Research Output 1972 2019

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2017

Beyond the sea: Crepidula atrasolea as a spiralian model system

Henry, J. J., Lesoway, M. P., Perry, K. J., Osborne, C. C., Shankland, M. & Lyons, D. C., Jan 1 2017, In : International Journal of Developmental Biology. 61, 8-9, p. 479-493 15 p.

Research output: Contribution to journalArticle

Snails
Oceans and Seas
Biological Models
Gastropoda
Organogenesis

Cap-n-Collar promotes tissue regeneration by regulating ROS and JNK signaling in the drosophila melanogaster wing imaginal disc

Brock, A. R., Seto, M. & Smith-Bolton, R., Jul 2017, In : Genetics. 206, 3, p. 1505-1520 16 p.

Research output: Contribution to journalArticle

Imaginal Discs
Drosophila melanogaster
Regeneration
Reactive Oxygen Species
JNK Mitogen-Activated Protein Kinases

Combinatorial Discovery of Defined Substrates That Promote a Stem Cell State in Malignant Melanoma

Zhang, D., Lee, J., Sun, M. B., Pei, Y., Chu, J., Gillette, M. L., Fan, T. M. & Kilian, K., May 24 2017, In : ACS Central Science. 3, 5, p. 381-393 13 p.

Research output: Contribution to journalArticle

Stem cells
Cells
Peptides
Proteoglycans
Substrates

Comparative analysis of weighted gene coexpression networks in human and mouse

Eidsaa, M., Stubbs, L. & Almaas, E., Nov 2017, In : PloS one. 12, 11, e0187611.

Research output: Contribution to journalArticle

Gene Regulatory Networks
Genes
mice
genes
Gene Ontology

CRMP-1 enhances EVL-mediated actin elongation to build lamellipodia and the actin cortex

Yu-Kemp, H. C., Kemp, J. P. & Brieher, W. M., Jan 1 2017, In : Journal of Cell Biology. 216, 8, p. 2463-2479 17 p.

Research output: Contribution to journalArticle

Pseudopodia
Actins
Actin Cytoskeleton
Polymerization
Madin Darby Canine Kidney Cells

Cytochrome P450 diversification and hostplant utilization patterns in specialist and generalist moths: Birth, death and adaptation

Calla, B., Noble, K., Johnson, R. M., Walden, K. K. O., Schuler, M. A., Robertson, H. M. & Berenbaum, M. R., Nov 2017, In : Molecular ecology. 26, 21, p. 6021-6035 15 p.

Research output: Contribution to journalArticle

Moths
cytochrome P-450
generalist
moth
Cytochrome P-450 Enzyme System
Honey
Bees
Quercetin
Triazoles
Phytochemicals
Metabolites
Ionization
Dopamine
Desorption
Brain

EPRS is a critical mTORC1-S6K1 effector that influences adiposity in mice

Arif, A., Terenzi, F., Potdar, A. A., Jia, J., Sacks, J., China, A., Halawani, D., Vasu, K., Li, X., Brown, J. M., Chen, J., Kozma, S. C., Thomas, G. & Fox, P. L., Feb 16 2017, In : Nature. 542, 7641, p. 357-361 5 p.

Research output: Contribution to journalArticle

Ribosomal Protein S6 Kinases
Adiposity
Fatty Acid Transport Proteins
Phosphorylation
Adipocytes

Establishment and activity of the D quadrant organizer in the marine gastropod Crepidula fornicata

Henry, J. J., Lyons, D. C., Perry, K. J. & Osborne, C. C., Nov 15 2017, In : Developmental Biology. 431, 2, p. 282-296 15 p.

Research output: Contribution to journalArticle

Gastropoda
Embryonic Structures
Asymmetric Cell Division
Mollusca
Snails

Integration of temporal and spatial patterning generates neural diversity

Erclik, T., Li, X., Courgeon, M., Bertet, C., Chen, Z., Baumert, R., Ng, J., Koo, C., Arain, U., Behnia, R., Del Valle Rodriguez, A., Senderowicz, L., Negre, N., White, K. P. & Desplan, C., Jan 19 2017, In : Nature. 541, 7637, p. 365-370 6 p.

Research output: Contribution to journalArticle

Neurons
Neuropil
Automatic Data Processing
Drosophila

Label-Free Imaging of Single Microtubule Dynamics Using Spatial Light Interference Microscopy

Kandel, M. E., Teng, K. W., Selvin, P. R. & Popescu, G., Jan 24 2017, In : ACS Nano. 11, 1, p. 647-655 9 p.

Research output: Contribution to journalArticle

Light interference
Labels
Microscopic examination
microscopy
interference

LanCL proteins are not Involved in Lanthionine Synthesis in Mammals

He, C., Zeng, M., Dutta, D., Koh, T. H., Chen, J. & Van Der Donk, W. A., Jan 20 2017, In : Scientific reports. 7, 40980.

Research output: Contribution to journalArticle

mammals
synthesis
biosynthesis
brain
proteins

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., Kannanganattu, P. K. & 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

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., Kannanganattu, P. K., 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

Morphogenesis along the animal-vegetal axis: Fates of primary quartet micromere daughters in the gastropod Crepidula fornicata

Lyons, D. C., Perry, K. J. & Henry, J. J., Sep 15 2017, In : BMC Evolutionary Biology. 17, 1, 217.

Research output: Contribution to journalArticle

morphogenesis
gastropod
Gastropoda
embryo
animal

Mov10 suppresses retroelements and regulates neuronal development and function in the developing brain

Skariah, G., Seimetz, J., Norsworthy, M., Lannom, M. C., Kenny, P. J., Elrakhawy, M., Forsthoefel, C., Drnevich, J., Kalsotra, A. & Ceman, S., Jun 29 2017, In : BMC biology. 15, 1, 54.

Research output: Contribution to journalArticle

Moloney murine leukemia virus
Retroelements
retrotransposons
leukemia
Viruses

Probing the Heterogeneity of Protein Kinase Activation in Cells by Super-resolution Microscopy

Zhang, R., Fruhwirth, G. O., Coban, O., Barrett, J. E., Burgoyne, T., Lee, S. H., Simonson, P. D., Baday, M., Kholodenko, B. N., Futter, C. E., Ng, T. & Selvin, P. R., Jan 24 2017, In : ACS Nano. 11, 1, p. 249-257 9 p.

Research output: Contribution to journalArticle

Epidermal Growth Factor Receptor
Protein Kinases
Microscopic examination
Mitogen-Activated Protein Kinases
Chemical activation

Prosurvival long noncoding RNA PINCR regulates a subset of p53 targets in human colorectal cancer cells by binding to Matrin 3

Chaudhary, R., Gryder, B., Woods, W. S., Subramanian, M., Jones, M. F., Li, X. L., Jenkins, L. M., Shabalina, S. A., Mo, M., Dasso, M., Yang, Y., Wakefield, L. M., Zhu, Y., Frier, S. M., Moriarity, B. S., Prasanth, K. V., Perez-Pinera, P. & Lal, A., Jun 5 2017, In : eLife. 6, e23244.

Research output: Contribution to journalArticle

Long Noncoding RNA
Untranslated RNA
Colorectal Neoplasms
Cells
DNA Damage

PSIP1/p75 promotes tumorigenicity in breast cancer cells by promoting the transcription of cell cycle genes

Singh, D. K., Gholamalamdari, O., Jadaliha, M., Li, X. L., Lin, Y. C., Zhang, Y., Guang, S., Hashemikhabir, S., Tiwari, S., Zhu, Y. J., Khan, A., Thomas, A., Chakraborty, A., Macias, V., Balla, A. K., Bhargava, R., Janga, S. C., Ma, J., Prasanth, S. G., Lal, A. & 1 others, Kannanganattu, P. K., Oct 1 2017, In : Carcinogenesis. 38, 10, p. 966-975 10 p., bgx062.

Research output: Contribution to journalArticle

Triple Negative Breast Neoplasms
cdc Genes
Breast Neoplasms
RNA Polymerase II
Cell Line

Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution

Fei, J., Jadaliha, M., Harmon, T. S., Li, I. T. S., Hua, B., Hao, Q., Holehouse, A. S., Reyer, M., Sun, Q., Freier, S. M., Pappu, R. V., Kannanganattu, P. K. & Ha, T., Dec 1 2017, In : Journal of cell science. 130, 24, p. 4180-4192 13 p.

Research output: Contribution to journalArticle

Nuclear RNA
RNA
Proteins
Small Nuclear RNA
Lighting

Site-specific regulation of histone H1 phosphorylation in pluripotent cell differentiation

Liao, R. & Mizzen, C. A., May 22 2017, In : Epigenetics and Chromatin. 10, 1, 29.

Research output: Contribution to journalArticle

Histones
Cell Differentiation
Phosphorylation
Interphase
Genes

Super-resolution imaging of synaptic and extra-synaptic AMPA receptors with Different-Sized fluorescent probes

Lee, S. H., Jin, C., Cai, E., Ge, P., Ishitsuka, Y., Teng, K. W., De Thomaz, A. A., Nall, D., Baday, M., Jeyifous, O., Demonte, D., Dundas, C. M., Park, S., Delgado, J. Y., Green, W. N. & Selvin, P. R., Jul 27 2017, In : eLife. 6, e27744.

Research output: Contribution to journalArticle

Post-Synaptic Density
Neurotransmitter Receptor
AMPA Receptors
Fluorescent Dyes
Imaging techniques

Temporal association of ORCA/LRWD1 to late-firing origins during G1 dictates heterochromatin replication and organization

Wang, Y., Khan, A., Marks, A. B., Smith, O. K., Giri, S., Lin, Y. C., Creager, R., MacAlpine, D. M., Kannanganattu, P. K., Aladjem, M. I. & Prasanth, S. G., Mar 17 2017, In : Nucleic acids research. 45, 5, p. 2490-2502 13 p.

Research output: Contribution to journalArticle

Heterochromatin
Chromatin
Origin Recognition Complex
DNA Replication
S Phase

Temporal dynamics of neurogenomic plasticity in response to social interactions in male threespined sticklebacks

Bukhari, S. A., Saul, M. C., Seward, C. H., Zhang, H., Bensky, M., James, N., Zhao, S. D., Chandrasekaran, S., Stubbs, L. J. & Bell, A. M., Jul 2017, In : PLoS Genetics. 13, 7, e1006840.

Research output: Contribution to journalArticle

Smegmamorpha
Gasterosteidae
Interpersonal Relations
plasticity
chromatin

The Drosophila Duox maturation factor is a key component of a positive feedback loop that sustains regeneration signaling

Khan, S. J., Abidi, S. N. F., Skinner, A., Tian, Y. & Smith-Bolton, R., Jul 2017, In : PLoS Genetics. 13, 7, e1006937.

Research output: Contribution to journalArticle

Drosophila
maturation
Regeneration
regeneration
imaginal discs

The maternal-zygotic transition and zygotic activation of the Mnemiopsis leidyi genome occurs within the first three cleavage cycles

Davidson, P. L., Koch, B. J., Schnitzler, C. E., Henry, J. J., Martindale, M. Q., Baxevanis, A. D. & Browne, W. E., Nov 2017, In : Molecular reproduction and development. 84, 11, p. 1218-1229 12 p.

Research output: Contribution to journalArticle

Ctenophora
Mothers
Genome
Transcriptional Activation
Stored Messenger RNA

Transcriptional regulatory dynamics drive coordinated metabolic and neural response to social challenge in mice

Saul, M. C., Seward, C. H., Troy, J. M., Zhang, H., Sloofman, L. G., Lu, X., Weisner, P. A., Caetano-Anolles, D., Sun, H., Zhao, S. D., Chandrasekaran, S., Sinha, S. & Stubbs, L., Jun 2017, In : Genome Research. 27, 6, p. 959-972 14 p.

Research output: Contribution to journalArticle

Chromatin
Frontal Lobe
Amygdala
Energy Metabolism
Hypothalamus

α7β1 integrin regulation of gene transcription in skeletal muscle following an acute bout of eccentric exercise

Mahmassani, Z. S., Son, K., Pincu, Y., Munroe, M., Drnevich, J., Chen, J. & Boppart, M., May 11 2017, In : American Journal of Physiology - Cell Physiology. 312, 5, p. 638-650 13 p.

Research output: Contribution to journalArticle

Integrins
Skeletal Muscle
Genes
Muscles
Costameres
2016

A rapid, gentle and scalable method for dissociation and fluorescent sorting of imaginal disc cells for mRNA sequencing

Khan, S. J., Abidi, S. N. F., Tian, Y., Skinner, A. & Smith-Bolton, R., Apr 2 2016, In : Fly. 10, 2, p. 73-80 8 p.

Research output: Contribution to journalArticle

imaginal discs
sorting
gene expression
cells
methodology

A Unique Class of Neural Progenitors in the Drosophila Optic Lobe Generates Both Migrating Neurons and Glia

Chen, Z., Del Valle Rodriguez, A., Li, X., Erclik, T., Fernandes, V. M. & Desplan, C., Apr 26 2016, In : Cell Reports. 15, 4, p. 774-786 13 p.

Research output: Contribution to journalArticle

Neuroglia
Drosophila
Neurons
Optics
Neurogenesis

Collapsin response mediator protein-1 regulates Arp2/3-dependent actin assembly

Yu-Kemp, H. C. & Brieher, W. M., Jan 8 2016, In : Journal of Biological Chemistry. 291, 2, p. 658-664 7 p.

Research output: Contribution to journalArticle

Listeria
Actins
Tail
Actin-Related Protein 2-3 Complex
Cytosol

Functional and prognostic significance of long non-coding RNA MALAT1 as a metastasis driver in ER negative lymph node negative breast cancer

Jadaliha, M., Zong, X., Malakar, P., Ray, T., Singh, D. K., Freier, S. M., Jensen, T., Prasanth, S. G., Karni, R., Ray, P. S. & Kannanganattu, P. K., Jan 1 2016, In : Oncotarget. 7, 26, p. 40418-40436 19 p.

Research output: Contribution to journalArticle

Long Noncoding RNA
Lymph Nodes
Breast Neoplasms
Neoplasm Metastasis
Triple Negative Breast Neoplasms

Hsp90 and p23 Molecular Chaperones Control Chromatin Architecture by Maintaining the Functional Pool of the RSC Chromatin Remodeler

Echtenkamp, F. J., Gvozdenov, Z., Adkins, N. L., Zhang, Y., Lynch-Day, M., Watanabe, S., Peterson, C. L. & Freeman, B. C., Dec 1 2016, In : Molecular cell. 64, 5, p. 888-899 12 p.

Research output: Contribution to journalArticle

Molecular Chaperones
Nucleosomes
Chromatin
Life Cycle Stages
Proteolysis

Interphase H1 phosphorylation: Regulation and functions in chromatin

Liao, R. & Mizzen, C. A., Mar 1 2016, In : Biochimica et Biophysica Acta - Gene Regulatory Mechanisms. 1859, 3, p. 476-485 10 p.

Research output: Contribution to journalArticle

Phosphorylation
Interphase
Chromatin
Histones
Transcription

Labeling proteins inside living cells using external fluorophores for microscopy

Teng, K. W., Ishitsuka, Y., Ren, P., Youn, Y., Deng, X., Ge, P., Belmont, A. S. & Selvin, P. R., Dec 9 2016, In : eLife. 5, DECEMBER2016, e20378.

Research output: Contribution to journalArticle

Fluorophores
Labeling
Microscopy
Microscopic examination
Fluorescence

Lens regeneration from the cornea requires suppression of Wnt/β-catenin signaling

Hamilton, P. W., Sun, Y. & Henry, J. J., Apr 1 2016, In : Experimental Eye Research. 145, p. 206-215 10 p.

Research output: Contribution to journalArticle

Catenins
Cornea
Lenses
Regeneration
Epithelium

Leucyl-tRNA Synthetase Activates Vps34 in Amino Acid-Sensing mTORC1 Signaling

Yoon, M. S., Son, K., Arauz, E., Han, J. M., Kim, S. & Chen, J., Aug 9 2016, In : Cell Reports. 16, 6, p. 1510-1517 8 p.

Research output: Contribution to journalArticle

Amino Acyl-tRNA Synthetases
Amino Acids
Chemical activation
Leucine
Transfer RNA Aminoacylation

Long non-coding RNA malat-1 is dispensable during pressure overload-induced cardiac remodeling and failure in mice

Peters, T., Hermans-Beijnsberger, S., Beqqali, A., Bitsch, N., Nakagawa, S., Kannanganattu, P. K., De Windt, L. J., Van Oort, R. J., Heymans, S. & Schroen, B., Feb 2016, In : PloS one. 11, 2, e0150236.

Research output: Contribution to journalArticle

Long Noncoding RNA
chest
Constriction
Thorax
Heart Failure

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. L., Jun 2016, In : PloS one. 11, 6, e0157824.

Research output: Contribution to journalArticle

Signal transduction
Suprachiasmatic Nucleus
melatonin
Melatonin
Transcription

Multidentate Polymer Coatings for Compact and Homogeneous Quantum Dots with Efficient Bioconjugation

Ma, L., Tu, C., Le, P., Chitoor, S., Lim, S. J., Zahid, M. U., Teng, K. W., Ge, P., Selvin, P. R. & Smith, A. M., Mar 16 2016, In : Journal of the American Chemical Society. 138, 10, p. 3382-3394 13 p.

Research output: Contribution to journalArticle

Quantum Dots
Nanoparticles
Semiconductor quantum dots
ligand
coating

Natural antisense RNA promotes 3′ end processing and maturation of MALAT1 lncRNA

Zong, X., Nakagawa, S., Freier, S. M., Fei, J., Ha, T., Prasanth, S. G. & Prasanth, K. V., Jan 29 2016, In : Nucleic acids research. 44, 6, p. 2898-2908 11 p.

Research output: Contribution to journalArticle

RNA 3' End Processing
Long Noncoding RNA
Antisense RNA
Ribonuclease P
RNA

Orc5 induces large-scale chromatin decondensation in a GCN5-dependent manner

Giri, S., Chakraborty, A., Sathyan, K. M., Prasanth, K. V. & Prasanth, S. G., Jan 1 2016, In : Journal of cell science. 129, 2, p. 417-429 13 p.

Research output: Contribution to journalArticle

Chromatin
Origin Recognition Complex
Histones
Centrosome
Cytokinesis

Paraspeckles modulate the intranuclear distribution of paraspeckle-associated Ctn RNA

Anantharaman, A., Jadaliha, M., Tripathi, V., Nakagawa, S., Hirose, T., Jantsch, M. F., Prasanth, S. G. & Kannanganattu, P. K., Sep 26 2016, In : Scientific Reports. 6, 34043.

Research output: Contribution to journalArticle

RNA
Long Noncoding RNA
Nuclear RNA
Proteasome Endopeptidase Complex
Lighting

Phase correlation imaging of unlabeled cell dynamics

Ma, L., Rajshekhar, G., Wang, R., Bhaduri, B., Sridharan, S., Mir, M., Chakraborty, A., Iyer, R., Prasanth, S. G., Millet, L., Gillette, M. L. & Popescu, G., Sep 12 2016, In : Scientific Reports. 6, 32702.

Research output: Contribution to journalArticle

Polymerization
Actins
Time-Lapse Imaging
Fluorescence

Regulation and integrated functions of the actin cytoskeleton

Charras, G. & Brieher, W. M., Mar 15 2016, In : Molecular biology of the cell. 27, 6, 1 p.

Research output: Contribution to journalArticle

Actin Cytoskeleton

Single-Molecule Analysis of Lipid-Protein Interactions in Crude Cell Lysates

Arauz, E., Aggarwal, V., Jain, A., Ha, T. & Chen, J., May 3 2016, In : Analytical chemistry. 88, 8, p. 4269-4276 8 p.

Research output: Contribution to journalArticle

Lipids
Molecules
Proteins
Assays
Phospholipids

Tbx18 Regulates the Differentiation of Periductal Smooth Muscle Stroma and the Maintenance of Epithelial Integrity in the Prostate

Bolt, C. C., Negi, S., Guimarães-Camboa, N., Zhang, H., Troy, J. M., Lu, X., Kispert, A., Evans, S. M. & Stubbs, L. J., Jan 1 2016, In : PloS one. 11, 4, p. e0154413

Research output: Contribution to journalArticle

smooth muscle
Smooth Muscle
Muscle
Prostate
sinuses

The lens regenerative competency of limbal vs. central regions of mature Xenopus cornea epithelium

Hamilton, P. W. & Henry, J. J., Nov 1 2016, In : Experimental Eye Research. 152, p. 94-99 6 p.

Research output: Contribution to journalArticle

Xenopus
Cornea
Lenses
Epithelium
Stem Cells