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INFORMATION FOR

Publications

2020-Present

  1. C. Zhang, B. Balbo, M. Ma, J. Zhao, X. Tian, Y. Kluger, and S. Somlo, "Cyclin-Dependent Kinase 1 Activity Is a Driver of Cyst Growth in Polycystic Kidney Disease," Journal of the American Society of Nephrology, vol. 32, pp. 41-51, 2021.
  2. E. Sefik, B. Israelow, J. Zhao, R. Qu, E. Song, H. Mirza, E. Kaffe, S. Halene, E. Meffre, and Y. Kluger, "A humanized mouse model of chronic COVID-19 to evaluate disease mechanisms and treatment options," 2021.
  3. M. S. B. Raredon, J. Yang, J. Garritano, M. Wang, D. Kushnir, J. C. Schupp, T. S. Adams, A. M. Greaney, K. L. Leiby, N. Kaminski, Y. Kluger, A. Levchenko, and L. E. Niklason, "Connectome: computation and visualization of cell-cell signaling topologies in single-cell systems data," bioRxiv, p. 2021.01.21.427529, 2021.
  4. T. Qing, H. Mohsen, V. L. Cannataro, M. Marczyk, M. Rozenblit, J. Foldi, M. F. Murray, J. P. Townsend, Y. Kluger, and M. Gerstein, "Cancer relevance of human genes," bioRxiv, 2021.
  5. Lindenbaum, N. Nouri, Y. Kluger, and S. H. Kleinstein, "Alignment free identification of clones in B cell receptor repertoires," Nucleic Acids Res, vol. 49, p. e21, Feb 26 2021.
  6. Y.-W. E. Lin, T. Shnitzer, R. Talmon, F. Villarroel-Espindola, S. Desai, K. Schalper, and Y. Kluger, "Graph of graphs analysis for multiplexed data with application to imaging mass cytometry," PLOS Computational Biology, vol. 17, p. e1008741, 2021.
  7. B. Landa, T. T. Zhang, and Y. Kluger, "Biwhitening Reveals the Rank of a Count Matrix," arXiv preprint arXiv:2103.13840, 2021.
  8. B. Landa, R. R. Coifman, and Y. Kluger, "Doubly Stochastic Normalization of the Gaussian Kernel Is Robust to Heteroskedastic Noise," SIAM Journal on Mathematics of Data Science, pp. 388-413, 2021/01/01 2021.
  9. A. Jaffe, N. Amsel, Y. Aizenbud, B. Nadler, J. T. Chang, and Y. Kluger, "Spectral Neighbor Joining for Reconstruction of Latent Tree Models," SIAM Journal on Mathematics of Data Science, vol. 3, pp. 113-141, 2021.
  10. Y. Aizenbud, A. Jaffe, M. Wang, A. Hu, N. Amsel, B. Nadler, J. T. Chang, and Y. Kluger, "Spectral Top-Down Recovery of Latent Tree Models," arXiv preprint arXiv:2102.13276, 2021.
  11. J. Zhao, A. Jaffe, H. Li, O. Lindenbaum, E. Sefik, R. Jackson, X. Cheng, R. Flavell, and Y. Kluger, "Detection of differentially abundant cell subpopulations discriminates biological states in scRNA-seq data," bioRxiv, p. 711929, 2020.
  12. H. Zhang, H. Zhu, G. Deng, C. R. Zito, V. O. Oria, C. K. Rane, S. Zhang, S. A. Weiss, T. Tran, A. Adeniran, F. Zhang , J. Zhou, Y. Kluger, M. W. Bosenberg , H. M. Kluger, and L. B. Jilaveanu, "PLEKHA5 regulates tumor growth in metastatic melanoma," Cancer, vol. 126, pp. 1016-1030, 2020.
  13. Y. Yamada, O. Lindenbaum, S. Negahban, and Y. Kluger, "Feature selection using stochastic gates," in International Conference on Machine Learning, 2020, pp. 10648-10659.
  14. M. Roulis, A. Kaklamanos, M. Schernthanner, P. Bielecki, J. Zhao, E. Kaffe, L. S. Frommelt, R. Qu, M. S. Knapp, A. Henriques, N. Chalkidi, V. Koliaraki, J. Jiao, J. R. Brewer, M. Bacher, H. N. Blackburn, X. Zhao, R. M. Breyer, V. Aidinis, D. Jain, B. Su, H. R. Herschman, Y. Kluger, G. Kollias, and R. A. Flavell, "Paracrine orchestration of intestinal tumorigenesis by a mesenchymal niche," Nature, vol. 580, pp. 524-529, Apr 2020.
  15. T. Qing, H. Mohsen, M. Marczyk, Y. Ye, T. O’Meara, H. Zhao, J. P. Townsend, M. Gerstein, T. Qing, H. Mohsen, M. Marczyk, Y. Ye, T. O’Meara, H. Zhao, J. P. Townsend, M. Gerstein, C. Hatzis, Y. Kluger, and L. Pusztai, "Germline variant burden in cancer genes correlates with age at diagnosis and somatic mutation burden," Nature communications, vol. 11, pp. 1-8, 2020.
  16. M. Marczyk, G. A. Patwardhan, J. Zhao, R. Qu, X. Li, V. B. Wali, A. K. Gupta, M. M. Pillai, Y. Kluger, Q. Yan, C. Hatzis, L. Pusztai, and V. Gunasekharan, "Multi-Omics Investigation of Innate Navitoclax Resistance in Triple-Negative Breast Cancer Cells," Cancers, vol. 12, p. 2551, 2020.
  17. Lindenbaum, U. Shaham, J. Svirsky, E. Peterfreund, and Y. Kluger, "Let the Data Choose its Features: Differentiable Unsupervised Feature Selection," arXiv preprint arXiv:2007.04728, 2020.
  18. Lindenbaum, M. Salhov, A. Averbuch, and Y. Kluger, "Deep Gated Canonical Correlation Analysis," arXiv preprint arXiv:2010.05620, 2020.
  19. B. Landa, R. Qu, J. Chang, and Y. Kluger, "Local Two-Sample Testing over Graphs and Point-Clouds by Random-Walk Distributions," arXiv preprint arXiv:2011.03418, 2020.
  20. D. M. Kluger, Y. Aizenbud, A. Jaffe, F. Parisi, L. Aizenbud, E. Minsky-Fenick, J. M. Kluger, S. Farhadian, H. M. Kluger, and Y. Kluger, "Impact of healthcare worker shift scheduling on workforce preservation during the COVID-19 pandemic," Infection Control & Hospital Epidemiology, vol. 41, pp. 1443-1445, 2020.
  21. A.Jarret, R. Jackson, C. Duizer, M. E. Healy, J. Zhao, J. M. Rone, P. Bielecki, E. Sefik, M. Roulis, T. Rice, K. N. Sivanathan, T. Zhou, A. G. Solis, H. Honcharova-Biletska, K. Vélez, S. Hartner, J. S. Low, R. Qu, M. R. de Zoete, N. W. Palm, A. M. Ring, A. Weber, A. E. Moor, Y. Kluger, R. Nowarski, and R. A. Flavell, "Enteric Nervous System-Derived IL-18 Orchestrates Mucosal Barrier Immunity," Cell, vol. 180, pp. 50-63.e12, 2020/01/09/ 2020.
  22. A. Jaffe, Y. Kluger, G. C. Linderman, G. Mishne, and S. Steinerberger, "Randomized near-neighbor graphs, giant components and applications in data science," Journal of applied probability, vol. 57, pp. 458-476, 2020.
  23. A. Jaffe, Y. Kluger, O. Lindenbaum, J. Patsenker, E. Peterfreund, and S. Steinerberger, "The Spectral Underpinning of word2vec," Frontiers in Applied Mathematics and Statistics, vol. 6, 2020-December-03 2020.
  24. S. B. Goldberg, K. A. Schalper, S. N. Gettinger, A. Mahajan, R. S. Herbst, A. C. Chiang, R. Lilenbaum, F. H. Wilson, S. B. Omay, J. B. Yu, L. Jilaveanu, T. Tran, K. Pavlik, E. Rowen, H. Gerrish, A. Komlo, R. Gupta, H. Wyatt, M. Ribeiro, Y. Kluger, G. Zhou, W. Wei, V. L. Chiang, and H. M. Kluger, "Pembrolizumab for management of patients with NSCLC and brain metastases: long-term results and biomarker analysis from a non-randomised, open-label, phase 2 trial," The Lancet Oncology, vol. 21, pp. 655-663, 2020/05/01/ 2020.

2010-2019

  1. M. C. Amezcua Vesely, P. Pallis, P. Bielecki, J. S. Low, J. Zhao, C. C. D. Harman, L. Kroehling, R. Jackson, W. Bailis, P. Licona-Limon, H. Xu, N. Iijima, P. S. Pillai, D. H. Kaplan, C. T. Weaver, Y. Kluger, M. S. Kowalczyk, A. Iwasaki, J. P. Pereira, E. Esplugues, N. Gagliani, and R. A. Flavell, "Effector TH17 Cells Give Rise to Long-Lived TRM Cells that Are Essential for an Immediate Response against Bacterial Infection," Cell, vol. 178, pp. 1176-1188 e15, Aug 22 2019.
  2. Z. Wang, M. D. Gearhart, Y. W. Lee, I. Kumar, B. Ramazanov, Y. Zhang, C. Hernandez, A. Y. Lu, N. Neuenkirchen, J. Deng, J. Jin, Y. Kluger, T. A. Neubert, V. J. Bardwell, and N. B. Ivanova, "A Non-canonical BCOR-PRC1.1 Complex Represses Differentiation Programs in Human ESCs," Cell Stem Cell, vol. 22, pp. 235-251 e9, Feb 1 2018.
  3. M. S. B. Raredon, T. S. Adams, Y. Suhail, J. C. Schupp, S. Poli, N. Neumark, K. L. Leiby, A. M. Greaney, Y. Yuan, C. Horien, G. Linderman, A. J. Engler, D. J. Boffa, Y. Kluger, I. O. Rosas, A. Levchenko, N. Kaminski, and L. E. Niklason, "Single-cell connectomic analysis of adult mammalian lungs," Sci Adv, vol. 5, p. eaaw3851, Dec 2019.
  4. G. C. Linderman, M. Rachh, J. G. Hoskins, S. Steinerberger, and Y. Kluger, "Fast interpolation-based t-SNE for improved visualization of single-cell RNA-seq data," Nature methods, vol. 16, p. 243, 2019.
  5. D. T. Li, G. C. Linderman, J. J. Cui, S. DeVries, A. D. Nicholson, E. Li, L. Petit, J. B. Kahan, R. Talty, Y. Kluger, D. R. Cooperman, and B. G. Smith, "The Proximal Humeral Ossification System Improves Assessment of Maturity in Patients with Scoliosis," J Bone Joint Surg Am, vol. 101, pp. 1868-1874, Oct 16 2019.
  6. A. Lahav, R. Talmon, and Y. Kluger, "Mahalanobis distance informed by clustering," Information and Inference: A Journal of the IMA, vol. 8, pp. 377-406, 2019.
  7. D. Kobak, G. Linderman, S. Steinerberger, Y. Kluger, and P. Berens, "Heavy-tailed kernels reveal a finer cluster structure in t-SNE visualisations," in Joint European Conference on Machine Learning and Knowledge Discovery in Databases, 2019, pp. 124-139.
  8. H. M. Kluger, V. Chiang, A. Mahajan, C. R. Zito, M. Sznol, T. Tran, S. A. Weiss, J. V. Cohen, J. Yu, and U. Hegde, "Long-term survival of patients with melanoma with active brain metastases treated with pembrolizumab on a phase II trial," Journal of Clinical Oncology, vol. 37, p. 52, 2019.
  9. L. Irshaid, E. Weinberger, J. Garritano, J. Patsenker, Y. Kluger, S. Katz, and M. Xu, "Histopathologic and Machine Deep Learning Criteria to Predict Lymphoma Transformation in Bone Marrow Biopsies," in LABORATORY INVESTIGATION, 2019.
  10. K. Gupta, J. Levinsohn, G. Linderman, D. Chen, T. Y. Sun, D. Dong, M. M. Taketo, M. Bosenberg, Y. Kluger, K. Choate, and P. Myung, "Single-Cell Analysis Reveals a Hair Follicle Dermal Niche Molecular Differentiation Trajectory that Begins Prior to Morphogenesis," Dev Cell, vol. 48, pp. 17-31 e6, Jan 7 2019.
  11. D. E. Carvajal-Hausdorf, J. Patsenker, K. P. Stanton, F. Villarroel-Espindola, A. Esch, R. R. Montgomery, A. Psyrri, K. T. Kalogeras, V. Kotoula, G. Foutzilas, K. A. Schalper, Y. Kluger, and D. L. Rimm, "Multiplexed (18-Plex) Measurement of Signaling Targets and Cytotoxic T Cells in Trastuzumab-Treated Patients using Imaging Mass Cytometry," Clin Cancer Res, vol. 25, pp. 3054-3062, May 15 2019.
  12. W. Bailis, J. A. Shyer, J. Zhao, J. C. G. Canaveras, F. J. Al Khazal, R. Qu, H. R. Steach, P. Bielecki, O. Khan, R. Jackson, Y. Kluger, L. J. Maher, 3rd, J. Rabinowitz, J. Craft, and R. A. Flavell, "Distinct modes of mitochondrial metabolism uncouple T cell differentiation and function," Nature, vol. 571, pp. 403-407, Jul 2019.
  13. Y. Yamada, O. Lindenbaum, S. Negahban, and Y. Kluger, "Feature Selection using Stochastic Gates," in Proceedings of the 37 th International Conference on Machine Learning, Vienna, Austria, PMLR 119, 2020, 2018.
  14. D. Ueno, Z. Xie, M. Boeke, J. Syed, K. A. Nguyen, P. McGillivray, A. Adeniran, P. Humphrey, G. M. Dancik, Y. Kluger, Z. Liu, H. Kluger, and B. Shuch, "Genomic Heterogeneity and the Small Renal Mass," Clin Cancer Res, vol. 24, pp. 4137-4144, Sep 1 2018.
  15. U. Shaham, K. Stanton, H. Li, R. Basri, B. Nadler, and Y. Kluger, "SpectralNet: Spectral Clustering using Deep Neural Networks," in International Conference on Learning Representations, 2018.
  16. U. Shaham, J. Garritano, Y. Yamada, E. Weinberger, A. Cloninger, X. Cheng, K. Stanton, and Y. Kluger, "Defending against adversarial images using basis functions transformations," arXiv preprint arXiv:1803.10840, 2018.
  17. G. C. Linderman, J. Zhao, and Y. Kluger, "Zero-preserving imputation of scRNA-seq data using low-rank approximation," bioRxiv, p. 397588, 2018.
  18. H. Li, Y. Kluger, and M. Tygert, "Randomized algorithms for distributed computation of principal component analysis and singular value decomposition," Advances in Computational Mathematics, vol. 44, pp. 1651-1672, 2018.
  19. J. L. Katzman, U. Shaham, A. Cloninger, J. Bates, T. Jiang, and Y. Kluger, "DeepSurv: personalized treatment recommender system using a Cox proportional hazards deep neural network," BMC Med Res Methodol, vol. 18, p. 24, Feb 26 2018.
  20. A. Jaffe, R. Weiss, B. Nadler, S. Carmi, and Y. Kluger, "Learning Binary Latent Variable Models: A Tensor Eigenpair Approach," presented at the Proceedings of the 35th International Conference on Machine Learning, Proceedings of Machine Learning Research, 2018.
  21. D. Herndler-Brandstetter, H. Ishigame, R. Shinnakasu, V. Plajer, C. Stecher, J. Zhao, M. Lietzenmayer, L. Kroehling, A. Takumi, K. Kometani, T. Inoue, Y. Kluger, S. M. Kaech, T. Kurosaki, T. Okada, and R. A. Flavell, "KLRG1(+) Effector CD8(+) T Cells Lose KLRG1, Differentiate into All Memory T Cell Lineages, and Convey Enhanced Protective Immunity," Immunity, vol. 48, pp. 716-729 e8, Apr 17 2018.
  22. S. Zhu, S. Ding, P. Wang, Z. Wei, W. Pan, N. W. Palm, Y. Yang, H. Yu, H. B. Li, G. Wang, X. Lei, M. R. de Zoete, J. Zhao, Y. Zheng, H. Chen, Y. Zhao, K. A. Jurado, N. Feng, L. Shan, Y. Kluger, J. Lu, C. Abraham, E. Fikrig, H. B. Greenberg, and R. A. Flavell, "Nlrp9b inflammasome restricts rotavirus infection in intestinal epithelial cells," Nature, vol. 546, pp. 667-670, Jun 29 2017.
  23. K. P. Stanton, J. Jin, R. R. Lederman, S. M. Weissman, and Y. Kluger, "Ritornello: high fidelity control-free chromatin immunoprecipitation peak calling," Nucleic acids research, vol. 45, pp. e173-e173, 2017.
  24. U. Shaham, K. P. Stanton, J. Zhao, H. Li, K. Raddassi, R. Montgomery, and Y. Kluger, "Removal of batch effects using distribution-matching residual networks," Bioinformatics, vol. 33, pp. 2539-2546, 2017.
  25. G. Mishne, R. Talmon, I. Cohen, R. R. Coifman, and Y. Kluger, "Data-driven tree transforms and metrics," IEEE transactions on signal and information processing over networks, vol. 4, pp. 451-466, 2017.
  26. H. B. Li, J. Tong, S. Zhu, P. J. Batista, E. E. Duffy, J. Zhao, W. Bailis, G. Cao, L. Kroehling, Y. Chen, G. Wang, J. P. Broughton, Y. G. Chen, Y. Kluger, M. D. Simon, H. Y. Chang, Z. Yin, and R. A. Flavell, "m(6)A mRNA methylation controls T cell homeostasis by targeting the IL-7/STAT5/SOCS pathways," Nature, vol. 548, pp. 338-342, Aug 17 2017.
  27. H. Li, U. Shaham, K. P. Stanton, Y. Yao, R. R. Montgomery, and Y. Kluger, "Gating mass cytometry data by deep learning," Bioinformatics, vol. 33, pp. 3423-3430, 2017.
  28. H. Li, G. C. Linderman, A. Szlam, K. P. Stanton, Y. Kluger, and M. Tygert, "Algorithm 971: An implementation of a randomized algorithm for principal component analysis," ACM Transactions on Mathematical Software (TOMS), vol. 43, pp. 1-14, 2017.
  29. H. M. Kluger, C. R. Zito, G. Turcu, M. K. Baine, H. Zhang, A. Adeniran, M. Sznol, D. L. Rimm, Y. Kluger, L. Chen, J. V. Cohen, and L. B. Jilaveanu, "PD-L1 Studies Across Tumor Types, Its Differential Expression and Predictive Value in Patients Treated with Immune Checkpoint Inhibitors," Clin Cancer Res, vol. 23, pp. 4270-4279, Aug 1 2017.
  30. Dror, B. Nadler, E. Bilal, and Y. Kluger, "Unsupervised ensemble regression," arXiv preprint arXiv:1703.02965, 2017.
  31. T. Jiang, U. Shaham, F. Parisi, R. Halaban, A. Safonov, H. Kluger, S. Weissman, J. Chang, and Y. Kluger, "Methods for detecting co-mutated pathways in cancer samples to inform treatment selection," bioRxiv, p. 082552, 2016.
  32. M. Vassilakopoulou, F. Parisi, S. Siddiqui, A. M. England, E. R. Zarella, V. Anagnostou, Y. Kluger, D. G. Hicks, D. L. Rimm, and V. M. Neumeister, "Preanalytical variables and phosphoepitope expression in FFPE tissue: quantitative epitope assessment after variable cold ischemic time," Laboratory investigation, vol. 95, pp. 334-341, 2015.
  33. B. Shuch, R. Falbo, F. Parisi, A. Adeniran, Y. Kluger, H. M. Kluger, and L. B. Jilaveanu, "MET expression in primary and metastatic clear cell renal cell carcinoma: implications of correlative biomarker assessment to MET pathway inhibitors," BioMed research international, vol. 2015, 2015.
  34. M. Murtha, F. Strino, Z. Tokcaer-Keskin, N. Sumru Bayin, D. Shalabi, X. Xi, Y. Kluger, and L. Dailey, "Comparative FAIRE-seq Analysis Reveals Distinguishing Features of the Chromatin Structure of Ground State-and Primed-Pluripotent Cells," Stem Cells, vol. 33, pp. 378-391, 2015.
  35. L. B. Jilaveanu, F. Parisi, M. L. Barr, C. R. Zito, W. Cruz-Munoz, R. S. Kerbel, D. L. Rimm, M. W. Bosenberg, R. Halaban, Y. Kluger, and H. M. Kluger, "PLEKHA5 as a Biomarker and Potential Mediator of Melanoma Brain Metastasis," Clin Cancer Res, vol. 21, pp. 2138-47, May 1 2015.
  36. Y. J. Jeon, S. Khelifa, B. Ratnikov, D. A. Scott, Y. Feng, F. Parisi, C. Ruller, E. Lau, H. Kim, L. M. Brill, T. Jiang, D. L. Rimm, R. D. Cardiff, G. B. Mills, J. W. Smith, A. L. Osterman, Y. Kluger, and Z. A. Ronai, "Regulation of glutamine carrier proteins by RNF5 determines breast cancer response to ER stress-inducing chemotherapies," Cancer Cell, vol. 27, pp. 354-69, Mar 9 2015.
  37. A. Jaffe, B. Nadler, and Y. Kluger, "Estimating the accuracies of multiple classifiers without labeled data," in Artificial Intelligence and Statistics, 2015, pp. 407-415.
  38. F. Parisi, F. Strino, B. Nadler, and Y. Kluger, "Ranking and combining multiple predictors without labeled data," Proceedings of the National Academy of Sciences, vol. 111, pp. 1253-1258, 2014.
  39. V. M. Neumeister, F. Parisi, A. M. England, S. Siddiqui, V. Anagnostou, E. Zarrella, M. Vassilakopolou, Y. Bai, S. Saylor, A. Sapino, Y. Kluger, D. G. Hicks, G. Bussolati, S. Kwei, and D. L. Rimm, "A tissue quality index: an intrinsic control for measurement of effects of preanalytical variables on FFPE tissue," Lab Invest, vol. 94, pp. 467-74, Apr 2014.
  40. M. Murtha, Z. Tokcaer-Keskin, Z. Tang, F. Strino, X. Chen, Y. Wang, X. Xi, C. Basilico, S. Brown, R. Bonneau, Y. Kluger, and L. Dailey, "FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells," Nat Methods, vol. 11, pp. 559-65, May 2014.
  41. L. K. Kim, E. Esplugues, C. E. Zorca, F. Parisi, Y. Kluger, T. H. Kim, N. J. Galjart, and R. A. Flavell, "Oct-1 regulates IL-17 expression by directing interchromosomal associations in conjunction with CTCF in T cells," Molecular cell, vol. 54, pp. 56-66, 2014.
  42. L. Jilaveanu, B. Shuch, C. Zito, F. Parisi, M. Barr, Y. Kluger, L. Chen, and H. Kluger, "PD-L1 expression in clear cell renal cell carcinoma: an analysis of nephrectomy and sites of metastases," Journal of Cancer, vol. 5, p. 166, 2014.
  43. T. Jiang, W. Shi, R. Natowicz, S. N. Ononye, V. B. Wali, Y. Kluger, L. Pusztai, and C. Hatzis, "Statistical measures of transcriptional diversity capture genomic heterogeneity of cancer," BMC genomics, vol. 15, pp. 1-11, 2014.
  44. E. Giesen, L. B. Jilaveanu, F. Parisi, Y. Kluger, R. L. Camp, and H. M. Kluger, "NY-ESO-1 as a potential immunotherapeutic target in renal cell carcinoma," Oncotarget, vol. 5, p. 5209, 2014.
  45. Y. Dong, J.-A. Richards, R. Gupta, P. Aung, A. Emley, Y. Kluger, S. Dogra, M. Mahalingam, and N. Wajapeyee, "PTEN functions as a melanoma tumor suppressor by promoting host immune response," Oncogene, vol. 33, pp. 4632-4642, 2014.
  46. R. Bonasio, E. Lecona, V. Narendra, P. Voigt, F. Parisi, Y. Kluger, and D. Reinberg, "Interactions with RNA direct the Polycomb group protein SCML2 to chromatin where it represses target genes," Elife, vol. 3, p. e02637, 2014.
  47. J. Zhang, R. Bonasio, F. Strino, Y. Kluger, J. K. Holloway, A. J. Modzelewski, P. E. Cohen, and D. Reinberg, "SFMBT1 functions with LSD1 to regulate expression of canonical histone genes and chromatin-related factors," Genes & development, vol. 27, pp. 749-766, 2013.
  48. F. Strino, F. Parisi, M. Micsinai, and Y. Kluger, "TrAp: a tree approach for fingerprinting subclonal tumor composition," Nucleic Acids Research, vol. 41, p. e165, 2013.
  49. K. P. Stanton, F. Parisi, F. Strino, N. Rabin, P. Asp, and Y. Kluger, "Arpeggio: harmonic compression of ChIP-seq data reveals protein-chromatin interaction signatures," Nucleic acids research, vol. 41, pp. e161-e161, 2013.
  50. J. Chaumeil, M. Micsinai, P. Ntziachristos, D. B. Roth, I. Aifantis, Y. Kluger, L. Deriano, and J. A. Skok, "The RAG2 C-terminus and ATM protect genome integrity by controlling antigen receptor gene cleavage," Nature communications, vol. 4, pp. 1-10, 2013.
  51. J. Chaumeil, M. Micsinai, P. Ntziachristos, L. Deriano, J. M. Wang, Y. Ji, E. P. Nora, M. J. Rodesch, J. A. Jeddeloh, I. Aifantis, Y. Kluger, D. G. Schatz, and J. A. Skok, "Higher-order looping and nuclear organization of Tcra facilitate targeted rag cleavage and regulated rearrangement in recombination centers," Cell Rep, vol. 3, pp. 359-70, Feb 21 2013.
  52. S. A. Aziz, J. A. Sznol, A. Adeniran, F. Parisi, Y. Kluger, R. L. Camp, and H. M. Kluger, "Expression of drug targets in primary and matched metastatic renal cell carcinoma tumors," BMC clinical pathology, vol. 13, pp. 1-9, 2013.
  53. P. P. Rocha, M. Micsinai, J. R. Kim, S. L. Hewitt, P. P. Souza, T. Trimarchi, F. Strino, F. Parisi, Y. Kluger, and J. A. Skok, "Close proximity to Igh is a contributing factor to AID-mediated translocations," Molecular cell, vol. 47, pp. 873-885, 2012.
  54. F. Parisi, M. Micsinai, F. Strino, S. Ariyan, D. Narayan, A. Bacchiocchi, E. Cheng, F. Xu, P. Li, H. Kluger, R. Halaban, and Y. Kluger, "Integrated analysis of tumor samples sheds light on tumor heterogeneity," Yale J Biol Med, vol. 85, pp. 347-61, Sep 2012.
  55. V. M. Neumeister, V. Anagnostou, S. Siddiqui, A. M. England, E. R. Zarrella, M. Vassilakopoulou, F. Parisi, Y. Kluger, D. G. Hicks, and D. L. Rimm, "Quantitative assessment of effect of preanalytic cold ischemic time on protein expression in breast cancer tissues," JNCI: Journal of the National Cancer Institute, vol. 104, pp. 1815-1824, 2012.
  56. 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, vol. 40, pp. e70-e70, 2012.
  57. K. Johnson, J. Chaumeil, M. Micsinai, J. M. H. Wang, L. B. Ramsey, G. V. Baracho, R. C. Rickert, F. Strino, Y. Kluger, M. A. Farrar, and J. A. Skok, "IL-7 Functionally Segregates the Pro-B Cell Stage by Regulating Transcription of Recombination Mediators across Cell Cycle," The Journal of Immunology, vol. 188, p. 6084, 2012.
  58. 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.
  59. 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.
  60. 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, pp. 1-14, 2011.
  61. 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, pp. 2417-2425, 2011.
  62. A. Collins, S. L. Hewitt, J. Chaumeil, M. Sellars, M. Micsinai, J. Allinne, F. Parisi, E. P. Nora, D. J. Bolland, A. E. Corcoran, Y. Kluger, R. Bosselut, W. Ellmeier, M. M. Chong, D. R. Littman, and J. A. Skok, "RUNX transcription factor-mediated association of Cd4 and Cd8 enables coordinate gene regulation," Immunity, vol. 34, pp. 303-14, Mar 25 2011.
  63. 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, pp. E149-E158, 2011.
  64. C. van Oevelen, C. Bowman, J. Pellegrino, P. Asp, J. Cheng, F. Parisi, M. Micsinai, Y. Kluger, A. Chu, A. Blais, G. David, and B. D. Dynlacht, "The mammalian Sin3 proteins are required for muscle development and sarcomere specification," Mol Cell Biol, vol. 30, pp. 5686-97, Dec 2010.
  65. F. Parisi, A. M. González, 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 Research, vol. 12, pp. 1-11, 2010.
  66. 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, pp. 466-473, 2010.
  67. 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.

2000-2009

  1. R. Halaban, M. Krauthammer, M. Pelizzola, E. Cheng, D. Kovacs, M. Sznol, S. Ariyan, D. Narayan, A. Bacchiocchi, A. Molinaro, Y. Kluger, M. Deng, N. Tran, W. Zhang, M. Picardo, and J. J. Enghild, "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 Research, vol. 10, pp. 1-12, 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, pp. 590-594, 2008.https://www.sciencedirect.com/science/article/pii/S0923753419411885
  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, 2008/06/03 2008.
  8. Y. Zhou, J. Ferguson, J. T. Chang, and Y. Kluger, "Inter-and intra-combinatorial regulation by transcription factors and microRNAs," BMC genomics, vol. 8, pp. 1-10, 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, pp. 2932-2937, 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. P. Tuck, H. M. Kluger, and Y. Kluger, "Characterizing disease states from topological properties of transcriptional regulatory networks," BMC bioinformatics, vol. 7, pp. 1-19, 2006.
  12. Y. Kluger, H. Kluger, and D. Tuck, "Association between pathways in regulatory networks," in 2006 International Conference of the IEEE Engineering in Medicine and Biology Society, 2006, pp. 2036-2040.
  13. H. Kim, W. Hu, and Y. Kluger, "Unraveling condition specific gene transcriptional regulatory networks in Saccharomyces cerevisiae," BMC bioinformatics, vol. 7, pp. 1-17, 2006.
  14. Z.-j. 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, vol. 102, pp. 18461-18466, 2005.
  15. H. M. Kluger, D. C. 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, pp. 5578-5587, 2005.
  16. 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, pp. 553-569, 2005.
  17. 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.
  18. Y. Kluger, D. P. Tuck, J. T. Chang, Y. Nakayama, R. Poddar, N. Kohya, Z. Lian, A. Ben Nasr, H. R. Halaban, D. S. Krause, X. Zhang, P. E. Newburger, and S. M. Weissman, "Lineage specificity of gene expression patterns," Proc Natl Acad Sci U S A, vol. 101, pp. 6508-13, Apr 27 2004.
  19. Y. Kluger, Z. Lian, X. Zhang, P. E. Newburger, and S. M. Weissman, "A panorama of lineage-specific transcription in hematopoiesis," Bioessays, vol. 26, pp. 1276-1287, 2004.
  20. 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.
  21. 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.
  22. 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.
  23. J. Qian, Y. Kluger, H. Yu, and M. Gerstein, "Identification and correction of spurious spatial correlations in microarray data," Biotechniques, vol. 35, pp. 42-48, 2003.
  24. Y. Kluger, H. Yu, J. Qian, and M. Gerstein, "Relationship between gene co-expression and probe localization on microarray slides," Bmc Genomics, vol. 4, pp. 1-6, 2003.
  25. 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.
  26. 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, pp. 449-453, 2003.
  27. 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, The Journal of the American Society of Hematology, vol. 100, pp. 3209-3220, 2002.
  28. Y. V. 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, The Journal of the American Society of Hematology, vol. 97, pp. 2457-2468, 2001.
  29. 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.
  30. 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.
  31. D. Christendat, A. Yee, A. Dharamsi, Y. Kluger, A. Savchenko, J. R. Cort, V. Booth, C. D. Mackereth, V. Saridakis, I. Ekiel, G. Kozlov, K. L. Maxwell, N. Wu, L. P. McIntosh, K. Gehring, M. A. Kennedy, A. R. Davidson, E. F. Pai, M. Gerstein, A. M. Edwards, and C. H. Arrowsmith, "Structural proteomics of an archaeon," Nat Struct Biol, vol. 7, pp. 903-9, Oct 2000.
  32. 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. 339-345, 2000.

1990-1999

  1. V. Koch, J. Randrup, X.-N. Wang, and Y. Kluger, "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, Dec 15 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 ? F 4 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, p. 4660, 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. Y. Kluger, "Back-reaction beyond the mean field approximation," in Hot and Dense Nuclear Matter, ed: Springer, 1994, pp. 635-646.
  11. 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.
  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. Y. Kluger, J. Eisenberg, and B. Svetitsky, "Pair production in a strong electric field: an initial value problem in quantum field theory," International Journal of Modern Physics E, vol. 2, pp. 333-380, 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, p. 2427, 1991.

1988-1989

  1. Transport equations for the quark–gluon plasma, J.M. Eisenberg, Y. Kluger and A. Rosenhauer, in The Nuclear Equation of State, W. Greiner, ed. (Plenum, New York, 1989) p. 501.
  2. Y. Kluger and J. M. Eisenberg, "THE ISOSCALAR CHARGE FORM FACTOR IN NUCLEI OF A=2, 3 OBTAINED IN THE SKYRME MODEL," International Journal of Modern Physics A, vol. 03, pp. 2127-2142, 1988/09/01 1988.