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  • 2020
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  • Hesham H Ali
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

Computational Approaches for Drug Design: A Focus on Drug Repurposing

Kim, S., Thapa, I., Samadi, F. & Ali, H., Jan 1 2020, Bioinformatics and Biomedical Engineering - 8th International Work-Conference, IWBBIO 2020, Proceedings. Rojas, I., Valenzuela, O., Rojas, F., Herrera, L. J. & Ortuño, F. (eds.). Springer, p. 213-223 11 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 12108 LNBI).

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

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
1 Scopus citations
Open Access
1 Scopus citations

Identifying Structural Changes in Correlation Networks Models of Cancer Gene Expression by Stage

Li, Q., Ghersi, D., Thapa, I., Zhang, L., Ali, H. & Cooper, K., Nov 2019, Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019. Yoo, I., Bi, J. & Hu, X. T. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 2075-2082 8 p. 8983069. (Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019).

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

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

1 Scopus citations

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

Cluster analysis of biological networks

Sharma, A., Ali, H. & Ghersi, D., Jan 1 2018, Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics. Elsevier, Vol. 1-3. p. 1036-1046 11 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

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

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

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

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 : 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

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 : 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 : 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

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