Publications

Christiaen Lab Publications

Access to our key publications and archives.
Up-to-date publication lists should be available here:

 
 

Our key publications by research aera

Gene regulation and cardiopharyngeal cell fate decision


Combinatorial chromatin dynamics foster accurate cardiopharyngeal fate choices.

Racioppi, C., Wiechecki, K.A., and L. Christiaen
2019, Elife. Nov 20;8. pii: e49921. doi: 10.7554/eLife.49921. [PDF]


A single cell transcriptional roadmap for cardiopharyngeal fate diversification.

Wang, W., Niu, X., Stuart, T., Jullian, E., Mauck, W., Kelly, R., Satija, R.*, and L. Christiaen*
Nat Cell Biol, 2019, 21(6):674-686. doi: 10.1038/s41556-019-0336-z. (* co-corresponding authors) [PDF]


An FGF-driven feed-forward circuit patterns the cardiopharyngeal mesoderm in space and time.

Razy-Krajka, F., Gravez, B., Nicole Kaplan, Claudia Racioppi, Wei Wang and L. Christiaen
eLife, 2018, 7. pii: e29656. doi: 10.7554/eLife.29656. PMCID: PMC5809146


A new heart for a new head in vertebrate cardiopharyngeal evolution.

Diogo, R.*, R. Kelly*, L. Christiaen*, M. Levine, J.M. Ziermann, J. Molnar & E. Tzahor*.
Nature, 2015, 520(7548):466-73 (* co-corresponding authors; invited review) [PDF]


Collier/Olf/EBF-dependent transcriptional dynamics control pharyngeal muscle specification from primed cardiopharyngeal progenitors

Razy-Krajka, F., K. Lam, W. Wang, E. Siu, A. Stolfi, R. Bonneau, and L. Christiaen
Dev Cell, 2014, 29(3):263-76 [PDF]


NK4 Antagonizes Tbx1/10 to Promote Cardiac Versus Pharyngeal Muscle Fate in the Ascidian Second Heart Field

Wang, W., Razy-Krajka, F., Siu, E., Ketcham, A., and L. Christiaen
PLOS Biology, 2013, 11(12):e1001725 [PDF]


Early chordate origins of the vertebrate second heart field.

Stolfi, A., T.B. Gainous, J.J. Young, A. Mori, M. Levine, and L. Christiaen
Science, 2010. 329(5991): p. 565-8. [PDF]


Methods and resources


Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data.

Tjärnberg, Andreas, Omar Mahmood, Christopher A Jackson, Giuseppe-Antonio Saldi, Kyunghyun Cho, Lionel Christiaen, Richard Bonneau
BioRxiv ; doi: https://doi.org/10.1101/2020.02.28.970202


Asymmetric Fitness of Second-Generation Interspecific Hybrids Between Ciona robusta and Ciona intestinalis.

Ohta, Naoyuki, Ng, J.T., Kaplan, N., Gravez, B.J., and Lionel Christiaen
G3 (Bethesda). 2020 Jun 9;g3.401427.2020. doi: 10.1534/g3.120.401427. BioRxiv; doi: https://doi.org/10.1101/2020.03.04.976837.


Simple method to quantify protein abundances from 1000 cells.

Vitrinel, Burcu, Dylan E. Iannitelli, Esteban O. Mazzoni, Lionel Christiaen, Christine Vogel
ACS Omega. 2020. Doi: 10.1021/acsomega.0c01191. BioRxiv 753582; doi: https://doi.org/10.1101/753582


Purification of Fluorescent Labelled Cells from Dissociated Ciona Embryos

Wang, W., Racioppi, C., Gravez, B., and L. Christiaen
Adv Exp Med Biol. 2018;1029:101-107. doi: 10.1007/978-981-10-7545-2_9.


Evaluation and rational design of guide RNAs for efficient CRISPR/Cas9-mediated mutagenesis in Ciona.

Gandhi, S., Haeussler, M., Razy-Krajka, F., Christiaen, L.*, and A. Stolfi*
Dev Biol, 2017, 425(1):8-20; doi: 10.1016/j.ydbio.2017.03.003; * co-corresponding authors). PMCID: PMC5502750


Tissue-specific genome editing in Ciona embryos by CRISPR/Cas9.

Stolfi, A., Gandhi, S., Salek, F., and L.Christiaen.
Development, 2014. 141(21):4115-20. doi: 10.1242/dev.114488.
 

Christian Lab Publications

Archives (2002-2020)

Simple method to quantify protein abundances from 1000 cells.

Vitrinel, Burcu, Dylan E. Iannitelli, Esteban O. Mazzoni, Lionel Christiaen, Christine Vogel. ACS Omega. 2020. Doi: 10.1021/acsomega.0c01191. BioRxiv 753582; doi: https://doi.org/10.1101/753582

Asymmetric Fitness of Second-Generation Interspecific Hybrids Between Ciona robusta and Ciona intestinalis

Ohta, Naoyuki, Ng, J.T., Kaplan, N., Gravez, B.J., and Lionel Christiaen. G3 (Bethesda). 2020 Jun 9;g3.401427.2020. doi: 10.1534/g3.120.401427. BioRxiv; doi: https://doi.org/10.1101/2020.03.04.976837

Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data.

Tjärnberg, Andreas, Omar Mahmood, Christopher A Jackson, Giuseppe-Antonio Saldi, Kyunghyun Cho, Lionel Christiaen, Richard Bonneau. BioRxiv ; doi: https://doi.org/10.1101/2020.02.28.970202

Combinatorial chromatin dynamics foster accurate cardiopharyngeal fate choices.

Racioppi, C., Wiechecki, K.A., and L. Christiaen. 2019, Elife. Nov 20;8. pii: e49921. doi: 10.7554/eLife.49921.

A conserved regulatory program drives emergence of the lateral plate mesoderm.

Hess, C., Dorien Prummel, K., Nieuwenhuize, S., Parker, H., Rogers, K.W., Kozmikova, I., Racioppi, C., Burger, S., Brombacher, E.C., Burger, A., Felker, A., Chiavacci, E., Shah, G., Huisken, J., Kozmik, Z., Christiaen, L., Mueller, P., Bronner, M., Krumlauf, R., and C. Mosimann. Nat Commun, 2019, 10(1):3857. doi: 10.1038/s41467-019-11561-7.

A single cell transcriptional roadmap for cardiopharyngeal fate diversification.

Wang, W., Niu, X., Stuart, T., Jullian, E., Mauck, W., Kelly, R., Satija, R.*, and L. Christiaen*. Nat Cell Biol, 2019, 21(6):674-686. doi: 10.1038/s41556-019-0336-z. (* co-corresponding authors)

A Complete Statistical Model for Calibration of RNA-seq Counts using External Spike-ins and Maximum Likelihood Theory.

Athanasiadou, R., Neymotin, B., Brandt, N., Wang, W., Christiaen, L., Gresham, D., and D. Tranchina. PLOS Comp Biol, 2019, 15(3):e1006794. doi: 10.1371/journal.pcbi.1006794.

Initial characterization of Wnt-Tcf functions during Ciona heart development.

Kaplan, N., Wang, W., and L. Christiaen. Dev Biol, 2019, pii: S0012-1606(18)30458-5. doi: 10.1016/j.ydbio.2018.12.018.

Transcriptional regulation of Rab32/38, a specific marker of pigment cell formation in Ciona robusta.

Racioppi C., Coppola U., Christiaen L., and F. Ristoratore. Dev Biol, 2019 pii: S0012-1606(18)30004-6. doi: 10.1016/j.ydbio.2018.11.013.

Discoidin-domain receptor coordinates cell-matrix adhesion and collective polarity in migratory cardiopharyngeal progenitors.

Bernadskaya, Y., Gline, S., Brahmbhatt, S., Wang, W., and L. Christiaen. Nat Commun, 2019, 10(1):57. doi: 10.1038/s41467-018-07976-3. PMCID:PMC6320373.

An FGF-driven feed-forward circuit patterns the cardiopharyngeal mesoderm in space and time.

Razy-Krajka, F., Gravez, B., Nicole Kaplan, Claudia Racioppi, Wei Wang and L. Christiaen. eLife, 2018, 7. pii: e29656. doi: 10.7554/eLife.29656. PMCID: PMC5809146

Evolutionary recruitment of flexible Esrp-dependent splicing programs into diverse embryonic morphogenetic processes.

Burguera D, Marquez Y, Racioppi C, Permanyer J, Torres-Méndez A, Esposito R, Albuixech-Crespo B, Fanlo L, D'Agostino Y, Gohr A, Navas-Perez E, Riesgo A, Cuomo C, Benvenuto G, Christiaen LA, Martí E, D'Aniello S, Spagnuolo A, Ristoratore F, Arnone MI, Garcia-Fernàndez J, Irimia M. Nat Commun. 2017. 8(1):1799. doi: 10.1038/s41467-017-01961-y.

ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets.

Brozovic M, Dantec C, Dardaillon J, Dauga D, Faure E, Gineste M, Louis A, Naville M, Nitta KR, Piette J, Reeves W, Scornavacca C, Simion P, Vincentelli R, Bellec M, Aicha SB, Fagotto M, Guéroult-Bellone M, Haeussler M, Jacox E, Lowe EK, Mendez M, Roberge A, Stolfi A, Yokomori R, Brown CT, Cambillau C, Christiaen L, Delsuc F, Douzery E, Dumollard R, Kusakabe T, Nakai K, Nishida H, Satou Y, Swalla B, Veeman M, Volff JN, Lemaire P. Nucleic Acids Res. 2018. 46(D1):D718-D725. doi: 10.1093/nar/gkx1108..

Evolutionary loss of melanogenesis in the tunicate Molgula occulta.

Racioppi C, Valoroso MC, Coppola U, Lowe EK, Brown CT, Swalla BJ, Christiaen L, Stolfi A, Ristoratore F. EvoDevo, 2017, 8(1). doi: 10.1186/s13227-017-0074-x.

CRISPR knockouts in Ciona embryos.

Gandhi, S., Razy-Krajka, F., Christiaen, L*, and A. Stolfi*. Adv Exp Med Biol. 2018;1029:141-152. doi: 10.1007/978-981-10-7545-2_13 (* co-corresponding authors).

Purification of Fluorescent Labelled Cells from Dissociated Ciona Embryos.

Wang, W., Racioppi, C., Gravez, B., and L. Christiaen. Adv Exp Med Biol. 2018;1029:101-107. doi: 10.1007/978-981-10-7545-2_9.

Evaluation and rational design of guide RNAs for efficient CRISPR/Cas9-mediated mutagenesis in Ciona.

Gandhi, S., Haeussler, M., Razy-Krajka, F., Christiaen, L.*, and A. Stolfi*. Dev Biol, 2017, 425(1):8-20; doi: 10.1016/j.ydbio.2017.03.003; * co-corresponding authors). PMCID: PMC5502750.

Fused Regression for Multi-source Gene Regulatory Network Inference.

Lam K.Y., Westrick Z.M., Müller C.L., Christiaen L., and R. Bonneau. PLoS Comp Biol, 2016, 12(12):e1005157. doi: 10.1371/journal.pcbi.1005157.

Rewiring of an ancestral Tbx1/10 - Ebf - Mrf network for pharyngeal muscle specification in distinct embryonic lineages.

Tolkin, T., and L. Christiaen. Development, 2016, 143(20):3852-62. doi: 10.1242/dev.136267

Ciona as a simple chordate model for heart development and regeneration.

Evans-Anderson, H., and L. Christiaen. J. Cardiovasc. Dev. Dis., 2016, 3(3). pii: 25. PMC5023151

Transcriptional control of developmental cell behaviors.

Bernadskaya, Y., and L. Christiaen. Ann Rev Cell Dev Biol, 2016, 32:77-101.

Collier/OLF/EBF-dependent transcriptional dynamics control pharyngeal muscle specification from primed cardiopharyngeal progenitors.

Razy-Krajka F, Lam K, Wang W, Stolfi A, Joly M, Bonneau R, Christiaen L.
Dev Cell. 2014 May 12;29(3):263-76. doi: 10.1016/j.devcel.2014.04.001. Epub 2014 May 1.

Fibroblast growth factor signalling controls nervous system patterning and pigment cell formation in Ciona intestinalis.

Racioppi C, Kamal AK, Razy-Krajka F, Gambardella G, Zanetti L, di Bernardo D, Sanges R, Christiaen LA, Ristoratore F.
Nat Commun. 2014 Sep 5;5:4830. doi: 10.1038/ncomms5830.

Divergent mechanisms regulate conserved cardiopharyngeal development and gene expression in distantly related ascidians.

Stolfi A, Lowe EK, Racioppi C, Ristoratore F, Brown CT, Swalla BJ, Christiaen L.
Elife. 2014 Sep 10;3:e03728. doi: 10.7554/eLife.03728.

Tissue-specific genome editing in Ciona embryos by CRISPR/Cas9.

Stolfi A, Gandhi S, Salek F, Christiaen L.
Development. 2014 Nov;141(21):4115-20. doi: 10.1242/dev.114488.

NK4 Antagonizes Tbx1/10 to Promote Cardiac versus Pharyngeal Muscle Fate in the Ascidian Second Heart Field.

Wang W, Razy-Krajka F, Siu E, Ketcham A, Christiaen L.
PLoS Biol. 2013 Dec;11(12):e1001725. doi: 10.1371/journal.pbio.1001725.

Cis-regulatory timers for developmental gene expression.

Christiaen, L.
PLoS Biol. 2013 Oct;11(10):e1001698. doi: 10.1371/journal.pbio.1001698.

p120RasGAP mediates ephrin/Eph-dependent attenuation of FGF/ERK signals during cell fate specification in ascidian embryos.

Haupaix N, Stolfi A, Sirour C, Picco V, Levine M, Christiaen L, Yasuo H. 
Development. 2013 Nov;140(21):4347-52.doi: 10.1242/dev.098756.

Genetic and Genomic Toolbox of the Chordate Ciona intestinalis.

Stolfi, A., and L. Christiaen 
Genetics, 2012. 192:55-66.

Developmental Cell Behavior.

Christiaen, L. 
Semin Cell Dev Biol, 2012, 23: p. 289.

Development and Evolution of the Ascidian Cardiogenic Mesoderm.

Tolkin, T., and L. Christiaen
Curr Top Dev Biol, 2012. 100: p. 107-42.

Transcriptional Enhancers in Ascidian Development.

Wang, W., and L. Christiaen
Curr Top Dev Biol, 2012. 98: p. 147-72.

The ANISEED database: digital representation, formalization, and elucidation of a chordate developmental program.

Tassy, O., D. Dauga, F. Daian, D. Sobral, L. Christiaen et al.
Genome Res, 2010. 20(10): p. 1459-68.

Early chordate origins of the vertebrate second heart field.

Stolfi, A., T.B. Gainous, J.J. Young, A. Mori, M. Levine, and L. Christiaen 
Science, 2010. 329(5991): p. 565-8.

A cis-regulatory signature for chordate anterior neuroectodermal genes.

Haeussler, M., Y. Jaszczyszyn, L. Christiaen, and J.S. Joly
PLoS Genet, 2010. 6(4): p. e1000912.

BMP signaling coordinates gene expression and cell migration during precardiac mesoderm development.

Christiaen, L., A. Stolfi, and M. Levine
Dev Biol, 2010. 340(2): p. 179-87.

The sea squirt Ciona intestinalis.

Christiaen, L., E. Wagner, W. Shi, and M. Levine
CSH Protoc, 2009. 2009(12): p. pdb emo138.

Isolation of sea squirt (Ciona) gametes, fertilization, dechorionation, and development.

Christiaen, L., E. Wagner, W. Shi, and M. Levine
CSH Protoc, 2009. 2009(12): p. pdb prot5344.

Electroporation of transgenic DNAs in the sea squirt Ciona.

Christiaen, L., E. Wagner, W. Shi, and M. Levine
CSH Protoc, 2009. 2009(12): p. pdb prot5345.

X-gal staining of electroporated sea squirt (Ciona) embryos.

Christiaen, L., E. Wagner, W. Shi, and M. Levine
CSH Protoc, 2009. 2009(12): p. pdb prot5346.

Microinjection of morpholino oligos and RNAs in sea squirt (Ciona) embryos.

Christiaen, L., E. Wagner, W. Shi, and M. Levine
CSH Protoc, 2009. 2009(12): p. pdb prot5347.

Whole-mount in situ hybridization on sea squirt (Ciona intestinalis) embryos.

Christiaen, L., E. Wagner, W. Shi, and M. Levine
CSH Protoc, 2009. 2009(12): p. pdb prot5348.

Isolation of individual cells and tissues from electroporated sea squirt (Ciona) embryos by fluorescence-activated cell sorting (FACS).

Christiaen, L., E. Wagner, W. Shi, and M. Levine
CSH Protoc, 2009. 2009(12): p. pdb prot5349.

Spatio-temporal intersection of Lhx3 and Tbx6 defines the cardiac field through synergistic activation of Mesp.

Christiaen, L., A. Stolfi, B. Davidson, and M. Levine
Dev Biol, 2009. 328(2): p. 552-60.

The transcription/migration interface in heart precursors of Ciona intestinalis.

Christiaen, L., B. Davidson, T. Kawashima, W. Powell, H. Nolla, K. Vranizan, and M. Levine
Science, 2008. 320(5881): p. 1349-52.

Evolutionary modification of mouth position in deuterostomes.

Christiaen, L., Y. Jaszczyszyn, M. Kerfant, S. Kano, V. Thermes, and J.S. Joly
Semin Cell Dev Biol, 2007. 18(4): p. 502-11.

FoxF is essential for FGF-induced migration of heart progenitor cells in the ascidian Ciona intestinalis.

Beh, J., W. Shi, M. Levine, B. Davidson, and L. Christiaen
Development, 2007. 134(18): p. 3297-305.

FGF signaling delineates the cardiac progenitor field in the simple chordate, Ciona intestinalis.

Davidson, B., W. Shi, J. Beh, L. Christiaen, and M. Levine
Genes Dev, 2006. 20(19): p. 2728-38.

Linking chordate gene networks to cellular behavior in ascidians.

Davidson, B. and L. Christiaen
Cell, 2006. 124(2): p. 247-50.

Embryonic versus blastogenetic development in the compound ascidian Botryllus schlosseri: insights from Pitx expression patterns.

Tiozzo, S., L. Christiaen, C. Deyts, L. Manni, J.S. Joly, and P. Burighel 
Dev Dyn, 2005. 232(2): p. 468-78.

Regulatory gene expressions in the ascidian ventral sensory vesicle: evolutionary relationships with the vertebrate hypothalamus.

Moret, F., L. Christiaen, C. Deyts, M. Blin, P. Vernier, and J.S. Joly
Dev Biol, 2005. 277(2): p. 567-79.

The dopamine-synthesizing cells in the swimming larva of the tunicate Ciona intestinalis are located only in the hypothalamus-related domain of the sensory vesicle.

Moret, F., L. Christiaen, C. Deyts, M. Blin, J.S. Joly, and P. Vernier
Eur J Neurosci, 2005. 21(11): p. 3043-55.

A modular cis-regulatory system controls isoform-specific pitx expression in ascidian stomodaeum.

Christiaen, L., F. Bourrat, and J.S. Joly
Dev Biol, 2005. 277(2): p. 557-66.

Culture of adult ascidians and ascidian genetics.

Hendrickson, C., L. Christiaen, K. Deschet, D. Jiang, J.S. Joly, L. Legendre, Y. Nakatani, J. Tresser, and W.C. Smith
Methods Cell Biol, 2004. 74: p. 143-70.

Pitx genes in Tunicates provide new molecular insight into the evolutionary origin of pituitary.

Christiaen, L., P. Burighel, W.C. Smith, P. Vernier, F. Bourrat, and J.S. Joly
Gene, 2002. 287(1-2): p. 107-13.