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Items: 1 to 50 of 65

1.

Preclinical rationale for entinostat in embryonal rhabdomyosarcoma.

Bharathy N, Berlow NE, Wang E, Abraham J, Settelmeyer TP, Hooper JE, Svalina MN, Bajwa Z, Goros MW, Hernandez BS, Wolff JE, Pal R, Davies AM, Ashok A, Bushby D, Mancini M, Noakes C, Goodwin NC, Ordentlich P, Keck J, Hawkins DS, Rudzinski ER, Mansoor A, Perkins TJ, Vakoc CR, Michalek JE, Keller C.

Skelet Muscle. 2019 May 21;9(1):12. doi: 10.1186/s13395-019-0198-x.

2.

RECAP reveals the true statistical significance of ChIP-seq peak calls.

Chitpin JG, Awdeh A, Perkins TJ.

Bioinformatics. 2019 Mar 1. pii: btz150. doi: 10.1093/bioinformatics/btz150. [Epub ahead of print]

PMID:
30824903
3.

The HDAC3-SMARCA4-miR-27a axis promotes expression of the PAX3:FOXO1 fusion oncogene in rhabdomyosarcoma.

Bharathy N, Berlow NE, Wang E, Abraham J, Settelmeyer TP, Hooper JE, Svalina MN, Ishikawa Y, Zientek K, Bajwa Z, Goros MW, Hernandez BS, Wolff JE, Rudek MA, Xu L, Anders NM, Pal R, Harrold AP, Davies AM, Ashok A, Bushby D, Mancini M, Noakes C, Goodwin NC, Ordentlich P, Keck J, Hawkins DS, Rudzinski ER, Chatterjee B, Bächinger HP, Barr FG, Liddle J, Garcia BA, Mansoor A, Perkins TJ, Vakoc CR, Michalek JE, Keller C.

Sci Signal. 2018 Nov 20;11(557). pii: eaau7632. doi: 10.1126/scisignal.aau7632.

4.

Targeting the MTF2-MDM2 Axis Sensitizes Refractory Acute Myeloid Leukemia to Chemotherapy.

Maganti HB, Jrade H, Cafariello C, Manias Rothberg JL, Porter CJ, Yockell-Lelièvre J, Battaion HL, Khan ST, Howard JP, Li Y, Grzybowski AT, Sabri E, Ruthenburg AJ, Dilworth FJ, Perkins TJ, Sabloff M, Ito CY, Stanford WL.

Cancer Discov. 2018 Nov;8(11):1376-1389. doi: 10.1158/2159-8290.CD-17-0841. Epub 2018 Aug 16.

PMID:
30115703
5.

Cis-regulatory determinants of MyoD function.

Soleimani VD, Nguyen D, Ramachandran P, Palidwor GA, Porter CJ, Yin H, Perkins TJ, Rudnicki MA.

Nucleic Acids Res. 2018 Aug 21;46(14):7221-7235. doi: 10.1093/nar/gky388.

6.

Mtf2-PRC2 control of canonical Wnt signaling is required for definitive erythropoiesis.

Rothberg JLM, Maganti HB, Jrade H, Porter CJ, Palidwor GA, Cafariello C, Battaion HL, Khan ST, Perkins TJ, Paulson RF, Ito CY, Stanford WL.

Cell Discov. 2018 May 1;4:21. doi: 10.1038/s41421-018-0022-5. eCollection 2018.

7.

Epigenetic Activation of Pro-angiogenic Signaling Pathways in Human Endothelial Progenitors Increases Vasculogenesis.

Fraineau S, Palii CG, McNeill B, Ritso M, Shelley WC, Prasain N, Chu A, Vion E, Rieck K, Nilufar S, Perkins TJ, Rudnicki MA, Allan DS, Yoder MC, Suuronen EJ, Brand M.

Stem Cell Reports. 2017 Nov 14;9(5):1573-1587. doi: 10.1016/j.stemcr.2017.09.009. Epub 2017 Oct 12.

8.

Uncovering robust patterns of microRNA co-expression across cancers using Bayesian Relevance Networks.

Ramachandran P, Sánchez-Taltavull D, Perkins TJ.

PLoS One. 2017 Aug 17;12(8):e0183103. doi: 10.1371/journal.pone.0183103. eCollection 2017.

9.

Reprogramming progeria fibroblasts re-establishes a normal epigenetic landscape.

Chen Z, Chang WY, Etheridge A, Strickfaden H, Jin Z, Palidwor G, Cho JH, Wang K, Kwon SY, Doré C, Raymond A, Hotta A, Ellis J, Kandel RA, Dilworth FJ, Perkins TJ, Hendzel MJ, Galas DJ, Stanford WL.

Aging Cell. 2017 Aug;16(4):870-887. doi: 10.1111/acel.12621. Epub 2017 Jun 8.

10.

Induction of senescence in primary glioblastoma cells by serum and TGFβ.

Kumar R, Gont A, Perkins TJ, Hanson JEL, Lorimer IAJ.

Sci Rep. 2017 May 19;7(1):2156. doi: 10.1038/s41598-017-02380-1.

11.

PCP and SAX-3/Robo Pathways Cooperate to Regulate Convergent Extension-Based Nerve Cord Assembly in C. elegans.

Shah PK, Tanner MR, Kovacevic I, Rankin A, Marshall TE, Noblett N, Tran NN, Roenspies T, Hung J, Chen Z, Slatculescu C, Perkins TJ, Bao Z, Colavita A.

Dev Cell. 2017 Apr 24;41(2):195-203.e3. doi: 10.1016/j.devcel.2017.03.024.

12.

Dynamics in Epistasis Analysis.

Awdeh A, Phenix H, Karn M, Perkins TJ.

IEEE/ACM Trans Comput Biol Bioinform. 2018 May-Jun;15(3):878-891. doi: 10.1109/TCBB.2017.2653110. Epub 2017 Jan 16.

PMID:
28092574
13.

Bayesian Correlation Analysis for Sequence Count Data.

Sánchez-Taltavull D, Ramachandran P, Lau N, Perkins TJ.

PLoS One. 2016 Oct 4;11(10):e0163595. doi: 10.1371/journal.pone.0163595. eCollection 2016.

14.

Induction of Activating Transcription Factor 3 Is Associated with Cisplatin Responsiveness in Non-Small Cell Lung Carcinoma Cells.

Bar J, Hasim MS, Baghai T, Niknejad N, Perkins TJ, Stewart DJ, Sekhon HS, Villeneuve PJ, Dimitroulakos J.

Neoplasia. 2016 Sep;18(9):525-35. doi: 10.1016/j.neo.2016.07.004.

15.

On cross-conditional and fluctuation correlations in competitive RNA networks.

Sánchez-Taltavull D, MacLeod M, Perkins TJ.

Bioinformatics. 2016 Sep 1;32(17):i790-i797. doi: 10.1093/bioinformatics/btw472.

PMID:
27587702
16.

Control of glioblastoma tumorigenesis by feed-forward cytokine signaling.

Jahani-Asl A, Yin H, Soleimani VD, Haque T, Luchman HA, Chang NC, Sincennes MC, Puram SV, Scott AM, Lorimer IA, Perkins TJ, Ligon KL, Weiss S, Rudnicki MA, Bonni A.

Nat Neurosci. 2016 Jun;19(6):798-806. doi: 10.1038/nn.4295. Epub 2016 Apr 25.

17.

UTX inhibition as selective epigenetic therapy against TAL1-driven T-cell acute lymphoblastic leukemia.

Benyoucef A, Palii CG, Wang C, Porter CJ, Chu A, Dai F, Tremblay V, Rakopoulos P, Singh K, Huang S, Pflumio F, Hébert J, Couture JF, Perkins TJ, Ge K, Dilworth FJ, Brand M.

Genes Dev. 2016 Mar 1;30(5):508-21. doi: 10.1101/gad.276790.115.

18.

BIDCHIPS: bias decomposition and removal from ChIP-seq data clarifies true binding signal and its functional correlates.

Ramachandran P, Palidwor GA, Perkins TJ.

Epigenetics Chromatin. 2015 Sep 17;8:33. doi: 10.1186/s13072-015-0028-2. eCollection 2015.

19.

Integrative genomics positions MKRN1 as a novel ribonucleoprotein within the embryonic stem cell gene regulatory network.

Cassar PA, Carpenedo RL, Samavarchi-Tehrani P, Olsen JB, Park CJ, Chang WY, Chen Z, Choey C, Delaney S, Guo H, Guo H, Tanner RM, Perkins TJ, Tenenbaum SA, Emili A, Wrana JL, Gibbings D, Stanford WL.

EMBO Rep. 2015 Oct;16(10):1334-57. doi: 10.15252/embr.201540974. Epub 2015 Aug 11.

20.

Gene selection for the reconstruction of stem cell differentiation trees: a linear programming approach.

Ghadie MA, Japkowicz N, Perkins TJ.

Bioinformatics. 2015 Aug 15;31(16):2676-82. doi: 10.1093/bioinformatics/btv192. Epub 2015 Apr 5.

PMID:
25847008
21.

Increased premotor cortex activation in high functioning autism during action observation.

Perkins TJ, Bittar RG, McGillivray JA, Cox II, Stokes MA.

J Clin Neurosci. 2015 Apr;22(4):664-9. doi: 10.1016/j.jocn.2014.10.007. Epub 2015 Feb 25.

PMID:
25726458
22.

miR Profiling Identifies Cyclin-Dependent Kinase 6 Downregulation as a Potential Mechanism of Acquired Cisplatin Resistance in Non-Small-Cell Lung Carcinoma.

Bar J, Gorn-Hondermann I, Moretto P, Perkins TJ, Niknejad N, Stewart DJ, Goss GD, Dimitroulakos J.

Clin Lung Cancer. 2015 Nov;16(6):e121-9. doi: 10.1016/j.cllc.2015.01.008. Epub 2015 Feb 3.

PMID:
25703099
23.

Learning a cost function for microscope image segmentation.

Nilufar S, Perkins TJ.

Conf Proc IEEE Eng Med Biol Soc. 2014;2014:5506-9. doi: 10.1109/EMBC.2014.6944873.

PMID:
25571241
24.

A scaling law for random walks on networks.

Perkins TJ, Foxall E, Glass L, Edwards R.

Nat Commun. 2014 Oct 14;5:5121. doi: 10.1038/ncomms6121.

25.

Increased left hemisphere impairment in high-functioning autism: a tract based spatial statistics study.

Perkins TJ, Stokes MA, McGillivray JA, Mussap AJ, Cox IA, Maller JJ, Bittar RG.

Psychiatry Res. 2014 Nov 30;224(2):119-23. doi: 10.1016/j.pscychresns.2014.08.003. Epub 2014 Aug 12.

PMID:
25159311
26.

Trichostatin A enhances vascular repair by injected human endothelial progenitors through increasing the expression of TAL1-dependent genes.

Palii CG, Vulesevic B, Fraineau S, Pranckeviciene E, Griffith AJ, Chu A, Faralli H, Li Y, McNeill B, Sun J, Perkins TJ, Dilworth FJ, Perez-Iratxeta C, Suuronen EJ, Allan DS, Brand M.

Cell Stem Cell. 2014 May 1;14(5):644-57. doi: 10.1016/j.stem.2014.03.003.

27.

Adaptive bandwidth kernel density estimation for next-generation sequencing data.

Ramachandran P, Perkins TJ.

BMC Proc. 2013 Dec 20;7(Suppl 7):S7. doi: 10.1186/1753-6561-7-S7-S7. Epub 2013 Dec 20.

28.

Pooled screening for synergistic interactions subject to blocking and noise.

Li K, Precup D, Perkins TJ.

PLoS One. 2014 Jan 16;9(1):e85864. doi: 10.1371/journal.pone.0085864. eCollection 2014.

29.

FiloDetect: automatic detection of filopodia from fluorescence microscopy images.

Nilufar S, Morrow AA, Lee JM, Perkins TJ.

BMC Syst Biol. 2013 Jul 23;7:66. doi: 10.1186/1752-0509-7-66.

30.

Chromatin tandem affinity purification sequencing.

Soleimani VD, Palidwor GA, Ramachandran P, Perkins TJ, Rudnicki MA.

Nat Protoc. 2013 Aug;8(8):1525-34. doi: 10.1038/nprot.2013.088. Epub 2013 Jul 11.

31.

MaSC: mappability-sensitive cross-correlation for estimating mean fragment length of single-end short-read sequencing data.

Ramachandran P, Palidwor GA, Porter CJ, Perkins TJ.

Bioinformatics. 2013 Feb 15;29(4):444-50. doi: 10.1093/bioinformatics/btt001. Epub 2013 Jan 7.

32.

What do molecules do when we are not looking? State sequence analysis for stochastic chemical systems.

Levin P, Lefebvre J, Perkins TJ.

J R Soc Interface. 2012 Dec 7;9(77):3411-25. doi: 10.1098/rsif.2012.0633. Epub 2012 Sep 12.

33.

Transcriptional dominance of Pax7 in adult myogenesis is due to high-affinity recognition of homeodomain motifs.

Soleimani VD, Punch VG, Kawabe Y, Jones AE, Palidwor GA, Porter CJ, Cross JW, Carvajal JJ, Kockx CE, van IJcken WF, Perkins TJ, Rigby PW, Grosveld F, Rudnicki MA.

Dev Cell. 2012 Jun 12;22(6):1208-20. doi: 10.1016/j.devcel.2012.03.014. Epub 2012 May 17.

34.

Neural population densities shape network correlations.

Lefebvre J, Perkins TJ.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Feb;85(2 Pt 1):021914. Epub 2012 Feb 17.

PMID:
22463251
35.

Methods for Determining the Statistical Significance of Enrichment or Depletion of Gene Ontology Classifications under Weighted Membership.

Iacucci E, Zingg HH, Perkins TJ.

Front Genet. 2012 Feb 23;3:24. doi: 10.3389/fgene.2012.00024. eCollection 2012.

36.

The show that started it all. Emergency! Debuted 40 years ago this month.

Perkins TJ.

EMS World. 2012 Jan;41(1):48-9. No abstract available.

PMID:
22299493
37.

Systematic discovery of Rab GTPases with synaptic functions in Drosophila.

Chan CC, Scoggin S, Wang D, Cherry S, Dembo T, Greenberg B, Jin EJ, Kuey C, Lopez A, Mehta SQ, Perkins TJ, Brankatschk M, Rothenfluh A, Buszczak M, Hiesinger PR.

Curr Biol. 2011 Oct 25;21(20):1704-15. doi: 10.1016/j.cub.2011.08.058. Epub 2011 Oct 13.

38.

Quantitative epistasis analysis and pathway inference from genetic interaction data.

Phenix H, Morin K, Batenchuk C, Parker J, Abedi V, Yang L, Tepliakova L, Perkins TJ, Kærn M.

PLoS Comput Biol. 2011 May;7(5):e1002048. doi: 10.1371/journal.pcbi.1002048. Epub 2011 May 12.

39.

Functional data analysis for identifying nonlinear models of gene regulatory networks.

Summer G, Perkins TJ.

BMC Genomics. 2010 Dec 2;11 Suppl 4:S18. doi: 10.1186/1471-2164-11-S4-S18.

40.

Robust patterns in the stochastic organization of filopodia.

Husainy AN, Morrow AA, Perkins TJ, Lee JM.

BMC Cell Biol. 2010 Nov 17;11:86. doi: 10.1186/1471-2121-11-86.

41.

A general model of codon bias due to GC mutational bias.

Palidwor GA, Perkins TJ, Xia X.

PLoS One. 2010 Oct 27;5(10):e13431. doi: 10.1371/journal.pone.0013431.

42.

Robust dynamics in minimal hybrid models of genetic networks.

Perkins TJ, Wilds R, Glass L.

Philos Trans A Math Phys Eng Sci. 2010 Nov 13;368(1930):4961-75. doi: 10.1098/rsta.2010.0139.

43.

Estimating the stochastic bifurcation structure of cellular networks.

Song C, Phenix H, Abedi V, Scott M, Ingalls BP, Kaern M, Perkins TJ.

PLoS Comput Biol. 2010 Mar 5;6(3):e1000699. doi: 10.1371/journal.pcbi.1000699. Erratum in: PLoS Comput Biol. 2010;6(3). doi: 10.1371/annotation/9a35fa58-f81c-41b4-9fa9-c1aeedbf0fff.

44.

A trade-off between sample complexity and computational complexity in learning Boolean networks from time-series data.

Perkins TJ, Hallett MT.

IEEE/ACM Trans Comput Biol Bioinform. 2010 Jan-Mar;7(1):118-25. doi: 10.1109/TCBB.2008.38.

PMID:
20150674
45.

Maximum probability reaction sequences in stochastic chemical kinetic systems.

Salehi M, Perkins TJ.

Front Physiol. 2010 Oct 19;1:170. doi: 10.3389/fphys.2010.00170. eCollection 2010.

46.

Strategies for cellular decision-making.

Perkins TJ, Swain PS.

Mol Syst Biol. 2009;5:326. doi: 10.1038/msb.2009.83. Epub 2009 Nov 17. Review.

47.

Statistical lower bounds on protein copy number from fluorescence expression images.

Zamparo L, Perkins TJ.

Bioinformatics. 2009 Oct 15;25(20):2670-6. doi: 10.1093/bioinformatics/btp415. Epub 2009 Jul 2.

48.

An evaluation of alcohol attendances to an inner city emergency department before and after the introduction of the UK Licensing Act 2003.

Durnford AJ, Perkins TJ, Perry JM.

BMC Public Health. 2008 Oct 31;8:379. doi: 10.1186/1471-2458-8-379.

49.

Views from the field. Interviewed by Raphael M Barishansky.

Moriguchi G, Perkins TJ, Studnek J.

EMS Mag. 2008 Oct;37(10):105-8. No abstract available.

PMID:
18959346
50.

"Level with me, sugar!" Dealing with diabetics and diabetic emergencies.

Perkins TJ.

EMS Mag. 2008 Aug;37(8):52, 54, 56. No abstract available.

PMID:
18814740

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