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

• Some Preprints:

• Explicit Computations for Delayed Semistatic Hedging
  Y. Dolinsky and O. Zuk.
  Code


• Selecting Covariates for Genome-Wide Association Studies
  E. Dor, I. Margaliot, N. Brandes, O. Zuk , M. Linial and N. Rappoport.
  


• Selecting Chromosomes for Polygenic Traits
  O. Zuk.
  Code


• A Correlation Inequality for Random Points in a Hypercube with Some Implications
  R. Jacobovic and O. Zuk.
  Slides     Code


• Enhancer Identification from DNA Sequence using Transfer and Adversarial Deep Learning
  D. Cohen, O. Zuk and T. Kaplan
  Supp. Info.


• Near-Optimal Pooling Designs for Biological Screens
  Y. Erlich, A. Gilbert, H. Ngo, A. Rudra, N. Thierry-Mieg, M. Wootters, D. Zielinski and O. Zuk
  biorxiv ver.: Biological Screens from Linear Codes: Theory and Tools


• Clustering Noisy Signals with Structured Sparsity Using Time-Frequency Representation
  T. Hope, A. Wagner and O. Zuk.
  Supp. Info.     Slides     Code

• Peer-Reviewed:

  1. Exponential Utility Maximization in a Discrete Time Gaussian Framework
     Y. Dolinsky and O. Zuk.
     SIAM Journal on Financial Mathematics to appear (2023)
     Code
  
  
  2. A Phase Transition for the Probability of Being a Maximum among Random Vectors with General iid Coordinates
     R. Jacobovic and O. Zuk.
     Statistics and Probability Letters 199:109847 (2023)
     
  
  
  3. Polygenic Embryo Screening: Four Clinical Considerations Warrant Further Attention
     S. Pereira, S. Carmi, G. Altarescu, J. Austin, D. Barlevy, A. Hershlag, E. Juengst, K. Kostick, E. Kovanci, R. Lathi, M. Mukherjee, I. Van-den Veyver, O. Zuk, G. Lazaro-Munoz and T. Lencz,
     Human Reproduction 37(7):1375 1378 (2022)
     
  
  
  4. Testing Independence with Biased Sampling
     Y. Tenzer, M. Mandel and O. Zuk.
     Journal of the American Statistics Association 17(540): 2194-2206 (2022)
     Supp. Info.     Code
  
  
  5. Co-Evolution Based Machine-Learning for Predicting Functional Interactions Between Human Genes
     D. Stupp, E. Sharon, I. Bloch, M. Zitnik, O. Zuk^* and Y. Tabach^*
     Nature Communications 12(1):1-14 (2021)
     Supp. Info.     Website
  
  
  6. Utility of Polygenic Embryo Screening for Disease Depends on the Selection Strategy
     T. Lencz, D. Backenroth, E. Granot-Hershkovitz, A. Green, K. Gettler, J.H. Cho, O. Weissbrod, O. Zuk and S. Carmi
     Elife DOI: 10.7554/eLife.64716 (2021)
     Supp. Info.     Code
  
  
  7. Comprehensive Gene Expression Analysis Detects Global Reduction of Proteasome Subunits in Schizophrenia
     L. Hertzberg, N. Maggio, I. Muler, A. Yitzhaky, M. Majer, V. Haroutaunian, O. Zuk, P. Katsel, E. Domany and M. Weiser
     Schizophrenia Bulletin 47(3):785-795 (2021)
     
  
  
  8. Deep Homology-Based Protein Contact-Map Prediction
     O. Ronen and O. Zuk
     Neurips Machine Learning in Computational Biology Workshop (2020)
     Code
  
  
  9. Screening Human Embryos for Polygenic Traits has Limited Utility
     E. Karavani^*, O. Zuk^*, D. Zeevi, N. Barzilai, N.C. Stefanis, A. Hatzimanolis, N. Smyrnis, D. Avramopoulos, L. Kruglyak, G. Atzmon, M. Lam, T. Lencz and S. Carmi
     Cell 179(6):1424-1435 (2019)
     Supp. Info.     Code
  
  
  10. ImmGen Report: Sexual Dimorphism in the Immune System Transcriptome
      S. Gal-Oz, B. Maier, H. Yoshida, K. Seddu, N. Elbaz, C. Czysz, O. Zuk, B.E. Stranger, H. Ner-Gaon and T. Shay
      Nature Communications 10:4295 (2019)
      Supp. Info.
  
  
  11. Substantial Batch Effects in TCGA Exome Sequences Undermine Pan-Cancer Analysis of Germline Variants
      R. Rasnic, N. Brandes, O. Zuk and M. Linial.
      BMC Cancer 19(1):1-10 (2019)
      Supp. Info.
  
  
  12. On The Asymptotic Efficiency of Selection Procedures for Independent Gaussian Populations
      R. Jacobovic and O. Zuk.
      Electronic Journal of Statistics 11(2): 5375-5405 (2017)
      Code
  
  
  13. Low-Rank Matrix Recovery from Row-and-Column Affine Measurements
      A. Wagner and O. Zuk.
      International Conference of Machine Learning 2012-2020 (2015)
      Supp. Info.     Slides     Code
  
  
  14. Exome Sequencing Identifies Rare LDLR and APOA5 Alleles Conferring Risk for Myocardial Infarction
      R. Do, N.O. Stitziel, H.H. Won, A.B. J rgensen, S. Duga, P.A. Merlini, A. Kiezun, M. Farrall, A. Goel, O. Zuk, I. Guella, R. Asselta, L.A. Lange, G.M. Peloso, P.L. Auer, NHLBI Exome Sequencing Project, D. Girelli, N. Martinelli, D.N. Farlow, M.A. DePristo, R. Roberts, A.F.R. Stewart, D. Saleheen, J. Danesh, S.E. Epstein, S. Sivapalaratnam, G.K. Hovingh, J.J. Kastelein, N.J. Samani, H. Schunkert, J. Erdmann, S.H. Shah, W.E. Kraus, R. Davies, M. Nikpay, C.T. Johansen, J. Wang, R.A. Hegele, E. Hechter, W. Marz, M.E. Kleber, J. Huang, A.D. Johnson, M. Li, G.L. Burke, M. Gross, Y. Liu, T.L. Assimes, G. Heiss, E.M. Lange, A.R. Folsom, H.A. Taylor, O. Olivieri, A. Hamsten, R. Clarke, D.F. Reilly, W. Yin, M.A. Rivas, P. Donnelly, J.E. Rossouw, B.M. Psaty, D.M. Herrington, J.G. Wilson, S.S. Rich, M.J. Bamshad, R.P. Tracy, L.A. Cupples, D.J. Rader, M.P. Reilly, J.A. Spertus, S. Cresci, J. Hartiala, W.H.W. Tang, S.L. Hazen, H. Allayee, A.P. Reiner, C.S. Carlson, C. Kooperberg, R.D. Jackson, E. Boerwinkle, E.S. Lander, S.M. Schwartz, D.S. Siscovick, R. McPherson, A. Tybjaerg-Hansen, G.R. Abecasis, H. Watkins, D.A. Nickerson, D. Ardissino, S.R. Sunyaev, C.J. O Donnell, D. Altshuler, S. Gabriel and S. Kathiresan.
      Nature 518(7537):102-106 (2015)
      Supp. Info.
  
  
  15. 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 111(4):E455 E464 (2014)
      Supp. Info.     Code
  
  
  16. 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)
      Supp. Info.     Code
  
  
  17. 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)
      Code
      
  
  
  18. 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)
      Supp. Info.
  
  
  19. 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)
      Supp. Info.
  
  
  20. 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)
      Supp. Info.
  
  
  21. 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  
  
  
  22. 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    
  
  
  23. 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)
                         Supp. Info.    
  
  
  24. 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    
  
  
  25. 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)
      Supp. Info.    
  
  
  26. 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)
      Supp. Info.    
  
  
  27. 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)
      Code    
  
  
  28. 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)
      Supp. Info.    
  
  
  29. 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)
      Supp. Info.    
  
  
  30. 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)
      Supp. Info.    
  
  
  31. 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)
      Supp. Info.    
  
  
  32. 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)
      Supp. Info.    
  
  
  33. Ranking under Uncertainty
      O. Zuk^*, L. Ein-Dor^* and E. Domany.
      Uncertainty in Artificial Intelligence 466-473 (2007)
      
  
  
  34. 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)
      Supp. Info.    
  
  
  35. 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    
  
  
  36. 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)
      
  
  
  37. The Relative Entropy Rate for two Hidden Markov Processes
      O. Zuk.
      ITG Turbo Coding (2006)
      Slides    
  
  
  38. 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)
      Supp. Info.    
  
  
  39. 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)
      Supp. Info.    
  
  
  40. Finding Motifs in Promoter Regions
      L. Hertzberg, O. Zuk, G. Getz and E. Domany.
      Journal of Computational Biology, 12(3):314-330 (2005)
      Slides    
  
  
  41. 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)
      
  
  
  42. Applications of the Montgomery Exponent
      S. Gueron and O. Zuk.
      International Conference on Information Technology: Coding and Computing, 1:620-625 (2005)
      
  
  
  43. Masked Inversion in GF (2ⁿ) Using Mixed Field Representations and its Efficient Implementation for AES
      S. Gueron, O. Parzanchevski and O. Zuk.
      Embedded Cryptographic Hardware: Methodologies and Architectures, 1-59454-012-8:213-228 (2004)
      
  
  
  44. Exponentiation Speed Up for Diffie-Hellman Key Agreement Protocol
      S. Gueron and O. Zuk.
      Intelligent Systems, New Generation (2004)
      
  
  
  45. 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. Conservation and Divergence in Modules of 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.
     Biorxiv (2018)
     
  
  
  2. Sparse Clustering of Noisy Signals in the Wavelets Domain
     T. Hope, A. Wagner and O. Zuk.
     Signal Processing with Adaptive Sparse Structured Representations (2015)    
  
  
  3. 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    
  
  
  4. 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)