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Publications

Selected publications (from over 100): 
 

J.S Bloom, I.M. Ehrenreich, W. Loo, T.L. Vo Lite and L. Kruglyak. (2013) Finding the sources of missing heritability in a yeast cross. Nature 494, 234–237.
 

A. Bendesky, J. Pitts, M.V. Rockman, L. Kruglyak and C.I. Bargmann (2012). Long-range regulatory polymorphisms affecting a GABA receptor constitute a quantitative trait locus (QTL) for social behavior in C. elegans. PLoS Genet. 8(12):e1003157.
 

B.E. Gaertner, M.R. Parmenter, M.V. Rockman, L. Kruglyak and P.C. Phillips (2012). More than the sum of its parts: a complex epistatic network underlies natural variation in thermal preference behavior in Caenorhabditis elegans. Genetics 192:1533-42.
 

R. Ghosh, A. Mohammadi, L. Kruglyak, W.S. Ryu. (2012) Multiparameter behavioral profiling reveals distinct thermal response regimes in Caenorhabditis elegans. BMC Biol. 2012 Oct 31;10 (1):85. [Epub ahead of print]
 

Z. Khan, J.S. Bloom, S. Amini, M. Singh, D.H. Perlman, A.A. Caudy and L. Kruglyak (2012). Quantitative measurement of allele specific protein expression in a diploid yeast hybrid by LC-MS. Mol. Syst. Biol. 8:602.
 

M. L. Reaves, S. Sinha, J. Rabinowitz, L. Kruglyak, R.J. Redfield (2012) Absence of Detectable Arsenate in DNA from Arsenate-Grown GFAJ-1 Cells. Science. 337. pp. 470-473.
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I.M. Ehrenreich, J.S. Bloom, N. Torabi, X. Wang, Y. Jia and L. Kruglyak (2012). Genetic architecture of highly complex chemical resistance traits across four yeast strains. PLoS Genet.e1002570. Published online 15 March 2012.


N. Torabi, L. Kruglyak (2012) Genetic Basis of Hidden Phenotypic Variation Revealed by Increased Translational Readthrough in Yeast. PLoS Genet 8(3) e1002546.
 

R. Ghosh, E.C.  Andersen, J.A. Shapiro, J.P. Gerke, L. Kruglyak. (2012) Natural variation in a chloride channel subunit confers avermectin resistance in C. elegans. Feb 3. 335(6068):574-8. ScienceReprints.

 
E.C. Andersen, J.P. Gerke, J.A. Shapiro, J.R. Crissman, R. Ghosh, J.S. Bloom, M.A. Félix, L. Kruglyak. (2012) Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversity. Nat Genet.  Jan. 29 doi: 10.1038/ng.1050. [Epub ahead of print]
 
E.J. Foss, D. Radulovic, S.A. Shaffer, D.R. Goodlett, L. Krugylak and A. Bedalov (2011). Natural genetic variation shapes protein networks mainly through non-transcriptional mechanisms. PLoS Biology 9(9): e1001144.
 
E.X. Kwan, E. Foss, L. Kruglyak and A. Bedalov (2011). Natural polymorphism in BUL2 links cellular amino acid availability with chronological aging and telomere maintenance in yeast. PLoS Genetics 7(8): e1002250. [Full Text]

N. Torabi and L. Kruglyak (2011). Variants in SUP45 and TRM10 underlie natural variation in translation termination efficiency inS. cerevisiae. PLoS Genetics 7(7): e1002211.
 
H.S. Seidel, M. Ailion, J. Li, A. van Oudenaarden, M.V. Rockman and L. Kruglyak (2011). A novel sperm-delivered toxin causes late-stage embryo lethality and transmission ratio distortion in C. elegans. PLoS Biology 9(7): e1001115. doi:10.1371/ journal.pbio.1001115.

A. Bendesky, M. Tsunozaki, M. V. Rockman, L. Kruglyak, C. I. Bargmann. (2011) Catecholamine receptor polymorphisms affect decision-making in C. elegans. Nature. April 21. [Full Text]
 
Z. Khan, S. Amini, J.S. Bloom, C. Ruse, A.A. Caudy, L. Kruglyak, M. Singh, D.H. Perlman and S. Tavazoie. (2011) Accurate proteome-wide protein quantification from high-resolution 15N mass spectra. Genome Biol.12(12):R122. 
 

M. V. Rockman, S. Skrovanek, L. Kruglyak. (2010) Selection at linked sites shapes heritable phenotypic variation in C. elegans. Science. Oct. 15; 330(6002):372-6. (link to publication) [Full Text}

 
I. M. Ehrenreich, N. Torabi, Y. Jia, J. Kent, S. Martis, J. A. Shapiro, D. Gresham, A. A. Caudy, L. Kruglyak. (2010) Dissection of genetically complex traits with extremely large pools of yeast segregants. Nature Letter, April 15. (link to publication) [Full Text].
 

D. Gresham, B. Curry, A. Ward, D.B. Gordon, L. Brizuela, L. Kruglyak, D. Botstein. (2010) Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with isothermal-melting probes. Proc Natl Acad Sci U S A. Jan 8. [link to publication] [Full Text].

 
T. A. Manolio, F. S. Collins, N. J. Cox, D. B. Goldstein, L. A. Hindorff, D. J. Hunter, M. I. McCarthy, E. M. Ramos, L. R. Cardon, A. Chakravarti, J. H. Cho, A. E. Guttmacher, A. Kong, L. Kruglyak, E. Mardis, C. N. Rotimi, M. Slatkin, D. Valle, A. S. Whittemore, M. Boehnke, A. G. Clark, E. E. Eichler, G. Gibson, J. L. Haines, T. F. C. Mackay, S. A. McCarroll & P. M. Visscher (2009) Finding the Missing Heritability of Complex Diseases, Nature, Oct 8 [link to publication] [Full Text].
 
L.N. Dimitrov, R.B. Brem, L. Kruglyak, D.E. Gottschling. (2009) Polymorphisms in Multiple Genes Contribute to the Spontaneous Mitochondrial Genome Instability of Saccharomyces cerevisiae S288C Strains. Genetics. Jul 6. [Full Text]

L. Kruglyak, J.D. Storey. (2009) Cause and express. Nat Biotechnol. 2009 Jun;27(6):544-5. [link to publication]
 
J.S. Bloom, Z. Khan, L. Kruglyak, M. Singh, A.A. Caudy. (2009) Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays. BMC Genomics. May 12;10:221. [link to publication]
 

Z. Khan, J. S. Bloom, L. Kruglyak, M. Singh (2009). A Practical Algorithm for Finding Maximal Exact Matches in Large Sequence Data Sets Using Sparse Suffix Arrays; Bioinformatics 2009; doi:10.1093/ bioinformatics/btp275 [link to publication]

 

P.T. McGrath, M.V. Rockman, M. Zimmer, H. Jang, E.Z. Macosko, L. Kruglyak and C.I. Bargmann (2009). Quantitative mapping of a digenic behavioral trait implicates globin variation in C. elegans sensory behaviors. Neuron Mar 12;61(5):692-9. [link to abstract]

 
M.V. Rockman and L. Kruglyak (2009). Recombinational Landscape and Population Genomics of C. elegans. PLoS Genet.  Mar;5(3):e1000419. [link to publication]
 
J. Schacherer, J.A. Shapiro, D.M. Ruderfer and L. Kruglyak (2009). Comprehensive polymorphism survey elucidates population structure of S. cerevisiae. Nature Mar 19;458(7236):342-5. [link to publication] [link to commentary in Nature Highlights]
 
K.C. Reddy, E.C. Andersen, L. Kruglyak, D.H. Kim. (2009) A polymorphism in npr-1 is a behavioral determinant of pathogen susceptibility in C. elegans. Science Jan 16;323(5912):382-4. [link to publication]
 
M.F. Palopoli, M.V. Rockman, A. TinMaung, C. Ramsey, S. Curwen, A. Aduna, J. Laurita and L. Kruglyak (2008). Molecular basis of the copulatory plug polymorphism in C. elegans. Nature Aug 21;454(7207):1019-22 [link to publication], [links to commentary in Current Biology and on Gene Expression blog]

A. Demogines, E.N. Smith, L. Kruglyak and E. Alani (2008). Identification and dissection of a complex DNA repair sensitivity phenotype in baker’s yeast. PLoS Genet. Jul 11;4(7):e1000123. [link to publication]

J. Zhu, B. Zhang, E.N. Smith, B. Drees, R. Brem, L. Kruglyak, R. Bumgarner and E.E. Schadt (2008). Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. Nat. Genet. (published online 15 June 2008; doi:10.1038/ng.167). [link to publication]

M.V. Rockman and L. Kruglyak (2008). Breeding designs for recombinant inbred advanced intercross lines. Genetics (published online May 27, 2008; doi:10.1534/genetics.107.083873). [link to publication]

E.N. Smith and L. Kruglyak (2008). Gene-environment interaction in yeast gene expression. PLoS Biol. 6(4): e83. doi:10.1371/journal.pbio.0060083. [link to publication]

L. Kruglyak (2008). The road to genome-wide association studies. Nat. Rev. Genet. 9:314-318 (published online 19 February 2008; doi:10.1038/nrg2316). [link to publication]

H.S. Seidel, M.V. Rockman and L. Kruglyak (2008). Widespread genetic incompatibility in C. elegans maintained by balancing selection. Science 319:589-594 (published online on Science Express January 10, 2008; doi:10.1126/science.1151107). [link to publication] [links to commentaries: Nature Reviews Genetics, Nature, This Week in Science, Nature Highlights]

E.J. Foss, D. Radulovic, S.A. Shaffer, D.M. Ruderfer, A. Bedalov, D.R. Goodlett and L. Kruglyak (2007). Genetic basis of proteome variation in yeast. Nat. Genet. 39:1369-1375 (published online 21 October 2007; doi:10.1038/ng.2007.22). [link to publication]

J. Schacherer, D. Ruderfer, D. Gresham, K. Dolinski, D. Botstein and L. Kruglyak (2007). Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains. PLoS ONE 2(3): e322. doi:10.1371/journal.pone.0000322. [link to publication]

Perlstein, Ruderfer, Roberts, Schreiber, Kruglyak (2007). Genetic basis of individual differences in the response to small-molecule drugs in yeast. Nat. Genet. 39:496-502. [link to publication]

Rockman, Kruglyak (2006). Genetics of global gene expression. Nat. Rev. Genet. 7:862-72. [link to publication

Ruderfer, Pratt, Seidel, Kruglyak (2006). Population genomic analysis of outcrossing and recombination in yeast. Nat. Genet. 38:1077-1081. [link to publication]

Riehle, Markianos, Niare, Xu, Li, Toure, Podiougou, Oduol, Diawara, Diallo, Coulibaly, Ouatara, Kruglyak, Traore, Vernick (2006). Natural malaria parasite infection in Anopheles gambiae is regulated by a single genomic control region. Science 312:577-579. [link to publication

Gresham, Ruderfer, Pratt, Schacherer, Dunham, Botstein, Kruglyak (2006). Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray. Science 311:1932-1936. [link to publication

Perlstein, Ramachandran, Ruderfer, Haggarty, Kruglyak, Schreiber (2006). Revealing complex traits using small molecules and naturally recombinant yeast strains. Chem Biol. 13:319-327. [link to publication]

Kruglyak (2005). Power tools for human genetics. Nature Genet. 37:1299-1300. [link to publication

Ronald, Brem, Whittle, Kruglyak (2005). Local regulatory variation in Saccharomyces cerevisiae. PLoS Genet. 1(2):e25. [link to publication]

Storey, Akey, Kruglyak (2005). Multiple locus linkage analysis of genomewide expression in yeast. PLoS Biol. 3(8):e267. [link to publication

Brem, Storey, Whittle, Kruglyak (2005). Genetic interactions between polymorphisms that affect gene expression in yeast. Nature 436:701-703. [link to publication]

Brem, Kruglyak (2005). The landscape of genetic complexity across 5,700 gene expression traits in yeast. Proc. Natl. Acad. Sci. USA; 102:5 1572-1577. [link to publication]

Ronald, Akey, Whittle, Smith, Yvert, Kruglyak (2005). Simultaneous genotyping, gene expression measurement, and detection of allele-specific expression with oligonucleotide arrays. Genome Res. 12:284-291. [link to publication]

Akey, Eberle, Rieder, Carlson, Shriver, Nickerson, Kruglyak. (2004). Population history and natural selection shape patterns of genetic variation in 132 genes. PLoS Biol. 2(10):e286. [link to publication]

Parker, Kim, Sutter, Carlson, Lorentzen, Johnson, DeFrance, Ostrander, Kruglyak (2004). Genetic structure of the purebred domestic dog. Science 304:1160-1164. [link to publication]

Carlson, Eberle, Kruglyak, Nickerson (2004). Mapping complex disease loci in whole-genome association studies. Nature 429:446-452. [link to publication]

The International HapMap Consortium (2003). The International HapMap Project. Nature 426:789-796. [link to publication]

Yvert, Brem, Whittle, Akey, Foss, Smith, Mackelprang, Kruglyak (2003). Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat. Genet. 35:57-64. [link to publication]

Carlson, Eberle, Rieder, Smith, Kruglyak, Nickerson (2003) Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans. Nat Genet 33:518-521. [link to publication]

Niaré, Markianos, Volz, Oduol, Touré, Bagayoko, Sangaré, Traoré, Wang, Blass, Dolo, Bouaré, Kafatos, Kruglyak, Touré, Vernick (2002) Genetic loci affecting resistance to human malaria parasites in a West African mosquito vector population. Science 298: 213-216. [link to publication]

Brem, Yvert, Clinton, Kruglyak (2002) Genetic dissection of transcriptional regulation in budding yeast. Science 296:752-755. [link to publication]

Eberle, Pfützer, Pogue-Geile, Bronner, Crispin, Kimmey, Duerr, Kruglyak, Whitcomb, Brentnall (2002) A new susceptibility locus for autosomal dominant pancreatic cancer maps to chromosome 4q32-34. Am J Hum Genet 70:1044-1048. [link to publication

Ardlie, Liu-Cordero, Eberle, Daly, Barrett, Winchester, Lander, Kruglyak (2001) Lower-than-expected linkage disequilibrium between tightly linked markers in humans suggests a role for gene conversion. Am J Hum Genet 69:582-589. [link to publication]

Kruglyak, Nickerson (2001) Variation is the spice of life. Nature Genetics 27:234-236. [link to publication]

Kruglyak (1999) Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat Genet 22:139. [link to publication]

Kruglyak (1997) The use of a genetic map of biallelic markers in linkage studies. Nat Genet 17:21 [link to publication]

Kruglyak, Daly, Reeve-Daly, Lander (1996) Parametric and nonparametric linkage analysis: A unified multipoint approach. Am J Hum Genet 58:1347. [link to publication]

Lander, Kruglyak (1995) Genetic dissection of complex traits: Guidelines for interpreting and reporting linkage results. Nat Genet 11:241. [link to publication