Debraj Ghosh, Ph.D. - Publications

Affiliations: 
University of California, Santa Cruz, Santa Cruz, CA, United States 
Area:
electrochemistry, nanomaterials

157 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 Anantharajan J, Zhou H, Zhang L, Hotz T, Vincent MY, Blevins MA, Jansson AE, Liang Kuan JW, Ng EY, Yeo K, Baburajendran N, Lin G, Hung AW, Joy J, Patnaik S, ... ... Ghosh D, et al. Structural and functional analyses of an allosteric Eya2 phosphatase inhibitor that has on target effects in human lung cancer cells. Molecular Cancer Therapeutics. PMID 31285279 DOI: 10.1158/1535-7163.MCT-18-1239  0.52
2019 Holleman AM, Broadaway KA, Duncan R, Todor A, Almli LM, Bradley B, Ressler KJ, Ghosh D, Mulle JG, Epstein MP. Powerful and Efficient Strategies for Genetic Association Testing of Symptom and Questionnaire Data in Psychiatric Genetic Studies. Scientific Reports. 9: 7523. PMID 31101869 DOI: 10.1038/s41598-019-44046-0  0.48
2019 Ozdemir T, Bowers DT, Zhan X, Ghosh D, Brown JL. Identification of Key Signaling Pathways Orchestrating Substrate Topography Directed Osteogenic Differentiation Through High-Throughput siRNA Screening. Scientific Reports. 9: 1001. PMID 30700820 DOI: 10.1038/s41598-018-37554-y  0.44
2019 Oliphant MUJ, Vincent MY, Galbraith MD, Pandey A, Zaberezhnyy V, Rudra P, Johnson KR, Costello JC, Ghosh D, DeGregori J, Espinosa JM, Ford HL. Six2 mediates late-stage metastasis via direct regulation of Sox2 and induction of a cancer stem cell program. Cancer Research. PMID 30606720 DOI: 10.1158/0008-5472.CAN-18-1791  0.52
2018 Zhang L, Zhou H, Li X, Vartuli RL, Rowse M, Xing Y, Rudra P, Ghosh D, Zhao R, Ford HL. Author Correction: Eya3 partners with PP2A to induce c-Myc stabilization and tumor progression. Nature Communications. 9: 3830. PMID 30224630 DOI: 10.1038/s41467-018-06265-3  0.52
2018 Vartuli RL, Zhou H, Zhang L, Powers RK, Klarquist J, Rudra P, Vincent MY, Ghosh D, Costello JC, Kedl RM, Slansky JE, Zhao R, Ford HL. Eya3 promotes breast tumor-associated immune suppression via threonine phosphatase-mediated PD-L1 upregulation. The Journal of Clinical Investigation. PMID 29757193 DOI: 10.1172/JCI96784  0.52
2018 Rudra P, Broadaway KA, Ware EB, Jhun MA, Bielak LF, Zhao W, Smith JA, Peyser PA, Kardia SLR, Epstein MP, Ghosh D. Testing cross-phenotype effects of rare variants in longitudinal studies of complex traits. Genetic Epidemiology. PMID 29601641 DOI: 10.1002/gepi.22121  0.52
2018 Zhang L, Zhou H, Li X, Vartuli RL, Rowse M, Xing Y, Rudra P, Ghosh D, Zhao R, Ford HL. Eya3 partners with PP2A to induce c-Myc stabilization and tumor progression. Nature Communications. 9: 1047. PMID 29535359 DOI: 10.1038/s41467-018-03327-4  0.52
2017 Zhang W, Ghosh D. On the use of kernel machines for Mendelian randomization. Quantitative Biology (Beijing, China). 5: 368-379. PMID 30221016 DOI: 10.1007/s40484-017-0124-3  0.32
2017 Zhu B, Song N, Shen R, Arora A, Machiela MJ, Song L, Landi MT, Ghosh D, Chatterjee N, Baladandayuthapani V, Zhao H. Integrating Clinical and Multiple Omics Data for Prognostic Assessment across Human Cancers. Scientific Reports. 7: 16954. PMID 29209073 DOI: 10.1038/s41598-017-17031-8  0.48
2017 Kim D, Volk H, Girirajan S, Pendergrass S, Hall MA, Verma SS, Schmidt RJ, Hansen RL, Ghosh D, Ludena-Rodriguez Y, Kim K, Ritchie MD, Hertz-Picciotto I, Selleck SB. The joint effect of air pollution exposure and copy number variation on risk for autism. Autism Research : Official Journal of the International Society For Autism Research. PMID 28448694 DOI: 10.1002/aur.1799  0.44
2017 O'Gorman WE, Kong DS, Balboni IM, Rudra P, Bolen CR, Ghosh D, Davis MM, Nolan GP, Hsieh EW. Mass cytometry identifies a distinct monocyte cytokine signature shared by clinically heterogeneous pediatric SLE patients. Journal of Autoimmunity. PMID 28389038 DOI: 10.1016/j.jaut.2017.03.010  0.52
2016 Zhan X, Girirajan S, Zhao N, Wu MC, Ghosh D. A novel copy number variants kernel association test with application to autism spectrum disorders studies. Bioinformatics (Oxford, England). PMID 27497442 DOI: 10.1093/bioinformatics/btw500  0.44
2016 McCammon KM, Panda SP, Xia C, Kim JP, Moutinho D, Kranendonk M, Auchus RJ, Lafer EM, Ghosh D, Martasek P, Kar R, Masters BS, Roman LJ. Instability of the Human Cytochrome P450 Reductase A287P Variant Is the Major Contributor to its Antley-Bixler Syndrome-Like Phenotype. The Journal of Biological Chemistry. PMID 27496950 DOI: 10.1074/jbc.M116.716019  0.32
2016 Ghosh D, Haswell KM, Sprada M, Gonzalez-Fernandez F. Fold conservation and proteolysis in zebrafish IRBP structure: Clues to possible enzymatic function? Experimental Eye Research. PMID 27155144 DOI: 10.1016/j.exer.2016.05.001  0.32
2016 Broadaway KA, Cutler DJ, Duncan R, Moore JL, Ware EB, Jhun MA, Bielak LF, Zhao W, Smith JA, Peyser PA, Kardia SL, Ghosh D, Epstein MP. A Statistical Approach for Testing Cross-Phenotype Effects of Rare Variants. American Journal of Human Genetics. 98: 525-540. PMID 26942286 DOI: 10.1016/j.ajhg.2016.01.017  0.48
2016 Ghosh DK, Wang D, Zhu T. On the transition of base flow recession from early stage to late stage Advances in Water Resources. 88: 8-13. DOI: 10.1016/j.advwatres.2015.11.015  0.4
2015 Zhan X, Epstein MP, Ghosh D. An Adaptive Genetic Association Test Using Double Kernel Machines. Statistics in Biosciences. 7: 262-281. PMID 26640602 DOI: 10.1007/s12561-014-9116-2  0.48
2015 Ghosh D, Haswell KM, Sprada M, Gonzalez-Fernandez F. Structure of zebrafish IRBP reveals fatty acid binding. Experimental Eye Research. PMID 26344741 DOI: 10.1016/j.exer.2015.08.026  0.32
2015 Zhan X, Patterson AD, Ghosh D. Kernel approaches for differential expression analysis of mass spectrometry-based metabolomics data. Bmc Bioinformatics. 16: 77. PMID 25887233 DOI: 10.1186/s12859-015-0506-3  0.44
2015 Hong JH, Chu H, Zhang C, Ghosh D, Gong X, Xu J. A quantitative analysis of stem cell homeostasis in the Arabidopsis columella root cap. Frontiers in Plant Science. 6: 206. PMID 25870608 DOI: 10.3389/fpls.2015.00206  0.4
2015 Bandyopadhyay S, Ghosh D, Mitra R, Zhao Z. MBSTAR: multiple instance learning for predicting specific functional binding sites in microRNA targets. Scientific Reports. 5: 8004. PMID 25614300 DOI: 10.1038/srep08004  0.32
2015 Ge T, Nichols TE, Ghosh D, Mormino EC, Smoller JW, Sabuncu MR. A kernel machine method for detecting effects of interaction between multidimensional variable sets: an imaging genetics application. Neuroimage. 109: 505-14. PMID 25600633 DOI: 10.1016/j.neuroimage.2015.01.029  0.44
2015 Liu Y, Ghosh D, Hallenbeck PC. Biological reformation of ethanol to hydrogen by Rhodopseudomonas palustris CGA009. Bioresource Technology. 176: 189-95. PMID 25461002 DOI: 10.1016/j.biortech.2014.11.047  0.6
2015 Zhan X, Ghosh D. Incorporating auxiliary information for improved prediction using combination of kernel machines. Statistical Methodology. 22: 47-57. PMID 25419198 DOI: 10.1016/j.stamet.2014.08.001  0.44
2015 Hua WY, Nichols TE, Ghosh D. Multiple comparison procedures for neuroimaging genomewide association studies. Biostatistics (Oxford, England). 16: 17-30. PMID 24963012 DOI: 10.1093/biostatistics/kxu026  0.44
2015 Ghosh D, Dey LK. On some parametric classifications of Quasi-symmetric 2-designs Tamkang Journal of Mathematics. 46: 269-280. DOI: 10.5556/j.tkjm.46.2015.1755  0.48
2015 Ghosh D, Hallenbeck PC. Cyanobacteria and photosynthetic bacteria: Metabolic engineering of hydrogen production Advances in Enzymatic Conversion of Biomass to Biofuels. 112-124. DOI: 10.4155/9781910420133.fseb2013.14.343  0.6
2015 Ghosh D, Hallenbeck PC. Metabolic engineering of hydrogen production by green algae Advances in Enzymatic Conversion of Biomass to Biofuels. 96-110. DOI: 10.4155/9781910420133.fseb2013.14.296  0.6
2015 Di Nardo G, Breitner M, Bandino A, Ghosh D, Jennings GK, Hackett JC, Gilardi G. Evidence for an elevated aspartate pKa in the active site of human aromatase Journal of Biological Chemistry. 290: 1186-1196. DOI: 10.1074/jbc.M114.595108  0.32
2015 Seelert T, Ghosh D, Yargeau V. Improving biohydrogen production using Clostridium beijerinckii immobilized with magnetite nanoparticles Applied Microbiology and Biotechnology. DOI: 10.1007/s00253-015-6484-6  0.6
2014 Ghosh D, Li S. Unsupervised outlier profile analysis. Cancer Informatics. 13: 25-33. PMID 25452686 DOI: 10.4137/CIN.S13969  1
2014 Almli LM, Duncan R, Feng H, Ghosh D, Binder EB, Bradley B, Ressler KJ, Conneely KN, Epstein MP. Correcting systematic inflation in genetic association tests that consider interaction effects: application to a genome-wide association study of posttraumatic stress disorder. Jama Psychiatry. 71: 1392-9. PMID 25354142 DOI: 10.1001/jamapsychiatry.2014.1339  0.44
2014 Xu J, Chatterjee M, Baguley TD, Brouillette J, Kurup P, Ghosh D, Kanyo J, Zhang Y, Seyb K, Ononenyi C, Foscue E, Anderson GM, Gresack J, Cuny GD, Glicksman MA, et al. Inhibitor of the tyrosine phosphatase STEP reverses cognitive deficits in a mouse model of Alzheimer's disease. Plos Biology. 12: e1001923. PMID 25093460 DOI: 10.1371/journal.pbio.1001923  0.56
2014 De Bekker C, Quevillon LE, Smith PB, Fleming KR, Ghosh D, Patterson AD, Hughes DP. Species-specific ant brain manipulation by a specialized fungal parasite Bmc Evolutionary Biology. 14. PMID 25085339 DOI: 10.1186/s12862-014-0166-3  0.48
2014 Li Y, Ghosh D. Meta-analysis based on weighted ordered P-values for genomic data with heterogeneity. Bmc Bioinformatics. 15: 226. PMID 24972803 DOI: 10.1186/1471-2105-15-226  1
2014 Lee Y, Ghosh D, Zhang Y. Regression hidden Markov modeling reveals heterogeneous gene expression regulation: a case study in mouse embryonic stem cells. Bmc Genomics. 15: 360. PMID 24884369 DOI: 10.1186/1471-2164-15-360  0.56
2014 Li Y, Ghosh D. A two-step hierarchical hypothesis set testing framework, with applications to gene expression data on ordered categories. Bmc Bioinformatics. 15: 108. PMID 24731138 DOI: 10.1186/1471-2105-15-108  1
2014 Lee Y, Ghosh D, Hardison RC, Zhang Y. MRHMMs: multivariate regression hidden Markov models and the variantS. Bioinformatics (Oxford, England). 30: 1755-6. PMID 24558116 DOI: 10.1093/bioinformatics/btu070  0.48
2014 Gonzalez-Fernandez F, Sung D, Haswell KM, Tsin A, Ghosh D. Thiol-dependent antioxidant activity of interphotoreceptor retinoid-binding protein. Experimental Eye Research. 120: 167-74. PMID 24424263 DOI: 10.1016/j.exer.2014.01.002  0.32
2014 Zhu Y, Ghosh D, Mitra N, Mukherjee B. A data-adaptive strategy for inverse weighted estimation of causal effects Health Services and Outcomes Research Methodology. 14: 69-91. DOI: 10.1007/s10742-014-0124-y  0.48
2013 Lee Y, Ghosh D, Zhang Y. Association testing to detect gene-gene interactions on sex chromosomes in trio data. Frontiers in Genetics. 4: 239. PMID 24312118 DOI: 10.3389/fgene.2013.00239  0.56
2013 Lo J, Di Nardo G, Griswold J, Egbuta C, Jiang W, Gilardi G, Ghosh D. Structural basis for the functional roles of critical residues in human cytochrome p450 aromatase. Biochemistry. 52: 5821-9. PMID 23899247 DOI: 10.1021/bi400669h  0.44
2013 Ghosh D. Genomic outlier detection in high-throughput data analysis. Methods in Molecular Biology (Clifton, N.J.). 972: 141-53. PMID 23385536 DOI: 10.1007/978-1-60327-337-4_9  0.48
2013 Choi H, Fermin D, Nesvizhskii AI, Ghosh D, Qin ZS. Sparsely correlated hidden Markov models with application to genome-wide location studies. Bioinformatics (Oxford, England). 29: 533-41. PMID 23325620 DOI: 10.1093/bioinformatics/btt012  0.48
2013 Schlicke H, Ghosh D, Fong LK, Xin HL, Zheng H, Alivisatos AP. Selective placement of faceted metal tips on semiconductor nanorods. Angewandte Chemie (International Ed. in English). 52: 980-2. PMID 23192900 DOI: 10.1002/anie.201205958  0.6
2013 Shrestha S, Pandey VP, Chanamai C, Ghosh DK. Green, Blue and Grey Water Footprints of Primary Crops Production in Nepal Water Resources Management. 27: 5223-5243. DOI: 10.1007/s11269-013-0464-3  0.4
2012 Ghosh D, Lo J, Morton D, Valette D, Xi J, Griswold J, Hubbell S, Egbuta C, Jiang W, An J, Davies HM. Novel aromatase inhibitors by structure-guided design. Journal of Medicinal Chemistry. 55: 8464-76. PMID 22951074 DOI: 10.1021/jm300930n  0.44
2012 Ghosh D. A causal framework for surrogate endpoints with semi-competing risks data. Statistics & Probability Letters. 82: 1898-1902. PMID 22899873 DOI: 10.1016/j.spl.2012.06.010  0.48
2012 Chen W, Ghosh D, Raghunathan TE, Norkin M, Sargent DJ, Bepler G. On Bayesian methods of exploring qualitative interactions for targeted treatment. Statistics in Medicine. 31: 3693-707. PMID 22733620 DOI: 10.1002/sim.5429  0.48
2012 Jain PK, Ghosh D, Baer R, Rabani E, Alivisatos AP. Near-field manipulation of spectroscopic selection rules on the nanoscale. Proceedings of the National Academy of Sciences of the United States of America. 109: 8016-9. PMID 22566662 DOI: 10.1073/pnas.1121319109  0.6
2012 Ghosh D, Taylor JM, Sargent DJ. Rejoinder for "Meta-analysis for surrogacy: accelerated failure time models and semi-competing risks modelling" Biometrics. 68: 245-247. PMID 22547832 DOI: 10.1111/j.1541-0420.2011.01638.x  0.48
2012 Poisson LM, Sreekumar A, Chinnaiyan AM, Ghosh D. Pathway-directed weighted testing procedures for the integrative analysis of gene expression and metabolomic data. Genomics. 99: 265-74. PMID 22497771 DOI: 10.1016/j.ygeno.2012.03.004  0.48
2012 Jiang W, Ghosh D. Motion and flexibility in human cytochrome p450 aromatase. Plos One. 7: e32565. PMID 22384274 DOI: 10.1371/journal.pone.0032565  0.44
2012 Li Y, Ghosh D. Assumption weighting for incorporating heterogeneity into meta-analysis of genomic data. Bioinformatics (Oxford, England). 28: 807-14. PMID 22285559 DOI: 10.1093/bioinformatics/bts037  1
2012 Tseng GC, Ghosh D, Feingold E. Comprehensive literature review and statistical considerations for microarray meta-analysis. Nucleic Acids Research. 40: 3785-99. PMID 22262733 DOI: 10.1093/nar/gkr1265  0.48
2012 Ghosh D, Taylor JM, Sargent DJ. Meta-analysis for surrogacy: accelerated failure time models and semicompeting risks modeling. Biometrics. 68: 226-32. PMID 21668903 DOI: 10.1111/j.1541-0420.2011.01633.x  0.48
2011 Poisson LM, Taylor JM, Ghosh D. Integrative set enrichment testing for multiple omics platforms. Bmc Bioinformatics. 12: 459. PMID 22118224 DOI: 10.1186/1471-2105-12-459  0.48
2011 Mortensen AH, MacDonald JW, Ghosh D, Camper SA. Candidate genes for panhypopituitarism identified by gene expression profiling. Physiological Genomics. 43: 1105-16. PMID 21828248 DOI: 10.1152/physiolgenomics.00080.2011  0.48
2011 Ghosh D. Propensity score modelling in observational studies using dimension reduction methods. Statistics & Probability Letters. 81: 813-820. PMID 21617766 DOI: 10.1016/j.spl.2011.03.002  0.48
2011 Chen F, Ding X, Ding Y, Xiang Z, Li X, Ghosh D, Schurig GG, Sriranganathan N, Boyle SM, He Y. Proinflammatory caspase-2-mediated macrophage cell death induced by a rough attenuated Brucella suis strain. Infection and Immunity. 79: 2460-9. PMID 21464087 DOI: 10.1128/IAI.00050-11  0.48
2011 Ghosh D, Jiang W, Lo J, Egbuta C. Higher order organization of human placental aromatase. Steroids. 76: 753-8. PMID 21392520 DOI: 10.1016/j.steroids.2011.02.030  0.44
2010 Ghosh D, Elliott MR, Taylor JM. Links between analysis of surrogate endpoints and endogeneity. Statistics in Medicine. 29: 2869-79. PMID 20803482 DOI: 10.1002/sim.4027  0.48
2010 Ghosh D. Discrete nonparametric algorithms for outlier detection with genomic data. Journal of Biopharmaceutical Statistics. 20: 193-208. PMID 20309754 DOI: 10.1080/10543400903572704  0.44
2010 Ghosh D. Semiparametric analysis of recurrent events: artificial censoring, truncation, pairwise estimation and inference. Lifetime Data Analysis. 16: 509-24. PMID 20063182 DOI: 10.1007/s10985-009-9150-4  0.44
2009 Pradhan S, Ghosh D, Chen S. Janus nanostructures based on Au-TiO2 heterodimers and their photocatalytic activity in the oxidation of methanol. Acs Applied Materials & Interfaces. 1: 2060-5. PMID 20355833 DOI: 10.1021/am900425v  0.6
2009 Wu J, Patwa TH, Lubman DM, Ghosh D. Identification of differentially expressed spatial clusters using humoral response microarray data. Computational Statistics & Data Analysis. 53: 3094-3102. PMID 19759808 DOI: 10.1016/j.csda.2008.04.026  0.32
2009 Khankal R, Chin JW, Ghosh D, Cirino PC. Transcriptional effects of CRP* expression in Escherichia coli. Journal of Biological Engineering. 3: 13. PMID 19703305 DOI: 10.1186/1754-1611-3-13  0.48
2009 Patwa TH, Li C, Poisson LM, Kim HY, Pal M, Ghosh D, Simeone DM, Lubman DM. The identification of phosphoglycerate kinase-1 and histone H4 autoantibodies in pancreatic cancer patient serum using a natural protein microarray. Electrophoresis. 30: 2215-26. PMID 19582723 DOI: 10.1002/elps.200800857  0.44
2009 Gudjonsson JE, Ding J, Li X, Nair RP, Tejasvi T, Qin ZS, Ghosh D, Aphale A, Gumucio DL, Voorhees JJ, Abecasis GR, Elder JT. Global gene expression analysis reveals evidence for decreased lipid biosynthesis and increased innate immunity in uninvolved psoriatic skin. The Journal of Investigative Dermatology. 129: 2795-804. PMID 19571819 DOI: 10.1038/jid.2009.173  0.44
2009 Ghosh D. Effect of preventive supplementation on young children in Niger. Jama. 301: 2208-9; author reply. PMID 19491177 DOI: 10.1001/jama.2009.740  0.44
2009 Choi H, Nesvizhskii AI, Ghosh D, Qin ZS. Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data. Bioinformatics (Oxford, England). 25: 1715-21. PMID 19447789 DOI: 10.1093/bioinformatics/btp312  0.44
2009 Davis SW, Potok MA, Brinkmeier ML, Carninci P, Lyons RH, MacDonald JW, Fleming MT, Mortensen AH, Egashira N, Ghosh D, Steel KP, Osamura RY, Hayashizaki Y, Camper SA. Genetics, gene expression and bioinformatics of the pituitary gland. Hormone Research. 71: 101-15. PMID 19407506 DOI: 10.1159/000192447  0.44
2009 McEwen LN, Kim C, Haan MN, Ghosh D, Lantz PM, Thompson TJ, Herman WH. Are health-related quality-of-life and self-rated health associated with mortality? Insights from Translating Research Into Action for Diabetes (TRIAD). Primary Care Diabetes. 3: 37-42. PMID 19269911 DOI: 10.1016/j.pcd.2009.01.001  0.44
2009 Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, ... Ghosh D, et al. Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 457: 910-4. PMID 19212411 DOI: 10.1038/nature07762  0.44
2009 Chen W, Ghosh D, Raghunathan TE, Sargent DJ. Bayesian variable selection with joint modeling of categorical and survival outcomes: an application to individualizing chemotherapy treatment in advanced colorectal cancer. Biometrics. 65: 1030-40. PMID 19210736 DOI: 10.1111/j.1541-0420.2008.01181.x  0.44
2009 Brinkmeier ML, Davis SW, Carninci P, MacDonald JW, Kawai J, Ghosh D, Hayashizaki Y, Lyons RH, Camper SA. Discovery of transcriptional regulators and signaling pathways in the developing pituitary gland by bioinformatic and genomic approaches. Genomics. 93: 449-60. PMID 19121383 DOI: 10.1016/j.ygeno.2008.11.010  0.44
2009 den Hollander AI, McGee TL, Ziviello C, Banfi S, Dryja TP, Gonzalez-Fernandez F, Ghosh D, Berson EL. A homozygous missense mutation in the IRBP gene (RBP3) associated with autosomal recessive retinitis pigmentosa. Investigative Ophthalmology & Visual Science. 50: 1864-72. PMID 19074801 DOI: 10.1167/iovs.08-2497  0.32
2009 Colón-López V, Haan MN, Aiello AE, Ghosh D. The effect of age at migration on cardiovascular mortality among elderly Mexican immigrants. Annals of Epidemiology. 19: 8-14. PMID 18922703 DOI: 10.1016/j.annepidem.2008.08.010  0.44
2009 Ghosh D. On assessing surrogacy in a single trial setting using a semicompeting risks paradigm. Biometrics. 65: 521-9. PMID 18759839 DOI: 10.1111/j.1541-0420.2008.01109.x  0.44
2009 Ghosh D, Poisson LM. "Omics" data and levels of evidence for biomarker discovery. Genomics. 93: 13-6. PMID 18723089 DOI: 10.1016/j.ygeno.2008.07.006  0.44
2008 Ghosh D. On the Plackett distribution with bivariate censored data. The International Journal of Biostatistics. 4: Article 7. PMID 22462114 DOI: 10.2202/1557-4679.1099  0.44
2008 Varambally S, Laxman B, Mehra R, Cao Q, Dhanasekaran SM, Tomlins SA, Granger J, Vellaichamy A, Sreekumar A, Yu J, Gu W, Shen R, Ghosh D, Wright LM, Kladney RD, et al. Golgi protein GOLM1 is a tissue and urine biomarker of prostate cancer. Neoplasia (New York, N.Y.). 10: 1285-94. PMID 18953438 DOI: 10.1593/neo.08922  0.44
2008 Shen R, Taylor JM, Ghosh D. Reconstructing tumor-wise protein expression in tissue microarray studies using a Bayesian cell mixture model. Bioinformatics (Oxford, England). 24: 2880-6. PMID 18922808 DOI: 10.1093/bioinformatics/btn536  0.48
2008 Shen R, Chinnaiyan AM, Ghosh D. Pathway analysis reveals functional convergence of gene expression profiles in breast cancer. Bmc Medical Genomics. 1: 28. PMID 18588682 DOI: 10.1186/1755-8794-1-28  0.48
2008 Liu D, Ghosh D, Lin X. Estimation and testing for the effect of a genetic pathway on a disease outcome using logistic kernel machine regression via logistic mixed models. Bmc Bioinformatics. 9: 292. PMID 18577223 DOI: 10.1186/1471-2105-9-292  0.72
2008 Yuan Z, Ghosh D. Combining multiple biomarker models in logistic regression. Biometrics. 64: 431-9. PMID 18325068 DOI: 10.1111/j.1541-0420.2007.00904.x  0.32
2008 Shen R, Ghosh D, Taylor JM. Modeling intra-tumor protein expression heterogeneity in tissue microarray experiments. Statistics in Medicine. 27: 1944-59. PMID 18300332 DOI: 10.1002/sim.3217  0.48
2008 Kwee LC, Liu D, Lin X, Ghosh D, Epstein MP. A powerful and flexible multilocus association test for quantitative traits. American Journal of Human Genetics. 82: 386-97. PMID 18252219 DOI: 10.1016/j.ajhg.2007.10.010  0.72
2008 Yu J, Yu J, Cordero KE, Johnson MD, Ghosh D, Rae JM, Chinnaiyan AM, Lippman ME. A transcriptional fingerprint of estrogen in human breast cancer predicts patient survival. Neoplasia (New York, N.Y.). 10: 79-88. PMID 18231641 DOI: 10.1593/neo.07859  0.32
2008 Choi H, Ghosh D, Nesvizhskii AI. Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling. Journal of Proteome Research. 7: 286-92. PMID 18078310 DOI: 10.1021/pr7006818  0.44
2008 Taylor BS, Pal M, Yu J, Laxman B, Kalyana-Sundaram S, Zhao R, Menon A, Wei JT, Nesvizhskii AI, Ghosh D, Omenn GS, Lubman DM, Chinnaiyan AM, Sreekumar A. Humoral response profiling reveals pathways to prostate cancer progression. Molecular & Cellular Proteomics : McP. 7: 600-11. PMID 18077443 DOI: 10.1074/mcp.M700263-MCP200  0.44
2008 Chen W, Ghosh D, Raghunathan TE, Sargent DJ. A false-discovery-rate-based loss framework for selection of interactions. Statistics in Medicine. 27: 2004-21. PMID 17979139 DOI: 10.1002/sim.3118  0.44
2008 Ghosh D. Semiparametric inference for surrogate endpoints with bivariate censored data Biometrics. 64: 149-156. PMID 17651457 DOI: 10.1111/j.1541-0420.2007.00834.x  0.44
2008 Ghosh D. Proportional hazards regression for cancer studies Biometrics. 64: 141-148. PMID 17573863 DOI: 10.1111/j.1541-0420.2007.00830.x  0.44
2008 Gonzalez-Fernandez F, Ghosh D. Focus on Molecules: interphotoreceptor retinoid-binding protein (IRBP). Experimental Eye Research. 86: 169-70. PMID 17222825 DOI: 10.1016/j.exer.2006.09.003  0.32
2008 Duax WL, Griffin JF, Ghosh D. Steroid Molecular Structure, Protein Interaction and Biological Function Structure Correlation. 1: 605-633. DOI: 10.1002/9783527616091.ch14  0.44
2007 Liu D, Lin X, Ghosh D. Semiparametric regression of multidimensional genetic pathway data: least-squares kernel machines and linear mixed models. Biometrics. 63: 1079-88. PMID 18078480 DOI: 10.1111/j.1541-0420.2007.00799.x  0.72
2007 Yu J, Yu J, Rhodes DR, Tomlins SA, Cao X, Chen G, Mehra R, Wang X, Ghosh D, Shah RB, Varambally S, Pienta KJ, Chinnaiyan AM. A polycomb repression signature in metastatic prostate cancer predicts cancer outcome. Cancer Research. 67: 10657-63. PMID 18006806 DOI: 10.1158/0008-5472.CAN-07-2498  0.32
2007 Yu J, Cao Q, Mehra R, Laxman B, Yu J, Tomlins SA, Creighton CJ, Dhanasekaran SM, Shen R, Chen G, Morris DS, Marquez VE, Shah RB, Ghosh D, Varambally S, et al. Integrative genomics analysis reveals silencing of beta-adrenergic signaling by polycomb in prostate cancer. Cancer Cell. 12: 419-31. PMID 17996646 DOI: 10.1016/j.ccr.2007.10.016  0.44
2007 Choi H, Shen R, Chinnaiyan AM, Ghosh D. A latent variable approach for meta-analysis of gene expression data from multiple microarray experiments. Bmc Bioinformatics. 8: 364. PMID 17900369 DOI: 10.1186/1471-2105-8-364  0.48
2007 Kim JH, Dhanasekaran SM, Mehra R, Tomlins SA, Gu W, Yu J, Kumar-Sinha C, Cao X, Dash A, Wang L, Ghosh D, Shedden K, Montie JE, Rubin MA, Pienta KJ, et al. Integrative analysis of genomic aberrations associated with prostate cancer progression. Cancer Research. 67: 8229-39. PMID 17804737 DOI: 10.1158/0008-5472.CAN-07-1297  0.44
2007 Pradhan S, Ghosh D, Xu LP, Chen S. Interparticle charge transfer mediated by pi-pi stacking of aromatic moieties. Journal of the American Chemical Society. 129: 10622-3. PMID 17696534 DOI: 10.1021/ja072597p  0.6
2007 Gonzalez-Fernandez F, Baer CA, Ghosh D. Module structure of interphotoreceptor retinoid-binding protein (IRBP) may provide bases for its complex role in the visual cycle - structure/function study of Xenopus IRBP. Bmc Biochemistry. 8: 15. PMID 17683573 DOI: 10.1186/1471-2091-8-15  0.32
2007 Tsai HJ, Tsai AC, Nriagu J, Ghosh D, Gong M, Sandretto A. Associations of BMI, TV-watching time, and physical activity on respiratory symptoms and asthma in 5th grade schoolchildren in Taipei, Taiwan. The Journal of Asthma : Official Journal of the Association For the Care of Asthma. 44: 397-401. PMID 17613637 DOI: 10.1080/02770900701364304  0.44
2007 Davila M, Jhala D, Ghosh D, Grizzle WE, Chakrabarti R. Expression of LIM kinase 1 is associated with reversible G1/S phase arrest, chromosomal instability and prostate cancer. Molecular Cancer. 6: 40. PMID 17559677 DOI: 10.1186/1476-4598-6-40  0.44
2007 Rhodes DR, Kalyana-Sundaram S, Tomlins SA, Mahavisno V, Kasper N, Varambally R, Barrette TR, Ghosh D, Varambally S, Chinnaiyan AM. Molecular concepts analysis links tumors, pathways, mechanisms, and drugs. Neoplasia (New York, N.Y.). 9: 443-54. PMID 17534450 DOI: 10.1593/neo.07292  0.32
2007 McEwen LN, Kim C, Karter AJ, Haan MN, Ghosh D, Lantz PM, Mangione CM, Thompson TJ, Herman WH. Risk factors for mortality among patients with diabetes: the Translating Research Into Action for Diabetes (TRIAD) Study. Diabetes Care. 30: 1736-41. PMID 17468353 DOI: 10.2337/dc07-0305  0.44
2007 Yu J, Yu J, Almal AA, Dhanasekaran SM, Ghosh D, Worzel WP, Chinnaiyan AM. Feature selection and molecular classification of cancer using genetic programming. Neoplasia (New York, N.Y.). 9: 292-303. PMID 17460773 DOI: 10.1593/neo.07121  0.32
2007 Chen G, Wang X, Yu J, Varambally S, Yu J, Thomas DG, Lin MY, Vishnu P, Wang Z, Wang R, Fielhauer J, Ghosh D, Giordano TJ, Giacherio D, Chang AC, et al. Autoantibody profiles reveal ubiquilin 1 as a humoral immune response target in lung adenocarcinoma. Cancer Research. 67: 3461-7. PMID 17409457 DOI: 10.1158/0008-5472.CAN-06-4475  0.32
2007 Rhodes DR, Kalyana-Sundaram S, Mahavisno V, Varambally R, Yu J, Briggs BB, Barrette TR, Anstet MJ, Kincead-Beal C, Kulkarni P, Varambally S, Ghosh D, Chinnaiyan AM. Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia (New York, N.Y.). 9: 166-80. PMID 17356713 DOI: 10.1593/neo.07112  0.32
2007 Mehra R, Tomlins SA, Shen R, Nadeem O, Wang L, Wei JT, Pienta KJ, Ghosh D, Rubin MA, Chinnaiyan AM, Shah RB. Comprehensive assessment of TMPRSS2 and ETS family gene aberrations in clinically localized prostate cancer. Modern Pathology : An Official Journal of the United States and Canadian Academy of Pathology, Inc. 20: 538-44. PMID 17334343 DOI: 10.1038/modpathol.3800769  0.48
2007 Ghosh D. Incorporating monotonicity into the evaluation of a biomarker Biostatistics. 8: 402-413. PMID 16905591 DOI: 10.1093/biostatistics/kxl018  0.44
2006 Ghosh D. Shrunken p-values for assessing differential expression with applications to genomic data analysis Biometrics. 62. PMID 17156284 DOI: 10.1111/j.1541-0420.2006.00616.x  0.44
2006 Tong MC, Chen W, Sun J, Ghosh D, Chen S. Dithiocarbamate-capped silver nanoparticles. The Journal of Physical Chemistry. B. 110: 19238-42. PMID 17004775 DOI: 10.1021/jp0631174  0.6
2006 Chang ST, Ghosh D, Kirschner DE, Linderman JJ. Peptide length-based prediction of peptide-MHC class II binding. Bioinformatics (Oxford, England). 22: 2761-7. PMID 17000752 DOI: 10.1093/bioinformatics/btl479  0.44
2006 Shen R, Ghosh D, Chinnaiyan A, Meng Z. Eigengene-based linear discriminant model for tumor classification using gene expression microarray data. Bioinformatics (Oxford, England). 22: 2635-42. PMID 16926220 DOI: 10.1093/bioinformatics/btl442  0.48
2006 Tsai HJ, Tsai AC, Nriagu J, Ghosh D, Gong M, Sandretto A. Risk factors for respiratory symptoms and asthma in the residential environment of 5th grade schoolchildren in Taipei, Taiwan. The Journal of Asthma : Official Journal of the Association For the Care of Asthma. 43: 355-61. PMID 16801139 DOI: 10.1080/02770900600705326  0.44
2006 McEwen LN, Kim C, Haan M, Ghosh D, Lantz PM, Mangione CM, Safford MM, Marrero D, Thompson TJ, Herman WH. Diabetes reporting as a cause of death: results from the Translating Research Into Action for Diabetes (TRIAD) study. Diabetes Care. 29: 247-53. PMID 16443868 DOI: 10.2337/diacare.29.02.06.dc05-0998  0.44
2006 Ghosh D. Modelling tumour biology-progression relationships in screening trials Statistics in Medicine. 25: 1872-1884. PMID 16220483 DOI: 10.1002/sim.2363  0.44
2006 Ghosh D. Semiparametric inferences for association with semi-competing risks data Statistics in Medicine. 25: 2059-2070. PMID 16196081 DOI: 10.1002/sim.2327  0.44
2006 Ghosh D. Finding cancer subtypes in microarray data using random projections Neurocomputing. 69: 2258-2267. DOI: 10.1016/j.neucom.2005.06.019  0.44
2005 Ghosh D. Three-dimensional structures of sulfatases Methods in Enzymology. 400: 273-293. PMID 16399355 DOI: 10.1016/S0076-6879(05)00016-9  0.32
2005 Mehra R, Varambally S, Ding L, Shen R, Sabel MS, Ghosh D, Chinnaiyan AM, Kleer CG. Identification of GATA3 as a breast cancer prognostic marker by global gene expression meta-analysis. Cancer Research. 65: 11259-64. PMID 16357129 DOI: 10.1158/0008-5472.CAN-05-2495  0.48
2005 Varambally S, Yu J, Laxman B, Rhodes DR, Mehra R, Tomlins SA, Shah RB, Chandran U, Monzon FA, Becich MJ, Wei JT, Pienta KJ, Ghosh D, Rubin MA, Chinnaiyan AM. Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression. Cancer Cell. 8: 393-406. PMID 16286247 DOI: 10.1016/j.ccr.2005.10.001  0.32
2005 Rhodes DR, Tomlins SA, Varambally S, Mahavisno V, Barrette T, Kalyana-Sundaram S, Ghosh D, Pandey A, Chinnaiyan AM. Probabilistic model of the human protein-protein interaction network. Nature Biotechnology. 23: 951-9. PMID 16082366 DOI: 10.1038/nbt1103  0.32
2005 Rubin MA, Bismar TA, Andrén O, Mucci L, Kim R, Shen R, Ghosh D, Wei JT, Chinnaiyan AM, Adami HO, Kantoff PW, Johansson JE. Decreased alpha-methylacyl CoA racemase expression in localized prostate cancer is associated with an increased rate of biochemical recurrence and cancer-specific death. Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association For Cancer Research, Cosponsored by the American Society of Preventive Oncology. 14: 1424-32. PMID 15941951 DOI: 10.1158/1055-9965.EPI-04-0801  0.48
2005 Witkiewicz AK, Varambally S, Shen R, Mehra R, Sabel MS, Ghosh D, Chinnaiyan AM, Rubin MA, Kleer CG. Alpha-methylacyl-CoA racemase protein expression is associated with the degree of differentiation in breast cancer using quantitative image analysis. Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association For Cancer Research, Cosponsored by the American Society of Preventive Oncology. 14: 1418-23. PMID 15941950 DOI: 10.1158/1055-9965.EPI-04-0607  0.48
2005 Wang Y, Feng L, Said M, Balderman S, Fayazi Z, Liu Y, Ghosh D, Gulick AM. Analysis of the 2.0 A crystal structure of the protein-DNA complex of the human PDEF Ets domain bound to the prostate specific antigen regulatory site. Biochemistry. 44: 7095-106. PMID 15882048 DOI: 10.1021/bi047352t  0.32
2005 Abecasis GR, Ghosh D, Nichols TE. Linkage disequilibrium: Ancient history drives the new genetics Human Heredity. 59: 118-124. PMID 15838181 DOI: 10.1159/000085226  0.44
2005 Levin AM, Ghosh D, Cho KR, Kardia SL. A model-based scan statistic for identifying extreme chromosomal regions of gene expression in human tumors. Bioinformatics (Oxford, England). 21: 2867-74. PMID 15814559 DOI: 10.1093/bioinformatics/bti417  0.44
2005 Shedden K, Chen W, Kuick R, Ghosh D, Macdonald J, Cho KR, Giordano TJ, Gruber SB, Fearon ER, Taylor JM, Hanash S. Comparison of seven methods for producing Affymetrix expression scores based on False Discovery Rates in disease profiling data. Bmc Bioinformatics. 6: 26. PMID 15705192 DOI: 10.1186/1471-2105-6-26  0.44
2005 Ghosh D. Nonparametric methods for analyzing replication origins in genomewide data Functional and Integrative Genomics. 5: 28-31. PMID 15599787 DOI: 10.1007/s10142-004-0122-1  0.44
2004 Ghosh D. Mutations in X-linked ichthyosis disrupt the active site structure of estrone/DHEA sulfatase Biochimica Et Biophysica Acta - Molecular Basis of Disease. 1739: 1-4. PMID 15607112 DOI: 10.1016/j.bbadis.2004.09.003  0.32
2004 Shah RB, Mehra R, Chinnaiyan AM, Shen R, Ghosh D, Zhou M, Macvicar GR, Varambally S, Harwood J, Bismar TA, Kim R, Rubin MA, Pienta KJ. Androgen-independent prostate cancer is a heterogeneous group of diseases: lessons from a rapid autopsy program. Cancer Research. 64: 9209-16. PMID 15604294 DOI: 10.1158/0008-5472.CAN-04-2442  0.48
2004 Shen R, Ghosh D, Chinnaiyan AM. Prognostic meta-signature of breast cancer developed by two-stage mixture modeling of microarray data. Bmc Genomics. 5: 94. PMID 15598354 DOI: 10.1186/1471-2164-5-94  0.48
2004 Ghosh D. Accelerated rates regression models for recurrent failure time data Lifetime Data Analysis. 10: 247-261. PMID 15456106 DOI: 10.1023/B:LIDA.0000036391.87081.e3  0.44
2004 Yu J, He S, Friedman JS, Akimoto M, Ghosh D, Mears AJ, Hicks D, Swaroop A. Altered expression of genes of the Bmp/Smad and Wnt/calcium signaling pathways in the cone-only Nrl-/- mouse retina, revealed by gene profiling using custom cDNA microarrays. The Journal of Biological Chemistry. 279: 42211-20. PMID 15292180 DOI: 10.1074/jbc.M408223200  0.44
2004 Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, Pandey A, Chinnaiyan AM. Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proceedings of the National Academy of Sciences of the United States of America. 101: 9309-14. PMID 15184677 DOI: 10.1073/pnas.0401994101  0.32
2004 Sreekumar A, Laxman B, Rhodes DR, Bhagavathula S, Harwood J, Giacherio D, Ghosh D, Sanda MG, Rubin MA, Chinnaiyan AM. Humoral immune response to alpha-methylacyl-CoA racemase and prostate cancer. Journal of the National Cancer Institute. 96: 834-43. PMID 15173267 DOI: 10.1093/jnci/djh145  0.32
2004 Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, Pandey A, Chinnaiyan AM. ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia (New York, N.Y.). 6: 1-6. PMID 15068665 DOI: 10.1016/S1476-5586(04)80047-2  0.32
2004 Zhang L, Srinivasan U, Marrs CF, Ghosh D, Gilsdorf JR, Foxman B. Library on a slide for bacterial comparative genomics. Bmc Microbiology. 4: 12. PMID 15035675 DOI: 10.1186/1471-2180-4-12  0.52
2004 Ghosh D. Mixture models for assessing differential expression in complex tissues using microarray data Bioinformatics. 20: 1663-1669. PMID 14988124 DOI: 10.1093/bioinformatics/bth139  0.44
2004 Ghosh D. Identification of shared components and sparse networks in gene expression time-course data Journal of Vlsi Signal Processing Systems For Signal, Image, and Video Technology. 38: 277-286. DOI: 10.1023/B:VLSI.0000042492.74928.1b  0.44
2003 Ghosh D. Penalized Discriminant Methods for the Classification of Tumors from Gene Expression Data Biometrics. 59: 992-1000. PMID 14969478 DOI: 10.1111/j.0006-341X.2003.00114.x  0.44
2003 Ghosh D. Goodness-of-fit methods for additive-risk models in tumorigenicity experiments Biometrics. 59: 721-726. PMID 14601774 DOI: 10.1111/1541-0420.00083  0.44
2003 Kleer CG, Cao Q, Varambally S, Shen R, Ota I, Tomlins SA, Ghosh D, Sewalt RG, Otte AP, Hayes DF, Sabel MS, Livant D, Weiss SJ, Rubin MA, Chinnaiyan AM. EZH2 is a marker of aggressive breast cancer and promotes neoplastic transformation of breast epithelial cells. Proceedings of the National Academy of Sciences of the United States of America. 100: 11606-11. PMID 14500907 DOI: 10.1073/pnas.1933744100  0.48
2003 Wu JH, Haan MN, Liang J, Ghosh D, Gonzalez HM, Herman WH. Impact of diabetes on cognitive function among older Latinos: a population-based cohort study. Journal of Clinical Epidemiology. 56: 686-93. PMID 12921938 DOI: 10.1016/S0895-4356(03)00077-5  0.44
2003 Wu JH, Haan MN, Liang J, Ghosh D, Gonzalez HM, Herman WH. Impact of antidiabetic medications on physical and cognitive functioning of older Mexican Americans with diabetes mellitus: a population-based cohort study. Annals of Epidemiology. 13: 369-76. PMID 12821276 DOI: 10.1016/S1047-2797(02)00464-7  0.44
2003 Wu JH, Haan MN, Liang J, Ghosh D, Gonzalez HM, Herman WH. Diabetes as a predictor of change in functional status among older Mexican Americans: a population-based cohort study. Diabetes Care. 26: 314-9. PMID 12547855 DOI: 10.2337/diacare.26.2.314  0.44
2002 Ghosh D. Resampling methods for variance estimation of singular value decomposition analyses from microarray experiments Functional and Integrative Genomics. 2: 92-97. DOI: 10.1007/s10142-002-0047-5  0.44
1997 Duax WL, Ghosh D. Structure and function of steroid dehydrogenases involved in hypertension, fertility, and cancer Steroids. 62: 95-100. PMID 9029722 DOI: 10.1016/S0039-128X(96)00166-3  0.32
1994 Ghosh D, Wawrzak Z, Weeks CM, Duax WL, Erman M. The refined three-dimensional structure of 3α,20β-hydroxysteroid dehydrogenase and possible roles of the residues conserved in short-chain dehydrogenases Structure. 2: 629-640. PMID 7922040 DOI: 10.1016/S0969-2126(00)00064-2  0.32
1994 Ghosh D, Erman M, Wawrzak Z, Duax WL, Pangborn W. Mechanism of inhibition of 3α,20β-hydroxysteroid dehydrogenaseby a licorice-derived steroidal inhibitor Structure. 2: 973-980. PMID 7866748 DOI: 10.1016/S0969-2126(94)00099-9  0.32
1993 Ghosh D, Erman M, Pangborn W, Duax WL, Nakajin S, Ohno S, Shinoda M. Crystallization and preliminary x-ray diffraction studies of a mammalian steroid dehydrogenase Journal of Steroid Biochemistry and Molecular Biology. 46: 103-104. PMID 8338786 DOI: 10.1016/0960-0760(93)90214-H  0.32
1992 Ghosh D, Erman M, Pangborn W, Duax WL, Baker ME. Inhibition of Streptomyces hydrogenans 3α,20β-hydroxysteroid dehydrogenase by licorice-derived compounds and crystallization of an enzyme-cofactor-inhibitor complex Journal of Steroid Biochemistry and Molecular Biology. 42: 849-853. PMID 1525045 DOI: 10.1016/0960-0760(92)90093-X  0.32
1991 Ghosh D, Erman M, Duax WL. Crystallization and preliminary diffraction analysis of cholesterol esterase from Candida cylindracea Journal of Steroid Biochemistry and Molecular Biology. 38: 663-665. PMID 2039758 DOI: 10.1016/0960-0760(91)90325-Y  0.32
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