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2017

Efficient Dual siRNA and Drug Delivery Using Engineered Lipoproteoplexes

Liu, C. F., Chen, R., Frezzo, J. A., Katyal, P., Hill, L. K., Yin, L., Srivastava, N., More, H. T., Renfrew, P. D., Bonneau, R. & Montclare, J., Sep 11 2017, In : Biomacromolecules. 18, 9, p. 2688-2698 11 p.

Research output: Contribution to journalArticle

Efficient Simulation of Financial Stress Testing Scenarios with Suppes-Bayes Causal Networks

Gao, G., Mishra, B. & Ramazzotti, D., 2017, In : Procedia Computer Science. 108, p. 272-284 13 p.

Research output: Contribution to journalArticle

Fast analytical methods for finding significant labeled graph motifs

Micale, G., Giugno, R., Ferro, A., Mongiovì, M., Shasha, D. & Pulvirenti, A., Nov 2 2017, (Accepted/In press) In : Data Mining and Knowledge Discovery. p. 1-28 28 p.

Research output: Contribution to journalArticle

Fast topological-shape optimization with boundary elements in two dimensions

Ostanin, I. A., Zorin, D. & Oseledets, I. V., Apr 1 2017, In : Russian Journal of Numerical Analysis and Mathematical Modelling. 32, 2, p. 127-133 7 p.

Research output: Contribution to journalArticle

Field-aligned online surface reconstruction Nico Schertler, New York University and TU Dresden

Tarini, M., Jakob, W., Kazhdan, M., Gumhold, S. & Panozzo, D., 2017, In : ACM Transactions on Graphics. 36, 4, 77.

Research output: Contribution to journalArticle

Finding All Potential Run-Time Errors and Data Races in Automotive Software

Kaestner, D., Miné, A., Schmidt, A., Hille, H., Mauborgne, L., Wilhelm, S., Rival, X., Feret, J., Cousot, P. & Ferdinand, C., Mar 28 2017, In : SAE Technical Papers. 2017-March, March

Research output: Contribution to journalArticle

Foreword to the Special Issue on Shape Modeling International 2017

Attene, M., Lefebvre, S. & Panozzo, D., 2017, (Accepted/In press) In : Computers and Graphics (Pergamon).

Research output: Contribution to journalArticle

Galton-watson probability contraction

Podder, M. & Spencer, J., 2017, In : Electronic Communications in Probability. 22, 20.

Research output: Contribution to journalArticle

Generalization bounds for learning weighted automata

Balle, B. & Mohri, M., Jan 1 2017, (Accepted/In press) In : Theoretical Computer Science.

Research output: Contribution to journalArticle

Hardness of coloring 2-colorable 12-uniform hypergraphs with 2(log n) ω(1) colors

Khot, S. & Saket, R., 2017, In : SIAM Journal on Computing. 46, 1, p. 235-271 37 p.

Research output: Contribution to journalArticle

Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets

Drew, K., Müller, C. L., Bonneau, R. & Marcotte, E. M., Oct 1 2017, In : PLoS Computational Biology. 13, 10, e1005625.

Research output: Contribution to journalArticle

Identifying potentially induced seismicity and assessing statistical significance in Oklahoma and California

McClure, M., Gibson, R., Chiu, K. K. & Ranganath, R., Mar 1 2017, In : Journal of Geophysical Research: Solid Earth. 122, 3, p. 2153-2172 20 p.

Research output: Contribution to journalArticle

Identifying unreliable and adversarial workers in crowdsourced labeling tasks

Jagabathula, S., Subramanian, L. & Venkataraman, A., Sep 1 2017, In : Journal of Machine Learning Research. 18, p. 1-67 67 p.

Research output: Contribution to journalArticle

Impact of phenylalanines outside the dimer interface on phosphotriesterase stability and function

Olsen, A. J., Halvorsen, L. A., Yang, C. Y., Barak Ventura, R., Yin, L., Renfrew, P. D., Bonneau, R. & Montclare, J., 2017, In : Molecular BioSystems. 13, 10, p. 2092-2106 15 p.

Research output: Contribution to journalArticle

Integrated Analysis of Biopsies from Inflammatory Bowel Disease Patients Identifies SAA1 as a Link between Mucosal Microbes with T H 17 and T H 22 Cells

Tang, M. S., Bowcutt, R., Leung, J. M., Wolff, M. J., Gundra, U. M., Hudesman, D., Malter, L. B., Poles, M. A., Chen, L. A., Pei, Z., Neto, A. G., Abidi, W. M., Ullman, T., Mayer, L., Bonneau, R., Cho, I. & Loke, P., Sep 1 2017, In : Inflammatory Bowel Diseases. 23, 9, p. 1544-1554 11 p.

Research output: Contribution to journalArticle

Introduction to the special issue on deep learning approaches for machine translation

Costa-jussà, M. R., Allauzen, A., Barrault, L., Cho, K. & Schwenk, H., Nov 1 2017, In : Computer Speech and Language. 46, p. 367-373 7 p.

Research output: Contribution to journalArticle

Learning a Health Knowledge Graph from Electronic Medical Records

Rotmensch, M., Halpern, Y., Tlimat, A., Horng, S. & Sontag, D., Dec 1 2017, In : Scientific Reports. 7, 1, 5994.

Research output: Contribution to journalArticle

Learning scalable deep kernels with recurrent structure

Al-Shedivat, M., Wilson, A. G., Saatchi, Y., Hu, Z. & Xing, E. P., Aug 1 2017, In : Journal of Machine Learning Research. 18, p. 1-37 37 p.

Research output: Contribution to journalArticle

Low-Grade Astrocytoma Mutations in IDH1, P53, and ATRX Cooperate to Block Differentiation of Human Neural Stem Cells via Repression of SOX2

Modrek, A. S., Golub, D., Khan, T., Bready, D., Prado, J., Bowman, C., Deng, J., Zhang, G., Rocha, P. P., Raviram, R., Lazaris, C., Stafford, J. M., LeRoy, G., Kader, M., Dhaliwal, J., Bayin, N. S., Frenster, J. D., Serrano, J., Chiriboga, L., Baitalmal, R. & 13 others, Nanjangud, G., Chi, A. S., Golfinos, J. G., Wang, J., Karajannis, M. A., Bonneau, R., Reinberg, D., Tsirigos, A., Zagzag, D., Snuderl, M., Skok, J. A., Neubert, T. A. & Placantonakis, D. G., Oct 31 2017, In : Cell Reports. 21, 5, p. 1267-1280 14 p.

Research output: Contribution to journalArticle

Low-Rank Spatial Channel Estimation for Millimeter Wave Cellular Systems

Eliasi, P. A., Rangan, S. & Rappaport, T., May 1 2017, In : IEEE Transactions on Wireless Communications. 16, 5, p. 2748-2759 12 p., 7891613.

Research output: Contribution to journalArticle

Lung microbiome and host immune tone in subjects with idiopathic pulmonary fibrosis treated with inhaled interferon-γ

Wang, J., Lesko, M., Badri, M. H., Kapoor, B. C., Wu, B. G., Li, Y., Smaldone, G. C., Bonneau, R., Kurtz, Z. D., Condos, R. & Segal, L. N., Jul 1 2017, In : ERS Monograph. 3, 3

Research output: Contribution to journalArticle

Mocap: Large-scale inference of transcription factor binding sites from chromatin accessibility

Chen, X., Yu, B., Carriero, N., Silva, C. & Bonneau, R., 2017, In : Nucleic Acids Research. 45, 8, p. 4315-4329 15 p.

Research output: Contribution to journalArticle

Overview of Millimeter Wave Communications for Fifth-Generation (5G) Wireless Networks-with a focus on Propagation Models

Rappaport, T., Xing, Y., MacCartney, G. R., Molisch, A. F., Mellios, E. & Zhang, J., Aug 1 2017, (Accepted/In press) In : IEEE Transactions on Antennas and Propagation.

Research output: Contribution to journalArticle

Parallel optimization with boundary elements and kernel independent fast multipole method

Ostanin, I., Zorin, D. & Oseledets, I., Jan 1 2017, In : International Journal of Computational Methods and Experimental Measurements. 5, 2, p. 154-162 9 p.

Research output: Contribution to journalArticle

Open Access

Position-based tensegrity design

Pietroni, N., Tarini, M., Vaxman, A., Panozzo, D. & Cignoni, P., Nov 20 2017, In : ACM Transactions on Graphics. 36, 6, a172.

Research output: Contribution to journalArticle

Project 1640 Observations of Brown Dwarf GJ 758 B: Near-infrared Spectrum and Atmospheric Modeling

Nilsson, R., Veicht, A., Godfrey, P. A. G., Rice, E. L., Aguilar, J., Pueyo, L., Roberts, L. C., Oppenheimer, R., Brenner, D., Luszcz-Cook, S. H., Bacchus, E., Beichman, C., Burruss, R., Cady, E., Dekany, R., Fergus, R., Hillenbrand, L., Hinkley, S., King, D., Lockhart, T. & 6 others, Parry, I. R., Sivaramakrishnan, A., Soummer, R., Vasisht, G., Zhai, C. & Zimmerman, N. T., Mar 20 2017, In : Astrophysical Journal. 838, 1, 64.

Research output: Contribution to journalArticle

Resource oblivious sorting on multicores

Cole, R. & Ramachandran, V., Mar 1 2017, In : ACM Transactions on Parallel Computing. 3, 4, a23.

Research output: Contribution to journalArticle

Rig animation with a tangible and modular input device

Glauser, O., Vartok, B., Ma, W. C., Panozzo, D., Jacobson, A., Pradalier, C., Hilliges, O. & Sorkine-Hornung, O., Mar 1 2017, Interactions, 24, 2, p. 16-17 2 p.

Research output: Contribution to specialist publicationArticle

Robust hex-dominant mesh generation using field-guided polyhedral agglomeration

Gao, X., Jakob, W., Tarini, M. & Panozzo, D., 2017, In : ACM Transactions on Graphics. 36, 4, 114.

Research output: Contribution to journalArticle

Robust structure simplification for hex Re-meshing

Gao, X., Panozzo, D., Wang, W., Deng, Z. & Chen, G., Nov 20 2017, In : ACM Transactions on Graphics. 36, 6, a185.

Research output: Contribution to journalArticle

Rotamer Libraries for the High-Resolution Design of β-Amino Acid Foldamers

Watkins, A. M., Craven, T. W., Renfrew, P. D., Arora, P. & Bonneau, R., 2017, (Accepted/In press) In : Structure.

Research output: Contribution to journalArticle

Rural macrocell path loss models for millimeter wave wireless communications

MacCartney, G. R. & Rappaport, T., Jul 1 2017, In : IEEE Journal on Selected Areas in Communications. 35, 7, p. 1663-1677 15 p., 7914696.

Research output: Contribution to journalArticle

Scalable locally injective mappings

Rabinovich, M., Poranne, R., Panozzo, D. & Sorkine-Hornung, O., Apr 1 2017, In : ACM Transactions on Graphics. 36, 2, 16.

Research output: Contribution to journalArticle

Scalable topology optimization with the kernel-independent fast multipole method

Ostanin, I., Tsybulin, I., Litsarev, M., Oseledets, I. & Zorin, D., Oct 1 2017, In : Engineering Analysis with Boundary Elements. 83, p. 123-132 10 p.

Research output: Contribution to journalArticle

Similarity maps and field-guided T-Splines: A perfect couple

Campen, M. & Zorin, D., 2017, In : ACM Transactions on Graphics. 36, 4, 91.

Research output: Contribution to journalArticle

Simplicial complex augmentation framework for bijective maps

Jiang, Z., Schaefer, S. & Panozzo, D., Nov 20 2017, In : ACM Transactions on Graphics. 36, 6, a186.

Research output: Contribution to journalArticle

Small-Scale, Local Area, and Transitional Millimeter Wave Propagation for 5G Communications

Rappaport, T., MacCartney, G. R., Sun, S., Yan, H. & Deng, S., Aug 1 2017, (Accepted/In press) In : IEEE Transactions on Antennas and Propagation.

Research output: Contribution to journalArticle

The first Winograd schema challenge at IJCAI-16

Davis, E., Morgenstern, L. & Ortiz, C. L., Sep 1 2017, In : AI Magazine. 38, 3, p. 97-98 2 p.

Research output: Contribution to journalArticle

The representational geometry of word meanings acquired by neural machine translation models

Hill, F., Cho, K., Jean, S. & Bengio, Y., Apr 29 2017, (Accepted/In press) In : Machine Translation. p. 1-16 16 p.

Research output: Contribution to journalArticle

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design

Alford, R. F., Leaver-Fay, A., Jeliazkov, J. R., O'Meara, M. J., DiMaio, F. P., Park, H., Shapovalov, M. V., Renfrew, P. D., Mulligan, V. K., Kappel, K., Labonte, J. W., Pacella, M. S., Bonneau, R., Bradley, P., Dunbrack, R. L., Das, R., Baker, D., Kuhlman, B., Kortemme, T. & Gray, J. J., Jun 13 2017, In : Journal of Chemical Theory and Computation. 13, 6, p. 3031-3048 18 p.

Research output: Contribution to journalArticle

Tight hardness of the non-commutative grothendieck problem

Briët, J., Regev, O. & Saket, R., Dec 2 2017, In : Theory of Computing. 13

Research output: Contribution to journalArticle

T-junctions in spline surfaces

Karčiauskas, K., Panozzo, D. & Peters, J., Oct 1 2017, In : ACM Transactions on Graphics. 36, 5, A170.

Research output: Contribution to journalArticle

Ubiquitous evaluation of layer potentials using Quadrature by Kernel-Independent Expansion

Rahimian, A., Barnett, A. & Zorin, D., Nov 6 2017, (Accepted/In press) In : BIT Numerical Mathematics. p. 1-34 34 p.

Research output: Contribution to journalArticle

What will 5G Antennas and Propagation Be?

Liu, D., Hong, W., Rappaport, T., Luxey, C. & Hong, W., Dec 1 2017, In : IEEE Transactions on Antennas and Propagation. 65, 12, p. 6205-6212 8 p., 8124182.

Research output: Contribution to journalArticle

Worst-case stress relief for microstructures

Panetta, J., Rahimian, A. & Zorin, D., 2017, In : ACM Transactions on Graphics. 36, 4, 122.

Research output: Contribution to journalArticle

2016

3-D Millimeter-Wave Statistical Channel Model for 5G Wireless System Design

Samimi, M. K. & Rappaport, T., Jun 28 2016, (Accepted/In press) In : IEEE Transactions on Microwave Theory and Techniques.

Research output: Contribution to journalArticle

4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments

Raviram, R., Rocha, P. P., Müller, C. L., Miraldi, E. R., Badri, S., Fu, Y., Swanzey, E., Proudhon, C., Snetkova, V., Bonneau, R. & Skok, J. A., Mar 1 2016, In : PLoS Computational Biology. 12, 3, e1004780.

Research output: Contribution to journalArticle

A BFGS-SQP method for nonsmooth, nonconvex, constrained optimization and its evaluation using relative minimization profiles

Curtis, F. E., Mitchell, T. & Overton, M., Jul 16 2016, (Accepted/In press) In : Optimization Methods and Software. p. 1-34 34 p.

Research output: Contribution to journalArticle

Accurate de novo design of hyperstable constrained peptides

Bhardwaj, G., Mulligan, V. K., Bahl, C. D., Gilmore, J. M., Harvey, P. J., Cheneval, O., Buchko, G. W., Pulavarti, S. V. S. R. K., Kaas, Q., Eletsky, A., Huang, P. S., Johnsen, W. A., Greisen, P. J., Rocklin, G. J., Song, Y., Linsky, T. W., Watkins, A., Rettie, S. A., Xu, X., Carter, L. P. & 7 others, Bonneau, R., Olson, J. M., Coutsias, E., Correnti, C. E., Szyperski, T., Craik, D. J. & Baker, D., 2016, In : Nature. 538, 7625, p. 329-335 7 p.

Research output: Contribution to journalArticle

A collaborative approach to computational reproducibility

Chirigati, F., Capone, R., Rampin, R., Freire, J. & Shasha, D., Jul 1 2016, In : Information Systems. 59, p. 95-97 3 p.

Research output: Contribution to journalArticle