Sample RA, Nogueira MF, Mitra RD, Puram SV. Epigenetic regulation of hybrid epithelial-mesenchymal cell states in cancer. Oncogene. 2023 Jul;42(29):2237-2248. doi: 10.1038/s41388-023-02749-9. Epub 2023 Jun 21. PMID: 37344626

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. 2023 Jun 9:2023.06.07.544098. doi: 10.1101/2023.06.07.544098. Preprint. PMID: 37333130

Recio PS, Mitra NJ, Shively CA, Song D, Jaramillo G, Lewis KS, Chen X, Mitra RD. Zinc cluster transcription factors frequently activate target genes using a non-canonical half-site binding mode.  Nucleic Acids Res. 2023 May 1:gkad320. doi: 10.1093/nar/gkad320. Online ahead of print.PMID: 37125648

Shively C, Dong F, Mitra RD, A Suite of New Strain Construction Vectors for Gene Expression Knockdown in Budding Yeast. ACS Synth Biol. 2023 Feb 17;12(2):624-633. doi: 10.1021/acssynbio.2c00547. Epub 2023 Jan 17.PMID: 36650116

Yenkin AL, Bramley JC, Kremitzki CL, Waligorski JE, Liebeskind MJ, Xu XE, Chandrasekaran VD, Vakaki MA, Bachman GW, Mitra RD, Milbrandt JD, Buchser WJ. Pooled image-base screening of mitochondria with microraft isolation distinguishes pathogenic mitofusin 2 mutations. Commun Biol. 2022 Oct 25;5(1):1128. doi: 10.1038/s42003-022-04089-y. PMID: 36284160

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 Genom Bioinform. 2022 Aug 31;4(3):lqac061. doi: 10.1093/nargab/lqac061. eCollection 2022 Sep.PMID: 36062164

Yim AKY, Wang PL, Bermingham JR Jr, Hackett A, Strickland A, Miller TM, Ly C, Mitra RD, Milbrandt J. Disentangling glial diversity in peripheral nerves at single-nuclei resolution. Nat Neurosci. 2022 Feb;25(2):238-251. doi: 10.1038/s41593-021-01005-1. Epub 2022 Feb 3.PMID: 35115729

Sams EI, Ng JK, Tate V, Claire Hou YC, Cao Y, Antonacci-Fulton L, Belhassan K, Neidich J, Mitra RD, Cole FS, Dickson P, Milbrandt J, Turner TN. From karyotypes to precision genomics in 9p deletion and duplication syndromes. HGG Adv. 2021 Dec 24;3(1):100081. doi: 10.1016/j.xhgg.2021.100081. eCollection 2022 Jan 13.PMID: 35047865

Kfoury N, Qi Z, Prager BC, Wilkinson M, Broestl L, Berrett KC, Moudgil A, Sankararaman S,  Chen X,  Gertz J,  Rich JN, Mitra RD, and Rubin JB. Brd4-bound enhancers drive cell-intrinsic sex differences in glioblastoma. Proc Natl Acad Sci USA April 20, 2021 118 (16) e2017148118; PMID:33850013

Liu C, Yang X, Duffy BF, Hoisington-Lopez J, Crosby M, Porche-Sorbet R, Saito K, Berry R, Swamidass V, Mitra RD. High-resolution HLA typing by long reads from the R10.3 Oxford nanopore flow cells. Hum Immunol. 2021 Apr;82(4):288-295. doi: 10.1016/j.humimm.2021.02.005. Epub 2021 Feb 19.PMID: 33612390

Lalli MA, Langmade JS, Chen X, Fronick CC, Sawyer CS, Burcea LC, Wilkinson MN, Fulton RS, Heinz M, Buchser WJ, Head RD, Mitra RD, Milbrandt J. Rapid and Extraction-Free Detection of SARS-CoV-2 from Saliva by Colorimetric Reverse-Transcription Loop-Mediated Isothermal Amplification. Clin Chem. 2021 Jan 30;67(2):415-424. doi: 10.1093/clinchem/hvaa267. pre-print May 2020 doi:10.1101/2020.05.07.20093542. PMID: 33098427 

Moudgil A, Li D, Hsu S, Purushotham, Wang T, Mitra RD. The qBED track: a novel genome browser visualization for point processes  Bioinformatics. 2021 May 23;37(8):1168-1170. doi: 10.1093/bioinformatics/btaa771. [preprint] April 2020  PMID: 32941613

Lalli M, 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 Res. 2020 Sep;30(9):1317-1331. doi: 10.1101/gr.262295.120. Epub 2020 Sep 4.PMID: 32887689 

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, 2020 July 28 PMID: 32722770

Liu J, Shively CA, Mitra RD. Quantitative analysis of transcription factor binding and expression using calling cards reporter arrays. Nucleic Acids Res. 2020 May 21;48(9):e50. doi: 10.1093/nar/gkaa141.PMID: 32133534

Shively CA, Liu J, Chen X, Loell K, Mitra RD. Homotypic cooperativity and collective binding are determinants of bHLH specificity and function. Proc Natl Acad Sci USA. 2019 Aug 6; 116(32):16143-16152. doi:10.1073/PNAS.1818015116. PMID:31341088

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 Res. 2020 Mar;30(3):459-471. doi: 10.1101/gr.259655.119. Epub 2020 Feb 14. PubMed PMID: 32060051.

Moudgil A, Wilkinson MN, Chen X, He J, Cammack AJ, Vasek MJ, Lagunas Jr. T, Qi Z, Morris SA, Dougherty JD, Mitra RD. Self-reporting transposons enable simultaneous readout of gene expression and transcription factor binding in single cells. Cell. 2020 Aug 20;182(4):992-1008.e21. doi: 10.1016/j.cell.2020.06.037. Epub 2020 Jul 24.PMID: 32710817

Cammack AJ, Moudgil A, Lagunas T, Vasek MJ, Shabsovich M, He J, Chen X, Wilkinson MN, Miller TM, Mitra RD, Dougherty JD. A viral toolkit for recording transcription factor-DNA interactions in live mouse tissues. Proc Natl Acad Sci U S A. 2020 May 5;117(18):10003-10014. doi: 10.1073/pnas.1918241117. Epub 2020 Apr 16.PMID: 32300008

Yen M, Qi Z, Chen X, Cooper JA, Mitra RD, Onken MD. Transposase mapping identifies the genomic targets of BAP1 in uveal melanoma. BMC Med Genomics. 2018 Nov 6;11(1):97. doi: 10.1186/s12920-018-0424-0. PMID: 30400891

Avey D, Sankararaman S, Yim A, Barve R, Milbrandt J†, Mitra RD†.Single-Cell RNA-Seq Uncovers a Robust Transcriptional Response to Morphine by Glia. Cell Rep. 2018 Sep 25;24(13):3619-3629.e4. doi: 10.1016/j.celrep.2018.08.080. PMID: 30257220

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. J Mol Diagn. 2018 Jul;20(4):428-435. doi: 10.1016/j.jmoldx.2018.02.006. Epub 2018 Apr 3. PMID: 29625249

Qi Z, Wilkinson MN, Chen X, Sankararaman S, Mayhew D, Mitra RD. An optimized, broadly applicable piggyBac transposon induction system. Nucleic Acids Res. 2017 Apr 20;45(7):e55. doi: 10.1093/nar/gkw1290. PubMed PMID: 28082389.

Haller G, Alvarado D, McCall K, Mitra RD, Dobbs MB, Gurnett CA.Massively parallel single-nucleotide mutagenesis using reversibly terminated inosine.. Nat Methods. 2016 Nov;13(11):923-924. doi: 10.1038/nmeth.4015. PubMed PMID: 27694911.

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, Luke B, Muzi-Falconi M, Myers CL, Mitra RD, Shore D, Brown GW, Zhang Z, Boone  C, Andrews BJ. Exploring Quantitative Yeast Phenomics with Single-Cell Analysis of DNA Damage Foci.. Cell Syst. 2016 Sep 28;3(3):264-277.e10. doi:10.1016/j.cels.2016.08.008. PubMed PMID: 27617677

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.erratum. JClin Invest. 2016 Apr 1;126(4):1603. doi: 10.1172/JCI87342. PubMed PMID: 26927868; PubMed Central PMCID: PMC4811140.

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.JClin Invest. 2016 Mar 1;126(3):1067-78. doi: 10.1172/JCI82592. Epub 2016 Feb 22. PubMed PMID: 26901816; PubMed Central PMCID: PMC4767358.

Mayhew D, Mitra RD. Transposon Calling Cards. Cold Spring Harb Protoc. 2016 Feb 1;2016(2):pdb.top077776. doi: 10.1101/pdb.top077776. PubMed PMID: 26832691

Mayhew D, Mitra RD.Calling Card Analysis in Budding Yeast. Cold Spring Harb Protoc. 2016 Feb 1;2016(2):pdb.prot086918. doi: 10.1101/pdb.prot086918. PubMed PMID: 26832687.

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 Res. 2015 Oct 15;43(18):9076-85. doi: 10.1093/nar/gkv901. Epub 2015 Sep 13. PubMed PMID: 26365240; PubMed Central PMCID: PMC4605323.

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. Ann Neurol. 2015 Jan;77(1):100-13. doi: 10.1002/ana.24306. Epub 2014 Nov 27. PMID: 25382069

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. Mol Cell Endocrinol. 2014 Dec 8. pii: S0303-7207(14)00396-7. doi: 10.1016/j.mce.2014.12.003. [Epub ahead of print] PMID: 25498963

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 Respir Res. 2014 Dec 10;1(1):e000057. doi: 10.1136/bmjresp-2014-000057. eCollection 2014. PMID: 25553246

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. Mol Cell Endocrinol. 2015 Jan 5;399:122-30. doi: 10.1016/j.mce.2014.09.029. Epub 2014 Oct 5. PubMed PMID: 25289806; PubMed Central PMCID: PMC4262703.

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. 2014 Sep 9;9(9):e107397. doi: 10.1371/journal.pone.0107397. eCollection 2014. PMID: 25203500

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. 2014 Jul 25;9(7):e102202. doi: 10.1371/journal.pone.0102202. eCollection 2014. PMID: 25062021

Bien-Willner GA, Mitra RD. Mutation and expression analysis in medulloblastoma yields prognostic variants and a putative mechanism of disease for i17q tumors. Acta Neuropathol Commun. 2014 Jul 17;2(1):74. [Epub ahead of print] PMID: 25030029

Mayhew D, Mitra RD.Transcription factor regulation and chromosome dynamics during pseudohyphal growth. Mol Biol Cell. 2014 Sep 1;25(17):2669-76. doi: 10.1091/mbc.E14-04-0871. Epub 2014 Jul 9. PMID: 25009286

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.J Pediatr. 2014 Jun;164(6):1316-21.e3. doi: 10.1016/j.jpeds.2014.02.021. Epub 2014 Mar 20. PMID: 24657120

Spencer DH, Tyagi M, Vallania F, Bredemeyer A, Pfeifer JD, Mitra RD, Duncavage EJ. Performance of Common Analysis Methods for Detecting Low-Frequency Single Nucleotide Variants in Targeted Next-Generation Sequence Data. J Mol Diagn. 2014 Jan;16(1):75-88. doi: 10.1016/j.jmoldx.2013.09.003. Epub 2013 Nov 5.PMID: 24211364.

Sharma MK, Phillips J, Agarwal S, Wiggins WS, Shrivastava S, Koul SB, Bhattacharjee M, Houchins CD, Kalakota RR, George B, Meyer RR, Spencer DH, Lockwood CM, Nguyen TT, Duncavage EJ, Al-Kateb H, Cottrell CE, Godala S, Lokineni R, Sawant SM, Chatti V, Surampudi S, Sunkishala RR, Darbha R, Macharla S, Milbrandt JD, Virgin HW, Mitra RD, Head RD, Kulkarni S, Bredemeyer A, Pfeifer JD, Seibert K, Nagarajan R. Clinical Genomics Workstation AMIA Summits Transl Sci Proc. 2013 Mar 18;2013:156-157. PubMed PMID: 24303327; PubMed Central PMCID: PMC3814481.

Liu C, Yang X, Duffy B, Mohanakumar T, Mitra RD, Zody M, Pfeifer J. Accurate Typing of Human Leukocyte Antigen (HLA) by Next-Generation Exome Sequencing. Human Immunology. 2013 Nov, Vol 74, Supplement, pg 11. doi:10.1016/j.humimm.2013.08.022

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, Brown JT, Cliften PF, George B, McIntosh LD, Shrivastava S, Nguyen TT, Payton JE, Watson MA, Crosby SD, Head RD, Mitra RD, Nagarajan R, Kulkarni S, Seibert K, Virgin HW 4th, Milbrandt J, Pfeifer JD. Validation of a Next-Generation Sequencing Assay for Clinical Molecular Oncology. J Mol Diagn. 2013 Nov 6. doi:pii: S1525-1578(13)00219-5. 10.1016/j.jmoldx.2013.10.002. [Epub ahead of print] PubMed PMID: 24211365.

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. 2013 Jul 9;8(7):e67801. doi:10.1371/journal.pone.0067801. Print 2013. PubMed PMID: 23874447; PubMed Central PMCID: PMC3706446.

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 Res. 2013 Aug;41(14):e142. doi: 10.1093/nar/gkt481. Epub 2013 Jun 8. PubMed PMID: 23748956; PubMed Central PMCID: PMC3737559.

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 Res. 2013 Apr 15. [Epub ahead of print]  PMID: 23589626

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. 2013 Mar 11. PMID: 23441808

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. Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):234-9. doi: 10.1073/pnas.1217548110. Epub 2012 Dec 17.  PMID: 23248290

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. 2012 Dec;130(6):e1575-82. doi: 10.1542/peds.2012-0918. Epub 2012 Nov 19. PMID: 23166334

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, Schwarzmüller T, Reynolds TB, Kuchler K, Gifford DK, Whiteway M, Giaever G, Nislow C, Costanzo M, Gingras AC, Mitra RD, Andrews B, Fink GR, Cowen LE, Boone C. Global gene deletion analysis exploring yeast filamentous growth.  Science. 2012 Sep 14;337(6100):1353-6. PMID: 22984072

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, Jain S.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.Hum Genet. 2012 Jun 23. [Epub ahead of print] PMID: 22729463

Vallania F, Ramos E, Cresci S, Mitra RD, Druley TE.  Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER.  J Vis Exp. 2012 June 23;(64). pii: 3943. Doi: 10.3791/3943  PMID: 22760212

Reyes A, Sandoval A, Cubillos-Ruiz A, Varley KE, Hernandez-Neuta I, Samper S, Martin C, Garcia MJ, Ritacco V, Lopez L, Roledo J, Zambrano MM Mmz, Mitra RD†, Del Portillo P†.  IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes.  BMC Genomics.  2012 Jun 15;13(1):249. PMID: 22703188

Yun Y, Adesanya TM, Mitra RD.  A systematic study of gene expression variation at single-nucleotide resolution reveals widespread regulatory roles for uAUGs  Genome Res. 2012 Jun; 22(6):1089-97. PMID:22454232.

Cruchaga C, 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, Ehm MG, Mayeux R, Goate AM; NIA-LOAD/NCRAD Family Study Consortium. Rare variants in APP PSEN1 and PSEN2 increase risk for AD in late-onset Alzheirmer’s disease families  PLoS One. 2012; 7(2):e31039

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 Res. 2012 Apr:22(4):681:92.  PMID: 22287102; PMCID: PMC3317150.

Wang H*, Mayhew D*, Chen X, Johnston M†, Mitra RD†.“Calling Cards” for DNA-Binding Proteins in Mammalian Cells.  Genetics. 2012 Jan 3. PMID: 22214611

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. Hum Mol Genet. 2011 Nov 16. PMID: 22042774

Tessler LA, Mitra RD.  (2011),  Sensitive single molecule protein quantification and protein complex detection in a microarray format. Proteomics, 11: 4731-4735.

Wang H*, Mayhew D*, Chen X, Johnston M†, Mitra RD†.  Calling Cards enable multiplexed identification of the genomic targets of DNA-binding proteins. Genome Res. 2011 May;21(5):748-55. Epub 2011 Apr 6. PMID: 21471402

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, 2011 Oct 7; 8(63):1400-8. Epub 2011 Feb 16. PMID: 21325313

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 Res. 2010 Dec; 20(12):1711-8. Epub November 1, 2010.  PMID 21041413

Varley KE, Mitra RD.  Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samples.  Genome Res. 2010 Sep;20(9):1279-87. Epub 2010 Jul 13.PMID: 20627893

Mogno I, Vallania F, Mitra RD, Cohen BA.  TATA is a modular component of synthetic promoters. Genome Res. 2010 Oct;20(10):1391-7. Epub 2010 Jul 13.PMID: 20627890

Varley KE, Mitra RD. (2009) Nested Patch PCR for Highly Multiplexed Amplification of Genomic Loci.  Cold Spring Harb Protoc. Jul;2009(7):pdb.prot5252.PMID: 20147217

Matkovich SJ, Van Booven DJ, Hindes A, Kang MY, Druley TE, Vallania FL, Mitra RD, Reilly MP, Cappola TP, Dorn GW 2nd.  (2010)  Cardiac signaling genes exhibit unexpected sequence diversity in sporadic cardiomyopathy, revealing HSPB7 polymorphisms associated with disease.  J Clin Invest. 2010 Jan 4;120(1):280-9.  PMID: 20038796

Goodman AL, McNulty NP, Zhao Y, Leip D, Mitra RD, Luzopone CA, Knight R, and Gordon JI.  Identifying genetic determinants needed to establish a human gut symbiont in its habitatCell Host and Microbe, 2009, Sep 17;6(3):279-89. PMID: 19748469

Tessler LA, Reifenberger J, Mitra RD.  Protein Quantification in Complex Mixtures by Solid Phase Single-Molecule CountingAnalytical Chemistry, 2009, Sep 1;81(17):7141-8. PMID: 19601620

Varley KE, Mutch DG, Edmonston TB, Goodfellow, PJ, Mitra, RD.  Intra-tumor heterogeneity of MLH1 promoter methylation revealed by deep single molecule bisulfite sequencingNucleic Acids Research 2009Aug; 37(14):4603-12. PMID: 19494183

Druley TE, Vallania FML, 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 DNANature Methods, 2009 Apr, 6(4): 263-5. PMID: 19252504 (PMCID: PMC2776647).

Wang, H, Heinz, ME, Crosby, SD, Johnston, HM, Mitra, RD.  ‘Calling Cards’ method for high-throughput identification of targets of yeast DNA-binding proteinsNature Protocols, 2008; 3:1569-1577. PMID: 18802438

Varley, KE, and Mitra, RD. Nested Patch PCR enables highly multiplexed mutation discovery in candidate genesGenome Research, 2008; 18(11):1844-50. PMID: 18849522

Rieger C, Poppino R, Sheridan R, Moley K, Mitra R, Gottlieb D.  Polony analysis of gene expression in ES cells and blastocystsNucleic Acids Research 2007; 35(22):e151. (PMCID: PMC2190707)

Leparc, GG and Mitra RD.  A sensitive procedure to detect alternatively spliced mRNA in pooled-tissue samplesNucleic Acids Research 2007; 35(21):e146.  PMID: 18000005 (PMCID: PMC2175357)

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 EyeGenetics 2007;  177(1):313-28.  PMID: 17890365 (PMCID: PMC2013731)

Wang, H, Johnston, M, Mitra, RD.  Calling cards for DNA-binding proteinsGenome Research 2007; 17: 1202-1209. PMID: 17623806 (PMCID: PMC1933518)

Leparc, GG and Mitra RD.  Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and humanNucleic Acids Research 2007;35(10):3192-202. PMID: 17452356 (PMCID: PMC1904267)

Zhang K, Zhu J, Shendure J, Porreca GJ, Aach JD, Mitra RD, Church GM.  Long-range polony haplotyping of individual human chromosome moleculesNature Genetics  2006; 38(3):382-7. PMID: 16493423

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 GenomeScience, 2005; 309:1728-32. PMID: 16081699

Shendure J, Mitra R, Varma C, Church GM. Advanced Sequencing Technologies: Methods and Goals. Nature Reviews of Genetics, 2004;5:335–344. PMID: 15143316

Buhler J, Souvenir R, Zhang W, Mitra RD. Design of a High-Throughput Assay for Alternative Splicing Using Polymerase Colonies. Pac Symp Biocomput. 2004:5-16. doi: 10.1142/9789812704856_0002. PMID: 14992488

Mikkilineni V, Mitra RD, Merritt J, DiTonno JR, Lemieux B, Church GM, Ogunnaike B Edwards JS. Digital Quantitative Measurements of Gene Expression. Biotechnology and Bioengineering 2004;86:117-124. PMID:15052631

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 Res 2003 Aug 1;31(15):e84. PMID: 12888536 (PMCID:PMC169973).

Zhu J*, Shendure J*, Mitra RD, Church GM. Single Molecule Profiling of Alternative Pre-mRNA Splicing. Science. 2003;301:836-838. PMID:12907803

Mitra RD, Shendure J, Olejnik J, Edyta-Krzymansk-Olejnik, Church GM. Fluorescent in situ sequencing on polymerase colonies. Anal Biochem 2003;320:55-65. PMID:12895469

Mitra RD, Butty V, Shendure J, Housman D, Church GM. Digital genotyping and haplotyping with polymerase colonies. Proc Natl Acad Sci 2003;100:5926-5931. PMID: 12730373

Cohen BA, Pilpel Y, Mitra RD, Church GM. Discrimination between Paralogs using Microarray Analysis: Application to the Yap1p and Yap2p Transcriptional Networks. Mol Biol Cell 2002;13:1608-1614. PMID:12006656

Cohen BA*, Mitra RD*, Hughes JD, Church GM. A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nature Genetics 2000;26:183-186. PMID:11017073

Mitra RD and Church GM. In-situ-localized amplification and contact replication of many individual DNA molecules. Nucleic Acids Res 1999;27:1-6. PMID:10572186

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* These authors contributed equally to this work.

† Corresponding authors.