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The differential response of the chicken trachea to chronic infection with virulent Mycoplasma gallisepticum strain Ap3AS and Vaxsafe MG (strain ts-304) - a transcriptional profile.

Kulappu Arachchige SN, Young ND, Shil PK, Legione AR, Kanci Condello A, Browning GF, Wawegama NK.

Infect Immun. 2020 Mar 2. pii: IAI.00053-20. doi: 10.1128/IAI.00053-20. [Epub ahead of print]


Expanded complement of Niemann-Pick type C2-like protein genes in Clonorchis sinensis suggests functions beyond sterol binding and transport.

Anari M, Stroehlein AJ, Hall RS, Chang BCH, Gasser RB, Young ND.

Parasit Vectors. 2020 Jan 23;13(1):38. doi: 10.1186/s13071-020-3910-0.


Gene content evolution in the arthropods.

Thomas GWC, Dohmen E, Hughes DST, Murali SC, Poelchau M, Glastad K, Anstead CA, Ayoub NA, Batterham P, Bellair M, Binford GJ, Chao H, Chen YH, Childers C, Dinh H, Doddapaneni HV, Duan JJ, Dugan S, Esposito LA, Friedrich M, Garb J, Gasser RB, Goodisman MAD, Gundersen-Rindal DE, Han Y, Handler AM, Hatakeyama M, Hering L, Hunter WB, Ioannidis P, Jayaseelan JC, Kalra D, Khila A, Korhonen PK, Lee CE, Lee SL, Li Y, Lindsey ARI, Mayer G, McGregor AP, McKenna DD, Misof B, Munidasa M, Munoz-Torres M, Muzny DM, Niehuis O, Osuji-Lacy N, Palli SR, Panfilio KA, Pechmann M, Perry T, Peters RS, Poynton HC, Prpic NM, Qu J, Rotenberg D, Schal C, Schoville SD, Scully ED, Skinner E, Sloan DB, Stouthamer R, Strand MR, Szucsich NU, Wijeratne A, Young ND, Zattara EE, Benoit JB, Zdobnov EM, Pfrender ME, Hackett KJ, Werren JH, Worley KC, Gibbs RA, Chipman AD, Waterhouse RM, Bornberg-Bauer E, Hahn MW, Richards S.

Genome Biol. 2020 Jan 23;21(1):15. doi: 10.1186/s13059-019-1925-7.


The developmental phosphoproteome of Haemonchus contortus.

Wang T, Ma G, Ang CS, Korhonen PK, Stroehlein AJ, Young ND, Hofmann A, Chang BCH, Williamson NA, Gasser RB.

J Proteomics. 2020 Feb 20;213:103615. doi: 10.1016/j.jprot.2019.103615. Epub 2019 Dec 14.


Genome-wide association study and genomic selection for soybean chlorophyll content associated with soybean cyst nematode tolerance.

Ravelombola WS, Qin J, Shi A, Nice L, Bao Y, Lorenz A, Orf JH, Young ND, Chen S.

BMC Genomics. 2019 Nov 27;20(1):904. doi: 10.1186/s12864-019-6275-z.


A Select and Resequence Approach Reveals Strain-Specific Effects of Medicago Nodule-Specific PLAT-Domain Genes.

Burghardt LT, Trujillo DI, Epstein B, Tiffin P, Young ND.

Plant Physiol. 2020 Jan;182(1):463-471. doi: 10.1104/pp.19.00831. Epub 2019 Oct 25.


High-quality Schistosoma haematobium genome achieved by single-molecule and long-range sequencing.

Stroehlein AJ, Korhonen PK, Chong TM, Lim YL, Chan KG, Webster B, Rollinson D, Brindley PJ, Gasser RB, Young ND.

Gigascience. 2019 Sep 1;8(9). pii: giz108. doi: 10.1093/gigascience/giz108.


Dafachronic acid promotes larval development in Haemonchus contortus by modulating dauer signalling and lipid metabolism.

Ma G, Wang T, Korhonen PK, Young ND, Nie S, Ang CS, Williamson NA, Reid GE, Gasser RB.

PLoS Pathog. 2019 Jul 23;15(7):e1007960. doi: 10.1371/journal.ppat.1007960. eCollection 2019 Jul.


An Evaluation of Machine Learning Approaches for the Prediction of Essential Genes in Eukaryotes Using Protein Sequence-Derived Features.

Campos TL, Korhonen PK, Gasser RB, Young ND.

Comput Struct Biotechnol J. 2019 Jun 8;17:785-796. doi: 10.1016/j.csbj.2019.05.008. eCollection 2019.


Effects of word overlap on generalized gains from a repeated readings intervention.

Martens BK, Young ND, Mullane MP, Baxter EL, Sallade SJ, Kellen D, Long SJ, Sullivan WE, Womack AJ, Underberg J.

J Sch Psychol. 2019 Jun;74:1-9. doi: 10.1016/j.jsp.2019.05.002. Epub 2019 May 13.


Comparative genome analysis indicates high evolutionary potential of pathogenicity genes in Colletotrichum tanaceti.

Lelwala RV, Korhonen PK, Young ND, Scott JB, Ades PK, Gasser RB, Taylor PWJ.

PLoS One. 2019 May 31;14(5):e0212248. doi: 10.1371/journal.pone.0212248. eCollection 2019.


Exploration of antibiotic resistance risks in a veterinary teaching hospital with Oxford Nanopore long read sequencing.

Kamathewatta KI, Bushell RN, Young ND, Stevenson MA, Billman-Jacobe H, Browning GF, Marenda MS.

PLoS One. 2019 May 30;14(5):e0217600. doi: 10.1371/journal.pone.0217600. eCollection 2019.


A systematic study towards evolutionary and epidemiological dynamics of currently predominant H5 highly pathogenic avian influenza viruses in Vietnam.

Nguyen LT, Firestone SM, Stevenson MA, Young ND, Sims LD, Chu DH, Nguyen TN, Van Nguyen L, Thanh Le T, Van Nguyen H, Nguyen HN, Tien TN, Nguyen TD, Tran BN, Matsuno K, Okamatsu M, Kida H, Sakoda Y.

Sci Rep. 2019 May 22;9(1):7723. doi: 10.1038/s41598-019-42638-4.


Long-read sequencing reveals a 4.4 kb tandem repeat region in the mitogenome of Echinococcus granulosus (sensu stricto) genotype G1.

Kinkar L, Korhonen PK, Cai H, Gauci CG, Lightowlers MW, Saarma U, Jenkins DJ, Li J, Li J, Young ND, Gasser RB.

Parasit Vectors. 2019 May 16;12(1):238. doi: 10.1186/s13071-019-3492-x.


High throughput LC-MS/MS-based proteomic analysis of excretory-secretory products from short-term in vitro culture of Haemonchus contortus.

Wang T, Ma G, Ang CS, Korhonen PK, Koehler AV, Young ND, Nie S, Williamson NA, Gasser RB.

J Proteomics. 2019 Jul 30;204:103375. doi: 10.1016/j.jprot.2019.05.003. Epub 2019 May 6.


Dauer signalling pathway model for Haemonchus contortus.

Ma G, Wang T, Korhonen PK, Stroehlein AJ, Young ND, Gasser RB.

Parasit Vectors. 2019 Apr 29;12(1):187. doi: 10.1186/s13071-019-3419-6.


Transcriptional alterations in Caenorhabditis elegans following exposure to an anthelmintic fraction of the plant Picria fel-terrae Lour.

Kumarasingha R, Young ND, Yeo TC, Lim DSL, Tu CL, Palombo EA, Shaw JM, Gasser RB, Boag PR.

Parasit Vectors. 2019 Apr 25;12(1):181. doi: 10.1186/s13071-019-3429-4.


Common workflow language (CWL)-based software pipeline for de novo genome assembly from long- and short-read data.

Korhonen PK, Hall RS, Young ND, Gasser RB.

Gigascience. 2019 Apr 1;8(4). pii: giz014. doi: 10.1093/gigascience/giz014.


Exploration of extracellular vesicles from Ascaris suum provides evidence of parasite-host cross talk.

Hansen EP, Fromm B, Andersen SD, Marcilla A, Andersen KL, Borup A, Williams AR, Jex AR, Gasser RB, Young ND, Hall RS, Stensballe A, Ovchinnikov V, Yan Y, Fredholm M, Thamsborg SM, Nejsum P.

J Extracell Vesicles. 2019 Feb 14;8(1):1578116. doi: 10.1080/20013078.2019.1578116. eCollection 2019.


Molecular evidence for distinct modes of nutrient acquisition between visceral and neurotropic schistosomes of birds.

Leontovyč R, Young ND, Korhonen PK, Hall RS, Bulantová J, Jeřábková V, Kašný M, Gasser RB, Horák P.

Sci Rep. 2019 Feb 4;9(1):1347. doi: 10.1038/s41598-018-37669-2.


Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium.

Oey H, Zakrzewski M, Gravermann K, Young ND, Korhonen PK, Gobert GN, Nawaratna S, Hasan S, Martínez DM, You H, Lavin M, Jones MK, Ragan MA, Stoye J, Oleaga A, Emery AM, Webster BL, Rollinson D, Gasser RB, McManus DP, Krause L.

PLoS Pathog. 2019 Jan 23;15(1):e1007513. doi: 10.1371/journal.ppat.1007513. eCollection 2019 Jan.


Nodule-specific PLAT domain proteins are expanded in the Medicago lineage and required for nodulation.

Trujillo DI, Silverstein KAT, Young ND.

New Phytol. 2019 May;222(3):1538-1550. doi: 10.1111/nph.15697. Epub 2019 Feb 27.


Programmed knockout mutation of liver fluke granulin attenuates virulence of infection-induced hepatobiliary morbidity.

Arunsan P, Ittiprasert W, Smout MJ, Cochran CJ, Mann VH, Chaiyadet S, Karinshak SE, Sripa B, Young ND, Sotillo J, Loukas A, Brindley PJ, Laha T.

Elife. 2019 Jan 15;8. pii: e41463. doi: 10.7554/eLife.41463.


Comparative bioinformatic analysis suggests that specific dauer-like signalling pathway components regulate Toxocara canis development and migration in the mammalian host.

Ma G, Wang T, Korhonen PK, Nie S, Reid GE, Stroehlein AJ, Koehler AV, Chang BCH, Hofmann A, Young ND, Gasser RB.

Parasit Vectors. 2019 Jan 14;12(1):32. doi: 10.1186/s13071-018-3265-y.


Interactive online application for the prediction, ranking and prioritisation of drug targets in Schistosoma haematobium.

Stroehlein AJ, Gasser RB, Hall RS, Young ND.

Parasit Vectors. 2018 Nov 27;11(1):605. doi: 10.1186/s13071-018-3197-6.


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. Review.


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. Review.


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.


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