All Publications

2023

2022

Athira, A., Dondorp, D., Rudolf, J., Peytral, O., & Chatzigeorgiou, M. (2022). Comprehensive analysis of locomotion dynamics in the protochordate Ciona intestinalis reveals how neuromodulators flexibly shape its behavioral repertoire. PLoS Biology, 20(8), e3001744.

Begik, O., Diensthuber, G., Liu, H., Delgado-Tejedor, A., Kontur, C., Niazi, A. M., Valen, E., Giraldez, A. J., Beaudoin, J. D., Mattick, J. S., & Novoa, E. M. (2022). Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing. Nature Methods, 20, 75–85.

Bizuayehu, T. T., Labun, K., Jakubec, M., Jefimov, K., Niazi, A. M., & Valen, E. (2022). Long-read single-molecule RNA structure sequencing using nanopore. Nucleic Acids Research, 50(20), e120-e120.

Burkhardt, P. (2022). Ctenophores and the evolutionary origin(s) of neurons. Trends in Neurosciences, 45(12), 878-880.

Colgren, J., & Burkhardt, P. (2022). The premetazoan ancestry of the synaptic toolkit and appearance of first neurons. Essays in Biochemistry, 66(6), 781–795.

Dandamudi, M., Hausen, H., & Lynagh, T. (2022). Comparative analysis defines a broader FMRFamide-gated sodium channel family and determinants of neuropeptide sensitivity. Journal of Biological Chemistry, 298(7), 102086.

Gahan, J. M., Kouzel, I. U., Jansen, K. O., Burkhardt, P., & Rentzsch, F. (2022). Histone demethylase Lsd1 is required for the differentiation of neural cells in Nematostella vectensis. Nature Communications, 13(1), 465.

Glover, J.C., Fritzsch, B. (2022). Molecular mechanisms governing development of the hindbrain choroid plexus and auditory projection: A validation of the seminal observations of Wilhelm His. IBRO Neuroscience Reports. 2022 Oct 3;13:306-313. doi: 10.1016/j.ibneur.2022.09.011. PMID: 36247525; PMCID: PMC9561746.

Henriet, S., Aasjord, A., & Chourrout, D. (2022). Laboratory study of Fritillaria lifecycle reveals key morphogenetic events leading to genus-specific anatomy. Frontiers in Zoology, 19(1), 26.

Kute, P. M., Soukarieh, O., Tjeldnes, H., Trégouët, D. A., & Valen, E. (2022). Small open reading frames, how to find them and determine their function. Frontiers in Genetics, 12, 2903.

Lebouvier, M., Miramón-Puértolas, P., & Steinmetz, P. R. H. (2022). Evolutionarily conserved aspects of animal nutrient uptake and transport in sea anemone vitellogenesis. Current Biology, 32(21), 4620-4630.e5. doi:10.1016/j.cub.2022.08.039

Lemaitre, Q. B., Bartsch, N., Kouzel, I. U., Busengdal, H., Richards, G. S., Steinmetz, PR., & Rentzsch, F. (2022). NvPrdm14d-expressing neural progenitor cells contribute to non-ectodermal neurogenesis in Nematostella vectensis. bioRxiv.

Ma, X., Øvrebø, J.I., Thompson, E.M. (2022). Evolution of CDK1 Paralog Specializations in a Lineage With Fast Developing Planktonic Embryos. Frontiers in Cell and Developmental Biology. 2022 Jan 28;9:770939. doi: 10.3389/fcell.2021.770939. PMID: 35155443; PMCID: PMC8832800.

Reint, G., Li, Z., Labun, K., Keskitalo, S., Soppa, I., Mamia, K., Tolo, E., Szymanska, M., Meza-Zepeda, L. A., Lorenz, S., Cieslar-Pobuda, A., Hu, X., Bordin, D. L., Staerk, J., Valen, E., Schmierer, B., Varjosalo, M., Taipale, J., & Haapaniemi, E. (2022). Rapid genome editing by CRISPR-Cas9-POLD3 fusion. Elife, 10, e75415.

Song M, Yuan X, Racioppi C, Leslie M, Stutt N, Aleksandrova A, Christiaen L, Wilson MD, Scott IC. (2022). GATA4/5/6 family transcription factors are conserved determinants of cardiac versus pharyngeal mesoderm fate. Science Advances. doi: 10.1126/sciadv.abg0834. PMCID: PMC8916722.

Tolstenkov, O., Mikhaleva, Y., Glover, J.C. (2022). Post-gastrulation transition from whole-body to tissue-specific intercellular calcium signaling in the appendicularian tunicate Oikopleura dioica. Developmental Biology. 2022 Dec; 492:37-46. doi: 10.1016/j.ydbio.2022.09.004. Epub 2022 Sep 24. PMID: 36162551.

Vitrinel, B., Vogel, C., Christiaen, L. (2022). Rnf149-related is an FGF/MAPK-independent regulator of pharyngeal muscle fate specification. BioRxiv 2022.01.07.475354. doi: 10.1101/2022.01.07.475354.

2021

AM Niazi, M Krause, E Valen (2021) Transcript Isoform-Specific Estimation of Poly (A) Tail Length by Nanopore Sequencing of Native RNA. Methods in Molecular Biology 2284, 543-567

Bernadskaya YY, Yue H, Copos C, Christiaen L, Mogilner A. (2021). Supracellular organization confers directionality and mechanical potency to migrating pairs of cardiopharyngeal progenitor cells. Elife. doi: 10.7554/eLife.70977. PubMed PMID: 34842140; PMCID: PMC8700272.

Burkhardt, P., & Jékely, G. (2021). Evolution of Synapses and Neurotransmitter Systems: The Divide-and-Conquer Model for Early Neural Cell-Type Evolution. Current Opinion in Neurobiology, 71, 127-138.

Goehde RA, Naumann B, Laundon D, Imig C, McDonald K, Cooper BH, Varoqueaux F, Fasshauer D, Burkhardt P (2021) Choanoflagellates and the ancestry of neurosecretory vesicles. Phil. Trans. R. Soc. B 20190759.

H Tjeldnes, K Labun, YT Cleuren, K Chyżyńska, M Świrski, E Valen (2021) ORFik: a comprehensive R toolkit for the analysis of translation BMC bioinformatics 22 (1), 1-16

K Chyżyńska, K Labun, C Jones, SN Grellscheid, E Valen (2021) Deep conservation of ribosome stall sites across RNA processing genes NAR genomics and bioinformatics 3 (2)

K Labun, M Krause, Y Torres Cleuren, E Valen (2021) CRISPR Genome Editing Made Easy Through the CHOPCHOP Website Current Protocols 1 (4), e46

Kolar, K., Dondorp, D., Zwiggelaar, J. C., Hoyer, J., & Chatzigeorgiou, M. (2021). Mesmerize is a dynamically adaptable user-friendly analysis platform for 2D and 3D calcium imaging data. Nature Communications, 12, 6569.

Lynagh T, Kiontke S, Meyhoff-Madsen M, Gless BH, Johannesen J, Kattelmann S, Christiansen A, Dufva M, Laustsen AH, Devkota K, Olsen CA, Kümmel D, Pless SA, Lohse B (2021) Peptide Inhibitors of the α-Cobratoxin-Nicotinic Acetylcholine Receptor Interaction. Journal of Medicinal Chemistry 63(22):13709-13718. doi: 10.1021/acs.jmedchem.0c01202

Martín-Durán JM, Vellutini BC, Marlétaz F, Cetrangolo V, Cvetesic N, Thiel D, Henriet S, Grau-Bové X, Carrillo-Baltodano AM, Gu W, Kerbl A, Marquez Y, Bekkouche N, Chourrout D, Gómez-Skarmeta JL, Irimia M, Lenhard B, Worsaae K, Hejnol A (2021) Conservative route to genome compaction in a miniature annelid. Nat Ecol Evol. 5(2):231-242

Nomaru H, Liu Y, De Bono C, Righelli D, Cirino A, Wang W, Song H, Racedo SE, Dantas AG, Zhang L, Cai CL, Angelini C, Christiaen L, Kelly RG, Baldini A, Zheng D, Morrow BE (2021). Single cell multi-omic analysis identifies a Tbx1-dependent multilineage primed population in murine cardiopharyngeal mesoderm. Nature Communications 12(1):6645. doi: 10.1038/s41467-021-26966-6. PMCID: PMC8599455.

Ohta, N., Christiaen, L. (2021). Cellular remodeling and JAK inhibition promote zygotic gene expression in the Ciona germline. BioRxiv 2021.07.12.452040. doi: 10.1101/2021.07.12.452040.

Orús-Alcalde, A., Lu, T.M., Børve, A., Hejnol, A. (2021). The evolution of the metazoan Toll receptor family and its expression during protostome development. BMC Ecology Evolution Nov 22;21(1):208. doi: 10.1186/s12862-021-01927-1. PMID: 34809567; PMCID: PMC8609888.

Sachkova MY, Nordmann EL, Soto Angel JJ, Meeda Y, Górski B, Naumann B, Dondorp D, Chatzigeorgiou M, Kittelmann M, Burkhardt, P (2021) Neuropeptide repertoire and 3D anatomy of the ctenophore nervous system. Current Biology

Sheikh ZP, Wulf M, Friis S, Althaus M, Lynagh T, Pless SA (2021) The M1 and pre-M1 segments contribute differently to ion selectivity in ASICs and ENaCs. Journal of General Physiology 153(10):e202112899. doi: 10.1085/jgp.202112899.

Thiel, D., Yañez-Guerra, L.A., Franz-Wachtel, M., Hejnol, A., Jékely, G (2021). Nemertean, Brachiopod, and Phoronid Neuropeptidomics Reveals Ancestral Spiralian Signaling Systems. Molecular Biology and Evolution Oct 27;38(11):4847-4866. doi: 10.1093/molbev/msab211. PMID: 34272863; PMCID: PMC8557429.

Tjärnberg, A., Omar Mahmood, Christopher A Jackson, Giuseppe-Antonio Saldi, Kyunghyun Cho, Lionel Christiaen, Richard Bonneau (2021). Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data. PLOS Computational Biology 17 (1), e1008569, 2021.

2020

Giess A, Torres Cleuren YN, Tjeldnes H, Krause M, Bizuayehu TT, Hiensch S, Okon A, Wagner CR, Valen E (2020) Profiling of Small Ribosomal Subunits Reveals Modes and Regulation of Translation Initiation. Cell Reports 10.1016/j.celrep.2020.107534

Gahan JM, Rentzsch F, Schnitzler CE (2020) The genetic basis for PRC1 complex diversity emerged early in animal evolution. Proc Nat Acad Sci 10.1073/pnas.2005136117

Tournière O, Dolan D, Richards GS, Sunagar K, Columbus-Shenkar YY, Moran Y, Rentzsch F (2020) NvPOU4/Brain3 Functions as a Terminal Selector Gene in the Nervous System of the Cnidarian Nematostella vectensis. Cell Rep 10.1016/j.celrep.2020.03.031.

Gasiorowski L, Hejnol, A (2020) Hox gene expression during development of the phoronid Phoronopsis harmeri. EvoDevo 11:2

Ramilowski JA, Yip CW, Agrawal S, Chang JC, Ciani Y, Kulakovskiy IV, Mendez M, Ooi JLC, Ouyang JF, Parkinson N, Petri A, Roos L, Severin J, Yasuzawa K, Abugessaisa I, Akalin A, Antonov IV, Arner E, Bonetti A, Bono H, Borsari B, Brombacher F, Cameron CJ, Cannistraci CV, Cardenas R, Cardon M, Chang H, Dostie J, Ducoli L, Favorov A, Fort A, Garrido D, Gil N, Gimenez J, Guler R, Handoko L, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto K, Hayatsu N, Heutink P, Hirose T, Imada EL, Itoh M, Kaczkowski B, Kanhere A, Kawabata E, Kawaji H, Kawashima T, Kelly ST, Kojima M, Kondo N, Koseki H, Kouno T, Kratz A, Kurowska-Stolarska M, Kwon ATJ, Leek J, Lennartsson A, Lizio M, López-Redondo F, Luginbühl J, Maeda S, Makeev VJ, Marchionni L, Medvedeva YA, Minoda A, Müller F, Muñoz-Aguirre M, Murata M, Nishiyori H, Nitta KR, Noguchi S, Noro Y, Nurtdinov R, Okazaki Y, Orlando V, Paquette D, Parr CJC, Rackham OJL, Rizzu P, Sánchez Martinez DF, Sandelin A, Sanjana P, Semple CAM, Shibayama Y, Sivaraman DM, Suzuki T, Szumowski SC, Tagami M, Taylor MS, Terao C, Thodberg M, Thongjuea S, Tripathi V, Ulitsky I, Verardo R, Vorontsov IE, Yamamoto C, et al.(2020) Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome Res 10.1101/gr.254219.119

Lewis SH, Ross L, Bain SA, Pahita E, Smith SA, Cordaux R, Miska EA, Lenhard B, Jiggins FM, Sarkies P (2020) Widespread conservation and lineage-specific diversification of genome-wide DNA methylation patterns across arthropods. PLOS Genetics 10.1371/journal.pgen.1008864

Nepal C, Taranta A, Hadzhiev Y, Pundhir S, Mydel P, Lenhard B, Müller F, Andersen JB (2020) Ancestrally Duplicated Conserved Noncoding Element Suggests Dual Regulatory Roles of HOTAIR in cis and trans. iScience 10.1016/j.isci.2020.101008

Bonetti A, Agostini F, Suzuki AM, Hashimoto K, Pascarella G, Gimenez J, Roos L, Nash AJ, Ghilotti M, Cameron CJF, Valentine M, Medvedeva YA, Noguchi S, Agirre E, Kashi K, Samudyata, Luginbühl J, Cazzoli R, Agrawal S, Luscombe NM, Blanchette M, Kasukawa T, Hoon M, Arner E, Lenhard B, Plessy C, Castelo-Branco G, Orlando V, Carninci P (2020) RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions. Nat Commun 10.1038/s41467-020-14337-6

Fornes O, Castro-Mondragon JA, Khan A, van der Lee R, Zhang X, Richmond PA, Modi BP, Correard S, Gheorghe M, Baranašić D, Santana-Garcia W, Tan G, Chèneby J, Ballester B, Parcy F, Sandelin A, Lenhard B, Wasserman WW, Mathelier A (2020) JASPAR 2020: update of the open-access database of transcription factor binding profiles Nucleic Acids Res 10.1093/nar/gkz1001

Barešić A, Nash AJ, Dahoun T, Howes O, Lenhard B (2020) Understanding the genetics of neuropsychiatric disorders: the potential role of genomic regulatory blocks. Mol Psychiatry 10.1038/s41380-019-0518-x

Poduval, DB, Ognedal, E, Sichmanova, Z, Valen, E, Iversen, GT, Minsaas, L, Lønning, PE, Knappskog, S (2020) Assessment of tumor suppressor promoter methylation in healthy individuals. Clinical Epigenetics 10.1186/s13148-020-00920-7

Rentzsch F, Renfer E, Technau U (2020) Generating Transgenic Reporter Lines for Studying Nervous System Development in the Cnidarian Nematostella vectensis. Methods Mol Biol 10.1007/978-1-4939-9732-9_3

Kumar S, Tumu SC, Helm C, Hausen H (2020) The development of early pioneer neurons in the annelid Malacoceros fuliginosus. BMC Evol Biol 10.1186/s12862-020-01680-x

Döring C. Kumar S., Tumu S.C., Kourtesis I, Hausen H (2020) The visual pigment xenopsin is widespread in protostome eyes and impacts the view on eye evolution. eLife 10.7554/eLife.55193

Lynagh T (2020) Characterization of Schistosoma mansoni Glutamate-Gated Chloride Channels. Methods Mol Biol 10.1007/978-1-0716-0635-3_14

Pálfy M, Schulze G, Valen E, Vastenhouw NL (2020) Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation. PLOS Genetics 10.1371/journal.pgen.1008546

2019

de Mendoza A, Hatleberg W, Pang K, Leininger S, Bogdanovic O, Pflueger J, Buckberry S, Technau U, Hejnol A, Adamska M, Degnan BM, Degnan SM, Lister R (2019) Convergent evolution of a vertebrate-like methylome in a marine sponge Nature Ecol Evol 3(10):1464-1473

Andrikou C, Passamaneck YJ, Lowe CJ, Martindale MQ, Hejnol A (2019) Molecular patterning during the development of Phoronopsis harmeri reveals similarities to rhynchonelliform brachiopods. Evodevo 10:33

Martín-Durán JM, Hejnol A (2019) A developmental perspective on the evolution of the nervous system. Dev Biol, doi:10.1016/j.ydbio.2019.10.003

Cvetesic N, Pahita E, Lenhard B (2019) Transcription Start Site Mapping Using Super-low Input Carrier-CAGE. J Vis Exp 10.3791/59805

Danks GB, Galbiati H, Raasholm M, Torres Cleuren YN, Valen E, Navratilova P, Thompson EM (2019) Trans-splicing of mRNAs links gene transcription to translational control regulated by mTOR. BMC Genomics

Henriet S, Sanmarti BC, Sumic S and Chourrout D* (2019) Evolution of the U2 Spliceosome for Processing Numerous and Highly Diverse Non-canonical Introns in the Chordate Fritillaria borealis. Current Biology 29 (19), R920-922, doi 10.1016/j.cub.2019.07.092

Nauman B, Burkhardt P (2019) Spatial cell disparity in the colonial choanoflagellate Salpingoeca rosetta. Frontiers in Cell and Developmental Biology 7 (231), doi 10.3389/fcell.2019.00231

Sachkova M, Burkhardt P (2019) Exciting times to study the identity and evolution of cell types. Development 146 (18), doi 10.1242/dev.178996

Annunziata R, Andrikou C, Perillo M (2019). Development and evolution of gut structures: from molecules to function. Cell and Tissue Research doi 10.1007/s00441-019-03093-9.

Steinmetz, P.R.H. (2019) A non-bilaterian perspective on the development and evolution of animal digestive systems. Cell and Tissue Research 377: 321. doi 10.1007/s00441-019-03075-x

Gasiorowski L, Furu A, Hejnol A (2019) Morphology of the nervous system of monogonont rotifer Epiphanes senta with a focus on sexual dimorphism between feeding females and dwarf males Frontiers in Zoology 16:33 doi: 10.1186/s12983-019-0334-9

Andrikou C, Thiel D, Ruiz-Santiesteban JA, Hejnol A (2019) Active mode of excretion across digestive tissues predates the origin of excretory organs. PLoS Biology 17 (7): e3000408. doi 10.1371/journal.pbio.3000408

Feng H, Raasholm M, Moosmann A, Campsteijn C, Thompson EM (2019) Switching of INCENP paralogs controls transitions in mitotic chromosomal passenger complex functions. Cell Cycle 18:17, 2006-2025, doi: 10.1080/15384101.2019.1634954

Memar N, Schiemann S, Hennig C, Findeis D, Conradt B, Schnabel R. (2019) Twenty million years of evolution: The embryogenesis of four Caenorhabditis species are indistinguishable despite extensive genome divergence. Dev Biol 447, 182-199

Thiel D, Bauknecht P, Jékely G, Hejnol A (2019) A nemertean excitatory peptide/CCHamide regulates ciliary swimming in the larvae of Lineus longissimus. Frontiers in Zoology 16:28. doi: 10.1186/s12983-019-0326-9

Hogvall M, Vellutini BC, Martin-Duran JM, Hejnol A, Budd GE, Janssen R (2019) Embryonic expression of priapulid Wnt genes. Development, Genes and Evolution doi: 10.1007/s00427-019-00636-6

Krause M, Niazi AM, Labun K, Torres Cleuren YN, Müller FS, Valen E (2019) tailfindr: Alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing. RNA doi: 10.1101/588343

Laundon D, Larson B, McDonald K, King N, Burkhardt P (2019) The architecture of cell differentiation in choanoflagellates and sponge choanocytes. PLoS Biology 17(4): e3000226.

Kondratskaya E, Ievglevskyi O, Züchner M, Samara A, Glover JC, Boulland JL. Locomotor central pattern generator excitability states and serotonin sensitivity after spontaneous recovery from a neonatal lumbar spinal cord injury. Brain Research 2019 Apr 1;1708:10-19. doi: 10.1016/j.brainres.2018.12.001. Epub 2018 Dec 4. PMID: 30521786

Labun K, Guo X, Chavez A, Church G, Gagnon JA, Valen E (2019) Accurate analysis of genuine CRISPR editing events with ampliCan. Genome research gr. 244293.118 PubMed 30850374

Naville M*, Henriet S*, Warren I, Reeve M, Volff JN, Chourrout D (2019) Massive Changes of Genome Size Driven by Expansions of Non-autonomous Transposable Elements. Current Biology 29(6) *co-first authors

Torres-Mèndez A, Bonnal S, Marquez Y, Roth J, Iglesias M, Permanyer J, Almudi I, O'Hanlon D, Guitart T, Soller M, Gingras AC, Gebauer F, Rentzsch F, Blencowe BJ, Valcàrcel J, Irimia M (2019) A novel protein domain in an ancestral splicing factor drove the evolution of neural microexons. Nature Ecology & Evolution 2019 Mar 4. doi: 10.1038/s41559-019-0813-6.

Labun K, Montage TG, Krause M, Torres Cleuren YN, Tjeldnes H, Valen E (2019) CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing Nucleic Acids Research, doi: 10.1093/nar/gkz365

Rentzsch F, Juliano C, Galliot B. (2019) Modern genomic tools reveal the structural and cellular diversity of cnidarian nervous systems. Curr Opin Neurobiol. 56:87-96. doi: 10.1016/j.conb.2018.12.004

Fromm B, Tosar JP, Aguilera F, Friedländer MR, Bachmann L, Hejnol A (2019) Evolutionary implications of the microRNA- and piRNA complement of Lepidodermella squamata (Gastrotricha). Non-Coding RNA 5(1), 19

Gasiorowski L, Hejnol A (2019) Hox gene expression in postmetamorphic juveniles of the brachiopod Terebratalia transversa. EvoDevo 10:1

2018

Ambrosino L, Vassalli QA, D'Agostino Y, Esposito R, Cetrangolo V, Caputi L, Amoroso A, Aniello F, D'Aniello S, Chatzigeorgiou M, Chiusano ML, Locascio A. (2018) Functional conserved non-coding elements among tunicates and chordates. Developmental Biology pii: S0012-1606(17)30909-0. doi: 10.1016/j.ydbio.2018.12.012.

Birkeland Å, ChyŻyńska K, Valen E. (2018) Shoelaces: an interactive tool for ribosome profiling processing and visualization. BMC Genomics 19(1):543. doi: 10.1186/s12864-018-4912-6.

Bouquet JM, Troedsson C, Novac A, Reeve M, Lechtenbörger AK, Massart W, Skaar KS, Aasjord A, Dupont S, Thompson EM. (2018) Increased fitness of a key appendicularian zooplankton species under warmer, acidified seawater conditions. PLoS One. 13(1):e0190625. doi: 10.1371/journal.pone.0190625.

Cvetesic N, Leitch HG, Borkowska M, Müller F, Carninci P, Hajkova P, Lenhard B. (2018) SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA. Genome Research 28(12):1943-1956.

Danks GB, Navratilova P, Lenhard B, Thompson EM. (2018) Distinct core promoter codes drive transcription initiation at key developmental transitions in a marine chordate. BMC Genomics 19(1):164. doi: 10.1186/s12864-018-4504-5.

Deng W, Henriet S, Chourrout D. (2018) PreValence of Mutation-Prone Microhomology-Mediated End Joining in a Chordate Lacking the c-NHEJ DNA Repair Pathway. Current Biology 28(20):3337-3341.

Dunn CW, Zapata F, Munro C, Siebert S, Hejnol A. (2018) Pairwise comparisons across species are problematic when analyzing functional genomic data. PNAS 115(3):E409-E417.

Martín-Durán JM, Pang K, Børve A, Semmler Lê H, Furu A, Taylor Cannon J, Jondelius U, Hejnol A (2018). Convergent evolution of bilaterian nerve cords. Nature 553, 45-50.

Feng H, Thompson EM.(2018) Specialization of CDK1 and cyclin B paralog functions in a coenocystic mode of oogenic meiosis. Cell Cycle 17(12):1425-1444. doi: 10.1080/15384101.2018.1486167.

Glover JC, Elliott KL, Erives A, Chizhikov VV, Fritzsch B. (2018) Wilhelm His' lasting insights into hindbrain and cranial ganglia development and evolution. Developmental Biology pii: S0012-1606(17)30584-5. doi: 10.1016/j.ydbio.2018.02.001.

Khan A, Fornes O, Stigliani A, Gheorghe M, Castro-Mondragon JA, van der Lee R, Bessy A, Chèneby J, Kulkarni SR, Tan G, Baranasic D, Arenillas DJ, Sandelin A, Vandepoele K, Lenhard B, Ballester B, Wasserman WW, Parcy F, Mathelier A. (2018) JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Research 46(D1):D260-D266.

Lekang K, Hadziavdic K, Sandnes Skaar K, Jonassen I, Thompson EM, Troedsson C. (2018) Development and testing of an 18S rRNA phylogenetic microarray for marine sediments. Journal of Microbiological Methods 154:95-106.

Li C, Lenhard B, Luscombe NM. (2018) Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome. Genome Research 28(5):676-688.

Lynagh T, Mikhaleva Y, Colding JM, Glover JC, Pless SA. (2018) Acid-sensing ion channels emerged over 600 Mya and are conserved throughout the deuterostomes. PNAS 115(33):8430-8435.

Marlétaz F, Firbas PN, Maeso I, Tena JJ, Bogdanovic O, Perry M, Wyatt CDR, de la Calle-Mustienes E, Bertrand S, Burguera D, Acemel RD, van Heeringen SJ, Naranjo S, Herrera-Ubeda C, Skvortsova K, Jimenez-Gancedo S, Aldea D, Marquez Y, Buono L, Kozmikova I, Permanyer J, Louis A, Albuixech-Crespo B, Le Petillon Y, Leon A, Subirana L, Balwierz PJ, Duckett PE, Farahani E, Aury JM, Mangenot S, Wincker P, Albalat R, Benito-Gutiérrez È, Cañestro C, Castro F, D'Aniello S, Ferrier DEK, Huang S, Laudet V, Marais GAB, Pontarotti P, Schubert M, Seitz H, Somorjai I, Takahashi T, Mirabeau O, Xu A, Yu JK, Carninci P, Martinez-Morales JR, Crollius HR, Kozmik Z, Weirauch MT, Garcia-Fernàndez J, Lister R, Lenhard B, Holland PWH, Escriva H, Gómez-Skarmeta JL, Irimia M. (2018) Amphioxus functional genomics and the origins of vertebrate gene regulation. Nature 564(7734):64-70.

Martín-Durán JM. (2018) General Principles of Planarian Embryogenesis and Its Analysis by In Situ Hybridization and Immunohistochemistry Methods. Methods in Molecular Biology 1774:405-421.

Memar N, Schiemann S, Hennig C, Findeis D, Conradt B, Schnabel R. (2018) Twenty million years of evolution: The embryogenesis of four Caenorhabditis species are indistinguishable despite extensive genome divergence. Developmental Biology pii: S0012-1606(18)30687-0. doi: 10.1016/j.ydbio.2018.12.022.

Mikhaleva Y, Skinnes R, Sumic S, Thompson EM, Chourrout D. (2018) Development of the house secreting epithelium, a major innovation of tunicate larvaceans, involves multiple homeodomain transcription factors. Developmental Biology 443(2):117-126.

Nash AJ, Lenhard B. (2018) A Novel Measure of Non-coding Genome Conservation Identifies Genomic Regulatory Blocks Within Primates. Bioinformatics. doi:10.1093/bioinformatics/bty1014.

Olsen LC, Kourtesis I, Busengdal H, Jensen MF, Hausen H, Chourrout D. Evidence for a centrosome-attracting body like structure in germ-soma segregation during early development, in the urochordate Oikopleura dioica. BMC Developmental Biology 2018 18(1) doi: 10.1186/s12861-018-0165-5.

Rentzsch F, Holstein TW. (2018) Making head or tail of cnidarian hox gene function. Nature Communication 9(1):2187. doi: 10.1038/s41467-018-04585-y.

Sebé-Pedrós A, Chomsky E, Pang K, Lara-Astiaso D, Gaiti F, Mukamel Z, Amit I, Hejnol A, Degnan BM, Tanay A. (2018) Early metazoan cell type diversity and the evolution of multicellular gene regulation. Nature Ecology & Evolution 2(7):1176-1188.

2017

Bosch TCG, Klimovich A, Domazet-Lošo T, Gründer S, Holstein TW, Jékely G, Miller DJ, Murillo-Rincon AP, Rentzsch F, Richards GS, Schröder K, Technau U, Yuste R. (2017) Back to the Basics: Cnidarians Start to Fire. Trends in Neuroscience 40(2):92-105.

Busengdal H, Rentzsch F. (2017) Unipotent progenitors contribute to the generation of sensory cell types in the nervous system of the cnidarian Nematostella vectensis. Developmental Biology 431(1):59-68.

Schiemann SM, Martín-Durán JM, Børve A, Vellutini BC, Passamaneck YJ, Hejnol A (2017). Clustered brachiopod Hox genes are not expressed collinearly and are associated with lophotrochozoan novelties. PNAS USA 114 (10) E1913– E1922.

Fritzsch B, Elliott KL, Glover JC. (2017) Gaskell revisited: new insights into spinal autonomics necessitate a revised motor neuron nomenclature. Cell and Tissue Research 370(2):195-209.

Conley KR, Gemmell BJ, Bouquet JM, Thompson EM, and Sutherland KR (2017). A self-cleaning biological filter: how appendicularians mechanically control particle adhesion and removal. Limnology and Oceanography, in press doi: 10.1002/lno.10680.

Giess A, Jonckheere V, Ndah E, Chyżyńska K, Van Damme P, Valen E. (2017) Ribosome signatures aid bacterial translation initiation site identification. BMC Biology 15(1):76. doi: 10.1186/s12915-017-0416-0.

Harmston N, Ing-Simmons E, Tan G, Perry M, Merkenschlager M, Lenhard B. (2017) Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation. Nature Communication 8(1):441. doi: 10.1038/s41467-017-00524-5.

Hejnol A, Vellutini BC. (2017) Larval Evolution: I'll Tail You Later…. Current Biology 27(1):R21-R24.

Helm C, Karl A, Beckers P, Kaul-Strehlow S, Ulbricht E, Kourtesis I, Kuhrt H, Hausen H, Bartolomaeus T, Reichenbach A, Bleidorn C. (2017) Early evolution of radial glial cells in Bilateria. Proceedings of the Royal Society B: Biological Sciences 284(1859). pii: 20170743. doi: 10.1098/rspb.2017.0743.

Holz O, Apel D, Steinmetz PR, Lange E, Hopfenmüller S, Olher K, Sudhop S, Hassel M. (2017) Bud detachment in Hydra requires activation of fibroblast growth factor receptor and a Rho-ROCK-myosin II signaling pathway to ensure formation of a basal constriction. Developmental Dynamics 246 (7):502-516.

Lanzén A, Lekang K, Jonassen I, Thompson EM, Troedsson C (2017). DNA extraction replicates improve diversity and compositional dissimilarity in metabarcoding of eukaryotes in marine sediments. PLoS One 12:e0179443. doi: 10.1371/journal.pone.0179443.

Martín-Durán JM, Pang K, Børve A, Lê HS, Furu A, Cannon JT, Jondelius U, Hejnol A. (2017) Convergent evolution of bilaterian nerve cords. Nature 553(7686):45-50.

Lawrence J, Topper J, Petelenz-Kurdziel E, Bratbak G, Larsen A, Thompson EM, Troedsson C, and Ray JL (2017). Viruses on the menu: The appendicularian Oikopleura dioica efficiently removes viruses from seawater. Limnology and Oceanography, in press.

Martín-Durán JM, Ryan JF, Vellutini BC, Pang, KS, Hejnol A (2017). A novel approach using increased taxon sampling reveals thousands of hidden orthologs in flatworms. Genome Research doi:10.1101/gr.216226.116

Navratilova P, Danks G, Long A, Butcher S, Manak JR, and EM Thompson (2017). Sex-specific chromatin landscapes in an ultra-compact chordate genome. BMC Epigenetics & Chromatin, 10:3.

Ndah E, Jonckheere V, Giess A, Valen E, Menschaert G, Van Damme P (2017). REPARATION: ribosome profiling assisted (re-)annotation of bacterial genomes. Nucleic Acids Research, gkx758

Omran H, Reiter JF. (2017) Evolutionary Proteomics Uncovers Ancient Associations of Cilia with Signaling Pathways. Developmental Cell 43(6):744-762.

Polychronopoulos D, King JWD, Nash AJ, Tan G, Lenhard B. (2017) Conserved non-coding elements: developmental gene regulation meets genome organization. Nucleic Acids Research 45(22):12611-12624.

Rentzsch F, Layden M, Manuel M. (2017) The cellular and molecular basis of cnidarian neurogenesis. Wiley Interdisciplinary Reviews: Developmental Biology 6(1). doi: 10.1002/wdev.257.

Sigg MA, Menchen T, Lee C, Johnson J, Jungnickel MK, Choksi SP, Garcia G 3rd, Busengdal H, Dougherty GW, Pennekamp P, Werner C, Rentzsch F, Florman HM, Krogan N, Wallingford JB, Omran H, Reiter JF. (2017) Evolutionary Proteomics Uncovers Ancient Associations of Cilia with Signaling Pathways. Developmental Cell 43(6):744-762.

Sinigaglia C, Thiel D, Hejnol A, Houliston E, Leclere L (2017). A safer, urea-based in situ hybridization method improves detection of gene expression in diverse animal species. Developmental Biology (doi:10.1016/j.ydbio.2017.11.015)

Siriboonpiputtana T, Zeisig BB, Zarowiecki M, Fung TK, Mallardo M, Tsai CT, Lau PNI, Hoang QC, Veiga P, Barnes J, Lynn C, Wilson A, Lenhard B, So CWE. (2017) Transcriptional memory of cells of origin overrides β-catenin requirement of MLL cancer stem cells. EMBO Journal 36(21):3139-3155.

Steinmetz PR, Aman A, Kraus JE, Technau U. (2017) Gut-like ectodermal tissue in a sea anemone challenges germ layer homology. Nature Ecology & Evolution 1:1535-1542.

Thiel D, Bauknecht P, Jékely G, Hejnol A (2017). An ancient FMRFamide-related peptide-receptor pair induces defence behaviour in a brachiopod larva, Open Biology 7:170136

Vellutini BC, Martín-Durán JM, Hejnol A (2017). Cleavage modification did not alter blastomere fates during bryozoan evolution. BMC Biology 15:33

Vöcking O, Kourtesis I, Tumu SC, Hausen H. (2017) Co-expression of xenopsin and rhabdomeric opsin in photoreceptors bearing microvilli and cilia. Elife. 2017 6. pii: e23435. doi: 10.7554/eLife.23435.

Wang S, Zhang J, Jiao W, Li J, Xun X, Sun Y, Guo X, Huan P, Dong B, Zhang L, Hu X, Sun X, Wang J, Zhao C, Wang Y, Wang D, Huang X, Wang R, Lv J, Li Y, Zhang Z, Liu B, Lu W, Hui Y, Liang J, Zhou Z, Hou R, Li X, Liu Y, Li H, Ning X, Lin Y, Zhao L, Xing Q, Dou J, Li Y, Mao J, Guo H, Dou H, Li T, Mu C, Jiang W, Fu Q, Fu X, Miao Y, Liu J, Yu Q, Li R, Liao H, Li X, Kong Y, Jiang Z, Chourrout D, Li R, Bao Z. (2017) Scallop genome provides insights into evolution of bilaterian karyotype and development. Nature Ecology & Evolution 1(5):120. doi:10.1038/s41559-017-0120.

Winder M, Bouquet JM, Bermúdez JR, Berger SA, Hansen T, Brandes J, Sazhin AF, Nejstgaard JC, Båmstedt U, Jakobsen HH, Dutz J, Frischer ME, Troedsson C, and EM Thompson (2017). Increased appendicularian zooplankton alter carbon cycling under warmer more acidified ocean conditions. Limnology and Oceanography, doi: 10.1002/lno.10516.

Hejnol A (2017). Ladders, trees, complexity and other metaphors in evolutionary thinking. (In "Arts of Living on a Damaged Planet: Ghosts and Monsters of the Anthropocene", eds. Tsing AL, Swanson HA, Gan E, Brubandt N, Minnesota University Press, Minnesota, pp. 110–117)

Hejnol A, Vellutini BC (2017) Larval Evolution: I'll tail you later... Curr Biol, 29, R21-R23

2016

Barberán S, Martín-Durán JM, Cebrìà F (2016). Evolution of the EGFR pathway in Metazoa and its diversification in the planarian Schmidtea mediterranea. Sci Rep 6:28071.

Bause M, van der Horst R, Rentzsch F (2016). Glypican1/2/4/6 and sulfated glycosaminoglycans regulate the patterning of the primary body axis in the cnidarian Nematostella vectensis. Dev Biol 414: 108-120.

Borisenko I, Adamski M, Ereskovsky A, Adamska A (2016). Surprisingly rich repertoire of Wnt genes in the demosponge Halisarca dujardini BMC Evol Biol 16:123. DOI: 10.1186/s12862-016-0700-6

Cannon J, Vellutini BC, Smith J, Ronquist F, Jondelius U, Hejnol A (2016). Xenacoelomorpha is the sister group of Nephrozoa. Nature 530, 89-93 doi:10.1038/nature16520

Helm C, Vöcking O, Kourtesis I and Hausen H (2016). Owenia fusiformis – a basally branching annelid suitable for studying ancestral features of annelid neural development. BMC Evol Biol, 16(1), 129. http://doi.org/10.1186/s12862-016-0690-4

Kerbl A, Martín-Durán JM, Worsaae K, Hejnol A (2016). Molecular regionalization in the compact brain of the meiofaunal annelid Dinophilus gyrociliatus (Dinophilidae). EvoDevo 7:20

Labun K, Montague TG, Gagnon JA, Thyme SB and Valen E (2016). CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering Nucleic Acids Research, Jul 8;44(W1):W272-6. doi: 10.1093/nar/gkw398.

Lanzén A, K Lekang, I Jonassen, EM Thompson and C Troedsson (2016). High-throughput metabarcoding of eukaryotic diversity for environmental monitoring of offshore oil-drilling activities. Mol Ecol 25:4392-4406.

Lavrov D, Adamski M, Chevaldonné P and Adamska M (2016). Extensive Mitochondrial mRNA Editing and Unusual Mitochondrial Genome Organization in Calcaronean Sponges. Curr Biol 26(1), 86–92

Leclére L, Bause M, Sinigaglia C, Steger J, Rentzsch F (2016). Development of the aboral domain in Nematostella requires β-catenin and the opposing activities of six3/6 and frizzled5/8. Development 143: 1766-1777.

Martín-Durán JM, Passamaneck YJ, Martindale Hejnol A (2016). The developmental basis for the recurrent evolution of deuterostomy and protostomy Nat Ecol Evol doi:10.1038/s41559-016-0005

Martín-Durán JM, Vellutini BC, Hejnol A (2016). Embryonic chirality and the evolution of spiralian left-right asymmetries Phil Trans R Soc Sci 371, 20150411

Martín-Durán JM, Wolff GH, Strausfeld NJ and Hejnol A (2016). The larval nervous system of the penis worm Priapulus caudatus (Ecdysozoa). Phil Trans R Soc Sci 271, doi:10.1098/rstb.2015.0050

Reitzel AM, Pang K and Martindale MQ (2016). Developmental expression of "germline"- and "sex determination"-related genes in the ctenophore Mnemiopsis leidyi. EvoDevo 7:17

Thyme SB, Akhmetova L, Montague TG, Valen E and Schier AF (2016). Internal guide RNA interactions interfere with Cas9-mediated cleavage Nature Communications, Jun 10;7:11750. doi: 10.1038/ncomms11750.

Vellutini, BC and Hejnol A (2016). Expression of segment polarity genes in brachiopods supports a non-segmental ancestral role of engrailed for bilaterians. Sci Rep 6, 32387; doi: 10.1038/srep32387

Hejnol A, Dunn CW (2016). Animal Evolution: Are Phyla Real? Curr Biol, 26, R424-R426

Ferrer M, Henriet S, Chamontin C, Lainé S and Mougel M (2016). From Cells to Virus Particles: Quantitative Methods to Monitor RNA Packaging. Viruses 8(8): 239 6:28071.

Hejnol A, Pang K (2016). Xenacoelomorpha’s significance for understanding bilaterian evolution Curr Opin Dev Gen 39, 48-54

Layden M, Rentzsch F, Röttinger E (2016). The rise of the starlet sea anemone Nematostella vectensis as a model system to investigate development and regeneration. Wiley Interdiscip Rev Dev Biol 2016 Jul;5(4):408-2 doi: 10.1002/wdev.222. Epub 2016 Feb 19

Rentzsch F, Technau U (2016). Genomics and development of Nematostella vectensis and other anthozoans Curr Opin Dev Gen 39, 63-70

2015

Bråte J, Adamski M, Neumann RS, Shalchian-Tabrizi K and Adamska M (2015). Regulatory RNA at the root of animals: dynamic expression of developmental lincRNAs in the calcisponge Sycon ciliatum. Proc R Soc B-Biol Sci 22;282(1821). pii: 20151746. doi: 10.1098/rspb.2015.1746

Church S, Ryan JF and Dunn CW (2015). Automation and Evaluation of the SOWH Test with SOWHAT Syst Bioldoi 10.1093/sysbio/syv055

Danks GB and EM Thompson (2015). Trans-splicing in metazoans: a link to translational control? Worm 4:3, e1046030, DOI: 10.1080/21624054.2015.1046030

Danks G, Raasholm M, Campsteijn C, Long AM, Manak JR, Lenhard B, Thompson EM (2015). Trans-splicing and operons in metazoans: translational control in maternally regulated development and recovery from growth arrest. Mol Biol Evol, 32: 585-599.

Denker E, Sehring IM, Dong B, Audisso J, Mathiesen B, Jiang D. (2015). Regulation by a TGFβ-ROCK-actomyosin axis secures a non-linear lumen expansion that is essential for tubulogenesis. Development pii: dev.117150

Fortunato S, Adamski M and Adamska M (2015). Comparative analyses of developmental transcription factor repertoires in sponges reveal unexpected complexity of the earliest animals. Mar Genom 24 Pt 2:121-9. doi: 10.1016/j.margen.2015.07.008. Epub 2015 Aug 5

Henriet S, Sumic S, Doufoundou-Guilengu C1, Flo Jensen M, Grandmougin C, Fal K, Thompson E, Volf JN and Chourrout D (2015). Embryonic expression of endogenous retroviral RNAs in somatic tissues adjacent to the Oikopleura germline Nucleic Acids Res doi:10.1093/nar/gkv169

Kreneisz O, Glover JC (2015). Developmental Characterization of Tail Movements in the Appendicularian Urochordate Oikopleura dioica. Brain Behav Evol 86(3-4):191-209.

Laumer CE, Bekkouche N, Kerbl A, Goetz F, Neves RC, Sørensen MV, Kristensen RM, Hejnol A, Dunn C, Giribet G, Worsaae K (2015). Spiralian phylogeny informs the evolution of microscopic lineages. Curr Biol, 25, 2000-6.

Laumer CE, Hejnol A, Giribet G (2015). Nuclear genomic signals of the “microturbellarian” roots of platyhelminth evolutionary innovation. eLife;10.7554/eLife.05503

Lekang K, Thompson EM and C Troedsson (2015). A comparison of DNA extraction methods for biodiversity studies of eukaryotes in marine sediments. Aquat Micr Ecol 75: 15-25.

Martí-Solans J, Ferrández-Roldán A, Godoy-Marín H, Badia-Ramentol J, Torres-Aguila NP, Rodríguez-Marí A, Bouquet JM, Chourrout D, Thompson EM, Albalat R, Cañestro C (2015). Oikopleura dioica culturing made easy: a low-cost facility for an emerging animal model in EvoDevo. Genesis 53:183-193.

Martín-Durán JM, Vellutini BC, Hejnol A (2015). The evolution and development of the adelphophagic, intracapsular Desor larva of the nemertean Lineus ruber. EvoDevo 6:28

Martín-Durán JM, Hejnol A (2015). The study of Priapulus caudatus reveals conserved molecular patterning underlying different gut morphogenesis in the Ecdysozoa. BMC Biol 13:29

Mikhaleva Y, Kreneisz O, Olsen LC, Glover JC, Chourrout D (2015). Modification of the larval swimming behavior in Oikopleura dioica, a chordate with a miniaturized central nervous system by dsRNA injection into fertilized eggs. J Exp Zool Part B 324:114-127.

Passamaneck YJ, Hejnol A, Martindale MQ (2015). Mesodermal gene expression during the embryonic and larval development of the articulate brachiopod Terebratalia transversa. EvoDevo 6:10

Richards GS, Rentzsch F (2015). Regulation of Nematostella neural progenitors by SoxB, Notch and bHLH genes. Development. 2015 142:3332-42.

Saina M, Busengdal H, Sinigaglia C, Petrone L, Oliveri P, Rentzsch, F, Benton R (2015). A cnidarian homologue of an insect gustatory receptor functions in developmental body patterning. Nat Commun, 6:6243. doi: 10.1038/ncomms7243

Sehring Y, Recho P, Denker E, Kourakis M, Mathiesen B, Hannezo E, Dong B, Jiang D (2015). Assembly and positioning of actomyosin rings by contractility and planar cell polarity. eLife;10.7554/eLife.09206

Sinigaglia C, Busengdal H, Lerner A, Oliveri P, Rentzsch F (2015). Molecular characterization of the apical organ of the anthozoan Nematostella vectensis. Dev Biol 398: 120-133.

Subramaniam G, Campsteijn C, and EM Thompson (2015). Co-expressed Cyclin D variants cooperate to regulate proliferation of germline nuclei in a syncytium. Cell Cycle 14: 2129-2141.

Vöcking O, Kourtesis I and Hausen H (2015). Posterior eyespots in larval chitons have a molecular identity similar to anterior cerebral eyes in other bilaterians. EvoDevo 6:40 DOI 10.1186/s13227-015-0036-0.

Øvrebø JI, Campsteijn C, Kourtesis I, Hausen H, Raasholm M, and EM Thompson (2015). Functional specialization of chordate CDK1 paralogs during oogenic meiosis. Cell Cycle 14: 880-893.

Hejnol A (2015). Acoelomorpha and Xenoturbellida. Evolutionary Developmental Biology of Invertebrates Volume 1, ed. Wanninger A., Springer Verlag, pp. 203-14.

Hejnol A (2015). Cycloneuralia. Evolutionary Developmental Biology of Invertebrates Volume 3, ed. Wanninger A, Springer Verlag, pp. 1-13.

Hejnol A (2015). Gnathifera. Evolutionary Developmental Biology of Invertebrates Volume 2, ed. Wanninger A, Springer Verlag, pp. 1-12.

Hejnol A (2015). Gastrotricha. Evolutionary Developmental Biology of Invertebrates Volume 2, ed. Wanninger A, Springer Verlag, pp. 13-19.

Hejnol A, Martín-Durán JM (2015). Getting to the bottom of anal evolution. Zool Anz, doi: 10.1016/j.jcz.2015.02.006

Hejnol A, Rentzsch F (2015). Primer: Neural Nets. Curr Biol 25:R782-R786

Adell T, Martín-Durán JM, Salo E, Cebria F (2015). Platyhelminthes. Evolutionary Developmental Biology of Invertebrates Volume 2, ed. Wanninger A, Springer Verlag, pp. 21-40.

Arnone MI, Hejnol A (2015). Genomics going wild: Marine sampling for studies of evolution and development Mar Genomics, doi:10.1016/j.margen.2015.11.003

Hejnol A, Lowe CJ (2015). Embracing the comparative approach: how robust phylogenies and broader developmental sampling impacts the understanding of nervous system evolution Phil Trans R Soc B 370: 20150045

Kelava I, Rentzsch F, Technau U (2015). Evolution of eumetazoan nervous systems: insights from cnidarians. Phil Trans R Soc B 2015 370 20150065; DOI: 10.1098/rstb.2015.0065. Published 9 November 2015

Hejnol A (2015). Acoelomorpha. Structure and Evolution of Invertebrate Nervous Systems eds. Schmidt-Rhaesa A, Hartzsch S, Purschke G, Oxford University Press, Oxford, pp. 56-61.

2014

Bekkouche N, Kristensen RM, Hejnol A, Sørensen, MV, Worsaae K (2014). Detailed reconstruction of the musculature in Limnognathia maerski (Micrognathozoa) and comparison with other Gnathifera. Front Zool 11:71

Buisson N, Sirour C, Moreau N, Denker E, Le Bouffant R, Goullancourt A, Darribere T, Bello V (2014). An adhesome comprising laminin, dystroglycan and myosin IIA is required during notochord development in Xenopus laevis. Development 141 (23) 4569-79.

Børve A, Hejnol A (2014). Development and juvenile anatomy of the nemertodermatid Meara stichopi (Bock) Westblad 1949 (Acoelomorpha). Front Zool 11:50

Calbet A, Sazhin AF, Nejstgaard JC, Berger SA, Tait ZS, Olmos L, Sousoni D, Isari S, Martínez RA, Bouquet JM, Thompson EM, Båmstedt U, Jakobsen HH (2014). Future climate scenarios for a coastal productive planktonic food web resulting in microplankton phenology changes and decreased trophic transfer efficiency. PLoS One, 9:e94388.

Fortunato S A V, Adamski M, Mendivil Ramos O, Leininger S, Liu J, Ferrier D E K and Adamska M (2014). Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes. Nature 514: 620–623 doi:10.1038/nature13881

Fortunato S, Leininger S, and Adamska M (2014). Evolution of the Pax-Six-Eya-Dach network: the calcisponge case study. EvoDevo, 5(23)

Grande C, Martín-Durán JM, Kenny NJ, Truchado-García M, Hejnol A (2014). Evolution, divergence and loss of the Nodal signalling pathway: new data and a synthesis across the Bilateria. Int J Dev Biol 58, 521-532

Hadziavdic K, Lekang K, Lanzen A, Jonassen I, Thompson EM and C Troedsson (2014). Characterization of the 18S rRNA Gene for Designing Universal Eukaryote Specific Primers. PLoS One, 9: e87624.

Leclère L, Rentzsch F (2014). RGM regulates BMP-mediated secondary axis formation in the sea anemone Nematostella vectensis. Cell Reports doi.org/10.1016/j.celrep.2014.11.009, Cell Podcast (starts at 9:35min)

Leininger S, Adamski M, Bergum B, Guder C, Liu J, Laplante M, Bråte, Hoffmann F, Fortunato S, Jordal S, Rapp HT and Adamska M (2014). Developmental gene expression provides clues to relationships between sponge and eumetazoan body plans Nat Commun doi:10.1038/ncomms4905.

Moran Y, Fredman D, Praher D, Li XZ, Wee LM, Rentzsch F, Zamore PD, Technau U, Seitz H (2014). Cnidarian microRNAs frequently regulate targets by cleavage. Genome Res 24(4):651-63.

Pascarella G, Lazarevic D, Plessy C, Bertin N, Akalin A, Vlachouli C, Simone R, Faulkner GJ, Zucchelli S, Kawai J, Daub CO, Hayashizaki Y, Lenhard B, Carninci P, Gustincich S (2014). NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elements. Front Cell Neurosci 8:41

Richards GS, Rentzsch F (2014). Transgenic analysis of a SoxB gene reveals neural progenitor cells in the cnidarian Nematostella vectensis. Development 141: 4681-4689 doi:10.1242

Schnitzler CE, Simmons DK, Pang K, Martindale MQ and Baxevanis AD (2014). Expression of multiple Sox genes through embryonic development in the ctenophore Mnemiopsis leidyi is spatially restricted to zones of cell proliferation EvoDevo, 5:15

Sehring IM, Dong B, Denker E, Bhattachan P, Deng W, Mathiesen BT, Jiang D (2014). An Equatorial Contractile Mechanism Drives Cell Elongation but not Cell Division PLoS Biol. 12(2):e1001781. doi: 10.1371/journal.pbio.1001781.

Subramaniam G, Campsteijn C, and EM Thompson (2014). Lifespan extension in a semelparous chordate occurs via developmental growth arrest just prior to meiotic entry. PLoS One, 9:e93787.

Voigt O, Adamski M, Sluzek K and Adamska M (2014). Calcareous sponge genomes reveal complex evolution of α-carbonic anhydrases and two key biomineralization enzymes. BMC Evol Biol doi:10.1186/s12862-014-0230-z

Zakrzewski A-C, Weigert A, Helm C, Adamski M, Adamska M, Bleidorn C, Raible F and Hausen H (2014). Early divergence, broad distribution and high diversity of animal chitin synthases. Genome Biol Evol 6(2):316-325.

Chiodin M, Børve A, Berezhikov E, Ladurner P, Martinez P, Hejnol A (2013). Mesodermal gene expression in the acoel Isodiametra pulchra indicates a low number of mesodermal cell types and the endomesodermal origin of the gonads. PLoS One 8(2): e55499 doi:10.1371/journal.pone.0055499

Hejnol A (2014). News and Views: Evolutionary Biology: Excitation about jelly nerves. Nature, 510, doi:10.1038/nature13340, Nature Podcast Not so Simple

Dunn CW, Giribet G, Edgecombe GD, Hejnol A (2014). Animal Phylogeny and Its Evolutionary Implications. Annu Rev Ecol Evol Syst 45:371-395

Hejnol A, Lowe C (2014). Animal Evolution: Stiff or Squishy Notochord Origins? Curr Biol 24, R1131-R1133

2013

Danks G, Campsteijn C, Parida M, Butcher S, Doddapaneni H, Fu B, Petrin R, Metpally R, Lenhard B, Wincker P, Chourrout D, Thompson EM and JR Manak (2013). OikoBase: A genomics and developmental transcriptomics resource for the urochordate Oikopleura dioica. Nucleic Acids Res. 41: 845-853.

Deng W, Niesb F, Feuerb A, Bocinac I, Oliverb D, and Di Jiang (2013) Anion translocation through an Slc26 transporter mediates lumen expansion during tubulogenesis. Proc Natl Acad Sci USA doi: 10.1073/pnas.1220884110.

Denker E, Boina A, Jiang D (2013). Tubulogenesis in a simple cell cord requires the formation of bi-apical cells through two discrete Par domains. Development 140(14):2985-96. doi: 10.1242/dev.092387. Epub 2013 Jun 12.

Flot JF, Hespeels B, Li X, Noel B, Arkhipova I, Danchin EGJ, Hejnol A, Henrissat B, Koszul R, Aury JM, Barbe V, Barthélémey R-M, Bast J, Bazykin GA, Chabrol O, Couloux A, Da Rocha M, Da Silva C, Gladyshev E, Gouret P, Hallatschek O, Hecox-Lea B, Lebadie K, Lejeune B, Piskurek O, Poulain J, Rodriguez F, Ryan JF, Vakhrusheva OA, Wajnberg E, Wirth B, Yushenova I, Kellis M, Kondrashov AS, Mark Welch DB, Pontarotti P, Weissenbach J, Wincker P, Jaillon O, Van Doninck K (2013). Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga. Nature 500, 453-457 (doi:10.1038/nature12326)

Gazave E, Lavrov DV, Cabrol J, Renard E, Rocher C, Vacelet J, Adamska M, Borchiellini C, Ereskovsky AV (2013). Systematics and molecular phylogeny of the family oscarellidae (homoscleromorpha) with description of two new oscarella species. PLoS ONE 30;8(5):e63976.

Hill MS, Hill AL, Lopez J, Peterson KJ, Pomponi S, Diaz MC, Thacker RW, Adamska M, Boury-Esnault N, Cáárdenas P, Chaves-Fonnegra A, Danka E, De Laine BO, Formica D, Hajdu E, Lobo-Hajdu G, Klontz S, Morrow CC, Patel J, Picton B, Pisani D, Pohlmann D, Redmond NE, Reed J, Richey S, Riesgo A, Rubin E, Russell Z, Rützler K, Sperling EA, di Stefano M, Tarver JE, Collins AG (2013). Reconstruction of Family-level Phylogenetic Relationships within Demospongiae (Porifera) Using Nuclear Encoded Housekeeping Genes. PLoS One 8(1):e50437.

Lobón CM, Bouquet JM, Reeve M, Novac A, Acuña JL, Thompson EM and C Troedsson (2013). Response of the pelagic Tunicate appendicularian, Oikopleura dioica to controlled simulations of a strong bloom condition: A bottom-up perspective. Limnol Oceanogr 58: 215-226.

Martín-Durán JM, Mendoza A, Sebé-Pedrós A, Ruiz-Trillo I, Hejnol A (2013). A broad genomic survey reveals multiple origins and frequent losses in the evolution of respiratory hemerythrins and hemocyanins Genome Biol Evol 5, 1435-1442 - abstract

Nosenko T, Schreiber F, Adamska M, Adamski M, Eitel M, Hammel J, Maldonado M, Müller WE, Nickel M, Schierwater B, Vacelet J, Wiens M, Wörheide G (2013). Deep metazoan phylogeny: When different genes tell different stories. Mol Phylogenet Evol Jan 23. pii: S1055-7903(13)00029-8. doi: 10.1016/j.ympev.2013.01.010. [Epub ahead of print]

Parlier D, Moers V, Van Campenhout C, Preillon J, Leclère L, Saulnier A, Sirakov M, Busengdal H, Kricha S, Marine JC, Rentzsch F, Bellefroid EJ (2013). The Xenopus doublesex-related gene Dmrt5 is required for olfactory placode neurogenesis. Dev Biol 373 (1): 39-52.

Robinson JM, Sperling EA, Bergum B, Adamski M, Nichols SA, Adamska M, Peterson KJ (2013). The Identification of microRNAs in Calcisponges: Independent Evolution of microRNAs in Basal Metazoans. J Exp Zool Part B Jan 24. doi: 10.1002/jez.b.22485. [Epub ahead of print]

Ryan JF, Pang K, Schnitzler CE, Nguyen AD, Moreland RT, Simmons DK, Koch BJ, Francis WR, Havlak P, NISC Comparative Sequencing Program, Smith SA, Putnam NH, Haddock SHD, Dunn CW, Wolfsberg TG, Mullikin JC, Martindale MQ, Baxevanis AD (2013). The Genome of the Ctenophore Mnemiopsis leidyi and Its Implications for Cell Type Evolution Science doi:10.1126/science.1242592

Sinigaglia C, Busengdal H, Leclère L, Technau U, Rentzsch F (2013). The bilaterian head patterning gene six3/6 controls aboral domain development in a cnidarian. PLoS Biol, 11(2): e1001488. doi:10.1371/journal.pbio.1001488

Troedsson C, Bouquet JM, Lobón CM, Novac A, Nejstgaard JC, Dupont S, Bosak S, Jakobsen HH, Romanova N, Pankoke LM, Isla A, Dutz J, Sazhin AF and EM Thompson (2013). Effects of ocean acidification, temperature and nutrient regimes on the appendicularian Oikopleura dioica: A mesocosm study. Mar Biol [special issue on ocean acidification], epub ahead of press DOI 10.1007/s00227-012-2137-9

2012

Campsteijn C, Øvrebø JI, Karlsen BO and EM Thompson (2012). Expansion of cyclin D and CDK1 paralogs in Oikopleura dioica, a chordate employing diverse cell cycle variants. Mol Biol Evol, 29: 487-502.

DuBuc TQ, Ryan JF, Shinzato C, Satoh N, Martindale MQ (2012). Coral Comparative Genomics Reveal Expanded Hox Cluster in the Cnidarian–Bilaterian Ancestor. Integr Comp Biol, 52(6): 835-841 doi:10.1093/icb/ics098.

Fortunato S, Adamski M, Bergum B, Guder C, Jordal S, Leininger S,Zwafink C, Rapp HT and Adamska M (2012). Genome-wide analysis of the sox family in the calcareous sponge Sycon ciliatum: multiple genes with unique expression patterns. EvoDevo, Jul 23;3(1):14. doi: 10.1186/2041-9139-3-14

Hosp J, Sagane Y, Danks G and EM Thompson (2012). The evolving proteome of a complex extracellular matrix, the Oikopleura house. PLoS One, 7(7): e40172.

Leclère L, Rentzsch F (2012). Repeated evolution of identical domain architecture in metazoan Netrin domain-containing proteins. Genome Biol Evol 4(9): 771-787.

Martín-Durán JM, Janssen R, Wennberg S, Budd GE, Hejnol A (2012). Deuterostomic Development in the Protostome Priapulus caudatus. Curr Biol 22:2161-2166.

Maxwell EK, Ryan JF, Schnitzler CE, Browne WE and Andreas D Baxevanis (2012). MicroRNAs and essential components of the microRNA processing machinery are not encoded in the genome of the ctenophore Mnemiopsis leidyi. BMC Genomics, 13:714

Nakanishi N, Renfer E, Technau U, Rentzsch F (2012). Nervous systems of the sea anemone Nematostella vectensis are generated by ectoderm and endoderm and shaped by distinct mechanisms. Development, 139:347-357

Santagata S, Resh C, Hejnol A, Martindale MQ, Passamaneck, YJ (2012). Development of the larval anterior neurogenic domains of Terebratalia transversa (Brachiopoda) provides insights into the diversification of larval apical organs and the spiralian nervous system. EvoDevo, 3:3

Schnitzler CE, Pang K, Powers ML, Reitzel AM, Ryan JF, Simmons D, Tada T, Park M, Gupta J, Brooks SY, Blakesley RW, Yokoyama S, Haddock SHD, Martindale MQ and Baxevanis AD (2012). Genomic organization, evolution, and expression of photoprotein and opsin genes in Mnemiopsis leidyi: a new view of ctenophore photocytes. BMC Biol, 10:107

Sommer F, Awazu S, Anton-Erxleben F, Jiang D, Klimovich AV, Klimovich BV, Samoilovich MP, Satou Y, Krüss M, Gelhaus C, Kürn U, Bosch TC, Khalturin K (2012). Blood System Formation in the Urochordate Ciona intestinalis Requires the Variable Receptor vCRL1. Mol Biol Evol Oct;29(10):3081-93.

Talbert PB, Ahmad K, Almouzni G, Ausió J, Berger F, Bhalla PL, Bonner WM, Cande WZ, Chadwick BP, Chan SWL, Cross GAM, Cui L, Dimitrov SI, Doenecke D, Eirin-López JM, Gorovsky MA, Hake SB, Hamkalo BA, Holec S, Jacobsen SE, Khochbin S, Ladurner AG, Landsman D, Latham JA, Loppin B, Malik HS, Marzluff WF, Pehrson JR, Postberg J, Singh MB, Schneider R, Smith MM, Thompson EM, Torres-Padilla M-E, Tremethick DJ, Turner BM, Waterborg JH, Wollmann H, Yelagandula R, Zhu B and S Henikoff (2012). A unified phylogeny-based nomenclature for histone variants. BMC Epigenetics & Chromatin, 5:7.

Yadetie F, Butcher S, Forde HE, Campsteijn C, Bouquet JM, Karlsen OA, Denoeud F, Metpally R, Thompson EM, Manak JR, Goksoyr A, and D Chourrout (2012). Conservation and divergence of chemical defence system in the tunicate Oikopleura dioica revealed by genome wide response to two xenobiotics. BMC Genomics. 13, 55.

Zakrzewski A-C, Suh A, Lüter C. (2012). New insights into the larval development of Macandrevia cranium (Müller, 1776) (Brachiopoda: Rhynchonelliformea). Zool Anz 251:263-269.

Denker E, Jiang D (2012). Ciona intestinalis notochord as a new model to investigate the cellular and molecular mechanisms of tubulogenesis. Semin Cell Dev Biol May;23(3):308-19. Epub 2012 Mar 23. Review

Hejnol A (2012). News and Views: Evolutionary Biology: Muscle's dual origins. Nature, 487, 181-182.

Martín-Durán JM, Egger B (2012). Developmental diversity in free-living flatworms. EvoDevo, 3:7

2011

Angotzi A, Mungpakdee S, Stefansson S, Male R, Chourrout D (2011). Involvement of Prop1 homeobox gene in the early development of fish pituitary gland. Gen Comp Endocrinol Volum 171.(3) s. 332-340.

Dong B, Deng W, Jiang D (2011). Distinct cytoskeleton population and extensive crosstalks control the Ciona notochord tubulogenesis. Development 138 (8):1631-1641.

Fuchs J, Martindale MQ and Hejnol A. (2011) Gene expression in bryozoan larvae suggest a fundamental importance of pre-patterned blastemic cells in the bryozoan life-cycle. EvoDevo, 2:13

José-Edwards DS, Kerner P, Kugler JE, Deng W, Jiang D, Di Gregorio A (2011). The identification of transcription factors expressed in the notochord of Ciona intestinalis adds new potential players to the brachyury gene regulatory network. Dev Dyn, 240:1793-1805.

Kugler JE, Kerner P, Bouquet JM, Jiang D, Di Gregorio A (2011). Evolutionary changes in the notochord genetic toolkit: a comparative analysis of notochord genes in the ascidian Ciona intestinalis ant the larvacean Oikopleura dioiac. BMC Evol Biol, 11:21-36.

Moosmann A, Campsteijn C, Jansen PWTC, Nasrallah C, Raasholm M, Stunnenberg HG and EM Thompson (2011). Histone variant innovation in a rapidly evolving chordate lineage. BMC Evol Biol, 11:208.

Passamaneck YJ, Furchheim N, Hejnol A, Martindale MQ, Lüter C (2011). Ciliary photoreceptors in the cerebral eyes of a protostome larva. EvoDevo, 2:6

Royo JL, Hidalgo C, Roncero Y, Angeles Seda M, Akalin A, Lenhard B, Casares F, Gomes-Skarmeta JL (2011). Dissecting the transcriptional regulatory properties of human chromosome 16 highly conserved non-coding regions. PLoS One, 6(9):e24824.

Sagane Y, Hosp J, Zech K and EM Thompson (2011). Cytoskeleton-mediated templating of complex cellulose-scaffolded extracellular structure in the urochordate Oikopleura. Cell Mol Life Sci, 68:1611-1622.

Suster, ML, Gembu A, Schouw A and Kawakami K. (2011). Transposon-mediated BAC transgenesis in zebrafish. Nature Protocols 1;6(12):1998-2021. doi: 10.1038/nprot.2011.416.

Ullrich-Lüter EM, Dupont S, Arbodela E, Hausen H, Arnone MI (2011). Unique system of photoreceptors in sea urchin tube feet. Proc Natl Acad Sci USA 108(20): 8367-8372.

Abe, G, Suster ML and Kawakami K (2011). Tol2-mediated Transgenesis, Gene Trapping, Enhancer Trapping, and the Gal4-UAS System. The Zebrafish: Genetics, Genomics and Informatics. Method Cell Biol, 104:23-49.

Adamska M, Degnan BM, Green K, Zwafink C (2011). What sponges can tell us about the evolution of developmental processes. Zoology (Jena), 114(1):1-10.

Edgecombe GD, Giribet G, Dunn CW, Hejnol A, Kristensen RM, Neves RC, Rouse GW, Worsaae K, Sørensen MV. (2011) Higher-level metazoan relationships: recent progress and remaining questions. Org Divers Evol, 11(2):151-172.

Hejnol A (2011). Mark Q. Martindale: Shedding new light on developmental diversity Int J Dev Biol, 55:237-242.

2010

Deng W, Niesb F, Feuerb A, Bocinac I, Oliverb D, and Di Jiang (2013) Anion translocation through an Slc26 transporter mediates lumen expansion during tubulogenesis. Proc Natl Acad Sci USA doi: 10.1073/pnas.1220884110.

Denoeud F, Henriet S, Mungpakdee S, Aury JM, Da Silva C, Brinkmann H, Mikhaleva J, Olsen LC, Jubin C, Cañestro C, Bouquet JM, Danks G, Poulain J, Campsteijn C, Adamski M, Cross I, Yadetie F, Muffato M, Louis A, Butcher S, Tsagkogeorga G, Konrad A. Singh S, Jensen MF, Cong EH, Eikeseth-Otteraa H, Anthouard V, Kachouri-Lafond R, Nishino A, Ugolini M, Chourrout P, Nishida H, Aasland R, Huzurbazar S, Westhof E, Delsuc F, Lehrach H, Reinhardt R, Weissenbach J, Roy SW, Artiguenave F, Postlethwait JH, Manak JR, Thompson EM, Jaillon O, Du Pasquier L, Boudinot P, Liberles DA, Volff JN, Philippe H, Lenhard B, Crollius HR, Wincker P and D Chourrout (2010). Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate. Science, 330:1381-1385.

Adamska M, Larroux C, Adamski M, Green K, Lovas E, Koop D, Richards GS, Zwafink C, Degnan BM (2010). Structure and expression of conserved wnt pathway components in the demosponge Amphimedon queenslandica. Evol Dev, 12:494-518.

Dong X, Navratilova P, Fredman D, Drivenes Ø, Becker TS, Lenhard B (2010). Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons. Nucleic Acids Res, 38:1071-1085

Navratilova P, Fredman D, Lenhard B, Becker TS (2010). Regulatory divergence of the duplicated chromosomal loci sox11a/b by subpartitioning and sequence evolution of enhancers in zebrafish. Mol Genet Genomics, 283:171-184.

Portales-Casamar E1, Thongjuea S1, Kwon AT, Arenillas D, Zhao X, Valen E, Yusuf D, Lenhard B, Wasserman WW, Sandelin A (2010). JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res, 38(Database Issue):D105-110.

Ragvin A, Moro E, Fredman D, Navratilova P, Drivenes Ø, Engström PG, Alonso ME, de la Calle Mustienes E, Gomez-Skarmeta JL, Tavares MJ, Casares F, Manzanares M, van Heyningen V, Molven A, Njølstad PR, Argenton F, Lenhard B, Becker TS (2010). Long-range Gene Regulation links Genomic Type 2 Diabetes and Obesity risk regions to HHEX, SOX4 and IRX3. Proc Natl Acad Sci USA, 107:775-780.

Renfer E, Amon-Hassenzahl A, Steinmetz Pr, Technau U (2010) A muscle-specific transgenic reporter line of the sea anemone, Nematostella vetensis. Proc Natl Acad Sci USA 107:104-108.

Sagane Y, Hosp J, Zech K and EM Thompson (2010). Cytoskeleton-mediated templating of complex cellulose-scaffolded extracellular structure and its association with oikosins in the urochordate Oikopleura. Cell Mol Life Sci, DOI 10.1007/s00018-010-0547-8.

Sagane Y, Zech K, Bouquet JM, Schmid M, Bal U and EM Thompson (2010). Functional specialization of cellulose synthase genes of prokaryotic origin in chordate larvaceans. Development, 137:1483-1492.

Soler E, Andrieu-Soler C, de Boer E, Bryne JC, Thongjuea S, Stadhouders R, Palstra RJ, Stevens M, Kockx C, van IJcken W, Hou J, Steinhoff C, Rijkers E, Lenhard B, Grosveld F (2010). The Genome-Wide Dynamics of the Binding of Ldb1 Complexes during Erythroid Differentiation. Genes Dev, 24:277-289.

Hejnol A (2010). A Twist in Time--The Evolution of Spiral Cleavage in the Light of Animal Phylogeny Integrative and Comparative Biology; 50, 695-706, doi: 10.1093/icb/icq103

2009

Hejnol A and Martindale MQ (2009). Coordinated spatial and temporal expression of Hox genes during embryogenesis in the acoel Convolutriloba longifissura. BMC Biol, 7:65.

Dong B, Horie T, Denker E, Kusakabe T, Tsuda M, Smith WC and Jiang D (2009). Tube formation by complex cellular processes in Ciona intestinalis notochord. Dev Biol 330:237-249.

Saina M, Genikhovich G, Renfer E and Technau U (2009). BMPs and Chordin regulate patterning of the directive axis in a sea anemone. Proc Natl Acad Sci USA, 106:18592-18597.

Saina M and Technau U (2009). Characterization of myostatin/gdf8/11 in the starlet sea anemone Nematostella vectensis. J Exp Zool Part B, 312:780-788

Amsterdam A, Lai K, Komisarczuk AZ, Becker TS, Borinson RT, Hopkins N, and Lees JA (2009). Zebrafish Hagoromo mutants upregulate fgf8 post-embryonically and develop neuroblastoma. Mol Cancer Res 7:841-850.

Komisarczuk AZ, Kawakami K and Becker TS (2009). Cis-regulation and chromosomal rearrangement of the fgf8 locus after the teleost/tetrapod split. Dev Biol, 336:301-312.

Akalin A, Fredman D, Arner E, Dong X, Bryne JC, Suzuki H, Daub CO, Hayashizaki Y and Lenhard B (2009). Transcriptional features of genomic regulatory blocks. Genome Biol 10(4):R38.

Chiba S, Jiang D, Satoh N, Smith WC (2009). Brachyury null mutant-induced defects in juvenile ascidian endodermal organs. Development 136(1):35-9.

Dong X, Fredman D AND Lenhard B (2009). Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes. Genome Biol 10:R86.

Navratilova P, Fredman D, Hawkins TA, Turner K, Lenhard B, and Becker TS (2009). Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes. Dev Biol 15;327:526-540.

Bouquet JM, Spriet E, Troedsson C, Ottera H, Chourrout D and Thompson EM (2009). Culture optimization for the emergent zooplanktonic model organism Oikopleura dioica. J Plankton Res, 31:359–370.

Troedsson C, Bouquet JM, Skinnes R., Acuña JL, Zech K, Frischer ME and EM Thompson (2009). Regulation of filter-feeding house components in response to varying food regimes in the Appendicularian, Oikopleura dioica. J Plankton Res 31, 1453-1463.

2008

Rentzsch F, Fritzenwanker JH, Scholz CB and Technau U (2008). FGF signalling controls formation of the apical sensory organ in the cnidarian Nematostella vectensis. Development, 135:1761-1769

Bessa J, Tavares MJ, Gómez-Skarmeta JL, Kikuta H, Laplante M, Becker TS and Casares F (2008). meis1 regulates cyclin D1 and c-myc expression, and controls the proliferation of the multipotent cells in the early developing zebrafish eye. Development, 135:799-803.

Ganot P, Moosmann-Schulmeister A and Thompson EM (2008). Oocyte selection is concurrent with meiosis resumption in the coenocystic oogenesis of Oikopleura. Dev Biol 324, 266-276.

Hill MM, Broman KW, Stupka E, Smith WC, Jiang D, Sidow A (2008) The C. savignyi genetic map and its integration with the reverence sequence facilitates insights into chordate genome evolution. Genome Res18:1369-1379

Hoppmann V, Wu J, Søviknes AM, Helvik JV and Becker TS (2008). Expression of the eight AMPA receptor subunit genes in the developing central nervous system and sensory organs of zebrafish. Dev Dyn, 237:788-799.

Komisarczuk AZ, Topp S, Stigloher C, Kapsimali M, Bally-Cuif L, and Becker TS (2008). Enhancer detection and developmental expression of zebrafish sprouty1, a member of the fgf8 synexpression group. Dev Dyn 237:2594-2603.

Pézeron G, Mourrain P, Sébastien C, Ghislain J, Becker TS, Rosa FM and David NB (2008). Live analysis of endodermal layer formation identifies random walk as a novel gastrulation movement. Curr Biol, 18:276-281.

Punnamoottil B, Kikuta H, Pézeron G, Erceg J, Becker TS and Rinkwitz, S (2008). Enhancer Detection in Zebrafish Permits the Identification of Neuronal Subtypes That Express Hox4 Paralogs. Dev Dyn 237:2195-2208.

Topp S, Stigloher C, Komisarczuk AZ, Adolf B, Becker TS, and Bally-Cuif L. (2008). Fgf signaling in the zebrafish adult brain: association of Fgf activity with ventricular zones but not cell proliferation. J Comp Neurol, 510:422-439.

Bryne JC, Valen E, Tang MHE, Marstrand T, Winther O, da Piedade I, Krogh A, Lenhard B and Sandelin A (2008). JASPAR, the open access database of transcription factor binding profiles: new content and tools in the 2008 update. Nucleic Acids Res 32:D102-106.

Kemmer D, Podowski RM, Yusuf D, Brumm J, Cheung W, Wahlestedt C, Lenhard B and Wasserman WW (2008). Gene characterization index: assessing the depth of gene annotation. PLoS One 3:e1440.

Engström PG, Fredman D and Lenhard B (2008). Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes. Genome Biol 9:R34.

Andersen M, Engström PG, Lithwick S, Arenillas D, Eriksson P, Lenhard B, Wasserman WW and Odeberg J (2008). In silico detection of sequence variations modifying transcriptional regulation. PLoS Comput Biol 4:e5.

Fu X, Adamski M and EM Thompson (2008). Altered miRNA Repertoire in the Simplified Chordate, Oikopleura dioica. Mol Biol Evol, 25:1067-1080.

Mungpakdee S, Seo HC and Chourrout D (2008). Spatio-temporal expression patterns of anterior Hox genes in Atlantic salmon (Salmo salar). Gene Expr Patterns, 8:508-514.

Stach T, Winter J, Bouquet JM, Chourrout D and Schnabel R (2008). Embryology of a planktonic tunicate reveals traces of sessility. Proc Natl Acad Sci USA, 105:7229-7234.

Mungpakdee S, Seo HC, Angotzi AR, Dong X, Akalin A and Chourrout D (2008). Differential Evolution of the Thirteen Atlantic Salmon Hox Clusters. Mol Biol Evol, 25:1333-1343.

Angotzi AR, Ersland KM, Mungpakdee S, Stefansson S and Chourrout D (2008). Independent and dynamic reallocation of pitx gene expression during vertebrate evolution, with emphasis on fish pituitary development. Gene, 417:19-26.

Søviknes AM and Glover JC (2008). Continued growth and cell proliferation into adulthood in the notochord of the appendicularian Oikopleura dioica. Biol Bull, 214:17-28.

Sardet C, Swalla BJ, Satoh N, Sasakura Y, Branno M, Thompson EM, Levine M and H Nishida (2008). Euro Chordates: Ascidian Community Swims Ahead. The 4th International Tunicate Meeting in Villefranche sur Mer. Dev Dyn 237, 1207–1213.

2007

Herpin A, Lelong C, Becker TS, Favrel P and Cunningham C (2007). A tolloid homologue from the Pacific oyster Crasseostrea gigas. Gene Expr Patterns, 7:700-708.

Becker TS, and Lenhard B (2007). The random versus fragile breakage models of chromosome evolution: A matter of resolution. Mol Genet Genomics, 278 (5): 487-491.

Bielen H, Oberleitner S, Marcellini S, Gee L, Lemaire P, Bode HR, Rupp R and Technau U (2007). Divergent functions of two ancient Hydra Brachyury paralogs suggest specific roles for their activation domains in tissue fate inductions. Development, 134:4187-4197.

Fritzenwanker J, Genikhovich G, Kraus Y, Technau U (2007). Early development and axis specification in the sea anemone Nematostella vectensis. Dev Biol, 310:264-279.

Kraus Y, Fritzenwanker J, Genikhovich G, Technau U (2007). The blastoporal organiser of a sea anemone. Curr Biol, 17:R874-R876.

Putnam NH, Srivastava M, Hellsten U, Dirks B, Chapman J, Salamov A, Terry A, Shapiro H, Lindquist E, Kapitonov V, Jurka J, Genikhovich G, Grigoriev I, Lucas S, Steele R, Finnerty J, Technau U, Martindale M, Rokhasr D. (2007). Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization. Science, 317:86-94.

Meijer AH, van der Sar AM, Cunha C, Lamers GEM, Laplante MA, Kikuta H, Bitter W, Becker TS and Spaink HP. (2007). Identification and real-time imaging of a myc-expressing neutrophil population involved in inflammation and mycobacterial granuloma formation in zebrafish. Dev Comp Immunol, 32:36-49.

Shankaran S, Sieger D, Schröter C, Czepe C, Pauly MC, Laplante MA, Becker TS, Oates AC, Gajewsky, M (2007). Completing the set of h/E(spl) cyclic genes in zebrafish: her12 and her15 reveal novel modes of expression and contribute to the segmentation clock. Dev Biol, 304:615-632.

Søviknes AM, Glover JC (2007). Spatiotemporal patterns of neurogenesis in the appendicularian Oikopleura dioica. Dev Biol Nov 1;311(1):264-75.

Søviknes AM, Chourrout D and Glover JC (2005). Development of putative GABAergic neurons in the appendicularian urochordate Oikoleura dioica. J Comp Neurol, 490:12-28.

Troedsson C, P Ganot, JM Bouquet, DL Aksnes, EM Thompson (2007). Endostyle cell recruitment as a frame of reference for development and growth in the Urochordate Oikopleura dioica. Biol Bull, Dec;213(3):325-334.

Weiner AMJ, Allende ML, Becker TS, Calcaterra NB. (2007). CNBP mediates neural crest cell expansion by controlling cell proliferation and cell survival during rostral head development. J Cell Biochem, 102:1553-1570.

Engström PG, Ho Sui S, Drivenes O, Becker TS, Lenhard B (2007). Genomic regulatory blocks underlie extensive microsynteny conservation in insects. Genome Res, 17:1898-1908.

Kikuta H, Laplante M, Navratilova P, Komisarczuk AZ, Engström PG, Fredman D, Akalin A, Caccamo M, Sealy I, Howe K, Ghislain J, Mourrain P, Adolf B, Pezeron G, Ellingsen E, Foucher I, Oates AC, Thisse C, Thisse B, Lenhard B, Becker TS (2007). Genomic Regulatory Blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome Res, 17:545-555.

Kikuta H, Fredman D, Rinkwitz S, Lenhard B and Becker TS (2007) Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks - a fundamental feature of vertebrate genomes. Genome Biol 8:suppl 1:4.

Clarke T, Bouquet JM, Fu X, Kallesøe T, and Thompson EM (2007). Rapidly evolving lamins in a chordate, Oikopleura dioica, with unusual nuclear architecture. Gene, 396:159-169.

Ganot P, Bouquet JM, Kallesøe T, Thompson EM (2007). The Oikopleura coenocyst, a unique chordate germ cell permitting rapid, extensive modulation of oocyte production. Dev Biol, 302, 302:591-600.

Ganot P, Kallesøe T, Thompson EM (2007). The cytoskeleton organizes germ nuclei with divergent fates and asynchronous cycles in a common cytoplasm during oogenesis in the chordate Oikopleura. Dev Biol, 302:577-590.

Schulmeister A, Schmid M, Thompson EM (2007). Phosphorylation of the histone H3.3 variant in mitosis and meiosis of the urochordate Oikopleura dioica. Chromosome Res, 15:189-201.

Spada F, Koch J, Sadoni N, Mitchell N, Ganot P, De Boni U, Zink D, Thompson EM (2007). Conserved patterns of nuclear compartmentalization are not observed in the chordate Oikopleura. Biol Cell, 99:273-287.

Troedsson C, Frischer ME, Nejstgaard JC, Thompson EM (2007). Molecular quantification of differential ingestion and particle trapping rates by the Appendicularian Oikopleura dioica as a function of prey size and shape. Limnol Oceanogr, 52:416–427.

Schuettengruber B, Chourrout D, Vervoort M, Leblanc B, Cavalli G (2007). Genome regulation by polycomb and trithorax proteins. Cell, 128:735-745.

Søviknes AM, Chourrout D, Glover JC (2007). Development of the caudal nerve cord, motoneurons, and muscle innervation in the appendicularian urochordate Oikopleura dioica. J Comp Neurol , 503:224-243

Søviknes AM and Glover JC (2007). Spatiotemporal patterns of neurogenesis in the appendicularian Oikopleura dioica. Dev Biol, 311:264-75.

Becker TS1, Lenhard B1 (2007). The Random vs. Fragile Breakage Models of Chromosome Evolution: A Matter of Resolution. Review Mol Genet Genomics 278:487-91

Kikuta H, Fredman D, Rinkwitz S, Lenhard B, Becker TS (2007). Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks - a fundamental feature of vertebrate genomes. Review Genome Biol 8(Suppl 1):S4

2006

Kraus Y, Technau U (2006). Gastrulation in the sea anemone Nematostella vectensis occurs by invagination and immigration: an ultrastructural study. Dev Genes Evol, 216:119-132.

Rentzsch F, Anton R, Saina M, Hammerschmidt M, Holstein TW, Technau U. (2006). Asymmetric expression of BMP antagonists in the sea anemone Nematostella vectensis: implications for the evolution of axial patterning. Dev Biol, 296:375-387.

Hadrys T, Punnamootil B, Pieper M, Kikuta H, Pezeron G, Becker TS, Prince VE, Baker R, Rinkwitz S (2006). Conserved co-regulation and promoter sharing of hoxb3a and hoxb4a in zebrafish. Dev Biol, 297:26-43.

Laplante M, Konig M, Kikuta H and Becker TS. (2006). Enhancer detection in the zebrafish using pseudotyped murine retroviruses. Methods, 39:189-198.

Pezeron, G, Anselme, I, Laplante, M, Ellingsen, S. Becker, TS, Charnay, P. Schneider-Manoury, S., Mourrain, P and Ghislain, J (2006). Duplicate sfrp1 genes in zebrafish: sfrp1a is dynamically expressed in the developing central nervous system, gut and lateral line. Gene Expr Patterns, 6:835-842.

Stigloher C, Nincovic J, Laplante M, Geling A, Tannhauser B, Topp S, Kikuta H, Becker TS, Houart C, Bally-Cuif L (2006). Segregation of telencephalic and eye field identities inside the zebrafish forebrain territory is controlled by Rx3. Development, 133:2925-2935.

Aksnes D, Troedsson C and Thompson EM (2006). A model of developmental time applied to planktonic embryos. Mar Ecol-Prog Ser, 318:75-80.

Aksnes D, Troedsson C and Thompson EM (2006). Integrating developmental clocking and growth in a life-history model for the planktonic chordate Oikopleura dioica. Mar Ecol-Prog Ser, 318:81-88.

Delsuc F, Brinkmann H, Chourrout D and Philippe H (2006). Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature, 439:965-968.

Ganot P, Bouquet JM and Thompson EM (2006). Comparative organisation of follicle, accessory cells and spawning anlagen in dynamic semelparous clutch manipulators, the urochordate Oikopleuridae. Biol Cell, 98:389-401.

Chourrout D, Delsuc F, Chourrout P, Edvardsen RB, Rentzsch F, Renfer E, Jensen MF, Zhu B, de Jong P, Steeele RE, Technau U (2006). Minimal ProtoHox cluster inferred from bilaterian and cnidarian Hox complements. Nature, 442:684-687.

Gómez-Skarmeta JL, Lenhard B and Becker TS (2006). New technologies, new findings and new concepts in the study of vertebrate cis-regulatory sequences. Review Dev Dyn 235:870-885.

2005

Herpin A, Lelong C, Becker TS, Rosa FM, Favrel P and Cunningham C (2005). Structural and functional evidences for a type 1 TGF-ß sensu stricto receptor in the lophotrochozoan Crasseostrea gigas suggest conserved molecular mechanisms controlling mesodermal patterning across bilateria. Mech Dev 122:695-705.

Herpin A, Lelong C, Becker TS, Rosa F, Favrel P, Cunningham C (2005). Structural and functional evidence for a singular repertoire of BMP receptor signal transducing proteins in the lophotrochozoan Crassostrea gigas suggests a shared ancestral BMP/activin pathway. FEBS J 272:3424-3440.

Kusserow A, Pang K, Sturm C, Hrouda M, Lentfer J, Schmidt HA, Technau U, von Haeseler A, Hobmayer B, Martindale MQ and Holstein TW (2005). Unexpected complexity of the Wnt gene family in a sea anemone. Nature 433:156-160.

Stansberg C, Subramaniam S, Collet B, Secombes CJ and Cunningham C (2005). Cloning of the Atlantic Salmon (salmo salar) IL-1 receptor associated protein. Fish Shellfish Immunol, 19:53-65.

Technau U, Rudd S, Maxwell P, Gordon PMK, Saina M, Grasso LC, Hayward DC, Sensen CW, Holstein TW, Ball EE, Miller DJ (2005). Maintenance of ancestral genetic complexity and non-metazoan genes in two basal cnidarians. Trends Genet 21:633-639.

Ellingsen S, Laplante M, Konig M, Furmanek T, Kikuta H, Høivik E and Becker TS (2005). Large-scale Enhancer Detection in the Zebrafish Genome. Development, 132:3799-3811.

Hardison AL, Lichten L, Banjeree-Basu S, Becker TS, Burgess S (2005). The zebrafish gene claudinj is essential for normal ear function and important for the formation of the otoliths. Mech Dev 122:949-958.

Spada F, Chioda M and Thompson EM (2005). Histone H4 post-translational modifications in chordate mitotic and endoreduplicative cell cycles. J Cell Biochem 95:885-901.

Spada F, Vincent M and Thompson EM (2005). Plasticity of histone modifications across the invertebrate to vertebrate transition: histone H3 lysine 4 trimethylation in heterochromatin. Chromosome Res 13:57-72.

Troedsson C, Grahl-Nielsen O and Thompson EM (2005). Variable fatty acid composition of the pelagic Appendicularian, Oikopleura dioica, in response to dietary quality and quantity. Mar Ecol-Prog Ser 289:165-176.

Edvardsen RB, Seo HC, Jensen MF, Mialon A, Mikhaleva J, Bjordal M, Cartry J, Reinhardt R, Weissenbach J, Wincker P & Chourrout D (2005). Remodelling of the homeobox gene complement in the tunicate Oikopleura dioica. Curr Biol, 15:R12-13.

Weill M, Philips A, Chourrout D and Fort P (2005). The caspase family in urochordates: distinct evolutionary fates in ascidians and larvaceans. Biol Cell, 97:857-866.

Søviknes AM, Chourrout D and Glover JC (2005). Development of putative GABAergic neurons in the appendicularian urochordate Oikoleura dioica. J Comp Neurol, 490:12-28.

Amsterdam A and Becker TS (2005). Transgenes as Screening Tools to Probe and Manipulate the Zebrafish Genome. Review Dev Dyn 234(2):255-268.

Miller DJ, Ball EE and Technau U (2005). Cnidarians and ancestral genetic complexity in the animal kingdom. Trends Genet (review) 21(10):536-9.

Thompson EM, Spada F and P Ganot (2005). Patterning and Organisation of the House Secreting Epithelium of Oikopleura dioica. In: Gorsky G, Youngbluth MJ and Deibel D (eds.) Response of Marine Ecosystems to Global Change: Ecological Impact of Appendicularians, Ed. G. Gorsky, Gordon and Breach, pp. 89-112.

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