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Long noncoding RNA MALAT1 promotes hepatocellular carcinoma development by SRSF1 upregulation and mTOR activation

Malakar, P., Shilo, A., Mogilevsky, A., Stein, I., Pikarsky, E., Nevo, Y., Benyamini, H., Elgavish, S., Zong, X., Prasanth, K. V. & Karni, R., Mar 1 2017, In : Cancer Research. 77, 5, p. 1155-1167 13 p.

Research output: Contribution to journalArticle

Long Noncoding RNA
Hepatocellular Carcinoma
Up-Regulation
Proto-Oncogenes
Alternative Splicing

Long Noncoding RNA PURPL Suppresses Basal p53 Levels and Promotes Tumorigenicity in Colorectal Cancer

Li, X. L., Subramanian, M., Jones, M. F., Chaudhary, R., Singh, D. K., Zong, X., Gryder, B., Sindri, S., Mo, M., Schetter, A., Wen, X., Parvathaneni, S., Kazandjian, D., Jenkins, L. M., Tang, W., Elloumi, F., Martindale, J. L., Huarte, M., Zhu, Y., Robles, A. I. & 9 others, Frier, S. M., Rigo, F., Cam, M., Ambs, S., Sharma, S., Harris, C. C., Dasso, M., Prasanth, K. V. & Lal, A., Sep 5 2017, In : Cell Reports. 20, 10, p. 2408-2423 16 p.

Research output: Contribution to journalArticle

Long Noncoding RNA
Colorectal Neoplasms
Cells
Cell Cycle Checkpoints
Cell culture

Long-Range Directional Movement of an Interphase Chromosome Site

Chuang, C. H., Carpenter, A. E., Fuchsova, B., Johnson, T., de Lanerolle, P. & Belmont, A. S., Apr 18 2006, In : Current Biology. 16, 8, p. 825-831 7 p.

Research output: Contribution to journalArticle

Interphase
Chromosomes
interphase
chromosomes
Genes

Luminescence resonance energy transfer measurements in myosin

Getz, E. B., Cooke, R. & Selvin, P. R., May 1998, In : Biophysical journal. 74, 5, p. 2451-2458 8 p.

Research output: Contribution to journalArticle

Energy Transfer
Myosins
Luminescence
Actins
Light

Lysine deacetylases regulate the heat shock response including the age-associated impairment of HSF1

Zelin, E. & Freeman, B. C., Apr 10 2015, In : Journal of Molecular Biology. 427, 7, p. 1644-1654 11 p.

Research output: Contribution to journalArticle

Heat-Shock Response
Lysine
Shock
Hot Temperature
Cell Aging

Magnetic Cytoskeleton Affinity Purification of Microtubule Motors Conjugated to Quantum Dots

Tjioe, M., Ryoo, H., Ishitsuka, Y., Ge, P., Bookwalter, C., Huynh, W., McKenney, R. J., Trybus, K. M. & Selvin, P. R., Jul 18 2018, In : Bioconjugate Chemistry. 29, 7, p. 2278-2286 9 p.

Research output: Contribution to journalArticle

Quantum Dots
Cytoskeleton
Microtubules
Semiconductor quantum dots
Purification

Malat1 is not an essential component of nuclear speckles in mice

Nakagawa, S., Ip, J. Y., Shioi, G., Tripathi, V., Zong, X., Hirose, T. & Prasanth, K. V., Aug 1 2012, In : RNA. 18, 8, p. 1487-1499 13 p.

Research output: Contribution to journalArticle

Long Noncoding RNA
RNA Precursors
Knockout Mice
Biological Phenomena
Homologous Recombination

Malat1 regulates myogenic differentiation and muscle regeneration through modulating MyoD transcriptional activity

Chen, X., He, L., Zhao, Y., Li, Y., Zhang, S., Sun, K., So, K., Chen, F., Zhou, L., Lu, L., Wang, L., Zhu, X., Bao, X., Esteban, M. A., Nakagawa, S., Prasanth, K. V., Wu, Z., Sun, H. & Wang, H., Mar 14 2017, In : Cell Discovery. 3, 17002.

Research output: Contribution to journalArticle

Muscle
Regeneration
Myoblasts
Gene expression
Muscles

Mammalian target of rapamycin (mTOR) signaling is required for a late-stage fusion process during skeletal myotube maturation

Park, I. H. & Chen, J., Sep 9 2005, In : Journal of Biological Chemistry. 280, 36, p. 32009-32017 9 p.

Research output: Contribution to journalArticle

Skeletal Muscle Fibers
Sirolimus
Fusion reactions
Phosphotransferases
Muscle Development

Mammalian target of rapamycin and Rictor control neutrophil chemotaxis by regulating Rac/Cdc42 activity and the actin cytoskeleton

He, Y., Li, D., Cook, S. L., Yoon, M. S., Kapoor, A., Rao, C. V., Kenis, P. J. A., Chen, J. & Wang, F., Nov 1 2013, In : Molecular biology of the cell. 24, 21, p. 3369-3380 12 p.

Research output: Contribution to journalArticle

Chemotaxis
Sirolimus
Actin Cytoskeleton
Neutrophils
Actins

Mammalian target of rapamycin regulates miRNA-1 and follistatin in skeletal myogenesis

Sun, Y., Ge, Y., Drnevich, J., Zhao, Y., Band, M. & Chen, J., Jun 28 2010, In : Journal of Cell Biology. 189, 7, p. 1157-1169 13 p.

Research output: Contribution to journalArticle

Follistatin
Muscle Development
Sirolimus
MicroRNAs
Histone Deacetylase 1

MAPK activation and the specification of the D quadrant in the gastropod mollusc, Crepidula fornicata

Henry, J. J. & Perry, K. J., Jan 1 2008, In : Developmental Biology. 313, 1, p. 181-195 15 p.

Research output: Contribution to journalArticle

Gastropoda
Mollusca
Mitogen-Activated Protein Kinase Kinases
Embryonic Structures
Embryonic Organizers

Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler

Chen, Y., Zhang, Y., Wang, Y., Zhang, L., Brinkman, E. K., Adam, S. A., Goldman, R., Van Steensel, B., Ma, J. & Belmont, A. S., Nov 1 2018, In : Journal of Cell Biology. 217, 11, p. 4025-4048 24 p.

Research output: Contribution to journalArticle

Chromosome Mapping
Genome
Chromosomes
Nuclear Lamina
Genes

Mass spectrometric characterization of human histone H3: A bird's eye view

Thomas, C. E., Kelleher, N. L. & Mizzen, C. A., Feb 1 2006, In : Journal of Proteome Research. 5, 2, p. 240-247 8 p.

Research output: Contribution to journalArticle

S 10
Acetylation
Methylation
Colchicine
HeLa Cells

Mass spectrometry-based discovery of circadian peptides

Hatcher, N. G., Atkins, N., Annangudi, S. P., Forbes, A. J., Kelleher, N. L., Gillette, M. U. & Sweedler, J. V., Aug 26 2008, In : Proceedings of the National Academy of Sciences of the United States of America. 105, 34, p. 12527-12532 6 p.

Research output: Contribution to journalArticle

Suprachiasmatic Nucleus
Mass Spectrometry
Peptides
Circadian Clocks
Solid Phase Extraction

Material properties of the cell dictate stress-induced spreading and differentiation in embryonic stemcells

Chowdhury, F., Na, S., Li, D., Poh, Y. C., Tanaka, T. S., Wang, F. & Wang, N., Jan 2010, In : Nature Materials. 9, 1, p. 82-88 7 p.

Research output: Contribution to journalArticle

Stem cells
Materials properties
stem cells
cells
softness

Maximum likelihood estimation of molecular motor kinetics from staircase dwell-time sequences

Milescu, L. S., Yildiz, A., Selvin, P. R. & Sachs, F., Jan 1 2006, In : Biophysical journal. 91, 4, p. 1156-1168 13 p.

Research output: Contribution to journalArticle

Likelihood Functions
Adenosine Triphosphate
Dyneins
Kinesin
Proton-Translocating ATPases

Mechanical force affects expression of an in vitro metastasis-like phenotype in HCT-8 cells

Tang, X., Kuhlenschmidt, T. B., Zhou, J., Bell, P., Wang, F., Kuhlenschmidt, M. S. & Saif, T. A., Oct 20 2010, In : Biophysical journal. 99, 8, p. 2460-2469 10 p.

Research output: Contribution to journalArticle

Neoplasm Metastasis
Phenotype
Cadherins
In Vitro Techniques
Cultured Cells

Mechanistic target of rapamycin controls homeostasis of adipogenesis

Yoon, M. S., Zhang, C., Sun, Y., Schoenherr, C. J. & Chen, J., Aug 1 2013, In : Journal of Lipid Research. 54, 8, p. 2166-2173 8 p.

Research output: Contribution to journalArticle

Adipogenesis
Sirolimus
Homeostasis
Peroxisome Proliferator-Activated Receptors
CCAAT-Enhancer-Binding Proteins

Mediation of pyrethroid insecticide toxicity to honey bees (Hymenoptera: Apidae) by cytochrome P450 monooxygenases

Johnson, R. M., Wen, Z., Schuler, M. A. & Berenbaum, M. R., Aug 2006, In : Journal of economic entomology. 99, 4, p. 1046-1050 5 p.

Research output: Contribution to journalArticle

pyrethroid insecticides
pyrethroid
Apidae
honey
fluvalinate

Melatonin action and signal transduction in the rat suprachiasmatic circadian clock: Activation of protein kinase C at dusk and dawn

Mcarthur, A. J., Hunt, A. E. & Gillette, M. U., Jan 1 1997, In : Endocrinology. 138, 2, p. 627-634 8 p.

Research output: Contribution to journalArticle

Circadian Clocks
Melatonin
Protein Kinase C
Signal Transduction
Suprachiasmatic Nucleus

Melatonin desensitizes endogenous MT2 melatonin receptors in the rat suprachiasmatic nucleus: Relevance for defining the periods of sensitivity of the mammalian circadian clock to melatonin

Gerdin, M. J., Masana, M. I., Rivera-Bermúdez, M. A., Hudson, R. L., Earnest, D. J., Gillette, M. U. & Dubocovich, M. L., Nov 1 2004, In : FASEB Journal. 18, 14, p. 1646-1656 11 p.

Research output: Contribution to journalArticle

Melatonin MT2 Receptor
Circadian Clocks
Suprachiasmatic Nucleus
melatonin
Melatonin

Melatonin directly resets the rat suprachiasmatic circadian clock in vitro

McArthur, A. J., Gillette, M. U. & Prosser, R. A., Nov 22 1991, In : Brain Research. 565, 1, p. 158-161 4 p.

Research output: Contribution to journalArticle

Circadian Clocks
Melatonin
Suprachiasmatic Nucleus
Biological Clocks
Pineal Gland

Melatonin signal transduction pathways require E-Box-Mediated transcription of Per1 and Per2 to reset the SCN clock at dusk

Kandalepas, P. C., Mitchell, J. W. & Gillette, M. U. G., Jun 2016, In : PloS one. 11, 6, e0157824.

Research output: Contribution to journalArticle

Signal transduction
Suprachiasmatic Nucleus
melatonin
Melatonin
Transcription
Papilio polyxenes
psoralens
NADPH-Ferrihemoprotein Reductase
cytochrome P-450
NADP (coenzyme)

Metabolism of myristicin by Depressaria pastinacella CYP6AB3v2 and inhibition by its metabolite

Mao, W., Zangerl, A. R., Berenbaum, M. R. & Schuler, M. A., Jun 1 2008, In : Insect Biochemistry and Molecular Biology. 38, 6, p. 645-651 7 p.

Research output: Contribution to journalArticle

Depressaria pastinacella
Enzyme inhibition
Metabolites
Pastinaca
Metabolism

Methods for examining lens regeneration in xenopus

Henry, J. J., Perry, K. J. & Hamilton, P. W., Apr 2019, In : Cold Spring Harbor protocols. 2019, 4, p. 268-273 6 p.

Research output: Contribution to journalArticle

Xenopus
Lenses
Regeneration
Corneal Epithelium
Anura

Microfluidic devices for culturing primary mammalian neurons at low densities

Millet, L. J., Stewart, M. E., Sweedler, J. V., Nuzzo, R. G. & Gillette, M. U., Jan 1 2007, In : Lab on a chip. 7, 8, p. 987-994 8 p.

Research output: Contribution to journalArticle

Lab-On-A-Chip Devices
Polydimethylsiloxane
Microfluidics
Neurons
Biocompatibility

MicroRNA-146b promotes myogenic differentiation and modulates multiple gene targets in muscle cells

Khanna, N., Ge, Y. & Chen, J., Jun 23 2014, In : PloS one. 9, 6, e100657.

Research output: Contribution to journalArticle

MicroRNAs
microRNA
myocytes
Muscle Cells
Muscle

Microtubule binding by dynactin is required for microtubule organization but not cargo transport

Kim, H., Ling, S. C., Rogers, G. C., Kural, C., Selvin, P. R., Rogers, S. L. & Gelfand, V. I., Feb 26 2007, In : Journal of Cell Biology. 176, 5, p. 641-651 11 p.

Research output: Contribution to journalArticle

Microtubules
Dyneins
Cytoplasmic Dyneins
Microtubule-Organizing Center
Cytochalasin D

Mild performic acid oxidation enhances chromatographic and top down mass spectrometric analyses of histones

Pesavento, J. J., Garcia, B. A., Streeky, J. A., Kelleher, N. L. & Mizzen, C. A., Sep 1 2007, In : Molecular and Cellular Proteomics. 6, 9, p. 1510-1526 17 p.

Research output: Contribution to journalArticle

Histones
Oxidation
Post Translational Protein Processing
Electrospray ionization
Reverse-Phase Chromatography

MIR100 host gene-encoded lncRNAs regulate cell cycle by modulating the interaction between HuR and its target mRNAs

Sun, Q., Tripathi, V., Yoon, J. H., Singh, D. K., Hao, Q., Min, K. W., Davila, S., Zealy, R. W., Li, X. L., Polycarpou-Schwarz, M., Lehrmann, E., Zhang, Y., Becker, K. G., Freier, S. M., Zhu, Y., Diederichs, S., Prasanth, S. G., Lal, A., Gorospe, M. & Prasanth, K. V., Jan 1 2018, In : Nucleic acids research. 46, 19, p. 10405-10416 12 p.

Research output: Contribution to journalArticle

Long Noncoding RNA
MicroRNAs
Cell Cycle
Messenger RNA
Genes

Mitotic chromosome structure: Reproducibility of folding and symmetry between sister chromatids

Strukov, Y. G. & Belmont, A. S., Feb 18 2009, In : Biophysical journal. 96, 4, p. 1617-1628 12 p.

Research output: Contribution to journalArticle

Chromosome Structures
Chromatids
Chromosomes
Metaphase
Chromatin
Sf9 Cells
Baculoviridae
Anchors
cytochrome P-450
Cytochrome P-450 Enzyme System

Modifications of H3 and H4 during chromatin replication, nucleosome assembly, and histone exchange

Benson, L. J., Gu, Y., Yakovleva, T., Tong, K., Barrows, C., Strack, C. L., Cook, R. G., Mizzen, C. A. & Annunziato, A. T., Apr 7 2006, In : Journal of Biological Chemistry. 281, 14, p. 9287-9296 10 p.

Research output: Contribution to journalArticle

Histone Code
Nucleosomes
Histones
Chromatin
Acetylation

Modified nodal integral method for the three-dimensional, time-dependent, incompressible Navier-Stokes equations

Wang, F. & Uddin, R., Jan 2005, In : Nuclear Science and Engineering. 149, 1, p. 107-114 8 p.

Research output: Contribution to journalArticle

Navier Stokes equations
Ordinary differential equations
Prisms
Partial differential equations
Convection

Modulation of histone acetylation by [4-(acetylamino)-N-(2-amino-phenyl) benzamide] in HCT-8 colon carcinoma

Kraker, A. J., Mizzen, C. A., Hartl, B. G., Miin, J., Allis, C. D. & Merriman, R. L., Apr 1 2003, In : Molecular Cancer Therapeutics. 2, 4, p. 401-408 8 p.

Research output: Contribution to journalArticle

Acetylation
Histones
Colon
Carcinoma
Histone Deacetylase 2

Molecular, phylogenetic and developmental analyses of Sall proteins in bilaterians

Lorente-Sorolla, J., Truchado-Garcia, M., Perry, K. J., Henry, J. Q. & Grande, C., Apr 10 2018, In : EvoDevo. 9, 1, 9.

Research output: Contribution to journalArticle

Zinc Fingers
Snails
zinc finger motif
phylogenetics
protein
Methoxsalen
Pheromones
Insecticides
Cytochrome P-450 Enzyme System
Zea mays

Molecular analysis of dicot and monocot small nuclear RNA populations.

Egeland, D. B., Sturtevant, A. P. & Schuler, M. A., Jun 1989, In : The Plant cell. 1, 6, p. 633-643 11 p.

Research output: Contribution to journalArticle

small nuclear RNA
Small Nuclear RNA
Magnoliopsida
Liliopsida
Population

Molecular analysis of mouse rab11b: A new type of mammalian ypt/rab protein

Lai, F., Stubbs, L. & Artzt, K., Aug 1994, In : Genomics. 22, 3, p. 610-616 7 p.

Research output: Contribution to journalArticle

Genes
Proteins
Chromosomes, Human, Pair 17
Chromosomes, Human, Pair 1
Protein Sequence Analysis

Molecular analysis of multiple CYP6B genes from polyphagous Papilio species

Li, W., Berenbaum, M. R. & Schuler, M. A., Sep 6 2001, In : Insect Biochemistry and Molecular Biology. 31, 10, p. 999-1011 13 p.

Research output: Contribution to journalArticle

Papilio glaucus
Papilio
psoralens
Genes
Methoxsalen

Molecular chaperone-mediated nuclear protein dynamics

Echtenkamp, F. J. & Freeman, B. C., Jan 1 2014, In : Current Protein and Peptide Science. 15, 3, p. 216-224 9 p.

Research output: Contribution to journalArticle

Molecular Chaperones
Nuclear Proteins
Proteins
Foster Home Care
Accessories

Molecular characterization of CYP73A9 and CYP82A1 P450 genes involved in plant defense in pea

Whitbred, J. M. & Schuler, M. A., Jan 1 2000, In : Plant physiology. 124, 1, p. 47-58 12 p.

Research output: Contribution to journalArticle

Peas
peas
Mixed Function Oxygenases
promoter regions
phenylpropanoids
methoxsalen
Methoxsalen
Helicoverpa zea
Cloning
Molecular Cloning

Molecular comparison of monocot and dicot U1 and U2 snRNAs

Musci, M. A., Egeland, D. B. & Schuler, M. A., Jul 1992, In : The Plant Journal. 2, 4, p. 589-599 11 p.

Research output: Contribution to journalArticle

small nuclear RNA
Small Nuclear Ribonucleoproteins
Magnoliopsida
Liliopsida
Triticum

Molecular definitions of fatty acid hydroxylases in Arabidopsis thaliana

Rupasinghe, S. G., Duan, H. & Schuler, M. A., Jul 1 2007, In : Proteins: Structure, Function and Genetics. 68, 1, p. 279-293 15 p.

Research output: Contribution to journalArticle

Mixed Function Oxygenases
Arabidopsis
Fatty Acids
lauric acid
Oleic Acid

Molecular docking of substrates and inhibitors in the catalytic site of CYP6B1, an insect cytochrome P450 monooxygenase

Baudry, J., Li, W., Pan, L., Berenbaum, M. R. & Schuler, M. A., Aug 1 2003, In : Protein Engineering. 16, 8, p. 577-587 11 p.

Research output: Contribution to journalArticle

Mixed Function Oxygenases
Cytochrome P-450 Enzyme System
Insects
Catalytic Domain
Substrates

Molecular markers for corneal epithelial cells in larval vs. adult Xenopus frogs

Sonam, S., Srnak, J. A., Perry, K. J. & Henry, J. J., Jul 2019, In : Experimental Eye Research. 184, p. 107-125 19 p.

Research output: Contribution to journalArticle

Xenopus
Anura
Cornea
Stem Cells
Epithelial Cells

Molecular motors one at a time: FIONA to the rescue

Kural, C., Balci, H. & Selvin, P. R., Nov 30 2005, In : Journal of Physics Condensed Matter. 17, 47, p. S3979-S3995

Research output: Contribution to journalArticle

myosins
Myosin Type V
Fluorescence
ribonucleic acids
Dyneins