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2016

A Damage-Independent Role for 53BP1 that Impacts Break Order and Igh Architecture during Class Switch Recombination

Rocha, P. P., Raviram, R., Fu, Y., Kim, J. H., Luo, V. M., Aljoufi, A., Swanzey, E., Pasquarella, A., Balestrini, A., Miraldi, E. R., Bonneau, R., Petrini, J., Schotta, G. & Skok, J. A., Feb 23 2016, (Accepted/In press) In : Cell Reports.

Research output: Contribution to journalArticle

Algorithmic methods to infer the evolutionary trajectories in cancer progression

Caravagna, G., Graudenzi, A., Ramazzotti, D., Sanz-Pamplona, R., De Sano, L., Mauri, G., Moreno, V., Antoniotti, M. & Mishra, B., Jul 12 2016, In : Proceedings of the National Academy of Sciences of the United States of America. 113, 28, p. E4025-E4034

Research output: Contribution to journalArticle

A mathematical motivation for complex-valued convolutional networks

Tygert, M., Bruna Estrach, J., Chintala, S., LeCun, Y., Piantino, S. & Szlam, A., May 1 2016, In : Neural Computation. 28, 5, p. 815-825 11 p.

Research output: Contribution to journalArticle

A Miniature Protein Stabilized by a Cation-π Interaction Network

Craven, T. W., Cho, M. K., Traaseth, N. J., Bonneau, R. & Kirshenbaum, K., Feb 17 2016, In : Journal of the American Chemical Society. 138, 5, p. 1543-1550 8 p.

Research output: Contribution to journalArticle

A near-optimal subdivision algorithm for complex root isolation based on the Pellet test and Newton iteration

Becker, R., Sagraloff, M., Sharma, V. & Yap, C., Jan 14 2016, (Accepted/In press) In : Journal of Symbolic Computation.

Research output: Contribution to journalArticle

An efficient SMT solver for string constraints

Liang, T., Reynolds, A., Tsiskaridze, N., Tinelli, C., Barrett, C. & Deters, M., Apr 5 2016, (Accepted/In press) In : Formal Methods in System Design. p. 1-29 29 p.

Research output: Contribution to journalArticle

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Jiang, Y., Oron, T. R., Clark, W. T., Bankapur, A. R., D'Andrea, D., Lepore, R., Funk, C. S., Kahanda, I., Verspoor, K. M., Ben-Hur, A., Koo, D. C. E., Penfold-Brown, D., Shasha, D., Youngs, N., Bonneau, R., Lin, A., Sahraeian, S. M. E., Martelli, P. L., Profiti, G., Casadio, R. & 127 others, Cao, R., Zhong, Z., Cheng, J., Altenhoff, A., Skunca, N., Dessimoz, C., Dogan, T., Hakala, K., Kaewphan, S., Mehryary, F., Salakoski, T., Ginter, F., Fang, H., Smithers, B., Oates, M., Gough, J., Törönen, P., Koskinen, P., Holm, L., Chen, C. T., Hsu, W. L., Bryson, K., Cozzetto, D., Minneci, F., Jones, D. T., Chapman, S., Bkc, D., Khan, I. K., Kihara, D., Ofer, D., Rappoport, N., Stern, A., Cibrian-Uhalte, E., Denny, P., Foulger, R. E., Hieta, R., Legge, D., Lovering, R. C., Magrane, M., Melidoni, A. N., Mutowo-Meullenet, P., Pichler, K., Shypitsyna, A., Li, B., Zakeri, P., ElShal, S., Tranchevent, L. C., Das, S., Dawson, N. L., Lee, D., Lees, J. G., Sillitoe, I., Bhat, P., Nepusz, T., Romero, A. E., Sasidharan, R., Yang, H., Paccanaro, A., Gillis, J., Sedeño-Cortés, A. E., Pavlidis, P., Feng, S., Cejuela, J. M., Goldberg, T., Hamp, T., Richter, L., Salamov, A., Gabaldon, T., Marcet-Houben, M., Supek, F., Gong, Q., Ning, W., Zhou, Y., Tian, W., Falda, M., Fontana, P., Lavezzo, E., Toppo, S., Ferrari, C., Giollo, M., Piovesan, D., Tosatto, S. C. E., del Pozo, A., Fernández, J. M., Maietta, P., Valencia, A., Tress, M. L., Benso, A., Di Carlo, S., Politano, G., Savino, A., Rehman, H. U., Re, M., Mesiti, M., Valentini, G., Bargsten, J. W., van Dijk, A. D. J., Gemovic, B., Glisic, S., Perovic, V., Veljkovic, V., Veljkovic, N., Almeida-e-Silva, D. C., Vencio, R. Z. N., Sharan, M., Vogel, J., Kansakar, L., Zhang, S., Vucetic, S., Wang, Z., Sternberg, M. J. E., Wass, M. N., Huntley, R. P., Martin, M. J., O'Donovan, C., Robinson, P. N., Moreau, Y., Tramontano, A., Babbitt, P. C., Brenner, S. E., Linial, M., Orengo, C. A., Rost, B., Greene, C. S., Mooney, S. D., Friedberg, I. & Radivojac, P., Sep 7 2016, In : Genome Biology. 17, 1, 184.

Research output: Contribution to journalArticle

An Explicit Implicit Scheme for Cut Cells in Embedded Boundary Meshes

May, S. & Berger, M., Dec 3 2016, (Accepted/In press) In : Journal of Scientific Computing. p. 1-25 25 p.

Research output: Contribution to journalArticle

Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet

Mahana, D., Trent, C. M., Kurtz, Z. D., Bokulich, N. A., Battaglia, T., Chung, J., Müller, C. L., Li, H., Bonneau, R. & Blaser, M. J., Apr 27 2016, In : Genome Medicine. 8, 1, 48.

Research output: Contribution to journalArticle

Assessment via the Oculus of Visual ‘Weighting’ and ‘Re-weighting’ in Young Adults

Lubetzky, A., Harel, D., Darmanin, H. & Perlin, K., 2016, In : Motor Control.

Research output: Contribution to journalArticle

Bijective maps from simplicial foliations

Campen, M., Silva, C. T. & Zorin, D., Jul 11 2016, In : ACM Transactions on Graphics. 35, 4, a74.

Research output: Contribution to journalArticle

Boosting with abstention

Cortes, C., De Salvo, G. & Mohri, M., 2016, In : Advances in Neural Information Processing Systems. p. 1668-1676 9 p.

Research output: Contribution to journalArticle

Bounded quantifier depth spectra for random graphs

Spencer, J. & Zhukovskii, M. E., Jun 6 2016, In : Discrete Mathematics. 339, 6, p. 1651-1664 14 p.

Research output: Contribution to journalArticle

Cancer megafunds with in silico and in vitro validation: Accelerating cancer drug discovery via financial engineering without financial crisis

Yang, X., Debonneuil, E., Zhavoronkov, A. & Mishra, B., 2016, In : Oncotarget. 7, 36, p. 57671-57678 8 p.

Research output: Contribution to journalArticle

Clawpack: Building an open source ecosystem for solving hyperbolic PDEs

Mandli, K. T., Ahmadia, A. J., Berger, M., Calhoun, D., George, D. L., Hadjimichael, Y., Ketcheson, D. I., Lemoine, G. I. & LeVeque, R. J., 2016, In : PeerJ Computer Science. 2016, 8, e68.

Research output: Contribution to journalArticle

Complete Instantiation-Based Interpolation

Totla, N. & Wies, T., Apr 15 2016, (Accepted/In press) In : Journal of Automated Reasoning. p. 1-29 29 p.

Research output: Contribution to journalArticle

Compliance signaling games: toward modeling the deterrence of insider threats

Casey, W., Morales, J. A., Wright, E., Zhu, Q. & Mishra, B., Apr 28 2016, (Accepted/In press) In : Computational and Mathematical Organization Theory. p. 1-32 32 p.

Research output: Contribution to journalArticle

Computational thermoforming

Schüller, C., Panozzo, D., Grundhöfer, A., Zimmer, H., Sorkine, E. & Sorkine-Hornung, O., Jul 11 2016, In : ACM Transactions on Graphics. 35, 4, a43.

Research output: Contribution to journalArticle

Confocal reference free traction force microscopy

Bergert, M., Lendenmann, T., Zündel, M., Ehret, A. E., Panozzo, D., Richner, P., Kim, D. K., Kress, S. J. P., Norris, D. J., Sorkine-Hornung, O., Mazza, E., Poulikakos, D. & Ferrari, A., Sep 29 2016, In : Nature Communications. 7, 12814.

Research output: Contribution to journalArticle

Context-dependent word representation for neural machine translation

Choi, H., Cho, K. & Bengio, Y., Apr 18 2016, (Accepted/In press) In : Computer Speech and Language.

Research output: Contribution to journalArticle

Corrigendum: DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions

Huang, W., Thomas, B., Flynn, R. A., Gavzy, S. J., Wu, L., Kim, S. V., Hall, J. A., Miraldi, E. R., Ng, C. P., Rigo, F., Meadows, S., Montoya, N. R., Herrera, N. G., Domingos, A. I., Rastinejad, F., Myers, R. M., Fuller-Pace, F. V., Bonneau, R., Chang, H. Y., Acuto, O. & 1 others, Littman, D. R., May 5 2016, In : Nature. 533, 7601, p. 130 1 p.

Research output: Contribution to journalArticle

Cut Cells: Meshes and Solvers

Berger, M., 2016, (Accepted/In press) In : Handbook of Numerical Analysis.

Research output: Contribution to journalArticle

Design of the TRONCO bioconductor package for TRanslational ONCOlogy

Antoniotti, M., Caravagna, G., De Sano, L., Graudenzi, A., Mauri, G., Mishra, B. & Ramazzotti, D., 2016, In : R Journal. 8, 2, p. 39-59 21 p.

Research output: Contribution to journalArticle

Directional field synthesis, design, and processing

Vaxman, A., Campen, M., Diamanti, O., Panozzo, D., Bommes, D., Hildebrandt, K. & Ben-Chen, M., May 1 2016, In : Computer Graphics Forum. 35, 2, p. 545-572 28 p.

Research output: Contribution to journalArticle

Directional Radio Propagation Path Loss Models for Millimeter-Wave Wireless Networks in the 28-, 60-, and 73-GHz Bands

Sulyman, A. I., Alwarafy, A., MacCartney, G. R., Rappaport, T. & Alsanie, A., Oct 1 2016, In : IEEE Transactions on Wireless Communications. 15, 10, p. 6939-6947 9 p., 7522613.

Research output: Contribution to journalArticle

Disentangling factors of variation in deep representations using adversarial training

Mathieu, M., Zhao, J., Sprechmann, P., Ramesh, A. & LeCun, Y., 2016, In : Advances in Neural Information Processing Systems. p. 5047-5055 9 p.

Research output: Contribution to journalArticle

Distributed representation learning for knowledge graphs with entity descriptions

Fan, M., Zhou, Q., Zheng, T. F. & Grishman, R., Apr 15 2016, (Accepted/In press) In : Pattern Recognition Letters.

Research output: Contribution to journalArticle

EGRINs (Environmental gene regulatory influence networks) in rice that function in the response to water deficit, high temperature, and agricultural environments

Wilkins, O., Hafemeister, C., Plessis, A., Holloway-Phillips, M. M., Pham, G. M., Nicotra, A. B., Gregorio, G. B., Krishna Jagadish, S. V., Septiningsih, E. M., Bonneau, R. & Purugganan, M., Oct 1 2016, In : Plant Cell. 28, 10, p. 2365-2384 20 p.

Research output: Contribution to journalArticle

Electronic medical record phenotyping using the anchor and learn framework

Halpern, Y., Horng, S., Choi, Y. & Sontag, D., 2016, In : Journal of the American Medical Informatics Association. 23, 4, p. 731-740 10 p.

Research output: Contribution to journalArticle

End-to-end goal-driven Web navigation

Nogueira, R. & Cho, K., 2016, In : Advances in Neural Information Processing Systems. p. 1911-1919 9 p.

Research output: Contribution to journalArticle

Epistatic Signaling and Minority Games, the Adversarial Dynamics in Social Technological Systems

Casey, W., Weaver, R., Morales, J. A., Wright, E. & Mishra, B., Feb 1 2016, In : Mobile Networks and Applications. 21, 1, p. 161-174 14 p.

Research output: Contribution to journalArticle

Erratum: An IL-23R/IL-22 Circuit Regulates Epithelial Serum Amyloid A to Promote Local Effector Th17 Responses (Cell (2015) 163 (381-393))

Sano, T., Huang, W., Hall, J. A., Yang, Y., Chen, A., Gavzy, S. J., Lee, J. Y., Ziel, J. W., Miraldi, E. R., Domingos, A. I., Bonneau, R. & Littman, D. R., Jan 14 2016, In : Cell. 164, 1-2, p. 324 1 p.

Research output: Contribution to journalArticle

Fine-grained dengue forecasting using telephone triage services

Abdur Rehman, N., Kalyanaraman, S., Ahmad, T., Pervaiz, F., Saif, U. & Subramanian, L., Jul 1 2016, In : Science advances. 2, 7, p. e1501215

Research output: Contribution to journalArticle

Fused Regression for Multi-source Gene Regulatory Network Inference

Lam, K. Y., Westrick, Z. M., Müller, C. L., Christiaen, L. & Bonneau, R., Dec 1 2016, In : PLoS Computational Biology. 12, 12, e1005157.

Research output: Contribution to journalArticle

Future Reality: How Emerging Technologies Will Change Language Itself

Perlin, K., May 1 2016, In : IEEE Computer Graphics and Applications. 36, 3, p. 84-89 6 p., 7466746.

Research output: Contribution to journalArticle

Generalization bounds for non-stationary mixing processes

Kuznetsov, V. & Mohri, M., Oct 3 2016, (Accepted/In press) In : Machine Learning. p. 1-25 25 p.

Research output: Contribution to journalArticle

Helminth infection promotes colonization resistance via type 2 immunity

Ramanan, D., Bowcutt, R., Lee, S. C., Tang, M. S., Kurtz, Z. D., Ding, Y., Honda, K., Gause, W. C., Blaser, M. J., Bonneau, R., Lim, Y. A. L., Loke, P. & Cadwell, K., Apr 14 2016, (Accepted/In press) In : Science. p. 1-9 9 p.

Research output: Contribution to journalArticle

High-Speed Atomic Force Microscopy Revealing Contamination in DNA Purification Systems

Mikheikin, A., Olsen, A., Picco, L., Payton, O., Mishra, B., Gimzewski, J. K. & Reed, J., Mar 1 2016, In : Analytical Chemistry. 88, 5, p. 2527-2532 6 p.

Research output: Contribution to journalArticle

Histological image processing features induce a quantitative characterization of chronic tumor hypoxia

Sundstrom, A., Grabocka, E., Bar-Sagi, D. & Mishra, B., Apr 1 2016, In : PLoS One. 11, 4, e0153623.

Research output: Contribution to journalArticle

How to Eat Your Entropy and Have it Too: Optimal Recovery Strategies for Compromised RNGs

Dodis, Y., Shamir, A., Stephens-Davidowitz, N. & Wichs, D., Nov 14 2016, (Accepted/In press) In : Algorithmica. p. 1-37 37 p.

Research output: Contribution to journalArticle

How to write science questions that are easy for people and hard for computers

Davis, E., 2016, In : AI Magazine. 37, 1, p. 13-22 10 p.

Research output: Contribution to journalArticle

Hybrid expansion-contraction: A robust scaleable method for approximating the H norm

Mitchell, T. & Overton, M., Jul 1 2016, In : IMA Journal of Numerical Analysis. 36, 3, p. 985-1014 30 p.

Research output: Contribution to journalArticle

Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions

Jiang, T., Raviram, R., Snetkova, V., Rocha, P. P., Proudhon, C., Badri, S., Bonneau, R., Skok, J. A. & Kluger, Y., Oct 14 2016, In : Nucleic Acids Research. 44, 18, p. 8714-8725 12 p.

Research output: Contribution to journalArticle

Inferring causal molecular networks: Empirical assessment through a community-based effort

HPN-DREAM Consortium, Mar 30 2016, In : Nature Methods. 13, 4, p. 310-322 13 p.

Research output: Contribution to journalArticle

Interactive modeling of mechanical objects

Ureta, F. G., Tymms, C. & Zorin, D., 2016, In : Eurographics Symposium on Geometry Processing. 35, 5, p. 145-155 11 p.

Research output: Contribution to journalArticle

Investigation of Prediction Accuracy, Sensitivity, and Parameter Stability of Large-Scale Propagation Path Loss Models for 5G Wireless Communications

Sun, S., Rappaport, T., Thomas, T. A., Ghosh, A., Nguyen, H. C., Kovacs, I. Z., Rodriguez, I., Koymen, O. & Partyka, A., May 1 2016, In : IEEE Transactions on Vehicular Technology. 65, 5, p. 2843-2860 18 p., 7434656.

Research output: Contribution to journalArticle

Iterative refinement of the approximate posterior for directed belief networks

Hjelm, R. D., Cho, K., Chung, J., Salakhutdinov, R., Calhoun, V. & Jojic, N., 2016, In : Advances in Neural Information Processing Systems. p. 4698-4706 9 p.

Research output: Contribution to journalArticle

Learning algorithms for second-price auctions with reserve

Mohri, M. & Muñoz Medina, A., Apr 1 2016, In : Journal of Machine Learning Research. 17

Research output: Contribution to journalArticle

Learning multiagent communication with backpropagation

Sukhbaatar, S., Szlam, A. & Fergus, R., 2016, In : Advances in Neural Information Processing Systems. p. 2252-2260 9 p.

Research output: Contribution to journalArticle

Learning N-gram language models from uncertain data

Kuznetsov, V., Liao, H., Mohri, M., Riley, M. & Roark, B., 2016, In : Unknown Journal. 08-12-September-2016, p. 2323-2327 5 p.

Research output: Contribution to journalArticle