Publications: (version displayed here might be slightly different from final version)

• Peer-Reviewed:

  1. Searching for Missing Heritability: Designing Rare Variants Association Studies
     O. Zuk, S. Schaffner, K. Samocha, R. Do, E. Hechter, S. Katherisan, M. Daly, B. Neale, S.R. Sunyaev and E.S. Lander
     Proceedings of the National Academy of Sciences, doi: 10.1073/pnas.1322563111 (2014)
     Supp. Info.     Code
  
  
  2. High Resolution Microbial Community Reconstruction by Integrating Short Reads from Multiple 16S rRNA Regions
     A. Amir^*, A. Zeisel^*, O. Zuk^*, M. Elgart, S. Stern, O. Shamir, P.J. Turnbaugh, Y. Soen and N. Shental
     Nucleic Acid Research, doi: 10.1093/nar/gkt1070 (2013)
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  3. Accurate Profiling of Microbial Communities from Massively Parallel Sequencing using Convex Optimization
     O. Zuk, A. Amir, A. Zeisel, O. Shamir and N. Shental
     String Processing and Information Retrieval, 279-297 (2013)
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  4. Identification of Transcriptional Regulators in the Mouse Immune System
     V. Jojic, T. Shay, K. Sylvia, O. Zuk, X. Sun, J. Kang, A. Regev, D. Koller and ImmGen Consortium
     Nature Immunology 14 (6):633-643 (2013)
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  5. Conservation and Divergence in the Transcriptional Programs of the Human and Mouse Immune Systems
     T. Shay, V. Jojic, O. Zuk, K. Rothamel, D. Puyraimond-Zemmour, T. Feng, E. Wakamatsu, C. Benoist, D. Koller, A. Regev and ImmGen Consortium
     Proceedings of the National Academy of Sciences 110(8):2946–2951 (2013)
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  6. Identification of Small RNA Pathway Genes using Patterns of Phylogenetic Conservation and Divergence
     Y. Tabach, A.C. Billi, G.D. Hayes, M.A. Newman, O. Zuk, H. Gabel, R. Kamath, K. Yacoby, B. Chapman, S.M. Garcia, M. Borowsky, J.K. Kim and G. Ruvkun
     Nature 493(7434):694–698 (2013)
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  7. The Mystery of Missing Heritability: Genetic Interactions Create Phantom Heritability
     O. Zuk, E. Hechter, S.R. Sunyaev and E.S. Lander
     Proceedings of the National Academy of Sciences 109(4): 1193-1198 (2012)
     Supp. Info.     Slides     Code  
  
  
  8. A High-Resolution Map of Human Evolutionary Constraint using 29 Mammals
     K. Lindblad-Toh, M. Garber^*, O. Zuk^*, M.F. Lin^*, B.J. Parker^*, S. Washietl^*, P. Kheradpour^*, J. Ernst^*, G. Jordan^*, E. Mauceli^*, L.D. Ward^*, C.B. Lowe^*, A.K. Holloway^*, M. Clamp^*, S. Gnerre^*, J. Alfoldi, K. Beal, J. Chang, H. Clawson, F. Di Palma, S. Fitzgerald, P. Flicek, M. Guttman, M.J. Hubisz, D.B. Jaffe, I. Jungreis, D. Kostka, M. Lara, A.L. Martins, T. Massingham, I. Moltke, B.J. Raney, M.D. Rasmussen, A. Stark, A.J. Vilella, J. Wen, X. Xie, M.C. Zody, Broad Institute Sequencing Platform, Whole Genome Assembly Team, K.C. Worley, C.L. Kovar, D.M. Muzny, R.A. Gibbs, Baylor College of Medicine Human Genome Sequencing Center, W.C. Warren, E.R. Mardis, G.M. Weinstoc, R.K. Wilson, Washington University Genome Center, E. Birney, E.H. Margulies, J. Herrero, E.D. Green, D. Haussler, A. Siepel, N. Goldman, K.S. Pollard, J.S. Pedersen, E.S. Lander and M. Kellis.
     Nature, 478(7370):476–482 (2011)
     Supp. Info.     Supp. Website    
  
  
  9. Bacterial Community Reconstruction Using Compressed Sensing
     A. Amir^* and O. Zuk^*.
     Journal of Computational Biology, 18(11):1723-1741 (2011)
     Supp. Website     Code    
     Conf. Ver:   Bacterial Community Reconstruction Using Compressed Sensing
                         Research in Computational Molecular Biology, 1-15 (2011)
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  10. FDR Control with Adaptive Procedures and FDR Monotonicity
      A. Zeisel^*, O. Zuk^* and E. Domany.
      Annals of Applied Statistics, 5(2A):943-968 (2011)
      Supp. Info.     Slides     Code    
  
  
  11. A Composite of Multiple Signals Distinguishes Causal Variants in Regions of Positive Selection
      S.R. Grossman, I. Shylakhter, E.K. Karlsson, E.H. Byrne, S. Morales, G. Frieden, E. Hostetter, E. Angelino, M. Garber, O. Zuk, E.S. Lander, S.F. Schaffner and P.C. Sabeti.
      Science, 327(5967):883-886 (2010)
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  12. A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response
      M. Huarte, M. Guttman, D. Feldser, M. Garber, M.J. Koziol, D. Kenzelmann-Broz, A.M. Khalil, O. Zuk, I. Amit, M. Rabani, L.D. Attardi, A. Regev,, E.S. Lander, T. Jacks and J.L. Rinn.
      Cell, 142(3):409-419 (2010)
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  13. Identification of Rare Alleles and their Carriers using Compressed Se (que) nsing
      N. Shental, A. Amir and O. Zuk.
      Nucleic Acids Research, 38(19):e179 (2010)
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  14. Chromatin Signature Reveals Over a Thousand Highly Conserved Large Non-coding RNAs in Mammals
      M. Guttman, I. Amit, M. Garber, C. French, M.F. Lin, D. Feldser, M. Huarte, O. Zuk, B.W. Carey, J.P. Cassady, M.N. Cabili, R. Jaenisch, T.S. Mikkelsen, T. Jacks, N. Hacohen, B.E. Bernstein, M. Kellis, A. Regev, J.L. Rinn and E.S. Lander.
      Nature, 458(7235):223-227 (2009)
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  15. Association of Survival and Disease Progression with Chromosomal Instability: A Genomic Exploration of Colorectal Cancer
      M. Sheffer, M.D. Bacolod, O. Zuk, S.F. Giardina, H. Pincas, F. Barany, P.B. Paty, W.L. Gerald, D.A. Notterman and E. Domany.
      Proceedings of the National Academy of Sciences, 106(17):7131-7136 (2009)
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  16. Chromatin Profiling by Directly Sequencing Small Quantities of Immunoprecipitated DNA
      A. Goren, F. Ozsolak, N. Shoresh, M. Ku, M. Adli, C. Hart, M. Gymrek, O. Zuk, A. Regev, P.M. Milos and B.E. Bernstein.
      Nature Methods, 7(1):47-49 (2009)
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  17. Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses
      I. Amit, M. Garber, N. Chevrier, A.P. Leite, Y. Donner, T. Eisenhaure, M. Guttman, J.K. Grenier, W. Li, O. Zuk, L.A. Schubert, B. Birditt, T. Shay, A. Goren, X. Zhang, Z. Smith, R. Deering, R.C. McDonald, M. Cabili, B.E. Bernstein, J.L. Rinn, A. Meissner, D.E. Root, N. Hacohen and A. Regev.
      Science, 326(5950):257-263 (2009)
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  18. Wide-scale Analysis of Human Functional Transcription Factor Binding Reveals a Strong Bias Towards the Transcription Start Site
      Y. Tabach, R. Brosh, Y. Buganim, A. Reiner, O. Zuk, A. Yitzhaky, M. Koudritsky, V. Rotter and E. Domany.
      PLoS One, 2(8):e807 (2007)
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  19. Ranking under Uncertainty
      O. Zuk^*, L. Ein-Dor^* and E. Domany.
      Uncertainty in Artificial Intelligence 466-473 (2007)
      
  
  
  20. Thousands of Samples are Needed to Generate a Robust Gene List for Predicting Outcome in Cancer
      L. Ein-Dor^*, O. Zuk^* and E. Domany.
      Proceedings of the National Academy of Sciences, 15(103):5923-5928 (2006)
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  21. On the Number of Samples Needed to Learn the Correct Structure of a Bayesian Network
      O. Zuk, S. Margel and E. Domany.
      Uncertainly in Artificial Intelligence 560-567 (2006)
      Slides     Errata    
  
  
  22. From Finite-System Entropy to Entropy Rate for a Hidden Markov Process
      O. Zuk, E. Domany, I. Kanter and M. Aizenman.
      IEEE Signal Processing Letters, 13(9):517-520 (2006)
      Conf. Ver:   Taylor Series Expansions for the Entropy Rate of Hidden Markov Processes
                          IEEE International Conference on Communications, 4, 1598-1604 (2006)
      
  
  
  23. The Relative Entropy Rate for two Hidden Markov Processes
      O. Zuk.
      ITG Turbo Coding (2006)
      Slides    
  
  
  24. Sorting Points into Neighborhoods (SPIN): Data Analysis and Visualization by Ordering Distance Matrices
      D. Tsafrir, I. Tsafrir, L. Ein-Dor, O. Zuk, D.A. Notterman and E. Domany.
      Bioinformatics, 21(10):2301-2308 (2005)
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  25. The Promoters of Human Cell Cycle Genes Integrate Signals from two Tumor Suppressive Pathways during Cellular Transformation
      Y. Tabach, M. Milyavsky, I. Shats, R. Brosh, O. Zuk, A. Yitzhaky, R. Mantovani, E. Domany, V. Rotter and Y. Pilpel.
      Molecular Systems Biology, 1:doi:10.1038/msb4100030 (2005)
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  26. Finding Motifs in Promoter Regions
      L. Hertzberg, O. Zuk, G. Getz and E. Domany.
      Journal of Computational Biology, 12(3):314-330 (2005)
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  27. The Entropy of a Binary Hidden Markov Process
      O. Zuk, I. Kanter and E. Domany.
      Journal of Statistical Physics, 121(3):343-360 (2005)
      Slides    
      Conf. Ver:   Asymptotics of the Entropy Rate for a Hidden Markov Process
                          Data Compression Conference , 173-182, (2005)
      
  
  
  28. Applications of the Montgomery Exponent
      S. Gueron and O. Zuk.
      International Conference on Information Technology: Coding and Computing, 1:620-625 (2005)
      
  
  
  29. Masked Inversion in GF (2ⁿ) Using Mixed Field Representations and its Efficient Implementation for AES
      S. Gueron, O. Parzanchevsky and O. Zuk.
      Embedded Cryptographic Hardware: Methodologies and Architectures, 1-59454-012-8:213-228 (2004)
      
  
  
  30. Exponentiation Speed Up for Diffie-Hellman Key Agreement Protocol
      S. Gueron and O. Zuk.
      Intelligent Systems, New Generation (2004)
      
  
  
  31. On Smoluchowski Equations for Coagulation Processes with Multiple Absorbing States
      S. Gueron and O. Zuk.
      Monte Carlo Methods and Applications, 7(1-2):203-212 (2001)
      
  
  

• Thesis:

  1. Graphical Models: Theory and Applications to Biological Data (Ph.D. Thesis)
     O. Zuk.
     thesis (2007)
     
  
  
  2. Stochastic Models and Their Application to Animal Behaviour (M.Sc. Thesis)
     O. Zuk.
     thesis (2001)
     
  
  

• Patent:

  1. Device and Method of Manipulating Masked Data
     S. Gueron, O. Parzanchevski and O. Zuk.
     WO Patent WO/2004/070,510 (2004)
     
  
  
  2. Method and Device of Manipulating Data in Finite Fields
     S. Gueron and O. Zuk.
     EP Patent 1,547,301 (2005)
     
  
  

• Other:

  1. Compressed Sensing-based Pooling Experiments using Next Generation Sequencing
     N. Shental, A. Amir and O. Zuk.
     Information Theory and Applications Workshop 1-2 (2010)
     Slides     Code    
  
  
  2. Compressed Sensing Approach for High Throughput Carrier Screen
     Y. Erlich, N. Shental, A. Amir and O. Zuk.
     47th Annual Allerton Conference on Communication, Control, and Computing 539-544 (2009)