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2017

Oligomerization and ATP stimulate condensin-mediated DNA compaction

Keenholtz, R. A., Dhanaraman, T., Palou, R., Yu, J., D'amours, D. & Marko, J. F., Dec 1 2017, In : Scientific reports. 7, 1, 14279.

Research output: Contribution to journalArticle

16 Scopus citations

Out of the testis: Biological impacts of new genes

Nyberg, K. G. & Carthew, R. W., Sep 15 2017, In : Genes and Development. 31, 18, p. 1825-1826 2 p.

Research output: Contribution to journalArticle

3 Scopus citations

Possibility and challenges of conversion of current virus species names to Linnaean binomials

Postler, T. S., Clawson, A. N., Amarasinghe, G. K., Basler, C. F., Bavari, S., Benko, M., Blasdell, K. R., Briese, T., Buchmeier, M. J., Bukreyev, A., Calisher, C. H., Chandran, K., Charrel, R., Clegg, C. S., Collins, P. L., De La Torre, J. C., DeRisi, J. L., Dietzgen, R. G., Dolnik, O., Dürrwald, R. & 52 others, Dye, J. M., Easton, A. J., Emonet, S., Formenty, P., Fouchier, R. A. M., Ghedin, E., Gonzalez, J. P., Harrach, B., Hewson, R., Horie, M., Jiāng, D., Kobinger, G., Kondo, H., Kropinski, A. M., Krupovic, M., Kurath, G., Lamb, R. A., Leroy, E. M., Lukashevich, I. S., Maisner, A., Mushegian, A. R., Netesov, S. V., Nowotny, N., Patterson, J. L., Payne, S. L., Paweska, J. T., Peters, C. J., Radoshitzky, S. R., Rima, B. K., Romanowski, V., Rubbenstroth, D., Sabanadzovic, S., Sanfaçon, H., Salvato, M. S., Schwemmle, M., Smither, S. J., Stenglein, M. D., Stone, D. M., Takada, A., Tesh, R. B., Tomonaga, K., Tordo, N., Towner, J. S., Vasilakis, N., Volchkov, V. E., Wahl-Jensen, V., Walker, P. J., Wang, L. F., Varsani, A., Whitfield, A. E., Murilo Zerbini, F. & Kuhn, J. H., May 1 2017, In : Systematic Biology. 66, 3, p. 463-473 11 p.

Research output: Contribution to journalArticle

8 Scopus citations

Protein homeostasis of a metastable subproteome associated with Alzheimer's disease

Kundra, R., Ciryam, P., Morimoto, R. I., Dobson, C. M. & Vendruscolo, M., Jul 11 2017, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 28, p. E5703-E5711

Research output: Contribution to journalArticle

29 Scopus citations

Proteoforms in Peripheral Blood Mononuclear Cells as Novel Rejection Biomarkers in Liver Transplant Recipients

Toby, T. K., Abecassis, M., Kim, K., Thomas, P. M., Fellers, R. T., LeDuc, R. D., Kelleher, N. L., Demetris, J. & Levitsky, J., Sep 2017, In : American Journal of Transplantation. 17, 9, p. 2458-2467 10 p.

Research output: Contribution to journalArticle

13 Scopus citations

Selective Targeting by a Mechanism-Based Inactivator against Pyridoxal 5′-Phosphate-Dependent Enzymes: Mechanisms of Inactivation and Alternative Turnover

Mascarenhas, R., Le, H. V., Clevenger, K. D., Lehrer, H. J., Ringe, D., Kelleher, N. L., Silverman, R. B. & Liu, D., Sep 19 2017, In : Biochemistry. 56, 37, p. 4951-4961 11 p.

Research output: Contribution to journalArticle

5 Scopus citations

Selective whole-genome amplification is a robust method that enables scalable whole-genome sequencing of Plasmodium vivax from unprocessed clinical samples

Cowell, A. N., Loy, D. E., Sundararaman, S. A., Valdivia, H., Fisch, K., Lescano, A. G., Baldeviano, G. C., Durand, S., Gerbasi, R. V., Sutherland, C. J., Nolder, D., Vinetz, J. M., Hahn, B. H. & Winzeler, E. A., Jan 1 2017, In : mBio. 8, 1, e02257-16.

Research output: Contribution to journalArticle

17 Scopus citations

Spinal motor neuron protein supersaturation patterns are associated with inclusion body formation in ALS

Ciryam, P., Lambert-Smith, I. A., Bean, D. M., Freer, R., Cid, F., Tartaglia, G. G., Saunders, D. N., Wilson, M. R., Oliver, S. G., Morimoto, R. I., Dobson, C. M., Vendruscolo, M., Favrin, G. & Yerbury, J. J., May 16 2017, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 20, p. E3935-E3943

Research output: Contribution to journalArticle

34 Scopus citations

Structural basis for antibody cross-neutralization of respiratory syncytial virus and human metapneumovirus

Wen, X., Mousa, J. J., Bates, J. T., Lamb, R. A., Crowe, J. E. & Jardetzky, T. S., Jan 30 2017, In : Nature Microbiology. 2, 16272.

Research output: Contribution to journalArticle

22 Scopus citations

Structural mechanism of ATP-independent transcription initiation by RNA polymerase I

Han, Y., Yan, C., Nguyen, T. H. D., Jackobel, A. J., Ivanov, I., Knutson, B. A. & He, Y., Jun 17 2017, In : eLife. 6, e27414.

Research output: Contribution to journalArticle

29 Scopus citations

Substrate Trapping in the Siderophore Tailoring Enzyme PvdQ

Clevenger, K. D., Mascarenhas, R., Catlin, D., Wu, R., Kelleher, N. L., Drake, E. J., Gulick, A. M., Liu, D. & Fast, W., Mar 17 2017, In : ACS chemical biology. 12, 3, p. 643-647 5 p.

Research output: Contribution to journalArticle

4 Scopus citations

Supercoiling DNA Locates Mismatches

Dittmore, A., Brahmachari, S., Takagi, Y., Marko, J. F. & Neuman, K. C., Oct 3 2017, In : Physical review letters. 119, 14, 147801.

Research output: Contribution to journalArticle

9 Scopus citations

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., Aug 1 2017, In : Archives of Virology. 162, 8, p. 2493-2504 12 p.

Research output: Contribution to journalArticle

124 Scopus citations

The dynamic three-dimensional organization of the diploid yeast genome

Kim, S., Liachko, I., Brickner, D. G., Cook, K., Noble, W. S., Brickner, J. H., Shendure, J. & Dunham, M. J., May 24 2017, In : eLife. 6, e23623.

Research output: Contribution to journalArticle

20 Scopus citations

The dynamic three-dimensional organization of the diploid yeast genome

Kim, S., Liachko, I., Brickner, D. G., Cook, K., Noble, W. S., Brickner, J. H., Shendure, J. & Dunham, M. J., May 24 2017, In : eLife. 6

Research output: Contribution to journalArticle

4 Scopus citations

The genetic basis of natural variation in a phoretic behavior

Lee, D., Yang, H., Kim, J., Brady, S., Zdraljevic, S., Zamanian, M., Kim, H., Paik, Y. K., Kruglyak, L., Andersen, E. C. & Lee, J., Dec 1 2017, In : Nature communications. 8, 1, 273.

Research output: Contribution to journalArticle

16 Scopus citations

The Intersection of Aging Biology and the Pathobiology of Lung Diseases: A Joint NHLBI/NIA Workshop

Budinger, G. S., Kohanski, R. A., Gan, W., Kobor, M. S., Amaral, L. A., Armanios, M., Kelsey, K. T., Pardo, A., Tuder, R., Macian, F., Chandel, N., Vaughan, D., Rojas, M., Mora, A. L., Kovacs, E., Duncan, S. R., Finkel, T., Choi, A., Eickelberg, O., Chen, D. & 8 others, Agusti, A., Selman, M., Balch, W. E., Busse, P., Lin, A., Morimoto, R., Sznajder, J. I. & Thannickal, V. J., Nov 1 2017, In : Journals of Gerontology - Series A Biological Sciences and Medical Sciences. 72, 11, p. 1492-1500 9 p.

Research output: Contribution to journalArticle

21 Scopus citations

The mechanisms and functions of interorganelle interactions

Lackner, L. L. & Voeltz, G. K., Mar 15 2017, In : Molecular biology of the cell. 28, 6, p. 703-704 2 p.

Research output: Contribution to journalArticle

1 Scopus citations

Therapeutic targeting of polycomb and BET bromodomain proteins in diffuse intrinsic pontine gliomas

Piunti, A., Hashizume, R., Morgan, M. A., Bartom, E. T., Horbinski, C. M., Marshall, S. A., Rendleman, E. J., Ma, Q., Takahashi, Y. H., Woodfin, A. R., Misharin, A. V., Abshiru, N. A., Lulla, R. R., Saratsis, A. M., Kelleher, N. L., James, C. D. & Shilatifard, A., Apr 1 2017, In : Nature Medicine. 23, 4, p. 493-500 8 p.

Research output: Contribution to journalArticle

115 Scopus citations

Torque and buckling in stretched intertwined double-helix DNAs

Brahmachari, S. & Marko, J. F., May 1 2017, In : Physical Review E. 95, 5, 052401.

Research output: Contribution to journalArticle

7 Scopus citations

Translation system engineering in Escherichia coli enhances non-canonical amino acid incorporation into proteins

Gan, R., Perez, J. G., Carlson, E. D., Ntai, I., Isaacs, F. J., Kelleher, N. L. & Jewett, M. C., May 1 2017, In : Biotechnology and Bioengineering. 114, 5, p. 1074-1086 13 p.

Research output: Contribution to journalArticle

20 Scopus citations

UTX/KDM6A Loss Enhances the Malignant Phenotype of Multiple Myeloma and Sensitizes Cells to EZH2 inhibition

Ezponda, T., Dupéré-Richer, D., Will, C. M., Small, E. C., Varghese, N., Patel, T., Nabet, B., Popovic, R., Oyer, J., Bulic, M., Zheng, Y., Huang, X., Shah, M. Y., Maji, S., Riva, A., Occhionorelli, M., Tonon, G., Kelleher, N., Keats, J. & Licht, J. D., Oct 17 2017, In : Cell reports. 21, 3, p. 628-640 13 p.

Research output: Contribution to journalArticle

33 Scopus citations

VCF-kit: Assorted utilities for the variant call format

Cook, D. E. & Andersen, E. C., May 15 2017, In : Bioinformatics. 33, 10, p. 1581-1582 2 p.

Research output: Contribution to journalArticle

15 Scopus citations
4 Scopus citations
2016

A Chimeric Pneumovirus Fusion Protein Carrying Neutralizing Epitopes of Both MPV and RSV

Wen, X., Pickens, J., Mousa, J. J., Leser, G. P., Lamb, R. A., Crowe, J. E. & Jardetzky, T. S., May 2016, In : PloS one. 11, 5, e0155917.

Research output: Contribution to journalArticle

9 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

29 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. & Wignall, S., Oct 15 2016, In : Molecular Biology of the Cell. 27, 20, p. 3122-3131 10 p.

Research output: Contribution to journalArticle

14 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

42 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-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

22 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

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

101 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

106 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

20 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

20 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

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
118 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

32 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

6 Scopus citations