SIFTER Search: A web server for accurate phylogeny-based protein function prediction
S.M.E. Sahraeian, K.R. Luo, and S.E. Brenner, Nucleic Acids Research, Web Server Issue 2015, to appear.
[SIFTER Web Server]

Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach.
Pablo Meyer, et al., Genome Research, 23:1928-1937, 2013
[Genome Research]

Digital genotyping of sorghum--a diverse plant species with a large repeat-rich genome.
D.T. Morishige, P.E. Klein, J.L. Hilley, S.M.E. Sahraeian, A. Sharma, and J.E. Mullet, BMC Genomics, 14:448, Jul. 2013.
[BMC Genomics]

SMETANA: accurate and scalable algorithm for probabilistic alignment of large-scale biological networks.
S.M.E. Sahraeian and B.J. Yoon, PLoS ONE, 8(7): e67995, Jul. 2013.
[PloS ONE] [Supplementary data]

Genetic Structure and Linkage Disequilibrium in a Diverse, Representative Collection of the C4 Model Plant, Sorghum bicolor.
Y.H. Wang, H.D. Upadhyaya, A.M. Burrell, S.M.E. Sahraeian, R.R. Klein, and P.E. Klein, G3: Genes Genomes Genetics, 3(5): 783-793, May 2013.
[G3]

A Network Synthesis Model for Generating Protein Interaction Network Families.
S.M.E. Sahraeian and B.J. Yoon, PLoS ONE, 7(8): e41474, 2012.
[PloS ONE] [Supplementary data]

RESQUE: Network reduction using semi-Markov random walk scores for efficient querying of biological networks.
S.M.E. Sahraeian and B.J. Yoon, Bioinformatics, 28(16): 2129-2136, 2012. (Presented in RECOMB 2012)
[Bioinformatics] [Supplementary data] [Recomb extended abstract]

Comparative analysis of biological networks using Markov chains and hidden Markov models.
B.J. Yoon, X. Qian, and S.M.E. Sahraeian, IEEE Signal Processing Magazine, 29(1): 22-34, Jan. 2012.
[IEEExplore]

Enhancing the accuracy of HMM-based conserved pathway prediction using global correspondence scores.
X. Qian, S.M.E. Sahraeian, and B.J. Yoon, BMC Bioinformatics, 12(Suppl 10):S6, 2011.
[BMC Bioinformatics] [Supplementary data]

PicXAA-Web: a web-based platform for non-progressive maximum expected accuracy alignment of multiple biological sequences
S.M.E. Sahraeian and B.J. Yoon, Nucleic Acids Research, Web Server Issue, doi:10.1093/nar/gkr244, Apr. 2011.
[PicXAA Web Server] [Nucleic Acid Research]

A Novel Low-Complexity HMM Similarity Measure.
S.M.E. Sahraeian and B.J. Yoon, IEEE Signal Processing Letters, 18(2): 87-90, Feb. 2011.
[IEEExplore]

PicXAA-R: Efficient structural alignment of multiple RNA sequences using a greedy approach.
S.M.E. Sahraeian and B.J. Yoon, BMC Bioinformatics, 12(Suppl 1):S38, 2011.
(Best Paper Award APBC 2011)
[BMC Bioinformatics]

PicXAA: Greedy probabilistic construction of maximum expected accuracy alignment of multiple sequences.
S.M.E. Sahraeian and B.J. Yoon, Nucleic Acids Research, 2010; 38(15): 4917-4928, 2010.
[Nucleic Acid Research]

Information hiding with maximum likelihood detector for correlated signals.
S.M.E. Sahraeian, M.A. Akhaee, B. Sankur, and F. Marvasti, Digital Signal Processing, 36: 144-155, 2015.
[ScienceDirect]

Scaling-based watermarking with universally optimum decoder.
M.A. Akhaee and S.M.E. Sahraeian, Multimedia Tools and Applications, 1-24, 2014.
[Springer]

Blind Image Watermarking Using a Sample Projection Approach.
M.A. Akhaee, S.M.E. Sahraeian, and C. Jin, IEEE Transactions on Information Forensics and Security, 6(3): 883-893, Sep. 2011.
[IEEExplore]

Contourlet Based Image Watermarking Using Optimum Detector in a Noisy Environment.
M.A. Akhaee, S.M.E. Sahraeian, and F. Marvasti, IEEE Trans. on Image Processing, 15(4): 967-980, Apr. 2010.
[IEEExplore]

Robust Scaling-Based Image Watermarking Using Maximum-Likelihood Decoder With Optimum Strength Factor.
M.A. Akhaee, S.M.E. Sahraeian, F. Marvasti, and B. Sankur, IEEE Trans. on Multimedia, 11(5):. 822-833, Aug. 2009.
[IEEExplore]

PicXAA: A Probabilistic Scheme for Finding the Maximum Expected Accuracy Alignment of Multiple Biological Sequences.
S.M.E. Sahraeian and B.J. Yoon, Multiple Sequence Alignment Methods, Methods in Molecular Biology, Edited by D. Russell, Springer, 1079: 203-210, 2014.
[Springer]

Probabilistic Consistency Transformation for Multiple alignment of Biological Networks
S.M.E. Sahraeian and B.J. Yoon, Proc. 9th IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), pp. 52-53, San Antonio, TX, Dec. 2011.
[IEEExplore]

Fast Network Querying Algorithm for Searching Large-scale Biological Networks
S.M.E. Sahraeian and B.J. Yoon, Proc. 36th IEEE Inter. Conf. on Acoustics, Speech, and Signal Processing (ICASSP), pp. 6008-6011, Prague, Czech Republic, May 2011.
[IEEExplore]

Distribution Independent Blind Watermarking.
S.M.E. Sahraeian, M.A. Akhaee, and F. Marvasti, Proc. 16th IEEE International Conference on Image Processing (ICIP), pp. 125-128, Cairo, Egypt, Nov. 2009.
[IEEExplore]

Information Hiding with Optimal Detector for Highly Correlated Signals.
S.M.E. Sahraeian, M.A. Akhaee, and F. Marvasti, Proc. 9th IEEE International Conference on Communications (ICC), Dresden, Germany, Jun. 2009.
[IEEExplore]

Blind Image Watermarking Based on Sample Rotation with Optimal Detector.
S.M.E. Sahraeian, M.A. Akhaee, and F. Marvasti, Proc. 17th European Signal Processing conference (EUSIPCO), pp. 278-282, Glasgow, Scotland, Aug. 2009.
[Eurasip]

Contourlet Based Image Watermarkin Using Optimum Detector in the Noisy Environment.
S.M.E. Sahraeian, M.A. Akhaee, S. A. Hejazi, and F. Marvasti, Proc. 15th IEEE International Conference on Image Processing (ICIP), pp. 429-432, San Diego, CA, Oct. 2008.
[IEEExplore]

Robust Multiplicative Watermarking Technique with Maximum Likelihood Detector.
S.M.E. Sahraeian, M.A. Akhaee, B. Sankur, and F. Marvasti, Proc. 16th European Signal Processing conference (EUSIPCO), Lausanne, Switzerland, Aug. 2008.
[Eurasip]

A new approach to assembly level programming.
S.M.E. Sahraeian and B. Vosoughi Vahdat, Proc. IEEE International Conference on Computer as a tool (EUROCON) pp. 439-445, Warsaw, Poland, Sep. 2007.
[IEEExplore]

Wavelet-based 2-D ECG Data Compression method using SPIHT and VQ coding.
S.M.E. Sahraeian and E. Fatemizadeh, Proc. IEEE International Conference on Computer as a tool (EUROCON), pp. 133-137, Warsaw, Poland, Sep. 2007.
[IEEExplore]

An Improved Image Denoising Technique Using Cycle Spinning.
S.M.E. Sahraeian and F. Marvasti, Proc. 14th IEEE International Conf. on Telecommunications (ICT), Malaysia, May 2007.
[IEEExplore]

Wavelet Image Denoising Based on Improved Thresholding Neural Network and Cycle Spinning.
S.M.E. Sahraeian, F. Marvasti, and N. Sadati, Proc. 32nd IEEE Inter. Conf. on Acoustics, Speech, and Signal Processing (ICASSP), vol. 1, pp. 585-588, Honolulu, HI, April 2007.
[IEEExplore]

Measuring the Geometrical Parameters of Steel Billets during Molding Process Using Image Processing.
N. Mohammadiha, S.M.E. Sahraeian, B. Vosoughi Vahdat, A. Azizi, and A. Shah Ahmadi, Proc. 6th IEEE Symposium on Signal Processing and Information Technology (ISSPIT), pp. 59-63, Vancouver, Canada, Aug. 2006.
[IEEExplore]

Predicting Protein Function for the CAFA 2014 Experiment using Phylogenetic Function Prediction Embedded in SIFTER.
S.M.E. Sahraeian, A.L. Lin, and S.E. Brenner, 22th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Automated Protein Function Prediction(AFP) SIG, Boston, MA, July 2014.
(Invited Talk as a top-performing group in CAFA 2014)
(Best Poster Award ISMB AFP-SIG 2014)

Automated function prediction using SIFTER: an application and validation on Desulfovibrio vulgaris Hildenborough genome.
S.M.E. Sahraeian and S.E. Brenner, 22th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2014), Boston, MA, July 2014.

Automated function prediction using SIFTER: an application and validation on Desulfovibrio vulgaris Hildenborough genome.
S.M.E. Sahraeian and M.L. Souza, B.E. Engelhardt, M.I. Jordan, and S.E. Brenner, Ecosystems and Networks Integrated with Genes and Molecular Assemblies retreat, Berkeley, CA, Aug 2013.

Efficient Maximum Expected Accuracy Alignment of Multiple Biological Networks.
S.M.E. Sahraeian and B.J. Yoon, 20th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2012), Long Beach, CA, July 2012.

Probabilistic Approaches in Comparative Studies of Biological Interaction Networks.
S.M.E. Sahraeian, Invited Talk, Shiraz University, Dept. Electrical Eng., Shiraz, Iran, May 2012.

Enhancing the accuracy of HMM-based conserved pathway prediction using global correspondence scores.
X. Qian, S.M.E. Sahraeian, and B.J. Yoon, 8th Annual Conference of the MidSouth Computational Biology and Bioinformatics Society (MCBIOS 2011), College Station, TX, April 2011.

Accurate and Scalable Network Querying Algorithm Using Semi-Markov Random Walk And Network Reduction Approach.
S.M.E. Sahraeian and B.J. Yoon, 8th Annual Conference of the MidSouth Computational Biology and Bioinformatics Society (MCBIOS 2011), College Station, TX, April 2011.

Efficient querying of protein interaction networks using semi-Markov random walk and network reduction approach.
S.M.E. Sahraeian and B.J. Yoon, 6th Annual RECOMB Satellite on Systems Biology, New York, NY, Nov. 2010.

PicXAA-R: Probabilistic Structural Alignment of Multiple RNA Sequences Using a Greedy Approach.
S.M.E. Sahraeian and B.J. Yoon, 8th IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), Cold Spring Harbor, NY, Nov. 2010.