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Items: 1 to 50 of 96

1.

Dinucleotide Degradation by REXO2 Maintains Promoter Specificity in Mammalian Mitochondria.

Nicholls TJ, Spåhr H, Jiang S, Siira SJ, Koolmeister C, Sharma S, Kauppila JHK, Jiang M, Kaever V, Rackham O, Chabes A, Falkenberg M, Filipovska A, Larsson NG, Gustafsson CM.

Mol Cell. 2019 Sep 27. pii: S1097-2765(19)30695-1. doi: 10.1016/j.molcel.2019.09.010. [Epub ahead of print]

2.

Author Correction: WWP2 regulates pathological cardiac fibrosis by modulating SMAD2 signaling.

Chen H, Moreno-Moral A, Pesce F, Devapragash N, Mancini M, Heng EL, Rotival M, Srivastava PK, Harmston N, Shkura K, Rackham OJL, Yu WP, Sun XM, Tee NGZ, Tan ELS, Barton PJR, Felkin LE, Lara-Pezzi E, Angelini G, Beltrami C, Pravenec M, Schafer S, Bottolo L, Hubner N, Emanueli C, Cook SA, Petretto E.

Nat Commun. 2019 Sep 9;10(1):4085. doi: 10.1038/s41467-019-12060-5.

3.

Integrated systems-genetic analyses reveal a network target for delaying glioma progression.

Laaniste L, Srivastava PK, Stylianou J, Syed N, Cases-Cunillera S, Shkura K, Zeng Q, Rackham OJL, Langley SR, Delahaye-Duriez A, O'Neill K, Williams M, Becker A, Roncaroli F, Petretto E, Johnson MR.

Ann Clin Transl Neurol. 2019 Sep;6(9):1616-1638. doi: 10.1002/acn3.50850. Epub 2019 Aug 17.

4.

WWP2 regulates pathological cardiac fibrosis by modulating SMAD2 signaling.

Chen H, Moreno-Moral A, Pesce F, Devapragash N, Mancini M, Heng EL, Rotival M, Srivastava PK, Harmston N, Shkura K, Rackham OJL, Yu WP, Sun XM, Tee NGZ, Tan ELS, Barton PJR, Felkin LE, Lara-Pezzi E, Angelini G, Beltrami C, Pravenec M, Schafer S, Bottolo L, Hubner N, Emanueli C, Cook SA, Petretto E.

Nat Commun. 2019 Aug 9;10(1):3616. doi: 10.1038/s41467-019-11551-9. Erratum in: Nat Commun. 2019 Sep 9;10(1):4085.

5.

Correction to: Molecular Interaction Networks to Select Factors for Cell Conversion.

Ouyang JF, Kamaraj US, Polo JM, Gough J, Rackham OJL.

Methods Mol Biol. 2019;1975:C1. doi: 10.1007/978-1-4939-9224-9_20.

PMID:
31290135
6.

Widespread Translational Control of Fibrosis in the Human Heart by RNA-Binding Proteins.

Chothani S, Schäfer S, Adami E, Viswanathan S, Widjaja AA, Langley SR, Tan J, Wang M, Quaife NM, Jian Pua C, D'Agostino G, Guna Shekeran S, George BL, Lim S, Yiqun Cao E, van Heesch S, Witte F, Felkin LE, Christodoulou EG, Dong J, Blachut S, Patone G, Barton PJR, Hubner N, Cook SA, Rackham OJL.

Circulation. 2019 Sep 10;140(11):937-951. doi: 10.1161/CIRCULATIONAHA.119.039596. Epub 2019 Jul 9.

7.

Modulation of miRNA function by natural and synthetic RNA-binding proteins in cancer.

Vos PD, Leedman PJ, Filipovska A, Rackham O.

Cell Mol Life Sci. 2019 Oct;76(19):3745-3752. doi: 10.1007/s00018-019-03163-9. Epub 2019 Jun 4. Review.

PMID:
31165201
8.

Molecular Interaction Networks to Select Factors for Cell Conversion.

Ouyang JF, Kamaraj US, Polo JM, Gough J, Rackham OJL.

Methods Mol Biol. 2019;1975:333-361. doi: 10.1007/978-1-4939-9224-9_16. Erratum in: Methods Mol Biol. 2019;1975:C1.

PMID:
31062318
9.

CirGO: an alternative circular way of visualising gene ontology terms.

Kuznetsova I, Lugmayr A, Siira SJ, Rackham O, Filipovska A.

BMC Bioinformatics. 2019 Feb 18;20(1):84. doi: 10.1186/s12859-019-2671-2.

10.

Let it RE:IN: integrating experimental observations to predict pluripotency network behaviour.

Rackham OJ, Polo JM.

EMBO J. 2019 Jan 3;38(1). pii: e101133. doi: 10.15252/embj.2018101133. Epub 2018 Dec 13. No abstract available.

PMID:
30545825
11.

Early-onset Parkinson disease caused by a mutation in CHCHD2 and mitochondrial dysfunction.

Lee RG, Sedghi M, Salari M, Shearwood AJ, Stentenbach M, Kariminejad A, Goullee H, Rackham O, Laing NG, Tajsharghi H, Filipovska A.

Neurol Genet. 2018 Oct 5;4(5):e276. doi: 10.1212/NXG.0000000000000276. eCollection 2018 Oct.

12.

Is mitochondrial gene expression coordinated or stochastic?

Lee RG, Rudler DL, Rackham O, Filipovska A.

Biochem Soc Trans. 2018 Oct 19;46(5):1239-1246. doi: 10.1042/BST20180174. Epub 2018 Oct 8. Review.

PMID:
30301847
13.

Concerted regulation of mitochondrial and nuclear non-coding RNAs by a dual-targeted RNase Z.

Siira SJ, Rossetti G, Richman TR, Perks K, Ermer JA, Kuznetsova I, Hughes L, Shearwood AJ, Viola HM, Hool LC, Rackham O, Filipovska A.

EMBO Rep. 2018 Oct;19(10). pii: e46198. doi: 10.15252/embr.201846198. Epub 2018 Aug 20.

14.

Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM.

Kummer E, Leibundgut M, Rackham O, Lee RG, Boehringer D, Filipovska A, Ban N.

Nature. 2018 Aug;560(7717):263-267. doi: 10.1038/s41586-018-0373-y. Epub 2018 Aug 8.

PMID:
30089917
15.

An Artificial Yeast Genetic Circuit Enables Deep Mutational Scanning of an Antimicrobial Resistance Protein.

Scott LH, Mathews JC, Flematti GR, Filipovska A, Rackham O.

ACS Synth Biol. 2018 Aug 17;7(8):1907-1917. doi: 10.1021/acssynbio.8b00121. Epub 2018 Jul 17.

PMID:
29979580
16.

Modular ssDNA binding and inhibition of telomerase activity by designer PPR proteins.

Spåhr H, Chia T, Lingford JP, Siira SJ, Cohen SB, Filipovska A, Rackham O.

Nat Commun. 2018 Jun 7;9(1):2212. doi: 10.1038/s41467-018-04388-1.

17.

Tighter Ligand Binding Can Compensate for Impaired Stability of an RNA-Binding Protein.

Wallis CP, Richman TR, Filipovska A, Rackham O.

ACS Chem Biol. 2018 Jun 15;13(6):1499-1505. doi: 10.1021/acschembio.8b00424. Epub 2018 May 29.

PMID:
29808990
18.

A modified yeast three-hybrid system enabling both positive and negative selections.

Wallis CP, Filipovska A, Rackham O.

Biotechnol Lett. 2018 Jul;40(7):1127-1134. doi: 10.1007/s10529-018-2567-7. Epub 2018 May 18.

PMID:
29777514
19.

PTCD1 Is Required for 16S rRNA Maturation Complex Stability and Mitochondrial Ribosome Assembly.

Perks KL, Rossetti G, Kuznetsova I, Hughes LA, Ermer JA, Ferreira N, Busch JD, Rudler DL, Spahr H, Schöndorf T, Shearwood AJ, Viola HM, Siira SJ, Hool LC, Milenkovic D, Larsson NG, Rackham O, Filipovska A.

Cell Rep. 2018 Apr 3;23(1):127-142. doi: 10.1016/j.celrep.2018.03.033.

20.

Mice lacking the mitochondrial exonuclease MGME1 accumulate mtDNA deletions without developing progeria.

Matic S, Jiang M, Nicholls TJ, Uhler JP, Dirksen-Schwanenland C, Polosa PL, Simard ML, Li X, Atanassov I, Rackham O, Filipovska A, Stewart JB, Falkenberg M, Larsson NG, Milenkovic D.

Nat Commun. 2018 Mar 23;9(1):1202. doi: 10.1038/s41467-018-03552-x.

21.

Cell Type of Origin Dictates the Route to Pluripotency.

Nefzger CM, Rossello FJ, Chen J, Liu X, Knaupp AS, Firas J, Paynter JM, Pflueger J, Buckberry S, Lim SM, Williams B, Alaei S, Faye-Chauhan K, Petretto E, Nilsson SK, Lister R, Ramialison M, Powell DR, Rackham OJL, Polo JM.

Cell Rep. 2017 Dec 5;21(10):2649-2660. doi: 10.1016/j.celrep.2017.11.029.

22.

IL-11 is a crucial determinant of cardiovascular fibrosis.

Schafer S, Viswanathan S, Widjaja AA, Lim WW, Moreno-Moral A, DeLaughter DM, Ng B, Patone G, Chow K, Khin E, Tan J, Chothani SP, Ye L, Rackham OJL, Ko NSJ, Sahib NE, Pua CJ, Zhen NTG, Xie C, Wang M, Maatz H, Lim S, Saar K, Blachut S, Petretto E, Schmidt S, Putoczki T, Guimarães-Camboa N, Wakimoto H, van Heesch S, Sigmundsson K, Lim SL, Soon JL, Chao VTT, Chua YL, Tan TE, Evans SM, Loh YJ, Jamal MH, Ong KK, Chua KC, Ong BH, Chakaramakkil MJ, Seidman JG, Seidman CE, Hubner N, Sin KYK, Cook SA.

Nature. 2017 Dec 7;552(7683):110-115. doi: 10.1038/nature24676. Epub 2017 Nov 13.

23.

LRPPRC-mediated folding of the mitochondrial transcriptome.

Siira SJ, Spåhr H, Shearwood AJ, Ruzzenente B, Larsson NG, Rackham O, Filipovska A.

Nat Commun. 2017 Nov 16;8(1):1532. doi: 10.1038/s41467-017-01221-z.

24.

RNA polymerase II primes Polycomb-repressed developmental genes throughout terminal neuronal differentiation.

Ferrai C, Torlai Triglia E, Risner-Janiczek JR, Rito T, Rackham OJ, de Santiago I, Kukalev A, Nicodemi M, Akalin A, Li M, Ungless MA, Pombo A.

Mol Syst Biol. 2017 Oct 16;13(10):946. doi: 10.15252/msb.20177754.

25.

Regulation of a minimal transcriptome by repeat domain proteins.

Ferreira N, Rackham O, Filipovska A.

Semin Cell Dev Biol. 2018 Apr;76:132-141. doi: 10.1016/j.semcdb.2017.08.037. Epub 2017 Aug 24. Review.

PMID:
28843979
26.

Adult-onset obesity is triggered by impaired mitochondrial gene expression.

Perks KL, Ferreira N, Richman TR, Ermer JA, Kuznetsova I, Shearwood AJ, Lee RG, Viola HM, Johnstone VPA, Matthews V, Hool LC, Rackham O, Filipovska A.

Sci Adv. 2017 Aug 16;3(8):e1700677. doi: 10.1126/sciadv.1700677. eCollection 2017 Aug.

27.

An atlas of human long non-coding RNAs with accurate 5' ends.

Hon CC, Ramilowski JA, Harshbarger J, Bertin N, Rackham OJ, Gough J, Denisenko E, Schmeier S, Poulsen TM, Severin J, Lizio M, Kawaji H, Kasukawa T, Itoh M, Burroughs AM, Noma S, Djebali S, Alam T, Medvedeva YA, Testa AC, Lipovich L, Yip CW, Abugessaisa I, Mendez M, Hasegawa A, Tang D, Lassmann T, Heutink P, Babina M, Wells CA, Kojima S, Nakamura Y, Suzuki H, Daub CO, de Hoon MJ, Arner E, Hayashizaki Y, Carninci P, Forrest AR.

Nature. 2017 Mar 9;543(7644):199-204. doi: 10.1038/nature21374. Epub 2017 Mar 1.

PMID:
28241135
28.

A Bayesian Approach for Analysis of Whole-Genome Bisulfite Sequencing Data Identifies Disease-Associated Changes in DNA Methylation.

Rackham OJ, Langley SR, Oates T, Vradi E, Harmston N, Srivastava PK, Behmoaras J, Dellaportas P, Bottolo L, Petretto E.

Genetics. 2017 Apr;205(4):1443-1458. doi: 10.1534/genetics.116.195008. Epub 2017 Feb 17.

29.

Simultaneous processing and degradation of mitochondrial RNAs revealed by circularized RNA sequencing.

Kuznetsova I, Siira SJ, Shearwood AJ, Ermer JA, Filipovska A, Rackham O.

Nucleic Acids Res. 2017 May 19;45(9):5487-5500. doi: 10.1093/nar/gkx104.

30.

Defects in RNA metabolism in mitochondrial disease.

Siira SJ, Shearwood AJ, Bracken CP, Rackham O, Filipovska A.

Int J Biochem Cell Biol. 2017 Apr;85:106-113. doi: 10.1016/j.biocel.2017.02.003. Epub 2017 Feb 9.

31.

Titin-truncating variants affect heart function in disease cohorts and the general population.

Schafer S, de Marvao A, Adami E, Fiedler LR, Ng B, Khin E, Rackham OJ, van Heesch S, Pua CJ, Kui M, Walsh R, Tayal U, Prasad SK, Dawes TJ, Ko NS, Sim D, Chan LL, Chin CW, Mazzarotto F, Barton PJ, Kreuchwig F, de Kleijn DP, Totman T, Biffi C, Tee N, Rueckert D, Schneider V, Faber A, Regitz-Zagrosek V, Seidman JG, Seidman CE, Linke WA, Kovalik JP, O'Regan D, Ware JS, Hubner N, Cook SA.

Nat Genet. 2017 Jan;49(1):46-53. doi: 10.1038/ng.3719. Epub 2016 Nov 21.

32.

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals.

Lizio M, Harshbarger J, Abugessaisa I, Noguchi S, Kondo A, Severin J, Mungall C, Arenillas D, Mathelier A, Medvedeva YA, Lennartsson A, Drabløs F, Ramilowski JA, Rackham O, Gough J, Andersson R, Sandelin A, Ienasescu H, Ono H, Bono H, Hayashizaki Y, Carninci P, Forrest AR, Kasukawa T, Kawaji H.

Nucleic Acids Res. 2017 Jan 4;45(D1):D737-D743. doi: 10.1093/nar/gkw995. Epub 2016 Oct 27.

33.

Computational methods for direct cell conversion.

Kamaraj US, Gough J, Polo JM, Petretto E, Rackham OJ.

Cell Cycle. 2016 Dec 16;15(24):3343-3354. doi: 10.1080/15384101.2016.1238119. Epub 2016 Oct 13. Review.

34.

Transcriptome-wide effects of a POLR3A gene mutation in patients with an unusual phenotype of striatal involvement.

Azmanov DN, Siira SJ, Chamova T, Kaprelyan A, Guergueltcheva V, Shearwood AJ, Liu G, Morar B, Rackham O, Bynevelt M, Grudkova M, Kamenov Z, Svechtarov V, Tournev I, Kalaydjieva L, Filipovska A.

Hum Mol Genet. 2016 Oct 1;25(19):4302-4314. doi: 10.1093/hmg/ddw263. Epub 2016 Aug 9.

PMID:
27506977
35.

Hierarchical RNA Processing Is Required for Mitochondrial Ribosome Assembly.

Rackham O, Busch JD, Matic S, Siira SJ, Kuznetsova I, Atanassov I, Ermer JA, Shearwood AM, Richman TR, Stewart JB, Mourier A, Milenkovic D, Larsson NG, Filipovska A.

Cell Rep. 2016 Aug 16;16(7):1874-90. doi: 10.1016/j.celrep.2016.07.031. Epub 2016 Aug 4.

36.

SLIRP stabilizes LRPPRC via an RRM-PPR protein interface.

Spåhr H, Rozanska A, Li X, Atanassov I, Lightowlers RN, Chrzanowska-Lightowlers ZM, Rackham O, Larsson NG.

Nucleic Acids Res. 2016 Aug 19;44(14):6868-82. doi: 10.1093/nar/gkw575. Epub 2016 Jun 28.

37.

Loss of the RNA-binding protein TACO1 causes late-onset mitochondrial dysfunction in mice.

Richman TR, Spåhr H, Ermer JA, Davies SM, Viola HM, Bates KA, Papadimitriou J, Hool LC, Rodger J, Larsson NG, Rackham O, Filipovska A.

Nat Commun. 2016 Jun 20;7:11884. doi: 10.1038/ncomms11884.

38.

A predictive computational framework for direct reprogramming between human cell types.

Rackham OJ, Firas J, Fang H, Oates ME, Holmes ML, Knaupp AS; FANTOM Consortium, Suzuki H, Nefzger CM, Daub CO, Shin JW, Petretto E, Forrest AR, Hayashizaki Y, Polo JM, Gough J.

Nat Genet. 2016 Mar;48(3):331-5. doi: 10.1038/ng.3487. Epub 2016 Jan 18.

PMID:
26780608
39.

Systems genetics identifies a convergent gene network for cognition and neurodevelopmental disease.

Johnson MR, Shkura K, Langley SR, Delahaye-Duriez A, Srivastava P, Hill WD, Rackham OJ, Davies G, Harris SE, Moreno-Moral A, Rotival M, Speed D, Petrovski S, Katz A, Hayward C, Porteous DJ, Smith BH, Padmanabhan S, Hocking LJ, Starr JM, Liewald DC, Visconti A, Falchi M, Bottolo L, Rossetti T, Danis B, Mazzuferi M, Foerch P, Grote A, Helmstaedter C, Becker AJ, Kaminski RM, Deary IJ, Petretto E.

Nat Neurosci. 2016 Feb;19(2):223-32. doi: 10.1038/nn.4205. Epub 2015 Dec 21.

40.

A mutation in MT-TW causes a tRNA processing defect and reduced mitochondrial function in a family with Leigh syndrome.

Duff RM, Shearwood AM, Ermer J, Rossetti G, Gooding R, Richman TR, Balasubramaniam S, Thorburn DR, Rackham O, Lamont PJ, Filipovska A.

Mitochondrion. 2015 Nov;25:113-9. doi: 10.1016/j.mito.2015.10.008. Epub 2015 Oct 30.

41.

Web-based Gene Pathogenicity Analysis (WGPA): a web platform to interpret gene pathogenicity from personal genome data.

Diaz-Montana JJ, Rackham OJ, Diaz-Diaz N, Petretto E.

Bioinformatics. 2016 Feb 15;32(4):635-7. doi: 10.1093/bioinformatics/btv598. Epub 2015 Oct 21.

42.

Function-selective domain architecture plasticity potentials in eukaryotic genome evolution.

Linkeviciute V, Rackham OJ, Gough J, Oates ME, Fang H.

Biochimie. 2015 Dec;119:269-77. doi: 10.1016/j.biochi.2015.05.003. Epub 2015 May 15.

43.

Mutation in MRPS34 compromises protein synthesis and causes mitochondrial dysfunction.

Richman TR, Ermer JA, Davies SM, Perks KL, Viola HM, Shearwood AM, Hool LC, Rackham O, Filipovska A.

PLoS Genet. 2015 Mar 27;11(3):e1005089. doi: 10.1371/journal.pgen.1005089. eCollection 2015 Mar.

44.

WGBSSuite: simulating whole-genome bisulphite sequencing data and benchmarking differential DNA methylation analysis tools.

Rackham OJ, Dellaportas P, Petretto E, Bottolo L.

Bioinformatics. 2015 Jul 15;31(14):2371-3. doi: 10.1093/bioinformatics/btv114. Epub 2015 Mar 15.

45.

EvoTol: a protein-sequence based evolutionary intolerance framework for disease-gene prioritization.

Rackham OJ, Shihab HA, Johnson MR, Petretto E.

Nucleic Acids Res. 2015 Mar 11;43(5):e33. doi: 10.1093/nar/gku1322. Epub 2014 Dec 29.

46.

An artificial PPR scaffold for programmable RNA recognition.

Coquille S, Filipovska A, Chia T, Rajappa L, Lingford JP, Razif MF, Thore S, Rackham O.

Nat Commun. 2014 Dec 17;5:5729. doi: 10.1038/ncomms6729.

47.

The SUPERFAMILY 1.75 database in 2014: a doubling of data.

Oates ME, Stahlhacke J, Vavoulis DV, Smithers B, Rackham OJ, Sardar AJ, Zaucha J, Thurlby N, Fang H, Gough J.

Nucleic Acids Res. 2015 Jan;43(Database issue):D227-33. doi: 10.1093/nar/gku1041. Epub 2014 Nov 20.

48.

Estrogen-mediated regulation of mitochondrial gene expression.

Sanchez MI, Shearwood AM, Chia T, Davies SM, Rackham O, Filipovska A.

Mol Endocrinol. 2015 Jan;29(1):14-27. doi: 10.1210/me.2014-1077.

49.

Genome3D: exploiting structure to help users understand their sequences.

Lewis TE, Sillitoe I, Andreeva A, Blundell TL, Buchan DW, Chothia C, Cozzetto D, Dana JM, Filippis I, Gough J, Jones DT, Kelley LA, Kleywegt GJ, Minneci F, Mistry J, Murzin AG, Ochoa-Montaño B, Oates ME, Punta M, Rackham OJ, Stahlhacke J, Sternberg MJ, Velankar S, Orengo C.

Nucleic Acids Res. 2015 Jan;43(Database issue):D382-6. doi: 10.1093/nar/gku973. Epub 2014 Oct 27.

50.

A proteome quality index.

Zaucha J, Stahlhacke J, Oates ME, Thurlby N, Rackham OJ, Fang H, Smithers B, Gough J.

Environ Microbiol. 2015 Jan;17(1):4-9. doi: 10.1111/1462-2920.12622. Epub 2014 Oct 22.

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