Cislo DJ, Yang F, Qin H, Pavlopoulos A, Bowick MJ, Streichan SJ. (2023) Active cell divisions generate exotic fourfold orientationally ordered phase in living tissue. Nat Phys. 19:1201.

Jain A, Ulman V, Mukherjee A, Prakash M, Cuenca MB, Pimpale LG, Münster S, Haase R, Panfilio KA, Jug F, Grill SW, Tomancak P, Pavlopoulos A. (2020) Regionalized tissue fluidization is required for epithelial gap closure during insect gastrulation. Nat Commun. 11:5604.

Münster S, Jain A, Mietke A, Pavlopoulos A, Grill SW, Tomancak P. (2019) Attachment of the blastoderm to the vitelline envelope affects gastrulation of insects. Nature 568:395-399.

Wolff C, Tinevez JY, Pietzsch T, Stamataki E, Harich B, Guignard L, Preibisch S, Shorte S, Keller PJ, Tomancak P, Pavlopoulos A. (2018) Multi-view light-sheet imaging and tracking with the MaMuT software reveals the cell lineage of a direct developing arthropod limb. Elife 7:e34410.

Kao D, Lai AG, Stamataki E, Rosic S, Konstantinides N, Jarvis E, Di Donfrancesco A, Pouchkina-Stancheva N, Semon M, Grillo M, Bruce H, Kumar S, Siwanowicz I, Le A, Lemire A, Eisen MB, Extavour C, Browne WE, Wolff C, Averof M, Patel NH, Sarkies P, Pavlopoulos A, Aboobaker A. (2016) The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion. Elife 5:e20062.

Kalogeridi M, Liaskas I, Rallis J, Pavlopoulos A. (2024) Lineage tracing by light-sheet microscopy and computational reconstruction. Methods in Molecular Biology, in press.

Mylonakis M, Tserevelakis GJ, Vlachos G, Fanouraki E, Pavlopoulos A, Pavlidis M, Zacharakis G. (2024) Bimodal optical and optoacoustic multiview microscope in the frequency-domain. Optics Letters, 49:462.

Cislo DJ, Yang F, Qin H, Pavlopoulos A, Bowick MJ, Streichan SJ. (2023) Active cell divisions generate exotic fourfold orientationally ordered phase in living tissue. Nature Physics, 19:1201.

Tserevelakis GJ, Barmparis GD, Kokosalis N, Giosa ES, Pavlopoulos A, Tsironis GP, Zacharakis G (2023) Deep learning-assisted frequency domain photoacoustic microscopy. (2023) Optics Letters, 48:2720.

Cislo DJ, Pavlopoulos A, Shraiman BI. (2023) A “morphogenetic action” principle for 3D shape formation by the growth of thin sheets. arXiv:2302.07839

Tserevelakis GJ, Tekonaki E, Kalogeridi M, Liaskas I, Pavlopoulos A, Zacharakis G. (2023) Hybrid Fluorescence and Frequency-Domain Photoacoustic Microscopy for Imaging Development of Parhyale hawaiensis Embryos. Photonics 10: 264.

Rallis J, Pavlopoulos A. (2022) Cellular basis of limb morphogenesis. Current Opinion in Insect Science, 50:100887.

Tserevelakis GJ, Velentza S, Liaskas I, Archontidis T, Pavlopoulos A, Zacharakis G. (2022) Imaging Parhyale hawaiensis embryogenesis with frequency domain photoacoustic microscopy: a novel tool in developmental biology.  Journal of Biophotonics, e202200202.

Rallis J, Kapai G, Pavlopoulos A. (2021) Parhyale hawaiensis, Crustacea. Chapter 16 in Handbook of Marine Model Organisms in Experimental Biology: Established and Emerging, CRC Press, 289-306.

Jain A, Ulman V, Mukherjee A, Prakash M, Cuenca MB, Pimpale LG, Münster S, Haase R, Panfilio KA, Jug F, Grill SW, Tomancak P, Pavlopoulos A. (2020) Regionalized tissue fluidization is required for epithelial gap closure during insect gastrulation. Nature Communications 11:5604.

Pavlopoulos A, Wolff C. (2020) Crustacean limb morphogenesis during normal development and regeneration. Oxford University Press, The Natural History of the Crustacea Volume VII - Chapter 2:45-78.

Münster S, Jain A, Mietke A, Pavlopoulos A, Grill SW, Tomancak P. (2019) Attachment of the blastoderm to the vitelline envelope affects gastrulation of insects. Nature 568:395-399.

Wolff C, Tinevez JY, Pietzsch T, Stamataki E, Harich B, Guignard L, Preibisch S, Shorte S, Keller PJ, Tomancak P, Pavlopoulos A. (2018) Multi-view light-sheet imaging and tracking with the MaMuT software reveals the cell lineage of a direct developing arthropod limb. Elife 7:e34410.

Stamataki E, Pavlopoulos A. (2016) Non-insect crustacean models in developmental genetics including an encomium to Parhyale hawaiensis. Current Opinion in Genetics & Development 39:149-156.

Kao D, Lai AG, Stamataki E, Rosic S, Konstantinides N, Jarvis E, Di Donfrancesco A, Pouchkina-Stancheva N, Semon M, Grillo M, Bruce H, Kumar S, Siwanowicz I, Le A, Lemire A, Eisen MB, Extavour C, Browne WE, Wolff C, Averof M, Patel NH, Sarkies P, Pavlopoulos A, Aboobaker A. (2016) The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion. Elife 5:e20062.

Benton MA, Pechmann M, Frey N, Stappert D, Conrads KH, Chen YT, Stamataki E, Pavlopoulos A, Roth S. (2016) Toll genes have an ancestral role in axis elongation. Current Biology 26:1609-1615.

Benton MA, Pavlopoulos A. (2014) Tribolium embryo morphogenesis: May the force be with you. Bioarchitecture 4:16-21.

Kontarakis Z, Pavlopoulos A. (2014) Transgenesis in non-model organisms: the case of Parhyale, Hox genes: Methods and Protocols. Methods in Molecular Biology 1196:145-181.

Benton MA, Akam M, Pavlopoulos A. (2013) Cell and tissue dynamics during Tribolium castaneum embryogenesis revealed by versatile fluorescence labeling approaches. Development 140:3210-3220.

Kontarakis Z, Konstantinides N, Pavlopoulos A, Averof M. (2011) Reconfiguring gene traps for new tasks using iTRAC. Fly 5:352-355.

Kontarakis Z, Pavlopoulos A, Kiupakis A, Konstantinides N, Douris V, Averof M. (2011) A versatile strategy for gene trapping and trap conversion in emerging model organisms. Development 138:2625-2630.

Pavlopoulos A. (2011) Identification of DNA sequences that flank a known region by inverse PCR, Molecular Methods for Evolutionary Genetics. Methods in Molecular Biology 772:267-275.

Pavlopoulos A, Akam M. (2011) Hox gene Ultrabithorax regulates distinct sets of target genes at successive stages of Drosophila haltere morphogenesis. Proceedings of the National Academy of Sciences USA 108:2855-2860.

Averof M, Pavlopoulos A, Kontarakis Z. (2010) Evolution of new appendage types by gradual changes in Hox gene expression – the case of crustacean maxillipeds. Palaeodiversity Suppl 3:141-146.

Pavlopoulos A, Kontarakis Z, Liubicich DM, Serano JM, Akam M, Patel NH, Averof M. (2009) Probing the evolution of appendage specialization by Hox gene misexpression in an emerging model crustacean. Proceedings of the National Academy of Sciences USA 106:13897-13902.

Liubicich DM, Serano JM, Pavlopoulos A, Kontarakis Z, Protas ME, Kwan E, Chatterjee S, Tran KD, Averof M, Patel NH (2009) Knockdown of Parhyale Ultrabithorax recapitulates evolutionary changes in crustacean appendage morphology. Proceedings of the National Academy of Sciences USA 106:13892-13896.

Pavlopoulos A, Oehler S, Kapetanaki MG, Savakis C. (2007) The DNA transposon Minos as a tool for transgenesis and functional genomic analysis in vertebrates and invertebrates. Genome Biology 8 Suppl 1:S2.

Pavlopoulos A, Akam M. (2007) Hox go omics: insights from Drosophila into Hox gene targets. Genome Biology 8:208.

Pavlopoulos A, Averof M. (2005) Establishing genetic transformation for comparative developmental studies in the crustacean Parhyale hawaiensis. Proceedings of the National Academy of Sciences USA 102:7888-7893.

Pavlopoulos A, Berghammer AJ, Averof M, Klingler M. (2004) Efficient transformation of the beetle Tribolium castaneum using the Minos transposable element: quantitative and qualitative analysis of genomic integration events. Genetics 167:737-746.

Pavlopoulos A, Averof M. (2002) Developmental evolution: Hox proteins ring the changes. Current Biology 12:R291-293.