Publications

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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.

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 R. Design of a High-Throughput Assay for Alternative Splicing Using Polymerase Colonies. Pac Symp Biocomput 2004;5-16. 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. Identifying genetic determinants needed to establish a human gut symbiont in its habitat. Nucleic Acids Res 1999;27:1-6. PMID:10572186

Mitra RD, Silva CM, Youvan DC. Fluorescence resonance energy transfer between blue-emitting and red-shifted excitation derivatives of the green fluorescent protein. Gene 1996;173:13-17. PMID:8707050

Jones HLJ, Mitra RD, Silva CM. Using GFP expressing E.coli to measure ingestion rates in mixotrophic algae and ciliates. European Journal of Protistology 1995;31:437.

* These authors contributed equally to this work.

† Corresponding authors.