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index medicus (13) 13
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corrigendum (2) 2
diet, high-fat (2) 2
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time (2) 2
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acetate-coa ligase - genetics (1) 1
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acute myeloid-leukemia (1) 1
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1. Full Text The Science of Santa Claus: Discussions on the Manna of Nicholas of Myra in the Modern Age
by de Ceglia, Francesco Paolo
Nuncius, ISSN 0394-7394, 2012, Volume 27, Issue 2, pp. 241 - 269
Nicholas of Myra, a bishop who lived between the third and fourth centuries AD, is considered to be the historical character on which the legendary figure of... 
Nicholas of Myra | relics and science | Fortunio Liceti | corpse medicine | MIRACLES | HISTORY & PHILOSOPHY OF SCIENCE | SAINTS
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2. Full Text Reprogramming of the Circadian Clock by Nutritional Challenge
by Eckel-Mahan, Kristin L and Patel, Vishal R and de Mateo, Sara and Orozco-Solis, Ricardo and Ceglia, Nicholas J and Sahar, Saurabh and Dilag-Penilla, Sherry A and Dyar, Kenneth A and Baldi, Pierre and Sassone-Corsi, Paolo
Cell, ISSN 0092-8674, 12/2013, Volume 155, Issue 7, pp. 1464 - 1478
Circadian rhythms and cellular metabolism are intimately linked. Here, we reveal that a high-fat diet (HFD) generates a profound reorganization of specific... 
GLUCOSE-HOMEOSTASIS | SHIFT WORK | DIET | METABOLISM | PYRUVATE-CARBOXYLASE | BIOCHEMISTRY & MOLECULAR BIOLOGY | GENE-EXPRESSION | FAT | PPAR-GAMMA | BODY-MASS | HEPATIC STEATOSIS | CELL BIOLOGY | Mice, Inbred C57BL | Gene Expression Regulation | Transcriptome | ARNTL Transcription Factors - metabolism | Male | Circadian Rhythm | PPAR gamma - metabolism | Obesity - metabolism | CLOCK Proteins - metabolism | Animals | Metabolic Networks and Pathways | Diet, High-Fat | Circadian Clocks | Mice | Metabolites | Physiological aspects
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3. Full Text Partitioning Circadian Transcription by SIRT6 Leads to Segregated Control of Cellular Metabolism
by Masri, Selma and Rigor, Paul and Cervantes, Marlene and Ceglia, Nicholas and Sebastian, Carlos and Xiao, Cuiying and Roqueta-Rivera, Manuel and Deng, Chuxia and Osborne, Timothy F and Mostoslavsky, Raul and Baldi, Pierre and Sassone-Corsi, Paolo
Cell, ISSN 0092-8674, 07/2014, Volume 158, Issue 3, pp. 659 - 672
Circadian rhythms are intimately linked to cellular metabolism. Specifically, the NAD -dependent deacetylase SIRT1, the founding member of the sirtuin family,... 
GENOMIC INSTABILITY | ACTIVATION | CLOCK-BMAL1 | ACETYLATION | BIOCHEMISTRY & MOLECULAR BIOLOGY | DEACETYLASE SIRT6 | GENE-EXPRESSION | REGULATORS | PROMOTER | IDENTIFICATION | CLOCK | CELL BIOLOGY | Sirtuin 1 - metabolism | Chromatin | Liver - metabolism | ARNTL Transcription Factors - metabolism | Gene Expression Profiling | Circadian Rhythm | Sirtuin 1 - genetics | Mice, Knockout | CLOCK Proteins - metabolism | Animals | Transcription, Genetic | Mice | Sirtuins - genetics | Sirtuins - metabolism | Computer science | Epigenetic inheritance | Metabolites | Analysis | Physiological aspects | Genetic research | Genetic transcription | Fatty acids
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4. Full Text Fasting Imparts a Switch to Alternative Daily Pathways in Liver and Muscle
by Kinouchi, Kenichiro and Magnan, Christophe and Ceglia, Nicholas and Liu, Yu and Cervantes, Marlene and Pastore, Nunzia and Huynh, Tuong and Ballabio, Andrea and Baldi, Pierre and Masri, Selma and Sassone-Corsi, Paolo
Cell Reports, ISSN 2211-1247, 12/2018, Volume 25, Issue 12, pp. 3299 - 3314.e6
The circadian clock operates as intrinsic time-keeping machinery to preserve homeostasis in response to the changing environment. While food is a known... 
circadian | RNA-seq | liver | transcriptome | muscle | metabolism | fasting | clock | rhythm | CIRCADIAN CLOCK | PPAR-ALPHA | LIPID-METABOLISM | TRANSCRIPTION | GENE-EXPRESSION | REV-ERB-ALPHA | MICE | TIME | INSULIN SENSITIVITY | BMAL1 | CELL BIOLOGY
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5. Full Text Bioinformatic Software Library for Circadian Analysis
by Ceglia, Nicholas
01/2018, ISBN 9780438745407
Circadian oscillations play a fundamental role in many biological processes including cell metabolism and cell cycle. As such, interest in understanding these... 
Computer science | Bioinformatics
Dissertation
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6. Full Text Mir-132/212 is required for maturation of binocular matching of orientation preference and depth perception
by Mazziotti, Raffaele and Baroncelli, Laura and Ceglia, Nicholas and Chelini, Gabriele and Sala, Grazia Della and Magnan, Christophe and Napoli, Debora and Putignano, Elena and Silingardi, Davide and Tola, Jonida and Tognini, Paola and Arthur, J. Simon C and Baldi, Pierre and Pizzorusso, Tommaso
Nature Communications, ISSN 2041-1723, 05/2017, Volume 8, Issue 1, p. 15488
MicroRNAs (miRNAs) are known to mediate post-transcriptional gene regulation, but their role in postnatal brain development is still poorly explored. We show... 
OLIGODENDROCYTE DIFFERENTIATION | PRIMARY VISUAL-CORTEX | CORTICAL MICROCIRCUITS | MENTAL-RETARDATION | MULTIDISCIPLINARY SCIENCES | SENSORY EXPERIENCE | MOUSE | ENVIRONMENTAL ENRICHMENT | DEPENDENT PLASTICITY | CRITICAL-PERIOD PLASTICITY | TRANSGENIC MICE | Up-Regulation | Mice, Inbred C57BL | Transcriptome | Electrophysiology | Genotype | Male | Mice, Transgenic | Visual Cortex | Orientation | Animals | Sequence Analysis, RNA | Neuronal Plasticity | Depth Perception | Gene Deletion | Neurons - physiology | Vision, Binocular | Female | Visual Perception | Mice | MicroRNAs - genetics | MicroRNAs - physiology
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7. Full Text SIRT6 Suppresses Cancer Stem-like Capacity in Tumors with PI3K Activation Independently of Its Deacetylase Activity
by Ioris, Rafael M and Galié, Mirco and Ramadori, Giorgio and Anderson, Jason G and Charollais, Anne and Konstantinidou, Georgia and Brenachot, Xavier and Aras, Ebru and Goga, Algera and Ceglia, Nicholas and Sebastián, Carlos and Martinvalet, Denis and Mostoslavsky, Raul and Baldi, Pierre and Coppari, Roberto
Cell Reports, ISSN 2211-1247, 02/2017, Volume 18, Issue 8, pp. 1858 - 1868
Cancer stem cells (CSCs) have high tumorigenic capacity. Here, we show that stem-like traits of specific human cancer cells are reduced by overexpression of... 
PI3K | SIRT6 | cancer stemness | BREAST-CANCER | GENE-EXPRESSION SIGNATURE | LUNG-CANCER | CELLS | AEROBIC GLYCOLYSIS | GROWTH | SELF-RENEWAL | MICE | ACUTE MYELOID-LEUKEMIA | IN-VITRO PROPAGATION | CELL BIOLOGY | Neoplasms - metabolism | Humans | Cell Proliferation - physiology | Phosphatidylinositol 3-Kinases - metabolism | Mice, SCID | Carcinogenesis - metabolism | Mutation - physiology | Transcription, Genetic - physiology | Animals | Neoplastic Stem Cells - metabolism | Cell Line, Tumor | Mice, Inbred NOD | Signal Transduction - physiology | Mice | Acetylation | Sirtuins - metabolism
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8. Full Text Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling
by Zhang, AW and O'Flanagan, C and Chavez, EA and Lim, JLP and Ceglia, N and McPherson, A and Wiens, M and Walters, P and Chan, T and Hewitson, B and Lai, D and Mottok, A and Sarkozy, C and Chong, L and Aoki, T and Wang, XH and Weng, AP and McAlpine, JN and Aparicio, S and Steidl, C and Campbell, KR and Shah, SP
NATURE METHODS, ISSN 1548-7091, 10/2019, Volume 16, Issue 10, pp. 1007 - 1007
Single-cell RNA sequencing has enabled the decomposition of complex tissues into functionally distinct cell types. Often, investigators wish to assign cells to... 
SMOOTH-MUSCLE-CELLS | MARKER | EXPRESSION | BIOCHEMICAL RESEARCH METHODS | RNA sequencing | Genetic markers | Tumor markers | Identification and classification | Analysis | Profiling | Ovarian carcinoma | Computer simulation | Probabilistic models | Mapping | Ribonucleic acid--RNA | Clustering | Lymphoma | Ovarian cancer | Gene sequencing | Annotations | Data sets | Tumors
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9. Full Text Dissociation of solid tumor tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses
by O'Flanagan, CH and Campbell, KR and Zhang, AW and Kabeer, F and Lim, JLP and Biele, J and Eirew, P and Lai, D and McPherson, A and Kong, E and Bates, C and Borkowski, K and Wiens, M and Hewitson, B and Hopkins, J and Pham, J and Ceglia, N and Moore, R and Mungall, AJ and McAlpine, JN and Shah, SP and Aparicio, S and CRUK IMAXT Grand Challenge Team and The CRUK IMAXT Grand Challenge Team
GENOME BIOLOGY, ISSN 1474-760X, 10/2019, Volume 20, Issue 1, pp. 1 - 13
Background Single-cell RNA sequencing (scRNA-seq) is a powerful tool for studying complex biological systems, such as tumor heterogeneity and tissue... 
HETEROGENEITY | RNA-seq | Tumor microenvironment | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | Quality control | GENETICS & HEREDITY | Single cell | GENE-EXPRESSION | Breast cancer | Gene expression | Tissue dissociation | Ovarian cancer | Transcription | Noise | Genomics | Proteinase | Genomes | Collagenase | Tumor cell lines | Ribonucleic acid--RNA | Experiments | Datasets | Major histocompatibility complex | Collagen | Cell lines | Xenografts | Population | Microenvironments | Solid tumors | Cellular stress response | Heat shock
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10. Full Text What time is it? Deep learning approaches for circadian rhythms
by Agostinelli, Forest and Ceglia, Nicholas and Shahbaba, Babak and Sassone-Corsi, Paolo and Baldi, Pierre
Bioinformatics, ISSN 1367-4803, 06/2016, Volume 32, Issue 12, pp. i8 - i17
Motivation: Circadian rhythms date back to the origins of life, are found in virtually every species and every cell, and play fundamental roles in functions... 
METABOLIC SYNDROME | KEY PATHWAYS | MOUSE | BIOCHEMICAL RESEARCH METHODS | PREDICTION | OBESITY | SHIFT WORK | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | MATHEMATICAL & COMPUTATIONAL BIOLOGY | GENE-EXPRESSION | ORCHESTRATED TRANSCRIPTION | OSCILLATIONS | CLOCK | Computational Biology - methods | Animals | Transcriptome | Circadian Clocks | Mice | Software | Circadian Rhythm | Machine Learning | Learning | Circadian rhythms | Databases | Cognition | Gene expression | Estimates | Bioinformatics | Computer programs | Ismb 2016 Proceedings July 8 to July 12, 2016, Orlando, Florida
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11. Full Text Distinct metabolic adaptation of liver circadian pathways to acute and chronic patterns of alcohol intake
by Gaucher, Jonathan and Kinouchi, Kenichiro and Ceglia, Nicholas and Montellier, Emilie and Peleg, Shahaf and Greco, Carolina Magdalen and Schmidt, Andreas and Forne, Ignasi and Masri, Selma and Baldi, Pierre and Imhof, Axel and Sassone-Corsi, Paolo
Proceedings of the National Academy of Sciences, ISSN 0027-8424, 11/2019, p. 201911189
Binge drinking and chronic exposure to ethanol contribute to alcoholic liver diseases (ALDs). A potential link between ALDs and circadian disruption has been... 
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12. Full Text What time is it? Deep learning approaches for circadian rhythms
by Agostinelli, Forest and Ceglia, Nicholas and Shahbaba, Babak and Sassone-Corsi, Paolo and Baldi, Pierre
Bioinformatics (Oxford, England), ISSN 1367-4803, 10/2016, Volume 32, Issue 19, pp. 3051 - 3051
Corrigendum
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13. Full Text Comparative circadian metabolomics reveal differential effects of nutritional challenge in the Serum and Liver
by Abbondante, Serena and Eckel-Mahan, Kristin L and Ceglia, Nicholas J and Baldi, Pierre and Sassone-Corsi, Paolo
Journal of Biological Chemistry, ISSN 0021-9258, 02/2016, Volume 291, Issue 6, pp. 2812 - 2828
Diagnosis and therapeutic interventions in pathological conditions rely upon clinical monitoring of key metabolites in the serum. Recent studies show that a... 
BETA-SITOSTEROL | SHIFT WORK | METABOLISM | KEY PATHWAYS | BIOCHEMISTRY & MOLECULAR BIOLOGY | GENE-EXPRESSION | BODY-MASS INDEX | INSULIN SENSITIVITY | CLOCK | CARDIOVASCULAR RISK-FACTORS | ADIPOSE-TISSUE | Metabolomics | Animals | Dietary Fats - pharmacology | Liver - metabolism | Male | Mice | Blood Proteins - metabolism | Circadian Rhythm | Metabolism | serum | liver | metabolomics | circadian rhythm
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14. Full Text CircadiOmics: circadian omic web portal
by Ceglia, Nicholas and Liu, Yu and Chen, Siwei and Agostinelli, Forest and Eckel-Mahan, Kristin and Sassone-Corsi, Paolo and Baldi, Pierre
Nucleic Acids Research, ISSN 0305-1048, 07/2018, Volume 46, Issue W1, pp. W157 - W162
Abstract Circadian rhythms play a fundamental role at all levels of biological organization. Understanding the mechanisms and implications of circadian... 
METABOLISM | RHYTHMS | TRANSCRIPTOME | BEHAVIOR | BIOCHEMISTRY & MOLECULAR BIOLOGY | ARCHITECTURE | COMPONENTS | COORDINATION | TIME | CLOCK | EXPRESSION | Web Server Issue
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15. Full Text What time is it? Deep learning approaches for circadian rhythms (vol 32, pg i8, 2016)
by Agostinelli, F and Ceglia, N and Shahbaba, B and Sassone-Corsi, P and Baldi, P
BIOINFORMATICS, ISSN 1367-4803, 10/2016, Volume 32, Issue 19, pp. 3051 - 3051
BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY
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16. Full Text The pervasiveness and plasticity of circadian oscillations: The coupled circadian-oscillators framework
by Patel, Vishal R and Ceglia, Nicholas and Zeller, Michael and Eckel-Mahan, Kristin and Sassone-Corsi, Paolo and Baldi, Pierre
Bioinformatics, ISSN 1367-4803, 10/2015, Volume 31, Issue 19, pp. 3181 - 3188
Motivation: Circadian oscillations have been observed in animals, plants, fungi and cyanobacteria and play a fundamental role in coordinating the homeostasis... 
METABOLIC SYNDROME | KEY PATHWAYS | REGULATORY MOTIF SITES | BIOCHEMICAL RESEARCH METHODS | LARGE GENE LISTS | DAVID BIOINFORMATICS RESOURCES | SHIFT WORK | RHYTHMS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | MATHEMATICAL & COMPUTATIONAL BIOLOGY | ORCHESTRATED TRANSCRIPTION | CLOCK | EXPRESSION | Animals | Circadian Rhythm Signaling Peptides and Proteins - metabolism | Time Factors | Circadian Rhythm Signaling Peptides and Proteins - genetics | Gene Expression Regulation | Transcriptome | Circadian Rhythm - physiology | Mice | Organ Specificity | Metabolomics - methods | Coupling (molecular) | Networks | Genes | Oscillations | Oscillating | Bioinformatics | Oscillators | Clocks | Original Papers
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