Timothy L Bailey

Timothy L Bailey

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Timothy L Bailey

Timothy L Bailey

Publications by authors named "Timothy L Bailey"

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MoMo: discovery of statistically significant post-translational modification motifs.

Bioinformatics 2019 Aug;35(16):2774-2782

Department of Pharmacology, University of Nevada, Reno, NV, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty1058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6691336PMC
August 2019

Homodimerization regulates an endothelial specific signature of the SOX18 transcription factor.

Nucleic Acids Res 2018 11;46(21):11381-11395

EMBL Australia node in Single Molecule Science and School of Medical Sciences, The University of New South Wales, Sydney, NSW 2031, Australia.

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http://dx.doi.org/10.1093/nar/gky897DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6265484PMC
November 2018

Krüppel-like factors compete for promoters and enhancers to fine-tune transcription.

Nucleic Acids Res 2017 Jun;45(11):6572-6588

Mater Research Institute, Translational Research Institute, University of Queensland, Brisbane 4102, Australia.

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http://dx.doi.org/10.1093/nar/gkx441DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5499887PMC
June 2017

CisMapper: predicting regulatory interactions from transcription factor ChIP-seq data.

Nucleic Acids Res 2017 02;45(4):e19

Department of Pharmacology, University of Nevada School of Medicine, Reno, NV 89557-0357, USA.

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http://dx.doi.org/10.1093/nar/gkw956DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389714PMC
February 2017

MCAST: scanning for cis-regulatory motif clusters.

Bioinformatics 2016 04 24;32(8):1217-9. Epub 2015 Dec 24.

Department of Genome Sciences, University of Washington, Seattle, WA, USA, Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA.

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http://bioinformatics.oxfordjournals.org/content/early/2015/
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http://bioinformatics.oxfordjournals.org/content/early/2016/
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http://bioinformatics.oxfordjournals.org/lookup/doi/10.1093/
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http://dx.doi.org/10.1093/bioinformatics/btv750DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4907379PMC
April 2016

EMX1 regulates NRP1-mediated wiring of the mouse anterior cingulate cortex.

Development 2015 Nov;142(21):3746-57

The University of Queensland, Queensland Brain Institute, Brisbane 4072, Australia The University of Queensland, The School of Biomedical Sciences, Brisbane 4072, Australia

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http://dx.doi.org/10.1242/dev.119909DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4647209PMC
November 2015

Conservation analysis of sequences flanking the testis-determining gene Sry in 17 mammalian species.

BMC Dev Biol 2015 Oct 6;15:34. Epub 2015 Oct 6.

Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.

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http://dx.doi.org/10.1186/s12861-015-0085-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4595323PMC
October 2015

Expansion of the lateral ventricles and ependymal deficits underlie the hydrocephalus evident in mice lacking the transcription factor NFIX.

Brain Res 2015 Aug 7;1616:71-87. Epub 2015 May 7.

The School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia; Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.brainres.2015.04.057DOI Listing
August 2015

The MEME Suite.

Nucleic Acids Res 2015 Jul 7;43(W1):W39-49. Epub 2015 May 7.

Department of Genome Sciences, Department of Computer Science and Engineering, University of Washington, Seattle, WA 98109, USA

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http://dx.doi.org/10.1093/nar/gkv416DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489269PMC
July 2015

Creating and validating cis-regulatory maps of tissue-specific gene expression regulation.

Nucleic Acids Res 2014 8;42(17):11000-10. Epub 2014 Sep 8.

Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia

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http://dx.doi.org/10.1093/nar/gku801DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4176179PMC
February 2015

Motif-based analysis of large nucleotide data sets using MEME-ChIP.

Nat Protoc 2014 22;9(6):1428-50. Epub 2014 May 22.

Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.

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http://dx.doi.org/10.1038/nprot.2014.083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4175909PMC
December 2014

GT-Scan: identifying unique genomic targets.

Bioinformatics 2014 Sep 23;30(18):2673-5. Epub 2014 May 23.

Genomics and Computational Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld. 4072, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btu354DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155256PMC
September 2014

Differential motif enrichment analysis of paired ChIP-seq experiments.

BMC Genomics 2014 Sep 2;15:752. Epub 2014 Sep 2.

Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, 4072 Brisbane, Australia.

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http://dx.doi.org/10.1186/1471-2164-15-752DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4167127PMC
September 2014

Improving MEME via a two-tiered significance analysis.

Bioinformatics 2014 Jul 24;30(14):1965-73. Epub 2014 Mar 24.

School of Mathematics and Statistics, University of Sydney, Sydney 2006, School of Mathematics and Applied Statistics, University of Wollongong, Wollongong 2522, New South Wales and Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btu163DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4080741PMC
July 2014

Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts.

Genome Res 2014 Jun 5;24(6):999-1011. Epub 2014 Feb 5.

Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; Department of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, USA.

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http://dx.doi.org/10.1101/gr.160374.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4032863PMC
June 2014

Switching on sex: transcriptional regulation of the testis-determining gene Sry.

Development 2014 Jun;141(11):2195-205

Institute for Molecular Bioscience, The University of Queensland, Brisbane QLD 4072, Australia

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http://dx.doi.org/10.1242/dev.107052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034426PMC
June 2014

Predicting the dynamics of protein abundance.

Mol Cell Proteomics 2014 May 16;13(5):1330-40. Epub 2014 Feb 16.

Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia;

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http://dx.doi.org/10.1074/mcp.M113.033076DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4014288PMC
May 2014

An overlapping set of genes is regulated by both NFIB and the glucocorticoid receptor during lung maturation.

BMC Genomics 2014 Mar 25;15:231. Epub 2014 Mar 25.

Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia 4072, Australia.

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http://dx.doi.org/10.1186/1471-2164-15-231DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4023408PMC
March 2014

NFIB-mediated repression of the epigenetic factor Ezh2 regulates cortical development.

J Neurosci 2014 Feb;34(8):2921-30

Queensland Brain Institute, Institute for Molecular Bioscience, and The School of Biomedical Sciences, The University of Queensland, Brisbane, Australia 4069, QIMR Berghofer Medical Research Institute, Brisbane, Australia 4029, and Department of Biochemistry, Program in Genetics, Genomics and Bioinformatics, Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, New York 14203.

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http://dx.doi.org/10.1523/JNEUROSCI.2319-13.2014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3931505PMC
February 2014

Nuclear factor one X regulates Bobby sox during development of the mouse forebrain.

Cell Mol Neurobiol 2013 Oct 14;33(7):867-73. Epub 2013 Jul 14.

The School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.

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http://dx.doi.org/10.1007/s10571-013-9961-4DOI Listing
October 2013

Triplex-Inspector: an analysis tool for triplex-mediated targeting of genomic loci.

Bioinformatics 2013 Aug 5;29(15):1895-7. Epub 2013 Jun 5.

Division of Genomics and Computational Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btt315DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3712220PMC
August 2013

Defining the RGG/RG motif.

Mol Cell 2013 Jun;50(5):613-23

Terry Fox Molecular Oncology Group and Bloomfield Center for Research on Aging, Lady Davis Institute for Medical Research and Departments of Oncology and Medicine, McGill University, Montreal, Quebec H3T 1E2, Canada.

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http://dx.doi.org/10.1016/j.molcel.2013.05.021DOI Listing
June 2013

DLocalMotif: a discriminative approach for discovering local motifs in protein sequences.

Bioinformatics 2013 Jan 9;29(1):39-46. Epub 2012 Nov 9.

Institute for Molecular Bioscience, The University of Queensland, Australia.

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http://dx.doi.org/10.1093/bioinformatics/bts654DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6636396PMC
January 2013

Novel roles for KLF1 in erythropoiesis revealed by mRNA-seq.

Genome Res 2012 Dec 26;22(12):2385-98. Epub 2012 Jul 26.

Mater Medical Research Institute, Mater Hospital, Brisbane, Queensland 4101, Australia.

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http://dx.doi.org/10.1101/gr.135707.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514668PMC
December 2012

Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study.

BMC Bioinformatics 2012 Dec 13;13:331. Epub 2012 Dec 13.

School of Information and Electrical Engineering, China University of Mining and Technology, Xuzhou, JiangSu 221008, PR China.

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http://dx.doi.org/10.1186/1471-2105-13-331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3577497PMC
December 2012

Genome-wide in silico prediction of gene expression.

Bioinformatics 2012 Nov 6;28(21):2789-96. Epub 2012 Sep 6.

Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.

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http://dx.doi.org/10.1093/bioinformatics/bts529DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3476338PMC
November 2012

Expression of nuclear factor one A and -B in the olfactory bulb.

J Comp Neurol 2012 Oct;520(14):3135-49

The University of Maryland, Baltimore, School of Medicine, Baltimore, Maryland 21201-1559, USA.

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http://dx.doi.org/10.1002/cne.23081DOI Listing
October 2012

Inferring direct DNA binding from ChIP-seq.

Nucleic Acids Res 2012 Sep 18;40(17):e128. Epub 2012 May 18.

Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia.

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http://nar.oxfordjournals.org/content/early/2012/05/18/nar.g
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http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gks433
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http://dx.doi.org/10.1093/nar/gks433DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3458523PMC
September 2012

Triplexator: detecting nucleic acid triple helices in genomic and transcriptomic data.

Genome Res 2012 Jul 1;22(7):1372-81. Epub 2012 May 1.

Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072 QLD, Australia.

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http://dx.doi.org/10.1101/gr.130237.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3396377PMC
July 2012

Cyclic peptides arising by evolutionary parallelism via asparaginyl-endopeptidase-mediated biosynthesis.

Plant Cell 2012 Jul 20;24(7):2765-78. Epub 2012 Jul 20.

Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia.

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http://dx.doi.org/10.1105/tpc.112.099085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3426113PMC
July 2012

Potential in vivo roles of nucleic acid triple-helices.

RNA Biol 2011 May-Jun;8(3):427-39. Epub 2011 May 1.

Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD Australia.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218511PMC
http://dx.doi.org/10.4161/rna.8.3.14999DOI Listing
May 2012

Epigenetic priors for identifying active transcription factor binding sites.

Bioinformatics 2012 Jan 8;28(1):56-62. Epub 2011 Nov 8.

Institute for Molecular Bioscience, The University of Queensland, Brisbane QLD 4072, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btr614DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3244768PMC
January 2012

Tissue-specific prediction of directly regulated genes.

Bioinformatics 2011 Sep 30;27(17):2354-60. Epub 2011 Jun 30.

Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btr399DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3157924PMC
September 2011

Inferring transcription factor complexes from ChIP-seq data.

Nucleic Acids Res 2011 Aug 20;39(15):e98. Epub 2011 May 20.

Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.

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http://dx.doi.org/10.1093/nar/gkr341DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159476PMC
August 2011

Sorting the nuclear proteome.

Bioinformatics 2011 Jul;27(13):i7-14

Queensland Brain Institute, School of Chemistry and Molecular Biosciences, Queensland Facility for Advanced Bioinformatics, The University of Queensland, St Lucia, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btr217DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117375PMC
July 2011

MEME-ChIP: motif analysis of large DNA datasets.

Bioinformatics 2011 Jun 12;27(12):1696-7. Epub 2011 Apr 12.

Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btr189DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3106185PMC
June 2011

DREME: motif discovery in transcription factor ChIP-seq data.

Authors:
Timothy L Bailey

Bioinformatics 2011 Jun 4;27(12):1653-9. Epub 2011 May 4.

Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btr261DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3106199PMC
June 2011

A probabilistic model of nuclear import of proteins.

Bioinformatics 2011 May 3;27(9):1239-46. Epub 2011 Mar 3.

Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btr121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6559714PMC
May 2011

FIMO: scanning for occurrences of a given motif.

Bioinformatics 2011 Apr 16;27(7):1017-8. Epub 2011 Feb 16.

Department of Genome Sciences, University of Washington, Seattle, WA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3065696PMC
April 2011

Dual-functioning transcription factors in the developmental gene network of Drosophila melanogaster.

BMC Bioinformatics 2010 Jul 2;11:366. Epub 2010 Jul 2.

Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072 Australia.

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http://dx.doi.org/10.1186/1471-2105-11-366DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2912886PMC
July 2010

Assigning roles to DNA regulatory motifs using comparative genomics.

Bioinformatics 2010 Apr 10;26(7):860-6. Epub 2010 Feb 10.

Institute for Molecular Bioscience, The University of Queensland, Brisbane QLD 4072, Australia.

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http://bioinformatics.oxfordjournals.org/content/early/2010/
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http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
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http://dx.doi.org/10.1093/bioinformatics/btq049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2844991PMC
April 2010

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data.

BMC Bioinformatics 2010 Apr 1;11:165. Epub 2010 Apr 1.

Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.

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http://www.biomedcentral.com/1471-2105/11/165
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http://dx.doi.org/10.1186/1471-2105-11-165DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2868005PMC
April 2010

The value of position-specific priors in motif discovery using MEME.

BMC Bioinformatics 2010 Apr 9;11:179. Epub 2010 Apr 9.

Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia.

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http://dx.doi.org/10.1186/1471-2105-11-179DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2868008PMC
April 2010

A Bayesian network model of proteins' association with promyelocytic leukemia (PML) nuclear bodies.

J Comput Biol 2010 Apr;17(4):617-30

Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland, Australia.

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http://dx.doi.org/10.1089/cmb.2009.0140DOI Listing
April 2010

Optimizing static thermodynamic models of transcriptional regulation.

Bioinformatics 2009 Jul 27;25(13):1640-6. Epub 2009 Apr 27.

Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btp283DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732318PMC
July 2009

MEME SUITE: tools for motif discovery and searching.

Nucleic Acids Res 2009 Jul 20;37(Web Server issue):W202-8. Epub 2009 May 20.

Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.

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http://nar.oxfordjournals.org/content/37/suppl_2/W202.full.p
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http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkp335
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http://dx.doi.org/10.1093/nar/gkp335DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703892PMC
July 2009

Assessing phylogenetic motif models for predicting transcription factor binding sites.

Bioinformatics 2009 Jun;25(12):i339-47

Institute for Molecular Bioscience, University of Queensland, Qld, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btp201DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687955PMC
June 2009

High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.

Nucleic Acids Res 2009 Jan 6;37(1):14-25. Epub 2008 Nov 6.

Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.

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http://dx.doi.org/10.1093/nar/gkn866DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2662491PMC
January 2009

STREAM: Static Thermodynamic REgulAtory Model of transcription.

Bioinformatics 2008 Nov 6;24(21):2544-5. Epub 2008 Sep 6.

Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld. 4072, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btn467DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732279PMC
November 2008

Associating transcription factor-binding site motifs with target GO terms and target genes.

Nucleic Acids Res 2008 Jul 10;36(12):4108-17. Epub 2008 Jun 10.

Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.

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http://dx.doi.org/10.1093/nar/gkn374DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2475605PMC
July 2008

Discovering sequence motifs.

Authors:
Timothy L Bailey

Methods Mol Biol 2008 ;452:231-51

ARC Centre of Excellence in Bioinformatics, and Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.

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http://dx.doi.org/10.1007/978-1-60327-159-2_12DOI Listing
July 2008

Discovering sequence motifs with arbitrary insertions and deletions.

PLoS Comput Biol 2008 May 9;4(4):e1000071. Epub 2008 May 9.

Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.

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http://dx.doi.org/10.1371/journal.pcbi.1000071DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2323616PMC
May 2008

Studying the functional conservation of cis-regulatory modules and their transcriptional output.

BMC Bioinformatics 2008 Apr 29;9:220. Epub 2008 Apr 29.

Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld. 4072 Australia.

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http://dx.doi.org/10.1186/1471-2105-9-220DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2386823PMC
April 2008

Discovering sequence motifs.

Authors:
Timothy L Bailey

Methods Mol Biol 2007 ;395:271-92

IMB/University of Queensland.

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http://dx.doi.org/10.1007/978-1-59745-514-5_17DOI Listing
March 2008

Splicing bypasses 3' end formation signals to allow complex gene architectures.

Gene 2007 Nov 30;403(1-2):188-93. Epub 2007 Aug 30.

Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Centre (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.

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http://dx.doi.org/10.1016/j.gene.2007.08.012DOI Listing
November 2007

Discriminative motif discovery in DNA and protein sequences using the DEME algorithm.

BMC Bioinformatics 2007 Oct 15;8:385. Epub 2007 Oct 15.

Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld, 4072 Australia.

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http://dx.doi.org/10.1186/1471-2105-8-385DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2194741PMC
October 2007

Discrimination of non-protein-coding transcripts from protein-coding mRNA.

RNA Biol 2006 Jan-Mar;3(1):40-8. Epub 2006 Apr 3.

Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Kanagawa, Japan.

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http://dx.doi.org/10.4161/rna.3.1.2789DOI Listing
September 2007

Quantifying similarity between motifs.

Genome Biol 2007 ;8(2):R24

Department of Genome Sciences, University of Washington, 1705 NE Pacific Street, Box 355065, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1186/gb-2007-8-2-r24DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852410PMC
July 2007

Prediction of protein solvent profile using SVR.

Conf Proc IEEE Eng Med Biol Soc 2004 ;4:2889-92

Inst. of Molecular Biosci., Queensland Univ., Brisbane, Qld., Australia.

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http://dx.doi.org/10.1109/IEMBS.2004.1403822DOI Listing
June 2007

Identifying sequence regions undergoing conformational change via predicted continuum secondary structure.

Bioinformatics 2006 Aug 23;22(15):1809-14. Epub 2006 May 23.

School of Information Technology and Electrical Engineering, QLD 4072, The University of Queensland Australia.

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http://dx.doi.org/10.1093/bioinformatics/btl198DOI Listing
August 2006

MEME: discovering and analyzing DNA and protein sequence motifs.

Nucleic Acids Res 2006 Jul;34(Web Server issue):W369-73

Institute of Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia.

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http://dx.doi.org/10.1093/nar/gkl198DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538909PMC
July 2006

Pseudo-messenger RNA: phantoms of the transcriptome.

PLoS Genet 2006 Apr 28;2(4):e23. Epub 2006 Apr 28.

Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan.

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http://dx.doi.org/10.1371/journal.pgen.0020023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449882PMC
April 2006

The abundance of short proteins in the mammalian proteome.

PLoS Genet 2006 Apr 28;2(4):e52. Epub 2006 Apr 28.

Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan.

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http://dx.plos.org/10.1371/journal.pgen.0020052
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http://dx.doi.org/10.1371/journal.pgen.0020052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449894PMC
April 2006

Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures.

BMC Bioinformatics 2006 Feb 14;7:68. Epub 2006 Feb 14.

School of Information Technology and Electrical Engineering, The University of Queensland, QLD 4072, St Lucia, Australia.

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http://dx.doi.org/10.1186/1471-2105-7-68DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1386714PMC
February 2006

GONOME: measuring correlations between GO terms and genomic positions.

BMC Bioinformatics 2006 Feb 25;7:94. Epub 2006 Feb 25.

Institute for Molecular Bioscience, University of Queensland, Brisbane 4072, Australia.

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http://dx.doi.org/10.1186/1471-2105-7-94DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1413564PMC
February 2006

Prediction of protein B-factor profiles.

Proteins 2005 Mar;58(4):905-12

Institute for Molecular Bioscience and ARC Centre in Bioinformatics, The University of Queensland, St. Lucia, Australia.

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http://dx.doi.org/10.1002/prot.20375DOI Listing
March 2005

Searching for statistically significant regulatory modules.

Bioinformatics 2003 Oct;19 Suppl 2:ii16-25

Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btg1054DOI Listing
October 2003

Estimating and evaluating the statistics of gapped local-alignment scores.

J Comput Biol 2002 ;9(3):575-93

ACMC, Mathematics Department, The University of Queensland, Brisbane, Queensland, 4072 Australia.

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http://dx.doi.org/10.1089/106652702760138637DOI Listing
January 2003

Discovering novel sequence motifs with MEME.

Authors:
Timothy L Bailey

Curr Protoc Bioinformatics 2002 Nov;Chapter 2:Unit 2.4

University of Queensland, Brisbane, Australia.

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November 2002