Robi D. Mitra - Publications

Biology & Biomedical Sciences (Computational Biology) Washington University, Saint Louis, St. Louis, MO 
Molecular Biology, Biochemistry, General

55 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
2016 Haller G, Alvarado D, McCall K, Mitra RD, Dobbs MB, Gurnett CA. Massively parallel single-nucleotide mutagenesis using reversibly terminated inosine. Nature Methods. PMID 27694911 DOI: 10.1038/Nmeth.4015  1
2016 Styles EB, Founk KJ, Zamparo LA, Sing TL, Altintas D, Ribeyre C, Ribaud V, Rougemont J, Mayhew D, Costanzo M, Usaj M, Verster AJ, Koch EN, Novarina D, Graf M, ... ... Mitra RD, et al. Exploring Quantitative Yeast Phenomics with Single-Cell Analysis of DNA Damage Foci. Cell Systems. PMID 27617677 DOI: 10.1016/J.Cels.2016.08.008  1
2016 Yu H, Artomov M, Brähler S, Stander MC, Shamsan G, Sampson MG, White JM, Kretzler M, Miner JH, Jain S, Winkler CA, Mitra RD, Kopp JB, Daly MJ, Shaw AS. A role for genetic susceptibility in sporadic focal segmental glomerulosclerosis. The Journal of Clinical Investigation. PMID 26901816 DOI: 10.1172/Jci82592  1
2016 Mayhew D, Mitra RD. Transposon Calling Cards. Cold Spring Harbor Protocols. 2016: pdb.top077776. PMID 26832691 DOI: 10.1101/Pdb.Top077776  1
2016 Mayhew D, Mitra RD. Calling Card Analysis in Budding Yeast. Cold Spring Harbor Protocols. 2016: pdb.prot086918. PMID 26832687 DOI: 10.1101/Pdb.Prot086918  1
2015 Zhang C, Myers CA, Qi Z, Mitra RD, Corbo JC, Havranek JJ. Redesign of the monomer-monomer interface of Cre recombinase yields an obligate heterotetrameric complex. Nucleic Acids Research. 43: 9076-85. PMID 26365240 DOI: 10.1093/Nar/Gkv901  1
2015 Röhrig T, Pihlajoki M, Ziegler R, Cochran RS, Schrade A, Schillebeeckx M, Mitra RD, Heikinheimo M, Wilson DB. Toying with fate: Redirecting the differentiation of adrenocortical progenitor cells into gonadal-like tissue. Molecular and Cellular Endocrinology. 408: 165-77. PMID 25498963 DOI: 10.1016/J.Mce.2014.12.003  1
2015 Cady J, Allred P, Bali T, Pestronk A, Goate A, Miller TM, Mitra RD, Ravits J, Harms MB, Baloh RH. Amyotrophic lateral sclerosis onset is influenced by the burden of rare variants in known amyotrophic lateral sclerosis genes. Annals of Neurology. 77: 100-13. PMID 25382069 DOI: 10.1002/Ana.24306  1
2015 Schillebeeckx M, Pihlajoki M, Gretzinger E, Yang W, Thol F, Hiller T, Löbs AK, Röhrig T, Schrade A, Cochran R, Jay PY, Heikinheimo M, Mitra RD, Wilson DB. Novel markers of gonadectomy-induced adrenocortical neoplasia in the mouse and ferret. Molecular and Cellular Endocrinology. 399: 122-30. PMID 25289806 DOI: 10.1016/J.Mce.2014.09.029  1
2014 Vallania FL, Sherman M, Goodwin Z, Mogno I, Cohen BA, Mitra RD. Origin and consequences of the relationship between protein mean and variance. Plos One. 9: e102202. PMID 25062021 DOI: 10.1371/Journal.Pone.0102202  1
2014 Mayhew D, Mitra RD. Transcription factor regulation and chromosome dynamics during pseudohyphal growth. Molecular Biology of the Cell. 25: 2669-76. PMID 25009286 DOI: 10.1091/Mbc.E14-04-0871  1
2014 Wambach JA, Wegner DJ, Heins HB, Druley TE, Mitra RD, Hamvas A, Cole FS. Synonymous ABCA3 variants do not increase risk for neonatal respiratory distress syndrome. The Journal of Pediatrics. 164: 1316-21.e3. PMID 24657120 DOI: 10.1016/J.Jpeds.2014.02.021  1
2014 Cottrell CE, Al-Kateb H, Bredemeyer AJ, Duncavage EJ, Spencer DH, Abel HJ, Lockwood CM, Hagemann IS, O'Guin SM, Burcea LC, Sawyer CS, Oschwald DM, Stratman JL, Sher DA, Johnson MR, ... ... Mitra RD, et al. Validation of a next-generation sequencing assay for clinical molecular oncology. The Journal of Molecular Diagnostics : Jmd. 16: 89-105. PMID 24211365 DOI: 10.1016/J.Jmoldx.2013.10.002  1
2014 Spencer DH, Tyagi M, Vallania F, Bredemeyer AJ, Pfeifer JD, Mitra RD, Duncavage EJ. Performance of common analysis methods for detecting low-frequency single nucleotide variants in targeted next-generation sequence data. The Journal of Molecular Diagnostics : Jmd. 16: 75-88. PMID 24211364 DOI: 10.1016/J.Jmoldx.2013.09.003  1
2013 Higdon CW, Mitra RD, Johnson SL. Gene expression analysis of zebrafish melanocytes, iridophores, and retinal pigmented epithelium reveals indicators of biological function and developmental origin. Plos One. 8: e67801. PMID 23874447 DOI: 10.1371/Journal.Pone.0067801  1
2013 Liu C, Yang X, Duffy B, Mohanakumar T, Mitra RD, Zody MC, Pfeifer JD. ATHLATES: accurate typing of human leukocyte antigen through exome sequencing. Nucleic Acids Research. 41: e142. PMID 23748956 DOI: 10.1093/Nar/Gkt481  1
2013 Schillebeeckx M, Schrade A, Löbs AK, Pihlajoki M, Wilson DB, Mitra RD. Laser capture microdissection-reduced representation bisulfite sequencing (LCM-RRBS) maps changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse. Nucleic Acids Research. 41: e116. PMID 23589626 DOI: 10.1093/Nar/Gkt230  1
2013 Donahoe CD, Cohen TL, Li W, Nguyen PK, Fortner JD, Mitra RD, Elbert DL. Ultralow protein adsorbing coatings from clickable PEG nanogel solutions: benefits of attachment under salt-induced phase separation conditions and comparison with PEG/albumin nanogel coatings. Langmuir : the Acs Journal of Surfaces and Colloids. 29: 4128-39. PMID 23441808 DOI: 10.1021/La3051115  1
2012 Wambach JA, Wegner DJ, Depass K, Heins H, Druley TE, Mitra RD, An P, Zhang Q, Nogee LM, Cole FS, Hamvas A. Single ABCA3 mutations increase risk for neonatal respiratory distress syndrome. Pediatrics. 130: e1575-82. PMID 23166334 DOI: 10.1542/Peds.2012-0918  1
2012 Ryan O, Shapiro RS, Kurat CF, Mayhew D, Baryshnikova A, Chin B, Lin ZY, Cox MJ, Vizeacoumar F, Cheung D, Bahr S, Tsui K, Tebbji F, Sellam A, Istel F, ... ... Mitra RD, et al. Global gene deletion analysis exploring yeast filamentous growth. Science (New York, N.Y.). 337: 1353-6. PMID 22984072 DOI: 10.1126/Science.1224339  1
2012 Vallania F, Ramos E, Cresci S, Mitra RD, Druley TE. Detection of rare genomic variants from pooled sequencing using SPLINTER. Journal of Visualized Experiments : Jove. PMID 22760212 DOI: 10.3791/3943  1
2012 Chatterjee R, Ramos E, Hoffman M, VanWinkle J, Martin DR, Davis TK, Hoshi M, Hmiel SP, Beck A, Hruska K, Coplen D, Liapis H, Mitra R, Druley T, Austin P, et al. Traditional and targeted exome sequencing reveals common, rare and novel functional deleterious variants in RET-signaling complex in a cohort of living US patients with urinary tract malformations. Human Genetics. 131: 1725-38. PMID 22729463 DOI: 10.1007/S00439-012-1181-3  1
2012 Reyes A, Sandoval A, Cubillos-Ruiz A, Varley KE, Hernández-Neuta I, Samper S, Martín C, García MJ, Ritacco V, López L, Robledo J, Zambrano MM, Mitra RD, Del Portillo P. IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes. Bmc Genomics. 13: 249. PMID 22703188 DOI: 10.1186/1471-2164-13-249  1
2012 Yun Y, Adesanya TM, Mitra RD. A systematic study of gene expression variation at single-nucleotide resolution reveals widespread regulatory roles for uAUGs. Genome Research. 22: 1089-97. PMID 22454232 DOI: 10.1101/Gr.117366.110  1
2012 Cruchaga C, Haller G, Chakraverty S, Mayo K, Vallania FL, Mitra RD, Faber K, Williamson J, Bird T, Diaz-Arrastia R, Foroud TM, Boeve BF, Graff-Radford NR, St Jean P, Lawson M, et al. Rare variants in APP, PSEN1 and PSEN2 increase risk for AD in late-onset Alzheimer's disease families. Plos One. 7: e31039. PMID 22312439 DOI: 10.1371/Journal.Pone.0031039  1
2012 Qi X, Daily K, Nguyen K, Wang H, Mayhew D, Rigor P, Forouzan S, Johnston M, Mitra RD, Baldi P, Sandmeyer S. Retrotransposon profiling of RNA polymerase III initiation sites. Genome Research. 22: 681-92. PMID 22287102 DOI: 10.1101/Gr.131219.111  1
2012 Wang H, Mayhew D, Chen X, Johnston M, Mitra RD. "Calling cards" for DNA-binding proteins in mammalian cells. Genetics. 190: 941-9. PMID 22214611 DOI: 10.1534/Genetics.111.137315  1
2012 Haller G, Druley T, Vallania FL, Mitra RD, Li P, Akk G, Steinbach JH, Breslau N, Johnson E, Hatsukami D, Stitzel J, Bierut LJ, Goate AM. Rare missense variants in CHRNB4 are associated with reduced risk of nicotine dependence. Human Molecular Genetics. 21: 647-55. PMID 22042774 DOI: 10.1093/Hmg/Ddr498  1
2011 Tessler LA, Mitra RD. Sensitive single-molecule protein quantification and protein complex detection in a microarray format. Proteomics. 11: 4731-5. PMID 22038904 DOI: 10.1002/Pmic.201100361  1
2011 Wang H, Mayhew D, Chen X, Johnston M, Mitra RD. Calling Cards enable multiplexed identification of the genomic targets of DNA-binding proteins. Genome Research. 21: 748-55. PMID 21471402 DOI: 10.1101/Gr.114850.110  1
2011 Tessler LA, Donahoe CD, Garcia DJ, Jun YS, Elbert DL, Mitra RD. Nanogel surface coatings for improved single-molecule imaging substrates. Journal of the Royal Society, Interface / the Royal Society. 8: 1400-8. PMID 21325313 DOI: 10.1098/Rsif.2010.0669  1
2010 Vallania FL, Druley TE, Ramos E, Wang J, Borecki I, Province M, Mitra RD. High-throughput discovery of rare insertions and deletions in large cohorts. Genome Research. 20: 1711-8. PMID 21041413 DOI: 10.1101/Gr.109157.110  1
2010 Varley KE, Mitra RD. Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samples. Genome Research. 20: 1279-87. PMID 20627893 DOI: 10.1101/Gr.101212.109  1
2010 Mogno I, Vallania F, Mitra RD, Cohen BA. TATA is a modular component of synthetic promoters. Genome Research. 20: 1391-7. PMID 20627890 DOI: 10.1101/Gr.106732.110  1
2010 Matkovich SJ, Van Booven DJ, Hindes A, Kang MY, Druley TE, Vallania FL, Mitra RD, Reilly MP, Cappola TP, Dorn GW. Cardiac signaling genes exhibit unexpected sequence diversity in sporadic cardiomyopathy, revealing HSPB7 polymorphisms associated with disease. The Journal of Clinical Investigation. 120: 280-9. PMID 20038796 DOI: 10.1172/Jci39085  1
2009 Varley KE, Mitra RD. Nested Patch PCR for highly multiplexed amplification of genomic loci. Cold Spring Harbor Protocols. 2009: pdb.prot5252. PMID 20147217 DOI: 10.1101/Pdb.Prot5252  1
2009 Goodman AL, McNulty NP, Zhao Y, Leip D, Mitra RD, Lozupone CA, Knight R, Gordon JI. Identifying genetic determinants needed to establish a human gut symbiont in its habitat. Cell Host & Microbe. 6: 279-89. PMID 19748469 DOI: 10.1016/J.Chom.2009.08.003  1
2009 Tessler LA, Reifenberger JG, Mitra RD. Protein quantification in complex mixtures by solid phase single-molecule counting. Analytical Chemistry. 81: 7141-8. PMID 19601620 DOI: 10.1021/Ac901068X  1
2009 Varley KE, Mutch DG, Edmonston TB, Goodfellow PJ, Mitra RD. Intra-tumor heterogeneity of MLH1 promoter methylation revealed by deep single molecule bisulfite sequencing. Nucleic Acids Research. 37: 4603-12. PMID 19494183 DOI: 10.1093/Nar/Gkp457  1
2009 Druley TE, Vallania FL, Wegner DJ, Varley KE, Knowles OL, Bonds JA, Robison SW, Doniger SW, Hamvas A, Cole FS, Fay JC, Mitra RD. Quantification of rare allelic variants from pooled genomic DNA. Nature Methods. 6: 263-5. PMID 19252504 DOI: 10.1038/Nmeth.1307  1
2008 Varley KE, Mitra RD. Nested Patch PCR enables highly multiplexed mutation discovery in candidate genes. Genome Research. 18: 1844-50. PMID 18849522 DOI: 10.1101/Gr.078204.108  1
2008 Wang H, Heinz ME, Crosby SD, Johnston M, Mitra RD. 'Calling Cards' method for high-throughput identification of targets of yeast DNA-binding proteins. Nature Protocols. 3: 1569-77. PMID 18802438 DOI: 10.1038/Nprot.2008.148  1
2007 Rieger C, Poppino R, Sheridan R, Moley K, Mitra R, Gottlieb D. Polony analysis of gene expression in ES cells and blastocysts. Nucleic Acids Research. 35: e151. PMID 18073198 DOI: 10.1093/Nar/Gkm1076  1
2007 Leparc GG, Mitra RD. A sensitive procedure to detect alternatively spliced mRNA in pooled-tissue samples. Nucleic Acids Research. 35: e146. PMID 18000005 DOI: 10.1093/Nar/Gkm989  1
2007 Rawls AS, Schultz SA, Mitra RD, Wolff T. Bedraggled, a putative transporter, influences the tissue polarity complex during the R3/R4 fate decision in the Drosophila eye. Genetics. 177: 313-28. PMID 17890365 DOI: 10.1534/Genetics.107.075945  1
2007 Wang H, Johnston M, Mitra RD. Calling cards for DNA-binding proteins. Genome Research. 17: 1202-9. PMID 17623806 DOI: 10.1101/Gr.6510207  1
2007 Leparc GG, Mitra RD. Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human. Nucleic Acids Research. 35: 3192-202. PMID 17452356 DOI: 10.1093/Nar/Gkm187  1
2004 Mikkilineni V, Mitra RD, Merritt J, DiTonno JR, Church GM, Ogunnaike B, Edwards JS. Digital quantitative measurements of gene expression. Biotechnology and Bioengineering. 86: 117-24. PMID 15052631 DOI: 10.1002/Bit.20048  1
2004 Buhler JD, Souvenir RM, Zhang W, Mitra RD. Design of a high-throughput assay for alternative splicing using polymerase colonies. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 5-16. PMID 14992488  1
2003 Merritt J, DiTonno JR, Mitra RD, Church GM, Edwards JS. Parallel competition analysis of Saccharomyces cerevisiae strains differing by a single base using polymerase colonies. Nucleic Acids Research. 31: e84. PMID 12888536 DOI: 10.1093/Nar/Gng084  1
2002 Cohen BA, Pilpel Y, Mitra RD, Church GM. Discrimination between paralogs using microarray analysis: application to the Yap1p and Yap2p transcriptional networks. Molecular Biology of the Cell. 13: 1608-14. PMID 12006656 DOI: 10.1091/Mbc.01-10-0472  1
2000 Cohen BA, Mitra RD, Hughes JD, Church GM. A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nature Genetics. 26: 183-6. PMID 11017073 DOI: 10.1038/79896  1
1999 Mitra RD, Church GM. In situ localized amplification and contact replication of many individual DNA molecules Nucleic Acids Research. 27: e34. PMID 10572186 DOI: 10.1093/Nar/27.24.E34  1
1998 Ostrowska E, Muralitharan M, Chandler S, Volker P, Hetherington S, Mitra R, Dunshea F. Optimized conditions for RAPD analysis in Pinus radiata In Vitro Cellular and Developmental Biology - Plant. 34: 225-230.  1
1996 Mitra RD, Silva CM, Youvan DC. Fluorescence resonance energy transfer between blue-emitting and red-shifted excitation derivatives of the green fluorescent protein. Gene. 173: 13-7. PMID 8707050 DOI: 10.1016/0378-1119(95)00768-7  1
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