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Bias-Corrected Targeted Next-Generation Sequencing for Rapid, Multiplexed Detection of Actionable Alterations in Cell-Free DNA from Advanced Lung Cancer Patients.

Paweletz CP, Sacher AG, Raymond CK, Alden RS, O'Connell A, Mach SL, Kuang Y, Gandhi L, Kirschmeier P, English JM, Lim LP, Jänne PA, Oxnard GR.

Clin Cancer Res. 2016 Feb 15;22(4):915-22. doi: 10.1158/1078-0432.CCR-15-1627-T. Epub 2015 Oct 12.


Activity of the Rhodopseudomonas palustris p-coumaroyl-homoserine lactone-responsive transcription factor RpaR.

Hirakawa H, Oda Y, Phattarasukol S, Armour CD, Castle JC, Raymond CK, Lappala CR, Schaefer AL, Harwood CS, Greenberg EP.

J Bacteriol. 2011 May;193(10):2598-607. doi: 10.1128/JB.01479-10. Epub 2011 Mar 4.


NSR-seq transcriptional profiling enables identification of a gene signature of Plasmodium falciparum parasites infecting children.

Vignali M, Armour CD, Chen J, Morrison R, Castle JC, Biery MC, Bouzek H, Moon W, Babak T, Fried M, Raymond CK, Duffy PE.

J Clin Invest. 2011 Mar;121(3):1119-29. doi: 10.1172/JCI43457. Epub 2011 Feb 7.


Unique signatures of long noncoding RNA expression in response to virus infection and altered innate immune signaling.

Peng X, Gralinski L, Armour CD, Ferris MT, Thomas MJ, Proll S, Bradel-Tretheway BG, Korth MJ, Castle JC, Biery MC, Bouzek HK, Haynor DR, Frieman MB, Heise M, Raymond CK, Baric RS, Katze MG.

MBio. 2010 Oct 26;1(5). pii: e00206-10. doi: 10.1128/mBio.00206-10.


Genetic validation of whole-transcriptome sequencing for mapping expression affected by cis-regulatory variation.

Babak T, Garrett-Engele P, Armour CD, Raymond CK, Keller MP, Chen R, Rohl CA, Johnson JM, Attie AD, Fraser HB, Schadt EE.

BMC Genomics. 2010 Aug 13;11:473. doi: 10.1186/1471-2164-11-473.


Digital genome-wide ncRNA expression, including SnoRNAs, across 11 human tissues using polyA-neutral amplification.

Castle JC, Armour CD, Löwer M, Haynor D, Biery M, Bouzek H, Chen R, Jackson S, Johnson JM, Rohl CA, Raymond CK.

PLoS One. 2010 Jul 26;5(7):e11779. doi: 10.1371/journal.pone.0011779.


DNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing.

Castle JC, Biery M, Bouzek H, Xie T, Chen R, Misura K, Jackson S, Armour CD, Johnson JM, Rohl CA, Raymond CK.

BMC Genomics. 2010 Apr 16;11:244. doi: 10.1186/1471-2164-11-244.


Digital transcriptome profiling using selective hexamer priming for cDNA synthesis.

Armour CD, Castle JC, Chen R, Babak T, Loerch P, Jackson S, Shah JK, Dey J, Rohl CA, Johnson JM, Raymond CK.

Nat Methods. 2009 Sep;6(9):647-9. doi: 10.1038/nmeth.1360. Epub 2009 Aug 9.


ACC2 is expressed at high levels in human white adipose and has an isoform with a novel N-terminus [corrected].

Castle JC, Hara Y, Raymond CK, Garrett-Engele P, Ohwaki K, Kan Z, Kusunoki J, Johnson JM.

PLoS One. 2009;4(2):e4369. doi: 10.1371/journal.pone.0004369. Epub 2009 Feb 3. Erratum in: PLoS One. 2009; 4(2) doi:10.1371/annotation/c921dfce-9702-4632-abbe-f13d62fdfde0.


Transcripts targeted by the microRNA-16 family cooperatively regulate cell cycle progression.

Linsley PS, Schelter J, Burchard J, Kibukawa M, Martin MM, Bartz SR, Johnson JM, Cummins JM, Raymond CK, Dai H, Chau N, Cleary M, Jackson AL, Carleton M, Lim L.

Mol Cell Biol. 2007 Mar;27(6):2240-52. Epub 2007 Jan 22.


The colorectal microRNAome.

Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O, Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H, Kinzler KW, Vogelstein B, Velculescu VE.

Proc Natl Acad Sci U S A. 2006 Mar 7;103(10):3687-92. Epub 2006 Feb 27.


DNA sequence and analysis of human chromosome 8.

Nusbaum C, Mikkelsen TS, Zody MC, Asakawa S, Taudien S, Garber M, Kodira CD, Schueler MG, Shimizu A, Whittaker CA, Chang JL, Cuomo CA, Dewar K, FitzGerald MG, Yang X, Allen NR, Anderson S, Asakawa T, Blechschmidt K, Bloom T, Borowsky ML, Butler J, Cook A, Corum B, DeArellano K, DeCaprio D, Dooley KT, Dorris L 3rd, Engels R, Glöckner G, Hafez N, Hagopian DS, Hall JL, Ishikawa SK, Jaffe DB, Kamat A, Kudoh J, Lehmann R, Lokitsang T, Macdonald P, Major JE, Matthews CD, Mauceli E, Menzel U, Mihalev AH, Minoshima S, Murayama Y, Naylor JW, Nicol R, Nguyen C, O'Leary SB, O'Neill K, Parker SC, Polley A, Raymond CK, Reichwald K, Rodriguez J, Sasaki T, Schilhabel M, Siddiqui R, Smith CL, Sneddon TP, Talamas JA, Tenzin P, Topham K, Venkataraman V, Wen G, Yamazaki S, Young SK, Zeng Q, Zimmer AR, Rosenthal A, Birren BW, Platzer M, Shimizu N, Lander ES.

Nature. 2006 Jan 19;439(7074):331-5.


Targeted, haplotype-resolved resequencing of long segments of the human genome.

Raymond CK, Subramanian S, Paddock M, Qiu R, Deodato C, Palmieri A, Chang J, Radke T, Haugen E, Kas A, Waring D, Bovee D, Stacy R, Kaul R, Olson MV.

Genomics. 2005 Dec;86(6):759-66. Epub 2005 Oct 24.


Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs.

Raymond CK, Roberts BS, Garrett-Engele P, Lim LP, Johnson JM.

RNA. 2005 Nov;11(11):1737-44.


Ancient haplotypes of the HLA Class II region.

Raymond CK, Kas A, Paddock M, Qiu R, Zhou Y, Subramanian S, Chang J, Palmieri A, Haugen E, Kaul R, Olson MV.

Genome Res. 2005 Sep;15(9):1250-7.


Expression of alternatively spliced sodium channel alpha-subunit genes. Unique splicing patterns are observed in dorsal root ganglia.

Raymond CK, Castle J, Garrett-Engele P, Armour CD, Kan Z, Tsinoremas N, Johnson JM.

J Biol Chem. 2004 Oct 29;279(44):46234-41. Epub 2004 Aug 9.


Hypervariability, suppressed recombination and the genetics of individuality.

Olson MV, Kas A, Bubb K, Qui R, Smith EE, Raymond CK, Kaul R.

Philos Trans R Soc Lond B Biol Sci. 2004 Jan 29;359(1441):129-40.


Whole-genome sequence variation among multiple isolates of Pseudomonas aeruginosa.

Spencer DH, Kas A, Smith EE, Raymond CK, Sims EH, Hastings M, Burns JL, Kaul R, Olson MV.

J Bacteriol. 2003 Feb;185(4):1316-25.


Effects of methanol concentration on expression levels of recombinant protein in fed-batch cultures of Pichia methanolica.

Mayson BE, Kilburn DG, Zamost BL, Raymond CK, Lesnicki GJ.

Biotechnol Bioeng. 2003 Feb 5;81(3):291-8.


Genetic variation at the O-antigen biosynthetic locus in Pseudomonas aeruginosa.

Raymond CK, Sims EH, Kas A, Spencer DH, Kutyavin TV, Ivey RG, Zhou Y, Kaul R, Clendenning JB, Olson MV.

J Bacteriol. 2002 Jul;184(13):3614-22.

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