Publications

  1. F. Parisi, F. Strino, B. Nadler, and Y. Kluger, "Ranking and combining multiple predictors without labeled data," PNAS, p. 201219097, 2014.
  2. Strino, F., Parisi, F., Micsinai, M., and Kluger,Y., TrAp: a Tree Approach for Fingerprinting Subclonal Tumor Composition, Nucleic Acids Research 2013; doi: 10.1093/nar/gkt641, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3783191/.
  3. Stanton, K., Parisi, F., Strino, F., Rabin, N., Asp, P. and Kluger,Y., Arpeggio: Harmonic compression of ChIP-seq data reveals protein-chromatin interaction signatures, Nucleic Acids Research 2013; doi: 10.1093/nar/gkt627.
  4. Chaumeil, J., Micsinai, M., Ntziachristos, P., Roth, D.B., Aifantis, I., Kluger, Y., Deriano, L., and Skok, J.A., The RAG2 C-terminus and ATM control cleavage to limit the number of potential translocation substrates, Nature Communications, 4, Article number: 2231 doi:10.1038/ncomms3231.
  5. Zhang, J., Bonasio, R. Strino, F., Kluger, Y., Holloway, K. Modzelewski, A., Cohen, P., Reinberg, D., SFMBT1 Functions with LSD1 to Regulate Expression of Canonical Histone Genes and Chromatin-Related Factors, Gene and Development 2013. 27: 749-766; PMC3639416
  6. Aziz, A.A., Sznol, J.A., Adeniran, A., Parisi, F. Kluger, Y. Camp, R.L. and Kluger, H.M., Expression of Drug Targets in Primary and Matched Metastatic Renal Cell Carcinoma Tumors, BMC Clinical Pathology, BMC Clinical Pathology 2013, 13:3; PMID: 23374878; PMC3575219
  7. Chaumeil J, Micsinai M, Ntziachristos P, Deriano L, Wang JMH, Ji Y, Nora E, Rodesch MJ, Jeddeloh JA, Kluger Y, Aifantis I, Schaatz DG, Skok JA. Higher-order looping and nuclear organization of antigen receptor loci facilities targeted RAG cleavage and regulated rearrangement in recombination centers. Cell Reports, Epub date 2013/02/19 PMID: 23416051
  8. Neumeister, V.M., Anagnostou, V., Siddiqui, S., England, A.M., Zarrella, E.R., Vassilakopoulou, M., Parisis, F., Kluger, Y., Hicks, D.G. and David L. Rimm, D.L. , Quantification of the Pre-analytic Effect of Cold Ischemic Time in Breast Cancer Tissue, JNCI 104(23): 1815-24 (2012); PMID: 23090068 ; PMCID: PMC3514166
  9. Rocha, P.P., Micsinai, M. Souza, P.P., Kim, J.R., Hewitt, S.L., Trimarchi, T., Strino, F., Parisi, F., Kluger, Y. and Skok, J.A., Close proximity to Igh is a contributing factor to AID mediated translocations, Molecular Cell 47(6): 873-85 (2012); PMID: 22864115 ; PMCID: PMC3571766
  10. Johnson, K., Chaumeil, J., Micsinai, M., Wang, J.M.H., Ramsey, L.B., Baracho, G.V., Rickert, R.C., Strino, F., Kluger, Y., Farrar, M.A., and Skok, J.A. IL-7 Functionally Segregates the Pro-B Cell Stage by Regulation Transcription of Recombination Mediators across Cell Cycle. Journal of Immunology 188(12):6084-92 (2012); PMID: 22581861 ; PMCID: PMC3370098  
  11. M. Micsinai, F. Parisi, F. Strino, P. Asp, B. D. Dynlacht, and Y. Kluger, "Picking ChIP-seq peak detectors for analyzing chromatin modification experiments," Nucleic Acids Research, 2012.
  12. Z. Gao, J. Zhang, R. Bonasio, F. Strino, A. Sawai, F. Parisi, Y. Kluger, and D. Reinberg, "PCGF Homologs, CBX Proteins, and RYBP Define Functionally Distinct PRC1 Family Complexes," Molecular Cell, vol. 45, pp. 344-356, 2012.
  13. F. Strino, F. Parisi, and Y. Kluger, "VDA, a Method of Choosing a Better Algorithm with Fewer Validations," PLoS One, vol. 6, p. e26074, 2011.
  14. F. Parisi, S. Ariyan, D. Narayan, A. Bacchiocchi, K. Hoyt, E. Cheng, F. Xu, P. Li, R. Halaban, and Y. Kluger, "Detecting copy number status and uncovering subclonal markers in heterogeneous tumor biopsies," BMC genomics, vol. 12, p. 230, 2011.
  15. H. M. Kluger, K. Hoyt, A. Bacchiocchi, T. Mayer, J. Kirsch, Y. Kluger, M. Sznol, S. Ariyan, A. Molinaro, and R. Halaban, "Plasma Markers for Identifying Patients with Metastatic Melanoma," Clinical Cancer Research, vol. 17, p. 2417, 2011.
  16. A. Collins, S. L. Hewitt, J. Chaumeil, M. L. Sellars, M. Micsinai, J. Allinne, F. Parisi, E. P. Nora, D. J. Bolland, and A. E. Corcoran, "RUNX transcription factor-mediated association of Cd4 and Cd8 enables coordinate gene regulation," Immunity, vol. 34, pp. 303-314, 2011.
  17. P. Asp, R. Blum, V. Vethantham, F. Parisi, M. Micsinai, J. Cheng, C. Bowman, Y. Kluger, and B. D. Dynlacht, "Genome-wide remodeling of the epigenetic landscape during myogenic differentiation," Proceedings of the National Academy of Sciences, vol. 108, p. E149, 2011.
  18. C. van Oevelen, C. Bowman, J. Pellegrino, P. Asp, J. Cheng, F. Parisi, M. Micsinai, Y. Kluger, A. Chu, and A. Blais, "The mammalian Sin3 proteins are required for muscle development and sarcomere specification," Molecular and cellular biology, vol. 30, p. 5686, 2010.
  19. F. Parisi, A. M. Gonzalez, Y. Nadler, R. L. Camp, D. L. Rimm, H. M. Kluger, and Y. Kluger, "Benefits of biomarker selection and clinico-pathological covariate inclusion in breast cancer prognostic models," Breast Cancer Res, vol. 12, p. R66, 2010.
  20. Y. Nadler, A. Gonzalez, R. Camp, D. Rimm, H. Kluger, and Y. Kluger, "Growth factor receptor-bound protein-7 (Grb7) as a prognostic marker and therapeutic target in breast cancer," Annals of Oncology, vol. 21, p. 466, 2010.
  21. R. Halaban, W. Zhang, A. Bacchiocchi, E. Cheng, F. Parisi, S. Ariyan, M. Krauthammer, J. P. McCusker, Y. Kluger, and M. Sznol, "PLX4032, a selective BRAFV600E kinase inhibitor, activates the ERK pathway and enhances cell migration and proliferation of BRAFWT melanoma cells," Pigment cell & melanoma research, vol. 23, pp. 190-200, 2010.

Publications

  1. R. Halaban, M. Krauthammer, M. Pelizzola, E. Cheng, D. Kovacs, M. Sznol, S. Ariyan, D. Narayan, A. Bacchiocchi, and A. Molinaro, "Integrative analysis of epigenetic modulation in melanoma cell response to decitabine: clinical implications," PLoS One, vol. 4, p. e4563, 2009.
  2. S. A. Aziz, M. Davies, E. Pick, C. Zito, L. Jilaveanu, R. L. Camp, D. L. Rimm, Y. Kluger, and H. M. Kluger, "Phosphatidylinositol-3-kinase as a therapeutic target in melanoma," Clinical Cancer Research, vol. 15, pp. 3029-3036, 2009.
  3. C. van Oevelen, J. Wang, P. Asp, Q. Yan, W. G. Kaelin Jr, Y. Kluger, and B. D. Dynlacht, "A role for mammalian Sin3 in permanent gene silencing," Molecular cell, vol. 32, pp. 359-370, 2008.
  4. Y. Nadler, R. L. Camp, C. Schwartz, D. L. Rimm, H. M. Kluger, and Y. Kluger, "Expression of Aurora A (but not Aurora B) is predictive of survival in breast cancer," Clinical Cancer Research, vol. 14, pp. 4455-4462, 2008.
  5. Y. Nadler, R. L. Camp, J. M. Giltnane, C. Moeder, D. L. Rimm, H. M. Kluger, and Y. Kluger, "Expression patterns and prognostic value of Bag-1 and Bcl-2 in breast cancer," Breast Cancer Res, vol. 10, p. R35, 2008.
  6. M. McCarthy, E. Pick, Y. Kluger, B. Gould-Rothberg, R. Lazova, R. Camp, D. Rimm, and H. Kluger, "HSP90 as a marker of progression in melanoma," Annals of oncology, vol. 19, p. 590, 2008.
  7. A. N. Kluger, D. Nir, and Y. Kluger, "Personal Position Repertoire (PPR) from a Bird's Eye View," Journal of Constructivist Psychology, vol. 21, pp. 223-238, 2008.
  8. Y. Zhou, J. Ferguson, J. Chang, and Y. Kluger, "Inter-and intra-combinatorial regulation by transcription factors and microRNAs," BMC genomics, vol. 8, p. 396, 2007.
  9. E. Pick, Y. Kluger, J. M. Giltnane, C. Moeder, R. L. Camp, D. L. Rimm, and H. M. Kluger, "High HSP90 expression is associated with decreased survival in breast cancer," Cancer research, vol. 67, p. 2932, 2007.
  10. D. Acosta-Alvear, Y. Zhou, A. Blais, M. Tsikitis, N. H. Lents, C. Arias, C. J. Lennon, Y. Kluger, and B. D. Dynlacht, "XBP1 controls diverse cell type-and condition-specific transcriptional regulatory networks," Molecular cell, vol. 27, pp. 53-66, 2007.
  11. D. Tuck, H. Kluger, and Y. Kluger, "Characterizing disease states from topological properties of transcriptional regulatory networks," BMC bioinformatics, vol. 7, p. 236, 2006.
  12. D. Mattoon, B. Love, Y. Kluger, G. Michaud, B. Schweitzer, P. Predki, G. Ritter, and R. Halaban, "OR. 65. Melanoma biomarker discovery through serum antibody profiling on protein microarrays," Clinical Immunology, vol. 119, pp. S28-S28, 2006.
  13. Y. Kluger, H. Kluger, and D. Tuck, "Association between pathways in regulatory networks," in 28th IEEE EMBS Annual International Conference (peer review), 2006, pp. 2036-2040.
  14. H. Kim, W. Hu, and Y. Kluger, "Unraveling condition specific gene transcriptional regulatory networks in Saccharomyces cerevisiae," BMC bioinformatics, vol. 7, p. 165, 2006.
  15. Z. Ye, Y. Kluger, Z. Lian, and S. M. Weissman, "Two types of precursor cells in a multipotential hematopoietic cell line," Proceedings of the National Academy of Sciences of the United States of America, vol. 102, p. 18461, 2005.
  16. J. E. Price, D. C. Lev, D. L. Rimm, Y. Kluger, and H. M. Kluger, "Using a xenograft model of breast cancer metastasis to identify genes associated with clinically aggressive disease," Proceedings of the American Association for Cancer Research, vol. 2005, p. 591, 2005.
  17. H. M. Kluger, D. Chelouche Lev, Y. Kluger, M. M. McCarthy, G. Kiriakova, R. L. Camp, D. L. Rimm, and J. E. Price, "Using a xenograft model of human breast cancer metastasis to find genes associated with clinically aggressive disease," Cancer research, vol. 65, p. 5578, 2005.
  18. A. Blais, M. Tsikitis, D. Acosta-Alvear, R. Sharan, Y. Kluger, and B. D. Dynlacht, "An initial blueprint for myogenic differentiation," Genes & development, vol. 19, p. 553, 2005.
  19. X. Zhang, Y. Kluger, Y. Nakayama, R. Poddar, C. Whitney, A. DeTora, S. M. Weissman, and P. E. Newburger, "Gene expression in mature neutrophils: early responses to inflammatory stimuli," Journal of leukocyte biology, vol. 75, pp. 358-372, 2004.
  20. H. Yu, J. Qian, Y. Kluger, and M. Gerstein, "Chromosomal location effects on gene expression: unraveling the contributions from chromatin super-structure and microarray artifacts," Department of Molecular Biophysics and Biochemistry Yale University, 2004.
  21. Y. Kluger, D. P. Tuck, J. T. Chang, Y. Nakayama, R. Poddar, N. Kohya, Z. Lian, A. B. Nasr, H. R. Halaban, and D. S. Krause, "Lineage specificity of gene expression patterns," Proceedings of the National Academy of Sciences of the United States of America, vol. 101, p. 6508, 2004.
  22. Y. Kluger, Z. Lian, X. Zhang, P. E. Newburger, and S. M. Weissman, "A panorama of lineage‚Äêspecific transcription in hematopoiesis," Bioessays, vol. 26, pp. 1276-1287, 2004.
  23. H. M. Kluger, Y. Kluger, M. Gilmore-Hebert, K. DiVito, J. T. Chang, S. Rodov, O. Mironenko, B. M. Kacinski, A. S. Perkins, and E. Sapi, "cDNA microarray analysis of invasive and tumorigenic phenotypes in a breast cancer model," Laboratory investigation, vol. 84, pp. 320-331, 2004.
  24. H. Cam, E. Balciunaite, A. Blais, A. Spektor, R. C. Scarpulla, R. Young, Y. Kluger, and B. D. Dynlacht, "A common set of gene regulatory networks links metabolism and growth inhibition," Molecular cell, vol. 16, pp. 399-411, 2004.
  25. Y. Tsukahara, Z. Lian, X. Zhang, C. Whitney, Y. Kluger, D. Tuck, S. Yamaga, Y. Nakayama, S. M. Weissman, and P. E. Newburger, "Gene expression in human neutrophils during activation and priming by bacterial lipopolysaccharide," Journal of cellular biochemistry, vol. 89, pp. 848-861, 2003.
  26. J. Qian, Y. Kluger, H. Yu, and M. Gerstein, "Identification and correction of spurious spatial correlations in microarray data," Biotechniques, vol. 35, pp. 42-49, 2003.
  27. Y. Kluger, H. Yu, J. Qian, and M. Gerstein, "Relationship between gene co-expression and probe localization on microarray slides," Bmc Genomics, vol. 4, p. 49, 2003.
  28. Y. Kluger, R. Basri, J. T. Chang, and M. Gerstein, "Spectral biclustering of microarray data: coclustering genes and conditions," Genome research, vol. 13, pp. 703-716, 2003.
  29. R. Jansen, H. Yu, D. Greenbaum, Y. Kluger, N. J. Krogan, S. Chung, A. Emili, M. Snyder, J. F. Greenblatt, and M. Gerstein, "A Bayesian networks approach for predicting protein-protein interactions from genomic data," Science, vol. 302, p. 449, 2003.
  30. Z. Lian, Y. Kluger, D. S. Greenbaum, D. Tuck, M. Gerstein, N. Berliner, S. M. Weissman, and P. E. Newburger, "Genomic and proteomic analysis of the myeloid differentiation program: global analysis of gene expression during induced differentiation in the MPRO cell line," Blood, vol. 100, p. 3209, 2002.
  31. Y. V. B. K. Subrahmanyam, S. Yamaga, Y. Prashar, H. H. Lee, N. P. Hoe, Y. Kluger, M. Gerstein, J. D. Goguen, P. E. Newburger, and S. M. Weissman, "RNA expression patterns change dramatically in human neutrophils exposed to bacteria," Blood, vol. 97, pp. 2457-2468, 2001.
  32. Z. Lian, L. Wang, S. Yamaga, W. Bonds, Y. Beazer-Barclay, Y. Kluger, M. Gerstein, P. E. Newburger, N. Berliner, and S. M. Weissman, "Genomic and proteomic analysis of the myeloid differentiation program," Blood, vol. 98, pp. 513-524, 2001.
  33. P. Bertone, Y. Kluger, N. Lan, D. Zheng, D. Christendat, A. Yee, A. M. Edwards, C. H. Arrowsmith, G. T. Montelione, and M. Gerstein, "SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics," Nucleic Acids Research, vol. 29, pp. 2884-2898, 2001.
  34. D. Christendat, A. Yee, A. Dharamsi, Y. Kluger, A. Savchenko, J. R. Cort, V. Booth, C. D. Mackereth, V. Saridakis, and I. Ekiel, "Structural proteomics of an archaeon," Nature Structural Biology, vol. 7, pp. 903-909, 2000.
  35. D. Christendat, A. Yee, A. Dharamsi, Y. Kluger, M. Gerstein, C. H. Arrowsmith, and A. M. Edwards, "Structural proteomics: prospects for high throughput sample preparation," Progress in biophysics and molecular biology, vol. 73, pp. 339-346, 2000.

Publications

  1. X. Wang, Y. Kluger, V. Koch, and J. Randrup, "Dileptons from Disoriented Chiral Condensates," Nuclear Physics A, vol. 638, pp. 447c-450c, 1998.
  2. Y. Kluger, E. Mottola, and J. M. Eisenberg, "Quantum Vlasov equation and its Markov limit," Physical Review D, vol. 58, p. 125015, 1998.
  3. Y. Kluger, V. Koch, J. Randrup, and X. N. Wang, "Dileptons from disoriented chiral condensates," Physical Review C, vol. 57, p. 280, 1998.
  4. F. Cooper, S. Habib, Y. Kluger, and E. Mottola, "Nonequilibrium dynamics of symmetry breaking in Φ4 theory," Physical Review D, vol. 55, p. 6471, 1997.
  5. S. Habib, Y. Kluger, E. Mottola, and J. P. Paz, "Dissipation and decoherence in mean field theory," Physical review letters, vol. 76, pp. 4660-4663, 1996.
  6. F. Cooper, Y. Kluger, and E. Mottola, "Anomalous transverse distribution of pions as a signal for the production of disoriented chiral condensates," Physical Review C, vol. 54, p. 3298, 1996.
  7. Y. Kluger, F. Cooper, E. Mottola, J. Paz, and A. Kovner, "Quantum evolution of the disoriented chiral condensates," Nuclear Physics A, vol. 590, pp. 581-584, 1995.
  8. F. Cooper, Y. Kluger, E. Mottola, and J. P. Paz, "Quantum evolution of disoriented chiral condensates," Physical Review D, vol. 51, p. 2377, 1995.
  9. F. Cooper, J. Dawson, S. Habib, Y. Kluger, D. Meredith, and H. Shepard, "Semiquantum chaos and the large N expansion," Physica D: Nonlinear Phenomena, vol. 83, pp. 74-97, 1995.
  10. F. Cooper, S. Habib, Y. Kluger, E. Mottola, J. P. Paz, and P. R. Anderson, "Nonequilibrium quantum fields in the large-N expansion," Physical Review D, vol. 50, p. 2848, 1994.
  11. F. Cooper, J. Dawson, Y. Kluger, and H. Shepard, "Time evolution of the quark-gluon plasma," Nuclear Physics A, vol. 566, pp. 395-398, 1994.
  12. G. Berman, E. Bulgakov, D. Holm, and Y. Kluger, "Dynamical chaos in SU (2) U (1) theory," Physics Letters A, vol. 194, pp. 251-264, 1994.
  13. V. Zelevinsky, Z. CHEN, Y. KLUGER, J. EISENBERG, B. SVETITSKY, M. EL-NADI, M. SHERIF, A. EL-SALAM, M. YASIN, and A. BAKR, "Limiting Anharmonicity of Soft Nuclei," International Journal of Modern Physics E, vol. 2, pp. 273-284, 1993.
  14. F. Cooper, J. Eisenberg, Y. Kluger, E. Mottola, and B. Svetitsky, "Particle production in the central rapidity region," Physical Review D, vol. 48, p. 190, 1993.
  15. Y. Kluger, J. Eisenberg, B. Svetitsky, F. Cooper, and E. Mottola, "Fermion pair production in a strong electric field," Physical Review D, vol. 45, p. 4659, 1992.
  16. Y. Kluger, J. Eisenberg, B. Svetitsky, F. Cooper, and E. Mottola, "Pair production in a strong electric field," Physical Review Letters, vol. 67, pp. 2427-2430, 1991.
  17. J. Eisenberg, Y. Kluger, and B. Svetitsky, "Pair production in a strong electric field with back reaction: An Interim summary," Acta Physica Polonica B, vol. 23, p. 577, 1991.

Publications

  1. J. Eisenberg, Y. Kluger, and A. Rosenhauer, "Transport Equations for the Quark-Gluon Plasma," 1989, p. 501.
  2. Y. Kluger and J. Eisenberg, "The isoscalar charge form factor in nuclei of A= 2, 3 obtained in the Skyrme model," International Journal of Modern Physics A;(USA), vol. 3, 1988.