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Items: 1 to 20 of 46


The effects of transcription and recombination on mutational dynamics of short tandem repeats.

Zavodna M, Bagshaw A, Brauning R, Gemmell NJ.

Nucleic Acids Res. 2018 Feb 16;46(3):1321-1330. doi: 10.1093/nar/gkx1253.


HISEA: HIerarchical SEed Aligner for PacBio data.

Khiste N, Ilie L.

BMC Bioinformatics. 2017 Dec 19;18(1):564. doi: 10.1186/s12859-017-1953-9.


Integrated analysis of individual codon contribution to protein biosynthesis reveals a new approach to improving the basis of rational gene design.

Villada JC, Brustolini OJB, Batista da Silveira W.

DNA Res. 2017 Aug 1;24(4):419-434. doi: 10.1093/dnares/dsx014.


Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae.

Sato TK, Tremaine M, Parreiras LS, Hebert AS, Myers KS, Higbee AJ, Sardi M, McIlwain SJ, Ong IM, Breuer RJ, Avanasi Narasimhan R, McGee MA, Dickinson Q, La Reau A, Xie D, Tian M, Reed JL, Zhang Y, Coon JJ, Hittinger CT, Gasch AP, Landick R.

PLoS Genet. 2016 Oct 14;12(10):e1006372. doi: 10.1371/journal.pgen.1006372. eCollection 2016 Oct. Erratum in: PLoS Genet. 2016 Nov 9;12 (11):e1006447.


Scarless Gene Tagging with One-Step Transformation and Two-Step Selection in Saccharomyces cerevisiae and Schizosaccharomyces pombe.

Landgraf D, Huh D, Hallacli E, Lindquist S.

PLoS One. 2016 Oct 13;11(10):e0163950. doi: 10.1371/journal.pone.0163950. eCollection 2016.


Leveraging Genetic-Background Effects in Saccharomyces cerevisiae To Improve Lignocellulosic Hydrolysate Tolerance.

Sardi M, Rovinskiy N, Zhang Y, Gasch AP.

Appl Environ Microbiol. 2016 Sep 16;82(19):5838-49. doi: 10.1128/AEM.01603-16. Print 2016 Oct 1.


Jabba: hybrid error correction for long sequencing reads.

Miclotte G, Heydari M, Demeester P, Rombauts S, Van de Peer Y, Audenaert P, Fostier J.

Algorithms Mol Biol. 2016 May 3;11:10. doi: 10.1186/s13015-016-0075-7. eCollection 2016.


Massive Amplification at an Unselected Locus Accompanies Complex Chromosomal Rearrangements in Yeast.

Thierry A, Khanna V, Dujon B.

G3 (Bethesda). 2016 May 3;6(5):1201-15. doi: 10.1534/g3.115.024547.


Extracting DNA words based on the sequence features: non-uniform distribution and integrity.

Li Z, Cao H, Cui Y, Zhang Y.

Theor Biol Med Model. 2016 Jan 25;13:2. doi: 10.1186/s12976-016-0028-3.


Concerted activities of Mcm4, Sld3, and Dbf4 in control of origin activation and DNA replication fork progression.

Sheu YJ, Kinney JB, Stillman B.

Genome Res. 2016 Mar;26(3):315-30. doi: 10.1101/gr.195248.115. Epub 2016 Jan 5.


Discovery of Novel ncRNA Sequences in Multiple Genome Alignments on the Basis of Conserved and Stable Secondary Structures.

Fu Y, Xu ZZ, Lu ZJ, Zhao S, Mathews DH.

PLoS One. 2015 Jun 15;10(6):e0130200. doi: 10.1371/journal.pone.0130200. eCollection 2015.


Macrotene chromosomes provide insights to a new mechanism of high-order gene amplification in eukaryotes.

Thierry A, Khanna V, Créno S, Lafontaine I, Ma L, Bouchier C, Dujon B.

Nat Commun. 2015 Jan 30;6:6154. doi: 10.1038/ncomms7154.


The accuracy, feasibility and challenges of sequencing short tandem repeats using next-generation sequencing platforms.

Zavodna M, Bagshaw A, Brauning R, Gemmell NJ.

PLoS One. 2014 Dec 1;9(12):e113862. doi: 10.1371/journal.pone.0113862. eCollection 2014.


Highly specific contractions of a single CAG/CTG trinucleotide repeat by TALEN in yeast.

Richard GF, Viterbo D, Khanna V, Mosbach V, Castelain L, Dujon B.

PLoS One. 2014 Apr 18;9(4):e95611. doi: 10.1371/journal.pone.0095611. eCollection 2014.


The reference genome sequence of Saccharomyces cerevisiae: then and now.

Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM.

G3 (Bethesda). 2014 Mar 20;4(3):389-98. doi: 10.1534/g3.113.008995.


Optimizing information in Next-Generation-Sequencing (NGS) reads for improving de novo genome assembly.

Liu T, Tsai CH, Lee WB, Chiang JH.

PLoS One. 2013 Jul 29;8(7):e69503. doi: 10.1371/journal.pone.0069503. Print 2013.


Starvation-associated genome restructuring can lead to reproductive isolation in yeast.

Kroll E, Coyle S, Dunn B, Koniges G, Aragon A, Edwards J, Rosenzweig F.

PLoS One. 2013 Jul 24;8(7):e66414. doi: 10.1371/journal.pone.0066414. Print 2013.


Genome sequencing and comparative genomics of honey bee microsporidia, Nosema apis reveal novel insights into host-parasite interactions.

Chen Yp, Pettis JS, Zhao Y, Liu X, Tallon LJ, Sadzewicz LD, Li R, Zheng H, Huang S, Zhang X, Hamilton MC, Pernal SF, Melathopoulos AP, Yan X, Evans JD.

BMC Genomics. 2013 Jul 5;14:451. doi: 10.1186/1471-2164-14-451.


Transcriptome-wide mapping of 5-methylcytidine RNA modifications in bacteria, archaea, and yeast reveals m5C within archaeal mRNAs.

Edelheit S, Schwartz S, Mumbach MR, Wurtzel O, Sorek R.

PLoS Genet. 2013 Jun;9(6):e1003602. doi: 10.1371/journal.pgen.1003602. Epub 2013 Jun 27.


A combined system for engineering glycosylation efficiency and glycan structure in Saccharomyces cerevisiae.

Parsaie Nasab F, Aebi M, Bernhard G, Frey AD.

Appl Environ Microbiol. 2013 Feb;79(3):997-1007. doi: 10.1128/AEM.02817-12. Epub 2012 Nov 30.

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