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The evolutionary making of SARS-CoV-2

Iruegas, R.; Dosch, J.; Sikora, M.; Hummer, G.; Covino, R.; Ebersberger, I.

doi: https://doi.org/10.1101/2021.01.29.428808

Endothelial versus pronephron fate decision is modulated by the transcription factors Cloche/Npas4l, Tal1, and Lmo2.

Mattonet, K.; Riemslagh, FW.; Guenther, S.; Prummel, KD.; Kesavan, G.; Hans, S.; Ebersberger, I.; Brand, M.; Burger, A.; Reischauer, S.; Mosimann, C.; Stainier, DYR.

Sci Adv. 2022 Sep 2;8(35):eabn2082. doi: 10.1126/sciadv.abn2082. Epub 2022 Aug 31.

InvL, an Invasin-Like Adhesin, Is a Type II Secretion System Substrate Required for Acinetobacter baumannii Uropathogenesis. 

Jackson-Litteken, CD.; Di Venanzio, G.; Le, NH.; Scott, NE.; Djahanschiri, B.; Distel, JS.; Pardue, EJ.; Ebersberger, I.; Feldman, MF. 

Bio. 2022 Jun 28;13(3):e0025822. doi: 10.1128/mbio.00258-22. Epub 2022 May 31.

Evolutionarily stable gene clusters shed light on the common grounds of pathogenicity in the Acinetobacter calcoaceticus-baumannii complex

Djahanschiri, B.; Di Venanzio, G.; Distel, J.S.; Breisch, J.; Dieckmann, M. A.; Goesmann, A.; Averhoff, B.; Göttig, S.; Wilharm, G.; Feldman, M.F.; Ebersberger, I.;

PLOS Genetics 2022

doi: https://doi.org/10.1101/2022.01.10.475602

Assembly and Functional Role of PACE Transporter PA2880 from Pseudomonas aeruginosa

Zhao, J.; Hellwig, N.; Djahanschiri, B.; Khera R.; Morgner N.; Ebersberger, I.; Wang , J.; Michel, H.

Microbiol Spectr 2022 Apr 4;e0145321. doi: 10.1128/spectrum.01453-21

The structure of the Aquifex aeolicus MATE family multidrug resistance transporter and sequence comparisons suggest the existence of a new subfamily

Zhao, J.; Xie, H.; Mehdipour, A. R.; Safarian, S.; Ermler, U.; Münke, C.; Thielmann, C.; Hummer, G.; Ebersberger, I.; Wang, J.; Michel, H.

PNAS November 16, 2021 118 (46) e2107335118; https://doi.org/10.1073/pnas.2107335118

Tracing Eukaryotic Ribosome Biogenesis Factors Into the Archaeal Domain Sheds Light on the Evolution of Functional Complexity

Birikmen, M.; Bohnsack, K. E.; Tran, V.; Somayaji, S.; Bohnsack, M. T.; Ebersberger, I.

Front. Microbiol., 16 September 2021 | https://doi.org/10.3389/fmicb.2021.739000

Ten years of collaborative progress in the Quest for Ortholog

Linard, B.; Ebersberger, I.; McGlynn, S. E.; Glover, N.; Mochizuki, T.; Patricio, M.; Lecompte, O.; Nevers, Y.; QFO Consortium; Thomas, P.D.; Gabaldón, T.; Sonnhammer, E.; Dessimoz, C.; Uchiyama, I.

Molecular Biology and Evolution 2021, msab098, https://doi.org/10.1093/molbev/msab098

Minimized combinatorial CRISPR screens identify genetic interactions in autophagy

Diehl, V.; Wegner, M.; Grumati, P.; Husnjak, K.; Schaubeck, S.; Gubas, A.; Jayeshkumar Shah, V.; Polat, I. H.; Langschied, F.; Prieto-Garcia, C.; Müller, K.; Kalousi, A.; Ebersberger, I.; Brandts, C. H.; Dikic, I.; Kaulich, M.

Nucleic Acids Research, Volume 49, Issue 10, 4 June 2021, Pages 5684–5704, https://doi.org/10.1093/nar/gkab309

Bacterial and Fungal Toll-Like Receptor Activation Elicits Type I IFN Responses in Mast Cells

Kornstädt, L.; Pierre, S.; Weigert, A.; Ebersberger, S.; Schäufele, T. J.; Kolbinger, A.; Schmid, T.; Cohnen, J.; Thomas, D.; Ferreirós, N.; Brüne, B.; Ebersberger, I., Scholich, K.

Front. Immunol. 2021, https://doi.org/10.3389/fimmu.2020.607048

Immune challenge reduces gut microbial diversity and triggers fertility-dependent gene expression changes in a social insect

Negroni, M. A.; Segers, F. H. I. D.; Vogelweith, F.; Foitzik, S.

BMC Genomics volume 21, Article number: 816 (2020)

https://doi.org/10.1186/s12864-020-07191-9

Peptidoglycanediting provides immunity to Acinetobacter baumannii during bacterial warfare

Nguyen, H. L.; Peters, K.; Espaillat, A.; Sheldon, J. R.; Gray, J.; Di Venanzio, G.; Lopez, J.; Djahanschiri, B.; Mueller, E. A.; Hennon, S. W.; Levin, P.-A.; Ebersberger, I.; Skaar, E. P.; Cava, F.; Vollmer, W.; Feldman M. F.;

Sci Adv . 2020 Jul 22;6(30):eabb5614. doi: 10.1126/sciadv.abb5614. eCollection 2020 Jul.

Tek/Tie2 is not required for cardiovascular development in zebrafish

Jiang, Z.; Carlantoni, C.; Allanki, S.; Ebersberger, I.; Stainier, D. Y. R. ;

Development 2020 : dev.193029 doi: 10.1242/dev.193029 Published 14 September 2020

Comparative transcriptomics reveal insights into the drought response of the three Panicum species P. bisulcatum, P. laetum and P. turgidum

Kotrade, P.; Werner, A.; Ebersberger, I.; Brüggemann, W.;

Plant Gene Volume 23, September 2020, https://doi.org/10.1016/j.plgene.2020.100232

Adjustment of photosynthetic activity to drought and fluctuating light in wheat

Grieco, M.; Roustan, R.; Dermendjiev, G.; Rantala, S.;Jain, J.; Leonardelli, M.; Neumann, K.; Berger, V.; Engelmeier, D.; Bachmann, B.; Ebersberger, I.; Aro, E.-M.; Weckwerth, W.; Teige, M.;

Plant Cell Environ. 2020;1–17; https://doi.org/10.1111/pce.13756

What is in Umbilicaria pustulata? A metagenomic approach to reconstruct the holo-genome of a lichen 

Greshake Tzovaras, B.; Segers, F.; Bicker,  A.; Dal Grande, F.; Otte, J.; Yahya Anvar, S.; Hankeln, T.; Schmitt, I.; Ebersberger, I.;

Genome Biology and Evolution 2020, eva0049, https://doi.org/10.1093/gbe/evaa049

The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation

Hildebrandt, A.; Brüggemann, M.; Rücklé, C.; Boerner, S.; Heidelberger, J. B.; Busch, A.; Hänel, H.; Voigt, A.; Möckel, M. M.; Ebersberger, S.; Scholz, A.; Dold, A.; Schmid, T.; Ebersberger, I.; Roignant, J.Y.; Zarnack, K.; König, J.; Beli, P.

Genome Biology volume 20, Article number: 216 (2019)

Advances and Applications in the Quest for Orthologs.

Glover N.; Dessimoz C.; Ebersberger I.; Forslund SK.; Gabaldón T.; Huerta-Cepas J.; Martin MJ.; Muffato M.; Patricio M.; Pereira C.; Sousa da Silva A.; Wang Y.; Sonnhammer E.; Thomas PD.; Quest for Orthologs Consortium.

Mol Biol Evol. 2019 Oct 1;36(10):2157-2164. doi: 10.1093/molbev/msz150.#

Identification of the novel class D β-lactamase OXA-679 involved in carbapenem resistance in Acinetobacter calcoaceticus

Tietgen, M.; Kramer, JS.; Brunst, S.; Djahanschiri, B.; Wohra, S.; Higgins, PG.; Weidensdorfer, M.; Riedel-Christ, S.; Pos, KM.; Gonzaga, A.; Steglich, M.; Nübel, U.; Ebersberger, I.; Proschak, E.; Göttig, S.

J Antimicrob Chemother. 2019 Jun 1;74(6):1494-1502. doi: 10.1093/jac/dkz080.

Apoptotic tumor cell-derived microRNA-375 uses CD36 to alter the tumor-associated macrophage phenotype

Frank, AC.; Ebersberger, S.; Fink, AF.; Lampe, S.; Weigert, A.; Schmid, T.; Ebersberger, I.; Syed, SN.; Brüne, B.

Nat Commun. 2019 Mar 8;10(1):1135. doi: 10.1038/s41467-019-08989-2.

Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity

Linker, SM.; Urban, L.; Clark, SJ.; Chhatriwala, M.; Amatya, S.; McCarthy, DJ.; Ebersberger, I.; Vallier, L.; Reik, W.; Stegle, O1.;, Bonder, MJ.

Genome Biol. 2019 Feb 11;20(1):30. doi: 10.1186/s13059-019-1644-0.

The Acinetobacter trimeric autotransporter adhesin Ata controls key virulence traits of Acinetobacter baumannii

Weidensdorfer, M.; Ishikawa, M.; Hori, K.; Linke, D.; Djahanschiri, B.; Iruegas, R.; Ebersberger, I.; Riedel-Christ, S.; Enders, G.; Leukert, L.; Kraiczy, P.; Rothweiler, F.; Cinatl, J.; Berger, J.; Hipp, K.; Kempf, V. A. J.; Göttig, S.

Virulence 2019, Jan, Pages 68-81, doi.org/10.1080/21505594.2018.1558693

The evolutionary traceability of a protein

Jain, A.; Persia, D.; Fliedner, F.; von Haesseler, A.; Ebersberger, I.

Genome Biol Evol. 2019 Feb 1;11(2):531-545. doi: 10.1093/gbe/evz008.

HEATSTER: A Database and Web Server for Identification and Classification of Heat Stress Transcription Factors in Plants.

Berz, J.; Simm, S.; Schuster, S.; Scharf, K.D.; Schleiff, E.; Ebersberger, I.

Bioinform Biol Insights. 2019 Jan 7;13:1177932218821365. doi: 10.1177/1177932218821365. eCollection 2019.

IL-6 augments IL-4-induced polarization of primary human macrophages through synergy of STAT3, STAT6 and BATF transcription factors

Conserved Gene Microsynteny Unveils Functional Interaction Between Protein Disulfide Isomerase and Rho Guanine-Dissociation Inhibitor Families

Moretti, A. I. S.; Pavanelli, J. C.; Nolasco, P.; Leisegang, M. S.; Tanaka, L. Y.; Fernandes, C. G.; Wosniak Jr, J.; Kajihara, D.; Dias, M. H.; Fernandes, D. C.; Jo, H.; Tran, N. V.; Ebersberger, I.; Brandes, R. P.; Bonatto, D.; Laurindo, F. R. M.

Scientific Reports 2017 Dec 8;7(1):17262. doi: 10.1038/s41598-017-16947-5.

Gearing up to handle the mosaic nature of life in the quest for orthologs

Forslund, K.; Pereira, C.; Capella-Gutierrez, S.; Sousa da Silva, A.; Altenhoff, A.; Huerta-Cepas, J.; Muffato, M.; Patricio, M.; Vandepoele, K.; Ebersberger, I.; Blake, J.; Breis, J.T.F.

The Quest for Orthologs Consortium: Boeckmann, B.; Gabaldón, T.; Sonnhammer, E.; Dessimoz, C.; Lewis, S.

Bioinformatics. 2018 Jan 15;34(2):323-329. doi: 10.1093/bioinformatics/btx542.

Natural product diversity associated with the nematode symbionts Photorhabdus and Xenorhabdus

Tobias, N.;  Wolff, H.;  Djahanschiri, B.;  Grundmann, F.;  Kronenwerth, M.;  Shi, Y.;  Simonyi, S.;  Grün, P.;  Shapiro-Ilan, D.;  Pidot, S.;  Stinear, T.;  Ebersberger, I.;  Bode, H.

Nat Microbiol. 2017 Dec;2(12):1676-1685. doi: 10.1038/s41564-017-0039-9. Epub 2017 Oct 9.

The draft genome of blunt snout bream (Megalobrama amblycephala) reveals the development of intermuscular bone and adaptation to herbivorous diet.

Liu, H.; Chen, C.; Gao, Z.; Min, J.; Gu, Y.; Jian, J.; Jiang, X.; Cai, H.; Ebersberger, I.; Xu, M.; Zhang, X.; Chen, J.; Luo, W.; Chen, B.; Chen, J.; Liu, H.; Li, J.; Lai, R.; Bai, M.; Wei, J.; Yi, S.; Wang, H.; Cao, X.; Zhou, X.; Zhao, Y.; Wei, K.; Yang, R.; Liu, B.; Zhao, S.; Fang, X.; Schartl, M.; Qian, X.; Wang, W.

Gigascience. 2017 Jul 1;6(7):1-13. doi: 10.1093/gigascience/gix039.

An annotated draft genome for Radix auricularia (Gastropoda, Mollusca)

Schell, T.; Feldmeyer, B.; Schmidt, H.; Greshake, B.; Tills, O.; Truebano, M.; Rundle, SD.; Paule, J.; Ebersberger, I.; Pfenninger, M.;

Genome Biology and Evolution, Volume 9, Issue 3, March 2017, Pages 585–592, https://doi.org/10.1093/gbe/evx032

Characterization of microsatellite loci in the lichen-forming fungus Cetraria aculeata (Parmeliaceae, Ascomycota).

Lutsak, T.; Fernández-Mendoza, F.; Greshake, B.; Dal Grande, F.; Ebersberger, I.; Ott, S.; Printzen, C.

Appl Plant Sci. 2016 Sep 19;4(9). pii: apps.1600047. doi: 10.3732/apps.1600047.

An evolutionary perspective of AMPK-TOR signaling in the three domains of life

Roustan, V.; Jain, A.; Teige, M.; Ebersberger, I.; Weckwerth, W.;

Acinetobacter equi sp. nov. isolated from horse faeces

Poppel, M.T.; Skiebe, E.; Laue, M.; Bergmann, H.; Ebersberger, I.; Garn, T.; Fruth, A.; Baumgardt, S.; Busse, H.J.; Wilharm, G.;

Int J Syst Evol Microbiol. 2015 Nov 30. doi: 10.1099/ijsem.0.000806

Acinetobacter baumannii Virulence Is Mediated by the Concerted Action of Three Phospholipases D

Stahl, J.; Bergmann, H.; Göttig, S.; Ebersberger, I.; Averhoff, B.;

PLoS One. 2015; 10(9): e0138360

Potential and pitfalls of eukaryotic metagenome skimming: A test case for lichens.

Greshake, B.; Zehr, S.; Dal Grande, F.; Meiser, A.; Schmitt, I.; Ebersberger, I.;

Mol Ecol Resour. 2015 Sep 8. doi: 10.1111/1755-0998.12463

The association of late-acting snoRNPs with human pre-ribosomal complexes requires the RNA helicase DDX21

Sloan, K. E.; Leisegang, M. S.; Doebele, C.; Ramírez, A. S.; Simm, S.; Safferthal, C.; Kretschmer, J.; Schorge, T.; Markoutsa, S.; Haag, S.; Karas, M.; Ebersberger, I.; Schleiff, E.; Watkins, N. J.; T. Bohnsack, M. T.

Nucl. Acids Res. (January 2015) 43 (1): 553-564

Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix

Feldmeyer, B.; Greshake, B.; Funke, E.; Patel, S.; Ebersberger, I.; Pfenninger, M.;

BMC Evolutionary Biology 2015, 15:164 doi:10.1186/s12862-015-0434-x

Higher plant proteins of cyanobacterial origin - are they or are they not preferentially targeted to chloroplasts?

Bayer, R.G.; Köstler, T.; Jain, A.; Stael, S.; Ebersberger, I.; Teige, M.;

Mol Plant. 2014 Dec;7(12):1797-800.

A transcriptome approach to ecdysozoan phylogeny

Borner, J.; Rehm, P.; Schill, R. O.; Ebersberger, I.; Burmester, T.;

Mol Phylogenet Evol. 2014 Nov; 80:79-87

The evolution of the ribosome biogenesis pathway from a yeast perspective

Ebersberger, I.: Simm, S.; Leisegang, M. S.; Schmitzberger, P.; Mirus, O.; von Haeseler, A.; Bohnsack, M. T.; Schleiff, E.;

Nucl. Acids Res. 2014 42: 1509-1523

Transcriptome Data Reveal Syndermatan Relationships and Suggest the Evolution of Endoparasitism in Acanthocephala via an Epizoic Stage

Wey-Fabrizius, A. R.; Herlyn, H.; Rieger, B.; Rosenkranz, D.; Witek, A.; Welch, D. B. M. ; Ebersberger, I.; Hankeln, T.;

PLOS ONE February 10, 2014; DOI: 10.1371/journal.pone.0088618

New phylogenomic data support the monophyly of Lophophorata and an Ectoproct-Phoronid clade and indicate that Polyzoa and Kryptrochozoa are caused by systematic bias

Nesnidal, M. P.; Helmkampf, M.; Meyer, A.; Witek, A.; Bruchhaus, I.; Ebersberger, I.; Hankeln, T.; Lieb, B.; Struck, T.H. and Hausdorf, B.;

BMC Evolutionary Biology.2013, 13:253; DOI: 10.1186/10.1186/1471-2148-13-253

Decisive Datasets in Phylogenomics: Lessons from Studies on the Phylogenetic Relationships of Primarily Wingless Insects

Mol Biol Evol 2013; DOI: 10.1093/molbev/mst196

Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and othereukaryotes for analysis of environmental sequencingdata

Bengtsson-Palme, J., Ryberg, M.; Hartmann, M.; Branco, S.; Wang, Z.; Godhe, A.; dee Wit, P.; Sánchez-García, M.; Ebersberger, I.; de Sousa, F.; Amend, A.; Jumpponen, A.; Unterseher, M.; Kristiansson, E.; Abarenkov, K.; Bertrand, Y.; Sanli, K.; Eriksson, K. M.; Vik, U.; Veldre, V.; Nilsson, R. H.

Methods in Ecology and Evolution 2013; DOI: 10.1111/2041-210X.12073

REvolver: Modeling sequence evolution under domain constraints.

Mol Biol Evol 2012; 29(9):2133-45

A Consistent Backbone for the Fungi.

Mol Biol Evol 2012; 29:1319-1334.

Pancrustacean phylogeny in the light of new phylogenomic data: support for Remipedia as the possible sister group of Hexapoda.

Mol Biol Evol 2012; 29:1031-1045

The plant heat stress transcription factor (Hsf) family: structure, function and evolution.

Scharf, KD.; Berberich, T.; Ebersberger, I. and Nover, L.;

BBA - Gene Regulatory Mechanisms. 2012; 1819(2):104-19, doi.org/10.1016/j.bbagrm.2011.10.002

Phylogenomic analyses of malaria parasites and evolution of their exported proteins.

Zygomycetes, microsporidia, and the evolutionary ancestry of sex determination.

Genome Biology and Evolution. 2011; 3:186-194

FACT: Functional annotation transfer between proteins with similar feature architecture.

Support for the monophyletic origin of Gnathifera from phylogenomics.

Science. 2009; 325(5938):340-343

Centrin4 coordinates cell and nuclear division in T. brucei.

J Cell Sci. 2008; 121(Pt 9):1538-1546

Targeted deletion of AIF decreases mitochondrial oxidative phosphorylation and protects from obesity and diabetes.

Mol Biol Evol. 2007; 24(10):2266-2276

Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae.

Cracks in the shell–zooming in on eggshell formation in the human parasite Schistosoma mansoni.

A neutral explanation for the correlation of diversity with recombination rates in humans.

Genomewide comparison of DNA sequences between humans and chimpanzees.

A variable intron distribution in globin genes of Chironomus: evidence for recent intron gain.