gobics.de: Publications

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.

2010

J.E. Stajich, ... , M. Stanke, ... , P.J. Pukkila (2010)
Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus)
Proc. Natl. Acad. Sci. USA, in press
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, 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)
To appear.
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., in press.
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 (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

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.

Created by Burkhard Morgenstern. Last modified: May 2010

gobics.de [Publications]