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Publications of Sayan Mukherjee    :chronological  alphabetical  combined  bibtex listing:

Papers Published

  1. Singleton, KR; Crawford, L; Tsui, E; Manchester, HE; Maertens, O; Liu, X; Liberti, MV; Magpusao, AN; Stein, EM; Tingley, JP; Frederick, DT; Boland, GM; Flaherty, KT; McCall, SJ; Krepler, C; Sproesser, K; Herlyn, M; Adams, DJ; Locasale, JW; Cichowski, K; Mukherjee, S; Wood, KC, Melanoma Therapeutic Strategies that Select against Resistance by Exploiting MYC-Driven Evolutionary Convergence., Cell Reports, vol. 21 no. 10 (December, 2017), pp. 2796-2812 [doi]  [abs]
  2. Gao, T; Yapuncich, GS; Daubechies, I; Mukherjee, S; Boyer, DM, Development and Assessment of Fully Automated and Globally Transitive Geometric Morphometric Methods, With Application to a Biological Comparative Dataset With High Interspecific Variation., The Anatomical Record : Advances in Integrative Anatomy and Evolutionary Biology (October, 2017) [doi]  [abs]
  3. Bobrowski, O; Mukherjee, S; Taylor, JE, Topological consistency via kernel estimation, Bernoulli : official journal of the Bernoulli Society for Mathematical Statistics and Probability, vol. 23 no. 1 (February, 2017), pp. 288-328 [doi]
  4. Snyder-Mackler, N; Majoros, WH; Yuan, ML; Shaver, AO; Gordon, JB; Kopp, GH; Schlebusch, SA; Wall, JD; Alberts, SC; Mukherjee, S; Zhou, X; Tung, J, Efficient Genome-Wide Sequencing and Low-Coverage Pedigree Analysis from Noninvasively Collected Samples., Genetics, vol. 203 no. 2 (June, 2016), pp. 699-714 [doi]  [abs]
  5. Zhao, S; Gao, C; Mukherjee, S; Engelhardt, BE, Bayesian group factor analysis with structured sparsity, Journal of machine learning research : JMLR, vol. 17 (April, 2016), pp. 1-47  [abs]
  6. Galinsky, KJ; Bhatia, G; Loh, P-R; Georgiev, S; Mukherjee, S; Patterson, NJ; Price, AL, Fast Principal-Component Analysis Reveals Convergent Evolution of ADH1B in Europe and East Asia., The American Journal of Human Genetics, vol. 98 no. 3 (March, 2016), pp. 456-472 [doi]  [abs]
  7. Munch, E; Turner, K; Bendich, P; Mukherjee, S; Mattingly, J; Harer, J, Probabilistic Fréchet means for time varying persistence diagrams, Electronic Journal of Statistics, vol. 9 no. 1 (January, 2015), pp. 1173-1204 [repository], [doi]  [abs]
  8. Raskutti, G; Mukherjee, S, The information geometry of mirror descent, Lecture notes in computer science, vol. 9389 (January, 2015), pp. 359-368, ISBN 9783319250397 [doi]  [abs]
  9. Stewart, L; MacLean, EL; Ivy, D; Woods, V; Cohen, E; Rodriguez, K; McIntyre, M; Mukherjee, S; Call, J; Kaminski, J; Miklósi, Á; Wrangham, RW; Hare, B, Citizen Science as a New Tool in Dog Cognition Research., PloS one, vol. 10 no. 9 (January, 2015), pp. e0135176 [doi]  [abs]
  10. Bonnefoi H, Potti A, Delorenzi M, Mauriac L, Campone M, Tubiana-Hulin M, Petit T, Rouanet P, Jassem J, Blot E, Becette V, Farmer P, André S, Acharya CR, Mukherjee S, Cameron D, Bergh J, Nevins JR, Iggo RD., Validation of gene signatures that predict the response of breast cancer to neoadjuvant chemotherapy: a substudy of the EORTC 10994/BIG 00-01 clinical trial., Lancet Oncology, vol. 8 no. 12 (December, 2007), pp. 1071-1078 [entrez]
  11. F. Liang, S. Mukherjee, M. West, Understanding the use of unlabelled data in predictive modelling, Statistical Science, vol. 22 no. 2 (Fall, 2007), pp. 189-205
  12. Jen-Tsan Chi1, Edwin H. Rodriguez, Zhen Wang, Dimitry S. A. Nuyten, Sayan Mukherjee, Matt van de Rijn, Marc J. van de Vijver, Trevor Hastie, Patrick O. Brown, Gene Expression Programs of Human Smooth Muscle Cells: Tissue-Specific Differentiation and Prognostic Significance in Breast Cancers, PLoS Genet, vol. 3 no. 9 (September, 2007), pp. 1770-1784 [pdf]
  13. Natesh Pillai, Qiang Wu, Feng Liang, Sayan Mukherjee, Robert L. Wolpert, Characterizing the function space for Bayesian kernel models, Journal of Machine Learning Research, vol. 8 (August, 2007), pp. 1769--1797 [html]  [abs]
  14. Liang Goh, Susan K. Murphy, Sayan Muhkerjee, and Terrence S. Furey, Genomic sweeping for hypermethylated genes, Bioinformatics, vol. 23 no. 3 (February, 2007), pp. 281-288 [btl620v1]
  15. Zhong Wang, Huntington F. Willard, Sayan Mukherjee, Terrence S. Furey, Evidence of Influence of Genomic DNA Sequence on Human X Chromosome Inactivation, Public Library of Science Computational Biology, vol. 2 no. 9 (Winter, 2006), pp. 979-988 [available here]
  16. S. Mukherjee and Q. Wu, Estimation of Gradients and Coordinate Covariation in Classification, Journal of Machine Learning Research, vol. 7 (November, 2006), pp. 2481--2514 [html]
  17. S. Mukherjee, DX. Zhou, Learning Coordinate Covariances via Gradients, Journal of Machine Learning Research, vol. 7 (March, 2006), pp. 519-549 [html]
  18. Elena Edelman, Alessandro Porrello, Justin Guinney, BalaBalakumaran, Andrea Bild, Phillip G. Febbo, and Sayan Mukherjee, Analysis of Sample Set Enrichment Scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles, Bioinformatics, vol. 22 no. 14 (2006), pp. e101-e116 [e108]
  19. Daniela Tropea, Gabriel Kreiman, Alvin Lyckman, Sayan Mukherjee, Hongbo Yu, Sam Horng and Mriganka Sur, Gene expression changes and molecular pathways mediating activity-dependent plasticity in visual cortex, Nature Neuroscience, vol. 9 (2006), pp. 660-668 [html]
  20. A. Potti, S. Mukherjee, R. Petersen, HK. Dressman, A. Bild, J. Koontz, R. Kratzke, MA. Watson, M. Kelley, A Genomic Strategy to Refine Prognosis in Early Stage Non-Small Cell Lung Carcinoma, New England Journal of Medicine, vol. 355 no. 6 (2006), pp. 570-580 [pdf]
  21. A. Subramanian, P. Tamayo, VK. Mootha, S. Mukherjee, BL. Ebert, MA. Gillette, A. Paulovich, SL. Pomeroy, TR. Golub, ES. Lander, JP. Mesirov, Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles, PNAS, vol. 102 no. 43 (October, 2005), pp. 15278-9 [15545]
  22. A. Rakhlin, D. Panchenko, S. Mukherjee, Risk Bounds for Mixture Density Estimation, ESAIM: Probability and Statistics, vol. 9 (June, 2005), pp. 220-229
  23. Sweet-Cordero, A., Mukherjee, S., You, H., Subramnian, S., Ladd, C., Roix, J., Mesirov, J.P., Golub, T.R., Jacks, T, An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis, Nature Genetics, vol. 37 no. 1 (January, 2005), pp. 48-55 [html]
  24. A. Rakhlin, S. Mukherjee, T. Poggio, Stability Results In Learning Theory, Analysis and Applications, vol. 3 no. 4 (2005), pp. 397–417 [html]
  25. P. Golland, F. Liang, S. Mukherjee, D. Panchenko, Permutation Tests for Classification, in Proceedings of Computational Learning Theory 2005, edited by P. Auer and R. Meir (2005), pp. 501-515, Springer-Verlag
  26. S. Mukherjee, P. Niyogi, T. Poggio, R. Rifkin, Statistical Learning: Stability is Sufficient for Generalization and Necessary and Sufficient for Consistency of Empirical Risk Minimization, Advances in Computational Mathematics, vol. 25 no. 1-3 (2005), pp. 161 - 193 [contribution.asp]
  27. R. Berger, PG. Febbo, PK. Majumder, JJ. Zhao, S. Mukherjee, T Campbell, WR. Sellers, TM. Roberts, M. Loda, TR. Golub, WC. Hahan, Androgen-Induced Differentiation and Tumorigenicity of Human Prostate Epithelial Cells, Cancer Research, vol. 64 (December, 2004), pp. 8867-8875 [8867]
  28. T. Poggio, R. Rifkin, S. Mukherjee, P. Niyogi, Learning Theory: general conditions for predictivity, Nature, vol. 428 (March, 2004), pp. 419-422 [html]
  29. R. Rifkin, S. Mukherjee, P. Tamayo, S. Ramaswamy, CH. Yeang, M. Reich, T. Poggio, ES. Lander, TR. Golub, JP. Mesirov, An Analytical Method for Multi-Class Cancer Classification, SIAM Reviews, vol. 45 no. 4 (Winter, 2003), pp. 706-723 [html]
  30. S. Mukherjee, P. Tamayo , S. Rogers, R. Rifkin, A. Engle, C. Campbell, TR. Golub, JP. Mesirov, Estimating Dataset Size Requirements for Classifying DNA Microarray Data, Journal of Computational Biology, vol. 10 no. 2 (April, 2003), pp. 119-142 [10.1089%2F106652703321825928]
  31. LD. Miller, PM. Long,L. Wong, S. Mukherjee, LM. McShane, ET. Liu, Optimal gene expression analysis by microarrays, Cancer Cell, vol. 2 (November, 2002), pp. 353-361 [abstract]
  32. S. Pomeroy, P. Tamayo, M. Gaasenbeek, L. Sturla, M. Angelo, M. McLaughlin, J. Kim, L. Goumnerova, P. Black, C. Lau, J. Allen, D. Zigzag, J. Olson, T. Curran, C. Wetmore, J. Biegel, T. Poggio, S. Mukherjee, R. Rifkin, A. Califano, G. Stolovitzky, D. Louis, Prediction of central nervous system embryonal tumour outcome based of gene expression, Nature, vol. 415 no. 24 (January, 2002), pp. 436-442 [html]
  33. Mukherjee, N; Mukherjee, S, Predicting signal peptides with support vector machines, Lecture notes in computer science, vol. 2388 (January, 2002), pp. 1-7, ISBN 354044016X [doi]  [abs]
  34. S. Ramaswamy, P. Tamayo, R. Rifkin, S. Mukherjee, CH Yeang, M. Angelo, C. Ladd, M. Reich, E. Latulippe, JP. Mesirov, T. Poggio, W. Gerald, M. Loda,, ES. Lander, TR. Golub, Multiclass cancer diagnosis using tumor gene expression signatures, PNAS, vol. 98 no. 26 (December, 2001), pp. 15149-15154 [15149]
  35. O. Chapelle, V. Vapnik, O. Bousquet, S. Mukherjee, Choosing Multiple Parameters for Support Vector Machines, Machine Learning, vol. 46 no. 1-3 (March, 2001), pp. 131-159 [contribution.asp]
  36. Peshkin, L; Mukherjee, S, Bounds on sample size for policy evaluation in Markov environments, Lecture notes in computer science, vol. 2111 (January, 2001), pp. 616-629, ISSN 0302-9743  [abs]
  37. J. Weston, S. Mukherjee, O. Chapelle, M. Pontil, T. Poggio, V. Vapnik, Feature Selection for SVMs, in Proceedings of Advances in Neural Information Processing Systems, vol. 14 (2001), pp. 668-674
  38. CH Yeang, S. Ramaswamy, P. Tamayo, S. Mukherjee, R. Rifkin, M. Angelo, M. Reich, E. Lander, J. Mesirov, T. Golub, Molecular classification of multiple tumor types, Bioinformatics, vol. 1 no. 1 (2001), pp. 1-7 [S316]
  39. Pontil, M; Mukherjee, S; Girosi, F, On the noise model of support vector machines regression, in Proceedings of Algorithmic Learning Theory 11th Conference, Lecture notes in computer science, vol. 1968 (2000), pp. 316-324, Springer, Berlin, ISBN 9783540412373  [abs]
  40. V. Vapnik, S. Mukherjee, Support vector method for multivariate density estimation, in Proceedings of Advances in Neural Information Processing Systems, edited by S. A. Solla, T. K. Leen, and K.R. Muller, vol. 12 (2000), pp. 659--665

Papers Accepted

  1. E. Edelman, J. Guinney, J-T. Chi, P.G. Febbo, and S. Mukherjee, Modeling Cancer Progression via Pathway Dependencies, Public Library of Science Computational Biology (2007) [html]

Papers Submitted

  1. Q. Wu, S. Mukherjee, F. Liang, Regularized sliced inverse regression for kernel models., Biometrika (2007) [html]
  2. F. Liang, K. Mao, M. Liao, S. Mukherjee and M. West, Non-parametric Bayesian kernel models, Biometrika (2007) [html]
  3. J. Guinney, Q. Wu, and S. Mukherjee, Estimating variable structure and dependence in Multi-task learning via gradients, Journal of Machine Learning Research (2007) [html]
  4. Q. Wu, J. Guinney, M. Maggioni, and S. Mukherjee, Learning gradients: predictive models that infer geometry and dependence, Journal of Machine Learning Research (2007) [html]
  5. S. Mukherjee, Q. Wu, D-X. Zhou, Learning Gradients and Feature Selection on Manifolds, Annals of Statistics (2007) [html]


  1. Huang, B; Jarrett, NWD; Babu, S; Mukherjee, S; Yang, J, Cümülön: MatrixBased data analytics in the cloud with spot instances, in Proceedings of the VLDB Endowment, vol. 9 (January, 2016), pp. 156-167  [abs]
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