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Items: 20

1.

Microbe-host interplay in atopic dermatitis and psoriasis.

Fyhrquist N, Muirhead G, Prast-Nielsen S, Jeanmougin M, Olah P, Skoog T, Jules-Clement G, Feld M, Barrientos-Somarribas M, Sinkko H, van den Bogaard EH, Zeeuwen PLJM, Rikken G, Schalkwijk J, Niehues H, Däubener W, Eller SK, Alexander H, Pennino D, Suomela S, Tessas I, Lybeck E, Baran AM, Darban H, Gangwar RS, Gerstel U, Jahn K, Karisola P, Yan L, Hansmann B, Katayama S, Meller S, Bylesjö M, Hupé P, Levi-Schaffer F, Greco D, Ranki A, Schröder JM, Barker J, Kere J, Tsoka S, Lauerma A, Soumelis V, Nestle FO, Homey B, Andersson B, Alenius H.

Nat Commun. 2019 Oct 16;10(1):4703. doi: 10.1038/s41467-019-12253-y.

2.

Survival prediction in mesothelioma using a scalable Lasso regression model: instructions for use and initial performance using clinical predictors.

Kidd AC, McGettrick M, Tsim S, Halligan DL, Bylesjo M, Blyth KG.

BMJ Open Respir Res. 2018 Jan 30;5(1):e000240. doi: 10.1136/bmjresp-2017-000240. eCollection 2018.

3.

Characterization of the human T cell response to in vitro CD27 costimulation with varlilumab.

Ramakrishna V, Sundarapandiyan K, Zhao B, Bylesjo M, Marsh HC, Keler T.

J Immunother Cancer. 2015 Aug 18;3:37. doi: 10.1186/s40425-015-0080-2. eCollection 2015.

4.

Extracting meaningful information from metabonomic data using multivariate statistics.

Bylesjö M.

Methods Mol Biol. 2015;1277:137-46. doi: 10.1007/978-1-4939-2377-9_11.

PMID:
25677152
5.

Identification and validation of an anthracycline/cyclophosphamide-based chemotherapy response assay in breast cancer.

Mulligan JM, Hill LA, Deharo S, Irwin G, Boyle D, Keating KE, Raji OY, McDyer FA, O'Brien E, Bylesjo M, Quinn JE, Lindor NM, Mullan PB, James CR, Walker SM, Kerr P, James J, Davison TS, Proutski V, Salto-Tellez M, Johnston PG, Couch FJ, Paul Harkin D, Kennedy RD.

J Natl Cancer Inst. 2014 Jan;106(1):djt335. doi: 10.1093/jnci/djt335.

6.

Development and independent validation of a prognostic assay for stage II colon cancer using formalin-fixed paraffin-embedded tissue.

Kennedy RD, Bylesjo M, Kerr P, Davison T, Black JM, Kay EW, Holt RJ, Proutski V, Ahdesmaki M, Farztdinov V, Goffard N, Hey P, McDyer F, Mulligan K, Mussen J, O'Brien E, Oliver G, Walker SM, Mulligan JM, Wilson C, Winter A, O'Donoghue D, Mulcahy H, O'Sullivan J, Sheahan K, Hyland J, Dhir R, Bathe OF, Winqvist O, Manne U, Shanmugam C, Ramaswamy S, Leon EJ, Smith WI Jr, McDermott U, Wilson RH, Longley D, Marshall J, Cummins R, Sargent DJ, Johnston PG, Harkin DP.

J Clin Oncol. 2011 Dec 10;29(35):4620-6. doi: 10.1200/JCO.2011.35.4498. Epub 2011 Nov 7.

PMID:
22067406
7.

Non-linear modeling of 1H NMR metabonomic data using kernel-based orthogonal projections to latent structures optimized by simulated annealing.

Fonville JM, Bylesjö M, Coen M, Nicholson JK, Holmes E, Lindon JC, Rantalainen M.

Anal Chim Acta. 2011 Oct 31;705(1-2):72-80. doi: 10.1016/j.aca.2011.04.016. Epub 2011 Apr 20.

PMID:
21962350
8.

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models.

Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, Shaughnessy JD Jr, Oberthuer A, Thomas RS, Paules RS, Fielden M, Barlogie B, Chen W, Du P, Fischer M, Furlanello C, Gallas BD, Ge X, Megherbi DB, Symmans WF, Wang MD, Zhang J, Bitter H, Brors B, Bushel PR, Bylesjo M, Chen M, Cheng J, Cheng J, Chou J, Davison TS, Delorenzi M, Deng Y, Devanarayan V, Dix DJ, Dopazo J, Dorff KC, Elloumi F, Fan J, Fan S, Fan X, Fang H, Gonzaludo N, Hess KR, Hong H, Huan J, Irizarry RA, Judson R, Juraeva D, Lababidi S, Lambert CG, Li L, Li Y, Li Z, Lin SM, Liu G, Lobenhofer EK, Luo J, Luo W, McCall MN, Nikolsky Y, Pennello GA, Perkins RG, Philip R, Popovici V, Price ND, Qian F, Scherer A, Shi T, Shi W, Sung J, Thierry-Mieg D, Thierry-Mieg J, Thodima V, Trygg J, Vishnuvajjala L, Wang SJ, Wu J, Wu Y, Xie Q, Yousef WA, Zhang L, Zhang X, Zhong S, Zhou Y, Zhu S, Arasappan D, Bao W, Lucas AB, Berthold F, Brennan RJ, Buness A, Catalano JG, Chang C, Chen R, Cheng Y, Cui J, Czika W, Demichelis F, Deng X, Dosymbekov D, Eils R, Feng Y, Fostel J, Fulmer-Smentek S, Fuscoe JC, Gatto L, Ge W, Goldstein DR, Guo L, Halbert DN, Han J, Harris SC, Hatzis C, Herman D, Huang J, Jensen RV, Jiang R, Johnson CD, Jurman G, Kahlert Y, Khuder SA, Kohl M, Li J, Li L, Li M, Li QZ, Li S, Li Z, Liu J, Liu Y, Liu Z, Meng L, Madera M, Martinez-Murillo F, Medina I, Meehan J, Miclaus K, Moffitt RA, Montaner D, Mukherjee P, Mulligan GJ, Neville P, Nikolskaya T, Ning B, Page GP, Parker J, Parry RM, Peng X, Peterson RL, Phan JH, Quanz B, Ren Y, Riccadonna S, Roter AH, Samuelson FW, Schumacher MM, Shambaugh JD, Shi Q, Shippy R, Si S, Smalter A, Sotiriou C, Soukup M, Staedtler F, Steiner G, Stokes TH, Sun Q, Tan PY, Tang R, Tezak Z, Thorn B, Tsyganova M, Turpaz Y, Vega SC, Visintainer R, von Frese J, Wang C, Wang E, Wang J, Wang W, Westermann F, Willey JC, Woods M, Wu S, Xiao N, Xu J, Xu L, Yang L, Zeng X, Zhang J, Zhang L, Zhang M, Zhao C, Puri RK, Scherf U, Tong W, Wolfinger RD; MAQC Consortium.

Nat Biotechnol. 2010 Aug;28(8):827-38. doi: 10.1038/nbt.1665. Epub 2010 Jul 30.

9.

Changes in diurnal patterns within the Populus transcriptome and metabolome in response to photoperiod variation.

Hoffman DE, Jonsson P, Bylesjö M, Trygg J, Antti H, Eriksson ME, Moritz T.

Plant Cell Environ. 2010 Aug 1;33(8):1298-313. doi: 10.1111/j.1365-3040.2010.02148.x. Epub 2010 Mar 18.

10.

A cross-species transcriptomics approach to identify genes involved in leaf development.

Street NR, Sjödin A, Bylesjö M, Gustafsson P, Trygg J, Jansson S.

BMC Genomics. 2008 Dec 5;9:589. doi: 10.1186/1471-2164-9-589.

11.

Integrated analysis of transcript, protein and metabolite data to study lignin biosynthesis in hybrid aspen.

Bylesjö M, Nilsson R, Srivastava V, Grönlund A, Johansson AI, Jansson S, Karlsson J, Moritz T, Wingsle G, Trygg J.

J Proteome Res. 2009 Jan;8(1):199-210. doi: 10.1021/pr800298s.

PMID:
19053836
12.

LAMINA: a tool for rapid quantification of leaf size and shape parameters.

Bylesjö M, Segura V, Soolanayakanahally RY, Rae AM, Trygg J, Gustafsson P, Jansson S, Street NR.

BMC Plant Biol. 2008 Jul 22;8:82. doi: 10.1186/1471-2229-8-82.

13.

Global expression profiling in leaves of free-growing aspen.

Sjödin A, Wissel K, Bylesjö M, Trygg J, Jansson S.

BMC Plant Biol. 2008 May 23;8:61. doi: 10.1186/1471-2229-8-61.

14.

K-OPLS package: kernel-based orthogonal projections to latent structures for prediction and interpretation in feature space.

Bylesjö M, Rantalainen M, Nicholson JK, Holmes E, Trygg J.

BMC Bioinformatics. 2008 Feb 19;9:106. doi: 10.1186/1471-2105-9-106.

15.

Data integration in plant biology: the O2PLS method for combined modeling of transcript and metabolite data.

Bylesjö M, Eriksson D, Kusano M, Moritz T, Trygg J.

Plant J. 2007 Dec;52(6):1181-91. Epub 2007 Oct 10.

16.

Orthogonal projections to latent structures as a strategy for microarray data normalization.

Bylesjö M, Eriksson D, Sjödin A, Jansson S, Moritz T, Trygg J.

BMC Bioinformatics. 2007 Jun 18;8:207.

17.

A multivariate approach to investigate docking parameters' effects on docking performance.

Andersson CD, Thysell E, Lindström A, Bylesjö M, Raubacher F, Linusson A.

J Chem Inf Model. 2007 Jul-Aug;47(4):1673-87. Epub 2007 Jun 9.

PMID:
17559207
18.

UPSC-BASE--Populus transcriptomics online.

Sjödin A, Bylesjö M, Skogström O, Eriksson D, Nilsson P, Rydén P, Jansson S, Karlsson J.

Plant J. 2006 Dec;48(5):806-17. Epub 2006 Nov 8.

19.

MASQOT-GUI: spot quality assessment for the two-channel microarray platform.

Bylesjö M, Sjödin A, Eriksson D, Antti H, Moritz T, Jansson S, Trygg J.

Bioinformatics. 2006 Oct 15;22(20):2554-5. Epub 2006 Aug 9.

PMID:
16899490
20.

MASQOT: a method for cDNA microarray spot quality control.

Bylesjö M, Eriksson D, Sjödin A, Sjöström M, Jansson S, Antti H, Trygg J.

BMC Bioinformatics. 2005 Oct 13;6:250.

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