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Items: 1 to 50 of 268

1.

Evaluating stably expressed genes in single cells.

Lin Y, Ghazanfar S, Strbenac D, Wang A, Patrick E, Lin DM, Speed T, Yang JYH, Yang P.

Gigascience. 2019 Sep 1;8(9). pii: giz106. doi: 10.1093/gigascience/giz106.

2.

DECENT: Differential Expression with Capture Efficiency adjustmeNT for single-cell RNA-seq data.

Ye C, Speed TP, Salim A.

Bioinformatics. 2019 Jun 14. pii: btz453. doi: 10.1093/bioinformatics/btz453. [Epub ahead of print]

PMID:
31197307
3.

Addressing the Opioid Crisis One Surgical Patient at a Time: Outcomes of a Novel Perioperative Pain Program.

Shechter R, Speed TJ, Blume E, Singh S, Williams K, Koch CG, Hanna MN.

Am J Med Qual. 2019 May 25:1062860619851170. doi: 10.1177/1062860619851170. [Epub ahead of print]

PMID:
31129979
4.

A new normalization for Nanostring nCounter gene expression data.

Molania R, Gagnon-Bartsch JA, Dobrovic A, Speed TP.

Nucleic Acids Res. 2019 Jul 9;47(12):6073-6083. doi: 10.1093/nar/gkz433.

5.

scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets.

Lin Y, Ghazanfar S, Wang KYX, Gagnon-Bartsch JA, Lo KK, Su X, Han ZG, Ormerod JT, Speed TP, Yang P, Yang JYH.

Proc Natl Acad Sci U S A. 2019 May 14;116(20):9775-9784. doi: 10.1073/pnas.1820006116. Epub 2019 Apr 26.

PMID:
31028141
6.

Using long-read sequencing to detect imprinted DNA methylation.

Gigante S, Gouil Q, Lucattini A, Keniry A, Beck T, Tinning M, Gordon L, Woodruff C, Speed TP, Blewitt ME, Ritchie ME.

Nucleic Acids Res. 2019 May 7;47(8):e46. doi: 10.1093/nar/gkz107.

7.

Maps of variability in cell lineage trees.

Hicks DG, Speed TP, Yassin M, Russell SM.

PLoS Comput Biol. 2019 Feb 12;15(2):e1006745. doi: 10.1371/journal.pcbi.1006745. eCollection 2019 Feb.

8.

Dysregulated IL-1β-GM-CSF Axis in Acute Rheumatic Fever That Is Limited by Hydroxychloroquine.

Kim ML, Martin WJ, Minigo G, Keeble JL, Garnham AL, Pacini G, Smyth GK, Speed TP, Carapetis J, Wicks IP.

Circulation. 2018 Dec 4;138(23):2648-2661. doi: 10.1161/CIRCULATIONAHA.118.033891.

PMID:
30571257
9.

Double jeopardy: a review of weight gain and weight management strategies for psychotropic medication prescribing during methadone maintenance treatment.

Schlienz NJ, Huhn AS, Speed TJ, Sweeney MM, Antoine DG.

Int Rev Psychiatry. 2018 Oct;30(5):147-154. doi: 10.1080/09540261.2018.1509843. Epub 2018 Nov 6. Review.

10.

Comorbid chronic pain and opioid use disorder: literature review and potential treatment innovations.

Speed TJ, Parekh V, Coe W, Antoine D.

Int Rev Psychiatry. 2018 Oct;30(5):136-146. doi: 10.1080/09540261.2018.1514369. Epub 2018 Nov 6. Review.

PMID:
30398071
11.

Sex differences in measures of central sensitization and pain sensitivity to experimental sleep disruption: implications for sex differences in chronic pain.

Smith MT Jr, Remeniuk B, Finan PH, Speed TJ, Tompkins DA, Robinson M, Gonzalez K, Bjurstrom MF, Irwin MR.

Sleep. 2019 Feb 1;42(2). doi: 10.1093/sleep/zsy209.

PMID:
30371854
12.

Publisher Correction: Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis.

Savas P, Virassamy B, Ye C, Salim A, Mintoff CP, Caramia F, Salgado R, Byrne DJ, Teo ZL, Dushyanthen S, Byrne A, Wein L, Luen SJ, Poliness C, Nightingale SS, Skandarajah AS, Gyorki DE, Thornton CM, Beavis PA, Fox SB; Kathleen Cuningham Foundation Consortium for Research into Familial Breast Cancer (kConFab), Darcy PK, Speed TP, Mackay LK, Neeson PJ, Loi S.

Nat Med. 2018 Dec;24(12):1941. doi: 10.1038/s41591-018-0176-6.

PMID:
30135555
13.

Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements.

Peters TJ, French HJ, Bradford ST, Pidsley R, Stirzaker C, Varinli H, Nair S, Qu W, Song J, Giles KA, Statham AL, Speirs H, Speed TP, Clark SJ.

Bioinformatics. 2019 Feb 15;35(4):560-570. doi: 10.1093/bioinformatics/bty675.

14.

The healthy ageing gene expression signature for Alzheimer's disease diagnosis: a random sampling perspective.

Jacob L, Speed TP.

Genome Biol. 2018 Jul 25;19(1):97. doi: 10.1186/s13059-018-1481-6.

15.

Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis.

Savas P, Virassamy B, Ye C, Salim A, Mintoff CP, Caramia F, Salgado R, Byrne DJ, Teo ZL, Dushyanthen S, Byrne A, Wein L, Luen SJ, Poliness C, Nightingale SS, Skandarajah AS, Gyorki DE, Thornton CM, Beavis PA, Fox SB; Kathleen Cuningham Foundation Consortium for Research into Familial Breast Cancer (kConFab), Darcy PK, Speed TP, Mackay LK, Neeson PJ, Loi S.

Nat Med. 2018 Jul;24(7):986-993. doi: 10.1038/s41591-018-0078-7. Epub 2018 Jun 25. Erratum in: Nat Med. 2018 Dec;24(12):1941.

PMID:
29942092
16.

Accurate RNA Sequencing From Formalin-Fixed Cancer Tissue To Represent High-Quality Transcriptome From Frozen Tissue.

Li J, Fu C, Speed TP, Wang W, Symmans WF.

JCO Precis Oncol. 2018;2018. doi: 10.1200/PO.17.00091. Epub 2018 Jan 26.

17.

Discrimination against Obese Exercise Clients: An Experimental Study of Personal Trainers.

Fontana F, Bopes J, Bendixen S, Speed T, George M, Mack M.

Int J Exerc Sci. 2018 May 1;11(5):116-128. eCollection 2018.

18.

An Innovative Perioperative Pain Program for Chronic Opioid Users: An Academic Medical Center's Response to the Opioid Crisis.

Hanna MN, Speed TJ, Shechter R, Grant MC, Sheinberg R, Goldberg E, Campbell CM, Theodore N, Koch CG, Williams K.

Am J Med Qual. 2019 Jan/Feb;34(1):5-13. doi: 10.1177/1062860618777298. Epub 2018 May 23.

PMID:
29790369
19.

Correction to: A statistical framework for analyzing deep mutational scanning data.

Rubin AF, Gelman H, Lucas N, Bajjalieh SM, Papenfuss AT, Speed TP, Fowler DM.

Genome Biol. 2018 Feb 7;19(1):17. doi: 10.1186/s13059-018-1391-7.

20.

RLE plots: Visualizing unwanted variation in high dimensional data.

Gandolfo LC, Speed TP.

PLoS One. 2018 Feb 5;13(2):e0191629. doi: 10.1371/journal.pone.0191629. eCollection 2018.

21.

Joint Modeling of Mixed Plasmodium Species Infections Using a Bivariate Poisson Lognormal Model.

Colborn KL, Mueller I, Speed TP.

Am J Trop Med Hyg. 2018 Jan;98(1):71-76. doi: 10.4269/ajtmh.17-0523.

22.

GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly.

Cameron DL, Schröder J, Penington JS, Do H, Molania R, Dobrovic A, Speed TP, Papenfuss AT.

Genome Res. 2017 Dec;27(12):2050-2060. doi: 10.1101/gr.222109.117. Epub 2017 Nov 2.

23.

Sex moderates the effects of positive and negative affect on clinical pain in patients with knee osteoarthritis.

Speed TJ, Richards JM, Finan PH, Smith MT.

Scand J Pain. 2017 Jul;16:66-73. doi: 10.1016/j.sjpain.2017.03.005. Epub 2017 Apr 19.

24.

A statistical framework for analyzing deep mutational scanning data.

Rubin AF, Gelman H, Lucas N, Bajjalieh SM, Papenfuss AT, Speed TP, Fowler DM.

Genome Biol. 2017 Aug 7;18(1):150. doi: 10.1186/s13059-017-1272-5. Erratum in: Genome Biol. 2018 Feb 7;19(1):17.

25.

Correction: The Subclonal Architecture of Metastatic Breast Cancer: Results from a Prospective Community-Based Rapid Autopsy Program "CASCADE".

Savas P, Teo ZL, Lefevre C, Flensburg C, Caramia F, Alsop K, Mansour M, Francis PA, Thorne HA, Silva MJ, Kanu N, Dietzen M, Rowan A, Kschischo M, Fox S, Bowtell DD, Dawson SJ, Speed TP, Swanton C, Loi S.

PLoS Med. 2017 Apr 21;14(4):e1002302. doi: 10.1371/journal.pmed.1002302. eCollection 2017 Apr.

26.

Deficiency of microRNA miR-34a expands cell fate potential in pluripotent stem cells.

Choi YJ, Lin CP, Risso D, Chen S, Kim TA, Tan MH, Li JB, Wu Y, Chen C, Xuan Z, Macfarlan T, Peng W, Lloyd KC, Kim SY, Speed TP, He L.

Science. 2017 Feb 10;355(6325). pii: eaag1927. doi: 10.1126/science.aag1927. Epub 2017 Jan 12.

27.

The Subclonal Architecture of Metastatic Breast Cancer: Results from a Prospective Community-Based Rapid Autopsy Program "CASCADE".

Savas P, Teo ZL, Lefevre C, Flensburg C, Caramia F, Alsop K, Mansour M, Francis PA, Thorne HA, Silva MJ, Kanu N, Dietzen M, Rowan A, Kschischo M, Fox S, Bowtell DD, Dawson SJ, Speed TP, Swanton C, Loi S.

PLoS Med. 2016 Dec 27;13(12):e1002204. doi: 10.1371/journal.pmed.1002204. eCollection 2016 Dec. Erratum in: PLoS Med. 2017 Apr 21;14 (4):e1002302.

28.

Characterization of pain, disability, and psychological burden in Marfan syndrome.

Speed TJ, Mathur VA, Hand M, Christensen B, Sponseller PD, Williams KA, Campbell CM.

Am J Med Genet A. 2017 Feb;173(2):315-323. doi: 10.1002/ajmg.a.38051. Epub 2016 Nov 14.

29.

Removal of unwanted variation reveals novel patterns of gene expression linked to sleep homeostasis in murine cortex.

Gerstner JR, Koberstein JN, Watson AJ, Zapero N, Risso D, Speed TP, Frank MG, Peixoto L.

BMC Genomics. 2016 Oct 25;17(Suppl 8):727.

30.

Contextual fear conditioning induces differential alternative splicing.

Poplawski SG, Peixoto L, Porcari GS, Wimmer ME, McNally AG, Mizuno K, Giese KP, Chatterjee S, Koberstein JN, Risso D, Speed TP, Abel T.

Neurobiol Learn Mem. 2016 Oct;134 Pt B:221-35. doi: 10.1016/j.nlm.2016.07.018. Epub 2016 Jul 20.

31.

Corrigendum to 'MicroRNAs in CD4+ T cell subsets are markers of disease risk and T cell dysfunction in individuals at risk for type 1 diabetes' [J. Autoimmun. 68C (2016) 52-61].

Zhang Y, Feng ZP, Naselli G, Bell F, Wettenhall J, Auyeung P, Ellis JA, Ponsonby AL, Speed TP, Chong MM, Harrison LC.

J Autoimmun. 2016 Sep;73:130. doi: 10.1016/j.jaut.2016.04.002. Epub 2016 Apr 25. No abstract available.

PMID:
27134182
32.

A molecular threshold for effector CD8(+) T cell differentiation controlled by transcription factors Blimp-1 and T-bet.

Xin A, Masson F, Liao Y, Preston S, Guan T, Gloury R, Olshansky M, Lin JX, Li P, Speed TP, Smyth GK, Ernst M, Leonard WJ, Pellegrini M, Kaech SM, Nutt SL, Shi W, Belz GT, Kallies A.

Nat Immunol. 2016 Apr;17(4):422-32. doi: 10.1038/ni.3410. Epub 2016 Mar 7.

33.

MicroRNAs in CD4(+) T cell subsets are markers of disease risk and T cell dysfunction in individuals at risk for type 1 diabetes.

Zhang Y, Feng ZP, Naselli G, Bell F, Wettenhall J, Auyeung P, Ellis JA, Ponsonby AL, Speed TP, Chong MM, Harrison LC.

J Autoimmun. 2016 Apr;68:52-61. doi: 10.1016/j.jaut.2015.12.006. Epub 2016 Jan 11.

PMID:
26786119
34.

Assessment of DNA methylation profiling and copy number variation as indications of clonal relationship in ipsilateral and contralateral breast cancers to distinguish recurrent breast cancer from a second primary tumour.

Huang KT, Mikeska T, Li J, Takano EA, Millar EK, Graham PH, Boyle SE, Campbell IG, Speed TP, Dobrovic A, Fox SB.

BMC Cancer. 2015 Oct 9;15:669. doi: 10.1186/s12885-015-1676-0.

35.

Systematic noise degrades gene co-expression signals but can be corrected.

Freytag S, Gagnon-Bartsch J, Speed TP, Bahlo M.

BMC Bioinformatics. 2015 Sep 24;16:309. doi: 10.1186/s12859-015-0745-3.

36.

Correcting gene expression data when neither the unwanted variation nor the factor of interest are observed.

Jacob L, Gagnon-Bartsch JA, Speed TP.

Biostatistics. 2016 Jan;17(1):16-28. doi: 10.1093/biostatistics/kxv026. Epub 2015 Aug 17.

37.

How data analysis affects power, reproducibility and biological insight of RNA-seq studies in complex datasets.

Peixoto L, Risso D, Poplawski SG, Wimmer ME, Speed TP, Wood MA, Abel T.

Nucleic Acids Res. 2015 Sep 18;43(16):7664-74. doi: 10.1093/nar/gkv736. Epub 2015 Jul 21.

38.

Removing unwanted variation in a differential methylation analysis of Illumina HumanMethylation450 array data.

Maksimovic J, Gagnon-Bartsch JA, Speed TP, Oshlack A.

Nucleic Acids Res. 2015 Sep 18;43(16):e106. doi: 10.1093/nar/gkv526. Epub 2015 May 18.

39.

Statistical methods for handling unwanted variation in metabolomics data.

De Livera AM, Sysi-Aho M, Jacob L, Gagnon-Bartsch JA, Castillo S, Simpson JA, Speed TP.

Anal Chem. 2015 Apr 7;87(7):3606-15. doi: 10.1021/ac502439y. Epub 2015 Mar 6.

40.

Distinct epigenetic signatures delineate transcriptional programs during virus-specific CD8(+) T cell differentiation.

Russ BE, Olshanksy M, Smallwood HS, Li J, Denton AE, Prier JE, Stock AT, Croom HA, Cullen JG, Nguyen ML, Rowe S, Olson MR, Finkelstein DB, Kelso A, Thomas PG, Speed TP, Rao S, Turner SJ.

Immunity. 2014 Nov 20;41(5):853-65. doi: 10.1016/j.immuni.2014.11.001. Epub 2014 Nov 6. Erratum in: Immunity. 2014 Dec 18;41(6):1064.

41.

Signatures of tumour immunity distinguish Asian and non-Asian gastric adenocarcinomas.

Lin SJ, Gagnon-Bartsch JA, Tan IB, Earle S, Ruff L, Pettinger K, Ylstra B, van Grieken N, Rha SY, Chung HC, Lee JS, Cheong JH, Noh SH, Aoyama T, Miyagi Y, Tsuburaya A, Yoshikawa T, Ajani JA, Boussioutas A, Yeoh KG, Yong WP, So J, Lee J, Kang WK, Kim S, Kameda Y, Arai T, Zur Hausen A, Speed TP, Grabsch HI, Tan P.

Gut. 2015 Nov;64(11):1721-31. doi: 10.1136/gutjnl-2014-308252. Epub 2014 Nov 10.

42.

Deciphering clonality in aneuploid breast tumors using SNP array and sequencing data.

Lönnstedt IM, Caramia F, Li J, Fumagalli D, Salgado R, Rowan A, Salm M, Kanu N, Savas P, Horswell S, Gade S, Loibl S, Neven P, Sotiriou C, Swanton C, Loi S, Speed TP.

Genome Biol. 2014 Oct 1;15(9):470. doi: 10.1186/s13059-014-0470-7.

43.

Normalization of RNA-seq data using factor analysis of control genes or samples.

Risso D, Ngai J, Speed TP, Dudoit S.

Nat Biotechnol. 2014 Sep;32(9):896-902. doi: 10.1038/nbt.2931. Epub 2014 Aug 24.

44.

Combining calls from multiple somatic mutation-callers.

Kim SY, Jacob L, Speed TP.

BMC Bioinformatics. 2014 May 21;15:154. doi: 10.1186/1471-2105-15-154.

45.

Dating rare mutations from small samples with dense marker data.

Gandolfo LC, Bahlo M, Speed TP.

Genetics. 2014 Aug;197(4):1315-27. doi: 10.1534/genetics.114.164616. Epub 2014 May 30.

46.

Silencing of odorant receptor genes by G protein βγ signaling ensures the expression of one odorant receptor per olfactory sensory neuron.

Ferreira T, Wilson SR, Choi YG, Risso D, Dudoit S, Speed TP, Ngai J.

Neuron. 2014 Feb 19;81(4):847-59. doi: 10.1016/j.neuron.2014.01.001.

47.

A positive feedback between p53 and miR-34 miRNAs mediates tumor suppression.

Okada N, Lin CP, Ribeiro MC, Biton A, Lai G, He X, Bu P, Vogel H, Jablons DM, Keller AC, Wilkinson JE, He B, Speed TP, He L.

Genes Dev. 2014 Mar 1;28(5):438-50. doi: 10.1101/gad.233585.113. Epub 2014 Feb 14.

48.

Investigating and correcting plasma DNA sequencing coverage bias to enhance aneuploidy discovery.

Chandrananda D, Thorne NP, Ganesamoorthy D, Bruno DL, Benjamini Y, Speed TP, Slater HR, Bahlo M.

PLoS One. 2014 Jan 29;9(1):e86993. doi: 10.1371/journal.pone.0086993. eCollection 2014.

49.

G protein-linked signaling pathways in bipolar and major depressive disorders.

Tomita H, Ziegler ME, Kim HB, Evans SJ, Choudary PV, Li JZ, Meng F, Dai M, Myers RM, Neal CR, Speed TP, Barchas JD, Schatzberg AF, Watson SJ, Akil H, Jones EG, Bunney WE, Vawter MP.

Front Genet. 2013 Dec 23;4:297. doi: 10.3389/fgene.2013.00297. eCollection 2013.

50.

A component of the mir-17-92 polycistronic oncomir promotes oncogene-dependent apoptosis.

Olive V, Sabio E, Bennett MJ, De Jong CS, Biton A, McGann JC, Greaney SK, Sodir NM, Zhou AY, Balakrishnan A, Foth M, Luftig MA, Goga A, Speed TP, Xuan Z, Evan GI, Wan Y, Minella AC, He L.

Elife. 2013 Oct 15;2:e00822. doi: 10.7554/eLife.00822.

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