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Items: 21

1.

Whole genome sequencing and variant discovery in the ASPIRE autism spectrum disorder cohort.

Callaghan DB, Rogic S, Tan PPC, Calli K, Qiao Y, Baldwin R, Jacobson M, Belmadani M, Holmes N, Yu C, Li Y, Li Y, Kurtzke FE, Kuzeljevic B, Yu AY, Hudson M, Mcaughton AJM, Xu Y, Dionne-Laporte A, Girard S, Liang P, Separovic ER, Liu X, Rouleau G, Pavlidis P, Lewis MES.

Clin Genet. 2019 Sep;96(3):199-206. doi: 10.1111/cge.13556. Epub 2019 May 30.

PMID:
31038196
2.

Interactive Exploration, Analysis, and Visualization of Complex Phenome-Genome Datasets with ASPIREdb.

Tan PP, Rogic S, Zoubarev A, McDonald C, Lui F, Charathsandran G, Jacobson M, Belmadani M, Leong J, Van Rossum T, Portales-Casamar E, Qiao Y, Calli K, Liu X, Hudson M, Rajcan-Separovic E, Lewis MS, Pavlidis P.

Hum Mutat. 2016 Aug;37(8):719-26. doi: 10.1002/humu.23011. Epub 2016 May 20.

3.

Meta-Analysis of Gene Expression Patterns in Animal Models of Prenatal Alcohol Exposure Suggests Role for Protein Synthesis Inhibition and Chromatin Remodeling.

Rogic S, Wong A, Pavlidis P.

Alcohol Clin Exp Res. 2016 Apr;40(4):717-27. doi: 10.1111/acer.13007. Epub 2016 Mar 20.

4.

Transcriptome sequencing of the anterior cingulate in bipolar disorder: dysregulation of G protein-coupled receptors.

Cruceanu C, Tan PP, Rogic S, Lopez JP, Torres-Platas SG, Gigek CO, Alda M, Rouleau GA, Pavlidis P, Turecki G.

Am J Psychiatry. 2015 Nov 1;172(11):1131-40. doi: 10.1176/appi.ajp.2015.14101279. Epub 2015 Aug 4.

PMID:
26238605
5.

Meta-Analysis of Gene Expression in Autism Spectrum Disorder.

Ch'ng C, Kwok W, Rogic S, Pavlidis P.

Autism Res. 2015 Oct;8(5):593-608. doi: 10.1002/aur.1475. Epub 2015 Feb 26.

6.

An RCOR1 loss-associated gene expression signature identifies a prognostically significant DLBCL subgroup.

Chan FC, Telenius A, Healy S, Ben-Neriah S, Mottok A, Lim R, Drake M, Hu S, Ding J, Ha G, Scott DW, Kridel R, Bashashati A, Rogic S, Johnson N, Morin RD, Rimsza LM, Sehn L, Connors JM, Marra MA, Gascoyne RD, Shah SP, Steidl C.

Blood. 2015 Feb 5;125(6):959-66. doi: 10.1182/blood-2013-06-507152. Epub 2014 Nov 13.

7.

Recurrent somatic mutations of PTPN1 in primary mediastinal B cell lymphoma and Hodgkin lymphoma.

Gunawardana J, Chan FC, Telenius A, Woolcock B, Kridel R, Tan KL, Ben-Neriah S, Mottok A, Lim RS, Boyle M, Rogic S, Rimsza LM, Guiter C, Leroy K, Gaulard P, Haioun C, Marra MA, Savage KJ, Connors JM, Shah SP, Gascoyne RD, Steidl C.

Nat Genet. 2014 Apr;46(4):329-35. doi: 10.1038/ng.2900. Epub 2014 Feb 16.

PMID:
24531327
8.

Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing.

Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA.

Blood. 2013 Aug 15;122(7):1256-65. doi: 10.1182/blood-2013-02-483727. Epub 2013 May 22.

9.

The E3 ubiquitin ligase UBR5 is recurrently mutated in mantle cell lymphoma.

Meissner B, Kridel R, Lim RS, Rogic S, Tse K, Scott DW, Moore R, Mungall AJ, Marra MA, Connors JM, Steidl C, Gascoyne RD.

Blood. 2013 Apr 18;121(16):3161-4. doi: 10.1182/blood-2013-01-478834. Epub 2013 Feb 13.

10.

Gene expression-based model using formalin-fixed paraffin-embedded biopsies predicts overall survival in advanced-stage classical Hodgkin lymphoma.

Scott DW, Chan FC, Hong F, Rogic S, Tan KL, Meissner B, Ben-Neriah S, Boyle M, Kridel R, Telenius A, Woolcock BW, Farinha P, Fisher RI, Rimsza LM, Bartlett NL, Cheson BD, Shepherd LE, Advani RH, Connors JM, Kahl BS, Gordon LI, Horning SJ, Steidl C, Gascoyne RD.

J Clin Oncol. 2013 Feb 20;31(6):692-700. doi: 10.1200/JCO.2012.43.4589. Epub 2012 Nov 26.

11.

Concurrent expression of MYC and BCL2 in diffuse large B-cell lymphoma treated with rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone.

Johnson NA, Slack GW, Savage KJ, Connors JM, Ben-Neriah S, Rogic S, Scott DW, Tan KL, Steidl C, Sehn LH, Chan WC, Iqbal J, Meyer PN, Lenz G, Wright G, Rimsza LM, Valentino C, Brunhoeber P, Grogan TM, Braziel RM, Cook JR, Tubbs RR, Weisenburger DD, Campo E, Rosenwald A, Ott G, Delabie J, Holcroft C, Jaffe ES, Staudt LM, Gascoyne RD.

J Clin Oncol. 2012 Oct 1;30(28):3452-9. Epub 2012 Jul 30.

12.

TBL1XR1/TP63: a novel recurrent gene fusion in B-cell non-Hodgkin lymphoma.

Scott DW, Mungall KL, Ben-Neriah S, Rogic S, Morin RD, Slack GW, Tan KL, Chan FC, Lim RS, Connors JM, Marra MA, Mungall AJ, Steidl C, Gascoyne RD.

Blood. 2012 May 24;119(21):4949-52. doi: 10.1182/blood-2012-02-414441. Epub 2012 Apr 11.

13.

Whole transcriptome sequencing reveals recurrent NOTCH1 mutations in mantle cell lymphoma.

Kridel R, Meissner B, Rogic S, Boyle M, Telenius A, Woolcock B, Gunawardana J, Jenkins C, Cochrane C, Ben-Neriah S, Tan K, Morin RD, Opat S, Sehn LH, Connors JM, Marra MA, Weng AP, Steidl C, Gascoyne RD.

Blood. 2012 Mar 1;119(9):1963-71. doi: 10.1182/blood-2011-11-391474. Epub 2011 Dec 30.

14.

SNP analysis of minimally evolved t(14;18)(q32;q21)-positive follicular lymphomas reveals a common copy-neutral loss of heterozygosity pattern.

Cheung KJ, Rogic S, Ben-Neriah S, Boyle M, Connors JM, Gascoyne RD, Horsman DE.

Cytogenet Genome Res. 2012;136(1):38-43. doi: 10.1159/000334265. Epub 2011 Nov 18.

PMID:
22104078
15.

Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma.

Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJ, Connors JM, Hirst M, Gascoyne RD, Marra MA.

Nature. 2011 Jul 27;476(7360):298-303. doi: 10.1038/nature10351.

16.

Meta-analysis of kindling-induced gene expression changes in the rat hippocampus.

Rogic S, Pavlidis P.

Front Neurosci. 2009 Sep 15;3:53. doi: 10.3389/neuro.15.001.2009. eCollection 2009.

17.

Correlation between the secondary structure of pre-mRNA introns and the efficiency of splicing in Saccharomyces cerevisiae.

Rogic S, Montpetit B, Hoos HH, Mackworth AK, Ouellette BF, Hieter P.

BMC Genomics. 2008 Jul 29;9:355. doi: 10.1186/1471-2164-9-355.

18.

GeneComber: combining outputs of gene prediction programs for improved results.

Shah SP, McVicker GP, Mackworth AK, Rogic S, Ouellette BF.

Bioinformatics. 2003 Jul 1;19(10):1296-7.

PMID:
12835277
19.

Improving gene recognition accuracy by combining predictions from two gene-finding programs.

Rogic S, Ouellette BF, Mackworth AK.

Bioinformatics. 2002 Aug;18(8):1034-45.

PMID:
12176826
20.

Evaluation of gene-finding programs on mammalian sequences.

Rogic S, Mackworth AK, Ouellette FB.

Genome Res. 2001 May;11(5):817-32.

21.

A physical map of the human genome.

McPherson JD, Marra M, Hillier L, Waterston RH, Chinwalla A, Wallis J, Sekhon M, Wylie K, Mardis ER, Wilson RK, Fulton R, Kucaba TA, Wagner-McPherson C, Barbazuk WB, Gregory SG, Humphray SJ, French L, Evans RS, Bethel G, Whittaker A, Holden JL, McCann OT, Dunham A, Soderlund C, Scott CE, Bentley DR, Schuler G, Chen HC, Jang W, Green ED, Idol JR, Maduro VV, Montgomery KT, Lee E, Miller A, Emerling S, Kucherlapati, Gibbs R, Scherer S, Gorrell JH, Sodergren E, Clerc-Blankenburg K, Tabor P, Naylor S, Garcia D, de Jong PJ, Catanese JJ, Nowak N, Osoegawa K, Qin S, Rowen L, Madan A, Dors M, Hood L, Trask B, Friedman C, Massa H, Cheung VG, Kirsch IR, Reid T, Yonescu R, Weissenbach J, Bruls T, Heilig R, Branscomb E, Olsen A, Doggett N, Cheng JF, Hawkins T, Myers RM, Shang J, Ramirez L, Schmutz J, Velasquez O, Dixon K, Stone NE, Cox DR, Haussler D, Kent WJ, Furey T, Rogic S, Kennedy S, Jones S, Rosenthal A, Wen G, Schilhabel M, Gloeckner G, Nyakatura G, Siebert R, Schlegelberger B, Korenberg J, Chen XN, Fujiyama A, Hattori M, Toyoda A, Yada T, Park HS, Sakaki Y, Shimizu N, Asakawa S, Kawasaki K, Sasaki T, Shintani A, Shimizu A, Shibuya K, Kudoh J, Minoshima S, Ramser J, Seranski P, Hoff C, Poustka A, Reinhardt R, Lehrach H; International Human Genome Mapping Consortium.

Nature. 2001 Feb 15;409(6822):934-41.

PMID:
11237014

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