Computational Science & Engineering

Research Output 2003 2019

Filter
Article
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

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
1 Citation (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
5 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

Exploring the molecular crosstalk between pancreatic bud and mesenchyme in embryogenesis: Novel signals involved

Guerriero, I., De Angelis, M. T., D'angelo, F., Leveque, R., Savignano, E., Roberto, L., Lucci, V., Mazzone, P., Laurino, S., Storto, G., Nardelli, A., Sgambato, A., Ceccarelli, M., De Felice, M., Amendola, E. & Falco, G., 1 Oct 2019, In : International journal of molecular sciences. 20, 19, 4900.

Research output: Contribution to journalArticle

Open Access
Mesoderm
Crosstalk
crosstalk
genes
Embryonic Development

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
1 Citation (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

Lifelong Exploratory Navigation: an Architecture for Safer Mobile Robots

de Chamisso, F. M., Cancila, D., Soulier, L., Passerone, R. & Aupetit, M., 1 Jan 2019, (Accepted/In press) In : IEEE Design and Test.

Research output: Contribution to journalArticle

Mobile robots
Navigation
Mechatronics
Sensors
Synchronization

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

Rumour verification through recurring information and an inner-attention mechanism

Aker, A., Sliwa, A., Dalvi, F. & Bontcheva, K., 1 Sep 2019, In : Online Social Networks and Media. 13, 100045.

Research output: Contribution to journalArticle

rumor
Neural networks
social media
neural network
news
4 Citations (Scopus)

The combination of neoantigen quality and T lymphocyte infiltrates identifies glioblastomas with the longest survival

Zhang, J., Caruso, F. P., Sa, J. K., Justesen, S., Nam, D. H., Sims, P., Ceccarelli, M., Lasorella, A. & Iavarone, A., 1 Dec 2019, In : Communications Biology. 2, 1, 135.

Research output: Contribution to journalArticle

Open Access
T-cells
Glioblastoma
Tumors
T-lymphocytes
T-Lymphocytes
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
24 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
10 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
2 Citations (Scopus)

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
2 Citations (Scopus)
Taxonomies
Guidelines
Visualization
Surveys and Questionnaires
10 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
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
2 Citations (Scopus)

Transcriptional landscape of mouse-aged ovaries reveals a unique set of non-coding RNAs associated with physiological and environmental ovarian dysfunctions

Cuomo, D., Porreca, I., Ceccarelli, M., Threadgill, D. W., Barrington, W. T., Petriella, A., D’Angelo, F., Cobellis, G., De Stefano, F., D’Agostino, M. N., De Felice, M., Mallardo, M. & Ambrosino, C., 1 Dec 2018, In : Cell Death Discovery. 4, 1, 112.

Research output: Contribution to journalArticle

Open Access
Untranslated RNA
Ovary
Follicular Atresia
Eukaryotic Initiation Factor-2
Small Nucleolar RNA
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
42 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
11 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
7 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
527 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
8 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
198 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
11 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
10 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
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
3 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

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
21 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
49 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