Computational Science & Engineering

Research Output 2003 2019

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
Physical Chemistry
Physical chemistry
machine learning
physical chemistry
Physics
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
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

Deep reinforcement learning for traffic light optimization

Coskun, M., Baggag, A. & Chawla, S., 7 Feb 2019, Proceedings - 18th IEEE International Conference on Data Mining Workshops, ICDMW 2018. Yu, J., Li, Z., Tong, H. & Zhu, F. (eds.). IEEE Computer Society, p. 564-571 8 p. 8637414. (IEEE International Conference on Data Mining Workshops, ICDMW; vol. 2018-November).

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

Reinforcement learning
Telecommunication traffic
Travel time
Simulators
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
1 Citation (Scopus)

Health Lifestyle Data-Driven Applications Using Pervasive Computing

Fernandez, L., Aupetit, M., Palotti, J., Singh, M., Fadlelbari, A., Baggag, A., Khowaja, K. & Al-Thani, D., 1 Jan 2019, Lecture Notes in Bioengineering. Springer, p. 115-126 12 p. (Lecture Notes in Bioengineering).

Research output: Chapter in Book/Report/Conference proceedingChapter

Ubiquitous computing
Life Style
Health
Ethics
Technology

Identifying and controlling important neurons in neural machine translation

Bau, A., Durrani, N., Belinkov, Y., Dalvi, F., Sajjad, H. & Glass, J., 1 Jan 2019.

Research output: Contribution to conferencePaper

Neurons
Linguistics
linguistics
intuition
Chemical activation

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
4 Citations (Scopus)

A twitter tale of three hurricanes: Harvey, Irma, and Maria

Alam, F., Ofli, F., Imran, M. & Aupetit, M., 1 Jan 2018, Conference Proceedings - 15th International Conference on Information Systems for Crisis Response and Management, ISCRAM 2018. Tomaszewski, B. & Boersma, K. (eds.). Information Systems for Crisis Response and Management, ISCRAM, Vol. 2018-May. p. 553-572 20 p.

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

Hurricanes
Disasters
Learning algorithms
Computer vision
Artificial intelligence
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
Qatar
Translational Medical Research
Medical problems
Type 2 Diabetes Mellitus
Medicine
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

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
2 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
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
2 Citations (Scopus)

Qlusty: Quick and dirty generation of event videos from written media coverage

Barron, A., Martino, G., Zhang, Y., Ali, A. & Dalvi, F., 1 Jan 2018, In : CEUR Workshop Proceedings. 2079, p. 27-32 6 p.

Research output: Contribution to journalConference article

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
2 Citations (Scopus)

VisCoDeR: A tool for visually comparing dimensionality reduction algorithms

Cutura, R., Holzer, S., Aupetit, M. & Sedlmair, M., 1 Jan 2018, ESANN 2018 - Proceedings, European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning. i6doc.com publication, p. 105-110 6 p. (ESANN 2018 - Proceedings, European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning).

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

Visualization

Visualizing geo-demographic urban data

Araujo, M., Aupetit, M., Mejova, Y. & Weber, I., 30 Oct 2018, CSCW 2018 Companion - Companion of the 2018 ACM Conference on Computer Supported Cooperative Work and Social Computing. Association for Computing Machinery, p. 45-48 4 p.

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

Visualization
Marketing
Data visualization
Application programming interfaces (API)
2017
1 Citation (Scopus)

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

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., Miller, L. D. & 2 others, Bedognetti, D. & Hendrickx, W. R., 1 Jan 2017, In : F1000Research. 6, 296.

Research output: Contribution to journalComment/debate

Transcriptome
Gene expression
Breast Neoplasms
Gene Expression
Genes

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)

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
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
3 Citations (Scopus)

Challenging language-Dependent segmentation for Arabic: An application to machine translation and part-of-Speech tagging

Sajjad, H., Dalvi, F., Durrani, N., Abdelali, A., Belinkov, Y. & Vogel, S., 1 Jan 2017, ACL 2017 - 55th Annual Meeting of the Association for Computational Linguistics, Proceedings of the Conference (Short Papers). Association for Computational Linguistics (ACL), Vol. 2. p. 601-607 7 p.

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

Convolution
Neural networks
language
dialect
neural network
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
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
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
9 Citations (Scopus)

In-memory distributed matrix computation processing & optimization

Yu, Y., Tang, M., Aref, W. G., Malluhi, Q. M., Abbas, M. & Ouzzani, M., 16 May 2017, Proceedings - 2017 IEEE 33rd International Conference on Data Engineering, ICDE 2017. IEEE Computer Society, p. 1047-1058 12 p. 7930046

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

Data storage equipment
Processing
Costs
Competitive intelligence
Communication
2 Citations (Scopus)

Interactive monitoring of critical situational information on social media

Aupetit, M. & Imran, M., 1 Jan 2017, In : Proceedings of the International ISCRAM Conference. 2017-May, p. 673-683 11 p.

Research output: Contribution to journalConference article

Monitoring
Managers
Disasters
Engines
Processing

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

On the role of political affiliation in human perception the case of Delhi OddEven experiment

Zanouda, T., Abbar, S., Berti-Equille, L., Shah, K., Baggag, A., Chawla, S. & Srivastava, J., 1 Jan 2017, Social Informatics - 9th International Conference, SocInfo 2017, Proceedings. Springer Verlag, p. 74-88 15 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 10540 LNCS).

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

Human Perception
Experiment
Experiments
India
Curbs