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Publications 2013

Clinical characteristics in patients with interstitial deletions of chromosome region 12q21-q22 and identification of a critical region associated with keratosis pilaris.
Al-Maawali A1, Marshall CR, Scherer SW, Dupuis L, Mendoza-Londono R, Stavropoulos DJ. Am J Med Genet A. 2014 Mar;164(3):796-800. doi: 10.1002/ajmg.a.36356. Epub 2013 Dec 20.

Nuclear localization of the transcriptional regulator MIER1a requires interaction with HDAC1/2 in breast cancer cells.
Li S and Paterno GD. PLoS One 2013 8: e84046

Polyploidy in myelofibrosis: analysis by cytogenetic and SNP array indicates association with advancing disease.
Singh NR1, Morris CM, Koleth M, Wong K, Ward CM, Stevenson WS. Mol Cytogenet 2013 6: 59

Defining the vulnerable period for reestablishment of Clostridium difficile colonization after treatment of C. difficile infection with oral vancomycin or metronidazole.
Abujamel T1, Cadnum JL, Jury LA, Sunkesula VC, Kundrapu S, Jump RL, Stintzi AC, Donskey CJ. PLoS One. 2013 8: e76269

Exploring high dimensional data with Butterfly: a novel classification algorithm based on discrete dynamical systems.
Geraci J1, Dharsee M, Nuin P, Haslehurst A, Koti M, Feilotter HE, Evans K. Bioinformatics 2014 Mar 1;30(5):712-8. doi: 10.1093/bioinformatics/btt602. Epub 2013 Oct 21.

Glucose transporter expression in an avian nectarivore: the rubythroated hummingbird (Archilochus colubris).
Welch KC Jr1, Allalou A, Sehgal P, Cheng J, Ashok A. PLoS One. 2013 8: e77003

Elastin binding protein and FKBP65 modulate in vitro self-assembly of human tropoelastin.
Miao M, Reichheld SE, Muiznieks LD, Huang Y, Keeley FW. Biochemistry 2013 52: 7731-41

miRNA-95 mediates radioresistance in tumors by targeting the sphingolipid phosphatise SGPP1.
Huang X1, Taeb S, Jahangiri S, Emmenegger U, Tran E, Bruce J, Mesci A, Korpela E, Vesprini D, Wong CS, Bristow RG, Liu FF, Liu SK. Cancer Res. 2013 73: 6972-86

Effect of glycogen synthase kinase-3 inactivation on mouse mammary gland development and oncogenesis.
Dembowy J, et al. bioRxiv. 2013 (Sanger sequencing and TCAG's Tara Paton)

Spindle cell oncocytomas and granular cell tumors of the pituitary are variants of pituicytoma.
Mete O and Lopes MB. Am J Surg Pathol. 2013 37: 1694-9

Fatal combined immunodeficiency associated with heterozygous mutation in STAT1.
Sharfe N, Nahum A, Newel A, Dadi H, Ngan B, Pereira SL, Herbrick JA, Roifman CM. J Allergy Clin Immunol. 2014 Mar;133(3):807-17. doi: 10.1016/j.jaci.2013.09.032. Epub 2013 Nov 13.

Genome-wide association study of subtype-specific epithelial ovarian cancer risk alleles using pooled DNA.
Earp MA, et al. Hum Genet. 2013 Nov 5. [Epub ahead of print] Abstract and full author's list

Association between early-onset Parkinson disease and 22q11.2 deletion syndrome: identification of a novel genetic form of Parkinson disease and its clinical implications.
Butcher NJ1, Kiehl TR, Hazrati LN, Chow EW, Rogaeva E, Lang AE, Bassett AS. JAMA Neurol. 2013 70: 1359-66 (qPCR)

Identification of three new Alu Yb subfamilies by source tracking of recently integrated Alu Yb elements.
Ahmed M and Li W. Mob DNA 2013 4: 25

Identification of the IGF1/PI3K/NF kB/ERK gene signalling networks associated with chemotherapy resistance and treatment response in high-grade serous epithelial ovarian cancer.
Koti M, Gooding RJ, Nuin P, Haslehurst A, Crane C, Weberpals J, Childs T, Bryson P, Dharsee M, Evans K, Feilotter HE, Park PC, Squire JA. BMC Cancer. 2013 13: 549

Recessive mutations in SLC38A8 cause foveal hypoplasia and optic nerve misrouting without albinism.
Poulter JA, Al-Araimi M, Conte I, van Genderen MM, Sheridan E, Carr IM, Parry DA, Shires M, Carrella S, Bradbury J, Khan K, Lakeman P, Sergouniotis PI, Webster AR, Moore AT, Pal B, Mohamed MD, Venkataramana A, Ramprasad V, Shetty R, Saktivel M, Kumaramanickavel G, Tan A, Mackey DA, Hewitt AW, Banfi S, Ali M, Inglehearn CF, Toomes C. Am J Hum Genet. 2013 93: 1143-50

Expression, purification, crystallization and preliminary X-ray analysis of the receiver domain of Staphylococcus aureus LytR protein.
Shala A, Patel KH, Golemi-Kotra D, Audette GF. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 69: 1418-21

Defining the vulnerable period for reestablishment of Clostridium difficile colonization after treatment of C. difficile infection with oral vancomycin or metronidazole.
Abujamel T, Cadnum JL, Jury LA, Sunkesula VC, Kundrapu S, Jump RL, Stintzi AC, Donskey CJ. PLoS One. 2013 8: e76269

Exploring high dimensional data with Butterfly: a novel classification algorithm based on discrete dynamical systems.
Geraci J1, Dharsee M, Nuin P, Haslehurst A, Koti M, Feilotter HE, Evans K. Bioinformatics. 2014 Mar 1;30(5):712-8. doi: 10.1093/bioinformatics/btt602. Epub 2013 Oct 21.

Glucose transporter expression in an avian nectarivore: the rubythroated hummingbird (Archilochus colubris).
Welch KC Jr, Allalou A, Sehgal P, Cheng J, Ashok A. PLoS One. 2013 8: e77003

Elastin binding protein and FKBP65 modulate in vitro self-assembly of human tropoelastin.
Miao M1, Reichheld SE, Muiznieks LD, Huang Y, Keeley FW. Biochemistry 2013 52: 7731-41

miRNA-95 mediates radioresistance in tumors by targeting the sphingolipid phosphatise SGPP1.
Huang X, Taeb S, Jahangiri S, Emmenegger U, Tran E, Bruce J, Mesci A, Korpela E, Vesprini D, Wong CS, Bristow RG, Liu FF, Liu SK. Cancer Res. 2013 73: 6972-86

Analysis of histomorphology in malignant hyperthermia-susceptible patients.
Orlov D, Keith J, Rosen D, Croul S, Kraeva N, Riazi S. Can J Anaesth. 2013 Oct;60(10):982-9.
PMID: 23888335

A genome-wide association study for malignant mesothelioma risk.
Cadby G, Mukherjee S, Musk AW, Reid A, Garlepp M, Dick I, Robinson C, Hui J, Fiorito G, Guarrera S, Beilby J, Melton PE, Moses EK, Ugolini D, Mirabelli D, Bonassi S, Magnani C, Dianzani I, Matullo G, Robinson B, Creaney J, Palmer LJ. Lung Cancer. 2013 Oct;82(1):1-8.
PMID: 23827383

The rad1 gene in Rainbow Trout (Oncorhynchus mykiss) is highly conserved and may express proteins from non-canonical spliced isoforms. Bozdarov J, Sherry JP, Duncker BP, Bols NC, Dixon B. Comp Biochem Physiol C Toxicol Pharmacol. 2013 157: 16-23

Hypoxic activation of the PERK/eIF2a arm of the unfolded protein response promotes metastasis through induction of LAMP3., Mujcic H, Nagelkerke A, Rouschop KM, Chung S, Chaudary N, Span PN, Clarke B, Milosevic M, Sykes J, Hill RP, Koritzinsky M, Wouters BG. Clin Cancer Res. 2013 19: 6126-37

The rad1 gene in Rainbow Trout (Oncorhynchus mykiss) is highly conserved and may express proteins from non-canonical spliced isoforms. Bozdarov J, Sherry JP, Duncker BP, Bols NC, Dixon B. Comp Biochem Physiol C Toxicol Pharmacol. 2013 157: 16-23

Detecting Alu insertions from high-throughput sequencing data.
David M, Mustafa H, Brudno M. Nucleic Acids Res. 2013 Sep;41(17):e169.
PMID: 23921633

Differentially methylated loci distinguish ovarian carcinoma histological types: evaluation of a DNA methylation assay in FFPE tissue.
Kelemen LE, Köbel M, Chan A, Taghaddos S, Dinu I. Biomed Res Int. 2013;2013:815894.
PMID: 24175302

Non-hodgkin lymphoma risk and variants in genes controlling lymphocyte development.
Schuetz JM, Daley D, Leach S, Conde L, Berry BR, Gallagher RP, Connors JM, Gascoyne RD, Bracci PM, Skibola CF, Spinelli JJ, Brooks-Wilson AR. PLoS One. 2013 Sep 30;8(9):e75170.
PMID: 24098683

A suppressor screen in Mecp2 mutant mice implicates cholesterol metabolism in Rett syndrome.
Buchovecky CM, Turley SD, Brown HM, Kyle SM, McDonald JG, Liu B, Pieper AA, Huang W, Katz DM, Russell DW, Shendure J, Justice MJ. Nat Genet. 2013 Sep;45(9):1013-20.
PMID: 23892605

Enu mutagenesis identifies a novel platelet phenotype in a loss-of-function jak2 allele.
Anderson NM, Javadi M, Berndl E, Berberovic Z, Bailey ML, Huang K, Flenniken AM, Osborne LR, Adamson SL, Rossant J, Carter-Su C, Wang C, McNagny KM, Paulson RF, Minden MD, Stanford WL, Barber DL. PLoS One. 2013 Sep 25;8(9):e75472.
PMID: 24086539

FOXP1 mutations cause intellectual disability and a recognizable phenotype.
Le Fevre AK, Taylor S, Malek NH, Horn D, Carr CW, Abdul-Rahman OA, O'Donnell S, Burgess T, Shaw M, Gecz J, Bain N, Fagan K, Hunter MF. Am J Med Genet A. 2013 Sep 24. [Epub ahead of print]
PMID: 24214399

Common variation contributes to the genetic architecture of social communication traits.
St Pourcain B, Whitehouse AJ, Ang WQ, Warrington NM, Glessner JT, Wang K, Timpson NJ, Evans DM, Kemp JP, Ring SM, McArdle WL, Golding J, Hakonarson H, Pennell CE, Smith GD. Mol Autism. 2013 Sep 18;4(1):34.
PMID: 24047820

Sex-and subtype-specific analysis of H2AFX polymorphisms in non-Hodgkin lymphoma.
Bretherick KL, Schuetz JM, Morton LM, Purdue MP, Conde L, Gallagher RP, Connors JM, Gascoyne RD, Berry BR, Armstrong B, Kricker A, Vajdic CM, Grulich A, Hjalgrim H, Smedby KE, Skibola CF, Rothman N, Spinelli JJ, Brooks-Wilson AR. PLoS One. 2013 Sep 17;8(9):e74619.
PMID: 24069324

Identification, expression, and taxonomic distribution of alternative oxidases in non-angiosperm plants.
Neimanis K, Staples JF, Hüner NP, McDonald AE. Gene. 2013 Sep 10;526(2):275-86.
PMID: 23664893

Interstitial deletions at 6q14.1q15 associated with developmental delay and a marfanoid phenotype.
Lowry RB, Chernos JE, Connelly MS, Wyse JP. Mol Syndromol. 2013 Sep;4(6):280-4.
PMID: 24167463

A comparison of the molecular organization of genomic regions associated with resistance to common bacterial blight in two Phaseolus vulgaris genotypes.
Perry G, Dinatale C, Xie W, Navabi A, Reinprecht Y, Crosby W, Yu K, Shi C, Pauls KP. Front Plant Sci. 2013 Aug 29;4:318.
PMID: 24009615

Genome-wide gene expression profiling of stress response in a spinal cord clip compression injury model.
Chamankhah M, Eftekharpour E, Karimi-Abdolrezaee S, Boutros PC, San-Marina S, Fehlings MG. BMC Genomics. 2013 Aug 28;14(1):583.
PMID: 23984903

Deletion of the Phytophthora sojae avirulence gene Avr1d causes gain of virulence on Rps1d.
Na R, Yu D, Qutob D, Zhao J, Gijzen M. Mol Plant Microbe Interact. 2013 Aug;26(8):969-76.
PMID: 23550527

Hemochromatosis enhances tumor progression via upregulation of intracellular iron in head and neck cancer.
Lenarduzzi M, Hui AB, Yue S, Ito E, Shi W, Williams J, Bruce J, Sakemura-Nakatsugawa N, Xu W, Schimmer A, Liu FF. PLoS One. 2013 Aug 26;8(8):e74075.
PMID: 23991213

Analysis of PAC1 receptor gene variants in Caucasian and African-American infants dying of sudden infant death syndrome.
Barrett KT, Rodikova E, Weese-Mayer DE, Rand CM, Marazita ML, Cooper ME, Berry-Kravis EM, Bech-Hansen NT, Wilson RJ. Acta Paediatr. 2013 Aug 26. [Epub ahead of print]

A Forward genetic screen in mice identifies mutants with abnormal cortical patterning.
Ha S, Stottmann RW, Furley AJ, Beier DR. Cereb Cortex. 2013 Aug22. [Epub ahead of print]
PMID: 23968836

Kinetics and epigenetics of retroviral silencing in mouse embryonic stem cells defined by deletion of the D4Z4 element.
Rival-Gervier S, Lo MY, Khattak S, Pasceri P, Lorincz MC, Ellis J. Mol Ther. 2013 Aug;21(8):1536-50.
PMID: 23752310

A mutation in the serine protease TMPRSS4 in a novel pediatric neurodegenerative disorder.
Lahiry P, Racacho L, Wang J, Robinson J, Gloor GB, Rupar CA, Siu VM, Bulman DE, Hegele RA. Orphanet J Rare Dis. 2013 Aug 17;8(1):126.
PMID: 23957953

UGT2B17 copy number gain in a large ankylosing spondylitis multiplex family.
Uddin M, Maksymowych WP, Inman R, Gladman D, Munn A, Yazdani R, Pellett F, Hamilton S, O'Rielly DD, Rahman P. BMC Genet. 2013 Aug 8;14:67.
PMID: 23927372

Reprever: resolving low-copy duplicated sequences using template driven assembly.
Kim S, Medvedev P, Paton TA, Bafna V. Nucleic Acids Res. 2013 Jul;41(12):e128.
PMID: 23658221

Engineering lentiviral vectors for modulation of dendritic cell apoptotic pathways.
Wang JC, Felizardo TC, Au BC, Fowler DH, Dekaban GA, Medin JA. Virol J. 2013 Jul 20;10:240.
PMID: 23870437

A synonymous change, p.Gly16Gly in MECP2 Exon 1, causes a cryptic splice event in a Rett syndrome patient.
Sheikh TI, Mittal K, Willis MJ, Vincent JB. Orphanet J Rare Dis. 2013 Jul 19;8:108.
PMID: 23866855

ENU-induced mutation in the DNA-binding domain of KLF3 reveals important roles for KLF3 in cardiovascular development and function in mice.
Kelsey L, Flenniken AM, Qu D, Funnell AP, Pearson R, Zhou YQ, Voronina I, Berberovic Z, Wood G, Newbigging S, Weiss ES, Wong M, Quach I, Yeh SY, Deshwar AR, Scott IC, McKerlie C, Henkelman M, Backx P, Simpson J, Osborne L, Rossant J, Crossley M, Bruneau B, Adamson SL. PLoS Genet. 2013 Jul;9(7):e1003612.
PMID: 23874215

Persistence of the oral probiotic Streptococcus salivarius M18 is dose dependent and megaplasmid transfer can augment their bacteriocin production and adhesion characteristics.
Burton JP, Wescombe PA, Macklaim JM, Chai MH, Macdonald K, Hale JD, Tagg J, Reid G, Gloor GB, Cadieux PA. PLoS One. 2013 Jun 13;8(6):e65991.
PMID: 23785463

MicroRNAs and their putative targets in Brassica napus seed maturation.
Huang D, Koh C, Feurtado JA, Tsang EW, Cutler AJ. BMC Genomics. 2013 Feb 28;14:140.
PMID: 23448243

Defining the functional potential and active community members of a sediment microbial community in a high-arctic hypersaline subzero spring.
Lay CY, Mykytczuk NC, Yergeau É, Lamarche-Gagnon G, Greer CW, Whyte LG. Appl Environ Microbiol. 2013 Jun;79(12):3637-48.
PMID: 23563939

Association between a multi-locus genetic risk score and inflammatory bowel disease.
Hu P, Muise AM, Xing X, Brumell JH, Silverberg MS, Xu W. Bioinform Biol Insights. 2013 May 19;7:143-52.
PMID: 23761965

Oral neutrophil transcriptome changes result in a pro-survival phenotype in periodontal diseases.
Lakschevitz FS, Aboodi GM, Glogauer M. PLoS One. 2013 Jul 11;8(7):e68983.
PMID: 23874838

Intellectual disability associated with a homozygous missense mutation in THOC6.
Beaulieu CL, Huang L, Innes AM, Akimenko MA, Puffenberger EG, Schwartz C, Jerry P, Ober C, Hegele RA, McLeod DR, Schwartzentruber J, Majewski J, Bulman DE, Parboosingh JS, Boycott KM. Orphanet J Rare Dis. 2013 Apr 26;8(1):62.
PMID: 23621916

Eukaryotic translation elongation factor 1-Alpha 1 inhibits p53 and p73 dependent apoptosis and chemotherapy sensitivity.
Blanch A, Robinson F, Watson IR, Cheng LS, Irwin MS. PLoS One. 2013 Jun 14;8(6):e66436.
PMID: 23799104

Identifying gene locus associations with promyelocytic leukemia nuclear bodies using immuno-TRAP.
Ching RW, Ahmed K, Boutros PC, Penn LZ, Bazett-Jones DP. J Cell Biol. 2013 Apr 15;201(2):325-35.
PMID: 23589495

Mutations in SCO2 are associated with autosomal-dominant high-grade myopia.
Tran-Viet KN, Powell C, Barathi VA, Klemm T, Maurer-Stroh S, Limviphuvadh V, Soler V, Ho C, Yanovitch T, Schneider G, Li YJ, Nading E, Metlapally R, Saw SM, Goh L, Rozen S, Young TL. Am J Hum Genet. 2013 May 2;92(5):820-6.
PMID: 23643385

MicroRNA-196b regulates the homeobox B7-vascular endothelial growth factor axis in cervical cancer.
How C, Hui AB, Alajez NM, Shi W, Boutros PC, Clarke BA, Yan R, Pintilie M, Fyles A, Hedley DW, Hill RP, Milosevic M, Liu FF. PLoS One. 2013 Jul 4;8(7):e67846.
PMID: 23861821

The Idd13 congenic interval defines the number of merocytic dendritic cells, a novel trait associated with autoimmune diabetes susceptibility.
Pelletier AN, Lesage S. J Autoimmun. 2013 Jun;43:70-7.
PMID: 23623717

γδ T cells are essential effectors of type 1 diabetes in the nonobese diabetic mouse model.
Markle JG, Mortin-Toth S, Wong AS, Geng L, Hayday A, Danska JS. J Immunol. 2013 Jun 1;190(11):5392-401.
PMID: 23626013

The molecular characterization of the kinin transcript and the physiological effects of kinins in the blood-gorging insect, Rhodnius prolixus.
Bhatt G, da Silva R, Nachman RJ, Orchard I. Peptides. 2013 Apr 26. doi:pii: S0196-9781(13)00152-6. 10.1016/j.peptides.2013.04.009.
PMID: 23624318

Characterization of a cruciferin deficient mutant of Arabidopsis and its utility for overexpression of foreign proteins in plants.
Lin Y, Pajak A, Marsolais F, McCourt P, Riggs CD. PLoS One. 2013 May 27;8(5):e64980.
PMID: 23724110

The cytokine ciliary neurotrophic factor (CNTF) activates hypothalamic urocortin-expressing neurons both in vitro and in vivo.
Purser MJ, Dalvi PS, Wang ZC, Belsham DD. PLoS One. 2013 Apr 23;8(4):e61616.
PMID: 23626705

PilMNOPQ from the Pseudomonas aeruginosa type IV pilus system form a transenvelope protein interaction network that interacts with PilA.
Tammam S, Sampaleanu LM, Koo J, Manoharan K, Daubaras M, Burrows LL, Howell PL. J Bacteriol. 2013 May;195(10):2126-35.
PMID: 23457250

Fibroblast growth factor receptor like-1 (FGFRL1) interacts with SHP-1 phosphatase at insulin secretory granules and induces beta-cell ERK1/2 protein activation.
Silva PN, Altamentova SM, Kilkenny DM, Rocheleau JV. J Biol Chem. 2013 Jun 14;288(24):17859-70.
PMID: 23640895

Interrogation of the platelet-derived growth factor receptor alpha locus and corneal astigmatism in Australians of Northern European ancestry: results of a genome-wide association study.
Yazar S, Mishra A, Ang W, Kearns LS, Mountain JA, Pennell C, Montgomery GW, Young TL, Hammond CJ, Macgregor S, Mackey DA, Hewitt AW. Mol Vis. 2013 Jun 6;19:1238-46.
PMID: 23761726

Raine eye health study: design, methodology and baseline prevalence of ophthalmic disease in a birth-cohort study of young adults.
Yazar S, Forward H, McKnight CM, Tan A, Soloshenko A, Oates SK, Ang W, Sherwin JC, Wood D, Mountain JA, Pennell CE, Hewitt AW, Mackey DA. Ophthalmic Genet. 2013 Jan 10.
PMID: 23301674

Genetic analyses of a three generation family segregating Hirschsprung disease and iris heterochromia.
Cui L, Wong EH, Cheng G, Firmato de Almeida M, So MT, Sham PC, Cherny SS, Tam PK, Garcia-Barceló MM. PLoS One. 2013 Jun 26;8(6):e66631.
PMID: 23840513

Causal relationship between adiponectin and metabolic traits: a Mendelian randomization study in a multiethnic population.
Mente A, Meyre D, Lanktree MB, Heydarpour M, Davis AD, Miller R, Gerstein H, Hegele RA, Yusuf S, Anand SS; SHARE and SHARE-AP Investigators. PLoS One. 2013 Jun 24;8(6):e66808.
PMID: 23826141

Changes in gene expression induced by aromatic amine drugs: testing the danger hypothesis.
Ng W, Uetrecht J. J Immunotoxicol. 2013 Apr-Jun;10(2):178-91.
PMID: 22970684

Quorum-sensing regulation of a capsular polysaccharide receptor for the Rhodobacter capsulatus gene transfer agent (RcGTA).
Brimacombe CA, Stevens A, Jun D, Mercer R, Lang AS, Beatty JT. Mol Microbiol. 2013 Feb;87(4):802-17.
PMID: 23279213