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1. Full Text Evidence for age-related changes in sensorimotor neuromagnetic responses during cued button pressing in a large open-access dataset
by Bardouille, Timothy and Bailey, Lyam and CamCAN Grp and CamCAN Group
NeuroImage, ISSN 1053-8119, 06/2019, Volume 193, pp. 25 - 34
Mu, beta, and gamma rhythms increase and decrease in amplitude during movement. This event-related synchronization (ERS) and desynchronization (ERD) can be... 
SURFACE-BASED ANALYSIS | VOLUNTARY MOVEMENTS | CORTICAL RHYTHMS | SPONTANEOUS MEG | GAMMA-OSCILLATIONS | NEUROSCIENCES | NEUROIMAGING | PRIMARY MOTOR CORTEX | HUMAN CEREBRAL-CORTEX | MOVEMENT BETA-SYNCHRONIZATION | FINGER MOVEMENT | TEMPORAL DYNAMICS | RADIOLOGY, NUCLEAR MEDICINE & MEDICAL IMAGING | Analysis | Neurophysiology | Automation | Young adults | EEG | Cortex | Event-related potentials | Nervous system | Rhythm | Synchronization | Latency | Datasets | Sensorimotor system | Aging | Thalamus | Age | Open access
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2. Full Text An injury risk function for the leg, foot, and ankle exposed to axial impact loading using force and impulse
by Bailey, Ann M and McMurry, Timothy L and Salzar, Robert S and Crandall, Jeff R
Journal of Biomechanical Engineering, ISSN 0148-0731, 02/2019, Volume 141, Issue 2, p. 21009
Most injury risk functions (IRFs) for dynamic axial loading of the leg have been targeted toward automotive applications such as predicting injury caused by... 
Axial impact | Lower extremity | Injury criterion | Force | Impulse | axial impact | BIOPHYSICS | ENGINEERING, BIOMEDICAL | TOLERANCE | force | impulse | CURVES | injury criterion | lower extremity
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3. Full Text MEME: Discovering and analyzing DNA and protein sequence motifs
by Bailey, Timothy L and Williams, Nadya and Misleh, Chris and Li, Wilfred W
Nucleic Acids Research, ISSN 0305-1048, 07/2006, Volume 34, Issue Web Server issue, pp. W369 - W373
MEME (Multiple EM for Motif Elicitation) is one of the most widely used tools for searching for novel 'signals' in sets of biological sequences. Applications... 
BIOCHEMISTRY & MOLECULAR BIOLOGY | Protein Structure, Tertiary | Transcription Factors - metabolism | Sequence Analysis, Protein - methods | User-Computer Interface | Sequence Alignment | Software | Internet | Binding Sites | Sequence Analysis, DNA - methods | Amino Acid Motifs | Index Medicus
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4. Full Text MEME Suite: tools for motif discovery and searching
by Bailey, Timothy L and Boden, Mikael and Buske, Fabian A and Frith, Martin and Grant, Charles E and Clementi, Luca and Ren, Jingyuan and Li, Wilfred W and Noble, William S
Nucleic Acids Research, ISSN 0305-1048, 7/2009, Volume 37, Issue suppl_2, pp. W202 - W208
The MEME Suite web server provides a unified portal for online discovery and analysis of sequence motifs representing features such as DNA binding sites and... 
SEQUENCE MOTIFS | BIOCHEMISTRY & MOLECULAR BIOLOGY | ENVIRONMENT | Transcription Factors - metabolism | Sequence Analysis, Protein | Algorithms | Regulatory Elements, Transcriptional | Databases, Genetic | Software | Internet | Binding Sites | Sequence Analysis, DNA | Index Medicus
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5. Full Text DREME: Motif discovery in transcription factor ChIP-seq data
by Bailey, Timothy L
Bioinformatics, ISSN 1367-4803, 06/2011, Volume 27, Issue 12, pp. 1653 - 1659
Motivation: Transcription factor (TF) ChIP-seq datasets have particular characteristics that provide unique challenges and opportunities for motif discovery.... 
DNA-BINDING | COMPLEX | ERYTHROPOIESIS | BIOCHEMICAL RESEARCH METHODS | FACTOR-BINDING SITES | GENOME | EVOLUTION | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | EMBRYONIC STEM-CELLS | SEQUENCE | GENES | MATHEMATICAL & COMPUTATIONAL BIOLOGY | EXPRESSION | Transcription Factors - metabolism | Cell Line | Algorithms | Animals | Chromatin Immunoprecipitation | Regulatory Elements, Transcriptional | Humans | Erythrocytes - metabolism | Mice | Sequence Analysis, DNA | Index Medicus | Original Papers
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6. Full Text Motif-based analysis of large nucleotide data sets using MEME-ChIP
by Ma, Wenxiu and Noble, William S and Bailey, Timothy L
Nature Protocols, ISSN 1754-2189, 2014, Volume 9, Issue 6, pp. 1428 - 1450
MEME-ChIP is a web-based tool for analyzing motifs in large DNA or RNA data sets. It can analyze peak regions identified by ChIP-seq, cross-linking sites... 
SEQ DATA | DNA-BINDING | HUMAN GENOME | CHROMATIN | PAR-CLIP | RESOLUTION | BIOCHEMICAL RESEARCH METHODS | SITES | IDENTIFICATION | DISCOVERY | RNA-BINDING PROTEIN | Algorithms | Nucleotide Motifs - genetics | Chromatin Immunoprecipitation - methods | Software | Binding Sites - genetics | High-Throughput Nucleotide Sequencing - methods | Cluster Analysis | RNA sequencing | Usage | Research | Nucleotide sequencing | Methods | DNA sequencing | Genetic algorithms | Index Medicus
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7. Full Text Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study
by Sun, Lei and Zhang, Zhihua and Bailey, Timothy L and Perkins, Andrew C and Tallack, Michael R and Xu, Zhao and Liu, Hui
BMC Bioinformatics, ISSN 1471-2105, 12/2012, Volume 13, Issue 1, pp. 331 - 331
Background: Study on long non-coding RNAs (lncRNAs) has been promoted by high-throughput RNA sequencing (RNA-Seq). However, it is still not trivial to identify... 
SEQUENCES | CHROMATIN | QUANTIFICATION | BIOCHEMICAL RESEARCH METHODS | PLURIPOTENCY | IDENTIFICATION | GENOME | INTEGRATIVE ANNOTATION | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | MATHEMATICAL & COMPUTATIONAL BIOLOGY | DIFFERENTIATION | TRANSCRIPTION FACTOR | REVEALS | Computational Biology - methods | Exons | Open Reading Frames | RNA, Long Noncoding - genetics | Transcriptome - genetics | Sequence Analysis, RNA - statistics & numerical data | Mice, Knockout | Sequence Analysis, RNA - methods | Animals | Base Sequence | High-Throughput Nucleotide Sequencing | Mice | Genome | Kruppel-Like Transcription Factors - genetics | RNA sequencing | Genomes | RNA | Analysis | Genomics | Studies | Rodents | Methods | Index Medicus | non-coding RNA | Computer applications | Data processing | Open reading frames | Gene expression | Bioinformatics
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8. Full Text Cyclic Peptides Arising by Evolutionary Parallelism via Asparaginyl-Endopeptidase—Mediated Biosynthesis
by Joshua S. Mylne and Lai Yue Chan and Aurelie H. Chanson and Norelle L. Daly and Hanno Schaefer and Timothy L. Bailey and Philip Nguyencong and Laura Cascales and David J. Craik
The Plant Cell, ISSN 1040-4651, 7/2012, Volume 24, Issue 7, pp. 2765 - 2778
The cyclic miniprotein Momordica cochinchinensis Trypsin Inhibitor II (MCoTI-II) (34 amino acids) is a potent trypsin inhibitor (TI) and a favored scaffold for... 
Proteins | Polymerase chain reaction | Cyclic peptides | DNA | Squashes | Protein precursors | Amino acids | Biosynthesis | Open reading frames | Free energy | CIRCULAR PROTEINS | CYSTINE KNOT MOTIF | ARABIDOPSIS-THALIANA | BACKBONE CYCLIZATION | MOMORDICA-COCHINCHINENSIS | BIOCHEMISTRY & MOLECULAR BIOLOGY | VACUOLAR PROCESSING ENZYME | STRUCTURAL MOTIFS | INHIBITOR MCOTI-II | PLANT SCIENCES | CELL BIOLOGY | PLANT CYCLOTIDES | TRYPSIN-INHIBITOR | Cyclotides - chemistry | Cystine-Knot Miniproteins - metabolism | Molecular Sequence Data | Cystine-Knot Miniproteins - genetics | Phylogeny | Peptides, Cyclic - chemistry | Peptides, Cyclic - metabolism | Cysteine Endopeptidases - metabolism | Peptides, Cyclic - genetics | Cystine-Knot Miniproteins - chemistry | DNA, Plant - genetics | Protein Structure, Tertiary | Amino Acid Sequence | Models, Molecular | Momordica - metabolism | Cyclotides - genetics | Arabidopsis - metabolism | Arabidopsis - genetics | Sequence Homology, Amino Acid | Sequence Alignment | Gene Amplification | Cyclotides - metabolism | Momordica - genetics | Protein Conformation | Evolution, Molecular | Arabidopsis thaliana | Synthesis | Peptides | Plant genetics | Genetic aspects | Research | Observations | Index Medicus
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9. Full Text Discovering sequence motifs with arbitrary insertions and deletions
by Frith, Martin C and Saunders, Neil F. W and Kobe, Bostjan and Bailey, Timothy L
PLoS Computational Biology, ISSN 1553-734X, 05/2008, Volume 4, Issue 5, pp. e1000071 - e1000071
Biology is encoded in molecular sequences: deciphering this encoding remains a grand scientific challenge. Functional regions of DNA, RNA, and protein... 
DATABASE | GENE | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | EUKARYOTIC PROTEINS | HIDDEN MARKOV-MODELS | FACTOR-BINDING SITES | ONLY PROTEIN LMO2 | REGULATORY ELEMENTS | EXPRESSION | COMPUTATIONAL ANALYSIS | MULTIPLE ALIGNMENT | Amino Acid Sequence | Sequence Alignment - methods | Algorithms | Sequence Analysis - methods | Base Sequence | Chromosome Mapping - methods | Gene Deletion | DNA Transposable Elements - genetics | Molecular Sequence Data | Amino Acid Motifs | Index Medicus | Studies | Proteins | Annealing | Cooling | Kinases | Data bases | Methods
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10. Full Text Repression of the genome organizer SATB1 in regulatory T cells is required for suppressive function and inhibition of effector differentiation
by Beyer, Marc and Thabet, Yasser and Müller, Roman-Ulrich and Sadlon, Timothy and Classen, Sabine and Lahl, Katharina and Basu, Samik and Zhou, Xuyu and Bailey-Bucktrout, Samantha L and Krebs, Wolfgang and Schönfeld, Eva A and Böttcher, Jan and Golovina, Tatiana and Mayer, Christian T and Hofmann, Andrea and Sommer, Daniel and Debey-Pascher, Svenja and Endl, Elmar and Limmer, Andreas and Hippen, Keli L and Blazar, Bruce R and Balderas, Robert and Quast, Thomas and Waha, Andreas and Mayer, Günter and Famulok, Michael and Knolle, Percy A and Wickenhauser, Claudia and Kolanus, Waldemar and Schermer, Bernhard and Bluestone, Jeffrey A and Barry, Simon C and Sparwasser, Tim and Riley, James L and Schultze, Joachim L
Nature Immunology, ISSN 1529-2908, 09/2011, Volume 12, Issue 9, pp. 898 - 907
Regulatory T cells (T-reg cells) are essential for self-tolerance and immune homeostasis. Lack of effector T cell (T-eff cell) function and gain of suppressive... 
TARGET GENES | MULTIPLE GENES | TGF-BETA | DISRUPTION | TRANSCRIPTION FACTOR FOXP3 | IN-VIVO | IMMUNOLOGY | BINDING PROTEIN | IDENTIFICATION | EXPRESSION | PLASTICITY | Forkhead Transcription Factors - immunology | T-Lymphocytes, Regulatory - metabolism | 3' Untranslated Regions - immunology | Self Tolerance - immunology | Humans | 3' Untranslated Regions - genetics | MicroRNAs - metabolism | Gene Expression Profiling | MicroRNAs - pharmacology | Chromatin Assembly and Disassembly - drug effects | T-Lymphocytes, Regulatory - immunology | Flow Cytometry | RNA Interference | RNA, Small Interfering - immunology | Forkhead Transcription Factors - metabolism | Self Tolerance - genetics | T-Lymphocytes, Regulatory - cytology | Self Tolerance - drug effects | Genome-Wide Association Study | Transduction, Genetic | Matrix Attachment Region Binding Proteins - metabolism | Mice, Inbred C57BL | RNA, Small Interfering - pharmacology | Gene Expression Regulation | Forkhead Transcription Factors - genetics | MicroRNAs - immunology | Reverse Transcriptase Polymerase Chain Reaction | Lentivirus | Matrix Attachment Region Binding Proteins - immunology | Chromatin Assembly and Disassembly - immunology | Mice, Knockout | Animals | Cell Differentiation - drug effects | Lymphocyte Activation - drug effects | Matrix Attachment Region Binding Proteins - genetics | Mice | Genome, Human | RNA, Small Interfering - metabolism | Physiological aspects | Chromatin | Genomes | Research | Gene expression | T cells | Index Medicus
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