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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

Analysis of the gradient method with an Armijo–Wolfe line search on a class of non-smooth convex functions

Asl, A. & Overton, M. L., Mar 3 2020, In : Optimization Methods and Software. 35, 2, p. 223-242 20 p.

Research output: Contribution to journalArticle

CDK7 Inhibition Potentiates Genome Instability Triggering Anti-tumor Immunity in Small Cell Lung Cancer

Zhang, H., Christensen, C. L., Dries, R., Oser, M. G., Deng, J., Diskin, B., Li, F., Pan, Y., Zhang, X., Yin, Y., Papadopoulos, E., Pyon, V., Thakurdin, C., Kwiatkowski, N., Jani, K., Rabin, A. R., Castro, D. M., Chen, T., Silver, H., Huang, Q. & 29 others, Bulatovic, M., Dowling, C. M., Sundberg, B., Leggett, A., Ranieri, M., Han, H., Li, S., Yang, A., Labbe, K. E., Almonte, C., Sviderskiy, V. O., Quinn, M., Donaghue, J., Wang, E. S., Zhang, T., He, Z., Velcheti, V., Hammerman, P. S., Freeman, G. J., Bonneau, R., Kaelin, W. G., Sutherland, K. D., Kersbergen, A., Aguirre, A. J., Yuan, G. C., Rothenberg, E., Miller, G., Gray, N. S. & Wong, K. K., Jan 13 2020, In : Cancer Cell. 37, 1, p. 37-54.e9

Research output: Contribution to journalArticle

Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection

Zhang, L., Forst, C. V., Gordon, A., Gussin, G., Geber, A. B., Fernandez, P. J., Ding, T., Lashua, L., Wang, M., Balmaseda, A., Bonneau, R., Zhang, B. & Ghedin, E., Mar 17 2020, In : Microbiome. 8, 1, 39.

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

Classification of the Molecular Defects Associated with Pathogenic Variants of the SLC6A8 Creatine Transporter

Salazar, M. D., Zelt, N. B., Saldivar, R., Kuntz, C. P., Chen, S., Penn, W. D., Bonneau, R., Koehler Leman, J. & Schlebach, J. P., Apr 7 2020, In : Biochemistry. 59, 13, p. 1367-1377 11 p.

Research output: Contribution to journalArticle

Classifier-agnostic saliency map extraction

Zolna, K., Geras, K. J. & Cho, K., Jul 2020, In : Computer Vision and Image Understanding. 196, 102969.

Research output: Contribution to journalArticle

Open Access

Clustering Complex Zeros of Triangular Systems of Polynomials

Imbach, R., Pouget, M. & Yap, C., 2020, (Accepted/In press) In : Mathematics in Computer Science.

Research output: Contribution to journalArticle

Computational limits don't fully explain human cognitive limitations

Davis, E. S. & Marcus, G. F., 2020, In : Behavioral and Brain Sciences. 43, e7.

Research output: Contribution to journalArticle

Data-driven physiologic thresholds for iron deficiency associated with hematologic decline

Foy, B. H., Li, A., McClung, J. P., Ranganath, R. & Higgins, J. M., Mar 1 2020, In : American Journal of Hematology. 95, 3, p. 302-309 8 p.

Research output: Contribution to journalArticle

Deep Neural Networks Improve Radiologists' Performance in Breast Cancer Screening

Wu, N., Phang, J., Park, J., Shen, Y., Huang, Z., Zorin, M., Jastrzebski, S., Fevry, T., Katsnelson, J., Kim, E., Wolfson, S., Parikh, U., Gaddam, S., Lin, L. L. Y., Ho, K., Weinstein, J. D., Reig, B., Gao, Y., Toth, H., Pysarenko, K. & 12 others, Lewin, A., Lee, J., Airola, K., Mema, E., Chung, S., Hwang, E., Samreen, N., Kim, S. G., Heacock, L., Moy, L., Cho, K. & Geras, K. J., Apr 2020, In : IEEE Transactions on Medical Imaging. 39, 4, p. 1184-1194 11 p., 8861376.

Research output: Contribution to journalArticle

Discrepancy-Based Theory and Algorithms for Forecasting Non-Stationary Time Series

Kuznetsov, V. & Mohri, M., Apr 1 2020, In : Annals of Mathematics and Artificial Intelligence. 88, 4, p. 367-399 33 p.

Research output: Contribution to journalArticle

Evaluation of Combined Artificial Intelligence and Radiologist Assessment to Interpret Screening Mammograms

and the DM DREAM Consortium, Mar 2 2020, In : JAMA network open. 3, 3, p. e200265

Research output: Contribution to journalArticle

Open Access

Fast radix-32 approximate dfts for 1024-beam digital rf beamforming

Madanayake, A., Cintra, R. J., Akram, N., Ariyarathna, V., Mandal, S., Coutinho, V. A., Bayer, F. M., Coelho, D. & Rappaport, T. S., 2020, In : IEEE Access. 8, p. 96613-96627 15 p., 9093889.

Research output: Contribution to journalArticle

Open Access

First-order perturbation theory for eigenvalues and eigenvectors

Greenbaum, A., Li, R. C. & Overton, M. L., 2020, In : SIAM Review. 62, 2, p. 463-482 20 p.

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

Global Identifiability of Differential Models

Hong, H., Ovchinnikov, A., Pogudin, G. & Yap, C., Sep 1 2020, In : Communications on Pure and Applied Mathematics. 73, 9, p. 1831-1879 49 p.

Research output: Contribution to journalArticle

Inference of bacterial small RNA regulatory networks and integration with transcription factor-driven regulatory networks

Arrieta-Ortiz, M. L., Arrieta-Ortiz, M. L., Hafemeister, C., Shuster, B., Baliga, N. S., Bonneau, R., Bonneau, R., Bonneau, R. & Eichenberger, P., Jun 2020, In : mSystems. 5, 3, e00057-20.

Research output: Contribution to journalArticle

Open Access

Interleukin-17 Inhibition in Spondyloarthritis Is Associated With Subclinical Gut Microbiome Perturbations and a Distinctive Interleukin-25–Driven Intestinal Inflammation

Manasson, J., Wallach, D. S., Guggino, G., Stapylton, M., Badri, M. H., Solomon, G., Reddy, S. M., Coras, R., Aksenov, A. A., Jones, D. R., Girija, P. V., Neimann, A. L., Heguy, A., Segal, L. N., Dorrestein, P. C., Bonneau, R., Guma, M., Ciccia, F., Ubeda, C., Clemente, J. C. & 1 others, Scher, J. U., Apr 1 2020, In : Arthritis and Rheumatology. 72, 4, p. 645-657 13 p.

Research output: Contribution to journalArticle

Kymatio: Scattering transforms in python

Andreux, M., Angles, T., Exarchakis, G., Leonarduzzi, R., Rochette, G., Thiry, L., Zarka, J., Mallat, S., Andén, J., Belilovsky, E., Bruna, J., Lostanlen, V., Chaudhary, M., Hirn, M. J., Oyallon, E., Zhang, S., Cella, C. & Eickenberg, M., Jan 1 2020, In : Journal of Machine Learning Research. 21

Research output: Contribution to journalArticle

Network architecture in the age of programmability

Sivaraman, A., Mason, T., Panda, A., Netravali, R. & Kondaveeti, S. A., Mar 23 2020, In : Computer Communication Review. 50, 1, p. 38-44 7 p.

Research output: Contribution to journalArticle

Open Access

OutPredict: multiple datasets can improve prediction of expression and inference of causality

Cirrone, J., Brooks, M. D., Bonneau, R., Coruzzi, G. M. & Shasha, D. E., Dec 1 2020, In : Scientific reports. 10, 1, 6804.

Research output: Contribution to journalArticle

Open Access
Open Access

Sepsis in the era of data-driven medicine: personalizing risks, diagnoses, treatments and prognoses

Liu, A. C., Patel, K., Vunikili, R. D., Johnson, K. W., Abdu, F., Belman, S. K., Glicksberg, B. S., Tandale, P., Fontanez, R., Mathew, O. K., Kasarskis, A., Mukherjee, P., Subramanian, L., Dudley, J. T. & Shameer, K., Jul 15 2020, In : Briefings in Bioinformatics. 21, 4, p. 1182-1195 14 p.

Research output: Contribution to journalArticle

Towards a Low-SWaP 1024-Beam Digital Array: A 32-Beam Subsystem at 5.8 GHz

Madanayake, A., Mandal, S., Rappaport, T. S., Ariyarathna, V., Madishetty, S., Pulipati, S., Cintra, R. J., Coelho, D., Oliviera, R., Bayer, F. M. & Belostotski, L., Feb 2020, In : IEEE Transactions on Antennas and Propagation. 68, 2, p. 900-912 13 p., 8826444.

Research output: Contribution to journalArticle

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

A hierarchical loss and its problems when classifying non-hierarchically

Wu, C., Tygert, M. & LeCun, Y., 2019, In : PloS one. 14, 12, e0226222.

Research output: Contribution to journalArticle

Open Access

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

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

Research output: Contribution to journalArticle

A recurrent COL6A1 pseudoexon insertion causes muscular dystrophy and is effectively targeted by splice-correction therapies

COL6A1 Intron 11 Study Group, Mar 21 2019, In : JCI Insight. 4, 6, e124403.

Research output: Contribution to journalArticle

Open Access

Bounded distortion tetrahedral metric interpolation

Aharon, I., Chen, R., Zorin, D. & Weber, O., Nov 2019, In : ACM Transactions on Graphics. 38, 6, 182.

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. B., 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

Comparing dynamics: deep neural networks versus glassy systems

Baity-Jesi, M., Sagun, L., Geiger, M., Spigler, S., Ben Arous, G., Cammarota, C., Lecun, Y., Wyart, M. & Biroli, G., Dec 20 2019, In : Journal of Statistical Mechanics: Theory and Experiment. 2019, 12, 124013.

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

Critical Velocity Ionization in Substellar Atmospheres

Wilson, A. D., Dobbs-Dixon, I., Diver, D. A. & Stark, C. R., Dec 1 2019, In : Astrophysical Journal. 887, 2, p. 138

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 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. A., Oct 1 2019, In : Political Science Research and Methods. 7, 4, p. 815-834 20 p.

Research output: Contribution to journalArticle

Open Access

Entropy-SGD: Biasing gradient descent into wide valleys

Chaudhari, P., Choromanska, A., Soatto, S., Lecun, Y., Baldassi, C., Borgs, C., Chayes, J., Sagun, L. & Zecchina, R., Dec 20 2019, In : Journal of Statistical Mechanics: Theory and Experiment. 2019, 12, 124018.

Research output: Contribution to journalArticle

Existential monadic second order logic on random rooted trees

Holroyd, A. E., Levy, A., Podder, M. & Spencer, J., Jan 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. S., 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., 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. A. & Bonneau, R., Apr 1 2019, In : SAGE Open. 9, 2

Research output: Contribution to journalArticle

Open Access