The Ramialison group is studying development and disease. They are a multidisciplinary team of computational and molecular biologists who specialise in genomics. The researchers answer complex questions using new genomic technology and the zebrafish as a model organism.

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The research team applies systems biology (the study of biological components, be it molecules, cells, organisms or entire species) to reconstruct the cardiac gene regulatory networks and to work out what leads to proper heart formation and what causes congenital heart disease.

Ramialison group photo


  • Dissecting cardiac gene regulatory networks in healthy and diseased hearts
  • Combining ‘wet’ and ‘dry’ lab: Using bioinformatics to decipher the regulatory code of vertebrate heart development 
  • Investigating the mechanisms of heart development and evolution
  • Identifying candidates for human congenital heart diseases
  • Role of ubiquitous transcription factor (compensation?) in heart disease

Featured Publications

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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 type of origin dictates the route to pluripotency.

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

Quaife-Ryan GA, Sim CB, Ziemann M, Kaspi A, Rafehi H, Ramialison M, El-Osta A, Hudson JE, Porrello ER.

Multicellular transcriptional analysis of mammalian heart regeneration.

Circulation. 2017 Sep 19;136(12):1123-1139. doi: 10.1161/CIRCULATIONAHA.117.028252. Epub 2017 Jul 21.

Chan AL, La HM, Legrand JMD, Mäkelä JA, Eichenlaub M, De Seram M, Ramialison M, Hobbs RM.

Germline stem cell activity is sustained by SALL4-dependent silencing of distinct tumor suppressor genes.

Stem Cell Reports. 2017 Sep 12;9(3):956-971. doi: 10.1016/j.stemcr.2017.08.001. Epub 2017 Aug 31.

Arumugam TV, Manzanero S, Furtado M, Biggins PJ, Hsieh YH, Gelderblom M, MacDonald KP, Salimova E, Li YI, Korn O, Dewar D, Macrae IM, Ashman RB, Tang SC, Rosenthal NA, Ruitenberg MJ, Magnus T, Wells CA.

An atypical role for the myeloid receptor Mincle in central nervous system injury.

J Cereb Blood Flow Metab. 2017 Jun;37(6):2098-2111. doi: 10.1177/0271678X16661201. Epub 2016 Jan 1.

Ta-Shma A, Zhang K, Salimova E, Zernecke A, Sieiro-Mosti D, Stegner D, Furtado M, Shaag A, Perles Z, Nieswandt B, Rein AJ, Rosenthal N, Neiman AM, Elpeleg O.

Congenital valvular defects associated with deleterious mutations in the PLD1 gene.

J Med Genet. 2017 Apr;54(4):278-286. doi: 10.1136/jmedgenet-2016-104259. Epub 2016 Oct 31.

Furtado M, Wilmanns J, Chandran A, Perera J, Hon O, Biben C, Willow T, Nim H, Kaur G, Simonds S, Wu Q, Williams D, Salimova E, Plachta N, Denegre J, Murray S, Fatkin D, Cowley M, Pearson J, Kaye D, Ramialison M, Harvey RP, Rosenthal N, Costa M.

Point mutations in murine Nkx2-5 phenocopies human congenital heart disease and induces pathogenic Wnt signaling.

JCI Insight. 2017 Mar 23; 2(6): e88271. doi: 10.1172/jci.insight.88271.

Ramialison M, Waardenberg AJ, Schonrock N, Doan T, de Jong D, Bouveret R, Harvey RP.

Analysis of steric effects in DamID profiling of transcription factor target genes.

Genomics. 2017 Mar;109(2):75-82. doi: 10.1016/j.ygeno.2017.01.006. Epub 2017 Feb 8.

Nim HT, Furtado MB, Ramialison M, Boyd SE.

Combinatorial ranking of gene sets to predict disease relapse: The retinoic acid pathway in early prostate cancer.

Frontiers in Oncology 2017;7:30. doi: 10.3389/fonc.2017.00030.

Furtado MB, Wilmanns JC, Chandran A, Tonta M, Biben C, Eichenlaub M, Coleman HA, Berger S, Bouveret R, Singh R, Harvey RP, Ramialison M, Pearson JT, Parkington HC, Rosenthal NA, Costa MW.

A novel conditional mouse model for Nkx2-5 reveals transcriptional regulation of cardiac ion channels.

Differentiation. 2016 Jan-Mar;91(1-3):29-41. doi: 10.1016/j.diff.2015.12.003. Epub 2016 Feb 17.

Bruckert H, Marchetti G, Ramialison M, Besse F.

Drosophila Hrp48 Is Required for Mushroom Body Axon Growth, Branching and Guidance.

PLoS One. 2015 Aug 27;10(8):e0136610.

Bouveret R, Waardenberg AJ, Schonrock N, Ramialison M, Doan T, de Jong D, Bondue A, Kaur G, Mohamed S, Fonoudi H, Chen CM, Wouters MA, Bhattacharya S, Plachta N, Dunwoodie SL, Chapman G, Blanpain C, Harvey RP.

NKX2-5 mutations causative for congenital heart disease retain functionality and are directed to hundreds of targets.

Elife. 2015 Jul 6;4. doi: 10.7554/eLife.06942.

Foster SR, Porrello ER, Stefani M, Smith NJ, Molenaar P, Dos Remedios CG, Thomas WG, Ramialison M.

Cardiac gene expression data and in silico analysis provide novel insights into human and mouse taste receptor gene regulation.

Naunyn Schmiedebergs Arch Pharmacol. 2015 388 (10), 1118, pp. 1009-27.

Paolini A, Duchemin AL, Albadri S, Patzel E, Bornhorst D, Avalos PG, Lemke S, Machate A, Brand M, Sel S, Di Donato V, Del Bene F, Zolessi FR, Ramialison M, Poggi L.

Asymmetric inheritance of the apical domain and self-renewal of retinal ganglion cell progenitors depend on Anillin function.

Development. 2015 142 (5), pp. 832-839.

Qing C, Su Y, Wesslowski J, Hagemann A, Ramialison M, Wittbrodt J, Scholpp S, Davidson G.

Tyrosine phosphorylation of LRP6 by Src and Fer inhibits Wnt/β­catenin signaling.

EMBO reports. 2014 15 (12), pp. 1254-1267.

Waardenberg AJ*, Ramialison M*, Bouveret R, Harvey RP.

Genetic networks governing heart development.

Cold Spring Harb Perspect Med. 2014 doi: 10.1101/cshperspect.a013839.

Nguyen PD, Hollway GE, Sonntag C, Miles LB, Hall TE, Berger S, Fernandez KJ, Gurevich DB, Cole NJ, Alaei S, Ramialison M, Sutherland RL, Polo JM, Lieschke GJ, Currie PD.

Haematopoietic stem cell induction by somite-derived endothelial cells controlled by meox1.

Nature. 2014 Aug 21;512(7514):314-8.

Medioni C, Ramialison M, Ephrussi A, Besse F.

Imp promotes axonal remodeling by regulating profilin mRNA during brain development.

Current Biology. 2014 Mar 18. pii: S0960-9822(14)00206-1.

Harden MV, Pereiro L, Ramialison M, Wittbrodt J, Prasad MK, McCallion A, Whitlock KE.

Close association of olfactory placode precursors and cranial neural crest cells does not predestine cell mixing.

Developmental Dynamics. 2012 Jul;241(7):1143-54.

Ramialison M*, Reinhardt R, Henrich T, Wittbrodt B, Kellner T, Lowy CM, Wittbrodt J*.

Cis-regulatory properties of medaka synexpression groups.

Development. 2012 Mar;139(5):917-28.

Schuhmacher LN, Albadri S, Ramialison M, Poggi L.

Evolutionary relationships and diversification of barhl genes within retinal cell lineages.

BMC Evolutionary Biology. 2011 Nov 21;11:340.

Bondue A, Tännler S, Chiapparo G, Chabab S, Ramialison M, Paulissen C, Beck B, Harvey R, Blanpain C.

Defining the earliest step of cardiovascular progenitor specification during embryonic stem cell differentiation.

Journal of Cell Biology. 2011 Mar 7;192(5):751-65.

Brown KE, Keller PJ, Ramialison M, Rembold M, Stelzer EH, Loosli F, Wittbrodt J.

Nlcam modulates midline convergence during anterior neural plate morphogenesis.

Developmental Biology. 2010 Mar 1;339(1):14-25.

Haudry Y*, Ramialison M*, Paten B, Wittbrodt J, Ettwiller L.

Using Trawler_standalone to discover overrepresented motifs in DNA and RNA sequences derived from various experiments including chromatin immunoprecipitation.

Nature Protocols. 2010;5(2):323-34.

Bajoghli B*, Ramialison M**, Aghaallaei N*, Czerny T, Wittbrodt J.

Identification of starmaker-like in medaka as a putative target gene of Pax2 in the otic vesicle.

Developmental Dynamics. 2009 Nov;238(11):2860-6.

Ramialison M, Bajoghli B, Aghaallaei N, Ettwiller L, Gaudan S, Wittbrodt B, Czerny T, Wittbrodt J.

Rapid identification of PAX2/5/8 direct downstream targets in the otic vesicle by combinatorial use of bioinformatics tools.

Genome Biology. 2008 Oct 1;9(10):R145.

Deutsch EW, Ball CA, Berman JJ, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen JH, Daian F, Dauga D, Davidson DR, Gimenez G, Goo YA, Grimmond S, Henrich T, Herrmann BG, Johnson MH, Korb M, Mills JC, Oudes AJ, Parkinson HE, Pascal LE, Pollet N, Quackenbush J, Ramialison M, Ringwald M, Salgado D, Sansone SA, Sherlock G, Stoeckert CJ Jr, Swedlow J, Taylor RC, Walashek L, Warford A, Wilkinson DG, Zhou Y, Zon LI, Liu AY, True LD.

Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE).

Nature Biotechnology. 2008 Mar;26(3):305-12.

Ettwiller L, Paten B, Ramialison M, Birney E, Wittbrodt J.

Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation.

Nature Methods. 2007 Jul;4(7):563-5.

Martinez-Morales JR*, Henrich T*, Ramialison M*, Wittbrodt J.

New genes in the evolution of the neural crest differentiation program.

Genome Biology. 2007;8(3):R36.

Deutsch EW, Ball CA, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen J, Davidson D, Eichner LJ, Goo YA, Grimmond S, Henrich T, Johnson MH, Korb M, Mills JC, Oudes A, Parkinson HE, Pascal LE, Quackenbush J, Ramialison M, Ringwald M, Sansone SA, Sherlock G, Stoeckert CJ Jr, Swedlow J, Taylor RC, Walashek L, Zhou Y, Liu AY, True LD.

Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE).

OMICS. 2006 Summer;10(2):205-8.

Henrich T*, Ramialison M*, Wittbrodt B, Assouline B, Bourrat F, Berger A, Himmelbauer H, Sasaki T, Shimizu N, Westerfield M, Kondoh H, Wittbrodt J.

MEPD: a resource for medaka gene expression patterns.

Bioinformatics. 2005 21 (14) 3195 – 3197.

Henrich T, Ramialison M, Segerdell E, Westerfield M, Furutani-Seiki M, Wittbrodt J, Kondoh H.

GSD: a genetic screen database.

Mechanisms of Development. 2004 Jul;121(7-8):959-63.

Furutani-Seiki M, Sasado T, Morinaga C, Suwa H, Niwa K, Yoda H, Deguchi T, Hirose Y, Yasuoka A, Henrich T, Watanabe T, Iwanami N, Kitagawa D, Saito K, Asaka S, Osakada M, Kunimatsu S, Momoi A, Elmasri H, Winkler C, Ramialison M, Loosli F, Quiring R, Carl M, Grabher C, Winkler S, Del Bene F, Shinomiya A, Kota Y, Yamanaka T, Okamoto Y, Takahashi K, Todo T, Abe K, Takahama Y, Tanaka M, Mitani H, Katada T, Nishina H, Nakajima N, Wittbrodt J, Kondoh H.

A systematic genome-wide screen for mutations affecting organogenesis in Medaka, Oryzias latipes.

Mechanisms of Development. 2004 Jul;121(7-8):647-58.

Quiring R, Wittbrodt B, Henrich T, Ramialison M, Burgtorf C, Lehrach H, Wittbrodt J.

Large-scale expression screening by automated whole-mount in situ hybridization.

Mechanisms of Development. 2004 Jul;121(7-8):971-6.

Henrich T, Ramialison M, Quiring R, Wittbrodt B, Furutani-Seiki M, Wittbrodt J, Kondoh H.

MEPD: a Medaka gene expression pattern database.

Nucleic Acids Research. 2003 Jan 1;31(1):72-4.

Ramialison M*, Mohr E*, Nal B*, Saboul T, Carrier A, Tagett R, Granjeaud S, Nguyen C, Gautheret D, Jordan BR, Ferrier P.

Expression profiling in mouse fetal thymus reveals clusters of coordinately expressed genes that mark individual stages of T-cell ontogeny.

Immunogenetics. 2002 Oct;54(7):469-78.