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2020

A Comprehensive Map of the Monocyte-Derived Dendritic Cell Transcriptional Network Engaged upon Innate Sensing of HIV

Johnson, J. S., De Veaux, N., Rives, A. W., Lahaye, X., Lucas, S. Y., Perot, B. P., Luka, M., Garcia-Paredes, V., Amon, L. M., Watters, A., Abdessalem, G., Aderem, A., Manel, N., Littman, D. R., Bonneau, R. & Ménager, M. M., Jan 21 2020, In : Cell Reports. 30, 3, p. 914-931.e9

Research output: Contribution to journalArticle

Open Access

Characterizing chromatin landscape from aggregate and single-cell genomic assays using flexible duration modeling

Gabitto, M. I., Rasmussen, A., Wapinski, O., Allaway, K., Carriero, N., Fishell, G. J. & Bonneau, R., Dec 1 2020, In : Nature communications. 11, 1, 747.

Research output: Contribution to journalArticle

Open Access

Gene regulatory network reconstruction using single-cell rna sequencing of barcoded genotypes in diverse environments

Jackson, C. A., Castro, D. M., Saldi, G. A., Bonneau, R. & Gresham, D., Jan 2020, In : eLife. 9, e51254.

Research output: Contribution to journalArticle

Open Access
2019

Adaptation based on generalized discrepancy

Cortes, C., Mohri, M. & Medina, A. M., Jan 1 2019, In : Journal of Machine Learning Research. 20, p. 1-30 30 p.

Research output: Contribution to journalArticle

An oculus rift assessment of dynamic balance by head mobility in a virtual park scene: A pilot study

Lubetzky, A., Hujsak, B. D., Fu, G. & Perlin, K., Jan 1 2019, In : Motor Control. 23, 1, p. 127-142 16 p.

Research output: Contribution to journalArticle

CAVE: Making collective virtual narrative

Layng, K., Perlin, K., Herscher, S., Brenner, C. & Meduri, T., Aug 1 2019, In : Leonardo. 52, 4, p. 349-356 8 p.

Research output: Contribution to journalArticle

Cellogram: On-the-Fly Traction Force Microscopy

Lendenmann, T., Schneider, T., Dumas, J., Tarini, M., Giampietro, C., Bajpai, A., Chen, W., Gerber, J., Poulikakos, D., Ferrari, A. & Panozzo, D., Oct 9 2019, In : Nano Letters. 19, 10, p. 6742-6750 9 p.

Research output: Contribution to journalArticle

Change surfaces for expressive multidimensional changepoints and counterfactual prediction

Herlands, W., Neill, D., Nickisch, H. & Wilson, A. G., Jun 1 2019, In : Journal of Machine Learning Research. 20

Research output: Contribution to journalArticle

Characterization of Transcriptional Regulatory Networks that Promote and Restrict Identities and Functions of Intestinal Innate Lymphoid Cells

Pokrovskii, M., Hall, J. A., Ochayon, D. E., Yi, R., Chaimowitz, N. S., Seelamneni, H., Carriero, N., Watters, A., Waggoner, S. N., Littman, D. R., Bonneau, R. & Miraldi, E. R., Jul 16 2019, In : Immunity. 51, 1, p. 185-197.e6

Research output: Contribution to journalArticle

Conditional Molecular Design with Deep Generative Models

Kang, S. & Cho, K., Jan 28 2019, In : Journal of Chemical Information and Modeling. 59, 1, p. 43-52 10 p.

Research output: Contribution to journalArticle

Curvislicer: Slightly curved slicing for 3-axis printers

Etienne, J., Ray, N., Panozzo, D., Hornus, S., Wang, C. C. L., Martínez, J., McMains, S., Alexa, M., Wyvill, B. & Lefebvre, S., Jul 2019, In : ACM Transactions on Graphics. 38, 4, 81.

Research output: Contribution to journalArticle

Deformation capture via soft and stretchable sensor arrays

Glauser, O., Panozzo, D., Hilliges, O. & Sorkine-Hornung, O., Apr 1 2019, In : ACM Transactions on Graphics. 38, 2, 16.

Research output: Contribution to journalArticle

Open Access

Distinct Polysaccharide Utilization Profiles of Human Intestinal Prevotella copri Isolates

Fehlner-Peach, H., Magnabosco, C., Raghavan, V., Scher, J. U., Tett, A., Cox, L. M., Gottsegen, C., Watters, A., Wiltshire-Gordon, J. D., Segata, N., Bonneau, R. & Littman, D. R., Nov 13 2019, In : Cell Host and Microbe. 26, 5, p. 680-690.e5

Research output: Contribution to journalArticle

Elites tweet to get feet off the streets: Measuring regime social media strategies during protest

Munger, K., Bonneau, R., Nagler, J. & Tucker, J., Oct 1 2019, In : Political Science Research and Methods. 7, 4, p. 815-834 20 p.

Research output: Contribution to journalArticle

Open Access

Existential monadic second order logic on random rooted trees

Holroyd, A. E., Levy, A., Podder, M. & Spencer, J., Jan 1 2019, In : Discrete Mathematics. 342, 1, p. 152-167 16 p.

Research output: Contribution to journalArticle

Exploiting high millimeter wave bands for military communications, applications, and design

Harvey, J. F., Steer, M. B. & Rappaport, T., Jan 1 2019, In : IEEE Access. 7, p. 52350-52359 10 p., 8692347.

Research output: Contribution to journalArticle

Fast methods for finding significant motifs on labelled multi-relational networks

Micale, G., Pulvirenti, A., Ferro, A., Giugno, R. & Shasha, D., Apr 15 2019, In : Journal of Complex Networks. 7, 6, p. 817-837 21 p.

Research output: Contribution to journalArticle

Fast Subgraph Matching Strategies Based on Pattern-Only Heuristics

Aparo, A., Bonnici, V., Micale, G., Ferro, A., Shasha, D., Pulvirenti, A. & Giugno, R., Mar 1 2019, In : Interdisciplinary Sciences: Computational Life Sciences. 11, 1, p. 21-32 12 p.

Research output: Contribution to journalArticle

Feature Preserving Octree-Based Hexahedral Meshing

Gao, X., Shen, H. & Panozzo, D., Jan 1 2019, In : Computer Graphics Forum. 38, 5, p. 135-149 15 p.

Research output: Contribution to journalArticle

For Whom the Bot Tolls: A Neural Networks Approach to Measuring Political Orientation of Twitter Bots in Russia

Stukal, D., Sanovich, S., Tucker, J. & Bonneau, R., Apr 1 2019, In : SAGE Open. 9, 2

Research output: Contribution to journalArticle

Open Access

High-definition spatial transcriptomics for in situ tissue profiling

Vickovic, S., Eraslan, G., Salmén, F., Klughammer, J., Stenbeck, L., Schapiro, D., Äijö, T., Bonneau, R., Bergenstråhle, L., Navarro, J. F., Gould, J., Griffin, G. K., Borg, Å., Ronaghi, M., Frisén, J., Lundeberg, J., Regev, A. & Ståhl, P. L., Oct 1 2019, In : Nature methods. 16, 10, p. 987-990 4 p.

Research output: Contribution to journalArticle

Integrative Protein Modeling in RosettaNMR from Sparse Paramagnetic Restraints

Kuenze, G., Bonneau, R., Leman, J. K. & Meiler, J., Nov 5 2019, In : Structure. 27, 11, p. 1721-1734.e5

Research output: Contribution to journalArticle

Interactive hand pose estimation using a stretch-sensing soft glove

Glauser, O., Wu, S., Panozzo, D., Hilliges, O. & Sorkine-Hornung, O., Jul 2019, In : ACM Transactions on Graphics. 38, 4, 41.

Research output: Contribution to journalArticle

Learning representations of microbe–metabolite interactions

Morton, J. T., Aksenov, A. A., Nothias, L. F., Foulds, J. R., Quinn, R. A., Badri, M. H., Swenson, T. L., Van Goethem, M. W., Northen, T. R., Vazquez-Baeza, Y., Wang, M., Bokulich, N. A., Watters, A., Song, S. J., Bonneau, R., Dorrestein, P. C. & Knight, R., Dec 1 2019, In : Nature methods. 16, 12, p. 1306-1314 9 p.

Research output: Contribution to journalArticle

Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells

Miraldi, E. R., Pokrovskii, M., Watters, A., Castro, D. M., De Veaux, N., Hall, J. A., Lee, J. Y., Ciofani, M., Madar, A., Carriero, N., Littman, D. R. & Bonneau, R., Mar 1 2019, In : Genome Research. 29, 3, p. 449-463 15 p.

Research output: Contribution to journalArticle

Open Access

Millimeter-wave base station diversity for 5G coordinated multipoint (CoMP) applications

MacCartney, G. R. & Rappaport, T., Jul 1 2019, In : IEEE Transactions on Wireless Communications. 18, 7, p. 3395-3410 16 p., 8705688.

Research output: Contribution to journalArticle

Molecular Geometry Prediction using a Deep Generative Graph Neural Network

Mansimov, E., Mahmood, O., Kang, S. & Cho, K., Dec 1 2019, In : Scientific reports. 9, 1, 20381.

Research output: Contribution to journalArticle

Open Access

Multi-study inference of regulatory networks for more accurate models of gene regulation

Castro, D. M., de Veaux, N. R., Miraldi, E. R. & Bonneau, R., Jan 1 2019, In : PLoS Computational Biology. 15, 1, e1006591.

Research output: Contribution to journalArticle

Network Walking charts transcriptional dynamics of nitrogen signaling by integrating validated and predicted genome-wide interactions

Brooks, M. D., Cirrone, J., Pasquino, A. V., Alvarez, J. M., Swift, J., Mittal, S., Juang, C. L., Varala, K., Gutiérrez, R. A., Krouk, G., Shasha, D. & Coruzzi, G., Dec 1 2019, In : Nature Communications. 10, 1, 1569.

Research output: Contribution to journalArticle

Open Access

NSD2 overexpression drives clustered chromatin and transcriptional changes in a subset of insulated domains

Lhoumaud, P., Badri, S., Rodriguez-Hernaez, J., Sakellaropoulos, T., Sethia, G., Kloetgen, A., Cornwell, M. I., Bhattacharyya, S., Ay, F., Bonneau, R., Tsirigos, A. & Skok, J. A., Dec 1 2019, In : Nature Communications. 10, 1, 4843.

Research output: Contribution to journalArticle

Open Access

On the origin of biomolecular networks

Janwa, H., Massey, S. E., Velev, J. & Mishra, B., Jan 1 2019, In : Frontiers in Genetics. 10, APR, 240.

Research output: Contribution to journalArticle

Open Access

Poly-spline finite-element method

Schneider, T., Dumas, J., Gao, X., Botsch, M., Panozzo, D. & Zorin, D., Jan 1 2019, In : ACM Transactions on Graphics. 38, 3, 19.

Research output: Contribution to journalArticle

Pre-detection history of extensively drug-resistant tuberculosis in KwaZulu-Natal, South Africa

Brown, T. S., Challagundla, L., Baugh, E. H., Omar, S. V., Mustaev, A., Auld, S. C., Shah, N. S., Kreiswirth, B. N., Brust, J. C. M., Nelson, K. N., Narechania, A., Kurepina, N., Mlisana, K., Bonneau, R., Eldholm, V., Ismail, N., Kolokotronis, S. O., Robinson, D. A., Gandhi, N. R. & Mathema, B., Nov 12 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 46, p. 23284-23291 8 p.

Research output: Contribution to journalArticle

Open Access

Progressive embedding

Shen, H., Jiang, Z., Zorin, D. & Panozzo, D., Jul 2019, In : ACM Transactions on Graphics. 38, 4, 32.

Research output: Contribution to journalArticle

QCD-aware recursive neural networks for jet physics

Louppe, G., Cho, K., Becot, C. & Cranmer, K., Jan 1 2019, In : Journal of High Energy Physics. 2019, 1, 57.

Research output: Contribution to journalArticle

Relative deviation learning bounds and generalization with unbounded loss functions

Cortes, C., Greenberg, S. & Mohri, M., Jan 1 2019, (Accepted/In press) In : Annals of Mathematics and Artificial Intelligence.

Research output: Contribution to journalArticle

Robust regularization of topology optimization problems with a posteriori error estimators

Ovchinnikov, G. V., Zorin, D. & Oseledets, I. V., Feb 1 2019, In : Russian Journal of Numerical Analysis and Mathematical Modelling. 34, 1, p. 57-69 13 p.

Research output: Contribution to journalArticle

Sian: A tool for assessing structural identifiability of parametric ODEs

Hong, H., Ovchinnikov, A., Pogudin, G. & Yap, C., Jun 2019, In : ACM Communications in Computer Algebra. 53, 2, p. 37-40 4 p.

Research output: Contribution to journalArticle

SIAN: software for structural identifiability analysis of ODE models

Hong, H., Ovchinnikov, A., Pogudin, G. & Yap, C., Aug 15 2019, In : Bioinformatics (Oxford, England). 35, 16, p. 2873-2874 2 p.

Research output: Contribution to journalArticle

Some complexity results for stateful network verification

Alpernas, K., Panda, A., Rabinovich, A., Sagiv, M., Shenker, S., Shoham, S. & Velner, Y., Jan 1 2019, (Accepted/In press) In : Formal Methods in System Design.

Research output: Contribution to journalArticle

Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis

Maniatis, S., Äijö, T., Vickovic, S., Braine, C., Kang, K., Mollbrink, A., Fagegaltier, D., Andrusivová, Ž., Saarenpää, S., Saiz-Castro, G., Cuevas, M., Watters, A., Lundeberg, J., Bonneau, R. & Phatnani, H., Apr 5 2019, In : Science. 364, 6435, p. 89-93 5 p.

Research output: Contribution to journalArticle

Spurious valleys in one-hidden-layer neural network optimization landscapes

Venturi, L., Bandeira, A. & Bruna Estrach, J., Aug 1 2019, In : Journal of Machine Learning Research. 20

Research output: Contribution to journalArticle

TACITuS: Transcriptomic data collector, integrator, and selector on big data platform

Alaimo, S., Di Maria, A., Shasha, D., Ferro, A. & Pulvirenti, A., Nov 22 2019, In : BMC Bioinformatics. 20, 366.

Research output: Contribution to journalArticle

Open Access

Tatonnement beyond gross substitutes? Gradient descent to the rescue

Cheung, Y. K., Cole, R. & Devanur, N. R., Jan 1 2019, In : Games and Economic Behavior.

Research output: Contribution to journalArticle

Thermoresponsive Protein-Engineered Coiled-Coil Hydrogel for Sustained Small Molecule Release

Hill, L. K., Meleties, M., Katyal, P., Xie, X., Delgado-Fukushima, E., Jihad, T., Liu, C. F., O'Neill, S., Tu, R. S., Renfrew, P. D., Bonneau, R., Wadghiri, Y. Z. & Montclare, J., Jan 1 2019, (Accepted/In press) In : Biomacromolecules.

Research output: Contribution to journalArticle

Thoughts on load distribution and the role of programmable switches

McCauley, J., Krishnamurthy, A., Panda, A. & Shenker, S., Jan 1 2019, In : Computer Communication Review. 49, 1, p. 18-23 6 p.

Research output: Contribution to journalArticle

Towards region-specific propagation of protein functions

Koo, D. C. E. & Bonneau, R., May 15 2019, In : Bioinformatics (Oxford, England). 35, 10, p. 1737-1744 8 p.

Research output: Contribution to journalArticle

Open Access

Triwild: Robust triangulation with curve constraints

Hu, Y., Schneider, T., Gao, X., Zhou, Q., Jacobson, A., Zorin, D. & Panozzo, D., Jul 2019, In : ACM Transactions on Graphics. 38, 4, 52.

Research output: Contribution to journalArticle