Peter F. Stadler

	2009
77		Andreas Heffel, Sonja J. Prohaska, Peter F. Stadler, Gerhard Kauer, Jens-Peer Kuska: Automatic Classification of Embryonic Fruit Fly Gene Expression Patterns. Bildverarbeitung für die Medizin 2009: 415-419
76		Markus Riester, Peter F. Stadler, Konstantin Klemm: FRANz: reconstruction of wild multi-generation pedigrees. Bioinformatics 25(16): 2134-2139 (2009)
75		David Langenberger, Clara Bermudez-Santana, Jana Hertel, Steve Hoffmann, Philipp Khaitovich, Peter F. Stadler: Evidence for human microRNA-offset RNAs in small RNA sequencing data. Bioinformatics 25(18): 2298-2301 (2009)
74		Fenix W. D. Huang, Jing Qin, Christian M. Reidys, Peter F. Stadler: Partition function and base pairing probabilities for RNA-RNA interaction prediction. Bioinformatics 25(20): 2646-2654 (2009)
73		Bogumil Kaczkowski, Elfar Torarinsson, Kristin Reiche, Jakob Hull Havgaard, Peter F. Stadler, Jan Gorodkin: Structural profiles of human miRNA families from pairwise clustering. Bioinformatics 25(3): 291-294 (2009)
72		Andreas W. M. Dress, Bülent Karasözen, Peter F. Stadler, Gerhard-Wilhelm Weber: Preface. Discrete Applied Mathematics 157(10): 2217-2220 (2009)
71		Konstantin Klemm, Peter F. Stadler: A note on fundamental, non-fundamental, and robust cycle bases. Discrete Applied Mathematics 157(10): 2432-2438 (2009)
70		Axel Mosig, Türker Bíyíkoglu, Sonja J. Prohaska, Peter F. Stadler: Discovering cis-regulatory modules by optimizing barbecues. Discrete Applied Mathematics 157(10): 2458-2468 (2009)
69		Frank Jühling, Mario Mörl, Roland K. Hartmann, Mathias Sprinzl, Peter F. Stadler, Joern Pütz: tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Research 37(Database-Issue): 159-162 (2009)
	2008
68		Ulrike Mückstein, Hakim Tafer, Stephan H. F. Bernhart, Maribel Hernandez-Rosales, Jörg Vogel, Peter F. Stadler, Ivo L. Hofacker: Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics. BIRD 2008: 114-127
67		Markus Riester, Peter F. Stadler, Konstantin Klemm: FRANz: Fast Reconstruction of Wild Pedigrees. German Conference on Bioinformatics 2008: 168-177
66		Andreas Heffel, Peter F. Stadler, Sonja J. Prohaska, Gerhard Kauer, Jens-Peer Kuska: Process flow for classification and clustering of fruit fly gene expression patterns. ICIP 2008: 721-724
65		Andreas W. M. Dress, Christoph Flamm, Guido Fritzsch, Stefan Grünewald, Matthias Kruspe, Sonja J. Prohaska, Peter F. Stadler: Noisy: Identification of problematic columns in multiple sequence alignments. Algorithms for Molecular Biology 3: (2008)
64		Stephan H. F. Bernhart, Ivo L. Hofacker, Sebastian Will, Andreas R. Gruber, Peter F. Stadler: RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics 9: (2008)
63		Jörg Lehmann, Peter F. Stadler, Sonja J. Prohaska: SynBlast: Assisting the analysis of conserved synteny information. BMC Bioinformatics 9: (2008)
62		Jana Hertel, Ivo L. Hofacker, Peter F. Stadler: SnoReport: computational identification of snoRNAs with unknown targets. Bioinformatics 24(2): 158-164 (2008)
61		Dominic Rose, Julian Jöris, Jörg Hackermüller, Kristin Reiche, Qiang Li, Peter F. Stadler: Duplicated RNA genes in teleost Fish genomes. J. Bioinformatics and Computational Biology 6(6): 1157-1175 (2008)
	2007
60		Christopher R. Stephens, Marc Toussaint, L. Darrell Whitley, Peter F. Stadler: Foundations of Genetic Algorithms, 9th International Workshop, FOGA 2007, Mexico City, Mexico, January 8-11, 2007, Revised Selected Papers Springer 2007
59		Christoph Flamm, Ivo L. Hofacker, Bärbel M. R. Stadler, Peter F. Stadler: Saddles and Barrier in Landscapes of Generalized Search Operators. FOGA 2007: 194-212
58		Axel Mosig, Peter Menzel, Peter F. Stadler: Tanimoto's Best Barbecue: Discovering Regulatory Modules using Tanimoto Scores. German Conference on Bioinformatics 2007: 68-77
57		Axel Mosig, Julian J.-L. Chen, Peter F. Stadler: Homology Search with Fragmented Nucleic Acid Sequence Patterns. WABI 2007: 335-345
56		Kristin Reiche, Peter F. Stadler: RNAstrand: reading direction of structured RNAs in multiple sequence alignments. Algorithms for Molecular Biology 2: (2007)
55		Matthias Kruspe, Peter F. Stadler: Progressive multiple sequence alignments from triplets. BMC Bioinformatics 8: (2007)
54		Matthias Bernt, Daniel Merkle, Kai Ramsch, Guido Fritzsch, Marleen Perseke, Detlef Bernhard, Martin Schlegel, Peter F. Stadler, Martin Middendorf: CREx: inferring genomic rearrangements based on common intervals. Bioinformatics 23(21): 2957-2958 (2007)
53		Manja Marz, Axel Mosig, Bärbel M. R. Stadler, Peter F. Stadler: U7 snRNAs: A Computational Survey. Genomics, Proteomics & Bioinformatics 5(3-4): 187-195 (2007)
	2006
52		Jana Hertel, Peter F. Stadler: Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data. ISMB (Supplement of Bioinformatics) 2006: 197-202
51		Sebastian Potzsch, Gerik Scheuermann, Peter F. Stadler, Michael T. Wolfinger, Christoph Flamm: Visualization of Lattice-Based Protein Folding Simulations. IV 2006: 89-94
50		Burkhard Morgenstern, Sonja J. Prohaska, Dirk Pöhler, Peter F. Stadler: Multiple sequence alignment with user-defined anchor points. Algorithms for Molecular Biology 1: (2006)
49		Burkhard Morgenstern, Peter F. Stadler: New journal: Algorithms for Molecular Biology. Algorithms for Molecular Biology 1: (2006)
48		Stephan H. F. Bernhart, Hakim Tafer, Ulrike Mückstein, Christoph Flamm, Peter F. Stadler, Ivo L. Hofacker: Partition function and base pairing probabilities of RNA heterodimers. Algorithms for Molecular Biology 1: (2006)
47		Christian V. Forst, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler: Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation. BMC Bioinformatics 7: 67 (2006)
46		Ivo L. Hofacker, Peter F. Stadler: Memory efficient folding algorithms for circular RNA secondary structures. Bioinformatics 22(10): 1172-1176 (2006)
45		Ulrike Mückstein, Hakim Tafer, Jörg Hackermüller, Stephan H. F. Bernhart, Peter F. Stadler, Ivo L. Hofacker: Thermodynamics of RNA-RNA binding. Bioinformatics 22(10): 1177-1182 (2006)
44		Stephan H. F. Bernhart, Ivo L. Hofacker, Peter F. Stadler: Local RNA base pairing probabilities in large sequences. Bioinformatics 22(5): 614-615 (2006)
43		Axel Mosig, Katrin Sameith, Peter F. Stadler: Fragrep: An Efficient Search Tool for Fragmented Patterns in Genomic Sequences. Genomics, Proteomics & Bioinformatics 4(1): 56-60 (2006)
42		Christian Heine, Gerik Scheuermann, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler: Visualization of Barrier Tree Sequences. IEEE Trans. Vis. Comput. Graph. 12(5): 781-788 (2006)
41		Paul Wei-Che Hsu, Hsien-Da Huang, Sheng-Da Hsu, Li-Zen Lin, Ann-Ping Tsou, Ching-Ping Tseng, Peter F. Stadler, Stefan Washietl, Ivo L. Hofacker: miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes. Nucleic Acids Research 34(Database-Issue): 135-139 (2006)
	2005
40		Camille Stephan-Otto Attolini, Peter F. Stadler, Christoph Flamm: CelloS: A Multi-level Approach to Evolutionary Dynamics. ECAL 2005: 500-509
39		Gil Benkö, Christoph Flamm, Peter F. Stadler: Explicit Collision Simulation of Chemical Reactions in a Graph Based Artificial Chemistry. ECAL 2005: 725-733
38		Kristin Missal, Dominic Rose, Peter F. Stadler: Non-coding RNAs in Ciona intestinalis. ECCB/JBI 2005: 78
37		Ivo L. Hofacker, Peter F. Stadler: Memory Efficient Folding Algorithms for Circular RNA Secondary Structures. German Conference on Bioinformatics 2005: 15-25
36		Ulrike Mückstein, Hakim Tafer, Jörg Hackermüller, Stephan H. F. Bernhart, Peter F. Stadler, Ivo L. Hofacker: Thermodynamics of RNA-RNA Binding. German Conference on Bioinformatics 2005: 3-13
35		Roman R. Stocsits, Ivo L. Hofacker, Claudia Fried, Peter F. Stadler: Multiple sequence alignments of partially coding nucleic acid sequences. BMC Bioinformatics 6: 160 (2005)
34		Burkhard Morgenstern, Nadine Werner, Sonja J. Prohaska, Rasmus Steinkamp, Isabelle Schneider, Amarendran R. Subramanian, Peter F. Stadler, Jan Weyer-Menkhoff: Multiple sequence alignment with user-defined constraints at GOBICS. Bioinformatics 21(7): 1271-1273 (2005)
33		Petra M. Gleiss, Josef Leydold, Peter F. Stadler: Minimum path bases and relevant paths. Networks 46(3): 119-123 (2005)
	2004
32		C. Thurner, Ivo L. Hofacker, Peter F. Stadler: Conserved RNA Pseudoknots. German Conference on Bioinformatics 2004: 207-216
31		Burkhard Morgenstern, Sonja J. Prohaska, Nadine Werner, Jan Weyer-Menkhoff, Isabelle Schneider, Amarendran R. Subramanian, Peter F. Stadler: Multiple sequence alignment with user-defined constraints. German Conference on Bioinformatics 2004: 25-36
30		Ivo L. Hofacker, Peter F. Stadler: The Partition Function Variant of Sankoff's Algorithm. International Conference on Computational Science 2004: 728-735
29		Ivo L. Hofacker, Peter F. Stadler, Roman R. Stocsits: Conserved RNA secondary structures in viral genomes: a survey. Bioinformatics 20(10): 1495-1499 (2004)
28		Ivo L. Hofacker, Stephan H. F. Bernhart, Peter F. Stadler: Alignment of RNA base pairing probability matrices. Bioinformatics 20(14): 2222-2227 (2004)
27		Ivo L. Hofacker, Barbara Priwitzer, Peter F. Stadler: Prediction of locally stable RNA secondary structures for genome-wide surveys. Bioinformatics 20(2): 186-190 (2004)
26		Christina Witwer, Ivo L. Hofacker, Peter F. Stadler: Prediction of Consensus RNA Secondary Structures Including Pseudoknots. IEEE/ACM Trans. Comput. Biology Bioinform. 1(2): 66-77 (2004)
25		Franziska Berger, Christoph Flamm, Petra M. Gleiss, Josef Leydold, Peter F. Stadler: Counterexamples in Chemical Ring Perception. Journal of Chemical Information and Modeling 44(2): 323-331 (2004)
24		Claudia Fried, Wim Hordijk, Sonja J. Prohaska, Claus R. Stadler, Peter F. Stadler: The Footprint Sorting Problem. Journal of Chemical Information and Modeling 44(2): 332-338 (2004)
	2003
23		Gil Benkö, Christoph Flamm, Peter F. Stadler: Generic Properties of Chemical Networks: Artificial Chemistry Based on Graph Rewriting. ECAL 2003: 10-19
22		Ingrid G. Abfalter, Christoph Flamm, Peter F. Stadler: Design of multi-stable nucleid acid sequences. German Conference on Bioinformatics 2003: 1-7
21		Ivo L. Hofacker, Peter F. Stadler, Roman R. Stocsits: Conserved RNA secondary structures in viral genomes: A survey. German Conference on Bioinformatics 2003: 57-62
20		Peter F. Stadler, Christoph Flamm: Barrier Trees on Poset-Valued Landscapes. Genetic Programming and Evolvable Machines 4(1): 7-20 (2003)
19		Gil Benkö, Christoph Flamm, Peter F. Stadler: A Graph-Based Toy Model of Chemistry. Journal of Chemical Information and Computer Sciences 43(4): 1085-1093 (2003)
	2002
18		Ulrike Mückstein, Ivo L. Hofacker, Peter F. Stadler: Stochastic pairwise alignments. ECCB 2002: 153-160
17		Bärbel M. R. Stadler, Peter F. Stadler: Generalized Topological Spaces in Evolutionary Theory and Combinatorial Chemistry. Journal of Chemical Information and Computer Sciences 42(3): 577-585 (2002)
	2000
16		Jan Cupal, Stephan Kopp, Peter F. Stadler: RNA Shape Space Topology. Artificial Life 6(1): 3-23 (2000)
15		Petra M. Gleiss, Josef Leydold, Peter F. Stadler: Interchangeability of Relevant Cycles in Graphs. Electr. J. Comb. 7: (2000)
14		Martin Fekete, Ivo L. Hofacker, Peter F. Stadler: Prediction of RNA Base Pairing Probabilities on Massively Parallel Computers. Journal of Computational Biology 7(1-2): 171-182 (2000)
	1999
13		G. Weberndorfer, Ivo L. Hofacker, Peter F. Stadler: An efficient potential for protein sequence design. German Conference on Bioinformatics 1999: 107-112
12		Roman R. Stocsits, Ivo L. Hofacker, Peter F. Stadler: Conserved secondary structures in hepatitis B virus DNA. German Conference on Bioinformatics 1999: 73-79
11		Ivo L. Hofacker, Peter F. Stadler: Automatic Detection of Conserved Base Pairing Patterns in RNA Virus Genomes. Computers & Chemistry 23(3-4): 401-414 (1999)
	1998
10		Ivo L. Hofacker, Peter Schuster, Peter F. Stadler: Combinatorics of RNA Secondary Structures. Discrete Applied Mathematics 88(1-3): 207-237 (1998)
9		Josef Leydold, Peter F. Stadler: Minimal Cycle Bases of Outerplanar Graphs. Electr. J. Comb. 5: (1998)
	1997
8		Jan Cupal, Christoph Flamm, Alexander Renner, Peter F. Stadler: Density of States, Metastable States, and Saddle Points: Exploring the Energy Landscape of an RNA Molecule. ISMB 1997: 88-91
7		Peter F. Stadler, Günter P. Wagner: Algebraic Theory of Recombination Spaces. Evolutionary Computation 5(3): 241-275 (1997)
	1996
6		Jan Cupal, Ivo L. Hofacker, Peter F. Stadler: Dynamic Programming Algorithm for the Density of States of RNA Secondary Structures. German Conference on Bioinformatics 1996: 184-186
5		Ivo L. Hofacker, Martijn A. Huynen, Peter F. Stadler, Paul E. Stolorz: Knowledge Discovery in RNA Sequence Families of HIV Using Scalable Computers. KDD 1996: 20-25
4		Christian M. Reidys, Peter F. Stadler: Bio-molecular Shapes and Algebraic Structures. Computers & Chemistry 20(1): 85-94 (1996)
3		Martijn A. Huynen, Alan S. Perelson, W. A. Vieira, Peter F. Stadler: Base Pairing Probabilities in a Complete HIV-1 RNA. Journal of Computational Biology 3(2): 253-274 (1996)
	1995
2		Peter F. Stadler: Random walks and orthogonal functions associated with highly symmetric graphs. Discrete Mathematics 145(1-3): 229-237 (1995)
	1994
1		Peter Schuster, Peter F. Stadler: Landscapes: Complex Optimization Problems and Biopolymer Structures. Computers & Chemistry 18(3): 295-324 (1994)

Coauthor Index

1	Ingrid G. Abfalter	[22]
2	Camille Stephan-Otto Attolini	[40]
3	Gil Benkö	[19] [23] [39]
4	Franziska Berger	[25]
5	Clara Bermudez-Santana	[75]
6	Detlef Bernhard	[54]
7	Stephan H. F. Bernhart	[28] [36] [44] [45] [48] [64] [68]
8	Matthias Bernt	[54]
9	Türker Bíyíkoglu	[70]
10	Julian J.-L. Chen	[57]
11	Jan Cupal	[6] [8] [16]
12	Andreas W. M. Dress	[65] [72]
13	Martin Fekete	[14]
14	Christoph Flamm	[8] [19] [20] [22] [23] [25] [39] [40] [42] [47] [48] [51] [59] [65]
15	Christian V. Forst	[47]
16	Claudia Fried	[24] [35]
17	Guido Fritzsch	[54] [65]
18	Petra M. Gleiss	[15] [25] [33]
19	Jan Gorodkin	[73]
20	Andreas R. Gruber	[64]
21	Stefan Grünewald	[65]
22	Jörg Hackermüller	[36] [45] [61]
23	Roland K. Hartmann	[69]
24	Jakob Hull Havgaard	[73]
25	Andreas Heffel	[66] [77]
26	Christian Heine	[42]
27	Maribel Hernandez-Rosales	[68]
28	Jana Hertel	[52] [62] [75]
29	Ivo L. Hofacker	[5] [6] [10] [11] [12] [13] [14] [18] [21] [26] [27] [28] [29] [30] [32] [35] [36] [37] [41] [42] [44] [45] [46] [47] [48] [59] [62] [64] [68]
30	Steve Hoffmann	[75]
31	Wim Hordijk	[24]
32	Paul Wei-Che Hsu	[41]
33	Sheng-Da Hsu	[41]
34	Fenix W. D. Huang	[74]
35	Hsien-Da Huang	[41]
36	Martijn A. Huynen	[3] [5]
37	Julian Jöris	[61]
38	Frank Jühling	[69]
39	Bogumil Kaczkowski	[73]
40	Bülent Karasözen	[72]
41	Gerhard Kauer	[66] [77]
42	Philipp Khaitovich	[75]
43	Konstantin Klemm	[67] [71] [76]
44	Stephan Kopp	[16]
45	Matthias Kruspe	[55] [65]
46	Jens-Peer Kuska	[66] [77]
47	David Langenberger	[75]
48	Jörg Lehmann	[63]
49	Josef Leydold	[9] [15] [25] [33]
50	Qiang Li	[61]
51	Li-Zen Lin	[41]
52	Manja Marz	[53]
53	Peter Menzel	[58]
54	Daniel Merkle	[54]
55	Martin Middendorf	[54]
56	Kristin Missal	[38]
57	Burkhard Morgenstern	[31] [34] [49] [50]
58	Mario Mörl	[69]
59	Axel Mosig	[43] [53] [57] [58] [70]
60	Ulrike Mückstein	[18] [36] [45] [48] [68]
61	Alan S. Perelson	[3]
62	Marleen Perseke	[54]
63	Dirk Pöhler	[50]
64	Sebastian Potzsch	[51]
65	Barbara Priwitzer	[27]
66	Sonja J. Prohaska	[24] [31] [34] [50] [63] [65] [66] [70] [77]
67	Joern Pütz	[69]
68	Jing Qin	[74]
69	Kai Ramsch	[54]
70	Kristin Reiche	[56] [61] [73]
71	Christian M. Reidys	[4] [74]
72	Alexander Renner	[8]
73	Markus Riester	[67] [76]
74	Dominic Rose	[38] [61]
75	Katrin Sameith	[43]
76	Gerik Scheuermann	[42] [51]
77	Martin Schlegel	[54]
78	Isabelle Schneider	[31] [34]
79	Peter Schuster	[1] [10]
80	Mathias Sprinzl	[69]
81	Bärbel M. R. Stadler	[17] [53] [59]
82	Claus R. Stadler	[24]
83	Rasmus Steinkamp	[34]
84	Christopher R. Stephens	[60]
85	Roman R. Stocsits	[12] [21] [29] [35]
86	Paul E. Stolorz	[5]
87	Amarendran R. Subramanian	[31] [34]
88	Hakim Tafer	[36] [45] [48] [68]
89	C. Thurner	[32]
90	Elfar Torarinsson	[73]
91	Marc Toussaint	[60]
92	Ching-Ping Tseng	[41]
93	Ann-Ping Tsou	[41]
94	W. A. Vieira	[3]
95	Jörg Vogel	[68]
96	Günter P. Wagner	[7]
97	Stefan Washietl	[41]
98	Gerhard-Wilhelm Weber	[72]
99	G. Weberndorfer	[13]
100	Nadine Werner	[31] [34]
101	Jan Weyer-Menkhoff	[31] [34]
102	L. Darrell Whitley (Darrell Whitley)	[60]
103	Sebastian Will	[64]
104	Christina Witwer	[26]
105	Michael T. Wolfinger	[51]

Colors in the list of coauthors