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Select item 90183821.

Thermodynamics-based modeling reveals regulatory effects of indirect transcription factor-DNA binding

Shounak Bhogale, Saurabh Sinha

iScience. 2022 May 20; 25(5): 104152. Published online 2022 Mar 24. doi: 10.1016/j.isci.2022.104152

PMCID:: PMC9018382

Abstract Article PDF–2.0M

Select item 66018682.

The Role of Chromatin Accessibility in cis-Regulatory Evolution

Pei-Chen Peng, Pierre Khoueiry, Charles Girardot, James P Reddington, David A Garfield, Eileen E M Furlong, Saurabh Sinha

Genome Biol Evol. 2019 Jul; 11(7): 1813–1828. Published online 2019 May 22. doi: 10.1093/gbe/evz103

PMCID:: PMC6601868

Abstract Article PDF–951K

Select item 55502763.

Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity

Pierre Khoueiry, Charles Girardot, Lucia Ciglar, Pei-Chen Peng, E Hilary Gustafson, Saurabh Sinha, Eileen EM Furlong

eLife. 2017; 6: e28440. Published online 2017 Aug 9. doi: 10.7554/eLife.28440

PMCID:: PMC5550276

Abstract Article PDF–2.7M

Select item 35272614.

Identifying targets of multiple co-regulating transcription factors from expression time-series by Bayesian model comparison

Michalis K Titsias, Antti Honkela, Neil D Lawrence, Magnus Rattray

BMC Syst Biol. 2012; 6: 53. Published online 2012 May 30. doi: 10.1186/1752-0509-6-53

PMCID:: PMC3527261

Abstract Article PDF–926K

Select item 33171585.

Cell-type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling

Florian A. Steiner, Paul B. Talbert, Sivakanthan Kasinathan, Roger B. Deal, Steven Henikoff

Genome Res. 2012 Apr; 22(4): 766–777. doi: 10.1101/gr.131748.111

PMCID:: PMC3317158

Abstract Article PDF–1.3M

Select item 29133986.

Dynamic CRM occupancy reflects a temporal map of developmental progression

Bartek Wilczyński, Eileen E M Furlong

Mol Syst Biol. 2010; 6: 383. Published online 2010 Jun 22. doi: 10.1038/msb.2010.35

PMCID:: PMC2913398

Abstract Article PDF–1.3M

Select item 34934607.

A Graphical Modelling Approach to the Dissection of Highly Correlated Transcription Factor Binding Site Profiles

Robert Stojnic, Audrey Qiuyan Fu, Boris Adryan

PLoS Comput Biol. 2012 Nov; 8(11): e1002725. Published online 2012 Nov 8. doi: 10.1371/journal.pcbi.1002725

PMCID:: PMC3493460

Abstract Article PDF–1.0M

Select item 14708128.

Nucleotide variation in the tinman and bagpipe homeobox genes of Drosophila melanogaster.

Evgeniy S Balakirev, Francisco J Ayala

Genetics. 2004 Apr; 166(4): 1845–1856. doi: 10.1534/genetics.166.4.1845

PMCID:: PMC1470812

Summary PDF–225K

Select item 2981419.

Drosophila NK-homeobox genes.

Y Kim, M Nirenberg

Proc Natl Acad Sci U S A. 1989 Oct; 86(20): 7716–7720. doi: 10.1073/pnas.86.20.7716

PMCID:: PMC298141

Summary Page Browse PDF–1.3M

Select item 889332110.

Simultaneous cellular and molecular phenotyping of embryonic mutants using single-cell regulatory trajectories

Stefano Secchia, Mattia Forneris, Tobias Heinen, Oliver Stegle, Eileen E.M. Furlong

Dev Cell. 2022 Feb 28; 57(4): 496–511.e8. doi: 10.1016/j.devcel.2022.01.016

PMCID:: PMC8893321

Abstract Article

Select item 2134411.

Differential rescue of visceral and cardiac defects in Drosophila by vertebrate tinman-related genes

Maijon Park, Carol Lewis, David Turbay, Amy Chung, Jau-Nian Chen, Sylvia Evans, Roger E. Breitbart, Mark C. Fishman, Seigo Izumo, Rolf Bodmer

Proc Natl Acad Sci U S A. 1998 Aug 4; 95(16): 9366–9371. doi: 10.1073/pnas.95.16.9366

Correction in:: Proc Natl Acad Sci U S A. 1998 Oct 27; 95(22): 13348.

PMCID:: PMC21344

Abstract Article PDF–468K

Select item 387920712.

Subtle Changes in Motif Positioning Cause Tissue-Specific Effects on Robustness of an Enhancer's Activity

Jelena Erceg, Timothy E. Saunders, Charles Girardot, Damien P. Devos, Lars Hufnagel, Eileen E. M. Furlong

PLoS Genet. 2014 Jan; 10(1): e1004060. Published online 2014 Jan 2. doi: 10.1371/journal.pgen.1004060

PMCID:: PMC3879207

Abstract Article PDF–9.8M

Select item 55669213.

Empty spiracles, a gap gene containing a homeobox involved in Drosophila head development.

U Walldorf, W J Gehring

EMBO J. 1992 Jun; 11(6): 2247–2259. doi: 10.1002/j.1460-2075.1992.tb05284.x

PMCID:: PMC556692

Summary Page Browse PDF–3.3M

Select item 373324514.

Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos

Stephen S. Gisselbrecht, Luis A. Barrera, Martin Porsch, Anton Aboukhalil, Preston W. Estep, 3rd, Anastasia Vedenko, Alexandre Palagi, Yongsok Kim, Xianmin Zhu, Brian W. Busser, Caitlin E. Gamble, Antonina Iagovitina, Aditi Singhania, Alan M. Michelson, Martha L. Bulyk

Nat Methods. Author manuscript; available in PMC 2014 Feb 1.

Published in final edited form as: Nat Methods. 2013 Aug; 10(8): 774–780. Published online 2013 Jul 14. doi: 10.1038/nmeth.2558