I am an Assistant Professor at the Department of Electrical and Computer Engineering at McGill University. Before joining McGill, I was a Postdoctoral Research Associate at the NIH KnowEnG Center of Excellence in Big Data Computing associated with the Department of Computer Science and the Institute for Genomic Biology (IGB) at the University of Illinois (UIUC). I received my PhD from UIUC in 2015, my MSc from the University of Alberta in 2009 and my BSc from Sharif University of Technology in 2007, all in Electrical and Computer Engineering.
Current Research Interests
My current research interests involve developing novel computational methods and algorithms based on machine learning, graph mining, and statistical methods to address various biological problems.
Currently, there are openings for motivated graduate students (PhD and Masters) in my lab. If you are interested in my research and have a strong programming background and knowledge in machine learning or bioinformatics, send me an email and include the following in the body of your email: the degree you are applying to (PhD, Masters), your undergrad and grad university and GPA, whether you are a domestic or international student, and whether you have applied to the ECE department. In addition, attach your CV (containing your GPA, publications, relevant courses, etc.), transcripts and up to 3 publications.
I also have some projects for undergraduate honour's thesis. If you are an undergraduate student at McGill and would like to have your honours thesis with me, send me an email and include your CV/resume (including your CGPA).
Women, Aboriginal persons, persons with disabilities, ethnic minorities, persons of minority sexual orientation or gender identity, and visible minorities are encouraged to apply.
Reconstruction of phenotype-relevant transcriptional regulatory networks.
Gene prioritization by combining transcriptomic data with prior network information.
A method based on community detection to identify cancer driver mutation modules.
A method for gene regulatory network reconstruction using times-series transcriptomic data.
▶ 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.
▶ 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.
▶ A. Emad, and S. Sinha, “Inference of phenotype-relevant transcriptional regulatory networks elucidates cancer type-specific regulatory mechanisms in a pan-cancer study,” Under revision, preprint: bioRxiv 389734, 2018.
▶ A. Emad, T. Ray, T. W. Jensen, M. Parat, R. Natrajan, S. Sinha, and P. S. Ray, “An epithelial-mesenchymal-amoeboid transition gene signature reveals subtypes of breast cancer progression and metastasis,” Submitted, preprint: bioRxiv 219410; https://doi.org/10.1101/219410.
Peer-reviewed journal papers
▶ 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.
▶ 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,” Scientific reports, 8, 2018. *Contributed equally
▶ 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
▶ 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.
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