Publications by authors named "Timothy R Hughes"

100Publications

Similarity regression predicts evolution of transcription factor sequence specificity.

Nat Genet 2019 06 27;51(6):981-989. Epub 2019 May 27.

Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/s41588-019-0411-1DOI Listing
June 2019

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

Nucleic Acids Res 2018 11;46(19):10514-10529

Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, School of Life Sciences, Peking University, Beijing 100871, China.

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https://academic.oup.com/nar/advance-article/doi/10.1093/nar
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http://dx.doi.org/10.1093/nar/gky836DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6212790PMC
November 2018

Motif models for RNA-binding proteins.

Curr Opin Struct Biol 2018 12 29;53:115-123. Epub 2018 Aug 29.

Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5T 3A1, Canada.

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http://dx.doi.org/10.1016/j.sbi.2018.08.001DOI Listing
December 2018

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

Fungal Biol 2018 06 1;122(6):570-582. Epub 2018 Mar 1.

Departamento de Bioquímica e Tecnologia Química, Instituto de Química, UNESP, Universidade Estadual Paulista, 14800-060, Araraquara, SP, Brazil. Electronic address:

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http://dx.doi.org/10.1016/j.funbio.2018.01.004DOI Listing
June 2018

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

J Biol Chem 2018 05 22;293(19):7344-7354. Epub 2018 Mar 22.

From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7,

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http://www.jbc.org/lookup/doi/10.1074/jbc.RA118.001785
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http://dx.doi.org/10.1074/jbc.RA118.001785DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5949999PMC
May 2018

The Human Transcription Factors.

Cell 2018 02;172(4):650-665

Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA; Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.01.029DOI Listing
February 2018

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

Structure 2018 01 21;26(1):85-95.e3. Epub 2017 Dec 21.

Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.str.2017.11.022DOI Listing
January 2018

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

J Immunol 2018 01 22;200(1):327-335. Epub 2017 Nov 22.

Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom; and

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http://www.jimmunol.org/lookup/doi/10.4049/jimmunol.1701238
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http://dx.doi.org/10.4049/jimmunol.1701238DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5739282PMC
January 2018

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

G3 (Bethesda) 2018 01 4;8(1):219-229. Epub 2018 Jan 4.

Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Ontario M5S 1A8, Canada

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http://dx.doi.org/10.1534/g3.117.300296DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5765350PMC
January 2018

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

Genome Biol 2017 09 6;18(1):167. Epub 2017 Sep 6.

Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.

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http://dx.doi.org/10.1186/s13059-017-1287-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5588721PMC
September 2017

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

Cancer Cell 2017 07;32(1):101-114.e8

Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2017.06.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5539779PMC
July 2017

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

Methods 2017 08 24;126:18-28. Epub 2017 Jun 24.

Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto M5S 2E4, Canada; Department of Electrical and Computer Engineering, University of Toronto, Toronto M5S 3G4, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2017.06.024DOI Listing
August 2017

Transcription factors read epigenetics.

Science 2017 05;356(6337):489-490

Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada.

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http://dx.doi.org/10.1126/science.aan2927DOI Listing
May 2017

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

Front Neurol 2017 7;8:78. Epub 2017 Mar 7.

Laboratorio de Fisiología Animal, Facultad de Ciencias, Departamento de Biología Celular, Genética y Fisiología, Instituto de Investigación Biomédica de Málaga (IBIMA), Universidad de Málaga , Málaga , Spain.

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http://dx.doi.org/10.3389/fneur.2017.00078DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5339270PMC
March 2017

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

Methods 2017 04 10;118-119:3-15. Epub 2016 Dec 10.

Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2016.12.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411283PMC
April 2017

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

Elife 2016 08 9;5. Epub 2016 Aug 9.

Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany.

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http://dx.doi.org/10.7554/eLife.16797DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4978528PMC
August 2016

Motif comparison based on similarity of binding affinity profiles.

Bioinformatics 2016 11 27;32(22):3504-3506. Epub 2016 Jul 27.

McGill University and Génome Québec Innovation Centre, Montreal, QC H3A 0G1, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btw489DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5181567PMC
November 2016

Complement Membrane Attack and Tumorigenesis: A SYSTEMS BIOLOGY APPROACH.

J Biol Chem 2016 07 19;291(29):14927-38. Epub 2016 May 19.

From the Complement Biology Group, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, Wales, United Kingdom

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http://dx.doi.org/10.1074/jbc.M115.708446DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4946912PMC
July 2016

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

J Neuroinflammation 2016 05 21;13(1):115. Epub 2016 May 21.

Departamento de Biología Celular, Genética y Fisiología, IBIMA, Facultad de Ciencias, Universidad de Málaga, Málaga, 29071, Spain.

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http://dx.doi.org/10.1186/s12974-016-0576-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4875702PMC
May 2016

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

Bone 2016 Mar 22;84:253-261. Epub 2015 Dec 22.

Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK; Arthritis Research UK Centre for Biomechanics and Bioengineering, Cardiff University, Cardiff, UK. Electronic address:

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http://dx.doi.org/10.1016/j.bone.2015.12.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4764651PMC
March 2016

Complementing the inflammasome.

Immunology 2016 Feb;147(2):152-64

Institute of Infection and Immunity, School of Medicine, University Hospital of Wales, Cardiff University, Cardiff, UK.

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http://dx.doi.org/10.1111/imm.12556DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4717242PMC
February 2016

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

Nat Biotechnol 2015 Dec 16;33(12):1242-1249. Epub 2015 Nov 16.

Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.

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http://dx.doi.org/10.1038/nbt.3343DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4871164PMC
December 2015

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

Nucleic Acids Res 2015 Oct 17;43(19):9147-57. Epub 2015 Sep 17.

Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto M5S 3E1, Canada Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada Department of Computer Science, University of Toronto, Toronto M5S 2E4, Canada

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http://dx.doi.org/10.1093/nar/gkv919DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4627083PMC
October 2015

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

PLoS Pathog 2015 Jun 11;11(6):e1004967. Epub 2015 Jun 11.

Beijing Nuclear Magnetic Resonance Center, School of Life Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.

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http://dx.doi.org/10.1371/journal.ppat.1004967DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4466236PMC
June 2015

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

J Immunol 2015 Jul 22;195(1):96-104. Epub 2015 May 22.

Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, Wales, United Kingdom; and

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http://dx.doi.org/10.4049/jimmunol.1402961DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4472944PMC
July 2015

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

Bioinformatics 2015 Sep 6;31(17):2879-81. Epub 2015 May 6.

Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada, Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada and Canadian Institute for Advanced Research, Toronto, ON, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btv284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547615PMC
September 2015

C2H2 zinc finger proteins greatly expand the human regulatory lexicon.

Nat Biotechnol 2015 May 18;33(5):555-62. Epub 2015 Feb 18.

1] Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada. [2] Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. [3] Canadian Institutes for Advanced Research, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/nbt.3128DOI Listing
May 2015

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

Science 2015 Jan 18;347(6218):1254806. Epub 2014 Dec 18.

Department of Electrical and Computer Engineering, University of Toronto, Toronto, Ontario M5S 3G4, Canada. Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada. Program on Genetic Networks and Program on Neural Computation & Adaptive Perception, Canadian Institute for Advanced Research, Toronto, Ontario M5G 1Z8, Canada. Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada. McLaughlin Centre, University of Toronto, Toronto, Ontario M5G 0A4, Canada. Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada. eScience Group, Microsoft Research, Redmond, WA 98052, USA.

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http://dx.doi.org/10.1126/science.1254806DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4362528PMC
January 2015

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

PLoS One 2014 29;9(10):e110479. Epub 2014 Oct 29.

Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0110479PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4212969PMC
June 2015

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

Mol Cell 2014 Jun 5;54(6):946-59. Epub 2014 Jun 5.

FAS Center for Systems Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2014.05.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4096705PMC
June 2014

A novel C2H2 transcription factor that regulates gliA expression interdependently with GliZ in Aspergillus fumigatus.

PLoS Genet 2014 May 1;10(5):e1004336. Epub 2014 May 1.

The University of Texas Graduate School of Biomedical Sciences at Houston, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America; Microbiology and Molecular Genetics, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America; Program in Genes and Development, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1004336DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4006717PMC
May 2014

Identifying mRNA sequence elements for target recognition by human Argonaute proteins.

Genome Res 2014 May 24;24(5):775-85. Epub 2014 Mar 24.

Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada;

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http://dx.doi.org/10.1101/gr.162230.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009607PMC
May 2014

Paralogs hnRNP L and hnRNP LL exhibit overlapping but distinct RNA binding constraints.

PLoS One 2013 11;8(11):e80701. Epub 2013 Nov 11.

Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0080701PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3823766PMC
February 2015

Early evolution of the T-box transcription factor family.

Proc Natl Acad Sci U S A 2013 Oct 16;110(40):16050-5. Epub 2013 Sep 16.

Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), 08003 Barcelona, Spain.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791752PMC
http://dx.doi.org/10.1073/pnas.1309748110DOI Listing
October 2013

Mapping yeast transcriptional networks.

Genetics 2013 Sep;195(1):9-36

Banting and Best Department of Medical Research and Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada.

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http://dx.doi.org/10.1534/genetics.113.153262DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3761317PMC
September 2013

A compendium of nucleosome and transcript profiles reveals determinants of chromatin architecture and transcription.

PLoS Genet 2013 May 2;9(5):e1003479. Epub 2013 May 2.

Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1003479DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3642058PMC
May 2013

The complement membrane attack complex triggers intracellular Ca2+ fluxes leading to NLRP3 inflammasome activation.

J Cell Sci 2013 Jul 23;126(Pt 13):2903-13. Epub 2013 Apr 23.

Institute of Infection and Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK.

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http://dx.doi.org/10.1242/jcs.124388DOI Listing
July 2013

Distribution and determinants of circulating complement factor H concentration determined by a high-throughput immunonephelometric assay.

J Immunol Methods 2013 Apr 30;390(1-2):63-73. Epub 2013 Jan 30.

Centre for Clinical Pharmacology, Division of Medicine, University College London, Rayne Building, 5 University Street, London, WC1E 6JJ, UK.

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http://dx.doi.org/10.1016/j.jim.2013.01.009DOI Listing
April 2013

C3-dependent mechanism of microglial priming relevant to multiple sclerosis.

Proc Natl Acad Sci U S A 2012 Jan 4;109(3):965-70. Epub 2012 Jan 4.

Department of Infection, Immunity, and Biochemistry, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom.

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http://dx.doi.org/10.1073/pnas.1111924109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3271873PMC
January 2012

YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities.

Nucleic Acids Res 2012 Jan 18;40(Database issue):D169-79. Epub 2011 Nov 18.

Department of Molecular Genetics, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada.

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http://dx.doi.org/10.1093/nar/gkr993DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245003PMC
January 2012

The draft genome and transcriptome of Cannabis sativa.

Genome Biol 2011 Oct 20;12(10):R102. Epub 2011 Oct 20.

Banting and Best Department of Medical Research and Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada.

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http://dx.doi.org/10.1186/gb-2011-12-10-r102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3359589PMC
October 2011

CD55 deficiency protects against atherosclerosis in ApoE-deficient mice via C3a modulation of lipid metabolism.

Am J Pathol 2011 Oct 2;179(4):1601-7. Epub 2011 Aug 2.

Complement Biology Group, Department of Infection, Immunity and Biochemistry, School of Medicine, Cardiff University, Cardiff, United Kingdom.

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http://dx.doi.org/10.1016/j.ajpath.2011.06.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3181373PMC
October 2011

BzpF is a CREB-like transcription factor that regulates spore maturation and stability in Dictyostelium.

Dev Biol 2011 Oct 23;358(1):137-46. Epub 2011 Jul 23.

Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.

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http://dx.doi.org/10.1016/j.ydbio.2011.07.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3180911PMC
October 2011

Structural basis for recognition of AT-rich DNA by unrelated xenogeneic silencing proteins.

Proc Natl Acad Sci U S A 2011 Jun 14;108(26):10690-5. Epub 2011 Jun 14.

Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8.

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http://dx.doi.org/10.1073/pnas.1102544108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3127928PMC
June 2011

Sequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays.

Nucleic Acids Res 2011 Jun 14;39(11):4680-90. Epub 2011 Feb 14.

Department of Molecular Genetics and Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada.

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http://dx.doi.org/10.1093/nar/gkq1303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3113560PMC
June 2011

Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology.

Genome Biol 2010 30;11(11):140. Epub 2010 Nov 30.

Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel.

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http://dx.doi.org/10.1186/gb-2010-11-11-140DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3156944PMC
June 2011

RBPDB: a database of RNA-binding specificities.

Nucleic Acids Res 2011 Jan 29;39(Database issue):D301-8. Epub 2010 Oct 29.

Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada.

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http://dx.doi.org/10.1093/nar/gkq1069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013675PMC
January 2011

Information propagation within the Genetic Network of Saccharomyces cerevisiae.

BMC Syst Biol 2010 Oct 26;4:143. Epub 2010 Oct 26.

Laboratory of Biosystem Dynamics, Computational Systems Biology Research Group, Tampere University of Technology, Tampere, Finland.

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http://dx.doi.org/10.1186/1752-0509-4-143DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2975643PMC
October 2010

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).

Mol Immunol 2010 Oct 9;47(16):2545-51. Epub 2010 Aug 9.

Department of Pharmacology, Oncology & Radiology, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK.

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http://dx.doi.org/10.1016/j.molimm.2010.07.002DOI Listing
October 2010

RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins.

PLoS Comput Biol 2010 Jul 1;6:e1000832. Epub 2010 Jul 1.

Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1371/journal.pcbi.1000832DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2895634PMC
July 2010

Dramatic changes in transcription factor binding over evolutionary time.

Genome Biol 2010 1;11(6):122. Epub 2010 Jun 1.

Banting and Best Department of Medical Research and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada.

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http://dx.doi.org/10.1186/gb-2010-11-6-122DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2911098PMC
November 2010

Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo.

EMBO J 2010 Jul 1;29(13):2147-60. Epub 2010 Jun 1.

Public Health Genomics Unit, National Institute for Health and Welfare (THL) and Genome-Scale Biology Program, Institute of Biomedicine and High Throughput Center, University of Helsinki, Biomedicum, Helsinki, Finland.

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http://dx.doi.org/10.1038/emboj.2010.106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2905244PMC
July 2010

Most "dark matter" transcripts are associated with known genes.

PLoS Biol 2010 May 18;8(5):e1000371. Epub 2010 May 18.

Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1371/journal.pbio.1000371DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872640PMC
May 2010

FuncBase: a resource for quantitative gene function annotation.

Bioinformatics 2010 Jul 21;26(14):1806-7. Epub 2010 May 21.

Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1093/bioinformatics/btq265DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2894510PMC
July 2010

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities.

Genome Res 2010 Jun 8;20(6):861-73. Epub 2010 Apr 8.

Department of Molecular Medicine, National Public Health Institute (KTL) and Genome-Scale Biology Program, Institute of Biomedicine and High Throughput Center, University of Helsinki, Biomedicum, Helsinki, Finland.

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http://dx.doi.org/10.1101/gr.100552.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877582PMC
June 2010

Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same.

Trends Genet 2010 Feb 18;26(2):66-74. Epub 2010 Jan 18.

Banting and Best Department of Medical Research and Donnelly Centre for Cellular and Biomolecular Research, Ontario, Canada.

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http://dx.doi.org/10.1016/j.tig.2009.12.002DOI Listing
February 2010

Conservation and regulatory associations of a wide affinity range of mouse transcription factor binding sites.

Genomics 2010 Apr 15;95(4):185-95. Epub 2010 Jan 15.

Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1016/j.ygeno.2010.01.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848887PMC
April 2010

G+C content dominates intrinsic nucleosome occupancy.

BMC Bioinformatics 2009 Dec 22;10:442. Epub 2009 Dec 22.

Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.

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http://dx.doi.org/10.1186/1471-2105-10-442DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808325PMC
December 2009

The membrane attack complex of complement drives the progression of atherosclerosis in apolipoprotein E knockout mice.

Mol Immunol 2010 Feb 2;47(5):1098-105. Epub 2009 Dec 2.

Department of Medical Biochemistry and Immunology, School of Medicine, Cardiff University, Cardiff, UK.

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http://linkinghub.elsevier.com/retrieve/pii/S016158900900808
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http://dx.doi.org/10.1016/j.molimm.2009.10.035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862291PMC
February 2010

Establishing legitimacy and function in the new transcriptome.

Brief Funct Genomic Proteomic 2009 Nov;8(6):424-36

Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada.

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http://dx.doi.org/10.1093/bfgp/elp037DOI Listing
November 2009

A systematic characterization of Cwc21, the yeast ortholog of the human spliceosomal protein SRm300.

RNA 2009 Dec 29;15(12):2174-85. Epub 2009 Sep 29.

Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.

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http://dx.doi.org/10.1261/rna.1790509DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779666PMC
December 2009

Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins.

Nat Biotechnol 2009 Jul 28;27(7):667-70. Epub 2009 Jun 28.

Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/nbt.1550DOI Listing
July 2009

Conservation of core gene expression in vertebrate tissues.

J Biol 2009 16;8(3):33. Epub 2009 Apr 16.

Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1186/jbiol130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689434PMC
October 2009