Research Output 1961 2017

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Chapter
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: ResearchChapter

Peptidomimetics
Proteins
Secondary Protein Structure
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: ResearchChapter

Cell Movement
Theoretical Models
Cell Separation
Zebrafish
Cues

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: ResearchChapter

Viral Encephalitis
Innate Immunity
Infection
Central Nervous System
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: ResearchChapter

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: ResearchChapter

Gene Expression Regulation
Proteins
Datasets
Proteolysis
Messenger RNA

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: ResearchChapter

Ubiquitinated Proteins
Ubiquitin
Mass Spectrometry
Mass spectrometry
Proteins

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: ResearchChapter

eyes
testing
Testing
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: ResearchChapter

sorting
gene expression
cells
tissues
Gene Expression Profiling
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: ResearchChapter

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: ResearchChapter

photoreceptors
Light
Drosophila
wavelengths
Diptera
2012

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: ResearchChapter

Salinity
Arabidopsis
Flow Cytometry
Oryza
Green Fluorescent Proteins

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: ResearchChapter

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: ResearchChapter

Molecular Evolution
Molecular Biology
Genetics
Angiosperms
Plant Development

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: ResearchChapter

Plasticity
Large scale systems
Animals
Cells
Systems Biology
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: ResearchChapter

Estuaries
DNA Adducts
Polycyclic Aromatic Hydrocarbons
DNA Repair
Neoplasms

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: ResearchChapter

sterility
lungs
microbiome
Microbiota
Lung
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: ResearchChapter

Plasmodium vivax
Culicidae
Genes
Plasmodium
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: ResearchChapter

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: ResearchChapter

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: ResearchChapter

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: ResearchChapter

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: ResearchChapter

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: ResearchChapter

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: ResearchChapter

Caenorhabditis elegans
Biological Sciences
animals
Systems Biology
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: ResearchChapter

Brugia malayi
Wolbachia
Tetracycline
Gene Expression
Therapeutics

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: ResearchChapter

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: ResearchChapter

Biological Sciences
Systems Biology
Ecosystem
organisms
Ecology

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: ResearchChapter

Cryptosporidium muris
genome
Cryptosporidium
Genome
parasites

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: ResearchChapter

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: ResearchChapter

Systems Biology
Research
Biological Sciences
organisms
plant biology

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: ResearchChapter

Vesicular Stomatitis
Virus Diseases
Viruses
Brain
Infection
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: ResearchChapter

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: ResearchChapter

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: ResearchChapter

Viral Encephalitis
Innate Immunity
Viruses
Central Nervous System
Brain

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: ResearchChapter

DNA Viruses
Prions
Retroviridae
Deltaretrovirus
HIV

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: ResearchChapter

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: ResearchChapter

RNA Viruses
Innate Immunity
Genome
Viruses
Hendra Virus
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: ResearchChapter

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: ResearchChapter

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: ResearchChapter

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: ResearchChapter

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: ResearchChapter

productivity
crop
land
Crops
Productivity
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: ResearchChapter

origin of life
surface temperature
weathering
land
atmosphere-ocean system

Volcanism, climatic change, and the geologic record

Rampino, M. R. 1991 Sedimentation in volcanic settings. Fisher, R. V. & Smith, G. A. (eds.). SEPM, Tulsa; Special Publication, 45, p. 9-18 10 p.

Research output: ResearchChapter

volcanism
climate change
climate
accretion
cooling
1990

The greenhouse effect, stratospheric ozone, marine productivity, and global hydrology: feedbacks in the global climate system

Rampino, M. R. & Etkins, R. 1990 Greenhouse effect, sea level and drought. Proc. workshop, Fuerteventura, 1989. Paepe, R. (ed.). Kluwer, for NATO ASI Series; Series C, 325, p. 3-20 18 p.

Research output: ResearchChapter

greenhouse effect
global climate
hydrology
ozone
productivity
1989

Sensitivity of climate and atmospheric CO2 to deep-ocean and shallow-ocean carbonate burial

Volk, T. 1989 Nature. 6208 ed. Vol. 337, p. 637-640 4 p.

Research output: ResearchChapter

carbonate
climate
ocean
mantle
geochemical cycle
1988

Volcanic winters

Rampino, M. R., Self, S. & Stothers, R. B. 1988 Annual review of earth and planetary sciences. Vol. 16. Wetherill, G. W. (ed.). Annual Reviews Inc., p. 73-99 27 p.

Research output: ResearchChapter

volcanic eruption
winter
sulfuric acid
aerosol
dust
1987

Feedbacks between weathering and atmospheric CO2 over the last 100 million years.

Volk, T. 1987 America Journal of Science. 8 ed. Vol. 287, p. 763-779 17 p.

Research output: ResearchChapter

weathering
effect
biosphere
productivity
soil
1985

Influence of the carcinogen 4-aminobiphenyl on DNA conformation

Broyde, S., Zawadzka, H. & Shapiro, R. 1985 Proceedings of the American Association for Cancer Research. Vol. VOL. 26

Research output: ResearchChapter

Ocean carbon pumps: analysis of relative strengths and efficiencies in ocean-driven atmospheric CO2 changes.

Volk, T. & Hoffert, M. I. 1985 The carbon cycle and atmospheric CO 2 : natural variations Archean to present. Chapman conference papers, 1984. Sundquist, E. T. & Broecker, W. S. (eds.). American Geophysical Union; Geophysical Monograph 32, p. 99-110 12 p.

Research output: ResearchChapter

pump
carbon
ocean
analysis
sea surface