Research Output 1961 2018

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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

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

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

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

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

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

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

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

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
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
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 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

A meeting that helped: Foster the acceptance of global tectonics

Rampino, M. R. 2017 In : Eos. 98, 2, p. 18-22 5 p.

Research output: Contribution to journalArticle

global perspective
conference proceeding
structural geology
tectonic setting
tectonics

An 18S rRNA Workflow for Characterizing Protists in Sewage, with a Focus on Zoonotic Trichomonads

Maritz, J. M., Rogers, K. H., Rock, T. M., Liu, N., Joseph, S., Land, K. M. & Carlton, J. M. May 24 2017 (Accepted/In press) In : Microbial Ecology. p. 1-14 14 p.

Research output: Contribution to journalArticle

Trichomonadida
protist
sewage
ribosomal RNA
DNA

An Engineered orco Mutation Produces Aberrant Social Behavior and Defective Neural Development in Ants

Yan, H. , Opachaloemphan, C. , Mancini, G. , Yang, H. , Gallitto, M. , Mlejnek, J. , Leibholz, A. , Haight, K. , Ghaninia, M. , Huo, L. , Perry, M. , Slone, J. , Zhou, X. , Traficante, M. , Penick, C. A. , Dolezal, K. , Gokhale, K. , Stevens, K. , Fetter-Pruneda, I. , Bonasio, R. & 5 others Zwiebel, L. J., Berger, S. L., Liebig, J., Reinberg, D. & Desplan, C. Aug 10 2017 In : Cell. 170, 4, p. 736-747.e9

Research output: Contribution to journalArticle

Odorant Receptors
Ants
Social Behavior
Mutation
Neurons

A non-canonical site reveals the cooperative mechanisms of microRNA-mediated silencing

Flamand, M. N., Gan, H. H., Mayya, V. K., Gunsalus, K. C. & Duchaine, T. F. Jul 1 2017 In : Nucleic Acids Research. 45, 12, p. 7212-7225 14 p.

Research output: Contribution to journalArticle

MicroRNAs
Structural Models
3' Untranslated Regions
Seeds
Protein Isoforms

Are some tillites impact-related debris-flow deposits?

Rampino, M. R. Mar 1 2017 In : Journal of Geology. 125, 2, p. 155-164 10 p.

Research output: Contribution to journalArticle

debris flow
clast
diamictite
brittle failure
iceberg

A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity

Ruiz, V. E., Battaglia, T., Kurtz, Z. D., Bijnens, L., Ou, A., Engstrand, I., Zheng, X., Iizumi, T., Mullins, B. J., Müller, C. L., Cadwell, K., Bonneau, R., Perez-Perez, G. I. & Blaser, M. J. Dec 1 2017 In : Nature Communications. 8, 1, 518

Research output: Contribution to journalArticle

antibiotics
Macrolides
immunity
Immunity
topology

Caenorhabditis elegans Dosage Compensation: Insights into Condensin-Mediated Gene Regulation

Albritton, S. E. & Ercan, S. 2017 (Accepted/In press) In : Trends in Genetics.

Research output: Contribution to journalArticle

Caenorhabditis elegans
Genes
X Chromosome
Chromosome Structures
Chromosomes

Changes in gene expression in space and time orchestrate environmentally mediated shaping of root architecture

Walker, L., Boddington, C., Jenkins, D., Wang, Y., Grønlund, J. T., Hulsmans, J., Kumar, S., Patel, D., Moore, J. D., Carter, A., Samavedam, S., Bonomo, G., Hersh, D. S., Coruzzi, G. M., Burroughs, N. J. & Gifford, M. L. Oct 1 2017 In : Plant Cell. 29, 10, p. 2393-2412 20 p.

Research output: Contribution to journalArticle

space and time
Gene Expression
gene expression
cells
Genes

Characterization of five unclassified orthobunyaviruses (Bunyaviridae) from Africa and the Americas

Rogers, M. B., Gulino, K. M., Tesh, R. B., Cui, L., Fitch, A., Unnasch, T. R., Popov, V. L., Travassos da Rosa, A. P. A., Guzman, H., Carrera, J. P., Vasilakis, N. & Ghedin, E. Sep 1 2017 In : Journal of General Virology. 98, 9, p. 2258-2266 9 p., 000899

Research output: Contribution to journalArticle

Orthobunyavirus
Bunyaviridae
Viruses
Simbu virus
California Encephalitis Viruses

Characterizing Antibody Responses to Plasmodium vivax and Plasmodium falciparum Antigens in India Using Genome-Scale Protein Microarrays

Uplekar, S. , Rao, P. N. , Ramanathapuram, L. , Awasthi, V. , Verma, K. , Sutton, P. , Ali, S. Z. , Patel, A. , Sri Lakshmi Priya, G. , Ravishankaran, S. , Desai, N. , Tandel, N. , Choubey, S. , Barla, P. , Kanagaraj, D. , Eapen, A. , Pradhan, K. , Singh, R. , Jain, A. , Felgner, P. L. & 3 others Davies, D. H., Carlton, J. M. & Das, J. Jan 24 2017 In : PLoS Neglected Tropical Diseases. 11, 1, e0005323

Research output: Contribution to journalArticle

Plasmodium vivax
Protein Array Analysis
Plasmodium falciparum
Malaria
Antibody Formation

Collective cell migration has distinct directionality and speed dynamics

Zhang, Y., Xu, G., Lee, R. M., Zhu, Z., Wu, J., Liao, S., Zhang, G., Sun, Y., Mogilner, A., Losert, W., Pan, T., Lin, F., Xu, Z. & Zhao, M. Jun 13 2017 (Accepted/In press) In : Cellular and Molecular Life Sciences. p. 1-10 10 p.

Research output: Contribution to journalArticle

Cell Movement
Rheology
flood basalt
volcanic eruption
extinction
ocean
mass extinction

Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP

Koehler Leman, J., Lyskov, S. & Bonneau, R. Feb 20 2017 In : BMC Bioinformatics. 18, 1, 115

Research output: Contribution to journalArticle

Membrane Protein
Lipids
Accessibility
Membrane Proteins
Proteins

Cooperation between a hierarchical set of recruitment sites targets the X chromosome for dosage compensation

Albritton, S. E., Kranz, A. L., Winterkorn, L. H., Street, L. A. & Ercan, S. May 30 2017 In : eLife. 6, e23645

Research output: Contribution to journalArticle

Nucleotide Motifs
X Chromosome
Regulator Genes
Chromosomes
Chromatin

Coordinated regulation of heterochromatin inheritance by Dpb3–Dpb4 complex

He, H., Li, Y., Dong, Q., Chang, A. Y., Gao, F., Chi, Z., Su, M., Zhang, F., Ban, H., Martienssen, R., Chen, Y. H. & Li, F. Nov 21 2017 In : Proceedings of the National Academy of Sciences of the United States of America. 114, 47, p. 12524-12529 6 p.

Research output: Contribution to journalArticle

Heterochromatin
Histones
DNA Replication
Epigenomics
Methylation