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Matthew Slattery

AddressChicago IL 60637
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. 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). PMID: 35195669.
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    2. 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. PMID: 33992677.
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    3. 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). PMID: 33681970.
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    4. 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. PMID: 32613751.
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    5. 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. PMID: 32052053.
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    6. 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. PMID: 30142157.
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    7. 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. PMID: 29242288.
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    8. 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. PMID: 27149848.
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    9. 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. PMID: 26823969.
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    10. 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. PMID: 26477561.
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    11. 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. PMID: 26468882.
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    12. 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. PMID: 26163000.
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    13. 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. PMID: 25843630.
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    14. 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. PMID: 25242320.
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    15. 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. PMID: 25164757.
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    16. 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. PMID: 25129887.
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    17. 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. PMID: 25017066.
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    18. 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. PMID: 24985914.
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    19. 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. PMID: 24985916.
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    20. Riley TR, Slattery M, Abe N, Rastogi C, Liu D, Mann RS, Bussemaker HJ. SELEX-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes. Methods Mol Biol. 2014; 1196:255-78. PMID: 25151169.
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    21. 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. PMID: 24039600.
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    22. 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. PMID: 23955773.
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    23. Slattery M, White KP. Enhanced dissection of the regulatory genome. Nat Methods. 2013 Aug; 10(8):710-2. PMID: 23900252.
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    24. 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. PMID: 23395637.
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    25. 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. PMID: 23063361.
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    26. 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. PMID: 22955991.
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    27. Slattery M, Nègre N, White KP. Interpreting the regulatory genome: the genomics of transcription factor function in Drosophila melanogaster. Brief Funct Genomics. 2012 Sep; 11(5):336-46. PMID: 23023663.
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    28. Lelli KM, Slattery M, Mann RS. Disentangling the many layers of eukaryotic transcriptional regulation. Annu Rev Genet. 2012; 46:43-68. PMID: 22934649.
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    29. 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. PMID: 22925885.
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    30. 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. PMID: 22522655.
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    31. 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. PMID: 22153072.
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    32. 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. PMID: 21483663.
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    33. Peng HW, Slattery M, 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 Oct 01; 23(19):2307-19. PMID: 19762509.
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    34. Affolter M, Slattery M, Mann RS. A lexicon for homeodomain-DNA recognition. Cell. 2008 Jun 27; 133(7):1133-5. PMID: 18585344.
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    35. Liko D, Slattery MG, Heideman W. 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. PMID: 17616518.
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    36. Liu K, Slattery M, Jacobs D, Cutter G, McDonald A, Van Horn L, Hilner JE, Caan B, Bragg C, Dyer A, et al. A study of the reliability and comparative validity of the cardia dietary history. Ethn Dis. 1994; 4(1):15-27. PMID: 7742729.
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    37. 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. The CARDIA dietary history: development, implementation, and evaluation. J Am Diet Assoc. 1991 Sep; 91(9):1104-12. PMID: 1918764.
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