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Publication List

This list contains papers from our bioinformatics group since it was set up in December 2002. For earlier publications from our group members, please visit our personal home pages.

2020

• M. Blanke, B. Morgenstern (2020)
  Phylogenetic placement of short reads without sequence alignment
  bioRxiv doi:10.1101/2020.10.19.344986
  
• M. Hosseini, D. Pratas, B Morgenstern, A.J. Pinho (2020)
  Smash++: an alignment-free and memory-efficient tool to find genomic rearrangements
  GigaScience 9, giaa048
• M. Leonard, A. Kühn, R. Harting, I. Maurus, A. Nagel, J. Starke, H. Kusch, O. Valerius, K. Feussner, I. Feussner, A. Kaever, M. Landesfeind, B. Morgenstern, D. Becher, M. Hecker, S. Braus-Stromeyer, J. Kronstad, G. Braus (2020)
  Verticillium longisporum elicits media-dependent secretome responses with capacity to distinguish between plant-related environments
  Frontiers in Microbiology 11, 1876
• S. Röhling, A. Linne, J. Schellhorn, M. Hosseini, T. Dencker, B. Morgenstern (2020)
  The number of k-mer matches between two DNA sequences as a function of k and applications to estimate phylogenetic distances
  PLOS ONE 15, e0228070
• B. Morgenstern (2020)
  Sequence Comparison without Alignment: The SpaM approaches
  In: K. Katoh (ed.) Multiple Sequence Alignment (to appear 12/2020)
  Book series Methods in Molecular Biology, Springer. Preprint available here
• B. Morgenstern (2020)
  Fake scientists on editorial boards can significantly enhance the visibility of junk journals.
  In: Mario Biagioli and Alexandra Lippman (Eds.)
  Gaming the Metrics: Misconduct and Manipulation in Academic Research, MIT Press, pp. 201-211.
  Book freely available as PDF, follow link "Open Access" in the middle of this page. Slides of my talk available here
• T. Dencker, C.-A. Leimeister, M. Gerth, C. Bleidorn, S. Snir, B. Morgenstern (2020)
  Multi-SpaM: a Maximum-Likelihood approach to Phylogeny reconstruction using Multiple Spaced-word Matches
  and Quartet Trees
  NAR Genomics and Bioinformatics 2, lqz013

2019

• A. Chakraborty, B. Morgenstern, S. Bandyopadhyay (2019)
  S-conLSH: Alignment-free gapped mapping of noisy long reads
  bioRxiv, doi:10.1101/801118v1
  
• A.K. Lau, S. Dörrer, C.-A. Leimeister, C. Bleidorn, B. Morgenstern (2019)
  Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage
  BMC Bioinformatics 20, 638 (Proceedings of RECOMB-CG 2019)
• B. Morgenstern (2019)
  Der Metrik-Wahn
  Laborjournal 7-8, 22-25
• A. Zielezinski, H.Z. Girgis, G. Bernard, C.-A. Leimeister, K. Tang, T. Dencker, A.K. Lau, S. Röhling, J. Choi, M.S. Waterman, M. Comin, S.-H. Kim, S. Vinga, J.S. Almeida, C.X. Chan, B. James, F. Sun, B. Morgenstern, W.M. Karlowski (2019)
  Benchmarking of alignment-free sequence comparison methods
  Genome Biology 20, 144
  
• C.-A. Leimeister, J. Schellhorn, S. Dörrer, M. Gerth, C. Bleidorn, B. Morgenstern (2019)
  Prot-SpaM: Fast alignment-free phylogeny reconstruction based on whole-proteome sequences
  GigaScience 8, giy148
  
• C.-A. Leimeister, T. Dencker, B. Morgenstern (2019)
  Accurate multiple alignment of distantly related genome sequences using Filtered Spaced Word Matches as anchor points
  Bioinformatics 35, 211-218

2018

• F. Wemheuer, J.-A. Taylor, R. Daniel, E. Johnston, P. Meinicke, T. Thomas, B. Wemheuer (2018)
  Tax4Fun2: a R-based tool for the rapid prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene marker gene sequences
  bioRxiv, 490037
  
• T. Dencker, C.-A. Leimeister, M. Gerth, C. Bleidorn, S. Snir, B. Morgenstern (2018)
  Multi-SpaM: a Maximum-Likelihood approach to Phylogeny reconstruction based on Multiple Spaced-Word Matches
  In: M. Blanchette, A. Ouangraoua (Eds.),
  Comparative Genomics, LNBI 11183, Springer, Proc. RECOMB-CG 2018, pp. 227-241.
  Preprint: arXiv:1803.09222 [q-bio.PE]
  

2017

• B. Morgenstern (2017)
  Virtual editors can significantly improve the visibility of junk journals - a case study.
  Talk at Gaming Metrics: Innovation & Surveillance in Academic Misconduct, UC Davis.
  
• B. Morgenstern, S. Schöbel, C.-A. Leimeister (2017)
  Phylogeny reconstruction based on the length distribution of k-mismatch common substrings
  Algorithms for Molecular Biology 12, 27
• A. Sczyrba, P. Hofmann, P. Belmann, D. Koslicki, S. Janssen, J. Droge, I. Gregor, S. Majda, J. Fiedler, E. Dahms, A. Bremges, A. Fritz, R. Garrido-Oter, T. S. Jorgensen, N. Shapiro, P. D. Blood, A. Gurevich, Y. Bai, D. Turaev, M. Z. DeMaere, R. Chikhi, N. Nagarajan, C. Quince, F. Meyer, M. Balvociute, Monika L. H. Hansen, S. J. Sorensen B. K. H. Chia, B. Denis, J.L. Froula, Z. Wang, R. Egan, D. Don Kang, J.J. Cook, C. Deltel, M. Beckstette, C. Lemaitre, P. Peterlongo, G. Rizk, D. Lavenier, Y. W. Wu, S. W. Singer, C. Jain, M. Strous, H. Klingenberg, P. Meinicke, M. D. Barton, T. Lingner, H. H. Lin, Y. C. Liao, G. G. Z. Silva, D. A. Cuevas, R. A. Edwards, S. Saha, V. C. Piro, B. Y. Renard, M. Pop, H. P. Klenk, M. Goker, N. C. Kyrpides, T. Woyke, J. A. Vorholt, P. Schulze-Lefert, E. M. Rubin, A. E. Darling, T. Rattei, A. C. McHardy (2017)
  Critical Assessment of Metagenome Interpretation - a benchmark of metagenomics software
  Nature Methods 14, 1063-1071
• H. Klingenberg, P. Meinicke (2017)
  How to normalize metatranscriptomic count data for differential expression analysis
  PeerJ 7:e3859
• I.J. Swierzy, U. Händel, A. Kaever, M. Jarek, M. Scharfe, D. Schlüter & C.G.K. Lüder (2017)
  Divergent co-transcriptomes of different host cells infected with Toxoplasma gondii reveal cell type-specific host-parasite interactions
  Scientific Reports 7, 7229
• C. Braun, A. Thürmer, R. Daniel, A.-K. Schultz, I. Bulla, H. Schirrmeier, D. Mayer, A. Neubert, C. Czerny (2017)
  Genetic Variability of Myxoma Virus Genomes
  Journal of Virology 91, e01570-16
• C.-A. Leimeister, S. Sohrabi-Jahromi, B. Morgenstern (2017)
  Fast and Accurate Phylogeny Reconstruction using Filtered Spaced-Word Matches
  Bioinformatics 33, 971-979

2016

• C.-A. Leimeister, L. Hahn, B. Morgenstern (2016)
  Fast alignment-free phylogeny reconstruction using spaced words
  Invited talk, SeqBio 2016, Nantes
• C. Nötzel, T. Lingner, H. Klingenberg, S. Thoms (2016)
  Identification of New Fungal Peroxisomal Matrix Proteins and Revision of the PTS1 Consensus
  Traffic 17, 1110-1124
• L. Hahn, C.-A. Leimeister, R. Ounit, S. Lonardi, B. Morgenstern (2016)
  rasbhari: optimizing spaced seeds for database searching, read mapping and alignment-free sequence comparison
  PLOS Computational Biology 12, e1005107
  
• S.K. Tschirner, H. Bähre, A. Kaever, E.H. Schneider, E. H., R. Seifert and V. Kaever (2016)
  Non-targeted metabolomics by high resolution mass spectrometry in HPRT knockout mice.
  Life Sciences 156, 68-73.

2015

• C.-A. Leimeister, M. Boden, Lindner, S. Horwege, B. Morgenstern (2015)
  Fast alignment-free sequence comparison using spaced-word frequencies (abstract)
  German Conference on Bioinformatics (GCB15), highlight talk
• C. Schmitt-Engel, D. Schultheis, J. Schwirz, N. Ströhlein, N. Troelenberg, U. Majumdar, V.A. Dao, D. Grossmann, T. Richter, M. Tech, J. Dönitz, L. Gerischer, M. Theis, I. Schild, J. Trauner, N. Koniszewski, E. Küster, S. Kittelmann, Y. Hu, S. Lehmann, J. Siemanowski, J. Ulrich, K. Panfilio, R. Schröder, B. Morgenstern, M. Stanke, F. Buchholz, M. Frasch, S. Roth, E. Wimmer, M. Schoppmeier, M. Klingler, and G. Bucher (2015)
  The iBeetle large scale RNAi screen reveals novel gene functions for insect development and physiology
  Nature Communications 6, 7822
• A. Kaever, M. Landesfeind, K. Feussner, A. Mosblech, I. Heilmann, B. Morgenstern, I. Feussner, P. Meinicke (2015)
  MarVis-Pathway: integrative and exploratory pathway analysis of non-targeted metabolomics data
  Metabolomics 11, 764-777
• K.P. Aßhauer, B. Wemheuer, R. Daniel, P. Meinicke (2015)
  Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data
  Bioinformatics 31, 2882-2884
• B. Morgenstern, B. Zhu, S. Horwege, C.-A Leimeister (2015)
  Estimating evolutionary distances between genomic sequences from spaced-word matches
  Algorithms for Molecular Biology 10, 5
• P. Meinicke (2015)
  UProC: tools for ultra-fast protein domain classification
  Bioinformatics 31, 1382-1388

2014

• F. Schueren, T. Lingner, R. George, J. Hofhuis, C. Dickel, J, Gärtner, S. Thom (2014)
  Peroxisomal lactate dehydrogenase is generated by translational readthrough in mammals
  eLife 2014;3:e03640
• M. Landesfeind, P. Meinicke (2014)
  Predicting the functional repertoire of an organism from unassembled RNA-seq data
  BMC Genomics 15, 1003
• J. Dönitz, C. Schmitt-Engel, D, Grossmann, L, Gerischer, M. Tech, M. Schoppmeier, M. Klingler, G. Bucher (2014)
  iBeetle-Base: a database for RNAi phenotypes in the red flour beetle Tribolium castaneum
  Nuc. Acids Research 43, D720-D725
• T. Lingner, P. Meinicke (2014)
  Characterizing metagenomic novelty with unexplained protein domain hits
  GCB 2014: 69-78
• K.P. Aßhauer, H. Klingenberg, T. Lingner, P. Meinicke (2014)
  Exploring Neighborhoods in the Metagenome Universe>
  International Journal of Molecular Sciences 15, 12364-12378
• B. Morgenstern, B. Zhu, S. Horwege, C.-A. Leimeister (2014)
  Estimating evolutionary distances from spaced-word matches
  In: Proceedings WABI 2014, Lecture Notes in Bioinformatics 8701, pp. 161-173
  Springer Verlag
• I. Bulla, A.-K. Schultz, C. Chesneau, T. Mark, F. Serea (2014)
  A model-based information sharing protocol for profile hidden Markov models used for HIV-1 recombination detection
  BMC Bioinformatics 15 ,205
• H. Nacke, C. Fischer, A. Thürmer, P. Meinicke, R. Daniel (2014)
  Land use type significantly affects microbial gene transcription in soil
  Microbial Ecology 67, 919-930
• C.-A. Leimeister, B. Morgenstern (2014)
  kmacs: the k-Mismatch Average Common Substring Approach to alignment-free sequence comparison
  Bioinformatics 30, 2000-2008
• C.-A. Leimeister, M. Boden, S. Horwege, S. Lindner, B. Morgenstern (2014)
  Fast alignment-free sequence comparison using spaced-word frequencies
  Bioinformatics 30, 1991-1999
• S. Horwege, S. Lindner, M. Boden, K. Hatje, M. Kollmar, C.-A. Leimeister, B. Morgenstern (2014)
  Spaced words and kmacs: fast alignment-free sequence comparison based on inexact word matches
  Nuc. Acids Research 42, W7-W11
• M. Landesfeind, A. Kaever, K. Feussner, C. Thurow, C. Gatz, I. Feussner, P. Meinicke (2014)
  Integrative study of Arabidopsis thaliana metabolomic and transcriptomic data with the interactive MarVis-Graph software.
  PeerJ 2:e239
• A. Kaever, M. Landesfeind, K. Feussner, B. Morgenstern, I. Feussner, P. Meinicke (2014)
  Meta-Analysis of Pathway Enrichment: Combining Independent and Dependent Omics Data Sets
  PLOS ONE, 9(2): e89297
• C.E. Hoppenau, V.-T. Tran, H. Kusch, K.P. Aßhauer, M. Landesfeind, P. Meinicke, B. Popova, S.A. Braus-Stromeyer, G.H. Braus(2014)
  Verticillium dahliae VdTHI4, involved in thiazole biosynthesis, stress response and DNA repair functions, is required for vascular disease induction in tomato.
  Environmental and Experimental Botany 108, 14-22
• V.T. Tran, S.A. Braus-Stromeyer, H. Kusch, M. Reusche, A. Kaever, A. Kühn, O. Valerius, M. Landesfeind, K. Aßhauer, M. Tech, K. Hoff, T.P. Centeno, M. Stanke, V. Lipka, G.H. Braus (2014)
  Verticillium transcription activator of adhesion Vta2 suppresses microsclerotia formation and is required for systemic infection of plant roots
  New Phytologist 202, 565-581
• S. König, K. Feussner, A. Kaever, M. Landesfeind, C. Herrfurth, C. Thurow, C. Gatz, P. Karlovsky, A. Polle, I. Feussner (2014)
  Soluble phenylpropanoids are involved in the defense response of Arabidopsis thaliana against Verticillium longisporum
  New Phytologist 202, 823-837
• J. Gamir, V. Pastor, A. Kaever, M. Cerezo, V. Flors (2014)
  Targeting novel chemical and constitutive primed metabolites against Plectosphaerella cucumerina
  Plant Journal 78, 227-240
• B. Morgenstern (2014)
  Multiple sequence alignment with DIALIGN (book chapter)
  In: Multiple Sequence Alignment Methods, pp. 191-202
  Humana Press
• G. Wörheide, T. Nosenko, F. Schreiber, B. Morgenstern (2014)
  Progress and perspectives of the deep non-bilaterian phylogeny, with focus on sponges (book chapter)
  In: Deep Metazoan Phylogeny: The Backbone of the Tree of Life, pp. 9-22
  De Gruyter

2013

• H. Klingenberg, R. Martinjak, F. O. Glöckner, R. Daniel, T. Lingner, P. Meinicke (2013)
  Dinucleotide distance histograms for fast detection of rRNA in metatranscriptomic sequences
  Proceedings German Conference on Bioinformatics (GCB'13), 80-89 (regular paper).
• K. P. Aßhauer, P. Meinicke (2013)
  On the estimation of metabolic profiles in metagenomics
  Proceedings German Conference on Bioinformatics (GCB'13), 1-13 (regular paper).
• T. Beißbarth, M. Kollmar, A. Leha, B. Morgenstern, A.-K. Schultz, S. Waack, E. Wingender (eds.):
  Proc. German Conference on Bioinformatics 2013, GCB 2013
  OASICS ISBN 978-3-939897-59-0, Schloss Dagstuhl - Leibniz-Zentrum für Informatik 2013
• M. Boden, M. Schöneich, S. Horwege, S. Lindner, C. Leimeister, B. Morgenstern (2013)
  Alignment-free sequence comparison with spaced k-mers
  Proceedings German Conference on Bioinformatics (GCB'13), 21-31 (regular paper).
• A. Kaever, M. Landesfeind, K. Feussner, I. Feussner, P. Meinicke (2013)
  Metabolite Clustering and Visualization of Mass Spectrometry Data Using One-Dimensional Self-Organizing Maps (book chapter)
  In: The Handbook of Plant Metabolomics, pp. 273 - 287
  Wiley-VCH
• L. Al Ait, Z. Yamak, B. Morgenstern (2013)
  DIALIGN at GOBICS - multiple sequence alignment using various sources of external information
  Nuc. Acids Research 41, W3-W7
• E. Corel (2013)
  Gérard-Levelt membranes
  Journal of Algebraic Combinatorics 37, 757-776.
• H. Klingenberg, K.P. Aßhauer, T. Lingner, P. Meinicke (2013)
  Protein signature-based estimation of metagenomic abundances including all domains of life and viruses
  Bioinformatics 29, 973-980.

2012

• L. Al Ait, E. Corel, B. Morgenstern (2012)
  Using protein-domain information for multiple sequence alignment
  Proc. IEEE 12th Int. Conf. on BioInformatics and BioEngineering (BIBE 12), pp. 164-168
• J. Gerke, O. Bayram, K. Feussner, M. Landesfeind, E. Shelest, I. Feussner, G. H. Braus (2012)
  Breaking the silence: protein stabilization uncovers silenced biosynthetic gene clusters in the fungus Aspergillus nidulans.
  Applied and Environmental Microbiology 78(23) pp.8234-8244
• S. König, K. Feussner, M. Schwarz, A. Kaever, T. Iven, M. Landesfeind, P. Ternes, P. Karlovsky, V. Lipka, I. Feussner (2012)
  Arabidopsis mutants of sphingolipid fatty acid alpha-hydroxylases accumulate ceramides and salicylates
  New Phytologist 196(4): 1086-1097.
• G. Didier, E. Corel, I. Laprevotte, A. Grossmann, C. Landès-Devauchele (2012)
  Variable length local decoding and alignment-free sequence comparison
  Theoretical Computer Science 462, 1 - 11
• S. Reumann, D. Buchwald, T. Lingner (2012)
  PredPlantPTS1: A Web Server for the Prediction of Plant Peroxisomal Proteins.
  Frontiers in Plant Science 3:194.
• L. Danielsen, A. Thürmer, P. Meinicke, M. Buée, E. Morin, F. Martin, G. Pilate, R. Daniel, A. Polle, M. Reich (2012)
  Fungal soil communities in a young transgenic poplar plantation form a rich reservoir for fungal root communities.
  Ecology and Evolution, 2(8):1935-1948
• A. Kaever, M. Landesfeind, M. Possienke, K. Feussner, I. Feussner, P. Meinicke (2012)
  MarVis-Filter: Ranking, Filtering, Adduct and Isotope Correction of Mass Spectrometry Data.
  Journal of Biomedicine and Biotechnology, 2012:263910
• G. Chowdhary, A.R. Kataya, T. Lingner, S. Reumann (2012)
  Non-canonical peroxisome targeting signals: identification of novel PTS1 tripeptides and characterization of enhancer elements by computational permutation analysis.
  BMC Plant Biology 12: 142.
• A.-K. Schultz, I. Bulla, M. Abdou-Chekaraou, E. Gordien, B. Morgenstern, F. Zoulim, P. Dény, M. Stanke (2012)
  jpHMM: Recombination analysis in viruses with circular genomes such as the hepatitis B virus
  Nuc. Acids Res. 40, W193-W198
• T. Lingner, A.R.A. Kataya, S. Reumann (2012)
  Experimental and statistical post-validation of positive example EST sequences carrying peroxisome targeting signals type 1 (PTS1)
  Plant Signaling and Behaviour: Vol. 7: Iss. 2, 263-268
• U. Großkathöfer, A. Sadeghipour, T. Lingner, P. Meinicke, T. Hermann, S. Kopp (2012)
  Low Latency Recognition and Reproduction of Natural Gesture Trajectories
  ICPRAM (2) 2012: 154-161.
• I. Bulla, A.-K. Schultz, P. Meinicke (2012)
  Improving Hidden Markov Models for Classification of Human Immunodeficiency Virus-1 Subtypes through Linear Classifier Learning
  Statistical Applications in Genetics and Molecular Biology: Vol. 11: Iss. 1, Article 1

2011

• A. Djamei, K. Schipper, F. Rabe, A. Ghosh, V. Vincon, J. Kahnt, S. Osorio, T. Tohge, A.R. Fernie, I. Feussner, K. Feussner, P. Meinicke, Y.-D. Stierhof, H. Schwarz, B. Macek, M. Mann, R. Kahmann (2011)
  Metabolic priming by a secreted fungal effector
  Nature 478, 395-398
• T. Lingner, K. P. Aßhauer, F. Schreiber, P. Meinicke (2011)
  CoMet -- a web server for comparative functional profiling of metagenomes
  Nucleic Acids Research 39, W518-W523
• P. Meinicke, K.P. Aßshauer, T Lingner (2011)
  Mixture models for analysis of the taxonomic composition of metagenomes
  Bioinformatics 27, 1618-1624.
• C.V.C. Truong, L.F. Groeneveld, B. Morgenstern, E. Groeneveld (2011)
  MolabIS - An Integrated Information System for Storing and Managing Molecular Genetics Data
  BMC Bioinformatics 12, 425
• T. Unterthiner, A.-K. Schultz, J. Bulla, B. Morgenstern, M. Stanke, I. Bulla (2011)
  Detection of viral sequence fragments of HIV-1 subfamilies yet unknown
  BMC Bioinformatics 12, 93
• N. Rachfall, I. Heinemeyer, B. Morgenstern, O. Valerius, G. Braus (2011)
  5'TRU: Identification and analysis of translationally regulative 5'untranslated regions in amino acid starved yeast cells
  Mol Cell Proteomics 10: M110.003350.
• T. Lingner, A. R. Kataya, G. E. Antonicelli, A. Benichou, K. Nilssen, X.-Y. Chen, T. Siemsen, B. Morgenstern, P. Meinicke, S. Reumann (2011)
  Identification of novel plant peroxisomal targeting signals by a combination of machine learning methods and in vivo subcellular targeting analyses
  The Plant Cell 23, 1556-1572

2010

• K. Nahlik, M. Dumkow, O. Bayram, K. Helmstaedt, S. Busch, O. Valerius, J. Gerke, M. Hoppert, E. Schwier, L. Opitz, M. Westermann, S. Grond, K. Feussner, C. Goebel, A. Kaever, P. Meinicke, I. Feussner, G. H. Braus (2010)
  The COP9 signalosome mediates transcriptional and metabolic response to hormones, oxidative stress protection and cell wall rearrangement during fungal development
  Molecular Microbiology 78, 964-979
• P. Arensburger, ... , M. Stanke, ... , P.W. Atkinson [76 authors] (2010)
  Sequencing of Culex quinquefasciatus Establishes a Platform for Mosquito Comparative Genomics
  Science 330, 86-88
• A. P. Chan, J. Crabtree, Q. Zhao, H. Lorenzi, J. Orvis, D. Puiu, A. Melake-Berhan, K. M. Jones, J. Redman, G. Chen, E. B. Cahoon, M. Gedil, M. Stanke, B. J. Haas, J. R. Wortman, C. M. Fraser-Liggett, J. Ravel, P. D. Rabinowiczi (2010)
  Draft genome sequence of the oilseed species Ricinus communis
  Nature Biotechnology 28, 951-956
• T. Lingner, S. Mühlhausen, T. Gabaldon , C. Notredame and P. Meinicke (2010)
  Predicting phenotypic traits of prokaryotes from protein domain frequencies
  BMC Bioinformatics 11, 481
• F. Pitschi, C. Devauchelle, E. Corel (2010)
  Automatic detection of anchor points for multiple sequence alignment
  BMC Bioinformatics 11, 445
• M. Srivastava, ... , M. Stanke, ... , D. S. Rokhsar [33 authors] (2010)
  The Amphimedon queenslandica genome and the evolution of animal complexity
  Nature 466, 720-726
• E. Corel, F. Pitschi, I. Laprevotte, G. Grasseau, G. Didier, C. Devauchelle (2010)
  MS4 - Multi-Scale Selector of Sequence Signatures: an alignment-free method for the classification of biological sequences
  BMC Bioinformatics 11, 406
• J. E. Stajich, ... , M. Stanke, ... , P. J. Pukkila [49 authors] (2010)
  Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus)
  Proc. Natl. Acad. Sci. USA 107, 11889-11894
• A. R. Subramanian, S. Hiran, R. Steinkamp, P. Meinicke, E. Corel, B. Morgenstern (2010)
  DIALIGN-TX and multiple protein alignment using secondary structure information at GOBICS
  Nucleic Acids Res. 38, W19-W22.
• I. Bulla, A.-K. Schultz, F. Schreiber, M. Zhang, T. Leitner, B. Korber, B. Morgenstern, M. Stanke (2010)
  HIV Classification using Coalescent Theory
  Bioinformatics 26, 1409-1415.
• K. Hoff, M. Tech, T. Lingner, R. Daniel, B. Morgenstern, P. Meinicke (2010)
  Gene prediction in metagenomic fragments with Orphelia: a large scale machine learning approach (book chapter)
  In: Handbook of Molecular Microbial Ecology I: Metagenomic and Complementary Approaches.
  Wiley
• K. Pick, F. Schreiber, D. Erpenbeck, D.J. Jackson, P. Wrede, M. Wiens, A. Alié, B. Morgenstern, M. Manuel, G. Wörheide (2010)
  Broader phylogenomic sampling improves the accuracy of non-bilaterian relationships
  Mol. Biol. Evol. 27, 1983-1987.
• M. Zhang, B. Foley, A.-K. Schultz, J. Macke, I. Bulla, M. Stanke, B. Morgenstern, B. Korber and T. Leitner (2010)
  The role of recombination in the emergence of a complex and dynamic HIV epidemic
  Retrovirology 7:25
• The International Aphid Genomics Consortium (2010)
  Genome Sequence of the Pea Aphid Acyrthosiphon pisum
  PLOS Biology 8(2): e1000313
• E. Corel, F. Pitschi, B. Morgenstern (2010)
  A min-cut Algorithm for the Consistency Problem in Multiple Sequence Alignment
  Bioinformatics 26, 1015-1021 (PDF)
• F. Schreiber, P. Gumrich, R. Daniel, P. Meinicke (2010)
  Treephyler: fast taxonomic profiling of metagenomes
  Bioinformatics 26, 960-961
• The Nasonia Genome Working Group (2010)
  Functional and Evolutionary Insights from the Genomes of Three Parasitoid Nasonia Species
  Science 327, 343-348
• S. K. Behura, M. Stanke, C.A. Desjardins, J. H. Werren, D. W. Severson (2010)
  Comparative Analysis of Nuclear tRNA Genes of Nasonia vitripennis with Apis mellifera and Other Sequenced Arthropods
  Insect Mol. Biol. 19, Suppl. 1, 49-58

2009

• C. Göbel, K. Feussner, A. Kaever, P. Meinicke, B. Morgenstern, I. Feussner (2009)
  Identification of metabolic changes after wounding in Arabidopsis thaliana by an unbiased UPLC-MS approach
  Chemistry and Physics of Lipids 160, S26
• K. J. Hoff (2009)
  The effect of sequencing errors on metagenomic gene prediction
  BMC Genomics 10, 520
• P. Meinicke (2009)
  UFO: a web server for ultra-fast functional profiling of whole genome protein sequences
  BMC Genomics 10, 409
• E. Corel (2009)
  Exponents of a meromorphic connection on a compact Riemann surface.
  Pacific Journal of Mathematics 242, 259-279
• F. Schreiber, K. Pick, D. Erpenbeck, G. Wörheide, B. Morgenstern (2009)
  OrthoSelect: a protocol for selecting orthologous groups in phylogenomics
  BMC Bioinformatics 10, 219
• M. Berriman, ... , M. Stanke, ... , N.M. El-Sayed [56 authors] (2009)
  The Genome of the blood fluke Schistosoma mansoni
  Nature 460, 352-358. See also the press release about this paper (in German)
• F. Schreiber, G. Wörheide, B. Morgenstern (2009)
  OrthoSelect: A web server for selecting orthologous gene alignments from EST sequences
  Nucleic Acids Research 37, W185-W188
• A.-K. Schultz, M. Zhang, I. Bulla, T. Leitner, B. Korber, B. Morgenstern, M. Stanke (2009)
  jpHMM: Improving the reliability of recombination prediction in HIV-1
  Nucleic Acids Research 37, W647-W651
• K. J. Hoff, T. Lingner, P. Meinicke, M. Tech (2009)
  Orphelia: predicting genes in metagenomic sequencing reads
  Nucleic Acids Research 37, W101-W105
• C. Schmeisser, H. Liesegang, D. Krysciak, N. Bakkou, A. LeQuéré, A. Wollherr, I. Heinemeyer, B. Morgenstern, A. Pommerening-Röser, M. Flores, R. Palacios, S. Brenner, G. Gottschalk, R. Schmitz, W. Broughton, X. Perret, A. Strittmatter, W. Streit (2009)
  Rhizobium sp. NGR234 possesses a remarkable number of secretion systems
  Applied and Environmental Microbiology 75, 4035-4045.
• A. Kaever, T. Lingner, K. Feussner, C. Gobel, I. Feussner, P. Meinicke (2009)
  MarVis: a tool for clustering and visualization of metabolic biomarkers
  BMC Bioinformatics 10, 92.
• H. Philippe, R. Derelle, P. Lopez, K. Pick, C. Borchiellini, N. Boury-Esnault, J. Vacelet, E. Renard, E. Houliston, E. Quéinnec, C. Da Silva, P. Wincker, H. Le Guyader, S. Leys, D.J. Jackson, F. Schreiber , D. Erpenbeck, B. Morgenstern, G. Wörheide, and M. Manuel (2009)
  Phylogenomics restores traditional views on deep animal relationships
  Current Biology 19, 706-712.
• N. Rachfall, I. Heinemeyer, O. Valerius (2009)
  5'-TRUE: Die wahre Translation?
  BIOspektrum 2/09:169-171
• D. Sommerfeld, T. Lingner, M. Stanke, B. Morgenstern, H. Richter (2009)
  AUGUSTUS at MediGRID: Adaption of a Bioinformatics Application to Grid Computing for Efficient Genome Analysis
  Future Generation Computer Systems 25, 337 - 345.
• D. Krefting, J. Bart, K. Beronow, O. Dzhimova, J. Falkner, M. Hartung, A. Hoheisel, T. Knoch, T. Lingner, Y. Mohammed, K. Peter, E. Rahm, U. Sax, D. Sommerfeld, T. Steinke, T. Tolxdorff, F. Vinzens, M, Vossberg, A. Weisbecker (2009)
  MediGRID - A User Friendly Secured Grid Infrastructure
  Future Generation Computer Systems 25, 326 - 336.
• B. Morgenstern (2009)
  Local versus global alignment (book chapter)
  In: Sequence Alignment, pp. 39 - 53.
  University of California Press.

2008

• N.E. Castellana, S.H. Payne, Z. Shen, M. Stanke, V. Bafna, S.P. Briggs
  Discovery and revision of Arabidopsis genes by proteogenomics
  Proc. Natl. Acad. Sci. USA 105, 21034-21038.
• A. Dress, B. Morgenstern, H. Wagner
  Stability of Multiple Alignments and Phylogenetic Trees: An Analysis of ABC-Transporter Proteins
  Algorithms for Molecular Biology 3, 15.
• A. Weiberg, D. Pöhler, B. Morgenstern, P. Karlovsky
  Improved coverage of cDNA-AFLP by sequential digestion of immobilized cDNA
  BMC Genomics 9, 480.
• B. Bunselmeyer, H. Laubach, M. Schiller, M. Stanke, T. Luger, R. Brehler
  Incremental build-up food challenge (IBUF) - A new diagnostic approach to evaluate pseudoallergic reactions in chronic urticaria: A pilot study - Stepwise food challenge in chronic urticaria
  Clinical and Experimental Allergy 39, 116-126.
• I. Bulla, J. Bulla, O. Nenadić
  hsmm - an R Package for Analyzing Hidden Semi-Markov Models
  Computational Statistics and Data Analysis, in press.
• P. Meinicke, T. Lingner, A. Kaever, K. Feussner, C. Gobel, I. Feussner, P. Karlovsky, B. Morgenstern
  Metabolite-based clustering and visualization of mass spectrometry data using one-dimensional self-organizing maps
  Algorithms for Molecular Biology 3, 9.
• T. Lingner and P. Meinicke
  Fast target set reduction for large-scale protein function prediction: a multi-class multi-label machine learning approach
  WABI 2008, Lecture Notes in Bioinformatics, 5251, 198-209.
• O. Keller, F. Odronitz, M. Stanke, M. Kollmar, S. Waack
  Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species
  BMC Bioinformatics 9, 278
• T. Lingner and P. Meinicke
  Word correlation matrices for protein sequence analysis and remote homology detection
  BMC Bioinformatics 9, 259
• A.R. Subramanian, M. Kaufmann, B. Morgenstern
  DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment
  Algorithms for Molecular Biology 3, 6.
• K. J. Hoff, M. Tech, T. Lingner, R. Daniel, B. Morgenstern, P. Meinicke
  Gene prediction in metagenomic fragments: a large scale machine learning approach
  BMC Bioinformatics 9, 217
• The Tribolium Genome Sequencing Consortium
  The genome of the beetle developmental model and pest Tribolium castaneum
  Nature 452, 949-955.
• M. Stanke, M. Diekhans, R. Baertsch, D. Haussler
  Using native and syntenically mapped cDNA alignments to improve de novo gene finding
  Bioinformatics 24, 637-644.
• A.-K. Schultz, M. Zhang, T. Leitner, B. Korber, B. Morgenstern, M. Stanke
  jpHMM: Erkennung von Rekombinationen bei HIV
  BIOforum 2/2008, 44-46.
  
• C. Oesterhelt, S. Vogelbein, R. P. Shrestha, M. Stanke and A. P. M. Weber
  The genome of the thermoacidophilic red microalga Galdieria sulphuraria encodes a small family of secreted class III peroxidases that might be involved in cell wall modification
  Planta 227, 353-362

2007

• L. Taher, P. Meinicke, B. Morgenstern
  On splice site prediction using weight array models: a comparison of smoothing techniques
  Journal of Physics: Conference Series 90, 012004
• B. Mersch, T. Glasmachers, P. Meinicke, C. Igel
  Evolutionary optimization of sequence kernels for detection of bacterial gene starts
  International Journal of Neural Systems 17, 369 - 381
• X.H. Chen, A. Koumoutsi, R. Scholz, A. Eisenreich, K. Schneider, I. Heinemeyer, B. Morgenstern, B. Voss, W.R. Hess, O. Reva, H. Junge, B. Voigt, P. R. Jungblut, J. Vater, R. Süssmuth, H. Liesegang, A. Strittmatter, G. Gottschalk, R. Borriss
  Genomanalyse eines phytostimulatorischen Bacillus-Stammes
  Genomxpress 3.07, 11-13.
• E. Ghedin, S. Wang, ... , M. Stanke, ... , M.L. Blaxter, and A.L. Scott
  Draft Genome of the Filarial Nematode Parasite Brugia malayi
  Science 317, 1756 - 1760.
  
• X.H. Chen, A. Koumoutsi, H. Liesegang, A. Strittmatter, O. Reva, R. Scholz, A. Eisenreich, K. Schneider, J. Vater, I. Heinemeyer, B. Morgenstern, B. Voss, W.R. Hess, B. Voigt, P. R. Jungblut, H. Junge, R. Süssmuth, G. Gottschalk, R. Borriss
  Comparative analysis of the complete genome sequence of the plant growth promoting Bacillus amyloliquefaciens FZB42
  Nature Biotechnology 25, 1007 - 1014.
  
• B. Morgenstern
  Book review: Computational Genome Analysis by R.C. Deonier, S. Tavare and M.S. Waterman
  Biometrical Journal 49, 789.
• B. Morgenstern
  Alignment of genomic sequences using DIALIGN (book chapter)
  In: Comparative Genomics, pp. 195 - 203
  Humana Press
• B. Morgenstern
  Multiple sequence alignment (book chapter)
  In: Bioinformatics (Methods Express Series), pp. 245 - 264
  Scion Publishing Ltd.
• V. Nene, J.R. Wortman, D. Lawson, ... , M. Stanke, ... , D. Werner, ... , C.M. Fraser-Liggett, D.W. Severson
  Genome Sequence of Aedes aegypti, a Major Arbovirus Vector
  Science 316, 1718-1723.
  
• G. Didier , L. Debomy , M. Pupin , M. Zhang , A. Grossmann, C. Devauchelle, I. Laprevotte
  Comparing sequences without using alignments: Application to HIV/SIV subtyping
  BMC Bioinformatics 8, 1.
  
• J. Xie, M. Zhang, T. Zhou, X. Hua, L. Tang, W. Wu
  Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs
  Nucleic Acids Res. 35, D183-D187.
  
• C. Igel, T. Glasmachers, B. Mersch, N. Pfeifer, P. Meinicke
  Gradient-based Optimization of Kernel-Target Alignment for Sequence Kernels Applied to Bacterial Gene Start Detection
  IEEE/ACM Transactions on Computational Biology and Bioinformatics 4, 216-226.
  

2006

• B. Mersch, T. Glasmachers, P. Meinicke, C. Igel
  Evolutionary optimization of sequence kernels for detection of bacterial gene starts
  Lecture Notes in Computer Science 4132, 827 - 836.
• T. Lingner and P. Meinicke
  Remote homology detection based on Oligomer Distances
  Bioinformatics 22, 2224 - 2231.
• P. Meinicke, T. Brodag, W.F. Fricke, S. Waack
  P-value based visualization of codon usage data
  Algorithms for Molecular Biology 1,10.
• A.-K. Schultz, M. Zhang, T. Leitner, C. Kuiken, B. Korber, B. Morgenstern, M. Stanke
  A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes
  BMC Bioinformatics 7, 265.
• B. Morgenstern, S.J. Prohaska, D. Pöhler, P.F. Stadler
  Multiple sequence alignment with user-defined anchor points
  Algorithms for Molecular Biology 1,6.
• M. Stanke, A. Tzvetkova, B. Morgenstern
  AUGUSTUS+ at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome.
  Genome Biology 7, S11.
• M. Tech, B. Morgenstern, P. Meinicke
  TICO: a tool for postprocessing the predictions of prokaryotic translation initiation sites
  Nucleic Acids Res. 34, W588 - W590.
• M. Zhang, A.-K. Schultz, C. Calef, C. Kuiken, T. Leitner, B. Korber, B. Morgenstern, M. Stanke
  jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1
  Nucleic Acids Res. 34, W463 - W465.
• M. Stanke, O. Keller, I. Gunduz, A. Hayes, S. Waack, B. Morgenstern
  AUGUSTUS: ab initio prediction of alternative transcripts
  Nucleic Acids Res. 34, W435 - W439.
• S. Waack, O. Keller, R. Asper, T. Brodag, C. Damm, W.F. Fricke, K. Surovcik, P. Meinicke, R. Merkl
  Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models
  BMC Bioinformatics 7, 142.
• M. Tech and P. Meinicke
  An unsupervised classification scheme for improving predictions of prokaryotic TIS
  BMC Bioinformatics 7, 121.
• B. Morgenstern and P.F. Stadler
  New journal: Algorithms for Molecular Biology (Editorial)
  Algorithms for Molecular Biology 1,1.
• M. Stanke, O. Schöffmann, B. Morgenstern, S. Waack
  Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources
  BMC Bioinformatics 7, 62.

2005

• M. Tech, N. Pfeifer, B. Morgenstern, P. Meinicke
  TICO: a tool for improving predictions of prokaryotic translation initiation sites
  Bioinformatics 21, 3568 - 3569.
• M. Stanke and B. Morgenstern (2005)
  AUGUSTUS: Genvorhersage in Eukaryoten mit Hidden-Markov-Modellen und vergleichender Sequenzanalyse
  BIOforum 9, 45 - 47.
  
• M. Zhang, A.-K. Schultz, B. Morgenstern, M. Stanke, B. Korber, T. Leitner
  Greater HIV Genome Diversities Inferred From Re-subtyping of HIV Database Sequences
  Proc. German Conference on Bioinformatics 2005 (Discovery Notes, Poster Abstracts), pp. 5 - 7.
• M. Zhang, K. Wilbe, N.D. Wolfe, B. Gaschen, J.K. Carr and T. Leitner
  HIV-1 CRF13_cpx revisited: identification of a new sequence from Cameroon and signal for sub-subtype J2
  AIDS Research and Human Retroviruses 21, 955-960.
• J. Weyer-Menkhoff, C. Devauchelle, A. Grossmann, S. Grünewald
  Integer linear programming as a tool for constructing trees from quartet data
  Computational Biology and Chemistry 29, 196-203. (preprint)
• B. Morgenstern (2005)
  Gene structure prediction by genomic sequence alignment (book chapter)
  In: Genetics, Genomics, Proteomics and Bioinformatics
  John Wiley & Sons
• M. Stanke and B. Morgenstern
  AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints
  Nucleic Acids Res. 33, W465 - W467.
• A.R. Subramanian, J. Weyer-Menkhoff, M. Kaufmann, B. Morgenstern
  DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment
  BMC Bioinformatics 6, 66.
• D. Pöhler, N. Werner, R. Steinkamp, B. Morgenstern
  Multiple Alignment of Genomic Sequences using CHAOS, DIALIGN and ABC
  Nucleic Acids Res. 33, W532 - W534.
• P. Meinicke, S. Klanke, R. Memisevic, H. Ritter (2005)
  Principal Surfaces from Unsupervised Kernel Regression
  IEEE Transactions on Pattern Analysis and Machine Intelligence 27, 1379 - 1391.
• A. Dress, B.Holland, K.T. Huber, J.H. Koolen, V. Moulton and J. Weyer-Menkhoff (2005)
  Delta additive and Delta ultra-additive maps, Gromov's trees, and the Farris transform
  Discrete Applied Mathematics 146, 51-73.
• B. Morgenstern, N. Werner, S.J. Prohaska, R. Steinkamp, I. Schneider, A.R. Subramanian, P.F. Stadler, J. Weyer-Menkhoff
  Multiple sequence alignment with user-defined constraints at GOBICS
  Bioinformatics 21, 1271-1273. (pdf)

2004

• P. Meinicke, M. Tech, B. Morgenstern, R. Merkl (2004)
  Oligo Kernels for datamining on biological sequences: A case study on prokaryotic translation initiation sites
  BMC Bioinformatics 5, 169.
• M. Schmollinger, K. Nieselt, M. Kaufmann, B. Morgenstern (2004)
  DIALIGN P: Fast pair-wise and multiple sequence alignment using parallel processors
  BMC Bioinformatics 5, 128.
• P. Meinicke, T. Hermann, H. Bekel, H. M. Müller, S. Weiss, H. Ritter (2004)
  Identification of Discriminative Features in EEG
  Intelligent Data Analysis, 8(1): 97-107
• M. Kaper, P. Meinicke, U. Grossekathoefer, T. Lingner, H. Ritter (2004)
  BCI competition 2003 - Data set IIb: Support vector machines for the P300 speller paradigm
  IEEE Transactions on Biomedical Engineering 51 (6): 1073-1076.
• L. Taher, O. Rinner, S. Garg, A. Sczyrba, B. Morgenstern (2004)
  AGenDA: Gene Prediction by Cross-Species Sequence Comparison
  Nucleic Acids Res. 32, W305-W308.
• M. Stanke, R. Steinkamp, S. Waack, B. Morgenstern (2004)
  AUGUSTUS: a web server for gene finding in eukaryotes
  Nucleic Acids Res. 32, W309-W312.
• B. Morgenstern, S.J. Prohaska, N. Werner, J. Weyer-Menkhoff, I. Schneider, A.R. Subramanian, P.F. Stadler (2004)
  Multiple sequence alignment with user-defined constraints (preprint)
  German Conference on Bioinformatics 2004; Lecture Notes in Informatics P-53, 25-36.
• B. Morgenstern (2004)
  DIALIGN: Multiple DNA and Protein Sequence Alignment at BiBiServ
  Nucleic Acids Res. 32, W33-W36.
• M. Brudno, R. Steinkamp, B. Morgenstern (2004)
  The CHAOS/DIALIGN WWW server for Multiple Alignment of Genomic Sequences
  Nucleic Acids Res. 32, W41-W44.
• M. Stanke (2004)
  Sequential selection of random vectors under a sum constraint.
  Journal of Applied Probability 41, 131-146. preprint
• B. Morgenstern (2004)
  The DIALIGN multiple alignment program: Recent developments and applications
  Cladistics 20, 89-90

2003

• M. Brudno, M. Chapman, B. Göttgens, S. Batzoglou, B. Morgenstern (2003)
  Fast and sensitive multiple alignment of large genomic sequences
  BMC Bioinformatics 4, 66.
• M. Stanke and S. Waack (2003)
  Gene Prediction with a Hidden Markov Model and new Intron Submodel.
  Bioinformatics 19, ii215-ii225 (ECCB 2003 special issue).
• M. Sammeth, B. Morgenstern, J. Stoye (2003)
  Divide-and-Conquer Multiple Alignment with Segment-Based Constraints
  Bioinformatics 19, ii189-ii195 (ECCB 2003 special issue).
• L. Taher, O. Rinner, S. Gargh, A. Sczyrba, M. Brudno, S. Batzoglou, B. Morgenstern (2003)
  AGenDA: Homology-based gene prediction.
  Bioinformatics 19, 1575-1577.