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Timothy Lawrence Bailey

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TOP 3
Ahmed M Mehdi; Muhammad Shoaib B Sehgal; Timothy Lawrence Bailey; Bostjan Kobe; Mikael Bodén
DLocalMotif: a discriminative approach for discovering local motifs in protein sequences.
Kevin A Peterson; Leila Shokri; Alexander van Oudenaarden; Anastasia Vedenko; Wing H Wong; Xiaoxiao Zhang; Tarjei Mikkelsen; Yuichi Nishi; Timothy Lawrence Bailey; José-Manuel Baizabal; Bradley E Bernstein; Martha L Bulyk; Jan Philipp Junker; Wenxiu Ma; Matthew McFarlane; Andrew P McMahon
Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning.
Michael R Tallack; Lei Sun; Timothy Lawrence Bailey; Benjamin Dartigues; Jessica M Fittock; Sally V Fry; Evgeny A Glazov; Stephen Huang; Graham W Magor; Andrew C Perkins
Novel roles for KLF1 in erythropoiesis revealed by mRNA-seq.

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All Publications

2013: Ahmed M Mehdi; Muhammad Shoaib B Sehgal; Timothy Lawrence Bailey; Bostjan Kobe; Mikael Bodén
DLocalMotif: a discriminative approach for discovering local motifs in protein sequences.
Bioinformatics (Oxford, England) 2013;29(1):39-46.
2012: Kevin A Peterson; Leila Shokri; Alexander van Oudenaarden; Anastasia Vedenko; Wing H Wong; Xiaoxiao Zhang; Tarjei Mikkelsen; Yuichi Nishi; Timothy Lawrence Bailey; José-Manuel Baizabal; Bradley E Bernstein; Martha L Bulyk; Jan Philipp Junker; Wenxiu Ma; Matthew McFarlane; Andrew P McMahon
Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning.
Genes & development 2012;26(24):2802-16.
2012: Michael R Tallack; Lei Sun; Timothy Lawrence Bailey; Benjamin Dartigues; Jessica M Fittock; Sally V Fry; Evgeny A Glazov; Stephen Huang; Graham W Magor; Andrew C Perkins
Novel roles for KLF1 in erythropoiesis revealed by mRNA-seq.
Genome research 2012;22(12):2385-98.
2012: Céline Plachez; Adam C Puche; Linda J Richards; Timothy Lawrence Bailey; Kathleen Cato; Richard M Gronostasjki; Yee Hsieh Evelyn Heng; Robert C McLeay; Michael Piper
Expression of nuclear factor one A and -B in the olfactory bulb.
The Journal of comparative neurology 2012;520(14):3135-49.
2012: Timothy Lawrence Bailey; Philip Machanick
Inferring direct DNA binding from ChIP-seq.
Nucleic acids research 2012;40(17):e128.
2012: Joshua S Mylne; Philip Nguyencong; Hanno Schaefer; Norelle L Daly; Timothy Lawrence Bailey; Laura Cascales; Lai Yue Chan; Aurelie H Chanson; David J Craik
Cyclic peptides arising by evolutionary parallelism via asparaginyl-endopeptidase-mediated biosynthesis.
The Plant cell 2012;24(7):2765-78.
2012: Fabian A Buske; John S Mattick; Denis C Bauer; Timothy Lawrence Bailey
Triplexator: detecting nucleic acid triple helices in genomic and transcriptomic data.
Genome research 2012;22(7):1372-81.
2012: Jing Yu; Timothy Lawrence Bailey; Mary Duah; Diane Faria; Kylie Georgas; Paul A Gray; Sean M Grimmond; Jin-Jin Guo; Jennifer K Hansard; Jan P Junker; A Michaela Krautzberger; Melissa H Little; Qiufu Ma; Philip Machanick; Jill McMahon; Qun Ren; David H Rowitch; Bree Rumballe; Karl Staser; Charles D Stiles; Rathi D Thiagarajan; Michael T Valerius; Alexander van Oudenaarden; Joe Vaughan; Andrew P McMahon
Identification of molecular compartments and genetic circuitry in the developing mammalian kidney.
Development (Cambridge, England) 2012;139(10):1863-73.
2012: Lei Sun; Michael R Tallack; Zhao Xu; Zhihua Zhang; Timothy Lawrence Bailey; Andrew C Perkins; Hui Liu
Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study.
BMC bioinformatics 2012;13():331.
2012: Gabriel Cuellar-Partida; William Stafford Noble; Fabian A Buske; Tom Whitington; Robert C McLeay; Timothy Lawrence Bailey
Epigenetic priors for identifying active transcription factor binding sites.
Bioinformatics (Oxford, England) 2012;28(1):56-62.
2011: Robert C McLeay; Chris J Leat; Timothy Lawrence Bailey
Tissue-specific prediction of directly regulated genes.
Bioinformatics (Oxford, England) 2011;27(17):2354-60.
2011: Tom Whitington; Martin C Frith; James Johnson; Timothy Lawrence Bailey
Inferring transcription factor complexes from ChIP-seq data.
Nucleic acids research 2011;39(15):e98.
2011: Denis C Bauer; Timothy Lawrence Bailey; Fabian A Buske; Graham Dellaire; Kim-Anh Lê Cao; Kai Willadsen; Mikael Bodén
Sorting the nuclear proteome.
Bioinformatics (Oxford, England) 2011;27(13):i7-14.
2011: Timothy Lawrence Bailey
DREME: motif discovery in transcription factor ChIP-seq data.
Bioinformatics (Oxford, England) 2011;27(12):1653-9.
2011: Philip Machanick; Timothy Lawrence Bailey
MEME-ChIP: motif analysis of large DNA datasets.
Bioinformatics (Oxford, England) 2011;27(12):1696-7.
2011: Fabian A Buske; John S Mattick; Timothy Lawrence Bailey
Potential in vivo roles of nucleic acid triple-helices.
RNA biology 2011;8(3):427-39.
2011: Ahmed M Mehdi; Muhammad Shoaib B Sehgal; Bostjan Kobe; Timothy Lawrence Bailey; Mikael Bodén
A probabilistic model of nuclear import of proteins.
Bioinformatics (Oxford, England) 2011;27(9):1239-46.
2011: Charles E Grant; Timothy Lawrence Bailey; William Stafford Noble
FIMO: scanning for occurrences of a given motif.
Bioinformatics (Oxford, England) 2011;27(7):1017-8.
2010: Michael R Tallack; Tom Whitington; Wai Shan Yuen; Elanor N Wainwright; Janelle R Keys; brooke gardiner; Ehsan Nourbakhsh; Nicole Cloonan; Sean M Grimmond; Timothy Lawrence Bailey; Andrew C Perkins
A global role for KLF1 in erythropoiesis revealed by ChIP-seq in primary erythroid cells.
Genome research 2010;20(8):1052-63.
2010: Michael Piper; Guy Barry; John Hawkins; Sharon Mason; Charlotta Lindwall; Erica Little; Anindita Sarkar; Aaron G Smith; Randal X Moldrich; Glen M Boyle; Shubha Tole; Richard M Gronostajski; Timothy Lawrence Bailey; Linda J Richards
NFIA controls telencephalic progenitor cell differentiation through repression of the Notch effector Hes1.
The Journal of neuroscience : the official journal of the Society for Neuroscience 2010;30(27):9127-39.
2010: Mikael Bodén; Graham Dellaire; Kevin Burrage; Timothy Lawrence Bailey
A Bayesian network model of proteins' association with promyelocytic leukemia (PML) nuclear bodies.
Journal of computational biology : a journal of computational molecular cell biology 2010;17(4):617-30.
2010: Fabian A Buske; Mikael Bodén; Denis Bauer; Timothy Lawrence Bailey
Assigning roles to DNA regulatory motifs using comparative genomics.
Bioinformatics (Oxford, England) 2010;26(7):860-6.
2010: Denis Bauer; Fabian A Buske; Timothy Lawrence Bailey
Dual-functioning transcription factors in the developmental gene network of Drosophila melanogaster.
BMC bioinformatics 2010;11():366.
2010: Timothy Lawrence Bailey; Mikael Bodén; Tom Whitington; Philip Machanick
The value of position-specific priors in motif discovery using MEME.
BMC bioinformatics 2010;11():179.
2010: Robert C McLeay; Timothy Lawrence Bailey
Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data.
BMC bioinformatics 2010;11():165.
2009: Timothy Lawrence Bailey; Mikael Boden; Fabian A Buske; Martin Frith; Charles E Grant; Luca Clementi; Jingyuan Ren; Wilfred Wenfeng Li; William S Noble
MEME SUITE: tools for motif discovery and searching.
Nucleic acids research 2009;37(Web Server issue):W202-8.
2009: Denis Bauer; Timothy Lawrence Bailey
Optimizing static thermodynamic models of transcriptional regulation.
Bioinformatics (Oxford, England) 2009;25(13):1640-6.
2009: John Hawkins; Charles Grant; William Stafford Noble; Timothy Lawrence Bailey
Assessing phylogenetic motif models for predicting transcription factor binding sites.
Bioinformatics (Oxford, England) 2009;25(12):i339-47.
2009: Tom Whitington; Andrew C Perkins; Timothy Lawrence Bailey
High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.
Nucleic acids research 2009;37(1):14-25.
2008: Denis Bauer; Timothy Lawrence Bailey
STREAM: Static Thermodynamic REgulAtory Model of transcription.
Bioinformatics (Oxford, England) 2008;24(21):2544-5.
2008: Mikael Bodén; Timothy Lawrence Bailey
Associating transcription factor-binding site motifs with target GO terms and target genes.
Nucleic acids research 2008;36(12):4108-17.
2008: Martin C Frith; Neil Saunders; Bostjan Kobe; Timothy Lawrence Bailey
Discovering sequence motifs with arbitrary insertions and deletions.
PLoS computational biology 2008;4(4):e1000071.
2008: Timothy Lawrence Bailey
Discovering sequence motifs.
Methods in molecular biology (Clifton, N.J.) 2008;452():231-51.
2008: Denis Bauer; Timothy Lawrence Bailey
Studying the functional conservation of cis-regulatory modules and their transcriptional output.
BMC bioinformatics 2008;9():220.
2007: Martin C Frith; piero carninci; Chikatoshi Kai; Jun Kawai; Timothy Lawrence Bailey; Yoshihide Hayashizaki; John S Mattick
Splicing bypasses 3' end formation signals to allow complex gene architectures.
Gene 2007;403(1-2):188-93.
2007: Timothy Lawrence Bailey
Discovering sequence motifs.
Methods in molecular biology (Clifton, N.J.) 2007;395():271-92.
2007: Emma Redhead; Timothy Lawrence Bailey
Discriminative motif discovery in DNA and protein sequences using the DEME algorithm.
BMC bioinformatics 2007;8():385.
2007: Shobhit Gupta; John A Stamatoyannopoulos; Timothy Lawrence Bailey; William Stafford Noble
Quantifying similarity between motifs.
Genome biology 2007;8(2):R24.
2006: Mikael Bodén; Timothy Lawrence Bailey
Identifying sequence regions undergoing conformational change via predicted continuum secondary structure.
Bioinformatics (Oxford, England) 2006;22(15):1809-14.
2006: Timothy Lawrence Bailey; Nadya Williams; Chris Misleh; Wilfred Wenfeng Li
MEME: discovering and analyzing DNA and protein sequence motifs.
Nucleic acids research 2006;34(Web Server issue):W369-73.
2006: Martin C Frith; Alistair Forrest; Ehsan Nourbakhsh; Ken C Pang; Chikatoshi Kai; Jun Kawai; piero carninci; Yoshihide Hayashizaki; Timothy Lawrence Bailey; Sean M Grimmond
The abundance of short proteins in the mammalian proteome.
PLoS genetics 2006;2(4):e52.
2006: Martin C Frith; Laurens G Wilming; Alistair Forrest; Hideya Kawaji; Sin Lam Tan; Claes Wahlestedt; Vladimir Bajic; Chikatoshi Kai; Jun Kawai; piero carninci; Yoshihide Hayashizaki; Timothy Lawrence Bailey; Lukasz Huminiecki
Pseudo-messenger RNA: phantoms of the transcriptome.
PLoS genetics 2006;2(4):e23.
2006: Martin C Frith; Timothy Lawrence Bailey; Takeya Kasukawa; Flavio Mignone; Sarah K Kummerfeld; Martin Madera; Sirisha Sunkara; Masaaki Furuno; Carol Bult; John Quackenbush; Chikatoshi Kai; Jun Kawai; piero carninci; Yoshihide Hayashizaki; Graziano Pesole; John S Mattick
Discrimination of non-protein-coding transcripts from protein-coding mRNA.
RNA biology 2006;3(1):40-8.
2006: Stefan M Stanley; Timothy Lawrence Bailey; John S Mattick
GONOME: measuring correlations between GO terms and genomic positions.
BMC bioinformatics 2006;7():94.
2006: Mikael Bodén; Zheng Yuan; Timothy Lawrence Bailey
Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures.
BMC bioinformatics 2006;7():68.
2005: piero carninci; T Kasukawa; S Katayama; J Gough; M C Frith; N Maeda; R Oyama; T Ravasi; B Lenhard; C Wells; R Kodzius; K Shimokawa; Vladimir Bajic; S E Brenner; S Batalov; Alistair Forrest; M Zavolan; M J Davis; L G Wilming; V Aidinis; J E Allen; A Ambesi-Impiombato; R Apweiler; R N Aturaliya; Timothy Lawrence Bailey; M Bansal; L Baxter; K W Beisel; Tom Bersano; H Bono; Alistair Chalk; K P Chiu; V Choudhary; A Christoffels; D R Clutterbuck; M L Crowe; E Dalla; B P Dalrymple; B de Bono; G Della Gatta; D di Bernardo; T Down; P Engstrom; M Fagiolini; G Faulkner; C F Fletcher; T Fukushima; M Furuno; S Futaki; manuela gariboldi; P Georgii-Hemming; Thomas Gingeras; Takashi Gojobori; R E Green; S Gustincich; M Harbers; Y Hayashi; T K Hensch; N Hirokawa; D Hill; L Huminiecki; M Iacono; Kazuho Ikeo; A Iwama; T Ishikawa; M Jakt; Alexander Kanapin; M Katoh; Y Kawasawa; J Kelso; H Kitamura; H Kitano; george kollias; S P T Krishnan; A Kruger; S K Kummerfeld; I V Kurochkin; L F Lareau; D Lazarevic; Leonard Lipovich; J Liu; S Liuni; S McWilliam; M Madan Babu; M Madera; LUIGI MARCHIONNI; H Matsuda; S Matsuzawa; H Miki; F Mignone; S Miyake; K Morris; S Mottagui-Tabar; N Mulder; N Nakano; H Nakauchi; P Ng; R Nilsson; S Nishiguchi; S Nishikawa; F Nori; O Ohara; Yasushi Okazaki; V Orlando; K C Pang; W J Pavan; G Pavesi; G Pesole; Nikolai Petrovsky; S Piazza; J Reed; J F Reid; B Z Ring; M Ringwald; B Rost; Y Ruan; Steven L Salzberg; A Sandelin; C Schneider; Christian Schönbach; K Sekiguchi; Colin Semple; S Seno; L Sessa; Y Sheng; Y Shibata; H Shimada; K Shimada; D Silva; B Sinclair; S Sperling; Elia Stupka; K Sugiura; R Sultana; Y Takenaka; K Taki; K Tammoja; S L Tan; S Tang; Martin Taylor; J Tegner; S A Teichmann; H R Ueda; E van Nimwegen; R Verardo; C L Wei; K Yagi; H Yamanishi; E Zabarovsky; S Zhu; A Zimmer; Winston Hide; Carol Bult; S M Grimmond; Rohan Teasdale; Edison Liu; V Brusic; John Quackenbush; Claes Wahlestedt; J S Mattick; D A Hume; C Kai; D Sasaki; Y Tomaru; S Fukuda; M Kanamori-Katayama; M Suzuki; J Aoki; T Arakawa; J Iida; K Imamura; Masayoshi Itoh; T Kato; Hideya Kawaji; N Kawagashira; T Kawashima; M Kojima; S Kondo; H Konno; K Nakano; N Ninomiya; T Nishio; M Okada; C Plessy; K Shibata; T Shiraki; S Suzuki; M Tagami; Kazunori Waki; A Watahiki; Y Okamura-Oho; H Suzuki; J Kawai; Y Hayashizaki
The transcriptional landscape of the mammalian genome.
Science (New York, N.Y.) 2005;309(5740):1559-63.
2005: Zheng Yuan; Timothy Lawrence Bailey; Rohan Teasdale
Prediction of protein B-factor profiles.
Proteins 2005;58(4):905-12.
2005: Martin Tompa; Nan Li; Timothy Lawrence Bailey; George M Church; Bart De Moor; Eleazar Eskin; Alexander Favorov; Martin C Frith; Yutao Fu; W James Kent; Vsevolod Makeev; Andrey A Mironov; William Stafford Noble; Giulio Pavesi; Graziano Pesole; Mireille Régnier; Nicolas Simonis; Saurabh sinha; Gert Thijs; Jacques Van Helden; Mathias Vandenbogaert; Zhiping Weng; Christopher Workman; Chun Ye; Zhou Zhu
Assessing computational tools for the discovery of transcription factor binding sites.
Nature biotechnology 2005;23(1):137-44.
2004: Zheng Yuan; Timothy Lawrence Bailey
Prediction of protein solvent profile using SVR.
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference 2004;4():2889-92.
2003: Timothy Lawrence Bailey; William Stafford Noble
Searching for statistically significant regulatory modules.
Bioinformatics (Oxford, England) 2003;19 Suppl 2():ii16-25.
2002: Timothy Lawrence Bailey
Discovering novel sequence motifs with MEME.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 2002;Chapter 2():Unit 2.4.
2002: Timothy Lawrence Bailey; Michael Gribskov
Estimating and evaluating the statistics of gapped local-alignment scores.
Journal of computational biology : a journal of computational molecular cell biology 2002;9(3):575-93.
2000: Timothy Lawrence Bailey; Michael Gribskov
Concerning the accuracy of MAST E-values.
Bioinformatics (Oxford, England) 2000;16(5):488-9.
1999: WN Grundy; Timothy Lawrence Bailey
Family pairwise search with embedded motif models.
Bioinformatics (Oxford, England) 1999;15(6):463-70.
1998: Timothy Lawrence Bailey; Michael Gribskov
Methods and statistics for combining motif match scores.
Journal of computational biology : a journal of computational molecular cell biology 1998;5(2):211-21.
1998: Timothy Lawrence Bailey; Michael Gribskov
Combining evidence using p-values: application to sequence homology searches.
Bioinformatics (Oxford, England) 1998;14(1):48-54.
1997: WN Grundy; Timothy Lawrence Bailey; CP Elkan; Michael E Baker
Meta-MEME: motif-based hidden Markov models of protein families.
Computer applications in the biosciences : CABIOS 1997;13(4):397-406.
1997: Timothy Lawrence Bailey; Michael E Baker; CP Elkan
An artificial intelligence approach to motif discovery in protein sequences: application to steriod dehydrogenases.
The Journal of steroid biochemistry and molecular biology 1997;62(1):29-44.
1997: WN Grundy; Timothy Lawrence Bailey; CP Elkan; Michael E Baker
Hidden Markov model analysis of motifs in steroid dehydrogenases and their homologs.
Biochemical and biophysical research communications 1997;231(3):760-6.
1997: Timothy Lawrence Bailey; Michael Gribskov
Score distributions for simultaneous matching to multiple motifs.
Journal of computational biology : a journal of computational molecular cell biology 1997;4(1):45-59.
1996: WN Grundy; Timothy Lawrence Bailey; CP Elkan
ParaMEME: a parallel implementation and a web interface for a DNA and protein motif discovery tool.
Computer applications in the biosciences : CABIOS 1996;12(4):303-10.
1996: Timothy Lawrence Bailey; Michael Gribskov
The megaprior heuristic for discovering protein sequence patterns.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1996;4():15-24.
1995: Timothy Lawrence Bailey; CP Elkan
The value of prior knowledge in discovering motifs with MEME.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1995;3():21-9.
1994: Timothy Lawrence Bailey; CP Elkan
Fitting a mixture model by expectation maximization to discover motifs in biopolymers.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1994;2():28-36.