Publications by authors named "Mika Gustafsson"

30Publications

MODifieR: an Ensemble R Package for Inference of Disease Modules from Transcriptomics Networks.

Bioinformatics 2020 Jun;36(12):3918-3919

School of Bioscience, Systems Biology Research Center, Skövde 541 45, Sweden.

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http://dx.doi.org/10.1093/bioinformatics/btaa235DOI Listing
June 2020

Pre- and postnatal Lactobacillus reuteri treatment alters DNA methylation of infant T helper cells.

Pediatr Allergy Immunol 2020 Jul 3;31(5):544-553. Epub 2020 Apr 3.

Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden.

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http://dx.doi.org/10.1111/pai.13240DOI Listing
July 2020

Deriving disease modules from the compressed transcriptional space embedded in a deep autoencoder.

Nat Commun 2020 02 12;11(1):856. Epub 2020 Feb 12.

Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.

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http://dx.doi.org/10.1038/s41467-020-14666-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7016183PMC
February 2020

LiPLike: towards gene regulatory network predictions of high certainty.

Bioinformatics 2020 04;36(8):2522-2529

Department of Physics, Chemistry and Biology, Linköping University, Linköping 581 83, Sweden.

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http://dx.doi.org/10.1093/bioinformatics/btz950DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7178405PMC
April 2020

Identification of DNA methylation patterns predisposing for an efficient response to BCG vaccination in healthy BCG-naïve subjects.

Epigenetics 2019 06 22;14(6):589-601. Epub 2019 Apr 22.

a Department of Clinical and Experimental Medicine (IKE), Faculty of Medicine and Health Sciences , Linköping University , Linköping , Sweden.

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http://dx.doi.org/10.1080/15592294.2019.1603963DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6557603PMC
June 2019

Potential Involvement of Type I Interferon Signaling in Immunotherapy in Seasonal Allergic Rhinitis.

J Immunol Res 2016 19;2016:5153184. Epub 2016 Dec 19.

The Centre for Personalized Medicine, Department of Clinical and Experimental Medicine, Division of Pediatrics, Linkoping University, Linkoping, Sweden.

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http://dx.doi.org/10.1155/2016/5153184DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5209614PMC
March 2017

Cross-talks via mTORC2 can explain enhanced activation in response to insulin in diabetic patients.

Biosci Rep 2017 02 24;37(1). Epub 2017 Jan 24.

Department of Biomedical Engineering, Linköping University, Sweden

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http://dx.doi.org/10.1042/BSR20160514DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5271673PMC
February 2017

Cancer network activity associated with therapeutic response and synergism.

Genome Med 2016 08 24;8(1):88. Epub 2016 Aug 24.

Breast Cancer and Systems Biology Lab, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), Gran via 199, L'Hospitalet del Llobregat, Barcelona, 08908, Catalonia, Spain.

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http://dx.doi.org/10.1186/s13073-016-0340-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4995628PMC
August 2016

Facing the challenges of multiscale modelling of bacterial and fungal pathogen-host interactions.

Brief Funct Genomics 2017 03;16(2):57-69

Leibniz-Institute for Natural Product Research and Infection Biology-Hans-Knoell-Institute, Jena, Germany.

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http://dx.doi.org/10.1093/bfgp/elv064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5439285PMC
March 2017

Targeted omics and systems medicine: personalising care.

Lancet Respir Med 2014 Oct 16;2(10):785-7. Epub 2014 Sep 16.

Centre for Individualised Medicine, Department of Pediatrics, Faculty of Medicine, Linköping University, Linköping, Sweden; Allergy Centre, Linköping University Hospital, Linköping, Sweden; Sweden Children's Clinic, Linköping University Hospital, Linköping, Sweden. Electronic address:

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http://dx.doi.org/10.1016/S2213-2600(14)70188-2DOI Listing
October 2014

Combining gene expression microarray- and cluster analysis with sequence-based predictions to identify regulators of IL-13 in allergy.

Cytokine 2012 Dec 13;60(3):736-40. Epub 2012 Sep 13.

The Center for Individualized Medication, Linköping University, Linköping, Sweden.

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http://dx.doi.org/10.1016/j.cyto.2012.08.009DOI Listing
December 2012

Combined multivariate and pathway analyses show that allergen-induced gene expression changes in CD4+ T cells are reversed by glucocorticoids.

PLoS One 2012 12;7(6):e39016. Epub 2012 Jun 12.

Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, Linköping, Sweden.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0039016PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3373548PMC
November 2012

Gene expression prediction by soft integration and the elastic net-best performance of the DREAM3 gene expression challenge.

PLoS One 2010 Feb 16;5(2):e9134. Epub 2010 Feb 16.

Department of Science and Technology, Linköping University, Norrköping, Sweden.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0009134PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2821917PMC
February 2010

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

Authors:
Harukazu Suzuki Alistair R R Forrest Erik van Nimwegen Carsten O Daub Piotr J Balwierz Katharine M Irvine Timo Lassmann Timothy Ravasi Yuki Hasegawa Michiel J L de Hoon Shintaro Katayama Kate Schroder Piero Carninci Yasuhiro Tomaru Mutsumi Kanamori-Katayama Atsutaka Kubosaki Altuna Akalin Yoshinari Ando Erik Arner Maki Asada Hiroshi Asahara Timothy Bailey Vladimir B Bajic Denis Bauer Anthony G Beckhouse Nicolas Bertin Johan Björkegren Frank Brombacher Erika Bulger Alistair M Chalk Joe Chiba Nicole Cloonan Adam Dawe Josee Dostie Pär G Engström Magbubah Essack Geoffrey J Faulkner J Lynn Fink David Fredman Ko Fujimori Masaaki Furuno Takashi Gojobori Julian Gough Sean M Grimmond Mika Gustafsson Megumi Hashimoto Takehiro Hashimoto Mariko Hatakeyama Susanne Heinzel Winston Hide Oliver Hofmann Michael Hörnquist Lukasz Huminiecki Kazuho Ikeo Naoko Imamoto Satoshi Inoue Yusuke Inoue Ryoko Ishihara Takao Iwayanagi Anders Jacobsen Mandeep Kaur Hideya Kawaji Markus C Kerr Ryuichiro Kimura Syuhei Kimura Yasumasa Kimura Hiroaki Kitano Hisashi Koga Toshio Kojima Shinji Kondo Takeshi Konno Anders Krogh Adele Kruger Ajit Kumar Boris Lenhard Andreas Lennartsson Morten Lindow Marina Lizio Cameron Macpherson Norihiro Maeda Christopher A Maher Monique Maqungo Jessica Mar Nicholas A Matigian Hideo Matsuda John S Mattick Stuart Meier Sei Miyamoto Etsuko Miyamoto-Sato Kazuhiko Nakabayashi Yutaka Nakachi Mika Nakano Sanne Nygaard Toshitsugu Okayama Yasushi Okazaki Haruka Okuda-Yabukami Valerio Orlando Jun Otomo Mikhail Pachkov Nikolai Petrovsky Charles Plessy John Quackenbush Aleksandar Radovanovic Michael Rehli Rintaro Saito Albin Sandelin Sebastian Schmeier Christian Schönbach Ariel S Schwartz Colin A Semple Miho Sera Jessica Severin Katsuhiko Shirahige Cas Simons George St Laurent Masanori Suzuki Takahiro Suzuki Matthew J Sweet Ryan J Taft Shizu Takeda Yoichi Takenaka Kai Tan Martin S Taylor Rohan D Teasdale Jesper Tegnér Sarah Teichmann Eivind Valen Claes Wahlestedt Kazunori Waki Andrew Waterhouse Christine A Wells Ole Winther Linda Wu Kazumi Yamaguchi Hiroshi Yanagawa Jun Yasuda Mihaela Zavolan David A Hume Takahiro Arakawa Shiro Fukuda Kengo Imamura Chikatoshi Kai Ai Kaiho Tsugumi Kawashima Chika Kawazu Yayoi Kitazume Miki Kojima Hisashi Miura Kayoko Murakami Mitsuyoshi Murata Noriko Ninomiya Hiromi Nishiyori Shohei Noma Chihiro Ogawa Takuma Sano Christophe Simon Michihira Tagami Yukari Takahashi Jun Kawai Yoshihide Hayashizaki

Nat Genet 2009 May 19;41(5):553-62. Epub 2009 Apr 19.

RIKEN Omics Science Center, RIKEN Yokohama Institute, Kanagawa, Japan.

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http://dx.doi.org/10.1038/ng.375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6711855PMC
May 2009

Constructing and analyzing a large-scale gene-to-gene regulatory network--lasso-constrained inference and biological validation.

IEEE/ACM Trans Comput Biol Bioinform 2005 Jul-Sep;2(3):254-61

Department of Science and Technology, Linköping University (Campus Norrköping), Norrköping, Sweden.

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http://dx.doi.org/10.1109/TCBB.2005.35DOI Listing
November 2006