publications – siegal lab

Buzby B, Plavskin Y, Sartori FMO, Tong Q, Vail JK and Siegal ML. 2024. Epistasis and cryptic QTL identified using modified bulk segregant analysis of copper resistance in budding yeast. bioRxiv 620582.

Plavskin Y, de Biase MS, Ziv N, Janská L, Zhu YO, Hall DW, Schwarz RF, Tranchina D and Siegal ML. 2024. Spontaneous single-nucleotide substitutions and microsatellite mutations have distinct distributions of fitness effects. PLOS Biology 22:e3002698.

Plavskin Y*, de Biase MS*, Schwarz RF and Siegal ML. 2023. The rate of spontaneous mutations in yeast deficient for MutSβ function. G3 jkac330.

Plavskin Y and Siegal ML. 2022. Systems Biology, in Oxford Bibliographies in Evolutionary Biology, Futuyma D, ed. New York: Oxford University Press.

Cinquin B, Kao JY and Siegal ML. 2022. Quantifying position effect variegation in Drosophila melanogaster, in Bioimage Data Analysis Workflows — Advanced Components and Methods, Miura K and Sladoje N, eds. Cham: Springer.

Plavskin Y*, Li S*, Jung H, Sartori FMO, Buzby C, Müller H, Ziv N, Levy SF and Siegal ML. 2021. High-throughput microcolony growth analysis from suboptimal low-magnification micrographs. bioRxiv 253724.

Sartori FMO, Buzby C, Plavskin Y, and Siegal ML. 2021. High-throughput live imaging of microcolonies to measure heterogeneity in growth and gene expression. Journal of Visualized Experiments 170:e62038.

Geiler-Samerotte KA, Li S, Lazaris C, Taylor A, Ziv N, Ramjeawan C, Paaby AB, and Siegal ML. 2020. Extent and context dependence of pleiotropy revealed by high-throughput single-cell phenotyping. PLOS Biology 18:e3000836.

Rice G, David JR, Kamimura Y, Masly JP, Mcgregor AP, Nagy O, Noselli S, Santos Nunes MD, O’Grady P, Sánchez-Herrero E, Siegal ML, Toda MJ, Rebeiz M, Courtier-Orgogozo V and Yassin A. 2019. A standardized nomenclature and atlas of the male terminalia of Drosophila melanogaster. Fly 13:51-64.

Xiong K, Lancaster AK, Siegal ML and Masel J. 2019. Feed-forward regulation adaptively evolves via dynamics rather than topology when there is intrinsic noise. Nature Communications 10:2418.

Geiler-Samerotte K, Sartori FMO and Siegal ML. 2019. Decanalizing thinking on genetic canalization. Seminars in Cell & Developmental Biology 88:54-66.

Li S, Giardina DM and Siegal ML. 2018. Control of nongenetic heterogeneity in growth rate and stress tolerance of Saccharomyces cerevisiae by cyclic AMP-regulated transcription factors. PLOS Genetics 14:e1007744.

Conley D, Johnson R, Domingue B, Dawes C, Boardman J and Siegal ML. 2018. A sibling method for identifying vQTLs. PLOS ONE 13:e0194541.

Assaf ZJ, Tilk S, Park J, Siegal ML and Petrov DA. 2017. Deep sequencing of natural and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations. Genome Research 27:1988-2000.

Ziv N, Shuster BM, Siegal ML and Gresham D. 2017. Resolving the complex genetic basis of phenotypic variation and variability of cellular growth. Genetics 206:1645-1657.

Siegal ML. 2017. Molecular genetics: Chaperone protein gets personal. Nature 545:36-37.

Geiler-Samerotte KA and Siegal ML. 2016. Questioning buffering. Cell Systems 3:407.

Geiler-Samerotte KA, Zhu YO, Goulet BE, Hall DW and Siegal ML. 2016. Selection transforms the landscape of genetic variation interacting with Hsp90. PLOS Biology 14:e2000465. [related PLOS Biology primer by R Schell et al.: Modifiers of the genotype-phenotype map: Hsp90 and beyond]

Rauscher E, Conley D and Siegal ML. 2015. Sibling genes as environment: sibling dopamine genotypes and adolescent health support frequency dependent selection. Social Science Research 54:209-220.

O’Malley MA, Soyer OS and Siegal ML. 2015. A philosophical perspective on evolutionary systems biology. Biological Theory 10:6-17.

Siegal ML. 2015. Shifting sugars and shifting paradigms. PLoS Biology 13:e1002068.

Bauer CR, Li S and Siegal ML. 2015. Essential gene disruptions reveal complex relationships between phenotypic robustness, pleiotropy, and fitness. Molecular Systems Biology 11:773.

Calcott B, Levy A, Siegal ML, Soyer O and Wagner A. 2015. Engineering & biology: counsel for a continued relationship. Biological Theory 10:50-59.

Siegal ML and Leu J-Y. 2014. On the nature and evolutionary impact of phenotypic robustness mechanisms. Annual Review of Ecology, Evolution, and Systematics 45:495-517.

Arbeitman M, Kopp A, Siegal ML and Van Doren M. 2014. The genetics of sex: exploring differences. Genetics 197:527-529.

Zhu YO, Siegal ML, Hall DW and Petrov DA. 2014. Precise estimates of mutation rate and spectrum in yeast. Proc Natl Acad Sci USA 111:E2310-8.

Also see: Zhu YO, Siegal ML, Hall DW and Petrov DA. 2014. Reply to Chen and Zhang: On interpreting genome-wide trends from yeast mutation accumulation data. Proc Natl Acad Sci USA 111:E4063.

Conley D, Domingue B, Harris KM, McQueen M, Siegal ML and Boardman J. 2014. Testing the key assumption of heritability estimates based on genome-wide genetic relatedness. Journal of Human Genetics 59:342-5.

Siegal ML. 2014. Systems Biology, in Oxford Bibliographies in Evolutionary Biology, Losos J, ed. New York: Oxford University Press.

Siegal ML. 2013. Evolution of molecular networks, in The Princeton Guide to Evolution, Losos J, ed. Princeton: Princeton University Press.

Ziv N, Siegal ML and Gresham D. 2013. Genetic and non-genetic determinants of cell-growth variation assessed by high-throughput microscopy. Molecular Biology and Evolution 30:2568-2578.

Richardson JB, Uppendahl LD, Traficante MK, Levy SF and Siegal ML. 2013. Histone variant HTZ1 shows extensive epistasis with, but does not increase robustness to, new mutations. PLOS Genetics 9:e1003733.

Conley D, Rauscher E, Dawes C, Magnusson PKE and Siegal ML. 2013. Heritability and the equal environments assumption: evidence from multiple samples of misclassified twins. Behavior Genetics 43:415-426.

Geiler-Samerotte K, Bauer C, Li S, Ziv N, Gresham D and Siegal ML. 2013. The details in the distributions: why and how to study phenotypic variability. Current Opinion in Biotechnology 24:752-759.

Conley D, Rauscher E and Siegal ML. 2013. Beyond orchids and dandelions: testing the 5-HTT “risky” allele for evidence of phenotypic capacitance and frequency-dependent selection. Biodemography and Social Biology 59:37-56.

Siegal ML. 2013. Crouching variation revealed. Molecular Ecology 22:1187-1189.

Schnakenberg SL, Siegal ML and Bloch Qazi MC. 2012. Oh, the places they’ll go: female sperm storage and sperm precedence in Drosophila melanogaster. Spermatogenesis 2:224-235.

Fraser HB, Levy S, Chavan A, Shah HB, Kowli S, Perez JC, Zhou Y, Siegal ML and Sinha H. 2012. Polygenic cis-regulatory adaptation in the evolution of yeast pathogenicity. Genome Research 22:1930-1939.

Levy SF and Siegal ML. 2012. The robustness continuum, pp. 431-452 in Evolutionary Systems Biology, Soyer O, ed. New York: Springer, Advances in Experimental Medicine and Biology Series, Volume 751.

Siegal ML and Rushlow C. 2012. Pausing on the path to robustness. Developmental Cell 22:905-906.

Levy SF, Ziv N and Siegal ML. 2012. Bet hedging in yeast by heterogeneous, age-correlated expression of a stress protectant. PLoS Biology 10:e1001325. [related PLoS Biology synopsis by R Meadows: Yeast survive by hedging their bets]

Siegal ML and Masel J. 2012. Hsp90 depletion goes wild. BMC Biol 10:14.

Schnakenberg SL, Matias WR and Siegal ML. 2011. Sperm-storage defects and live birth in Drosophila females lacking spermathecal secretory cells. PLoS Biology 9:e1001192. [related PLoS Biology primer by MF Wolfner: Precious essences: Female secretions promote sperm storage in Drosophila]

Chatterjee SS, Uppendahl LD, Chowdhury MA, Ip PL and Siegal ML. 2011. The female-specific Doublesex isoform regulates pleiotropic transcription factors to pattern genital development in Drosophila. Development 138:1099-1109.

Arbeitman MN, Kopp A, Siegal ML and Van Doren M. 2010. Everything you always wanted to know about sex … in flies. Sex Dev 4:315-320.

Chen K, van Nimwegen E, Rajewsky N and Siegal ML. 2010. Correlating gene expression variation with cis-regulatory polymorphism in Saccharomyces cerevisiae. Genome Biol Evol 2:697-707.

Masel J and Siegal ML. 2009. Robustness: mechanisms and consequences. Trends Genet 25:395-403.

Chen K, Maaskola J, Siegal ML and Rajewsky N. 2009. Reexamining microRNA site accessibility in Drosophila: a population genomics study. PLoS ONE 4:e5681.

Levy SF and Siegal ML. 2008. Network hubs buffer environmental variation in Saccharomyces cerevisiae. PLoS Biology 6:e264.

Siegal ML, Promislow DEL and Bergman A. 2007. Functional and evolutionary inference in gene networks: does topology matter? Genetica 129:83-103.

Siegal ML and Bergman A. 2006. Canalization, pp. 235-251 in Evolutionary Genetics: Concepts and Case Studies, Fox CW and Wolf JB, eds. New York: Oxford University Press.

Siegal ML and Baker BS. 2005. Functional conservation and divergence of intersex, a gene required for female differentiation in Drosophila melanogaster. Dev Genes Evol 215:1-12.

Arbeitman MN, Fleming AA, Siegal ML, Null BH and Baker BS. 2004. A genomic analysis of Drosophila somatic sexual differentiation and its regulation. Development 131:2007-2021.

Bergman A and Siegal ML. 2003. Evolutionary capacitance as a general feature of complex gene networks. Nature 424:549-552. [related Nature News and Views by SC Stearns: Safeguards and spurs]

Garrett-Engele CM, Siegal ML, Manoli DS, Williams BC, Li H and Baker BS. 2002. intersex, a gene required for female sexual development in Drosophila, is expressed in both sexes and functions together with doublesex to regulate terminal differentiation. Development 129:4661-4675.

Siegal ML and Bergman A. 2002. Waddington’s canalization revisited: developmental stability and evolution. Proc Natl Acad Sci USA 99:10528-10532. [related PNAS commentary by SC Stearns: Progress on canalization]

Marín I, Siegal ML and Baker BS. 2000. The evolution of dosage-compensation mechanisms. BioEssays 22:1106-1114.

Siegal ML and Hartl DL. 2000. Application of Cre/loxP in Drosophila. Site-specific recombination and transgene coplacement. Methods Mol Biol 136:487-495.

Siegal ML and Hartl DL. 1999. Oviposition-site preference in Drosophila following interspecific gene transfer of the Alcohol dehydrogenase locus. Behav Genet 29:199-204.

Siegal ML and Hartl DL. 1998. An experimental test for lineage-specific position effects on alcohol dehydrogenase (Adh) genes in Drosophila. Proc Natl Acad Sci USA 95:15513-15518.

Siegal ML and Hartl DL. 1996. Transgene coplacement and high efficiency site-specific recombination with the Cre/loxP system in Drosophila. Genetics 144:715-726.

Siegal ML, Petrov DA and De Aguiar D. 1996. Triple-ligation strategy with advantages over directional cloning. BioTechniques 21:614-619.

Plavskin Y, de Biase MS, Schwarz RF and Siegal ML. 2023. The rate of spontaneous mutations in yeast deficient for MutSβ function. G3 jkac330.

Plavskin Y, Li S, Jung H, Sartori FMO, Buzby C, Müller H, Ziv N, Levy SF and Siegal ML. 2021. High-throughput microcolony growth analysis from suboptimal low-magnification micrographs. bioRxiv 253724.