Epub 2014 Oct 20. Review.

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