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2010

A hybrid, de novo based, genome-wide database search approach applied to the sea urchin neuropeptidome

Menschaert, G., Vandekerckhove, T. T. M., Baggerman, G., Landuyt, B., Sweedler, J. V., Schoofs, L., Luyten, W. & Van Criekinge, W., Feb 5 2010, In : Journal of Proteome Research. 9, 2, p. 990-996 7 p.

Research output: Contribution to journalArticle

Sea Urchins
Genes
Genome
Databases
Search Engine

A mass spectrometry primer for mass spectrometry imaging

Rubakhin, S. S. & Sweedler, J. V., Dec 1 2010, Mass Spectrometry Imaging: Principles and Protocols. Rubakhin, S. & Sweedler, J. (eds.). p. 21-49 29 p. (Methods in Molecular Biology; vol. 656).

Research output: Chapter in Book/Report/Conference proceedingChapter

Tandem Mass Spectrometry
Mass Spectrometry
Molecular Biology
Research Personnel
Guidelines

Base-induced delignification of miscanthus x giganteus studied by three-dimensional confocal raman imaging

Chu, L. Q., Masyuko, R., Sweedler, J. V. & Bohn, P. W., Jul 1 2010, In : Bioresource Technology. 101, 13, p. 4919-4925 7 p.

Research output: Contribution to journalArticle

Delignification
Lignin
lignin
Cellulose
Cells

Circadian integration of glutamatergic signals by little SAAS in novel suprachiasmatic circuits

Atkins, N., Mitchell, J. W., Romanova, E. V., Morgan, D. J., Cominski, T. P., Ecker, J. L., Pintar, J. E., Sweedler, J. V. & Gillette, M. U., Nov 1 2010, In : PloS one. 5, 9, p. 1-13 13 p., e12612.

Research output: Contribution to journalArticle

Suprachiasmatic Nucleus
Gastrin-Releasing Peptide
Light
Networks (circuits)
Vasoactive Intestinal Peptide

Comparison of sample pre-treatments for laser desorption ionization and secondary ion mass spectrometry imaging of Miscanthus × giganteus

Li, Z., Bohn, P. W. & Sweedler, J. V., Jul 1 2010, In : Bioresource Technology. 101, 14, p. 5578-5585 8 p.

Research output: Contribution to journalArticle

Secondary ion mass spectrometry
Ionization
Mass spectrometry
Desorption
desorption

Composite modulatory feedforward loop contributes to the establishment of a network state

Wu, J. S., Vilim, F. S., Hatcher, N. G., Due, M. R., Sweedler, J. V., Weiss, K. R. & Jing, J., Apr 1 2010, In : Journal of neurophysiology. 103, 4, p. 2174-2184 11 p.

Research output: Contribution to journalArticle

Interneurons
Central Pattern Generators
Aplysia
Peptides
Cheek

Direct cellular peptidomics of supraoptic magnocellular and hippocampal neurons in low-density cocultures

Millet, L. J., Bora, A., Sweedler, J. V. & Gillette, M. U., Jan 20 2010, In : ACS Chemical Neuroscience. 1, 1, p. 36-48 13 p.

Research output: Contribution to journalArticle

Coculture Techniques
Neurons
Peptides
Neurokinin B
Chromogranins

Distinct mechanisms produce functionally complementary actions of neuropeptides that are structurally related but derived from different precursors

Vilim, F. S., Sasaki, K., Rybak, J., Alexeeva, V., Cropper, E. C., Jing, J., Orekhova, I. V., Brezina, V., Price, D., Romanova, E. V., Rubakhin, S. S., Hatcher, N., Sweedler, J. V. & Weiss, K. R., Jan 6 2010, In : Journal of Neuroscience. 30, 1, p. 131-147 17 p.

Research output: Contribution to journalArticle

FMRFamide
Neuropeptides
Sensory Receptor Cells
Aplysia
Muscles

Electrokinetic control of fluid transport in gold-coated nanocapillary array membranes in hybrid nanofluidic-microfluidic devices

Piruska, A., Branagan, S. P., Minnis, A. B., Wang, Z., Cropek, D. M., Sweedler, J. V. & Bohn, P. W., 2010, In : Lab on a chip. 10, 10, p. 1237-1244 8 p.

Research output: Contribution to journalArticle

Lab-On-A-Chip Devices
Nanofluidics
Neural Cell Adhesion Molecules
Microfluidics
Gold

Endogenous peptide discovery of the rat circadian clock: A focused study of the suprachiasmatic nucleus by ultrahigh performance tandem mass spectrometry

Lee, J. E., Atkins, N., Hatcher, N. G., Zamdborg, L., Gillette, M. U., Sweedler, J. V. & Kelleher, N. L., Feb 1 2010, In : Molecular and Cellular Proteomics. 9, 2, p. 285-297 13 p.

Research output: Contribution to journalArticle

Circadian Clocks
Suprachiasmatic Nucleus
Tandem Mass Spectrometry
Mass spectrometry
Rats

Feedforward compensation mediated by the central and peripheral actions of a single neuropeptide discovered using representational difference analysis

Jing, J., Sweedler, J. V., Cropper, E. C., Alexeeva, V., Park, J. H., Romanova, E. V., Xie, F., Dembrow, N. C., Ludwar, B. C., Weiss, K. R. & Vilim, F. S., Dec 8 2010, In : Journal of Neuroscience. 30, 49, p. 16545-16558 14 p.

Research output: Contribution to journalArticle

Neuropeptides
Cheek
Interneurons
Peptides
Aplysia

Fishing for the hidden peptidome in health and disease (Drug Abuse)

Fricker, L. D. & Sweedler, J. V., Dec 1 2010, In : AAPS Journal. 12, 4, p. 679-682 4 p.

Research output: Contribution to journalReview article

Substance-Related Disorders
Health
Proteins
Peptides
Peptide Receptors

Genome-wide analyses reveal a role for peptide hormones in planarian germline development

Collins, J. J., Hou, X., Romanova, E. V., Lambrus, B. G., Miller, C. M., Saberi, A., Sweedler, J. V. & Newmark, P. A., Oct 1 2010, In : PLoS biology. 8, 10, e1000509.

Research output: Contribution to journalArticle

Platyhelminths
Planarians
peptide hormones
Peptide Hormones
Platyhelminthes

Genome-wide census and expression profiling of chicken neuropeptide and prohormone convertase genes

Delfino, K. R., Southey, B. R., Sweedler, J. V. & Rodriguez-Zas, S. L., Feb 1 2010, In : Neuropeptides. 44, 1, p. 31-44 14 p.

Research output: Contribution to journalArticle

Proprotein Convertases
Censuses
Neuropeptides
Chickens
Genome

Mass spectrometry–based methodologies for single-cell metabolite detection and identification

Knolhoff, A. M., Nemes, P., Rubakhin, S. & Sweedler, J. V., Jan 1 2010, Methodologies for Metabolomics: Experimental Strategies and Techniques. Cambridge University Press, p. 119-139 21 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Metabolites
Fluorescence
Tissue
Metabolomics
Biochemistry

Mass Spectrometry Imaging: Principles and Protocols

Rubakhin, S. (ed.) & Sweedler, J. V. (ed.), 2010, Humana Press. 488 p. (Methods in Molecular Biology; vol. 656)

Research output: Book/ReportBook

Mass spectrometry
Imaging techniques
Molecular biology
Xenobiotics
Metabolites

Mass spectrometry imaging using the stretched sample approach

Zimmerman, T. A., Rubakhin, S. S. & Sweedler, J. V., Dec 1 2010, Mass Spectrometry Imaging: Principles and Protocols. Rubakhin, S. & Sweedler, J. (eds.). p. 465-479 15 p. (Methods in Molecular Biology; vol. 656).

Research output: Chapter in Book/Report/Conference proceedingChapter

Mass Spectrometry
Membranes
Lasers
Computer-Assisted Image Processing
Matrix-Assisted Laser Desorption-Ionization Mass Spectrometry
Mass Screening
Prefrontal Cortex
Cocaine
Mass Spectrometry
Peptides

Methodologies for metabolomics: Experimental strategies and techniques

Lutz, N. W., Sweedler, J. V. & Wevers, R. A., Jan 1 2010, Cambridge University Press. 627 p.

Research output: Book/ReportBook

Metabolomics
Metabolites
Physiological Phenomena
Pathologic Processes
Metabolic Networks and Pathways

Nanofluidics in chemical analysis

Piruska, A., Gong, M., Sweedler, J. V. & Bohn, P. W., Mar 1 2010, In : Chemical Society Reviews. 39, 3, p. 1060-1072 13 p.

Research output: Contribution to journalReview article

Nanofluidics
Nanopores
Chemical analysis
Microfluidics
Microsensors

Neuropeptide release is impaired in a mouse model of fragile x mental retardation syndrome

Annangudi, S. P., Luszpak, A. E., Kim, S. H., Ren, S., Hatcher, N. G., Weiler, I. J., Thornley, K. T., Kile, B. M., Wightman, R. M., Greenough, W. T. & Sweedler, J. V., Apr 21 2010, In : ACS Chemical Neuroscience. 1, 4, p. 306-314 9 p.

Research output: Contribution to journalArticle

Fragile X Mental Retardation Protein
Neuropeptides
Intellectual Disability
Fragile X Syndrome
Messenger RNA

Preface

Rubakhin, S. & Sweedler, J. V., Dec 1 2010, In : Methods in Molecular Biology. 656

Research output: Contribution to journalArticle

Production of nitric oxide within the aplysia californica nervous system

Ye, X., Xie, F., Romanova, E. V., Rubakhin, S. S. & Sweedler, J. V., Mar 17 2010, In : ACS Chemical Neuroscience. 1, 3, p. 182-193 12 p.

Research output: Contribution to journalArticle

Aplysia
Neurology
Nervous System
Nitric Oxide
Fluorescence

Quantitative neuroproteomics of the synapse.

Ramos-Ortolaza, D. L., Bushlin, I., Abul-Husn, N., Annangudi, S. P., Sweedler, J. V. & Devi, L. A., 2010, In : Methods in molecular biology (Clifton, N.J.). 615, p. 227-246 20 p.

Research output: Contribution to journalArticle

Proteomics
Synapses
Neurodegenerative Diseases
Proteins
Brain

Serotonin and its metabolism in basal deuterostomes: Insights from Strongylocentrotus purpuratus and Xenoturbella bocki

Squires, L. N., Rubakhin, S. S., Wadhams, A. A., Talbot, K. N., Nakano, H., Moroz, L. L. & Sweedler, J. V., Aug 1 2010, In : Journal of Experimental Biology. 213, 15, p. 2647-2654 8 p.

Research output: Contribution to journalArticle

Strongylocentrotus purpuratus
basal metabolism
Basal Metabolism
Strongylocentrotus
serotonin

Single-Cell Mass Spectrometry

Knolhoff, A. M., Rubakhin, S. & Sweedler, J. V., Mar 19 2010, Chemical Cytometry: Ultrasensitive Analysis of Single Cells. Wiley-VCH, p. 197-218 22 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Single-Cell Analysis
Aplysia
Drosophila melanogaster
Mass spectrometry
Mass Spectrometry

Spatial correlation of confocal raman scattering and secondary ion mass spectrometric molecular images of lignocellulosic materials

Li, Z., Chu, L. Q., Sweedler, J. V. & Bohn, P. W., Apr 1 2010, In : Analytical chemistry. 82, 7, p. 2608-2611 4 p.

Research output: Contribution to journalArticle

Molecular mass
Secondary ion mass spectrometry
Raman scattering
Ions
Biofuels

Synthesis, accumulation, and release of d-aspartate in the Aplysia californica CNS

Scanlan, C., Shi, T., Hatcher, N. G., Rubakhin, S. & Sweedler, J. V., Dec 1 2010, In : Journal of Neurochemistry. 115, 5, p. 1234-1244 11 p.

Research output: Contribution to journalArticle

Aplysia
Aspartic Acid
Ganglia
Neurons
Tissue

The genome of a songbird

Warren, W. C., Clayton, D. F., Ellegren, H., Arnold, A. P., Hillier, L. W., Künstner, A., Searle, S., White, S., Vilella, A. J., Fairley, S., Heger, A., Kong, L., Ponting, C. P., Jarvis, E. D., Mello, C. V., Minx, P., Lovell, P., Velho, T. A. F., Ferris, M., Balakrishnan, C. N. & 62 others, Sinha, S., Blatti, C., London, S. E., Li, Y., Lin, Y. C., George, J., Sweedler, J., Southey, B., Gunaratne, P., Watson, M., Nam, K., Backström, N., Smeds, L., Nabholz, B., Itoh, Y., Whitney, O., Pfenning, A. R., Howard, J., Völker, M., Skinner, B. M., Griffin, D. K., Ye, L., McLaren, W. M., Flicek, P., Quesada, V., Velasco, G., Lopez-Otin, C., Puente, X. S., Olender, T., Lancet, D., Smit, A. F. A., Hubley, R., Konkel, M. K., Walker, J. A., Batzer, M. A., Gu, W., Pollock, D. D., Chen, L., Cheng, Z., Eichler, E. E., Stapley, J., Slate, J., Ekblom, R., Birkhead, T., Burke, T., Burt, D., Scharff, C., Adam, I., Richard, H., Sultan, M., Soldatov, A., Lehrach, H., Edwards, S. V., Yang, S. P., Li, X., Graves, T., Fulton, L., Nelson, J., Chinwalla, A., Hou, S., Mardis, E. R. & Wilson, R. K., Apr 1 2010, In : Nature. 464, 7289, p. 757-762 6 p.

Research output: Contribution to journalArticle

Finches
Songbirds
Equidae
Genome
Molecular Evolution

The zebra finch neuropeptidome: Prediction, detection and expression

Xie, F., London, S. E., Southey, B. R., Annangudi, S. P., Amare, A., Rodriguez-Zas, S. L., Clayton, D. F. & Sweedler, J. V., Apr 1 2010, In : BMC biology. 8, 28.

Research output: Contribution to journalArticle

Finches
Taeniopygia guttata
Equidae
peptide
learning

Transcriptional Orchestration of the Regulated Secretory Pathway in Neurons by the bHLH protein DIMM

Hamanaka, Y., Park, D., Yin, P., Annangudi, S. P., Edwards, T. N., Sweedler, J. V., Meinertzhagen, I. A. & Taghert, P. H., Jan 12 2010, In : Current Biology. 20, 1, p. 9-18 10 p.

Research output: Contribution to journalArticle

Secretory Pathway
neuropeptides
Neuropeptides
Neurons
photoreceptors
2011

A diverse family of novel peptide toxins from an unusual cone snail, Conus californicus

Gilly, W. F., Richmond, T. A., Duda, T. F., Elliger, C., Lebaric, Z., Schulz, J., Bingham, J. P. & Sweedler, J. V., Jan 1 2011, In : Journal of Experimental Biology. 214, 1, p. 147-161 15 p.

Research output: Contribution to journalArticle

Conus Snail
seed cones
peptide
snail
toxin

A novel pyridoxal 5'-phosphate-dependent amino acid racemase in the aplysia californica central nervous system

Wang, L., Ota, N., Romanova, E. V. & Sweedler, J. V., Apr 15 2011, In : Journal of Biological Chemistry. 286, 15, p. 13765-13774 10 p.

Research output: Contribution to journalArticle

aspartate racemase
Amino Acid Isomerases
D-Aspartic Acid
Aplysia
Pyridoxal Phosphate

Chronic morphine alters the presynaptic protein profile: Identification of novel molecular targets using proteomics and network analysis

Abul-Husn, N. S., Annangudi, S. P., Ma'ayan, A., Ramos-Ortolaza, D. L., Stockton, S. D., Gomes, I., Sweedler, J. V. & Devi, L. A., Oct 17 2011, In : PloS one. 6, 10, e25535.

Research output: Contribution to journalArticle

morphine
Electric network analysis
Proteomics
proteomics
Morphine
ethylenediamine
Neurons
Ionization
Mass spectrometry
Pyrrolidinones

Comparison of tandem mass spectrometry search methods to identify neuropeptides

Akhtar, M. N., Southey, B. R., Porter, K. I., Sweedler, J. V. & Rodriguez-Zas, S. L., Dec 1 2011, 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011. p. 982-984 3 p. 6112530. (2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Tandem Mass Spectrometry
Neuropeptides
Mass spectrometry
Peptides
Amino acids

Direct cellular peptidomics of hypothalamic neurons

Mitchell, J. W., Atkins, N., Sweedler, J. V. & Gillette, M. L., Oct 1 2011, In : Frontiers in Neuroendocrinology. 32, 4, p. 377-386 10 p.

Research output: Contribution to journalReview article

Neurons
Peptides
Cell signaling
Supraoptic Nucleus
Suprachiasmatic Nucleus
Neuropeptides
Neurons
Mass spectrometry
Amino Acids
Peptides

Diversity of conotoxin types from Conus californicus reflects a diversity of prey types and a novel evolutionary history

Elliger, C. A., Richmond, T. A., Lebaric, Z. N., Pierce, N. T., Sweedler, J. V. & Gilly, W. F., Feb 1 2011, In : Toxicon. 57, 2, p. 311-322 12 p.

Research output: Contribution to journalArticle

Conotoxins
History
Peptides
Complementary DNA
Molluscs

Integration of sequence and functional information to identify and annotate neuropeptides in the pig genome

Porter, K. I., Southey, B. R., Akhtar, M. N., Sweedler, J. V. & Rodriguez-Zas, S. L., Dec 1 2011, 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011. p. 988-990 3 p. 6112532. (2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Neuropeptides
Swine
Genes
Genome
Proprotein Convertases

MALDI mass spectrometry imaging of neuronal cell cultures

Zimmerman, T. A., Rubakhin, S. S. & Sweedler, J. V., May 1 2011, In : Journal of the American Society for Mass Spectrometry. 22, 5, p. 828-836 9 p.

Research output: Contribution to journalArticle

Matrix-Assisted Laser Desorption-Ionization Mass Spectrometry
Cell culture
Mass spectrometry
Aplysia
Mass Spectrometry

Metabolic differentiation of neuronal phenotypes by single-cell capillary electrophoresis-electrospray ionization-mass spectrometry

Nemes, P., Knolhoff, A. M., Rubakhin, S. & Sweedler, J. V., Sep 1 2011, In : Analytical chemistry. 83, 17, p. 6810-6817 8 p.

Research output: Contribution to journalArticle

Capillary electrophoresis
Electrospray ionization
Neurons
Mass spectrometry
Neurology

Mice deficient in endothelin-converting enzyme-2 exhibit abnormal responses to morphine and altered peptide levels in the spinal cord

Miller, L. K., Hou, X., Rodriguiz, R. M., Gagnidze, K., Sweedler, J. V., Wetsel, W. C. & Devi, L. A., Dec 1 2011, In : Journal of Neurochemistry. 119, 5, p. 1074-1085 12 p.

Research output: Contribution to journalArticle

Endothelins
Morphine
Spinal Cord
Peptides
Enzymes

Model of ion intensity from tandem mass spectra for improved peptide identification and simulation

Fazal, Z., Southey, B. R., Sadeque, A., Sweedler, J. V. & Rodriguez-Zas, S. L., Dec 1 2011, 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011. p. 994-996 3 p. 6112534. (2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Peptides
Ions
Mass spectrometry
Tandem Mass Spectrometry
Protons

Molecular organization of drosophila neuroendocrine cells by dimmed

Park, D., Hadžić, T., Yin, P., Rusch, J., Abruzzi, K., Rosbash, M., Skeath, J. B., Panda, S., Sweedler, J. V. & Taghert, P. H., Sep 27 2011, In : Current Biology. 21, 18, p. 1515-1524 10 p.

Research output: Contribution to journalArticle

Neuroendocrine Cells
Drosophila
Secretory Vesicles
Assays
Proteins

Neuropeptidomics: Mass spectrometry-based qualitative and quantitative analysis

Yin, P., Hou, X., Romanova, E. V. & Sweedler, J. V., Oct 24 2011, Neuropeptides: Methods and Protocols. Merighi, A. (ed.). p. 223-236 14 p. (Methods in Molecular Biology; vol. 789).

Research output: Chapter in Book/Report/Conference proceedingChapter

Neuropeptides
Mass Spectrometry
Liquid Chromatography
Peptides
Protein Precursors

Neuropeptidomics

Sweedler, J. V., Xie, F. & Bora, A., Sep 23 2011, Protein and Peptide Mass Spectrometry in Drug Discovery. John Wiley and Sons, p. 393-433 41 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Neuropeptidomics of the mammalian brain

Xie, F., Romanova, E. V. & Sweedler, J. V., Jun 3 2011, Neuroproteomics. Li, K. W. (ed.). p. 229-242 14 p. (Neuromethods; vol. 57).

Research output: Chapter in Book/Report/Conference proceedingChapter

Brain
Peptides
Mass spectrometry
Mass Spectrometry
Liquid chromatography

Probing the production of amidated peptides following genetic and dietary copper manipulations

Yin, P., Bousquet-Moore, D., Annangudi, S. P., Southey, B. R., Mains, R. E., Eipper, B. A. & Sweedler, J. V., Dec 16 2011, In : PloS one. 6, 12, e28679.

Research output: Contribution to journalArticle

Mixed Function Oxygenases
Copper
copper
peptides
Peptides

Profiling metabolites and peptides in single cells

Rubakhin, S., Romanova, E. V., Nemes, P. & Sweedler, J. V., Apr 2011, In : Nature Methods. 8, 4, p. S20-S29

Research output: Contribution to journalArticle

Metabolites
Cytology
Peptides
Stem cells
Chemical analysis