Research Output 1961 2017

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2017

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

Acetylcholine
actin
Actins
Feedback
adhesion

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 In : Microbial Ecology. p. 1-14 14 p.

Research output: Contribution to journalArticle

sewage
sampling
protist
Trichomonadida
ribosomal RNA

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
Insects

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

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 In : Cellular and Molecular Life Sciences. p. 1-10 10 p.

Research output: Contribution to journalArticle

Cell Movement
Rheology
flood basalt
extinction
volcanic eruption
mass extinction
crater

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 Proteins
Lipids
Proteins
Membranes
Membrane protein

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
Chromatin
Chromosomes

Correlated Mutations and Homologous Recombination Within Bacterial Populations

Lin, M. & Kussell, E. Feb 1 2017 In : Genetics. 205, 2, p. 891-917 27 p.

Research output: Contribution to journalArticle

Homologous Recombination
Mutation
Genetic Recombination
Datasets
Bacterial DNA
extinction
crater
cratering
ejecta
damage

Critical role of IRF1 and BATF in forming chromatin landscape during type 1 regulatory cell differentiation

Karwacz, K., Miraldi, E. R., Pokrovskii, M., Madi, A., Yosef, N., Wortman, I., Chen, X., Watters, A., Carriero, N., Awasthi, A., Regev, A., Bonneau, R., Littman, D. & Kuchroo, V. K. Feb 6 2017 In : Nature Immunology.

Research output: Contribution to journalArticle

Regulatory T-Lymphocytes
Chromatin
Cell Differentiation
Interleukin-27
Transcription Factors

Defining Brugia malayi and Wolbachia symbiosis by stage-specific dual RNA-seq

Grote, A., Voronin, D., Ding, T., Twaddle, A., Unnasch, T. R., Lustigman, S. & Ghedin, E. Mar 30 2017 In : PLoS Neglected Tropical Diseases. 11, 3, e0005357

Research output: Contribution to journalArticle

Brugia malayi
Wolbachia
Symbiosis
RNA
Parasites

Detecting and Trapping of a Single C. elegans Worm in a Microfluidic Chip for Automated Microplate Dispensing

Desta, I. T., Al-Sharif, A., AlGharibeh, N., Mustafa, N., Orozaliev, A., Giakoumidis, N., Gunsalus, K. C. & Song, Y. A. Aug 1 2017 In : SLAS Technology. 22, 4, p. 431-436 6 p.

Research output: Contribution to journalArticle

Microfluidics
Caenorhabditis elegans
Polydimethylsiloxane
Throughput
Microfluidic Analytical Techniques

Digital Dissent: Informational and Motivational Pathways to Political Protests Through Social Media

Tucker, J., Jost, J., Barberá, P., Bonneau, R., MacDuffee Metzger, M., Nagler, J. & Sterling, J. L. 2017 In : Advances in Political Psychology.

Research output: Contribution to journalArticle

Disrupting hepatocyte Cyp51 from cholesterol synthesis leads to progressive liver injury in the developing mouse and decreases RORC signalling

Urlep, Ž., Lorbek, G., Perše, M., Jeruc, J., Juvan, P., Matz-Soja, M., Gebhardt, R., Björkhem, I., Hall, J. A., Bonneau, R., Littman, D. R. & Rozman, D. Jan 18 2017 In : Scientific Reports. 7, 40775

Research output: Contribution to journalArticle

Hepatocytes
Cholesterol
Liver
Wounds and Injuries
Lanosterol

Electric fields accelerate cell polarization and bypass myosin action in motility initiation

Sun, Y. H., Sun, Y., Zhu, K., Reid, B., Gao, X., Draper, B. W., Zhao, M. & Mogilner, A. 2017 In : Journal of Cellular Physiology.

Research output: Contribution to journalArticle

Gamma Rays
Myosins
Polarization
Cell Movement
Fishes

Evolution and cryo-electron microscopy capsid structure of a north american bat adenovirus and its relationship to other mastadenoviruses

Hackenbrack, N., Rogers, M. B., Ashley, R. E., Keel, M. K., Kubiski, S. V., Bryan, J. A., Ghedin, E., Holmes, E. C., Hafenstein, S. L. & Allison, A. B. 2017 In : Journal of Virology. 91, 2, e01504-16

Research output: Contribution to journalArticle

Mastadenovirus
Cryoelectron Microscopy
Capsid
Adenoviridae
Chiroptera

Evolutionary loss of melanogenesis in the tunicate Molgula occulta

Racioppi, C., Valoroso, M. C., Coppola, U., Lowe, E. K., Brown, C. T., Swalla, B. J., Christiaen, L., Stolfi, A. & Ristoratore, F. Jul 18 2017 In : EvoDevo. 8, 1, 11

Research output: Contribution to journalArticle

Tunicata
gene
Urochordata
Monophenol Monooxygenase
Molgula oculata

Filthy lucre: A metagenomic pilot study of microbes found on circulating currency in New York City

Maritz, J. M., Sullivan, S. A., Prill, R. J., Aksoy, E., Scheid, P. & Carlton, J. M. Apr 1 2017 In : PLoS ONE. 12, 4, e0175527

Research output: Contribution to journalArticle

Edema Disease of Swine
Skin
Metagenomics
microorganisms
Bufo arenarum

Fundamental cell cycle kinases collaborate to ensure timely destruction of the synaptonemal complex during meiosis

Argunhan, B., Leung, W. K., Afshar, N., Terentyev, Y., Subramanian, V. V., Murayama, Y., Hochwagen, A., Iwasaki, H., Tsubouchi, T. & Tsubouchi, H. 2017 In : EMBO Journal.

Research output: Contribution to journalArticle

Synaptonemal Complex
Meiosis
Cell Cycle
Phosphotransferases
Meiotic Prophase I

Genomic and phenotypic characterization of myxoma virus from Great Britain reveals multiple evolutionary pathways distinct from those in Australia

Kerr, P. J., Cattadori, I. M., Rogers, M. B., Fitch, A., Geber, A., Liu, J., Sim, D. G., Boag, B., Eden, J. S., Ghedin, E., Read, A. F. & Holmes, E. C. Mar 1 2017 In : PLoS Pathogens. 13, 3, e1006252

Research output: Contribution to journalArticle

Myxoma virus
Virulence
Viruses
Phenotype
Rabbits

Geophysical evidence for a large impact structure on the Falkland (Malvinas) Plateau

Rocca, M. C. L., Rampino, M. R. & Báez Presser, J. L. 2017 In : Terra Nova.

Research output: Contribution to journalArticle

basin
impact structure
gravity anomaly
plateau
anomaly

Inferring fitness landscapes and selection on phenotypic states from single-cell genealogical data

Nozoe, T., Kussell, E. & Wakamoto, Y. Mar 1 2017 In : PLoS Genetics. 13, 3, e1006653

Research output: Contribution to journalArticle

cells
fitness
methodology
phenotype
Phenotype

Integrated Analysis of Biopsies from Inflammatory Bowel Disease Patients Identifies SAA1 as a Link between Mucosal Microbes with T H 17 and T H 22 Cells

Tang, M. S., Bowcutt, R., Leung, J. M., Wolff, M. J., Gundra, U. M., Hudesman, D., Malter, L. B., Poles, M. A., Chen, L. A., Pei, Z., Neto, A. G., Abidi, W. M., Ullman, T., Mayer, L., Bonneau, R. A., Cho, I. & Loke, P. Sep 1 2017 In : Inflammatory Bowel Diseases. 23, 9, p. 1544-1554 11 p.

Research output: Contribution to journalArticle

Inflammatory Bowel Diseases
Biopsy
T-Lymphocytes
Pediatrics
Datasets

Integration of temporal and spatial patterning generates neural diversity

Erclik, T., Li, X., Courgeon, M., Bertet, C., Chen, Z., Baumert, R., Ng, J., Koo, C., Arain, U., Behnia, R., del Valle Rodriguez, A., Senderowicz, L., Negre, N., White, K. P. & Desplan, C. Jan 19 2017 In : Nature. 541, 7637, p. 365-370 6 p.

Research output: Contribution to journalArticle

Neurons
Automatic Data Processing
Drosophila
Cell Body

L-2-Hydroxyglutarate production arises from noncanonical enzyme function at acidic pH

Intlekofer, A. M., Wang, B., Liu, H., Shah, H., Carmona-Fontaine, C., Rustenburg, A. S., Salah, S., Gunner, M. R., Chodera, J. D., Cross, J. R. & Thompson, C. B. Mar 6 2017 In : Nature Chemical Biology.

Research output: Contribution to journalArticle

Enzymes
Physiological Adaptation
Isocitrate Dehydrogenase
Hypoxia-Inducible Factor 1
Malate Dehydrogenase

Lessons from the genomes and transcriptomes of filarial nematodes

Grote, A., Lustigman, S. & Ghedin, E. Jan 11 2017 In : Molecular and Biochemical Parasitology.

Research output: Contribution to journalArticle

Transcriptome
Genome
Infection
Gene Expression Profiling
Sequence Analysis

Liberal and Conservative Values: What We Can Learn From Congressional Tweets

Jones, K. L., Noorbaloochi, S., Jost, J. T., Bonneau, R., Nagler, J. & Tucker, J. A. 2017 In : Political Psychology.

Research output: Contribution to journalArticle

Security Measures
Beneficence
Social Security
Self Report
Observational Study

Lung microbiome and host immune tone in subjects with idiopathic pulmonary fibrosis treated with inhaled interferon-γ

Wang, J., Lesko, M., Badri, M. H., Kapoor, B. C., Wu, B. G., Li, Y., Smaldone, G. C., Bonneau, R., Kurtz, Z. D., Condos, R. & Segal, L. N. Jul 1 2017 In : ERS Monograph. 3, 3

Research output: Contribution to journalArticle

Idiopathic Pulmonary Fibrosis
Microbiota
Interferon-gamma
Lung
Biological Markers

Mechanosensitive Adhesion Explains Stepping Motility in Amoeboid Cells

Copos, C. A., Walcott, S., del Álamo, J. C., Bastounis, E., Mogilner, A. & Guy, R. D. Jun 20 2017 In : Biophysical Journal. 112, 12, p. 2672-2682 11 p.

Research output: Contribution to journalArticle

Dictyostelium
Traction
Locomotion
Amoeba
Surface Properties

Metabolic origins of spatial organization in the tumor microenvironment

Carmona-Fontaine, C., Deforet, M., Akkari, L., Thompson, C. B., Joyce, J. A. & Xavier, J. B. Mar 14 2017 In : Proceedings of the National Academy of Sciences of the United States of America. 114, 11, p. 2934-2939 6 p.

Research output: Contribution to journalArticle

Tumor Microenvironment
Neoplasms
Macrophages
Arginase
Embryology

Mocap: Large-scale inference of transcription factor binding sites from chromatin accessibility

Chen, X., Yu, B., Carriero, N., Silva, C. & Bonneau, R. 2017 In : Nucleic Acids Research. 45, 8, p. 4315-4329 15 p.

Research output: Contribution to journalArticle

Chromatin
Transcription Factors
Binding Sites
CpG Islands
Base Composition

Myosin Clusters of Finite Size Develop Contractile Stress in 1D Random Actin Arrays

Rubinstein, B. Y. & Mogilner, A. Aug 22 2017 In : Biophysical Journal. 113, 4, p. 937-947 11 p.

Research output: Contribution to journalArticle

Myosins
Actins
Actomyosin
Stress Fibers
Structural Models
Nucleosomes
Benzo(a)pyrene
Acetylation
Histones
Lysine
Benzo(a)pyrene
DNA Repair
DNA
Proteins
Repair

Reduced dosage of the chromosome axis factor Red1 selectively disrupts the meiotic recombination checkpoint in Saccharomyces cerevisiae

Markowitz, T. E., Suarez, D., Blitzblau, H. G., Patel, N. J., Markhard, A. L., MacQueen, A. J. & Hochwagen, A. Jul 1 2017 In : PLoS Genetics. 13, 7, e1006928

Research output: Contribution to journalArticle

Chromosome Pairing
Genetic Recombination
Saccharomyces cerevisiae
Chromosomes
Alleles

Regulatory logic driving stable levels of defective proventriculus expression during terminal photoreceptor specification in flies

Yan, J., Anderson, C., Viets, K., Tran, S., Goldberg, G., Small, S. & Johnston, R. J. Mar 1 2017 In : Development (Cambridge). 144, 5, p. 844-855 12 p.

Research output: Contribution to journalArticle

Proventriculus
Diptera
Transcription Factors
Gene Expression
Neurons

Resolving the complex genetic basis of phenotypic variation and variability of cellular growth

Ziv, N., Shuster, B. M., Siegal, M. L. & Gresham, D. Jul 1 2017 In : Genetics. 206, 3, p. 1645-1657 13 p.

Research output: Contribution to journalArticle

Glucose
Quantitative Trait Loci
Genotype
Gene-Environment Interaction
Saccharomycetales

Seed plant-specific gene lineages involved in carpel development

Pfannebecker, K. C., Lange, M., Rupp, O., Becker, A. & Purugganan, M. Apr 1 2017 In : Molecular Biology and Evolution. 34, 4, p. 925-942 18 p.

Research output: Contribution to journalArticle

Plant Genes
Seeds
Genes
carpels
gene

Selective growth inhibition of cancer cells with doxorubicin-loaded CB[7]-modified iron-oxide nanoparticles

Benyettou, F., Fahs, H., Elkharrag, R., Bilbeisi, R. A., Asma, B., Rezgui, R., Motte, L., Magzoub, M., Brandel, J., Olsen, J. C., Piano, F., Gunsalus, K. C., Platas-Iglesias, C. & Trabolsi, A. 2017 In : RSC Advances. 7, 38, p. 23827-23834 8 p.

Research output: Contribution to journalArticle

Myosins
Nanoparticles
Castration
Cells
Acetanilides

Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput

Gierahn, T. M., Wadsworth, M. H., Hughes, T. K., Bryson, B. D., Butler, A., Satija, R., Fortune, S., Love, J. C. & Shalek, A. K. Feb 13 2017 In : Nature Methods.

Research output: Contribution to journalArticle

RNA Sequence Analysis
Costs and Cost Analysis
Costs
RNA
Bronchiolo-Alveolar Adenocarcinoma

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

Villani, A. C. , Satija, R. , Reynolds, G. , Sarkizova, S. , Shekhar, K. , Fletcher, J. , Griesbeck, M. , Butler, A. , Zheng, S. , Lazo, S. , Jardine, L. , Dixon, D. , Stephenson, E. , Nilsson, E. , Grundberg, I. , McDonald, D. , Filby, A. , Li, W. , De Jager, P. L. , Rozenblatt-Rosen, O. & 4 others Lane, A. A., Haniffa, M., Regev, A. & Hacohen, N. Apr 21 2017 In : Science. 356, 6335, eaah4573

Research output: Contribution to journalArticle

RNA Sequence Analysis
Dendritic Cells
Monocytes
Blood Cells
Immunologic Monitoring

Specialized odorant receptors in social insects that detect cuticular hydrocarbon cues and candidate pheromones

Pask, G. M., Slone, J. D., Millar, J. G., Das, P., Moreira, J. A., Zhou, X., Bello, J., Berger, S. L., Bonasio, R., Desplan, C., Reinberg, D., Liebig, J., Zwiebel, L. J. & Ray, A. Dec 1 2017 In : Nature Communications. 8, 1, 297

Research output: Contribution to journalArticle

Odorant Receptors
Pheromones
Hydrocarbons
Cues
Insects

Taxonomy of the order Mononegavirales: update 2017

Amarasinghe, G. K. , Bào, Y. , Basler, C. F. , Bavari, S. , Beer, M. , Bejerman, N. , Blasdell, K. R. , Bochnowski, A. , Briese, T. , Bukreyev, A. , Calisher, C. H. , Chandran, K. , Collins, P. L. , Dietzgen, R. G. , Dolnik, O. , Dürrwald, R. , Dye, J. M. , Easton, A. J. , Ebihara, H. , Fang, Q. & 53 others Formenty, P., Fouchier, R. A. M., Ghedin, E., Harding, R. M., Hewson, R., Higgins, C. M., Hong, J., Horie, M., James, A. P., Jiāng, D., Kobinger, G. P., Kondo, H., Kurath, G., Lamb, R. A., Lee, B., Leroy, E. M., Li, M., Maisner, A., Mühlberger, E., Netesov, S. V., Nowotny, N., Patterson, J. L., Payne, S. L., Paweska, J. T., Pearson, M. N., Randall, R. E., Revill, P. A., Rima, B. K., Rota, P., Rubbenstroth, D., Schwemmle, M., Smither, S. J., Song, Q., Stone, D. M., Takada, A., Terregino, C., Tesh, R. B., Tomonaga, K., Tordo, N., Towner, J. S., Vasilakis, N., Volchkov, V. E., Wahl-Jensen, V., Walker, P. J., Wang, B., Wang, D., Wang, F., Wang, L. F., Werren, J. H., Whitfield, A. E., Yan, Z., Ye, G. & Kuhn, J. H. Apr 7 2017 In : Archives of Virology. p. 1-12 12 p.

Research output: Contribution to journalArticle

Mononegavirales
Pneumovirus
Rhabdoviridae
Viruses
Permian
acritarch
Permian-Triassic boundary
woody debris
gymnosperm

The genome and phenome of the green alga chloroidium sp. UTEX 3007 reveal adaptive traits for desert acclimatization

Nelson, D. R., Khraiwesh, B., Fu, W., Alseekh, S., Jaiswal, A., Chaiboonchoe, A., Hazzouri, K. M., O’Connor, M. J., Butterfoss, G. L., Drou, N., Rowe, J. D., Harb, J., Fernie, A. R., Gunsalus, K. C. & Salehi-Ashtiani, K. Jun 17 2017 In : eLife. 6, e25783

Research output: Contribution to journalArticle

Chlorophyta
Acclimatization
Genome
Algae
Carbon

The Nonbulky DNA Lesions Spiroiminodihydantoin and 5-Guanidinohydantoin Significantly Block Human RNA Polymerase II Elongation in Vitro

Kolbanovskiy, M., Chowdhury, M. A., Nadkarni, A., Broyde, S., Geacintov, N. E., Scicchitano, D. A. & Shafirovich, V. Jun 20 2017 In : Biochemistry. 56, 24, p. 3008-3018 11 p.

Research output: Contribution to journalArticle

RNA Polymerase II
DNA Repair
DNA
In Vitro Techniques
Transcription

The rice paradox: Multiple origins but single domestication in Asian Rice

Choi, J. Y., Platts, A. E., Fuller, D. Q., Hsing, Y. I., Wing, R. A., Purugganan, M. D. & Kim, Y. Apr 1 2017 In : Molecular Biology and Evolution. 34, 4, p. 969-979 11 p.

Research output: Contribution to journalArticle

rice
Oryza sativa
domestication
wild rice
introgression