Liu K, Slattery M, Jacobs D, Cutter G, McDonald A, Van Horn L, Hilner JE, Caan B, Bragg C, Dyer A
A study of the reliability and comparative validity of the cardia dietary history. Ethn Dis. 1994; 4(1):15-27.
A study of the reliability and comparative validity of the cardia dietary history.
Newcomb S, Voutev R, Jory A, Delker RK, Slattery M, Mann RS
cis-regulatory architecture of a short-range EGFR organizing center in the Drosophila melanogaster leg. PLoS Genet. 2018 08; 14(8):e1007568.
cis-regulatory architecture of a short-range EGFR organizing center in the Drosophila melanogaster leg.
McDonald A, Van Horn L, Slattery M, Hilner J, Bragg C, Caan B, Jacobs D, Liu K, Hubert H, Gernhofer N, Betz E, Havlik D
Journal of the American Dietetic Association
The CARDIA dietary history: development, implementation, and evaluation. J Am Diet Assoc. 1991 Sep; 91(9):1104-12.
The CARDIA dietary history: development, implementation, and evaluation.
Wang L, Joshi P, Miller EL, Higgins L, Slattery M, Simon JA
A Role for Monomethylation of Histone H3-K27 in Gene Activity in Drosophila. Genetics. 2018 03; 208(3):1023-1036.
A Role for Monomethylation of Histone H3-K27 in Gene Activity in Drosophila.
Zraly CB, Zakkar A, Perez JH, Ng J, White KP, Slattery M, Dingwall AK
The Drosophila MLR COMPASS complex is essential for programming cis-regulatory information and maintaining epigenetic memory during development. Nucleic Acids Res. 2020 04 17; 48(7):3476-3495.
The Drosophila MLR COMPASS complex is essential for programming cis-regulatory information and maintaining epigenetic memory during development.
Quiquand M, Rimesso G, Qiao N, Suo S, Zhao C, Slattery M, White KP, Han JJ, Baker NE
New regulators of Drosophila eye development identified from temporal transcriptome changes. Genetics. 2021 04 15; 217(4).
New regulators of Drosophila eye development identified from temporal transcriptome changes.
Johnson DM, Wells MB, Fox R, Lee JS, Loganathan R, Levings D, Bastien A, Slattery M, Andrew DJ
CrebA increases secretory capacity through direct transcriptional regulation of the secretory machinery, a subset of secretory cargo, and other key regulators. Traffic. 2020 09; 21(9):560-577.
CrebA increases secretory capacity through direct transcriptional regulation of the secretory machinery, a subset of secretory cargo, and other key regulators.
Slattery M, Ma L, Négre N, White KP, Mann RS
Genome-wide tissue-specific occupancy of the Hox protein Ultrabithorax and Hox cofactor Homothorax in Drosophila. PLoS One. 2011 Apr 05; 6(4):e14686.
Genome-wide tissue-specific occupancy of the Hox protein Ultrabithorax and Hox cofactor Homothorax in Drosophila.
Chen Y, Negre N, Li Q, Mieczkowska JO, Slattery M, Liu T, Zhang Y, Kim TK, He HH, Zieba J, Ruan Y, Bickel PJ, Myers RM, Wold BJ, White KP, Lieb JD, Liu XS
Systematic evaluation of factors influencing ChIP-seq fidelity. Nat Methods. 2012 Jun; 9(6):609-14.
Systematic evaluation of factors influencing ChIP-seq fidelity.
Interpreting the regulatory genome: the genomics of transcription factor function in Drosophila melanogaster. Brief Funct Genomics. 2012 Sep; 11(5):336-46.
Interpreting the regulatory genome: the genomics of transcription factor function in Drosophila melanogaster.
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.
Control of mitochondrial structure and function by the Yorkie/YAP oncogenic pathway.
Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 2012 Sep; 22(9):1813-31.
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.
Levings DC, Lacher SE, Palacios-Moreno J, Slattery M
Transcriptional reprogramming by oxidative stress occurs within a predefined chromatin accessibility landscape. Free Radic Biol Med. 2021 08 01; 171:319-331.
Transcriptional reprogramming by oxidative stress occurs within a predefined chromatin accessibility landscape.
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 Oct 01; 23(19):2307-19.
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.
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.
A survey of 6,300 genomic fragments for cis-regulatory activity in the imaginal discs of Drosophila melanogaster.
Loganathan R, Levings DC, Kim JH, Wells MB, Chiu H, Wu Y, Slattery M, Andrew DJ
Ribbon boosts ribosomal protein gene expression to coordinate organ form and function. J Cell Biol. 2022 04 04; 221(4).
Ribbon boosts ribosomal protein gene expression to coordinate organ form and function.
Rhee DY, Cho DY, Zhai B, Slattery M, Ma L, Mintseris J, Wong CY, White KP, Celniker SE, Przytycka TM, Gygi SP, Obar RA, Artavanis-Tsakonas S
Transcription factor networks in Drosophila melanogaster. Cell Rep. 2014 Sep 25; 8(6):2031-2043.
Transcription factor networks in Drosophila melanogaster.
Arthur RK, Ma L, Slattery M, Spokony RF, Ostapenko A, Nègre N, White KP
Evolution of H3K27me3-marked chromatin is linked to gene expression evolution and to patterns of gene duplication and diversification. Genome Res. 2014 Jul; 24(7):1115-24.
Evolution of H3K27me3-marked chromatin is linked to gene expression evolution and to patterns of gene duplication and diversification.
Hattori T, Taft JM, Swist KM, Luo H, Witt H, Slattery M, Koide A, Ruthenburg AJ, Krajewski K, Strahl BD, White KP, Farnham PJ, Zhao Y, Koide S
Recombinant antibodies to histone post-translational modifications. Nat Methods. 2013 Oct; 10(10):992-5.
Recombinant antibodies to histone post-translational modifications.
Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, Ma L, Niu W, Rehm EJ, Rozowsky J, Slattery M, Spokony R, Terrell R, Vafeados D, Wang D, Weisdepp P, Wu YC, Xie D, Yan KK, Feingold EA, Good PJ, Pazin MJ, Huang H, Bickel PJ, Brenner SE, Reinke V, Waterston RH, Gerstein M, White KP, Kellis M, Snyder M
Comparative analysis of regulatory information and circuits across distant species. Nature. 2014 Aug 28; 512(7515):453-6.
Comparative analysis of regulatory information and circuits across distant species.
Slattery M, Voutev R, Ma L, Nègre N, White KP, Mann RS
Divergent transcriptional regulatory logic at the intersection of tissue growth and developmental patterning. PLoS Genet. 2013; 9(9):e1003753.
Divergent transcriptional regulatory logic at the intersection of tissue growth and developmental patterning.
Slattery M, Ma L, Spokony RF, Arthur RK, Kheradpour P, Kundaje A, Nègre N, Crofts A, Ptashkin R, Zieba J, Ostapenko A, Suchy S, Victorsen A, Jameel N, Grundstad AJ, Gao W, Moran JR, Rehm EJ, Grossman RL, Kellis M, White KP
Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster. Genome Res. 2014 Jul; 24(7):1224-35.
Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster.
Oh H, Slattery M, Ma L, White KP, Mann RS, Irvine KD
Yorkie promotes transcription by recruiting a histone methyltransferase complex. Cell Rep. 2014 Jul 24; 8(2):449-59.
Yorkie promotes transcription by recruiting a histone methyltransferase complex.
Regulatory Precision in Stress Responsive Transcriptional Networks
Indentification of Hox target genes controlling tissue growth
Riley TR, Slattery M, Abe N, Rastogi C, Liu D, Mann RS, Bussemaker HJ
Methods in molecular biology (Clifton, N.J.)
SELEX-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes. Methods Mol Biol. 2014; 1196:255-78.
SELEX-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.
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 09; 147(6):1270-82.
Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins.
Stb3 binds to ribosomal RNA processing element motifs that control transcriptional responses to growth in Saccharomyces cerevisiae. J Biol Chem. 2007 Sep 07; 282(36):26623-8.
Stb3 binds to ribosomal RNA processing element motifs that control transcriptional responses to growth in Saccharomyces cerevisiae.
Abe N, Dror I, Yang L, Slattery M, Zhou T, Bussemaker HJ, Rohs R, Mann RS
Deconvolving the recognition of DNA shape from sequence. Cell. 2015 Apr 09; 161(2):307-18.
Deconvolving the recognition of DNA shape from sequence.
Enhanced dissection of the regulatory genome. Nat Methods. 2013 Aug; 10(8):710-2.
Enhanced dissection of the regulatory genome.
Disentangling the many layers of eukaryotic transcriptional regulation. Annu Rev Genet. 2012; 46:43-68.
Disentangling the many layers of eukaryotic transcriptional regulation.
A lexicon for homeodomain-DNA recognition. Cell. 2008 Jun 27; 133(7):1133-5.
A lexicon for homeodomain-DNA recognition.
Bieli D, Kanca O, Requena D, Hamaratoglu F, Gohl D, Schedl P, Affolter M, Slattery M, Müller M, Estella C
Establishment of a Developmental Compartment Requires Interactions between Three Synergistic Cis-regulatory Modules. PLoS Genet. 2015 Oct; 11(10):e1005376.
Establishment of a Developmental Compartment Requires Interactions between Three Synergistic Cis-regulatory Modules.
Loganathan R, Lee JS, Wells MB, Grevengoed E, Slattery M, Andrew DJ
Ribbon regulates morphogenesis of the Drosophila embryonic salivary gland through transcriptional activation and repression. Dev Biol. 2016 Jan 01; 409(1):234-250.
Ribbon regulates morphogenesis of the Drosophila embryonic salivary gland through transcriptional activation and repression.
Slattery M, Zhou T, Yang L, Dantas Machado AC, Gordân R, Rohs R
Absence of a simple code: how transcription factors read the genome. Trends Biochem Sci. 2014 Sep; 39(9):381-99.
Absence of a simple code: how transcription factors read the genome.
Lacher SE, Lee JS, Wang X, Campbell MR, Bell DA, Slattery M
Beyond antioxidant genes in the ancient Nrf2 regulatory network. Free Radic Biol Med. 2015 Nov; 88(Pt B):452-465.
Beyond antioxidant genes in the ancient Nrf2 regulatory network.
Zhang Y, Lee JK, Toso EA, Lee JS, Choi SH, Slattery M, Aihara H, Kyba M
DNA-binding sequence specificity of DUX4. Skelet Muscle. 2016; 6:8.
DNA-binding sequence specificity of DUX4.
Lacher SE, Alazizi A, Wang X, Bell DA, Pique-Regi R, Luca F, Slattery M
A hypermorphic antioxidant response element is associated with increased MS4A6A expression and Alzheimer's disease. Redox Biol. 2018 04; 14:686-693.
A hypermorphic antioxidant response element is associated with increased MS4A6A expression and Alzheimer's disease.
Lacher SE, Skon-Hegg C, Ruis BL, Krznarich J, Slattery M
An antioxidant response element regulates the HIF1a axis in breast cancer cells. Free Radic Biol Med. 2023 08 01; 204:243-251.
An antioxidant response element regulates the HIF1a axis in breast cancer cells.
Levings DC, Wang X, Kohlhase D, Bell DA, Slattery M
A distinct class of antioxidant response elements is consistently activated in tumors with NRF2 mutations. Redox Biol. 2018 10; 19:235-249.
A distinct class of antioxidant response elements is consistently activated in tumors with NRF2 mutations.
Levings DC, Pathak SS, Yang YM, Slattery M
bioRxiv : the preprint server for biology
Limited Expression of Nrf2 in Neurons Across the Central Nervous System. bioRxiv. 2023 May 09.
Limited Expression of Nrf2 in Neurons Across the Central Nervous System.
Buford M, Lacher S, Slattery M, Levings DC, Postma B, Holian A, Migliaccio C
A mouse model of wildfire smoke-induced health effects: sex differences in acute and sustained effects of inhalation exposures. Inhal Toxicol. 2024 07; 36(6):367-377.
A mouse model of wildfire smoke-induced health effects: sex differences in acute and sustained effects of inhalation exposures.
Limited expression of Nrf2 in neurons across the central nervous system. Redox Biol. 2023 09; 65:102830.
Limited expression of Nrf2 in neurons across the central nervous system.
Lacher SE, Krznarich J, Levings DC, Pathak SS, Pufall M, Yang YM, Slattery M
The Glucocorticoid Receptor Inhibits NRF2-Mediated Expression of SLC7A11. Free Radic Biol Med. 2025 Dec 16; 241:53-63.
The Glucocorticoid Receptor Inhibits NRF2-Mediated Expression of SLC7A11.
Krznarich J, Schumann T, Bjork J, Slattery M, Lacher SE
An economical in vitro model of wood smoke exposure. Inhal Toxicol. 2025 Apr; 37(4):208-215.
An economical in vitro model of wood smoke exposure.
Lacher SE, Levings DC, Freeman S, Slattery M
Identification of a functional antioxidant response element at the HIF1A locus. Redox Biol. 2018 10; 19:401-411.
Identification of a functional antioxidant response element at the HIF1A locus.
Gene regulatory effects of disease-associated variation in the NRF2 network. Curr Opin Toxicol. 2016 Dec; 1:71-79.
Gene regulatory effects of disease-associated variation in the NRF2 network.
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.
Genome-wide association of Yorkie with chromatin and chromatin-remodeling complexes.
Wang X, Campbell MR, Lacher SE, Cho HY, Wan M, Crowl CL, Chorley BN, Bond GL, Kleeberger SR, Slattery M, Bell DA
A Polymorphic Antioxidant Response Element Links NRF2/sMAF Binding to Enhanced MAPT Expression and Reduced Risk of Parkinsonian Disorders. Cell Rep. 2016 Apr 26; 15(4):830-842.
A Polymorphic Antioxidant Response Element Links NRF2/sMAF Binding to Enhanced MAPT Expression and Reduced Risk of Parkinsonian Disorders.