Waksman Institute of Microbiology

Research Output 1972 2019

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Review article
2019
2 Citations (Scopus)

Auxin EvoDevo: Conservation and Diversification of Genes Regulating Auxin Biosynthesis, Transport, and Signaling

Matthes, M. S., Best, N. B., Robil, J. M., Malcomber, S., Gallavotti, A. & McSteen, P., Mar 4 2019, In : Molecular Plant. 12, 3, p. 298-320 23 p.

Research output: Contribution to journalReview article

Indoleacetic Acids
Arabidopsis
Zea mays
auxins
biosynthesis

Discovery, properties, and biosynthesis of pseudouridimycin, an antibacterial nucleoside-analog inhibitor of bacterial RNA polymerase

Maffioli, S. I., Sosio, M., Ebright, R. & Donadio, S., Mar 29 2019, In : Journal of Industrial Microbiology and Biotechnology. 46, 3-4, p. 335-343 9 p.

Research output: Contribution to journalReview article

Bacterial RNA
Biosynthesis
DNA-Directed RNA Polymerases
RNA
Nucleosides
1 Citation (Scopus)

Post-transcriptional adaptation of the aquatic plant Spirodela polyrhiza under stress and hormonal stimuli

Fourounjian, P., Tang, J., Tanyolac, B., Feng, Y., Gelfand, B., Kakrana, A., Tu, M., Wakim, C., Meyers, B. C., Ma, J. & Messing, J., Jun 1 2019, In : Plant Journal. 98, 6, p. 1120-1133 14 p.

Research output: Contribution to journalReview article

Spirodela polyrhiza
aquatic plants
MicroRNAs
microRNA
Araceae
9 Citations (Scopus)
Open Access
United States Food and Drug Administration
Communicable Diseases
Anti-Bacterial Agents
Pharmaceutical Preparations
Carbapenems
2 Citations (Scopus)

Xenogeneic Regulation of the Bacterial Transcription Machinery

Tabib-Salazar, A., Mulvenna, N., Severinov, K., Matthews, S. J. & Wigneshweraraj, S., Jan 1 2019, In : Journal of molecular biology.

Research output: Contribution to journalReview article

Open Access
Bacteriophages
DNA-Directed RNA Polymerases
Bacterial RNA
Coliphages
Viruses
2018
4 Citations (Scopus)

Cell–cell communication via ciliary extracellular vesicles: clues from model systems

Wang, J. & Barr, M., May 15 2018, In : Essays in biochemistry. 62, 2, p. 205-213 9 p.

Research output: Contribution to journalReview article

Cilia
Communication
Health
Flagella
Human Development
2 Citations (Scopus)

Cell polarity: compassing cell division and differentiation in plants

Zhang, Y. & Dong, J., Oct 1 2018, In : Current Opinion in Plant Biology. 45, p. 127-135 9 p.

Research output: Contribution to journalReview article

cell differentiation
cell division
proteins
cell walls
cells
18 Citations (Scopus)

The hippo signaling network and its biological functions

Misra, J. R. & Irvine, K., Nov 23 2018, In : Annual Review of Genetics. 52, p. 65-87 23 p.

Research output: Contribution to journalReview article

Cues
Long-Acting Thyroid Stimulator
Cell Proliferation
Cell Polarity
Intercellular Junctions
2017
18 Citations (Scopus)

Mechanical control of growth: Ideas, facts and challenges

Irvine, K. & Shraiman, B. I., Dec 1 2017, In : Development (Cambridge). 144, 23, p. 4238-4248 11 p.

Research output: Contribution to journalReview article

Growth
Mechanical Stress
Morphogenesis
Biological Phenomena
Physics
216 Citations (Scopus)

Multiplex gene editing by CRISPR-Cpf1 using a single crRNA array

Zetsche, B., Heidenreich, M., Mohanraju, P., Fedorova, I., Kneppers, J., Degennaro, E. M., Winblad, N., Choudhury, S. R., Abudayyeh, O. O., Gootenberg, J. S., Wu, W. Y., Scott, D. A., Severinov, K., Van Der Oost, J. & Zhang, F., Jan 1 2017, In : Nature biotechnology. 35, 1, p. 31-34 4 p.

Research output: Contribution to journalReview article

Clustered Regularly Interspaced Short Palindromic Repeats
RNA
Genes
Brain
Cells
1 Citation (Scopus)

Novel RNA polymerase inhibitor found in soil extracts provides hope for future antibacterial drugs

Ebright, R., Oct 1 2017, In : Future Medicinal Chemistry. 9, 16, p. 1857-1861 5 p.

Research output: Contribution to journalReview article

DNA-Directed RNA Polymerases
Soil
Pharmaceutical Preparations
New Brunswick
Patents
11 Citations (Scopus)

The chromosomal basis of meiotic acentrosomal spindle assembly and function in oocytes

Radford, S. J., Nguyen, A. L., Schindler, K. & McKim, K., Jun 1 2017, In : Chromosoma. 126, 3, p. 351-364 14 p.

Research output: Contribution to journalReview article

Spindle Apparatus
Oocytes
Centrosome
Chromosomes
Meiosis
2016
13 Citations (Scopus)

Asymmetric cell division in plants: mechanisms of symmetry breaking and cell fate determination

Pillitteri, L. J., Guo, X. & Dong, J., Jun 10 2016, In : Cellular and Molecular Life Sciences. 73, 22, p. 4213-4229 17 p.

Research output: Contribution to journalReview article

Asymmetric Cell Division
Cell Polarity
Indoleacetic Acids
Plant Cells
DNA Methylation
46 Citations (Scopus)

Cellular Organization and Cytoskeletal Regulation of the Hippo Signaling Network

Sun, S. & Irvine, K., Sep 1 2016, In : Trends in Cell Biology. 26, 9, p. 694-704 11 p.

Research output: Contribution to journalReview article

Cytoskeleton
Cell Polarity
Growth
Proteins
27 Citations (Scopus)

Ciliary Extracellular Vesicles: Txt Msg Organelles

Wang, J. & Barr, M., Apr 1 2016, In : Cellular and Molecular Neurobiology. 36, 3, p. 449-457 9 p.

Research output: Contribution to journalReview article

Organelles
Cilia
Caenorhabditis elegans
Chlamydomonas
Extracellular Vesicles
30 Citations (Scopus)

Expanding the Regulatory Network for Meristem Size in Plants

Galli, M. & Gallavotti, A., Jun 1 2016, In : Trends in Genetics. 32, 6, p. 372-383 12 p.

Research output: Contribution to journalReview article

Meristem
Stem Cells
Plant Development
Lycopersicon esculentum
Arabidopsis
10 Citations (Scopus)

Phage M13 for the treatment of Alzheimer and Parkinson disease

Messing, J., Jun 1 2016, In : Gene. 583, 2, p. 85-89 5 p.

Research output: Contribution to journalReview article

Bacteriophage M13
Protein Biosynthesis
DNA Replication
Neurodegenerative Diseases
Bacteriophages
16 Citations (Scopus)

Polarity in plant asymmetric cell division: Division orientation and cell fate differentiation

Shao, W. & Dong, J., Nov 1 2016, In : Developmental Biology. 419, 1, p. 121-131 11 p.

Research output: Contribution to journalReview article

Asymmetric Cell Division
Plant Cells
Cell Differentiation
Cell Division
Proteins
39 Citations (Scopus)

Structural basis for differing electrocatalytic water oxidation by the cubic, layered and spinel forms of lithium cobalt oxides

Gardner, G., Al-Sharab, J., Danilovic, N., Go, Y. B., Ayers, K., Greenblatt, M. & Charles Dismukes, G., Jan 2016, In : Energy and Environmental Science. 9, 1, p. 184-192 9 p.

Research output: Contribution to journalReview article

catalysis
lithium
cobalt
spinel
electrolyte
2015
9 Citations (Scopus)

Focusing on the focus: What else beyond the master switches for polar cell growth?

Qin, Y. & Dong, J., Apr 6 2015, In : Molecular Plant. 8, 4, p. 582-594 13 p.

Research output: Contribution to journalReview article

Polar Bodies
cell growth
Growth
Asymmetric Cell Division
Cell Polarity
30 Citations (Scopus)

Matters of context guide future research in TGFβ superfamily signaling

Akhurst, R. J. & Padgett, R., Oct 20 2015, In : Science signaling. 8, 399, p. re10

Research output: Contribution to journalReview article

Transforming Growth Factors
Research
Electric wiring
2 Citations (Scopus)

RNA polymerase molecular beacon as tool for studies of RNA polymerase-promoter interactions

Mekler, V. & Severinov, K., Sep 15 2015, In : Methods. 86, p. 19-26 8 p.

Research output: Contribution to journalReview article

DNA-Directed RNA Polymerases
Transcription
Assays
Bacterial RNA
Holoenzymes
9 Citations (Scopus)

Status of duckweed genomics and transcriptomics

Wang, W. & Messing, J., Jan 1 2015, In : Plant Biology. 17, s1, p. 10-15 6 p.

Research output: Contribution to journalReview article

Spirodela
transcriptomics
genomics
genome
DNA barcoding
2014
3 Citations (Scopus)

Decoding the role of chromatin architecture in development: Coming closer to the end of the tunnel

Luo, C., Dong, J., Zhang, Y. & Lam, E., Aug 21 2014, In : Frontiers in Plant Science. 5, AUG, 374.

Research output: Contribution to journalReview article

chromatin
genome
Biological Sciences
gene expression
monitoring
18 Citations (Scopus)

Mating behavior, male sensory cilia, and polycystins in caenorhabditis elegans

O'Hagan, R., Wang, J. & Barr, M., Jan 1 2014, In : Seminars in Cell and Developmental Biology. 33, p. 25-33 9 p.

Research output: Contribution to journalReview article

TRPP Cation Channels
Cilia
Caenorhabditis elegans
Autosomal Dominant Polycystic Kidney
Neurons
2013
6 Citations (Scopus)

A non-bacterial transcription factor inhibits bacterial transcription by a multipronged mechanism

Sheppard, C., James, E., Barton, G., Matthews, S., Severinov, K. & Wigneshweraraj, S., Jan 1 2013, In : RNA Biology. 10, 4, p. 495-501 7 p.

Research output: Contribution to journalReview article

DNA-Directed RNA Polymerases
Transcription Factors
Enzymes
Bacteria
Bacteriophages
180 Citations (Scopus)

Photosystem II: The reaction center of oxygenic photosynthesis

Vinyard, D. J., Ananyev, G. M. & Dismukes, G., Jun 1 2013, In : Annual review of biochemistry. 82, p. 577-606 30 p.

Research output: Contribution to journalReview article

Photosystem II Protein Complex
Photosynthesis
Water
Oxidation
Planets
786 Citations (Scopus)

Ribosomally synthesized and post-translationally modified peptide natural products: Overview and recommendations for a universal nomenclature

Arnison, P. G., Bibb, M. J., Bierbaum, G., Bowers, A. A., Bugni, T. S., Bulaj, G., Camarero, J. A., Campopiano, D. J., Challis, G. L., Clardy, J., Cotter, P. D., Craik, D. J., Dawson, M., Dittmann, E., Donadio, S., Dorrestein, P. C., Entian, K. D., Fischbach, M. A., Garavelli, J. S., Göransson, U. & 45 others, Gruber, C. W., Haft, D. H., Hemscheidt, T. K., Hertweck, C., Hill, C., Horswill, A. R., Jaspars, M., Kelly, W. L., Klinman, J. P., Kuipers, O. P., Link, A. J., Liu, W., Marahiel, M. A., Mitchell, D. A., Moll, G. N., Moore, B. S., Müller, R., Nair, S. K., Nes, I. F., Norris, G. E., Olivera, B. M., Onaka, H., Patchett, M. L., Piel, J., Reaney, M. J. T., Rebuffat, S., Ross, R. P., Sahl, H. G., Schmidt, E. W., Selsted, M. E., Severinov, K., Shen, B., Sivonen, K., Smith, L., Stein, T., Süssmuth, R. D., Tagg, J. R., Tang, G. L., Truman, A. W., Vederas, J. C., Walsh, C. T., Walton, J. D., Wenzel, S. C., Willey, J. M. & Van Der Donk, W. A., Jan 2013, In : Natural Product Reports. 30, 1, p. 108-160 53 p.

Research output: Contribution to journalReview article

Biosynthesis
Terminology
Biological Products
Peptides
compound 20

Science signaling podcast: 10 september 2013

Irvine, K., Sun, G. & VanHook, A. M., Sep 10 2013, In : Science signaling. 6, 292, pc23.

Research output: Contribution to journalReview article

Webcasts
Solar System
Growth and Development
Diptera
Sun
51 Citations (Scopus)

The role of auxin in shaping shoot architecture

Gallavotti, A., Jun 1 2013, In : Journal of Experimental Botany. 64, 9, p. 2593-2608 16 p.

Research output: Contribution to journalReview article

Indoleacetic Acids
plant architecture
auxins
stem elongation
meristems
2012
151 Citations (Scopus)

Hippo signaling in Drosophila: Recent advances and insights

Staley, B. K. & Irvine, K. D., Jan 1 2012, In : Developmental Dynamics. 241, 1, p. 3-15 13 p.

Research output: Contribution to journalReview article

Drosophila
Arthropods
Tumor Suppressor Genes
Vertebrates
Regeneration
55 Citations (Scopus)

Integration of intercellular signaling through the Hippo pathway

Irvine, K., Jan 1 2012, In : Seminars in Cell and Developmental Biology. 23, 7, p. 812-817 6 p.

Research output: Contribution to journalReview article

Signal Transduction
Growth
Transcription Factors
Proteins
24 Citations (Scopus)

Microcin C: Biosynthesis and mechanisms of bacterial resistance

Severinov, K. & Nair, S. K., Feb 1 2012, In : Future Microbiology. 7, 2, p. 281-289 9 p.

Research output: Contribution to journalReview article

Aspartate-tRNA Ligase
Bacterial Drug Resistance
Anti-Bacterial Agents
Amino Acyl-tRNA Synthetases
Bacteria
87 Citations (Scopus)

Sweet sorghum as a model system for bioenergy crops

Calviño, M. & Messing, J., Jun 1 2012, In : Current Opinion in Biotechnology. 23, 3, p. 323-329 7 p.

Research output: Contribution to journalReview article

Sorghum
Crops
Genes
Genetic Crosses
Costs and Cost Analysis
19 Citations (Scopus)

Towards hydrogen energy: Progress on catalysts for water splitting

Swiegers, G. F., MacFarlane, D. R., Officer, D. L., Ballantyne, A., Boskovic, D., Chen, J., Dismukes, G., Gardner, G. P., Hocking, R. K., Smith, P. F., Spiccia, L., Wagner, P., Wallace, G. G., Winther-Jensen, B. & Winther-Jensen, O., Jul 3 2012, In : Australian Journal of Chemistry. 65, 6, p. 577-582 6 p.

Research output: Contribution to journalReview article

Hydrogen
Oxidation
Catalysts
Water
Harvesters
2011
20 Citations (Scopus)

NanoRNAs: A class of small RNAs that can prime transcription initiation in bacteria

Nickels, B. & Dove, S. L., Oct 7 2011, In : Journal of molecular biology. 412, 5, p. 772-781 10 p.

Research output: Contribution to journalReview article

RNA
Bacteria
Gene Expression
DNA-Directed RNA Polymerases
In Vitro Techniques
87 Citations (Scopus)

New target for inhibition of bacterial RNA polymerase: 'switch region'

Srivastava, A., Talaue, M., Liu, S., Degen, D., Ebright, R. Y., Sineva, E., Chakraborty, A., Druzhinin, S. Y., Chatterjee, S., Mukhopadhyay, J., Ebright, Y. W., Zozula, A., Shen, J., Sengupta, S., Niedfeldt, R. R., Xin, C., Kaneko, T., Irschik, H., Jansen, R., Donadio, S. & 2 others, Connell, N. & Ebright, R. H., Oct 1 2011, In : Current Opinion in Microbiology. 14, 5, p. 532-543 12 p.

Research output: Contribution to journalReview article

Bacterial RNA
DNA-Directed RNA Polymerases
Anti-Bacterial Agents
Drug Discovery
Binding Sites
2010
57 Citations (Scopus)

Chloroplasts as expression platforms for plant-produced vaccines

Cardi, T., Lenzi, P. & Maliga, P., Jan 1 2010, In : Expert Review of Vaccines. 9, 8, p. 893-911 19 p.

Research output: Contribution to journalReview article

Chloroplasts
Transgenes
Synthetic Vaccines
Plastids
Vaccines
13 Citations (Scopus)

Fertilization and the oocyte-to-embryo transition in C. elegans

Marcello, M. R. & Singson, A., Jan 1 2010, In : BMB Reports. 43, 6, p. 389-399 11 p.

Research output: Contribution to journalReview article

Fertilization
Oocytes
Caenorhabditis elegans
Embryonic Structures
Sperm-Ovum Interactions
69 Citations (Scopus)

RNA remodeling and gene regulation by cold shock proteins

Phadtare, S. & Severinov, K., Jan 1 2010, In : RNA Biology. 7, 6, p. 788-795 8 p.

Research output: Contribution to journalReview article

Cold Shock Proteins and Peptides
RNA
Temperature
RNA Stability
Genes
105 Citations (Scopus)

Yorkie: the final destination of Hippo signaling

Oh, H. & Irvine, K., Jul 1 2010, In : Trends in Cell Biology. 20, 7, p. 410-417 8 p.

Research output: Contribution to journalReview article

DNA-Binding Proteins
Growth
Drosophila
Vertebrates
Genes
2009
18 Citations (Scopus)

Cytological analysis of meiosis in fixed Drosophila ovaries.

McKim, K., Joyce, E. F. & Jang, J. K., Jan 1 2009, In : Methods in molecular biology (Clifton, N.J.). 558, p. 197-216 20 p.

Research output: Contribution to journalReview article

Meiosis
Drosophila
Ovary
Pachytene Stage
Metaphase
32 Citations (Scopus)

Genetic assays to define and characterize protein-protein interactions involved in gene regulation

Nickels, B., Jan 1 2009, In : Methods. 47, 1, p. 53-62 10 p.

Research output: Contribution to journalReview article

DNA-Directed RNA Polymerases
Transcription
Gene expression
Assays
Substitution reactions
1 Citation (Scopus)

Mechanisms of action of RNA polymerase-binding transcription factors that do not bind to DNA

Stepanova, E. V., Shevelev, A. B., Borukhov, S. I. & Severinov, K., Sep 1 2009, In : Biofizika. 54, 5, p. 773-790 18 p.

Research output: Contribution to journalReview article

DNA-Directed RNA Polymerases
Transcription Factors
DNA
Gene Expression Regulation
Enzymes
80 Citations (Scopus)

Structures of RNA polymerase-antibiotic complexes

Ho, M. X., Hudson, B. P., Das, K., Arnold, E. & Ebright, R. H., Dec 1 2009, In : Current Opinion in Structural Biology. 19, 6, p. 715-723 9 p.

Research output: Contribution to journalReview article

DNA-Directed RNA Polymerases
Anti-Bacterial Agents
Rifamycins
Bacterial RNA
DNA
6 Citations (Scopus)

Synergy of two reference genomes for the grass family

Messing, J., Jan 1 2009, In : Plant physiology. 149, 1, p. 117-124 8 p.

Research output: Contribution to journalReview article

Plant Genome
Retroelements
DNA Transposable Elements
Gene Duplication
Sorghum
111 Citations (Scopus)

The 'inner circle' of the cereal genomes

Bolot, S., Abrouk, M., Masood-Quraishi, U., Stein, N., Messing, J., Feuillet, C. & Salse, J., Apr 1 2009, In : Current Opinion in Plant Biology. 12, 2, p. 119-125 7 p.

Research output: Contribution to journalReview article

genome
grasses
chromosomes
linkage groups
ancestry
2008
26 Citations (Scopus)

Genes required for the common miracle of fertilization in Caenorhabditis elegans

Singson, A., Hang, J. S. & Parry, J. M., Oct 27 2008, In : International Journal of Developmental Biology. 52, 5-6, p. 647-656 10 p.

Research output: Contribution to journalReview article

Sperm-Ovum Interactions
Caenorhabditis elegans
Fertilization
Ovum
Genetic Association Studies
117 Citations (Scopus)

Photoassembly of the water-oxidizing complex in photosystem II

Dasgupta, J., Ananyev, G. M. & Dismukes, G. C., Feb 1 2008, In : Coordination Chemistry Reviews. 252, 3-4, p. 347-360 14 p.

Research output: Contribution to journalReview article

Photosystem II Protein Complex
Oxidation
Water
water
oxidation
9 Citations (Scopus)

Regulation of gene expression in a type II restriction-modification system

Nagornykh, M. O., Bogdanova, E. S., Protsenko, A. S., Solonin, A. S., Zakharova, M. V. & Severinov, K., May 1 2008, In : Russian Journal of Genetics. 44, 5, p. 523-532 10 p.

Research output: Contribution to journalReview article

DNA Restriction-Modification Enzymes
Endonucleases
Gene Expression Regulation
Methyltransferases
Type II Site Specific Deoxyribonucleases