פרופ' מאלכ יוסף

abeer A, Temiz M, Bakir-Gungor B and Yousef M (2023) miRdisNET: Discovering microRNA biomarkers that are associated with diseases utilizing biological knowledge-based machine learning. Front. Genet. 13:1076554

Yousef, M., Ozdemir, F., Jaber, A. et al. PriPath: identifying dysregulated pathways from differential gene expression via grouping, scoring, and modeling with an embedded feature selection approach. BMC Bioinformatics 24, 60 (2023).

Voskergian D, Bakir-Gungor B, Yousef M. TextNetTopics Pro, a topic model-based text classification for short text by integration of semantic and document-topic distribution information. Front Genet. 2023 Oct 5;14:1243874.

Unlu Yazici M, Marron JS, Bakir-Gungor B, Zou F and Yousef M (2023) Invention of 3Mint for feature grouping and scoring in multi-omics. Front. Genet. 14:1093326.

Söylemez, Ü. G., Yousef, M., & Bakir-Gungor, B. (2023). AMP-GSM: Prediction of Antimicrobial Peptides via a Grouping–Scoring–Modeling Approach. Applied Sciences, 13(8), 5106. MDPI AG.

Marcos-Zambrano LJ, López-Molina VM, Bakir-Gungor B, Frohme M, Karaduzovic-Hadziabdic K, Klammsteiner T, Ibrahimi E, Lahti L, Loncar-Turukalo T, Dhamo X, Simeon A, Nechyporenko A, Pio G, Przymus P, Sampri A, Trajkovik V, Lacruz-Pleguezuelos B, Aasmets O, Araujo R, Anagnostopoulos I, Aydemir &, Berland M, Calle ML, Ceci M, Duman H, Gündoğdu A, Havulinna AS, Kaka Bra KHN, Kalluci E, Karav S, Lode D, Lopes MB, May P, Nap B, Nedyalkova M, Paciência I, Pasic L, Pujolassos M, Shigdel R, Susín A, Thiele I, Truică C-O, Wilmes P, Yilmaz E, Yousef M, Claesson MJ, Truu J and Carrillo de Santa Pau E (2023) A toolbox of machine learning software to support microbiome analysis. Front. Microbiol. 14:1250806.

Kuzudisli C, Bakir-Gungor B, Bulut N, Qaqish B, Yousef M. 2023. Review of feature selection approaches based on grouping of features. PeerJ 11:e15666

Khatib, M.; Mansbach-Kleinfeld, I.; Zaid, D.; Ifrah, A.; Yousef, M.; Sheikh Muhammad, A. Compliance with COVID-19 Regulations among Palestinian Citizens of Israel in the Context of Social Norms and Gender Roles. Sustainability 2023, 15, 11354.

Emma Qumsiyeh, Zaidoun Salah, Malik Yousef, miRGediNET: A comprehensive examination of common genes in miRNA-Target interactions and disease associations: Insights from a grouping-scoring-modeling approach, Heliyon, Volume 9, Issue 12, 2023

Odenthal L., Allmer J., Yousef M. (2022) Ensemble Classifiers for Multiclass MicroRNA Classification. In: Allmer J., Yousef M. (eds) miRNomics. Methods in Molecular Biology, vol 2257. Humana, New York, NY.

Bakir-Gungor B, Hacılar H, Jabeer A, Nalbantoglu OU, Aran O, Yousef M. 2022. Inflammatory bowel disease biomarkers of human gut microbiota selected via different feature selection methods. PeerJ 10:e13205

Khan F.N., Yousef M., Raza K. (2022) Machine Learning-Based Models in the Diagnosis, Prognosis and Effective Cancer Therapeutics: Current State-of-the-Art. In: Raza K. (eds) Computational Intelligence in Oncology. Studies in Computational Intelligence, vol 1016. Springer, Singapore.

Khatib M, Sheikh Muhammad A, Hadid S, Ben Shlomo I, Yousef M. Correlates of Hookah Smoking among Arab Adults in Israel Identified by a Machine Learning Algorithm. Isr Med Assoc J. 2022 Apr;24(4):246-252.

Yousef M., Parveen A., Kumar A. (2022) Computational Methods for Predicting Mature microRNAs. In: Allmer J., Yousef M. (eds) miRNomics. Methods in Molecular Biology, vol 2257. Humana, New York, NY.

Qumsiyeh, E., Showe, L. & Yousef, M. GediNET for discovering gene associations across diseases using knowledge based machine learning approach. Sci Rep 12, 19955 (2022).

Söylemez, Ü.G.; Yousef, M.; Kesmen, Z.; Büyükkiraz, M.E.; Bakir-Gungor, B. Prediction of Linear Cationic Antimicrobial Peptides Active against Gram-Negative and Gram-Positive Bacteria Based on Machine Learning Models. Appl. Sci. 2022, 12, 3631.

Yousef M, Goy G and Bakir-Gungor B (2022) miRModuleNet: Detecting miRNA-mRNA Regulatory Modules. Front. Genet. 13:767455

Yousef M, Voskergian D. TextNetTopics: Text Classification Based Word Grouping as Topics and Topics' Scoring. Front Genet. 2022 Jun 20;13:893378.PMID: 35795215; PMCID: PMC9251539.

Akgül B. et al. (2022) 44 Current Challenges in miRNomics. In: Allmer J., Yousef M. (eds) miRNomics. Methods in Molecular Biology, vol 2257. Humana, New York, NY.

Yousef, M.; Kumar, A.; Bakir-Gungor, B. Application of Biological Domain Knowledge Based Feature Selection on Gene Expression Data. Entropy 2021, 23, 2.

Yousef, M.; Allmer, J. Classification of Precursor MicroRNAs from Different Species Based on K-mer Distance Features. Algorithms 2021, 14, 132.

Yousef M, Ülgen E, Uğur Sezerman O. 2021. CogNet: classification of gene expression data based on ranked active-subnetwork-oriented KEGG pathway enrichment analysis. PeerJ Computer Science 7:e336

Yousef M, Goy G, Mitra R, Eischen CM, Jabeer A, Bakir-Gungor B. 2021. miRcorrNet: machine learning-based integration of miRNA and mRNA expression profiles, combined with feature grouping and ranking. PeerJ 9:e11458

Uttarilli, A., Amalakanti, S., Kommoju, P., Sharma, S., Goyal, P., Manjunath, G., Upadhayay, V., Parveen, A., Tandon, R., Prasad, K., Dakal, T., Ben Shlomo, I., Yousef, M., Neerathilingam, M. & Kumar, A. (2021). Super-rapid race for saving lives by developing COVID-19 vaccines: . Journal of Integrative Bioinformatics, 18(1), 27-43.

Rohit Satyam, Malik Yousef, Sahar Qazi, Adil Manzoor Bhat, Khalid Raza, COVIDium: a COVID-19 resource compendium, Database, Volume 2021, 2021, baab057,

Marcos-Zambrano LJ, Karaduzovic-Hadziabdic K, Loncar Turukalo T, Przymus P, Trajkovik V, Aasmets O, Berland M, Gruca A, Hasic J, Hron K, Klammsteiner T, Kolev M, Lahti L, Lopes MB, Moreno V, Naskinova I, Org E, Paciência I, Papoutsoglou G, Shigdel R, Stres B, Vilne B, Yousef M, Zdravevski E, Tsamardinos I, Carrillo de Santa Pau E, Claesson MJ, Moreno-Indias I and Truu J (2021) Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment. Front. Microbiol. 12:634511.

Abdallah, L.; Badarna, M.; Khalifa, W.; Yousef, M. MultiKOC: Multi-One-Class Classifier Based K-Means Clustering. Algorithms 2021, 14, 134.

Yousef, M., Showe, L. & Ben Shlomo, I. (2021). Clinical presentation of COVID-19 – a model derived by a machine learning algorithm: . Journal of Integrative Bioinformatics, 18(1), 3-8.

Malik Yousef, Burcu Bakir-Gungor, Amhar Jabeer, Rehman Qureshi and Louise C. Showe(2020), Recursive Cluster Elimination based Rank Function (SVM-RCE-R) Implemented in Knime. F1000Research

Jamal Alqunds and Malik yousef (2020), Exploring the Effects of Text Complexity on its Quality in Social Medi, Journal of Enterprise Information Management.

Abdallah, L., Yousef, M. GrpClassifierEC: a novel classification approach based on the ensemble clustering space. Algorithms Mol Biol 15, 3 (2020).

Al Qundus, J., Paschke, A., Gupta, S., Alzouby, A.M. and Yousef, M. (2020), "Exploring the impact of short-text complexity and structure on its quality in social media", Journal of Enterprise Information Management, Vol. 33 No. 6, pp. 1443-1466.

Malik Yousef, Jamal Al Qundus, Adrian Paschke, Silvio Peikert(2020), TopicsRanksDC: Distance-based Topic Ranking applied on Two-Class Data. DEXA 2020. Communications in Computer and Information Science, Springer, Cham

Luise Odenthal1, Jens Allmer and Malik Yousef (2020), A Machine Learning-based Approach for the Categorization of MicroRNAs to their Species of Origin, International Conference on Bioinformatics Models, Methods and Algorithms. Proceedings of BIOSTEC 2020, 13th International Joint Conference on Biomedical Engineering Systems and Technologies

Malik Yousef, Louise Show and Izhar Ben Shlomo(2020), Machine Learning Analysis of National Vaccination Schedules and Rates of Compliance Reveals Correlation with COVID_19 Mortality. International Journal for Computational Biology (IJCB)

Malik Youse, Loai Abdalla and Jens Allmer (2019), maTE: Discovering Expressed MicroRNA - Target Interactions. Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4020–4028.

Saçar Demirci, M.D., Yousef, M., Allmer, J. (2019). Computational Prediction of Functional MicroRNA–mRNA Interactions. In: Lai, X., Gupta, S., Vera, J. (eds) Computational Biology of Non-Coding RNA. Methods in Molecular Biology, vol 1912. Humana Press, New York, NY.

Malik Yousef and Jens Allmer (2019), Classification of Pre-Cursor microRNAs from Different Species using a New Set of Features. In: Elloumi M. et al. (eds) Database and Expert Systems Applications. DEXA 2019. Communications in Computer and Information Science, Springer, Cham.

Malik Yousef (2019), Hamming Distance and K-mer Features for Classification of Pre-Cursor microRNAs from Different Species. In: Benavente-Peces C., Slama S., Zafar B. (eds) Proceedings of the 1st International Conference on Smart Innovation, Ergonomics and Applied Human Factors (SEAHF). SEAHF 2019. Smart Innovation, Systems and Technologies, vol 150. Springer, Cham

Yousef, M., Khalifa, W., Acar, İ.E. et al. MicroRNA categorization using sequence motifs and k-mers. BMC Bioinformatics 18, 170 (2017).

Yousef, M., Nigatu, D., Levy, D. et al. Categorization of species based on their microRNAs employing sequence motifs, information-theoretic sequence feature extraction, and k-mers. EURASIP J. Adv. Signal Process. 2017, 70 (2017).

Nigatu, D., Sobetzko, P., Yousef, M. et al. Sequence-based information-theoretic features for gene essentiality prediction. BMC Bioinformatics 18, 473 (2017).