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2018

Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines

MC3 Working Group & The Cancer Genome Atlas Research Network, Mar 28 2018, In : Cell Systems. 6, 3, p. 271-281.e7

Research output: Contribution to journalArticle

93 Scopus citations

Secure estimation based Kalman Filter for cyber–physical systems against sensor attacks

Chang, Y. H., Hu, Q. & Tomlin, C. J., Sep 1 2018, In : Automatica. 95, p. 399-412 14 p.

Research output: Contribution to journalArticle

15 Scopus citations

Secure state estimation and control for cyber security of the nonlinear power systems

Hu, Q., Fooladivanda, D., Chang, Y. H. & Tomlin, C. J., Sep 1 2018, In : IEEE Transactions on Control of Network Systems. 5, 3, p. 1310-1321 12 p., 7929374.

Research output: Contribution to journalArticle

6 Scopus citations

Simultaneous Multicolor Single-Molecule Tracking with Single-Laser Excitation via Spectral Imaging

Huang, T., Phelps, C., Wang, J., Lin, L. J., Bittel, A., Scott, Z., Jacques, S., Gibbs, S., Gray, J. & Nan, X., Jan 23 2018, In : Biophysical Journal. 114, 2, p. 301-310 10 p.

Research output: Contribution to journalArticle

13 Scopus citations

Snaptron: Querying splicing patterns across tens of thousands of RNA-seq samples

Wilks, C., Gaddipati, P., Nellore, A. & Langmead, B., Jan 1 2018, In : Bioinformatics. 34, 1, p. 114-116 3 p.

Research output: Contribution to journalArticle

6 Scopus citations

Stereotactic body proton therapy for liver tumors: Dosimetric advantages and their radiobiological and clinical implications

Arscott, W. T., Thompson, R. F., Yin, L., Burgdorf, B., Kirk, M. & Ben-Josef, E., Oct 2018, In : Physics and Imaging in Radiation Oncology. 8, p. 17-22 6 p.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Structure of native lens connexin 46/50 intercellular channels by cryo-EM

Myers, J. B., Haddad, B. G., O’Neill, S. E., Chorev, D. S., Yoshioka, C. C., Robinson, C. V., Zuckerman, D. M. & Reichow, S. L., Dec 20 2018, In : Nature. 564, 7736, p. 372-377 6 p.

Research output: Contribution to journalArticle

10 Scopus citations

Structure of the human epithelial sodium channel by cryo-electron microscopy

Noreng, S., Bharadwaj, A., Posert, R., Yoshioka, C. & Baconguis, I., Sep 25 2018, In : eLife. 7

Research output: Contribution to journalArticle

18 Scopus citations

Superresolution microscopy with novel BODIPY-based fluorophores

Bittel, A. M., Saldivar, I. S., Dolman, N. J., Nan, X. & Gibbs, S., Jan 1 2018, In : PLoS One. 13, 10, p. e0206104

Research output: Contribution to journalArticle

3 Scopus citations

Supramolecular self assembly of nanodrill-like structures for intracellular delivery

Ashwanikumar, N., Plaut, J. S., Mostofian, B., Patel, S., Kwak, P., Sun, C., McPhail, K., Zuckerman, D., Esener, S. & Sahay, G., Jan 1 2018, (Accepted/In press) In : Journal of Controlled Release.

Research output: Contribution to journalArticle

5 Scopus citations

Systematic Testing of Belief-Propagation Estimates for Absolute Free Energies in Atomistic Peptides and Proteins

Donovan-Maiye, R. M., Langmead, C. J. & Zuckerman, D., Jan 9 2018, In : Journal of Chemical Theory and Computation. 14, 1, p. 426-443 18 p.

Research output: Contribution to journalArticle

The effect of exercise on sleep in adults with type 1 diabetes

Reddy, R., El Youssef, J., Winters-Stone, K., Branigan, D., Leitschuh, J., Castle, J. & Jacobs, P., Feb 1 2018, In : Diabetes, Obesity and Metabolism. 20, 2, p. 443-447 5 p.

Research output: Contribution to journalArticle

8 Scopus citations

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

Afgan, E., Baker, D., Batut, B., Van Den Beek, M., Bouvier, D., Ech, M., Chilton, J., Clements, D., Coraor, N., Grüning, B. A., Guerler, A., Hillman-Jackson, J., Hiltemann, S., Jalili, V., Rasche, H., Soranzo, N., Goecks, J., Taylor, J., Nekrutenko, A. & Blankenberg, D., Jul 2 2018, In : Nucleic acids research. 46, W1, p. W537-W544

Research output: Contribution to journalArticle

363 Scopus citations

The Role of AcrAB–TolC Efflux Pumps on Quinolone Resistance of E. coli ST131

Atac, N., Kurt-Azap, O., Dolapci, I., Yesilkaya, A., Ergonul, O., Gonen, M. & Can, F., Dec 1 2018, In : Current Microbiology. 75, 12, p. 1661-1666 6 p.

Research output: Contribution to journalArticle

3 Scopus citations

Toward Minimal Residual Disease-Directed Therapy in Melanoma

Rambow, F., Rogiers, A., Marin-Bejar, O., Aibar, S., Femel, J., Dewaele, M., Karras, P., Brown, D., Chang, Y. H., Debiec-Rychter, M., Adriaens, C., Radaelli, E., Wolter, P., Bechter, O., Dummer, R., Levesque, M., Piris, A., Frederick, D. T., Boland, G., Flaherty, K. T. & 5 others, van den Oord, J., Voet, T., Aerts, S., Lund, A. & Marine, J. C., Aug 9 2018, In : Cell. 174, 4, p. 843-855.e19

Research output: Contribution to journalArticle

63 Scopus citations

Transcriptional Programming of Normal and Inflamed Human Epidermis at Single-Cell Resolution

Cheng, J. B., Sedgewick, A. J., Finnegan, A. I., Harirchian, P., Lee, J., Kwon, S., Fassett, M. S., Golovato, J., Gray, M., Ghadially, R., Liao, W., Perez White, B. E., Mauro, T. M., Mully, T., Kim, E. A., Sbitany, H., Neuhaus, I. M., Grekin, R. C., Yu, S. S., Gray, J. W. & 6 others, Purdom, E., Paus, R., Vaske, C. J., Benz, S. C., Song, J. S. & Cho, R. J., Oct 23 2018, In : Cell Reports. 25, 4, p. 871-883 13 p.

Research output: Contribution to journalArticle

19 Scopus citations

Valection: Design optimization for validation and verification studies

Cooper, C. I., Yao, D., Sendorek, D. H., Yamaguchi, T. N., P'ng, C., Houlahan, K. E., Caloian, C., Fraser, M., Ellrott, K., Margolin, A. A., Bristow, R. G., Stuart, J. M. & Boutros, P. C., Sep 25 2018, In : BMC bioinformatics. 19, 1, 339.

Research output: Contribution to journalArticle

2 Scopus citations

Varied Length Stokes Shift BODIPY-Based Fluorophores for Multicolor Microscopy

Bittel, A. M., Davis, A. M., Wang, L., Nederlof, M. A., Escobedo, J. O., Strongin, R. M. & Gibbs, S., Dec 1 2018, In : Scientific Reports. 8, 1, 4590.

Research output: Contribution to journalArticle

5 Scopus citations

VIPER is a genetically encoded peptide tag for fluorescence and electron microscopy

Doh, J. K., White, J. D., Zane, H. K., Chang, Y. H., Lopez, C., Enns, C. & Beatty, K., Dec 18 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 51, p. 12961-12966 6 p.

Research output: Contribution to journalArticle

6 Scopus citations

α 2 -Macroglobulin Is a Significant In Vivo Inhibitor of Activated Protein C and Low APC: α 2 M Levels Are Associated with Venous Thromboembolism

Martos, L., Ramón, L. A., Oto, J., Fernández-Pardo, Á., Bonanad, S., Cid, A. R., Gruber, A., Griffin, J. H., España, F., Navarro, S. & Medina, P., Feb 15 2018, (Accepted/In press) In : Thrombosis and Haemostasis.

Research output: Contribution to journalArticle

5 Scopus citations
2017

Aberrant plasticity of peripheral sensory axons in a painful neuropathy

Hirai, T., Mulpuri, Y., Cheng, Y., Xia, Z., Li, W., Ruangsri, S., Spigelman, I. & Nishimura, I., Dec 1 2017, In : Scientific Reports. 7, 1, 3407.

Research output: Contribution to journalArticle

13 Scopus citations

A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines

Gonen, M., Weir, B. A., Cowley, G. S., Vazquez, F., Guan, Y., Jaiswal, A., Karasuyama, M., Uzunangelov, V., Wang, T., Tsherniak, A., Howell, S., Marbach, D., Hoff, B., Norman, T. C., Airola, A., Bivol, A., Bunte, K., Carlin, D., Chopra, S., Deran, A. & 25 others, Ellrott, K., Gopalacharyulu, P., Graim, K., Kaski, S., Khan, S. A., Newton, Y., Ng, S., Pahikkala, T., Paull, E., Sokolov, A., Tang, H., Tang, J., Wennerberg, K., Xie, Y., Zhan, X., Zhu, F., Aittokallio, T., Mamitsuka, H., Stuart, J. M., Boehm, J. S., Root, D. E., Xiao, G., Stolovitzky, G., Hahn, W. C. & Margolin, A., 2017, (Accepted/In press) In : Cell Systems.

Research output: Contribution to journalArticle

7 Scopus citations

Activated protein C inhibits neutrophil extracellular trap formation in vitro and activation in vivo

Healy, L. D., Puy, C., Fernández, J. A., Mitrugno, A., Keshari, R. S., Taku, N. A., Chu, T. T., Xu, X., Gruber, A., Lupu, F., Griffin, J. H. & McCarty, O., May 26 2017, In : Journal of Biological Chemistry. 292, 21, p. 8616-8629 14 p.

Research output: Contribution to journalArticle

29 Scopus citations

Activity of distinct growth factor receptor network components in breast tumors uncovers two biologically relevant subtypes

Rahman, M., MacNeil, S. M., Jenkins, D. F., Shrestha, G., Wyatt, S. R., McQuerry, J. A., Piccolo, S. R., Heiser, L. M., Gray, J. W., Johnson, W. E. & Bild, A. H., Apr 26 2017, In : Genome Medicine. 9, 1, 40.

Research output: Contribution to journalArticle

5 Scopus citations

A fully integrated, three-dimensional fluorescence to electron microscopy correlative workflow

Lopez, C., Bouchet-Marquis, C., Arthur, C. P., McQuiston, J., Heiss, G., Thibault, G., Pullan, L., Kwon, S. & Gray, J., 2017, (Accepted/In press) In : Methods in Cell Biology.

Research output: Contribution to journalArticle

7 Scopus citations

Analysis of K-Ras interactions by biotin ligase tagging

Ritchie, C., Mack, A., Harper, L., Alfadhli, A., Stork, P. J. S., Nan, X. & Barklis, E., Jul 1 2017, In : Cancer Genomics and Proteomics. 14, 4, p. 225-239 15 p.

Research output: Contribution to journalArticle

1 Scopus citations

A Novel Strategy to Engineer Pre-Vascularized Full-Length Dental Pulp-like Tissue Constructs

Athirasala, A., Lins, F., Tahayeri, A., Hinds, M., Smith, A. J., Sedgley, C., Ferracane, J. & Bertassoni, L., Dec 1 2017, In : Scientific Reports. 7, 1, 3323.

Research output: Contribution to journalArticle

23 Scopus citations

Anti-diabetic drug binding site in a mammalian KATP channel revealed by Cryo-EM

Martin, G. M., Kandasamy, B., Dimaio, F., Yoshioka, C. & Shyng, S-L., Oct 16 2017, In : eLife. 6, e31054.

Research output: Contribution to journalArticle

38 Scopus citations

Aspirin therapy reduces the ability of platelets to promote colon and pancreatic cancer cell proliferation: Implications for the oncoprotein c-MYC

Mitrugno, A., Sylman, J. L., Ngo, A. T. P., Pang, J., Sears, R. C., Williams, C. D. & McCarty, O. J. T., Feb 8 2017, In : American Journal of Physiology - Cell Physiology. 312, 2, p. C176-C189

Research output: Contribution to journalArticle

33 Scopus citations

Assessment and rehabilitation of central sensory impairments for balance in mTBI using auditory biofeedback: A randomized clinical trial

Fino, P. C., Peterka, R. J., Hullar, T. E., Murchison, C., Horak, F. B., Chesnutt, J. C. & King, L. A., Feb 23 2017, In : BMC Neurology. 17, 1, 41.

Research output: Contribution to journalArticle

8 Scopus citations

Assessment of roles for the rho-specific guanine nucleotide dissociation inhibitor Ly-GDI in platelet function: A spatial systems approach

Ngo, A. T. P., Thierheimer, M. L. D., Babur, O., Rocheleau, A. D., Huang, T., Pang, J., Rigg, R. A., Mitrugno, A., Theodorescu, D., Burchard, J., Nan, X., Demir, E., McCarty, O. & Aslan, J., Apr 7 2017, In : American Journal of Physiology - Cell Physiology. 312, 4, p. C527-C536

Research output: Contribution to journalArticle

7 Scopus citations

Bayesian network inference modeling identifies TRIB1 as a novel regulator of cell-cycle progression and survival in cancer cells

Gendelman, R., Xing, H., Mirzoeva, O. K., Sarde, P., Curtis, C., Feiler, H., McDonagh, P., Gray, J., Khalil, I. & Korn, W. M., 2017, In : Cancer Research. 77, 7, p. 1575-1585 11 p.

Research output: Contribution to journalArticle

21 Scopus citations
Open Access

Blood flow patterns underlie developmental heart defects

Midgett, M., Thornburg, K. & Rugonyi, S., Mar 13 2017, In : American Journal of Physiology - Heart and Circulatory Physiology. 312, 3, p. H632-H642

Research output: Contribution to journalArticle

19 Scopus citations

Chromatin and Transcriptional Analysis of Mesoderm Progenitor Cells Identifies HOPX as a Regulator of Primitive Hematopoiesis

Palpant, N. J., Wang, Y., Hadland, B., Zaunbrecher, R. J., Redd, M., Jones, D., Pabon, L., Jain, R., Epstein, J., Ruzzo, W. L., Zheng, Y., Bernstein, I., Margolin, A. & Murry, C. E., Aug 15 2017, In : Cell Reports. 20, 7, p. 1597-1608 12 p.

Research output: Contribution to journalArticle

9 Scopus citations

Combating subclonal evolution of resistant cancer phenotypes

Brady, S. W., McQuerry, J. A., Qiao, Y., Piccolo, S. R., Shrestha, G., Jenkins, D. F., Layer, R. M., Pedersen, B. S., Miller, R. H., Esch, A., Selitsky, S. R., Parker, J. S., Anderson, L. A., Dalley, B. K., Factor, R. E., Reddy, C. B., Boltax, J. P., Li, D. Y., Moos, P. J., Gray, J. W. & 8 others, Heiser, L. M., Buys, S. S., Cohen, A. L., Johnson, W. E., Quinlan, A. R., Marth, G., Werner, T. L. & Bild, A. H., Dec 1 2017, In : Nature communications. 8, 1, 1231.

Research output: Contribution to journalArticle

29 Scopus citations

Combinatorial Microenvironments Impose a Continuum of Cellular Responses to a Single Pathway-Targeted Anti-cancer Compound

Lin, C. H., Jokela, T., Gray, J. & LaBarge, M. A., Oct 10 2017, In : Cell Reports. 21, 2, p. 533-545 13 p.

Research output: Contribution to journalArticle

10 Scopus citations

Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma

The Cancer Genome Atlas Research Network, Jun 15 2017, In : Cell. 169, 7, p. 1327-1341.e23

Research output: Contribution to journalArticle

400 Scopus citations

Context Specificity in Causal Signaling Networks Revealed by Phosphoprotein Profiling

Hill, S. M., Nesser, N. K., Johnson-Camacho, K., Jeffress, M., Johnson, A., Boniface, C., Spencer, S. E. F., Lu, Y., Heiser, L. M., Lawrence, Y., Pande, N. T., Korkola, J. E., Gray, J. W., Mills, G. B., Mukherjee, S. & Spellman, P. T., Jan 25 2017, In : Cell Systems. 4, 1, p. 73-83.e10

Research output: Contribution to journalArticle

11 Scopus citations

Cryo-EM structure of the ATP-sensitive potassium channel illuminates mechanisms of assembly and gating

Martin, G. M., Yoshioka, C., Rex, E. A., Fay, J. F., Xie, Q., Whorton, M., Chen, J. Z. & Shyng, S-L., Jan 16 2017, In : eLife. 6, e24149.

Research output: Contribution to journalArticle

69 Scopus citations

DCE-MRI Texture Features for Early Prediction of Breast Cancer Therapy Response

Thibault, G., Tudorica, A., Afzal, A., Chui, S. Y. C., Naik, A., Troxell, M. L., Kemmer, K. A., Oh, K. Y., Roy, N., Jafarian, N., Holtorf, M. L., Huang, W. & Song, X., Mar 1 2017, In : Tomography (Ann Arbor, Mich.). 3, 1, p. 23-32 10 p.

Research output: Contribution to journalArticle

Open Access

Deep nuclear invaginations are linked to cytoskeletal filaments - integrated bioimaging of epithelial cells in 3D culture

Jorgens, D. M., Inman, J. L., Wojcik, M., Robertson, C., Palsdottir, H., Tsai, W. T., Huang, H., Bruni-Cardoso, A., López, C. S., Bissell, M. J., Xu, K. & Auer, M., Jan 1 2017, In : Journal of Cell Science. 130, 1, p. 177-189 13 p.

Research output: Contribution to journalArticle

26 Scopus citations

Differential Roles for the Coagulation Factors XI and XII in Regulating the Physical Biology of Fibrin

Sylman, J. L., Daalkhaijav, U., Zhang, Y., Gray, E. M., Farhang, P. A., Chu, T. T., Zilberman-Rudenko, J., Puy, C., Tucker, E. I., Smith, S. A., Morrissey, J. H., Walker, T. W., Nan, X. L., Gruber, A. & McCarty, O. J. T., May 1 2017, In : Annals of Biomedical Engineering. 45, 5, p. 1328-1340 13 p.

Research output: Contribution to journalArticle

2 Scopus citations

Direct administration of nerve-specific contrast to improve nerve sparing radical prostatectomy

Barth, C. W. & Gibbs, S., 2017, In : Theranostics. 7, 3, p. 573-593 21 p.

Research output: Contribution to journalArticle

20 Scopus citations

Epigenomic inactivation of RasGAPs activates RAS signaling in a subset of luminal B breast cancers

Sears, R. & Gray, J., Feb 1 2017, In : Cancer Discovery. 7, 2, p. 131-133 3 p.

Research output: Contribution to journalArticle

6 Scopus citations

Evaluation of model complexity in model predictive control within an exercise-enabled artificial pancreas

Resalat, N., El Youssef, J., Reddy, R. & Jacobs, P., Jul 1 2017, In : IFAC-PapersOnLine. 50, 1, p. 7756-7761 6 p.

Research output: Contribution to journalArticle

7 Scopus citations

Extensive alternative splicing transitions during postnatal skeletal muscle development are required for calcium handling functions

Brinegar, A. E., Xia, Z., Loehr, J. A., Li, W., Rodney, G. G. & Cooper, T. A., Aug 11 2017, In : eLife. 6, e27192.

Research output: Contribution to journalArticle

15 Scopus citations

Falls, functioning, and disability among women with persistent symptoms of chemotherapy-induced peripheral neuropathy

Winters-Stone, K. M., Horak, F., Jacobs, P. G., Trubowitz, P., Dieckmann, N. F., Stoyles, S. & Faithfull, S., Aug 10 2017, In : Journal of Clinical Oncology. 35, 23, p. 2604-2612 9 p.

Research output: Contribution to journalArticle

73 Scopus citations

Far-Red and Near-Infrared Seminaphthofluorophores for Targeted Pancreatic Cancer Imaging

Wang, L., Barth, C. W., Sibrian-Vazquez, M., Escobedo, J. O., Lowry, M., Muschler, J., Li, H., Gibbs, S. L. & Strongin, R. M., Jan 31 2017, In : ACS Omega. 2, 1, p. 154-163 10 p.

Research output: Contribution to journalArticle

11 Scopus citations

Hepatocytic expression of human sodium-taurocholate cotransporting polypeptide enables hepatitis B virus infection of macaques /631/326/596/1550 /631/326/596/2555 /631/326/596/2557 article

Burwitz, B. J., Wettengel, J. M., Mück-Häusl, M. A., Ringelhan, M., Ko, C., Festag, M. M., Hammond, K. B., Northrup, M., Bimber, B. N., Jacob, T., Reed, J. S., Norris, R., Park, B., Moller-Tank, S., Esser, K., Greene, J. M., Wu, H. L., Abdulhaqq, S., Webb, G., Sutton, W. F. & 8 others, Klug, A., Swanson, T., Legasse, A. W., Vu, T. Q., Asokan, A., Haigwood, N. L., Protzer, U. & Sacha, J. B., Dec 1 2017, In : Nature communications. 8, 1, 2146.

Research output: Contribution to journalArticle

14 Scopus citations