Research Output 1961 2019

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Review article
2019

An evolving view of copy number variants

Lauer, S. & Gresham, D., Jan 1 2019, In : Current Genetics.

Research output: Contribution to journalReview article

Inverted Repeat Sequences
Archaea
DNA Replication
Population
Saccharomyces cerevisiae

Cell reprogramming: The many roads to success

Aydin, B. & Mazzoni, E., Jan 1 2019, In : Annual Review of Cell and Developmental Biology. 35, p. 433-452 20 p.

Research output: Contribution to journalReview article

Transcription Factors
Cellular Reprogramming

Classical and emerging regulatory mechanisms of cytokinesis in animal cells

Verma, V., Mogilner, A. & Maresca, T. J., Sep 1 2019, In : Biology. 8, 3, 55.

Research output: Contribution to journalReview article

Open Access
Myosin Type II
Actomyosin
Cytokinesis
cytokinesis
Chromosomes

Coordination of neural patterning in the Drosophila visual system

Courgeon, M. & Desplan, C., Jun 1 2019, In : Current Opinion in Neurobiology. 56, p. 153-159 7 p.

Research output: Contribution to journalReview article

Neuropil
Drosophila
Gene Expression

Copy Number Variation in Domestication

Lye, Z. N. & Purugganan, M., Jan 1 2019, In : Trends in Plant Science.

Research output: Contribution to journalReview article

domestication
mutation
genetic variation
animals
genes

Evolutionary Insights into the Nature of Plant Domestication

Purugganan, M., Jul 22 2019, In : Current Biology. 29, 14, p. R705-R714

Research output: Contribution to journalReview article

Open Access
domestication
Crops
crops
Genomics
genomics

Exploiting Interdata Relationships in Next-generation Proteomics Analysis

Vitrinel, B., Koh, H. W. L., Mujgan Kar, F., Maity, S., Rendleman, J., Choi, H. & Vogel, C., Aug 9 2019, In : Molecular & cellular proteomics : MCP. 18, 8, p. S5-S14

Research output: Contribution to journalReview article

Open Access
Proteomics
Messenger RNA
Molecules
Data integration
Mass spectrometry

Towards Building a Plant Cell Atlas

Rhee, S. Y., Birnbaum, K. & Ehrhardt, D. W., Jan 1 2019, In : Trends in Plant Science.

Research output: Contribution to journalReview article

cells
immune system
climate change
brain
carbon
2018

Evolution of human malaria

Carlton, J., Jun 1 2018, In : Nature Microbiology. 3, 6, p. 642-643 2 p.

Research output: Contribution to journalReview article

Hominidae
Plasmodium falciparum
Genomics
Malaria
Genes

Integration of large-scale multi-omic datasets: A protein-centric view

Rendleman, J., Choi, H. & Vogel, C., Oct 1 2018, In : Current Opinion in Systems Biology. 11, p. 74-81 8 p.

Research output: Contribution to journalReview article

Proteomics
Proteins
Protein
Gene expression regulation
Genes

Intracellular Fluid Mechanics: Coupling Cytoplasmic Flow with Active Cytoskeletal Gel

Mogilner, A. & Manhart, A., Jan 5 2018, In : Annual Review of Fluid Mechanics. 50, p. 347-370 24 p.

Research output: Contribution to journalReview article

fluid mechanics
gels
cytology
continuum mechanics
organelles

Malaria parasite evolution in a test tube

Carlton, J., Jan 12 2018, In : Science. 359, 6372, p. 159-160 2 p.

Research output: Contribution to journalReview article

Biological Evolution
host-parasite interaction
Host-Parasite Interactions
disease transmission
Plasmodium

Neuro-evo-devo in the single cell sequencing era

Konstantinides, N., Degabriel, S. & Desplan, C., Oct 1 2018, In : Current Opinion in Systems Biology. 11, p. 32-40 9 p.

Research output: Contribution to journalReview article

Clustered Regularly Interspaced Short Palindromic Repeats
Transcription factors
Neurology
Sequencing
Explosions

Neuronal specification in space and time

Holguera, I. & Desplan, C., Oct 12 2018, In : Science. 362, 6411, p. 176-180 5 p.

Research output: Contribution to journalReview article

Invertebrates
Cues
Vertebrates
Transcription Factors
Maintenance

Power in numbers: Single-cell RNA-seq strategies to dissect complex tissues

Birnbaum, K., Nov 23 2018, In : Annual Review of Genetics. 52, p. 203-221 19 p.

Research output: Contribution to journalReview article

Cell Count
RNA
RNA Sequence Analysis
Phenotype
Genetic Testing

Recent advances in behavioral (epi)genetics in eusocial insects

Opachaloemphan, C., Yan, H., Leibholz, A., Desplan, C. & Reinberg, D., Nov 23 2018, In : Annual Review of Genetics. 52, p. 489-510 22 p.

Research output: Contribution to journalReview article

Behavioral Genetics
Insects
Social Behavior
Pheromones
Epigenomics

Single-cell RNA sequencing to explore immune cell heterogeneity

Papalexi, E. & Satija, R., Jan 1 2018, In : Nature Reviews Immunology. 18, 1, p. 35-45 11 p.

Research output: Contribution to journalReview article

RNA Sequence Analysis
Immune System
Cell Lineage
Systems Analysis
Epigenomics

The metabolic axis of macrophage and immune cell polarization

Hobson-Gutierrez, S. A. & Carmona Fontaine, C., Aug 1 2018, In : DMM Disease Models and Mechanisms. 11, 8, dmm034462.

Research output: Contribution to journalReview article

Macrophages
Tumors
Polarization
Neoplasms
Tumor Microenvironment

Why are there hotspot mutations in the TP53 gene in human cancers?

Baugh, E. H., Ke, H., Levine, A. J., Bonneau, R. & Chan, C. S., Jan 1 2018, In : Cell Death and Differentiation. 25, 1, p. 154-160 7 p.

Research output: Contribution to journalReview article

p53 Genes
Mutation
Mutant Proteins
Alleles
Neoplasms
2017

Are all repeats created equal? Understanding DNA repeats at an individual level

Yang, J. & Li, F., Feb 1 2017, In : Current Genetics. 63, 1, p. 57-63 7 p.

Research output: Contribution to journalReview article

Centromere
Epigenomics
Chromatin
DNA
Genome

Biophysically motivated regulatory network inference: Progress and prospects

Äijö, T. & Bonneau, R., Jan 1 2017, In : Human Heredity. 81, 2, p. 62-77 16 p.

Research output: Contribution to journalReview article

Technology
Chromatin
Research Design
Learning
Genome

Generation and Evolution of Neural Cell Types and Circuits: Insights from the Drosophila Visual System

Perry, M., Konstantinides, N., Pinto-Teixeira, F. & Desplan, C., Nov 27 2017, In : Annual Review of Genetics. 51, p. 501-577 77 p.

Research output: Contribution to journalReview article

Drosophila
Neurons
Diptera
Brain
Insects

Getting the flu: 5 key facts about influenza virus evolution

Johnson, K. E. E., Song, T., Greenbaum, B. & Ghedin, E., Aug 1 2017, In : PLoS Pathogens. 13, 8, e1006450.

Research output: Contribution to journalReview article

Orthomyxoviridae

Quantifying protein (dis)order: A study of bacteria, yeast, and mammalian cells maps the melting behavior of cellular proteins

Vogel, C., Feb 24 2017, In : Science. 355, 6327, p. 794-795 2 p.

Research output: Contribution to journalReview article

cells and cell components
Freezing
yeast
melting
Yeasts

Repair-Resistant DNA Lesions

Geacintov, N. & Broyde, S., Aug 21 2017, In : Chemical Research in Toxicology. 30, 8, p. 1517-1548 32 p.

Research output: Contribution to journalReview article

DNA Repair
Repair
DNA
Nucleotides
Drug Design

Retinal perception and ecological significance of color vision in insects

Lebhardt, F. & Desplan, C., Dec 1 2017, In : Current Opinion in Insect Science. 24, p. 75-83 9 p.

Research output: Contribution to journalReview article

color vision
wavelengths
eyes
insect
opsin

The lung mycobiome in the next-generation sequencing era

Tipton, L., Ghedin, E. & Morris, A., Apr 3 2017, In : Virulence. 8, 3, p. 334-341 8 p.

Research output: Contribution to journalReview article

Lung
Fungi
Respiratory Tract Diseases
Names
Mycobiome

The role of 'omics' in the quest to eliminate human filariasis

Lustigman, S., Grote, A. & Ghedin, E., Apr 20 2017, In : PLoS Neglected Tropical Diseases. 11, 4, e0005464.

Research output: Contribution to journalReview article

Timing temporal transitions during brain development

Rossi, A. M., Fernandes, V. M. & Desplan, C., Feb 1 2017, In : Current Opinion in Neurobiology. 42, p. 84-92 9 p.

Research output: Contribution to journalReview article

Brain
Aptitude
Neural Stem Cells
Invertebrates
Nervous System
2016

A Case for Distributed Control of Local Stem Cell Behavior in Plants

Rahni, R., Efroni, I. & Birnbaum, K., Sep 26 2016, In : Developmental Cell. 38, 6, p. 635-642 8 p.

Research output: Contribution to journalReview article

Stem cells
Stem Cells
Tissue
Decentralized control
Meristem

Agent-based modeling: Case study in cleavage furrow models

Mogilner, A. & Manhart, A., Nov 7 2016, In : Molecular Biology of the Cell. 27, 22, p. 3379-3384 6 p.

Research output: Contribution to journalReview article

Systems Analysis
Cell Biology
History
Recognition (Psychology)

A synopsis on aging—Theories, mechanisms and future prospects

da Costa, J. P., Vitorino, R., Silva, G. M., Vogel, C., Duarte, A. C. & Rocha-Santos, T., Aug 1 2016, In : Ageing Research Reviews. 29, p. 90-112 23 p.

Research output: Contribution to journalReview article

Biochemical Phenomena
Aging of materials
Systems Biology
Research
Therapeutics

How many ways are there to make a root?

Birnbaum, K., Dec 1 2016, In : Current Opinion in Plant Biology. 34, p. 61-67 7 p.

Research output: Contribution to journalReview article

blood vessels
ontogeny
embryogenesis
tissues

Network inference from multimodal data: A review of approaches from infectious disease transmission

Ray, B., Ghedin, E. & Chunara, R., Dec 1 2016, In : Journal of Biomedical Informatics. 64, p. 44-54 11 p.

Research output: Contribution to journalReview article

Infectious Disease Transmission
Electric power transmission networks
Metagenomics
Epidemiology
Biomarkers

Nitrate Transport, Sensing, and Responses in Plants

O'Brien, JA. A., Vega, A., Bouguyon, E., Krouk, G., Gojon, A., Coruzzi, G. & Gutiérrez, RA. A., 2016, In : Molecular Plant. 9, 6, p. 837-856 20 p.

Research output: Contribution to journalReview article

Nitrates
plant response
nitrates
Growth and Development
Imino Acids

Programmed cell death acts at different stages of Drosophila neurodevelopment to shape the central nervous system

Pinto-Teixeira, F., Konstantinides, N. & Desplan, C., Aug 1 2016, In : FEBS Letters. p. 2435-2453 19 p.

Research output: Contribution to journalReview article

Neurology
Cell death
Drosophila
Cell Death
Central Nervous System

Transcriptional Control of Developmental Cell Behaviors

Bernadskaya, Y. & Christiaen, L., Oct 6 2016, In : Annual Review of Cell and Developmental Biology. 32, p. 77-101 25 p.

Research output: Contribution to journalReview article

Gene Regulatory Networks
Cues
Cell-Matrix Junctions
Developmental Genes
Cell Shape
2015

Mechanisms of X chromosome dosage compensation

Ercan, S., Jan 1 2015, In : Journal of Genomics. 3, p. 1-19 19 p.

Research output: Contribution to journalReview article

X Chromosome
Chromosomes
Transcription
Animals
Compensation and Redress
2013

Are mantle plumes periodic?

Rampino, M. & Prokoph, A., Mar 19 2013, In : Eos. 94, 12, p. 113-114 2 p.

Research output: Contribution to journalReview article

mantle plume
2010

Keeping in touch with contact inhibition of locomotion

Mayor, R. & Carmona Fontaine, C., Jun 2010, In : Trends in Cell Biology. 20, 6, p. 319-328 10 p.

Research output: Contribution to journalReview article

Contact Inhibition
Locomotion
rho GTP-Binding Proteins
Monomeric GTP-Binding Proteins
Cell Movement
2005

Genetic network during neural crest induction: From cell specification to cell survival

Steventon, B., Carmona Fontaine, C. & Mayor, R., Dec 2005, In : Seminars in Cell and Developmental Biology. 16, 6, p. 647-654 8 p.

Research output: Contribution to journalReview article

Neural Crest
Cell Survival
Transcription Factors
Maintenance

Pseudomonas aeruginosa Genome Database and PseudoCAP: Facilitating community-based, continually updated, genome annotation

Winsor, G. L., Lo, R., Ho Sui, S. J., Ung, K. S. E., Huang, S-S., Cheng, D., Ching, W. K. H., Hancock, R. E. W. & Brinkman, F. S. L., Jan 1 2005, In : Nucleic Acids Research. 33, DATABASE ISS.

Research output: Contribution to journalReview article

Pseudomonas aeruginosa
Genome
Databases
Licensure
Research Personnel