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Zeba B. Wunderlich, Ph.D. - Publications

Affiliations: 
2008 Harvard University, Cambridge, MA, United States 
Area:
Population genetics and evolutionary theory; Polymer physics theory and simulation; Statistical interpretation of genome-wide data
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27 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Waymack R, Gad M, Wunderlich Z. Molecular competition can shape enhancer activity in the embryo. Iscience. 24: 103034. PMID 34568782 DOI: 10.1016/j.isci.2021.103034  0.326
2020 Lopez-Rivera F, Foster Rhoades OK, Vincent BJ, Pym ECG, Bragdon MDJ, Estrada J, DePace AH, Wunderlich Z. A Mutation in the Stripe 2 Minimal Enhancer Is Buffered by Flanking Sequences. G3 (Bethesda, Md.). PMID 33037064 DOI: 10.1534/g3.120.401777  0.312
2019 Park J, Estrada J, Johnson G, Vincent BJ, Ricci-Tam C, Bragdon MD, Shulgina Y, Cha A, Wunderlich Z, Gunawardena J, DePace AH. Dissecting the sharp response of a canonical developmental enhancer reveals multiple sources of cooperativity. Elife. 8. PMID 31223115 DOI: 10.7554/Elife.41266  0.389
2019 Wunderlich Z, Fowlkes CC, Eckenrode KB, Bragdon MDJ, Abiri A, DePace AH. Quantitative Comparison of the Anterior-Posterior Patterning System in the Embryos of Five Species. G3 (Bethesda, Md.). PMID 31048401 DOI: 10.1534/G3.118.200953  0.366
2018 Osman NM, Kitapci TH, Vlaho S, Wunderlich Z, Nuzhdin SV. Inference of Transcription Factor Regulation Patterns Using Gene Expression Covariation in Natural Populations of . Biophysics. 63: 43-51. PMID 30739944 DOI: 10.1134/S0006350918010128  0.429
2018 Vincent BJ, Staller MV, Lopez-Rivera F, Bragdon MDJ, Pym ECG, Biette KM, Wunderlich Z, Harden TT, Estrada J, DePace AH. Hunchback is counter-repressed to regulate even-skipped stripe 2 expression in Drosophila embryos. Plos Genetics. 14: e1007644. PMID 30192762 DOI: 10.1371/Journal.Pgen.1007644  0.417
2018 Wang X, Zhou T, Wunderlich Z, Maurano MT, DePace AH, Nuzhdin SV, Rohs R. Analysis of Genetic Variation Indicates DNA Shape Involvement in Purifying Selection. Molecular Biology and Evolution. PMID 29850830 DOI: 10.1093/Molbev/Msy099  0.421
2017 Samee MAH, Lydiard-Martin T, Biette KM, Vincent BJ, Bragdon MD, Eckenrode KB, Wunderlich Z, Estrada J, Sinha S, DePace AH. Quantitative Measurement and Thermodynamic Modeling of Fused Enhancers Support a Two-Tiered Mechanism for Interpreting Regulatory DNA. Cell Reports. 21: 236-245. PMID 28978476 DOI: 10.1016/J.Celrep.2017.09.033  0.365
2017 Li L, Wunderlich Z. An Enhancer's Length and Composition Are Shaped by Its Regulatory Task. Frontiers in Genetics. 8: 63. PMID 28588608 DOI: 10.3389/Fgene.2017.00063  0.365
2016 Estrada J, Ruiz-Herrero T, Scholes C, Wunderlich Z, DePace AH. SiteOut: An Online Tool to Design Binding Site-Free DNA Sequences. Plos One. 11: e0151740. PMID 26987123 DOI: 10.1371/Journal.Pone.0151740  0.448
2015 Wunderlich Z, Bragdon MD, Vincent BJ, White JA, Estrada J, DePace AH. Krüppel Expression Levels Are Maintained through Compensatory Evolution of Shadow Enhancers. Cell Reports. 12: 1740-7. PMID 26344774 DOI: 10.1016/J.Celrep.2015.08.021  0.336
2015 Staller MV, Fowlkes CC, Bragdon MD, Wunderlich Z, Estrada J, DePace AH. A gene expression atlas of a bicoid-depleted Drosophila embryo reveals early canalization of cell fate. Development (Cambridge, England). 142: 587-96. PMID 25605785 DOI: 10.1242/Dev.117796  0.349
2015 Staller MV, Vincent BJ, Bragdon MD, Lydiard-Martin T, Wunderlich Z, Estrada J, DePace AH. Shadow enhancers enable Hunchback bifunctionality in the Drosophila embryo. Proceedings of the National Academy of Sciences of the United States of America. 112: 785-90. PMID 25564665 DOI: 10.1073/Pnas.1413877112  0.349
2014 Wunderlich Z, Bragdon MD, DePace AH. Comparing mRNA levels using in situ hybridization of a target gene and co-stain. Methods (San Diego, Calif.). 68: 233-41. PMID 24434507 DOI: 10.1016/J.Ymeth.2014.01.003  0.303
2012 Wunderlich Z, Bragdon MD, Eckenrode KB, Lydiard-Martin T, Pearl-Waserman S, DePace AH. Dissecting sources of quantitative gene expression pattern divergence between Drosophila species. Molecular Systems Biology. 8: 604. PMID 22893002 DOI: 10.1038/Msb.2012.35  0.391
2011 Fowlkes CC, Eckenrode KB, Bragdon MD, Meyer M, Wunderlich Z, Simirenko L, Luengo Hendriks CL, Keränen SV, Henriquez C, Knowles DW, Biggin MD, Eisen MB, DePace AH. A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila. Plos Genetics. 7: e1002346. PMID 22046143 DOI: 10.1371/Journal.Pgen.1002346  0.34
2011 Wunderlich Z, DePace AH. Modeling transcriptional networks in Drosophila development at multiple scales. Current Opinion in Genetics & Development. 21: 711-8. PMID 21889888 DOI: 10.1016/J.Gde.2011.07.005  0.325
2009 Wunderlich Z, Mirny LA. Different gene regulation strategies revealed by analysis of binding motifs. Trends in Genetics : Tig. 25: 434-40. PMID 19815308 DOI: 10.1016/J.Tig.2009.08.003  0.636
2009 Wunderlich Z, Mirny LA. Using genome-wide measurements for computational prediction of SH2-peptide interactions. Nucleic Acids Research. 37: 4629-41. PMID 19502496 DOI: 10.1093/Nar/Gkp394  0.557
2009 Mirny L, Slutsky M, Wunderlich Z, Tafvizi A, Leith J, Kosmrlj A. How a protein searches for its site on DNA: The mechanism of facilitated diffusion Journal of Physics a: Mathematical and Theoretical. 42. DOI: 10.1088/1751-8113/42/43/434013  0.635
2008 Tian W, Zhang LV, TaÅŸan M, Gibbons FD, King OD, Park J, Wunderlich Z, Cherry JM, Roth FP. Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function. Genome Biology. 9: S7. PMID 18613951 DOI: 10.1186/Gb-2008-9-S1-S7  0.334
2008 Wunderlich Z, Mirny LA. Spatial effects on the speed and reliability of protein-DNA search. Nucleic Acids Research. 36: 3570-8. PMID 18453629 DOI: 10.1093/Nar/Gkn173  0.625
2008 Wunderlich Z, Mirny L. Fundamentally different strategies for transcriptional regulation are revealed by analysis of binding motifs Nature Precedings. DOI: 10.1038/Npre.2008.2688.2  0.596
2008 Wunderlich Z, Mirny L. An optimized energy potential can predict SH2 domain-peptide interactions Nature Precedings. DOI: 10.1038/Npre.2008.1881.1  0.509
2007 Kolesov G, Wunderlich Z, Laikova ON, Gelfand MS, Mirny LA. How gene order is influenced by the biophysics of transcription regulation. Proceedings of the National Academy of Sciences of the United States of America. 104: 13948-53. PMID 17709750 DOI: 10.1073/Pnas.0700672104  0.612
2006 Wunderlich Z, Mirny LA. Using the topology of metabolic networks to predict viability of mutant strains. Biophysical Journal. 91: 2304-11. PMID 16782788 DOI: 10.1529/Biophysj.105.080572  0.544
2005 Wunderlich Z, Mirny L. Genome Biology. 6: P15. DOI: 10.1186/Gb-2005-6-13-P15  0.546
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