Group's Papers and Thesas

Dr. Himanshu Agrawal

  • Extreme Self-Organization in Networks Constructed from Gene Expression DataHimanshu Agrawal (2002), Physical Review Letters 89(26),   268702-(1-4). Download PDF

 

  • Potts Ferromagnets on Coexpressed Gene Networks:Identifying Maximally Stable Partitions, Himanshu Agrawal and Eytan Domany         (2003), Physical Review Letters 90(15), 158102-(1-4). Download PDF

 

  • Expression profiles of acute lymphoblastic and myeloblastic leukemias with ALL-1 rearrangements, T.Rozovskaia, O. Ravid-Amir, S. Tillib, G. Getz, E. Feinstein, H. Agrawal, A.Nagler, E.F. Rappaport, I. Issaeva, Y. Matsuo h ,U.R. Kees, T. Lapidot, F. Lo Coco, R. Foa, A. Mazo, T. Nakamura, C.M. Croce, G. Cimino, E. Domany and E. Canaani (2003), PNAS 100(13), 7853–7858 Download PDF

Omer Barad

  • Advanced Clustering Algorithm for Gene Expression Analysis using Statistical Physics Methods, M.Sc Thesis (2003). Download PDF

 

  • Design Principle of Gene Expression Used by Human Stem Cells; Implication for Pluripotency, Michal Golan-Mashiach, Jean-Eudes Dazard, Sharon Gerecht-Nir, Ninette Amariglio, Tamar Fisher, Jasmine Jacob-Hirsch, Bella Bielorai, Sivan Osenberg, Omer Barad, Gad Getz, Amos Toren, Gideon Rechavi, Joseph Eldor-Itskovitz, Eytan Domany, David Givol (2004), FASEB Download PDF

Hila Benjamin

  • GeneNote: whole genome expression profiles in normal human tissues, Orit Shmueli, Shirley Horn-Saban, Vered Chalifa-Caspi, Michael Shmoish, Ron Ophir, Hila Benjamin-Rodrig, Marilyn Safran, Eytan Domany, Doron Lancet (2003), C.R.Biologies 326, 1067–1072 Download PDF
     

  • Analysis of Gene Expression Data from Normal Human Tissues, M.Sc Thesis (2004). Download PDF
     

  • Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification, Itai Yanai, Hila Benjamin, Michael Shmoish, Vered Chalifa-Caspi, Maxim Shklar, Ron Ophir, Arren Bar-Even, Shirley Horn-Saban, Marilyn Safran, Eytan Domany, Doron Lancet and Orit Shmueli (2004), Bioinformatics Download PDF

 

Noa Bossel Ben-Moshe

 

 

 

Yotam Drier

 

  • Punctuated Evolution of Prostate Cancer Genomes, Baca SC, Prandi D, Lawrence MS, Mosquera JM, Romanel A, Drier Y, Park K, Kitabayashi N, MacDonald TY, Van Allen E, Kryukov GV, Theurillat JP, Soong TD, Nickerson E, Auclair D, Tewari A, Beltran H, Onofrio RC, Boysen G, Guiducci C, Barbieri CE, ibulskis K, Sivachenko A, Carter SL, Saksena G, Voet D, Ramos AH, Winckler W, Redman MC, Ardlie K, Kantoff PW, Gabriel SB, Golub TR, Meyerson M, Lander ES, Elemento O, Getz G, Demichelis F, Rubin MA, Garraway LA: Cell 2013, 153(3):666-677. 

 

 

 

  • Melanoma genome sequencing reveals frequent PREX2 mutations, Berger MF, Hodis E, Heffernan TP, Deribe YL, Lawrence MS, Protopopov A, Ivanova E, Watson IR, Nickerson E, Ghosh P, Zhang H, Zeid R, Ren X, Cibulskis K, Sivachenko AY, Wagle N, Sucker A, Sougnez C, Onofrio R, Ambrogio L, Auclair D, Fennell T, Carter SL, Drier Y, Stojanov P, Singer MA, Voet D, Jing R, Saksena G, Barretina J, Ramos AH, Pugh TJ, Stransky N, Parkin M, Winckler W, Mahan S, Ardlie K, Baldwin J, Wargo J, Schadendorf D, Meyerson M, Gabriel SB, Golub TR, Wagner SN, Lander ES, Getz G, Chin L, Garraway LA: Nature 2012, 485(7399):502-6.

 

 

  • The genomic complexity of primary human prostate cancer, Berger MF*, Lawrence MS*, Demichelis F*, Drier Y*, Cibulskis K, Sivachenko AY, Sboner A, Esgueva R, Pflueger D, Sougnez C, Onofrio R, Carter SL, Park K, Habegger L, Ambrogio L, Fennell T, Parkin M, Saksena G, Voet D, Ramos AH, Pugh TJ, Wilkinson J, Fisher S, Winckler W, Mahan S, Ardlie K, Baldwin J, Simons JW, Kitabayashi N, MacDonald TY, Kantoff PW, Chin L, Gabriel SB, Gerstein MB, Golub TR, Meyerson M, Tewari A, Lander ES, Getz G, Rubin MA, Garraway LA, Nature 2011, 470(7333):214-220.
    *These authors contributed equally to this work.

     

 

  • Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion, Bass AJ, Lawrence MS, Brace LE, Ramos AH, Drier Y, Cibulskis K, Sougnez C, Voet D, Saksena G, Sivachenko A, Jing R, Parkin M, Pugh T, Verhaak RG, Stransky N, Boutin AT, Barretina J, Solit DB, Vakiani E, Shao W, Mishina Y, Warmuth M, Jimenez J, Chiang DY, Signoretti S, Kaelin WG, Spardy N, Hahn WC, Hoshida Y, Ogino S, Depinho RA, Chin L, Garraway LA, Fuchs CS, Baselga J, Tabernero J, Gabriel S, Lander ES, Getz G, Meyerson M, Nat Genet. 2011 43(10):964-8.

 

 

  • Initial genome sequencing and analysis of multiple myeloma, Chapman MA, Lawrence MS, Keats JJ, Cibulskis K, Sougnez C, Schinzel AC, Harview CL, Brunet JP, Ahmann GJ, Adli M, Anderson KC, Ardlie KG, Auclair D, Baker A, Bergsagel PL, Bernstein BE, Drier Y, Fonseca R, Gabriel SB, Hofmeister CC, Jagannath S, Jakubowiak AJ, Krishnan A, Levy J, Liefeld T, Lonial S, Mahan S, Mfuko B, Monti S, Perkins LM, Onofrio R, Pugh TJ, Rajkumar SV, Ramos AH, Siegel DS, Sivachenko A, Stewart AK, Trudel S, Vij R, Voet D, Winckler W, Zimmerman T, Carpten J, Trent J, Hahn WC, Garraway LA, Meyerson M, Lander ES, Getz G, Golub TR, Nature 2011,471(7339):467-472.

     

     

 

Uri Einav

  • Class Discovery in Acute Lymphoblastic Leukemia using Gene Expression Analysis, M.Sc Thesis (2003).Download PDF

 

  • Gene expression analysis reveals a strong signature of an interferon-induced pathway in childhood lymphoblastic leukemia as well as in breast and ovarian cancer, Uri Einav, Yuval Tabach, Gad Getz, Assif Yitzhaky, Ugur Ozbek, Ninette Amariglio, Shai Izraeli, Gideon Rechavi and Eytan Domany (2005),Oncogene (2005), 1-9  Download PDF

 

Dr. Liat Ein-Dor

  • Outcome signature genes in breast cancer: is there a unique set? Liat Ein-Dor, Itai Kela, Gad Getz, David Givol and Eytan Domany (2004), Bioinformatics Download PDF

 

  • Sorting Points Into Neighborhoods (SPIN): Data Analysis and Visualization by Ordering Distance Matrices, D. Tsafrir, I. Tsafrir, L. Ein-Dor, O. Zuk, D. Notterman and E. Domany (2005), Bioinformatics21, 2301 Download PDF

 

Gad Elizur

  • Antigen Chip: Development and analysis; An application to autoimmune diseases, M.Sc Thesis (2004).Download PDF

 

  • Functional immunomics: Microarray analysis of IgG autoantibody repertoires predicts the future response of mice to induced diabetes, Francisco J. Quintana, Peter H. Hagedorn, Gad Elizur, Yifat Merbl, Eytan Domany, and Irun R. Cohen (2004). PNAS Download PDF

     

 

Hila Gal

  • Genome-Wide Expression Analysis using Novel Clustering Methods; Implications for Colon and Skin Cancer, M.Sc Thesis (2003). Download PDF

     

  • Coupled two-way clustering analysis of breast cancer and colon cancer gene expression data, Gad Getz, Hilah Gal, Itai Kela, Daniel A.Notterman and Eytan Domany (2003), Bioinformatics 19(9), 1079–1089Download PDF

 

  • Genome-wide comparison of human keratinocyte and squamous cell carcinoma responses to UVB irradiation:implications for skin and epithelial cancer, Jean-Eudes Dazard ,Hilah Gal, Ninette Amariglio, Gideon Rechavi, Eytan Domany and David Givol (2003), Oncogene 22, 2993–3006 Download PDF

 

  • Inhibition of p53-induced apoptosis without affecting expression of p53-regulated genes, Joseph Lotem, Hilah Gal, Rachel Kama, Ninette Amariglio, Gideon Rechavi, Eytan Domany, Leo Sachs, David Givol (2003), PNAS 100(11), 6718–6723 Download PDF

     

 

Dr. Gaddy Getz

  • Classification and Clustering of Protein Structures, M.Sc Thesis (1998). Download PDF

 

  • Super-paramagnetic clustering of yeast gene expression profiles, G. Getz, E. Levine, E. Domany, M. Q. Zhang (2000). Download PDF

 

  • Coupled two-way clustering analysis of gene microarray data, Gad Getz, Erel Levine and Eytan Domany (2000), PNAS 97(22) 12079–12084 Download PDF

 

  • DNA microarrays identification of primary and secondary target genes regulated by p53, Karuppiah Kannan, Ninette Amariglio, Gideon Rechavi, Jasmine Jakob-Hirsch, Itai Kela, Naftali Kaminski, Gad Getz, Eytan Domany and David Givol (2001), Oncogene 20, 2225 - 2234 Download PDF

 

  • Coupled two-way clustering server, Gad Getz and Eytan Domany (2002), Bioinformatics 19(9), 1153–1154Download PDF

 

  • Automated Assignment of SCOP and CATH Protein Structure Classifications From FSSP Scores, Gad Getz, Michele Vendruscolo, David Sachs, Eytan Domany (2002), PROTEINS: Structure, Function, and Genetics 46, 405–415 Download PDF

 

  • Coupled two-way clustering analysis of breast cancer and colon cancer gene expression data, Gad Getz, Hilah Gal, Itai Kela, Daniel A.Notterman and Eytan Domany (2003), Bioinformatics 19(9) 1079–1089Download PDF

 

  • Cluster analysis of human autoantibody reactivities in health and in type 1 diabetes mellitus: a bio-informatic approach to immune complexity, Francisco J.Quintana, Gad Getz, Guy Hed, Eytan Domany, Irun R.Cohen (2003), Journal of Autoimmunity 21, 65–75 Download PDF

 

  • Classification of Human Astrocytic Gliomas on the Basis of Gene Expression: A Correlated Group of Genes with Angiogenic Activity Emerges As a Strong Predictor of Subtypes, Sophie Godard, Gad Getz, Mauro Delorenzi, Pierre Farmer, Hiroyuki Kobayashi, Isabelle Desbaillets, Michimasa Nozaki, Annie-Claire Diserens, Marie-France Hamou, Pierre-Yves Dietrich, Luca Regli, Robert C. Janzer, Philipp Bucher, Roger Stupp, Nicolas de Tribolet, Eytan Domany, and Monika E.Hegi (2003), Cancer Research 63,6613–6625 Download PDF

 

  • Expression profiles of acute lymphoblastic and myeloblastic leukemias with ALL-1 rearrangements, T.Rozovskaia, O. Ravid-Amir, S. Tillib, G. Getz, E. Feinstein, H. Agrawal, A.Nagler, E.F. Rappaport, I. Issaeva, Y. Matsuo h ,U.R. Kees, T. Lapidot, F. Lo Coco, R. Foa, A. Mazo, T. Nakamura, C.M. Croce, G. Cimino, E. Domany and E. Canaani (2003), PNAS 100(13), 7853–7858 Download PDF

 

  • Large Scale Analysis of Biological Data using Physically Motivated Techniques, Ph.D Thesis (2003).Download PDF

 

  • FSSP to SCOP and CATH (F2CS) Prediction Server, Gad Getz, Alina Starovolsky and Eytan Domany (2004), Bioinformatics 20(13) 2150–2152 Download PDF

 

  • Design Principle of Gene Expression Used by Human Stem Cells; Implication for Pluripotency, Michal Golan-Mashiach, Jean-Eudes Dazard, Sharon Gerecht-Nir, Ninette Amariglio, Tamar Fisher, Jasmine Jacob-Hirsch, Bella Bielorai, Sivan Osenberg, Omer Barad, Gad Getz, Amos Toren, Gideon Rechavi, Joseph Eldor-Itskovitz, Eytan Domany, David Givol (2004), FASEB Download PDF

 

  • Outcome signature genes in breast cancer: is there a unique set? Liat Ein-Dor, Itai Kela, Gad Getz, David Givol and Eytan Domany (2004), Bioinformatics Download PDF

 

  • Finding Motifs in Promoter Regions, Libi Hertzberg,Or Zuk,Gad Getz and Eytan Domany (2005),JOURNAL OF COMPUTATIONAL BIOLOGY 12(3), 314-330 Download PDF

 

  • Gene expression analysis reveals a strong signature of an interferon-induced pathway in childhood lymphoblastic leukemia as well as in breast and ovarian cancer, Uri Einav, Yuval Tabach, Gad Getz, Assif Yitzhaky, Ugur Ozbek, Ninette Amariglio, Shai Izraeli, Gideon Rechavi and Eytan Domany (2005),Oncogene (2005), 1-9  Download PDF

 

  • Semi Supervised Learning - a Statistical Physics Approach, G. Getz, N. Shental and E. Domany (2005),Proceedings of "Learning with partially classified training data - ICML 2005" workshop. Download PDF

 

Guy Hed

  • The Nature of the Spin Glass Phase in Finite Dimension: Correlated Spin Domains Generate Hierarchical Structure in State Space, M.Sc Thesis (2001). Download PDF

 

  • Spin Domains Generate Hierarchical Ground State Structure in J = ± 1 Spin Glasses, Guy Hed, Alexander K.Hartmann, Dietrich Stauffer, and Eytan Domany (2001), Physical Review Letters 86(14),   3148-3151.Download PDF

 

  • State hierarchy induced by correlated spin domains in short-range spin glasses, Eytan Domany, Guy Hed, Matteo Palassini,  A.P. Young (2001), Physical Review B 64, 224406(1-21) Download PDF

 

  • New extrapolation of overlap distribution in spin glasses, G. Hed, A.K. Hartmann, E. Domany (2001),Europhysics Letters 55(1), 112-118 Download PDF

 

  • Cluster analysis of human autoantibody reactivities in health and in type 1 diabetes mellitus: a bio-informatic approach to immune complexity, Francisco J.Quintana, Gad Getz, Guy Hed, Eytan Domany, Irun R.Cohen (2003), Journal of Autoimmunity 21, 65–75 Download PDF

 

  • Lack of Ultrametricity in the Low Temperature phase of 3D Ising Spin Glasses, Guy Hed, A. P. Young, Eytan Domany (2003), (submitted) Download PDF

 

Libi Hertzberg

  • Probabilistic Motif Searching, M.Sc Thesis (2003). Download PDF

 

  • Finding Motifs in Promoter Regions, Libi Hertzberg,Or Zuk,Gad Getz and Eytan Domany (2005),JOURNAL OF COMPUTATIONAL BIOLOGY 12(3), 314-330 Download PDF

 

  • STOP: searching for transcription factor motifs using gene expression, Hertzberg L, Izraeli S, Domany E. (2007), Bioinformatics 23, 1737-1743 Download PDF

 

  • Prediction of chromosomal aneuploidy from gene expression data, Hertzberg L, Betts DR, Raimondi SC, et al (2007), Genes Chromosomes Cancer 46,75-86 Download PDF

     

  • Trisomy of chromosome 21 in leukemogenesis, Izraeli S, Rainis L, Hertzberg L, Smooha G, Birger Y. (2007),  Blood Cells Mol Dis 39, 156-159 Download PDF

 

Itai Kela

  • Unraveling Biological Information from Gene Expression Data  using Advanced Clustering Techniques ,M.Sc Thesis (2001). Download PDF

 

  • DNA microarrays identification of primary and secondary target genes regulated by p53, Karuppiah Kannan, Ninette Amariglio, Gideon Rechavi, Jasmine Jakob-Hirsch, Itai Kela, Naftali Kaminski, Gad Getz, Eytan Domany and David Givol (2001), Oncogene 20, 2225 - 2234 Download PDF

 

  • Identification of Direct p73 Target Genes Combining DNA Microarray and Chromatin Immunoprecipitation Analyses, Giulia Fontemaggi, Itai Kela, Ninette Amariglio, Gideon Rechavi, Janakiraman Krishnamurthy, Sabrina Strano, Ada Sacchi, David Givol, Giovanni Blandino (2002), The Journal of Biological Chemistry 277(45) 43359–43368 Download PDF

     

  • Coupled two-way clustering analysis of breast cancer and colon cancer gene expression data, Gad Getz, Hilah Gal, Itai Kela, Daniel A.Notterman and Eytan Domany (2003), Bioinformatics 19(9), 1079–1089Download PDF

 

  • Outcome signature genes in breast cancer: is there a unique set? Liat Ein-Dor, Itai Kela, Gad Getz, David Givol and Eytan Domany (2004), Bioinformatics Download PDF

 

Mark Koudritsky

  • Wide-Scale Analysis of Human Functional Transcription Factor Binding Reveals a Strong Bias towards the Transcription Start Site, Yuval Tabach, Ran Brosh, Yossi Buganim, Anat Reiner, Or Zuk, Assif Yitzhaky, Mark Koudritsky, Varda Rotter, Eytan Domany (2007), PLOS ONE Download PDF

     

Erel Levine

 

  • Un-Supervised Estimation of Cluster Validity - Methods and Applications, M.Sc Thesis (1999). Download PDF

     

  • Super-paramagnetic clustering of yeast gene expression profiles, G. Getz, E. Levine, E. Domany, M. Q. Zhang (2000). Download PDF

 

  • Coupled two-way clustering analysis of gene microarray data, Gad Getz, Erel Levine and Eytan Domany (2000), PNAS 97(22) 12079–12084 Download PDF

 

  • Resampling Method for Unsupervised Estimation of Cluster Validity, Erel Levine, Eytan Domany (2001),Neural Computation 13, 2573–2593 Download PDF

     

    Shiri Margel

     

  • A Method For Reconstructing Transcriptional Regulatory Networks, M.Sc Thesis (2005). Download PDF

     

    Michal Mashiach

     

  • The Secret of Stem Cells; Transcriptional Profiling of Human Stem Cells M.Sc Thesis (2003). Download PDF

 

  • Design Principle of Gene Expression Used by Human Stem Cells; Implication for Pluripotency, Michal Golan-Mashiach, Jean-Eudes Dazard, Sharon Gerecht-Nir, Ninette Amariglio, Tamar Fisher, Jasmine Jacob-Hirsch, Bella Bielorai, Sivan Osenberg, Omer Barad, Gad Getz, Amos Toren, Gideon Rechavi, Joseph Eldor-Itskovitz, Eytan Domany, David Givol (2004), FASEB Download PDF

 

  • Vascular Gene Expression and Phenotypic Correlation during Differentiation of Human Embryonic Stem Cells, Sharon Gerecht-Nir, Jean-Eudes Dazard, Michal Golan-Mashiach, Sivan Osenberg, Alex Botvinnik, Ninette Amariglio, Eytan Domany, Gideon Rechavi, David Givol and Joseph Itskovitz-Eldor (2004),Developmental Dynamics Download PDF

 

Dvir Netanely

  • Induction in myeloid leukemic cells of genes that are expressed in different normal tissues, Lotem J, Benjamin H, Netanely D, Domany E, Sachs L. (2004)  PNAS 101(45), 16022-7 Download PDF

 

  • Network analysis of protein structures identifies functional residues, Amitai G, Shemesh A, Sitbon E, Shklyar M, Netanely D, Venger I & Pietrokovski S (2004)  Journal of Molecular Biology, Volume 344(4),1135-1146 Download PDF

 

  • Human cancers overexpress genes that are specific to a variety of normal human tissues, Joseph Lotem, Dvir Netanely, Eytan Domany, and Leo Sachs (2005), PNAS, 102(51), 18556 - 18561 Download PDF

 

  • Gene Expression Analysis of Mesenchymal Stem Cell Differentiation and Leukemic Over Expression of Tissue Specific Genes, M.Sc Thesis (2006) Download PDF

     

Osnat Ravid

  • DNA Microarray Analysis Using Statistical Methods and Clustering: Three Case Studies. M.Sc Thesis (2003). Download PDF

 

  • Expression profiles of acute lymphoblastic and myeloblastic leukemias with ALL-1 rearrangements, T.Rozovskaia, O. Ravid-Amir, S. Tillib, G. Getz, E. Feinstein, H. Agrawal, A.Nagler, E.F. Rappaport, I. Issaeva, Y. Matsuo h ,U.R. Kees, T. Lapidot, F. Lo Coco, R. Foa, A. Mazo, T. Nakamura, C.M. Croce, G. Cimino, E. Domany and E. Canaani (2003), PNAS 100(13), 7853–7858 Download PDF

Anat Reiner

  • Wide-Scale Analysis of Human Functional Transcription Factor Binding Reveals a Strong Bias towards the Transcription Start Site, Yuval Tabach, Ran Brosh, Yossi Buganim, Anat Reiner, Or Zuk, Assif Yitzhaky, Mark Koudritsky, Varda Rotter, Eytan Domany (2007), PLOS ONE Download PDF

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Tal Shay

  •  From DNA Copy Number to Gene Expression: Local aberrations, Trisomies and Monosomies, Ph.D Thesis (2008). Download PDF

Michal Sheffer

  • Genome Wide Expression Analysis of Colorectal Cancer and Cervical Cancer, M.Sc Thesis (2005)Download PDF

 

  • Identification of a Proliferation Gene Cluster Associated with HPV E6/E7 Expression Level and Viral DNA Load in     Invasive Cervical Carcinoma, Christophe Rosty, Michal Sheffer, Dafna Tsafrir, Nicolas Stransky, Ilan Tsafrir, Martine Peter, Patricia de Cremoux, Anne de La Rochefordiere, Remy Salmon, Thierry Dorval, Jean Paul Thiery, Jerome Couturier, Francois Radvanyi, Eytan Domany and Xavier Sastre-Garau (2005), Oncogene (2005), 1-11  Download PDF

 

Noam Shental

  • Adjustment Learning and Relevant Component AnalysisNoam Shental, Tomer Hertz, Daphna Weinshall and Misha Pavel , 7th European conference of Computer Vision. Download PDF

 

  • Enhancing Image and Video Retrieval: Learning Via Equivalence ConstraintsTomer Hertz, Aharon Bar-Hillel, Noam Shental and Daphna Weinshall, IEEE Conf. on Computer Vision & Pattern Recognition, Madison WI, June 2003. Download PDF

 

  • Computing Gaussian Mixture Models with EM using Side Information, Noam Shental, Aharon Bar-Hillel, Tomer Hertz and Daphna Weinshall, Workshop on "The Continuum from Labeled to Unlabeled Data in Machine Learning and Data Mining", 20th International Conference on Machine Learning (ICML 2003), Washington DC, August 2003. Download PDF

 

  • Learning Distance Functions Using Equivalence Relations, Aharon Bar-Hillel, Tomer Hertz, Noam Shental and Daphna Weinshall, 20th International Conference on Machine Learning (ICML 2003), Washington DC, August 2003. Download PDF

 

  • Learning and Inferring Image Segmentations Using the GBP Typical Cut, Noam Shental, Assaf Zomet, Tomer Hertz and Yair Weiss, 9th International Conference on Computer Vision, Nice, France, October 2003. Download PDF

 

  • Pairwise Clustering and Graphical Models, Noam Shental, Assaf Zomet, Tomer Hertz and Yair Weiss,(accepted to NIPS 03) Download PDF

 

  • Computing Gaussian Mixture Models with EM using Side Information, Noam Shental, Aharon Bar-Hillel, Tomer Hertz and Daphna Weinshall, (accepted to NIPS03) Download PDF

 

  • Semi Supervised Learning - a Statistical Physics Approach, G. Getz, N. Shental and E. Domany (2005),Proceedings of "Learning with partially classified training data - ICML 2005" workshop. Download PDF

     

Yuval Tabach

  • Gene expression analysis reveals a strong signature of an interferon-induced pathway in childhood lymphoblastic leukemia as well as in breast and ovarian cancer, Uri Einav, Yuval Tabach, Gad Getz, Assif Yitzhaky, Ugur Ozbek, Ninette Amariglio, Shai Izraeli, Gideon Rechavi and Eytan Domany (2005),Oncogene (2005), 1-9  Download PDF

 

  • Transcriptional programs following genetic alterations in p53, INK4A, and H-Ras genes along defined stages of malignant transformation, Michael Milyavsky, Yuval Tabach, Igor Shats, Neta Erez, Yehudit Cohen, Xiaohu Tang, Marina Kalis, Ira Kogan, Yosef Buganim, Naomi Goldfinger, Doron Ginsberg, Curtis C. Harris, Eytan Domany and Varda Rotter (2005), Cancer Research, 65, 4531 Download PDF

 

 

  • Wide-Scale Analysis of Human Functional Transcription Factor Binding Reveals a Strong Bias towards the Transcription Start Site, Yuval Tabach, Ran Brosh, Yossi Buganim, Anat Reiner, Or Zuk, Assif Yitzhaky, Mark Koudritsky, Varda Rotter, Eytan Domany (2007), PLOS ONE Download PDF

 

Dafna Tsafrir

  • Sorting Points Into Neighborhoods (SPIN): Data Analysis and Visualization by Ordering Distance Matrices, D. Tsafrir, I. Tsafrir, L. Ein-Dor, O. Zuk, D. Notterman and E. Domany (2005), Bioinformatics21, 2301 Download PDF

 

  • Identification of a Proliferation Gene Cluster Associated with HPV E6/E7 Expression Level and Viral DNA Load in     Invasive Cervical Carcinoma, Christophe Rosty, Michal Sheffer, Dafna Tsafrir, Nicolas Stransky, Ilan Tsafrir, Martine Peter, Patricia de Cremoux, Anne de La Rochefordiere, Remy Salmon, Thierry Dorval, Jean Paul Thiery, Jerome Couturier, Francois Radvanyi, Eytan Domany and Xavier Sastre-Garau (2005), Oncogene (2005), 1-11  Download PDF

 

Dr. Ilan Tsafrir

  • Sorting Points Into Neighborhoods (SPIN): Data Analysis and Visualization by Ordering Distance Matrices, D. Tsafrir, I. Tsafrir, L. Ein-Dor, O. Zuk, D. Notterman and E. Domany (2005), Bioinformatics21, 2301 Download PDF

 

  • Identification of a Proliferation Gene Cluster Associated with HPV E6/E7 Expression Level and Viral DNA Load in     Invasive Cervical Carcinoma, Christophe Rosty, Michal Sheffer, Dafna Tsafrir, Nicolas Stransky, Ilan Tsafrir, Martine Peter, Patricia de Cremoux, Anne de La Rochefordiere, Remy Salmon, Thierry Dorval, Jean Paul Thiery, Jerome Couturier, Francois Radvanyi, Eytan Domany and Xavier Sastre-Garau (2005), Oncogene (2005), 1-11  Download PDF

 

Assif Yitzhaky

  • Gene expression analysis reveals a strong signature of an interferon-induced pathway in childhood lymphoblastic leukemia as well as in breast and ovarian cancer, Uri Einav, Yuval Tabach, Gad Getz, Assif Yitzhaky, Ugur Ozbek, Ninette Amariglio, Shai Izraeli, Gideon Rechavi and Eytan Domany (2005),Oncogene (2005), 1-9  Download PDF

 

 

 

  • Wide-Scale Analysis of Human Functional Transcription Factor Binding Reveals a Strong Bias towards the Transcription Start Site, Yuval Tabach, Ran Brosh, Yossi Buganim, Anat Reiner, Or Zuk, Assif Yitzhaky, Mark Koudritsky, Varda Rotter, Eytan Domany (2007), PLOS ONE Download PDF

 

 

 

 

 

 

 

 

 

 

Amit Zeisel

 

  • Amit Zeisel, Michael Stiassnie, and Yehuda Agnon. Viscous effects on wave generation by strong winds. Journal of Fluid Mechanics, 597, 343-369 (2008) Download PDF

 

  • Amit Zeisel*, Amnon Amir*, Wolfgang J. Koestler, Eytan Domany. Intensity dependent estimation of noise in microarrays improves detection of differentially expressed genes. BMC Bioinformatics 2010, 11:400 Download PDF

 

  • Libbat Tirosh-Finkel*, Amit Zeisel*, Miriam Brodt-Ivenshitz*, Ayelet Shamai, Zhong Yao, Rony Seger, Eytan Domany and Eldad Tzahor. BMP-mediated inhibition of FGF signaling promotes cardiomyocyte differentiation of anterior heart field progenitors. Development 137, 2989-3000 (2010) Download PDF

 

  • Avraham Roi, Sas-Chen Aldema, Manor Ohad, Steinfeld Israel, Shalgi Reut, Tarcic Gabi, Bossel Noa, Zeisel Amit, Amit Ido, Zwang Yaara, Enerly Espen, Russnes G. Hege, Biagioni Francesca, Mottolese Marcella, Strano Sabrina, Blandino Giovanni, Brresen-Dale Anne-Lise, Pilpel Yitzhak, Yakhini Zohar, Segal Eran, Yarden Yosef. EGF decreases the abundance of microRNAs that restrain oncogenic transcription factors. Science Signaling 2010 3:124 Download PDF

 

  • Amit Zeisel*, Or Zuk*, Eytan Domany. FDR control with adaptive procedures and FDR monotonicity. The Annals of Applied Statistics, 2011, Vol. 5, No. 2A, 943968 Download PDF

 

  • Amit Zeisel*, Wolfgang J. Koestler*, Natali Molotski, Jonathan M. Tsai, Rita Krauthgamer, Jasmine Jacob-Hirsch, Gideon Rechavi, Yoav Soen, Steffen Jung, Yosef Yarden, and Eytan Domany. Coupled pre-mRNA and mRNA dynamics unveil operational strategies underlying transcriptional responses to stimuli. Molecular Systems Biology, 2011, 7:529 Download PDF

 

  • Chaluvally-Raghavan Pradeep, Amit Zeisel, Wolfgang J. Koestler, Jasmine Jacob-Hirsch, Benjamin HaibeKains, Ninette Amariglio, Nir Ben-Chetrit, Anna Emde, Inna Solomonov, Gera Neufeld, Martine Piccart, Irit Sagi, Christos Sotiriou, Gideon Rechavi, Eytan Domany, Christine Desmedt and Yosef Yarden. Modeling invasive breast cancer: growth factors propel progression of HER2-positive premalignant lesions. Oncogene 2011 doi:10.1038/onc.2011.547 Download PDF

 

  • Development of mathematical and statistical methods and their application to the analysis of high throughput biological data, Ph.D Thesis (2012) Download PDF

 

 

 

 

Or Zuk

  • Sorting Points Into Neighborhoods (SPIN): Data Analysis and Visualization by Ordering Distance Matrices, D. Tsafrir, I. Tsafrir, L. Ein-Dor, O. Zuk, D. Notterman and E. Domany (2005), Bioinformatics21, 2301 Download PDF

 

  • Finding Motifs in Promoter Regions, Libi Hertzberg,Or Zuk,Gad Getz and Eytan Domany (2005),JOURNAL OF COMPUTATIONAL BIOLOGY 12(3), 314-330 Download PDF

 

  • Asymptotics of the Entropy Rate for a Hidden Markov Process, Or Zuk, Ido Kanter and Eytan Domany (2005), Proceedings of Data Compression Conference DCC2005, Snowbird, Utah, Ed. J.A. Storer and M. Cohn, IEEE Computer Society, p. 173. Download PDF

 

  • The Entropy of a binary Hidden Markov Process, Or Zuk, Ido Kanter and Eytan Domany (2005), J. Stat. Phys. (in print) Download PDF

 

 

  • Wide-Scale Analysis of Human Functional Transcription Factor Binding Reveals a Strong Bias towards the Transcription Start Site, Yuval Tabach, Ran Brosh, Yossi Buganim, Anat Reiner, Or Zuk, Assif Yitzhaky, Mark Koudritsky, Varda Rotter, Eytan Domany (2007), PLOS ONE Download PDF