Research Output 1961 2018

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2018

Antibody pull-down experiments in fission yeast

Dong, Q. & Li, F. Jan 1 2018 Methods in Molecular Biology. Humana Press Inc., Vol. 1721, p. 117-123 7 p. (Methods in Molecular Biology; vol. 1721)

Research output: Chapter in Book/Report/Conference proceedingChapter

Schizosaccharomyces
Antibodies
Proteins

CRISPR knockouts in Ciona embryos

Gandhi, S., Razy-Krajka, F., Christiaen, L. & Stolfi, A. Jan 1 2018 Advances in Experimental Medicine and Biology. Springer New York LLC, p. 141-152 12 p. (Advances in Experimental Medicine and Biology; vol. 1029)

Research output: Chapter in Book/Report/Conference proceedingChapter

Clustered Regularly Interspaced Short Palindromic Repeats
Gene Knockout Techniques
Embryonic Structures
Zinc plating
Urochordata

Determining mRNA decay rates using RNA approach to equilibrium sequencing (RATE-seq)

Abdul-Rahman, F. & Gresham, D. Jan 1 2018 Methods in Molecular Biology. Humana Press Inc., Vol. 1720, p. 15-24 10 p. (Methods in Molecular Biology; vol. 1720)

Research output: Chapter in Book/Report/Conference proceedingChapter

RNA Stability
RNA
Nonlinear Dynamics
Streptavidin
Uracil

In situ chromatin-binding assay using epifluorescent microscopy in S. pombe

Yang, J. & Li, F. Jan 1 2018 Methods in Molecular Biology. Humana Press Inc., Vol. 1721, p. 155-165 11 p. (Methods in Molecular Biology; vol. 1721)

Research output: Chapter in Book/Report/Conference proceedingChapter

Schizosaccharomyces
Chromatin
Microscopy
Epigenomics
Proteins

Purification of fluorescent labeled cells from dissociated Ciona embryos

Wang, W., Racioppi, C., Gravez, B. & Christiaen, L. Jan 1 2018 Advances in Experimental Medicine and Biology. Springer New York LLC, p. 101-107 7 p. (Advances in Experimental Medicine and Biology; vol. 1029)

Research output: Chapter in Book/Report/Conference proceedingChapter

Embryonic Structures
Population
Singapore
Larva
Flow Cytometry

μChIP-seq for genome-wide mapping of in vivo TF-DNA interactions in Arabidopsis root protoplasts

Para, A., Li, Y. & Coruzzi, G. M. Jan 1 2018 Methods in Molecular Biology. Humana Press Inc., p. 249-261 13 p. (Methods in Molecular Biology; vol. 1761)

Research output: Chapter in Book/Report/Conference proceedingChapter

Protoplasts
Chromatin Immunoprecipitation
Chromosome Mapping
Arabidopsis
Leucine Zippers
2017

Modeling and design of peptidomimetics to modulate protein–protein interactions

Watkins, A. M., Bonneau, R. & Arora, P. S. 2017 Methods in Molecular Biology. Humana Press Inc., Vol. 1561, p. 291-307 17 p. (Methods in Molecular Biology; vol. 1561)

Research output: Chapter in Book/Report/Conference proceedingChapter

Peptidomimetics
Secondary Protein Structure
Proteins
Tertiary Protein Structure
Software
2016

An experimental model for simultaneous study of migration of cell fragments, single cells, and cell sheets

Sun, Y. H., Sun, Y., Zhu, K., Draper, B. W., Zeng, Q., Mogilner, A. & Zhao, M. 2016 Methods in Molecular Biology. Humana Press Inc., Vol. 1407, p. 251-272 22 p. (Methods in Molecular Biology; vol. 1407)

Research output: Chapter in Book/Report/Conference proceedingChapter

Cell Movement
Theoretical Models
Cell Separation
Zebrafish
Cues

Innate immunity in viral encephalitis

Reiss, C. S. Nov 2016 Neurotropic viral infections: Neurotropic retroviruses, DNA viruses, Immunity and transmission. Reiss, C. S. (ed.). 2 ed. Switzerland: Springer , Vol. 2, p. 251-304

Research output: Chapter in Book/Report/Conference proceedingChapter

Innate immunity in viral encephalitis

Reiss, C. S. Jan 1 2016 Neurotropic Viral Infections: Volume 2: Neurotropic Retroviruses, DNA Viruses, Immunity and Transmission. Springer International Publishing, p. 251-303 53 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Viral Encephalitis
Innate Immunity
Central Nervous System
Infection
Microglia
2015

A mass-action-based model for gene expression regulation in dynamic systems

Teo, G., Vogel, C., Ghosh, D., Kim, S. & Choi, H. Jan 1 2015 Integrating Omics Data. Cambridge University Press, p. 362-379 18 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Gene Expression Regulation
Proteolysis
Proteins
Stochastic Processes
Controlled Environment

Identification and quantification of K63-ubiquitinated proteins in neuronal cells by high-resolution mass spectrometry

Silva, G. M., Wei, W., Manohar, S. & Vogel, C. Nov 18 2015 Neuromethods. Humana Press Inc., Vol. 114, p. 111-125 15 p. (Neuromethods; vol. 114)

Research output: Chapter in Book/Report/Conference proceedingChapter

Ubiquitinated Proteins
Ubiquitin
Mass spectrometry
Mass Spectrometry
Ubiquitination

Regressive Evolution: Testing Hypotheses of Selection and Drift

Borowsky, R. Oct 12 2015 Biology and Evolution of the Mexican Cavefish. Elsevier Inc., p. 93-109 17 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Genetic Drift
eyes
Genetic Selection
genetic drift
natural selection

Tissue-specific gene expression profiling by cell sorting

Ip, P. L. & Birnbaum, K. D. Mar 11 2015 Plant Functional Genomics: Methods and Protocols: Second Edition. Springer New York, p. 175-183 9 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Gene Expression Profiling
sorting
gene expression
Flow Cytometry
cells
2013

The SATOL project: An interdisciplinary model of technology transfer for research-to-practice in clinical supervision for addiction treatment

Straussner, S. L. A., Naegle, M. A., Gillespie, C., Wolkstein, E., Donath, R. & Azmitia, E. C. 2013 Information Technology and Evidence-Based Social Work Practice. Taylor and Francis, p. 39-54 16 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Technology transfer
Supervisory personnel
Quality of service

Vision

Vogt, N. & Desplan, C. Jan 1 2013 Behavioral Genetics of the Fly (Drosophila Melanogaster). Cambridge University Press, p. 37-48 12 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

photoreceptors
Drosophila
Light
Diptera
wavelengths
2012

Brain Chemicals: Global Projections of Ancient Aromatic Neurotransmitters

Azmitia, E. C. Jan 1 2012 Encyclopedia of Human Behavior: Second Edition. Elsevier Inc., p. 396-405 10 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Hallucinogens
Photosynthesis
Mixed Function Oxygenases
Benzene
Catecholamines

Fluorescence-activated cell sorting for analysis of cell type-specific responses to salinity stress in Arabidopsis and rice.

Evrard, A., Bargmann, B. O. R., Birnbaum, K. D., Tester, M., Baumann, U. & Johnson, A. A. T. 2012 Plant Salt Tolerance: Methods and Protocols. Humana Press Inc., Vol. 913, p. 265-276 12 p. (Methods in Molecular Biology; vol. 913)

Research output: Chapter in Book/Report/Conference proceedingChapter

Salinity
Arabidopsis
Flow Cytometry
Green Fluorescent Proteins
Genetically Modified Plants

Label-free protein quantitation using weighted spectral counting

Vogel, C. & Marcotte, E. M. 2012 Quantitative Methods in Proteomics. Vol. 893, p. 321-341 21 p. (Methods in Molecular Biology; vol. 893)

Research output: Chapter in Book/Report/Conference proceedingChapter

Proteins
Tandem Mass Spectrometry
Mass Spectrometry
Peptides
Firearms

The Evolution of Plant Form: A Summary Perspective

Purugganan, M. Nov 27 2012 The Evolution of Plant Form. John Wiley and Sons Ltd., Vol. 45, p. 357-366 10 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Molecular Evolution
Molecular Biology
Angiosperms
Plant Development
Population Genetics

The robustness continuum

Levy, S. F. & Siegal, M. L. 2012 Evolutionary Systems Biology. Springer New York LLC, Vol. 751, p. 431-452 22 p. (Advances in Experimental Medicine and Biology; vol. 751)

Research output: Chapter in Book/Report/Conference proceedingChapter

Plasticity
Large scale systems
Animals
Cells
Phenotype
2011

Covalent polycyclic aromatic hydrocarbon-DNA adducts: Carcinogenicity, structure, and function

Broyde, S., Wang, L., Cai, Y., Jia, L., Shapiro, R., Patel, D. J. & Geacintov, N. E. 2011 Chemical Carcinogenesis. Vol. 6, p. 181-207 27 p. (Current Cancer Research; vol. 6)

Research output: Chapter in Book/Report/Conference proceedingChapter

Estuaries
DNA Adducts
Polycyclic Aromatic Hydrocarbons
Polycyclic Aromatic Hydrocarbon Bay-Region
DNA Repair

The human lung microbiome

Losada, L., Ghedin, E., Morris, A., Chu, H. W. & Nierman, W. C. 2011 Metagenomics of the Human Body. Springer New York, p. 117-143 27 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

sterility
Microbiota
lungs
Lung
immune system
2010

A systems-based analysis of Plasmodium vivax lifecycle transcription from human to mosquito

Westenberger, S. J., McClean, C. M., Chattopadhyay, R., Dharia, N. V., Carlton, J. M., Barnwell, J. W., Collins, W. E., Hoffman, S. L., Zhou, Y., Vinetz, J. M. & Winzeler, E. A. Apr 2010 PLoS Neglected Tropical Diseases. 4 ed. Vol. 4

Research output: Chapter in Book/Report/Conference proceedingChapter

Plasmodium vivax
Culicidae
Plasmodium
Genes
Vivax Malaria

DNA Damage and Transcription Elongation: Consequences and RNA Integrity

Dreij, K., Burns, J. A., Dimitri, A., Nirenstein, L., Noujnykh, T. & Scicchitano, D. A. Oct 11 2010 The Chemical Biology of DNA Damage. Wiley-VCH, p. 399-437 39 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Thermionic emission
DNA-Directed RNA Polymerases
DNA Damage
RNA

Elucidating Structure-Function Relationships in Bulky DNA Lesions: From Solution Structures to Polymerases

Broyde, S., Wang, L., Patel, D. J. & Geacintov, N. E. Oct 11 2010 The Chemical Biology of DNA Damage. Wiley-VCH, p. 331-352 22 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Mutagenesis
Computer Simulation
Carcinogenesis
DNA

Introduction and Perspectives on the Chemistry and Biology of DNA Damage

Geacintov, N. E. & Broyde, S. Oct 11 2010 The Chemical Biology of DNA Damage. Wiley-VCH, p. 1-20 20 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Reactive Nitrogen Species
DNA Repair
DNA Damage
Reactive Oxygen Species
Drug Therapy

Mathematical and physical modeling of actin dynamics in motile cells

Carlsson, A. E. & Mogilner, A. 2010 Actin-based Motility: Cellular, Molecular and Physical Aspects. Springer Netherlands, p. 381-412 32 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Actins
Cohort Effect
Pseudopodia
Actin Cytoskeleton

Population Density Methods in Large-Scale Neural Network Modelling

Tranchina, D. Feb 1 2010 Stochastic Methods in Neuroscience. Oxford University Press

Research output: Chapter in Book/Report/Conference proceedingChapter

Network Modeling
Neural Networks
Density Function
Computational Neuroscience
Dynamic Neural Networks

Recognition and Removal of Bulky DNA Lesions by the Nucleotide Excision Repair System

Cai, Y., Kropachev, K., Kolbanovskiy, M., Kolbanovskiy, A., Broyde, S., Patel, D. J. & Geacintov, N. E. Oct 11 2010 The Chemical Biology of DNA Damage. Wiley-VCH, p. 261-298 38 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Reactor startup
Nucleic Acid Conformation
DNA Adducts
Benzo(a)pyrene
DNA Repair
2009

Animal Systems Biology: Towards a Systems View of Development in C. elegans

Fernandez, A., Piano, F. & Gunsalus, K. C. Aug 18 2009 Plant Systems Biology. Blackwell Publishing Ltd., Vol. 35, p. 137-165 29 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Systems Biology
Caenorhabditis elegans
Biological Sciences
Embryonic Development
early development

Brugia malayi gene expression in response to the targeting of the Wolbachia endosymbiont by tetracycline treatment

Ghedin, E., Hailemariam, T., DePasse, J. V., Zhang, X., Oksov, Y., Unnasch, T. R. & Lustigman, S. Oct 2009 PLoS Neglected Tropical Diseases. 10 ed. Vol. 3, e525

Research output: Chapter in Book/Report/Conference proceedingChapter

Brugia malayi
Wolbachia
Tetracycline
Gene Expression
Down-Regulation

Gene orthology assessment with orthologID

Egan, M., Lee, E. K., Chiu, J. C., Coruzzi, G. & Desalle, R. 2009 Bioinformatics for DNA Sequence Analysis. Vol. 537, p. 23-38 16 p. (Methods in Molecular Biology; vol. 537)

Research output: Chapter in Book/Report/Conference proceedingChapter

Genes
Pedigree
Genome

Perspectives on Ecological and Evolutionary Systems Biology

Richards, C. L., Hanzawa, Y., Katari, M. S., Ehrenreich, I. M., Engelmann, K. E. & Purugganan, M. D. Aug 18 2009 Plant Systems Biology. Blackwell Publishing Ltd., Vol. 35, p. 331-349 19 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Systems Biology
Ecosystem
Ecology
Biological Sciences
Biota

Preliminary analysis of the cryptosporidium muris genome

Widmer, G., London, E., Zhang, L., Ge, G., Tzipori, S., Carlton, J. M. & Da Silva, J. C. Feb 25 2009 Giardia and Cryptosporidium: From Molecules to Diseases. CABI Publishing, p. 320-327 8 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Cryptosporidium muris
Cryptosporidium
Genome
genome
Cryptosporidium hominis

Prokaryotic Systems Biology

Kacmarczyk, T., Waltman, P. & Bonneau, R. Aug 18 2009 Plant Systems Biology. Blackwell Publishing Ltd., Vol. 35, p. 67-136 70 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Systems Biology
Technology
Biological Sciences
Genomics
Computational Biology

Systems Biology: Principles and Applications in Plant Research

Coruzzi, G. M., Burga, A. R., Katari, M. S. & Gutiérrez, R. A. Aug 18 2009 Plant Systems Biology. Blackwell Publishing Ltd., Vol. 35, p. 1-40 40 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Systems Biology
Biological Sciences
Research
Planets
Chemical Industry

VSV infection elicits distinct host responses in the periphery and the brain

Reiss, C. S. Jan 1 2009 RNA Viruses: Host Gene Responses to Infections. World Scientific Publishing Co., p. 229-246 18 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Vesicular Stomatitis
Virus Diseases
Viruses
Brain
Psychodidae
2008

De Novo Structure Prediction: Methods and Applications

Bonneau, R. Feb 5 2008 Bioinformatics-From Genomes to Therapies. Wiley-VCH Verlag GmbH, Vol. 1, p. 389-418 30 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Mutagenesis

Development of the Drosophila Melanogaster Eye: From Precursor Specification to Terminal Differentiation

Sprecher, S. G. & Desplan, C. 2008 Animal Models in Eye Research. Elsevier Ltd, p. 27-47 21 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Drosophila melanogaster
eyes
toys
Play and Playthings
instars

Innate immunity in viral encephalitis

Reiss, C. S. Jan 1 2008 Neurotropic Viral Infections. Cambridge University Press, p. 265-291 27 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Viral Encephalitis
Innate Immunity
Viruses
Central Nervous System
West Nile virus

Introduction: Immunity, diagnosis, vector, and beneficial uses of neurotropic viruses

Reiss, C. S. Jan 1 2008 Neurotropic Viral Infections. Cambridge University Press, p. 263-264 2 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Virus Diseases
Innate Immunity
Immunity
Viruses
Infection

Introduction: RNA viruses

Reiss, C. S. Jan 1 2008 Neurotropic Viral Infections. Cambridge University Press, p. 1-2 2 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

RNA Viruses
Innate Immunity
Hendra Virus
Fomites
Nipah Virus

Introduction: Retroviruses, DNA viruses, and prions

Reiss, C. S. Jan 1 2008 Neurotropic Viral Infections. Cambridge University Press, p. 139-140 2 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

DNA Viruses
Prions
Retroviridae
Deltaretrovirus
RNA-Directed DNA Polymerase
2005

Analysis of glutamate receptor genes in plants: Progress and prospects

Chiu, J. C., Brenner, E. D., Desalle, R., Barboza, N. M. & Coruzzi, G. M. 2005 Glutamate Receptors in Peripheral Tissue: Excitatory Transmission Outside the CNS. Springer US, p. 245-255 11 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Plant Genes
Glutamate Receptors
Genes
Arabidopsis
Metabotropic Glutamate Receptors

Erosion processes

Rampino, M. R. 2005 Encyclopedia of Earth Sciences Series. Springer Netherlands, Vol. 14, p. 432-433 2 p. (Encyclopedia of Earth Sciences Series; vol. 14)

Research output: Chapter in Book/Report/Conference proceedingChapter

erosion
2004

Culture of Adult Ascidians and Ascidian Genetics

Hendrickson, C., Christiaen, L., Deschet, K., Jiang, D., Joly, J. S., Legendre, L., Nakatani, Y., Tresser, J. & Smith, W. C. 2004 Development of Sea Urchins, Ascidians, and Other Invertebrate Deuterostomes: Experimental Approaches. Vol. 74, p. 143-170 28 p. (Methods in Cell Biology; vol. 74)

Research output: Chapter in Book/Report/Conference proceedingChapter

Biological Metamorphosis
Urochordata
Aquaculture
Chromosome Mapping
Cytogenetic Analysis
1997

Evolution

Fitch, D. H. A. & Kelley Thomas, W. 1997 C. elegans II. Riddle, D. L., Blumenthal, T., Meyer, B. J. & Priess, J. R. (eds.). Cold Spring Harbor (NY): Cold Spring Harbor Laboratory Press

Research output: Chapter in Book/Report/Conference proceedingChapter

1996

Assessing long-term impacts of increased crop productivity on atmospheric CO2

Cavazzoni, J. & Volk, T. 1996 Energy Policy. 5 ed. Vol. 24, p. 403-411 9 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Crops
Productivity
Fossil fuels
productivity
crop
1991

Biotic enhancement of weathering and surface temperatures on Earth since the origin of life

Schwartzman, D. W. & Volk, T. 1991 Palaeogeography, Palaeoclimatology, Palaeoecology (Global & Planetary Change Section). 4 ed. Vol. 90, p. 357-371 15 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

origin of life
surface temperature
weathering
atmosphere-ocean system
microbial activity