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Baker's Yeast Clinical Isolates Provide a Model for How Pathogenic Yeasts Adapt to Stress.

Raghavan V, Aquadro CF, Alani E.

Trends Genet. 2019 Nov;35(11):804-817. doi: 10.1016/j.tig.2019.08.002. Epub 2019 Sep 13. Review.


Chromatin Modifiers Alter Recombination Between Divergent DNA Sequences.

Chakraborty U, Mackenroth B, Shalloway D, Alani E.

Genetics. 2019 Aug;212(4):1147-1162. doi: 10.1534/genetics.119.302395. Epub 2019 Jun 20.


A mutation in the endonuclease domain of mouse MLH3 reveals novel roles for MutLγ during crossover formation in meiotic prophase I.

Toledo M, Sun X, Brieño-Enríquez MA, Raghavan V, Gray S, Pea J, Milano CR, Venkatesh A, Patel L, Borst PL, Alani E, Cohen PE.

PLoS Genet. 2019 Jun 6;15(6):e1008177. doi: 10.1371/journal.pgen.1008177. eCollection 2019 Jun.


Intrinsically disordered regions regulate both catalytic and non-catalytic activities of the MutLα mismatch repair complex.

Kim Y, Furman CM, Manhart CM, Alani E, Finkelstein IJ.

Nucleic Acids Res. 2019 Feb 28;47(4):1823-1835. doi: 10.1093/nar/gky1244.


Incompatibilities in Mismatch Repair Genes MLH1-PMS1 Contribute to a Wide Range of Mutation Rates in Human Isolates of Baker's Yeast.

Raghavan V, Bui DT, Al-Sweel N, Friedrich A, Schacherer J, Aquadro CF, Alani E.

Genetics. 2018 Dec;210(4):1253-1266. doi: 10.1534/genetics.118.301550. Epub 2018 Oct 22.


Genomic Instability Promoted by Overexpression of Mismatch Repair Factors in Yeast: A Model for Understanding Cancer Progression.

Chakraborty U, Dinh TA, Alani E.

Genetics. 2018 Jun;209(2):439-456. doi: 10.1534/genetics.118.300923. Epub 2018 Apr 13.


mlh3 mutations in baker's yeast alter meiotic recombination outcomes by increasing noncrossover events genome-wide.

Al-Sweel N, Raghavan V, Dutta A, Ajith VP, Di Vietro L, Khondakar N, Manhart CM, Surtees JA, Nishant KT, Alani E.

PLoS Genet. 2017 Aug 21;13(8):e1006974. doi: 10.1371/journal.pgen.1006974. eCollection 2017 Aug. Erratum in: PLoS Genet. 2017 Oct 24;13(10 ):e1007067.


DNA replication and mismatch repair safeguard against metabolic imbalances.

Manhart CM, Alani E.

Proc Natl Acad Sci U S A. 2017 May 30;114(22):5561-5563. doi: 10.1073/pnas.1705971114. Epub 2017 May 22. No abstract available.


The mismatch repair and meiotic recombination endonuclease Mlh1-Mlh3 is activated by polymer formation and can cleave DNA substrates in trans.

Manhart CM, Ni X, White MA, Ortega J, Surtees JA, Alani E.

PLoS Biol. 2017 Apr 28;15(4):e2001164. doi: 10.1371/journal.pbio.2001164. eCollection 2017 Apr.


Mismatch Repair Incompatibilities in Diverse Yeast Populations.

Bui DT, Friedrich A, Al-Sweel N, Liti G, Schacherer J, Aquadro CF, Alani E.

Genetics. 2017 Apr;205(4):1459-1471. doi: 10.1534/genetics.116.199513. Epub 2017 Feb 13.


Understanding how mismatch repair proteins participate in the repair/anti-recombination decision.

Chakraborty U, Alani E.

FEMS Yeast Res. 2016 Sep;16(6). pii: fow071. Epub 2016 Aug 28.


Roles for mismatch repair family proteins in promoting meiotic crossing over.

Manhart CM, Alani E.

DNA Repair (Amst). 2016 Feb;38:84-93. doi: 10.1016/j.dnarep.2015.11.024. Epub 2015 Dec 2. Review.


A Delicate Balance Between Repair and Replication Factors Regulates Recombination Between Divergent DNA Sequences in Saccharomyces cerevisiae.

Chakraborty U, George CM, Lyndaker AM, Alani E.

Genetics. 2016 Feb;202(2):525-40. doi: 10.1534/genetics.115.184093. Epub 2015 Dec 17.


High-Throughput Universal DNA Curtain Arrays for Single-Molecule Fluorescence Imaging.

Gallardo IF, Pasupathy P, Brown M, Manhart CM, Neikirk DP, Alani E, Finkelstein IJ.

Langmuir. 2015 Sep 22;31(37):10310-7. doi: 10.1021/acs.langmuir.5b02416. Epub 2015 Sep 8.


A Genetic Incompatibility Accelerates Adaptation in Yeast.

Bui DT, Dine E, Anderson JB, Aquadro CF, Alani EE.

PLoS Genet. 2015 Jul 31;11(7):e1005407. doi: 10.1371/journal.pgen.1005407. eCollection 2015 Jul.


Mlh1-Mlh3, a meiotic crossover and DNA mismatch repair factor, is a Msh2-Msh3-stimulated endonuclease.

Rogacheva MV, Manhart CM, Chen C, Guarne A, Surtees J, Alani E.

J Biol Chem. 2014 Feb 28;289(9):5664-73. doi: 10.1074/jbc.M113.534644. Epub 2014 Jan 8.


Pch2 is a hexameric ring ATPase that remodels the chromosome axis protein Hop1.

Chen C, Jomaa A, Ortega J, Alani EE.

Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):E44-53. doi: 10.1073/pnas.1310755111. Epub 2013 Dec 23.


Genetic analysis of mlh3 mutations reveals interactions between crossover promoting factors during meiosis in baker's yeast.

Sonntag Brown M, Lim E, Chen C, Nishant KT, Alani E.

G3 (Bethesda). 2013 Jan;3(1):9-22. doi: 10.1534/g3.112.004622. Epub 2013 Jan 1.


Evolutionary rate covariation in meiotic proteins results from fluctuating evolutionary pressure in yeasts and mammals.

Clark NL, Alani E, Aquadro CF.

Genetics. 2013 Feb;193(2):529-38. doi: 10.1534/genetics.112.145979. Epub 2012 Nov 26.


Single-molecule imaging reveals target-search mechanisms during DNA mismatch repair.

Gorman J, Wang F, Redding S, Plys AJ, Fazio T, Wind S, Alani EE, Greene EC.

Proc Natl Acad Sci U S A. 2012 Nov 6;109(45):E3074-83. doi: 10.1073/pnas.1211364109. Epub 2012 Sep 24.


Mutation hot spots in yeast caused by long-range clustering of homopolymeric sequences.

Ma X, Rogacheva MV, Nishant KT, Zanders S, Bustamante CD, Alani E.

Cell Rep. 2012 Jan 26;1(1):36-42. doi: 10.1016/j.celrep.2011.10.003. Epub 2012 Jan 26.


The unstructured linker arms of Mlh1-Pms1 are important for interactions with DNA during mismatch repair.

Plys AJ, Rogacheva MV, Greene EC, Alani E.

J Mol Biol. 2012 Sep 14;422(2):192-203. doi: 10.1016/j.jmb.2012.05.030. Epub 2012 May 30.


Multiple cellular mechanisms prevent chromosomal rearrangements involving repetitive DNA.

George CM, Alani E.

Crit Rev Biochem Mol Biol. 2012 May-Jun;47(3):297-313. doi: 10.3109/10409238.2012.675644. Epub 2012 Apr 12. Review.


Evolutionary rate covariation reveals shared functionality and coexpression of genes.

Clark NL, Alani E, Aquadro CF.

Genome Res. 2012 Apr;22(4):714-20. doi: 10.1101/gr.132647.111. Epub 2012 Jan 27.


The DNA damage checkpoint allows recombination between divergent DNA sequences in budding yeast.

George CM, Lyndaker AM, Alani E.

DNA Repair (Amst). 2011 Nov 10;10(11):1086-94. doi: 10.1016/j.dnarep.2011.07.007. Epub 2011 Oct 5.


Multiple factors insulate Msh2-Msh6 mismatch repair activity from defects in Msh2 domain I.

Kumar C, Piacente SC, Sibert J, Bukata AR, O'Connor J, Alani E, Surtees JA.

J Mol Biol. 2011 Aug 26;411(4):765-80. doi: 10.1016/j.jmb.2011.06.030. Epub 2011 Jun 25.


Pch2 modulates chromatid partner choice during meiotic double-strand break repair in Saccharomyces cerevisiae.

Zanders S, Sonntag Brown M, Chen C, Alani E.

Genetics. 2011 Jul;188(3):511-21. doi: 10.1534/genetics.111.129031. Epub 2011 Apr 21.


Sustained and rapid chromosome movements are critical for chromosome pairing and meiotic progression in budding yeast.

Sonntag Brown M, Zanders S, Alani E.

Genetics. 2011 May;188(1):21-32. doi: 10.1534/genetics.110.125575. Epub 2011 Feb 21.


Genetic analysis of baker's yeast Msh4-Msh5 reveals a threshold crossover level for meiotic viability.

Nishant KT, Chen C, Shinohara M, Shinohara A, Alani E.

PLoS Genet. 2010 Aug 26;6(8). pii: e1001083. doi: 10.1371/journal.pgen.1001083.


The baker's yeast diploid genome is remarkably stable in vegetative growth and meiosis.

Nishant KT, Wei W, Mancera E, Argueso JL, Schlattl A, Delhomme N, Ma X, Bustamante CD, Korbel JO, Gu Z, Steinmetz LM, Alani E.

PLoS Genet. 2010 Sep 9;6(9):e1001109. doi: 10.1371/journal.pgen.1001109.


Detection of heterozygous mutations in the genome of mismatch repair defective diploid yeast using a Bayesian approach.

Zanders S, Ma X, Roychoudhury A, Hernandez RD, Demogines A, Barker B, Gu Z, Bustamante CD, Alani E.

Genetics. 2010 Oct;186(2):493-503. doi: 10.1534/genetics.110.120105. Epub 2010 Jul 26.


Visualizing one-dimensional diffusion of eukaryotic DNA repair factors along a chromatin lattice.

Gorman J, Plys AJ, Visnapuu ML, Alani E, Greene EC.

Nat Struct Mol Biol. 2010 Aug;17(8):932-8. doi: 10.1038/nsmb.1858. Epub 2010 Jul 25.


Genomic mutation rates: what high-throughput methods can tell us.

Nishant KT, Singh ND, Alani E.

Bioessays. 2009 Sep;31(9):912-20. doi: 10.1002/bies.200900017. Review.


The pch2Delta mutation in baker's yeast alters meiotic crossover levels and confers a defect in crossover interference.

Zanders S, Alani E.

PLoS Genet. 2009 Jul;5(7):e1000571. doi: 10.1371/journal.pgen.1000571. Epub 2009 Jul 24.


A tale of tails: insights into the coordination of 3' end processing during homologous recombination.

Lyndaker AM, Alani E.

Bioessays. 2009 Mar;31(3):315-21. doi: 10.1002/bies.200800195. Review.


Csm4, in collaboration with Ndj1, mediates telomere-led chromosome dynamics and recombination during yeast meiosis.

Wanat JJ, Kim KP, Koszul R, Zanders S, Weiner B, Kleckner N, Alani E.

PLoS Genet. 2008 Sep 26;4(9):e1000188. doi: 10.1371/journal.pgen.1000188.


Identification and dissection of a complex DNA repair sensitivity phenotype in Baker's yeast.

Demogines A, Smith E, Kruglyak L, Alani E.

PLoS Genet. 2008 Jul 11;4(7):e1000123. doi: 10.1371/journal.pgen.1000123.


Mutants defective in Rad1-Rad10-Slx4 exhibit a unique pattern of viability during mating-type switching in Saccharomyces cerevisiae.

Lyndaker AM, Goldfarb T, Alani E.

Genetics. 2008 Aug;179(4):1807-21. doi: 10.1534/genetics.108.090654. Epub 2008 Jun 24.


A mutation in the putative MLH3 endonuclease domain confers a defect in both mismatch repair and meiosis in Saccharomyces cerevisiae.

Nishant KT, Plys AJ, Alani E.

Genetics. 2008 Jun;179(2):747-55. doi: 10.1534/genetics.108.086645. Epub 2008 May 27.


Broad overexpression of ribonucleotide reductase genes in mice specifically induces lung neoplasms.

Xu X, Page JL, Surtees JA, Liu H, Lagedrost S, Lu Y, Bronson R, Alani E, Nikitin AY, Weiss RS.

Cancer Res. 2008 Apr 15;68(8):2652-60. doi: 10.1158/0008-5472.CAN-07-5873.


Dynamic basis for one-dimensional DNA scanning by the mismatch repair complex Msh2-Msh6.

Gorman J, Chowdhury A, Surtees JA, Shimada J, Reichman DR, Alani E, Greene EC.

Mol Cell. 2007 Nov 9;28(3):359-70.


The effect of genetic background on the function of Saccharomyces cerevisiae mlh1 alleles that correspond to HNPCC missense mutations.

Wanat JJ, Singh N, Alani E.

Hum Mol Genet. 2007 Feb 15;16(4):445-52. Epub 2007 Jan 8.


Negative epistasis between natural variants of the Saccharomyces cerevisiae MLH1 and PMS1 genes results in a defect in mismatch repair.

Heck JA, Argueso JL, Gemici Z, Reeves RG, Bernard A, Aquadro CF, Alani E.

Proc Natl Acad Sci U S A. 2006 Feb 28;103(9):3256-61. Epub 2006 Feb 21.


Detection of high-affinity and sliding clamp modes for MSH2-MSH6 by single-molecule unzipping force analysis.

Jiang J, Bai L, Surtees JA, Gemici Z, Wang MD, Alani E.

Mol Cell. 2005 Dec 9;20(5):771-81.


Analysis of interactions between mismatch repair initiation factors and the replication processivity factor PCNA.

Lee SD, Alani E.

J Mol Biol. 2006 Jan 13;355(2):175-84. Epub 2005 Nov 8.


Competing crossover pathways act during meiosis in Saccharomyces cerevisiae.

Argueso JL, Wanat J, Gemici Z, Alani E.

Genetics. 2004 Dec;168(4):1805-16.

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