Publications

in press

• H.Q. Dinh, B.Q. Minh, H.X. Huan and A. von Haeseler (2010) ACOPHY: A simple and general ant colony optimization approach for phylogenetic tree reconstruction. to be published in Proceedings of the 7th Intl. Conference on Swarm Inteligence (ANTS 2010), accepted.
• K.A. Gurley, S.A. Elliot, O. Simakov, H.A. Schmidt, T.W. Holstein and A. Sánchez Alvarado (2009) Expression of secreted Wnt pathway components reveals unexpected complexity of the planarian amputation response. Dev. Biol., accepted. (DOI: 10.1016/j.ydbio.2010.08.007, PMID: 20707997)
• K. Meusemann, B.M. von Reumont, S. Simon, F. Roeding, S. Strauss, P. Kück, I. Ebersberger, M. Walzl, G. Pass, S. Breuers, V. Achter, A. von Haeseler, T. Burmester, H. Hadrys, W.W. Wägele and B. Misof (2010) A phylogenomic approach to resolve the arthropod tree of life. Mol. Biol. Evol., 27, in press. (DOI: 10.1093/molbev/msq130, PMID: 20534705)
• M. A. T. Nguyen, S. Klaere, and A. von Haeseler (2010) MISFITS: Evaluating the goodness of fit between a phylogenetic model and an alignment. Mol. Biol. Evol., 27, in press. (free copy, DOI: 10.1093/molbev/msq180, PMID: 20643866)
• S. Washietl and T. Gesell (2010) Graph Representations and Algorithms in Computational Biology of RNA Secondary Structure. In M. Dehmer (ed.) Structural Analysis of Complex Networks., in press, Birkhäuser, Boston, USA. (ISBN: 978-0-8176-4788-9)
• L.S. Vinh, A. Fuehrer, and A. von Haeseler (2010) Random Tree-Puzzle leads to the Yule-Harding Distribution. Mol. Biol. Evol., in press.

2010

• T. Baubec, H.Q. Dinh, A. Pecinka, B. Rakic, W. Rozhon, B. Wohlrab, A. von Haeseler and O. Mittelsten Scheid (2010) Cooperation of Multiple Chromatin Modifications Can Generate Unanticipated Stability of Epigenetic States in Arabidopsis. Plant Cell, 22, 34-47. (DOI: 10.1105/tpc.109.072819, PMID: 20097869)
• J. Hofmann, K. Frenzel, B. Q. Minh, A. von Haeseler, A. Edelmann, R.S. Ross, D.H. Krueger, H. Meisel (2010) Quantitative detection and typing of Hepatitis D virus in human serum by real-time PCR and melting curve analysis. Diagn. Microbiol. Infect. Dis., 67, 172-179. (DOI: 10.1016/j.diagmicrobio.2010.02.003, PMID: 20466196)
• T. Köstler, A. von Haeseler, and I. Ebersberger (2010) FACT: Functional annotation transfer between proteins with similar feature architecture. BMC Bioinform., 11, 417. (DOI: 10.1186/1471-2105-11-417, PMID: 20696036)
• C. Lorenz, T. Gesell, B. Zimmermann, U. Schoeberl, I. Bilusic, L. Rajkowitsch, C. Waldsich, A. von Haeseler and R. Schroeder (2010) Genomic SELEX for Hfq-binding RNAs identifies genomic aptamers predominantly in antisense transcripts. Nucleic Acids Res., 38, 3794-3808. (DOI: 10.1093/nar/gkq032, PMID: 20348540)
• B. Zimmermann^e, T. Gesell^e, D. Chen, C. Lorenz and R. Schroeder (2010) Monitoring Genomic Sequences during SELEX Using High-Throughput Sequencing: Neutral SELEX. PLoS ONE, 5, e9169. (DOI: 10.1371/journal.pone.0009169, PMID: 20161784)
  ^e contributed equally

2009

• F. Catalanotti, G. Reyes, V. Jesenberger, G. Galabova-Kovacs, R. de Matos Simoes, O. Carugo, M. Baccarini (2009) A Mek1-Mek2 heterodimer determines the strength and duration of the Erk signal. Nat. Struct. Mol. Biol., 16, 294-303. (DOI: 10.1038/nsmb.1564, PMID: 19219045)
• S. J. F. Cronin, N. T. Nehme, S. Limmer, S. Liegeois, J. A. Pospisilik, D. Schramek, A. Leibbrandt, R. de Matos Simoes, S. Gruber, U. Puc, I. Ebersberger, T. Zoranovic, G. G. Neely, A. von Haeseler, D. Ferrandon and J. M. Penninger (2009) A genome-wide in vivo RNAi screen on innate immunity to intestinal pathogenic infections. Science, 325, 340-343. (DOI: 10.1126/science.1173164, PMID: 19520911)
• I. Ebersberger, S. Strauss, and A. von Haeseler (2009) HaMStR: Profile Hidden Markov Model Based Search for Orthologs in ESTs. BMC Evol. Biol., 9, 157. (DOI: 10.1186/1471-2148-9-157, PMID: 19586527)
• R. Hanada, A. Leibbrandt, T. Hanada, S. Kitaoka, T. Furuyashiki, H. Fujihara, J. Trichereau, M. Paolino, F. Qadri, R. Plehm, S. Klaere, V. Komnenovic, H. Mimata, H. Yoshimatsu, N. Takahashi, A. von Haeseler, M. Bader, S. Sebnem Kilic, Y. Ueta, C. Pifl, S. Narumiya and J.M. Penninger (2009) Central control of fever and female body temperature by RANKL/RANK. Nature, 462, 505-509. (DOI: 10.1038/nature08596, PMID: 19940926)
• U. Krauss^e, B.Q. Minh^e, A. Losi, W. Gaertner, T. Eggert, A. von Haeseler^c, and K.E. Jaeger (2009) Distribution and phylogeny of light-oxygen-voltage-blue-light-signaling proteins in the three kingdoms of life. J. Bacteriol., 191, 7234-7242. (DOI: 10.1128/JB.00923-09, PMID: 19783626)
  ^e contributed equally, ^c corresponding author
• A. Kupczok and A. von Haeseler (2009) Comment on: A congruency index for testing topological similarity between trees. Bioinformatics, 25, 147-149. (DOI: 10.1093/bioinformatics/btn539, PMID: 18922807)
• M. Knapp, N. Rohland, J. Weinstock, G. Baryshnikov, A. Sher, D. Nagel, G. Rabeder, R. Pinhasi, H.A. Schmidt, and M. Hofreiter (2009) First DNA sequences from Asian cave bear fossils reveal deep divergences and complex phylogeographic patterns. Mol. Ecol., 18, 1225-1238. (DOI: 10.1111/j.1365-294X.2009.04088.x, PMID: 19226321)
• T. Lengfeld, H. Watanabe, O. Simakov, D. Lindgens, L. Gee, L. Law, H.A. Schmidt, S. Ozbek, H. Bode, and T.W. Holstein (2009) Multiple Wnts are involved in Hydra organizer formation and regeneration. Dev. Biol., 330, 186-199. (DOI: 10.1016/j.ydbio.2009.02.004, PMID: 19217898)
• B. Q. Minh, S. Klaere, and A. von Haeseler (2009) Taxon Selection under Split Diversity. Syst. Biol., 57, 586-594. (DOI: 10.1093/sysbio/syp058)
• B.Q. Minh, F. Pardi, S. Klaere, and A. von Haeseler (2009) Budgeted Phylogenetic Diversity on Circular Split Systems. IEEE/ACM Trans. Comput. Biol. Bioinform., 6, 22-29. (DOI: 10.1109/TCBB.2008.54, PMID: 19179696)
• O. Mirus, T. Bionda, A. von Haeseler, and E. Schleiff (2009) Evolutionarily evolved discriminators in the TPR domain of the Toc64 family involved in protein translocation at the outer membrane of chloroplasts and mitochondria. J. Mol. Mod., 15, 971-982. (DOI: 10.1007/s00894-008-0449-y, PMID: 19198901)
• O. Mirus^e, S. Strauss^e, K. Nicolaisen, A. von Haeseler, E. Schleiff (2009) TonB-dependent transporters and their occurrence in cyanobacteria. BMC Biol., 7, 68. (DOI: 10.1186/1741-7007-7-68, PMID: 19821963)
  ^e contributed equally
• H.A. Schmidt (2009) Testing Tree Topologies. In P. Lemey, M. Salemi, A.M. Vandamme (eds.)The Phylogenetic Handbook: a Practical Approach to Phylogenetic Analysis and Hypothesis Testing., 2nd Edition, 381-404, Cambridge University Press, Cambridge. (ISBN: paperback: 9780521730716, hardcover: 9780521877107)
• H.A. Schmidt and A. von Haeseler (2009) Phylogenetic Inference Using Maximum Likelihood Methods. In P. Lemey, M. Salemi, A.M. Vandamme (eds.)The Phylogenetic Handbook: a Practical Approach to Phylogenetic Analysis and Hypothesis Testing., 2nd Edition, 181-209, Cambridge University Press, Cambridge. (ISBN: paperback: 9780521730716, hardcover: 9780521877107)
• S. Simon, S. Strauss, A. von Haeseler, and H. Hadrys (2009) A phylogenomic approach to resolve the basal pterygote divergence. Mol. Biol. Evol., 26, 2719-2730. (DOI: 10.1093/molbev/msp191, PMID: 19713325)
• K. Strimmer and A. von Haeseler (2009) Nucleotide Substitition Models. In P. Lemey, M. Salemi, A.M. Vandamme (eds.)The Phylogenetic Handbook: a Practical Approach to Phylogenetic Analysis and Hypothesis Testing., 2nd Edition, 111-141, Cambridge University Press, Cambridge. (ISBN: paperback: 9780521730716, hardcover: 9780521877107)
• M. Tillich, L. S. Vinh, K. Schulerowitz, A. von Haeseler, U. G. Maier and C. Schmitz-Linneweber (2009) Loss of MatK RNA Editing in Seed Plant Chloroplasts. BMC Evol. Biol., 9, 201. (DOI: 10.1186/1471-2148-9-201) PMID: 19678945)
• C. Weber, A. Pickl-Herk, S. Strauss, O. Carugo and D. Blaas (2009) Predictive bioinformatic identification of minor receptor group human rhinoviruses. FEBS Lett., 583, 2547-2551. (DOI: 10.1016/j.febslet.2009.07.015, PMID: 19615999)
• A. Witek, H. Herlyn, I. Ebersberger, D. B. M. Welch and T. Hankeln (2009) Support for the Monophyletic Origin of Gnathifera from Phylogenomics. Mol. Phylogenet. Evol., 53, 1037-1041. (DOI: 10.1016/j.ympev.2009.07.031, PMID: 19654049)

2008

• I. Barinaga-Rementeria Ramirez, C.L. de Graffenried, I. Ebersberger, J. Yelinek, C.Y. He, A. Price, and G. Warren (2008) TbG63, a golgin involved in Golgi architecture in Trypanosoma brucei. J. Cell Sci., 121, 1538-1546. (DOI: 10.1242/jcs.014324, PMID: 18411253)
• I. Bruns, Ingmar and U. Steidl, Ulrich and J.C. Fischer, A. Czibere, G. Kobbe, S. Raschke, R. Singh, R. Fenk, M. Rosskopf, S. Pechtel, A. von Haeseler, P. Wernet, D. Tenen, R. Haas, and R. Kronenwett (2008) Pegylated G-CSF mobilizes CD34+ cells with different stem and progenitor subsets and distinct functional properties in comparison with unconjugated G-CSF. Haematologica, 93, 347-355. (DOI: 10.3324/haematol.12081, PMID: 18268278)
• M. Dehmer, F. Emmert-Streib, and T. Gesell (2008) A comparative analysis of multidimensional features of objects resembling sets of graphs. Appl. Math. Comput., 196, 221-235. (DOI: 10.1016/j.amc.2007.05.058)
• G.B. Ewing, I. Ebersberger, H.A. Schmidt, and A. von Haeseler (2008) Rooted Triple Consensus and Anomalous Gene Trees. BMC Evol. Biol., 8, 118. (DOI: 10.1186/1471-2148-8-118, PMID: 18439266)
• T. Gesell and S. Washietl (2008) Dinucleotide Controlled Null Models for Comparative RNA Gene Prediction. BMC Bioinform., 9, 248. (DOI: 10.1186/1471-2105-9-248, PMID: 18505553)
• S. Klaere, T. Gesell, and A. von Haeseler (2008) The impact of single substitutions on multiple sequence alignments. Phil. Trans. R. Soc. Lond. B, 363, 4041-4047. (DOI: 10.1098/rstb.2008.0140, PMID: 18852110)
• A. Kupczok, A. von Haeseler, and S. Klaere (2008) An Exact Algorithm for the Geodesic Distance between Phylogenetic Trees. J. Comput. Biol., 15, 577-591. (DOI: 10.1089/cmb.2008.0068, PMID: 18631022)
• G. Magiorkinis, D. Paraskevis, H.A. Schmidt, and A. Hatzakis (2008) The phylogenetic information profile of HIV-1 and the degradation effect of recombination. Infect. Genet. Evol., 8, 139-145. (DOI: 10.1016/j.meegid.2007.11.002, PMID: 18093883)
• D. Mainz, I. Paulsen, I. Mainz, K. Weller, J. Kohl, and A. von Haeseler (2008) Knowledge Acquisition Focused Cooperative Development of Bio-Ontologies - A Case Study with BIO2Me. In M. Elloumi, J. Küng, M. Linial, R.F. Murphy, K. Schneider, T. Cristian (eds.) Bioinformatics Research and Development., 258-272, Springer, Berlin. (ISBN 978-3-540-70598-7)
• I. Mainz, K. Weller, I. Paulsen, D. Mainz, J. Kohl, and A. von Haeseler (2008) Ontoverse: Collaborative Ontology Engineering for the Life Sciences. Inform. Wiss. Praxis, 2, 91-99. (online access)
• A. Rohrbeck, J. Neukirchen, M. Rosskopf, G.G. Pardillos, H. Geddert, A. Schwalen, H.E. Gabbert, A. von Haeseler, G. Pitschke, M. Schott, R. Kronenwett, R. Haas, Rainer U.-P. Rohr (2008) Gene expression profiling for molecular discrimination and characterization of laser captured primary lung cancers. J. Translat. Med., 6, 69. (DOI: 10.1186/1479-5876-6-69)
• H. Schabauer, J. Zottl, A. von Haeseler, W.N. Gansterer, and H.A. Schmidt (2008) Phylogenetic Quality Assessment for Campus Grids. In J. Küng, K. Schneider, R. Wagner (eds.) BIRD'08 -- 2nd International Conference on Bioinformatics and Development (Articles on Poster Presentations)., Schriftenreihe Informatik, 109-114, Trauner Verlag, Linz. (ISBN 978-3-85499-422-0)
• J. Shi, J. Franklin, J. Yelinek, I. Ebersberger, G. Warren, and C. Y. He (2008) Centrin4 coordinates cell and nuclear division in Trypanosoma brucei. J. Cell Sci., 121, 3062-3070. (DOI: 10.1242/jcs.030643, PMID: 18768932)
• L. S. Vinh and A. von Haeseler (2008) Bookreview on "Computational Molecular Evolution by Ziheng Yang, 2006, Oxford University Press, Oxford". Syst. Biol., 56, 1024-1026. (DOI: 10.1080/10635150701752532, PMID: 18066933)

2007

• R. Bredemeier, T. Schlegel, F. Ertel, A. Vojita, L. Borissenko, M.T. Bohnsack, M. Groll, A. von Haeseler, and E. Schleiff (2007) Functional and phylogenetic properties of the pore forming β-barrel transporter of the Omp85 family. J. Biol. Chem., 282, 1882-1890. (DOI: 10.1074/jbc.M609598200, PMID: 17088246)
• M. Dehmer and F. Emmert-Streib (2007) Comparing large graphs efficiently by margins of feature vectors. Appl. Math. Comput., 188, 1699-1710. (DOI: 10.1016/j.amc.2006.11.185)
• M. Dehmer and F. Emmert-Streib (2007) Structural similarity of directed universal hierarchical graphs: A low computational complexity approach. Appl. Math. Comput., 194, 7-20. (DOI: 10.1016/j.amc.2007.04.006)
• E. Diaz-Blanco, I. Bruns, F. Neumann, J.C. Fischer, T. Graef, M. Rosskopf, B. Brors, S. Pechtel, S. Bork, A. Koch, A. Baer, U.-P. Rohr, G. Kobbe, A. von Haeseler, N. Gattermann, and R. Kronenwett (2007) Molecular signature of CD34+ hematopoietic stem and progenitor cells of patients with CML in chronic phase. Leukemia, 21, 494-504. (DOI: 10.1038/sj.leu.2404549, PMID: 17252012)
• I. Ebersberger, P. Galgoczy, S. Taudien, S. Taenzer, M. Platzer, and A. von Haeseler (2007) Mapping human genetic ancestry. Mol. Biol. Evol., 24, 2266-2276. (DOI: 10.1093/molbev/msm156, PMID: 17660505)
• I. Ebersberger, A. von Haeseler, and H.A. Schmidt (2007) Phylogeny Reconstruction. In T. Lengauer (ed.) Bioinformatics: From Genomes to Therapies 83-128, Wiley-VCH, Weinheim. (ISBN 978-3-527-31278-8)
• M.R. Eckert, T. Gesell, M. Grabner, A. Gruber, K. Gonzales, I.L. Hofacker, A. von Haeseler, and E. Charpentier (2007) A bioinformatic screen reveals novel small noncoding RNAs in Streptococcus pyogenes FEBS J., 274, 189. (DOI: 10.1111/j.0014-2956.2007.05861.x)
• F. Emmert-Streib and M. Dehmer (2007) Information theoretic measures of UHG graphs with low computational complexity. Appl. Math. Comput., 190, 1783-1794. (DOI: 10.1016/j.amc.2007.02.095)
• W. Glaser, T. Schwarzmüller, K. Kuchler, and M. Grabner (2007) Automated generation of PCR primers for a genomewide knock-out in Candida glabrata FEBS J., 274, 246. (DOI: 10.1111/j.0014-2956.2007.05861_5.x)
• T. Laubach and A. von Haeseler (2007) TreeSnatcher: Coding trees from images. Bioinformatics, 23, 3384-3385. (DOI: 10.1093/bioinformatics/btm438, PMID: 17893085)
• S. Linz, A. Radtke, A. von Haeseler (2007) A maximum likelihood framework to measure horizontal gene transfer. Mol. Biol. Evol., 24, 1312-1319. (DOI: 10.1093/molbev/msm052, PMID: 17374878)
• W. Löffelhardt, A. von Haeseler, E. Schleiff (2007) The β-barrel shaped polypeptide transporter, an old concept for precursor protein transfer across membranes. Symbiosis, 44, 33-42.
• S. Piskacek, M. Gregor, M. Nemethova, M. Grabner, P. Kovarik and M. Piskacek (2007) Nine-amino-acid transactivation domain: Establishment and prediction utilities. Genomics, 89, 756-768. (DOI: 10.1016/j.ygeno.2007.02.003, PMID: 17467953)
• J.A. Pospisilik, C. Knauf, N. Joza, P. Benit, M. Orthofer, P.D. Cani, I. Ebersberger, T. Nakashima, R. Sarao, G. Neely, H. Esterbauer, A. Kozlov, C.R. Kahn, G. Kroemer, P. Rustin, R. Burcelin, and J.M. Penninger (2007) Targeted deletion of AIF decreases mitochondrial oxidative phosphorylation and protects from obesity and diabetes. Cell, 131, 476-491. (DOI: 10.1016/j.cell.2007.08.047, PMID: 17981116)
• F. Roeding, S. Hagner-Holler, H. Ruhberg, I. Ebersberger, A. von Haeseler, M. Kube, R. Reinhardt, and Burmester, T. (2007) EST sequencing of Onychophora and phylogenomic analysis of Metazoa. Mol. Phylogenet. Evol., 45, 942-951. (DOI: 10.1016/j.ympev.2007.09.002, PMID: 17933557)
• U. Schauer, C. Lorenz, T. Gesell, C. Waldsich, A. von Haeseler, and R. Schroeder (2007) Characterization of high affinity Hfq binding sites FEBS J., 274, 86. (DOI: 10.1111/j.0014-2956.2007.05861_1.x)
• T. Schlegel, O. Mirus, A. von Haeseler and E. Schleiff (2007) The tetratricopeptide repeats of receptors involved in protein translocation across membranes. Mol. Biol. Evol., 24, 2763-2774. (DOI: 10.1093/molbev/msm211, PMID: 17905998)
• H.A. Schmidt and A. von Haeseler (2007) Maximum Likelihood Analysis using TREE-PUZZLE. (revised version) In A.D. Baxevanis, D.B. Davison, R.D.M. Page, G. Stormo, and L. Stein (eds.) Current Protocols in Bioinformatics, Unit 6.6, pages 6.6.1-6.6.23, Wiley and Sons, New York. (DOI: 10.1002/0471250953.bi0606s17, PMID: 18428792, ISBN 0-471-25093-7, CP online)
• H.A. Schmidt, A. von Haeseler, and J. Buschbom (2007) pIPHULA - Parallel Inference of Population Parameters Using a Likelihood Approach. Bioinformatics, 23, 2636-2637. (free reprint, DOI: 10.1093/bioinformatics/btm391, PMID: 17698495)

2006

• I. Bruns, U. Steidl, J.C. Fischer, S. Raschke, G. Kobbe, R. Fenk, M. Rosskopf, S. Pechtel, U.-P. Rohr, A. von Haeseler, P. Wernet, D. Tenen, R. Haas, and R. Kronenwett (2006) Meeting Abstract: Pegylated G-CSF Mobilizes CD34+ Cells with Different Stem and Progenitor Cell Subsets and Distinct Functional Properties in Comparison with Unconjugated G-CSF. Blood, 108, 3382. (Journal site)
• F. Emmert-Streib and M. Dehmer (2006) Topological Mappings between Graphs, Trees and Generalized Trees. Appl. Math. Comput., 186, 1326-1333. (DOI: 10.1016/j.amc.2006.07.162)
• F. Emmert-Streib, M. Dehmer, and C. Seidel (2006) Influence of Prior Information on the Reconstruction of the Yeast Cell Cycle from Microarray Data. Proceedings of the Workshop 'Gene Networks: Theory and Application' at the 2006 International Conference on Bioinformatics and Computational Biology (BIOCOMP'06). 477-482. (PDF)
• F. Emmert-Streib and M. Dehmer (2006) Theoretical Bounds for the Number of inferable Edges in sparse Random Networks. Proceedings of the Workshop 'Gene Networks: Theory and Application' at the 2006 International Conference on Bioinformatics and Computational Biology (BIOCOMP'06). 477-482. (PDF)
• T. Gesell and A. von Haeseler (2006) In silico sequence evolution with site-specific interactions along phylogenetic trees. Bioinformatics, 22, 716-722. (DOI: 10.1093/bioinformatics/bti812, PMID: 16332711)
• C. Guder, S. Pinho, T.G. Nacak, H.A. Schmidt, B. Hobmayer, C. Niehrs, and T.W. Holstein (2006) An ancient Wnt-Dickkopf antagonism in Hydra. Development, 133, 901-911. (DOI: 10.1242/dev.02265, PMID: 16452091)
• B. Kilian, H. Özkan, J. Kohl, A. von Haeseler, O. Deusch, A. Brandolini, C. Yucel, W. Martin, and F. Salamini (2006) Haplotype structure at seven barley genes: relevance to gene pool bottlenecks, phylogeny of ear type and site of barley domestication. Mol. Genet. Genomics, 275, 230-241. (DOI: 10.1007/s00438-006-0136-6, PMID: 16758198)
• J. Kohl, I. Paulsen, T. Laubach, A. Radtke, and A. von Haeseler (2006) HvrBase++: A phylogenetic database for primate species. Nucl. Acids Res., 34, D700-D704. (DOI: 10.1093/nar/gkj030, PMID: 16381963)
• J. Krause, P. H. Dear, J. L. Pollack, M. Slatkin, H. Spriggs, I. Barnes, A. Lister, I. Ebersberger, S. Pääbo, and M. Hofreiter (2006) Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae. Nature, 439, 724-727. (DOI: 10.1038/nature04432)
• B.Q. Minh, S. Klaere, and A. von Haeseler (2006) Phylogenetic Diversity within Seconds. Syst. Biol., 55, 769-773. (DOI: 10.1080/10635150600981604)
• B.Q. Minh, L.S. Vinh, H.A. Schmidt, and A. von Haeseler (2006) Large Maximum Likelihood Trees. Proceedings of the NIC Symposium 2006. 357-365, Forschunungszentrum Jülich, Germany. (free reprint, ISBN 3-00-017351-X)
• I. Paulsen and A. von Haeseler (2006) INVHOGEN: A database of homologous invertebrate genes. Nucl. Acids Res., 34, D349-D353. (DOI: 10.1093/nar/gkj100, PMID: 16381884)
• E. Petzold, D. Merkle, M. Middendorf, A. von Haeseler, and H.A. Schmidt (2006) Phylogenetic Parameter Estimation on COWs. In A.Y. Zomaya (ed.) Parallel Computing for Bioinformatics and Computational Biology 347-368, Wiley and Sons, New York. (ISBN 0-471-71848-3)
• S. Taudien, I. Ebersberger, Gernot Glöckner, and Mattias Platzer (2006) Should the draft chimpanzee sequence be finished? Trends Genet., 22, 122-125. (DOI: 10.1016/j.tig.2005.12.007, PMID: 16406850)

2005

• J. Buschbom and A. von Haeseler (2005) Introduction to applications of the likelihood function in molecular evolution. In R. Nielsen (ed.) Statistical Methods in Molecular Evolution 25-44, Springer, New York. (ISBN: 0-387-22333-9)
• I. Ebersberger, J. Knobloch, and W. Kunz (2005) Cracks in the shell: zooming in on eggshell formation in the human parasite Schistosoma mansoni. Dev. Genes Evol., 215, 261-267. (DOI: 10.1007/s00427-005-0467-z, PMID: 15747129)
• I. Ebersberger and M. Meyer (2005) A genomic region evolving toward different GC contents in humans and chimpanzees indicates a recent and regionally limited shift in the mutation pattern. Mol. Biol. Evol., 22, 1240-1245. (DOI: 10.1093/molbev/msi109, PMID: 15703238)
• R. Fleißner, D. Metzler, and A. von Haeseler (2005) Simultaneous statistical multiple alignment and phylogeny reconstruction. Syst. Biol., 54, 548-561. (DOI: 10.1080/10635150590950371, PMID: 16085574)
• P. Khaitovich, S. Pääbo, and G. Weiss (2005) Toward a Neutral Evolutionary Model of Gene Expression. Genetics, 170, 929-939. (DOI: 10.1534/genetics.104.037135, PMID: 15834146)
  
• J. Kohl and A. von Haeseler (2005) Bookreview on "Perl Programming for Biologists by D.C. Jamison. Wiley-Liss, Chichester, 2003". Biometrics, 61, 316. (DOI: 10.1111/j.0006-341X.2005.20050217-2_6.x)
  
• A. Kusserow, K. Pang, C. Sturm, M. Hrouda, J. Lentfer, H.A. Schmidt, U. Technau, A. von Haeseler, B. Hobmayer, M.Q. Martindale, and T.W. Holstein (2005) Unexpected complexity of Wnt gene family in a sea anemone. Nature, 433, 156-160. (DOI: 10.1038/nature03158, PMID: 15650739)
  Press releases by FZ Jülich (follow-ups: Bionity, Radio-Luma, Google search), Heidelberg University
• D. Metzler, R. Fleißner, A. Wakolbinger, and A. von Haeseler (2005) Stochastic insertion-deletion processes and statistical sequence alignment. In A. Greven and D. Deuschel (eds.) Interacting Stochastic Systems, 247-267, Springer, Heidelberg/Berlin. (ISBN: 3-540-23033-5)
• B.Q. Minh, L.S. Vinh, A. von Haeseler, and H.A. Schmidt (2005) pIQPNNI -- Parallel Reconstruction of Large Maximum Likelihood Phylogenies. Bioinformatics, 21:3794-3796. (free reprint, DOI: 10.1093/bioinformatics/bti594, PMID: 16046495)
• S. Moslavac, O. Mirus, R. Bredemeier, J. Soll, A. von Haeseler, and E. Schleiff (2005) Conserved pore-forming regions in polypeptide-transporting proteins. FEBS Journal (formerly: European Journal of Biochemistry), 272, 1367-1378. (DOI: 10.1111/j.1742-4658.2005.04569.x, PMID: 15752354)
• H. Oota, B. Pakendorf, G. Weiss, A. von Haeseler, S. Pookajorn, W. Settheetham-Ishida, D. Tiwawech, T. Ishida, and M. Stoneking (2005) Recent Origin and Cultural Reversion of a Hunter-Gatherer Group. PLoS Biology, 3, e71. (DOI: 10.1371/journal.pbio.0030071, PMID: 15736978)
• L.S. Vinh, H.A. Schmidt, and A. von Haeseler (2005) PhyNav: A novel approach to reconstruct large phylogenies. In C. Weihs and W. Gaul (eds.) Classification, the Ubiquitous Challenge Series Studies in Classification, Data Analysis, and Knowledge Organization, 386-393, Springer, Heidelberg/New York.
• L. S. Vinh and A. von Haeseler (2005) Shortest triplet clustering: reconstructing large phylogenies using representative sets. BMC Bioinform., 6, 92. (DOI: 10.1186/1471-2105-6-92, PMID: 15819989)