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Sayan Mukherjee - Publications

Affiliations: 
Duke University, Durham, NC 
Area:
Computational biology , statistical learning , Laplacian statistics
Website:
http://www.stat.duke.edu/~sayan/
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52 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Cakir M, Mukherjee S, Wood KC. Label propagation defines signaling networks associated with recurrently mutated cancer genes. Scientific Reports. 9: 9401. PMID 31253832 DOI: 10.1038/s41598-019-45603-3  0.318
2019 Gao T, Brodzki J, Mukherjee S. The Geometry of Synchronization Problems and Learning Group Actions Discrete and Computational Geometry. 1-62. DOI: 10.1007/S00454-019-00100-2  0.316
2018 Zhao S, Engelhardt BE, Mukherjee S, Dunson DB. Fast Moment Estimation for Generalized Latent Dirichlet Models. Journal of the American Statistical Association. 113: 1528-1540. PMID 35875263 DOI: 10.1080/01621459.2017.1341839  0.321
2018 Crawford L, Wood KC, Zhou X, Mukherjee S. Bayesian Approximate Kernel Regression with Variable Selection. Journal of the American Statistical Association. 113: 1710-1721. PMID 30799887 DOI: 10.1080/01621459.2017.1361830  0.345
2017 Crawford L, Zeng P, Mukherjee S, Zhou X. Detecting epistasis with the marginal epistasis test in genetic mapping studies of quantitative traits. Plos Genetics. 13: e1006869. PMID 28746338 DOI: 10.1371/Journal.Pgen.1006869  0.31
2017 Sun S, Hood M, Scott L, Peng Q, Mukherjee S, Tung J, Zhou X. Differential expression analysis for RNAseq using Poisson mixed models. Nucleic Acids Research. PMID 28369632 DOI: 10.1093/Nar/Gkx204  0.338
2017 Bobrowski O, Mukherjee S, Taylor JE. Topological consistency via kernel estimation Bernoulli. 23: 288-328. DOI: 10.3150/15-BEJ744  0.309
2017 Lunagómez S, Mukherjee S, Wolpert RL, Airoldi EM. Geometric Representations of Random Hypergraphs Journal of the American Statistical Association. 112: 363-383. DOI: 10.1080/01621459.2016.1141686  0.738
2016 Mukherjee S, Steenbergen J. Random walks on simplicial complexes and harmonics. Random Structures & Algorithms. 49: 379-405. PMID 28303080 DOI: 10.1002/Rsa.20645  0.666
2016 Galinsky KJ, Bhatia G, Loh PR, Georgiev S, Mukherjee S, Patterson NJ, Price AL. Response to Shen et al. American Journal of Human Genetics. 99: 1220-1221. PMID 27814525 DOI: 10.1016/J.Ajhg.2016.09.013  0.569
2016 Galinsky KJ, Bhatia G, Loh PR, Georgiev S, Mukherjee S, Patterson NJ, Price AL. Fast Principal-Component Analysis Reveals Convergent Evolution of ADH1B in Europe and East Asia. American Journal of Human Genetics. PMID 26924531 DOI: 10.1016/J.Ajhg.2015.12.022  0.602
2015 Boyer DM, Puente J, Gladman JT, Glynn C, Mukherjee S, Yapuncich GS, Daubechies I. A new fully automated approach for aligning and comparing shapes. Anatomical Record (Hoboken, N.J. : 2007). 298: 249-76. PMID 25529243 DOI: 10.1002/Ar.23084  0.306
2015 McGoff K, Mukherjee S, Pillai N. Statistical inference for dynamical systems: A review Statistics Surveys. 9: 209-252. DOI: 10.1214/15-Ss111  0.511
2015 McGoff K, Mukherjee S, Nobel A, Pillai N. Consistency of maximum likelihood estimation for some dynamical systems Annals of Statistics. 43: 1-29. DOI: 10.1214/14-Aos1259  0.534
2015 Raskutti G, Mukherjee S. The information geometry of mirror descent Ieee Transactions On Information Theory. 61: 1451-1457. DOI: 10.1109/Tit.2015.2388583  0.338
2014 Whitney O, Pfenning AR, Howard JT, Blatti CA, Liu F, Ward JM, Wang R, Audet JN, Kellis M, Mukherjee S, Sinha S, Hartemink AJ, West AE, Jarvis ED. Core and region-enriched networks of behaviorally regulated genes and the singing genome. Science (New York, N.Y.). 346: 1256780. PMID 25504732 DOI: 10.1126/Science.1256780  0.304
2014 Weiser M, Mukherjee S, Furey TS. Novel distal eQTL analysis demonstrates effect of population genetic architecture on detecting and interpreting associations. Genetics. 198: 879-93. PMID 25230953 DOI: 10.1534/Genetics.114.167791  0.331
2014 Xiong Q, Mukherjee S, Furey TS. GSAASeqSP: a toolset for gene set association analysis of RNA-Seq data. Scientific Reports. 4: 6347. PMID 25213199 DOI: 10.1038/Srep06347  0.334
2014 Steenbergen J, Klivans C, Mukherjee S. A Cheeger-type inequality on simplicial complexes Advances in Applied Mathematics. 56: 56-77. DOI: 10.1016/J.Aam.2014.01.002  0.656
2013 Blum JM, Añó L, Li Z, Van Mater D, Bennett BD, Sachdeva M, Lagutina I, Zhang M, Mito JK, Dodd LG, Cardona DM, Dodd RD, Williams N, Ma Y, Lepper C, ... ... Mukherjee S, et al. Distinct and overlapping sarcoma subtypes initiated from muscle stem and progenitor cells. Cell Reports. 5: 933-40. PMID 24239359 DOI: 10.1016/J.Celrep.2013.10.020  0.499
2013 Stifanelli PF, Creanza TM, Anglani R, Liuzzi VC, Mukherjee S, Schena FP, Ancona N. A comparative study of covariance selection models for the inference of gene regulatory networks. Journal of Biomedical Informatics. 46: 894-904. PMID 23876513 DOI: 10.1016/j.jbi.2013.07.002  0.342
2013 Runcie DE, Mukherjee S. Dissecting high-dimensional phenotypes with bayesian sparse factor analysis of genetic covariance matrices. Genetics. 194: 753-67. PMID 23636737 DOI: 10.1534/Genetics.113.151217  0.349
2013 Wu Q, Liang F, Mukherjee S. Kernel sliced inverse regression: Regularization and consistency Abstract and Applied Analysis. 2013. DOI: 10.1155/2013/540725  0.449
2012 Bennett BD, Xiong Q, Mukherjee S, Furey TS. A predictive framework for integrating disparate genomic data types using sample-specific gene set enrichment analysis and multi-task learning. Plos One. 7: e44635. PMID 23028573 DOI: 10.1371/Journal.Pone.0044635  0.585
2012 Xiong Q, Ancona N, Hauser ER, Mukherjee S, Furey TS. Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets. Genome Research. 22: 386-97. PMID 21940837 DOI: 10.1101/Gr.124370.111  0.35
2012 Anglani R, Creanza T, Liuzzi V, Stifanelli P, Maglietta R, Piepoli A, Mukherjee S, Schena F, Ancona N. Topological analysis of co-expression networks in neoplastic tissues Embnet.Journal. 18: 127. DOI: 10.14806/Ej.18.A.457  0.337
2011 Garman KS, Acharya CR, Edelman E, Grade M, Gaedcke J, Sud S, Barry W, Diehl AM, Provenzale D, Ginsburg GS, Ghadimi BM, Ried T, Nevins JR, Mukherjee S, Hsu D, et al. Retraction for Garman et al: A genomic approach to colon cancer risk stratification yields biologic insights into therapeutic opportunities. Proceedings of the National Academy of Sciences of the United States of America. 108: 17569. PMID 21969600 DOI: 10.1073/pnas.1115170108  0.413
2011 D'Addabbo A, Palmieri O, Maglietta R, Latiano A, Mukherjee S, Annese V, Ancona N. Discovering genetic variants in Crohn's disease by exploring genomic regions enriched of weak association signals. Digestive and Liver Disease : Official Journal of the Italian Society of Gastroenterology and the Italian Association For the Study of the Liver. 43: 623-31. PMID 21411385 DOI: 10.1016/j.dld.2011.02.010  0.313
2011 Guinney J, Wu Q, Mukherjee S. Estimating variable structure and dependence in multitask learning via gradients Machine Learning. 83: 265-287. DOI: 10.1007/S10994-010-5217-4  0.624
2010 Georgiev S, Boyle AP, Jayasurya K, Ding X, Mukherjee S, Ohler U. Evidence-ranked motif identification. Genome Biology. 11: R19. PMID 20156354 DOI: 10.1186/Gb-2010-11-2-R19  0.584
2010 Maglietta R, Distaso A, Piepoli A, Palumbo O, Carella M, D'Addabbo A, Mukherjee S, Ancona N. On the reproducibility of results of pathway analysis in genome-wide expression studies of colorectal cancers. Journal of Biomedical Informatics. 43: 397-406. PMID 19796710 DOI: 10.1016/j.jbi.2009.09.005  0.37
2010 Mukherjee S, Wu Q, Zhou DX. Learning gradients on manifolds Bernoulli. 16: 181-207. DOI: 10.3150/09-BEJ206  0.449
2010 Wu Q, Liang F, Mukherjee S. Localized sliced inverse regression Journal of Computational and Graphical Statistics. 19: 843-860. DOI: 10.1198/jcgs.2010.08080  0.429
2010 Edelman E, Garman K, Potti A, Mukherjee S. Making Mountains out of Molehills: Moving from Single Gene to Pathway Based Models of Colon Cancer Progression Medical Biostatistics For Complex Diseases. 73-87. DOI: 10.1002/9783527630332.ch4  0.447
2009 Abatangelo L, Maglietta R, Distaso A, D'Addabbo A, Creanza TM, Mukherjee S, Ancona N. Comparative study of gene set enrichment methods. Bmc Bioinformatics. 10: 275. PMID 19725948 DOI: 10.1186/1471-2105-10-275  0.343
2009 Tung J, Fédrigo O, Haygood R, Mukherjee S, Wray GA. Genomic features that predict allelic imbalance in humans suggest patterns of constraint on gene expression variation. Molecular Biology and Evolution. 26: 2047-59. PMID 19506001 DOI: 10.1093/Molbev/Msp113  0.334
2008 Garman KS, Acharya CR, Edelman E, Grade M, Gaedcke J, Sud S, Barry W, Diehl AM, Provenzale D, Ginsburg GS, Ghadimi BM, Ried T, Nevins JR, Mukherjee S, Hsu D, et al. A genomic approach to colon cancer risk stratification yields biologic insights into therapeutic opportunities. Proceedings of the National Academy of Sciences of the United States of America. 105: 19432-7. PMID 19050079 DOI: 10.1073/Pnas.0806674105  0.519
2008 Edelman EJ, Guinney J, Chi JT, Febbo PG, Mukherjee S. Modeling cancer progression via pathway dependencies. Plos Computational Biology. 4: e28. PMID 18282083 DOI: 10.1371/Journal.Pcbi.0040028  0.667
2007 Liang F, Mukherjee S, West M. The use of unlabeled data in predictive modeling Statistical Science. 22: 189-205. DOI: 10.1214/088342307000000032  0.349
2006 Edelman E, Porrello A, Guinney J, Balakumaran B, Bild A, Febbo PG, Mukherjee S. Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles. Bioinformatics (Oxford, England). 22: e108-16. PMID 16873460 DOI: 10.1093/Bioinformatics/Btl231  0.678
2006 Tropea D, Kreiman G, Lyckman A, Mukherjee S, Yu H, Horng S, Sur M. Gene expression changes and molecular pathways mediating activity-dependent plasticity in visual cortex. Nature Neuroscience. 9: 660-8. PMID 16633343 DOI: 10.1038/Nn1689  0.557
2006 Mukherjee S, Niyogi P, Poggio T, Rifkin R. Learning theory: Stability is sufficient for generalization and necessary and sufficient for consistency of empirical risk minimization Advances in Computational Mathematics. 25: 161-193. DOI: 10.1007/s10444-004-7634-z  0.676
2005 Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America. 102: 15545-50. PMID 16199517 DOI: 10.1073/Pnas.0506580102  0.35
2005 Sweet-Cordero A, Mukherjee S, Subramanian A, You H, Roix JJ, Ladd-Acosta C, Mesirov J, Golub TR, Jacks T. An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis. Nature Genetics. 37: 48-55. PMID 15608639 DOI: 10.1038/Ng1490  0.326
2005 Rakhlin A, Mukherjee S, Poggio T. Stability Results In Learning Theory Analysis and Applications. 3: 397-417. DOI: 10.1142/S0219530505000650  0.689
2005 Rakhlin A, Panchenko D, Mukherjee S. Risk bounds for mixture density estimation Esaim - Probability and Statistics. 9: 220-229. DOI: 10.1051/ps:2005011  0.594
2004 Poggio T, Rifkin R, Mukherjee S, Niyogi P. General conditions for predictivity in learning theory. Nature. 428: 419-22. PMID 15042089 DOI: 10.1038/nature02341  0.673
2003 Mukherjee S, Tamayo P, Rogers S, Rifkin R, Engle A, Campbell C, Golub TR, Mesirov JP. Estimating dataset size requirements for classifying DNA microarray data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 10: 119-42. PMID 12804087 DOI: 10.1089/106652703321825928  0.343
2003 Rifkin R, Mukherjee S, Tamayo P, Ramaswamy S, Yeang CH, Angelo M, Reich M, Poggio T, Lander ES, Golub TR, Mesirov JP. An analytical method for multiclass molecular cancer classification Siam Review. 45: 706-723. DOI: 10.1137/S0036144502411986  0.552
2002 Miller LD, Long PM, Wong L, Mukherjee S, McShane LM, Liu ET. Optimal gene expression analysis by microarrays. Cancer Cell. 2: 353-61. PMID 12450790 DOI: 10.1016/S1535-6108(02)00181-2  0.328
2001 Ramaswamy S, Tamayo P, Rifkin R, Mukherjee S, Yeang CH, Angelo M, Ladd C, Reich M, Latulippe E, Mesirov JP, Poggio T, Gerald W, Loda M, Lander ES, Golub TR. Multiclass cancer diagnosis using tumor gene expression signatures. Proceedings of the National Academy of Sciences of the United States of America. 98: 15149-54. PMID 11742071 DOI: 10.1073/Pnas.211566398  0.552
2001 Yeang CH, Ramaswamy S, Tamayo P, Mukherjee S, Rifkin RM, Angelo M, Reich M, Lander E, Mesirov J, Golub T. Molecular classification of multiple tumor types. Bioinformatics (Oxford, England). 17: S316-22. PMID 11473023 DOI: 10.1093/Bioinformatics/17.Suppl_1.S316  0.314
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