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Publication

 

MALIK YOUSEF

Patent

1.    U.S. Provisional Patent Application No. 61/005,569 “Recursive Cluster Elimination (RCE) for Classification and Feature Selection from Gene Expression Data”. Filed December 05, 2007 with Louise Showe, Wistar Institute

2.    PCT Patent Application No. PCT/US2008/013450 “Method for Diagnosing Lung Cancers using Gene Expression Profiles in Peripheral Blood Mononuclear Cells”. Filed December 05, 2008 Louise Showe, Wistar Institute

Books:

1.      Malik Yousef, One-class Document Classification, VDM Verlag Dr. Müller AG & Co. KG, 2009, ISBN 978-3-639-14869-5

 

Publications in Journals:

 

2.      Fang Lu, William Stedman, Malik Yousef, Rolf Renne, Paul M Lieberman, Epigenetic Regulation of KSHV Latency by Viral-Encoded MicroRNAs that Target Rta and the Cellular Rbl2-DNMT Pathway. Journal of virology. 01/2010.

3.      Malik Yousef,  Naim Najami and Walid Khaliefa ,A Comparison Study Between One-Class and Two-Class Machine Learning for MicroRNA Target Detection  ,Journal of Biomedical Science and Engineering (2009) (Accepted to Appear)

4.      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 ,Circulating Monocytes in HIV-1-Infected Viremic Subjects Exhibit an Antiapoptosis Gene Signature and Virus- and Host-Mediated Apoptosis Resistance . The Journal of Immunology, 2009, 182, 4459 -4470

5.      Michael Showe, Anil Vachani, Andrew Kossenkov, Malik Yousef, Calen Nichols, Elena Nikonova, Celia Chang, John Kucharczuk, Bao Tran, Elliot Wakeam, Ting-An Yie, David Speicher, William Rom, Steven Albelda, Louise Showe, 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, 2009

6.      Malik Yousef, Mohamed Ketany, Larry Manevitz , Louise C Showe, Michael K. Showe  , Classification and biomarker identification using gene network modules and support vector machines. BMC Bioinformatics 2009, 10:337 [Highly Accessed]

7.      Malik Yousef,  Louise C Showe and Michael K Showe,  A study of microRNAs in silico and in vivo: Bioinformatics approaches to microRNA Discovery and Target Identification,  FEBS J. 2009 Apr;276(8):2150-6

8.      Malik Yousef, Segun Jung, Louise C Showe and Michael K Showe, Learning from Positive Examples when the Negative Class is Undetermined- microRNA gene identification, Algorithms for Molecular Biology, 3:2 (2008) [Highly Accessed]

9.      Malik Yousef, Segun Jung, Andrew V. Kossenkov, Louise C. Showe and Michael K. Showe, Naïve Bayes classifier for microRNA target gene identification, Bioinformatics, 23: 2987 - 2992 (2007)

10. Jiajing Wang , Huai Li, Yitan Zhu, Malik Yousef , Michael Nebozhyn, Michael Showe, Louise Showe, Jason Xuan, Robert Clarke, Yue Wang1, VISDA: A free, open-source caBIGTM analytical tool for clustering and beyond, Bioinformatics,23: 2024 – 2027, (2007)

11. Malik Yousef, Louise C. Showe and Michael K. Showe, Recursive Cluster Elimination (RCE) for Classification and Feature Selection from Gene Expression Data. BMC Bioinformatics  8:144 (2007)  [Highly Accessed]

12. Larry M. Manevitz and Malik Yousef, One-Class Document Classification via Neural Networks , Neurocomputing 70(7-9):1466-1481,(2007)

13. Malik Yousef, Hagit Shatkay, Michael Nebozhyn, Louise C. Showe and Michael K. Showe, Combining Multi-Species Genomic Data for MicroRNA Identification Using Naïve Bayes Classifier. Bioinformatics, Vol. 22, No. 11, p. 1325-1334 (2006)(in Bioinformatics  2006 among the top 32  most-frequently read articles at the Bioinformatics journal)

14. 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, 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 (2006)

15. Malik Yousef, Andrei Kouranov, Zissimos Mourelatos, Artemis G. Hatzigeorgiou, Prediction of Human microRNA Targets Using Parallel Computing, WSEAS Transactions on Information Science and Applications, Vol. 1, p. 581-586 (2004)

16.  Larry M. Manevitz and Malik Yousef, 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 (2004).

17. Larry M. Manevitz and Malik Yousef, One-Class SVM for Document Classification, Journal of Machine Learning Research (JMLR), Vol. 2, p. 139-154 (2001)

18. Larry M. Manevitz, Malik Yousef and Dan Givoli, Finite Element Mesh Generation Using Self Organizing Neural Networks, Special Issue on Machine Learning. MicroComputers in Civil Engineering, Vol. 12, No. 4, 3-250 (1997).

Publication in Magazine

19. Malik Yousef and Waleed  Khalifa, MiRNAs: a review of bioinformatics approaches. Biotech International ,July 2009.

Refereed Papers in Conference Proceedings:

 

20.  Naim Najami, Alon Friedman, Malik Yousef, Regulation Profile of miRNAs hsa-miR-342 and hsa-miR-326 in Experimental Blood Brain Barrier Disruption, 5th International Symposium on Health Informatics and Bioinformatics, Turkey 2010 (HIBIT2010) (Abstract)

21.  Waleed Khalifa and Malik Yousef, Using Threshold Backward Feature Selection for Improving the Performance of One Class MicroRNA Target Predictions. IBS 2010. The Israeli Bioinformatics annual Symposium (2010)(Abstract)

22.  Malik Yousef and Waleed  Khalifa, 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, Turkey 2010 (HIBIT2010)

23.  Malik Yousef, Mohamed Ketany, Larry Manevitz , Louise C Showe, Michael K. Showe  , Classification and biomarker identification using gene network modules and support vector machines. BBC09, the fifth Benelux Bioinformatics Conference.

24.  Malik Yousef , Mohamed Ketany and  Larry Manevitz, Recursive gene Networks Elimination (RNE) For Feature Selection and Classification from Gene Expression data. The 10th Bar-Ilan Symposium on the Foundations of Artificial Intelligence (BISFAI),09

25.  Malik Yousef and Waleed  Khalifa, One-Class or Two-Class Machine Learning for MicroRNA Target Prediction. The 10th Bar-Ilan Symposium on the Foundations of Artificial Intelligence (BISFAI),09

26.  Waleed Khalifa, Naim Najami, Malik Youse (2009), MicroRNA Target Predictions Based Exclusively On Positive Examples. IBS 2009. The Israeli Bioinformatics annual Symposium (2009)(Abstract)

27.  Malik Yousef,  Naim Najami and Walid Khaliefa (2009), One-Class Machine Learning for MicroRNA Target Detection. 4th International Symposium on Health Informatics and Bioinformatics, Turkey’09 ((HIBIT2009)

28.  Trinh, H.V., Lesage, G., Malik Yousef , Greber, U. and Hemmi, S. (2008). Computational and Experimental Analysis of Potential miRNAs Encoded by Human Adenoviruses. RNAi – The RIGHT Track to Therapy. Abstract, Nov 03-05, Brussels, Belgium(Abstract)

29.  M. K. SHOWE, A. Vachani, A. Kossenkov, Malik Yousef, E. Nikonova, S. Albelda, L. C. Showe, Gene expression in peripheral blood cells detects early stage non-small cell lung cancer. ASCO-NCI-EORTC Annual Meeting on Molecular Markers in Cancer. Florida,USA, (2008) (Abstract)

30.  Malik Yousef, Segun Jung, Andrew V. Kossenkov, Louise C. Showe and Michael K. A web-server applying Naïve Bayes and SVM for microRNA gene prediction. ECAI08-BIGPAIA. Greece (2008)

31.  Mohamed Ketany, Larry Manevitz, Louise C Showe, Michael K. Showe and Malik Yousef, Recursive Cluster Elimination using Biological gene Network For classification and feature selection from gene expression data.  IBS 2008. The Israeli Bioinformatics annual Symposium (2008)(Abstract)

32.  Malik Yousef, Louise C Showe, Roola Agbaria, Hung V Trinh, Guillaume Lesage and Michael K. Showe, Predicting MicroRNA Genes and Their Target Site using Structural and Sequence Features: Machine Learning Approach. Non-Coding RNAs: Computational Challenges and Applications, Antalya, Turkey (2008)

33.  Naim Najami, Hung V Trinh  and Malik Yousef. Developing Tolerant Crop Plants to Abiotic Stresses Possible Role of miRNAs. Non-Coding RNAs: Computational Challenges and Applications, Antalya, Turkey (2008)

34.  Malik Yousef, Segun Jung, Louise C. Showe and Michael K. Showe, A Web-Server Predicting MicroRNAs based on Machine Learning Approaches, Greater Philadelphia Bioinformatics Alliance (2007)(poster).

35.  Hsiuan-Lin Wu, Malik Yousef, Michael Nebozhyn, Celia Chang and Louise Showe, Microarray Analysis In Macrophages Infected With Suicidal Transgenic Leishmania Spp, Greater Philadelphia Bioinformatics Alliance, (2005) (poster)

36.  Andrei Kouranov, Marianthi Kiriakidou, Peter T. Nelson, Petko Fitziev, Costas Bouyioukos, Malik Yousef, Zissimos Mourelatos, Artemis Hatzigeorgiou,  A Combined Computational-Experimental Approach Predicts Human microRNA Targets, 12th International Conference On Intelligent Systems For Molecular Biology & 3rd European Conference On Computational Biology, ISMB/ECCB (2004)

37.  Manevitz, L. and Malik Yousef*, Document Classification on Neural Networks Using Only Positive Examples, Proc. of ACM SIGIR Conference on Research and Development in Information Retrieval, Athens, Greece (2000)

38.  Manevitz, L. and Malik Yousef*, The Surfer’s Apprentice, Neural Network Models and Intelligent Data Mining, BRAIN-MACHINE 2000 Workshop, 20-22 December (2000), Ankara, Turkey

39.  Manevitz, L., Givoli, D., Malik Yousef and Margi, M., 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 (1996)

40.  Manevitz, L., Givoli, D. and Malik Yousef*, Automatic Mesh Generation using Self Organizing Neural Networks, Proc. of Bar-Hillel Memorial Symposium, (Editor M. Kopple and E. Shamir), p.144-158 (1997)

41.  Manevitz, L., Givoli, D. and Malik Yousef, Placing Geometry and Topology in Meshes, Proc. of IAICV-12, p.102-112 (1996)

42.  Manevitz, L., Givoli, D and Malik Yousef*, Grid Generation using a Self-Organizing Neural Network, Proc. of BISFAI'95, The Fourth Bar-Ilan Symposium on Foundations of Artificial Intelligence, Israel (1995)

* Presenter