Original research papers

1. Caglar C, Ereskovsky A, Laplante M, Tokina D, Leininger S, Borisenko I, Aisbett G, Pan D, Adamski M*, Adamska M* (2023) Fast transcriptional activation of developmental signalling pathways during wound healing of the calcareous sponge Sycon ciliatum. In final revision in Development (available on BioRXiv). *co-corresponding
2. Xu J, Mead O, Moya A, Caglar C, Miller D, Adamski M, Adamska M, 2023. Wound healing and regeneration in the reef building coral Acropora millepora. Frontiers in Ecology and Evolution, 10, 979278.
3. Arsov T, Sofijanova A, Adamski M, Vinuesa C, 2022. WES result reanalysis and CAMK2B variant causing developmental delay. European Journal Of Human Genetics, 30, SUPPL 1, 257-257.
4. Arsov T, Kelecic J, Frkovic SH, Sestan M, Kifer N, Andrews D, Adamski M, Jelusic M, Cook M, 2021. Expanding the clinical spectrum of pathogenic variation in NR2F2: Asplenia. European Journal of Medical Genetics, 64, 12, 104347.
5. He Y, Gallman AE, Xie C, Shen Q, Ma J, Wolfreys FD, Sandy M, Arsov T, Wu X, Qin Y, Zhang P, Jiang S, Stanley M, Wu P, Tan J, Ding H, Xue H, Chen W, Xu J, Lindsey A, Criswell A Nititham J, Adamski M, Kitching RA, Cook M, Cao L, Shen N, Cyster JG, Vinuesa C, 2021. P2RY8 variants in lupus patients uncover a role for the receptor in immunological tolerance. Journal of Experimental Medicine, 219, 1, e20211004.
6. Somasiri P, Behm CA, Adamski M, Wen J, Verma NK. 2020. Transcriptional response of Caenorhabditis elegans when exposed to Shigella flexneri. Genomics. S0888-7543(18)30727-4.
7. Pett W, Adamski M, Adamska M, Francis WR, Eitel M, Pisani D, Wörheide G. 2019. The Role of Homology and Orthology in the Phylogenomic Analysis of Metazoan Gene Content. Mol Biol Evol.  1;36(4).
8. Parajuli P, Adamski M, Verma NK. 2017. Bacteriophages are the major drivers of Shigella flexneri serotype 1c genome plasticity: a complete genome analysis. BMC Genomics. 12;18(1):722.
9. Voolstra CR; GIGA Community of Scientists (including Adamski M), Wörheide G, Lopez JV. 2017. Advancing Genomics through the Global Invertebrate Genomics Alliance (GIGA). Invertebr. Syst. 31(1):1-7.
10. Voigt O, Adamska M, Adamski M, Kittelmann A, Wencker L, Wörheide G. 2017. Spicule formation in calcareous sponges: Coordinated expression of biomineralization genes and spicule-type specific genes. Sci Rep. 13;7:45658
11. Fortunato SA, Vervoort M, Adamski M, Adamska M. 2016. Conservation and divergence of bHLH genes in the calcisponge Sycon ciliatum. Evodevo. 14:7
12. Borisenko I, Adamski M, Ereskovsky A, Adamska M. 2016. Surprisingly rich repertoire of Wnt genes in the demosponge Halisarca dujardini. BMC Evol Biol. 16:123
13. Lavrov DV, Adamski M, Chevaldonné P, Adamska M. 2016. Extensive Mitochondrial mRNA Editing and Unusual Mitochondrial Genome Organization in Calcaronean Sponges. Curr Biol. 26:86-92.
14. Bråte J, Adamski M, Neumann RS, Shalchian-Tabrizi K, Adamska M. 2015. Regulatory RNA at the root of animals: dynamic expression of developmental lincRNAs in the calcisponge Sycon ciliatum. Proc Biol Sci. 282(1821). pii: 20151746
15. Voigt O, Adamski M, Sluzek K, Adamska M. 2014. Genome-wide screening identifies two carbonic anhydrases involved in biomineralization in calcareous sponges. BMC Evol. Biology. 14:230
16. Fortunato SA, Adamski M, Mendivil O, Leininger S, Ferrier DEK, Adamska M. 2014. Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes. Nature.  514(7524):620
17. Leininger S*, Adamski M*, Bergum B, Guder C, Liu J, Naranjo Durán S, Ariza-Cosano A, Laplante M, Hoffmann F, Fortunato S, Jordal S, Rapp HT, Gomez-Skarmeta JL, Adamska M. 2014. Developmental gene expression indicates homology of poriferan and eumetazoan body plans. Nature Communications. 5:3905. *equal contribution
18. Zakrzewski AC, Weigert A, Helm C, Adamski M, Adamska M, Bleidorn C, Raible F, Hausen H. 2014. Early divergence, broad distribution and high diversity of animal chitin synthases. Genome Biol. Evolution. 6:316.
19. Sebé-Pedrós A, Ariza-Cosano A, Weirauch MT, Leininger S, Yang A, Torruella G, Adamski M, Adamska M, Hughes TR, Gómez-Skarmeta JL, Ruiz-Trillo I. 2013. Early evolution of the T-box transcription factor family. PNAS. 110:16050.
20. 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. 67:223.
21. 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 B Mol Dev Evol. 320:84.
22. Fortunato S, Adamski M, Bergum B, Guder C, Jordal S, Leininger S, Zwafink C, Rapp HT, Adamska M. 2012. Genome-wide analysis of the sox family in the calcareous sponge Sycon ciliatum: multiple genes with unique expression patterns. Evodevo. 3:14.
23. 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, […], Chourrout D. 2010. Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate. Science. 330:1381.
24. 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.
25. Erpenbeck D, Voigt O, Adamski M, Woodcroft BJ, Hooper JN, Wörheide G, Degnan BM. 2011. NUMTs in the sponge genome reveal conserved transposition mechanisms in metazoans. Mol Biol Evol. 28:1.
26. Srivastava M, Simakov O, Chapman J, Fahey B, Gauthier M, Mitros T, Richards GS, Conaco C, Dacre M, Hellsten U, Larroux C, Putnam NH, Stanke M, Adamska M, Darling A, Degnan SM, Oakley TH, Plachetzki D, Zhai Y,  Adamski M, Calcino A, Cummins SF, Goodstein DM, Harris C, Jackson DJ, Leys SP, Shu S, Woodcroft BJ; Vervoort M, Kosik KS, Manning G, Degnan BM and Rokhsar DS. 2010. The Amphimedon queenslandica genome and the evolution of animal complexity. Nature. 466:720.
27. Frentiu FD, Adamski M, McGraw EA, Blows MW, Chenoweth SF. 2009. An expressed sequence tag (EST) library for Drosophila serrata, a model system for sexual selection and climatic adaptation studies. BMC Genomics. 10:40.
28. Fu X, Adamski M, Thompson EM. 2008. Altered miRNA repertoire in the simplified chordate, Oikopleura dioica. Mol Biol Evol. 25:1067.
29. Adamska M, Degnan SM, Green KM, Adamski M, Craigie A, Larroux C, Degnan BM. 2007. Wnt and TGF-beta expression in the sponge Amphimedon queenslandica and the origin of metazoan embryonic patterning. PLoS ONE. 2:e1031.
30. Adamska M, Matus DQ, Adamski M, Green K, Rokhsar DS, Martindale MQ, Degnan BM. 2007. The evolutionary origin of hedgehog proteins. Curr Biol. 17:R836.
31. Sakarya O, Armstrong KA, Adamska M, Adamski M, Wang IF, Tidor B, Degnan BM, Oakley TH, Kosik KS. 2007. A post-synaptic scaffold at the origin of the animal kingdom. PLoS ONE. 2:e506.
32. Brownlie JC, Adamski M, Slatko B, McGraw EA. 2007. Diversifying selection and host adaptation in two endosymbiont genomes. BMC Evol Biol. 7:68.
33. Larroux C, Fahey B, Degnan SM, Adamski M, Rokhsar DS, Degnan BM. 2007. The NK homeobox gene cluster predates the origin of Hox genes. Curr Biol. 17:706.
34. Erpenbeck D, Voigt O, Adamski M, Adamska M, Hooper JN, Wörheide G, Degnan BM. 2007. Mitochondrial diversity of early-branching metazoa is revealed by the complete mtgenome of a haplosclerid demosponge. Mol Biol Evol. 24:19.
35. Fermin D, Allen BB, Blackwell TW, Menon R, Adamski M, Xu Y, Ulintz P, Omenn GS, States DJ. 2006. Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics. Genome Biol. 7(4).
36. Adamski M, Blackwell T, Menon R, Martens L, Hermjakob H, Taylor C, Omenn GS, States DJ. 2005. Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project. Proteomics. 5:3246.
37. Omenn GS, States DJ, Adamski M, et al. 2005. Overview of the HUPO Plasma Proteome Project: results from the pilot phase with35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics. 5:3226.
38. Martens L, Hermjakob H, Jones P, Adamski M, Taylor C, States D, Gevaert K, Vandekerckhove J, Apweiler R. 2005. PRIDE: the proteomics identifications database. Proteomics. 5:3537.
39. Martens L, Nesvizhskii AI, Hermjakob H, Adamski M, Omenn GS, Vandekerckhove J, Gevaert K. 2005. Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories. Proteomics. 5:3501.
40. Adamska M, Herbrand H, Adamski M, Krüger M, Braun T, Bober E. 2001. FGFs control the patterning of the inner ear but are not able to induce the full ear program. Mech Dev. 109:303.

Review paper

1. Fortunato SA, Adamski M, Adamska M. 2015. Comparative analyses of developmental transcription factor repertoires in sponges reveal unexpected complexity of the earliest animals. Mar Genomics. S1874-7787:30014.

Books and Book Chapters

1. Omenn GS, Menon R, Adamski M, Blackwell T, Haab BB, States DJ: The Human Plasma and Serum Proteome, book chapter in Proteomics of Human Body Fluids: Principles, Methods, and Applications. Springer 2007; ISBN 978-1-58829-657-3
2. Omenn GS, States DJ, Adamski M, Blackwell TW, Menon R, Hermjakob H, Apweiler R, Haab BB, Simpson RJ, Eddes JS, Kapp EA, Moritz RL, Chan DW, Rai AJ, Admon A, Aebersold R, Eng J, Hancock WS, Hefta SA, Meyer H, Paik JK, Yoo JS, Ping P, Pounds J, Adkins J, Qian X, Wang R, Wasinger V, Wu CY, Zhao X, Zeng R, Archakov A, Tsugita A, Beer I, Pandey A, Pisano M, Andrews P, Tammen H, Speicher DW, Hanash SM: Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database, book chapter in Exploring the Human Plasma Proteome. Viley-Vch 2006; ISBN: 9783527317578
3. Adamski M, Blackwell T, Menon R, Martens L, Hermjakob H, Taylor C, Omenn GS, States DJ: Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project, book chapter in Exploring the Human Plasma Proteome. Viley-Vch 2006; ISBN: 9783527317578
4. Martens L, Nesvizhskii AI, Hermjakob H, Adamski M, Omenn GS, Vandekerckhove J, Gevaert K: Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories, book chapter in Exploring the Human Plasma Proteome. Viley-Vch 2006; ISBN: 9783527317578
5. Adamski M, States DJ, Omenn GS: Data Standardization and Integration in Collaborative Proteomics Studies, book chapter in Informatics in Proteomics. Taylor and Francis Books 2005; ISBN 1574-444808
6. Laczny JM, Adamski M: Environmental impact of power plant waste disposal sites: A mathematical model, Institute of Environmental Engineering of the Polish Academy of Science, 2002, ISBN 83-04-04603-2

Personally Delivered Conference and Workshop Talks

1. Adamski M. Assembly strategies and approaches to difficult invertebrate genomes and transcriptomes. Invited keynote lecture. 2^nd Global Invertebrate Genomics Alliance (GIGA) workshop 2015, March 2015, München Germany.
2. Adamski M, Leininger S, Fortunato S, Rapp HT, Adamska M: Surprisingly complex genomes of calcisponges. Society for Molecular Biology and Evolution Conference June 2014, Puerto Rico.
3. Adamski M, Leininger S, Fortunato S, Rapp HT, Adamska M: Genomes of calcaronean sponges: simple body plans and surprisingly complex developmental toolkits. 10^th International Marine Biotechnology Conference November 2013, Brisbane Australia
4. Adamski M, Leininger S, Fortunato S, Bergum B, Rapp HT, Adamska M: Genomes of calcareous sponges reveal surprisingly complex developmental toolkits. 9th World Sponge Conference, November 2013, Fremantle Australia
5. Adamski M, Leininger S, Fortunato S, Rapp HT, Adamska M: Surprisingly complex genomes of calcisponges  ICREA Conference on the evolution of multicellularity, 2013, Barcelona
6. Adamski M, Leininger S, Fortunato S, Rapp HT, Adamska M: Surprisingly complex developmental toolkits of calcisponge. International Hydra Workshop: Unravelling the Developmental Regulatory Network in Early Animals September 2013, Tutzing Germany
7. Adamski M: Surprisingly complex developmental toolkits of calcaronean sponges, Euro Evo Devo, Conference July 2012 Lisbon
8. Adamski M: Calcaronean sponges: simple body plans and surprisingly complex developmental toolkits September 2012, COMBIO Conference, Adelaide Australia
9. Adamski M, Leininger S, Adamska M: Genome of Sycon ciliatum reveals differences between developmental toolkits of the Demospongia and the Calcarea. International Hydra Workshop “Searching for Eve: basal metazoans and the evolution of multicellular complexity” Tutzing, Germany, September 2011
10. Adamski M, Fortunato S, Leininger S, Adamska M: Transcriptome resources in Sycon ciliatum, a calcareous sponge.  International Workshop: Novel Approaches in Sponge and Cnidarian Research: Focus on Genomics and Metagenomics. September 2009, Aidling Germany.
11. Adamski M: Modelling of ion transport in structure of solidified fly-ashes (in Polish). 4^th Workshop of Polish Society for Computer Simulation, 1997, Jelenia Gora Poland.

Sellected Personally Presented Conference Posters

1. Adamski M, Fortunato S, Laplante M, Bråte J, Leon A, Borisenko I, Aisbett G, Rathjen R, McFetridge M, Adamska M: Developmental Genomics of Sponges. Society for Molecular Biology and Evolution Conference July 2016, Gold Coast Australia.
2. Adamski M, Fortunato S, Adamska M: Sponge genomes reveal spectacular diversity and complexity of developmental toolkit genes. ComBio September 2015, Melbourne Australia.
3. Adamski M, Leininger S, Fortunato S, Rapp HT, Adamska M: RNA-Seq analysis of gene expression in sponges provides clues to axial patterning in the first multicellular animals. Society for Molecular Biology and Evolution Conference June 2014, Puerto Rico.
4. Adamski M: Do developmental toolkits of the basal metazoans carry phylogenetic signal? Deep Metazoan Phylogeny Workshop, October 2011, Munich Germany.