Research Output

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2020

Evolution of serotonin: sunlight to suicide

Azmitia, E. C., 2020, Handbook of Behavioral Neuroscience. Elsevier B.V., p. 3-22 20 p. (Handbook of Behavioral Neuroscience; vol. 31).

Research output: Chapter in Book/Report/Conference proceedingChapter

Gene regulatory networks during the development of the Drosophila visual system

Chen, Y. C. & Desplan, C., 2020, Current Topics in Developmental Biology. Academic Press Inc., p. 89-125 37 p. (Current Topics in Developmental Biology; vol. 139).

Research output: Chapter in Book/Report/Conference proceedingChapter

Just passing through: The auxin gradient of the root meristem

Guillotin, B. & Birnbaum, K. D., 2020, Current Topics in Developmental Biology. Small, S. & Briscoe, J. (eds.). Academic Press Inc., p. 433-454 22 p. (Current Topics in Developmental Biology; vol. 137).

Research output: Chapter in Book/Report/Conference proceedingChapter

2019

Nucleobindins and encoded peptides: From cell signaling to physiology

Leung, A. K. W., Ramesh, N., Vogel, C. & Unniappan, S., 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

The Role of Tertiary Structure in MicroRNA Target Recognition

Gan, H. H. & Gunsalus, K. C., 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

2018

Antibody pull-down experiments in fission yeast

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

Research output: Chapter in Book/Report/Conference proceedingChapter

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

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., p. 15-24 10 p. (Methods in Molecular Biology; vol. 1720).

Research output: Chapter in Book/Report/Conference proceedingChapter

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

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., p. 155-165 11 p. (Methods in Molecular Biology; vol. 1721).

Research output: Chapter in Book/Report/Conference proceedingChapter

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

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

2017

Modeling and design of peptidomimetics to modulate protein–protein interactions

Watkins, A. M., Bonneau, R. & Arora, P. S., Jan 1 2017, Methods in Molecular Biology. Humana Press Inc., p. 291-307 17 p. (Methods in Molecular Biology; vol. 1561).

Research output: Chapter in Book/Report/Conference proceedingChapter

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., Jan 1 2016, Methods in Molecular Biology. Humana Press Inc., p. 251-272 22 p. (Methods in Molecular Biology; vol. 1407).

Research output: Chapter in Book/Report/Conference proceedingChapter

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

Tucker, J. A., 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

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

Regressive Evolution: Testing Hypotheses of Selection and Drift

Borowsky, R., Jan 1 2016, Biology and Evolution of the Mexican Cavefish. Elsevier Inc., p. 93-109 17 p.

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

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., p. 111-125 15 p. (Neuromethods; vol. 114).

Research output: Chapter in Book/Report/Conference proceedingChapter

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

2014

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

Azmitia, E. C., 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

Population Genomics of Plant Species

Hazzouri, K. M., Purugganan, M. D. & Flowers, J. M., 2014, Advances in Botanical Research. Academic Press Inc., p. 311-334 24 p. (Advances in Botanical Research; vol. 69).

Research output: Chapter in Book/Report/Conference proceedingChapter

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

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., Dec 1 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

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

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

Development and Evolution of the Ascidian Cardiogenic Mesoderm

Tolkin, T. & Christiaen, L., 2012, Current Topics in Developmental Biology. Academic Press Inc., p. 107-142 36 p. (Current Topics in Developmental Biology; vol. 100).

Research output: Chapter in Book/Report/Conference proceedingChapter

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: 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

Label-free protein quantitation using weighted spectral counting

Vogel, C. & Marcotte, E. M., Jul 27 2012, Quantitative Methods in Proteomics. Katrin, M. (ed.). p. 321-341 21 p. (Methods in Molecular Biology; vol. 893).

Research output: Chapter in Book/Report/Conference proceedingChapter

Swimming Upstream: Identifying Proteomic Signals that Drive Transcriptional Changes using the Interactome and Multiple " -Omics" Datasets

Huang, S. S. C. & Fraenkel, E., 2012, Methods in Cell Biology. Academic Press Inc., p. 57-80 24 p. (Methods in Cell Biology; vol. 110).

Research output: Chapter in Book/Report/Conference proceedingChapter

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

The robustness continuum

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

Research output: Chapter in Book/Report/Conference proceedingChapter

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., Dec 1 2011, Chemical Carcinogenesis. Penning, T. (ed.). p. 181-207 27 p. (Current Cancer Research; vol. 6).

Research output: Chapter in Book/Report/Conference proceedingChapter

RNAi Methods and Screening: RNAi Based High-Throughput Genetic Interaction Screening

Cipriani, P. G. & Piano, F., 2011, Methods in Cell Biology. Academic Press Inc., p. 89-111 23 p. (Methods in Cell Biology; vol. 106).

Research output: Chapter in Book/Report/Conference proceedingChapter

The human lung microbiome

Losada, L., Ghedin, E., Morris, A., Chu, H. W. & Nierman, W. C., Jan 1 2011, Metagenomics of the Human Body. Springer New York, p. 117-143 27 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

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

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

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

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

Mathematical and physical modeling of actin dynamics in motile cells

Carlsson, A. E. & Mogilner, A., Jan 1 2010, Actin-based Motility: Cellular, Molecular and Physical Aspects. Springer Netherlands, p. 381-412 32 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

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

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

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

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

Annual Plant Reviews

Coruzzi, G. M. & Gutiérrez, R. A., Aug 18 2009, Plant Systems Biology. Blackwell Publishing Ltd, Vol. 35. p. 1-360 360 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Bolide impacts and climat

Rampino, M. R., 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

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

Gene orthology assessment with orthologID

Egan, M., Lee, E. K., Chiu, J. C., Coruzzi, G. & Desalle, R., Dec 1 2009, Bioinformatics for DNA Sequence Analysis. Posada, D. (ed.). p. 23-38 16 p. (Methods in Molecular Biology; vol. 537).

Research output: Chapter in Book/Report/Conference proceedingChapter

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