Publications

 Articles in Refereed Journals

  1. *Malik Youse, Loai Abdalla and Jens Allmer (2018), maTE: Discovering Expressed MicroRNA – Target Interactions, Bioinformatics(revised),IF:5.481
  2. *Dawit Nigatu, Patrick Sobetzko, Malik Yousef, Werner Henkel(2017), Sequence-based information-theoretic features for gene essentiality prediction. BMC Bioinformatics, 18(1), 473. https://doi.org/10.1186/s12859-017-1884-5, IF: 2.435.
  3. *Malik Yousef, Dawit Nigatu and Loai Abdalla (2017), Automatic Categorization of PubMed microRNA Target Abstracts Based on Text Classification Techniques. Journal of Applied Bioinformatics and Computational Biology, J Appl Bioinforma Comput Biol 2017, 6:3DOI: 10.4172/2329-9533.1000138. IF:1.0.
  4. *Malik Yousef , Dawit Nigatu, Dalit Levy, Jens Allmer, and Werner Henkel (2017), Categorization of Species based on their MicroRNAs Employing Sequence Motifs, Information-Theoretic Sequence Feature Extraction, and k-mers. EURASIP Journal on Advances in Signal Processing 2017:70 DOI 10.1186/s13634-017-0506-8, IF: 1.961.
  5. *Loai Abdalla, Waleed Khalifa, Louise C.Show3 and Malik Yousef (2017), Selecting Significant Clusters of Genes based on Ensemble Clustering using Recursive Cluster Elimination (RCE), Journal of Proteomics & Bioinformatics 10: 186-192. doi: 10.4172/jpb.1000439. IF:1.57 (3.14 5 Year Journal Impact Factor).
  6. *Malik Yousef, Waleed Khalifa, ?lhan Erkin Acar and Jens Allmer(2017), MicroRNA Categorization using Sequence Motifs and k-mers. BMC Bioinformatics 18:170. IF: 2.435.
  7. *Jens Allmer and *Malik Yousef (2016). Editorial: Computational miRNomics. Journal of Integrative Bioinformatics, 13(5):302, 2016. http://journal.imbio.de/index.php?paper_id=302. SJR =0.42, RGIF:0.81
  8. *Malik Yousef, Waleed Khalifa and Loai AbdAllah(2016). Ensemble Clustering Classification compete SVM and One-Class classifiers applied on plant microRNAs Data. Journal of Integrative Bioinformatics, 13(5):304, 2016. Online Journal: http://journal.imbio.de/index.php?paper_id=304. SJR =0.42, RGIF:0.81
  9. *Waleed Khalifa, Malik Yousef, Duygu Sacar and MD, Jens Allmer (2016). The impact of feature selection on one and two-class classification performance for plant microRNAs. PeerJ 4:e2135 https://doi.org/10.7717/peerj.2135. IF: 2.18.
  10. *Malik Yousef, Duygu Sacar, Waleed Khalifa and Jens Allmer (2016). Feature Selection has a Large Impact on One-Class Classification Accuracy for MicroRNAs in Plants. Advances in Bioinformatics, vol. 2016, Article ID 5670851, 6 pages, 2016. doi:10.1155/2016/5670851. SJR:0.5, RGIF:2.39
  11. *Malik Yousef , Jens Allmer and Waldi Khaleifa (2016). Accurate Plant MicroRNA Prediction can be Achieved using Sequence Motif Features. Journal of Intelligent Learning Systems and Applications, 8, 9-22. doi: 10.4236/jilsa.2016.81002, Google-based Impact Factor: 1.73
  12. *Malik Yousef , Jens Allmer and Waldi Khaleifa (2015). Sequence Motif-based One-Class Classifiers can Achieve Comparable Acuracy to Two-Class Learners for Plant MicroRNA Detection. Journal of Biomedical Science and Engineering, 8, 684-694. doi: 10.4236/jbise.2015.810065, Google-based Impact Factor: 0.83.
  13. *Malik Yousef , Naim Najami , Loai Abedallah and Waldi Khaleifa (2014), Computational Approaches for Biomarker Discovery, Journal of Intelligent Learning Systems and Applications, 6, 153-161, Google-based Impact Factor: 1.21
  14. *Malik Yousef, Trinh HV, and Jens Allmer (2014). Intersection of MicroRNA and Gene Regulatory Networks and their Implication in Cancer, Current Pharmaceutical Biotechnology, pages:445 – 454, doi: 10.2174/1389201015666140519120855, IF:2.511 ,GS-Cited: 4
  15. *Jens Allmer and Malik Yousef, (2012). Computational methods for ab initio detection of microRNAs, Frontiers in Genetics, vol. 3, pages:5 . doi: 0.3389/fgene.2012.00209, SJR:1.46, GS-Cited:14
  16. *Bethsebah Gekonge; Malavika S Giri; Andrew V Kossenkov; Karam Mounzer; Michael Nebozyhn; Louise C Showe; Malik Yousef; Luis J Montaner (2012) Constitutive gene expression in monocytes from chronic HIV-1 infection overlaps with acute Toll-like receptor induced monocyte activation profiles. PloS one 2012;7(7):e41153. SJR:1.5 IF:3.73, GS-Cited:12
  17. *Sujoy Dutta, Celia Chang, Bala Krishna Kolli, §Shigeru Sassa, Malik Yousef, Michael Showe, Louise Showe, and Kwang-Poo Chang, (2012). Delta-aminolevulinate-induced host-parasite porphyric disparity for selective photolysis of transgenic Leishmania in the phagolysosomes of mononuclear phagocytes: A potential novel platform for vaccine delivery. Eukaryotic Cell 11(4): 430-441. SJR:19.85,IF: 2.82, GS-Cited: 2
  18. *Malik Yousef, Naim Najami and Walid Khaliefa , (2010). A Comparison Study Between One-Class and Two-Class Machine Learning for MicroRNA Target Detection . Journal of Biomedical Science and Engineering 2010, 3, 247-252, Google-based Impact Factor: 0.83, GS-Cited: 14
  19. *Andrea Raymond, Bethsebah Gekonge, Malavika S. Giri, Aidan Hancock Emmanouil Papasavvas, Jihed Chehimi, Andrew Kossevkov, Calen Nicols, Malik Yousef, Karam Mounzer, Jane Shull, Jay Kostman, Louise Showe, Luis J. (2010). Montaner, Increased metallothionein gene expression, zinc, and zinc dependent resistance to apoptosis in circulating monocytes during HIV viremia. The Journal of Leukocyte Biology. vol. 88 no. 3 P. 589-596 doi:10.1189/jlb.0110051. SJR:0.85, IF:1.606, GS-Cited:29
  20. *Fang Lu, William Stedman, Malik Yousef, Rolf Renne, Paul M Lieberman,(2010). Epigenetic Regulation of KSHV Latency by Viral-Encoded MicroRNAs that Target Rta and the Cellular Rbl2-DNMT Pathway. Journal of virology 84(6): 2697-2706, SJR:2.56, IF:5.076
  21. *Fang Lu; William Stedman; Malik Yousef; Rolf Renne; Paul M Lieberman,(2010). Epigenetic regulation of Kaposi’s sarcoma-associated herpesvirus latency by virus-encoded microRNAs that target Rta and the cellular Rbl2-DNMT pathway. Journal of virology 2010;84(6):2697-706 SJR:2.56, IF:5.076, GS-Cited: 154
  22. *Malik Yousef, Mohamed Ketany, Larry Manevitz , Louise C Showe, Michael K. Showe , (2009). Classification and biomarker identification using gene network modules and support vector machines. BMC Bioinformatics, 10:337 doi:10.1186/1471-2105-10-337, SJR:1.52, IF: 2.58, GS-Cited: 26
  23. *Malik Yousef, Louise C Showe and Michael K Showe,(2009). A study of microRNAs in silico and in vivo: Bioinformatics approaches to microRNA Discovery and Target Identification, Federation of European Biochemical Societies FEBS Journal ;276(8):2150-2156. IF: 4.25, GS-Cited: 45
  24. *Malavika S. Giri, Michael Nebozyhn, Andrea Raymond , Bethsebah Gekonge, Aidan Hancock, Shenoa Creer, Calen Nicols, Malik Yousef, Andrea S. Foulkes, Karam Mounzer, Jane Shull, Guido Silvestri, Jay Kostman, Ronald G. Collman, Louise Showe and Luis J. Montaner ,(2009). Circulating Monocytes in HIV-1-Infected Viremic Subjects Exhibit an Antiapoptosis Gene Signature and Virus- and Host-Mediated Apoptosis Resistance . The Journal of Immunology, 182, 4459 -4470 . IF: 5.520, GS-Cited: 63
  25. *Michael Showe, Anil Vachani, Andrew Kossenkov, Malik Yousef, Calen Nichols, Elena Nikonova, Celia Chang, John Kucharczuk, Bao Tran, Elliot Wakeam, Ting-An
  26. Yie, David Speicher, William Rom, Steven Albelda, Louise Showe,(2009). Gene Expression Profiles in Peripheral Blood Mononuclear Cells Can Distinguish Patients with Non-Small-Cell Lung Cancer from Patients with Non-Malignant Lung Disease. Cancer Research, 69(24):9202-10. IF: 8.650, GS-Cited: 106
  27. Malik Yousef, Segun Jung, Louise C Showe and Michael K Showe, (2008). Learning from Positive Examples when the Negative Class is Undetermined- microRNA gene identification. Algorithms for Molecular Biology, 3:2.doi:10.1186/1748-7188-3-2, SJR :0.85, IF :1.46,GS:-Cited: 57
  28. Malik Yousef, Segun Jung, Andrew V. Kossenkov, Louise C. Showe and Michael K. Showe, (2007). Naïve Bayes classifier for microRNA target gene identification. Bioinformatics, 23: 2987 – 299, IF :5.766, GS-Cited: 123
  29. Malik Yousef, Louise C. Showe and Michael K. Showe(2007), Recursive Cluster Elimination (RCE) for Classification and Feature Selection from Gene Expression Data. BMC Bioinformatics 8:144. doi: 10.1186/1471-2105-8-144 SJR:1.52, IF: 2.58, GS-Cited: 60
  30. Larry Manevitz and Malik Yousef (2007), One-Class Document Classification via Neural Networks. Neurocomputing 70(7-9):1466-1481,SJR:0.99, IF: 2.083, GS-Cited: 91
    Jiajing Wang , Huai Li, Yitan Zhu, Malik Yousef , Michael Nebozhyn, Michael Showe,
  31. Louise Showe, Jason Xuan, Robert Clarke, Yue Wang1, (2007), VISDA: an open-source caBIG™ analytical tool for data clustering and beyond. Bioinformatics,23: 2024 – 2027. IF: 5.766, GS-Cited: 17
  32. Malik Yousef, Hagit Shatkay, Michael Nebozhyn, Louise C. Showe and Michael K. Showe, (2006), Combining Multi-Species Genomic Data for MicroRNA Identification Using Naïve Bayes Classifier. Bioinformatics, Vol. 22, No. 11, p. 1325-1334, SJR:0.524.2, IF: 5.766, GS-Cited : 169
  33. Michael Nebozhyn, Laszlo Kari, Andrey Loboda, Calen Nichols, Malik Yousef, Alain H. Rook, Eric C. Vonderheid, Stuart Lessin, Lalitha Gudipati, Meiling Shang, Michael K. Showe and Louise C. Showe(2006), Quantitative PCR on 5 Genes Reliably Identifies CTCL Patients with 5-99% Circulating Tumor Cells with 90% Accuracy. Blood, Vol. 107, No. 8, p. 3189-3196. IF: 9.898, GS-Cited: 78
  34. Malik Yousef, Andrei Kouranov, Zissimos Mourelatos, Artemis G. Hatzigeorgiou (2004), Prediction of Human microRNA Targets Using Parallel Computing. WSEAS Transactions on Information Science and Applications, Vol. 1, p. 581-586. SJR :0.18, GS-Cited: 1
  35. Larry Manevitz and Malik Yousef (2004), A Web Navigation System Based on a Neural Network User-Model Trained with Only Positive Web Documents. Web Intelligence and Agent Systems (WIAS) Vol. 2, No.2 , p.137-144. SJR:0.39,GS-Cited: 4
  36. Larry Manevitz and Malik Yousef (2001), One-Class SVM for Document Classification. Journal of Machine Learning Research (JMLR), Vol. 2, p. 139-154. SJR :2.69, IF:3.42, GS-Cited: 902
  37. Larry Manevitz, Malik Yousef and Dan Givoli(1997), Finite Element Mesh Generation Using Self Organizing Neural Networks. Special Issue on Machine Learning. MicroComputers in Civil Engineering (12) 4, 233-250. IF: 5.625 GS-Cited: 30 (Computer-Aided Civil and Infrastructure Engineering Formerly: Microcomputers in Civil Engineering)

Articles in Conference Proceedings

  1. Larry Manevitz, Dan Givoli, Malik Yousef and Margi, M.(1996). AI and NN Tools for the Finite Element Method. Proc. of the First World Online Symposium of Soft Computing, Nagoya, Japan, (Editor T. Furuhoshi) p. 192-197. GS-Cited: 1
  2. Larry Manevitz., Dan Givoli. and Malik Yousef, (1996). Placing Geometry and Topology in Meshes, Proc. of IAICV-12 (Israeli Symposium on Artificial Intelligence and Computer Vision), p.102-112
  3. Larry Manevitz., Malik Yousef and Dan Givoli, (1997). Automatic Mesh Generation using Self Organizing Neural Networks, of Bar-Hillel Memorial Symposium, (Editor M. Kopple and E. Shamir), p.144-158
  4. Larry Manevitz, . and Malik Yousef (2000). Document Classification on Neural Networks Using Only Positive Examples.  Proceedings of 23rd ACM SIGIR Conference on Research in Information Retrieval (Sigir 2000), p. 304-307,Athens.
  5. Larry Manevitz. and Malik Yousef (2000). The Surfer’s Apprentice, Neural Network Models and Intelligent Data Mining. BRAIN-MACHINE 2000 Workshop, pages: 12, 20-22 December, Ankara, Turkey
  6. Malik Yousef, Segun Jung, Andrew V. Kossenkov, Louise C. Showe and Michael K (2008). A web-server applying Naïve Bayes and SVM for microRNA gene prediction. European Conference on Artificial Intelligence, Workshop Bioinformatics, Genomics & Proteomics, an Artificial Intelligence Approach (ECAI08-BIGPAIA), Pages:4, 22 July, Patras, Greece0
  7. *Malik Yousef, Naim Najami and Walid Khaliefa (2009). One-Class Machine Learning for MicroRNA Target Detection. 4th International Symposium on Health Informatics and Bioinformatics, (HIBIT2009), pages:7 April 16-18, 2009 METU Informatics Institute, Ankara, Turkey
  8. *Malik Yousef and Waleed Khalifa,(2010). A Zero-Norm Feature Selection Method for Improving the Performance of the One-Class Machine Learning for MicroRNA Target Detection. 5th International Symposium on Health Informatics and Bioinformatics, (HIBIT2010), 45–50, 20-22 April 2010, Antalya, Turkey, doi:  10.1109/HIBIT.2010.5478907. GS-Cited: 1
  9. *Najami Naim, Friedman Alon, Khalifa Waleed and Malik Yousef, (2011). Experimental Analysis Of Potential MicroRNAs Encoded During and After Blood Brain Barrier Disruption. 6th International Symposium on Health Informatics and Bioinformatics, (HIBIT2011), 108-115,2-5 May 2011,Izmir, Turkey, doi: 10.1109/HIBIT.2011.6450818
  10. Khalid Arar, Mahmood Khalil and Malik Yousef (2014), Leading change: Collaboration between Sakhnin Arab Teacher Education College and Al-Bashaer High School. ECER 2014, The Past, the Present and the Future of Educational Research. Dublin.
  11. *Malik Yousef , Jens Allmer and Waldi Khaleifa (2016), Feature Selection for MicroRNA Target Prediction: A Comparison of One-Class Feature Selection Methodologies, In Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2016) – Volume 3: BIOINFORMATICS, pages 216-225, ISBN: 978-989-758-170-0. February , Rome, Italy.
  12. *Malik Yousef and Naela hello(2017), What is an effective rubric, characteristics and principles of its construction. Intercollegiate Conference for Presenting the Final Master’s Degree Projects, MOFET, Israel.
  13. *Malik Yousef , Waldi Khaleifa, İlhan Erkin Acar and Jens Allmer (2017), Distinguishing Between MicroRNA Targets From Diverse Species Using Sequence Motifs And K-Mers, Proceedings of BIOSTEC 2017, 10th International Joint Conference on Biomedical Engineering Systems and Technologies, Porto., vol. 3, 2017
  14. *Malik Yousef, Dalit Levi and Jens Allmer(2018), Species categorization based on 3’UTR microRNA target sites using sequence features. International Conference on Bioinformatics Models, Methods and Algorithms. Proceedings of BIOSTEC 2018, 11th International Joint Conference on Biomedical Engineering Systems and Technologies. Volume 3: BIOINFORMATICS, pages 112-118 ,ISBN: 978-989-758-280-6, Finchal-Maderi , Portugal.
  15. Loai Abdallah and *Malik Yousef (2018), Decision Trees Applied on Ensemble Clustering Distance Space, ICDM 2018: 20th International Conference on Data Mining,Istanbul,Turkey Jul23-24,2018.
  16. Loai Abdallah and *Malik Yousef (2018), Ensemble Clustering based Dimensional Reduction. 8th International Workshop on Biological Knowledge Discovery from Data, DEXA-BIOKDD’18. Regensburg, Germany.

Articles or Chapters in Scientific Books

  1. *Malik Yousef, Naim Najami and Walid Khaleifa (2011). MicroRNA Identification Based on Bioinformatics Approaches, In Ning-Sun Yang (Eds.), Systems and Computational Biology – Molecular and Cellular Experimental Systems (pp. 205-216),   ISBN 978-953-307-280-7,  InTech Press, DOI: 10.5772/78.
  2. *Hamid Hamzeiy, Jens Allmer, and Malik Yousef (2014). Computational Methods for MicroRNA Target Prediction. In Malik Yousef and Jens Allemer(Eds.), miRNomics: MicroRNA Biology and Computational Analysis, Methods in Molecular Biology , Volume: 1107 (pp. 207-221), Humana Press, USA (Part of the Springer publishing group). DOI: 10.1007/978-1-62703-748-8_12. GS-Cited: 14
  3. Khalid Arar, Malik Yousef ,Rania Ismael and Amer Badarni (2016), Leading change: Collaboration between Sakhnin Arab Teacher Education College and Al-Bashaer High School.  In book: Building and Maintaining Collaborative Communities: Schools, University, and Community Organizations. Editors: J, Slater, R, Ravid, M, Reardon .
  4. *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.

Edited Books 

* Malik Yousef and Jens Allemer (2014), Editors of volume – miRNomics: MicroRNA Biology and Computational Analysis.  Series: Methods in Molecular Biology, Volume:1107, ISBN: 978-1-62703-747-1, 320 pages, Humana Press, USA (Part of the Springer publishing group). (50,000 downloads)GS-Cited: 1

Books

*Malik Yousef (2009), One-class Document Classification: One-class Document Classification via Neural Networks and Support Vector Machines, SBN 978-3-639-14869-5. 108 pages. Publisher: VDM  Verlag, Saarbrücken, Germany.

Dissertation

Automated Document Classification Trained with Positive Examples Exclusively, year 2002, pages 111, Language English, University of Haifa, Mathematics and Computer Sciences, Israel.Advisor: Prof. Larry Manevitz.