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Towards a mechanistic understanding of DNA methylation readout by transcription factors.

Kribelbauer JF, Lu XJ, Rohs R, Mann RS, Bussemaker HJ.

J Mol Biol. 2019 Nov 2. pii: S0022-2836(19)30617-5. doi: 10.1016/j.jmb.2019.10.021. [Epub ahead of print] Review.


Low affinity binding sites in an activating CRM mediate negative autoregulation of the Drosophila Hox gene Ultrabithorax.

Delker RK, Ranade V, Loker R, Voutev R, Mann RS.

PLoS Genet. 2019 Oct 7;15(10):e1008444. doi: 10.1371/journal.pgen.1008444. eCollection 2019 Oct.


In vivo Hox binding specificity revealed by systematic changes to a single cis regulatory module.

Sánchez-Higueras C, Rastogi C, Voutev R, Bussemaker HJ, Mann RS, Hombría JC.

Nat Commun. 2019 Aug 9;10(1):3597. doi: 10.1038/s41467-019-11416-1.


Low-Affinity Binding Sites and the Transcription Factor Specificity Paradox in Eukaryotes.

Kribelbauer JF, Rastogi C, Bussemaker HJ, Mann RS.

Annu Rev Cell Dev Biol. 2019 Oct 6;35:357-379. doi: 10.1146/annurev-cellbio-100617-062719. Epub 2019 Jul 5.


The development and assembly of the Drosophila adult ventral nerve cord.

Venkatasubramanian L, Mann RS.

Curr Opin Neurobiol. 2019 Jun;56:135-143. doi: 10.1016/j.conb.2019.01.013. Epub 2019 Feb 28. Review.


Stereotyped terminal axon branching of leg motor neurons mediated by IgSF proteins DIP-α and Dpr10.

Venkatasubramanian L, Guo Z, Xu S, Tan L, Xiao Q, Nagarkar-Jaiswal S, Mann RS.

Elife. 2019 Feb 4;8. pii: e42692. doi: 10.7554/eLife.42692.


TP901-1 Phage Recombinase Facilitates Genome Engineering in Drosophila melanogaster.

Voutev R, Mann RS.

G3 (Bethesda). 2019 Apr 9;9(4):983-986. doi: 10.1534/g3.119.0002.


Visualize Drosophila Leg Motor Neuron Axons Through the Adult Cuticle.

Guan W, Venkatasubramanian L, Baek M, Mann RS, Enriquez J.

J Vis Exp. 2018 Oct 30;(140). doi: 10.3791/58365.


Improved reference genome of Aedes aegypti informs arbovirus vector control.

Matthews BJ, Dudchenko O, Kingan SB, Koren S, Antoshechkin I, Crawford JE, Glassford WJ, Herre M, Redmond SN, Rose NH, Weedall GD, Wu Y, Batra SS, Brito-Sierra CA, Buckingham SD, Campbell CL, Chan S, Cox E, Evans BR, Fansiri T, Filipović I, Fontaine A, Gloria-Soria A, Hall R, Joardar VS, Jones AK, Kay RGG, Kodali VK, Lee J, Lycett GJ, Mitchell SN, Muehling J, Murphy MR, Omer AD, Partridge FA, Peluso P, Aiden AP, Ramasamy V, Rašić G, Roy S, Saavedra-Rodriguez K, Sharan S, Sharma A, Smith ML, Turner J, Weakley AM, Zhao Z, Akbari OS, Black WC 4th, Cao H, Darby AC, Hill CA, Johnston JS, Murphy TD, Raikhel AS, Sattelle DB, Sharakhov IV, White BJ, Zhao L, Aiden EL, Mann RS, Lambrechts L, Powell JR, Sharakhova MV, Tu Z, Robertson HM, McBride CS, Hastie AR, Korlach J, Neafsey DE, Phillippy AM, Vosshall LB.

Nature. 2018 Nov;563(7732):501-507. doi: 10.1038/s41586-018-0692-z. Epub 2018 Nov 14.


Intrinsic DNA Shape Accounts for Affinity Differences between Hox-Cofactor Binding Sites.

Zeiske T, Baburajendran N, Kaczynska A, Brasch J, Palmer AG 3rd, Shapiro L, Honig B, Mann RS.

Cell Rep. 2018 Aug 28;24(9):2221-2230. doi: 10.1016/j.celrep.2018.07.100.


cis-regulatory architecture of a short-range EGFR organizing center in the Drosophila melanogaster leg.

Newcomb S, Voutev R, Jory A, Delker RK, Slattery M, Mann RS.

PLoS Genet. 2018 Aug 24;14(8):e1007568. doi: 10.1371/journal.pgen.1007568. eCollection 2018 Aug.


Accurate and sensitive quantification of protein-DNA binding affinity.

Rastogi C, Rube HT, Kribelbauer JF, Crocker J, Loker RE, Martini GD, Laptenko O, Freed-Pastor WA, Prives C, Stern DL, Mann RS, Bussemaker HJ.

Proc Natl Acad Sci U S A. 2018 Apr 17;115(16):E3692-E3701. doi: 10.1073/pnas.1714376115. Epub 2018 Apr 2.


Robust ΦC31-Mediated Genome Engineering in Drosophila melanogaster Using Minimal attP/attB Phage Sites.

Voutev R, Mann RS.

G3 (Bethesda). 2018 May 4;8(5):1399-1402. doi: 10.1534/g3.118.200051.


Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein-DNA binding.

Rao S, Chiu TP, Kribelbauer JF, Mann RS, Bussemaker HJ, Rohs R.

Epigenetics Chromatin. 2018 Feb 6;11(1):6. doi: 10.1186/s13072-018-0174-4.


Differing Strategies Despite Shared Lineages of Motor Neurons and Glia to Achieve Robust Development of an Adult Neuropil in Drosophila.

Enriquez J, Rio LQ, Blazeski R, Bellemin S, Godement P, Mason C, Mann RS.

Neuron. 2018 Feb 7;97(3):538-554.e5. doi: 10.1016/j.neuron.2018.01.007. Epub 2018 Jan 27.


Origins and Specification of the Drosophila Wing.

Requena D, Álvarez JA, Gabilondo H, Loker R, Mann RS, Estella C.

Curr Biol. 2017 Dec 18;27(24):3826-3836.e5. doi: 10.1016/j.cub.2017.11.023. Epub 2017 Dec 7.


From Reductionism to Holism: Toward a More Complete View of Development Through Genome Engineering.

Delker RK, Mann RS.

Adv Exp Med Biol. 2017;1016:45-74. doi: 10.1007/978-3-319-63904-8_3. Review.


Genome-wide prediction of minor-groove electrostatic potential enables biophysical modeling of protein-DNA binding.

Chiu TP, Rao S, Mann RS, Honig B, Rohs R.

Nucleic Acids Res. 2017 Dec 1;45(21):12565-12576. doi: 10.1093/nar/gkx915.


Quantitative Analysis of the DNA Methylation Sensitivity of Transcription Factor Complexes.

Kribelbauer JF, Laptenko O, Chen S, Martini GD, Freed-Pastor WA, Prives C, Mann RS, Bussemaker HJ.

Cell Rep. 2017 Jun 13;19(11):2383-2395. doi: 10.1016/j.celrep.2017.05.069.


Bxb1 phage recombinase assists genome engineering in Drosophila melanogaster.

Voutev R, Mann RS.

Biotechniques. 2017 Jan 1;62(1):37-38. doi: 10.2144/000114494.


To Be Specific or Not: The Critical Relationship Between Hox And TALE Proteins.

Merabet S, Mann RS.

Trends Genet. 2016 Jun;32(6):334-347. doi: 10.1016/j.tig.2016.03.004. Epub 2016 Apr 8. Review.


Streamlined scanning for enhancer elements in Drosophila melanogaster.

Voutev R, Mann RS.

Biotechniques. 2016 Mar 1;60(3):141-4. doi: 10.2144/000114391. eCollection 2016.


The Importance of Timing.

Mann RS, Howard CE.

Cell. 2016 Jan 28;164(3):347-8. doi: 10.1016/j.cell.2016.01.010.


Building accurate sequence-to-affinity models from high-throughput in vitro protein-DNA binding data using FeatureREDUCE.

Riley TR, Lazarovici A, Mann RS, Bussemaker HJ.

Elife. 2015 Dec 23;4. pii: e06397. doi: 10.7554/eLife.06397.


How Genomes Generate Animals: A View from Pasadena Genomic Control Process: Development and Evolution.

Mann RS.

FASEB J. 2015 Dec;29(12):4764-4765. doi: 10.1096/fj.15-1203ufm. No abstract available.


Asparagine deamidation reduces DNA-binding affinity of the Drosophila melanogaster Scr homeodomain.

O'Connell NE, Lelli K, Mann RS, Palmer AG 3rd.

FEBS Lett. 2015 Oct 24;589(21):3237-41. doi: 10.1016/j.febslet.2015.09.020. Epub 2015 Oct 3.


Quantification of gait parameters in freely walking rodents.

Mendes CS, Bartos I, Márka Z, Akay T, Márka S, Mann RS.

BMC Biol. 2015 Jul 22;13:50. doi: 10.1186/s12915-015-0154-0.


Identification of Suitable Reference Genes for Real Time Quantitative Polymerase Chain Reaction Assays on Pectoralis major Muscle in Chicken (Gallus gallus ).

Nascimento CS, Barbosa LT, Brito C, Fernandes RP, Mann RS, Pinto AP, Oliveira HC, Dodson MV, Guimarães SE, Duarte MS.

PLoS One. 2015 May 28;10(5):e0127935. doi: 10.1371/journal.pone.0127935. eCollection 2015.


Specification of individual adult motor neuron morphologies by combinatorial transcription factor codes.

Enriquez J, Venkatasubramanian L, Baek M, Peterson M, Aghayeva U, Mann RS.

Neuron. 2015 May 20;86(4):955-970. doi: 10.1016/j.neuron.2015.04.011. Epub 2015 May 7.


Deconvolving the recognition of DNA shape from sequence.

Abe N, Dror I, Yang L, Slattery M, Zhou T, Bussemaker HJ, Rohs R, Mann RS.

Cell. 2015 Apr 9;161(2):307-18. doi: 10.1016/j.cell.2015.02.008. Epub 2015 Apr 2.


Quantitative modeling of transcription factor binding specificities using DNA shape.

Zhou T, Shen N, Yang L, Abe N, Horton J, Mann RS, Bussemaker HJ, Gordân R, Rohs R.

Proc Natl Acad Sci U S A. 2015 Apr 14;112(15):4654-9. doi: 10.1073/pnas.1422023112. Epub 2015 Mar 9.


Is there a role for community pharmacists in promoting oral health?

Mann RS, Marcenes W, Gillam DG.

Br Dent J. 2015 Mar 13;218(5):E10. doi: 10.1038/sj.bdj.2015.172.


Swept confocally-aligned planar excitation (SCAPE) microscopy for high speed volumetric imaging of behaving organisms.

Bouchard MB, Voleti V, Mendes CS, Lacefield C, Grueber WB, Mann RS, Bruno RM, Hillman EM.

Nat Photonics. 2015 Feb;9(2):113-119.


Low affinity binding site clusters confer hox specificity and regulatory robustness.

Crocker J, Abe N, Rinaldi L, McGregor AP, Frankel N, Wang S, Alsawadi A, Valenti P, Plaza S, Payre F, Mann RS, Stern DL.

Cell. 2015 Jan 15;160(1-2):191-203. doi: 10.1016/j.cell.2014.11.041. Epub 2014 Dec 31.


Kinematic responses to changes in walking orientation and gravitational load in Drosophila melanogaster.

Mendes CS, Rajendren SV, Bartos I, Márka S, Mann RS.

PLoS One. 2014 Oct 28;9(10):e109204. doi: 10.1371/journal.pone.0109204. eCollection 2014.


cgChIP: a cell type- and gene-specific method for chromatin analysis.

Agelopoulos M, McKay DJ, Mann RS.

Methods Mol Biol. 2014;1196:291-306. doi: 10.1007/978-1-4939-1242-1_18.


SELEX-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.

Riley TR, Slattery M, Abe N, Rastogi C, Liu D, Mann RS, Bussemaker HJ.

Methods Mol Biol. 2014;1196:255-78. doi: 10.1007/978-1-4939-1242-1_16.


Yorkie promotes transcription by recruiting a histone methyltransferase complex.

Oh H, Slattery M, Ma L, White KP, Mann RS, Irvine KD.

Cell Rep. 2014 Jul 24;8(2):449-59. doi: 10.1016/j.celrep.2014.06.017. Epub 2014 Jul 10.


Neuroscience. The Michael Jackson fly.

Mann RS.

Science. 2014 Apr 4;344(6179):48-9. doi: 10.1126/science.1252431. No abstract available.


The LIM and POU homeobox genes ttx-3 and unc-86 act as terminal selectors in distinct cholinergic and serotonergic neuron types.

Zhang F, Bhattacharya A, Nelson JC, Abe N, Gordon P, Lloret-Fernandez C, Maicas M, Flames N, Mann RS, Colón-Ramos DA, Hobert O.

Development. 2014 Jan;141(2):422-35. doi: 10.1242/dev.099721. Epub 2013 Dec 18.


OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites.

Shazman S, Lee H, Socol Y, Mann RS, Honig B.

Nucleic Acids Res. 2014 Jan;42(Database issue):D167-71. doi: 10.1093/nar/gkt1165. Epub 2013 Nov 22.


Divergent transcriptional regulatory logic at the intersection of tissue growth and developmental patterning.

Slattery M, Voutev R, Ma L, Nègre N, White KP, Mann RS.

PLoS Genet. 2013;9(9):e1003753. doi: 10.1371/journal.pgen.1003753. Epub 2013 Sep 5.


Chemical and behavioral analysis of the cuticular hydrocarbons from Asian citrus psyllid, Diaphorina citri.

Mann RS, Rouseff RL, Smoot J, Rao N, Meyer WL, Lapointe SL, Robbins PS, Cha D, Linn CE, Webster FX, Tiwari S, Stelinski LL.

Insect Sci. 2013 Jun;20(3):367-78. doi: 10.1111/j.1744-7917.2012.01541.x. Epub 2012 Jul 31.


Dual role for Hox genes and Hox co-factors in conferring leg motoneuron survival and identity in Drosophila.

Baek M, Enriquez J, Mann RS.

Development. 2013 May;140(9):2027-38. doi: 10.1242/dev.090902. Epub 2013 Mar 27.


Genome-wide association of Yorkie with chromatin and chromatin-remodeling complexes.

Oh H, Slattery M, Ma L, Crofts A, White KP, Mann RS, Irvine KD.

Cell Rep. 2013 Feb 21;3(2):309-18. doi: 10.1016/j.celrep.2013.01.008. Epub 2013 Feb 8.


Quantification of gait parameters in freely walking wild type and sensory deprived Drosophila melanogaster.

Mendes CS, Bartos I, Akay T, Márka S, Mann RS.

Elife. 2013 Jan 8;2:e00231. doi: 10.7554/eLife.00231. Erratum in: Elife. 2013 Feb 11;2:e00565.


Abdominal color of the Asian citrus psyllid, Diaphorina citri, is associated with susceptibility to various insecticides.

Tiwari S, Killiny N, Mann RS, Wenninger EJ, Stelinski LL.

Pest Manag Sci. 2013 Apr;69(4):535-41. doi: 10.1002/ps.3407. Epub 2012 Nov 28.


A survey of 6,300 genomic fragments for cis-regulatory activity in the imaginal discs of Drosophila melanogaster.

Jory A, Estella C, Giorgianni MW, Slattery M, Laverty TR, Rubin GM, Mann RS.

Cell Rep. 2012 Oct 25;2(4):1014-24. doi: 10.1016/j.celrep.2012.09.010. Epub 2012 Oct 12.


Disentangling the many layers of eukaryotic transcriptional regulation.

Lelli KM, Slattery M, Mann RS.

Annu Rev Genet. 2012;46:43-68. doi: 10.1146/annurev-genet-110711-155437. Epub 2012 Aug 28. Review.


Engrailed cooperates directly with Extradenticle and Homothorax on a distinct class of homeodomain binding sites to repress sloppy paired.

Fujioka M, Gebelein B, Cofer ZC, Mann RS, Jaynes JB.

Dev Biol. 2012 Jun 15;366(2):382-92. doi: 10.1016/j.ydbio.2012.04.004. Epub 2012 Apr 20.

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