Diego Miranda-Saavedra

Diego Miranda-Saavedra

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Diego Miranda-Saavedra

Diego Miranda-Saavedra

Publications by authors named "Diego Miranda-Saavedra"

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51Publications

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Predicting conformational ensembles and genome-wide transcription factor binding sites from DNA sequences.

Sci Rep 2017 06 22;7(1):4071. Epub 2017 Jun 22.

National Institutes of Biomedical Innovation Health and Nutrition, 7-6-8, Saito-Asagi, Ibaraki, Osaka, 5670085, Japan.

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http://dx.doi.org/10.1038/s41598-017-03199-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5481346PMC
June 2017

A Drosophila-centric view of protein tyrosine phosphatases.

FEBS Lett 2015 Apr 13;589(9):951-66. Epub 2015 Mar 13.

World Premier International (WPI) Immunology Frontier Research Center (IFReC), Osaka University, 3-1 Yamadaoka, Suita 565-0871, Osaka, Japan; Centro de Biología Molecular Severo Ochoa, CSIC/Universidad Autónoma de Madrid, 28049 Madrid, Spain; IE Business School, IE University, María de Molina 31 bis, 28006 Madrid, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.febslet.2015.03.005DOI Listing
April 2015

Genomic analysis of LPS-stimulated myeloid cells identifies a common pro-inflammatory response but divergent IL-10 anti-inflammatory responses.

Sci Rep 2015 Mar 13;5:9100. Epub 2015 Mar 13.

1] World Premier International (WPI) Immunology Frontier Research Center (IFReC), Osaka University, 3-1 Yamadaoka, Suita, 565-0871 Osaka, Japan [2] Centro de Biología Molecular Severo Ochoa, CSIC/Universidad Autónoma de Madrid, 28049 Madrid, Spain [3] IE Business School, IE University, María de Molina 31 bis, 28006 Madrid, Spain.

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http://dx.doi.org/10.1038/srep09100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4650320PMC
March 2015

glbase: a framework for combining, analyzing and displaying heterogeneous genomic and high-throughput sequencing data.

Cell Regen (Lond) 2014 24;3(1). Epub 2014 Jan 24.

Fibrosis Laboratories, Institute of Cellular Medicine, Newcastle University Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH UK.

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http://dx.doi.org/10.1186/2045-9769-3-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4230833PMC
November 2014

rTRM-web: a web tool for predicting transcriptional regulatory modules for ChIP-seq-ed transcription factors.

Gene 2014 Aug 11;546(2):417-20. Epub 2014 Jun 11.

Fibrosis Laboratories, Institute of Cellular Medicine, Newcastle University Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom. Electronic address:

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http://dx.doi.org/10.1016/j.gene.2014.06.016DOI Listing
August 2014

PTP1B: a simple enzyme for a complex world.

Crit Rev Biochem Mol Biol 2013 Sep-Oct;48(5):430-45. Epub 2013 Jul 23.

Goodman Cancer Research Center .

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http://dx.doi.org/10.3109/10409238.2013.819830DOI Listing
May 2014

Protein tyrosine phosphatase 1B is a regulator of the interleukin-10-induced transcriptional program in macrophages.

Sci Signal 2014 May 6;7(324):ra43. Epub 2014 May 6.

1Goodman Cancer Research Centre, McGill University, 1160 Pine Avenue, Montreal, Quebec H3A 1A3, Canada.

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http://dx.doi.org/10.1126/scisignal.2005020DOI Listing
May 2014

PTP-central: a comprehensive resource of protein tyrosine phosphatases in eukaryotic genomes.

Methods 2014 Jan 31;65(2):156-64. Epub 2013 Jul 31.

Bioinformatics and Genomics Laboratory, World Premier International (WPI), Immunology Frontier Research Center (IFReC), Osaka University, 3-1 Yamadaoka, Suita, 565-0871 Osaka, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2013.07.031DOI Listing
January 2014

Characterization of PTPN2 and its use as a biomarker.

Methods 2014 Jan 30;65(2):239-46. Epub 2013 Aug 30.

Goodman Cancer Research Center, McGill University, Montreal, QC, Canada; Department of Biochemistry, McGill University, Montreal, QC, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2013.08.020DOI Listing
January 2014

Systematic identification of transcriptional regulatory modules from protein-protein interaction networks.

Nucleic Acids Res 2014 Jan 16;42(1):e6. Epub 2013 Oct 16.

World Premier International (WPI) Immunology Frontier Research Center (IFReC), Osaka University, 3-1 Yamadaoka, Suita 565-0871, Osaka, Japan, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Ave, Guangzhou 510663, China and Fibrosis Laboratories, Institute of Cellular Medicine, Newcastle University Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom.

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http://dx.doi.org/10.1093/nar/gkt913DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3874207PMC
January 2014

The IL-10/STAT3-mediated anti-inflammatory response: recent developments and future challenges.

Brief Funct Genomics 2013 Nov 12;12(6):489-98. Epub 2013 Aug 12.

Bioinformatics and Genomics Laboratory, World Premier International (WPI) Immunology Frontier Research Center (IFReC), Osaka University, 3-1 Yamadaoka, Suita, 565-0871 Osaka, Japan. Tel.: +81 6 6879 4269; Fax: +81 6 6879 4272;

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http://dx.doi.org/10.1093/bfgp/elt028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3838198PMC
November 2013

Cellular network entropy as the energy potential in Waddington's differentiation landscape.

Sci Rep 2013 Oct 24;3:3039. Epub 2013 Oct 24.

1] Statistical Cancer Genomics, Paul O'Gorman Building, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, United Kingdom [2] Centre for Mathematics and Physics in the Life Sciences and Experimental Biology, University College London, London WC1E6BT United Kingdom.

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http://dx.doi.org/10.1038/srep03039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3807110PMC
October 2013

Genomic and computational approaches to dissect the mechanisms of STAT3's universal and cell type-specific functions.

JAKSTAT 2013 Oct 20;2(4):e25097. Epub 2013 May 20.

Bioinformatics and Genomics Laboratory; World Premier International (WPI) Immunology Frontier Research Center (IFReC); Osaka University; Suita, Osaka Japan.

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http://dx.doi.org/10.4161/jkst.25097DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3876425PMC
October 2013

Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model.

Bioinformatics 2013 Jul;29(13):i80-8

IBIVU Centre for Integrative Bioinformatics, VU University Amsterdam, AIMMS Amsterdam Institute for Molecules Medicines and Systems, VU University Amsterdam, De Boelelaan 1081, NKI-AVL The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btt243DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694641PMC
July 2013

The repertoires of ubiquitinating and deubiquitinating enzymes in eukaryotic genomes.

Mol Biol Evol 2013 May 7;30(5):1172-87. Epub 2013 Feb 7.

Bioinformatics and Genomics Laboratory, World Premier International Immunology Frontier Research Center, Osaka University, Osaka, Japan.

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http://dx.doi.org/10.1093/molbev/mst022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3670738PMC
May 2013

Distinct transcriptional regulatory modules underlie STAT3's cell type-independent and cell type-specific functions.

Nucleic Acids Res 2013 Feb 7;41(4):2155-70. Epub 2013 Jan 7.

World Premier International (WPI) Immunology Frontier Research Center (IFReC), Osaka University, 3-1 Yamadaoka, Suita, 565-0871 Osaka, Japan.

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http://dx.doi.org/10.1093/nar/gks1300DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3575808PMC
February 2013

Discovery and characterization of new transcripts from RNA-seq data in mouse CD4(+) T cells.

Genomics 2012 Nov 4;100(5):303-13. Epub 2012 Aug 4.

World Premier International Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, 565-0871, Osaka, Japan.

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http://dx.doi.org/10.1016/j.ygeno.2012.07.014DOI Listing
November 2012

Chemical proteomic analysis reveals the drugability of the kinome of Trypanosoma brucei.

ACS Chem Biol 2012 Nov 23;7(11):1858-65. Epub 2012 Aug 23.

Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K.

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http://dx.doi.org/10.1021/cb300326zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3621575PMC
November 2012

The kinomes of apicomplexan parasites.

Microbes Infect 2012 Aug 26;14(10):796-810. Epub 2012 Apr 26.

Bioinformatics and Genomics Laboratory, World Premier International (WPI) Immunology Frontier Research Center (IFReC), Osaka University, 3-1 Yamadaoka, Suita, 565-0871 Osaka, Japan.

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http://dx.doi.org/10.1016/j.micinf.2012.04.007DOI Listing
August 2012

Deep evolutionary conservation of an intramolecular protein kinase activation mechanism.

PLoS One 2012 3;7(1):e29702. Epub 2012 Jan 3.

Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0029702PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3250476PMC
May 2012

Genome-wide enhancer prediction from epigenetic signatures using genetic algorithm-optimized support vector machines.

Nucleic Acids Res 2012 May 10;40(10):e77. Epub 2012 Feb 10.

Bioinformatics and Genomics Laboratory, WPI-Immunology Frontier Research Center (IFReC), Osaka University, 3-1 Yamadaoka, Suita 565-0871, Osaka, Japan.

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http://dx.doi.org/10.1093/nar/gks149DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3378905PMC
May 2012

Genome-wide analysis of STAT3 binding in vivo predicts effectors of the anti-inflammatory response in macrophages.

Blood 2012 Mar 9;119(13):e110-9. Epub 2012 Feb 9.

World Premier International (WPI) Immunology Frontier Research Centre (IFReC), Osaka University, Osaka, Japan.

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http://www.bloodjournal.org/cgi/doi/10.1182/blood-2011-09-38
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http://dx.doi.org/10.1182/blood-2011-09-381483DOI Listing
March 2012

An essential Aurora-related kinase transiently associates with spindle pole bodies during Plasmodium falciparum erythrocytic schizogony.

Mol Microbiol 2011 Jan 10;79(1):205-21. Epub 2010 Nov 10.

INSERM-EPFL Joint Laboratory, Global Health Institute, EPFL-SV-GHI, Station 19, CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1111/j.1365-2958.2010.07442.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3025120PMC
January 2011

RNA-binding E3 ubiquitin ligases: novel players in nucleic acid regulation.

Biochem Soc Trans 2010 Dec;38(6):1621-6

Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK.

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http://dx.doi.org/10.1042/BST0381621DOI Listing
December 2010

The Ectocarpus genome and the independent evolution of multicellularity in brown algae.

Nature 2010 Jun;465(7298):617-21

UPMC Université Paris 6, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France.

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http://dx.doi.org/10.1038/nature09016DOI Listing
June 2010

Characterization of a domain that transiently converts class 2 DYRKs into intramolecular tyrosine kinases.

Sci Signal 2010 Mar 2;3(111):ra16. Epub 2010 Mar 2.

1Department of Immunology, Infection and Inflammation, Glasgow Biomedical Research Centre, University of Glasgow, 120 University Place, Glasgow G12 8TA, UK.

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http://stke.sciencemag.org/cgi/doi/10.1126/scisignal.2000579
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http://dx.doi.org/10.1126/scisignal.2000579DOI Listing
March 2010

ID1 promotes expansion and survival of primary erythroid cells and is a target of JAK2V617F-STAT5 signaling.

Blood 2009 Aug 1;114(9):1820-30. Epub 2009 Jul 1.

Department of Hematology, Cambridge Institute for Medical Research, Addenbrooke's Hospital, Cambridge, United Kingdom.

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http://dx.doi.org/10.1182/blood-2009-02-206573DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3942052PMC
August 2009

The phosphoproteome of bloodstream form Trypanosoma brucei, causative agent of African sleeping sickness.

Mol Cell Proteomics 2009 Jul 4;8(7):1527-38. Epub 2009 Apr 4.

Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom.

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http://www.mcponline.org/lookup/doi/10.1074/mcp.M800556-MCP2
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http://dx.doi.org/10.1074/mcp.M800556-MCP200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2716717PMC
July 2009

Kinomer v. 1.0: a database of systematically classified eukaryotic protein kinases.

Nucleic Acids Res 2009 Jan 30;37(Database issue):D244-50. Epub 2008 Oct 30.

College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkn834DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686601PMC
January 2009

BloodExpress: a database of gene expression in mouse haematopoiesis.

Nucleic Acids Res 2009 Jan 4;37(Database issue):D873-9. Epub 2008 Nov 4.

Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK.

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http://dx.doi.org/10.1093/nar/gkn854DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686428PMC
January 2009

Transcriptional regulatory networks in haematopoiesis.

Curr Opin Genet Dev 2008 Dec 7;18(6):530-5. Epub 2008 Oct 7.

Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.

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http://dx.doi.org/10.1016/j.gde.2008.09.001DOI Listing
December 2008

Classification and functional annotation of eukaryotic protein kinases.

Proteins 2007 Sep;68(4):893-914

School of Life Sciences Research, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK.

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http://doi.wiley.com/10.1002/prot.21444
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http://dx.doi.org/10.1002/prot.21444DOI Listing
September 2007

Draft genome of the filarial nematode parasite Brugia malayi.

Science 2007 Sep;317(5845):1756-60

Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.

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http://www.sciencemag.org/cgi/doi/10.1126/science.1145406
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http://dx.doi.org/10.1126/science.1145406DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2613796PMC
September 2007

Emerging roles of pseudokinases.

Trends Cell Biol 2006 Sep 1;16(9):443-52. Epub 2006 Aug 1.

MRC Protein Phosphorylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH , UK.

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http://dx.doi.org/10.1016/j.tcb.2006.07.003DOI Listing
September 2006

GOLD.db: genomics of lipid-associated disorders database.

BMC Genomics 2004 Dec 10;5(1):93. Epub 2004 Dec 10.

Institute for Genomics and Bioinformatics and Christian-Doppler-Laboratory for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria.

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http://dx.doi.org/10.1186/1471-2164-5-93DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC544894PMC
December 2004