Research Output

2016

Structure and stabilization of the Hendra virus F glycoprotein in its prefusion form

Wong, J. J. W., Paterson, R. G., Lamb, R. A. & Jardetzky, T. S., Jan 26 2016, In : Proceedings of the National Academy of Sciences of the United States of America. 113, 4, p. 1056-1061 6 p.

Research output: Contribution to journalArticle

34 Scopus citations

Structure of promoter-bound TFIID and model of human pre-initiation complex assembly

Louder, R. K., He, Y., López-Blanco, J. R., Fang, J., Chacón, P. & Nogales, E., Mar 31 2016, In : Nature. 531, 7596, p. 604-609 6 p.

Research output: Contribution to journalArticle

107 Scopus citations

Subnuclear positioning and interchromosomal clustering of the GAL1-10 locus are controlled by separable, interdependent mechanisms

Brickner, D. G., Sood, V., Tutucci, E., Coukos, R., Viets, K., Singer, R. H. & Brickner, J. H., Oct 1 2016, In : Molecular biology of the cell. 27, 19, p. 2980-2993 14 p.

Research output: Contribution to journalArticle

20 Scopus citations

Susan Lindquist 1949-2016

Morimoto, R. I., Dec 6 2016, In : Nature structural & molecular biology. 23, 12, p. 1072-1073 2 p.

Research output: Contribution to journalArticle

1 Scopus citations

Systems Proteomics View of the Endogenous Human Claudin Protein Family

Liu, F., Koval, M., Ranganathan, S., Fanayan, S., Hancock, W. S., Lundberg, E. K., Beavis, R. C., Lane, L., Duek, P., McQuade, L., Kelleher, N. L. & Baker, M. S., Feb 5 2016, In : Journal of Proteome Research. 15, 2, p. 339-359 21 p.

Research output: Contribution to journalReview article

13 Scopus citations

Targeted analysis of recombinant NF kappa B (RelA/p65) by denaturing and native top down mass spectrometry

Savaryn, J. P., Skinner, O. S., Fornelli, L., Fellers, R. T., Compton, P. D., Terhune, S. S., Abecassis, M. M. & Kelleher, N. L., Feb 16 2016, In : Journal of Proteomics. 134, p. 76-84 9 p.

Research output: Contribution to journalArticle

8 Scopus citations

Taxonomy of the order Mononegavirales: update 2016

Afonso, C. L., Amarasinghe, G. K., Bányai, K., Bào, Y., Basler, C. F., Bavari, S., Bejerman, N., Blasdell, K. R., Briand, F. X., Briese, T., Bukreyev, A., Calisher, C. H., Chandran, K., Chéng, J., Clawson, A. N., Collins, P. L., Dietzgen, R. G., Dolnik, O., Domier, L. L., Dürrwald, R. & 63 others, Dye, J. M., Easton, A. J., Ebihara, H., Farkas, S. L., Freitas-Astúa, J., Formenty, P., Fouchier, R. A. M., Fù, Y., Ghedin, E., Goodin, M. M., Hewson, R., Horie, M., Hyndman, T. H., Jiāng, D., Kitajima, E. W., Kobinger, G. P., Kondo, H., Kurath, G., Lamb, R. A., Lenardon, S., Leroy, E. M., Li, C. X., Lin, X. D., Liú, L., Longdon, B., Marton, S., Maisner, A., Mühlberger, E., Netesov, S. V., Nowotny, N., Patterson, J. L., Payne, S. L., Paweska, J. T., Randall, R. E., Rima, B. K., Rota, P., Rubbenstroth, D., Schwemmle, M., Shi, M., Smither, S. J., Stenglein, M. D., Stone, D. M., Takada, A., Terregino, C., Tesh, R. B., Tian, J. H., Tomonaga, K., Tordo, N., Towner, J. S., Vasilakis, N., Verbeek, M., Volchkov, V. E., Wahl-Jensen, V., Walsh, J. A., Walker, P. J., Wang, D., Wang, L. F., Wetzel, T., Whitfield, A. E., Xiè, J., Yuen, K. Y., Zhang, Y. Z. & Kuhn, J. H., Aug 1 2016, In : Archives of Virology. 161, 8, p. 2351-2360 10 p.

Research output: Contribution to journalArticle

257 Scopus citations

The CopC Family: Structural and Bioinformatic Insights into a Diverse Group of Periplasmic Copper Binding Proteins

Lawton, T. J., Kenney, G. E., Hurley, J. D. & Rosenzweig, A. C., Apr 3 2016, In : Biochemistry. 55, 15, p. 2278-2290 13 p.

Research output: Contribution to journalArticle

33 Scopus citations

The genetic basis of natural variation in Caenorhabditis elegans telomere length

Cook, D. E., Zdraljevic, S., Tanny, R. E., Seo, B., Riccardi, D. D., Noble, L. M., Rockman, M. V., Alkema, M. J., Braendle, C., Kammenga, J. E., Wang, J., Kruglyak, L., Félix, M. A., Lee, J. & Andersen, E. C., Sep 2016, In : Genetics. 204, 1, p. 371-383 13 p.

Research output: Contribution to journalArticle

38 Scopus citations

The NuRD complex component p66 suppresses photoreceptor neuron regeneration in planarians

Vásquez-Doorman, C. & Petersen, C. P., Jun 2016, In : Regeneration (Oxford, England). 3, 3, p. 168-78 11 p.

Research output: Contribution to journalArticle

The pathogen-occupied vacuoles of Anaplasma phagocytophilum and Anaplasma marginale interact with the endoplasmic reticulum

Truchan, H. K., Cockburn, C. L., Hebert, K. S., Magunda, F., Noh, S. M. & Carlyon, J. A., Mar 1 2016, In : Frontiers in Cellular and Infection Microbiology. 6, MAR, 22.

Research output: Contribution to journalArticle

Open Access
18 Scopus citations

The search engine for multi-proteoform complexes: An online tool for the identification and stoichiometry determination of protein complexes

Skinner, O. S., Schachner, L. F. & Kelleher, N. L., Jan 1 2016, In : Current Protocols in Bioinformatics. 2016, p. 13.30.1-13.30.11

Research output: Contribution to journalArticle

2 Scopus citations

The TAR-RNA binding protein is required for immunoresponses triggered by Cardiovirus infection

Komuro, A., Homma, Y., Negoro, T., Barber, G. N. & Horvath, C. M., Nov 11 2016, In : Biochemical and Biophysical Research Communications. 480, 2, p. 187-193 7 p.

Research output: Contribution to journalArticle

13 Scopus citations

Transcription factors dynamically control the spatial organization of the yeast genome

Randise-Hinchliff, C. & Brickner, J. H., Jul 3 2016, In : Nucleus. 7, 4, p. 369-374 6 p.

Research output: Contribution to journalReview article

13 Scopus citations

Unabridged analysis of human histone H3 by differential top-down mass spectrometry reveals hypermethylated proteoforms from MMSET/NSD2 overexpression

Zheng, Y., Fornelli, L., Compton, P. D., Sharma, S., Canterbury, J., Mullen, C., Zabrouskov, V., Fellers, R. T., Thomas, P. M., Licht, J. D., Senko, M. W. & Kelleher, N. L., Mar 2016, In : Molecular and Cellular Proteomics. 15, 3, p. 776-790 15 p.

Research output: Contribution to journalArticle

35 Scopus citations

Wnt, Ptk7, and FGFRL expression gradients control trunk positional identity in planarian regeneration

Lander, R. & Petersen, C. P., Apr 13 2016, In : eLife. 5, April 2016, e12850.

Research output: Contribution to journalArticle

39 Scopus citations
2015
14 Scopus citations

Allosteric transcriptional regulation via changes in the overall topology of the core promoter

Philips, S. J., Canalizo-Hernandez, M., Yildirim, I., Schatz, G. C., Mondragón, A. & O'Halloran, T. V., Aug 21 2015, In : Science. 349, 6250, p. 877-881 5 p.

Research output: Contribution to journalArticle

59 Scopus citations

Analyzing internal fragmentation of electrosprayed ubiquitin ions during beam-type collisional dissociation

Durbin, K. R., Skinner, O. S., Fellers, R. T. & Kelleher, N. L., Feb 26 2015, In : Journal of the American Society for Mass Spectrometry. 26, 5, p. 782-787 6 p., 1078.

Research output: Contribution to journalArticle

17 Scopus citations

A new metal binding domain involved in cadmium, cobalt and zinc transport

Smith, A. T., Barupala, D., Stemmler, T. L. & Rosenzweig, A. C., Sep 20 2015, In : Nature Chemical Biology. 11, 9, p. 678-684 7 p.

Research output: Contribution to journalArticle

15 Scopus citations

A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63

Bao, X., Rubin, A. J., Qu, K., Zhang, J., Giresi, P. G., Chang, H. Y. & Khavari, P. A., Dec 18 2015, In : Genome biology. 16, 1, 284.

Research output: Contribution to journalArticle

52 Scopus citations

Antibiotics and the developing infant gut microbiota and resistome

Gibson, M. K., Crofts, T. S. & Dantas, G., Oct 1 2015, In : Current Opinion in Microbiology. 27, p. 51-56 6 p.

Research output: Contribution to journalReview article

77 Scopus citations

A powerful new quantitative genetics platform, combining caenorhabditis elegans high-throughput fitness assays with a large collection of recombinant strains

Andersen, E. C., Shimko, T. C., Crissman, J. R., Ghosh, R., Bloom, J. S., Seidel, H. S., Gerke, J. P. & Kruglyak, L., 2015, In : G3: Genes, Genomes, Genetics. 5, 5, p. 911-920 10 p.

Research output: Contribution to journalArticle

33 Scopus citations

Architecture of the human XPC DNA repair and stem cell coactivator complex

Zhang, E. T., He, Y., Grob, P., Fong, Y. W., Nogales, E. & Tjian, R., Dec 1 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 48, p. 14817-14822 6 p.

Research output: Contribution to journalArticle

13 Scopus citations

A serpin takes a bite out of the flu

Horvath, C. M., Mar 11 2015, In : Cell Host and Microbe. 17, 3, p. 283-284 2 p.

Research output: Contribution to journalShort survey

A Small Molecule That Switches a Ubiquitin Ligase from a Processive to a Distributive Enzymatic Mechanism

Kathman, S. G., Span, I., Smith, A. T., Xu, Z., Zhan, J., Rosenzweig, A. C. & Statsyuk, A. V., Oct 7 2015, In : Journal of the American Chemical Society. 137, 39, p. 12442-12445 4 p.

Research output: Contribution to journalArticle

38 Scopus citations

A Wild C. Elegans Strain Has Enhanced Epithelial Immunity to a Natural Microsporidian Parasite

Balla, K. M., Andersen, E. C., Kruglyak, L. & Troemel, E. R., 2015, In : PLoS pathogens. 11, 2, e1004583.

Research output: Contribution to journalArticle

21 Scopus citations

Biochemistry: Breaking methane

Rosenzweig, A. C., Feb 19 2015, In : Nature. 518, 7539, p. 309-310 2 p.

Research output: Contribution to journalShort survey

10 Scopus citations

Biophysics of protein-DNA interactions and chromosome organization

Marko, J. F., Jan 15 2015, In : Physica A: Statistical Mechanics and its Applications. 418, p. 126-153 28 p.

Research output: Contribution to journalArticle

28 Scopus citations

Cell division: Stem cells take the stage

Wignall, S. M., May 4 2015, In : Current Biology. 25, p. 376-378

Research output: Contribution to journalArticle

1 Scopus citations

Change in the gastro-intestinal tract by overexpressed activin beta A

Kim, M. N., Kim, Y. I., Cho, C., Mayo, K. E. & Cho, B. N., Nov 24 2015, In : Molecules and Cells. 38, 12, p. 1079-1085 7 p.

Research output: Contribution to journalArticle

3 Scopus citations

Comparative genomic analysis of Leishmania (Viannia) peruviana and Leishmania (Viannia) braziliensis

Valdivia, H. O., Reis-Cunha, J. L., Rodrigues-Luiz, G. F., Baptista, R. P., Baldeviano, G. C., Gerbasi, R. V., Dobson, D. E., Pratlong, F., Bastien, P., Lescano, A. G., Beverley, S. M. & Bartholomeu, D. C., Sep 18 2015, In : BMC Genomics. 16, 1, 715.

Research output: Contribution to journalArticle

32 Scopus citations

Conformational dynamics of a class C G-protein-coupled receptor

Vafabakhsh, R., Levitz, J. & Isacoff, E. Y., Aug 27 2015, In : Nature. 524, 7566, p. 497-501 5 p.

Research output: Contribution to journalArticle

84 Scopus citations

Control of the dynamics and homeostasis of the Drosophila Hedgehog receptor Patched by two C2-WW-HECT-E3 Ubiquitin ligases

Brigui, A., Hofmann, L., Argüelles, C., Sanial, M., Holmgren, R. A. & Plessis, A., Oct 7 2015, In : Open Biology. 5, 10, 150112.

Research output: Contribution to journalArticle

4 Scopus citations

Coordinating Cell Cycle Remodeling with Transcriptional Activation at the Drosophila MBT

Blythe, S. A. & Wieschaus, E. F., Jan 1 2015, Current Topics in Developmental Biology: The Maternal-to-Zygotic Transition, 2015. Lipshitz, H. D. (ed.). Academic Press Inc, p. 113-148 36 p. (Current Topics in Developmental Biology; vol. 113).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

28 Scopus citations

Crucial HSP70 co-chaperone complex unlocks metazoan protein disaggregation

Nillegoda, N. B., Kirstein, J., Szlachcic, A., Berynskyy, M., Stank, A., Stengel, F., Arnsburg, K., Gao, X., Scior, A., Aebersold, R., Guilbride, D. L., Wade, R. C., Morimoto, R. I., Mayer, M. P. & Bukau, B., Aug 13 2015, In : Nature. 524, 7564, p. 247-251 5 p.

Research output: Contribution to journalArticle

152 Scopus citations

Defining the neuropeptidome of the spiny lobster Panulirus interruptus brain using a multidimensional mass spectrometry-based platform

Ye, H., Wang, J., Zhang, Z., Jia, C., Schmerberg, C., Catherman, A. D., Thomas, P. M., Kelleher, N. L. & Li, L., Nov 6 2015, In : Journal of Proteome Research. 14, 11, p. 4776-4791 16 p.

Research output: Contribution to journalArticle

17 Scopus citations

Design and Mechanism of Tetrahydrothiophene-Based γ-Aminobutyric Acid Aminotransferase Inactivators

Le, H. V., Hawker, D. D., Wu, R., Doud, E., Widom, J., Sanishvili, R., Liu, D., Kelleher, N. L. & Silverman, R. B., Mar 17 2015, In : Journal of the American Chemical Society. 137, 13, p. 4525-4533 9 p.

Research output: Contribution to journalArticle

12 Scopus citations

Differential association of chromatin proteins identifies BAF60a/SMARCD1 as a regulator of embryonic stem cell differentiation

Alajem, A., Biran, A., Harikumar, A., Sailaja, B. S., Aaronson, Y., Livyatan, I., Nissim-Rafinia, M., Sommer, A. G., Mostoslavsky, G., Gerbasi, V. R., Golden, D. E., Datta, A., Sze, S. K. & Meshorer, E., Mar 31 2015, In : Cell reports. 10, 12, p. 2019-2031 13 p.

Research output: Contribution to journalArticle

23 Scopus citations

Differential nucleosome occupancies across Oct4-Sox2 binding sites in murine embryonic stem cells

Sebeson, A., Xi, L., Zhang, Q., Sigmund, A., Wang, J. P., Widom, J. & Wang, X., May 18 2015, In : PloS one. 10, 5, e0127214.

Research output: Contribution to journalArticle

6 Scopus citations

Distinct mechanisms regulating mechanical force-induced Ca2+ signals at the plasma membrane and the ER in human MSCs

Kim, T. J., Joo, C., Seong, J., Vafabakhsh, R., Botvinick, E. L., Berns, M. W., Palmer, A. E., Wang, N., Ha, T., Jakobsson, E., Sun, J. & Wang, Y., Feb 10 2015, In : eLife. 2015, 4, e04876.

Research output: Contribution to journalArticle

33 Scopus citations

DNA-Segment-Facilitated Dissociation of Fis and NHP6A from DNA Detected via Single-Molecule Mechanical Response

Giuntoli, R. D., Linzer, N. B., Banigan, E. J., Sing, C. E., De La Cruz, M. O., Graham, J. S., Johnson, R. C. & Marko, J. F., Sep 25 2015, In : Journal of Molecular Biology. 427, 19, p. 3123-3136 14 p.

Research output: Contribution to journalArticle

24 Scopus citations

DNase H Activity of Neisseria meningitidis Cas9

Zhang, Y., Rajan, R., Seifert, H., Mondragon, A. & Sontheimer, E. J., Oct 15 2015, In : Molecular cell. 60, 2, p. 242-255 14 p.

Research output: Contribution to journalArticle

35 Scopus citations

Dynamics and heterogeneity of a fate determinant during transition towards cell differentiation

Peláez, N., Gavalda-Miralles, A., Wang, B., Navarro, H. T., Gudjonson, H., Rebay, I., Dinner, A. R., Katsaggelos, A. K., Amaral, L. A. N. & Carthew, R. W., Nov 19 2015, In : eLife. 4, NOVEMBER2015, e08924.

Research output: Contribution to journalArticle

15 Scopus citations

Editorial overview: Catalysis and regulation

Klinman, J. P. & Rosenzweig, A. C., Dec 1 2015, In : Current Opinion in Structural Biology. 35, p. iv-vi

Research output: Contribution to journalEditorial

Editorial overview: Antiviral strategies

Gale, M. & Horvath, C. M., Jun 14 2015, In : Current Opinion in Virology. 12, p. v-vii

Research output: Contribution to journalEditorial

1 Scopus citations

Enzymatic oxidation of methane

Sirajuddin, S. & Rosenzweig, A. C., Apr 14 2015, In : Biochemistry. 54, 14, p. 2283-2294 12 p.

Research output: Contribution to journalArticle

130 Scopus citations

Essential Domains of Anaplasma phagocytophilum Invasins Utilized to Infect Mammalian Host Cells

Seidman, D., Hebert, K. S., Truchan, H. K., Miller, D. P., Tegels, B. K., Marconi, R. T. & Carlyon, J. A., 2015, In : PLoS pathogens. 11, 2, e1004669.

Research output: Contribution to journalArticle

Open Access
24 Scopus citations

Evolution of translation machinery in recoded bacteria enables multi-site incorporation of nonstandard amino acids

Amiram, M., Haimovich, A. D., Fan, C., Wang, Y. S., Aerni, H. R., Ntai, I., Moonan, D. W., Ma, N. J., Rovner, A. J., Hong, S. H., Kelleher, N. L., Goodman, A. L., Jewett, M. C., Söll, D., Rinehart, J. & Isaacs, F. J., Dec 1 2015, In : Nature biotechnology. 33, 12, p. 1272-1279 8 p.

Research output: Contribution to journalArticle

110 Scopus citations