Research Output 1961 2018

2018

An FGF-driven feed-forward circuit patterns the cardiopharyngeal mesoderm in space and time

Razy-Krajka, F., Gravez, B., Kaplan, N., Racioppi, C., Wang, W. & Christiaen, L. Feb 6 2018 In : eLife. 7, e29656

Research output: Contribution to journalArticle

Mesoderm
Muscles
Pharyngeal Muscles
Urochordata
Cardiac Myocytes

ANISEED 2017: Extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets

Brozovic, M. , Dantec, C. , Dardaillon, J. , Dauga, D. , Faure, E. , Gineste, M. , Louis, A. , Naville, M. , Nitta, K. R. , Piette, J. , Reeves, W. , Scornavacca, C. , Simion, P. , Vincentelli, R. , Bellec, M. , Aicha, S. B. , Fagotto, M. , Guéroult-Bellone, M. , Haeussler, M. , Jacox, E. & 19 others Lowe, E. K., Mendez, M., Roberge, A., Stolfi, A., Yokomori, R., Brown, C. T., Cambillau, C., Christiaen, L., Delsuc, F., Douzery, E., Dumollard, R., Kusakabe, T., Nakai, K., Nishida, H., Satou, Y., Swalla, B., Veeman, M., Volff, J. N. & Lemaire, P. Jan 1 2018 In : Nucleic acids research. 46, D1, p. D718-D725

Research output: Contribution to journalArticle

Urochordata
Genome
Databases
Gene Expression
Vertebrates

A Novel Domain Assembly Routine for Creating Full-Length Models of Membrane Proteins from Known Domain Structures

Koehler Leman, J. & Bonneau, R. Apr 3 2018 In : Biochemistry. 57, 13, p. 1939-1944 6 p.

Research output: Contribution to journalArticle

Photosensitizers
Membrane Proteins
Slip forming
Membranes
Hand

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

A sibling method for identifying vQTLs

Conley, D., Johnson, R., Domingue, B., Dawes, C., Boardman, J. & Siegal, M. Apr 1 2018 In : PLoS ONE. 13, 4, e0194541

Research output: Contribution to journalArticle

Siblings
genetic relationships
Single Nucleotide Polymorphism
Genotype
Phenotype

Availability of Data Supporting Tables and Figures in Articles

Reiss, C. S. Jan 1 2018 In : DNA and Cell Biology. 37, 1, 1 p.

Research output: Contribution to journalEditorial

cAMPr: A single-wavelength fluorescent sensor for cyclic AMP

Hackley, C. R., Mazzoni, E. O. & Blau, J. Mar 6 2018 In : Science Signaling. 11, 520, eaah3738

Research output: Contribution to journalArticle

Acoustic logging
Cyclic AMP
Photons
Drosophila
Neurons

Cavefishes

Borowsky, R. Jan 22 2018 In : Current Biology. 28, 2, p. R60-R64

Research output: Contribution to journalShort survey

caves
Fishes
fish
Food
food availability

Cherub versus brat

Malin, J. A. & Desplan, C. Mar 27 2018 In : eLife. 7, e36030

Research output: Contribution to journalArticle

Long Noncoding RNA
Neoplasms

C-MAF-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont

Xu, M., Pokrovskii, M., Ding, Y., Yi, R., Au, C., Harrison, O. J., Galan, C., Belkaid, Y., Bonneau, R. & Littman, D. R. Feb 15 2018 In : Nature. 554, 7692, p. 373-377 5 p.

Research output: Contribution to journalArticle

Regulatory T-Lymphocytes
Helicobacter hepaticus
Bacteria
T-Lymphocytes
Inflammatory Bowel Diseases

Condition-Specific Modeling of Biophysical Parameters Advances Inference of Regulatory Networks

Tchourine, K., Vogel, C. & Bonneau, R. Apr 10 2018 In : Cell Reports. 23, 2, p. 376-388 13 p.

Research output: Contribution to journalArticle

Thermionic emission
RNA Stability
Chaperonin Containing TCP-1
Chaperonins
Gene Regulatory Networks

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

Developmental diversification of cortical inhibitory interneurons

Mayer, C., Hafemeister, C., Bandler, R. C., Machold, R., Batista Brito, R., Jaglin, X., Allaway, K., Butler, A., Fishell, G. & Satija, R. Mar 22 2018 In : Nature. 555, 7697, p. 457-462 6 p.

Research output: Contribution to journalArticle

Interneurons
Transcription Factors
RNA Sequence Analysis
Parvalbumins
Gene Regulatory Networks

Developmental dynamics of gene expression and alternative polyadenylation in the Caenorhabditis elegans germline

West, S. M., Mecenas, D., Gutwein, M., Aristizábal-Corrales, D., Piano, F. & Gunsalus, K. C. Jan 24 2018 In : Genome Biology. 19, 1, 8

Research output: Contribution to journalArticle

Developmental Genes
Polyadenylation
Caenorhabditis elegans
3' Untranslated Regions
3' untranslated regions

Development of Concurrent Retinotopic Maps in the Fly Motion Detection Circuit

Pinto-Teixeira, F., Koo, C., Rossi, A. M., Neriec, N., Bertet, C., Li, X., Del-Valle-Rodriguez, A. & Desplan, C. Apr 5 2018 In : Cell. 173, 2, p. 485-498.e11

Research output: Contribution to journalArticle

Neurons
Motion Perception
Birth Order
Neuropil
Neurogenesis

Does the common sexually transmitted parasite Trichomonas vaginalis have sex?

Bradic, M. & Carlton, J. M. Mar 1 2018 In : PLoS Pathogens. 14, 3, e1006831

Research output: Contribution to journalArticle

Trichomonas vaginalis
Parasites

Enhanced spontaneous DNA twisting/bending fluctuations unveiled by fluorescence lifetime distributions promote mismatch recognition by the Rad4 nucleotide excision repair complex

Chakraborty, S., Steinbach, P. J., Paul, D., Mu, H., Broyde, S., Min, J. H. & Ansari, A. Feb 16 2018 In : Nucleic acids research. 46, 3, p. 1240-1255 16 p.

Research output: Contribution to journalArticle

DNA Repair
Fluorescence
DNA
Nucleic Acid Conformation
DNA Adducts

ERK inhibition represses gefitinib resistance in non-small cell lung cancer cells

Qi, M., Tian, Y., Li, W., Li, D., Zhao, T., Yang, Y., Li, Q., Chen, S., Yang, Y., Zhang, Z., Tang, L., Liu, Z., Su, B., Li, F., Feng, Y., Fei, K., Zhang, P., Zhang, F. & Zhang, L. Jan 1 2018 In : Oncotarget. 9, 15, p. 12020-12034 15 p.

Research output: Contribution to journalArticle

Autophagy
Non-Small Cell Lung Carcinoma
Phosphorylation
gefitinib
Extracellular Signal-Regulated MAP Kinases
color vision
insect
insects

Evolutionary epigenomics of retrotransposon-mediated methylation spreading in rice

Choi, J. Y. & Purugganan, M. D. Feb 1 2018 In : Molecular Biology and Evolution. 35, 2, p. 365-382 18 p.

Research output: Contribution to journalArticle

Retroelements
DNA Transposable Elements
terminal repeat sequences
Terminal Repeat Sequences
retrotransposons

Fungi stabilize connectivity in the lung and skin microbial ecosystems

Tipton, L., Müller, C. L., Kurtz, Z. D., Huang, L., Kleerup, E., Morris, A., Bonneau, R. & Ghedin, E. Jan 1 2018 In : Microbiome. 6, 1, 12

Research output: Contribution to journalArticle

Ecosystem
Fungi
Microbiota
Lung
Skin

How Social Media Facilitates Political Protest: Information, Motivation, and Social Networks

Jost, J. T., Barberá, P., Bonneau, R., Langer, M., Metzger, M., Nagler, J., Sterling, J. & Tucker, J. A. Feb 1 2018 In : Political Psychology. 39, p. 85-118 34 p.

Research output: Contribution to journalArticle

Social Media
Information Services
social media
Social Support
protest

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

Insulin resistance in cavefish as an adaptation to a nutrient-limited environment

Riddle, M. R., Aspiras, A. C., Gaudenz, K., Peuß, R., Sung, J. Y., Martineau, B., Peavey, M., Box, A. C., Tabin, J. A., McGaugh, S., Borowsky, R., Tabin, C. J. & Rohner, N. Mar 29 2018 In : Nature. 555, 7698, p. 647-651 5 p.

Research output: Contribution to journalArticle

Insulin Resistance
Food
Mutation
Insulin Receptor
Insulin

Integrating single-cell transcriptomic data across different conditions, technologies, and species

Butler, A., Hoffman, P., Smibert, P., Papalexi, E. & Satija, R. Jun 1 2018 In : Nature Biotechnology. 36, 5, p. 411-420 10 p.

Research output: Contribution to journalArticle

Thermionic emission
RNA
Technology
Blood
Cells

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

Large-Scale CRISPR-Mediated Somatic Mutagenesis Identifies a Signaling Pathway that Guides Retinal Development

Minkina, O. & Desplan, C. Apr 4 2018 In : Neuron. 98, 1, p. 1-3 3 p.

Research output: Contribution to journalShort survey

Clustered Regularly Interspaced Short Palindromic Repeats
Mutagenesis
Retina
Retinal Cone Photoreceptor Cells
Retinal Rod Photoreceptor Cells

Malaria parasite evolution in a test tube

Carlton, J. M. 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

Mapping of HKT1;5 gene in barley using gwas approach and its implication in salt tolerance mechanism

Hazzouri, K. M., Khraiwesh, B., Amiri, K. M. A., Pauli, D., Blake, T., Shahid, M., Mullath, S. K., Nelson, D., Mansour, A. L., Salehi-Ashtiani, K., Purugganan, M. & Masmoudi, K. Feb 19 2018 In : Frontiers in Plant Science. 9, 156

Research output: Contribution to journalArticle

salt tolerance
barley
sodium
genes
leaves

Molecular transitions in early progenitors during human cord blood hematopoiesis

Zheng, S., Papalexi, E., Butler, A., Stephenson, W. & Satija, R. Mar 1 2018 In : Molecular Systems Biology. 14, 3, e8041

Research output: Contribution to journalArticle

Hematopoiesis
Thermionic emission
hematopoiesis
Fetal Blood
Blood

Multiple origin but single domestication led to Oryza sativa

Choi, J. Y. & Purugganan, M. D. Mar 1 2018 In : G3: Genes, Genomes, Genetics. 8, 3, p. 797-803 7 p.

Research output: Contribution to journalArticle

Genomics
Population
Alleles
Domestication
Oryza

O6-methylguanine–induced transcriptional mutagenesis reduces p53 tumor-suppressor function

Ezerskyte, M., Paredes, J. A., Malvezzi, S., Burns, J. A., Margison, G. P., Olsson, M., Scicchitano, D. A. & Dreij, K. May 1 2018 In : Proceedings of the National Academy of Sciences of the United States of America. 115, 18, p. 4731-4736 6 p.

Research output: Contribution to journalArticle

Mutagenesis
Neoplasms
Carcinogenesis
G1 Phase Cell Cycle Checkpoints
RNA Sequence Analysis

Phenazines regulate Napdependent denitrification in Pseudomonas aeruginosa biofilms

Lin, Y. C., Sekedat, M. D., Cornell, W. C., Silva, G. M., Okegbe, C., Price-Whelan, A., Vogel, C. & Dietrich, L. E. P. May 1 2018 In : Journal of Bacteriology. 200, 9, e00031-18

Research output: Contribution to journalArticle

Phenazines
Denitrification
Biofilms
Pseudomonas aeruginosa
Nitrates

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

Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation

Stephenson, W., Donlin, L. T., Butler, A., Rozo, C., Bracken, B., Rashidfarrokhi, A., Goodman, S. M., Ivashkiv, L. B., Bykerk, V. P., Orange, D. E., Darnell, R. B., Swerdlow, H. P. & Satija, R. Dec 1 2018 In : Nature Communications. 9, 1, 791

Research output: Contribution to journalArticle

droplet
instrumentation
RNA
cost
subpopulation

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

Statistically derived asymmetric membrane potentials from α-helical and β-barrel membrane proteins

Koehler Leman, J., Bonneau, R. & Ulmschneider, M. B. Dec 1 2018 In : Scientific Reports. 8, 1, 4446

Research output: Contribution to journalArticle

Membrane Potentials
Energy Transfer
Membrane Proteins
Membranes
Proteins

Statistics about recent journal performance

Reiss, C. S. Mar 1 2018 In : DNA and Cell Biology. 37, 3, 1 p.

Research output: Contribution to journalEditorial

Strength in numbers from integrated single-cell neuroscience

Satija, R. Jan 10 2018 In : Nature Biotechnology. 36, 1, p. 41-42 2 p.

Research output: Contribution to journalShort survey

Neurosciences
Reactor startup
Nucleosomes
DNA Repair
Fault tolerance
Genome

Taxonomy of the order Mononegavirales: update 2018

Amarasinghe, G. K. , Aréchiga Ceballos, N. G. , Banyard, A. C. , Basler, C. F. , Bavari, S. , Bennett, A. J. , Blasdell, K. R. , Briese, T. , Bukreyev, A. , Caì, Y. , Calisher, C. H. , Campos Lawson, C. , Chandran, K. , Chapman, C. A. , Chiu, C. Y. , Choi, K. S. , Collins, P. L. , Dietzgen, R. G. , Dolja, V. V. , Dolnik, O. & 30 others Domier, L. L., Dürrwald, R., Dye, J. M., Easton, A. J., Ebihara, H., Echevarría, J. E., Fooks, A. R., Formenty, P. B. H., Fouchier, R. A. M., Freuling, C. M., Ghedin, E., Goldberg, T. L., Hewson, R., Horie, M., Hyndman, T. H., Jiāng, D., Kityo, R., Kobinger, G. P., Kondō, H., Koonin, E. V., Krupovic, M., Kurath, G., Lamb, R. A., Lee, B., Leroy, E. M., Maes, P., Maisner, A., Marston, D. A., Mor, S. K. & Müller, T. Apr 11 2018 (Accepted/In press) In : Archives of Virology. p. 1-12 12 p.

Research output: Contribution to journalArticle

Mononegavirales
Viruses

Temperature preference of cave and surface populations of Astyanax mexicanus

Tabin, J. A., Aspiras, A., Martineau, B., Riddle, M., Kowalko, J., Borowsky, R., Rohner, N. & Tabin, C. J. Jan 1 2018 (Accepted/In press) In : Developmental Biology.

Research output: Contribution to journalArticle

Temperature
Population
Fever
Fishes
Behavioral Genetics

Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing

Äijö, T., Müller, C. L. & Bonneau, R. Feb 1 2018 In : Bioinformatics. 34, 3, p. 372-380 9 p.

Research output: Contribution to journalArticle

Probabilistic Modeling
Sequencing
Metagenomics
Sampling
Chemical analysis

β-Actin-dependent global chromatin organization and gene expression programs control cellular identity

Xie, X., Almuzzaini, B., Drou, N., Kremb, S., Yousif, A., Farrants, A. K. Ö., Gunsalus, K. & Percipalle, P. Mar 1 2018 In : FASEB Journal. 32, 3, p. 1296-1314 19 p.

Research output: Contribution to journalArticle

Efflorescence
Epigenomics
Chemical properties
Chromatin
Actins

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

Actin Turnover in Lamellipodial Fragments

Raz-Ben Aroush, D., Ofer, N., Abu-Shah, E., Allard, J., Krichevsky, O., Mogilner, A. & Keren, K. Oct 9 2017 In : Current Biology. 27, 19, p. 2963-2973.e14

Research output: Contribution to journalArticle

actin
Actins
pseudopodia
Pseudopodia
Oligomers

Adhesion-Dependent Wave Generation in Crawling Cells

Barnhart, E. L., Allard, J., Lou, S. S., Theriot, J. A. & Mogilner, A. Jan 9 2017 In : Current Biology. 27, 1, p. 27-38 12 p.

Research output: Contribution to journalArticle

actin
adhesion
Actins
Adhesion
Feedback

A Feast of Malaria Parasite Genomes

Carlton, J. M. & Sullivan, S. A. Mar 8 2017 In : Cell Host and Microbe. 21, 3, p. 310-312 3 p.

Research output: Contribution to journalShort survey

Plasmodium
Malaria
Parasites
Genome

A free-boundary model of a motile cell explains turning behavior

Nickaeen, M., Novak, I. L., Pulford, S., Rumack, A., Brandon, J., Slepchenko, B. M. & Mogilner, A. Nov 1 2017 In : PLoS Computational Biology. 13, 11, e1005862

Research output: Contribution to journalArticle

Myosin
Myosins
myosin
Free Boundary
Actin