Research Output 1961 2019

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2019

Nucleobindins and encoded peptides: From cell signaling to physiology

Leung, A. K. W., Ramesh, N., Vogel, C. & Unniappan, S., Jan 1 2019, Advances in Protein Chemistry and Structural Biology. Donev, R. (ed.). Academic Press Inc., p. 91-133 43 p. (Advances in Protein Chemistry and Structural Biology; vol. 116).

Research output: Chapter in Book/Report/Conference proceedingChapter

Cell signaling
Physiology
Peptides
Cytology
Proprotein Convertases

The Role of Tertiary Structure in MicroRNA Target Recognition

Gan, H. H. & Gunsalus, K., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 43-64 22 p. (Methods in Molecular Biology; vol. 1970).

Research output: Chapter in Book/Report/Conference proceedingChapter

MicroRNAs
Ribonucleoproteins
Physics
Single Nucleotide Polymorphism
Genome
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
Genes
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

Generative models for quantification of DNA modifications

Äijö, T., Bonneau, R. & Lähdesmäki, H., Jan 1 2018, Methods in Molecular Biology. Humana Press Inc., p. 37-50 14 p. (Methods in Molecular Biology; vol. 1807).

Research output: Chapter in Book/Report/Conference proceedingChapter

Cytosine
DNA
Methylation
Research Design
Statistical Models

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

Purification
Embryonic Structures
Cells
Sorting
Population

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

Para, A., Li, Y. & Coruzzi, G., 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
Transcription Factors
2017

Modeling and design of peptidomimetics to modulate protein–protein interactions

Watkins, A. M., Bonneau, R. & Arora, P., 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
Tertiary Protein Structure
Software
Databases
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

Big data, social media, and protest: Foundations for a research agenda

Tucker, J., Nagler, J., MacDuffee, M. M., Barberá, P., Penfold-Brown, D. & Bonneau, R., Mar 7 2016, Computational Social Science: Discovery and Prediction. Cambridge University Press, p. 199-224 26 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

social media
protest

Innate immunity in viral encephalitis

Reiss, C., 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

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

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., 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
2014

Impact of drugs and alcohol on the brain through the life cycle: Knowledge for social workers

Azmitia, E., Jan 1 2014, Neurobiology of Addictions: Implications for Clinical Practice. Taylor and Francis, p. 41-63 23 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Life Cycle Stages
life cycle
social worker
brain
alcohol
2013

Actomyosin-dependent cortical dynamics

Sommi, P., Cheerambathur, D., Brust-Mascher, I. & Mogilner, A., Jan 1 2013, Trends in Biophysics: From Cell Dynamics Toward Multicellular Growth Phenomena. Apple Academic Press, p. 49-69 21 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Myosin Type II
Dyneins
Prophase
Kinesin
Actomyosin

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

Research output: Chapter in Book/Report/Conference proceedingChapter

Neurotransmitter Agents
Brain
Catechols
Hallucinogens
Indoles

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., 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

DNA-Directed RNA Polymerases
Transcription
Elongation
RNA
DNA

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
Computer simulation

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
Chemotherapy
DNA Repair
DNA Damage
Reactive Oxygen Species

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

Nucleic Acid Conformation
DNA Adducts
Benzo(a)pyrene
DNA sequences
DNA Repair

The evolutionary genetics of cave fishes: Convergence, adaptation and pleiotropy

Borowsky, R., Jan 1 2010, Biology of Subterranean Fishes. CRC Press, p. 115-139 25 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

pleiotropy
caves
Fishes
fish
eyes
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

Bolide impacts and climat

Rampino, M., Jan 1 2009, Encyclopedia of Earth Sciences Series. Springer Netherlands, p. 972-975 4 p. (Encyclopedia of Earth Sciences Series).

Research output: Chapter in Book/Report/Conference proceedingChapter

bolide

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., 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., 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: 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