Publications

  1. Fok ET, Fanucchi S, Bystricky K, Mhlanga MM. Visualization of Chromatin Dynamics by Live Cell Microscopy Using CRISPR/Cas9 Gene Editing and ANCHOR Labeling. Methods Mol Biol. 2021;2157:197-212. doi:10.1007/978-1-0716-0664-3_11. PMID: 32820405.
  2. de Bruijn SE, Fiorentino A, Ottaviani D, Fanucchi S, Melo US, Corral-Serrano JC, Mulders T, Georgiou M, Rivolta C, Pontikos N, Arno G, Roberts L, Greenberg J, Albert S, Gilissen C, Aben M, Rebello G, Mead S, Raymond FL, Corominas J, Smith CEL, Kremer H, Downes S, Black GC, Webster AR, Inglehearn CF, van den Born LI, Koenekoop RK, Michaelides M, Ramesar RS, Hoyng CB, Mundlos S, Mhlanga MM, Cremers FPM, Cheetham ME, Roosing S, Hardcastle AJ. Structural Variants Create New Topological-Associated Domains and Ectopic Retinal Enhancer-Gene Contact in Dominant Retinitis Pigmentosa. Am J Hum Genet. 2020 Nov 5;107(5):802-814. doi: 10.1016/j.ajhg.2020.09.002. Epub 2020 Oct 5. PMID: 33022222.
  3. Majumder PP, Mhlanga MM, Shalek AK. The Human Cell Atlas and equity: lessons learned. Nat Med. 2020 Oct;26(10):1509-1511. doi: 10.1038/s41591-020-1100-4. PMID: 33029017.
  4. de Wet TJ, Winkler KR, Mhlanga M, Mizrahi V, Warner DF. Arrayed CRISPRi and quantitative imaging describe the morphotypic landscape of essential mycobacterial genes. Elife. 2020 Nov 6;9:e60083. doi: 10.7554/eLife.60083. PMID: 33155979; PMCID: PMC7647400.
  5. Savulescu AF, Jacobs C, Negishi Y, Davignon L, Mhlanga MM. Pinpointing Cell Identity in Time and Space. Front Mol Biosci. 2020 Aug 14;7:209. doi: 10.3389/fmolb.2020.00209. PMID: 32923457; PMCID: PMC7456825.
  6. Pereira PM, Gustafsson N, Marsh M, Mhlanga MM, Henriques R. Super-beacons: Open-source probes with spontaneous tuneable blinking compatible with live-cell super-resolution microscopy. Traffic. 2020 May;21(5):375-385. doi: 10.1111/tra.12728. Epub 2020 Mar 30. PMID: 32170988.
  7. Keating ST, Groh L, van der Heijden CDCC, Rodriguez H, Dos Santos JC, Fanucchi S, Okabe J, Kaipananickal H, van Puffelen JH, Helder L, Noz MP, Matzaraki V, Li Y, de Bree LCJ, Koeken VACM, Moorlag SJCFM, Mourits VP, Domínguez-Andrés J, Oosting M, Bulthuis EP, Koopman WJH, Mhlanga M, El-Osta A, Joosten LAB, Netea MG, Riksen NP. The Set7 Lysine Methyltransferase Regulates Plasticity in Oxidative Phosphorylation Necessary for Trained Immunity Induced by β-Glucan. Cell Rep. 2020 Apr 21;31(3):107548. doi: 10.1016/j.celrep.2020.107548. PMID: 32320649; PMCID: PMC7184679.
  8. Netea MG, Domínguez-Andrés J, Barreiro LB, Chavakis T, Divangahi M, Fuchs E, Joosten LAB, van der Meer JWM, Mhlanga MM, Mulder WJM, Riksen NP, Schlitzer A, Schultze JL, Stabell Benn C, Sun JC, Xavier RJ, Latz E. Defining trained immunity and its role in health and disease. Nat Rev Immunol. 2020 Jun;20(6):375-388. doi: 10.1038/s41577-020-0285-6. Epub 2020 Mar 4. PMID: 32132681; PMCID: PMC7186935.
  9. Khader SA, Divangahi M, Hanekom W, Hill PC, Maeurer M, Makar KW, Mayer-Barber KD, Mhlanga MM, Nemes E, Schlesinger LS, van Crevel R, Vankayalapati R, Xavier RJ, Netea MG; Bill and Melinda Gates Foundation Collaboration for TB Vaccine Discovery Innate Immunity Working Group18. Targeting innate immunity for tuberculosis vaccination. J Clin Invest. 2019 Sep 3;129(9):3482-3491. doi: 10.1172/JCI128877. PMID: 31478909; PMCID: PMC6715374.
  10. Fanucchi S, Fok ET, Dalla E, Shibayama Y, Börner K, Chang EY, Stoychev S, Imakaev M, Grimm D, Wang KC, Li G, Sung WK, Mhlanga MM. Immune genes are primed for robust transcription by proximal long noncoding RNAs located in nuclear compartments. Nat Genet. 2019 Jan;51(1):138-150. doi: 10.1038/s41588-018-0298-2. Epub 2018 Dec 10. Erratum in: Nat Genet. 2019 Feb;51(2):364. PMID: 30531872.
  11. Denisenko E, Guler R, Mhlanga M, Suzuki H, Brombacher F, Schmeier S. Transcriptionally induced enhancers in the macrophage immune response to Mycobacterium tuberculosis infection. BMC Genomics. 2019 Jan 22;20(1):71. doi: 10.1186/s12864-019-5450-6. PMID: 30669987; PMCID: PMC6341744.
  12. Fanucchi S, Fok ET, Dalla E, Shibayama Y, Börner K, Chang EY, Stoychev S, Imakaev M, Grimm D, Wang KC, Li G, Sung WK, Mhlanga MM. Publisher Correction: Immune genes are primed for robust transcription by proximal long noncoding RNAs located in nuclear compartments. Nat Genet. 2019 Feb;51(2):364. doi: 10.1038/s41588-018-0341-3. Erratum for: Nat Genet. 2019 Jan;51(1):138-150. PMID: 30647470.
  13. Domínguez-Andrés J, Fanucchi S, Joosten LAB, Mhlanga MM, Netea MG. Advances in understanding molecular regulation of innate immune memory. Curr Opin Cell Biol. 2020 Apr;63:68-75. doi: 10.1016/j.ceb.2019.12.006. Epub 2020 Jan 25. PMID: 31991317.
  14. Fok ET, Davignon L, Fanucchi S, Mhlanga MM. The lncRNA Connection Between Cellular Metabolism and Epigenetics in Trained Immunity. Front Immunol. 2019 Jan 29;9:3184. doi: 10.3389/fimmu.2018.03184. PMID: 30761161; PMCID: PMC6361822.
  15. Fanucchi S, Mhlanga MM. Lnc-ing Trained Immunity to Chromatin Architecture. Front Cell Dev Biol. 2019 Jan 24;7:2. doi: 10.3389/fcell.2019.00002. PMID: 30733945; PMCID: PMC6353842.
  16. Govender NP, Magobo RE, Mpembe R, Mhlanga M, Matlapeng P, Corcoran C, Govind C, Lowman W, Senekal M, Thomas J. Candida auris in South Africa, 2012-2016. Emerg Infect Dis. 2018 Nov;24(11):2036-2040. doi: 10.3201/eid2411.180368. PMID: 30334713; PMCID: PMC6200016.
  17. Barichievy S, Naidoo J, Boullé M, Scholefield J, Parihar SP, Coussens AK, Brombacher F, Sigal A, Mhlanga MM. Viral Apoptosis Evasion via the MAPK Pathway by Use of a Host Long Noncoding RNA. Front Cell Infect Microbiol. 2018 Aug 3;8:263. doi: 10.3389/fcimb.2018.00263. PMID: 30123777; PMCID: PMC6086015.
  18. Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe’er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M,  Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N; Human Cell Atlas Meeting Participants. The Human Cell Atlas. Elife. 2017 Dec 5;6:e27041. doi: 10.7554/eLife.27041. PMID: 29206104; PMCID: PMC5762154.
  19. Fok ET, Scholefield J, Fanucchi S, Mhlanga MM. The emerging molecular biology toolbox for the study of long noncoding RNA biology. Epigenomics. 2017 Oct;9(10):1317-1327. doi: 10.2217/epi-2017-0062. Epub 2017 Sep 6. PMID: 28875715.
  20. Denisenko E, Guler R, Mhlanga MM, Suzuki H, Brombacher F, Schmeier S. Genome-wide profiling of transcribed enhancers during macrophage activation. Epigenetics Chromatin. 2017 Oct 23;10(1):50. doi: 10.1186/s13072-017-0158-9. PMID: 29061167; PMCID: PMC5654053.
  21. Shibayama Y, Fanucchi S, Mhlanga MM. Visualization of Enhancer-Derived Noncoding RNA. Methods Mol Biol. 2017;1468:19-32. doi: 10.1007/978-1-4939-4035-6_3. PMID: 27662867.
  22. Magagula L, Gagliardi M, Naidoo J, Mhlanga M. Lnc-ing inflammation to disease. Biochem Soc Trans. 2017 Aug 15;45(4):953-62. doi: 10.1042/BST20160377. Epub 2017 Jul 7. PMID: 28687714.
  23. Warrell J, Mhlanga M. Stability and structural properties of gene regulation networks with coregulation rules. J Theor Biol. 2017 May 7;420:304-317. doi: 10.1016/j.jtbi.2016.10.020. Epub 2016 Nov 17. PMID: 27866978.
  24. Fanucchi S, Mhlanga MM. Enhancer-Derived lncRNAs Regulate Genome Architecture: Fact or Fiction? Trends Genet. 2017 Jun;33(6):375-377. doi: 10.1016/j.tig.2017.03.004. Epub 2017 Mar 27. PMID: 28359583.
  25. Scholefield J, Henriques R, Savulescu AF, Fontan E, Boucharlat A, Laplantine E, Smahi A, Israël A, Agou F, Mhlanga MM. Super-resolution microscopy reveals a preformed NEMO lattice structure that is collapsed in incontinentia pigmenti. Nat Commun. 2016 Sep 2;7:12629. doi:  10.1038/ncomms12629. PMID: 27586688; PMCID: PMC5025789.
  26. Barichievy S, Naidoo J, Mhlanga MM. Non-coding RNAs and HIV: viral manipulation of host dark matter to shape the cellular environment. Front Genet. 2015 Mar 26;6:108. doi: 10.3389/fgene.2015.00108. PMID: 25859257; PMCID: PMC4374539.
  27. Parihar SP, Guler R, Khutlang R, Lang DM, Hurdayal R, Mhlanga MM, Suzuki H, Marais AD, Brombacher F. Statin therapy reduces the mycobacterium tuberculosis burden in human macrophages and in mice by enhancing autophagy and phagosome maturation. J Infect Dis. 2014 Mar 1;209(5):754-63. doi: 10.1093/infdis/jit550. Epub 2013 Oct 16. PMID: 24133190.
  28. Fanucchi S, Shibayama Y, Mhlanga MM. Are genes switched on when they kiss? Nucleus. 2014 Mar-Apr;5(2):103-12. doi: 10.4161/nucl.28352. Epub 2014 Feb 25. PMID: 24637837; PMCID: PMC4049915.
  29. Shibayama Y, Fanucchi S, Magagula L, Mhlanga MM. lncRNA and gene looping: what’s the connection? Transcription. 2014;5(3):e28658. doi: 10.4161/trns.28658. PMID: 25764331; PMCID: PMC4215167.
  30. Tarantino N, Tinevez JY, Crowell EF, Boisson B, Henriques R, Mhlanga M, Agou F, Israël A, Laplantine E. TNF and IL-1 exhibit distinct ubiquitin requirements for inducing NEMO-IKK supramolecular structures. J Cell Biol. 2014 Jan 20;204(2):231-45. doi: 10.1083/jcb.201307172. PMID: 24446482; PMCID: PMC3897181.
  31. Fanucchi S, Shibayama Y, Burd S, Weinberg MS, Mhlanga MM. Chromosomal contact permits transcription between coregulated genes. Cell. 2013 Oct 24;155(3):606-20. doi: 10.1016/j.cell.2013.09.051. Epub 2013 Oct 24. PMID: 24243018.
  32. Meliopoulos VA, Andersen LE, Birrer KF, Simpson KJ, Lowenthal JW, Bean AG, Stambas J, Stewart CR, Tompkins SM, van Beusechem VW, Fraser I, Mhlanga M, Barichievy S, Smith Q, Leake D, Karpilow J, Buck A, Jona G, Tripp RA. Host gene targets for novel influenza therapies elucidated by high-throughput RNA interference screens. FASEB J. 2012 Apr;26(4):1372-86. doi: 10.1096/fj.11-193466. Epub 2012 Jan 12. PMID: 22247330; PMCID: PMC3316894.
  33. Henriques R, Griffiths C, Hesper Rego E, Mhlanga MM. PALM and STORM: unlocking live-cell super-resolution. Biopolymers. 2011 May;95(5):322-31. doi: 10.1002/bip.21586. Epub 2011 Jan 19. PMID: 21254001.
  34. Rolando M, Stefani C, Flatau G, Auberger P, Mettouchi A, Mhlanga M, Rapp U, Galmiche A, Lemichez E. Transcriptome dysregulation by anthrax lethal toxin plays a key role in induction of human endothelial cell cytotoxicity. Cell Microbiol. 2010 Jul;12(7):891-905. doi: 10.1111/j.1462-5822.2010.01438.x. Epub 2010 May 20. PMID: 20088950.
  35. Henriques R, Lelek M, Fornasiero EF, Valtorta F, Zimmer C, Mhlanga MM. QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ. Nat Methods. 2010 May;7(5):339-40. doi: 10.1038/nmeth0510-339. PMID: 20431545.
  36. Mhlanga MM, Bratu DP, Genovesio A, Rybarska A, Chenouard N, Nehrbass U, Olivo-Marin JC. In vivo colocalisation of oskar mRNA and trans-acting proteins revealed by quantitative imaging of the Drosophila oocyte. PLoS One. 2009 Jul 14;4(7):e6241. doi: 10.1371/journal.pone.0006241. PMID: 19597554; PMCID: PMC2705681.
  37. Henriques R, Mhlanga MM. PALM and STORM: what hides beyond the Rayleigh limit? Biotechnol J. 2009 Jun;4(6):846-57. doi: 10.1002/biot.200900024. PMID: 19548237.
  38. Barreiro LB, Henriques R, Mhlanga MM. High-throughput SNP genotyping: combining tag SNPs and molecular beacons. Methods Mol Biol. 2009;578:255-76. doi: 10.1007/978-1-60327-411-1_17. PMID: 19768600; PMCID: PMC7121513.
  39. Lewenza S, Mhlanga MM, Pugsley AP. Novel inner membrane retention signals in Pseudomonas aeruginosa lipoproteins. J Bacteriol. 2008 Sep;190(18):6119-25. doi: 10.1128/JB.00603-08. Epub 2008 Jul 18. PMID: 18641140; PMCID: PMC2546801.
  40. Mhlanga MM, Tyagi S. Using tRNA-linked molecular beacons to image cytoplasmic mRNAs in live cells. Nat Protoc. 2006;1(3):1392-8. doi: 10.1038/nprot.2006.242. PMID: 17406426.
  41. Mhlanga MM, Vargas DY, Fung CW, Kramer FR, Tyagi S. tRNA-linked molecular beacons for imaging mRNAs in the cytoplasm of living cells. Nucleic Acids Res. 2005 Apr 4;33(6):1902-12. doi: 10.1093/nar/gki302. PMID: 15809226; PMCID: PMC1074395.
  42. Bratu DP, Cha BJ, Mhlanga MM, Kramer FR, Tyagi S. Visualizing the distribution and transport of mRNAs in living cells. Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13308-13. doi: 10.1073/pnas.2233244100. Epub 2003 Oct 28. PMID: 14583593; PMCID: PMC263795.
  43. Mhlanga MM, Malmberg L. Using molecular beacons to detect single-nucleotide polymorphisms with real-time PCR. Methods. 2001 Dec;25(4):463-71. doi: 10.1006/meth.2001.1269. PMID: 11846616.
  44. Kostrikis LG, Tyagi S, Mhlanga MM, Ho DD, Kramer FR. Spectral genotyping of human alleles. Science. 1998 Feb 20;279(5354):1228-9. doi: 10.1126/science.279.5354.1228. PMID: 9508692.