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Items: 1 to 50 of 53

1.

p38γ is essential for cell cycle progression and liver tumorigenesis.

Tomás-Loba A, Manieri E, González-Terán B, Mora A, Leiva-Vega L, Santamans AM, Romero-Becerra R, Rodríguez E, Pintor-Chocano A, Feixas F, López JA, Caballero B, Trakala M, Blanco Ó, Torres JL, Hernández-Cosido L, Montalvo-Romeral V, Matesanz N, Roche-Molina M, Bernal JA, Mischo H, León M, Caballero A, Miranda-Saavedra D, Ruiz-Cabello J, Nevzorova YA, Cubero FJ, Bravo J, Vázquez J, Malumbres M, Marcos M, Osuna S, Sabio G.

Nature. 2019 Apr;568(7753):557-560. doi: 10.1038/s41586-019-1112-8. Epub 2019 Apr 10.

PMID:
30971822
2.

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

Pike KA, Hatzihristidis T, Bussières-Marmen S, Robert F, Desai N, Miranda-Saavedra D, Pelletier J, Tremblay ML.

Sci Rep. 2017 Oct 16;7(1):13275. doi: 10.1038/s41598-017-13673-w.

3.

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

Andrabi M, Hutchins AP, Miranda-Saavedra D, Kono H, Nussinov R, Mizuguchi K, Ahmad S.

Sci Rep. 2017 Jun 22;7(1):4071. doi: 10.1038/s41598-017-03199-6.

4.

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

Woo YH, Ansari H, Otto TD, Klinger CM, Kolisko M, Michálek J, Saxena A, Shanmugam D, Tayyrov A, Veluchamy A, Ali S, Bernal A, del Campo J, Cihlář J, Flegontov P, Gornik SG, Hajdušková E, Horák A, Janouškovec J, Katris NJ, Mast FD, Miranda-Saavedra D, Mourier T, Naeem R, Nair M, Panigrahi AK, Rawlings ND, Padron-Regalado E, Ramaprasad A, Samad N, Tomčala A, Wilkes J, Neafsey DE, Doerig C, Bowler C, Keeling PJ, Roos DS, Dacks JB, Templeton TJ, Waller RF, Lukeš J, Oborník M, Pain A.

Elife. 2015 Jul 15;4:e06974. doi: 10.7554/eLife.06974.

5.

A Drosophila-centric view of protein tyrosine phosphatases.

Hatzihristidis T, Desai N, Hutchins AP, Meng TC, Tremblay ML, Miranda-Saavedra D.

FEBS Lett. 2015 Apr 13;589(9):951-66. doi: 10.1016/j.febslet.2015.03.005. Epub 2015 Mar 13. Review.

6.
7.

Population of Monocyte-Derived Macrophages.

McGovern N, Schlitzer A, Gunawan M, Jardine L, Shin A, Poyner E, Green K, Dickinson R, Wang XN, Low D, Best K, Covins S, Milne P, Pagan S, Aljefri K, Windebank M, Miranda-Saavedra D, Larbi A, Wasan PS, Kaibo D, Poidinger M, Bigley V, Ginhoux F, Collin M, Haniffa M.

Immunity. 2015 Feb 17;42(2):391. doi: 10.1016/j.immuni.2015.01.018. Epub 2015 Feb 17. No abstract available.

8.

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

Hutchins AP, Jauch R, Dyla M, Miranda-Saavedra D.

Cell Regen (Lond). 2014 Jan 24;3(1):1. doi: 10.1186/2045-9769-3-1. eCollection 2014.

9.

Human dermal CD14⁺ cells are a transient population of monocyte-derived macrophages.

McGovern N, Schlitzer A, Gunawan M, Jardine L, Shin A, Poyner E, Green K, Dickinson R, Wang XN, Low D, Best K, Covins S, Milne P, Pagan S, Aljefri K, Windebank M, Miranda-Saavedra D, Larbi A, Wasan PS, Duan K, Poidinger M, Bigley V, Ginhoux F, Collin M, Haniffa M.

Immunity. 2014 Sep 18;41(3):465-477. doi: 10.1016/j.immuni.2014.08.006. Epub 2014 Sep 4. Erratum in: Immunity. 2015 Feb 17;42(2):391. Saavedra, Diego Miranda [corrected to Miranda-Saavedra, Diego]. Immunity. 2015 Feb 17;42(2):391.

10.

Genomic analysis of the causative agents of coccidiosis in domestic chickens.

Reid AJ, Blake DP, Ansari HR, Billington K, Browne HP, Bryant J, Dunn M, Hung SS, Kawahara F, Miranda-Saavedra D, Malas TB, Mourier T, Naghra H, Nair M, Otto TD, Rawlings ND, Rivailler P, Sanchez-Flores A, Sanders M, Subramaniam C, Tay YL, Woo Y, Wu X, Barrell B, Dear PH, Doerig C, Gruber A, Ivens AC, Parkinson J, Rajandream MA, Shirley MW, Wan KL, Berriman M, Tomley FM, Pain A.

Genome Res. 2014 Oct;24(10):1676-85. doi: 10.1101/gr.168955.113. Epub 2014 Jul 11.

11.

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

Liu F, Miranda-Saavedra D.

Gene. 2014 Aug 10;546(2):417-20. doi: 10.1016/j.gene.2014.06.016. Epub 2014 Jun 11.

PMID:
24927962
12.

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

Pike KA, Hutchins AP, Vinette V, Théberge JF, Sabbagh L, Tremblay ML, Miranda-Saavedra D.

Sci Signal. 2014 May 6;7(324):ra43. doi: 10.1126/scisignal.2005020.

PMID:
24803538
13.

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

Hardy S, Uetani N, Wong N, Kostantin E, Labbé DP, Bégin LR, Mes-Masson A, Miranda-Saavedra D, Tremblay ML.

Oncogene. 2015 Feb 19;34(8):986-95. doi: 10.1038/onc.2014.33. Epub 2014 Mar 17.

PMID:
24632616
14.

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

Hutchins AP, Diez D, Miranda-Saavedra D.

JAKSTAT. 2013 Oct 1;2(4):e25097. doi: 10.4161/jkst.25097. Epub 2013 May 20. Review.

15.

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

Banerji CR, Miranda-Saavedra D, Severini S, Widschwendter M, Enver T, Zhou JX, Teschendorff AE.

Sci Rep. 2013 Oct 24;3:3039. doi: 10.1038/srep03039.

16.

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

Diez D, Hutchins AP, Miranda-Saavedra D.

Nucleic Acids Res. 2014 Jan;42(1):e6. doi: 10.1093/nar/gkt913. Epub 2013 Oct 16.

17.

Characterization of PTPN2 and its use as a biomarker.

Bussières-Marmen S, Hutchins AP, Schirbel A, Rebert N, Tiganis T, Fiocchi C, Miranda-Saavedra D, Tremblay ML.

Methods. 2014 Jan 15;65(2):239-46. doi: 10.1016/j.ymeth.2013.08.020. Epub 2013 Aug 30.

PMID:
23994241
18.

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

Hutchins AP, Diez D, Miranda-Saavedra D.

Brief Funct Genomics. 2013 Nov;12(6):489-98. doi: 10.1093/bfgp/elt028. Epub 2013 Aug 12. Review.

19.

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

Hatzihristidis T, Liu S, Pryszcz L, Hutchins AP, Gabaldón T, Tremblay ML, Miranda-Saavedra D.

Methods. 2014 Jan 15;65(2):156-64. doi: 10.1016/j.ymeth.2013.07.031. Epub 2013 Jul 31.

PMID:
23911837
20.

PTP1B: a simple enzyme for a complex world.

Feldhammer M, Uetani N, Miranda-Saavedra D, Tremblay ML.

Crit Rev Biochem Mol Biol. 2013 Sep-Oct;48(5):430-45. doi: 10.3109/10409238.2013.819830. Epub 2013 Jul 23. Review.

PMID:
23879520
21.

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

Bonzanni N, Garg A, Feenstra KA, Schütte J, Kinston S, Miranda-Saavedra D, Heringa J, Xenarios I, Göttgens B.

Bioinformatics. 2013 Jul 1;29(13):i80-8. doi: 10.1093/bioinformatics/btt243.

22.

The repertoires of ubiquitinating and deubiquitinating enzymes in eukaryotic genomes.

Hutchins AP, Liu S, Diez D, Miranda-Saavedra D.

Mol Biol Evol. 2013 May;30(5):1172-87. doi: 10.1093/molbev/mst022. Epub 2013 Feb 7.

23.

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

Clarke M, Lohan AJ, Liu B, Lagkouvardos I, Roy S, Zafar N, Bertelli C, Schilde C, Kianianmomeni A, Bürglin TR, Frech C, Turcotte B, Kopec KO, Synnott JM, Choo C, Paponov I, Finkler A, Heng Tan CS, Hutchins AP, Weinmeier T, Rattei T, Chu JS, Gimenez G, Irimia M, Rigden DJ, Fitzpatrick DA, Lorenzo-Morales J, Bateman A, Chiu CH, Tang P, Hegemann P, Fromm H, Raoult D, Greub G, Miranda-Saavedra D, Chen N, Nash P, Ginger ML, Horn M, Schaap P, Caler L, Loftus BJ.

Genome Biol. 2013 Feb 1;14(2):R11. doi: 10.1186/gb-2013-14-2-r11.

24.

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

Hutchins AP, Diez D, Takahashi Y, Ahmad S, Jauch R, Tremblay ML, Miranda-Saavedra D.

Nucleic Acids Res. 2013 Feb 1;41(4):2155-70. doi: 10.1093/nar/gks1300. Epub 2013 Jan 7.

25.

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

Bruna A, Greenwood W, Le Quesne J, Teschendorff A, Miranda-Saavedra D, Rueda OM, Sandoval JL, Vidakovic AT, Saadi A, Pharoah P, Stingl J, Caldas C.

Nat Commun. 2012;3:1055. doi: 10.1038/ncomms2039.

PMID:
22968701
26.

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

Urbaniak MD, Mathieson T, Bantscheff M, Eberhard D, Grimaldi R, Miranda-Saavedra D, Wyatt P, Ferguson MA, Frearson J, Drewes G.

ACS Chem Biol. 2012 Nov 16;7(11):1858-65. doi: 10.1021/cb300326z. Epub 2012 Aug 23.

27.

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

Hutchins AP, Poulain S, Fujii H, Miranda-Saavedra D.

Genomics. 2012 Nov;100(5):303-13. doi: 10.1016/j.ygeno.2012.07.014. Epub 2012 Aug 4.

28.

The kinomes of apicomplexan parasites.

Miranda-Saavedra D, Gabaldón T, Barton GJ, Langsley G, Doerig C.

Microbes Infect. 2012 Aug;14(10):796-810. doi: 10.1016/j.micinf.2012.04.007. Epub 2012 Apr 26. Review.

PMID:
22587893
29.

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

Fernández M, Miranda-Saavedra D.

Nucleic Acids Res. 2012 May;40(10):e77. doi: 10.1093/nar/gks149. Epub 2012 Feb 10.

30.

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

Hutchins AP, Poulain S, Miranda-Saavedra D.

Blood. 2012 Mar 29;119(13):e110-9. doi: 10.1182/blood-2011-09-381483. Epub 2012 Feb 9.

PMID:
22323479
31.

Deep evolutionary conservation of an intramolecular protein kinase activation mechanism.

Han J, Miranda-Saavedra D, Luebbering N, Singh A, Sibbet G, Ferguson MA, Cleghon V.

PLoS One. 2012;7(1):e29702. doi: 10.1371/journal.pone.0029702. Epub 2012 Jan 3.

32.

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

Reininger L, Wilkes JM, Bourgade H, Miranda-Saavedra D, Doerig C.

Mol Microbiol. 2011 Jan;79(1):205-21. doi: 10.1111/j.1365-2958.2010.07442.x. Epub 2010 Nov 10.

33.

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

Cano F, Miranda-Saavedra D, Lehner PJ.

Biochem Soc Trans. 2010 Dec;38(6):1621-6. doi: 10.1042/BST0381621.

PMID:
21118137
34.

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

Bachmann PS, Piazza RG, Janes ME, Wong NC, Davies C, Mogavero A, Bhadri VA, Szymanska B, Geninson G, Magistroni V, Cazzaniga G, Biondi A, Miranda-Saavedra D, Göttgens B, Saffery R, Craig JM, Marshall GM, Gambacorti-Passerini C, Pimanda JE, Lock RB.

Blood. 2010 Oct 21;116(16):3013-22. doi: 10.1182/blood-2010-05-284968. Epub 2010 Jul 20.

PMID:
20647567
35.

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

Cock JM, Sterck L, Rouzé P, Scornet D, Allen AE, Amoutzias G, Anthouard V, Artiguenave F, Aury JM, Badger JH, Beszteri B, Billiau K, Bonnet E, Bothwell JH, Bowler C, Boyen C, Brownlee C, Carrano CJ, Charrier B, Cho GY, Coelho SM, Collén J, Corre E, Da Silva C, Delage L, Delaroque N, Dittami SM, Doulbeau S, Elias M, Farnham G, Gachon CM, Gschloessl B, Heesch S, Jabbari K, Jubin C, Kawai H, Kimura K, Kloareg B, Küpper FC, Lang D, Le Bail A, Leblanc C, Lerouge P, Lohr M, Lopez PJ, Martens C, Maumus F, Michel G, Miranda-Saavedra D, Morales J, Moreau H, Motomura T, Nagasato C, Napoli CA, Nelson DR, Nyvall-Collén P, Peters AF, Pommier C, Potin P, Poulain J, Quesneville H, Read B, Rensing SA, Ritter A, Rousvoal S, Samanta M, Samson G, Schroeder DC, Ségurens B, Strittmatter M, Tonon T, Tregear JW, Valentin K, von Dassow P, Yamagishi T, Van de Peer Y, Wincker P.

Nature. 2010 Jun 3;465(7298):617-21. doi: 10.1038/nature09016.

PMID:
20520714
36.

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium.

Ma LJ, van der Does HC, Borkovich KA, Coleman JJ, Daboussi MJ, Di Pietro A, Dufresne M, Freitag M, Grabherr M, Henrissat B, Houterman PM, Kang S, Shim WB, Woloshuk C, Xie X, Xu JR, Antoniw J, Baker SE, Bluhm BH, Breakspear A, Brown DW, Butchko RA, Chapman S, Coulson R, Coutinho PM, Danchin EG, Diener A, Gale LR, Gardiner DM, Goff S, Hammond-Kosack KE, Hilburn K, Hua-Van A, Jonkers W, Kazan K, Kodira CD, Koehrsen M, Kumar L, Lee YH, Li L, Manners JM, Miranda-Saavedra D, Mukherjee M, Park G, Park J, Park SY, Proctor RH, Regev A, Ruiz-Roldan MC, Sain D, Sakthikumar S, Sykes S, Schwartz DC, Turgeon BG, Wapinski I, Yoder O, Young S, Zeng Q, Zhou S, Galagan J, Cuomo CA, Kistler HC, Rep M.

Nature. 2010 Mar 18;464(7287):367-73. doi: 10.1038/nature08850.

37.

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

Kinstrie R, Luebbering N, Miranda-Saavedra D, Sibbet G, Han J, Lochhead PA, Cleghon V.

Sci Signal. 2010 Mar 2;3(111):ra16. doi: 10.1126/scisignal.2000579.

38.

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

Kantorovitz MR, Kazemian M, Kinston S, Miranda-Saavedra D, Zhu Q, Robinson GE, Göttgens B, Halfon MS, Sinha S.

Dev Cell. 2009 Oct;17(4):568-79. doi: 10.1016/j.devcel.2009.09.002.

39.

Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication.

Ma LJ, Ibrahim AS, Skory C, Grabherr MG, Burger G, Butler M, Elias M, Idnurm A, Lang BF, Sone T, Abe A, Calvo SE, Corrochano LM, Engels R, Fu J, Hansberg W, Kim JM, Kodira CD, Koehrsen MJ, Liu B, Miranda-Saavedra D, O'Leary S, Ortiz-Castellanos L, Poulter R, Rodriguez-Romero J, Ruiz-Herrera J, Shen YQ, Zeng Q, Galagan J, Birren BW, Cuomo CA, Wickes BL.

PLoS Genet. 2009 Jul;5(7):e1000549. doi: 10.1371/journal.pgen.1000549. Epub 2009 Jul 3.

40.

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

Wood AD, Chen E, Donaldson IJ, Hattangadi S, Burke KA, Dawson MA, Miranda-Saavedra D, Lodish HF, Green AR, Göttgens B.

Blood. 2009 Aug 27;114(9):1820-30. doi: 10.1182/blood-2009-02-206573. Epub 2009 Jul 1.

41.

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

Nett IR, Martin DM, Miranda-Saavedra D, Lamont D, Barber JD, Mehlert A, Ferguson MA.

Mol Cell Proteomics. 2009 Jul;8(7):1527-38. doi: 10.1074/mcp.M800556-MCP200. Epub 2009 Apr 4.

42.

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

Wilson NK, Miranda-Saavedra D, Kinston S, Bonadies N, Foster SD, Calero-Nieto F, Dawson MA, Donaldson IJ, Dumon S, Frampton J, Janky R, Sun XH, Teichmann SA, Bannister AJ, Göttgens B.

Blood. 2009 May 28;113(22):5456-65. doi: 10.1182/blood-2009-01-200048. Epub 2009 Apr 3.

PMID:
19346495
43.

A HaemAtlas: characterizing gene expression in differentiated human blood cells.

Watkins NA, Gusnanto A, de Bono B, De S, Miranda-Saavedra D, Hardie DL, Angenent WG, Attwood AP, Ellis PD, Erber W, Foad NS, Garner SF, Isacke CM, Jolley J, Koch K, Macaulay IC, Morley SL, Rendon A, Rice KM, Taylor N, Thijssen-Timmer DC, Tijssen MR, van der Schoot CE, Wernisch L, Winzer T, Dudbridge F, Buckley CD, Langford CF, Teichmann S, Göttgens B, Ouwehand WH; Bloodomics Consortium.

Blood. 2009 May 7;113(19):e1-9. doi: 10.1182/blood-2008-06-162958. Epub 2009 Feb 19.

44.

BloodExpress: a database of gene expression in mouse haematopoiesis.

Miranda-Saavedra D, De S, Trotter MW, Teichmann SA, Göttgens B.

Nucleic Acids Res. 2009 Jan;37(Database issue):D873-9. doi: 10.1093/nar/gkn854. Epub 2008 Nov 4.

45.

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

Martin DM, Miranda-Saavedra D, Barton GJ.

Nucleic Acids Res. 2009 Jan;37(Database issue):D244-50. doi: 10.1093/nar/gkn834. Epub 2008 Oct 30.

46.

Transcriptional regulatory networks in haematopoiesis.

Miranda-Saavedra D, Göttgens B.

Curr Opin Genet Dev. 2008 Dec;18(6):530-5. doi: 10.1016/j.gde.2008.09.001. Epub 2008 Oct 7. Review.

PMID:
18838119
47.
48.

Draft genome of the filarial nematode parasite Brugia malayi.

Ghedin E, Wang S, Spiro D, Caler E, Zhao Q, Crabtree J, Allen JE, Delcher AL, Guiliano DB, Miranda-Saavedra D, Angiuoli SV, Creasy T, Amedeo P, Haas B, El-Sayed NM, Wortman JR, Feldblyum T, Tallon L, Schatz M, Shumway M, Koo H, Salzberg SL, Schobel S, Pertea M, Pop M, White O, Barton GJ, Carlow CK, Crawford MJ, Daub J, Dimmic MW, Estes CF, Foster JM, Ganatra M, Gregory WF, Johnson NM, Jin J, Komuniecki R, Korf I, Kumar S, Laney S, Li BW, Li W, Lindblom TH, Lustigman S, Ma D, Maina CV, Martin DM, McCarter JP, McReynolds L, Mitreva M, Nutman TB, Parkinson J, Peregrín-Alvarez JM, Poole C, Ren Q, Saunders L, Sluder AE, Smith K, Stanke M, Unnasch TR, Ware J, Wei AD, Weil G, Williams DJ, Zhang Y, Williams SA, Fraser-Liggett C, Slatko B, Blaxter ML, Scott AL.

Science. 2007 Sep 21;317(5845):1756-60.

49.
50.

Classification and functional annotation of eukaryotic protein kinases.

Miranda-Saavedra D, Barton GJ.

Proteins. 2007 Sep 1;68(4):893-914.

PMID:
17557329

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