Research Output

2016

Anaplasma phagocytophilum APH0032 is exposed on the cytosolic face of the pathogen-occupied vacuole and co-opts host cell SUMOylation

Oki, A. T., Huang, B., Beyer, A. R., May, L. J., Truchan, H. K., Walker, N. J., Galloway, N. L., Borjesson, D. L. & Carlyon, J. A., Sep 22 2016, In : Frontiers in Cellular and Infection Microbiology. 6, SEP, 108.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Anaplasma phagocytophilum-occupied vacuole interactions with the host cell cytoskeleton

Truchan, H. K., Cockburn, C. L., May, L. J., VieBrock, L. & Carlyon, J. A., Sep 1 2016, In : Veterinary Sciences. 3, 3, 25.

Research output: Contribution to journalArticle

Open Access
5 Scopus citations

Anaplasma phagocytophilum Rab10-dependent parasitism of the trans-Golgi network is critical for completion of the infection cycle

Truchan, H. K., Viebrock, L., Cockburn, C. L., Ojogun, N., Griffin, B. P., Wijesinghe, D. S., Chalfant, C. E. & Carlyon, J. A., Feb 1 2016, In : Cellular Microbiology. 18, 2, p. 260-281 22 p.

Research output: Contribution to journalArticle

15 Scopus citations

An assay for 26S proteasome activity based on fluorescence anisotropy measurements of dye-labeled protein substrates

Bhattacharyya, S., Renn, J. P., Yu, H., Marko, J. F. & Matouschek, A., Sep 15 2016, In : Analytical Biochemistry. 509, p. 50-59 10 p.

Research output: Contribution to journalArticle

13 Scopus citations

A network approach to discerning the identities of C. elegans in a free moving population

Winter, P. B., Brielmann, R. M., Timkovich, N. P., Navarro, H. T., Teixeira-Castro, A., Morimoto, R. I. & Amaral, L. A. N., Oct 11 2016, In : Scientific reports. 6, 34859.

Research output: Contribution to journalArticle

3 Scopus citations

An informatic framework for decoding protein complexes by top-down mass spectrometry

Skinner, O. S., Havugimana, P. C., Haverland, N. A., Fornelli, L., Early, B. P., Greer, J. B., Fellers, R. T., Durbin, K. R., Do Vale, L. H. F., Melani, R. D., Seckler, H. S., Nelp, M. T., Belov, M. E., Horning, S. R., Makarov, A. A., LeDuc, R. D., Bandarian, V., Compton, P. D. & Kelleher, N. L., Feb 25 2016, In : Nature Methods. 13, 3, p. 237-240 4 p.

Research output: Contribution to journalArticle

38 Scopus citations

Antibiotic perturbation of the preterm infant gut microbiome and resistome

Gasparrini, A. J., Crofts, T. S., Gibson, M. K., Tarr, P. I., Warner, B. B. & Dantas, G., Aug 18 2016, In : Gut Microbes. 7, 5, p. 443-449 7 p.

Research output: Contribution to journalArticle

33 Scopus citations

Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation

Hattori, T., Lai, D., Dementieva, I. S., Montaño, S. P., Kurosawa, K., Zheng, Y., Akin, L. R., ͆wist-Rosowska, K. M., Grzybowski, A. T., Koide, A., Krajewski, K., Strahl, B. D., Kelleher, N. L., Ruthenburg, A. J. & Koide, S., Feb 23 2016, In : Proceedings of the National Academy of Sciences of the United States of America. 113, 8, p. 2092-2097 6 p.

Research output: Contribution to journalArticle

12 Scopus citations

A researcher's guide to mass spectrometry-based proteomics

Savaryn, J. P., Toby, T. K. & Kelleher, N. L., Sep 1 2016, In : Proteomics. 16, 18, p. 2435-2443 9 p.

Research output: Contribution to journalArticle

15 Scopus citations

Assembly of Caenorhabditis elegans acentrosomal spindles occurs without evident microtubuleorganizing centers and requires microtubule sorting by KLP-18/kinesin-12 and MESP-1

Wolff, I. D., Tran, M. V., Mullen, T. J., Villeneuve, A. M. & Wignalla, S. M., Oct 15 2016, In : Molecular biology of the cell. 27, 20, p. 3122-3131 10 p.

Research output: Contribution to journalArticle

15 Scopus citations

A transcriptional signature of Alzheimer's disease is associated with a metastable subproteome at risk for aggregation

Ciryam, P., Kundra, R., Freer, R., Morimoto, R. I., Dobson, C. M. & Vendruscolo, M., Apr 26 2016, In : Proceedings of the National Academy of Sciences of the United States of America. 113, 17, p. 4753-4758 6 p.

Research output: Contribution to journalArticle

44 Scopus citations

Biocatalysts for methane conversion: big progress on breaking a small substrate

Lawton, T. J. & Rosenzweig, A. C., Dec 1 2016, In : Current Opinion in Chemical Biology. 35, p. 142-149 8 p.

Research output: Contribution to journalReview article

9 Scopus citations

Bone protein "extractomics": Comparing the efficiency of bone protein extractions of Gallus gallus in tandem mass spectrometry, with an eye towards paleoproteomics

Schroeter, E. R., DeHart, C. J., Schweitzer, M. H., Thomas, P. M. & Kelleher, N. L., 2016, In : PeerJ. 2016, 10, e2603.

Research output: Contribution to journalArticle

21 Scopus citations

Cell division: A sticky problem for chromosomes

Brangwynne, C. P. & Marko, J. F., Jan 1 2016, In : Nature. 535, 7611, p. 234-235 2 p.

Research output: Contribution to journalComment/debate

1 Scopus citations

Cell-free protein synthesis enables high yielding synthesis of an active multicopper oxidase

Li, J., Lawton, T. J., Kostecki, J. S., Nisthal, A., Fang, J., Mayo, S. L., Rosenzweig, A. C. & Jewett, M. C., Feb 1 2016, In : Biotechnology Journal. 11, 2, p. 212-218 7 p.

Research output: Contribution to journalArticle

26 Scopus citations

Characterization of Methanobactin from Methylosinus sp. LW4

Kenney, G. E., Goering, A. W., Ross, M. O., DeHart, C. J., Thomas, P. M., Hoffman, B. M., Kelleher, N. L. & Rosenzweig, A. C., Sep 7 2016, In : Journal of the American Chemical Society. 138, 35, p. 11124-11127 4 p.

Research output: Contribution to journalArticle

13 Scopus citations

Charge-Disproportionation Symmetry Breaking Creates a Heterodimeric Myoglobin Complex with Enhanced Affinity and Rapid Intracomplex Electron Transfer

Trana, E. N., Nocek, J. M., Woude, J. V., Span, I., Smith, S. M., Rosenzweig, A. C. & Hoffman, B. M., Sep 28 2016, In : Journal of the American Chemical Society. 138, 38, p. 12615-12628 14 p.

Research output: Contribution to journalArticle

4 Scopus citations

Chimeric coupling proteins mediate transfer of heterologous type IV effectors through the Escherichia coli pKM101-encoded conjugation machine

Whitaker, N., Berry, T. M., Rosenthal, N., Gordon, J. E., Gonzalez-Rivera, C., Sheehan, K. B., Truchan, H. K., VieBrock, L., Newton, I. L. G., Carlyon, J. A. & Christie, P. J., 2016, In : Journal of bacteriology. 198, 19, p. 2701-2718 18 p.

Research output: Contribution to journalArticle

Open Access
18 Scopus citations

Chromosome Compaction by Active Loop Extrusion

Goloborodko, A., Marko, J. F. & Mirny, L. A., May 24 2016, In : Biophysical Journal. 110, 10, p. 2162-2168 7 p.

Research output: Contribution to journalArticle

102 Scopus citations

CN-GELFrEE - Clear native gel-eluted liquid fraction entrapment electrophoresis

Melani, R. D., Seckler, H. S., Skinner, O. S., Do Vale, L. H. F., Catherman, A. D., Havugimana, P. C., de Sousa, M. V., Domont, G. B., Kelleher, N. L. & Compton, P. D., Feb 29 2016, In : Journal of Visualized Experiments. 2016, 108, e53597.

Research output: Contribution to journalArticle

6 Scopus citations

Compaction and segregation of sister chromatids via active loop extrusion

Goloborodko, A., Imakaev, M. V., Marko, J. F. & Mirny, L., May 18 2016, In : eLife. 5, MAY2016, e14864.

Research output: Contribution to journalArticle

108 Scopus citations

Comparative top down proteomics of peripheral blood mononuclear cells from kidney transplant recipients with normal kidney biopsies or acute rejection

Savaryn, J. P., Toby, T. K., Catherman, A. D., Fellers, R. T., LeDuc, R. D., Thomas, P. M., Friedewald, J. J., Salomon, D. R., Abecassis, M. M. & Kelleher, N. L., Jul 1 2016, In : Proteomics. 16, 14, p. 2048-2058 11 p.

Research output: Contribution to journalArticle

12 Scopus citations

Controlled rotation mechanism of DNA strand exchange by the Hin serine recombinase

Xiao, B., McLean, M. M., Lei, X., Marko, J. F. & Johnson, R. C., Apr 1 2016, In : Scientific reports. 6, 23697.

Research output: Contribution to journalArticle

4 Scopus citations

Copper oxide nanoparticles impact several toxicological endpoints and cause neurodegeneration in caenorhabditis elegans

Mashock, M. J., Zanon, T., Kappell, A. D., Petrella, L. N., Andersen, E. C. & Hristova, K. R., Dec 2016, In : PloS one. 11, 12, e0167613.

Research output: Contribution to journalArticle

23 Scopus citations

Copper-responsive gene expression in the methanotroph: Methylosinus trichosporium OB3b

Kenney, G. E., Sadek, M. & Rosenzweig, A. C., Sep 2016, In : Metallomics. 8, 9, p. 931-940 10 p.

Research output: Contribution to journalArticle

22 Scopus citations

Crossover-site sequence and DNA torsional stress control strand interchanges by the Bxb1 site-specific serine recombinase

Keenholtz, R. A., Grindley, N. D. F., Hatfull, G. F. & Marko, J. F., Oct 14 2016, In : Nucleic acids research. 44, 18, p. 8921-8932 12 p.

Research output: Contribution to journalArticle

8 Scopus citations

Cryo-EM in the study of challenging systems: the human transcription pre-initiation complex

Nogales, E., Louder, R. K. & He, Y., Oct 1 2016, In : Current Opinion in Structural Biology. 40, p. 120-127 8 p.

Research output: Contribution to journalReview article

14 Scopus citations

Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments

Van Valen, D. A., Kudo, T., Lane, K. M., Macklin, D. N., Quach, N. T., DeFelice, M. M., Maayan, I., Tanouchi, Y., Ashley, E. A. & Covert, M. W., Nov 2016, In : PLoS computational biology. 12, 11, e1005177.

Research output: Contribution to journalArticle

Open Access
124 Scopus citations

Dependence of the structure and mechanics of metaphase chromosomes on oxidized cysteines

Eastland, A., Hornick, J., Kawamura, R., Nanavati, D. & Marko, J. F., Sep 1 2016, In : Chromosome Research. 24, 3, p. 339-353 15 p.

Research output: Contribution to journalArticle

1 Scopus citations

Differential masking of natural genetic variation by miR-9a in Drosophila

Cassidy, J. J., Straughan, A. J. & Carthew, R. W., Feb 2016, In : Genetics. 202, 2, p. 675-687 13 p.

Research output: Contribution to journalArticle

10 Scopus citations

E2F coregulates an essential HSF developmental program that is distinct from the heat-shock response

Li, J., Chauve, L., Phelps, G., Brielmann, R. M. & Morimoto, R. I., Sep 15 2016, In : Genes and Development. 30, 18, p. 2062-2075 14 p.

Research output: Contribution to journalArticle

36 Scopus citations

Elucidating the Rimosamide-Detoxin Natural Product Families and Their Biosynthesis Using Metabolite/Gene Cluster Correlations

McClure, R. A., Goering, A. W., Ju, K. S., Baccile, J. A., Schroeder, F. C., Metcalf, W. W., Thomson, R. J. & Kelleher, N. L., Dec 16 2016, In : ACS chemical biology. 11, 12, p. 3452-3460 9 p.

Research output: Contribution to journalArticle

8 Scopus citations

Enhanced binding of antibodies generated during chronic HIV infection to mucus component MUC16

Gunn, B. M., Shansab, M., Schneider, J. R., Bastian, A. R., Fahrbach, K. M., SmithIV, A. D., Mahan, A. E., Karim, M. M., Licht, A. F., Zvonar, I., Tedesco, J., Anderson, M. R., Chapel, A., Suscovich, T. J., Malaspina, D. C., Streeck, H., Walker, B. D., Kim, A., Lauer, G., Altfeld, M. & 6 others, Pillai, S., Szleifer, I., Kelleher, N. L., Kiser, P. F., Hope, T. J. & Alter, G., Nov 1 2016, In : Mucosal Immunology. 9, 6, p. 1549-1558 10 p.

Research output: Contribution to journalArticle

29 Scopus citations

Epigenetic Profiling Reveals a Unique Histone Code in Chordoma

Moussazadeh, N., Berman, S. H., Laufer, I., Gounder, M., Zheng, Y., Sommer, J., Bilsky, M. H., Kelleher, N. L. & Brennan, C., 2016, In : Neurosurgery. 63, CN_suppl 1, p. 208

Research output: Contribution to journalArticle

Epiproteomics: Quantitative analysis of histone marks and codes by mass spectrometry

Zheng, Y., Huang, X. & Kelleher, N. L., Aug 1 2016, In : Current Opinion in Chemical Biology. 33, p. 142-150 9 p.

Research output: Contribution to journalReview article

30 Scopus citations

Establishment and maintenance of heritable chromatin structure during early drosophila embryogenesis

Blythe, S. A. & Wieschaus, E. F., Nov 23 2016, In : eLife. 5, NOVEMBER2016, e20148.

Research output: Contribution to journalArticle

53 Scopus citations

Eukaryotic transcription initiation machinery visualized at molecular level

Han, Y. & He, Y., Oct 19 2016, In : Transcription. 7, 5, p. 203-208 6 p.

Research output: Contribution to journalReview article

2 Scopus citations

Expression and Characterization of Hyperthermostable Exo-polygalacturonase TtGH28 from Thermotoga thermophilus

Wagschal, K., Rose Stoller, J., Chan, V. J., Lee, C. C., Grigorescu, A. A. & Jordan, D. B., Jul 1 2016, In : Molecular Biotechnology. 58, 7, p. 509-519 11 p.

Research output: Contribution to journalArticle

3 Scopus citations

Facilitated dissociation of a nucleoid protein from the bacterial chromosome

Hadizadeh, N., Johnson, R. C. & Marko, J. F., Jun 1 2016, In : Journal of bacteriology. 198, 12, p. 1735-1742 8 p.

Research output: Contribution to journalArticle

22 Scopus citations

Flexibility of the head-stalk linker domain of paramyxovirus HN glycoprotein is essential for triggering virus fusion

Adu-Gyamfi, E., Kim, L. S., Jardetzky, T. S. & Lamb, R. A., Jan 1 2016, In : Journal of virology. 90, 20, p. 9172-9181 10 p.

Research output: Contribution to journalArticle

9 Scopus citations

Focused Screening Identifies Evoxine as a Small Molecule That Counteracts CO2-Induced Immune Suppression

Helenius, I. T., Nair, A., Bittar, H. E. T., Sznajder, J. I., Sporn, P. H. S. & Beitel, G. J., Apr 1 2016, In : Journal of Biomolecular Screening. 21, 4, p. 363-371 9 p.

Research output: Contribution to journalArticle

3 Scopus citations

Hexagonal Patterning of the Insect Compound Eye: Facet Area Variation, Defects, and Disorder

Kim, S., Cassidy, J. J., Yang, B., Carthew, R. W. & Hilgenfeldt, S., Dec 20 2016, In : Biophysical Journal. 111, 12, p. 2735-2746 12 p.

Research output: Contribution to journalArticle

10 Scopus citations

Human fallopian tube epithelium co-culture with murine ovarian follicles reveals crosstalk in the reproductive cycle

Zhu, J., Xu, Y., Rashedi, A. S., Pavone, M. E., Julie Kim, J., Woodruff, T. K. & Burdette, J. E., Nov 1 2016, In : Molecular human reproduction. 22, 11, p. 756-767 12 p.

Research output: Contribution to journalArticle

13 Scopus citations

Identification of drosophila Zfh2 as a mediator of hypercapnic immune regulation by a genome-wide RNA interference screen

Helenius, I. T., Haake, R. J., Kwon, Y. J., Hu, J. A., Krupinski, T., Marina Casalino-Matsuda, S., Sporn, P. H. S., Sznajder, J. I. & Beitel, G. J., Jan 15 2016, In : Journal of Immunology. 196, 2, p. 655-667 13 p.

Research output: Contribution to journalArticle

9 Scopus citations

Immobilization of the N-terminal helix stabilizes prefusion paramyxovirus fusion proteins

Albert, S. S., Taylor, A. P., Luciano, A. A., Theodore, S. J., Matteo, D. P. & Lamb, R. A., Jul 5 2016, In : Proceedings of the National Academy of Sciences of the United States of America. 113, 27, p. E3844-E3851

Research output: Contribution to journalArticle

2 Scopus citations

Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping

Voong, L. N., Xi, L., Sebeson, A. C., Xiong, B., Wang, J. & Wang, X., Dec 1 2016, In : Cell. 167, 6, p. 1555-1570.e15

Research output: Contribution to journalArticle

64 Scopus citations

Integrated bottom-up and top-down proteomics of patient-derived breast tumor xenografts

Ntai, I., LeDuc, R. D., Fellers, R. T., Erdmann-Gilmore, P., Davies, S. R., Rumsey, J., Early, B. P., Thomas, P. M., Li, S., Compton, P. D., Ellis, M. J. C., Ruggles, K. V., Fenyö, D., Boja, E. S., Rodriguez, H., Townsend, R. R. & Kelleher, N. L., Jan 2016, In : Molecular and Cellular Proteomics. 15, 1, p. 45-56 12 p.

Research output: Contribution to journalArticle

40 Scopus citations

Lactate Dehydrogenase C Produces S-2-Hydroxyglutarate in Mouse Testis

Teng, X., Emmett, M. J., Lazar, M. A., Goldberg, E. & Rabinowitz, J. D., Sep 16 2016, In : ACS chemical biology. 11, 9, p. 2420-2427 8 p.

Research output: Contribution to journalArticle

15 Scopus citations

Male fertility and obesity: Are ghrelin, leptin and glucagon-like peptide-1 pharmacologically relevant?

Alves, M. G., Jesus, T. T., Sousa, M., Goldberg, E., Silva, B. M. & Oliveira, P. F., Feb 1 2016, In : Current Pharmaceutical Design. 22, 7, p. 783-791 9 p.

Research output: Contribution to journalArticle

29 Scopus citations