D. Miranda-Saavedra

发表

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

Michael Fernández, D. Miranda-Saavedra, Diego Miranda-Saavedra, 2012, Nucleic acids research.

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

Corinne Da Silva, Susana M. Coelho, J. Poulain, 2010, Nature.

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

K. Mizuguchi, R. Nussinov, H. Kono, 2017, Scientific Reports.

Genome-wide transcription factor activities are explained by intrinsic conformational dynamics of binding-sites and distal flanking-regions

K. Mizuguchi, R. Nussinov, H. Kono, 2015, bioRxiv.

Source (or Part of the following Source): Type Article Title Comparative Genomics Reveals Mobile Pathogenicity Chromosomes in Fusarium Author(s)

Christina A. Cuomo, M. Grabherr, Q. Zeng, 2022 .

Classification and functional annotation of eukaryotic protein kinases

G. Barton, D. Miranda-Saavedra, Diego Miranda-Saavedra, 2007, Proteins.

The Repertoires of Ubiquitinating and Deubiquitinating Enzymes in Eukaryotic Genomes

Diego Miranda-Saavedra, Diego Diez, Andrew Paul Hutchins, 2013, Molecular biology and evolution.

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

S. Severini, A. Teschendorff, M. Widschwendter, 2013, Scientific Reports.

Genomic Analysis of the Basal Lineage Fungus Rhizopus oryzae Reveals a Whole-Genome Duplication

Ashraf S. Ibrahim, Diego Miranda-Saavedra, Marek Elias, 2009, PLoS genetics.

Draft Genome Sequence of the Sexually Transmitted Pathogen Trichomonas vaginalis

Richard D. Hayes, Shelby L. Bidwell, Joana C. Silva, 2007, Science.

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

H. Lodish, B. Göttgens, A. Green, 2009, Blood.

Draft Genome of the Filarial Nematode Parasite Brugia malayi

Jonathan E. Allen, Matthew W. Dimmic, David M. A. Martin, 2007, Science.

A HaemAtlas: characterizing gene expression in differentiated human blood cells

S. Teichmann, W. Ouwehand, A. Attwood, 2008, Blood.

Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse.

Diego Miranda-Saavedra, Berthold Göttgens, Marc S. Halfon, 2009, Developmental cell.

TGFβ induces the formation of tumour-initiating cells in claudinlow breast cancer

Diego Miranda-Saavedra, Carlos Caldas, Alejandra Bruna, 2012, Nature Communications.

Genomic analysis of the causative agents of coccidiosis in domestic chickens

Tareq B. Malas, B. Barrell, J. Parkinson, 2014, Genome research.

Computational analysis of apicomplexan kinomes.

N. Kannan, D. Miranda-Saavedra, Eric Talevich, 2013 .

1 The kinomes of apicomplexan parasites

G. Barton, D. Miranda-Saavedra, T. Gabaldón, 2013 .

Systematic identification of transcriptional regulatory modules from protein–protein interaction networks

Diego Miranda-Saavedra, Diego Diez, Andrew Paul Hutchins, 2013, Nucleic acids research.

Transcriptional regulatory networks in haematopoiesis.

B. Göttgens, D. Miranda-Saavedra, Diego Miranda-Saavedra, 2008, Current opinion in genetics & development.

TC-PTP regulates the IL-7 transcriptional response during murine early T cell development

J. Pelletier, D. Miranda-Saavedra, M. Tremblay, 2017, Scientific Reports.

The Phosphoproteome of Bloodstream Form Trypanosoma brucei, Causative Agent of African Sleeping Sickness

Jonathan D. Barber, Diego Miranda-Saavedra, David M. A. Martin, 2009, Molecular & Cellular Proteomics.

The complement of protein kinases of the microsporidium Encephalitozoon cuniculi in relation to those of Saccharomyces cerevisiae and Schizosaccharomyces pombe

G. Barton, D. Miranda-Saavedra, M. Stark, 2007, BMC Genomics.

The protein tyrosine phosphatase PRL-2 interacts with the magnesium transporter CNNM3 to promote oncogenesis

L. Bégin, A. Mes-Masson, S. Hardy, 2014, Oncogene.

Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling

Klaus O. Kopec, P. Hegemann, A. Bateman, 2013, Genome Biology.

Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites

Diego Miranda-Saavedra, Neil D Rawlings, Chris Bowler, 2015, eLife.

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

D. Miranda-Saavedra, C. Doerig, L. Reininger, 2011, Molecular microbiology.

p38γ is essential for cell cycle progression and liver tumorigenesis

M. Malumbres, J. Bravo, F. Feixas, 2019, Nature.

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

D. Miranda-Saavedra, A. Hutchins, Diego Diez, 2013, Briefings in functional genomics.

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

Geoffrey J. Barton, Diego Miranda-Saavedra, David M. A. Martin, 2008, Nucleic Acids Res..

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

Diego Miranda-Saavedra, Andrew Paul Hutchins, D. Miranda-Saavedra, 2015, Scientific Reports.

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

D. Miranda-Saavedra, A. Hutchins, Diego Diez, 2013, JAK-STAT.

domestic chickens Genomic analysis of the causative agents of coccidiosis in Material Supplemental

Tareq B. Malas, B. Barrell, J. Parkinson, 2017 .

PTP1B: A simple enzyme for a complex world

D. Miranda-Saavedra, M. Tremblay, N. Uetani, 2013, Critical reviews in biochemistry and molecular biology.

The transcriptional program controlled by the stem cell leukemia gene Scl/Tal1 during early embryonic hematopoietic development.

Mark A. Dawson, Diego Miranda-Saavedra, Sarah A. Teichmann, 2009, Blood.

The kinomes of apicomplexan parasites.

G. Barton, D. Miranda-Saavedra, T. Gabaldón, 2012, Microbes and infection.

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

D. Miranda-Saavedra, A. Hutchins, S. Poulain, 2012, Blood.

Emerging roles of pseudokinases.

G. Barton, D. Alessi, D. Miranda-Saavedra, 2006, Trends in cell biology.

A Drosophila‐centric view of protein tyrosine phosphatases

D. Miranda-Saavedra, A. Hutchins, M. Tremblay, 2015, FEBS letters.

Characterization of PTPN2 and its use as a biomarker.

D. Miranda-Saavedra, A. Hutchins, M. Tremblay, 2014, Methods.

The Ectocarpus genome and brown algal genomics: the Ectocarpus Genome Consortium

Corinne Da Silva, Gildas Le Corguillé, Susana M. Coelho, 2012 .

Characterization of a Domain That Transiently Converts Class 2 DYRKs into Intramolecular Tyrosine Kinases

D. Miranda-Saavedra, P. Lochhead, Nathan Luebbering, 2010, Science Signaling.

Epigenetic silencing of BIM in glucocorticoid poor-responsive pediatric acute lymphoblastic leukemia, and its reversal by histone deacetylase inhibition.

B. Göttgens, J. Pimanda, A. Mogavero, 2010, Blood.

The IL-10 / STAT 3-mediated anti-inflammatory response : recent developments and future challenges

D. Miranda-Saavedra, A. Hutchins, Diego Diez, 2013 .

Genome Analysis of the Unicellular Green Alga Chlamydomonas reinhardtii Indicates an Ancient Evolutionary Origin for Key Pattern Recognition and Cell-Signaling Protein Families

G. Barton, D. Miranda-Saavedra, G. Wheeler, 2008, Genetics.

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

P. Lehner, D. Miranda-Saavedra, F. Cano, 2010, Biochemical Society transactions.

p38γ is essential for cell cycle progression and liver tumorigenesis

M. Malumbres, J. Bravo, F. Feixas, 2019, Nature.

Chemical Proteomic Analysis Reveals the Drugability of the Kinome of Trypanosoma brucei

Michael D. Urbaniak, G. Drewes, M. Bantscheff, 2012, ACS chemical biology.

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

D. Miranda-Saavedra, A. Hutchins, H. Fujii, 2012, Genomics.

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

Ioannis Xenarios, Jaap Heringa, Diego Miranda-Saavedra, 2013, Bioinform..

BloodExpress: a database of gene expression in mouse haematopoiesis

Subhajyoti De, Diego Miranda-Saavedra, Matthew W. Trotter, 2008, Nucleic Acids Res..

inhibition acute lymphoblastic leukemia, and its reversal by histone deacetylase in glucocorticoid poor-responsive pediatric BIM Epigenetic silencing of

B. Göttgens, J. Pimanda, D. Miranda-Saavedra, 2012 .

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

Diego Miranda-Saavedra, Toni Gabaldón, Andrew P Hutchins, 2014, Methods.

Deep Evolutionary Conservation of an Intramolecular Protein Kinase Activation Mechanism

M. Ferguson, D. Miranda-Saavedra, Nathan Luebbering, 2012, PloS one.

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

Ralf Jauch, Andrew Paul Hutchins, Mateusz Dyla, 2014, Cell Regeneration.

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

Diego Miranda-Saavedra, Diego Diez, Ralf Jauch, 2013, Nucleic acids research.

Population of Monocyte-Derived Macrophages

N. McGovern, F. Ginhoux, A. Schlitzer, 2015, Immunity.

TC-PTP regulates the IL-7 transcriptional response during murine early T cell development

J. Pelletier, D. Miranda-Saavedra, M. Tremblay, 2017, Scientific Reports.

Protein Tyrosine Phosphatase 1B Is a Regulator of the Interleukin-10–Induced Transcriptional Program in Macrophages

D. Miranda-Saavedra, A. Hutchins, M. Tremblay, 2014, Science Signaling.