Publications by authors named "Zeba Wunderlich"

30Publications

A Mutation in the Stripe 2 Minimal Enhancer Is Buffered by Flanking Sequences.

G3 (Bethesda) 2020 Dec 3;10(12):4473-4482. Epub 2020 Dec 3.

Department of Systems Biology, Harvard Medical School, Boston, MA 02115

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http://dx.doi.org/10.1534/g3.120.401777DOI Listing
December 2020

Shadow enhancers can suppress input transcription factor noise through distinct regulatory logic.

Elife 2020 08 17;9. Epub 2020 Aug 17.

Department of Developmental and Cell Biology, University of California, Irvine, Irvine, United States.

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http://dx.doi.org/10.7554/eLife.59351DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7556877PMC
August 2020

Quantitative Comparison of the Anterior-Posterior Patterning System in the Embryos of Five Species.

G3 (Bethesda) 2019 07 9;9(7):2171-2182. Epub 2019 Jul 9.

Department of Systems Biology, Harvard Medical School, Boston, MA, 20115.

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http://dx.doi.org/10.1534/g3.118.200953DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6643877PMC
July 2019

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

Mol Biol Evol 2018 08;35(8):1958-1967

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA.

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http://dx.doi.org/10.1093/molbev/msy099DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6063282PMC
August 2018

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

Front Genet 2017 23;8:63. Epub 2017 May 23.

Department of Developmental and Cell Biology, University of California, IrvineIrvine, CA, United States.

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http://dx.doi.org/10.3389/fgene.2017.00063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5440464PMC
May 2017

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

PLoS One 2016 17;11(3):e0151740. Epub 2016 Mar 17.

Department of Systems Biology, Harvard Medical School, Boston, MA, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0151740PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4795680PMC
July 2016

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

Cell Rep 2015 Sep 3;12(11):1740-7. Epub 2015 Sep 3.

Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.08.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4581983PMC
September 2015

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

Mol Cell 2015 Jun;58(5):718-21

Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2015.04.025DOI Listing
June 2015

Shadow enhancers enable Hunchback bifunctionality in the Drosophila embryo.

Proc Natl Acad Sci U S A 2015 Jan 6;112(3):785-90. Epub 2015 Jan 6.

Department of Systems Biology, Harvard Medical School, Boston, MA 02115

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http://dx.doi.org/10.1073/pnas.1413877112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4311800PMC
January 2015

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

Methods 2014 Jun 13;68(1):233-41. Epub 2014 Jan 13.

Department of Systems Biology, Harvard Medical School, 200 Longwood Ave., Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2014.01.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4048779PMC
June 2014

Modeling transcriptional networks in Drosophila development at multiple scales.

Curr Opin Genet Dev 2011 Dec 1;21(6):711-8. Epub 2011 Sep 1.

Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1016/j.gde.2011.07.005DOI Listing
December 2011

Different gene regulation strategies revealed by analysis of binding motifs.

Trends Genet 2009 Oct 6;25(10):434-40. Epub 2009 Oct 6.

Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S01689525090016
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http://dx.doi.org/10.1016/j.tig.2009.08.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3697852PMC
October 2009

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

Nucleic Acids Res 2009 Aug 5;37(14):4629-41. Epub 2009 Jun 5.

Biophysics Program, Harvard University, Cambridge, MA 02138, USA.

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http://dx.doi.org/10.1093/nar/gkp394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2724268PMC
August 2009

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

Genome Biol 2008 27;9 Suppl 1:S7. Epub 2008 Jun 27.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Longwood Avenue, Boston, Massachusetts 02115, USA.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2008-9-s1-s7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447541PMC
August 2008

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

Nucleic Acids Res 2008 Jun 3;36(11):3570-8. Epub 2008 May 3.

Biophysics Program, Harvard University, Cambridge, MA 02138, USA.

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http://dx.doi.org/10.1093/nar/gkn173DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2441786PMC
June 2008

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

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

Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0700672104
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http://dx.doi.org/10.1073/pnas.0700672104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1955771PMC
August 2007

Assessing model accuracy using the homology modeling automatically software.

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

Center for Advanced Biotechnology and Medicine (CABM), Rutgers University and Robert Wood Johnson Medical School (UMDNJ), Piscataway, New Jersey 08854, USA.

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http://dx.doi.org/10.1002/prot.21466DOI Listing
January 2008

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

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

Biophysics Program, Harvard University, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1529/biophysj.105.080572DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1557581PMC
September 2006