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Homotypic cooperativity and collective binding are determinants of bHLH specificity and function.

Shively CA, Liu J, Chen X, Loell K, Mitra RD.

Proc Natl Acad Sci U S A. 2019 Aug 6;116(32):16143-16152. doi: 10.1073/pnas.1818015116. Epub 2019 Jul 24.


Transposase mapping identifies the genomic targets of BAP1 in uveal melanoma.

Yen M, Qi Z, Chen X, Cooper JA, Mitra RD, Onken MD.

BMC Med Genomics. 2018 Nov 6;11(1):97. doi: 10.1186/s12920-018-0424-0.


Single-Cell RNA-Seq Uncovers a Robust Transcriptional Response to Morphine by Glia.

Avey D, Sankararaman S, Yim AKY, Barve R, Milbrandt J, Mitra RD.

Cell Rep. 2018 Sep 25;24(13):3619-3629.e4. doi: 10.1016/j.celrep.2018.08.080.


Accurate Typing of Human Leukocyte Antigen Class I Genes by Oxford Nanopore Sequencing.

Liu C, Xiao F, Hoisington-Lopez J, Lang K, Quenzel P, Duffy B, Mitra RD.

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


An optimized, broadly applicable piggyBac transposon induction system.

Qi Z, Wilkinson MN, Chen X, Sankararaman S, Mayhew D, Mitra RD.

Nucleic Acids Res. 2017 Apr 20;45(7):e55. doi: 10.1093/nar/gkw1290.


Massively parallel single-nucleotide mutagenesis using reversibly terminated inosine.

Haller G, Alvarado D, McCall K, Mitra RD, Dobbs MB, Gurnett CA.

Nat Methods. 2016 Nov;13(11):923-924. doi: 10.1038/nmeth.4015. Epub 2016 Oct 3.


Exploring Quantitative Yeast Phenomics with Single-Cell Analysis of DNA Damage Foci.

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.

Cell Syst. 2016 Sep 28;3(3):264-277.e10. doi: 10.1016/j.cels.2016.08.008. Epub 2016 Sep 8.


A role for genetic susceptibility in sporadic focal segmental glomerulosclerosis.

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.

J Clin Invest. 2016 Apr 1;126(4):1603. doi: 10.1172/JCI87342. Epub 2016 Mar 1. No abstract available.


A role for genetic susceptibility in sporadic focal segmental glomerulosclerosis.

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.

J Clin Invest. 2016 Mar 1;126(3):1067-78. doi: 10.1172/JCI82592. Epub 2016 Feb 22. Erratum in: J Clin Invest. 2016 Apr 1;126(4):1603.


Transposon Calling Cards.

Mayhew D, Mitra RD.

Cold Spring Harb Protoc. 2016 Feb 1;2016(2):pdb.top077776. doi: 10.1101/pdb.top077776.


Calling Card Analysis in Budding Yeast.

Mayhew D, Mitra RD.

Cold Spring Harb Protoc. 2016 Feb 1;2016(2):pdb.prot086918. doi: 10.1101/pdb.prot086918.


Redesign of the monomer-monomer interface of Cre recombinase yields an obligate heterotetrameric complex.

Zhang C, Myers CA, Qi Z, Mitra RD, Corbo JC, Havranek JJ.

Nucleic Acids Res. 2015 Oct 15;43(18):9076-85. doi: 10.1093/nar/gkv901. Epub 2015 Sep 13.


Sequencing of idiopathic pulmonary fibrosis-related genes reveals independent single gene associations.

Coghlan MA, Shifren A, Huang HJ, Russell TD, Mitra RD, Zhang Q, Wegner DJ, Cole FS, Hamvas A.

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


Toying with fate: Redirecting the differentiation of adrenocortical progenitor cells into gonadal-like tissue.

Röhrig T, Pihlajoki M, Ziegler R, Cochran RS, Schrade A, Schillebeeckx M, Mitra RD, Heikinheimo M, Wilson DB.

Mol Cell Endocrinol. 2015 Jun 15;408:165-77. doi: 10.1016/j.mce.2014.12.003. Epub 2014 Dec 8. Review.


Amyotrophic lateral sclerosis onset is influenced by the burden of rare variants in known amyotrophic lateral sclerosis genes.

Cady J, Allred P, Bali T, Pestronk A, Goate A, Miller TM, Mitra RD, Ravits J, Harms MB, Baloh RH.

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


Novel markers of gonadectomy-induced adrenocortical neoplasia in the mouse and ferret.

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.

Mol Cell Endocrinol. 2015 Jan 5;399:122-30. doi: 10.1016/j.mce.2014.09.029. Epub 2014 Oct 5.


PDE7B is a novel, prognostically significant mediator of glioblastoma growth whose expression is regulated by endothelial cells.

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.

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


Origin and consequences of the relationship between protein mean and variance.

Vallania FL, Sherman M, Goodwin Z, Mogno I, Cohen BA, Mitra RD.

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


Mutation and expression analysis in medulloblastoma yields prognostic variants and a putative mechanism of disease for i17q tumors.

Bien-Willner GA, Mitra RD.

Acta Neuropathol Commun. 2014 Jul 17;2:74. doi: 10.1186/s40478-014-0074-1.


Transcription factor regulation and chromosome dynamics during pseudohyphal growth.

Mayhew D, Mitra RD.

Mol Biol Cell. 2014 Sep 1;25(17):2669-76. doi: 10.1091/mbc.E14-04-0871. Epub 2014 Jul 9.


Synonymous ABCA3 variants do not increase risk for neonatal respiratory distress syndrome.

Wambach JA, Wegner DJ, Heins HB, Druley TE, Mitra RD, Hamvas A, Cole FS.

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


Clinical genomicist workstation.

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.

AMIA Jt Summits Transl Sci Proc. 2013 Mar 18;2013:156-7. eCollection 2013.


Validation of a next-generation sequencing assay for clinical molecular oncology.

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.

J Mol Diagn. 2014 Jan;16(1):89-105. doi: 10.1016/j.jmoldx.2013.10.002. Epub 2013 Nov 6.


Performance of common analysis methods for detecting low-frequency single nucleotide variants in targeted next-generation sequence data.

Spencer DH, Tyagi M, Vallania F, Bredemeyer AJ, Pfeifer JD, Mitra RD, Duncavage EJ.

J Mol Diagn. 2014 Jan;16(1):75-88. doi: 10.1016/j.jmoldx.2013.09.003. Epub 2013 Nov 5.


ATHLATES: accurate typing of human leukocyte antigen through exome sequencing.

Liu C, Yang X, Duffy B, Mohanakumar T, Mitra RD, Zody MC, Pfeifer JD.

Nucleic Acids Res. 2013 Aug;41(14):e142. doi: 10.1093/nar/gkt481. Epub 2013 Jun 8.


Laser capture microdissection-reduced representation bisulfite sequencing (LCM-RRBS) maps changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse.

Schillebeeckx M, Schrade A, Löbs AK, Pihlajoki M, Wilson DB, Mitra RD.

Nucleic Acids Res. 2013 Jun;41(11):e116. doi: 10.1093/nar/gkt230. Epub 2013 Apr 15.


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.

Donahoe CD, Cohen TL, Li W, Nguyen PK, Fortner JD, Mitra RD, Elbert DL.

Langmuir. 2013 Mar 26;29(12):4128-39. doi: 10.1021/la3051115. Epub 2013 Mar 11.


Functional characterization of piggyBat from the bat Myotis lucifugus unveils an active mammalian DNA transposon.

Mitra R, Li X, Kapusta A, Mayhew D, Mitra RD, Feschotte C, Craig NL.

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


Single ABCA3 mutations increase risk for neonatal respiratory distress syndrome.

Wambach JA, Wegner DJ, Depass K, Heins H, Druley TE, Mitra RD, An P, Zhang Q, Nogee LM, Cole FS, Hamvas A.

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


Global gene deletion analysis exploring yeast filamentous growth.

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.

Science. 2012 Sep 14;337(6100):1353-6. doi: 10.1126/science.1224339.


Detection of rare genomic variants from pooled sequencing using SPLINTER.

Vallania F, Ramos E, Cresci S, Mitra RD, Druley TE.

J Vis Exp. 2012 Jun 23;(64). pii: 3943. doi: 10.3791/3943.


IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes.

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.

BMC Genomics. 2012 Jun 15;13:249. doi: 10.1186/1471-2164-13-249.


A systematic study of gene expression variation at single-nucleotide resolution reveals widespread regulatory roles for uAUGs.

Yun Y, Adesanya TM, Mitra RD.

Genome Res. 2012 Jun;22(6):1089-97. doi: 10.1101/gr.117366.110. Epub 2012 Mar 27.


Rare variants in APP, PSEN1 and PSEN2 increase risk for AD in late-onset Alzheimer's disease families.

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, Ehm MG, Mayeux R, Goate AM; NIA-LOAD/NCRAD Family Study Consortium.

PLoS One. 2012;7(2):e31039. doi: 10.1371/journal.pone.0031039. Epub 2012 Feb 1. Erratum in: PLoS One. 2012;7(5): doi/10.1371/annotation/c92e16da-7733-421d-b063-1db19488daa6. Haller, Gabe [added]..


Retrotransposon profiling of RNA polymerase III initiation sites.

Qi X, Daily K, Nguyen K, Wang H, Mayhew D, Rigor P, Forouzan S, Johnston M, Mitra RD, Baldi P, Sandmeyer S.

Genome Res. 2012 Apr;22(4):681-92. doi: 10.1101/gr.131219.111. Epub 2012 Jan 27.


"Calling cards" for DNA-binding proteins in mammalian cells.

Wang H, Mayhew D, Chen X, Johnston M, Mitra RD.

Genetics. 2012 Mar;190(3):941-9. doi: 10.1534/genetics.111.137315. Epub 2012 Jan 3.


Rare missense variants in CHRNB4 are associated with reduced risk of nicotine dependence.

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.

Hum Mol Genet. 2012 Feb 1;21(3):647-55. doi: 10.1093/hmg/ddr498. Epub 2011 Oct 31.


Sensitive single-molecule protein quantification and protein complex detection in a microarray format.

Tessler LA, Mitra RD.

Proteomics. 2011 Dec;11(24):4731-5. doi: 10.1002/pmic.201100361. Epub 2011 Nov 23.


Calling Cards enable multiplexed identification of the genomic targets of DNA-binding proteins.

Wang H, Mayhew D, Chen X, Johnston M, Mitra RD.

Genome Res. 2011 May;21(5):748-55. doi: 10.1101/gr.114850.110. Epub 2011 Apr 6.


Nanogel surface coatings for improved single-molecule imaging substrates.

Tessler LA, Donahoe CD, Garcia DJ, Jun YS, Elbert DL, Mitra RD.

J R Soc Interface. 2011 Oct 7;8(63):1400-8. doi: 10.1098/rsif.2010.0669. Epub 2011 Feb 16.


High-throughput discovery of rare insertions and deletions in large cohorts.

Vallania FL, Druley TE, Ramos E, Wang J, Borecki I, Province M, Mitra RD.

Genome Res. 2010 Dec;20(12):1711-8. doi: 10.1101/gr.109157.110. Epub 2010 Nov 1.


Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samples.

Varley KE, Mitra RD.

Genome Res. 2010 Sep;20(9):1279-87. doi: 10.1101/gr.101212.109. Epub 2010 Jul 13.


TATA is a modular component of synthetic promoters.

Mogno I, Vallania F, Mitra RD, Cohen BA.

Genome Res. 2010 Oct;20(10):1391-7. doi: 10.1101/gr.106732.110. Epub 2010 Jul 13.


Nested Patch PCR for highly multiplexed amplification of genomic loci.

Varley KE, Mitra RD.

Cold Spring Harb Protoc. 2009 Jul;2009(7):pdb.prot5252. doi: 10.1101/pdb.prot5252.


Cardiac signaling genes exhibit unexpected sequence diversity in sporadic cardiomyopathy, revealing HSPB7 polymorphisms associated with disease.

Matkovich SJ, Van Booven DJ, Hindes A, Kang MY, Druley TE, Vallania FL, Mitra RD, Reilly MP, Cappola TP, Dorn GW 2nd.

J Clin Invest. 2010 Jan;120(1):280-9. doi: 10.1172/JCI39085. Epub 2009 Dec 14.


Identifying genetic determinants needed to establish a human gut symbiont in its habitat.

Goodman AL, McNulty NP, Zhao Y, Leip D, Mitra RD, Lozupone CA, Knight R, Gordon JI.

Cell Host Microbe. 2009 Sep 17;6(3):279-89. doi: 10.1016/j.chom.2009.08.003.


Protein quantification in complex mixtures by solid phase single-molecule counting.

Tessler LA, Reifenberger JG, Mitra RD.

Anal Chem. 2009 Sep 1;81(17):7141-8. doi: 10.1021/ac901068x.


Intra-tumor heterogeneity of MLH1 promoter methylation revealed by deep single molecule bisulfite sequencing.

Varley KE, Mutch DG, Edmonston TB, Goodfellow PJ, Mitra RD.

Nucleic Acids Res. 2009 Aug;37(14):4603-12. doi: 10.1093/nar/gkp457. Epub 2009 Jun 3.


Quantification of rare allelic variants from pooled genomic DNA.

Druley TE, Vallania FL, Wegner DJ, Varley KE, Knowles OL, Bonds JA, Robison SW, Doniger SW, Hamvas A, Cole FS, Fay JC, Mitra RD.

Nat Methods. 2009 Apr;6(4):263-5. doi: 10.1038/nmeth.1307. Epub 2009 Mar 1.

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