• 2023
  • Stepankiw N, Yang AWH, Hughes TR. The human genome contains over a million autonomous exons. Genome Res. 2023 Nov 9;33(11):1865–78. doi: 10.1101/gr.277792.123. Epub ahead of print. PMID: 37945377; PMCID: PMC10760453. Web Supplement
  • Sharma S, Kajjo S, Harra Z, Hasaj B, Delisle V, Ray D, Gutierrez RL, Carrier I, Kleinman C, Morris Q, Hughes TR, McInnes R, Fabian MR. Uncovering a mammalian neural-specific poly(A) binding protein with unique properties. Genes Dev. 2023 Aug 1;37(15-16):760-777. doi: 10.1101/gad.350597.123. Epub 2023 Sep 13. PMID: 37704377; PMCID: PMC10546976.
  • Brennan KJ, Weilert M, Krueger S, Pampari A, Liu HY, Yang AWH, Morrison JA, Hughes TR, Rushlow CA, Kundaje A, Zeitlinger J. Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation. Dev Cell. 2023 Oct 9;58(19):1898-1916.e9. doi: 10.1016/j.devcel.2023.07.007. Epub 2023 Aug 8. PMID: 37557175; PMCID: PMC10592203.
  • Coyle MC, Tajima AM, Leon F, Choksi SP, Yang A, Espinoza S, Hughes TR, Reiter JF, Booth DS, King N. An RFX transcription factor regulates ciliogenesis in the closest living relatives of animals. Curr Biol. 2023 Sep 11;33(17):3747-3758.e9. doi: 10.1016/j.cub.2023.07.022. Epub 2023 Aug 7. PMID: 37552984; PMCID: PMC10530576.
  • Liu K, Zhang J, Xiao Y, Yang A, Song X, Li Y, Chen Y, Hughes TR, Min J. Structural insights into DNA recognition by the BEN domain of the transcription factor BANP. J Biol Chem. 2023 Jun;299(6):104734. doi: 10.1016/j.jbc.2023.104734. Epub 2023 Apr 20. PMID: 37086783; PMCID: PMC10206803.
  • Ray D, Laverty KU, Jolma A, Nie K, Samson R, Pour SE, Tam CL, von Krosigk N, Nabeel-Shah S, Albu M, Zheng H, Perron G, Lee H, Najafabadi H, Blencowe B, Greenblatt J, Morris Q, Hughes TR. (2023). RNA-binding proteins that lack canonical RNA-binding domains are rarely sequence-specific. Sci Rep. 2023 Mar 31;13(1):5238 Web Supplement
  • Shkurin A, Pour SE, Hughes TR. (2023). Known sequence features explain half of all human gene ends. NAR Genom Bioinform. 2023 Apr 5;5(2) Web Supplement
  • Ichikawa DM, Abdin O, Alerasool N, Kogenaru M, Mueller AL, Wen H, Giganti DO, Goldberg GW, Adams S, Spencer JM, Razavi R, Nim S, Zheng H, Gionco C, Clark FT, Strokach A, Hughes TR, Lionnet T, Taipale M, Kim PM, Noyes MB. (2023). A universal deep-learning model for zinc finger design enables transcription factor reprogramming. Nat Biotechnol. 2023 Jan 26. doi: 10.1038/s41587-022-01624-4.
  • IRF4 International Consortium (50+ authors) (2023). A multimorphic mutation in IRF4 causes human autosomal dominant combined immunodeficiency. 8(79):eade7953.
• 2022
  • Zheng, L., Liu J., Niu, L., Kamran, M., Yang, A.W.H., Jolma, A., Dai, Q., Hughes, T.R., Patel, D.J., Zhang, L., Prasanth, S.G., Yu, Y., Ren, A., Lai, E.C. (2022). Distinct structural bases for sequence-specific DNA binding by mammalian BEN domain proteins Genes Dev 36(3-4):225-240.
  • Laverty KU, Jolma A, Pour SE, Zheng H, Ray D, Morris Q, Hughes TR. (2022). PRIESSTESS: interpretable, high-performing models of the sequence and structure preferences of RNA-binding proteins. Nucleic Acids Res. 2022 Oct 28;50(19). GitHub Code
  • Campitelli L., Yellan I., Albu M., Barazandeh M., Patel Z.M., Blanchette M., Hughes TR. (2022). Reconstruction of full-length LINE-1 progenitors from ancestral genomes . Genetics .221 (3):1943-2631 Web Supplement
  • Song, J., Nabeel-Shah, S., Pu, S., Lee, H., Braunschweig, U., Ni, Z., Ahmed, N., Marcon, E., Zhong, G., Ray, D., Ha, K.C.H., Guo, X., Zhang, Z., Hughes TR, Blencowe, B.J., Greenblatt, J.F. (2022). Regulation of alternative polyadenylation by the C2H2-zinc-finger protein Sp1. Mol Cell. 2022 82(17):3135-3150.e9.
  • Spruce, T., Plass, M., Gohr, A., Ray, D., Martínez de Lagrán, M., Rot, G., Nóvoa, A., Burguera, D., Permanyer, J., Miret, M., Zheng, H., Swanson, M.S., Morris, Q., Mallo, M., Dierssen, M., Hughes TR, Pernaute, B., Irimia, M. (2022). The X-linked splicing regulator MBNL3 has been co-opted to restrict placental growth in eutherians. PLoS Biol. 20(4):e3001615.
• 2021
  • Patel, Z.M. and Hughes, T.R. (2021) Global properties of regulatory sequences are predicted by transcription factor recognition mechanisms. Genome Biol. 7;22(1):285.
  • Yellan, I., Yang, A.W.H., and Hughes, T.R. (2021) Diverse Eukaryotic CGG-Binding Proteins Produced by Independent Domestications of hAT Transposons. Mol Biol Evol. 38(5):2070-2075. Web Supplement
  • Zhang, M., Lei, M., Qin, S., Dong, A., Yang, A., Li, Y., Loppnau, P., Hughes, T.R., Min, J., Liu, Y. (2021) Crystal structure of the BRPF2 PWWP domain in complex with DNA reveals a different binding mode than the HDGF family of PWWP domains. Biochim Biophys Acta Gene Regul Mech. 1864(3):194688.
• 2020
  • Kosti, A., de Araujo, P.R., Li, W.Q., Guardia, G.D.A., Chiou, J., Yi, C., Ray, D., Meliso, F., Li, Y.M., Delambre, T., Qiao, M., Burns, S.S., Lorbeer, F.K., Georgi, F., Flosbach, M., Klinnert, S., Jenseit, A., Lei, X., Sandoval, C.R., Ha, K., Zheng, H., Pandey, R., Gruslova, A., Gupta, Y.K., Brenner, A., Kokovay, E., Hughes, T.R., Morris, Q.D., Galante, P.A.F., Tiziani, S., Penalva, L.O.F. (2020). The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation. Genome Biol. 21(1):195.
  • Jolma, A., Zhang, J., Mondragón, E., Morgunova, E., Kivioja, T., Laverty, K.U., Yin, Y., Zhu, F., Bourenkov, G., Morris, Q., Hughes, T.R., Maher, L.J., and Taipale, J. (2020) Binding specificities of human RNA binding proteins towards structured and linear RNA sequences. Genome Research, 30(7):962-973. 
  • Chakraborti, S., Balakrishnan, D., Trotter, A.J., Gittens, W.H., Yang, A.W.H., Jolma, A., Paterson, J.R., Świątek, S., Plewka, J., Curtis, F.A., Bowers, L.Y., Pålsson, L.O., Hughes, T.R., Taube, M., Kozak, M., Heddle, J.G., Sharples, G.J. (2020). A bacteriophage mimic of the bacterial nucleoid-associated protein Fis. Biochem J. 2020 477(7):1345-1362.
• 2019
  • Lambert, S.A., Yang, A.W.H., Sasse, A., Cowley, G., Albu, M., Caddick, M.X., Morris, Q.D., Weirauch, M.T., Hughes, T.R. (2019). Similarity regression predicts evolution of transcription factor sequence specificity. Nat Genet. 51(6):981-989. CisBP Webserver
  • 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, G.D., Hughes, T.R., Morris, Q.D., Scott, M.S., Krause, H., Angers, S., Blencowe, B.J., Cummins, C.L. (2019). ARGLU1 is a transcriptional coactivator and splicing regulator important for stress hormone signaling and development. Nucleic Acids Res. 47(6):2856-2870. ProteomeXchange
  • Buckley, M.A., Woods, N.T., Tyrer, J.P., Mendoza-Fandiño, G., Lawrenson, K., Hazelett, D.J., Najafabadi, H.S., Gjyshi, A., Carvalho, R.S., Lyra, P.C. Jr, Coetzee, S.G., Shen, H.C., Yang, A.W., Earp, M.A., Yoder, S.J., Risch, H., Chenevix-Trench, G., Ramus, S.J., Phelan, C.M., Coetzee, G.A., Noushmehr, H., Hughes, T.R., Sellers, T.A., Goode, E.L., Pharoah, P.D., Gayther, S.A., Monteiro, A.N.A.; Ovarian Cancer Association Consortium. (2019). Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus. Cancer Res. 79(3):467-481
  • Laverty, K.U., Stout, J.M., Sullivan, M.J., Shah, H., Gill, N., Holbrook, L., Deikus, G., Sebra, R., Hughes, T.R.*, Page, J.E.*, van Bakel, H.* (2019). A physical and genetic map of Cannabis sativa identifies extensive rearrangements at the THC/CBD acid synthase loci. Genome Res. 29(1):146-156.
• 2018
  • Lambert SA, Jolma A, Campitelli LF, Das PK, Yin Y, Albu M, Chen X, Taipale J, Hughes TR, Weirauch MT.(2018) The Human Transcription Factors. Cell. 172(4):650-665. doi: 10.1016/j.cell.2018.01.029. Review HumantTFs Webserver
  • Davis, G.M., Tu, S., Anderson, J.W., Colson, R.N., Gunzburg, M.J., Francisco, M.A., Ray, D., Shrubsole, S.P., Sobotka, J.A., Seroussi, U., Lao, R.X., Maity, T., Wu, M.Z., McJunkin, K., Morris, Q.D., Hughes, T.R., Wilce, J.A., Claycomb, J.M., Weng, Z., Boag, P.R. (2018). The TRIM-NHL protein NHL-2 is a co-factor in the nuclear and somatic RNAi pathways in C. elegans. Elife. 21;7. pii: e35478.
  • Duan, B., Ding, P., Hughes, T.R., Navarre, W.W., Liu, J., Xia, B. (2018). How bacterial xenogeneic silencer rok distinguishes foreign from self DNA in its resident genome. Nucleic Acids Res. 46(19):10514-10529.
  • François-Moutal, L., Jahanbakhsh, S., Nelson, A.D.L., Ray, D., Scott, D.D., Hennefarth, M.R., Moutal, A., Perez-Miller, S., Ambrose, A.J., Al-Shamari, A., Coursodon, P., Meechoovet, B., Reiman, R., Lyons, E., Beilstein, M., Chapman, E., Morris, Q.D., Van Keuren-Jensen, K., Hughes, T.R., Khanna, R., Koehler, C., Jen, J., Gokhale, V., Khanna, M. (2018). A Chemical Biology Approach to Model Pontocerebellar Hypoplasia Type 1B (PCH1B). ACS Chem Biol. 13(10):3000-3010.
  • Boni, A.C., Ambrósio, D.L., Cupertino, F.B., Montenegro-Montero, A., Virgilio, S., Freitas, F.Z., Corrocher, F.A., Gonçalves, R.D., Yang, A., Weirauch, M.T., Hughes, T.R., Larrondo, L.F., Bertolini, M.C. (2018). Neurospora crassa developmental control mediated by the FLB-3 transcription factor. Fungal Biol. 122(6):570-582.
  • Liu, K., Xu, C., Lei, M., Yang, A., Loppnau, P., Hughes, T.R., Min, J. (2018). Structural basis for the ability of MBD domains to bind methyl-CG and TG sites in DNA. J Biol Chem. 2018 Mar 22. [Epub ahead of print]
  • Xu, C., Liu, K., Lei, M., Yang, A., Li, Y., Hughes, T.R., Min, J. (2018). DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants. Structure 26:85-95
  • Townsend, P.D., Dixon, C.H., Slootweg, E.J., Sukarta, O.C.A., Yang, A.W.H., Hughes, T.R., Sharples, G.J., Pålsson, L.O., Takken, F.L.W., Goverse, A., Cann, M.J. (2018). The intracellular immune receptor Rx1 regulates the DNA-binding activity of a Golden2-like transcription factor. J Biol Chem. 293:3218-3233.
• 2017
  • Barazandeh, M., Lambert, S.A., Albu, M., Hughes, T.R. (2017). Comparison of ChIP-Seq Data and a Reference Motif Set for Human KRAB C2H2 Zinc Finger Proteins. G3 (Bethesda). 8:219-229. Web Supplement
  • Dang, H., Takai, A., Forgues, M., Pomyen, Y., Mou, H., Xue, W., Ray, D., Ha, K.C.H., Morris, Q.D., Hughes, T.R., Wang, X.W. (2017). Oncogenic Activation of the RNA Binding Protein NELFE and MYC Signaling in Hepatocellular Carcinoma. Cancer Cell 32:101-114.e8.
  • Najafabadi, H.S., Garton, M., Weirauch, M.T., Mnaimneh, S., Yang, A., Kim, P.M., Hughes, T.R. (2017). Non-base-contacting residues enable kaleidoscopic evolution of metazoan C2H2 zinc finger DNA binding. Genome Biol 18:167.
  • Cook, K.B., Vembu, S., Ha, K.C.H., Zheng, H., Laverty, K.U., Hughes, T.R., Ray, D., Morris, Q.D. (2017). RNAcompete-S: Combined RNA sequence/structure preferences for RNA binding proteins derived from a single-step in vitro selection. Methods 126:18-28. Web Supplement
  • Han, H., Braunschweig, U., Gonatopoulos-Pournatzis, T., Weatheritt, R.J., Hirsch, C.L., Ha, K.C., 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, C.L., Hughes, T.R., Greenblatt, J.F., Wrana, J.L., Moffat, J., Blencowe, B.J. (2017). Multilayered Control of Alternative Splicing Regulatory Networks by Transcription Factors. Mol Cell 65:539-553.
• 2016
  • Ray, D., Ha, K.C., Nie, K., Zheng, H., Hughes, T.R., Morris, Q.D. (2016). RNAcompete methodology and application to determine sequence preferences of unconventional RNA-binding proteins. Methods S1046-2023(16)30472-8.
  • van der Does, H.C., Fokkens, L., Yang, A., Schmidt, S.M., Langereis, L., Lukasiewicz, J.M., Hughes, T.R., Rep, M. (2016). Transcription Factors Encoded on Core and Accessory Chromosomes of Fusarium oxysporum Induce Expression of Effector Genes. PLoS Genet 12:e1006401.
  • Schmitges, F.W., Radovani, E., Najafabadi, H.S., Barazandeh, M., Campitelli, L.F., Yin, Y., Jolma, A., Zhong, G., Guo, H., Kanagalingan, T., Dai, W.F., Taipale, J., Emili, A., Greenblatt, J.F., and Hughes, T.R. (2016). Multiparameter functional diversity of human C2H2 zinc finger proteins. Genome Research, 26:1742. Web Supplement
  • Solana, J., Irimia, M., Ayoub, S., Orejuela, M.R., Zywitza, V., Jens, M., Tapiale, J., Ray, D., Morris, Q., Hughes, T.R., Blencowe, B.J., and Rajewsky, N. (2016). Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians. Elife 5:e16797.
  • Lambert, S.A., Albu, M., Hughes, T.R., Najafabadi, H.S. (2016). Motif comparison based on similarity of binding affinity profiles. Bioinformatics 32:3504-3506. Mosbat Webserver
• 2015
  • Pelossof, R., Singh, I., Yang, J.L., Weirauch, M., Hughes, T.R., and Leslie, C.S. (2015). Affinity regression predicts the recognition code of nucleic acid binding proteins. Nature Biotechnology 33:1242-1249.
  • Loedige, I., Jakob, L., Treiber, T., Ray, D., Stotz, M., Treiber, N., Hennig, J., Cook, K.B., Morris, Q.D., Hughes, T.R., Engelmann, J.C., Krahn, M., and Meister, G. (2015). The crystal structure of the NHL domain in complex with RNA reveals the molecular basis of Drosophila Brain tumor-mediated gene regulation. Cell Reports, 13:1206-20.
  • Garton, M., Najafabadi, H., Schmitges, F., Radovani, E., Hughes, T.R., and Kim, P.M. (2015). A structural approach reveals how neighboring C2H2 zinc-fingers influence DNA binding specificity. Nucleic Acids Research, 43:9147-57.
  • Ding, P., McFarland, K.A., Jin, S., Tong, G., Duan, B., Yang, A., Hughes, T.R., Liu, J., Dove, S.L., Navarre, W.W., Xia, B. (2015) A Novel AT-Rich DNA Recognition Mechanism for Bacterial Xenogeneic Silencer MvaT. PLoS Pathog. 11:e1004967.
  • Laver, J.D., Li, X., Ray, D., Cook, K.B., Hahn, N.A., Nabeel-Shah, S., Kekis, M., Luo, H., Marsolais, A.J., Fung, K.Y., Hughes, T.R., Westwood, J.T., Sidhu, S.S., Morris, Q., Lipshitz, H.D., Smibert, C.A. (2015). Brain tumor is a sequence-specific RNA-binding protein that directs maternal mRNA clearance during the Drosophila maternal-to-zygotic transition. Genome Biology, 16:94.
  • Najafabadi, H.S., Albu, M., Hughes, T.R. (2015). Identification of C2H2-ZF binding preferences from ChIP-seq data using RCADE. Bioinformatics, 31:2879-81. RCADE Webserver
  • Narasimhan, K., Lambert, S.A., Yang, A.W., Riddell, J., Mnaimneh, S., Zheng, H., Albu, M., Najafabadi, H.S., Reece-Hoyes, J.S., Fuxman-Bass, J.I., Walhout, A.J., Weirauch, M.T., Hughes, T.R. (2015). Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities. Elife. 2015 Apr 23;4. CisBP Webserver Web Supplement
  • Najafabadi, H.S.*, Mnaimneh, S.*, Schmitges, F.W.*, Garton, M., Lam, K.N., Yang, A., Albu, M., Weirauch, M.T., Radovani, E., Kim, P.M., Greenblatt, J., Frey, B.J., Hughes, T.R. (2015). C2H2 zinc finger proteins greatly expand the human regulatory lexicon. Nature Biotechnology. 33(5):555-62. Web Supplement
  • Xiong, H.Y., Alipanahi, B., Lee, L.J., Bretschneider, H., Merico, D., Yuen, R.K., Hua, Y., Gueroussov, S., Najafabadi, H.S., Hughes, T.R., Morris, Q., Barash, Y., Krainer, A.R., Jojic, N., Scherer, S.W., Blencowe, B.J., Frey, B.J. (2015). RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease. Science. 347(6218):1254806.
• 2014
  • de Boer, C.G,, Hughes, T.R. (2014). Poly-dA:dT tracts form an in vivo nucleosomal turnstile. PLoS One. 9(10):e110479.
  • Sullivan, A.M., Arsovski, A.A., Lempe, J., Bubb, K.L., Weirauch, M.T., Sabo, P.J., Sandstrom, R., Thurman, R.E., Neph, S., Reynolds, A.P., Stergachis, A.B., Vernot, B., Johnson, A.K., Haugen, E., Sullivan, S.T., Thompson, A., Neri, F.V. 3rd, Weaver, M., Diegel, M., Mnaimneh, S., Yang, A., Hughes, T.R., Nemhauser, J.L., Queitsch, C., Stamatoyannopoulos, J.A. (2014). Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A. thaliana. Cell Rep. 8:2015-30
  • Weirauch, M.T., Yang, A., Albu, M., Cote, A.G., Montenegro-Montero, A., Drewe, P., Najafabadi, H.S., Lambert, S.A., Mann, I., Cook, K., Zheng, H., Goity, A., van Bakel, H., Lozano, J.C., Galli, M., Lewsey, M.G., Huang, E., Mukherjee, T., Chen, X., Reece-Hoyes, J.S., Govindarajan, S., Shaulsky, G., Walhout, A.J., Bouget, F.Y., Ratsch, G., Larrondo, L.F., Ecker, J.R., Hughes, T.R. (2014). Determination and inference of eukaryotic transcription factor sequence specificity. Cell 158:1431-43. CisBP Webserver Web Supplement
  • Norris, A.D., Gao, S., Norris, M.L., Ray, D., Ramani, A.K., Fraser, A.G., Morris, Q., Hughes, T.R., Zhen, M., Calarco, J.A. (2014). A pair of RNA-binding proteins controls networks of splicing events contributing to specialization of neural cell types. Mol Cell 54:946-59.
  • Schoberle, T.J., Nguyen-Coleman, C.K., Herold, J., Yang, A., Weirauch, M., Hughes, T.R., McMurray, J.S., May, G.S. (2014). A Novel C2H2 Transcription Factor that Regulates gliA Expression Interdependently with GliZ in Aspergillus fumigatus. PLoS Genet. 10(5):e1004336
  • Li, J., Kim, T., Nutiu, R., Ray, D., Hughes, T.R., Zhang, Z. (2014). Identifying mRNA sequence elements for target recognition by human Argonaute proteins. Genome Res. 24:775-785.
• 2013
  • de Boer, C.G., van Bakel, H., Tsui, K., Li, J., Morris, Q.D., Nislow, C., Greenblatt, J.F., Hughes, T.R. (2013). A Unified Model for yeast transcript definition. Genome Research 24:154-66. Web Supplement
  • Smith, S.A., Ray, D., Cook, K.B., Mallory, M.J., Hughes, T.R., Lynch, K.W. (2013). Paralogs hnRNP L and hnRNP LL Exhibit Overlapping but Distinct RNA Binding Constraints. PLoS One. 8(11):e80701
  • Sebé-Pedrós, A., Ariza-Cosano, A., Weirauch, M.T., Leininger, S., Yang, A., Torruella, G., Adamski, M., Adamska, M., Hughes, T.R., Gómez-Skarmeta, J.L., and Ruiz-Trillo, I. (2013). Early evolution of the T-box transcription factor family. Proc Natl Acad Sci U S A. 110:16050-5
  • Ray, D., Kazan, H., Cook, K.B., Weirauch, M.T., Najafabadi, H.S., Li, X., Guerousov, S., Albu, M., Zheng, H., Yang, A., Na, H., Irimia, M., Matzat, L.H., Dale, R.K., Smith, S.A., Yarosh, C.A., Kelly, S.M., Nabet, B., Mecenas, D., Li, W., Laishram, R.S., Qiao, M., Lipshitz, H.D. Piano, F., Corbett, A.H., Carstens, R.P., Frey, B.J., Anderson, R.A., Lynch, K.W., Penalva, L.O.F., Lei, E.P., Fraser, A.G., Blencowe, B.J., Morris, Q.D.* and Hughes, T.R.* (2013). A compendium of RNA binding motifs for decoding gene regulation. Nature 499:172-7. CisBP-RNA Webserver
  • Chang, K.N., Zhong, S., Weirauch, M.T., Hon, G., Pelizzola, M., Li, H., Huang, S.S., Schmitz, R.J., Urich, M.A., Kuo, D., Nery, J.R., Qiao, H., Yang, A., Jamali, A., Chen, H., Ideker, T., Ren, B., Bar-Joseph, Z., Hughes, T.R. and Ecker, J.R. (2013). Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis. Elife 2:e00675.
  • Reece-Hoyes, J.S., Pons, C., Diallo, A., Mori, A., Shrestha, S., Kadreppa, S., Nelson, J., Diprima, S., Dricot, A., Lajoie, B.R., Ribeiro, P.S., Weirauch, M.T., Hill, D.E., Hughes, T.R., Myers, C.L., and Walhout, A.J. (2013). Extensive Rewiring and Complex Evolutionary Dynamics in a C. elegans Multiparameter Transcription Factor Network. Mol Cell. 51:116-27
  • van Bakel, H., Tsui, K., Gebbia, M., Mnaimneh, S., Hughes, T.R., and Nislow, C. (2013). A compendium of nucleosome and transcript profiles reveals determinants of chromatin architecture and transcription. PLoS Genet. 9(5):e1003479 Web Supplement
  • Mann, I.K., Chatterjee, R., Zhao, J., He, X., Weirauch, M.T., Hughes, T.R., and Vinson, C. (2013). CG methylated microarrays identify a novel methylated sequence bound by the CEBPB|ATF4 heterodimer that is active in vivo. Genome Res. 23:988-97.
  • Weirauch, M.T., Cote, A., Norel, R., Annala, M., Zhao, Y., Riley, T.R., Saez-Rodriguez, J., Cokelaer, T., Vedenko, A., Talukder, S., DREAM5 consortium, Bussemaker, H.J., Morris, Q.D., Bulyk, M.L., Stolovitzky, G. and Hughes, T. R. (2013). Evaluation of methods for modeling transcription factor sequence specificity. Nature Biotechnology 31(2):126-34. Web Supplement
  • Jolma, A., Yan, J., Whitington, T., Toivonen, J., Nitta, K.R., Rastas, P., Morgunova, E., Enge1, M., Taipale, M., Wei, G., Palin, K., Vaquerizas, J.M., Vincentelli, R., Luscombe, N.M., Hughes, T.R., Lemaire, P., Ukkonen, E., Kivioja, T.,and Taipale, J. (2013). Binding specificities of human transcription factors. Cell 152(1-2):327-39.
• 2012
  • de Boer, C.G., and Hughes, T.R. (2012). YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities. Nucleic Acids Research 40(Database issue):D169-79. Yetfasco Server
• 2011
  • van Bakel, H., Stout, J., Cote, A.G., Tallon, C., Morris, Q., Hughes, T.R.* and Page, J.E.* (2011). The draft genome and transcriptome of Cannabis sativa. Genome Biology 12(10):R102. *co-communicating Canabis Genome Browser
  • Gabut, M., Samavarchi-Tehrani, P., Wang, X., Slobodeniuc, V., O'Hanlon, D., Sung, H.K., Alvarez, M., Talukder, S., Pan, Q., Mazzoni, E.O., Nedelec, S., Wichterle, H., Woltjen, K., Hughes, T.R., Zandstra, P.W., Nagy, A., Wrana, J.L., Blencowe, B.J. (2011). An alternative splicing switch regulates embryonic stem cell pluripotency and reprogramming. Cell 147(1):132-46.
  • Huang, E., Talukder, S., Hughes, T.R., Curk, T., Zupan, B., Shaulsky, G., Katoh-Kurasawa, M. (2011). BzpF is a CREB-like transcription factor that regulates spore maturation and stability in Dictyostelium. Dev Biol. 358(1):137-46.
  • Gordon, B.R., Li, Y., Cote, A., Weirauch, M.T., Ding, P., Hughes, T.R., Navarre, W.W., Xia, B., and Liu, J. (2011). Structural basis for recognition of AT-rich DNA by unrelated xenogeneic silencing proteins. Proc Natl Acad Sci U S A. 108(26):10690-5.
  • Lam, K.N, van Bakel, H., Cote, A.G., van der Ven, A. and Hughes, T.R. (2011). Sequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays. Nucleic Acids Res. 39(11):4680-90. Web Supplement
  • Stead, M.B., Marshburn, S., Mohanty, B.K., Mitra, J., Castillo, L.P., Ray, D., van Bakel, H., Hughes, T.R., Kushner, S.R. (2011). Analysis of Escherichia coli RNase E and RNase III activity in vivo using tiling microarrays. Nucleic Acids Res. 39(8):3188-203.
• 2010
  • Cook, K.B., Kazan, H., Zuberi, K., Morris, Q., Hughes, T.R. (2010). RBPDB: a database of RNA-binding specificities. Nucleic Acids Res. 39(Database issue):D301-8 RBPDB Server
  • Chowdhury, S., Lloyd-Price, J., Smolander, O.P., Baici, W.C., Hughes, T.R., Yli-Harja, O., Chua, G., Ribeiro, A.S. (2010). Information propagation within the Genetic Network of Saccharomyces cerevisiae. BMC Syst Biol. 4:143.
  • Santos, M.A., Turinsky, A.L., Ong, S., Tsai, J., Berger, M.F., Badis, G., Talukder, S., Gehrke, A.R., Bulyk, M.L., Hughes, T.R., Wodak, S.J. (2010). Objective sequence-based subfamily classifications of mouse homeodomains reflect their in vitro DNA-binding preferences. Nucleic Acids Res. 38(22):7927-42
  • Kazan, H., Ray, D., Chan, E.T., Hughes, T.R., Morris, Q. (2010). RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins. PLoS Comput Biol. 1;6:e1000832.
  • van Bakel, H., Blencowe, B.J., Nislow, C., Hughes T.R. (2010). Most “Dark Matter” Transcripts are Associated with Known Genes. PLoS Biology 8(5):e1000371. Web Supplement
  • Wei, G.H., Badis, G., Berger, M.F., Kivioja, T., Palin, K., Enge, M., Bonke, M., Jolma, A., Varjosalo, M., Gehrke, A.R., Yan, J., Talukder, S., Turunen, M., Taipale, M., Stunnenberg, H.G., Ukkonen, E., Hughes, T.R., Bulyk, M.L., Taipale, J. (2010). Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo. EMBO J. 29:2147-60.
  • Beaver, J.E., Tasan, M., Gibbons, F.D., Tian, W., Hughes, T.R., Roth, F.P. (2010). FuncBase: a resource for quantitative gene function annotation. Bioinformatics. 26:1806-7.
  • Jolma, A., Kivioja, T., Toivonen, J., Cheng, L., Wei, G., Enge, M., Taipale, M., Vaquerizas, J.M., Yan, J., Sillanpää, M.J., Bonke, M., Palin, K., Talukder, S., Hughes, T.R., Luscombe, N.M., Ukkonen, E., Taipale, J. (2010). Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Res. 20:861-73.
  • Tillo, D., Kaplan, N., Moore, I.K., Fondufe-Mittendorf, Y., Gossett, A.J., Field, Y., Lieb, J.D., Widom, J., Segal, E., Hughes, T.R. (2010). High Nucleosome Occupancy Is Encoded at Human Regulatory Sequences. PLoS ONE 5(2):e9129.
  • Jaeger, S.A., Chan, E.T., Berger, M.F., Stottmann, R., Hughes, T.R., Bulyk, M.L. (2010). Conservation and regulatory associations of a wide affinity range of mouse transcription factor binding sites. Genomics Jan 15. 95(4):185-95
• 2009
  • Tillo, D., Hughes, T.R. (2009) G+C content dominates intrinsic nucleosome occupancy. BMC Bioinformatics 10:442.
  • Khanna, M., Van Bakel, H., Tang, X., Calarco, J.A., Babak, T., Guo, G., Emili, A., Greenblatt, J.F., Hughes, T.R., Krogan, N.J., Blencowe, B.J. (2009). A systematic characterization of Cwc21, the yeast ortholog of the human spliceosomal protein SRm300. RNA. 15:2174-85.
  • Fillingham J, Kainth P, Lambert JP, van Bakel H, Tsui K, Peña-Castillo L, Nislow C, Figeys D, Hughes TR, Greenblatt J, Andrews BJ. (2009). Two-color cell array screen reveals interdependent roles for histone chaperones and a chromatin boundary regulator in histone gene repression. Mol Cell. 35:340-51.
  • Ray, D., Kazan, H., Chan, E.T., Castillo, L.P., Chaudhry, S., Talukder, S., Blencowe, B.J., Morris, Q., Hughes, T.R. (2009) Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins. Nature Biotechnology 27:667-70. Web Supplement
  • Badis, G., Berger, M.F., Philippakis, A.A., Gehrke, A.R., Talukder, S, Jaeger, S.A., Chan, E.T., Metzler, G., Vedenko, A., Chen, X., Kuznetsov, H., Wang, C.-F., Coburn, D., Newburger, D., Morris, Q., Hughes, T.R.*, Bulyk, M.L.* (2009) Diversity and Complexity in DNA Recognition by Transcription Factors. Science 324:1720. *co-communicating.
  • Chan, E.T., Quon, G.T., Chua,G., Babak, T., Trochesset, M., Zirngibl, R.A., Aubin, J., Ratcliffe, M., Wilde, A., Brudno, M., Morris, Q.D. and Hughes, T.R. (2009) Conservation of gene expression in vertebrate tissues. Journal of Biology 8:33. Web Supplement
  • Fulton, D.L., Sundararajan, S., Badis, G., Hughes, T.R., Sladek, R., Roach, J.C., and Wasserman, W.W. (2009) TFCat: the curated catalog of mouse and human transcription factors. Genome Biology 10:R29.
  • Kainth, P., Sassi, H.E., Peña-Castillo, L., Chua, G., Hughes, T.R., and Andrews, B. (2009) Comprehensive genetic analysis of transcription factor pathways using a dual reporter gene system in budding yeast. Methods 48:258-64.
  • Coughlin, D.J., Babak, T., Nihranz, C., Hughes, T.R., and Engelke, D.R. (2009) Prediction and verification of mouse tRNA gene families. RNA Biol 6:195-202.
  • Kaplan, N., Moore, I., Fondufe-Mittendorf, Y., Gossett, A., Tillo, D., Field, Y., LeProust, E.M., Hughes, T.R., Lieb, J.D., Widom, J., Segal, E. (2009) The DNA-Encoded Nucleosome Organization of a Eukaryotic Genome. Nature 458:362-6.
  • Alleyne, T.M., Peña-Castillo, L., Badis, G., Talukder, S., Berger, M.F., Gehrke, A.R., Philippakis, A.A., Bulyk, M.L., Morris, Q.D., and Hughes, T.R. (2009) Predicting the Binding Preference of Transcription Factors to Individual DNA k-mers. Bioinformatics 25:1012-8 Web Supplement
• 2008
  • Badis, G., Chan, E.T., van Bakel, H., Pena-Castillo, L., Tillo, D., Tsui, K., Carlson, C.D, Gossett, A.J., Hasinoff, M.J., Warren, C.L., Gebbia, M., Talukder, S., Yang, A., Mnaimneh, S., Terterov, D., Coburn, D., Yeo, A.L., Yeo, Z.X., Clarke, N.D., Lieb, J.D., Ansari, A.Z., Nislow, C., and Hughes, T.R. (2008) A new library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell 32:878-87. Web Supplement
  • Cheung, V., Chua, G., Batada, N.N., Landry, C.R., Michnick, S.W., Hughes, T.R., Winston, F. (2008) Chromatin- and transcription-related factors repress transcription from within coding regions throughout the Saccharomyces cerevisiae genome. PLoS Biol. 6:e277.
  • Berger, M.F.*, Badis, G.*, Gehrke, A.R.*, Talukder, S.*, Philippakis, A.A., Pena-Castillo, L., Alleyne, T., Mnaimneh, S., Botvinnik, O.B., Chan, E.T., Khalid, F., Zhang, W., Newburger, D., Jaeger, S., Morris, Q.D., Bulyk, M.L. and Hughes, T.R. (2008). Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell, 133(7):1266-76. Web Supplement
  • Peña-Castillo, L., Tasan, M., Myers, C.L., Lee, H., Joshi, T., Zhang, C., Guan, Y., Leone, M., Pagnani, A., Kim, W.K., Krumpelman, C., Tian, W-d., Obozinski, G., Qi, Y., Mostafavi, S., Lin G.N., Berriz, G., Gibbons, F., Lanckriet, G., Qiu, J., Grant, C., Barutcuoglu, Z., Hill, D.P., Wade-Farley, D., Grouios, C., Ray, D., Blake, J.A., Deng, M., Jordan, M., Noble, W.S., Morris, Q., Klein-Seetharaman, J., Bar-Joseph, Z., Chen, T., Sun, F., Troyanskaya, O.G., Marcotte, E.M., Xu, D., Hughes, T.R.*, and Roth, F.P.* (2008). A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biology 2008:9 Suppl 1:S2. (*co-communicating)
  • Lovegrove, F.E., Gharib, S.A., Peña-Castillo, L., Patel, S.N., Ruzinski, J.T., Hughes, T.R., Liles, W.C., Kain, K.C. (2008). Parasite burden and CD36-mediated sequestration are determinants of acute lung injury in an experimental malaria model. PLoS Pathog. 4(5):e1000068.
  • Willis, I.M., Chua, G., Tong, A.H., Brost, R.L., Hughes, T.R., Boone, C., Moir, R.D. (2008). Genetic interactions of MAF1 identify a role for Med20 in transcriptional repression of ribosomal protein genes. PLoS Genet. 4(7):e1000112.
  • Rutherford, J.C., Chua, G., Hughes, T., Cardenas, M.E., Heitman, J. (2008). A Mep2-dependent Transcriptional Profile Links Permease Function to Gene Expression during Pseudohyphal Growth in Saccharomyces cerevisiae. Mol Biol Cell. 19(7):3028-39.
  • Zhao, R., Kakihara, Y., Gribun, A., Huen, J., Yang, G., Khanna, M., Costanzo, M., Brost, R.L., Boone, C., Hughes, T.R., Yip, C.M., Houry, W.A. (2008). Molecular chaperone Hsp90 stabilizes Pih1/Nop17 to maintain R2TP complex activity that regulates snoRNA accumulation. J Cell Biol. 180(3):563-78.
  • Sandhu, C., Hewel, J.A., Badis, G., Talukder, S., Liu, J., Hughes, T.R., and Emili, A. Evaluation of Data-Dependent versus Targeted Shotgun Proteomic Approaches for Monitoring Transcription Factor Expression in Breast Cancer. (2008) J Proteome Res. 7:1529.
  • Marcon, E., Babak, T., Chua, G., Hughes, T., Moens, P.B. (2008). miRNA and piRNA localization in the male mammalian meiotic nucleus. Chromosome Res. 16(2):243-60.
• 2007
  • Zhang, J., Harnpicharnchai, P., Jakovljevic, J., Tang, L., Guo, Y., Oeffinger, M., Rout, M.P., Hiley, S., Hughes, T.R., and Woolford, J.L. (2007) Assembly Factors Rpf2 and Rrs1 Recruit 5S rRNA and Ribosomal Proteins rpL5 and rpL11 into Nascent Ribosomes. Genes Dev. 21(20):2580-92.
  • Huang, J.C., Babak, T., Corson, T.W., Chua, G., Khan, S., Gallie, B.L., Hughes, T.R., Blencowe, B.J., Frey, B.J., Morris, Q.D. (2007) Using expression profiling data to identify human microRNA targets. Nature Methods 4:1045-9.
  • Lécuyer, E., Yoshida, H., Parthasarathy, N., Alm, C., Cerovina, T., Babak, T., Hughes, T.R., Tomancak, P., and Krause, H.M. (2007). Global analysis of subcellular mRNA localization during early Drosophila development. Cell. 131(1):174-87.
  • Lee, W., Tillo, D., Bray, N., Morse, R.H., Davis, R.W., Hughes, T.R. and Nislow, C. (2007). A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet. 39(10):1235-44. Web Supplement
  • Walker, E., Ohishi, M., Davey, R.E., Zhang, W., Cassar, P.A., Tanaka, T.S., Der, S.D., Morris, Q., Hughes, T.R., Zandstra, P.W., and Stanford, W.L. Prediction and Testing of Novel Transcriptional Networks Regulating Embryonic Stem Cell Self-Renewal and Commitment. Cell Stem Cell 1(1):71-86.
  • Chen, X., Hughes, T.R., and Morris, Q. (2007). RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors. Bioinformatics. 23(13):i72-i79.
  • Wyce, A., Xiao, T., Whelan, K.A., Kosman, C., Walter, W., Eick, D., Hughes, T.R., Krogan, N.J., Strahl, B.D., and Berger, S.L. (2007). H2B Ubiquitylation Acts as a Barrier to Ctk1 Nucleosomal Recruitment Prior to Removal by Ubp8 within a SAGA-Related Complex. Mol Cell. 27(2):275-88.
  • Jeronimo, C., Forget, D., Bouchard, A., Li, Q., Chua, G., Poitras, C., Therien, C., Bergeron, D., Bourassa, S., Greenblatt, J., Chabot, B., Poirier, G.G., Hughes, T.R., Blanchette, M., Price, D.H., and Coulombe, B. (2007). Systematic Analysis of the Protein Interaction Network for the Human Transcription Machinery Reveals the Identity of the 7SK Capping Enzyme. Mol Cell. 27(2):262-274. Web Supplement
  • Fagnani, M., Barash, Y., Ip, J., Misquitta, C., Pan, Q., Saltzman, A.L., Shai, O., Lee, L., Rozenhek, A., Mohammad, N., Willaime-Morawek, S., Babak, T., Zhang, W., Hughes, T.R., van der Kooy, D., Frey, B.J., and Blencowe, B.J. (2007). Functional coordination of alternative splicing in the mammalian central nervous system. Genome Biol. 8(6):R108
  • Babak, T., Blencowe, B.J., and Hughes, T.R. (2007). Considerations in the identification of functional RNA structural elements in genomic alignments. BMC Bioinformatics. 2007 8:33.
  • Tadros, W., Goldman, A.L., Babak, T., Menzies, F., Vardy, L., Orr-Weaver, T., Hughes, T.R., Westwood, J.T., Smibert, C.A., and Lipshitz, H.D. (2007). SMAUG is a major regulator of maternal mRNA destabilization in Drosophila and its translation is activated by the PAN GU kinase. Dev Cell 12(1):143-55.
• 2006
  • Lovegrove, F.E., Pena-Castillo, L., Mohammad, N., Liles, W.C., Hughes, T.R., Kain, K.C. (2006). Simultaneous host and parasite expression profiling identifies tissue-specific transcriptional programs associated with susceptibility or resistance to experimental cerebral malaria. BMC Genomics. 7:295. Web Supplement
  • Zhang, W., Walker, A., Tamplin, O., Rossant, J., Stanford, W.L., and Hughes, T.R. (2006). Zfp206 regulates ES cell gene expression and differentiation. Nucleic Acids Research 34:4780-90. Web Supplement
  • Yu, L., P Castillo, L., Mnaimneh, S., Hughes, T.R., and Brown, G.W. (2006). A Survey of Essential Gene Function in the Yeast Cell Division Cycle. Mol Biol Cell. 17:4736-47.
  • Chua, G., Morris, Q.D., Sopko, R., Robinson, M.D., Ryan, O., Chan, E.T., Frey, B.J., Andrews, B.J., Boone, C., and Hughes, T.R. (2006). Identifying transcription factor functions and targets by phenotypic activation. Proc Natl Acad Sci 103:12045-50 Web Supplement
  • Parsons, A.B., Lopez, A., Givoni, I.E., Williams, D.E., Gray, C., Porter, J., Chua, G., Sopko, R., Ho, C.H., Brost, R.L., Ketela, T., Brenner, C., Payne, G., Ishihara, S., Ohya, Y., Andrews, B., Hughes, T.R., Frey, B., Graham, T.R., Andersen, R.J., and Boone, C. (2006). Exploring the Mode-of-Action of Bioactive Compounds by Chemical-Genetic Profiling in Yeast. Cell 126:611-25
  • Krogan, N. J., G. Cagney, H. Yu, G. Zhong, X. Guo, A. Ignatchenko, J. Li, S. Pu, N. Datta, A. P. Tikuisis, T. Punna, J. M. Peregrin-Alvarez, M. Shales, X. Zhang, M. Davey, M. D. Robinson, A. Paccanaro, J. E. Bray, A. Sheung, B. Beattie, D. P. Richards, V. Canadien, A. Lalev, F. Mena, P. Wong, A. Starostine, M. M. Canete, J. Vlasblom, S. Wu, C. Orsi, S. R. Collins, S. Chandran, R. Haw, J. Rilestone, K. Gandi, N. J. Thompson, G. Musso, P. St. Onge, S. Ghanny, M. H. Y. Lam, G. Butland, A. Altaf, S. Kanaya, A. Shilatifard, E. O’Shea, J. S. Weissman, C. J. Ingles, T. R. Hughes, J. Parkinson, M. Gerstein, S. J. Wodak, A. Emili and J. F. Greenblatt. (2006.) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440:637-43
  • Sopko, R., Huang, D., Preston, N., Chua, G., Papp, B., Kafadar, K., Snyder, M., Oliver, S., Cyert, M., Hughes, T., Boone, C., and Andrews, B. (2006). Mapping pathways and phenotypes by systematic gene overexpression. Molecular Cell 21:319-30.
  • Kislinger, T., Cox, B., Kannan, A., Chung, C., Hu, P., Ignatchenko, A., Scott, M.S., Gramolini, A.O., Morris, Q., Hallett, M.T., Rossant, J., Hughes, T.R., Frey, J. and Emili, A.E. (2006). Global Survey of Organ and Organelle Protein Expression in Mouse: Combined Proteomic and Transcriptomic Profiling. Cell 125:173-86
  • Alto, N.M., Shao, F., Lazar, C.S., Brost, R.L., Chua, G., Mattoo, S., McMahon, S.A., Ghosh, P., Hughes, T.R., Boone, C., and Dixon, J.E. (2006). Identification of a Bacterial Type III Effector Family with G-protein Mimicry Functions. Cell 124:133-45.
  • Leeds, N.B, Hiley, S.L., Small, E., Hughes, T.R. and Staley, J.P. (2006). The Splicing Factor Prp43, a DEAH box ATPase, Functions in Ribosome Biogenesis. Molecular and Cellular Biology 26:513-22. Web Supplement
  • Alexandrov, A., Chernyakov, I., Gu, W., Hiley, S., Hughes, T.R., Grayhack, E.J., and Phizicky, E.M. (2006). Rapid tRNA Decay Can Result from Lack of Nonessential Modifications. Molecular Cell 21:87-96
• 2005
  • Keogh, M.C., Kurdistani, S.K., Morris, S.A., Ahn, S.H., Podolny, V., Collins, S.R., Schuldiner, M., Chin, K., Punna, T., Thompson, N.J., Boone, C., Emili, A., Weissman, J.S., Hughes, T.R., Strahl, B.D., Grunstein, M., Greenblatt, J.F., Buratowski, S., Krogan, N.J. (2005). Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 123:593-605.
  • Davierwala, A.P., Haynes, J., Li, Z., Brost, R.L., Robinson, M.D., Yu, L., Mnaimneh, S., Preston, N., Zhu, H., Chen, Y., Cheng, X., Brown, G.W., Boone, C., Andrews, B.J. and Hughes, T.R. (2005) The synthetic genetic interaction spectrum of essential genes. Nature Genetics 37:1147-52. Web Supplement
  • Frey, B.J.*, Mohammad, N.*, Morris, Q.D.*, Zhang, W.*, Robinson, M.D., Mnaimneh, S., Shai, O., Chang, R., Pan, Q., Sat, E., Rossant, J., Bruneau, B.G., Aubin, J.E., Blencowe, B.J., and Hughes, T.R. (2005) Genome-wide analysis of mouse transcription using exon-resolution microarrays and factor graphs. Nature Genetics 37:991-996. Web Supplement
  • Babak, T., Blencowe, B.J., and Hughes, T.R. (2005) A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription. BMC Genomics 2005 6:104 Web Supplement
  • Laribee, R.N., Krogan, N.J., Xiao, T., Shibata, Y., Hughes, T.R., Greenblatt, J.F., Strahl, B.D. (2005). BUR Kinase Selectively Regulates H3 K4 Trimethylation and H2B Ubiquitylation through Recruitment of the PAF Elongation Complex. Curr Biol. 15:1487-93.
  • Henras, A.K., Sam, M., Hiley, S.L., Wu, H., Hughes, T.R., Feigon, J., Chanfreau, G.F. (2005). Biochemical and genomic analysis of substrate recognition by the double-stranded RNA binding domain of yeast RNase III. RNA 11:1225-37.
  • Hoang, T.*, Peng, W.-T.*, Vanrobays, E.*, Krogan, N., Hiley, S., Beyer, A.L., Osheim, Y.N., Greenblatt, J.F., Hughes, T.R., and Lafontaine, D.L.J. (2005). Esf2p, a u3-associated factor required for small-subunit processome assembly and compaction. Molecular and Cellular Biology 25:5523-34. Web Supplement
  • Hiley, S.L., Babak, T., and Hughes, T.R. (2005). Global analysis of yeast RNA processing by microarray identifies new targets of Rnase III and uncovers a link between tRNA 5'-end processing and tRNA splicing. Nucleic Acids Res. 33:3048-56. Web Supplement
  • Ingvarsdottir, K. Krogan, N.M., Emre, N.C., Wyce, A., Thompson, N.J., Emili, A., Hughes, T.R., Greenblatt, J.F., and Berger, S.L. (2005). H2B ubiquitin protease Ubp8 and Sgf11 constitute a discrete functional module within the S. cerevisiae SAGA complex. Mol Cell Biol. 25:1162-72.
  • Pan, Q., Bakowski, M.A., Morris, Q., Zhang, W., Frey, B., Hughes, T.R. and Blencowe, B.J. (2005). Alternative splicing of conserved exons is frequently species-specific in human and mouse. Trends Genet. 21:73-77.
  • Hiley, S.L., Jackman, J., Babak, T., Trochesset, M., Morris, Q., Phizicky, E., and Hughes, T.R. (2005). Detection and discovery of RNA modifications using microarrays. Nucleic Acids Res. 33(1):e2. Web Supplement
• 2004
  • Pan, Q., Shai, O., Misquitta, C., Zhang, W., Saltzman, A.L., Mohammad, N., Babak, T., Siu, H., Hughes, T.R., Morris, Q.D., Frey, B.J., Blencowe, B.J. (2004). Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Mol Cell 16:929-41.
  • Zhang, W., Morris, Q., Chang, R., Shai, O., Bakowski, M.A., Mitsakakis, N., Mohammad, N., Robinson, M., Zirnglibl, R., Somogyi, E., Laurin, N., Eftekharpour, E., Sat, E., Grigull, J., Pan, Q., Peng, W.-T., Krogan, N.J., Greenblatt, J.F., Fehlings, M., van der Kooy, D., Aubin, J., Bruneau, B.G., Rossant, J., Blencowe, B.J., Frey, B.J., and Hughes, T.R. (2004). The functional landscape of mouse gene expression. J Biol 3:21. Web Supplement
  • Lewis, K., Robinson, M., Hughes, T.R., and Hogue, C. (2004). MyMed: A database system for biomedical research on MEDLINE data. IBM Systems Journal 43:4.
  • Krogan, N.J., Baetz, K., Keogh, M.C., Datta, N., Sawa, C., Kwok, T.C., Thompson, N.J., Davey, M.G., Pootoolal, J., Hughes, T.R., Emili, A., Buratowski, S., Hieter, P., Greenblatt, J.F. (2004). Regulation of chromosome stability by the histone H2A variant Htz1, the Swr1 chromatin remodeling complex, and the histone acetyltransferase NuA4. Proc Natl Acad Sci U S A. 101:13513-8.
  • Babak, T., Zhang, W., Morris, Q., Blencowe, B.J., and Hughes, T.R. (2004). Profiling microRNAs with microarrays: tissue specificity and functional inference. RNA 10:1813-9. Web Supplement
  • Jeronimo, C., Langelier, M.F., Zeghouf, M., Cojocaru, M., Bergeron, D., Baali, D., Forget, D., Mnaimneh, S., Davierwala, A.P., Pootoolal, J., Chandy, M., Canadien, V., Beattie, B.K., Richards, D.P., Workman, J.L., Hughes, T.R., Greenblatt, J. and Coulombe, B. (2004) RPAP1, a novel human RNA polymerase II-associated protein affinity purified using recombinant wild type and mutated polymerase subunits. Mol Cell Biol. 24:7043-58.
  • Mnaimneh, S., Davierwala, A.P., Haynes, J., Moffat, J., Peng W.T., Zhang, W., Yang, X., Pootoolal, J., Chua, G., Lopez, A., Trochesset, M., Morse, D., Krogan, N.J., Hiley, S.L., Li, Z., Morris, Q., Grigull, J., Mitsakakis, N., Roberts, C.J., Greenblatt, J.F., Boone, C., Kaiser, C.A., Andrews, B.J. and Hughes, T.R. (2004) Exploration of essential gene functions via titratable promoter alleles. Cell 118:31-44. Web Supplement
  • Grigull, J., Mnaimneh, S., Pootoolal, J., Robinson, M. and Hughes, T.R. (2004) Genome-wide analysis of mRNA decay using transcription inhibitors and microarrays reveals post-transcriptional control of ribosome biogenesis factors. Molecular and Cellular Biology 24:5534-47 Web Supplement
  • Peng, W.-T., Krogan, N.J., Richards, D.P., Greenblatt, J.F. and Hughes, T.R. (2004). ESF1 is required for 18S rRNA synthesis in Saccharomyces cerevisiae. Nucleic Acids Research 32:1993-9.
  • Xing, F., Hiley, S.L., Hughes, T.R., and Phizicky, E.M. (2004). The specificities of four yeast dihydrouridine synthetases for cytoplasmic tRNAs. Journal of Biological Chemistry 279:17850-60. Web Supplement
  • Krogan, N., Cagney, G., Peng, W.-T., Lalev, A. Robinson, M., Grigull, J., Canadien, V., Richards, D., Beattie, B., Hughes, T.R., Emili, A., and Greenblatt, J. (2004). High-definition macromolecular composition of yeast RNA processing complexes. Molecular Cell 13:225-39. Web Supplement
  • Parsons, A.B., Brost, R.L., Ding, H., Li, Z., Zhang, C., Sheikh, B., Brown, G.W., Kane, P.M., Hughes, T.R., and Boone, C. (2004). Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways. Nature Biotechnology 22:62-9.
• 2003
  • Krogan, N., Keogh, M-C., Datta, N., Sawa, C., Ryan, O.W., Ding, H., Haw, R.A., Pootoolal, J., Tong, A., Canadien, V., Richards, D., Wu, X., Emili, A., Hughes, T.R., Buratowski, S., and Greenblatt, J. (2003). A Snf2-Family ATPase Complex Required for Recruitment of the Histone H2A Variant Htz1. Molecular Cell 12:1565-76.
  • Peng, W-T, Robinson, M.D., Mnaimneh, S., Krogan, N., Cagney, G., Davierwala, A.P., Grigull, J., Yang, X., Zhang, W., Mitsakakis, N., Ryan, O.W., Datta, N., Jojic, V., Pal, C., Morris, Q., Frey, B.J., Canadien, V., Richards, D., Beattie, B., Wu, L.F., Altschuler, S.J., Boone, C., Emili, A., Greenblatt, J. and Hughes, T.R. (2003). A panoramic view of yeast non-coding RNA processing. Cell 113:919-33.
  • Nelson, B., Kurischko, C., Horecka, J., Mody, M., Nair, P., Pratt, L., Zoughman, A., McBroom, L.D.B., Hughes, T.R., Boone, C. and Luca, F.C. (2003). RAM: a conserved signaling network that regulates Ace2p transcriptional activity and polarized morphogenesis. Mol Biol Cell. 14:3782-803.
  • Nedea, E., He, X., Kim, M., Pootoolal, J., Zhong, G., Canadien, V., Hughes, T.R., Buratowski, S., Moore, C.L. and Greenblatt, J. (2003). Organization and function of APT, a subcomplex of the yeast cleavage and polyadenylation factor involved in the formation of mRNA and small nucleolar RNA 3'-ends. J Biol Chem. 278:33000-10. Web Supplement
• 2002
  • Robinson, M.D., Grigull, J., Mohammad, N. and Hughes, T.R. (2002) FUNSPEC: A Web-Based Cluster Interpreter for Yeast. BMC Bioinformatics. 3:35. Funspec Server
  • Wu, L.F.*, Hughes, T.R.*, Davierwala, A.P., Robinson, M.D., Stoughton, R. and Altschuler, S.J. (2002). Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nature Genetics 31:255-65. (* indicates equal contribution) Web Supplement
  • Mitton-Fry, R.M., Anderson, E.M., Hughes, T.R., Lundblad, V., and Wuttke, D.S. (2002). Conserved structure for single-stranded telomeric DNA recognition. Science 296:145-7.
• 2001
  • Hughes, T.R., Mao, M., Jones, A., Burchard, J., Marton, M.J., Schelter, J., Meyer, M.R., Kobayashi, S., Dai, H., He, Y., Stephaniants, S., West, A., Coffey, E., Shoemaker, D., Stoughton, R., Blanchard, A., Friend, S.H., and Linsley, P.S. (2001). Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nature Biotechnology 19:342-7.
  • Harris, K., Lamson, R.E., Nelson, B., Hughes, T.R., Marton, M.J., Roberts, C.J., Boone, C., Pryciak, P.M. (2001). Role of scaffolds in MAP kinase pathway specificity revealed by custom design of pathway-dedicated signaling proteins. Curr Biol 11:1815-24 .
  • Chandra, A., Hughes, T.R., Nugent, C. I. and Lundblad, V. (2001). A role for Cdc13p in negative telomere length regulation. Genes and Development 15:404-14.
  • Gachotte, D., Eckstein, J., Barbuch, R., Hughes, T., Roberts, C., and Bard, M. (2001). A novel gene conserved from yeast to humans is involved in sterol biosynthesis. Journal of Lipids Research 42:150-154.
• 2000
  • Hughes, T.R., Marton, M.J., Jones, A.R., Roberts, C.J., Stoughton, R., Armour, C.D., Bennett, H.A., Dai, H., He, Y.D., Kidd, M.J., King, A.M., Meyer, M.R., Slade, D., Lum, P.Y., Stepaniants, S.B., Shoemaker, D.D., Gachotte, D., Chakraburtty, K., Simon, J., Bard, M. and Friend, S.H. (2000). Functional discovery via a compendium of expression profiles. Cell 102:109-126. Web Supplement
  • Hughes, T.R., Roberts, C.J., Dai, H., Jones, A.R., Meyer, M.R., Slade, D., Burchard, J., Dow, S., Ward, T.R., Kidd, M.J., Friend, S.H. and Marton, M.J. (2000). Widespread Aneuploidy Revealed by DNA Microarray Expression Profiling. Nature Genetics 25:333-337. Web Supplement
  • Hughes, T.R., Evans, S.K., Weilbaecher, R.G., and Lundblad, V. (2000). The Est3 protein is a subunit of yeast telomerase. Current Biology 10:809-812.
  • Hughes, T.R., Weilbaecher, R.G., Waltersheid, M., and Lundblad, V. (2000). Identification of the single-strand telomeric DNA binding domain of the Saccharomyces cerevisiae Cdc13 protein. Proc. Natl. Acad. Sci. U. S. A. 97:6457-62.
  • Roberts, C.J., Nelson, B., Marton, M.J., Stoughton, R., Meyer, M.R., Bennett, H.A., He, Y.D., Dai, H., Walker, W.L., Hughes, T.R., Tyers, M., Boone, C., and Friend, S.H. (2000). Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science 287:873-80. Web Supplement
• 1999
  • Norman, T.C., Smith, D.L., Sorger, P.K., Drees, B.L., O'Rourke, S.M., Hughes, T.R., Roberts, C.J., Friend, S.H., Fields, S., and Murray, A.W. (1999). Genetic selection of peptide inhibitors of biological pathways. Science 285:591-5.
• 1997
  • Lingner, J., Cech, T.R., Hughes, T.R., and Lundblad, V. (1997). Three Ever Shorter Telomere (EST) genes are dispensable for in vitro yeast telomerase activity. Proc. Natl. Acad. Sci. U. S. A. 94:11190-5.
  • Lingner, J., Hughes, T.R., Shevchenko, A., Mann, M., Lundblad, V., and Cech, T.R. (1997). Reverse transcriptase motifs in the catalytic subunit of telomerase. Science 27:561-7.
• 1996
  • Nugent, C.I.*, Hughes, T.R.*, Lue, N.F., and Lundblad, V. (1996). Cdc13p: a single-strand telomeric DNA-binding protein with a dual role in yeast telomere maintenance. Science 274:249-52. (* indicates equal contribution)
• 1995
  • Maghsoudlou, S.S., Hughes, T.R., and Hornsby, P.J. (1995). Analysis of the distal 5' region of the human CYP17 gene. Genome 38:825-9.