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Items: 29

1.

Inference of Transcription Factor Regulation Patterns Using Gene Expression Covariation in Natural Populations of Drosophila melanogaster.

Osman NM, Kitapci TH, Vlaho S, Wunderlich Z, Nuzhdin SV.

Biophysics (Oxf). 2018 Jan;63(1):43-51. doi: 10.1134/S0006350918010128. Epub 2018 Apr 23.

2.

Hunchback is counter-repressed to regulate even-skipped stripe 2 expression in Drosophila embryos.

Vincent BJ, Staller MV, Lopez-Rivera F, Bragdon MDJ, Pym ECG, Biette KM, Wunderlich Z, Harden TT, Estrada J, DePace AH.

PLoS Genet. 2018 Sep 7;14(9):e1007644. doi: 10.1371/journal.pgen.1007644. eCollection 2018 Sep.

3.

Analysis of Genetic Variation Indicates DNA Shape Involvement in Purifying Selection.

Wang X, Zhou T, Wunderlich Z, Maurano MT, DePace AH, Nuzhdin SV, Rohs R.

Mol Biol Evol. 2018 Aug 1;35(8):1958-1967. doi: 10.1093/molbev/msy099.

4.

Quantitative Measurement and Thermodynamic Modeling of Fused Enhancers Support a Two-Tiered Mechanism for Interpreting Regulatory DNA.

Samee MAH, Lydiard-Martin T, Biette KM, Vincent BJ, Bragdon MD, Eckenrode KB, Wunderlich Z, Estrada J, Sinha S, DePace AH.

Cell Rep. 2017 Oct 3;21(1):236-245. doi: 10.1016/j.celrep.2017.09.033.

5.

An Enhancer's Length and Composition Are Shaped by Its Regulatory Task.

Li L, Wunderlich Z.

Front Genet. 2017 May 23;8:63. doi: 10.3389/fgene.2017.00063. eCollection 2017.

6.

Krüppel Expression Levels Are Maintained through Compensatory Evolution of Shadow Enhancers.

Wunderlich Z, Bragdon MD, Vincent BJ, White JA, Estrada J, DePace AH.

Cell Rep. 2016 Mar 29;14(12):3030. doi: 10.1016/j.celrep.2016.03.032. No abstract available.

7.

SiteOut: An Online Tool to Design Binding Site-Free DNA Sequences.

Estrada J, Ruiz-Herrero T, Scholes C, Wunderlich Z, DePace AH.

PLoS One. 2016 Mar 17;11(3):e0151740. doi: 10.1371/journal.pone.0151740. eCollection 2016.

8.

Krüppel Expression Levels Are Maintained through Compensatory Evolution of Shadow Enhancers.

Wunderlich Z, Bragdon MD, Vincent BJ, White JA, Estrada J, DePace AH.

Cell Rep. 2015 Sep 22;12(11):1740-7. doi: 10.1016/j.celrep.2015.08.021. Epub 2015 Sep 3. Erratum in: Cell Rep. 2016 Mar 29;14(12):3030.

9.

Yearly planning meetings: individualized development plans aren't just more paperwork.

Vincent BJ, Scholes C, Staller MV, Wunderlich Z, Estrada J, Park J, Bragdon MD, Lopez Rivera F, Biette KM, DePace AH.

Mol Cell. 2015 Jun 4;58(5):718-21. doi: 10.1016/j.molcel.2015.04.025.

10.

A gene expression atlas of a bicoid-depleted Drosophila embryo reveals early canalization of cell fate.

Staller MV, Fowlkes CC, Bragdon MD, Wunderlich Z, Estrada J, DePace AH.

Development. 2015 Feb 1;142(3):587-96. doi: 10.1242/dev.117796.

11.

Shadow enhancers enable Hunchback bifunctionality in the Drosophila embryo.

Staller MV, Vincent BJ, Bragdon MD, Lydiard-Martin T, Wunderlich Z, Estrada J, DePace AH.

Proc Natl Acad Sci U S A. 2015 Jan 20;112(3):785-90. doi: 10.1073/pnas.1413877112. Epub 2015 Jan 6.

12.

Comparing mRNA levels using in situ hybridization of a target gene and co-stain.

Wunderlich Z, Bragdon MD, DePace AH.

Methods. 2014 Jun 15;68(1):233-41. doi: 10.1016/j.ymeth.2014.01.003. Epub 2014 Jan 13.

13.

Depleting gene activities in early Drosophila embryos with the "maternal-Gal4-shRNA" system.

Staller MV, Yan D, Randklev S, Bragdon MD, Wunderlich ZB, Tao R, Perkins LA, Depace AH, Perrimon N.

Genetics. 2013 Jan;193(1):51-61. doi: 10.1534/genetics.112.144915. Epub 2012 Oct 26.

14.

Dissecting sources of quantitative gene expression pattern divergence between Drosophila species.

Wunderlich Z, Bragdon MD, Eckenrode KB, Lydiard-Martin T, Pearl-Waserman S, DePace AH.

Mol Syst Biol. 2012;8:604. doi: 10.1038/msb.2012.35.

15.

A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila.

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.

PLoS Genet. 2011 Oct;7(10):e1002346. doi: 10.1371/journal.pgen.1002346. Epub 2011 Oct 27.

16.

Modeling transcriptional networks in Drosophila development at multiple scales.

Wunderlich Z, DePace AH.

Curr Opin Genet Dev. 2011 Dec;21(6):711-8. doi: 10.1016/j.gde.2011.07.005. Epub 2011 Sep 1. Review.

17.

Different gene regulation strategies revealed by analysis of binding motifs.

Wunderlich Z, Mirny LA.

Trends Genet. 2009 Oct;25(10):434-40. doi: 10.1016/j.tig.2009.08.003. Epub 2009 Oct 6.

18.

Using genome-wide measurements for computational prediction of SH2-peptide interactions.

Wunderlich Z, Mirny LA.

Nucleic Acids Res. 2009 Aug;37(14):4629-41. doi: 10.1093/nar/gkp394. Epub 2009 Jun 5.

19.

Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function.

Tian W, Zhang LV, Taşan M, Gibbons FD, King OD, Park J, Wunderlich Z, Cherry JM, Roth FP.

Genome Biol. 2008;9 Suppl 1:S7. doi: 10.1186/gb-2008-9-s1-s7. Epub 2008 Jun 27.

20.

Spatial effects on the speed and reliability of protein-DNA search.

Wunderlich Z, Mirny LA.

Nucleic Acids Res. 2008 Jun;36(11):3570-8. doi: 10.1093/nar/gkn173. Epub 2008 May 3.

21.

Non-traditional publishing choices can enrich science.

Wunderlich Z, Kuchibhotla K.

Nature. 2008 Feb 21;451(7181):887. doi: 10.1038/451887a. No abstract available.

PMID:
18288164
22.

How gene order is influenced by the biophysics of transcription regulation.

Kolesov G, Wunderlich Z, Laikova ON, Gelfand MS, Mirny LA.

Proc Natl Acad Sci U S A. 2007 Aug 28;104(35):13948-53. Epub 2007 Aug 20.

23.

Assessing model accuracy using the homology modeling automatically software.

Bhattacharya A, Wunderlich Z, Monleon D, Tejero R, Montelione GT.

Proteins. 2008 Jan 1;70(1):105-18.

PMID:
17640066
24.

Using the topology of metabolic networks to predict viability of mutant strains.

Wunderlich Z, Mirny LA.

Biophys J. 2006 Sep 15;91(6):2304-11. Epub 2006 Jun 16.

25.

The protein target list of the Northeast Structural Genomics Consortium.

Wunderlich Z, Acton TB, Liu J, Kornhaber G, Everett J, Carter P, Lan N, Echols N, Gerstein M, Rost B, Montelione GT.

Proteins. 2004 Aug 1;56(2):181-7. No abstract available.

PMID:
15211503
26.

SPINE 2: a system for collaborative structural proteomics within a federated database framework.

Goh CS, Lan N, Echols N, Douglas SM, Milburn D, Bertone P, Xiao R, Ma LC, Zheng D, Wunderlich Z, Acton T, Montelione GT, Gerstein M.

Nucleic Acids Res. 2003 Jun 1;31(11):2833-8.

27.

[Effect of antioxidants on the psoralen photo-oxidation process].

Potapenko AIa, Bezdetnaia LN, Wunderlich Z, Sukhorukov VL, Pliquett F.

Biofizika. 1986 Jul-Aug;31(4):549-54. Russian.

PMID:
3756226
28.

[Action of natural and synthetic antioxidants on the electrical parameters and stability of natural and artificial membranes].

Ivanov II, Korolev NP, Semin BK, Lap V, Wunderlich Z.

Nauchnye Doki Vyss Shkoly Biol Nauki. 1986;(5):35-40. Russian.

PMID:
3730453
29.

[Changes in the passive electrical properties of the erythrocytes during hemosorption].

Pliquett F, Sergienko VI, Wunderlich Z, Kagan VE.

Biull Eksp Biol Med. 1984 Oct;98(10):414-6. Russian.

PMID:
6498317

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