2019

[1]	Abdolhosseini, F., Azarkhalili, B., Maazallahi, A., Kamal, A., Motahari, S.A., Sharifi-Zarchi, A. & Chitsaz, H. Cell Identity Codes: Understanding Cell Identity from Gene Expression Profiles using Deep Neural Networks. Nature Scientific Reports (Accepted), 2019.
[2]	Kashani, B., Bidgoli, M.H., Motahari, S.A., Sedaghat, N. & Modarressi, M.H. You are What You Eat: Sequence Analysis Reveals How Plant MicroRNAs May Regulate the Human Genome. Computers in Biology and Medicine (Accepted), 2019.
[3]	Yousefi, M.H.N., Goudarzi, M. & Motahari, S.A. Improved Meta-aligner and Minimap2 On Spark. BMC Bioinformatics (Accepted), 2019.
[4]	Sanjaroon, V., Farhadi, A., Khalaj, B.H. & Motahari, A.S. Estimation and stability over AWGN channel in the presence of fading, noisy feedback channel and different sample rates. Systems \& Control Letters, 123:75-84, North-Holland, 2019.
[5]	Tavassolipour, M., Motahari, S.A. & Shalmani, M.T.M. Learning of Tree-Structured Gaussian Graphical Models on Distributed Data Under Communication Constraints. IEEE Transactions on Signal Processing, 67(1):17-28, IEEE, 2019.

2018

[1]	Roushdy, A., Motahari, A.S., Nafie, M. & Gündüz, D. Cache-aided fog radio access networks with partial connectivity. In Wireless Communications and Networking Conference (WCNC), 2018 IEEE, pages 1-6, 2018.
[2]	Sanjaroon, V., Motahari, a., Farhadi, A. & Khalaj, B. Delay-limited Joint Source Channel Coding over Parallel AWGN Channels with Feedback. Submitted to IEEE Trans. on Communications, 2018.
[3]	Hossein, M., Mahboubi, P. & Motahari, A. Achieving the Total DoF of MIMO X-Channels Through a Joint Processing Technique. Submitted to IEEE Trans. on Communications, 2018.
[4]	Salehi, M.J., Motahari, S.A., Khalaj, B.H. & Shariatpanahi, S.P. Content Delivery Networks: Interactions between storage/delay/cost. In 2018 Iran Workshop on Communication and Information Theory (IWCIT), 2018.
[5]	Salehi, M.J., Motahari, S.A. & Khalaj, B.H. On the Optimality of 0–1 Data Placement in Cache Networks. IEEE Transactions on Communications, 66(3):1053-1063, IEEE, 2018.
[6]	Sanjaroon, V., Farhadi, A., Motahari, a. & Khalaj, B. Stability of Nonlinear Dynamic Systems over Limited Capacity Communication Channels. Submitted to IEEE Trans. on Automatic Control, 2018.
[7]	Sanjaroon, V., Farhadi, A., Motahari, A.S. & Khalaj, B.H. Estimation of Nonlinear Dynamic Systems over Communication Channels. IEEE Transactions on Automatic Control, 2018.
[8]	Tahmasebi, B., Motahari, A.S. & Maddah–Ali, M.A. On the identifiability of parameters in the population stratification problem: A worst-case analysis. In 2018 IEEE International Symposium on Information Theory (ISIT), pages 1051-1055, 2018.
[9]	Tavassolipour, M., Motahari, S.A. & Shalmani, M.T.M. Learning of Gaussian Processes in Distributed and Communication Limited Systems. Submitted to IEEE Trans. on Pattern Analysis and Machine Intelligence (Revised), 2018.
[10]	Tahmasebi, B., Maddah-Ali, M.A. & Motahari, S.A. Information theoretic limits of learning of the causal features in a linear model. In 2018 Iran Workshop on Communication and Information Theory (IWCIT), 2018.
[11]	Nashtaali, D., Motahari, S.A. & Khalaj, B.H. Paired-end sequencing method. , 2018., (US Patent App. 15/667,269).
[12]	Tahmasebi, B., Maddah-Ali, M.A. & Motahari, A.S. Genome-wide association studies: Information theoretic limits of reliable learning. In 2018 IEEE International Symposium on Information Theory (ISIT), pages 2231-2235, 2018.
[13]	Tahmasebi, B., Motahari, S.A. & Maddah-Ali, M.A. On the Identifiability of Finite Mixtures of Finite Product Measures. arXiv preprint arXiv:1807.05444, 2018.

2017

[1]	Najafi, A., Janghorbani, S., Motahari, S. & Fatemizadeh, E. Statistical Association Mapping of Population-Structured Genetic Data. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2017.
[2]	Roig, J.S.P., Motahari, S.A., Tosato, F. & Gündüz, D. Fundamental limits of latency in a cache-aided 4\times 4 interference channel. In Information Theory Workshop (ITW), 2017 IEEE, pages 16-20, 2017.
[3]	Nashtaali, D., Motahari, S.A., Mehrbod, M., Khalaj, B.H. & Taghivand, M. Dna sequencing and processing. , 2017., (US Patent App. 15/442,864).
[4]	Nashta-ali, D., Aliyari, A., Moghadam, A.A., Edrisi, M.A., Motahari, S.A. & Khalaj, B.H. Meta-aligner: long-read alignment based on genome statistics. BMC bioinformatics, 18(1):126, BioMed Central, 2017.
[5]	Najafi, A., Motahari, A. & Rabiee, H.R. Reliable learning of bernoulli mixture models. arXiv preprint arXiv:1710.02101, 2017.
[6]	Seraji, M.R. & Motahari, S.A. SureMap: Versatile, Error Tolerant, and High Sensitive Read Mapper. bioRxiv, pages 173740, Cold Spring Harbor Laboratory, 2017.

2016

[1]	Ghareghani, M., Motahari, S.A., Khazaei, S. & Tavassolipour, M. GW-CALL: Accurate Genome-Wide Variant Caller. bioRxiv, pages 079905, Cold Spring Harbor Laboratory, 2016.
[2]	Akhoundi, F., Ghobeh, M., Ghiasvand, E., Akbari-Roshan, K. & Motahari, S.A. Performance characterization of a low-cost dual-channel camera-based microarray scanner. In Electrical Engineering (ICEE), 2016 24th Iranian Conference on, pages 1534-1538, 2016.
[3]	Najafi, A., Nashta-ali, D., Motahari, S.A., Khani, M., Khalaj, B.H. & Rabiee, H.R. Fundamental Limits of Pooled-DNA Sequencing. arXiv preprint arXiv:1604.04735, 2016.
[4]	Shariatpanahi, S.P., Motahari, S.A. & Khalaj, B.H. Multi-server coded caching. IEEE Transactions on Information Theory, pages 7253-7271, 2016.
[5]	Nashta-ali, D., Motahari, S.A. & Khalaj, B.H. Breaking Lander-Waterman’s Coverage Bound. PloS one, pages 060384, Public Library of Science, 2016.

2015

[1]	Shariatpanahi, S.P., Motahari, S.A. & Khalaj, B.H. Content delivery via multi-server coded caching in linear networks. In Information Theory Workshop-Fall (ITW), 2015 IEEE, pages 267-271, 2015.

2014

[1]	Bagheri, H., Motahari, A.S. & Khandani, A.K. On the capacity of the half-duplex diamond channel under fixed scheduling. IEEE Transactions on Information Theory, 60(6):3544-3558, IEEE, 2014.
[2]	Motahari, A.S., Oveis-Gharan, S., Maddah-Ali, M.A. & Khandani, A.K. Real interference alignment: Exploiting the potential of single antenna systems. IEEE Transactions on Information Theory, 60(8):4799-4810, IEEE, 2014.

2013

[1]	Bagherikaram, G., Motahari, A.S. & Khandani, A.K. The Secrecy Capacity Region of the Gaussian MIMO Broadcast Channel. IEEE Transactions on Information Theory, 59(5):2673-2682, 2013.
[2]	Pourahmadi, V., Motahari, A.S. & Khandani, A.K. Multilayer codes for broadcasting over quasi-static fading MIMO networks. IEEE Transactions on Communications, 61(4):1573-1583, IEEE, 2013.
[3]	Motahari, A., Ramchandran, K., Tse, D. & Ma, N. Optimal DNA shotgun sequencing: Noisy reads are as good as noiseless reads. Information Theory Proceedings (ISIT), 2013 IEEE International Symposium on, 2013.
[4]	Pourahmadi, V., Motahari, A.S. & Khandani, A.K. Degrees of freedom of MIMO-MAC with random access. IEEE Transactions on Communications, 61(5):1956-1967, IEEE, 2013.
[5]	Mohajer, S., Motahari, A. & Tse, D. Reference-based DNA shotgun sequencing: Information theoretic limits. In Information Theory Proceedings (ISIT), 2013 IEEE International Symposium on, pages 1635-1639, 2013.
[6]	Motahari, A.S., Bresler, G. & David, N. Information theory of DNA shotgun sequencing. IEEE Transactions on Information Theory, 59(10):6273-6289, IEEE, 2013.

2012

[1]	Maddah-Ali, M.A., Motahari, S.A., Khandani, A., Baligh, M., Jia, M., Ma, J., Zhu, P. & Tong, W. X-MIMO systems with multi-transmitters and multi-receivers. , 2012., (US Patent 8,340,235).
[2]	Motahari, A., Bresler, G. & Tse, D. Information theory for DNA sequencing: Part I: A basic model. In Information Theory Proceedings (ISIT), 2012 IEEE International Symposium on, pages 2741-2745, 2012.

2011

[1]	Ghasemi, A., Motahari, A.S. & Khandani, A.K. Interference alignment for the MIMO interference channel with delayed local CSIT. arXiv preprint arXiv:1102.5673, 2011.
[2]	Motahari, A.S. & Khandani, A.K. To decode the interference or to consider it as noise. IEEE Transactions on Information Theory, 57(3):1274-1283, IEEE, 2011.
[3]	Ghasemi, A., Motahari, A.S. & Khandani, A.K. On the degrees of freedom of X channel with delayed CSIT. In Information Theory Proceedings (ISIT), 2011 IEEE International Symposium on, pages 767-770, 2011.
[4]	Pourahmadi, V., Motahari, A.S. & Khandani, A.K. Degrees of freedom of two-user MIMO networks with random medium access control mechanism. In Information Theory Proceedings (ISIT), 2011 IEEE International Symposium on, pages 1980-1984, 2011.

2010

[1]	Ahmadzadeh, S.A., Motahari, S.A. & Khandani, A.K. Signal space cooperative communication. IEEE transactions on wireless communications, 9(4):1266-1271, IEEE, 2010.
[2]	Bagherikaram, G., Motahari, A.S. & Khandani, A.K. On the secure degrees-of-freedom of the multiple-access-channel. arXiv preprint arXiv:1003.0729, 2010.
[3]	Bagheri, H., Motahari, A.S. & Khandani, A.K. The approximate capacity region of the Gaussian z-interference channel with conferencing encoders. arXiv preprint arXiv:1005.1635, 2010.
[4]	Ghasemi, A., Motahari, A.S. & Khandani, A.K. Interference alignment for the K user MIMO interference channel. In 2010 IEEE International Symposium on Information Theory, pages 360-364, 2010.
[5]	Bagheri, H., Motahari, A.S. & Khandani, A.K. On the capacity of the half-duplex diamond channel. In 2010 IEEE International Symposium on Information Theory, pages 649-653, 2010.
[6]	Bagherikaram, G., Motahari, A.S. & Khandani, A.K. On the secure dof of the single-antenna mac. In 2010 IEEE International Symposium on Information Theory, pages 2588-2592, 2010.
[7]	Bagheri, H., Motahari, A.S. & Khandani, A.K. Zero-forcing for the symmetric interference channel with conferencing encoders. In 2010 IEEE International Symposium on Information Theory, pages 370-374, 2010.
[8]	Mahboubi, S.H., Motahari, A.S. & Khandani, A.K. Layered interference alignment: achieving the total DOF of MIMO X-channels. In 2010 IEEE International Symposium on Information Theory, pages 355-359, 2010.
[9]	Nourani, B., Motahari, S.A. & Khandani, A.K. Relay-aided interference alignment for the quasi-static interference channel. In 2010 IEEE International Symposium on Information Theory, pages 405-409, 2010.

2009

[1]	Motahari, A.S. & Khandani, A.K. Capacity bounds for the Gaussian interference channel. IEEE Transactions on Information Theory, 55(2):620-643, IEEE, 2009.
[2]	Ahmadzadeh, S.A., Motahari, S.A. & Khandani, A.K. Constellation Design for Cooperative Communication. In Information Sciences and Systems, 2009. CISS 2009. 43rd Annual Conference on, pages 657-662, 2009.
[3]	Bagherikaram, G., Motahari, A.S. & Khandani, A.K. Secrecy capacity region of gaussian broadcast channel. In Information Sciences and Systems, 2009. CISS 2009. 43rd Annual Conference on, pages 152-157, 2009.
[4]	Bagheri, H., Motahari, A.S. & Khandani, A.K. Generalized degrees of freedom of the symmetric Gaussian interference channel with partial unidirectional transmitter cooperation. In Information Sciences and Systems, 2009. CISS 2009. 43rd Annual Conference on, pages 307-312, 2009.
[5]	Bagherikaram, G., Motahari, A.S. & Khandani, A.K. Secrecy rate region of the broadcast channel with an eavesdropper. arXiv preprint arXiv:0910.3658, 2009.
[6]	Motahari, A.S., Gharan, S.O. & Khandani, A.K. On the Degrees of Freedom of the 3-user Gaussian interference channel: The symmetric case. In 2009 IEEE International Symposium on Information Theory, pages 1914-1918, 2009.
[7]	Motahari, S.A. Interference Management in Non-cooperative Networks. University of Waterloo, 2009.
[8]	Bagherikaram, G., Motahari, A.S. & Khandani, A.K. The secrecy capacity region of the degraded vector Gaussian broadcast channel. In 2009 IEEE International Symposium on Information Theory, pages 2772-2776, 2009.
[9]	Pourahmadi, V., Motahari, A.S. & Khandani, A.K. Infinite-layer codes for single-user slowly fading MIMO channels. In 2009 IEEE International Symposium on Information Theory, pages 1525-1529, 2009.
[10]	Bagheri, H., Motahari, A.S. & Khandani, A.K. On the symmetric Gaussian interference channel with partial unidirectional cooperation. arXiv preprint arXiv:0909.2777, 2009.
[11]	Bagherikaram, G., Motahari, A.S. & Khandani, A.K. The secrecy capacity region of the Gaussian MIMO broadcast channel. arXiv preprint arXiv:0903.3261, 2009.
[12]	Nourani, B., Motahari, S.A. & Khandani, A.K. Relay-aided interference alignment for the quasi-static X channel. In 2009 IEEE International Symposium on Information Theory, pages 1764-1768, 2009.

2008

[1]	Maddah-Ali, M.A., Motahari, A.S. & Khandani, A.K. Communication over MIMO X channels: Interference alignment, decomposition, and performance analysis. Information Theory, IEEE Transactions on, 54(8):3457-3470, IEEE, 2008.
[2]	Bagherikaram, G., Motahari, A.S. & Khandani, A.K. Secure broadcasting: The secrecy rate region. In Communication, Control, and Computing, 2008 46th Annual Allerton Conference on, pages 834-841, 2008.

2007

[1]	Maddah-Ali, M.A., Motahari, A.S. & Khandani, A.K. Decomposition of the MIMO X Channels. In Information Theory, 2007. CWIT’07. 10th Canadian Workshop on, pages 110-113, 2007.
[2]	Motahari, A.S. & Khandani, A.K. M-user Gaussian interference channels: To decode the interference or to consider it as noise. In 2007 IEEE International Symposium on Information Theory, pages 2196-2200, 2007.

2006

[1]	Maddah-Ali, M.A., Motahari, A.S. & Khandani, A.K. Signaling over MIMO multi-base systems: Combination of multi-access and broadcast schemes. In 2006 IEEE International Symposium on Information Theory, pages 2104-2108, 2006.

2004

[1]	Motahari, A.S. & Nasiri-Kenari, M. Multiuser detections for optical CDMA networks based on expectation-maximization algorithm. IEEE transactions on communications, 52(4):652-660, IEEE, 2004.

2002

[1]	Motahary, A. & Nasiri-Kenari, M. EM-based multiuser detections for optical CDMA networks. In Spread Spectrum Techniques and Applications, 2002 IEEE Seventh International Symposium on, 3:731-735, 2002.