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Targeted metagenomics approach to capture the biodiversity of Saccharomyces genus in wild environments.

Alsammar HF, Naseeb S, Brancia LB, Gilman RT, Wang P, Delneri D.

Environ Microbiol Rep. 2018 Dec 3. doi: 10.1111/1758-2229.12724. [Epub ahead of print]


Whole Genome Sequencing, de Novo Assembly and Phenotypic Profiling for the New Budding Yeast Species Saccharomyces jurei.

Naseeb S, Alsammar H, Burgis T, Donaldson I, Knyazev N, Knight C, Delneri D.

G3 (Bethesda). 2018 Aug 30;8(9):2967-2977. doi: 10.1534/g3.118.200476.


Large-scale profiling of noncoding RNA function in yeast.

Parker S, Fraczek MG, Wu J, Shamsah S, Manousaki A, Dungrattanalert K, de Almeida RA, Invernizzi E, Burgis T, Omara W, Griffiths-Jones S, Delneri D, O'Keefe RT.

PLoS Genet. 2018 Mar 12;14(3):e1007253. doi: 10.1371/journal.pgen.1007253. eCollection 2018 Mar.


History of genome editing in yeast.

Fraczek MG, Naseeb S, Delneri D.

Yeast. 2018 May;35(5):361-368. doi: 10.1002/yea.3308. Epub 2018 Feb 26. Review.


Rapid functional and evolutionary changes follow gene duplication in yeast.

Naseeb S, Ames RM, Delneri D, Lovell SC.

Proc Biol Sci. 2017 Aug 30;284(1861). pii: 20171393. doi: 10.1098/rspb.2017.1393.


Saccharomyces jurei sp. nov., isolation and genetic identification of a novel yeast species from Quercus robur.

Naseeb S, James SA, Alsammar H, Michaels CJ, Gini B, Nueno-Palop C, Bond CJ, McGhie H, Roberts IN, Delneri D.

Int J Syst Evol Microbiol. 2017 Jun;67(6):2046-2052. doi: 10.1099/ijsem.0.002013. Epub 2017 Jun 22.


A resource for functional profiling of noncoding RNA in the yeast Saccharomyces cerevisiae.

Parker S, Fraczek MG, Wu J, Shamsah S, Manousaki A, Dungrattanalert K, de Almeida RA, Estrada-Rivadeneyra D, Omara W, Delneri D, O'Keefe RT.

RNA. 2017 Aug;23(8):1166-1171. doi: 10.1261/rna.061564.117. Epub 2017 May 3.


Non-coding RNAs and disease: the classical ncRNAs make a comeback.

de Almeida RA, Fraczek MG, Parker S, Delneri D, O'Keefe RT.

Biochem Soc Trans. 2016 Aug 15;44(4):1073-8. doi: 10.1042/BST20160089. Review.


Novel Intronic RNA Structures Contribute to Maintenance of Phenotype in Saccharomyces cerevisiae.

Hooks KB, Naseeb S, Parker S, Griffiths-Jones S, Delneri D.

Genetics. 2016 Jul;203(3):1469-81. doi: 10.1534/genetics.115.185363. Epub 2016 May 18.


Widespread Impact of Chromosomal Inversions on Gene Expression Uncovers Robustness via Phenotypic Buffering.

Naseeb S, Carter Z, Minnis D, Donaldson I, Zeef L, Delneri D.

Mol Biol Evol. 2016 Jul;33(7):1679-96. doi: 10.1093/molbev/msw045. Epub 2016 Feb 28.


Intron evolution in Saccharomycetaceae.

Hooks KB, Delneri D, Griffiths-Jones S.

Genome Biol Evol. 2014 Sep;6(9):2543-56.


Environmental systems biology of cold-tolerant phenotype in Saccharomyces species adapted to grow at different temperatures.

Paget CM, Schwartz JM, Delneri D.

Mol Ecol. 2014 Nov;23(21):5241-57. doi: 10.1111/mec.12930.


Sequencing and characterisation of rearrangements in three S. pastorianus strains reveals the presence of chimeric genes and gives evidence of breakpoint reuse.

Hewitt SK, Donaldson IJ, Lovell SC, Delneri D.

PLoS One. 2014 Mar 18;9(3):e92203. doi: 10.1371/journal.pone.0092203. eCollection 2014.


Chimeric protein complexes in hybrid species generate novel phenotypes.

Piatkowska EM, Naseeb S, Knight D, Delneri D.

PLoS Genet. 2013;9(10):e1003836. doi: 10.1371/journal.pgen.1003836. Epub 2013 Oct 3.


Osteoblastic cell secretome: a novel role for progranulin during risedronate treatment.

Romanello M, Piatkowska E, Antoniali G, Cesaratto L, Vascotto C, Iozzo RV, Delneri D, Brancia FL.

Bone. 2014 Jan;58:81-91. doi: 10.1016/j.bone.2013.10.003. Epub 2013 Oct 11.


Characterization and prediction of haploinsufficiency using systems-level gene properties in yeast.

Norris M, Lovell S, Delneri D.

G3 (Bethesda). 2013 Nov 6;3(11):1965-77. doi: 10.1534/g3.113.008144.


The yeast factory.

Delneri D.

Genome Biol. 2012;13(9):320.


Impact of chromosomal inversions on the yeast DAL cluster.

Naseeb S, Delneri D.

PLoS One. 2012;7(8):e42022. doi: 10.1371/journal.pone.0042022. Epub 2012 Aug 14.


Non-coding RNAs in Saccharomyces cerevisiae: what is the function?

Wu J, Delneri D, O'Keefe RT.

Biochem Soc Trans. 2012 Aug;40(4):907-11. doi: 10.1042/BST20120042. Review.


Genome-wide analysis of longevity in nutrient-deprived Saccharomyces cerevisiae reveals importance of recycling in maintaining cell viability.

Davey HM, Cross EJ, Davey CL, Gkargkas K, Delneri D, Hoyle DC, Oliver SG, Kell DB, Griffith GW.

Environ Microbiol. 2012 May;14(5):1249-60. doi: 10.1111/j.1462-2920.2012.02705.x. Epub 2012 Feb 22.


Genome-wide analysis of yeast stress survival and tolerance acquisition to analyze the central trade-off between growth rate and cellular robustness.

Zakrzewska A, van Eikenhorst G, Burggraaff JE, Vis DJ, Hoefsloot H, Delneri D, Oliver SG, Brul S, Smits GJ.

Mol Biol Cell. 2011 Nov;22(22):4435-46. doi: 10.1091/mbc.E10-08-0721. Epub 2011 Sep 30.


Knock-in reconstitution studies reveal an unexpected role of Cys-65 in regulating APE1/Ref-1 subcellular trafficking and function.

Vascotto C, Bisetto E, Li M, Zeef LA, D'Ambrosio C, Domenis R, Comelli M, Delneri D, Scaloni A, Altieri F, Mavelli I, Quadrifoglio F, Kelley MR, Tell G.

Mol Biol Cell. 2011 Oct;22(20):3887-901. doi: 10.1091/mbc.E11-05-0391. Epub 2011 Aug 24.


Competition experiments coupled with high-throughput analyses for functional genomics studies in yeast.

Delneri D.

Methods Mol Biol. 2011;759:271-82. doi: 10.1007/978-1-61779-173-4_16.


Barcode technology in yeast: application to pharmacogenomics.

Delneri D.

FEMS Yeast Res. 2010 Dec;10(8):1083-9. doi: 10.1111/j.1567-1364.2010.00676.x. Review.


Evolutionary systems biology of amino acid biosynthetic cost in yeast.

Barton MD, Delneri D, Oliver SG, Rattray M, Bergman CM.

PLoS One. 2010 Aug 17;5(8):e11935. doi: 10.1371/journal.pone.0011935. Erratum in: PLoS One. 2010;5(10) doi: 10.1371/annotation/b60feca4-9a4f-4311-8a07-4bf16a2f9316.


Gene duplication and environmental adaptation within yeast populations.

Ames RM, Rash BM, Hentges KE, Robertson DL, Delneri D, Lovell SC.

Genome Biol Evol. 2010;2:591-601. doi: 10.1093/gbe/evq043. Epub 2010 Jul 21.


Fusel alcohols regulate translation initiation by inhibiting eIF2B to reduce ternary complex in a mechanism that may involve altering the integrity and dynamics of the eIF2B body.

Taylor EJ, Campbell SG, Griffiths CD, Reid PJ, Slaven JW, Harrison RJ, Sims PF, Pavitt GD, Delneri D, Ashe MP.

Mol Biol Cell. 2010 Jul 1;21(13):2202-16. doi: 10.1091/mbc.E09-11-0962. Epub 2010 May 5.


Identification of secondary targets of N-containing bisphosphonates in mammalian cells via parallel competition analysis of the barcoded yeast deletion collection.

Bivi N, Romanello M, Harrison R, Clarke I, Hoyle DC, Moro L, Ortolani F, Bonetti A, Quadrifoglio F, Tell G, Delneri D.

Genome Biol. 2009;10(9):R93. doi: 10.1186/gb-2009-10-9-r93. Epub 2009 Sep 10.


Transcriptome and proteome analysis of osteocytes treated with nitrogen-containing bisphosphonates.

Bivi N, Bereszczak JZ, Romanello M, Zeef LA, Delneri D, Quadrifoglio F, Moro L, Brancia FL, Tell G.

J Proteome Res. 2009 Mar;8(3):1131-42. doi: 10.1021/pr8005606.


Genome-wide analysis and proteomic studies reveal APE1/Ref-1 multifunctional role in mammalian cells.

Vascotto C, Cesaratto L, Zeef LA, Deganuto M, D'Ambrosio C, Scaloni A, Romanello M, Damante G, Taglialatela G, Delneri D, Kelley MR, Mitra S, Quadrifoglio F, Tell G.

Proteomics. 2009 Feb;9(4):1058-74. doi: 10.1002/pmic.200800638.


Probing (macro)molecular transport through cell walls.

Kilcher G, Delneri D, Duckham C, Tirelli N.

Faraday Discuss. 2008;139:199-212; discussion 213-28, 419-20.


Identification and characterization of high-flux-control genes of yeast through competition analyses in continuous cultures.

Delneri D, Hoyle DC, Gkargkas K, Cross EJ, Rash B, Zeef L, Leong HS, Davey HM, Hayes A, Kell DB, Griffith GW, Oliver SG.

Nat Genet. 2008 Jan;40(1):113-7. Epub 2007 Dec 23.


Application of the comprehensive set of heterozygous yeast deletion mutants to elucidate the molecular basis of cellular chromium toxicity.

Holland S, Lodwig E, Sideri T, Reader T, Clarke I, Gkargkas K, Hoyle DC, Delneri D, Oliver SG, Avery SV.

Genome Biol. 2007;8(12):R268.


Development of novel guanidino-labelling derivatisation (GLaD) reagents for liquid chromatography/matrix-assisted laser desorption/ionisation analysis.

Brancia FL, Bereszczak JZ, Piatkowska E, Delneri D.

Rapid Commun Mass Spectrom. 2007;21(18):3069-76.


Plasticity of genetic interactions in metabolic networks of yeast.

Harrison R, Papp B, Pál C, Oliver SG, Delneri D.

Proc Natl Acad Sci U S A. 2007 Feb 13;104(7):2307-12. Epub 2007 Feb 6.


Cellular processes and pathways that protect Saccharomyces cerevisiae cells against the plasma membrane-perturbing compound chitosan.

Zakrzewska A, Boorsma A, Delneri D, Brul S, Oliver SG, Klis FM.

Eukaryot Cell. 2007 Apr;6(4):600-8. Epub 2007 Jan 26.


GIMS: an integrated data storage and analysis environment for genomic and functional data.

Cornell M, Paton NW, Hedeler C, Kirby P, Delneri D, Hayes A, Oliver SG.

Yeast. 2003 Nov;20(15):1291-306.


Engineering evolution to study speciation in yeasts.

Delneri D, Colson I, Grammenoudi S, Roberts IN, Louis EJ, Oliver SG.

Nature. 2003 Mar 6;422(6927):68-72.


Tools for the study of genome rearrangements in laboratory and industrial yeast strains.

Lockhart L, Oliver SG, Delneri D.

Yeast. 2002 Mar 30;19(5):441-8.


Towards a truly integrative biology through the functional genomics of yeast.

Delneri D, Brancia FL, Oliver SG.

Curr Opin Biotechnol. 2001 Feb;12(1):87-91. Review.


Exploring redundancy in the yeast genome: an improved strategy for use of the cre-loxP system.

Delneri D, Tomlin GC, Wixon JL, Hutter A, Sefton M, Louis EJ, Oliver SG.

Gene. 2000 Jul 11;252(1-2):127-35.


Characterization of microbial cellulose from a high-producing mutagenized Acetobacter pasteurianus strain.

Bertocchi C, Delneri D, Signore S, Weng Z, Bruschi CV.

Biochim Biophys Acta. 1997 Aug 29;1336(2):211-7.


The nucleotide sequence of Saccharomyces cerevisiae chromosome VII.

Tettelin H, Agostoni Carbone ML, Albermann K, Albers M, Arroyo J, Backes U, Barreiros T, Bertani I, Bjourson AJ, Brückner M, Bruschi CV, Carignani G, Castagnoli L, Cerdan E, Clemente ML, Coblenz A, Coglievina M, Coissac E, Defoor E, Del Bino S, Delius H, Delneri D, de Wergifosse P, Dujon B, Kleine K, et al.

Nature. 1997 May 29;387(6632 Suppl):81-4.


Sequencing of a 40.5 kb fragment located on the left arm of chromosome VII from Saccharomyces cerevisiae.

Coglievina M, Klima R, Bertani I, Delneri D, Zaccaria P, Bruschi CV.

Yeast. 1997 Jan;13(1):55-64.


Degradation of trans-ferulic and p-coumaric acid by Acinetobacter calcoaceticus DSM 586.

Delneri D, Degrassi G, Rizzo R, Bruschi CV.

Biochim Biophys Acta. 1995 Jun 9;1244(2-3):363-7.


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