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Research Output 1996 2019

  • 816 Citations
  • 14 h-Index
  • 35 Article
  • 18 Conference contribution
  • 3 Chapter
  • 2 Comment/debate
2019

Accurate Prediction for Antibody Resistance of Clinical HIV-1 Isolates

Rawi, R., Mall, R., Shen, C. H., Farney, S. K., Shiakolas, A., Zhou, J., Bensmail, H., Chun, T. W., Doria-Rose, N. A., Lynch, R. M., Mascola, J. R., Kwong, P. D. & Chuang, G. Y., 1 Dec 2019, In : Scientific reports. 9, 1, 14696.

Research output: Contribution to journalArticle

Open Access
HIV-1
Neutralizing Antibodies
Antibodies
Clinical Trials
env Gene Products
2 Citations (Scopus)

Clustme: A visual quality measure for ranking monochrome scatterplots based on cluster patterns

Abbas, M., Aupetit, M., Sedlmair, M. & Bensmail, H., 1 Jan 2019, In : Computer Graphics Forum. 38, 3, p. 225-236 12 p.

Research output: Contribution to journalArticle

Merging
Physical Chemistry
Physical chemistry
machine learning
physical chemistry
Physics
3 Citations (Scopus)

Deepcrystal: A deep learning framework for sequence-based protein crystallization prediction

Elbasir, A., Moovarkumudalvan, B., Kunji, K., Kolatkar, P., Mall, R. & Bensmail, H., 1 Jul 2019, In : Bioinformatics. 35, 13, p. 2216-2225 10 p.

Research output: Contribution to journalArticle

Crystallization
Learning
Proteins
Protein
Prediction
1 Citation (Scopus)

DeepCrystal: A Deep Learning Framework for Sequence-based Protein Crystallization Prediction

Elbasir, A., Moovarkumudalvan, B., Kunji, K., Kolatkar, P., Bensmail, H. & Mall, R., 21 Jan 2019, Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. Schmidt, H., Griol, D., Wang, H., Baumbach, J., Zheng, H., Callejas, Z., Hu, X., Dickerson, J. & Zhang, L. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 2747-2749 3 p. 8621202. (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Crystallization
Learning
Proteins
Diffraction
Crystals
7 Citations (Scopus)

Exploring new approaches towards the formability of mixed-ion perovskites by DFT and machine learning

Park, H., Mall, R., Alharbi, F., Sanvito, S., Tabet, N., Bensmail, H. & El-Mellouhi, F., 1 Jan 2019, In : Physical Chemistry Chemical Physics. 21, 3, p. 1078-1088 11 p.

Research output: Contribution to journalArticle

machine learning
perovskites
Formability
Discrete Fourier transforms
learning

KinVis: A visualization tool to detect cryptic relatedness in genetic datasets

Ullah, E., Aupetit, M., Das, A., Patil, A., Al Muftah, N., Rawi, R., Saad, M. & Bensmail, H., 1 Aug 2019, In : Bioinformatics. 35, 15, p. 2683-2685 3 p.

Research output: Contribution to journalArticle

Genome-Wide Association Study
Computational Biology
Visualization
Hot Temperature
Bar chart
2 Citations (Scopus)

Learn-and-Match Molecular Cations for Perovskites

Park, H., Mall, R., Alharbi, F., Sanvito, S., Tabet, N., Bensmail, H. & El-Mellouhi, F., 1 Jan 2019, In : Journal of Physical Chemistry A.

Research output: Contribution to journalArticle

perovskites
machine learning
Cations
Learning systems
cations

Prediction of protein group function by iterative classification on functional relevance network

Khan, I. K., Jain, A., Rawi, R., Bensmail, H. & Kihara, D., 1 Jan 2019, In : Bioinformatics. 35, 8, p. 1388-1394 7 p.

Research output: Contribution to journalArticle

Proteins
Protein
Prediction
Proteomics
Graphical Models
2018
11 Citations (Scopus)

DeepSol: A deep learning framework for sequence-based protein solubility prediction

Khurana, S., Rawi, R., Kunji, K., Chuang, G. Y., Bensmail, H. & Mall, R., 1 Jan 2018, In : Bioinformatics. 34, 15, p. 2605-2613 9 p.

Research output: Contribution to journalArticle

Solubility
Learning
Proteins
Protein
Prediction
Qatar
Translational Medical Research
Medical problems
Type 2 Diabetes Mellitus
Medicine
1 Citation (Scopus)

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. & Bensmail, H., 12 Apr 2018, In : Journal of Translational Medicine. 16, 1, 99.

Research output: Contribution to journalArticle

Qatar
Medical problems
Type 2 Diabetes Mellitus
Obesity
Insulin

ISaaC: Identifying structural relations in biological data with copula-based kernel dependency measures

Al Meer, H., Mall, R., Ullah, E., Megrez, N. & Bensmail, H., 1 Jan 2018, Bioinformatics and Biomedical Engineering - 6th International Work-Conference, IWBBIO 2018, Proceedings. Springer Verlag, p. 71-82 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 10813 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Copula
Genes
kernel
Reverse engineering
Reverse Engineering
3 Citations (Scopus)

Microbiomarkers Discovery in Inflammatory Bowel Diseases using Network-Based Feature Selection

Abbas, M., Le, T., Bensmail, H., Honavar, V. & El-Manzalawy, Y., 15 Aug 2018, ACM-BCB 2018 - Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. Association for Computing Machinery, Inc, p. 172-177 6 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Biomarkers
Inflammatory Bowel Diseases
Feature extraction
Metagenomics
Phenotype
6 Citations (Scopus)

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. & Ceccarelli, M., 20 Apr 2018, In : Nucleic Acids Research. 46, 7, p. e39

Research output: Contribution to journalArticle

Gene Regulatory Networks
Regulator Genes
Glioblastoma
Transcriptome
Brain Neoplasms
2017

Advanced computation of sparse precision matrices for big data

Baggag, A., Bensmail, H. & Srivastava, J., 1 Jan 2017, Advances in Knowledge Discovery and Data Mining - 21st Pacific-Asia Conference, PAKDD 2017, Proceedings. Springer Verlag, p. 27-38 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 10235 LNAI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Covariance matrix
Method of multipliers
Alternating Direction Method
Positive Definiteness
Stopping Criterion
1 Citation (Scopus)

An adaptive refinement for community detection methods for disease module identification in biological networks using novel metric based on connectivity, conductance & modularity

Mall, R., Ullah, E., Kunji, K., Bensmail, H. & Ceccarelli, M., 15 Dec 2017, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Institute of Electrical and Electronics Engineers Inc., Vol. 2017-January. p. 2282-2284 3 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Benchmarking
Genes
Genome-Wide Association Study
Merging
Biomedical Research
9 Citations (Scopus)

Detection of statistically significant network changes in complex biological networks

Mall, R., Cerulo, L., Bensmail, H., Iavarone, A. & Ceccarelli, M., 4 Mar 2017, In : BMC Systems Biology. 11, 1, 32.

Research output: Contribution to journalArticle

Biological Networks
Electric wiring
Complex Networks
Genes
Hamming distance
1 Citation (Scopus)

Differential community detection in paired biological networks

Mall, R., D'Angelo, F., Ullah, E., Bensmail, H., Kunji, K. & Ceccarelli, M., 20 Aug 2017, ACM-BCB 2017 - Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. Association for Computing Machinery, Inc, p. 330-339 10 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Genes
Methylation
Molecular interactions
Electric wiring
Gene expression

Identification of cancer drug sensitivity biomarkers

Ullah, E., Mall, R., Bensmail, H., Rawi, R., Shama, S., Muftah, N. A. & Thmpson, I. R., 15 Dec 2017, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Institute of Electrical and Electronics Engineers Inc., Vol. 2017-January. p. 2322-2324 3 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Biomarkers
Cells
Gene expression
Pharmaceutical Preparations
Medicine
1 Citation (Scopus)

Metabolomic Data Profiling for Diabetes Research in Qatar

Mall, R., Berti-Equille, L. & Bensmail, H., 12 Jan 2017, Proceedings - 27th International Workshop on Database and Expert Systems Applications, DEXA 2016. Institute of Electrical and Electronics Engineers Inc., p. 39-43 5 p. 7816621

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Medical problems
Biomarkers
Metabolites
Nuclear magnetic resonance spectroscopy
Nuclear magnetic resonance
2016
1 Citation (Scopus)

A design study to identify inconsistencies in kinship information: The case of the 1000 Genomes project

Aupetit, M., Ullah, E., Rawi, R. & Bensmail, H., 4 May 2016, 2016 IEEE Pacific Visualization Symposium, PacificVis 2016 - Proceedings. IEEE Computer Society, Vol. 2016-May. p. 254-258 5 p. 7465281

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Genes
Data visualization
Empirical Bayes
Contact
Proteins
Protein
Estimator
1 Citation (Scopus)

Denoised Kernel Spectral data Clustering

Mall, R., Bensmail, H., Langone, R., Varon, C. & Suykens, J. A. K., 31 Oct 2016, 2016 International Joint Conference on Neural Networks, IJCNN 2016. Institute of Electrical and Electronics Engineers Inc., Vol. 2016-October. p. 3709-3716 8 p. 7727677

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Principal component analysis
Heuristic methods
Bandwidth
14 Citations (Scopus)

Supervised Cross-Modal Factor Analysis for Multiple Modal Data Classification

Wang, J., Zhou, Y., Duan, K., Wang, J. J. Y. & Bensmail, H., 12 Jan 2016, Proceedings - 2015 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2015. Institute of Electrical and Electronics Engineers Inc., p. 1882-1888 7 p. 7379461

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Factor analysis
Labels
Hinges
Objective function
Experiments
2015
5 Citations (Scopus)

Coevolution analysis of HIV-1 envelope glycoprotein complex

Rawi, R., Kunji, K., Haoudi, A. & Bensmail, H., 1 Nov 2015, In : PLoS One. 10, 11, 0143245.

Research output: Contribution to journalArticle

coevolution
Human immunodeficiency virus 1
HIV-1
glycoproteins
Glycoproteins
1 Citation (Scopus)

Erratum: Coevolution analysis of HIV-1 envelope glycoprotein complex (PLoS ONE (2015) 10:11 (e0143245) DOI:10.1371/journal.pone.0143245)

Rawi, R., Kunji, K., Haoudi, A. & Bensmail, H., 1 Dec 2015, In : PLoS One. 10, 12, e0145974.

Research output: Contribution to journalArticle

Glycoproteins

Model selection emphasises the importance of non-chromosomal information in genetic studies

Rawi, R., Anbari, M. E. & Bensmail, H., 27 Jan 2015, In : PLoS One. 10, 1, e0117014.

Research output: Contribution to journalArticle

Yeast
heritability
Yeasts
Phenotype
Growth

Residue-residue contact prediction in the HIV-1 envelope glycoprotein complex

Rawi, R., Kunji, K., Haoudi, A. & Bensmail, H., 16 Dec 2015, Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. Institute of Electrical and Electronics Engineers Inc., p. 1709-1711 3 p. 7359933

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Glycoproteins
env Gene Products
HIV-1
Proteins
Fusion reactions
22 Citations (Scopus)

Systems biology analysis reveals NFAT5 as a novel biomarker and master regulator of inflammatory breast cancer

Remo, A., Simeone, I., Pancione, M., Parcesepe, P., Finetti, P., Cerulo, L., Bensmail, H., Birnbaum, D., Van Laere, S. J., Colantuoni, V., Bonetti, F., Bertucci, F., Manfrin, E. & Ceccarelli, M., 1 May 2015, In : Journal of Translational Medicine. 13, 1, 138.

Research output: Contribution to journalArticle

Inflammatory Breast Neoplasms
Catenins
Systems Biology
Biomarkers
Genes
2014
3 Citations (Scopus)

COFADMM: A computational features selection with alternating Direction Method of Multipliers

El Anbari, M., Alam, S. & Bensmail, H., 2014, Procedia Computer Science. Elsevier, Vol. 29. p. 821-830 10 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Feature extraction
Convex optimization
Combinatorial optimization
Distributed computer systems
Explosions

Computational neuro-modeling of visual memory: Multimodal imaging and analysis

El Anbari, M., Nemmour, N., Bouhali, O., Rawi, R., Sheharyar, A. & Bensmail, H., 1 Jan 2014, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Springer Verlag, Vol. 8609 LNAI. p. 21-32 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8609 LNAI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Imaging
Imaging techniques
Data storage equipment
Functional Magnetic Resonance Imaging
Overfitting
3 Citations (Scopus)

Domain transfer nonnegative matrix factorization

Wang, J. J. Y., Sun, Y. & Bensmail, H., 1 Jan 2014, Proceedings of the International Joint Conference on Neural Networks. Institute of Electrical and Electronics Engineers Inc., p. 3605-3612 8 p. 6889428

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Factorization
Classifiers
Vector spaces
Labels
Learning algorithms
50 Citations (Scopus)

Feature selection and multi-kernel learning for sparse representation on a manifold

Wang, J. J. Y., Bensmail, H. & Gao, X., 1 Mar 2014, In : Neural Networks. 51, p. 9-16 8 p.

Research output: Contribution to journalArticle

Feature extraction
Learning
Glycosylation
Medical imaging
Diagnostic Imaging

Unified framework for representing and ranking

Wang, J. J. Y. & Bensmail, H., 1 Jun 2014, In : Pattern Recognition. 47, 6, p. 2293-2300 8 p.

Research output: Contribution to journalArticle

Magnetic resonance imaging
Feature extraction
Tumors
Brain
Proteins
2013
2 Citations (Scopus)

Cross-domain sparse coding

Wang, J. J. Y. & Bensmail, H., 11 Dec 2013, International Conference on Information and Knowledge Management, Proceedings. p. 1461-1464 4 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Spam
Oil
Discrepancy
Experiment
30 Citations (Scopus)

Discriminative sparse coding on multi-manifolds

Wang, J. J. Y., Bensmail, H., Yao, N. & Gao, X., 1 Jan 2013, In : Knowledge-Based Systems. 54, p. 199-206 8 p.

Research output: Contribution to journalArticle

Labels
Medical imaging
Bioinformatics
Computer vision
Tumors
41 Citations (Scopus)

Joint learning and weighting of visual vocabulary for bag-of-feature based tissue classification

Wang, J. J. Y., Bensmail, H. & Gao, X., 1 Dec 2013, In : Pattern Recognition. 46, 12, p. 3249-3255 7 p.

Research output: Contribution to journalArticle

Tissue
Tomography
Brain
1 Citation (Scopus)

Metflexo: An automated simulation of realistic H1-NMR spectra

Atieh, Z., Suhre, K. & Bensmail, H., 2013, Procedia Computer Science. Elsevier, Vol. 18. p. 1382-1391 10 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Metabolites
Nuclear magnetic resonance
Magnetic fields
Deconvolution
Biological systems
79 Citations (Scopus)

Multiple graph regularized nonnegative matrix factorization

Wang, J. J. Y., Bensmail, H. & Gao, X., 1 Oct 2013, In : Pattern Recognition. 46, 10, p. 2840-2847 8 p.

Research output: Contribution to journalArticle

Factorization
Proteins
Experiments
2012
6 Citations (Scopus)

Efficient feature selection and multiclass classification with integrated instance and model based learning

Liu, Z., Bensmail, H. & Tan, M., 15 May 2012, Evolutionary Bioinformatics. 8 ed. Vol. 2012. p. 197-205 9 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Feature extraction
learning
Learning
Logistics
Medical applications
37 Citations (Scopus)

Multiple graph regularized protein domain ranking

Wang, J. J. Y., Bensmail, H. & Gao, X., 19 Nov 2012, In : BMC Bioinformatics. 13, 1, 307.

Research output: Contribution to journalArticle

Ranking
Proteins
Protein
Graph in graph theory
Protein Databases

RAFNI: Robust analysis of functional neuroimages with non-normal α-stable error

Bensmail, H., Anjum, S., Bouhali, O. & El Anbari, M., 19 Nov 2012, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). PART 1 ed. Vol. 7663 LNCS. p. 624-631 8 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 7663 LNCS, no. PART 1).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Functional Magnetic Resonance Imaging
Stable Distribution
Neuroscience
Neuroimaging
Fat Tails
2009
1 Citation (Scopus)

Performance of model selection criteria in Bayesian Threshold VAR (TVAR) models

Kwon, Y., Bozdogan, H. & Bensmail, H., 1 Jan 2009, In : Econometric Reviews. 28, 1-3, p. 83-101 19 p.

Research output: Contribution to journalArticle

Model selection criteria
VAR model
Bayesian modeling
Burden
Bayes factor
2008
27 Citations (Scopus)

A comparison of multiple linear regression and quantite regression for modeling the internal bond of medium density fiberboard

Young, T. M., Shaffer, L. B., Guess, F. M., Bensmail, H. & León, R. V., 1 Apr 2008, In : Forest Products Journal. 58, 4, p. 39-48 10 p.

Research output: Contribution to journalArticle

medium density fiberboards
Linear regression
modeling
comparison
refiners
2007
1 Citation (Scopus)

Clustering proteomics data using bayesian principal component analysis

Bensmail, H., Semmes, O. J. & Haoudi, A., 2007, Springer Optimization and Its Applications. Springer International Publishing, Vol. 7. p. 339-362 24 p. (Springer Optimization and Its Applications; vol. 7).

Research output: Chapter in Book/Report/Conference proceedingChapter

Proteomics
Bayesian Analysis
Principal Component Analysis
Clustering
Bayesian Model
2006
31 Citations (Scopus)

Bioinformatics and data mining in proteomics

Haoudi, A. & Bensmail, H., 7 Jul 2006, In : Expert Review of Proteomics. 3, 3, p. 333-343 11 p.

Research output: Contribution to journalArticle

Data Mining
Bioinformatics
Computational Biology
Proteomics
Data mining
44 Citations (Scopus)

Detection and classification of defect patterns on semiconductor wafers

Wang, C. H., Kuo, W. & Bensmail, H., 1 Dec 2006, In : IIE Transactions (Institute of Industrial Engineers). 38, 12, p. 1059-1068 10 p.

Research output: Contribution to journalArticle

Semiconductor materials
Defects
Engineers
Electron microscopes
Scanning
2005
29 Citations (Scopus)

A novel approach for clustering proteomics data using Bayesian fast Fourier transform

Bensmail, H., Golek, J., Moody, M. M., Semmes, J. O. & Haoudi, A., 15 May 2005, In : Bioinformatics. 21, 10, p. 2210-2224 15 p.

Research output: Contribution to journalArticle

Proteomics
Fourier Analysis
Fast Fourier transform
Fast Fourier transforms
Cluster Analysis
8 Citations (Scopus)

Clustering gene expression data with kernel principal components

Liu, Z., Chen, D., Bensmail, H. & Xu, Y., 1 Apr 2005, In : Journal of Bioinformatics and Computational Biology. 3, 2, p. 303-316 14 p.

Research output: Contribution to journalArticle

Principal Component Analysis
Gene expression
Principal component analysis
Cluster Analysis
Microarrays