Publications

You can find our latest publications on these websites:

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Patents

• A. Emad, C. J. Nuzman, and E. Soljanin, “Methods and systems for determining crosstalk for a line in a vectored system,” United States patent granted, US9948769B2, 2018.

Book Chapter

• D. M. Malioutov, K. R. Varshney, A. Emad, and S. Dash, “Learning Interpretable Classification Rules with Boolean Compressed Sensing,” in Transparent Data Mining for Big and Small Data, Studies in Big Data, 11, Springer, 2017, pp. 95-121.

Preprints

• C. Su, S. Rousseau, and A. Emad “Identification of COVID-19-relevant transcriptional regulatory networks and associated kinases as potential therapeutic targets,” Submitted, preprint: bioRxiv 2020.12.23.424177.

• J. Ding, D. E. Hostallero, et al., “A network-informed analysis of SARS-CoV-2 and hemophagocytic lymphohistiocytosis genes’ interactions points to Neutrophil Extracellular Traps as mediators of thrombosis in COVID-19,” Submitted, preprint: medRxiv 2020.07.01.20144121.

Peer-Reviewed Journal Papers

• J. Szymborski, and A. Emad, “RAPPPID: towards generalizable protein interaction prediction with AWD-LSTM twin networks.” Bioinformatics 38.16 (2022): 3958-3967.

• A. Emad, and S. Sinha, “Inference of phenotype-relevant transcriptional regulatory networks elucidates cancer type-specific regulatory mechanisms in a pan-cancer study,” In Press, NPJ Systems Biology and Applications, 2021.

• C. A. Blatti*, A. Emad*, et al., “Knowledge-guided analysis of ‘omics’ data using the KnowEnG cloud platform,” PLoS Biology, 18 (1), e3000583, 2020. *Contributed equally

• E. W. Huang, A. Bhope, J. Lim, S. Sinha, and A. Emad, “Tissue-guided LASSO for prediction of clinical drug response using preclinical samples,” PLoS Computational Biology, 16(1): e1007607, 2020.

• A. Emad, T. Ray, et al., “Superior breast cancer metastasis risk stratification using an epithelial-mesenchymal-amoeboid transition gene signature,” Breast Cancer Research, 22(1), pp. 1-13, 2020.

• C. Qian, A. Emad, and N. D. Sidiropoulos, “A recursive framework for predicting the time-course of drug sensitivity,” Scientific Reports, 10 (1), 1-12, 2020.

• K. O’Dowd, M. Emam, et al., “Distinct miRNA Profile of Cellular and Extracellular Vesicles Released from Chicken Tracheal Cells Following Avian Influenza Virus Infection,” Vaccines 8 (3), 438, 2020.

• S. Tabe Bordbar*, A. Emad*, S. D. Zhao, S. Sinha, “A closer look at cross-validation approaches for assessing the accuracy of gene regulatory networks and models,” Nature Scientific Reports, 8, 2018. *Contributed equally

• A. Emad, J. Cairns, K. R. Kalari, L. Wang, and S. Sinha, “Knowledge-guided gene prioritization reveals new insights into the mechanisms of chemoresistance,” Genome Biology, 18(1), 153, 2017.

• J. P. Hou*, A. Emad*, G. J. Puleo, J. Ma, and O. Milenkovic, “A new correlation clustering method for cancer mutation analysis,” Bioinformatics, 32 (24), pp. 3717-3728, 2016. *Contributed equally

• A. Emad and O. Milenkovic, “Code Construction and Decoding Algorithms for Semi-Quantitative Group Testing with Nonuniform Thresholds,” IEEE Trans. Inf. Theory, vol. 62, pp. 1674-1687, 2016.

• A. Emad and O. Milenkovic, “Poisson Group Testing: A Probabilistic Model for Boolean Compressed Sensing,” IEEE Trans. Signal Proc., vol. 63, pp. 4396-4410, 2015.

• A. Emad and O. Milenkovic, “Semiquantitative Group Testing,” IEEE Trans. Inf. Theory, vol. 60, pp. 4614-4636, 2014.

• A. Emad and O. Milenkovic, “CaSPIAN: A Causal Compressive Sensing Algorithm for Discovering Directed Interactions in Gene Networks,” PLOS ONE, vol. 9, no. 3, e90781, March 2014. doi:10.1371/journal.pone.0090781.

• A. Emad and N. C. Beaulieu, “On the Performance of an Automatic Frequency Control Loop in Dissimilar Fading Channels in the Presence of Interference,” IEEE Trans. Commun., vol. 59, pp. 3234-3239, Dec. 2011.

• A. Emad and N. C. Beaulieu, “Lower Bounds to the Performance of Bit Synchronization for Bandwidth Efficient Pulse-Shaping,” IEEE Trans. Commun., vol. 58, pp. 2789-2794, Oct. 2010.

• A. Emad and N. C. Beaulieu, “Performance of an AFC Loop in the Presence of a Single Interferer in a Fading Channel,” IEEE Trans. Commun., vol. 58, pp. 3386-3391, Dec. 2010.

Peer-Reviewed Conference Papers

• C. Qian, N. D. Sidiropoulos, M. Amiridi, and A. Emad, “From Gene Expression to Drug Response: A Collaborative Filtering Approach,” Proc. IEEE Int. Conf. Acoustics, Speech, and Signal Processing (ICASSP’19), 2019, pp. 7465-7469.

• A. Emad, K. R. Varshney, and D. Malioutov, “Learning Interpretable Clinical Prediction Rules using Threshold Group Testing,’ NIPS Workshop on Machine Learning in Healthcare, 2015.

• A. Emad, K. R. Varshney, and D. Malioutov, “A Semiquantitative Group Testing Approach for Learning Interpretable Clinical Prediction Rules,” Signal Processing with Adaptive Sparse Structured Representations (SPARS’15), 2015.

• A. Emad and O. Milenkovic, “Group Testing for Non-Uniformly Quantized Adder Channels,” Proc. IEEE Int. Symp. Inf. Theory (ISIT’14), July 2014, pp. 2351-2355.

• A. Emad and O. Milenkovic, “Poisson Group Testing: A Probabilistic Model for Nonadaptive Streaming Boolean Compressed Sensing,” Proc. IEEE Int. Conf. Acoustics, Speech, and Signal Processing (ICASSP’14), 2014, pp. 3335-3339.

• M. Kim, J. G. Ligo, A. Emad, F. Farnoud (Hassanzadeh), O. Milenkovic, V. V. Veeravalli, “MetaPar: Metagenomic Sequence Assembly via Iterative Reclassification,” Proc. IEEE GlobalSIP, 2013, pp. 43-46.

• J. G. Ligo, M. Kim, A. Emad, O. Milenkovic, V. V. Veeravalli, “MCUIUC – A New Framework for Metagenomic Read Compression,” Proc. IEEE Inf. Theory Workshop (ITW’13), 2013.

• A. Emad and O. Milenkovic, “Compression of Noisy Signals with Information Bottlenecks,” Proc. IEEE Inf. Theory Workshop (ITW’13), 2013.

• P. Johnstone, A. Emad, O. Milenkovic, and P. Moulin, “RFIT: A New Algorithm for Matrix Rank Minimization,” Signal Processing with Adaptive Sparse Structured Representations (SPARS’13), 2013.

• M. Deng, A. Emad and O. Milenkovic, “Causal Compressive Sensing for Gene Network Inference,” Proc. IEEE Statistical Signal Processing Workshop (SSP’12), Aug. 2012, pp. 696 – 699.

• A. Emad and O. Milenkovic, “Semi-quantitative Group Testing,” Proc. IEEE Int. Symp. Inf. Theory (ISIT’12), July 2012, pp. 1847 – 1851.

• A. Emad and O. Milenkovic, “Information Theoretic Bounds for Tensor Rank Minimization over Finite Fields,” Proc. IEEE Global Commun. Conf. (Globecom’11), Dec. 2011, pp. 1-5.

• A. Emad and O. Milenkovic, “Symmetric Group Testing and Superimposed Codes,” Proc. IEEE Inf. Theory Workshop (ITW’11), Oct. 2011, pp. 20 – 24, invited.

• A. Emad, W. Dai, and O. Milenkovic, “Protein-Protein Interaction Prediction using Non-Linear Matrix Completion Methods,” 15th Int. Conf. Research Computational Molecular Biology (RECOMB’11), March 2011.

• A. Emad and N. C. Beaulieu, “On the Performance of Bit-Synchronizers in an ISI Channel and a Related Lower Bound,” Proc. IEEE Global Commun. Conf. (Globecom’09), Dec. 2009, pp. 1-6.

• A. Emad and N. C. Beaulieu, “Mean Time to Loss of Lock and Average Switching Rate of an Automatic Frequency Control Loop with an Interferer and Noise in a Fading Channel,” Proc. IEEE Int. Conf. Commun. (ICC’09), June 2009, pp. 1-6.

• A. Emad and N. C. Beaulieu, “Effect of a Cochannel Interferer on an Automatic Frequency Control Loop in Fading Channels,” Proc. IEEE Wireless Commun. Netw. Conf. (WCNC’09), April 2009, pp. 1-6.

• A. Emad and N. C. Beaulieu, “Performance Measures of Automatic Frequency Control Corrupted by Interference and Fading in Dual Dissimilar Channels,” Proc. IEEE 69th Veh. Technol. Conf. (VTC’09), April 2009, pp. 1-5.

• A. Emad and M. B. Shamsollahi, “ECG Denoising Using M-Band Wavelet Transform,” 12th Int. Conf. Biomed. Engin. (ICBME’05), Dec. 2005.