Specification of individual adult motor neuron morphologies by combinatorial transcription factor codes. Enriquez J, Venkatasubramanian L, Baek M, Peterson M, Aghayeva U, et al. Neuron. 2015; 86(4):955-70. NIHMSID: NIHMS681022 PubMed [journal] PMID: 25959734 PMCID: PMC4441546.


Quantitative modeling of transcription factor binding specificities using DNA shape. Zhou T, Shen N, Yang L, Abe N, Horton J, et al. Proceedings of the National Academy of Sciences of the United States of America. 2015; 112(15):4654-9. PubMed [journal] PMID: 25775564 PMCID: PMC4403198.


Deconvolving the recognition of DNA shape from sequence. Abe N, Dror I, Yang L, Slattery M, Zhou T, et al. Cell. 2015; 161(2):307-18. NIHMSID: NIHMS663346 PubMed [journal] PMID: 25843630 PMCID: PMC4422406.


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, et al. Nature photonics. 2015; 9(2):113-119. NIHMSID: NIHMS647115 PubMed [journal] PMID: 25663846 PMCID: PMC4317333.



Low affinity binding site clusters confer hox specificity and regulatory robustness. Crocker J, Abe N, Rinaldi L, McGregor AP, Frankel N, et al. Cell. 2015; 160(1-2):191-203. NIHMSID: NIHMS690323 PubMed [journal] PMID: 25557079 PMCID: PMC4449256.


Yorkie promotes transcription by recruiting a histone methyltransferase complex. Oh H, Slattery M, Ma L, White KP, Mann RS, et al. Cell reports. 2014; 8(2):449-59. NIHMSID: NIHMS618331 PubMed [journal] PMID: 25017066 PMCID: PMC4152371.


Neuroscience. The Michael Jackson fly. Mann RS. Science (New York, N.Y.). 2014; 344(6179):48-9. NIHMSID: NIHMS610641 PubMed [journal] PMID: 24700848 PMCID: PMC4143233.


cgChIP: a cell type- and gene-specific method for chromatin analysis. Agelopoulos M, McKay DJ, Mann RS. Methods in molecular biology (Clifton, N.J.). 2014; 1196:291-306. NIHMSID: NIHMS690319 PMID: 25151171  PMCID: PMC4439094


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; 9(10):e109204. PubMed [journal] PMID: 25350743 PMCID: PMC4211655.


Shazman S, Lee H, Socol Y, Mann RS, Honig B (2013) OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites. Nucleic acids research. 2014; 42(Database issue):D167-71. PMID: 24271386  PMCID:PMC3965123

Zhang F, Bhattacharya A, Nelson JC, Abe N, Gordon P, Lloret-Fernandez C, Maicas M, Flames N, Mann RS, Colon-Ramos DA, Hobert O. (2013) The LIM and POU homeobox genes ttx-3 and unc-86 act as terminal selectors in distinct cholinergic and serotonergic neuron types. Development (Cambridge, England). 2014; 141(2):422-35PMID:24353061  PMCID:PMC3879818

Slattery M, Voutev R, Ma L, Negre N, White KP, Mann RS. Divergent transcriptional regulatory logic at the intersection of tissue growth and developmental patterning. PLoS Genetics 2013 e1003753.



Oh H, Slattery M, Ma L, Crofts A, White KP, Mann RS, Irvine KD. Genome-wide Association of Yorkie with Chromatin and Chromatin-Remodeling Complexes.  Cell Rep. 2013 Feb 21;3(2):309-18. doi: 10.1016/j.celrep.2013.01.008.


Doitsidou M, Flames N, Topalidou I, Abe N, Felton T, Remesal L, Popovitchenko T, Mann R, Chalfie M, Hobert O. (2013) A combinatorial regulatory signature controls terminal differentiation of the dopaminergic nervous system in C. elegans. Genes Dev. 2013 Jun 15;27(12):1391-405. PMID:23788625.

César S Mendes, Imre Bartos, Turgay Akay, Szabolcs Márka, Richard S Mann. Quantification of gait parameters in freely walking wild type and sensory deprived Drosophila melanogaster. eLife 2013 10.7554/eLife.00231


Jory A, Estella C, Giorgianni MW, Slattery M, Laverty TR, Rubin GM, Mann RS.  A Survey of 6,300 Genomic Fragments for cis-Regulatory Activity in the Imaginal Discs of Drosophila melanogaster.  Cell Rep. 2012 Oct 25;2(4):1014-24.


Lelli KM, Slattery M, Mann RS.  Disentangling the many layers of eukaryotic transcriptional regulation.  Annu Rev Genet. 2012 Dec 15;46:43-68. doi: 10.1146/annurev-genet-110711-155437.


Nagaraj R, Gururaja-Rao S, Jones KT, Slattery M, Negre N, Braas D, Christofk H, White KP, Mann R, Banerjee U.  Control of mitochondrial structure and function by the Yorkie/YAP oncogenic pathway.  Genes Dev. 2012 Sep 15;26(18):2027-37.


Agelopoulos, M., McKay, D., and Mann, RS. Developmental regulation of chromatin conformation by Hox proteins in Drosophila.  Cell Rep. 2012 Apr 5;1(4):350-359.


Fujioka M, Gebelein B, Cofer ZC, Mann RS, Jaynes JB. Engrailed cooperates directly with Extradenticle and Homothorax on a distinct class of homeodomain binding sites to repress sloppy paired. Dev Biol. 2012 Jun 15;366(2):382-92. Epub 2012 Apr 20.


Estella C, Voutev R, Mann RS. A dynamic network of morphogens and transcription factors patterns the fly leg. Curr Top Dev Biol. 2012;98:173-98.


Lelli KM, Noro B, Mann RS. Variable motif utilization in homeotic selector (Hox)-cofactor complex formation controls specificity. Proc Natl Acad Sci U S A. 2011 Dec 27;108(52):21122-7.


Slattery M, Riley T, Liu P, Abe N, Gomez-Alcala P, Dror I, Zhou T, Rohs R, Honig B, Bussemaker HJ, Mann RS. Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins. Cell. 2011 Dec 9;147(6):1270-82.


Noro B, Lelli K, Sun L, Mann RS. Competition for cofactor-dependent DNA binding underlies Hox phenotypic suppression. Genes Dev. 2011 Nov 15;25(22):2327-32. doi: 10.1101/gad.175539.111.


Bishop EP, Rohs R, Parker SC, West SM, Liu P, Mann RS, Honig B, Tullius TD. A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA. ACS Chem Biol. 2011 Dec 16;6(12):1314-20.


Slattery, M. Négre, N. Ma, L., White, KP, and Mann, RS. Genome-wide tissue-specific occupancy of the Hox protein Ultrabithorax and Hox cofactor Homothorax in Drosophila. PLoS ONE 2011:6(4): e14686. doi:10.1371/journal.pone.0014686

PDF: Slattery et al PLoSONE


Giorgianni, M. and Mann, RS. Establishment of medial fates along the proximodistal axis of the Drosophila leg through direct activation of dachshund by DistallessDev Cell. 2011 Apr 19;20(4):455-68.


West SM, Rohs R, Mann RS, Honig B. Electrostatic interactions between arginines and the minor groove in the nucleosome. J Biomol Struct Dyn. 2010 Jun;27(6):861-6.


Rohs, R., Jin, X., West, S. Joshi, R., Honig, B. and Mann, RS. Origins of Specificity in Protein-DNA Recognition. Annual Review of Biochemistry (2010), Volume 79:233-269.

PDF: Rohs et al., AnnRev


Joshi, R., Sun, L. and Mann, RS. Dissecting the functional specificities of two Hox proteins. Genes Dev. 2010:24(14); 1533-1545.

PDF: Joshi et al G&D


Estella, C. and Mann, R.S. Non-redundant selector and growth-promoting functions of two sister genes, buttonhead and Sp1, in Drosophila leg development. PLoS Genet. 2010 Jun 24;6(6):e1001001.


Crickmore M, Mann RS. A new chisel for sculpting Darwin’s endless forms. Nat Cell Biol. 2010 Jun;12(6):528-9.


Baek M, Mann RS. Lineage and birth date specify motor neuron targeting and dendritic architecture in adult Drosophila. J Neurosci. (2009) May 27;29(21):6904-16.

PDF: Baek and Mann JNeuro


McKay, D., Estella, C. and Mann R.S. The origins of the Drosophila leg as revealed by the cis-regulatory architecture of the Distalless gene. Development. 2009 Jan;136(1):61-71.

PDF: McKay_etal


Peng, W., Slattery, M. and Mann RS. Transcription factor choice in the Hippo signaling pathway: homothorax and yorkie regulation of the microRNA bantam in the progenitor domain of the Drosophila eye imaginal disc. Genes Dev (2009) 23(19):2307-19.

PDF: Peng et al_G&D


Crickmore MA, Ranade V, Mann RS. Regulation of Ubx expression by epigenetic enhancer silencing in response to Ubx levels and genetic variation. PLoS Genet. 2009 Sep;5(9):e1000633.

PDF: Crickmore etalPG


Rohs, R., West, S., Sosinsky, A., Liu, P. Mann, RS, and Honig, B. The role of DNA shape in protein-DNA recognition. Nature (article) (2009) 461(7268):1248-53.

PDF: Rohs et al_Nature


Mann RS, Lelli KM, Joshi R. Hox specificity: unique roles for cofactors and collaborators. Curr Top Dev Biol. 2009;88:63-101


Estella, C., McKay, D., and Mann, R.S. Direct integrations of Wingless, Decapentaplegic, and autoregulatory inputs into Distalless during Drosophila leg development. Dev. Cell, (2008) 14:86-96.

PDF: Estella et al PLoSG


Affolter, M., Slattery, M., and Mann, R.S. A lexicon for homeodomain-DNA recognition. Cell (2008) 133:1133-1135.


Estella, C. and Mann, R.S. Logic of Wg and Dpp induction of distal and medial fates in the Drosophila leg. Development, (2008), 135:627-636.

PDF: EstellaMannDev


Crickmore MA, Mann RS. The control of size in animals: insights from selector genes. Bioessays. 2008 Sep;30(9):843-53.


Joshi, R. Passner, J., Rohs, R., Jain, R. Sosinsky, A., Crickmore, M.A., Jacob, V., Aggarwal, A.K., Honig, B. and Mann, RS. Functional specificity of a Hox protein mediated by the recognition of minor groove structure. Cell. (2007) 131(3):530-43.

PDF: joshi_etal


Sosinsky, A., Honig, B., Mann, R.S., and Califano, A. Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting. Proc Natl Acad Sci U S A, 2007. 104(15): p. 6305-10.



Zirin, JD and Mann, RS. Nubbin and Teashirt mark barriers to clonal growth along the proximal-distal axis of the Drosophila wing. Dev Biol. 2007 Apr 15;304(2):745-58.


Gebelein B, Mann RS. Compartmental modulation of abdominal Hox expression by engrailed and sloppy-paired patterns the fly ectoderm. Dev Biol. 2007 Aug 15;308(2):593-605.


Stevens KE, Mann RS. A balance between two nuclear localization sequences and a nuclear export sequence governs extradenticle subcellular localization. Genetics. 2007 Apr;175(4):1625-36.


Crickmore, MA and R.S. Mann (2006) Hox Control of Organ Size by Regulation of Morphogen Production and Mobility. Science (Article), 313(5783):63-8.

PDF: Crickmore+Mann_text+SOM


Crickmore MA, Mann RS. (2006) Hox control of morphogen mobility and organ development through regulation of glypican expression. Development. 2007 Jan;134(2):327-34.

PDF: Crickmore+MannDev


Noro B, Culi J, McKay DJ, Zhang W, Mann RS. Distinct functions of homeodomain-containing and homeodomain-less isoforms encoded by homothorax. Genes Dev. 2006 Jun 15;20(12):1636-50.


Culi J, Aroca P, Modolell J, Mann RS. jing is required for wing development and to establish the proximo-distal axis of the leg in Drosophila melanogaster. Genetics. 2006 May;173(1):255-66.


Wildonger J, Mann RS. Evidence that nervy, the Drosophila homolog of ETO/MTG8, promotes mechanosensory organ development by enhancing Notch signaling. Dev Biol. 2005 Oct 15;286(2):507-20.


Ice RJ, Wildonger J, Mann RS, Hiebert SW. Comment on “Nervy links protein kinase A to plexin-mediated semaphorin repulsion”.  Science. 2005 Jul 22;309(5734):558


Wildonger J, Sosinsky A, Honig B, Mann RS. Lozenge directly activates argos and klumpfuss to regulate programmed cell death. Genes Dev. 2005 May 1;19(9):1034-9.


Mann RS, Culi J. Developmental biology: morphogens hitch a greasy ride. Nature. 2005 May 5;435(7038):30-3.


Wildonger J, Mann RS. The t(8;21) translocation converts AML1 into a constitutive transcriptional repressor. Development. 2005 May;132(10):2263-72.


Zirin JD, Mann RS. Differing strategies for the establishment and maintenance of teashirt and homothorax repression in the Drosophila wing. Development. 2004 Nov;131(22):5683-93.


Gebelein B, McKay DJ, Mann RS. Direct integration of Hox and segmentation gene inputs during Drosophila development. Nature. 2004 Oct 7;431(7009):653-9.


Bonin CP, Mann RS. A piggyBac transposon gene trap for the analysis of gene expression and function in Drosophila. Genetics. 2004 Aug;167(4):1801-11.


Culi J, Springer TA, Mann RS. Boca-dependent maturation of beta-propeller/EGF modules in low-density lipoprotein receptor proteins. EMBO J. 2004 Mar 24;23(6):1372-80.


Mann RS. Two Pax are better than one. Nat Genet. 2004 Jan;36(1):10-1.


Sosinsky A., Bonin K., Mann R.S., Honig B. (2003) Target Explorer: an automated tool for the identification of new target genes for a specified set of transcription factors. NAR, 31:3589-92.


Wang Z, Mann RS. Requirement for two nearly identical TGIF-related homeobox genes in Drosophila spermatogenesis. Development. 2003 Jul;130(13):2853-65.


Culi J, Mann RS. Boca, an endoplasmic reticulum protein required for wingless signaling and trafficking of LDL receptor family members in Drosophila. Cell. 2003 Feb 7;112(3):343-54.


Kobayashi M, Fujioka M, Tolkunova EN, Deka D, Abu-Shaar M, Mann RS, Jaynes JB. Engrailed cooperates with extradenticle and homothorax to repress target genes in Drosophila. Development. 2003 Feb;130(4):741-51.


Gebelein B, Culi J, Ryoo HD, Zhang W, Mann RS. Specificity of Distalless repression and limb primordia development by abdominal Hox proteins. Dev Cell. 2002 Oct;3(4):487-98.


Mann RS, Carroll SB. Molecular mechanisms of selector gene function and evolution. Curr Opin Genet Dev. 2002 Oct;12(5):592-600.


Mann RS, Casares F. Developmental biology: signalling legacies. Nature. 2002 Aug 15;418(6899):737-9.


Bessa J, B. Gebelein, F. Pichaud, F. Casares, and R.S. Mann (2002) Combinatorial control of Drosophila eye development by Eyeless, Homothorax, and Teashirt. Genes Dev. 16:2415-2427.


Casares F, Mann RS. The ground state of the ventral appendage in Drosophila. Science. 2001 Aug 24;293(5534):1477-80.


Mann RS, Morata G. The developmental and molecular biology of genes that subdivide the body of Drosophila. Annu Rev Cell Dev Biol. 2000;16:243-71.


Casares F, Mann RS. A dual role for homothorax in inhibiting wing blade development and specifying proximal wing identities in Drosophila. Development. 2000 Apr;127(7):1499-508.


Ryoo HD, Marty T, Casares F, Affolter M, Mann RS. Regulation of Hox target genes by a DNA bound Homothorax/Hox/Extradenticle complex.  Development. 1999 Nov;126(22):5137-48.


Ryoo HD, Mann RS. The control of trunk Hox specificity and activity by Extradenticle. Genes Dev. 1999 Jul 1;13(13):1704-16.


Abu-Shaar M, Ryoo HD, Mann RS. Control of the nuclear localization of Extradenticle by competing nuclear import and export signals. Genes Dev. 1999 Apr 15;13(8):935-45.


Passner JM, Ryoo HD, Shen L, Mann RS, Aggarwal AK. Structure of a DNA-bound Ultrabithorax-Extradenticle homeodomain complex. Nature. 1999 Feb 25;397(6721):714-9.


Mann RS, Affolter M. Hox proteins meet more partners. Curr Opin Genet Dev. 1998 Aug;8(4):423-9.


Abu-Shaar M, Mann RS. Generation of multiple antagonistic domains along the proximodistal axis during Drosophila leg development. Development. 1998 Oct;125(19):3821-30.


González-Crespo S, Abu-Shaar M, Torres M, Martínez-A C, Mann RS, Morata G. Antagonism between extradenticle function and Hedgehog signalling in the developing limb. Nature. 1998 Jul 9;394(6689):196-200.


Casares F, Mann RS. Control of antennal versus leg development in Drosophila. Nature. 1998 Apr 16;392(6677):723-6.


Grieder NC, Marty T, Ryoo HD, Mann RS, Affolter M. Synergistic activation of a Drosophila enhancer by HOM/EXD and DPP signaling. EMBO J. 1997 Dec 15;16(24):7402-10.


Rieckhof GE, Casares F, Ryoo HD, Abu-Shaar M, Mann RS. Nuclear translocation of extradenticle requires homothorax, which encodes an extradenticle-related homeodomain protein. Cell. 1997 Oct 17;91(2):171-83.


Mann RS. Why are Hox genes clustered? Bioessays. 1997 Aug;19(8):661-4.


Maconochie MK, Nonchev S, Studer M, Chan SK, Pöpperl H, Sham MH, Mann RS, Krumlauf R. Cross-regulation in the mouse HoxB complex: the expression of Hoxb2 in rhombomere 4 is regulated by Hoxb1. Genes Dev. 1997 Jul 15;11(14):1885-95.


Jaffe L, Ryoo HD, Mann RS. A role for phosphorylation by casein kinase II in modulating Antennapedia activity in Drosophila. Genes Dev. 1997 May 15;11(10):1327-40.


Chan SK, Ryoo HD, Gould A, Krumlauf R, Mann RS. Switching the in vivo specificity of a minimal Hox-responsive element. Development. 1997 May;124(10):2007-14.


Mann RS, Abu-Shaar M. Nuclear import of the homeodomain protein extradenticle in response to Wg and Dpp signalling. Nature. 1996 Oct 17;383(6601):630-3.


Mann RS, Chan SK. Extra specificity from extradenticle: the partnership between HOX and PBX/EXD homeodomain proteins. Trends Genet. 1996 Jul;12(7):258-62.


Chan SK, Mann RS. A structural model for a homeotic protein-extradenticle-DNA complex accounts for the choice of HOX protein in the heterodimer. Proc Natl Acad Sci U S A. 1996 May 28;93(11):5223-8.


Chan SK, Pöpperl H, Krumlauf R, Mann RS. An extradenticle-induced conformational change in a HOX protein overcomes an inhibitory function of the conserved hexapeptide motif. EMBO J. 1996 May 15;15(10):2476-87.


Mann RS. The specificity of homeotic gene function. Bioessays. 1995 Oct;17(10):855-63.


Pöpperl H, Bienz M, Studer M, Chan SK, Aparicio S, Brenner S, Mann RS, Krumlauf R. Segmental expression of Hoxb-1 is controlled by a highly conserved autoregulatory loop dependent upon exd/pbx. Cell. 1995 Jun 30;81(7):1031-42.


Feinstein PG, Kornfeld K, Hogness DS, Mann RS. Identification of homeotic target genes in Drosophila melanogaster including nervy, a proto-oncogene homologue. Genetics. 1995 Jun;140(2):573-86.


Mann, RS. Engrailed-mediated repression of Ultrabithorax is necessary for the parasegment 6 identity in Drosophila. Development. 1994 Nov;120(11):3205-12.


Chan SK, Jaffe L, Capovilla M, Botas J, Mann RS. The DNA binding specificity of Ultrabithorax is modulated by cooperative interactions with extradenticle, another homeoprotein. Cell. 1994 Aug 26;78(4):603-15.


Chan SK, Mann RS. The segment identity functions of Ultrabithorax are contained within its homeo domain and carboxy-terminal sequences. Genes Dev. 1993 May;7(5):796-811.


Irvine KD, Botas J, Jha S, Mann RS, Hogness DS. Negative autoregulation by Ultrabithorax controls the level and pattern of its expression. Development. 1993 Jan;117(1):387-99.


Mann RS, Hogness DS. Functional dissection of Ultrabithorax proteins in D. melanogaster. Cell. 1990 Feb 23;60(4):597-610.


Additional PDFs:




Genes Dev.-2006-Noro-1636-50


The Laboratory of Richard S Mann
Department of Biochemistry and Molecular Biophysics
Columbia University Medical Center
701 West 168th Street, HHSC 1104
New York, NY 10032

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