​Publications - Research Paper

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Publications

 

2024


Genomic evidence for the wide-spread presence of GH45 cellulases among soil invertebrates 

H. Muelbaier, F. Arthen, G. Collins, T. Hickler, K. Hohberg , R. Lehmitz, Y. Pauchet,
M. Pfenninger, A. Potapov , J. Romahn, I. Schaefer, S. Scheu, C. Schneider, I. Ebersberger, M.  Bálint

Molecular Ecology 2024      accepted

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2023


The MetaInvert soil invertebrate genome resource provides insights into below-ground biodiversity and evolution

G. Collins, C. Schneider, L. L. Boštjančić, U. Burkhardt, A. Christian, P. Decker, I. Ebersberger, K. Hohberg, O. Lecompte, D. Merges, H. Muelbaier, J. Romahn, J. Römbke, C. Rutz, R. Schmelz, A. Schmidt, K. Theissinger, R. Veres, R. Lehmitz, M. Pfenninger, Mi. Bálint

Communications Biology, Volume 6, Article number: 1241 (2023)


Sequencing the Genomes of the First Terrestrial Fungal Lineages: What Have We Learned? 

A. P. Grygansky, J. Golan, A. Muszewska, A. Idnurm, S. Dolatabadi, S. J. Mondo, V. B. Kutovenko, V. O. Kutovenko, M. T. Gajdeczka, I. M. Anishchenko, J. Pawlowska, N. V. Tran, I. Ebersberger, K. Voigt, Y. Wang, Y. Chang, T. E. Pawlowska, J. Heitman, R. Vilgalys, G. Bonito, G. L. Benny, M. E. Smith, N. Reynolds, T. Y. James, I. V. Grigoriev, J. W. Spatafora, J. E. Stajich

Microorganisms 2023, 11(7), 1830; https://doi.org/10.3390/microorganisms11071830


FUBP1 is a general splicing factor facilitating 3' splice site recognition and splicing of long introns

S. Ebersberger, C. Hipp, M. M. Mulorz, A. Buchbender, D. Hubrich, H. Kang, S. Martinez-Lumbreras, P. Kristofori, R. Sutandy, L. Llacsahuanga Allcca, J. Schönfeld, C. Bakisoglu, A. Busch, H. Hänel, K. Tretow, M. Welzel, A. Di Liddo, M. M. Möckel, K. Zarnack, I. Ebersberger, S. Legewie, K. Luck, M. Sattler, J. König

Molecular Cell (2023), https://doi.org/10.1016/j.molcel.2023.07.002


Better integration of chemical pollution research will further our understanding of biodiversity loss

F. Sylvester, F. G. Weichert, V. L. Lozano, K. J. Groh, M. Bálint, L. Baumann, C. Bässler, W. Brack, B. Brandl, J. Curtius, P. Dierkes, P. Döll, I. Ebersberger, S. Fragkostefanakis, E. J. N. Helfrich, T. Hickler, S. Johann, J. Jourdan, S. Klimpel, H. Kminek, F. Liquin, D. Möllendorf, T. Mueller, J. Oehlmann, R. Ottermanns, S. U. Pauls, M. Piepenbring, J. Pfefferle, G. J. Schenk, J. F. Scheepens, M. Scheringer, S. Schiwy, A. Schlottmann, F. Schneider, L. M. Schulte, M. Schulze-Sylvester, E. Stelzer, F. Strobl, A. Sundermann, K. Tockner, T. Tröger, A. Vilcinskas, C. Völker, R. Winkelmann, H. Hollert

nature ecology & evolution, June 2023, https://doi.org/10.1038/s41559-023-02117-6


Feature architecture aware phylogenetic profiling indicates a functional diversification of type IVa pili in the nosocomial pathogen Acinetobacter baumannii

R. Iruegas, K. Pfefferle, S. Goettig, B. Averhoff, I. Ebersberger

PLOS Genetics, July 27, 2023, https://doi.org/10.1371/journal.pgen.1010646


ncOrtho: Efficient and reliable identification of miRNA orthologs

F. Langschied, M. Leisegang, R. Brandes, I. Ebersberger

Nucleic Acids Research, June 2023, gkad467, https://doi.org/10.1093/nar/gkad467


FAS: Assessing the similarity between proteins using multi-layered feature architectures 

J. Dosch, H. Bergmann, V. Tran, I. Ebersberger

Bioinformatics, April 2023, btad226, https://doi.org/10.1093/bioinformatics/btad226

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2022


The Quest for Orthologs orthology benchmark service in 2022. 

Nevers Y, Jones TEM, Jyothi D, Yates B, Ferret M, Portell-Silva L, Codo L, Cosentino S, Marcet-Houben M, Vlasova A, Poidevin L, Kress A, Hickman M, Persson E, Piližota I, Guijarro-Clarke C; OpenEBench team the Quest for Orthologs Consortium; Iwasaki W, Lecompte O, Sonnhammer E, Roos DS, Gabaldón T, Thybert D, Thomas PD, Hu Y, Emms DM, Bruford E, Capella-Gutierrez S, Martin MJ, Dessimoz C, Altenhoff A. 

Nucleic Acids Res. 2022 May 12;50(W1):W623-32. doi: 10.1093/nar/gkac330


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. 

mBio. 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

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2021


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

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2020


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

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2019


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.

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2018


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


Gupta, S.; Jain, A.; Syed, S. N. .; Snodgrass, R. G.; Pflüger-Müller, B.; Leisegang, M. S. .; Weigert, A.; Brandes, R. P. .; Ebersberger, .I; Brüne, B.; Namgaladze, D.

OncoImmunology 2018, 7:10 , doi.org/10.1080/2162402X.2018.1494110


Recombinant production of A1S_0222 from Acinetobacter baumannii ATCC 17978 and confirmation of its DNA-(adenine N6)-methyltransferase activity

Blaschke, U.; Suwono, B.; Zafari, S.; Ebersberger, I.; Skiebe, E.; Jeffries, C. M.; Svergun, D.I.; Wilharm, G.

Protein Expr Purif. 2018 Nov;151:78-85. doi: 10.1016/j.pep.2018.06.009. Epub 2018 Jun 22.


PhyloProfile: Dynamic visualization and exploration of multi-layered phylogenetic profiles

Tran, N. V; Greshake Tzovaras, B; Ebersberger, I;

Bioinformatics. 2018 Sep 1;34(17):3041-3043. doi: 10.1093/bioinformatics/bty225.


Studying AMPK in an Evolutionary Context.

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

Methods Mol Biol. 2018;1732:111-142. doi: 10.1007/978-1-4939-7598-3_8.

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2017


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

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2016


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.;

Exp Bot. 2016 Jun;67(13):3897-907. doi: 10.1093/jxb/erw211


The calmodulin-like proteins AtCML4 and AtCML5 are single-pass membrane proteins targeted to the endomembrane system by an N-terminal signal anchor sequence

Ruge, R.; Flosdorff, S.; Ebersberger, I.; Chigri, F.; Vothknecht, U.;

J Exp Bot. 2016 Jun;67(13):3985-96. doi: 10.1093/jxb/erw101. Epub 2016 Mar 29.


An evolutionary view on thylakoid protein phosphorylation to uncover novel phosphorylation hotspots with potential functional implications

Grieco M.; Jain, A.; Ebersberger, I.; Teige, M.;

J Exp Bot. 2016 Jun;67(13):3883-96. doi: 10.1093/jxb/erw164. Epub 2016 Apr 25. Review.

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2015


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

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2014


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

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2013


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

Dell'Ampio, E.; Meusemann, K.; Szucsich, N. U.; Peters, R. S.; Meyer, B.; Borner, J.; Petersen, M.; Aberer, A. J. ; Stamatakis, A.; Walzl, M. G.; Minh, B. Q.; von Haeseler, A.; Ebersberger, I.; Pass, G.; Misof, B.;

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

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2012


REvolver: Modeling sequence evolution under domain constraints.

Koestler, T.; von Haeseler, A.; Ebersberger, I.;

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


A Consistent Backbone for the Fungi.

Ebersberger, I.; de Matos Simoes, R.; Kupczok, A.; Gube, M.; Kothe, E.; Voigt, K.; von Haeseler, A.;

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.

von Reumont, BM.; Jenner, RA.; Wills, MA.; DellAmpio, E.; Pass, G.; Ebersberger, I.; Meyer, B.; Koenemann, S.; Iliffe, TM.; Stamatakis, A.; Niehuis, O.; Meusemann, K.; Misof, B.;

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

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2011


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

Pick, C.; Ebersberger, I.; Spielmann, T.; Bruchhaus, I. and Burmester, T.;

BMC Evolutionary Biology. 2011; 11:167


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

Koestler, T.; Ebersberger, I.;

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

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2010


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

Koestler, T.; von Haeseler, A.; Ebersberger, I.;

BMC Bioinformatics. 2010; 11:417


A phylogenomic approach to resolve the arthropod tree of life.

Meusemann, K.; von Reumont, BM.; Simon, S.; Roeding, F.; Strauss, S.; Kück, P.; Ebersberger, I.; Walzl, M.; Pass, G.; Breuers, S.; Achter, V.; von Haeseler, A.; Burmester, T.; Hadrys, H.; Wägele, JW.; Misof, B.;

Mol Biol Evol. 2010; 27(11):2451-2464

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2009


Support for the monophyletic origin of Gnathifera from phylogenomics.

Witek, A.; Herlyn, H.; Ebersberger, I.; Mark Welch, DB.; Hankeln, T.;

Mol Phylogenet Evol. 2009; 53(3):1037-1041


HaMStR: profile hidden markov model based search for orthologs in ESTs.

Ebersberger, I.; Strauss, S.; von Haeseler, A.;

BMC Evol Biol. 2009; 9:157


Genome-wide RNAi screen identifies genes involved in intestinal pathogenic bacterial infection.

Cronin, SJ.; Nehme, NT.; Limmer, S.; Liegeois, S.; Pospisilik, JA.; Schramek, D.; Leibbrandt, A.; Simoes Rde, M.; Gruber, S.; Puc, U.; Ebersberger, I.; Zoranovic, T.; Neely, GG.; von Haeseler, A.; Ferrandon, D.; Penninger, JM.;

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

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2008


Centrin4 coordinates cell and nuclear division in T. brucei.

Shi, J.; Franklin, JB.; Yelinek, JT.; Ebersberger, I.; Warren, G.; He, CY;.

J Cell Sci. 2008; 121(Pt 18):3062-3070


Rooted triple consensus and anomalous gene trees.

Ewing, GB.; Ebersberger, I.; Schmidt, HA.; von Haeseler, A.;

BMC Evol Biol. 2008; 8:118


TbG63, a golgin involved in Golgi architecture in Trypanosoma brucei.

Ramirez, IB.; de Graffenried, CL.; Ebersberger, I.; Yelinek, J.; He, CY.; Price, A.; Warren, G.;

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

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2007


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

Pospisilik, JA.; Knauf, C.; Joza, N.; Benit, P.; Orthofer, M.; Cani, PD.; Ebersberger, I.; Nakashima, T.; Sarao, R.; Neely, G.; Esterbauer, H.; Kozlov, A.; Kahn, CR.; Kroemer, G.; Rustin, P.; Burcelin, R.; Penninger, JM.;

Cell. 2007; 131(3):476-491


EST sequencing of Onychophora and phylogenomic analysis of Metazoa.

Roeding, F.; Hagner-Holler, S.; Ruhberg, H.; Ebersberger, I.; von Haeseler, A.; Kube, M.; Reinhardt, R.; Burmester, T.;

Mol Phylogenet Evol. 2007; 45(3):942-951


Mapping human genetic ancestry.

Ebersberger, I.; Galgoczy, P.; Taudien, S.; Taenzer, S.; Platzer, M.; von Haeseler, A.;

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

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2006


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

Krause, J.; Dear, PH.; Pollack, JL.; Slatkin, M.; Spriggs, H.; Barnes, I.; Lister, AM.; Ebersberger, I.; Pääbo, S.; Hofreiter, M.;

Nature. 2006; 439(7077):724-727


Should the draft chimpanzee sequence be finished?

Taudien, S.; Ebersberger, I.; Glöckner, G.; Platzer, M.;

Trends Genet. 2006; 22(3):122-125; doi.org/10.1016/j.tig.2005.12.007

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2005

                                                                                                                                         back

2003


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

Hellmann, I.; Ebersberger, I.; Ptak, SE.; Płłbo, S.; Przeworski, M.;

Am J Hum Genet. 2003 Jun;72(6):1527-1535


Selection on human genes as revealed by comparisons to chimpanzee cDNA.

Hellmann, I.; Zollner, S.; Enard, W.; Ebersberger, I.; Nickel, B.; Paabo, S.;

Genome Res. 2003; 13(5):831-837

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2002


Genomewide comparison of DNA sequences between humans and chimpanzees.

Ebersberger, I.; Metzler, D.; Schwarz, C.; Pääbo, S.;

Am J Hum Genet. 2002; 70(6):1490-1497

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1997


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

Hankeln, T.; Friedl, H.; Ebersberger, I.; Martin, J.; Schmidt, ER.;

Gene. 1997; 205(1-2):151-160

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​Preprints

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Kontakt

Goethe-University Frankfurt/Main

Department for Applied Bioinformatics

Institute for Cell Biology and Neuroscience

Prof. Dr. Ingo Ebersberger

Max-von-Laue Str. 13
D-60438 Frankfurt
GERMANY

Phone   +49 69 798 - 42112

Secretary
Anne Hänel
Campus Riedberg
Biologicum; Room 3.205
Phone   +49 69 798-42110
Mail       haenel@bio.uni-frankfurt.de

How to reach us