Recent Papers
Harnessing Qatar Biobank to understand type 2 diabetes and obesity in adult Qataris from the First Qatar Biobank Project
Ullah, E., Mall, R., Rawi, R., Moustaid, N.M., Butt, A.A. and Bensmail, H., 2018.
Journal of translational medicine, 16(1), p.99.
ISaaC: Identifying Structural Relations in Biological Data with Copula-Based Kernel Dependency Measures
Al Meer, H., Mall, R., Ullah, E., Megrez, N. and Bensmail, H., 2018, April.
In International Conference on Bioinformatics and Biomedical Engineering (pp. 71-82). Springer, Cham.
An unsupervised disease module identification technique in biological networks using novel quality metric based on connectivity, conductance and modularity
Mall, R., Ullah, E., Kunji, K., Ceccarelli, M. and Bensmail, H., 2018.
F1000Research, 7.
RGBM: regularized gradient boosting machines for identification of the transcriptional regulators of discrete glioma subtypes
Mall, R., Cerulo, L., Garofano, L., Frattini, V., Kunji, K., Bensmail, H., Sabedot, T.S., Noushmehr, H., Lasorella, A., Iavarone, A. and Ceccarelli, M., 2018.
Nucleic Acids Research.
Whole genome sequencing of Caribbean Hispanic families with late‐onset Alzheimer's disease
Vardarajan, B.N., Barral, S., Jaworski, J., .., Saad, M., .., Koboldt, D.C. and Waligorski, J., 2018.
Annals of clinical and translational neurology, 5(4), pp.406-417.
Quality Control and Integration of Genotypes from Two Calling Pipelines for Whole Genome Sequence Data in the Alzheimer's Disease Sequencing Project
Naj, A.C., Lin, H., .., Saad, M., .., Martin, E. and DeStefano, A.L., 2018.
bioRxiv, p.318857.
A metabolic function of FGFR3-TACC3 gene fusions in cancer
Frattini, V., Pagnotta, S.M., .., Mall, R., .., Ceccarelli, M., .., Lasorella, A. and Iavarone, A., 2018.
Nature.
DeepSol: A Deep Learning Framework for Sequence-Based Protein Solubility Prediction
Khurana, S., Rawi, R., Kunji, K., Chuang, G.Y., Bensmail, H. and Mall, R., 2018.
Bioinformatics.
Open community challenge reveals molecular network modules with key roles in diseases
Choobdar, S., Ahsen, M.E., DREAM Module Identification Challenge Consortium: Kunji, K., .., Mall, R., .. and Ullah, E., Bergmann, S. and Marbach, D., 2018.
bioRxiv, p.265553.
DeepCrystal: A Deep Learning Framework for Sequence-based Protein Crystallization Prediction
Elbasir, A., Moovarkumudalvan, B., Kunji, K., Kolatkar, P. R., Mall, R., Bensmail, H., 2018.
Bioinformatics.
PaRSnIP: sequence-based protein solubility prediction using gradient boosting machine
Rawi, R., Mall, R., Kunji, K., Shen, C.H., Kwong, P.D. and Chuang, G.Y., 2017.
Bioinformatics
Differential Community Detection in Paired Biological Networks
Mall, R., Ullah, E., Kunji, K., D'Angelo, F., Bensmail, H. and Ceccarelli, M., 2017, August.
Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (pp. 330-339). ACM.
Detection of statistically significant network changes in complex biological networks
Mall, R., Cerulo, L., Bensmail, H., Iavarone, A. and Ceccarelli, M., 2017.
BMC systems biology, 11(1), p.32.
Advanced Computation of Sparse Precision Matrices for Big Data
Baggag, A., Bensmail, H. and Srivastava, J., 2017, May.
Pacific-Asia Conference on Knowledge Discovery and Data Mining (pp. 27-38). Springer, Cham.
Integrative Statistical Inferences for Drug Sensitivity Biomarkers in Cancer
Ullah, E., Shama, S., Al Muftah, N., Thompson, I.R., Rawi, R., Mall, R. and Bensmail, H., 2017.
bioRxiv, p.194670.
GIGI-Quick: A Fast Approach to Impute Missing Genotypes in Genome-Wide Association Family Data.
Kunji, K., Ullah, E., Nato, A.Q., Wijsman, E.M. and Saad, M., 2017.
Bioinformatics, p.btx782.
An adaptive refinement for community detection methods for disease module identification in biological networks using novel metric based on connectivity, conductance and modularity
Mall, R.,Ullah, E.,Kunji, K., Bensmail, H. and M Ceccarelli
Bioinformatics and Biomedicine (BIBM)
Application of High-Dimensional Statistics and Network based Visualization techniques on Arab Diabetes and Obesity data
Mall, R., Ullah, E., Kunji, K., Bensmail, H. and Ceccarelli, M., 2017, November.
Bioinformatics and Biomedicine (BIBM), 2017 IEEE International Conference on (pp. 2282-2284). IEEE.
Identification of cancer drug sensitivity biomarkers
Ullah, E., Mall, R., Bensmail, H., Rawi, R., Shama, S., Al Muftah, N. and Thmpson, I.R., 2017, November.
Bioinformatics and Biomedicine (BIBM), 2017 IEEE International Conference on (pp. 2322-2324). IEEE.
Selection Finder (SelFi): A computational metabolic engineering tool to enable directed evolution of enzymes
Hassanpour, N., Ullah, E., Yousofshahi, M., Nair, N.U. and Hassoun, S., 2017.
Metabolic Engineering Communications, 4, pp.37-47.
Discovery and functional prioritization of Parkinson’s disease candidate genes from large-scale whole exome sequencing
Jansen, I.E., Ye, H., .., IPDGC consortium members and affiliations: .., Saad, M., .., .., Shulman, J.M. and Heutink, P., 2017.
Genome biology, 18(1), p.22.
Excessive burden of lysosomal storage disorder gene variants in Parkinson’s disease
Robak, L.A., Jansen, I.E., Van Rooij, J., Uitterlinden, A.G., Kraaij, R., Jankovic, J., International Parkinson’s Disease Genomics Consortium (IPDGC): .., Saad, M., .., Heutink, P. and Shulman, J.M., 2017.
Brain, 140(12), pp.3191-3203.
Association Score Testing for Rare Variants and Binary Traits in Family Data with Common Controls
Saad, M. and Wijsman, E.M., 2017.
Briefings in bioinformatics.
Accounting for Cryptic Relatedness across Families in Family-based Association Testing
Wijsman, E.M., Blue, E.E., Day, T.R., Nato Jr, A.Q., Sohi, H.K., Horimoto, A.R., Nafikov, R., Saad, M.H. and Thornton, T.A., 2017, November.
GENETIC EPIDEMIOLOGY (Vol. 41, No. 7, pp. 707-707). 111 RIVER ST, HOBOKEN 07030-5774, NJ USA: WILEY.
Predictive and Comparative Network Analysis of the Gut Microbiota in Type 2 Diabetes
Abbas, M. and EL-Manzalawy, Y., 2017, August.
Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (pp. 313-320). ACM.
Parallelizing Partial Digest Problem on Multicore System
Bahig, H.M., Abbas, M.M. and Mohie-Eldin, M.M., 2017, April.
International Conference on Bioinformatics and Biomedical Engineering (pp. 95-104). Springer, Cham.
In-Memory Distributed Matrix Computation Processing and Optimization
Yu, Y., Tang, M., Aref, W.G., Malluhi, Q.M., Abbas, M.M. and Ouzzani, M., 2017, April.
Data Engineering (ICDE), 2017 IEEE 33rd International Conference on (pp. 1047-1058). IEEE.
Denoised Kernel Spectral Data Clustering
Mall, R., Bensmail, H., Langone, R., Varon, C. and Suykens, J.A., 2016, July.
Neural Networks (IJCNN), 2016 International Joint Conference on (pp. 3709-3716). IEEE..
Metabolomic Data Profiling for Diabetes Research in Qatar
Mall, R., Berti-Equille, L. and Bensmail, H., 2016, September
Database and Expert Systems Applications (DEXA), 2016 27th International Workshop on (pp. 39-43). IEEE.
COUSCOus: improved protein contact prediction using an empirical Bayes covariance estimator
Rawi, R., Mall, R., Kunji, K., El Anbari, M., Aupetit, M., Ullah, E. and Bensmail, H., 2016
BMC bioinformatics, 17(1), p.533.
A design study to identify inconsistencies in kinship information: The case of the 1000 Genomes project
Aupetit, M., Ullah, E., Rawi, R. and Bensmail, H., 2016, April
2016 IEEE (pp. 254-258). IEEE.
Fast in-memory spectral clustering using a fixed-size approach
Langone, R., Mall, R., Vilen Jumutc, V. and Suykens, J., 2016, April
Proc. of the 24th european symposium on artificial neural networks, computational intelligence and machine learning (pp. 557-562).
Statistical and Network Analysis of Metabolomics Data
Ullah, E., Mall, R., Rawi, R. and Bensmail, H., 2016, October
Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (pp. 544-545). ACM.
Kernel spectral clustering and applications
Langone, R., Mall, R., Alzate, C. and Suykens, J.A., 2016
In Unsupervised Learning Algorithms (pp. 135-161). Springer, Cham.
Cell Line Screens Identify Biomarkers of Drug Sensitivity in GLIOMA Cancer
Al Muftah, N., Rawi, R., Thompson, R. and Bensmail, H. , 2016
World Academy of Science, Engineering and Technology, International Journal of Bioengineering and Life Sciences, 3(2).
gEFM: an algorithm for computing elementary flux modes using graph traversal
Ullah, E., Aeron, S. and Hassoun, S., 2016
IEEE/ACM transactions on computational biology and bioinformatics, 13(1), pp.122-134.
A fast exact sequential algorithm for the partial digest problem
Abbas, M.M. and Bahig, H.M., 2016
BMC bioinformatics, 17(19), p.510.