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Best practice data life cycle approaches for the life sciences.

Griffin PC, Khadake J, LeMay KS, Lewis SE, Orchard S, Pask A, Pope B, Roessner U, Russell K, Seemann T, Treloar A, Tyagi S, Christiansen JH, Dayalan S, Gladman S, Hangartner SB, Hayden HL, Ho WWH, Keeble-Gagnère G, Korhonen PK, Neish P, Prestes PR, Richardson MF, Watson-Haigh NS, Wyres KL, Young ND, Schneider MV.

Version 2. F1000Res. 2017 Aug 31 [revised 2018 Jan 1];6:1618. doi: 10.12688/f1000research.12344.2. eCollection 2017.


Sequential Screening to Improve Behavioral Health Needs Detection in Primary Care.

Young ND, Takala CR.

J Am Acad Child Adolesc Psychiatry. 2018 Aug;57(8):603-609. doi: 10.1016/j.jaac.2018.04.017. Epub 2018 Jun 22.


Opisthorchis viverrini Draft Genome - Biomedical Implications and Future Avenues.

Young ND, Gasser RB.

Adv Parasitol. 2018;101:125-148. doi: 10.1016/bs.apar.2018.05.005. Epub 2018 Jun 6.


The small RNA complement of adult Schistosoma haematobium.

Stroehlein AJ, Young ND, Korhonen PK, Hall RS, Jex AR, Webster BL, Rollinson D, Brindley PJ, Gasser RB.

PLoS Negl Trop Dis. 2018 May 29;12(5):e0006535. doi: 10.1371/journal.pntd.0006535. eCollection 2018 May.


Molecular alterations during larval development of Haemonchus contortus in vitro are under tight post-transcriptional control.

Ma G, Wang T, Korhonen PK, Ang CS, Williamson NA, Young ND, Stroehlein AJ, Hall RS, Koehler AV, Hofmann A, Gasser RB.

Int J Parasitol. 2018 Aug;48(9-10):763-772. doi: 10.1016/j.ijpara.2018.03.008. Epub 2018 May 22.


Clonorchis sinensis and Clonorchiasis: The Relevance of Exploring Genetic Variation.

Wang D, Young ND, Korhonen PK, Gasser RB.

Adv Parasitol. 2018;100:155-208. doi: 10.1016/bs.apar.2018.03.006. Epub 2018 May 4.


Complete Genome Sequence of Sinorhizobium meliloti Bacteriophage HMSP1-Susan.

Fleagle B, Imamovic A, Toledo S, Couves M, Jensen A, Vang M, Steevens A, Young ND, Sadowsky MJ, Martinez-Vaz BM.

Genome Announc. 2018 May 3;6(18). pii: e01450-17. doi: 10.1128/genomeA.01450-17.


Improved strategy for the curation and classification of kinases, with broad applicability to other eukaryotic protein groups.

Stroehlein AJ, Young ND, Gasser RB.

Sci Rep. 2018 May 1;8(1):6808. doi: 10.1038/s41598-018-25020-8.


A Novel Glaesserella sp. Isolated from Pigs with Severe Respiratory Infections Has a Mosaic Genome with Virulence Factors Putatively Acquired by Horizontal Transfer.

Watt AE, Browning GF, Legione AR, Bushell RN, Stent A, Cutler RS, Young ND, Marenda MS.

Appl Environ Microbiol. 2018 May 17;84(11). pii: e00092-18. doi: 10.1128/AEM.00092-18. Print 2018 Jun 1.


Advances in kinome research of parasitic worms - implications for fundamental research and applied biotechnological outcomes.

Stroehlein AJ, Young ND, Gasser RB.

Biotechnol Adv. 2018 Jul - Aug;36(4):915-934. doi: 10.1016/j.biotechadv.2018.02.013. Epub 2018 Mar 19. Review.


Improved genomic resources and new bioinformatic workflow for the carcinogenic parasite Clonorchis sinensis: Biotechnological implications.

Wang D, Korhonen PK, Gasser RB, Young ND.

Biotechnol Adv. 2018 Jul - Aug;36(4):894-904. doi: 10.1016/j.biotechadv.2018.02.008. Epub 2018 Feb 15. Review.


Select and resequence reveals relative fitness of bacteria in symbiotic and free-living environments.

Burghardt LT, Epstein B, Guhlin J, Nelson MS, Taylor MR, Young ND, Sadowsky MJ, Tiffin P.

Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):2425-2430. doi: 10.1073/pnas.1714246115. Epub 2018 Feb 16.


Use of a bioinformatic-assisted primer design strategy to establish a new nested PCR-based method for Cryptosporidium.

Koehler AV, Korhonen PK, Hall RS, Young ND, Wang T, Haydon SR, Gasser RB.

Parasit Vectors. 2017 Oct 23;10(1):509. doi: 10.1186/s13071-017-2462-4.


The Battle Against Flystrike - Past Research and New Prospects Through Genomics.

Anstead CA, Perry T, Richards S, Korhonen PK, Young ND, Bowles VM, Batterham P, Gasser RB.

Adv Parasitol. 2017;98:227-281. doi: 10.1016/bs.apar.2017.03.001. Epub 2017 May 5.


Innate immune genes in persistent mating-induced endometritis in horses.

Marth CD, Firestone SM, Hanlon D, Glenton LY, Browning GF, Young ND, Krekeler N.

Reprod Fertil Dev. 2018 Mar;30(3):533-545. doi: 10.1071/RD17157.


ODG: Omics database generator - a tool for generating, querying, and analyzing multi-omics comparative databases to facilitate biological understanding.

Guhlin J, Silverstein KAT, Zhou P, Tiffin P, Young ND.

BMC Bioinformatics. 2017 Aug 10;18(1):367. doi: 10.1186/s12859-017-1777-7.


Transcriptomic basis of genome by genome variation in a legume-rhizobia mutualism.

Burghardt LT, Guhlin J, Chun CL, Liu J, Sadowsky MJ, Stupar RM, Young ND, Tiffin P.

Mol Ecol. 2017 Nov;26(21):6122-6135. doi: 10.1111/mec.14285. Epub 2017 Sep 5.


Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula.

Moll KM, Zhou P, Ramaraj T, Fajardo D, Devitt NP, Sadowsky MJ, Stupar RM, Tiffin P, Miller JR, Young ND, Silverstein KAT, Mudge J.

BMC Genomics. 2017 Aug 4;18(1):578. doi: 10.1186/s12864-017-3971-4.


Hybrid assembly with long and short reads improves discovery of gene family expansions.

Miller JR, Zhou P, Mudge J, Gurtowski J, Lee H, Ramaraj T, Walenz BP, Liu J, Stupar RM, Denny R, Song L, Singh N, Maron LG, McCouch SR, McCombie WR, Schatz MC, Tiffin P, Young ND, Silverstein KAT.

BMC Genomics. 2017 Jul 19;18(1):541. doi: 10.1186/s12864-017-3927-8.


Deguelin exerts potent nematocidal activity via the mitochondrial respiratory chain.

Preston S, Korhonen PK, Mouchiroud L, Cornaglia M, McGee SL, Young ND, Davis RA, Crawford S, Nowell C, Ansell BRE, Fisher GM, Andrews KT, Chang BCH, Gijs MAM, Sternberg PW, Auwerx J, Baell J, Hofmann A, Jabbar A, Gasser RB.

FASEB J. 2017 Oct;31(10):4515-4532. doi: 10.1096/fj.201700288R. Epub 2017 Jul 7.


Whipworm kinomes reflect a unique biology and adaptation to the host animal.

Stroehlein AJ, Young ND, Korhonen PK, Chang BCH, Nejsum P, Pozio E, La Rosa G, Sternberg PW, Gasser RB.

Int J Parasitol. 2017 Nov;47(13):857-866. doi: 10.1016/j.ijpara.2017.04.005. Epub 2017 Jun 10.


Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes.

Zhou P, Silverstein KA, Ramaraj T, Guhlin J, Denny R, Liu J, Farmer AD, Steele KP, Stupar RM, Miller JR, Tiffin P, Mudge J, Young ND.

BMC Genomics. 2017 Mar 27;18(1):261. doi: 10.1186/s12864-017-3654-1.


All roads lead to weediness: Patterns of genomic divergence reveal extensive recurrent weedy rice origins from South Asian Oryza.

Huang Z, Young ND, Reagon M, Hyma KE, Olsen KM, Jia Y, Caicedo AL.

Mol Ecol. 2017 Jun;26(12):3151-3167. doi: 10.1111/mec.14120. Epub 2017 May 5.


Genome-wide association studies with proteomics data reveal genes important for synthesis, transport and packaging of globulins in legume seeds.

Le Signor C, Aimé D, Bordat A, Belghazi M, Labas V, Gouzy J, Young ND, Prosperi JM, Leprince O, Thompson RD, Buitink J, Burstin J, Gallardo K.

New Phytol. 2017 Jun;214(4):1597-1613. doi: 10.1111/nph.14500. Epub 2017 Mar 21.


Mitochondrial genomic comparison of Clonorchis sinensis from South Korea with other isolates of this species.

Wang D, Young ND, Koehler AV, Tan P, Sohn WM, Korhonen PK, Gasser RB.

Infect Genet Evol. 2017 Jul;51:160-166. doi: 10.1016/j.meegid.2017.02.015. Epub 2017 Feb 22.


Exploring the molecular mechanisms of parasite-host interactions with a view towards new therapeutics and vaccines.

Cross M, Klepzig E, Dallaston M, Young ND, Bailey UM, Mason L, Jones MK, Gasser RB, Hofmann A.

Postepy Biochem. 2016;62(3):370-376. Review.


Validating Genome-Wide Association Candidates Controlling Quantitative Variation in Nodulation.

Curtin SJ, Tiffin P, Guhlin J, Trujillo DI, Burghart LT, Atkins P, Baltes NJ, Denny R, Voytas DF, Stupar RM, Young ND.

Plant Physiol. 2017 Feb;173(2):921-931. doi: 10.1104/pp.16.01923. Epub 2017 Jan 5.


Isolation of Tasmanian Rickettsia-like organism (RLO) from farmed salmonids: identification of multiple serotypes and confirmation of pathogenicity.

Morrison RN, Young ND, Knowles G, Cornish MC, Carson J.

Dis Aquat Organ. 2016 Dec 21;122(2):85-103. doi: 10.3354/dao03057.


The apicoplast genomes of two taxonomic units of Babesia from sheep.

Wang T, Guan G, Korhonen PK, Koehler AV, Hall RS, Young ND, Yin H, Gasser RB.

Vet Parasitol. 2017 Jan 15;233:123-128. doi: 10.1016/j.vetpar.2016.11.004. Epub 2016 Nov 6.


Population Structure in the Model Grass Is Highly Correlated with Flowering Differences across Broad Geographic Areas.

Tyler L, Lee SJ, Young ND, DeIulio GA, Benavente E, Reagon M, Sysopha J, Baldini RM, Troìa A, Hazen SP, Caicedo AL.

Plant Genome. 2016 Jul;9(2). doi: 10.3835/plantgenome2015.08.0074.


Probing function and structure of trehalose-6-phosphate phosphatases from pathogenic organisms suggests distinct molecular groupings.

Cross M, Lepage R, Rajan S, Biberacher S, Young ND, Kim BN, Coster MJ, Gasser RB, Kim JS, Hofmann A.

FASEB J. 2017 Mar;31(3):920-926. doi: 10.1096/fj.201601149R. Epub 2016 Nov 18.


Mitochondrial genomes of two Babesia taxa from sheep in China as a foundation for population genetic and epidemiological investigations.

Wang T, Guan G, Korhonen PK, Koehler AV, Young ND, Hall RS, Yin H, Gasser RB.

Infect Genet Evol. 2017 Jan;47:51-55. doi: 10.1016/j.meegid.2016.11.002. Epub 2016 Nov 11.


Oestrous cycle-dependent equine uterine immune response to induced infectious endometritis.

Marth CD, Firestone SM, Glenton LY, Browning GF, Young ND, Krekeler N.

Vet Res. 2016 Nov 8;47(1):110.


Genomic resources for a unique, low-virulence Babesia taxon from China.

Guan G, Korhonen PK, Young ND, Koehler AV, Wang T, Li Y, Liu Z, Luo J, Yin H, Gasser RB.

Parasit Vectors. 2016 Oct 27;9(1):564.


Analyses of Compact Trichinella Kinomes Reveal a MOS-Like Protein Kinase with a Unique N-Terminal Domain.

Stroehlein AJ, Young ND, Korhonen PK, Chang BC, Sternberg PW, La Rosa G, Pozio E, Gasser RB.

G3 (Bethesda). 2016 Sep 8;6(9):2847-56. doi: 10.1534/g3.116.032961.


CAP protein superfamily members in Toxocara canis.

Stroehlein AJ, Young ND, Hall RS, Korhonen PK, Hofmann A, Sternberg PW, Jabbar A, Gasser RB.

Parasit Vectors. 2016 Jun 24;9(1):360. doi: 10.1186/s13071-016-1642-y.


Understanding Haemonchus contortus Better Through Genomics and Transcriptomics.

Gasser RB, Schwarz EM, Korhonen PK, Young ND.

Adv Parasitol. 2016;93:519-67. doi: 10.1016/bs.apar.2016.02.015. Epub 2016 Apr 5. Review.


Adaptation to climate through flowering phenology: a case study in Medicago truncatula.

Burgarella C, Chantret N, Gay L, Prosperi JM, Bonhomme M, Tiffin P, Young ND, Ronfort J.

Mol Ecol. 2016 Jul;25(14):3397-415. doi: 10.1111/mec.13683. Epub 2016 Jun 30.


MicroRNAs of Toxocara canis and their predicted functional roles.

Ma G, Luo Y, Zhu H, Luo Y, Korhonen PK, Young ND, Gasser RB, Zhou R.

Parasit Vectors. 2016 Apr 23;9:229. doi: 10.1186/s13071-016-1508-3.


Harnessing the Toxocara Genome to Underpin Toxocariasis Research and New Interventions.

Gasser RB, Korhonen PK, Zhu XQ, Young ND.

Adv Parasitol. 2016;91:87-110. doi: 10.1016/bs.apar.2015.12.001. Epub 2016 Feb 28. Review.


Pipeline for the identification and classification of ion channels in parasitic flatworms.

Nor B, Young ND, Korhonen PK, Hall RS, Tan P, Lonie A, Gasser RB.

Parasit Vectors. 2016 Mar 16;9:155. doi: 10.1186/s13071-016-1428-2.


Making sense of genomes of parasitic worms: Tackling bioinformatic challenges.

Korhonen PK, Young ND, Gasser RB.

Biotechnol Adv. 2016 Sep-Oct;34(5):663-686. doi: 10.1016/j.biotechadv.2016.03.001. Epub 2016 Mar 5. Review.


A blow to the fly - Lucilia cuprina draft genome and transcriptome to support advances in biology and biotechnology.

Anstead CA, Batterham P, Korhonen PK, Young ND, Hall RS, Bowles VM, Richards S, Scott MJ, Gasser RB.

Biotechnol Adv. 2016 Sep-Oct;34(5):605-620. doi: 10.1016/j.biotechadv.2016.02.009. Epub 2016 Mar 2. Review.


Comparative Transcriptomic Exploration Reveals Unique Molecular Adaptations of Neuropathogenic Trichobilharzia to Invade and Parasitize Its Avian Definitive Host.

Leontovyč R, Young ND, Korhonen PK, Hall RS, Tan P, Mikeš L, Kašný M, Horák P, Gasser RB.

PLoS Negl Trop Dis. 2016 Feb 10;10(2):e0004406. doi: 10.1371/journal.pntd.0004406. eCollection 2016 Feb.


Exploring structural variants in environmentally sensitive gene families.

Young ND, Zhou P, Silverstein KA.

Curr Opin Plant Biol. 2016 Apr;30:19-24. doi: 10.1016/j.pbi.2015.12.012. Epub 2016 Feb 8. Review.


Reconstruction of the insulin-like signalling pathway of Haemonchus contortus.

Mohandas N, Hu M, Stroehlein AJ, Young ND, Sternberg PW, Lok JB, Gasser RB.

Parasit Vectors. 2016 Feb 3;9:64. doi: 10.1186/s13071-016-1341-8.


Phylogenomic and biogeographic reconstruction of the Trichinella complex.

Korhonen PK, Pozio E, La Rosa G, Chang BC, Koehler AV, Hoberg EP, Boag PR, Tan P, Jex AR, Hofmann A, Sternberg PW, Young ND, Gasser RB.

Nat Commun. 2016 Feb 1;7:10513. doi: 10.1038/ncomms10513.


Genomics of worms, with an emphasis on Opisthorchis viverrini - opportunities for fundamental discovery and biomedical outcomes.

Gasser RB, Tan P, Teh BT, Wongkham S, Young ND.

Parasitol Int. 2017 Aug;66(4):341-345. doi: 10.1016/j.parint.2016.01.005. Epub 2016 Jan 12. Review.


An Alternative Approach to "Identification of Unknowns": Designing a Protocol to Verify the Identities of Nitrogen Fixing Bacteria.

Martinez-Vaz BM, Denny R, Young ND, Sadowsky MJ.

J Microbiol Biol Educ. 2015 Dec 1;16(2):247-53. doi: 10.1128/jmbe.v16i2.973. eCollection 2015 Dec.


The Haemonchus contortus kinome--a resource for fundamental molecular investigations and drug discovery.

Stroehlein AJ, Young ND, Korhonen PK, Jabbar A, Hofmann A, Sternberg PW, Gasser RB.

Parasit Vectors. 2015 Dec 8;8:623. doi: 10.1186/s13071-015-1231-5.

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