Publications - Research Paper

2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 |

2003 | 2002 | 1997 |


2019 top



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 PD23; Quest for Orthologs Consortium.

Mol Biol Evol. 2019 Jun 26. pii: msz150. doi: 10.1093/molbev/msz150. [Epub ahead of print]


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

Tietgen et al.

J. Antimicrobial Therapy, , Accepted


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

Frank et al.

Nature Comm, Accepted


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

Lindner et al.

Genome Biology, Accepted


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 Jan 15. doi: 10.1093/gbe/evz008. [Epub ahead of print]


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.


2018 top

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 Jun 22;151:78-85. doi: 10.1016/j.pep.2018.06.009. [Epub ahead of print]


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

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

Bioinformatics 2018 Apr 6. doi: 10.1093/bioinformatics/bty225. [Epub ahead of print]


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.



2017 top

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 2017 Aug 30. doi: 10.1093/bioinformatics/btx542. [Epub ahead of print]


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 Biol Evol. 2017 Feb 15. doi: 10.1093/gbe/evx032. [Epub ahead of print]


2016 top

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.


2015 top

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


2014 top

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


2013 top

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


2012 top

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


Review:    

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


2011 top

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


2010 top

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


2009 top

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


2008 top

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


2007 top

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


2006 top

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


Review:    

Should the draft chimpanzee sequence be finished?

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

Trends Genet. 2006; 22(3):122-125


2005 top

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

Ebersberger, I.; Knobloch, J.; Kunz, W.;

Dev Genes Evol. 2005; 215(5):261-267


A genomic region evolving toward different GC contents in humans and chimpanzees indicates a recent and regionally limited shift in the mutation pattern.

Ebersberger, I.; Meyer, M.;

Mol Biol Evol. 2005; 22(5):1240-1245


2003 top

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


2002 top

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


1997 top

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

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

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