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Similarity regression predicts evolution of transcription factor sequence specificity.

Lambert SA, Yang AWH, Sasse A, Cowley G, Albu M, Caddick MX, Morris QD, Weirauch MT, Hughes TR.

Nat Genet. 2019 Jun;51(6):981-989. doi: 10.1038/s41588-019-0411-1. Epub 2019 May 27.


In vitro neuroprotective activities of two distinct probiotic consortia.

Michael DR, Davies TS, Loxley KE, Allen MD, Good MA, Hughes TR, Plummer SF.

Benef Microbes. 2019 Apr 19;10(4):437-447. doi: 10.3920/BM2018.0105. Epub 2019 Mar 4.


ARGLU1 is a transcriptional coactivator and splicing regulator important for stress hormone signaling and development.

Magomedova L, Tiefenbach J, Zilberman E, Le Billan F, Voisin V, Saikali M, Boivin V, Robitaille M, Gueroussov S, Irimia M, Ray D, Patel R, Xu C, Jeyasuria P, Bader GD, Hughes TR, Morris QD, Scott MS, Krause H, Angers S, Blencowe BJ, Cummins CL.

Nucleic Acids Res. 2019 Apr 8;47(6):2856-2870. doi: 10.1093/nar/gkz010.


The TRIM-NHL protein NHL-2 is a co-factor in the nuclear and somatic RNAi pathways in C. elegans.

Davis GM, Tu S, Anderson JW, Colson RN, Gunzburg MJ, Francisco MA, Ray D, Shrubsole SP, Sobotka JA, Seroussi U, Lao RX, Maity T, Wu MZ, McJunkin K, Morris QD, Hughes TR, Wilce JA, Claycomb JM, Weng Z, Boag PR.

Elife. 2018 Dec 21;7. pii: e35478. doi: 10.7554/eLife.35478.


Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus.

Buckley MA, Woods NT, Tyrer JP, Mendoza-Fandiño G, Lawrenson K, Hazelett DJ, Najafabadi HS, Gjyshi A, Carvalho RS, Lyra PC Jr, Coetzee SG, Shen HC, Yang AW, Earp MA, Yoder SJ, Risch H, Chenevix-Trench G, Ramus SJ, Phelan CM, Coetzee GA, Noushmehr H, Hughes TR, Sellers TA, Goode EL, Pharoah PD, Gayther SA, Monteiro ANA; Ovarian Cancer Association Consortium.

Cancer Res. 2019 Feb 1;79(3):467-481. doi: 10.1158/0008-5472.CAN-17-3864. Epub 2018 Nov 28.


A physical and genetic map of Cannabis sativa identifies extensive rearrangements at the THC/CBD acid synthase loci.

Laverty KU, Stout JM, Sullivan MJ, Shah H, Gill N, Holbrook L, Deikus G, Sebra R, Hughes TR, Page JE, van Bakel H.

Genome Res. 2019 Jan;29(1):146-156. doi: 10.1101/gr.242594.118. Epub 2018 Nov 8.


The Human Transcription Factors.

Lambert SA, Jolma A, Campitelli LF, Das PK, Yin Y, Albu M, Chen X, Taipale J, Hughes TR, Weirauch MT.

Cell. 2018 Oct 4;175(2):598-599. doi: 10.1016/j.cell.2018.09.045. No abstract available.


How bacterial xenogeneic silencer rok distinguishes foreign from self DNA in its resident genome.

Duan B, Ding P, Hughes TR, Navarre WW, Liu J, Xia B.

Nucleic Acids Res. 2018 Nov 2;46(19):10514-10529. doi: 10.1093/nar/gky836.


Motif models for RNA-binding proteins.

Sasse A, Laverty KU, Hughes TR, Morris QD.

Curr Opin Struct Biol. 2018 Dec;53:115-123. doi: 10.1016/ Epub 2018 Aug 29. Review.


A Chemical Biology Approach to Model Pontocerebellar Hypoplasia Type 1B (PCH1B).

François-Moutal L, Jahanbakhsh S, Nelson ADL, Ray D, Scott DD, Hennefarth MR, Moutal A, Perez-Miller S, Ambrose AJ, Al-Shamari A, Coursodon P, Meechoovet B, Reiman R, Lyons E, Beilstein M, Chapman E, Morris QD, Van Keuren-Jensen K, Hughes TR, Khanna R, Koehler C, Jen J, Gokhale V, Khanna M.

ACS Chem Biol. 2018 Oct 19;13(10):3000-3010. doi: 10.1021/acschembio.8b00745. Epub 2018 Sep 6.


Neurospora crassa developmental control mediated by the FLB-3 transcription factor.

Boni AC, Ambrósio DL, Cupertino FB, Montenegro-Montero A, Virgilio S, Freitas FZ, Corrocher FA, Gonçalves RD, Yang A, Weirauch MT, Hughes TR, Larrondo LF, Bertolini MC.

Fungal Biol. 2018 Jun;122(6):570-582. doi: 10.1016/j.funbio.2018.01.004. Epub 2018 Mar 1.


Structural basis for the ability of MBD domains to bind methyl-CG and TG sites in DNA.

Liu K, Xu C, Lei M, Yang A, Loppnau P, Hughes TR, Min J.

J Biol Chem. 2018 May 11;293(19):7344-7354. doi: 10.1074/jbc.RA118.001785. Epub 2018 Mar 22.


The Human Transcription Factors.

Lambert SA, Jolma A, Campitelli LF, Das PK, Yin Y, Albu M, Chen X, Taipale J, Hughes TR, Weirauch MT.

Cell. 2018 Feb 8;172(4):650-665. doi: 10.1016/j.cell.2018.01.029. Review. Erratum in: Cell. 2018 Oct 4;175(2):598-599.


DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants.

Xu C, Liu K, Lei M, Yang A, Li Y, Hughes TR, Min J.

Structure. 2018 Jan 2;26(1):85-95.e3. doi: 10.1016/j.str.2017.11.022. Epub 2017 Dec 21.


The intracellular immune receptor Rx1 regulates the DNA-binding activity of a Golden2-like transcription factor.

Townsend PD, Dixon CH, Slootweg EJ, Sukarta OCA, Yang AWH, Hughes TR, Sharples GJ, Pålsson LO, Takken FLW, Goverse A, Cann MJ.

J Biol Chem. 2018 Mar 2;293(9):3218-3233. doi: 10.1074/jbc.RA117.000485. Epub 2017 Dec 7.


Absence of CD59 in Guinea Pigs: Analysis of the Cavia porcellus Genome Suggests the Evolution of a CD59 Pseudogene.

Boshra H, Zelek WM, Hughes TR, Rodriguez de Cordoba S, Morgan BP.

J Immunol. 2018 Jan 1;200(1):327-335. doi: 10.4049/jimmunol.1701238. Epub 2017 Nov 22.


Comparison of ChIP-Seq Data and a Reference Motif Set for Human KRAB C2H2 Zinc Finger Proteins.

Barazandeh M, Lambert SA, Albu M, Hughes TR.

G3 (Bethesda). 2018 Jan 4;8(1):219-229. doi: 10.1534/g3.117.300296.


Non-base-contacting residues enable kaleidoscopic evolution of metazoan C2H2 zinc finger DNA binding.

Najafabadi HS, Garton M, Weirauch MT, Mnaimneh S, Yang A, Kim PM, Hughes TR.

Genome Biol. 2017 Sep 6;18(1):167. doi: 10.1186/s13059-017-1287-y.


Oncogenic Activation of the RNA Binding Protein NELFE and MYC Signaling in Hepatocellular Carcinoma.

Dang H, Takai A, Forgues M, Pomyen Y, Mou H, Xue W, Ray D, Ha KCH, Morris QD, Hughes TR, Wang XW.

Cancer Cell. 2017 Jul 10;32(1):101-114.e8. doi: 10.1016/j.ccell.2017.06.002.


RNAcompete-S: Combined RNA sequence/structure preferences for RNA binding proteins derived from a single-step in vitro selection.

Cook KB, Vembu S, Ha KCH, Zheng H, Laverty KU, Hughes TR, Ray D, Morris QD.

Methods. 2017 Aug 15;126:18-28. doi: 10.1016/j.ymeth.2017.06.024. Epub 2017 Jun 24.


The anti-cholesterolaemic effect of a consortium of probiotics: An acute study in C57BL/6J mice.

Michael DR, Davies TS, Moss JWE, Calvente DL, Ramji DP, Marchesi JR, Pechlivanis A, Plummer SF, Hughes TR.

Sci Rep. 2017 Jun 6;7(1):2883. doi: 10.1038/s41598-017-02889-5.


Direct Binding of the pH-Regulated Protein 1 (Pra1) from Candida albicans Inhibits Cytokine Secretion by Mouse CD4+ T Cells.

Bergfeld A, Dasari P, Werner S, Hughes TR, Song WC, Hortschansky P, Brakhage AA, Hünig T, Zipfel PF, Beyersdorf N.

Front Microbiol. 2017 May 11;8:844. doi: 10.3389/fmicb.2017.00844. eCollection 2017.


Transcription factors read epigenetics.

Hughes TR, Lambert SA.

Science. 2017 May 5;356(6337):489-490. doi: 10.1126/science.aan2927. No abstract available.


Microbial Neuraminidase Induces a Moderate and Transient Myelin Vacuolation Independent of Complement System Activation.

Granados-Durán P, López-Ávalos MD, Cifuentes M, Pérez-Martín M, Fernández-Arjona MD, Hughes TR, Johnson K, Morgan BP, Fernández-Llebrez P, Grondona JM.

Front Neurol. 2017 Mar 7;8:78. doi: 10.3389/fneur.2017.00078. eCollection 2017.


Multilayered Control of Alternative Splicing Regulatory Networks by Transcription Factors.

Han H, Braunschweig U, Gonatopoulos-Pournatzis T, Weatheritt RJ, Hirsch CL, Ha KCH, Radovani E, Nabeel-Shah S, Sterne-Weiler T, Wang J, O'Hanlon D, Pan Q, Ray D, Zheng H, Vizeacoumar F, Datti A, Magomedova L, Cummins CL, Hughes TR, Greenblatt JF, Wrana JL, Moffat J, Blencowe BJ.

Mol Cell. 2017 Feb 2;65(3):539-553.e7. doi: 10.1016/j.molcel.2017.01.011.


RNAcompete methodology and application to determine sequence preferences of unconventional RNA-binding proteins.

Ray D, Ha KCH, Nie K, Zheng H, Hughes TR, Morris QD.

Methods. 2017 Apr 15;118-119:3-15. doi: 10.1016/j.ymeth.2016.12.003. Epub 2016 Dec 10.


Transcription Factors Encoded on Core and Accessory Chromosomes of Fusarium oxysporum Induce Expression of Effector Genes.

van der Does HC, Fokkens L, Yang A, Schmidt SM, Langereis L, Lukasiewicz JM, Hughes TR, Rep M.

PLoS Genet. 2016 Nov 17;12(11):e1006401. doi: 10.1371/journal.pgen.1006401. eCollection 2016 Nov. Erratum in: PLoS Genet. 2016 Dec 29;12 (12 ):e1006527.


Multiparameter functional diversity of human C2H2 zinc finger proteins.

Schmitges FW, Radovani E, Najafabadi HS, Barazandeh M, Campitelli LF, Yin Y, Jolma A, Zhong G, Guo H, Kanagalingam T, Dai WF, Taipale J, Emili A, Greenblatt JF, Hughes TR.

Genome Res. 2016 Dec;26(12):1742-1752. Epub 2016 Nov 16.


Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians.

Solana J, Irimia M, Ayoub S, Orejuela MR, Zywitza V, Jens M, Tapial J, Ray D, Morris Q, Hughes TR, Blencowe BJ, Rajewsky N.

Elife. 2016 Aug 9;5. pii: e16797. doi: 10.7554/eLife.16797.


Motif comparison based on similarity of binding affinity profiles.

Lambert SA, Albu M, Hughes TR, Najafabadi HS.

Bioinformatics. 2016 Nov 15;32(22):3504-3506. Epub 2016 Jul 27.


Complement Membrane Attack and Tumorigenesis: A SYSTEMS BIOLOGY APPROACH.

Towner LD, Wheat RA, Hughes TR, Morgan BP.

J Biol Chem. 2016 Jul 15;291(29):14927-38. doi: 10.1074/jbc.M115.708446. Epub 2016 May 19.


Complement system activation contributes to the ependymal damage induced by microbial neuraminidase.

Granados-Durán P, López-Ávalos MD, Hughes TR, Johnson K, Morgan BP, Tamburini PP, Fernández-Llebrez P, Grondona JM.

J Neuroinflammation. 2016 May 21;13(1):115. doi: 10.1186/s12974-016-0576-9.


Deletion of the membrane complement inhibitor CD59a drives age and gender-dependent alterations to bone phenotype in mice.

Bloom AC, Collins FL, Van't Hof RJ, Ryan ES, Jones E, Hughes TR, Morgan BP, Erlandsson M, Bokarewa M, Aeschlimann D, Evans BAJ, Williams AS.

Bone. 2016 Mar;84:253-261. doi: 10.1016/j.bone.2015.12.014. Epub 2015 Dec 22.


Complementing the inflammasome.

Triantafilou M, Hughes TR, Morgan BP, Triantafilou K.

Immunology. 2016 Feb;147(2):152-64. doi: 10.1111/imm.12556. Review.


Affinity regression predicts the recognition code of nucleic acid-binding proteins.

Pelossof R, Singh I, Yang JL, Weirauch MT, Hughes TR, Leslie CS.

Nat Biotechnol. 2015 Dec;33(12):1242-1249. doi: 10.1038/nbt.3343. Epub 2015 Nov 16.


The Crystal Structure of the NHL Domain in Complex with RNA Reveals the Molecular Basis of Drosophila Brain-Tumor-Mediated Gene Regulation.

Loedige I, Jakob L, Treiber T, Ray D, Stotz M, Treiber N, Hennig J, Cook KB, Morris Q, Hughes TR, Engelmann JC, Krahn MP, Meister G.

Cell Rep. 2015 Nov 10;13(6):1206-1220. doi: 10.1016/j.celrep.2015.09.068. Epub 2015 Oct 29.


A structural approach reveals how neighbouring C2H2 zinc fingers influence DNA binding specificity.

Garton M, Najafabadi HS, Schmitges FW, Radovani E, Hughes TR, Kim PM.

Nucleic Acids Res. 2015 Oct 30;43(19):9147-57. doi: 10.1093/nar/gkv919. Epub 2015 Sep 17.


A Novel AT-Rich DNA Recognition Mechanism for Bacterial Xenogeneic Silencer MvaT.

Ding P, McFarland KA, Jin S, Tong G, Duan B, Yang A, Hughes TR, Liu J, Dove SL, Navarre WW, Xia B.

PLoS Pathog. 2015 Jun 11;11(6):e1004967. doi: 10.1371/journal.ppat.1004967. eCollection 2015 Jun.


Skin Metabolites Define a New Paradigm in the Localization of Skin Tropic Memory T Cells.

McCully ML, Collins PJ, Hughes TR, Thomas CP, Billen J, O'Donnell VB, Moser B.

J Immunol. 2015 Jul 1;195(1):96-104. doi: 10.4049/jimmunol.1402961. Epub 2015 May 22.


Brain tumor is a sequence-specific RNA-binding protein that directs maternal mRNA clearance during the Drosophila maternal-to-zygotic transition.

Laver JD, Li X, Ray D, Cook KB, Hahn NA, Nabeel-Shah S, Kekis M, Luo H, Marsolais AJ, Fung KY, Hughes TR, Westwood JT, Sidhu SS, Morris Q, Lipshitz HD, Smibert CA.

Genome Biol. 2015 May 12;16:94. doi: 10.1186/s13059-015-0659-4.


Identification of C2H2-ZF binding preferences from ChIP-seq data using RCADE.

Najafabadi HS, Albu M, Hughes TR.

Bioinformatics. 2015 Sep 1;31(17):2879-81. doi: 10.1093/bioinformatics/btv284. Epub 2015 May 6.


Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities.

Narasimhan K, Lambert SA, Yang AW, Riddell J, Mnaimneh S, Zheng H, Albu M, Najafabadi HS, Reece-Hoyes JS, Fuxman Bass JI, Walhout AJ, Weirauch MT, Hughes TR.

Elife. 2015 Apr 23;4. doi: 10.7554/eLife.06967.


C2H2 zinc finger proteins greatly expand the human regulatory lexicon.

Najafabadi HS, Mnaimneh S, Schmitges FW, Garton M, Lam KN, Yang A, Albu M, Weirauch MT, Radovani E, Kim PM, Greenblatt J, Frey BJ, Hughes TR.

Nat Biotechnol. 2015 May;33(5):555-62. doi: 10.1038/nbt.3128. Epub 2015 Feb 18.


Complement activation and expression during chronic relapsing experimental autoimmune encephalomyelitis in the Biozzi ABH mouse.

Ramaglia V, Jackson SJ, Hughes TR, Neal JW, Baker D, Morgan BP.

Clin Exp Immunol. 2015 Jun;180(3):432-41. doi: 10.1111/cei.12595. Epub 2015 Apr 24.


RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease.

Xiong HY, Alipanahi B, Lee LJ, Bretschneider H, Merico D, Yuen RK, Hua Y, Gueroussov S, Najafabadi HS, Hughes TR, Morris Q, Barash Y, Krainer AR, Jojic N, Scherer SW, Blencowe BJ, Frey BJ.

Science. 2015 Jan 9;347(6218):1254806. doi: 10.1126/science.1254806. Epub 2014 Dec 18.


High-throughput characterization of protein-RNA interactions.

Cook KB, Hughes TR, Morris QD.

Brief Funct Genomics. 2015 Jan;14(1):74-89. doi: 10.1093/bfgp/elu047. Epub 2014 Dec 13. Review.


Poly-dA:dT tracts form an in vivo nucleosomal turnstile.

de Boer CG, Hughes TR.

PLoS One. 2014 Oct 29;9(10):e110479. doi: 10.1371/journal.pone.0110479. eCollection 2014.


Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana.

Sullivan AM, Arsovski AA, Lempe J, Bubb KL, Weirauch MT, Sabo PJ, Sandstrom R, Thurman RE, Neph S, Reynolds AP, Stergachis AB, Vernot B, Johnson AK, Haugen E, Sullivan ST, Thompson A, Neri FV 3rd, Weaver M, Diegel M, Mnaimneh S, Yang A, Hughes TR, Nemhauser JL, Queitsch C, Stamatoyannopoulos JA.

Cell Rep. 2014 Sep 25;8(6):2015-2030. doi: 10.1016/j.celrep.2014.08.019. Epub 2014 Sep 15.


Determination and inference of eukaryotic transcription factor sequence specificity.

Weirauch MT, Yang A, Albu M, Cote AG, Montenegro-Montero A, Drewe P, Najafabadi HS, Lambert SA, Mann I, Cook K, Zheng H, Goity A, van Bakel H, Lozano JC, Galli M, Lewsey MG, Huang E, Mukherjee T, Chen X, Reece-Hoyes JS, Govindarajan S, Shaulsky G, Walhout AJM, Bouget FY, Ratsch G, Larrondo LF, Ecker JR, Hughes TR.

Cell. 2014 Sep 11;158(6):1431-1443. doi: 10.1016/j.cell.2014.08.009.


A pair of RNA-binding proteins controls networks of splicing events contributing to specialization of neural cell types.

Norris AD, Gao S, Norris ML, Ray D, Ramani AK, Fraser AG, Morris Q, Hughes TR, Zhen M, Calarco JA.

Mol Cell. 2014 Jun 19;54(6):946-59. doi: 10.1016/j.molcel.2014.05.004. Epub 2014 Jun 5.

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