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Robi D. Mitra - Publications

Affiliations: 
Biology & Biomedical Sciences (Computational Biology) Washington University, Saint Louis, St. Louis, MO 
Area:
Molecular Biology, Biochemistry, General
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72 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
2023 Yen A, Mateusiak C, Sarafinovska S, Gachechiladze MA, Guo J, Chen X, Moudgil A, Cammack AJ, Hoisington-Lopez J, Crosby M, Brent MR, Mitra RD, Dougherty JD. Calling Cards: A Customizable Platform to Longitudinally Record Protein-DNA Interactions Over Time in Cells and Tissues. Current Protocols. 3: e883. PMID 37755132 DOI: 10.1002/cpz1.883  0.309
2023 Yen A, Mateusiak C, Sarafinovska S, Gachechiladze MA, Guo J, Chen X, Moudgil A, Cammack AJ, Hoisington-Lopez J, Crosby M, Brent MR, Mitra RD, Dougherty JD. Calling Cards: a customizable platform to longitudinally record protein-DNA interactions over time in cells and tissues. Biorxiv : the Preprint Server For Biology. PMID 37333130 DOI: 10.1101/2023.06.07.544098  0.321
2022 Lalli M, Yen A, Thopte U, Dong F, Moudgil A, Chen X, Milbrandt J, Dougherty JD, Mitra RD. Measuring transcription factor binding and gene expression using barcoded self-reporting transposon calling cards and transcriptomes. Nar Genomics and Bioinformatics. 4: lqac061. PMID 36062164 DOI: 10.1093/nargab/lqac061  0.319
2020 Moudgil A, Li D, Hsu S, Purushotham D, Wang T, Mitra RD. The qBED track: a novel genome browser visualization for point processes. Bioinformatics (Oxford, England). PMID 32941613 DOI: 10.1093/Bioinformatics/Btaa771  0.365
2020 Lalli MA, Avey D, Dougherty JD, Milbrandt J, Mitra RD. High-throughput single-cell functional elucidation of neurodevelopmental disease-associated genes reveals convergent mechanisms altering neuronal differentiation. Genome Research. PMID 32887689 DOI: 10.1101/Gr.262295.120  0.375
2020 Chen D, Cremona MA, Qi Z, Mitra RD, Chiaromonte F, Makova KD. Human L1 Transposition Dynamics Unraveled with Functional Data Analysis. Molecular Biology and Evolution. PMID 32722770 DOI: 10.1093/Molbev/Msaa194  0.309
2020 Moudgil A, Wilkinson MN, Chen X, He J, Cammack AJ, Vasek MJ, Lagunas T, Qi Z, Lalli MA, Guo C, Morris SA, Dougherty JD, Mitra RD. Self-Reporting Transposons Enable Simultaneous Readout of Gene Expression and Transcription Factor Binding in Single Cells. Cell. PMID 32710817 DOI: 10.1016/J.Cell.2020.06.037  0.428
2020 Cammack AJ, Moudgil A, Chen J, Vasek MJ, Shabsovich M, McCullough K, Yen A, Lagunas T, Maloney SE, He J, Chen X, Hooda M, Wilkinson MN, Miller TM, Mitra RD, et al. A viral toolkit for recording transcription factor-DNA interactions in live mouse tissues. Proceedings of the National Academy of Sciences of the United States of America. PMID 32300008 DOI: 10.1073/Pnas.1918241117  0.439
2020 Liu J, Shively CA, Mitra RD. Quantitative analysis of transcription factor binding and expression using calling cards reporter arrays. Nucleic Acids Research. PMID 32133534 DOI: 10.1093/Nar/Gkaa141  0.364
2020 Kang Y, Patel NR, Shively C, Recio PS, Chen X, Wranik BJ, Kim G, McIsaac RS, Mitra R, Brent MR. Dual threshold optimization and network inference reveal convergent evidence from TF binding locations and TF perturbation responses. Genome Research. PMID 32060051 DOI: 10.1101/Gr.259655.119  0.363
2020 Kfoury-Beaumont N, Qi Z, Wilkinson M, Broestl L, Berrett K, Moudgil A, Sankararaman S, Chen X, Gertz J, Mitra R, Rubin JB. Abstract 3658: Brd4-bound enhancers drive critical sex differences in glioblastoma Cancer Research. 80: 3658-3658. DOI: 10.1158/1538-7445.Am2020-3658  0.315
2019 Shively CA, Liu J, Chen X, Loell K, Mitra RD. Homotypic cooperativity and collective binding are determinants of bHLH specificity and function. Proceedings of the National Academy of Sciences of the United States of America. PMID 31341088 DOI: 10.1073/Pnas.1818015116  0.396
2018 Yen M, Qi Z, Chen X, Cooper JA, Mitra RD, Onken MD. Transposase mapping identifies the genomic targets of BAP1 in uveal melanoma. Bmc Medical Genomics. 11: 97. PMID 30400891 DOI: 10.1186/S12920-018-0424-0  0.42
2018 Avey D, Sankararaman S, Yim AKY, Barve R, Milbrandt J, Mitra RD. Single-Cell RNA-Seq Uncovers a Robust Transcriptional Response to Morphine by Glia. Cell Reports. 24: 3619-3629.e4. PMID 30257220 DOI: 10.1016/J.Celrep.2018.08.080  0.316
2018 Liu C, Xiao F, Hoisington-Lopez J, Lang K, Quenzel P, Duffy B, Mitra RD. Accurate typing of Human Leukocyte Antigen class I genes by Oxford nanopore sequencing. The Journal of Molecular Diagnostics : Jmd. PMID 29625249 DOI: 10.1016/J.Jmoldx.2018.02.006  0.328
2017 Qi Z, Wilkinson MN, Chen X, Sankararaman S, Mayhew D, Mitra RD. An optimized, broadly applicable piggyBac transposon induction system. Nucleic Acids Research. PMID 28082389 DOI: 10.1093/Nar/Gkw1290  0.76
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  0.35
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  0.758
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  0.34
2016 Mayhew D, Mitra RD. Transposon Calling Cards. Cold Spring Harbor Protocols. 2016: pdb.top077776. PMID 26832691 DOI: 10.1101/Pdb.Top077776  0.749
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  0.761
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  0.332
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  0.763
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  0.773
2014 Coghlan MA, Shifren A, Huang HJ, Russell TD, Mitra RD, Zhang Q, Wegner DJ, Cole FS, Hamvas A. Sequencing of idiopathic pulmonary fibrosis-related genes reveals independent single gene associations. Bmj Open Respiratory Research. 1: e000057. PMID 25553246 DOI: 10.1136/Bmjresp-2014-000057  0.318
2014 Brooks MD, Jackson E, Warrington NM, Luo J, Forys JT, Taylor S, Mao DD, Leonard JR, Kim AH, Piwnica-Worms D, Mitra RD, Rubin JB. PDE7B is a novel, prognostically significant mediator of glioblastoma growth whose expression is regulated by endothelial cells. Plos One. 9: e107397. PMID 25203500 DOI: 10.1371/Journal.Pone.0107397  0.631
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  0.322
2014 Bien-Willner GA, Mitra RD. Mutation and expression analysis in medulloblastoma yields prognostic variants and a putative mechanism of disease for i17q tumors. Acta Neuropathologica Communications. 2: 74. PMID 25030029 DOI: 10.1186/S40478-014-0074-1  0.334
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  0.756
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  0.373
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  0.362
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  0.308
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  0.768
2013 Mitra R, Li X, Kapusta A, Mayhew D, Mitra RD, Feschotte C, Craig NL. Functional characterization of piggyBat from the bat Myotis lucifugus unveils an active mammalian DNA transposon. Proceedings of the National Academy of Sciences of the United States of America. 110: 234-9. PMID 23248290 DOI: 10.1073/Pnas.1217548110  0.747
2013 Brooks MD, Jackson E, Piwnica-Worms D, Mitra RD, Rubin JB. Abstract 366: Downregulation of THBS1 is a critical step in glioblastoma angiogenesis. Cancer Research. 73: 366-366. DOI: 10.1158/1538-7445.Am2013-366  0.62
2013 Liu C, Yang X, Duffy B, Mohanakumar T, Mitra RD, Zody MC, Pfeifer JD. 11-OR Human Immunology. 74: 11. DOI: 10.1016/J.Humimm.2013.08.022  0.333
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  0.737
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  0.396
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  0.697
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  0.792
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  0.756
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  0.764
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  0.763
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  0.777
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  0.741
2011 Chiappinelli KB, Haynes BC, Schillebeeckx M, Mitra RD, Brent MR, Goodfellow PJ. Abstract 1173: A genomics approach to understanding DICER1's role in tumorigenesis Cancer Research. 71: 1173-1173. DOI: 10.1158/1538-7445.Am2011-1173  0.767
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  0.365
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  0.733
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  0.364
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  0.319
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  0.71
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  0.328
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  0.752
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  0.693
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  0.72
2009 Matkovich SJ, Druley TE, Van Booven DJ, Chun S, Vallania FM, Hindes A, Fay JC, Mitra RD, Dorn II GW. Genetic Diversity and Novel SNP Discovery in Signaling Genes Revealed by Pooled Sequencing of Cardiomyopathy DNAs Journal of Cardiac Failure. 15: S40. DOI: 10.1016/J.Cardfail.2009.06.297  0.365
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  0.719
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  0.423
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  0.745
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  0.369
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  0.462
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  0.335
2006 Zhang K, Zhu J, Shendure J, Porreca GJ, Aach JD, Mitra RD, Church GM. Long-range polony haplotyping of individual human chromosome molecules. Nature Genetics. 38: 382-7. PMID 16493423 DOI: 10.1038/Ng1741  0.357
2005 Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, Wang MD, Zhang K, Mitra RD, Church GM. Accurate multiplex polony sequencing of an evolved bacterial genome. Science (New York, N.Y.). 309: 1728-32. PMID 16081699 DOI: 10.1126/Science.1117389  0.372
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  0.366
2003 Zhu J, Shendure J, Mitra RD, Church GM. Single molecule profiling of alternative pre-mRNA splicing. Science (New York, N.Y.). 301: 836-8. PMID 12907803 DOI: 10.1126/Science.1085792  0.318
2003 Mitra RD, Shendure J, Olejnik J, Edyta-Krzymanska-Olejnik, Church GM. Fluorescent in situ sequencing on polymerase colonies. Analytical Biochemistry. 320: 55-65. PMID 12895469 DOI: 10.1016/S0003-2697(03)00291-4  0.363
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  0.353
2003 Mitra RD, Butty VL, Shendure J, Williams BR, Housman DE, Church GM. Digital genotyping and haplotyping with polymerase colonies. Proceedings of the National Academy of Sciences of the United States of America. 100: 5926-31. PMID 12730373 DOI: 10.1073/Pnas.0936399100  0.342
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  0.408
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  0.337
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  0.355
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