CURRICULUM VITAE

MALIK YOUSEF

Cell phone: 052-643-7156

Date of Birth:            September, 4, 1970
Citizenship:               Israel
Marital Status:           Married +       4

Last Title:

Member of the Academic committee, The College of Sakhnin (2010)
Dean of Graduate Studies, The College of Sakhnin (2010)                       
Senior Lecture at Al-Qasemi College  (2010)                         במכללת אלקאסמי מרצה בכיר  
    Researcher, GS & Haifa University      חוקר , מכון מחקר אגודת הגליל ואוניברסיטת חיפה  
    Postdoctoral, University of Pennsylvania, USA   פוסט דוקטורט, אונ' פינסילבניה
Mayor of Dabburiya Local Council   ראש המועצה המקומית דבוריה                     

Research Interests:

• Machine Learning
• Text Mining - Document Classification Trained with Positive Examples Exclusively
• ­Bioinformatics – Machine Learning for microRNA Gene and Target Prediction  
• Bioinformatics:  Machine Learning for  Microarray Dataset Analysis

Current Projects:

          Bioinformatics

• microRNA gene prediction using Machine Learning approaches.
• microRNA target genes prediction using Machine Learning approaches.
• SVM-RCE - Recursive Cluster Elimination for Classification and Feature Selection from gene expression dataset
•  

Funded Projects

2009-210         פיתוח גישות חישוביות חדשות לניתוח קבוצות נתונים של ביטויים גנטיים וגילוי רשתות
 גנים משמעותיות, מכון מופ"ת  
2009-2011       MO-1, Novel Obesity Gene: Genotype and Phenotype 
Characterization of Obese and Lean Arab Groups from the Galilee.
                        Funded by ministry of science culture and sport. (Malik Yousef is the PI of
                         the project)                      
2008-2011       Naïve Bayes/SVM for MicroRNA Gene Target Predictions. Postdoctoral
that funded by the ESHKOL scholarship  program of the ministry of             
science culture and sport (Malik Yousef is the PI of the project)                      

Educational Background:

1997-2002:      Ph.D., Mathematics and Computer Science - Haifa University, Haifa, Israel
Dissertation: Automated Document Classification Trained with Positive Examples Exclusively. Thesis Advisor: Dr. Larry Manevitz

1993-1996:      M.A., Mathematics and Computer Science - Haifa University, Haifa, Israel Thesis: Automatic Mesh Generation Using Self-Organizing Neural Networks. Thesis Advisor: Dr. Larry Manevitz, Co-Advisor: Dr. Dan Givoli, Technion Institute
 Graduated CUM LAUDE
1991-1993:      B.A., Mathematics and Computer Science - Haifa University, Haifa, Israel

Work Experience:

2008 – current:   Computer Science Department, Hiafa University, Researcher
2007 – current:  Sakhnin+Alqasemi Colleges and G&S research Institute, Israel.
2007-current   Consulting Service for Lousie Showe laboratory,
Wistar Institute, UPENN, USA
200 3 - 2007: Postdoctoral Fellow, The Wistar Institute, University of  
Pennsylvania, Philadelphia, PA 19104, USA and Center for
Bioinformatics (UPENN)

2001-2002:      Postdoctoral, The Caesarea Edmond Benjamin de Rothschild Foundation, Institute for Interdisciplinary Applications of Computer Science,
University of Haifa, Mount Carmel, 31905 Haifa, Israel

1993-1999:      Graduate Assistant in Computer Science, Haifa University, Haifa, Israel
Courses:
1. An Introduction to Computer Science
2. An Introduction to Programming Methods with C++

1994–2000:     Lecturer in Computer Science in different colleges (Beit-Berl College, Baqa Gharbieh ,E-bleen)

 

PROFESSIONAL EXPERIENCE

2008 – 2011       Supervision for Postdoctoral that funded by the ESHKOL scholarship
program of the ministry of science culture and sport                      
2007 – Current    Supervision for Graduate student (M.A.) at CS-Haifa University, Israel
2005-2007          Supervisor for graduate students at Showe Lab, Wistar Institute, USA
2005-2007         Leader of the Statistical Data Analyzer (VISDA) in collaboration               
with the National Cancer Institute’s Cancer Bioinformatics Grid. Showe
Lab, Wistar Institute, USA

• The mayor of Dabburia Village, Israel. Manage a town and town budget.

PROFESSIONAL MEMEBRSHIP

2009-current        Associate Editor, Research Journal of Applied Science, Engineering
& Technology
2008-current        Member of the Alnbras Journal –Sakhnin College
2008-current        Management Committee of COST Action IC0602-Algorithmic Decision
Theory
2005-current       ISCB- International Society for Computational Biology

Professional Courses Attended:

2005                Intelligent Extraction of Information from Graphs and High Dimensional   
Data. The Institute for Pure and Applied Mathematics (IPAM), UCLA, Los Angeles, CA

Conference Committees and chair:

2010                 Program Committee. The 6th International Symposium on Health Informatics and Bioinformatics, (HIBIT 2011

2009                Session Chair. 1st BIOmics Workshop & Conference, Aug 30-Sep 4, Weizmann Institute of Science, Rehovot, Israel
2008               Program Committee. ECAI'08 Workshop on Bioinformatics, Genomics & Proteomics, an Artificial Intelligence Approach. Tuesday 22 July, 2008 Patras, Greece.

2005               Program Committee. The IADIS e-Society 2005 Conference

2004                Program Committee, Semantic Web Workshop, 27th Annual International ACM SIGIR Conference, July 25-July 29, 2004, Sheffield, UK

2003                Program Committee, Semantic Web Workshop, Workshop at SIGIR 2003 funded by Ontoweb (http://www.ontoweb.org/) (http://www.sigir2003.org/), 26th Annual International ACM SIGIR Conference July 28 - August 1, 2003, Toronto, Canada

Honors & awards:

2010                Excellent lecturer – Al-Qasemi College, Israel
1996                Graduated CUM LAUDE
1995                Faculty of Science and Science Education, Haifa University  

Journal Reviewer:

2009      to present         Journal of Machine Learning Research (JMLR)
2009      to present         Journal of Computer Science and System Biology
2009    to present         IEEE Transactions on Knowledge and Data Engineering (TKDE)
2009       to present          Biotechnology Progress
2008        to present       Algorithms for Molecular Biology
2008        to present       Bioinformatics (Oxford)
2007        to present         Nucleic Acids Research (NAR)
2007      to present       BMC-Bioinformatics
2007      to present       Cancer Informatics
2007      to present       Genomics
2006        to present         Frontiers in Bioscience
2006        to present         Journal In Silico Biology (ISB)
2004      to present       JZUS- “Biomedicine, Biochemistry & Biotechnology”

Invited Talks:

Invited talks in Conference

• ECAI'08 Workshop on Bioinformatics, Genomics & Proteomics, an Artificial Intelligence Approach. Tuesday 22 July, 2008 Patras, Greece.

Publication

MALIK YOUSEF

Patent

• 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
• 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:

• Malik Yousef, One-class Document Classification, VDM Verlag Dr. Müller AG & Co. KG, 2009, ISBN 978-3-639-14869-5
• Editor of volume “Computer-based Micro-RNA Gene Prediction” for Methods in Molecular Biology published by Humana Press, USA (part of the Springer publishing group).  In preparation (2010)

Publications in Journals:

• 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. Montaner, Increased metallothionein gene expression, zinc, and zincdependent resistance to apoptosis in circulating monocytes during HIV viremia. The Journal of Leukocyte Biology, 2010
• 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.
• 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 2010, 3, 247-252
• 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
• 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
• 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]
• 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
• 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]
• 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)
• 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)
• 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]
• Larry M. Manevitz and Malik Yousef, One-Class Document Classification via Neural Networks , Neurocomputing 70(7-9):1466-1481,(2007)
• 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)
• 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)
• 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)
•  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).
• Larry M. Manevitz and Malik Yousef, One-Class SVM for Document Classification, Journal of Machine Learning Research (JMLR), Vol. 2, p. 139-154 (2001)
• 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

• Malik Yousef and Waleed  Khalifa, MiRNAs: a review of bioinformatics approaches. Biotech International ,July 2 009.

Refereed Papers in Conference Proceedings:

• Waleed Khalifa and Malik Yousef , Feature elimination for one-class microRNA target prediction and gene identification. ECCB10, Belgium,2010(poster)
• 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)
• 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)
• 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)
• 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.
• 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
• 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
• Waleed Khalifa, Naim Najami, Malik Youse (2009), MicroRNA Target Predictions Based Exclusively On Positive Examples. IBS 2009. The Israeli Bioinformatics annual Symposium (2009)(Abstract)
• 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)
• 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)
• 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)
• 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)
• 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)
• 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)
• 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)
• 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).
• 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)
• 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)
• 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)
• 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
• 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)
• 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)
• Manevitz, L., Givoli, D. and Malik Yousef, Placing Geometry and Topology in Meshes, Proc. of IAICV-12, p.102-112 (1996)
• 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