Recent Publications

An ancient yet flexible cis-regulatory architecture allows localized Hedgehog tuning by patched/PTCH1.
David S. Lorberbaum*, Andrea I. Ramos*, Kevin Peterson, Brandon Carpenter, David Parker, Sandip De, Lauren Hillers+, Victoria Blake+, Yuichi Nishi, Matthew McFarlane+, C.-Y. Chiang, Judith Kassis, Benjamin Allen, Andrew McMahon, and Scott Barolo
eLife 5:e13550 (2016). *Co-first authors; +Undergraduate co-authors.


How to tune an enhancer.
Scott Barolo
Proc Natl Acad Sci U S A 113(23):6330-1 (2016).


Identification and validation of novel Hedgehog-responsive enhancers predicted by computational analysis of Ci/Gli binding site density.
Katherine Gurdziel*, Aaron M. Udager*, David S. Lorberbaum*, Jane Y. Song, Neil Richards, David S. Parker, Lisa A. Johnson, Benjamin L. Allen+, Scott Barolo+, Deborah L. Gumucio+ 
PLoS One 10(12):e0145225 (2015). *Co-first authors; +Co-corresponding authors.


Enhancer biology: Holding out for the right promoter. David S. Lorberbaum & Scott Barolo
Current Biology 25:R290-3 (2015).


Genome evolution: How sister genes grow apart.       Victoria M. Blake & Scott Barolo
Current Biology 24: R695-697 (2014).


Gene regulation: When analog beats digital.
David S. Lorberbaum & Scott Barolo
Current Biology 23: R1054-1056 (2013).


Low-affinity transcription factor binding sites shape morphogen responses and enhancer evolution. 
Andrea I. Ramos & Scott Barolo
Philosophical Transactions of the Royal Society B, theme issue on “Molecular and Functional Evolution of Transcriptional Enhancers,” 368: 20130018 (2013).


Evolution of gene regulation: Hybrid networks breed diversity.
Andrea I. Ramos & Scott Barolo
Current Biology  22(23): R1009–1011 (2012).


A model of spatially restricted transcription in opposing gradients of activators and repressors.
Michael A. White, David S. Parker, Scott Barolo, & Barak A. Cohen
Molecular Systems Biology  8, 614 (2012).             -Recommended Article at F1000Prime



Sparkling insights into enhancer structure, function, and evolution.
Nicole C. Evans, Christina I. Swanson, & Scott Barolo
Current Topics in Developmental Biology  98, 97-120 (2012).


Rapid evolutionary rewiring of a structurally constrained eye enhancer.
Christina I. Swanson, David B. Schwimmer, & Scott Barolo
Current Biology  21(14), 1186-1196 (2011). [cover image] -Featured in a Dispatch in Current Biology, 26 June 2011.


The cis-regulatory logic of Hedgehog gradient responses: Key roles for Gli binding affinity, competition, and cooperativity. 
David S. Parker, Michael A. White, Andrea I. Ramos, Barak A. Cohen, & Scott Barolo
Science Signaling  4(176), ra38 (2011). [cover image]   -Featured in a "Perspective" in Science Signaling, 7 June 2011.


Using the game of Mastermind to teach, practice, and discuss scientific reasoning skills.
Amy R. Strom & Scott Barolo
PLoS Biology  9(1), e1000578 (2011). 
-Selected as an "Editors' Pick" by PLoS Biology, 18 Jan 2011.


Structural rules and complex regulatory circuitry constrain expression of a Notch- and EGFR-regulated eye enhancer.
Christina I. Swanson, Nicole C. Evans, & Scott Barolo
Developmental Cell  18(3), 359-370 (2010). 
-Selected as a "Must Read" by Faculty of 1000 Biology.
-Selected as a Science  Editors' Choice, 16 April 2010.


Reverse-engineering a transcriptional enhancer: a case study in Drosophila.
Lisa A. Johnson, Ying Zhao, Krista Golden, & Scott Barolo
Tissue Engineering  14(9), 1549-1559 (2008). 


The chromatin remodelers ISWI and ACF1 directly repress Wingless transcriptional targets.
Yan Liu, Mikyung Chang, Hui Lee, Scott Barolo, Jinhee Chang, Tim A. Blauwkamp, & Ken M. Cadigan
Developmental Biology  323, 41-52 (2008). 


A directional recombination cloning system for restriction- and ligation-free construction of GFP, DsRed, and lacZ transgenic Drosophila reporters.  
Christina I. Swanson, Trish Hinrichs, Lisa A. Johnson, Ying Zhao, & Scott Barolo
Gene  408, 180-186 (2008). 


Regulation of the feedback antagonist naked cuticle by Wingless signaling.
Jinhee Chang, Mikyung Chang, Scott Barolo, & Ken M. Cadigan
Developmental Biology  321, 446-454 (2008).