Hesham H Ali, PhD

Dean

  • 1162 Citations
  • 15 h-Index
1990 …2020

Research output per year

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Research Output

2020

A bag-of-words feature engineering approach for assessing health conditions using accelerometer data

Rastegari, E. & Ali, H., May 2020, In : Smart Health. 16, 100116.

Research output: Contribution to journalArticle

2019

A Graph-Theoretic Approach for Identifying Bacterial Inter-correlations and Functional Pathways in Microbiome Data

Kim, S., Thapa, I. & Ali, H. H., Jan 21 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. 405-411 7 p. 8621179. (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018).

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

1 Scopus citations

A novel graph theoretical approach for modeling microbiomes and inferring microbial ecological relationships

Kim, S., Thapa, I., Zhang, L. & Ali, H., Dec 20 2019, In : BMC genomics. 20, 945.

Research output: Contribution to journalArticle

Open Access
Open Access

On Identifying Candidates for Drug Repurposing for the Treatment of Ulcerative Colitis using Gene Expression Data

Kim, S., Thapa, I., Zhang, L. & Ali, H., Jan 1 2019, Bioinformatics and Biomedical Engineering - 7th International Work-Conference, IWBBIO 2019, Proceedings. Valenzuela, O., Rojas, F., Ortuño, F., Ortuño, F. & Rojas, I. (eds.). Springer Verlag, p. 513-521 9 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11465 LNBI).

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

Uncovering and characterizing splice variants associated with survival in lung cancer patients

West, S., Kumar, S., Batra, S. K., Ali, H. & Ghersi, D., Jan 1 2019, In : PLoS computational biology. 15, 10, e1007469.

Research output: Contribution to journalArticle

Open Access
2018

Heterogeneity of Ly6G+ Ly6C+ myeloid-derived suppressor cell infiltrates during Staphylococcus aureus biofilm infection

Heim, C. E., West, S. C., Ali, H. & Kielian, T., Dec 1 2018, In : Infection and immunity. 86, 12, e00684.

Research output: Contribution to journalArticle

7 Scopus citations

Preface

Ali, H. H., Oct 11 2018, Proceedings of 2018 2nd International Conference on Computational Biology and Bioinformatics, ICCBB 2018. Association for Computing Machinery, p. 12-17 6 p. (ACM International Conference Proceeding Series).

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

Preface

Peixoto, N., Silveira, M., Ali, H. H., Maciel, C. & van den Broek, E. L., Jan 1 2018, In : Communications in Computer and Information Science. 881, p. V

Research output: Contribution to journalEditorial

2017

A correlation network model utilizing gait parameters for evaluating health levels

Rastegari, E. & Ali, H. H., Aug 20 2017, ACM-BCB 2017 - Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. Association for Computing Machinery, Inc, p. 568-574 7 p. (ACM-BCB 2017 - Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics).

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

2 Scopus citations

A hierarchical learning model for extracting public health data from social media

Rastegari, E., Ali, H. H. & Azizian, S., Jan 1 2017, AMCIS 2017 - America's Conference on Information Systems: A Tradition of Innovation. Americas Conference on Information Systems, (AMCIS 2017 - America's Conference on Information Systems: A Tradition of Innovation; vol. 2017-August).

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

1 Scopus citations

Analysis of clustering algorithms in biological networks

Sharma, A. & Ali, H. H., Dec 15 2017, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Yoo, I., Zheng, J. H., Gong, Y., Hu, X. T., Shyu, C-R., Bromberg, Y., Gao, J. & Korkin, D. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 2303-2305 3 p. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; vol. 2017-January).

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

1 Scopus citations

A network-based approach to mine temporal genes exhibiting significant expression variation in Caenorhabditis elegans

Cooper, K., Hassan, W. & Ali, H., Dec 15 2017, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Yoo, I., Zheng, J. H., Gong, Y., Hu, X. T., Shyu, C-R., Bromberg, Y., Gao, J. & Korkin, D. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 2151-2156 6 p. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; vol. 2017-January).

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

An evolutionary graph-based approach for managing self-organized IoT networks

Haddad, Y. M. & Ali, H. H., Nov 21 2017, MobiWac 2017 - Proceedings of the 15th ACM International Symposium on Mobility Management and Wireless Access, Co-located with MSWiM 2017. Association for Computing Machinery, Inc, p. 113-120 8 p. (MobiWac 2017 - Proceedings of the 15th ACM International Symposium on Mobility Management and Wireless Access, Co-located with MSWiM 2017).

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

A systems biology approach for modeling microbiomes using split graphs

Kim, S., Thapa, I., Lu, G., Zhu, L. & Ali, H. H., Dec 15 2017, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Yoo, I., Zheng, J. H., Gong, Y., Hu, X. T., Shyu, C-R., Bromberg, Y., Gao, J. & Korkin, D. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 2062-2068 7 p. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; vol. 2017-January).

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

2 Scopus citations

Evaluation of the oral microbiome as a biomarker for early detection of human oral carcinomas

Warnke-Sommer, J. D. & Ali, H. H., Dec 15 2017, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Yoo, I., Zheng, J. H., Gong, Y., Hu, X. T., Shyu, C-R., Bromberg, Y., Gao, J. & Korkin, D. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 1-8 8 p. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; vol. 2017-January).

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

1 Scopus citations

Granularity-aware fusion of biological networks for information extraction

West, S. & Ali, H., Dec 15 2017, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Yoo, I., Zheng, J. H., Gong, Y., Hu, X. T., Shyu, C-R., Bromberg, Y., Gao, J. & Korkin, D. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 638-642 5 p. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; vol. 2017-January).

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

Graph-based analysis of genetic features associated with mobile elements in Crohn’s disease and healthy gut microbiomes

Warnke-Sommer, J. & Ali, H., Jan 1 2017, BIOINFORMATICS 2017 - 8th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 10th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2017. Fred, A., Ali, H., Gamboa, H. & Vaz, M. (eds.). SciTePress, p. 104-114 11 p. (BIOINFORMATICS 2017 - 8th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 10th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2017; vol. 3).

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

On the integration of assembly and non-assembly approaches for comparing biological sequences

Dam, V. & Ali, H. H., Dec 15 2017, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Yoo, I., Zheng, J. H., Gong, Y., Hu, X. T., Shyu, C-R., Bromberg, Y., Gao, J. & Korkin, D. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 2232-2234 3 p. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; vol. 2017-January).

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

Parallel NGS assembly using distributed assembly graphs enriched with biological knowledge

Warnke-Sommer, J. D. & Ali, H. H., Jun 30 2017, Proceedings - 2017 IEEE 31st International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2017. Institute of Electrical and Electronics Engineers Inc., p. 273-282 10 p. 7965056. (Proceedings - 2017 IEEE 31st International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2017).

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

Preface

Ali, H., Khazanchi, D., Shi, Y., Ras, Z. W., Li, Y., Klusch, M., Reformat, M., Belkasim, S. & Ferilli, S., Jan 11 2017, In : Proceedings - 2016 IEEE/WIC/ACM International Conference on Web Intelligence Workshops, WIW 2016. p. ix-x 7814456.

Research output: Contribution to journalEditorial

Preface

Ali, H., Khazanchi, D., Shi, Y., Ras, Z. W., Li, Y., Klusch, M., Reformat, M., Belkasim, S. & Ferilli, S., Jan 12 2017, In : Proceedings - 2016 IEEE/WIC/ACM International Conference on Web Intelligence, WI 2016. p. xv-xvi 7817022.

Research output: Contribution to journalEditorial

Sensitivity analysis of granularity levels in complex biological networks

West, S. & Ali, H., Jan 1 2017, Biomedical Engineering Systems and Technologies - 9th International Joint Conference, BIOSTEC 2016, Revised Selected Papers. Gamboa, H. & Fred, A. (eds.). Springer Verlag, p. 167-188 22 p. (Communications in Computer and Information Science; vol. 690).

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

2 Scopus citations

Using gait parameters to recognize various stages of Parkinson's disease

Rastegari, E., Marmelat, V., Najjar, L., Bastola, D. & Ali, H. H., Dec 15 2017, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Yoo, I., Zheng, J. H., Gong, Y., Hu, X. T., Shyu, C-R., Bromberg, Y., Gao, J. & Korkin, D. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 1647-1651 5 p. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; vol. 2017-January).

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

2 Scopus citations
2016

A dynamic run-profile energy-aware approach for scheduling computationally intensive bioinformatics applications

Pawaskar, S. & Ali, H. H., Sep 13 2016, 2016 International Conference on High Performance Computing and Simulation, HPCS 2016. Zeljkovic, V. & Smari, W. W. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 427-434 8 p. 7568366. (2016 International Conference on High Performance Computing and Simulation, HPCS 2016).

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

1 Scopus citations

Foreword

Fred, A., Gamboa, H., Gilbert, J., Azhari, H., Ali, H., Quintão, C., Sliwa, J. & Ruiz, C., Jan 1 2016, In : BIOSIGNALS 2016 - 9th International Conference on Bio-Inspired Systems and Signal Processing, Proceedings; Part of 9th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2016. p. IX-X

Research output: Contribution to journalEditorial

Foreword

Fred, A., Gamboa, H., Gilbert, J., Azhari, H., Ali, H., Quintão, C., Sliwa, J. & Ruiz, C., Jan 1 2016, In : BIOINFORMATICS 2016 - 7th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 9th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2016. p. IX-X

Research output: Contribution to journalEditorial

Foreword

Fred, A., Gamboa, H., Gilbert, J., Azhari, H., Ali, H., Quintão, C., Sliwa, J. & Ruiz, C., Jan 1 2016, In : BIODEVICES 2016 - 9th International Conference on Biomedical Electronics and Devices, Proceedings; Part of 9th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2016. p. IX-X

Research output: Contribution to journalEditorial

Foreword

Fred, A., Gamboa, H., Gilbert, J., Azhari, H., Ali, H., Quintão, C., Sliwa, J. & Ruiz, C., Jan 1 2016, In : BIOIMAGING 2016 - 3rd International Conference on Bioimaging, Proceedings; Part of 9th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2016. p. IX-X

Research output: Contribution to journalEditorial

Graph mining for next generation sequencing: Leveraging the assembly graph for biological insights

Warnke-Sommer, J. & Ali, H., May 6 2016, In : BMC genomics. 17, 1, 340.

Research output: Contribution to journalArticle

2 Scopus citations

On the impact of granularity in extracting knowledge from bioinformatics data

West, S. & Ali, H., Jan 1 2016, BIOINFORMATICS 2016 - 7th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 9th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2016. Azhari, H., Ruiz, C., Ali, H., Gilbert, J., Sliwa, J., Fred, A., Gamboa, H. & Quintao, C. (eds.). SciTePress, p. 92-103 12 p. (BIOINFORMATICS 2016 - 7th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 9th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2016).

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

1 Scopus citations

Preface

Ascoli, G. A., Hawrylycz, M., Ali, H., Khazanchi, D. & Shi, Y., Jan 1 2016, In : Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9919 LNAI, p. V-VI

Research output: Contribution to journalEditorial

2015

A multi-stage graph approach for efficient clustering in self-organized wireless sensor networks

Karpate, A. & Ali, H. H., Jan 1 2015, SENSORNETS 2015 - 4th International Conference on Sensor Networks, Proceedings. Plainchault, P., Benavente-Peces, C. & Postolache, O. (eds.). SciTePress, p. 56-62 7 p. (SENSORNETS 2015 - 4th International Conference on Sensor Networks, Proceedings).

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

Applications of high performance computing in bioinformatics, computational biology and computational chemistry

Pèrèz-Sànchez, H., Fassihi, A., Cecilia, J. M., Ali, H. H. & Cannataro, M., Jan 1 2015, Bioinformatics and Biomedical Engineering - 3rd International Conference, IWBBIO 2015, Proceedings. Ortuño, F. & Rojas, I. (eds.). Springer Verlag, p. 527-541 15 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9044).

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

8 Scopus citations

Evaluating the robustness of correlation network analysis in the aging mouse hypothalamus

Cooper, K. M., Bonasera, S. & Ali, H., Jan 1 2015, Biomedical Engineering Systems and Technologies - 8th International Joint Conference, BIOSTEC 2015, Revised Selected Papers. Elias, D., Fred, A. & Gamboa, H. (eds.). Springer Verlag, p. 224-238 15 p. (Communications in Computer and Information Science; vol. 574).

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

Identification of biologically significant elements using correlation networks in high performance computing environments

Cooper, K. D., Pawaskar, S. & Ali, H. H., Jan 1 2015, Bioinformatics and Biomedical Engineering - 3rd International Conference, IWBBIO 2015, Proceedings. Ortuño, F. & Rojas, I. (eds.). Springer Verlag, p. 607-619 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9044).

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

1 Scopus citations

Identifying aging genes in the aging mouse hypothalamus using gateway node analysis of correlation networks

Cooper, K. M., Bonasera, S. & Ali, H., Jan 1 2015, BIOINFORMATICS 2015 - 6th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 8th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2015. Sinoquet, C., Pastor, O., Gamboa, H., Fred, A. & Elias, D. (eds.). SciTePress, p. 36-43 8 p. (BIOINFORMATICS 2015 - 6th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 8th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2015).

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

1 Scopus citations

Next generation sequence assembler mis-assembly of phage genomes with terminal redundancy

Warnke-Sommer, J., Thapa, I. & Ali, H., Dec 16 2015, Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. Schapranow, L. M., Zhou, J., Hu, X. T., Ma, B., Rajasekaran, S., Miyano, S., Yoo, I., Pierce, B., Shehu, A., Gombar, V. K., Chen, B., Pai, V. & Huan, J. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 1102-1108 7 p. 7359836. (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015).

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

On the comparison of state-and transition-based analysis of biological relevance in gene co-expression networks

Cooper, K., Vemuri, P. & Ali, H., Dec 16 2015, Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. Schapranow, L. M., Zhou, J., Hu, X. T., Ma, B., Rajasekaran, S., Miyano, S., Yoo, I., Pierce, B., Shehu, A., Gombar, V. K., Chen, B., Pai, V. & Huan, J. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 1197-1203 7 p. 7359852. (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015).

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

2014

An integrated model of human biomedical and clinical data structures

Paliulis, E. & Ali, H. H., Jul 24 2014, 2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2014. Institute of Electrical and Electronics Engineers Inc., 6863910. (2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2014).

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

1 Scopus citations

Focus: A new multilayer graph model for short read analysis and extraction of biologically relevant features

Warnke, J. & Ali, H., Sep 20 2014, ACM BCB 2014 - 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. Association for Computing Machinery, Inc, p. 489-498 10 p. (ACM BCB 2014 - 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics).

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

4 Scopus citations

Identifying aging-related genes in mouse hippocampus using gateway nodes

Dempsey, K. M. & Ali, H. H., May 27 2014, In : BMC systems biology. 8, 1, 62.

Research output: Contribution to journalArticle

10 Scopus citations

On the impact of data integration and edge enrichment in mining significant signals from biological networks

West, S. & Ali, H., Sep 20 2014, ACM BCB 2014 - 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. Association for Computing Machinery, Inc, p. 760-767 8 p. (ACM BCB 2014 - 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics).

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

On the robustness of the biological correlation network model

Dempsey, K. M. & Ali, H. H., Jan 1 2014, BIOINFORMATICS 2014 - 5th Int. Conf. on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 7th Int. Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2014. SciTePress, p. 186-195 10 p. (BIOINFORMATICS 2014 - 5th Int. Conf. on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 7th Int. Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2014).

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

3 Scopus citations

Optimisation of miRNA-mRNA relationship prediction using biological features

Banwait, J. K., Ali, H. H. & Bastola, D. R., Jan 27 2014, In : International Journal of Computational Biology and Drug Design. 7, 1, p. 45-60 16 p.

Research output: Contribution to journalArticle

2 Scopus citations

Special Issue on ICCS 2012

Ali, H., Shi, Y. & Khazanchi, D., Mar 1 2014, In : Journal of Computational Science. 5, 2, p. 63-64 2 p.

Research output: Contribution to journalEditorial

2 Scopus citations
2013

A base composition analysis of natural patterns for the preprocessing of metagenome sequences.

Bonham-Carter, O., Ali, H. & Bastola, D., 2013, In : BMC bioinformatics. 14 Suppl 11, p. S5

Research output: Contribution to journalArticle

Open Access
4 Scopus citations