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Next Generation Sequencing Core

Publications

Kurian SM, Williams AN, Gelbart T, Campbell D, Mondala TS, Head SR, Horvath S, Gaber L, Thompson R, Whisenant T, Lin W, Langfelder P, Robison EH, Schaffer RL, Fisher JS, Friedewald J, Flechner SM, Chan LK, Wiseman AC, Shidban H, Mendez R, Heilman R, Abecassis MM, Marsh CL, Salomon DR. (2014) Molecular classifiers for acute kidney transplant rejection in peripheral blood by whole genome gene expression profiling. Am J Transplant. May;14(5):1164-72. doi: 10.1111/ajt.12671. Epub 2014 Apr 11.

Zilio N, Codlin S, Vashisht AA, Bitton DA, Head SR, Wohlschlegel JA, Bähler J, Boddy MN (2014) A novel histone deacetylase complex in the control of transcription and genome stability. Mol Cell Biol. Sep 15;34(18):3500-14. doi: 10.1128/MCB.00519-14. Epub 2014 Jul 7.

Lin N, Chang KY, Li Z, Gates K, Rana ZA, Dang J, Zhang D, Han T, Yang CS, Cunningham TJ, Head SR, Duester G, Si Dong PD, Rana TM. (2014) An Evolutionarily Conserved Long Noncoding RNA TUNA Controls Pluripotency and Neural Lineage Commitment. Mol Cell. 2014 Feb 11. pii: S1097-2765(14)00082-3. doi: 10.1016/j.molcel.2014.01.021

Head SR, Komori HK, Lamere SA, Whisenant T, Van Nieuwerburgh F, Salomon DR, Ordoukhanian P (2014). Library construction for next-generation sequencing: Overviews and challenges. Biotechniques. Feb 1;56(2):61-77.

Ruwona TB, McBride R, Chappel R, Head SR, Ordoukhanian P, Burton DR, Law M. Optimization of peptide arrays for studying antibodies to hepatitis C virus continuous epitopes (2014).  J Immunol Methods. Jan 15;402(1-2):35-42.

Bhargava V, Head SR, Ordoukhanian P, Mercola M, Subramaniam S (2014). Technical Variations in Low-Input RNA-seq Methodologies. Sci Rep. Jan 14;4:3678.

Li Z, Chao TC, Chang KY, Lin N, Patil VS, Shimizu C, Head SR, Burns JC, Rana TM (2014). The long noncoding RNA THRIL regulates TNF? expression through its interaction with hnRNPL. Proc Natl Acad Sci U S A. Jan 21;111(3):1002-7.

Krishnaswami SR, Kumar S, Ordoukhanian P, Yu BD (2014) Fate and Plasticity of the Epidermis in Response to Congenital Activation of BRAF. J Invest Dermatol. 2014 Sep 9. doi: 10.1038/jid.2014.388. [Epub ahead of print] PMID: 25202828

Helsmoortel C, Vandeweyer G, Ordoukhanian P, Van Nieuwerburgh F, Van der Aa N, Kooy RF. Challenges and opportunities in the investigation of unexplained intellectual disability using family based whole exome sequencing. Clin Genet. (2014) doi: 10.1111/cge.12470. PMID: 25081361

Dosanjh A, Robison E, Mondala T, Head SR, Salomon DR, Kurian SM, (2013). Genomic meta-analysis of growth factor and integrin pathways in chronic kidney transplant injury. BMC Genomics. Apr 23;14:275. doi: 10.1186/1471-2164-14-275.

Verma-Gaur J, Torkamani A, Schaffer L, Head SR, Schork NJ, Feeney AJ (2012). Noncoding transcription within the Igh distal V(H) region at PAIR elements affects the 3D structure of the Igh locus in pro-B cells. Proc Natl Acad Sci U S A. Oct 16;109(42):17004-9.

Routh A, Ordoukhanian P, Johnson JE (2012). Nucleotide-resolution profiling of RNA recombination in the encapsidated genome of a eukaryotic RNA virus by next-generation sequencing. J Mol Biol 424, 257-69. PMC 3502730

Van Nieuwerburgh F, Thompson RC, Ledesma J, Deforce D, Gaasterland T, Ordoukhanian P, Head SR. (2012) Illumina mate-paired DNA sequencing-library preparation using Cre-Lox recombination. Nucleic Acids Res. Feb 1;40(3):e24. Epub 2011 Nov 29.

Van Nieuwerburgh F, Soetaert S, Podshivalova K, Ay-Lin Wang E, Schaffer L, Deforce D, Salomon DR, Head SR, Ordoukhanian P (2011). Quantitative bias in Illumina TruSeq and a novel post amplification barcoding strategy for multiplexed DNA and small RNA deep sequencing. PLoS One.;6(10):e26969. Epub 2011 Oct 28.

Grigoryev YA, Kurian SM, Hart T, Nakorchevsky AA, Chen C, Campbell D, Head SR, Yates JR 3rd, Salomon DR. (2011). MicroRNA Regulation of Molecular Networks Mapped by Global MicroRNA, mRNA, and Protein Expression in Activated T Lymphocytes. J Immunol. Sep 1;187(5):2233-43. Epub Jul 25.

Chang LM, Maheshwari P, Werth S, Schaffer L, Head SR, Kovarik C, Werth VP (2011).Identification and molecular analysis of glycosaminoglycans in cutaneous lupus erythematosus and dermatomyositis. J Histochem Cytochem. Mar;59(3):336-45. Epub 2011 Jan 12.

Head SR, Komori HK, Hart GT, Shimashita J, Schaffer L, Salomon DR, Ordoukhanian PT (2011). Method for improved Illumina sequencing library preparation using NuGEN Ovation RNA-Seq System. Biotechniques. Mar;50(3):177-80.

Flaherty BL, Van Nieuwerburgh F, Head SR, Golden JW (2011). Directional RNA deep sequencing sheds new light on the transcriptional response of Anabaena sp. strain PCC 7120 to combined-nitrogen deprivation. BMC Genomics. Jun 28;12:332. PMC3141674

Komori HK, Lamere SA, Torkamani A, Hart GT, Kotsopoulos S, Warner J, Samuels ML, Olson J, Head SR, Ordoukhanian P, Lee PL, Link DR, Salomon DR (2011). Application of microdroplet PCR for large-scale targeted bisulfite sequencing. Genome Res. Aug 25. [Epub ahead of print].

Grigoryev YA, Kurian SM, Hart T, Nakorchevsky AA, Chen C, Campbell D, Head SR, Yates JR 3rd, Salomon DR. (2011). MicroRNA Regulation of Molecular Networks Mapped by Global MicroRNA, mRNA, and Protein Expression in Activated T Lymphocytes. J Immunol. Sep 1;187(5):2233-43. Epub Jul 25.

Tang B, Di Lena P, Schaffer L, Head SR, Baldi P, Thomas EA  (2011). Genome-wide identification of bcl11b gene targets reveals role in brain-derived neurotrophic factor signaling. PLoS One. 2011;6(9):e23691. Epub Sep 1.

Grigoryev YA, Kurian SM, Avnur Z, Borie D, Deng J, Campbell D, Sung J, Nikolcheva T, Quinn A, Schulman H, Peng SL, Schaffer R, Fisher J, Mondala T, Head S, Flechner SM, Kantor AB, Marsh C, Salomon DR (2010). Deconvoluting post-transplant immunity: cell subset-specific mapping reveals pathways for activation and expansion of memory T, monocytes and B cells. PLoS One. Oct 14;5(10):e13358.

Rozenzhak S, Mejía-Ramírez E, Williams JS, Schaffer L, Hammond JA, Head SR, Russell P (2010). Rad3 decorates critical chromosomal domains with gammaH2A to protect genome integrity during S-Phase in fission yeast. PLoS Genet. Jul 22;6(7):e1001032. 

Greenbaum JA, Assarsson E, Chung JL, Head S, Sette A, Peters B (2010). TiArA: a virtual appliance for the analysis of Tiling Array data. PLoS One. Apr 1;5(4):e9993.

Nakorchevsky A, Hewel JA, Kurian SM, Mondala TS, Campbell D, Head SR, Marsh CL, Yates JR 3rd, Salomon DR (2010). Molecular mechanisms of chronic kidney transplant rejection via large-scale proteogenomic analysis of tissue biopsies. J Am Soc Nephrol. Feb;21(2):362-73. Epub Jan 2

Moutaftsi M, Tscharke DC, Vaughan K, Koelle DM, Stern L, Calvo-Calle M, Ennis F, Terajima M, Sutter G, Crotty S, Drexler I, Franchini G, Yewdell JW, Head SR, Blum J, Peters B, Sette A (2010). Uncovering the interplay between CD8, CD4 and antibody responses to complex pathogens. Future Microbiol. Feb;5(2):221-39.

Robison EH, Mondala TS, Williams AR, Head SR, Salomon DR, Kurian SM (2009). Whole genome transcript profiling from fingerstick blood samples: a comparison and feasibility study. BMC Genomics. Dec 17;10:617.

Grigoryev YA, Kurian SM, Nakorchevskiy AA, Burke JP, Campbell D, Head SR, Deng J, Kantor AB, Yates JR 3rd, Salomon DR. (2009 ). Genome-wide analysis of immune activation in human T and B cells reveals distinct classes of alternatively spliced genes. PLoS One. Nov 19;4(11):e7906.

Montpetit ML, Stocker PJ, Schwetz TA, Harper JM, Norring SA, Schaffer L, North SJ, Jang-Lee J, Gilmartin T, Head SR, Haslam SM, Dell A, Marth JD, Bennett ES, (2009). Regulated and aberrant glycosylation modulate cardiac electrical signaling. Proc Natl Acad Sci U S A. Aug 7. [Epub ahead of print]

Kurian SM, Heilman R, Mondala TS, Nakorchevsky A, Hewel JA, Campbell D, Robison EH, Wang L, Lin W, Gaber L, Solez K, Shidban H, Mendez R, Schaffer RL, Fisher JS, Flechner SM, Head SR, Horvath S, Yates JR, Marsh CL, Salomon DR. (2009). Biomarkers for early and late stage chronic allograft nephropathy by proteogenomic profiling of peripheral blood. PLoS One. Jul 10;4(7):e6212.

Pebernard S, Schaffer L, Campbell D, Head SR, Boddy MN (2008). Localization of Smc5/6 to centromeres and telomeres requires heterochromatin and SUMO, respectively. EMBO J. 2008 Nov 19;27(22):3011-23. Epub 2008 Oct 16.

Xu CR, Schaffer L, Head SR, Feeney AJ. (2008) Reciprocal patterns of methylation of H3K36 and H3K27 on proximal vs. distal IgVH genes are modulated by IL-7 and Pax5. Proc Natl Acad Sci U S A. Jun 24;105(25):8685-90. Epub 2008 Jun 17.

Marcos NT, Magalhães A, Ferreira B, Oliveira MJ, Carvalho AS, Mendes N, Gilmartin T, Head SR, Figueiredo C, David L, Santos-Silva F, Reis CA. (2008) Helicobacter pylori induces beta3GnT5 in human gastric cell lines, modulating expression of the SabA ligand sialyl-Lewis x. J Clin Invest. Jun;118(6):2325-36. 

Benhnia MR, McCausland MM, Su HP, Singh K, Hoffmann J, Davies DH, Felgner PL, Head S, Sette A, Garboczi DN, Crotty S (2008). Redundancy and plasticity of neutralizing antibody responses are cornerstone attributes of the human immune response to the smallpox vaccine. J Virol. Apr;82(7):3751-68.

Assarsson E, Greenbaum JA, Sundström M, Schaffer L, Hammond JA, Pasquetto V, Oseroff C, Hendrickson RC, Lefkowitz EJ, Tscharke DC, Sidney J, Grey HM, Head SR, Peters B, Sette A. (2008). Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genes. Proc Natl Acad Sci U S A. Feb 12;105(6):2140-5.

Bax M, García-Vallejo JJ, Jang-Lee J, North SJ, Gilmartin TJ, Hernández G, Crocker PR, Leffler H, Head SR, Haslam SM, Dell A, van Kooyk Y (2007). Dendritic cell maturation results in pronounced changes in glycan expression affecting recognition by siglecs and galectins. J Immunol. Dec 15;179 (12):8216-24.

Desplats PA, Denny CA, Kass KE, Gilmartin T, Head SR, Sutcliffe JG, Seyfried TN, Thomas EA. (2007) Glycolipid and ganglioside metabolism imbalances in Huntington's disease. Neurobiol Dis. Sep;27 (3): 265-77

Kurian S, Grigoryev Y, Head S, Campbell D, Mondala T, Salomon DR. (2007) Applying genomics to organ transplantation medicine in both discovery and validation of biomarkers. Int Immunopharmacol. Dec 20;7(14):1948-60.

Sampathkumar SG, Jones MB, Meledeo MA, Campbell CT, Choi SS, Hida K, Gomutputra P, Sheh A, Gilmartin T, Head SR, Yarema KJ (2006). Targeting glycosylation pathways and the cell cycle: sugar-dependent activity of butyrate-carbohydrate cancer prodrugs. Chem Biol. Dec;13(12):1265-75.

Hammond JA, Head SR (2006). Expression profiling of glycosyltransferases and related enzymes using gene microarrays. Methods Enzymol.416:141-56.

Cirz RT, O'neill BM, Hammond JA, Head SR, Romesberg FE. (2006). Defining the Pseudomonas aeruginosa SOS Response and Its Role in the Global Response to the Antibiotic Ciprofloxacin. J Bacteriol. Oct;188(20):7101-10. 

Liang FS, Greenberg WA, Hammond JA, Hoffmann J, Head SR, Wong CH (2006). Evaluation of RNA-binding specificity of aminoglycosides with DNA microarrays. Proc Natl Acad Sci U S A. Aug 15;103(33):12311-6.

Comelli EM, Sutton-Smith M, Yan Q, Amado M, Panico M, Gilmartin T, Whisenant T, Lanigan CM, Head SR, Goldberg D, Morris H, Dell A, and James Paulson JC (2006). Activation of CD4+ and CD8+ T Lymphocytes Leads to Dramatic Remodeling of N-linked Glycans. Aug 15;177(4):2431-40 The Journal of Immunology.

Huang CY, Thayer DA, Chang AY, Best MD, Hoffmann J, Head S, Wong CH. (2006). Carbohydrate microarray for profiling the antibodies interacting with Globo H tumor antigen. Proc Natl Acad Sci U S A. Jan 3;103(1):15-20. Epub 2005 Dec 22.

Desplats PA, Kass KE, Gilmartin T, Stanwood GD, Woodward EL, Head SR, Sutcliffe JG, Thomas EA. (2006). Selective deficits in the expression of striatal-enriched mRNAs in Huntington's disease. J Neurochem. Feb;96(3):743-57

Kurian SM, Flechner SM, Kaouk J, Modlin C, Goldfarb D, Cook DJ, Head S, Salomon DR (2005). Laparoscopic donor nephrectomy gene expression profiling reveals upregulation of stress and ischemia associated genes compared to control kidneys. Transplantation. Oct 27;80(8):1067-71.

Blixt O, Head S, Mondala T, Scanlan C, Huflejt ME, Alvarez R, Bryan MC, Fazio F, Calarese D, Stevens J, Razi N, Stevens DJ, Skehel JJ, van Die I, Burton DR, Wilson IA, Cummings R, Bovin N, Wong C-H and Paulson JC (2004). Printed covalent glycan array for ligand profiling of diverse glycan binding proteins. Proc Natl Acad Sci U S A. Dec 7;101(49):17033-8.

Sieber SA, Mondala TS, Head SR, Cravatt BF (2004). A microarray platform for profiling enzyme activities in complex proteomes. J Am Chem Soc. Dec 8;126(48):15640-1.

Flechner SM, Kurian SM, Solez K, Cook DJ, Burke JT, Rollin H, Hammond JA, Whisenant T, Lanigan CM, Head SR, Salomon DR (2004). De novo kidney transplantation without use of calcineurin inhibitors preserves renal structure and function at two years. Am J Transplant. Nov;4(11):1776-85.

Kunicki TJ, Federici AB, Salomon DR, Koziol JA, Head SR, Mondala TS, Chismar JD, Baronciani L, Canciani MT, Peake IR. (2004). An association of candidate gene haplotypes and bleeding severity in Von Willebrand Disease (VWD) type 1 pedigrees. Blood. Oct 15;104(8):2359-67.

Flechner SM, Kurian SM, Head SR, Sharp SM, Whisenant TC, Zhang J, Horvath S, Mondala T, Gilmartin T, Cook DJ, Kay SA, Walker, JR, and Salomon DR (2004). Characterizing Acute Kidney Transplant Rejection by Gene Profiling of Biopsies and Peripheral Blood Lymphocytes. Am J Transplant. 2004 Sep;4(9):1475-89.

Chismar, J, Mondala, T, Fox, H, Roberts, E,  Langford, D,  Masliah, E, Salomon, DR ,and Head, SR. (2002) Analysis of result variability from high-density Affymetrix oligonucleotide arrays comparing same-species (human/human) and cross-species (human/monkey) hybridizations. Biotechniques.Sep;33(3):516-524.

Head SR, Parikh K, Rogers Y, Bishai W, Goelet P, Boyce-Jacino MT (1999).  Solid-phase sequence scanning for drug resistance detection in tuberculosis. Mol Cell Probes 13(2):81-87.

Head SR, Rogers Y-H, Parikh K, Lan G, Anderson S, Goelet P, & Boyce-Jacino, MT, (1997).  Nested Genetic Bit Analysis (N-GBA) for mutation detection in the human p53 gene.  Nucleic Acids Res 25 (24): 5065-5071