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1. Full Text Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning
by Alipanahi, Babak and Delong, Andrew and Weirauch, Matthew T and Frey, Brendan J
Nature biotechnology, ISSN 1087-0156, 08/2015, Volume 33, Issue 8, pp. 831 - 838
Life Sciences & Biomedicine | Biotechnology & Applied Microbiology | Science & Technology | Sequence Analysis, Protein - methods | Computational Biology - methods | Software | Position-Specific Scoring Matrices | DNA-Binding Proteins - chemistry | RNA-Binding Proteins - chemistry | Usage | Nucleotide sequence | Neural networks | Genetic research | Genetic aspects | DNA binding proteins | Research | Protein binding | Proteins | Ribonucleic acid--RNA | Genomics | Deoxyribonucleic acid--DNA | Cancer | Index Medicus
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2. Full Text Genomic programming of IRF4-expressing human Langerhans cells
by Sirvent, Sofia and Vallejo, Andres F and Davies, James and Clayton, Kalum and Wu, Zhiguo and Woo, Jeongmin and Riddell, Jeremy and Chaudhri, Virendra K and Stumpf, Patrick and Nazlamova, Liliya Angelova and Wheway, Gabrielle and Rose-Zerilli, Matthew and West, Jonathan and Pujato, Mario and Chen, Xiaoting and Woelk, Christopher H and MacArthur, Ben and Ardern-Jones, Michael and Friedmann, Peter S and Weirauch, Matthew T and Singh, Harinder and Polak, Marta E
Nature communications, ISSN 2041-1723, 01/2020, Volume 11, Issue 1, pp. 313 - 313
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Proto-Oncogene Proteins - metabolism | Up-Regulation | Basic-Leucine Zipper Transcription Factors - metabolism | Cytokines - metabolism | Genomics | Humans | Transcriptional Activation | Histocompatibility Antigens Class I | Interferon Regulatory Factors - metabolism | Interferon Regulatory Factors - genetics | Antigen Presentation - genetics | NF-kappa B - metabolism | Gene Expression Profiling | Gene Editing | CRISPR-Cas Systems | Langerhans Cells - immunology | Histocompatibility Antigens Class II | Trans-Activators - metabolism | Transcription, Genetic | Langerhans Cells - metabolism | Repressor Proteins - metabolism | Cell Movement | ETS protein | Oxidative stress | Chromatin | Transcription factors | Profiling | Genes | Antigen processing | Editing | Inflammatory response | Regulatory sequences | PU.1 protein | Attenuation | CRISPR | Antigen presentation | NF-κB protein | Antigens | Maturation | Cytokines | Activator protein 1 | Epidermis | Inflammation | Gene expression | Major histocompatibility complex | Immunogenicity | Tumor necrosis factor | Interferon regulatory factor 4 | Langerhans cells | Skin | Index Medicus
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3. Full Text AMP kinase promotes glioblastoma bioenergetics and tumour growth
by Chhipa, Rishi Raj and Fan, Qiang and Anderson, Jane and Muraleedharan, Ranjithmenon and Huang, Yan and Ciraolo, Georgianne and Chen, Xiaoting and Waclaw, Ronald and Chow, Lionel M and Khuchua, Zaza and Kofron, Matthew and Weirauch, Matthew T and Kendler, Ady and McPherson, Christopher and Ratner, Nancy and Nakano, Ichiro and Dasgupta, Nupur and Komurov, Kakajan and Dasgupta, Biplab
Nature cell biology, ISSN 1465-7392, 07/2018, Volume 20, Issue 7, pp. 823 - 835
Life Sciences & Biomedicine | Science & Technology | Cell Biology | AMP-Activated Protein Kinases - metabolism | Glioblastoma - enzymology | Neoplastic Stem Cells - drug effects | Humans | Brain Neoplasms - pathology | Gene Expression Regulation, Neoplastic | Male | Autophagy | Glioblastoma - genetics | Time Factors | Hypoxia-Inducible Factor 1, alpha Subunit - metabolism | HEK293 Cells | Neoplastic Stem Cells - pathology | Female | Transcription, Genetic | Antineoplastic Agents - pharmacology | Tumor Cells, Cultured | Brain Neoplasms - enzymology | Signal Transduction | Hypoxia-Inducible Factor 1, alpha Subunit - genetics | AMP-Activated Protein Kinases - antagonists & inhibitors | Brain Neoplasms - genetics | Tumor Burden | Brain Neoplasms - drug therapy | Mice, SCID | GA-Binding Protein Transcription Factor - genetics | Xenograft Model Antitumor Assays | Cyclic AMP Response Element-Binding Protein - genetics | Animals | Glioblastoma - pathology | Cyclic AMP Response Element-Binding Protein - metabolism | Cell Line, Tumor | Mice, Inbred NOD | Cell Proliferation - drug effects | Protein Kinase Inhibitors - pharmacology | Glioblastoma - drug therapy | Neoplastic Stem Cells - enzymology | AMP-Activated Protein Kinases - genetics | Energy Metabolism - drug effects | Apoptosis | GA-Binding Protein Transcription Factor - metabolism | Physiological aspects | Development and progression | Genetic aspects | Research | Adenylic acid | Protein kinases | Glioblastoma multiforme | Stresses | Transcription factors | Cell survival | AMP | Glioblastoma | Muscles | Stem cell transplantation | Genomes | Pharmacology | Metabolism | Kinases | Skeletal muscle | Stress | Protein turnover | Proteins | Glucose metabolism | Clonal deletion | Bioenergetics | Isoforms | Stem cells | Viability | Cellular stress response | Cancer | Tumors | Index Medicus
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4. Full Text SpDamID: Marking DNA Bound by Protein Complexes Identifies Notch-Dimer Responsive Enhancers
by Hass, Matthew R and Liow, Hien-haw and Chen, Xiaoting and Sharma, Ankur and Inoue, Yukiko U and Inoue, Takayoshi and Reeb, Ashley and Martens, Andrew and Fulbright, Mary and Raju, Saravanan and Stevens, Michael and Boyle, Scott and Park, Joo-Seop and Weirauch, Matthew T and Brent, Michael R and Kopan, Raphael
Molecular cell, ISSN 1097-2765, 08/2015, Volume 59, Issue 4, pp. 685 - 697
Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Science & Technology | Cell Biology | DNA - genetics | Cell Line | Molecular Probe Techniques | Animals | Enhancer Elements, Genetic | Base Sequence | Molecular Sequence Data | Protein Binding | Receptors, Notch - physiology | Mice, Transgenic | DNA - metabolism | Binding Sites | Purines | Neurosciences | Developmental biology | Analysis | Transferases | Genomics | DNA | Genetic research | Methylation | Protein binding | Chromatin | Resveratrol | DNA binding proteins | Genetic transcription | Index Medicus | DamID | transcription | method | ChIP | Notch
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5. Full Text Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A. thaliana
by Sullivan, Alessandra M and Arsovski, Andrej A and Lempe, Janne and Bubb, Kerry L and Weirauch, Matthew T and Sabo, Peter J and Sandstrom, Richard and Thurman, Robert E and Neph, Shane and Reynolds, Alex P and Stergachis, Andrew B and Vernot, Benjamin and Johnson, Audra K and Haugen, Eric and Sullivan, Shawn T and Thompson, Agnieszka and Neri, Fidencio V and Weaver, Molly and Diegel, Morgan and Mnaimneh, Sanie and Yang, Ally and Hughes, Timothy R and Nemhauser, Jennifer L and Queitsch, Christine and Stamatoyannopoulos, John A
Cell reports (Cambridge), ISSN 2211-1247, 09/2014, Volume 8, Issue 6, pp. 2015 - 2030
Life Sciences & Biomedicine | Science & Technology | Cell Biology | Chromatin - metabolism | Arabidopsis Proteins - genetics | Genome-Wide Association Study | Arabidopsis - growth & development | Exons | Seedlings - genetics | Chromosome Mapping | Genome, Plant | Transcription Factors - genetics | Gene Regulatory Networks | Plant Development - genetics | Arabidopsis - metabolism | Arabidopsis - genetics | Arabidopsis Proteins - metabolism | Transcription Factors - metabolism | Deoxyribonuclease I - metabolism | Codon | Light | Protein Binding | Regulatory Elements, Transcriptional - genetics | Index Medicus
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6. Full Text Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same
by Weirauch, Matthew T and Hughes, Timothy R
Trends in genetics, ISSN 0168-9525, 2009, Volume 26, Issue 2, pp. 66 - 74
Medical Education | Life Sciences & Biomedicine | Genetics & Heredity | Science & Technology | Fundamental and applied biological sciences. Psychology | Biological and medical sciences | Molecular and cellular biology | Genetics of eukaryotes. Biological and molecular evolution | Gene Expression | Animals | Humans | Regulatory Sequences, Nucleic Acid | Selection, Genetic | Conserved Sequence | Transcription, Genetic | Evolution, Molecular | Index Medicus | Conserved sequence
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7. Full Text C2H2 zinc finger proteins greatly expand the human regulatory lexicon
by Najafabadi, Hamed S and Mnaimneh, Sanie and Schmitges, Frank W and Garton, Michael and Lam, Kathy N and Yang, Ally and Albu, Mihai and Weirauch, Matthew T and Radovani, Ernest and Kim, Philip M and Greenblatt, Jack and Frey, Brendan J and Hughes, Timothy R
Nature biotechnology, ISSN 1087-0156, 05/2015, Volume 33, Issue 5, pp. 555 - 562
Life Sciences & Biomedicine | Biotechnology & Applied Microbiology | Science & Technology | Chromatin - metabolism | Humans | Regulatory Sequences, Nucleic Acid | Gene Expression Regulation | Repressor Proteins - genetics | Nuclear Proteins - metabolism | DNA-Binding Proteins - genetics | Retroelements - genetics | Carrier Proteins - genetics | Carrier Proteins - metabolism | Protein Binding | Genome, Human | Nuclear Proteins - genetics | Repressor Proteins - metabolism | Protein research | Transcription factors | Research | Properties | Protein binding | Index Medicus
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8. Full Text Determination and inference of eukaryotic transcription factor sequence specificity
by Weirauch, Matthew T and Weirauch, Matthew T and Yang, Ally and Albu, Mihai and Cote, Atina G and Montenegro-Montero, Alejandro and Montenegro-Montero, Alejandro and Drewe, Philipp and Drewe, Philipp and Najafabadi, Hamed S and Lambert, Samuel A and Lambert, Samuel A and Mann, Ishminder and Mann, Ishminder and Cook, Kate and Cook, Kate and Zheng, Hong and Goity, Alejandra and Goity, Alejandra and Van Bakel, Harm and van Bakel, Harm and Lozano, Jean-Claude and Lozano, Jean-Claude and Galli, Mary and Galli, Mary and Lewsey, Mathew G and Lewsey, Mathew G and Huang, Eryong and Huang, Eryong and Mukherjee, Tuhin and Mukherjee, Tuhin and Chen, Xiaoting and Chen, Xiaoting and Reece-Hoyes, John S and Reece-Hoyes, John S and Govindarajan, Sridhar and Govindarajan, Sridhar and Shaulsky, Gad and Shaulsky, Gad and Walhout, Albertha J. M and Walhout, Albertha J M and Bouget, François-Yves and Bouget, Franc¸ois-Yves and Ratsch, Gunnar and Ratsch, Gunnar and Larrondo, Luis F and Larrondo, Luis F and Ecker, Joseph R and Ecker, Joseph R and Hughes, Timothy R and Hughes, Timothy R
Cell (Cambridge), ISSN 0092-8674, 2014, Volume 158, Issue 6, pp. 1431 - 1443
Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Science & Technology | Cell Biology | Arabidopsis - genetics | Transcription Factors - metabolism | Promoter Regions, Genetic | Chromatin Immunoprecipitation | Nucleotide Motifs | Humans | Protein Binding | Polymorphism, Single Nucleotide | Quantitative Trait Loci | Sequence Analysis, DNA | Arabidopsis - metabolism | Arabidopsis thaliana | Quantitative genetics | Plant physiology | Developmental biology | Analysis | Single nucleotide polymorphisms | Nucleotide sequencing | DNA sequencing | Index Medicus
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