Alani Lab Publications

Dr. Alani's Pubmed Listing

Representative Publications


  • Al-Sweel N, Raghavan V, Dutta A, Ajith VP, Di Vietro L, Khondakar N, Manhart CM, Surtees JA, Nishant KT, Alani E. (2017). mlh3 mutations in baker's yeast alter meiotic recombination outcomes by increasing noncrossover events genome-wide. PLoS Genetics, 13(8), e1006974. doi: 10.1371/journal.pgen.1006974
  • Manhart CM, Alani E. (2017). DNA replication and mismatch repair safeguard against metabolic imbalances. Proceedings of the National Academy of Sciences of the United States of America, 114(22):5561-5563. doi: 10.1073/pnas.1705971114
  • Manhart CM, Ni X, White MA, Ortega J, Surtees JA, Alani E. (2017). The mismatch repair and meiotic recombination endonuclease Mlh1-Mlh3 is activated by polymer formation and can cleave DNA substrates in trans. PLoS Biology, 15(4):e2001164. doi: 10.1371/journal.pbio.2001164
  • Bui DT, Friedrich A, Al-Sweel N, Liti G, Schacherer J, Aquadro CF, Alani E. Mismatch Repair Incompatibilities in Diverse Yeast Populations. Genetics, 205(4):1459-1471. doi: 10.1534/genetics.116.199513


  • Chakraborty U, Alani E. (2016). Understanding how mismatch repair proteins participate in the repair/anti-recombination decision. FEMS Yeast Research, 16(6). pii: fow071
  • Manhart CM, Alani E. (2016). Roles for mismatch repair family proteins in promoting meiotic crossing over. DNA Repair, 38:84-93. doi: 10.1016/j.dnarep.2015.11.024
  • Chakraborty U, George CM, Lyndaker AM, Alani E. (2016). A Delicate Balance Between Repair and Replication Factors Regulates Recombination Between Divergent DNA Sequences in Saccharomyces cerevisiae. Genetics, 202(2):525-40. doi: 10.1534/genetics.115.184093


  • Gallardo, I. F., Pasupathy, P., Brown, M., Manhart, C. M., Neikirk, D. P., Alani, E., & Finkelstein, I. J. (2015). High-Throughput Universal DNA Curtain Arrays for Single-Molecule Fluorescence Imaging. Langmuir, 150901130712008. doi:10.1021/acs.langmuir.5b02416
  • Bui, D. T., Dine, E., Anderson, J. B., Aquadro, C. F., & Alani, E. E. (2015). A Genetic Incompatibility Accelerates Adaptation in Yeast. PLoS Genetics, 11(7), e1005407. doi:10.1371/journal.pgen.1005407


  • Chen, C., Jomaa, A., Ortega, J., & Alani, E. E. (2014). Pch2 is a hexameric ring ATPase that remodels the chromosome axis protein Hop1. Proceedings of the National Academy of Sciences of the United States of America, 111(1), E44–53. doi:10.1073/pnas.1310755111
  • Rogacheva, M. V., Manhart, C. M., Chen, G., Guarne, A., Surtees, J., & Alani, E. (2014). Mlh1-Mlh3, a meiotic crossover and DNA mismatch repair factor,is a Msh2-Msh3-stimulated endonuclease. Journal of Biological Chemistry, 289(9), 5664–5673. doi:10.1074/jbc.M113.534644


  • Brown, M. S., Lim, E., Chen, C., Nishant, K. T., & Alani, E. (2013). Genetic Analysis of mlh3 Mutations Reveals Interactions Between Crossover Promoting Factors During Meiosis in Baker’s Yeast. G3 (Bethesda, Md.), 3(1), 9–22. doi:10.1534/g3.112.004622


  • Ma, X.,* Rogacheva, M.,* Nishant, K.T., Zanders, S., Bustamante, C. D., Alani, E. (2012) Mutation hotspots in yeast caused by long-range clustering of homopolymeric sequences. Cell Reports1,36-42. *co-first authors. PMC3408629
  • Clark, N., Alani, E., Aquadro, C.F.(2012) Evolutionary rate covariation reveals shared functionality, but notintermolecular coevolution, of genes. Genome Research22, 714-720.
  • George, C. M., Alani, E. (2012)Multiple cellular mechanisms prevent chromosomal rearrangements involving repetitive DNA. Critical Rev. Biochem. Mol. Biol.47, 297-313.
  • Plys, A. J., Rogacheva, M. V.,Greene, E. C., and Alani, E. (2012) The unstructured linker arms of Mlh1-Pms1are important for interactions with DNA during mismatch repair. J. Mol. Biol. 422,192-203.
  • Gorman, J. Wang, F., Redding, S.,Plys, A. J., Fazio, T., Wind, S., Reichman, D., Alani, E., Greene, E. C. (2012)Single-molecule imaging reveals target search mechanisms during DNA mismatchrepair. Proc. Natl. Acad. Sci. USA


  • Brown, S. M., Zanders, S., and Alani, E. (2011) Sustained and rapid chromosome movements are critical for chromosome pairing and meiotic
  • progression in budding yeast. Genetics188,21-32.PMC3120158. Issue highlights.
  • Zanders, S., Sonntag Brown, M., Chen, C., and Alani, E.  (2011)Pch2 modulates partner choice during meiotic double-strand break repair. Genetics188, 511-521.  PMCID in process.
  • Kumar, C., Piacente, S.C., Sibert, J., Bukata, A.R., O'Connor, J., Alani, E., and Surtees, J.A. (2011) Multiple factors insulate Msh2-Msh6 mismatch repair activity from defects in Msh2 Domain I. J. Mol. Biol. 411, 765-780. PMCID in process.


  • Plys, A.J. and Alani, E. (2010).  DNA mismatch repair in mammals.  Encyclopedia of Biological Chemistry, 2nd edition.  Elsevier Press.
  • Gorman, J.*, Plys, A.J.,* Visnapuu, M.L., Alani, E., Greene, E. (2010).  Visualizing 1D-diffusion of eukaryotic DNA repair factors along a chromatin lattice.  Nat. Struct. Mol. Biol. 12,1124-1125.PMC2953804.  *co-first authors.  Recommended, Faculty of 1000 Biology
  • Nishant, K.T., Cheng, C., Shinohara, M., Shinohara, A, Alani, E. (2010). Genetic analysis of baker's yeast Msh4-Msh5 reveals a threshold crossover level for meiotic viability. PLoS Genetics,6, e1001083. PMC2928781
  • Nishant, K.T., Wei, Wl, Mancera, E. Argueso, J.L., Schlattl, A., Delhomme, N., Ma, X., Bustamante, C., Korbel, J.O., Gu, Z., Steinmetz, L.M., Alani, E. (2010).The baker's yeast diploid genome is remarkably stable in vegetative growth and meiosis.  PLoS Genetics 6, e1001109.PMC2936533.  Recommended, Faculty of 1000 Biology
  • Zanders, S., Ma, X., RoyChoudhury, A., Hernandez, R.D., Demogines, A., Barker, B., Gu, Z., Bustamante, C.D., Alani, E. (2010) Detection of heterozygous mutations in the genome of mismatch repair defective diploid yeast using a Bayesian approach.  Genetics, 186, 493-503.PMC2954485.  


  • Zanders, S., and Alani, E. (2009). The pch2D mutation in baker's yeast alters meiotic crossover levels and confers a defect in crossover interference.  PLoS Genetics 5, e1000571.  Featured in Perspective (Thacker and Keeney), PLoS Genetics 5, e1000576.
  • Nishant, K. T., Singh, N. D. and Alani, E. (2009).  Genomic mutation rates: What high-throughput methods can tell us.  BioEssays 31, 912-920. PMC2952423


  • Nishant, K.T., Plys, A., and Alani, E. (2008) A mutation in the putative MLH3 endonuclease domain confers a defect in both mismatch repair and meiosis in Saccharomyces cerevisiae. Genetics 179, 747-755.
  • Demogines, A., Wong, A., Aquadro, C., and Alani, E. (2008) Incompatibilities involving yeast mismatch repair genes: a role for genetic modifiers and implications for disease penetrance and variation in genomic mutation rates. PLoS Genetics 4, e1000103.
  • Demogines, A., Smith, E., Kruglyak, L., and Alani, E. (2008) Identification and dissection of a complex DNA repair sensitivity phenotype in baker's yeast. PLoS Genetics 4, e1000123.
  • Lyndaker, A.M., Goldfarb, T., and Alani, E. (2008) Mutants defective in Rad1-Rad10-Slx4 exhibit a unique pattern of viability during mating type switching in S. cerevisiae. Genetics 179, 1807-1821.
  • Wanat, J., Kim, K., P., Kozul, R., Zanders, S., Weiner, B., Kleckner, N., and Alani, E. (2008) Csm4, in collaboration with Ndj1, mediates telomere-led chromosome dynamics and recombination during yeast meiosis. PLoS Genetics 4, e1000188.  Featured in Perspective (M Dresser), PLoS Genetics 4, e1000210.


  • Lee, S. D., Surtees, J. A., and Alani, E. (2007). Saccharomyces cerevisiae MSH2-MSH3 and MSH2-MSH6 complexes display distinct requirements for DNA binding Domain I in mismatch recognition.  J. Mol. Biol.366, 53-66.
  • Gorman, J., Chowdhury, A., Surtees, J. A., Shimada, J., Reichman, D. R., Alani, E., and Greene, E. (2007)Dynamic basis for one-dimensional DNA scanning by the mismatch repair complex Msh2-Msh6. Mol. Cell28, 359-370.


  • Heck, J. A., Argueso, J. L., Gemici, Z., Reeves, G. R., Bernard, A., Aquadro, C. F., and Alani, E. (2006). Negative epistasis between natural variants of the Saccharomyces cerevisiae MLH1 and PMS1 genes results in a defect in mismatch repair.  Proc. Natl. Acad. Sci. USA 103, 3256-3261.
  • Surtees J. A., and Alani, E. (2006).  Mismatch Repair Factor MSH2-MSH3 binds and alters the conformation of branched DNA structures predicted to form during genetic recombination.  J. Mol. Biol. 360, 523-536.
  • Heck, J. A., Gresham, D., Botstein, D., and Alani, E.  (2006).  Accumulation of recessive lethal mutations in S. cerevisiae mlh1 mismatch repair mutants is not associated with gross chromosomal rearrangements.  Genetics 174, 519-523.


  • Goldfarb, T., and Alani, E. (2005). Distinct roles for the Saccharomyces cerevisiae mismatch repair proteins in heteroduplex rejection, mismatch repair, and non-homologous tail removal.  Genetics 169, 563-574.
  • Jiang, J., Bai, L., Surtees, J. A., Gemici, Z., Wang, M. D., and Alani, E. (2005).  Detection of high affinity mismatch binding and sliding clamp modes for the MSH2-MSH6 mismatch recognition complex by single-molecule unzipping force analysis. Mol. Cell 20, 771-781.
  • Sugawara, N., Goldfarb, T., Studamire, B., Alani, E., and Haber, J. E. (2004)  Heteroduplex  rejection during single-strand annealing requires Sgs1 helicase and mismatch repair  proteins Msh2 and msh6 but not Pms1.  Proc. Natl. Acad. Sci. USA  101, 9315-9320.
  • Argueso, J. L., Wanat, J., Gemici, Z., and Alani, E.  (2004).  Competing crossover pathways act during meiosis in Saccharomyces cerevisiae.  Genetics, 168, 1805-1816.
  • Argueso, J. L., Kijas, A. W., Sarin, S., Heck, J., Waase, M., and Alani, E. (2003). Systematic mutagenesis of the Saccharomyces cerevisiae MLH1 gene reveals distinct roles for Mlh1p in meiotic crossing over and in vegetative and meiotic mismatch repair.  Mol. Cell. Biol. 23, 873-886..
  • Alani, E., Lee, J. Y., Schofield, M. J., Kijas, A. W., Hsieh, P.  and Yang, W. (2003)  Crystal structure and biochemical analysis of the MutS-ADP· BeFx complex suggests a conserved mechanism for ATP interactions in mismatch repair.  J. Biol. Chem. 278, 16088-16094.
  • Kijas, A. W., Studamire, B., and Alani, E. (2003)  msh2 separation of function mutations confer defects in the initiation steps of mismatch repair.  J. Mol. Biol. 331,123-138.
  • Evans, E., Sugawara, N., Haber, J. E., and Alani, E. (2000).  The Saccharomyces cerevisiae Msh2 mismatch repair protein localizes to recombination intermediates in vivo. Mol. Cell 5,
  • 789-799.