Timothy Hughes - Publications

Affiliations: 
University of Oslo, Oslo, Oslo, Norway 
Website:
http://ous-research.no/hughes/

103 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2015 Hughes T, Hansson L, Sønderby IE, Athanasiu L, Zuber V, Tesli M, Song J, Hultman CM, Bergen SE, Landén M, Melle I, Andreassen OA, Djurovic S. A Loss-of-Function Variant in a Minor Isoform of ANK3 Protects Against Bipolar Disorder and Schizophrenia. Biological Psychiatry. PMID 26682468 DOI: 10.1016/j.biopsych.2015.09.021  0.92
2015 Pelossof R, Singh I, Yang JL, Weirauch MT, Hughes TR, Leslie CS. Affinity regression predicts the recognition code of nucleic acid-binding proteins. Nature Biotechnology. PMID 26571099 DOI: 10.1038/nbt.3343  0.92
2015 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. The Crystal Structure of the NHL Domain in Complex with RNA Reveals the Molecular Basis of Drosophila Brain-Tumor-Mediated Gene Regulation. Cell Reports. PMID 26527002 DOI: 10.1016/j.celrep.2015.09.068  0.92
2015 Garton M, Najafabadi HS, Schmitges FW, Radovani E, Hughes TR, Kim PM. A structural approach reveals how neighbouring C2H2 zinc fingers influence DNA binding specificity. Nucleic Acids Research. 43: 9147-57. PMID 26384429 DOI: 10.1093/nar/gkv919  0.92
2015 Ding P, McFarland KA, Jin S, Tong G, Duan B, Yang A, Hughes TR, Liu J, Dove SL, Navarre WW, Xia B. A Novel AT-Rich DNA Recognition Mechanism for Bacterial Xenogeneic Silencer MvaT. Plos Pathogens. 11: e1004967. PMID 26068099 DOI: 10.1371/journal.ppat.1004967  0.92
2015 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, et al. 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. PMID 25962635 DOI: 10.1186/s13059-015-0659-4  0.92
2015 Najafabadi HS, Albu M, Hughes TR. Identification of C2H2-ZF binding preferences from ChIP-seq data using RCADE. Bioinformatics (Oxford, England). 31: 2879-81. PMID 25953800 DOI: 10.1093/bioinformatics/btv284  0.92
2015 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. Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities. Elife. 4. PMID 25905672 DOI: 10.7554/eLife.06967  0.92
2015 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. C2H2 zinc finger proteins greatly expand the human regulatory lexicon. Nature Biotechnology. 33: 555-62. PMID 25690854 DOI: 10.1038/nbt.3128  0.92
2015 Ramaglia V, Jackson SJ, Hughes TR, Neal JW, Baker D, Morgan BP. Complement activation and expression during chronic relapsing experimental autoimmune encephalomyelitis in the Biozzi ABH mouse. Clinical and Experimental Immunology. 180: 432-41. PMID 25619542 DOI: 10.1111/cei.12595  0.92
2015 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, et al. RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease. Science (New York, N.Y.). 347: 1254806. PMID 25525159 DOI: 10.1126/science.1254806  0.92
2015 Cook KB, Hughes TR, Morris QD. High-throughput characterization of protein-RNA interactions. Briefings in Functional Genomics. 14: 74-89. PMID 25504152 DOI: 10.1093/bfgp/elu047  0.92
2014 de Boer CG, Hughes TR. Poly-dA:dT tracts form an in vivo nucleosomal turnstile. Plos One. 9: e110479. PMID 25353956 DOI: 10.1371/journal.pone.0110479  0.92
2014 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, ... ... Hughes TR, et al. Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana. Cell Reports. 8: 2015-30. PMID 25220462 DOI: 10.1016/j.celrep.2014.08.019  0.92
2014 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, ... ... Hughes TR, et al. Determination and inference of eukaryotic transcription factor sequence specificity. Cell. 158: 1431-43. PMID 25215497 DOI: 10.1016/j.cell.2014.08.009  0.92
2014 Norris AD, Gao S, Norris ML, Ray D, Ramani AK, Fraser AG, Morris Q, Hughes TR, Zhen M, Calarco JA. A pair of RNA-binding proteins controls networks of splicing events contributing to specialization of neural cell types. Molecular Cell. 54: 946-59. PMID 24910101 DOI: 10.1016/j.molcel.2014.05.004  0.92
2014 Schoberle TJ, Nguyen-Coleman CK, Herold J, Yang A, Weirauch M, Hughes TR, McMurray JS, May GS. A Novel C2H2 Transcription Factor that Regulates gliA Expression Interdependently with GliZ in Aspergillus fumigatus Plos Genetics. 10. PMID 24784729 DOI: 10.1371/journal.pgen.1004336  0.92
2014 Steiner T, Francescut L, Byrne S, Hughes T, Jayanthi A, Guschina I, Harwood J, Cianflone K, Stover C, Francis S. Protective role for properdin in progression of experimental murine atherosclerosis. Plos One. 9: e92404. PMID 24667818 DOI: 10.1371/journal.pone.0092404  0.92
2014 Li J, Kim T, Nutiu R, Ray D, Hughes TR, Zhang Z. Identifying mRNA sequence elements for target recognition by human Argonaute proteins. Genome Research. 24: 775-85. PMID 24663241 DOI: 10.1101/gr.162230.113  0.92
2014 de Boer CG, van Bakel H, Tsui K, Li J, Morris QD, Nislow C, Greenblatt JF, Hughes TR. A unified model for yeast transcript definition. Genome Research. 24: 154-66. PMID 24170600 DOI: 10.1101/gr.164327.113  0.92
2013 Smith SA, Ray D, Cook KB, Mallory MJ, Hughes TR, Lynch KW. Paralogs hnRNP L and hnRNP LL exhibit overlapping but distinct RNA binding constraints. Plos One. 8: e80701. PMID 24244709 DOI: 10.1371/journal.pone.0080701  0.92
2013 Sivasankar B, Hughes TR, Morgan BP, Gray LC, Van Den Berg CW. Retraction: Modulation of CD59 expression by restrictive silencer factor-derived peptides in cancer immunotherapy for neuroblastoma (Cancer Research (2008) 68, (5979-5987)) Cancer Research. 73: 6839. PMID 24204029 DOI: 10.1158/0008-5472.CAN-13-2936  0.92
2013 Cole DS, Sivasankar B, Hughes TR, Morgan BP. Retraction: P53 regulates cellular resistance to complement lysis through enhanced expression of CD59 (Cancer Research (2006) 66, (2451-2458)) Cancer Research. 73: 6838. PMID 24204028 DOI: 10.1158/0008-5472.CAN-13-2935  0.92
2013 Sebé-Pedrós A, Ariza-Cosano A, Weirauch MT, Leininger S, Yang A, Torruella G, Adamski M, Adamska M, Hughes TR, Gómez-Skarmeta JL, Ruiz-Trillo I. Early evolution of the T-box transcription factor family. Proceedings of the National Academy of Sciences of the United States of America. 110: 16050-5. PMID 24043797 DOI: 10.1073/pnas.1309748110  0.92
2013 Hughes TR, de Boer CG. Mapping yeast transcriptional networks. Genetics. 195: 9-36. PMID 24018767 DOI: 10.1534/genetics.113.153262  0.92
2013 Ray D, Kazan H, Cook KB, Weirauch MT, Najafabadi HS, Li X, Gueroussov S, Albu M, Zheng H, Yang A, Na H, Irimia M, Matzat LH, Dale RK, Smith SA, ... ... Hughes TR, et al. A compendium of RNA-binding motifs for decoding gene regulation. Nature. 499: 172-7. PMID 23846655 DOI: 10.1038/nature12311  0.92
2013 Laudisi F, Spreafico R, Evrard M, Hughes TR, Mandriani B, Kandasamy M, Morgan BP, Sivasankar B, Mortellaro A. Cutting edge: the NLRP3 inflammasome links complement-mediated inflammation and IL-1β release. Journal of Immunology (Baltimore, Md. : 1950). 191: 1006-10. PMID 23817414 DOI: 10.4049/jimmunol.1300489  0.92
2013 Chang KN, Zhong S, Weirauch MT, Hon G, Pelizzola M, Li H, Huang SS, Schmitz RJ, Urich MA, Kuo D, Nery JR, Qiao H, Yang A, Jamali A, Chen H, ... ... Hughes TR, et al. Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis. Elife. 2: e00675. PMID 23795294 DOI: 10.7554/eLife.00675  0.92
2013 Reece-Hoyes JS, Pons C, Diallo A, Mori A, Shrestha S, Kadreppa S, Nelson J, Diprima S, Dricot A, Lajoie BR, Ribeiro PS, Weirauch MT, Hill DE, Hughes TR, Myers CL, et al. Extensive rewiring and complex evolutionary dynamics in a C. elegans multiparameter transcription factor network. Molecular Cell. 51: 116-27. PMID 23791784 DOI: 10.1016/j.molcel.2013.05.018  0.92
2013 van Bakel H, Tsui K, Gebbia M, Mnaimneh S, Hughes TR, Nislow C. A compendium of nucleosome and transcript profiles reveals determinants of chromatin architecture and transcription. Plos Genetics. 9: e1003479. PMID 23658529 DOI: 10.1371/journal.pgen.1003479  0.92
2013 Triantafilou K, Hughes TR, Triantafilou M, Morgan BP. The complement membrane attack complex triggers intracellular Ca2+ fluxes leading to NLRP3 inflammasome activation. Journal of Cell Science. 126: 2903-13. PMID 23613465 DOI: 10.1242/jcs.124388  0.92
2013 Mann IK, Chatterjee R, Zhao J, He X, Weirauch MT, Hughes TR, Vinson C. CG methylated microarrays identify a novel methylated sequence bound by the CEBPB|ATF4 heterodimer that is active in vivo. Genome Research. 23: 988-97. PMID 23590861 DOI: 10.1101/gr.146654.112  0.92
2013 Sofat R, Mangione PP, Gallimore JR, Hakobyan S, Hughes TR, Shah T, Goodship T, D'Aiuto F, Langenberg C, Wareham N, Morgan BP, Pepys MB, Hingorani AD. Distribution and determinants of circulating complement factor H concentration determined by a high-throughput immunonephelometric assay. Journal of Immunological Methods. 390: 63-73. PMID 23376722 DOI: 10.1016/j.jim.2013.01.009  0.92
2013 Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S, Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, ... Hughes TR, et al. Evaluation of methods for modeling transcription factor sequence specificity. Nature Biotechnology. 31: 126-34. PMID 23354101 DOI: 10.1038/nbt.2486  0.92
2013 Jolma A, Yan J, Whitington T, Toivonen J, Nitta KR, Rastas P, Morgunova E, Enge M, Taipale M, Wei G, Palin K, Vaquerizas JM, Vincentelli R, Luscombe NM, Hughes TR, et al. DNA-binding specificities of human transcription factors. Cell. 152: 327-39. PMID 23332764 DOI: 10.1016/j.cell.2012.12.009  0.92
2013 Kandasamy M, Ying PC, Ho AW, Sumatoh HR, Schlitzer A, Hughes TR, Kemeny DM, Morgan BP, Ginhoux F, Sivasankar B. Complement mediated signaling on pulmonary CD103(+) dendritic cells is critical for their migratory function in response to influenza infection. Plos Pathogens. 9: e1003115. PMID 23326231 DOI: 10.1371/journal.ppat.1003115  0.92
2013 Killick R, Hughes TR, Morgan BP, Lovestone S. Deletion of Crry, the murine ortholog of the sporadic Alzheimer's disease risk gene CR1, impacts tau phosphorylation and brain CFH. Neuroscience Letters. 533: 96-9. PMID 23153828 DOI: 10.1016/j.neulet.2012.11.008  0.92
2013 Killick R, Hughes TR, Morgan BP, Lovestone S. Corrigendum to Deletion of Crry, the murine ortholog of the sporadic Alzheimer's disease risk gene CR1, impacts tau phosphorylation and brain CFH [Neurosci. Lett. 533 (2013) 96-99] Neuroscience Letters. 545: 144. DOI: 10.1016/j.neulet.2013.05.004  0.92
2012 Gilfillan GD, Hughes T, Sheng Y, Hjorthaug HS, Straub T, Gervin K, Harris JR, Undlien DE, Lyle R. Limitations and possibilities of low cell number ChIP-seq. Bmc Genomics. 13: 645. PMID 23171294 DOI: 10.1186/1471-2164-13-645  0.92
2012 Xu M, Soloveychik M, Ranger M, Schertzberg M, Shah Z, Raisner R, Venkatasubrahmanyan S, Tsui K, Gebbia M, Hughes T, van Bakel H, Nislow C, Madhani HD, Meneghini MD. Timing of transcriptional quiescence during gametogenesis is controlled by global histone H3K4 demethylation. Developmental Cell. 23: 1059-71. PMID 23123093 DOI: 10.1016/j.devcel.2012.10.005  0.92
2012 Hamfjord J, Stangeland AM, Hughes T, Skrede ML, Tveit KM, Ikdahl T, Kure EH. Differential expression of miRNAs in colorectal cancer: Comparison of paired tumor tissue and adjacent normal mucosa using high-throughput sequencing Plos One. 7. PMID 22529906 DOI: 10.1371/journal.pone.0034150  0.92
2012 Ramaglia V, Hughes TR, Donev RM, Ruseva MM, Wu X, Huitinga I, Baas F, Neal JW, Morgan BP. C3-dependent mechanism of microglial priming relevant to multiple sclerosis. Proceedings of the National Academy of Sciences of the United States of America. 109: 965-70. PMID 22219359 DOI: 10.1073/pnas.1111924109  0.92
2012 De Boer CG, Hughes TR. YeTFaSCo: A database of evaluated yeast transcription factor sequence specificities Nucleic Acids Research. 40: D169-D179. PMID 22102575 DOI: 10.1093/nar/gkr993  0.92
2012 Selmer KK, Gilfillan GD, Strømme P, Lyle R, Hughes T, Hjorthaug HS, Brandal K, Nakken S, Misceo D, Egeland T, Munthe LA, Braekken SK, Undlien DE. A mild form of Mucopolysaccharidosis IIIB diagnosed with targeted next-generation sequencing of linked genomic regions European Journal of Human Genetics. 20: 58-63. PMID 21712855 DOI: 10.1038/ejhg.2011.126  0.92
2011 van Bakel H, Stout JM, Cote AG, Tallon CM, Sharpe AG, Hughes TR, Page JE. The draft genome and transcriptome of Cannabis sativa. Genome Biology. 12: R102. PMID 22014239 DOI: 10.1186/gb-2011-12-10-r102  0.92
2011 Gabut M, Samavarchi-Tehrani P, Wang X, Slobodeniuc V, O'Hanlon D, Sung HK, Alvarez M, Talukder S, Pan Q, Mazzoni EO, Nedelec S, Wichterle H, Woltjen K, Hughes TR, Zandstra PW, et al. An alternative splicing switch regulates embryonic stem cell pluripotency and reprogramming. Cell. 147: 132-46. PMID 21924763 DOI: 10.1016/j.cell.2011.08.023  0.92
2011 Lewis RD, Perry MJ, Guschina IA, Jackson CL, Morgan BP, Hughes TR. CD55 deficiency protects against atherosclerosis in ApoE-deficient mice via C3a modulation of lipid metabolism. The American Journal of Pathology. 179: 1601-7. PMID 21816131 DOI: 10.1016/j.ajpath.2011.06.015  0.92
2011 Huang E, Talukder S, Hughes TR, Curk T, Zupan B, Shaulsky G, Katoh-Kurasawa M. BzpF is a CREB-like transcription factor that regulates spore maturation and stability in Dictyostelium. Developmental Biology. 358: 137-46. PMID 21810415 DOI: 10.1016/j.ydbio.2011.07.017  0.92
2011 Gordon BR, Li Y, Cote A, Weirauch MT, Ding P, Hughes TR, Navarre WW, Xia B, Liu J. Structural basis for recognition of AT-rich DNA by unrelated xenogeneic silencing proteins. Proceedings of the National Academy of Sciences of the United States of America. 108: 10690-5. PMID 21673140 DOI: 10.1073/pnas.1102544108  0.92
2011 Morris Q, Bulyk ML, Hughes TR. Jury remains out on simple models of transcription factor specificity. Nature Biotechnology. 29: 483-4. PMID 21654663 DOI: 10.1038/nbt.1892  0.92
2011 Lueck K, Wasmuth S, Williams J, Hughes TR, Morgan BP, Lommatzsch A, Greenwood J, Moss SE, Pauleikhoff D. Sub-lytic C5b-9 induces functional changes in retinal pigment epithelial cells consistent with age-related macular degeneration. Eye (London, England). 25: 1074-82. PMID 21597483 DOI: 10.1038/eye.2011.109  0.92
2011 Weirauch MT, Hughes TR. A catalogue of eukaryotic transcription factor types, their evolutionary origin, and species distribution. Sub-Cellular Biochemistry. 52: 25-73. PMID 21557078 DOI: 10.1007/978-90-481-9069-0_3  0.92
2011 Lam KN, van Bakel H, Cote AG, van der Ven A, Hughes TR. Sequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays. Nucleic Acids Research. 39: 4680-90. PMID 21321018 DOI: 10.1093/nar/gkq1303  0.92
2011 Stead MB, Marshburn S, Mohanty BK, Mitra J, Pena Castillo L, Ray D, van Bakel H, Hughes TR, Kushner SR. Analysis of Escherichia coli RNase E and RNase III activity in vivo using tiling microarrays. Nucleic Acids Research. 39: 3188-203. PMID 21149258 DOI: 10.1093/nar/gkq1242  0.92
2011 Cook KB, Kazan H, Zuberi K, Morris Q, Hughes TR. RBPDB: a database of RNA-binding specificities. Nucleic Acids Research. 39: D301-8. PMID 21036867 DOI: 10.1093/nar/gkq1069  0.92
2011 van Bakel H, Nislow C, Blencowe BJ, Hughes TR. Response to "The reality of pervasive transcription" Plos Biology. 9. DOI: 10.1371/journal.pbio.1001102  0.92
2011 Hughes TR. Introduction to “a handbook of transcription factors” Sub-Cellular Biochemistry. 52. DOI: 10.1007/978-90-481-9069-0_1  0.92
2010 Kaplan N, Hughes TR, Lieb JD, Widom J, Segal E. Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology. Genome Biology. 11: 140. PMID 21118582 DOI: 10.1186/gb-2010-11-11-140  0.92
2010 Chowdhury S, Lloyd-Price J, Smolander OP, Baici WCV, Hughes TR, Yli-Harja O, Chua G, Ribeiro AS. Information propagation within the Genetic Network of Saccharomyces cerevisiae Bmc Systems Biology. 4. PMID 20977725 DOI: 10.1186/1752-0509-4-143  0.92
2010 Santos MA, Turinsky AL, Ong S, Tsai J, Berger MF, Badis G, Talukder S, Gehrke AR, Bulyk ML, Hughes TR, Wodak SJ. Objective sequence-based subfamily classifications of mouse homeodomains reflect their in vitro DNA-binding preferences. Nucleic Acids Research. 38: 7927-42. PMID 20705649 DOI: 10.1093/nar/gkq714  0.92
2010 Gray LC, Hughes TR, Van den Berg CW. Binding of human antigen R (HuR) to an AU-rich element (ARE) in the 3′untranslated region (3′UTR) reduces the expression of decay accelerating factor (DAF) Molecular Immunology. 47: 2545-2551. PMID 20692039 DOI: 10.1016/j.molimm.2010.07.002  0.92
2010 Kaplan N, Moore I, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, Hughes TR, Lieb JD, Widom J, Segal E. Nucleosome sequence preferences influence in vivo nucleosome organization. Nature Structural & Molecular Biology. 17: 918-20; author reply. PMID 20683473 DOI: 10.1038/nsmb0810-918  0.92
2010 Kazan H, Ray D, Chan ET, Hughes TR, Morris Q. RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins. Plos Computational Biology. 6: e1000832. PMID 20617199 DOI: 10.1371/journal.pcbi.1000832  0.92
2010 Weirauch MT, Hughes TR. Dramatic changes in transcription factor binding over evolutionary time. Genome Biology. 11: 122. PMID 20519030 DOI: 10.1186/gb-2010-11-6-122  0.92
2010 Wei GH, Badis G, Berger MF, Kivioja T, Palin K, Enge M, Bonke M, Jolma A, Varjosalo M, Gehrke AR, Yan J, Talukder S, Turunen M, Taipale M, Stunnenberg HG, ... ... Hughes TR, et al. Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo. The Embo Journal. 29: 2147-60. PMID 20517297 DOI: 10.1038/emboj.2010.106  0.92
2010 van Bakel H, Nislow C, Blencowe BJ, Hughes TR. Most "dark matter" transcripts are associated with known genes. Plos Biology. 8: e1000371. PMID 20502517 DOI: 10.1371/journal.pbio.1000371  0.92
2010 Beaver JE, Tasan M, Gibbons FD, Tian W, Hughes TR, Roth FP. FuncBase: a resource for quantitative gene function annotation. Bioinformatics (Oxford, England). 26: 1806-7. PMID 20495000 DOI: 10.1093/bioinformatics/btq265  0.92
2010 Jolma A, Kivioja T, Toivonen J, Cheng L, Wei G, Enge M, Taipale M, Vaquerizas JM, Yan J, Sillanpää MJ, Bonke M, Palin K, Talukder S, Hughes TR, Luscombe NM, et al. Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Research. 20: 861-73. PMID 20378718 DOI: 10.1101/gr.100552.109  0.92
2010 Tillo D, Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Field Y, Lieb JD, Widom J, Segal E, Hughes TR. High nucleosome occupancy is encoded at human regulatory sequences. Plos One. 5: e9129. PMID 20161746 DOI: 10.1371/journal.pone.0009129  0.92
2010 Weirauch MT, Hughes TR. Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same. Trends in Genetics : Tig. 26: 66-74. PMID 20083321 DOI: 10.1016/j.tig.2009.12.002  0.92
2010 Jaeger SA, Chan ET, Berger MF, Stottmann R, Hughes TR, Bulyk ML. Conservation and regulatory associations of a wide affinity range of mouse transcription factor binding sites. Genomics. 95: 185-95. PMID 20079828 DOI: 10.1016/j.ygeno.2010.01.002  0.92
2010 Copland DA, Hussain K, Baalasubramanian S, Hughes TR, Morgan BP, Xu H, Dick AD, Nicholson LB. Systemic and local anti-C5 therapy reduces the disease severity in experimental autoimmune uveoretinitis. Clinical and Experimental Immunology. 159: 303-14. PMID 20002447 DOI: 10.1111/j.1365-2249.2009.04070.x  0.92
2010 Lewis RD, Jackson CL, Morgan BP, Hughes TR. The membrane attack complex of complement drives the progression of atherosclerosis in apolipoprotein E knockout mice. Molecular Immunology. 47: 1098-105. PMID 19959238 DOI: 10.1016/j.molimm.2009.10.035  0.92
2010 Gould CM, Diella F, Via A, Puntervoll P, Gemünd C, Chabanis-Davidson S, Michael S, Sayadi A, Bryne JC, Chica C, Seiler M, Davey NE, Haslam N, Weatheritt RJ, Budd A, ... Hughes T, et al. ELM: the status of the 2010 eukaryotic linear motif resource. Nucleic Acids Research. 38: D167-80. PMID 19920119 DOI: 10.1093/nar/gkp1016  0.92
2009 Tillo D, Hughes TR. G+C content dominates intrinsic nucleosome occupancy Bmc Bioinformatics. 10. PMID 20028554 DOI: 10.1186/1471-2105-10-442  0.92
2009 van Bakel H, Hughes TR. Establishing legitimacy and function in the new transcriptome Briefings in Functional Genomics and Proteomics. 8: 424-436. PMID 19833698 DOI: 10.1093/bfgp/elp037  0.92
2009 Khanna M, Van Bakel H, Tang X, Calarco JA, Babak T, Guo G, Emili A, Greenblatt JF, Hughes TR, Krogan NJ, Blencowe BJ. A systematic characterization of Cwc21, the yeast ortholog of the human spliceosomal protein SRm300. Rna (New York, N.Y.). 15: 2174-85. PMID 19789211 DOI: 10.1261/rna.1790509  0.92
2009 Fillingham J, Kainth P, Lambert JP, van Bakel H, Tsui K, Peña-Castillo L, Nislow C, Figeys D, Hughes TR, Greenblatt J, Andrews BJ. Two-color cell array screen reveals interdependent roles for histone chaperones and a chromatin boundary regulator in histone gene repression. Molecular Cell. 35: 340-51. PMID 19683497 DOI: 10.1016/j.molcel.2009.06.023  0.92
2009 Ray D, Kazan H, Chan ET, Peña Castillo L, Chaudhry S, Talukder S, Blencowe BJ, Morris Q, Hughes TR. Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins. Nature Biotechnology. 27: 667-70. PMID 19561594 DOI: 10.1038/nbt.1550  0.92
2009 Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, Chan ET, Metzler G, Vedenko A, Chen X, Kuznetsov H, Wang CF, Coburn D, Newburger DE, Morris Q, ... Hughes TR, et al. Diversity and complexity in DNA recognition by transcription factors. Science (New York, N.Y.). 324: 1720-3. PMID 19443739 DOI: 10.1126/science.1162327  0.92
2009 Chan ET, Quon GT, Chua G, Babak T, Trochesset M, Zirngibl RA, Aubin J, Ratcliffe MJ, Wilde A, Brudno M, Morris QD, Hughes TR. Conservation of core gene expression in vertebrate tissues. Journal of Biology. 8: 33. PMID 19371447 DOI: 10.1186/jbiol130  0.92
2009 Fulton DL, Sundararajan S, Badis G, Hughes TR, Wasserman WW, Roach JC, Sladek R. TFCat: the curated catalog of mouse and human transcription factors. Genome Biology. 10: R29. PMID 19284633 DOI: 10.1186/gb-2009-10-3-r29  0.92
2009 Kainth P, Sassi HE, Peña-Castillo L, Chua G, Hughes TR, Andrews B. Comprehensive genetic analysis of transcription factor pathways using a dual reporter gene system in budding yeast. Methods (San Diego, Calif.). 48: 258-64. PMID 19269327 DOI: 10.1016/j.ymeth.2009.02.015  0.92
2009 Coughlin DJ, Babak T, Nihranz C, Hughes TR, Engelke DR. Prediction and verification of mouse tRNA gene families Rna Biology. 6. PMID 19246989  0.92
2009 Hughes TR. 'Validation' in genome-scale research Journal of Biology. 8. PMID 19222867 DOI: 10.1186/jbiol104  0.92
2009 Blencowe B, Brenner S, Hughes T, Morris Q. Post-transcriptional gene regulation: RNA-protein interactions, RNA processing, mRNA stability and localization. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 545-8. PMID 19209730  0.92
2009 Hughes TR, Ross KS, Cowan GJ, Sivasankar B, Harris CL, Mitchell TJ, Morgan BP. Identification of the high affinity binding site in the Streptococcus intermedius toxin intermedilysin for its membrane receptor, the human complement regulator CD59. Molecular Immunology. 46: 1561-7. PMID 19200600 DOI: 10.1016/j.molimm.2009.01.003  0.92
2009 Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, LeProust EM, Hughes TR, Lieb JD, Widom J, Segal E. The DNA-encoded nucleosome organization of a eukaryotic genome. Nature. 458: 362-6. PMID 19092803 DOI: 10.1038/nature07667  0.92
2009 Alleyne TM, Peña-Castillo L, Badis G, Talukder S, Berger MF, Gehrke AR, Philippakis AA, Bulyk ML, Morris QD, Hughes TR. Predicting the binding preference of transcription factors to individual DNA k-mers. Bioinformatics (Oxford, England). 25: 1012-8. PMID 19088121 DOI: 10.1093/bioinformatics/btn645  0.92
2009 Ruseva MM, Hughes TR, Donev RM, Sivasankar B, Pickering MC, Wu X, Harris CL, Morgan BP. Crry deficiency in complement sufficient mice: C3 consumption occurs without associated renal injury. Molecular Immunology. 46: 803-11. PMID 18947875 DOI: 10.1016/j.molimm.2008.09.003  0.92
2009 Quon G, Teh YW, Chan E, Hughes T, Brudno M, Morris Q. A mixture model for the evolution of gene expression in non-homogeneous datasets Advances in Neural Information Processing Systems 21 - Proceedings of the 2008 Conference. 1297-1304.  0.92
2008 Badis G, Chan ET, van Bakel H, Pena-Castillo L, Tillo D, Tsui K, Carlson CD, Gossett AJ, Hasinoff MJ, Warren CL, Gebbia M, Talukder S, Yang A, Mnaimneh S, Terterov D, ... ... Hughes TR, et al. A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Molecular Cell. 32: 878-87. PMID 19111667 DOI: 10.1016/j.molcel.2008.11.020  0.92
2008 Cheung V, Chua G, Batada NN, Landry CR, Michnick SW, Hughes TR, Winston F. Chromatin- and transcription-related factors repress transcription from within coding regions throughout the Saccharomyces cerevisiae genome. Plos Biology. 6: e277. PMID 18998772 DOI: 10.1371/journal.pbio.0060277  0.92
2008 Hughes T, Liberles DA. Whole-genome duplications in the ancestral vertebrate are detectable in the distribution of gene family sizes of tetrapod species. Journal of Molecular Evolution. 67: 343-57. PMID 18815825 DOI: 10.1007/s00239-008-9145-x  0.92
2008 Harris SM, Harvey EJ, Hughes TR, Ramji DP. The interferon-gamma-mediated inhibition of lipoprotein lipase gene transcription in macrophages involves casein kinase 2- and phosphoinositide-3-kinase-mediated regulation of transcription factors Sp1 and Sp3. Cellular Signalling. 20: 2296-301. PMID 18793716 DOI: 10.1016/j.cellsig.2008.08.016  0.92
2008 Donev RM, Gray LC, Sivasankar B, Hughes TR, van den Berg CW, Morgan BP. Modulation of CD59 expression by restrictive silencer factor-derived peptides in cancer immunotherapy for neuroblastoma. Cancer Research. 68: 5979-87. PMID 18632654 DOI: 10.1158/0008-5472.CAN-07-6828  0.92
2008 Willis IM, Chua G, Tong AH, Brost RL, Hughes TR, Boone C, Moir RD. Genetic interactions of MAF1 identify a role for Med20 in transcriptional repression of ribosomal protein genes. Plos Genetics. 4: e1000112. PMID 18604275 DOI: 10.1371/journal.pgen.1000112  0.92
2008 Lovegrove FE, Peña-Castillo L, Liles WC, Hughes TR, Kain KC. Plasmodium falciparum shows transcriptional versatility within the human host. Trends in Parasitology. 24: 288-91. PMID 18538633 DOI: 10.1016/j.pt.2008.04.004  0.92
2008 Rutherford JC, Chua G, Hughes T, Cardenas ME, Heitman J. A Mep2-dependent transcriptional profile links permease function to gene expression during pseudohyphal growth in Saccharomyces cerevisiae. Molecular Biology of the Cell. 19: 3028-39. PMID 18434596 DOI: 10.1091/mbc.E08-01-0033  0.92
2008 Hughes T, Liberles DA. The power-law distribution of gene family size is driven by the pseudogenisation rate's heterogeneity between gene families. Gene. 414: 85-94. PMID 18378100 DOI: 10.1016/j.gene.2008.02.014  0.92
2007 Hughes T, Liberles DA. The pattern of evolution of smaller-scale gene duplicates in mammalian genomes is more consistent with neo- than subfunctionalisation. Journal of Molecular Evolution. 65: 574-88. PMID 17957399 DOI: 10.1007/s00239-007-9041-9  0.92
2007 Hughes T, Ekman D, Ardawatia H, Elofsson A, Liberles DA. Evaluating dosage compensation as a cause of duplicate gene retention in Paramecium tetraurelia. Genome Biology. 8: 213. PMID 17521457 DOI: 10.1186/gb-2007-8-5-213  0.92
2004 Hughes T, Hyun Y, Liberles DA. Visualising very large phylogenetic trees in three dimensional hyperbolic space. Bmc Bioinformatics. 5: 48. PMID 15117420 DOI: 10.1186/1471-2105-5-48  0.92
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