Computational Science & Engineering

Research Output 2003 2019

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2019

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
1 Citation (Scopus)

Comparison and assessment of family- and population-based genotype imputation methods in large pedigrees

Ullah, E., Mall, R., Abbas, M. M., Kunji, K., Nato, A. Q., Bensmail, H., Wijsman, E. M. & Saad, M., 1 Jan 2019, In : Genome Research. 29, 1, p. 125-134 10 p.

Research output: Contribution to journalArticle

Pedigree
Genotype
Population
Neurofibromin 2
Genome-Wide Association Study

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
2 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

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

A collection of annotated and harmonized human breast cancer transcriptome datasets, including immunologic classification

Miller, L. D., Roelands, J., Decock, J., Boughorbel, S., Rinchai, D., Maccalli, C., Ceccarelli, M., Black, M., Print, C., Chou, J., Presnell, S., Quinn, C., Jithesh, P. V., Syed, N., Al Bader, S. B. J., Bedri, S., Wang, E., Marincola, F. M., Chaussabel, D. J., Kuppen, P. & 2 others, Bedognetti, D. & Hendrickx, W. R., 1 Jan 2018, In : F1000Research. 6, 296.

Research output: Contribution to journalArticle

Transcriptome
Gene expression
Breast Neoplasms
Gene Expression
Genes
19 Citations (Scopus)

A metabolic function of FGFR3-TACC3 gene fusions in cancer

Frattini, V., Pagnotta, S. M., Tala, Fan, J. J., Russo, M. V., Lee, S. B., Garofano, L., Zhang, J., Shi, P., Lewis, G., Sanson, H., Frederick, V., Castano, A. M., Cerulo, L., Rolland, D. C. M., Mall, R., Mokhtari, K., Elenitoba-Johnson, K. S. J., Sanson, M., Huang, X. & 3 others, Ceccarelli, M., Lasorella, A. & Iavarone, A., 11 Jan 2018, In : Nature. 553, 7687, p. 222-227 6 p.

Research output: Contribution to journalArticle

Gene Fusion
Neoplasms
Oncogene Fusion
Respiration
Phosphopeptides

Application of FTIR and LA-ICPMS spectroscopies as a possible approach for biochemical analyses of different rat brain regions

Hosni M. Ali, M., Rakib, F., Nischwitz, V., Ullah, E., Mall, R., Shraim, A. M., Ahmad, M. I., Ghouri, Z. K., McNaughton, D., Küppers, S., Ahmed, T. & Al-Saad, K., 1 Dec 2018, In : Applied Sciences (Switzerland). 8, 12, 2436.

Research output: Contribution to journalArticle

rats
brain
Fourier transform infrared spectroscopy
Rats
Brain
4 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

Fourier-transform infrared imaging spectroscopy and laser ablation -ICPMS new vistas for biochemical analyses of ischemic stroke in rat brain

Hosni M. Ali, M., Rakib, F., Mohamed, E., Limbeck, A., Mall, R., Ullah, E., Mesaeli, N., McNaughton, D., Ahmed, T. & Al-Saad, K., 19 Sep 2018, In : Frontiers in Neuroscience. 12, SEP, 647.

Research output: Contribution to journalArticle

Laser Therapy
Fourier Transform Infrared Spectroscopy
Stroke
Brain
Lipids
1 Citation (Scopus)

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. & Saad, M., 1 May 2018, In : Bioinformatics. 34, 9, p. 1591-1593 3 p.

Research output: Contribution to journalArticle

Imputation
Pedigree
Genotype
Genome
Genes

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
1 Citation (Scopus)
Taxonomies
Guidelines
Visualization
Surveys and Questionnaires
6 Citations (Scopus)

PaRSnIP: Sequence-based protein solubility prediction using gradient boosting machine

Rawi, R., Mall, R., Kunji, K., Shen, C. H., Kwong, P. D. & Chuang, G. Y., 1 Apr 2018, In : Bioinformatics. 34, 7, p. 1092-1098 7 p.

Research output: Contribution to journalArticle

Solubility
Boosting
Gradient
Proteins
Protein

Resilience analytics: coverage and robustness in multi-modal transportation networks

Baggag, A., Abbar, S., Zanouda, T. & Srivastava, J., 1 Dec 2018, In : EPJ Data Science. 7, 1, 14.

Research output: Contribution to journalArticle

Multimodal transportation
Transportation Networks
Resilience
Coverage
Robustness
4 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
1 Citation (Scopus)

A multiplex approach to urban mobility

Baggag, A., Abba, S., Zanouda, T., Borge-Holthoefer, J. & Srivastava, J., 2017, In : Studies in Computational Intelligence. 693, p. 551-563 13 p.

Research output: Contribution to journalArticle

Multimodal transportation
Multilayers
8 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
37 Citations (Scopus)

Identification of genetic determinants of breast cancer immune phenotypes by integrative genome-scale analysis

Hendrickx, W. R., Simeone, I., Anjum, S., Mokrab, Y., Bertucci, F., Finetti, P., Curigliano, G., Seliger, B., Cerulo, L., Tomei, S., Delogu, L. G., Maccalli, C., Wang, E., Miller, L. D., Marincola, F. M., Ceccarelli, M. & Bedognetti, D., 1 Feb 2017, In : OncoImmunology. 6, 2, e1253654.

Research output: Contribution to journalArticle

Genome
Breast Neoplasms
Phenotype
Mutation
Atlases
4 Citations (Scopus)
Qatar
Social Media
Pediatric Obesity
Feasibility Studies
Weight Loss
3 Citations (Scopus)

The possible role of chromosome X variability in hypertensive familiarity

Ciccarelli, M., Finelli, R., Rivera, N., Santulli, G., Izzo, R., De Luca, N., Rozza, F., Ceccarelli, M., Pagnotta, S., Uliano, F., Tremigliozzi, R., Condorelli, G., Trimarco, V. & Iaccarino, G., 1 Jan 2017, In : Journal of Human Hypertension. 31, 1, p. 37-42 6 p.

Research output: Contribution to journalArticle

X Chromosome
Mothers
Hypertension
Odds Ratio
Confidence Intervals
2016
2 Citations (Scopus)

A fast exact sequential algorithm for the partial digest problem

Abbas, M. & Bahig, H. M., 22 Dec 2016, In : BMC Bioinformatics. 17, 510.

Research output: Contribution to journalArticle

Sequential Algorithm
Exact Algorithms
Partial
Digestion
Restriction
Empirical Bayes
Contact
Proteins
Protein
Estimator
10 Citations (Scopus)

Disentangling the relationship between tumor genetic programs and immune responsiveness

Bedognetti, D., Hendrickx, W. R., Ceccarelli, M., Miller, L. D. & Seliger, B., 1 Apr 2016, In : Current Opinion in Immunology. 39, p. 150-158 9 p.

Research output: Contribution to journalArticle

Phenotype
Neoplasms
Chemokines
Genes
Cytokines
6 Citations (Scopus)

FastRNABindR: Fast and accurate prediction of protein-RNA interface residues

El-Manzalawy, Y., Abbas, M., Malluhi, Q. & Honavar, V., 1 Jul 2016, In : PLoS One. 11, 7, e0158445.

Research output: Contribution to journalArticle

RNA
prediction
Position-Specific Scoring Matrices
Proteins
amino acid sequences
476 Citations (Scopus)

Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma

TCGA Research Network, 28 Jan 2016, In : Cell. 164, 3, p. 550-563 14 p.

Research output: Contribution to journalArticle

Glioma
Genes
Genome
Mutation
Atlases
7 Citations (Scopus)

Retinoic acid specifically enhances embryonic stem cell metastate marked by Zscan4

Tagliaferri, D., De Angelis, M. T., Russo, N. A., Marotta, M., Ceccarelli, M., Del Vecchio, L., De Felice, M. & Falco, G., 1 Feb 2016, In : PLoS One. 11, 2, e0147683.

Research output: Contribution to journalArticle

retinoic acid
embryonic stem cells
Embryonic Stem Cells
Tretinoin
Stem cells
156 Citations (Scopus)

TCGAbiolinks: An R/Bioconductor package for integrative analysis of TCGA data

Colaprico, A., Silva, T. C., Olsen, C., Garofano, L., Cava, C., Garolini, D., Sabedot, T. S., Malta, T. M., Pagnotta, S. M., Castiglioni, I., Ceccarelli, M., Bontempi, G. & Noushmehr, H., 5 May 2016, In : Nucleic Acids Research. 44, 8, p. e71

Research output: Contribution to journalArticle

Atlases
Genome
Neoplasms
Computational Biology
Workflow
8 Citations (Scopus)

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages

Silva, T. C., Colaprico, A., Olsen, C., D'Angelo, F., Bontempi, G., Ceccarelli, M. & Noushmehr, H., 2016, In : F1000Research. 5, 1542.

Research output: Contribution to journalArticle

Workflow
Atlases
Genomics
Epigenomics
Tumors
7 Citations (Scopus)

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages [version 1; referees: 1 approved, 1 approved with reservations]

Silva, T. C., Colaprico, A., Olsen, C., D'Angelo, F., Bontempi, G., Ceccarelli, M. & Noushmehr, H., 2016, In : F1000Research. 5, 1542.

Research output: Contribution to journalArticle

Workflow
Atlases
Genomics
Epigenomics
Tumors
2015
3 Citations (Scopus)

Assessing the effects of data selection and representation on the development of reliable E. coli sigma 70 promoter region predictors

Abbas, M., Mohie-Eldin, M. M. & El-Manzalawy, Y., 24 Mar 2015, In : PLoS One. 10, 3

Research output: Contribution to journalArticle

Genetic Promoter Regions
Escherichia coli
promoter regions
Classifiers
Transcriptional Regulatory Elements
2 Citations (Scopus)

ClassiMap: A New Dimension Reduction Technique for Exploratory Data Analysis of Labeled Data

Lespinats, S., Aupetit, M. & Meyer-Baese, A., 14 Sep 2015, In : International Journal of Pattern Recognition and Artificial Intelligence. 29, 6, 1551008.

Research output: Contribution to journalArticle

Labels
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

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

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

Introduction to the special issue on visual analytics using multidimensional projections

Aupetit, M. & van der Maaten, L., 2015, In : Neurocomputing. 150, PB, p. 543-545 3 p.

Research output: Contribution to journalArticle

3 Citations (Scopus)

Irish: A Hidden Markov Model to detect coded information islands in free text

Cerulo, L., Di Penta, M., Bacchelli, A., Ceccarelli, M. & Canfora, G., 1 Jul 2015, In : Science of Computer Programming. 105, p. 26-43 18 p.

Research output: Contribution to journalArticle

Electronic mail
Hidden Markov models
Textbooks
Communication
Software engineering

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
20 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
1 Citation (Scopus)

VEGAWES: Variational segmentation on whole exome sequencing for copy number detection

Anjum, S., Morganella, S., D'Angelo, F., Iavarone, A. & Ceccarelli, M., 29 Sep 2015, In : BMC Bioinformatics. 16, 1, 315.

Research output: Contribution to journalArticle

Exome
Sequencing
Segmentation
Tumors
Tumor
2014
48 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
1 Citation (Scopus)

Parallelizing exact motif finding algorithms on multi-core

Abbas, M., Bahig, H. M., Abouelhoda, M. & Mohie-Eldin, M. M., 1 Aug 2014, In : Journal of Supercomputing. 69, 2, p. 814-826 13 p.

Research output: Contribution to journalArticle

Sequential Algorithm
Scalability
OpenMP
Bioinformatics
Computational Complexity

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)

An Efficient Algorithm to Identify DNA Motifs

Abbas, M. & Bahig, H. M., 1 Dec 2013, In : Mathematics in Computer Science. 7, 4, p. 387-399 13 p.

Research output: Contribution to journalArticle

DNA
Efficient Algorithms
Voting
Pattern Matching
Pattern matching
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
75 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
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