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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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58 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  0.32
2019 Wu F, Lopatkin AJ, Needs DA, Lee CT, Mukherjee S, You L. A unifying framework for interpreting and predicting mutualistic systems. Nature Communications. 10: 242. PMID 30651549 DOI: 10.1038/s41467-018-08188-5  0.52
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  0.32
2017 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, ... ... Mukherjee S, et al. Melanoma Therapeutic Strategies that Select against Resistance by Exploiting MYC-Driven Evolutionary Convergence. Cell Reports. 21: 2796-2812. PMID 29212027 DOI: 10.1016/j.celrep.2017.11.022  0.32
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  0.32
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  0.32
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  1
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  0.44
2016 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 Non-invasively Collected Samples. Genetics. PMID 27098910 DOI: 10.1534/genetics.116.187492  0.72
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  0.72
2015 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. 10: e0135176. PMID 26376443 DOI: 10.1371/journal.pone.0135176  0.72
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  0.72
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  0.72
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  0.72
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  0.72
2014 Kapur A, Schneider JA, Heard D, Mukherjee S, Schumm P, Oruganti G, Laumann EO. A digital network approach to infer sex behavior in emerging HIV epidemics. Plos One. 9: e101416. PMID 24992340 DOI: 10.1371/journal.pone.0101416  0.72
2014 Fusco D, Barnum TJ, Bruno AE, Luft JR, Snell EH, Mukherjee S, Charbonneau P. Statistical analysis of crystallization database links protein physico-chemical features with crystallization mechanisms. Plos One. 9: e101123. PMID 24988076 DOI: 10.1371/journal.pone.0101123  0.72
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  0.72
2013 Megraw M, Mukherjee S, Ohler U. Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits. Genome Biology. 14: R85. PMID 23972209 DOI: 10.1186/gb-2013-14-8-r85  0.72
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  0.72
2013 Hafez D, Ni T, Mukherjee S, Zhu J, Ohler U. Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation. Bioinformatics (Oxford, England). 29: i108-16. PMID 23812974 DOI: 10.1093/bioinformatics/btt233  0.72
2013 Winter DR, Song L, Mukherjee S, Furey TS, Crawford GE. DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types. Genome Research. 23: 1118-29. PMID 23657885 DOI: 10.1101/gr.150482.112  0.72
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  0.72
2013 Perez BA, Ghafoori AP, Lee CL, Johnston SM, Li Y, Moroshek JG, Ma Y, Mukherjee S, Kim Y, Badea CT, Kirsch DG. Assessing the radiation response of lung cancer with different gene mutations using genetically engineered mice. Frontiers in Oncology. 3: 72. PMID 23565506 DOI: 10.3389/fonc.2013.00072  0.72
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  0.72
2012 Runcie DE, Garfield DA, Babbitt CC, Wygoda JA, Mukherjee S, Wray GA. Genetics of gene expression responses to temperature stress in a sea urchin gene network. Molecular Ecology. 21: 4547-62. PMID 22856327 DOI: 10.1111/j.1365-294X.2012.05717.x  0.72
2012 Tung J, Charpentier MJ, Mukherjee S, Altmann J, Alberts SC. Genetic effects on mating success and partner choice in a social mammal. The American Naturalist. 180: 113-29. PMID 22673655 DOI: 10.1086/665993  0.72
2012 Simmons Kovacs LA, Mayhew MB, Orlando DA, Jin Y, Li Q, Huang C, Reed SI, Mukherjee S, Haase SB. Cyclin-dependent kinases are regulators and effectors of oscillations driven by a transcription factor network. Molecular Cell. 45: 669-79. PMID 22306294 DOI: 10.1016/j.molcel.2011.12.033  0.72
2012 Acharya CR, Hsu DS, Anders CK, Anguiano A, Salter KH, Walters KS, Redman RC, Tuchman SA, Moylan CA, Mukherjee S, Barry WT, Dressman HK, Ginsburg GS, Marcom KP, Garman KS, et al. Retraction: Acharya CR, et al. Gene expression signatures, clinicopathological features, and individualized therapy in breast cancer. JAMA. 2008;299(13):1574-1587. Jama. 307: 453. PMID 22228686 DOI: 10.1001/jama.2012.2  0.72
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  0.72
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  0.72
2011 D'Addabbo A, Palmieri O, Latiano A, Annese V, Mukherjee S, Ancona N. RS-SNP: a random-set method for genome-wide association studies. Bmc Genomics. 12: 166. PMID 21450072 DOI: 10.1186/1471-2164-12-166  0.72
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  0.72
2011 Potti A, Mukherjee S, Petersen R, Dressman HK, Bild A, Koontz J, Kratzke R, Watson MA, Kelley M, Ginsburg GS, West M, Harpole DH, Nevins JR. Retraction: A genomic strategy to refine prognosis in early-stage non-small-cell lung cancer. N Engl J Med 2006;355:570-80. The New England Journal of Medicine. 364: 1176. PMID 21366430 DOI: 10.1056/NEJMc1101915  0.72
2011 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, et al. Retraction--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. The Lancet. Oncology. 12: 116. PMID 21277543 DOI: 10.1016/S1470-2045(11)70011-0  0.72
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  0.72
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  0.72
2009 Mito JK, Riedel RF, Dodd L, Lahat G, Lazar AJ, Dodd RD, Stangenberg L, Eward WC, Hornicek FJ, Yoon SS, Brigman BE, Jacks T, Lev D, Mukherjee S, Kirsch DG. Cross species genomic analysis identifies a mouse model as undifferentiated pleomorphic sarcoma/malignant fibrous histiocytoma. Plos One. 4: e8075. PMID 19956606 DOI: 10.1371/journal.pone.0008075  0.72
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  0.72
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  0.72
2009 Jesneck JL, Mukherjee S, Yurkovetsky Z, Clyde M, Marks JR, Lokshin AE, Lo JY. Do serum biomarkers really measure breast cancer? Bmc Cancer. 9: 164. PMID 19476629 DOI: 10.1186/1471-2407-9-164  0.72
2009 Hsu DS, Acharya CR, Balakumaran BS, Riedel RF, Kim MK, Stevenson M, Tuchman S, Mukherjee S, Barry W, Dressman HK, Nevins JR, Powers S, Mu D, Potti A. Characterizing the developmental pathways TTF-1, NKX2-8, and PAX9 in lung cancer. Proceedings of the National Academy of Sciences of the United States of America. 106: 5312-7. PMID 19279207 DOI: 10.1073/pnas.0900827106  0.72
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  0.72
2008 Acharya CR, Hsu DS, Anders CK, Anguiano A, Salter KH, Walters KS, Redman RC, Tuchman SA, Moylan CA, Mukherjee S, Barry WT, Dressman HK, Ginsburg GS, Marcom KP, Garman KS, et al. Gene expression signatures, clinicopathological features, and individualized therapy in breast cancer. Jama. 299: 1574-87. PMID 18387932 DOI: 10.1001/jama.299.13.1574  0.72
2008 Salter KH, Acharya CR, Walters KS, Redman R, Anguiano A, Garman KS, Anders CK, Mukherjee S, Dressman HK, Barry WT, Marcom KP, Olson J, Nevins JR, Potti A. An integrated approach to the prediction of chemotherapeutic response in patients with breast cancer. Plos One. 3: e1908. PMID 18382681 DOI: 10.1371/journal.pone.0001908  0.72
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  0.72
2008 Anders CK, Acharya CR, Hsu DS, Broadwater G, Garman K, Foekens JA, Zhang Y, Wang Y, Marcom K, Marks JR, Mukherjee S, Nevins JR, Blackwell KL, Potti A. Age-specific differences in oncogenic pathway deregulation seen in human breast tumors. Plos One. 3: e1373. PMID 18167534 DOI: 10.1371/journal.pone.0001373  0.72
2007 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, et al. 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. The Lancet. Oncology. 8: 1071-8. PMID 18024211 DOI: 10.1016/S1470-2045(07)70345-5  0.72
2007 Chi JT, Rodriguez EH, Wang Z, Nuyten DS, Mukherjee S, van de Rijn M, van de Vijver MJ, Hastie T, Brown PO. Gene expression programs of human smooth muscle cells: tissue-specific differentiation and prognostic significance in breast cancers. Plos Genetics. 3: 1770-84. PMID 17907811 DOI: 10.1371/journal.pgen.0030164  0.72
2006 Wang Z, Willard HF, Mukherjee S, Furey TS. Evidence of influence of genomic DNA sequence on human X chromosome inactivation Plos Computational Biology. 2: 0979-0988. PMID 16948528 DOI: 10.1371/journal.pcbi.0020113  0.72
2006 Potti A, Mukherjee S, Petersen R, Dressman HK, Bild A, Koontz J, Kratzke R, Watson MA, Kelley M, Ginsburg GS, West M, Harpole DH, Nevins JR. A genomic strategy to refine prognosis in early-stage non-small-cell lung cancer. The New England Journal of Medicine. 355: 570-80. PMID 16899777 DOI: 10.1056/NEJMoa060467  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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  0.72
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