Research Output 1961 2018

2018

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: Research - peer-reviewEditorial

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: ResearchChapter

RNA Stability
RNA
4-thiouracil
Nonlinear Dynamics
Streptavidin

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: Research - peer-reviewReview article

fluid mechanics
gels
cells
cytology
continuum mechanics

Malaria parasite evolution in a test tube

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

Research output: Research - peer-reviewReview article

Biological Evolution
Host-Parasite Interactions
Plasmodium
Malaria
Parasites

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: Research - peer-reviewReview article

RNA Sequence Analysis
Immune System
Cell Lineage
Systems Analysis
Epigenomics

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: Research - peer-reviewShort survey

Neurosciences
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: Research - peer-reviewArticle

Actins
actin
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: Research - peer-reviewArticle

actin
adhesion
cells
Actins
Adhesion

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: Research - peer-reviewShort 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: Research - peer-reviewArticle

Myosin
Free Boundary
Cell
Model
myosin

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

Trichomonadida
sewage
ribosomal RNA
protists
protist

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

MicroRNAs
Structural Models
3' Untranslated Regions
Seeds
Protein Isoforms

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: Research - peer-reviewReview article

DNA
Centromere
Epigenomics
Chromatin
Genome

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

Macrolides
Immunity
Anti-Bacterial Agents
Topology
antibiotics

Asymmetric Notch Amplification to Secure Stem Cell Identity

Rossi, A. M. & Desplan, C. Mar 27 2017 In : Developmental Cell. 40, 6, p. 513-514 2 p.

Research output: Research - peer-reviewShort survey

Stem Cells
Neural Stem Cells

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: Research - peer-reviewReview article

Technology
Chromatin
Research Design
Learning
Genome

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: Research - peer-reviewArticle

Caenorhabditis elegans
Genes
condensin complexes
X Chromosome
Chromosome Structures

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: Research - peer-reviewArticle

space and time
gene expression
cells
Gene Expression
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: Research - peer-reviewArticle

Orthobunyavirus
Bunyaviridae
Viruses
Serogroup
Simbu virus

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

Cell Movement
Rheology
flood basalt
volcanic eruption
extinction
ocean
comparison

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: Research - peer-reviewArticle

Membrane Protein
Lipids
Accessibility
Computing
Membrane 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: Research - peer-reviewArticle

Nucleotide Motifs
X Chromosome
Regulator Genes
Chromatin
Chromosomes

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: Research - peer-reviewArticle

Heterochromatin
Histones
DNA Replication
Epigenomics
Methylation

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: Research - peer-reviewArticle

Homologous Recombination
Mutation
Population
Genetic Recombination
Datasets

Correlation of the largest craters, stratigraphic impact signatures, and extinction events over the past 250 Myr

Rampino, M. R. & Caldeira, K. Jan 27 2017 (Accepted/In press) In : Geoscience Frontiers.

Research output: Research - peer-reviewArticle

crater
extinction
cratering
ejecta
effect

Corrigendum to: CTCF-mediated topological boundaries during development foster appropriate gene regulation (Genes & Development, (2016), 30, (2657–2662), 10.1101/gad.288324.116)

Narendra, V., Bulajić, M., Dekker, J., Mazzoni, E. O. & Reinberg, D. Aug 15 2017 In : Genes and Development. 31, 16, p. 2657-2662 6 p.

Research output: Research - peer-reviewComment/debate

Organized Financing
National Institutes of Health (U.S.)
Genes
corrigendum

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 (Accepted/In press) In : Nature Immunology.

Research output: Research - peer-reviewArticle

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

Deconvolving sequence features that discriminate between overlapping regulatory annotations

Kakumanu, A., Velasco, S., Mazzoni, E. & Mahony, S. Oct 1 2017 In : PLoS Computational Biology. 13, 10, e1005795

Research output: Research - peer-reviewArticle

Overlapping
Annotation
Cell
cells
Labels

Deep sequencing of natural and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations

Assaf, Z. J., Tilk, S., Park, J., Siegal, M. L. & Petrov, D. A. Dec 1 2017 In : Genome Research. 27, 12, p. 1988-2000 13 p.

Research output: Research - peer-reviewArticle

High-Throughput Nucleotide Sequencing
Drosophila melanogaster
Mutation
Population
Mutation Accumulation

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: Research - peer-reviewArticle

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: Research - peer-reviewArticle

Microfluidics
Caenorhabditis elegans
baysilon
Polydimethylsiloxane
Throughput

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 (Accepted/In press) In : Advances in Political Psychology.

Research output: Research - peer-reviewArticle

Discovery of peptide ligands through docking and virtual screening at nicotinic acetylcholine receptor homology models

Leffler, A. E., Kuryatov, A., Zebroski, H. A., Powell, S. R., Filipenko, P., Hussein, A. K., Gorson, J., Heizmann, A., Lyskov, S., Tsien, R. W., Poget, S. F., Nicke, A., Lindstrom, J., Rudy, B., Bonneau, R. & Holford, M. Sep 19 2017 In : Proceedings of the National Academy of Sciences of the United States of America. 114, 38, p. E8100-E8109

Research output: Research - peer-reviewArticle

Nicotinic Receptors
Screening
Ligands
Peptides
Conotoxins

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: Research - peer-reviewArticle

Hepatocytes
Cholesterol
Liver
Wounds and Injuries
Lanosterol

Efficient Dual siRNA and Drug Delivery Using Engineered Lipoproteoplexes

Liu, C. F., Chen, R., Frezzo, J. A., Katyal, P., Hill, L. K., Yin, L., Srivastava, N., More, H. T., Renfrew, P. D., Bonneau, R. & Montclare, J. K. Sep 11 2017 In : Biomacromolecules. 18, 9, p. 2688-2698 11 p.

Research output: Research - peer-reviewArticle

Drug delivery
Doxorubicin
Small Interfering RNA
Cells
Lipofectamine
Peer Review
Publications

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 (Accepted/In press) In : Journal of Cellular Physiology.

Research output: Research - peer-reviewArticle

Myosins
Electric fields
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: Research - peer-reviewArticle

Mastadenovirus
capsid
Adenoviridae
Chiroptera
cryo-electron microscopy

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: Research - peer-reviewArticle

Molgula
melanogenesis
Tunicata
gene
loss

Evolutionary recruitment of flexible Esrp-dependent splicing programs into diverse embryonic morphogenetic processes

Burguera, D. , Marquez, Y. , Racioppi, C. , Permanyer, J. , Torres-Méndez, A. , Esposito, R. , Albuixech-Crespo, B. , Fanlo, L. , D'Agostino, Y. , Gohr, A. , Navas-Perez, E. , Riesgo, A. , Cuomo, C. , Benvenuto, G. , Christiaen, L. A. , Martí, E. , D'Aniello, S. , Spagnuolo, A. , Ristoratore, F. , Arnone, M. I. & 2 others Garcia-Fernàndez, J. & Irimia, M. Dec 1 2017 In : Nature Communications. 8, 1, 1799

Research output: Research - peer-reviewArticle

Vertebrates
Animals
Genes
Tissue
Defects

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: Research - peer-reviewArticle

Skin
DNA
microorganisms
Metagenomics
Dairies

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 (Accepted/In press) In : EMBO Journal.

Research output: Research - peer-reviewArticle

Synaptonemal Complex
Meiosis
Cell Cycle
Phosphotransferases
Cells

G9A promotes tumor cell growth and invasion by silencing CASP1 in non-small-cell lung cancer cells

Huang, T., Zhang, P., Li, W., Zhao, T., Zhang, Z., Chen, S., Yang, Y., Feng, Y., Li, F., Shirley Liu, X., Zhang, L., Jiang, G. & Zhang, F. Jan 1 2017 In : Cell Death and Disease. 8, 4, e2726

Research output: Research - peer-reviewArticle

Neoplasm Proteins
Neoplasm Invasiveness
Histone-Lysine N-Methyltransferase
Inbred BALB C Mouse
Caspase 1

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: Research - peer-reviewReview article

Drosophila
Neurons
Diptera
Brain
Insects

Genome Architecture and Evolution of a Unichromosomal Asexual Nematode

Fradin, H., Kiontke, K., Zegar, C., Gutwein, M., Lucas, J., Kovtun, M., Corcoran, D. L., Baugh, L. R., Fitch, D. H. A., Piano, F. & Gunsalus, K. C. 2017 (Accepted/In press) In : Current Biology.

Research output: Research - peer-reviewArticle

heterozygosity
Nematoda
chromosomes
genome
Genome