The Ramialison Group located at the Murdoch Children’s Research Institute and affiliated with ARMI is studying embryonic development and congenital disease. They are a multidisciplinary team of computational biologists, molecular biologists, mathematicians and software engineers specialised in genomics and transcriptomics.

The research team is dedicated to improve diagnosis, treatment and prevention of congenital disease by developing novel analytics methods dedicated to mining multi-omics big data. They have pioneered the design and application of cutting-edge computer programs that successfully led to a better understanding of the genetic mechanisms in place to form a healthy embryo, and how perturbations in these processes lead to congenital disease.

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Group Members

Research Themes

  • 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

Authors Title Published In

del Monte-Nieto G, Ramialison M, Cherian A, Wu B, Aharonov A, D’Uva G, Bourke LM, Pitulescu ME, Chen H, Shou W, Adams RH, Harten SK, Tzahor E, Zhou B, Stainier D and Harvey RP.

Extracellular matrix dynamics reveals the building plan for cardiac trabeculation.

Nature. 2018 May;557(7705):439-445. (IF: 40.137)

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. (IF: 41.458; 31 cites)

Haudry Y# & Ramialison M#, Paten B, Wittbrodt J, Ettwiller L. (#: co-first authors)

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. (IF: 11.296; 11 cites)

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. (IF: 35.028; 73 cites)

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. (IF: 41.388; 90 cites)

Chahal G, Tyagi S#, Ramialison M#. (#: co-corresponding authors)

Navigating the non-coding genome in heart development and Congenital Heart Disease.

Differentiation. 2019 May 8;107:11-23.

Dang LT, Tondl M, Chiu MHH, Revote J, Paten B, Besse F, Quaife-Ryan G, Tano V, Cumming H, Drvodelic MJ, Eichenlaub MP, Hallab JC, Nim HT, Stolper JS, Tokolyi A, Bogoyevitch MA, Jans DA, Porello ER, Hudson JE, Ramialison M.

TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets.

BMC Genomics. 2018  Apr 5;19(1):238. (IF 3.867)

Ramialison M@, Reinhardt R, Henrich T, Wittbrodt B, Kellner T, Lowy CM and Wittbrodt J@. (@: co-corresponding authors).

Cis-regulatory properties of medaka synexpression groups. 

Development. 2012 Mar; 139:917-928. (IF: 6.231; 8 cites)

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. (IF: 13.168; 13 cites)

Henrich T# & Ramialison M#, Wittbrodt B, Assouline B, Bourrat F, Berger A, Himmelbauer H, Sasaki T, Shimizu N, Westerfield M, Kondoh H, Wittbrodt J. (#: co-first authors).

MEPD: a resource for medaka gene expression patterns.

Bioinformatics. 2005 Jul 15;21(14):3195-7. (IF: 7.685; 25 cites)

More Publications

Authors Title Published In

Salimova E, Nowak KJ, Estrada AC, Furtado MB, McNamara E, Nguyen Q, Balmer L, Preuss C, Holmes JW, Ramialison M, Morahan G, Rosenthal NA.

Variable outcomes of human heart attack recapitulated in genetically diverse mice.

NPJ Regen Med. 2019 Mar 4;4:5. (IF=NA)

Wilmanns, JC, Pandey, R, Hon, O, Chandran, A, Schilling, JM, Forte, E, Wu, Q, Cagnone, G, Bais, P, Philip, V, Coleman, D, Kocalis, H, Archer, SK, Pearson, JT, Ramialison, M, Heineke, J, Patel, HH, Rosenthal, NA, Furtado, MB & Costa, MW.

Metformin intervention prevents cardiac dysfunction in a murine model of adult congenital heart disease.

Molecular Metabolism. 2019 Fe;20:1202-114. (IF: 6.291)

Fahey, JK, Williams, SM, Tyagi, S, Powell, DR, Hallab, JC, Chahal, G, Ramialison, MSM & White, AJ.

The Intercellular Tight Junction and Spontaneous Coronary Artery Dissection.

Journal of the American College of Cardiology. 2018 vol. 72, no. 14, pp. 1752-1753. (IF: 16.834)

Sibbritt, T, Ip, CK, Khoo, PL, Wilkie, E, Jones, V, Sun, JQJ, Shen, JX, Peng, G, Han, JDJ, Jing, N, Osteil, P, Ramialison, M, Tam, PPL & Fossat, N.

A gene regulatory network anchored by LIM homeobox 1 for embryonic head development.

Genesis. 2018 vol. 56, no. 9, e23246. (IF=2.272)

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 Reports. 2017 Dec 5;21(10):2649-2660. (IF: 8.282)

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. (IF: 7.338)

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. (IF: 19.309).

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.

Front Oncol. 2017 Mar 15;7:30. (IF: 3.566)

Ramialison M#, Waardenberg AJ#, Schonrock N, Doan T, de Jong D, Bouveret R, Harvey RP. (#: co-first authors)

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

Genomics. 2017 Mar;109(2):75-82. (IF: 2.896)

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. (IF: not yet attributed)

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 (IF: 2.934; 4 cites).

Tam PPL, Fossat N, Wilkie E, Loebel DAF, Ip CK, Ramialison M.

Formation of the Embryonic Head in the Mouse: Attributes of a Gene Regulatory Network. 

Current Topics in Developmental Biology. 2016;117:497-521. (IF: 5.188)

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. (IF: 3.535; 1 cite)

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; 9014(4) (IF: 8.512; 14 cites)

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):1009-27. (IF: 2.226; 5 cites)

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 Feb 5; 142(5):832-839 (IF: 6.231; 4 cites)

Waardenberg AJ# & Ramialison M#, Bouveret R, Harvey RP. (#: co-first authors)

Genetic networks governing heart development.

Cold Spring Harb Perspect Med. 2014 Oct 3;4(11)a013839–a013839.  (IF: 8.945; 1 cite)

Chen Q, 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 Dec; 15(12):1254-67. (IF: 7.413; 7 cites)

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

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

Current Biology. 2014 Mar; pii: S0960-9822(14)00206-1. (IF: 9.733; 18 cites)

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. (IF: 2.388; 13 cites)

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. (IF: 3.608; 9 cites)

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. (IF: 9.886; 89 cites)

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. (IF: 3.481; 32 cites)

Bajoghli B# & Ramialison M#@, Aghaallaei N, Czerny T, Wittbrodt J@. (#: co-first authors, @: co-corresponding authors).

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. (IF: 2.388; 14 cites)

Martinez-Morales JR# & Henrich T# & Ramialison M#, Wittbrodt J. (#: co-first authors).

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

Genome Biology. 2007;8(3):R36. (IF: 13.168; 40 cites)

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. (IF: 2.651; 12 cites)

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. (IF: 2.028; 7 cites)

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. (IF: 2.028; 118 cites)

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. (IF: 2.028; 41 cites)

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. (IF: 8.647; 26 cites)

Ramialison M# & Mohr E# & Nal B#, Saboul T, Carrier A, Tagett R, Granjeaud S, Nguyen C, Gautheret D, Jordan BR, Ferrier P. (#: co-first authors).

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. (IF: 2.415; 5 cites)

Ramialison Group [Affiliate]


Group members

Research themes