Research Output 1972 2019

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2012

Glycerolipid signals alter mTOR complex 2 (mTORC2) to diminish insulin signaling

Zhang, C., Wendel, A. A., Keogh, M. R., Harris, T. E., Chen, J. & Coleman, R. A., Jan 31 2012, In : Proceedings of the National Academy of Sciences of the United States of America. 109, 5, p. 1667-1672 6 p.

Research output: Contribution to journalArticle

Acyltransferases
Phosphatidic Acids
Insulin
Hepatocytes
Diglycerides

Identification of key regulatory pathways of myeloid differentiation using an mESC-based karyotypically normal cell model

Li, D., Yang, H., Nan, H., Liu, P., Pang, S., Zhao, Q., Karni, R., Kamps, M. P., Xu, Y., Zhou, J., Wiedmer, T., Sims, P. J. & Wang, F., Dec 6 2012, In : Blood. 120, 24, p. 4712-4719 8 p.

Research output: Contribution to journalArticle

Embryonic Stem Cells
Stem cells
Karyotyping
Estrogens
Neutrophils

Malat1 is not an essential component of nuclear speckles in mice

Nakagawa, S., Ip, J. Y., Shioi, G., Tripathi, V., Zong, X., Hirose, T. & Kannanganattu, P. K., 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

Multicolor super-resolution DNA imaging for genetic analysis

Baday, M., Cravens, A., Hastie, A., Kim, H., Kudeki, D. E., Kwok, P. Y., Xiao, M. & Selvin, P. R., Jul 11 2012, In : Nano Letters. 12, 7, p. 3861-3866 6 p.

Research output: Contribution to journalArticle

DNA
deoxyribonucleic acid
Endonucleases
Imaging techniques
enzymes

Orc2 protects ORCA from ubiquitin-mediated degradation

Shen, Z. & Prasanth, S. G., Oct 1 2012, In : Cell Cycle. 11, 19, p. 3578-3589 12 p.

Research output: Contribution to journalArticle

Origin Recognition Complex
Ubiquitin
Ubiquitination
Chromatin
Cell Cycle

Over a century of neuron culture: From the hanging drop to microfluidic devices

Millet, L. J. & Gillette, M. L., Dec 1 2012, In : Yale Journal of Biology and Medicine. 85, 4, p. 501-521 21 p.

Research output: Contribution to journalArticle

Lab-On-A-Chip Devices
Microfluidics
Neurons
Brain
Hydrogels

Peptidomic analyses of mouse astrocytic cell lines and rat primary cultured astrocytes

Yin, P., Knolhoff, A. M., Rosenberg, H. J., Millet, L. J., Gillette, M. L. & Sweedler, J. V., Aug 3 2012, In : Journal of Proteome Research. 11, 8, p. 3965-3973 9 p.

Research output: Contribution to journalArticle

Astrocytes
Rats
Cells
Cell Line
Peptides

Reactive and bioactive cationic α-helical polypeptide template for nonviral gene delivery

Gabrielson, N. P., Lu, H., Yin, L., Li, D., Wang, F. & Cheng, J., Jan 27 2012, In : Angewandte Chemie - International Edition. 51, 5, p. 1143-1147 5 p.

Research output: Contribution to journalArticle

Polypeptides
Glutamic Acid
Genes
Peptides
Polyethyleneimine

Replicating and transcribing on twisted roads of chromatin

Giri, S. & Prasanth, S. G., May 1 2012, In : Briefings in Functional Genomics. 11, 3, p. 188-204 17 p., elr047.

Research output: Contribution to journalArticle

Chromatin
DNA
Histones
DNA Replication
Transcription

SRSF1 regulates the assembly of pre-mRNA processing factors in nuclear speckles

Tripathi, V., Song, D. Y., Zong, X., Shevtsov, S. P., Hearn, S., Fu, X. D., Dundr, M. & Kannanganattu, P. K., Sep 15 2012, In : Molecular biology of the cell. 23, 18, p. 3694-3706 13 p.

Research output: Contribution to journalArticle

RNA Precursors
Interphase
Cell Nucleus
RNA
Gene Expression

The natural product cucurbitacin e inhibits depolymerization of actin filaments

Sörensen, P. M., Iacob, R. E., Fritzsche, M., Engen, J. R., Brieher, W. M., Charras, G. & Eggert, U. S., Sep 21 2012, In : ACS chemical biology. 7, 9, p. 1502-1508 7 p.

Research output: Contribution to journalArticle

Cucurbitacins
Depolymerization
Biological Products
Actin Cytoskeleton
Actins

The p23 Molecular Chaperone and GCN5 Acetylase Jointly Modulate Protein-DNA Dynamics and Open Chromatin Status

Zelin, E., Zhang, Y., Toogun, O. A., Zhong, S. & Freeman, B. C., Nov 9 2012, In : Molecular cell. 48, 3, p. 459-470 12 p.

Research output: Contribution to journalArticle

Acetylesterase
Molecular Chaperones
Chromatin
DNA
Proteins

The recruitment of the U5 snRNP to nascent transcripts requires internal loop 1 of U5 snRNA

Kim, R., Paschedag, J., Novikova, N. & Bellini, M., Dec 1 2012, In : Chromosome Research. 20, 8, p. 943-951 9 p.

Research output: Contribution to journalArticle

U5 Small Nuclear Ribonucleoproteins
Oocytes
Spliceosomes
U5 small nuclear RNA
RNA Precursors

The transcription factor ultraspiracle influences honey bee social behavior and behavior-related gene expression

Ament, S. A., Wang, Y., Chen, C. C., Blatti, C. A., Hong, F., Liang, Z. S., Negre, N., White, K. P., Rodriguez-Zas, S. L., Mizzen, C. A., Sinha, S., Zhong, S. & Robinson, G. E., Mar 1 2012, In : PLoS genetics. 8, 3, e1002596.

Research output: Contribution to journalArticle

Fat Body
Honey
Social Behavior
Gene Regulatory Networks
Bees

Using fixed fiduciary markers for stage drift correction

Lee, S. H., Baday, M., Tjioe, M., Simonson, P. D., Zhang, R., Cai, E. & Selvin, P. R., May 21 2012, In : Optics Express. 20, 11, p. 12177-12183 7 p.

Research output: Contribution to journalArticle

fiduciaries
markers
fluorescence
walking
clocks

VITAL NMR: Using chemical shift derived secondary structure information for a limited set of amino acids to assess homology model accuracy

Brothers, M. C., Nesbitt, A. E., Hallock, M. J., Rupasinghe, S. G., Tang, M., Harris, J., Baudry, J., Schuler, M. A. & Rienstra, C. M., Jan 1 2012, In : Journal of Biomolecular NMR. 52, 1, p. 41-56 16 p.

Research output: Contribution to journalArticle

Chemical shift
Nuclear magnetic resonance
Amino Acids
Proteins
Labeling

Williams Syndrome Transcription Factor is critical for neural crest cell function in Xenopus laevis

Barnett, C., Yazgan, O., Kuo, H. C., Malakar, S., Thomas, T., Fitzgerald, A., Harbour, W., Henry, J. J. & Krebs, J. E., Sep 1 2012, In : Mechanisms of Development. 129, 9-12, p. 324-338 15 p.

Research output: Contribution to journalArticle

Williams Syndrome
Neural Crest
Xenopus laevis
Transcription Factors
Embryonic Structures

α-Actinin-4/FSGS1 is required for Arp2/3-dependent actin assembly at the adherens junction

Tang, V. & Brieher, W. M., Jan 1 2012, In : Journal of Cell Biology. 196, 1, p. 115-130 16 p.

Research output: Contribution to journalArticle

Actinin
Adherens Junctions
Actins
Cadherins
Intercellular Junctions
2011

3D microperiodic hydrogel scaffolds for robust neuronal cultures

Hanson Shepherd, J. N., Parker, S. T., Shepherd, R. F., Gillette, M. L., Lewis, J. A. & Nuzzo, R. G., Jan 7 2011, In : Advanced Functional Materials. 21, 1, p. 47-54 8 p.

Research output: Contribution to journalArticle

Hydrogel
Hydrogels
Scaffolds
inks
cells

A BEN-domain-containing protein associates with heterochromatin and represses transcription

Sathyan, K. M., Shen, Z., Tripathi, V., Kannanganattu, P. K. & Prasanth, S. G., Sep 15 2011, In : Journal of cell science. 124, 18, p. 3149-3163 15 p.

Research output: Contribution to journalArticle

Heterochromatin
Chromatin
Histone Deacetylases
Cell Cycle Checkpoints
Eukaryota

A cell-instructive hydrogel to regulate malignancy of 3D tumor spheroids with matrix rigidity

Liang, Y., Jeong, J., DeVolder, R. J., Cha, C., Wang, F., Tong, Y. W. & Kong, H., Dec 1 2011, In : Biomaterials. 32, 35, p. 9308-9315 8 p.

Research output: Contribution to journalArticle

Hydrogel
Hydrogels
Rigidity
Tumors
Gels

A new regulatory function of the region proximal to the RGG box in the fragile X mental retardation protein

Blackwell, E. & Ceman, S., Sep 15 2011, In : Journal of cell science. 124, 18, p. 3060-3065 6 p.

Research output: Contribution to journalArticle

Fragile X Mental Retardation Protein
Nucleic Acid Regulatory Sequences
Exons
Protein Isoforms
Aptitude

A substrate-specific cytochrome P450 monooxygenase, CYP6AB11, from the polyphagous navel orangeworm (Amyelois transitella)

Niu, G., Rupasinghe, S. G., Zangerl, A. R., Siegel, J. P., Schuler, M. A. & Berenbaum, M. R., Apr 1 2011, In : Insect Biochemistry and Molecular Biology. 41, 4, p. 244-253 10 p.

Research output: Contribution to journalArticle

Amyelois transitella
piperonyl butoxide
synergists
Mixed Function Oxygenases
Piperonyl Butoxide
Glycogen Synthase Kinase 3
Apigenin
Luteolin
Citrus
Quercetin

Class III PI-3-kinase activates phospholipase D in an amino acid-sensing mTORC1 pathway

Yoon, M. S., Du, G., Backer, J. M., Frohman, M. A. & Chen, J., Oct 31 2011, In : Journal of Cell Biology. 195, 3, p. 435-447 13 p.

Research output: Contribution to journalArticle

Phospholipase D
Phosphatidylinositol 3-Kinases
Amino Acids
Aminoacylation
Sirolimus

Crystal structure of a phenol-coupling P450 monooxygenase involved in teicoplanin biosynthesis

Li, Z., Rupasinghe, S. G., Schuler, M. A. & Nair, S. K., Jun 1 2011, In : Proteins: Structure, Function and Bioinformatics. 79, 6, p. 1728-1738 11 p.

Research output: Contribution to journalArticle

Teicoplanin
Biosynthesis
Mixed Function Oxygenases
Phenol
Glycopeptides
Acaricides
Honey
Bees
Coumaphos
Pesticides

Dispersion-relation phase spectroscopy of intracellular transport

Wang, R., Wang, Z., Millet, L., Gillette, M. L., Levine, A. J. & Popescu, G., Oct 10 2011, In : Optics Express. 19, 21, p. 20571-20579 9 p.

Research output: Contribution to journalArticle

cytoplasm
mass distribution
spectroscopy
decay rates
diffusion coefficient

Extension of a three-helix bundle domain of myosin VI and key role of calmodulins

Liu, Y., Hsin, J., Kim, H. J., Selvin, P. R. & Schulten, K., Jan 1 2011, In : Biophysical journal. 100, 12, p. 2964-2973 10 p.

Research output: Contribution to journalArticle

Calmodulin
Molecular Motor Proteins
Protein Unfolding
Dimerization
Molecular Dynamics Simulation

Facioscapulohumeral muscular dystrophy region gene 1 Is a dynamic RNA-associated and actin-bundling protein

Sun, C. Y. J., Van Koningsbruggen, S., Long, S. W., Straasheijm, K., Klooster, R., Jones, T. I., Bellini, M., Levesque, L., Brieher, W. M., Van Der Maarel, S. M. & Jones, P. L., Aug 12 2011, In : Journal of Molecular Biology. 411, 2, p. 397-416 20 p.

Research output: Contribution to journalArticle

Facioscapulohumeral Muscular Dystrophy
Actins
RNA
Genes
Proteins

FGF signaling is required for lens regeneration in Xenopus Laevis

Fukui, L. & Henry, J. J., Jan 1 2011, In : Biological Bulletin. 221, 1, p. 137-145 9 p.

Research output: Contribution to journalArticle

Xenopus laevis
Lens
Lenses
Regeneration
Fibroblast Growth Factor Receptors

Function and evolution of C2H2 zinc finger arrays

Stubbs, L. J., Sun, Y. & Caetano-Anolles, D., Jan 1 2011, In : Sub-Cellular Biochemistry. 52, p. 75-94 20 p.

Research output: Contribution to journalArticle

Zinc
Transcription Factors
Nucleotide Motifs
Proteins
DNA

Gain, loss and divergence in primate Zinc-Finger genes: A rich resource for evolution of gene regulatory differences between species

Nowick, K., Fields, C. J., Gernat, T., Caetano-Anolles, D., Kholina, N. & Stubbs, L. J., Jul 1 2011, In : PloS one. 6, 6, e21553.

Research output: Contribution to journalArticle

zinc finger motif
Zinc Fingers
Regulator Genes
regulator genes
Primates

Generation of melanocytes from induced pluripotent stem cells

Yang, R., Jiang, M., Kumar, S. M., Xu, T., Wang, F., Xiang, L. & Xu, X., Dec 2011, In : Journal of Investigative Dermatology. 131, 12, p. 2458-2466 9 p.

Research output: Contribution to journalArticle

Induced Pluripotent Stem Cells
Melanocytes
Stem cells
Fibroblasts
Tail

Global Functional Map of the p23 Molecular Chaperone Reveals an Extensive Cellular Network

Echtenkamp, F. J., Zelin, E., Oxelmark, E., Woo, J. I., Andrews, B. J., Garabedian, M. & Freeman, B. C., Jul 22 2011, In : Molecular cell. 43, 2, p. 229-241 13 p.

Research output: Contribution to journalArticle

Molecular Chaperones
Yeasts
Validation Studies
Mutagens
Ribosomes

IGF-II is regulated by microRNA-125b in skeletal myogenesis

Ge, Y., Sun, Y. & Chen, J., Jan 10 2011, In : Journal of Cell Biology. 192, 1, p. 69-81 13 p.

Research output: Contribution to journalArticle

Insulin-Like Growth Factor II
Muscle Development
MicroRNAs
Sirolimus
Muscles

Label-free intracellular transport measured by spatial light interference microscopy

Wang, Z., Millet, L., Chan, V., Ding, H., Gillette, M. U., Bashir, R. & Popescu, G., Feb 1 2011, In : Journal of biomedical optics. 16, 2, 026019.

Research output: Contribution to journalArticle

Light interference
organelles
Labels
Microscopic examination
microscopy

Larval environmental stress alters Aedes aegypti competence for Sindbis virus

Muturi, E. J., Kim, C-H., Alto, B. W., Berenbaum, M. R. & Schuler, M. A., Aug 1 2011, In : Tropical Medicine and International Health. 16, 8, p. 955-964 10 p.

Research output: Contribution to journalArticle

Sindbis Virus
Cecropins
Aedes
Defensins
Culicidae

Live-cell chromosome dynamics and outcome of X chromosome pairing events during ES cell differentiation

Masui, O., Bonnet, I., Le Baccon, P., Brito, I., Pollex, T., Murphy, N., Hupé, P., Barillot, E., Belmont, A. S. & Heard, E., Apr 29 2011, In : Cell. 145, 3, p. 447-458 12 p.

Research output: Contribution to journalArticle

Chromosome Pairing
X Chromosome
Chromosomes
Cell Differentiation
X Chromosome Inactivation

One-dimensional deterministic transport in neurons measured by dispersion-relation phase spectroscopy

Wang, R., Wang, Z., Leigh, J., Sobh, N., Millet, L., Gillette, M. L., Levine, A. J. & Popescu, G., Sep 21 2011, In : Journal of Physics Condensed Matter. 23, 37, 374107.

Research output: Contribution to journalArticle

neurons
Neurons
Spectroscopy
cargo
spectroscopy

Optical measurement of cycle-dependent cell growth

Mir, M., Wang, Z., Shen, Z., Bednarz, M., Bashir, R., Golding, I., Prasanth, S. G. & Popescu, G., Aug 9 2011, In : Proceedings of the National Academy of Sciences of the United States of America. 108, 32, p. 13124-13129 6 p.

Research output: Contribution to journalArticle

Cell Cycle
Growth
Interference Microscopy
Cell Size
Light

"ORCanization" On heterochromatin linking DNA replication initiation to chromatin organization

Chakraborty, A., Shen, Z. & Prasanth, S. G., Jun 2011, In : Epigenetics. 6, 6, p. 665-670 6 p.

Research output: Contribution to journalArticle

Origin Recognition Complex
Heterochromatin
DNA Replication
Chromatin
Histone Code

Phosphatidic acid activates mammalian target of rapamycin complex 1 (mTORC1) kinase by displacing FK506 binding protein 38 (FKBP38) and exerting an allosteric effect

Yoon, M. S., Sun, Y., Arauz, E., Jiang, Y. & Chen, J., Aug 26 2011, In : Journal of Biological Chemistry. 286, 34, p. 29568-29574 7 p.

Research output: Contribution to journalArticle

Tacrolimus Binding Proteins
Phosphatidic Acids
Phosphotransferases
Tacrolimus Binding Protein 1A
Chemical activation

Probing cellular protein complexes using single-molecule pull-down

Jain, A., Liu, R., Ramani, B., Arauz, E., Ishitsuka, Y., Ragunathan, K., Park, J., Chen, J., Xiang, Y. K. & Ha, T., May 26 2011, In : Nature. 473, 7348, p. 484-488 5 p.

Research output: Contribution to journalArticle

Proteins
Macromolecular Substances
Tissue Extracts
Cyclic AMP-Dependent Protein Kinases
Fluorescence Microscopy

Raptor and rheb negatively regulate skeletal myogenesis through suppression of insulin receptor substrate 1 (IRS1)

Ge, Y., Yoon, M. S. & Chen, J., Oct 14 2011, In : Journal of Biological Chemistry. 286, 41, p. 35675-35682 8 p.

Research output: Contribution to journalArticle

Raptors
Insulin Receptor Substrate Proteins
Muscle Development
Sirolimus
Phosphorylation

Ring-opening polymerization of γ-(4-vinylbenzyl)-l-glutamate N-carboxyanhydride for the synthesis of functional polypeptides

Lu, H., Bai, Y., Wang, J., Gabrielson, N. P., Wang, F., Lin, Y. & Cheng, J., Aug 23 2011, In : Macromolecules. 44, 16, p. 6237-6240 4 p.

Research output: Contribution to journalArticle

Polypeptides
Ring opening polymerization
Glutamic Acid
Polymerization
Amination

Role of mechanical factors in fate decisions of stem cells

Li, D., Zhou, J., Chowdhury, F., Cheng, J., Wang, N. & Wang, F., Mar 1 2011, In : Regenerative Medicine. 6, 2, p. 229-240 12 p.

Research output: Contribution to journalArticle

Blastocyst Inner Cell Mass
Adult Stem Cells
Cell Shape
Embryonic Stem Cells
Stem cells

Single-molecule-based super-resolution images in the presence of multiple fluorophores

Simonson, P. D., Rothenberg, E. & Selvin, P. R., Nov 9 2011, In : Nano letters. 11, 11, p. 5090-5096 7 p.

Research output: Contribution to journalArticle

Fluorophores
image resolution
Image resolution
Molecules
diffraction

Single-virus tracking reveals a spatial receptor-dependent search mechanism

Rothenberg, E., Sepúlveda, L. A., Skinner, S. O., Zeng, L., Selvin, P. R. & Golding, I., Jan 1 2011, In : Biophysical journal. 100, 12, p. 2875-2882 8 p.

Research output: Contribution to journalArticle

Viruses
Virus Attachment
Virus Receptors
Viral Genome
Virus Diseases

Spatial light interference microscopy (SLIM)

Wang, Z., Millet, L., Mir, M., Ding, H., Unarunotai, S., Rogers, J. A., Gillette, M. L. & Popescu, G., Jan 17 2011, In : Optics Express. 19, 2, p. 1016-1026 11 p.

Research output: Contribution to journalArticle

microscopy
interference
phase contrast
cells
optical paths