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Peter F. Stadler - Publications

Affiliations: 
Interdisciplinary Centre for Bioinformatics Leipzig University, Leipzig, Sachsen, Germany 
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460 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Triebel S, Lamkiewicz K, Ontiveros N, Sweeney B, Stadler PF, Petrov AI, Niepmann M, Marz M. Comprehensive survey of conserved RNA secondary structures in full-genome alignment of Hepatitis C virus. Scientific Reports. 14: 15145. PMID 38956134 DOI: 10.1038/s41598-024-62897-0  0.587
2024 Backofen R, Gorodkin J, Hofacker IL, Stadler PF. Comparative RNA Genomics. Methods in Molecular Biology (Clifton, N.J.). 2802: 347-393. PMID 38819565 DOI: 10.1007/978-1-0716-3838-5_12  0.312
2024 Hellmuth M, Stadler PF. The Theory of Gene Family Histories. Methods in Molecular Biology (Clifton, N.J.). 2802: 1-32. PMID 38819554 DOI: 10.1007/978-1-0716-3838-5_1  0.61
2024 Kühnl F, Stadler PF, Findeiß S. Assessing the Quality of Cotranscriptional Folding Simulations. Methods in Molecular Biology (Clifton, N.J.). 2726: 347-376. PMID 38780738 DOI: 10.1007/978-1-0716-3519-3_14  0.725
2024 Freudiger A, Jovanovic VM, Huang Y, Snyder-Mackler N, Conrad DF, Miller B, Montague MJ, Westphal H, Stadler PF, Bley S, Horvath JE, Brent LJN, Platt ML, Ruiz-Lambides A, Tung J, et al. Taking identity-by-descent analysis into the wild: Estimating realized relatedness in free-ranging macaques. Biorxiv : the Preprint Server For Biology. PMID 38260273 DOI: 10.1101/2024.01.09.574911  0.673
2023 Schaller D, Hartmann T, Lafond M, Stadler PF, Wieseke N, Hellmuth M. Relative timing information and orthology in evolutionary scenarios. Algorithms For Molecular Biology : Amb. 18: 16. PMID 37940998 DOI: 10.1186/s13015-023-00240-4  0.609
2023 Klapproth C, Zötzsche S, Kühnl F, Fallmann J, Stadler PF, Findeiß S. Tailored machine learning models for functional RNA detection in genome-wide screens. Nar Genomics and Bioinformatics. 5: lqad072. PMID 37608800 DOI: 10.1093/nargab/lqad072  0.705
2023 Hellmuth M, Schaller D, Stadler PF. Clustering systems of phylogenetic networks. Theory in Biosciences = Theorie in Den Biowissenschaften. PMID 37573261 DOI: 10.1007/s12064-023-00398-w  0.584
2023 Schuster P, Stadler PF. Virus Evolution on Fitness Landscapes. Current Topics in Microbiology and Immunology. 439: 1-94. PMID 36592242 DOI: 10.1007/978-3-031-15640-3_1  0.437
2022 Müller S, Flamm C, Stadler PF. What makes a reaction network "chemical"? Journal of Cheminformatics. 14: 63. PMID 36123755 DOI: 10.1186/s13321-022-00621-8  0.531
2022 Leal W, Llanos EJ, Bernal A, Stadler PF, Jost J, Restrepo G. The expansion of chemical space in 1826 and in the 1840s prompted the convergence to the periodic system. Proceedings of the National Academy of Sciences of the United States of America. 119: e2119083119. PMID 35867818 DOI: 10.1073/pnas.2119083119  0.768
2022 Ender A, Stadler PF, Mörl M, Findeiß S. RNA Design Principles for Riboswitches that Regulate RNase P-Mediated tRNA Processing. Methods in Molecular Biology (Clifton, N.J.). 2518: 179-202. PMID 35666446 DOI: 10.1007/978-1-0716-2421-0_11  0.715
2022 Engelhardt J, Scheer O, Stadler PF, Prohaska SJ. Evolution of DNA Methylation Across Ecdysozoa. Journal of Molecular Evolution. 90: 56-72. PMID 35089376 DOI: 10.1007/s00239-021-10042-0  0.58
2022 Schaller D, Geiss M, Hellmuth M, Stadler PF. Best Match Graphs with Binary Trees. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 35044918 DOI: 10.1109/TCBB.2022.3143870  0.606
2022 Ender A, Grafl N, Kolberg T, Findeiss S, Stadler PF, Mörl M. Synthetic Riboswitches for the Analysis of tRNA Processing by eukaryotic RNase P Enzymes. Rna (New York, N.Y.). PMID 35022261 DOI: 10.1261/rna.078814.121  0.668
2021 Klapproth C, Sen R, Stadler PF, Findeiß S, Fallmann J. Common Features in lncRNA Annotation and Classification: A Survey. Non-Coding Rna. 7. PMID 34940758 DOI: 10.3390/ncrna7040077  0.725
2021 Schaller D, Hellmuth M, Stadler PF. A simpler linear-time algorithm for the common refinement of rooted phylogenetic trees on a common leaf set. Algorithms For Molecular Biology : Amb. 16: 23. PMID 34872590 DOI: 10.1186/s13015-021-00202-8  0.589
2021 Schaller D, Geiß M, Hellmuth M, Stadler PF. Heuristic algorithms for best match graph editing. Algorithms For Molecular Biology : Amb. 16: 19. PMID 34404422 DOI: 10.1186/s13015-021-00196-3  0.626
2021 Schaller D, Lafond M, Stadler PF, Wieseke N, Hellmuth M. Indirect identification of horizontal gene transfer. Journal of Mathematical Biology. 83: 10. PMID 34218334 DOI: 10.1007/s00285-021-01631-0  0.603
2021 Kolora SRR, Gysi DM, Schaffer S, Grimm-Seyfarth A, Szabolcs M, Faria R, Henle K, Stadler PF, Schlegel M, Nowick K. Accelerated evolution of tissue-specific genes mediates divergence amidst gene flow in European green lizards. Genome Biology and Evolution. PMID 33988711 DOI: 10.1093/gbe/evab109  0.671
2021 Schaller D, Geiß M, Chávez E, González Laffitte M, López Sánchez A, Stadler BMR, Valdivia DI, Hellmuth M, Hernández Rosales M, Stadler PF. Corrigendum to "Best match graphs". Journal of Mathematical Biology. 82: 47. PMID 33818665 DOI: 10.1007/s00285-021-01601-6  0.581
2021 Schaller D, Geiß M, Stadler PF, Hellmuth M. Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs. Journal of Mathematical Biology. 82: 20. PMID 33606106 DOI: 10.1007/s00285-021-01564-8  0.633
2021 Ender A, Etzel M, Hammer S, Findeiß S, Stadler P, Mörl M. Ligand-dependent tRNA processing by a rationally designed RNase P riboswitch. Nucleic Acids Research. PMID 33469651 DOI: 10.1093/nar/gkaa1282  0.704
2020 Günzel C, Kühnl F, Arnold K, Findeiß S, Weinberg CE, Stadler PF, Mörl M. Beyond Plug and Pray: Context Sensitivity and Design of Artificial Neomycin Riboswitches. Rna Biology. PMID 32882151 DOI: 10.1080/15476286.2020.1816336  0.738
2020 Flamm C, Hellmuth M, Merkle D, Nojgaard N, Stadler PF. Generic Context-Aware Group Contributions. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 32750852 DOI: 10.1109/Tcbb.2020.2998948  0.735
2020 Erber L, Hoffmann A, Fallmann J, Hagedorn M, Hammann C, Stadler PF, Betat H, Prohaska S, Mörl M. Unusual Occurrence of Two Bona-Fide CCA-Adding Enzymes in . International Journal of Molecular Sciences. 21. PMID 32717856 DOI: 10.3390/Ijms21155210  0.645
2020 Balogh G, Bernhart SH, Stadler PF, Schor J. A probabilistic version of Sankoff's maximum parsimony algorithm. Journal of Bioinformatics and Computational Biology. 18: 2050004. PMID 32336248 DOI: 10.1142/S0219720020500043  0.326
2020 Stadler PF, Geiß M, Schaller D, López Sánchez A, González Laffitte M, Valdivia DI, Hellmuth M, Hernández Rosales M. From pairs of most similar sequences to phylogenetic best matches. Algorithms For Molecular Biology : Amb. 15: 5. PMID 32308731 DOI: 10.1186/S13015-020-00165-2  0.654
2020 Corona-Gomez JA, Garcia-Lopez IJ, Stadler PF, Fernandez-Valverde SL. Splicing conservation signals in plant long non-coding RNAs. Rna (New York, N.Y.). PMID 32241834 DOI: 10.1261/Rna.074393.119  0.399
2020 Nitsche A, Arnold C, Ueberham U, Reiche K, Fallmann J, Hackermüller J, Horn F, Stadler PF, Arendt T. Alzheimer-related genes show accelerated evolution. Molecular Psychiatry. PMID 32203153 DOI: 10.1038/S41380-020-0680-1  0.317
2020 Seal RL, Chen LL, Griffiths-Jones S, Lowe TM, Mathews MB, O'Reilly D, Pierce AJ, Stadler PF, Ulitsky I, Wolin SL, Bruford EA. A guide to naming human non-coding RNA genes. The Embo Journal. e103777. PMID 32090359 DOI: 10.15252/Embj.2019103777  0.369
2020 Binder S, Zipfel I, Friedrich M, Riedel D, Ende S, Kämpf C, Wiedemann K, Buschmann T, Puppel SH, Reiche K, Stadler PF, Horn F. Master and servant: LINC00152 - a STAT3-induced long noncoding RNA regulates STAT3 in a positive feedback in human multiple myeloma. Bmc Medical Genomics. 13: 22. PMID 32041604 DOI: 10.1186/S12920-020-0692-3  0.365
2020 Berkemer SJ, Maier LK, Amman F, Bernhart SH, Wörtz J, Märkle P, Pfeiffer F, Stadler PF, Marchfelder A. Identification of RNA 3´ ends and termination sites in . Rna Biology. 1-14. PMID 32041469 DOI: 10.1080/15476286.2020.1723328  0.417
2020 Geiß M, Laffitte MEG, Sánchez AL, Valdivia DI, Hellmuth M, Rosales MH, Stadler PF. Best match graphs and reconciliation of gene trees with species trees. Journal of Mathematical Biology. PMID 32002659 DOI: 10.1007/S00285-020-01469-Y  0.647
2020 Fritz A, Hellmuth M, Stadler PF, Wieseke N. Cograph editing: Merging modules is equivalent to editing P_4s The Art of Discrete and Applied Mathematics. 3: #P2.01. DOI: 10.26493/2590-9770.1252.e71  0.549
2020 Hellmuth M, Geiß M, Stadler PF. Complexity of modification problems for reciprocal best match graphs Theoretical Computer Science. 809: 384-393. DOI: 10.1016/J.Tcs.2019.12.033  0.636
2020 Hellmuth M, Seemann CR, Stadler PF. Generalized Fitch graphs II: Sets of binary relations that are explained by edge-labeled trees Discrete Applied Mathematics. 283: 495-511. DOI: 10.1016/J.Dam.2020.01.036  0.607
2019 Geiß M, Stadler PF, Hellmuth M. Reciprocal best match graphs. Journal of Mathematical Biology. PMID 31691135 DOI: 10.1007/S00285-019-01444-2  0.647
2019 Donath A, Jühling F, Al-Arab M, Bernhart SH, Reinhardt F, Stadler PF, Middendorf M, Bernt M. Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes. Nucleic Acids Research. PMID 31584075 DOI: 10.1093/Nar/Gkz833  0.343
2019 Nowick K, Walter Costa MB, Höner Zu Siederdissen C, Stadler PF. Selection Pressures on RNA Sequences and Structures. Evolutionary Bioinformatics Online. 15: 1176934319871919. PMID 31496634 DOI: 10.1177/1176934319871919  0.725
2019 Erber L, Hoffmann A, Fallmann J, Betat H, Stadler PF, Mörl M. LOTTE-seq (Long hairpin oligonucleotide based tRNA high-throughput sequencing): specific selection of tRNAs with 3'-CCA end for high-throughput sequencing. Rna Biology. 1-10. PMID 31486704 DOI: 10.1080/15476286.2019.1664250  0.375
2019 Kirsch R, Olzog VJ, Bonin S, Weinberg CE, Betat H, Stadler PF, Mörl M. A streamlined protocol for the detection of mRNA-sRNA interactions using AMT-crosslinking . Biotechniques. PMID 31462065 DOI: 10.2144/Btn-2019-0047  0.366
2019 Llanos EJ, Leal W, Luu DH, Jost J, Stadler PF, Restrepo G. Exploration of the chemical space and its three historical regimes. Proceedings of the National Academy of Sciences of the United States of America. PMID 31186353 DOI: 10.1073/Pnas.1816039116  0.775
2019 Keller M, Spyrou MA, Scheib CL, Neumann GU, Kröpelin A, Haas-Gebhard B, Päffgen B, Haberstroh J, Ribera I Lacomba A, Raynaud C, Cessford C, Durand R, Stadler P, Nägele K, Bates JS, et al. Ancient genomes from across Western Europe reveal early diversification during the First Pandemic (541-750). Proceedings of the National Academy of Sciences of the United States of America. PMID 31164419 DOI: 10.1073/Pnas.1820447116  0.309
2019 Fallmann J, Videm P, Bagnacani A, Batut B, Doyle MA, Klingstrom T, Eggenhofer F, Stadler PF, Backofen R, Grüning B. The RNA workbench 2.0: next generation RNA data analysis. Nucleic Acids Research. PMID 31073612 DOI: 10.1093/Nar/Gkz353  0.39
2019 Gatter T, Stadler PF. Ryūtō: network-flow based transcriptome reconstruction. Bmc Bioinformatics. 20: 190. PMID 30991937 DOI: 10.1186/S12859-019-2786-5  0.401
2019 Geiß M, Chávez E, González Laffitte M, López Sánchez A, Stadler BMR, Valdivia DI, Hellmuth M, Hernández Rosales M, Stadler PF. Best match graphs. Journal of Mathematical Biology. PMID 30968198 DOI: 10.1007/S00285-019-01332-9  0.634
2019 López C, Kleinheinz K, Aukema SM, Rohde M, Bernhart SH, Hübschmann D, Wagener R, Toprak UH, Raimondi F, Kreuz M, Waszak SM, Huang Z, Sieverling L, Paramasivam N, Seufert J, ... ... Stadler PF, et al. Genomic and transcriptomic changes complement each other in the pathogenesis of sporadic Burkitt lymphoma. Nature Communications. 10: 1459. PMID 30926794 DOI: 10.1038/S41467-019-08578-3  0.313
2019 Walter Costa MB, Höner Zu Siederdissen C, Dunjić M, Stadler PF, Nowick K. SSS-test: a novel test for detecting positive selection on RNA secondary structure. Bmc Bioinformatics. 20: 151. PMID 30898084 DOI: 10.1186/S12859-019-2711-Y  0.745
2019 Sweeney BA, Petrov AI, Burkov B, Finn RD, Bateman A, Szymanski M, Karlowski WM, Gorodkin J, Seemann SE, Cannone JJ, Gutell RR, Fey P, Basu S, Kay S, Cochrane G, ... ... Stadler PF, et al. RNAcentral: a hub of information for non-coding RNA sequences Nucleic Acids Research. 47. PMID 30395267 DOI: 10.1093/Nar/Gky1034  0.411
2019 Silva WMCd, Andersen JL, Holanda MT, Walter MEMT, Brigido MM, Stadler PF, Flamm C. Exploring Plant Sesquiterpene Diversity by Generating Chemical Networks Processes. 7: 240. DOI: 10.3390/PR7040240  0.533
2018 Kirsch R, Seemann SE, Ruzzo WL, Cohen SM, Stadler PF, Gorodkin J. Identification and characterization of novel conserved RNA structures in Drosophila. Bmc Genomics. 19: 899. PMID 30537930 DOI: 10.1186/S12864-018-5234-4  0.442
2018 Kolora SRR, Weigert A, Saffari A, Kehr S, Costa MBW, Spröer C, Indrischek H, Chintalapati M, Lohse K, Doose G, Overmann J, Bunk B, Bleidorn C, Grimm-Seyfarth A, Henle K, ... ... Stadler PF, et al. Divergent evolution in the genomes of closely-related lacertids, Lacerta viridis and L. bilineata and implications for speciation. Gigascience. PMID 30535196 DOI: 10.1093/Gigascience/Giy160  0.716
2018 Kutsche LK, Gysi DM, Fallmann J, Lenk K, Petri R, Swiersy A, Klapper SD, Pircs K, Khattak S, Stadler PF, Jakobsson J, Nowick K, Busskamp V. Combined Experimental and System-Level Analyses Reveal the Complex Regulatory Network of miR-124 during Human Neurogenesis. Cell Systems. PMID 30292704 DOI: 10.1016/J.Cels.2018.08.011  0.685
2018 Gärtner F, Höner Zu Siederdissen C, Müller L, Stadler PF. Coordinate systems for supergenomes. Algorithms For Molecular Biology : Amb. 13: 15. PMID 30258487 DOI: 10.1186/S13015-018-0133-4  0.351
2018 Wiegreffe D, Alexander D, Stadler PF, Zeckzer D. RNApuzzler: Efficient Outerplanar Drawing of RNA-Secondary Structures. Bioinformatics (Oxford, England). PMID 30239566 DOI: 10.1093/Bioinformatics/Bty817  0.387
2018 Skrzypczyk A, Kehr S, Krystel I, Bernhart SH, Giri S, Bader A, Stadler PF. Noncoding RNA Transcripts during Differentiation of Induced Pluripotent Stem Cells into Hepatocytes. Stem Cells International. 2018: 5692840. PMID 30210551 DOI: 10.1155/2018/5692840  0.308
2018 Velandia-Huerto CA, Brown FD, Gittenberger A, Stadler PF, Bermúdez-Santana CI. Nonprotein-Coding RNAs as Regulators of Development in Tunicates. Results and Problems in Cell Differentiation. 65: 197-225. PMID 30083922 DOI: 10.1007/978-3-319-92486-1_11  0.403
2018 Waldl M, Thiel BC, Ochsenreiter R, Holzenleiter A, de Araujo Oliveira JV, Walter MEMT, Wolfinger MT, Stadler PF. TERribly Difficult: Searching for Telomerase RNAs in Saccharomycetes. Genes. 9. PMID 30049970 DOI: 10.3390/Genes9080372  0.735
2018 Donath A, Stadler PF. Split-inducing indels in phylogenomic analysis. Algorithms For Molecular Biology : Amb. 13: 12. PMID 30026791 DOI: 10.1186/S13015-018-0130-7  0.301
2018 Geiß M, Anders J, Stadler PF, Wieseke N, Hellmuth M. Reconstructing gene trees from Fitch's xenology relation. Journal of Mathematical Biology. PMID 29951855 DOI: 10.1007/S00285-018-1260-8  0.641
2018 Retzlaff N, Stadler PF. Phylogenetics beyond biology. Theory in Biosciences = Theorie in Den Biowissenschaften. PMID 29931521 DOI: 10.1007/S12064-018-0264-7  0.335
2018 Sutandy FXR, Ebersberger S, Huang L, Busch A, Bach M, Kang HS, Fallmann J, Maticzka D, Backofen R, Stadler PF, Zarnack K, Sattler M, Legewie S, König J. In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactors. Genome Research. PMID 29643205 DOI: 10.1101/Gr.229757.117  0.327
2018 Fagerberg R, Flamm C, Kianian R, Merkle D, Stadler PF. Finding the K best synthesis plans. Journal of Cheminformatics. 10: 19. PMID 29623440 DOI: 10.1186/S13321-018-0273-Z  0.566
2018 Nøjgaard N, Geiß M, Merkle D, Stadler PF, Wieseke N, Hellmuth M. Time-consistent reconciliation maps and forbidden time travel. Algorithms For Molecular Biology : Amb. 13: 2. PMID 29441122 DOI: 10.1186/S13015-018-0121-8  0.634
2018 Laubichler MD, Prohaska SJ, Stadler PF. Toward a mechanistic explanation of phenotypic evolution: The need for a theory of theory integration. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. PMID 29356321 DOI: 10.1002/Jez.B.22785  0.609
2018 Backofen R, Gorodkin J, Hofacker IL, Stadler PF. Comparative RNA Genomics. Methods in Molecular Biology (Clifton, N.J.). 1704: 363-400. PMID 29277874 DOI: 10.1007/978-1-4939-7463-4_14  0.422
2018 Setubal JC, Stadler PF. Gene Phylogenies and Orthologous Groups. Methods in Molecular Biology (Clifton, N.J.). 1704: 1-28. PMID 29277861 DOI: 10.1007/978-1-4939-7463-4_1  0.339
2018 Walter Costa MB, Höner Zu Siederdissen C, Tulpan D, Stadler PF, Nowick K. Temporal ordering of substitutions in RNA evolution: Uncovering the structural evolution of the Human Accelerated Region 1. Journal of Theoretical Biology. 438: 143-150. PMID 29175608 DOI: 10.1016/J.Jtbi.2017.11.015  0.727
2018 Hellmuth M, Long Y, Geiß M, Stadler PF. A short note on undirected Fitch graphs The Art of Discrete and Applied Mathematics. 1: #1.08. DOI: 10.26493/2590-9770.1245.98C  0.566
2018 Retzlaff N, Stadler PF. Partially Local Multi-way Alignments Mathematics in Computer Science. 12: 207-234. DOI: 10.1007/S11786-018-0338-4  0.358
2017 Andersen JL, Flamm C, Merkle D, Stadler PF. Chemical Transformation Motifs --- Modelling Pathways as Integer Hyperflows. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 29990045 DOI: 10.1109/Tcbb.2017.2781724  0.589
2017 Sen R, Doose G, Stadler PF. Rare Splice Variants in Long Non-Coding RNAs. Non-Coding Rna. 3. PMID 29657294 DOI: 10.3390/Ncrna3030023  0.422
2017 Canzler S, Stadler PF, Hertel J. Evolution of Fungal U3 snoRNAs: Structural Variation and Introns. Non-Coding Rna. 3. PMID 29657275 DOI: 10.3390/Ncrna3010003  0.433
2017 Prohaska SJ, Berkemer SJ, Gärtner F, Gatter T, Retzlaff N, Höner Zu Siederdissen C, Stadler PF. Expansion of gene clusters, circular orders, and the shortest Hamiltonian path problem. Journal of Mathematical Biology. PMID 29260295 DOI: 10.1007/S00285-017-1197-3  0.649
2017 Hoffmann A, Fallmann J, Mörl M, Stadler PF, Amman F. Accurate Mapping of tRNA Reads. Bioinformatics (Oxford, England). PMID 29228294 DOI: 10.1093/Bioinformatics/Btx756  0.357
2017 Yazbeck AM, Tout KR, Stadler PF. Detailed Secondary Structure Models of Invertebrate 7SK RNAs. Rna Biology. 0. PMID 29219696 DOI: 10.1080/15476286.2017.1412913  0.424
2017 Hellmuth M, Hernandez-Rosales M, Long Y, Stadler PF. Inferring phylogenetic trees from the knowledge of rare evolutionary events. Journal of Mathematical Biology. PMID 29218395 DOI: 10.1007/S00285-017-1194-6  0.635
2017 Canzler S, Stadler PF, Schoor J. The Fungal snoRNAome. Rna (New York, N.Y.). PMID 29196413 DOI: 10.1261/Rna.062778.117  0.38
2017 Andersen JL, Flamm C, Merkle D, Stadler PF. An intermediate level of abstraction for computational systems chemistry. Philosophical Transactions. Series a, Mathematical, Physical, and Engineering Sciences. 375. PMID 29133452 DOI: 10.1098/Rsta.2016.0354  0.586
2017 Berkemer SJ, Hoffmann A, Murray CRA, Stadler PF. SMORE: Synteny Modulator of Repetitive Elements. Life (Basel, Switzerland). 7. PMID 29088079 DOI: 10.3390/Life7040042  0.426
2017 Valach M, Moreira S, Hoffmann S, Stadler PF, Burger G. Keeping it complicated: Mitochondrial genome plasticity across diplonemids. Scientific Reports. 7: 14166. PMID 29074957 DOI: 10.1038/S41598-017-14286-Z  0.39
2017 Kühnl F, Stadler PF, Will S. Tractable RNA-ligand interaction kinetics. Bmc Bioinformatics. 18: 424. PMID 29072147 DOI: 10.1186/S12859-017-1823-5  0.38
2017 Schneider HW, Raiol T, Brigido MM, Walter MEMT, Stadler PF. A Support Vector Machine based method to distinguish long non-coding RNAs from protein coding transcripts. Bmc Genomics. 18: 804. PMID 29047334 DOI: 10.1186/S12864-017-4178-4  0.377
2017 Richards CL, Alonso C, Becker C, Bossdorf O, Bucher E, Colomé-Tatché M, Durka W, Engelhardt J, Gaspar B, Gogol-Döring A, Grosse I, van Gurp TP, Heer K, Kronholm I, Lampei C, ... ... Stadler PF, et al. Ecological plant epigenetics: Evidence from model and non-model species, and the way forward. Ecology Letters. PMID 29027325 DOI: 10.1111/Ele.12858  0.646
2017 Machné R, Murray DB, Stadler PF. Similarity-Based Segmentation of Multi-Dimensional Signals. Scientific Reports. 7: 12355. PMID 28955039 DOI: 10.1038/S41598-017-12401-8  0.312
2017 Findeiß S, Etzel M, Will S, Mörl M, Stadler PF. Design of Artificial Riboswitches as Biosensors. Sensors (Basel, Switzerland). 17. PMID 28867802 DOI: 10.3390/S17091990  0.737
2017 Al Arab M, Bernt M, Höner Zu Siederdissen C, Tout K, Stadler PF. Partially local three-way alignments and the sequence signatures of mitochondrial genome rearrangements. Algorithms For Molecular Biology : Amb. 12: 22. PMID 28852417 DOI: 10.1186/S13015-017-0113-0  0.339
2017 Binder S, Hösler N, Riedel D, Zipfel I, Buschmann T, Kämpf C, Reiche K, Burger R, Gramatzki M, Hackermüller J, Stadler PF, Horn F. STAT3-induced long noncoding RNAs in multiple myeloma cells display different properties in cancer. Scientific Reports. 7: 7976. PMID 28801664 DOI: 10.1038/S41598-017-08348-5  0.333
2017 Fallmann J, Will S, Engelhardt J, Grüning B, Backofen R, Stadler PF. Recent advances in RNA folding. Journal of Biotechnology. PMID 28690134 DOI: 10.1016/J.Jbiotec.2017.07.007  0.4
2017 Indrischek H, Prohaska SJ, Gurevich VV, Gurevich EV, Stadler PF. Uncovering missing pieces: duplication and deletion history of arrestins in deuterostomes. Bmc Evolutionary Biology. 17: 163. PMID 28683816 DOI: 10.1186/S12862-017-1001-4  0.616
2017 Yazbeck AM, Tout KR, Stadler PF, Hertel J. Towards a Consistent, Quantitative Evaluation of MicroRNA Evolution. Journal of Integrative Bioinformatics. 14. PMID 28637930 DOI: 10.1515/Jib-2016-0013  0.357
2017 Grüning BA, Fallmann J, Yusuf D, Will S, Erxleben A, Eggenhofer F, Houwaart T, Batut B, Videm P, Bagnacani A, Wolfien M, Lott SC, Hoogstrate Y, Hess WR, Wolkenhauer O, ... ... Stadler PF, et al. The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy. Nucleic Acids Research. PMID 28582575 DOI: 10.1093/Nar/Gkx409  0.384
2017 Backofen R, Engelhardt J, Erxleben A, Fallmann J, Grüning B, Ohler U, Rajewsky N, Stadler PF. RNA-bioinformatics: Tools, Services and Databases for the Analysis of RNA-based Regulation. Journal of Biotechnology. PMID 28554830 DOI: 10.1016/J.Jbiotec.2017.05.019  0.406
2017 Alkan F, Wenzel A, Palasca O, Kerpedjiev P, Rudebeck AF, Stadler PF, Hofacker IL, Gorodkin J. RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets. Nucleic Acids Research. PMID 28108657 DOI: 10.1093/Nar/Gkw1325  0.391
2017 Hölzer M, Krähling V, Amman F, Barth E, Bernhart SH, Carmelo VA, Collatz M, Doose G, Eggenhofer F, Ewald J, Fallmann J, Feldhahn LM, Fricke M, Gebauer J, Gruber AJ, ... ... Stadler PF, et al. Corrigendum: Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells. Scientific Reports. 7: 39421. PMID 28074834 DOI: 10.1038/Srep39421  0.718
2017 Petrov AI, Kay SJE, Kalvari I, Howe KL, Gray KA, Bruford EA, Kersey PJ, Cochrane G, Finn RD, Bateman A, Kozomara A, Griffiths-Jones S, Frankish A, Zwieb CW, ... ... Stadler PF, et al. RNAcentral: a comprehensive database of non-coding RNA sequences. Nucleic Acids Research. 45: D128-D134. PMID 27794554 DOI: 10.1093/Nar/Gkw1008  0.415
2016 de Araujo Oliveira JV, Costa F, Backofen R, Stadler PF, Machado Telles Walter ME, Hertel J. SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification. Bmc Bioinformatics. 17: 464. PMID 28105919 DOI: 10.1186/S12859-016-1345-6  0.306
2016 Domin G, Findeiß S, Wachsmuth M, Will S, Stadler PF, Mörl M. Applicability of a computational design approach for synthetic riboswitches. Nucleic Acids Research. PMID 27994029 DOI: 10.1093/Nar/Gkw1267  0.726
2016 Hellmuth M, Stadler PF, Wieseke N. The mathematics of xenology: di-cographs, symbolic ultrametrics, 2-structures and tree-representable systems of binary relations. Journal of Mathematical Biology. PMID 27904954 DOI: 10.1007/S00285-016-1084-3  0.665
2016 Patra Bhattacharya D, Canzler S, Kehr S, Hertel J, Grosse I, Stadler PF. Phylogenetic distribution of plant snoRNA families. Bmc Genomics. 17: 969. PMID 27881081 DOI: 10.1186/S12864-016-3301-2  0.363
2016 Krakauer DC, Müller L, Prohaska SJ, Stadler PF. Design specifications for cellular regulation. Theory in Biosciences = Theorie in Den Biowissenschaften. PMID 27864730 DOI: 10.1007/S12064-016-0239-5  0.637
2016 Hölzer M, Krähling V, Amman F, Barth E, Bernhart SH, Carmelo VA, Collatz M, Doose G, Eggenhofer F, Ewald J, Fallmann J, Feldhahn LM, Fricke M, Gebauer J, Gruber AJ, ... ... Stadler PF, et al. Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells. Scientific Reports. 6: 34589. PMID 27713552 DOI: 10.1038/Srep34589  0.731
2016 Al Arab M, Höner Zu Siederdissen C, Tout K, Sahyoun AH, Stadler PF, Bernt M. Accurate annotation of protein-coding genes in mitochondrial genomes. Molecular Phylogenetics and Evolution. 106: 209-216. PMID 27693569 DOI: 10.1016/J.Ympev.2016.09.024  0.367
2016 Velandia-Huerto CA, Gittenberger AA, Brown FD, Stadler PF, Bermúdez-Santana CI. Automated detection of ncRNAs in the draft genome sequence of a colonial tunicate: the carpet sea squirt Didemnum vexillum. Bmc Genomics. 17: 691. PMID 27576499 DOI: 10.1186/S12864-016-2934-5  0.334
2016 Velandia-Huerto CA, Berkemer SJ, Hoffmann A, Retzlaff N, Romero Marroquín LC, Hernández-Rosales M, Stadler PF, Bermúdez-Santana CI. Orthologs, turn-over, and remolding of tRNAs in primates and fruit flies. Bmc Genomics. 17: 617. PMID 27515907 DOI: 10.1186/S12864-016-2927-4  0.403
2016 Nitsche A, Stadler PF. Evolutionary clues in lncRNAs. Wiley Interdisciplinary Reviews. Rna. PMID 27436689 DOI: 10.1002/Wrna.1376  0.417
2016 Righetti F, Nuss AM, Twittenhoff C, Beele S, Urban K, Will S, Bernhart SH, Stadler PF, Dersch P, Narberhaus F. Temperature-responsive in vitro RNA structurome of Yersinia pseudotuberculosis. Proceedings of the National Academy of Sciences of the United States of America. PMID 27298343 DOI: 10.1073/Pnas.1523004113  0.372
2016 Jorjani H, Kehr S, Jedlinski DJ, Gumienny R, Hertel J, Stadler PF, Zavolan M, Gruber AR. An updated human snoRNAome. Nucleic Acids Research. PMID 27174936 DOI: 10.1093/Nar/Gkw386  0.419
2016 Lorenz R, Hofacker IL, Stadler PF. RNA folding with hard and soft constraints. Algorithms For Molecular Biology : Amb. 11: 8. PMID 27110276 DOI: 10.1186/S13015-016-0070-Z  0.374
2016 Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, Berlin AM, Campbell MS, Barrell D, Martin KJ, Mulley JF, ... ... Stadler PF, et al. The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nature Genetics. 48: 427-37. PMID 26950095 DOI: 10.1038/Ng.3526  0.354
2016 Indrischek H, Wieseke N, Stadler PF, Prohaska SJ. The paralog-to-contig assignment problem: high quality gene models from fragmented assemblies. Algorithms For Molecular Biology : Amb. 11: 1. PMID 26913054 DOI: 10.1186/S13015-016-0063-Y  0.674
2016 Westermann AJ, Förstner KU, Amman F, Barquist L, Chao Y, Schulte LN, Müller L, Reinhardt R, Stadler PF, Vogel J. Dual RNA-seq unveils noncoding RNA functions in host-pathogen interactions. Nature. 529: 496-501. PMID 26789254 DOI: 10.1038/Nature16547  0.37
2016 Lorenz R, Luntzer D, Hofacker IL, Stadler PF, Wolfinger MT. SHAPE directed RNA folding. Bioinformatics (Oxford, England). 32: 145-7. PMID 26353838 DOI: 10.7490/F1000Research.1097918.1  0.719
2016 Stadler PF. Evolution of RNA-Based Networks. Current Topics in Microbiology and Immunology. 392: 43-59. PMID 26336964 DOI: 10.1007/82_2015_470  0.418
2016 Riechert M, Höner zu Siederdissen C, Stadler PF. Algebraic dynamic programming for multiple context-free grammars Theoretical Computer Science. 639: 91-109. DOI: 10.1016/J.Tcs.2016.05.032  0.315
2016 Flamm C, Stadler BMR, Stadler PF. Generalized Topologies: Hypergraphs, Chemical Reactions, and Biological Evolution Advances in Mathematical Chemistry and Applications. 2: 300-328. DOI: 10.1016/B978-1-68108-053-6.50013-2  0.557
2016 Hammack RH, Hellmuth M, Ostermeier L, Stadler PF. Associativity and Non-Associativity of Some Hypergraph Products Mathematics in Computer Science. 10: 403-408. DOI: 10.1007/S11786-016-0276-Y  0.592
2016 Andersen JL, Flamm C, Merkle D, Stadler PF. A software package for chemically inspired graph transformation Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9761: 73-88. DOI: 10.1007/978-3-319-40530-8_5  0.545
2016 Flamm C, Merkle D, Stadler PF, Thorsen U. Automatic inference of graph transformation rules using the cyclic nature of chemical reactions Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9761: 206-222. DOI: 10.1007/978-3-319-40530-8_13  0.552
2015 Agrisani A, Tafer H, Stadler PF, Furia M. Unusual Novel SnoRNA-Like RNAs in Drosophila melanogaster. Non-Coding Rna. 1: 139-150. PMID 29861420 DOI: 10.3390/Ncrna1020139  0.439
2015 Kolora SR, Faria R, Weigert A, Schaffer S, Grimm A, Henle K, Sahyoun AH, Stadler PF, Nowick K, Bleidorn C, Schlegel M. The complete mitochondrial genome of Lacerta bilineata and comparison with its closely related congener L. Viridis. Mitochondrial Dna. 1-3. PMID 26709540 DOI: 10.3109/19401736.2015.1111349  0.702
2015 zu Siederdissen CH, Prohaska SJ, Stadler PF. Algebraic Dynamic Programming over general data structures. Bmc Bioinformatics. 16: S2. PMID 26695390 DOI: 10.1186/1471-2105-16-S19-S2  0.674
2015 Jühling F, Kretzmer H, Bernhart SH, Otto C, Stadler PF, Hoffmann S. metilene: Fast and sensitive calling of differentially methylated regions from bisulfite sequencing data. Genome Research. PMID 26631489 DOI: 10.1101/Gr.196394.115  0.301
2015 Laubichler MD, Stadler PF, Prohaska SJ, Nowick K. The relativity of biological function. Theory in Biosciences = Theorie in Den Biowissenschaften. 134: 143-7. PMID 26449352 DOI: 10.1007/S12064-015-0215-5  0.777
2015 Kucharík M, Hofacker IL, Stadler PF, Qin J. Pseudoknots in RNA folding landscapes. Bioinformatics (Oxford, England). PMID 26428288 DOI: 10.1093/Bioinformatics/Btv572  0.366
2015 Höner Zu Siederdissen C, Hofacker IL, Stadler PF. Product Grammars for Alignment and Folding. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 12: 507-19. PMID 26357262 DOI: 10.1109/Tcbb.2014.2326155  0.301
2015 Engelhardt J, Stadler PF. Evolution of the unspliced transcriptome. Bmc Evolutionary Biology. 15: 166. PMID 26289325 DOI: 10.1186/S12862-015-0437-7  0.365
2015 Hecker N, Christensen-Dalsgaard M, Seemann SE, Havgaard JH, Stadler PF, Hofacker IL, Nielsen H, Gorodkin J. Optimizing RNA structures by sequence extensions using RNAcop. Nucleic Acids Research. 43: 8135-45. PMID 26283181 DOI: 10.1093/Nar/Gkv813  0.378
2015 Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, ... ... Stadler PF, et al. Third Report on Chicken Genes and Chromosomes 2015. Prepared by. Cytogenetic and Genome Research. 145: 78-179. PMID 26282327 DOI: 10.1159/000430927  0.342
2015 Sahyoun AH, Hölzer M, Jühling F, Höner zu Siederdissen C, Al-Arab M, Tout K, Marz M, Middendorf M, Stadler PF, Bernt M. Towards a comprehensive picture of alloacceptor tRNA remolding in metazoan mitochondrial genomes. Nucleic Acids Research. 43: 8044-56. PMID 26227972 DOI: 10.1093/Nar/Gkv746  0.582
2015 Arruda WC, Souza DS, Ralha CG, Walter ME, Raiol T, Brigido MM, Stadler PF. Knowledge-based reasoning to annotate noncoding RNA using multi-agent system. Journal of Bioinformatics and Computational Biology. 1550021. PMID 26223200 DOI: 10.1142/S0219720015500213  0.323
2015 Le Duc D, Renaud G, Krishnan A, Almén MS, Huynen L, Prohaska SJ, Ongyerth M, Bitarello BD, Schiöth HB, Hofreiter M, Stadler PF, Prüfer K, Lambert D, Kelso J, Schöneberg T. Kiwi genome provides insights into evolution of a nocturnal lifestyle. Genome Biology. 16: 147. PMID 26201466 DOI: 10.1186/S13059-015-0711-4  0.643
2015 Lyubetsky V, Piel WH, Stadler PF. Molecular Phylogenetics 2014. Biomed Research International. 2015: 919251. PMID 26161422 DOI: 10.1155/2015/919251  0.446
2015 Betat H, Mede T, Tretbar S, Steiner L, Stadler PF, Mörl M, Prohaska SJ. The ancestor of modern Holozoa acquired the CCA-adding enzyme from Alphaproteobacteria by horizontal gene transfer. Nucleic Acids Research. 43: 6739-46. PMID 26117543 DOI: 10.1093/Nar/Gkv631  0.652
2015 Wachsmuth M, Domin G, Lorenz R, Serfling R, Findeiß S, Stadler PF, Mörl M. Design criteria for synthetic riboswitches acting on transcription. Rna Biology. 12: 221-31. PMID 25826571 DOI: 10.1080/15476286.2015.1017235  0.72
2015 Gardner PP, Fasold M, Burge SW, Ninova M, Hertel J, Kehr S, Steeves TE, Griffiths-Jones S, Stadler PF. Conservation and losses of non-coding RNAs in avian genomes. Plos One. 10: e0121797. PMID 25822729 DOI: 10.1371/Journal.Pone.0121797  0.409
2015 Nitsche A, Rose D, Fasold M, Reiche K, Stadler PF. Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well conserved. Rna (New York, N.Y.). 21: 801-12. PMID 25802408 DOI: 10.1261/Rna.046342.114  0.433
2015 Hoffmann S, Stadler PF, Strimmer K. A simple data-adaptive probabilistic variant calling model. Algorithms For Molecular Biology : Amb. 10: 10. PMID 25788974 DOI: 10.1186/S13015-015-0037-5  0.331
2015 Hertel J, Stadler PF. The Expansion of Animal MicroRNA Families Revisited. Life (Basel, Switzerland). 5: 905-20. PMID 25780960 DOI: 10.3390/Life5010905  0.357
2015 Hellmuth M, Wieseke N, Lechner M, Lenhof HP, Middendorf M, Stadler PF. Phylogenomics with paralogs. Proceedings of the National Academy of Sciences of the United States of America. 112: 2058-63. PMID 25646426 DOI: 10.1073/Pnas.1412770112  0.662
2015 Angrisani A, Tafer H, Stadler PF, Furia M. Developmentally regulated expression and expression strategies of Drosophila snoRNAs. Insect Biochemistry and Molecular Biology. 61: 69-78. PMID 25641266 DOI: 10.1016/J.Ibmb.2015.01.013  0.368
2015 Findeiß S, Wachsmuth M, Mörl M, Stadler PF. Design of transcription regulating riboswitches. Methods in Enzymology. 550: 1-22. PMID 25605378 DOI: 10.1016/Bs.Mie.2014.10.029  0.718
2015 Qi X, Rand DP, Podlevsky JD, Li Y, Mosig A, Stadler PF, Chen JJ. Prevalent and distinct spliceosomal 3'-end processing mechanisms for fungal telomerase RNA. Nature Communications. 6: 6105. PMID 25598218 DOI: 10.1038/Ncomms7105  0.369
2015 Berkemer SJ, Höner zu Siederdissen C, Amman F, Wintsche A, Will S, Hofacker I, Prohaska S, Stadler P. Processed Small RNAs in Archaea and BHB Elements Genomics and Computational Biology. 1: 18. DOI: 10.18547/GCB.2015.VOL1.ISS1.E18  0.677
2015 Engelhardt J, Stadler PF. Evolution of 3'UTR-associated RNAs Bmc Bioinformatics. 16. DOI: 10.1186/1471-2105-16-S8-A7  0.351
2015 Hoell JI, Das Mahapatra K, Hezaveh K, Kloetgen A, Bernhart S, Hoffmann S, Stadler P, Lenze D, Haake A, Richter J, Truemper LH, Burkhardt B, Klapper W, Moeller P, Rosenstiel P, et al. Identification of Blut, a Novel Long-Noncoding RNA Differentially Expressed in Burkitt Lymphoma Blood. 126: 3875-3875. DOI: 10.1182/Blood.V126.23.3875.3875  0.388
2015 Berkemer SJ, Chaves RRC, Fritz A, Hellmuth M, Hernandez-Rosales M, Stadler PF. Spiders can be Recognized by Counting Their Legs Mathematics in Computer Science. 9: 437-441. DOI: 10.1007/S11786-015-0233-1  0.643
2015 Andersen JL, Flamm C, Merkle D, Stadler PF. In silico Support for Eschenmoser's Glyoxylate Scenario Israel Journal of Chemistry. 55: 919-933. DOI: 10.1002/Ijch.201400187  0.601
2014 Patra D, Fasold M, Langenberger D, Steger G, Grosse I, Stadler PF. plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants. Frontiers in Plant Science. 5: 708. PMID 25566282 DOI: 10.3389/Fpls.2014.00708  0.388
2014 Machyna M, Kehr S, Straube K, Kappei D, Buchholz F, Butter F, Ule J, Hertel J, Stadler PF, Neugebauer KM. The coilin interactome identifies hundreds of small noncoding RNAs that traffic through Cajal bodies. Molecular Cell. 56: 389-99. PMID 25514182 DOI: 10.1016/J.Molcel.2014.10.004  0.378
2014 Mann M, Nahar F, Schnorr N, Backofen R, Stadler PF, Flamm C. Atom mapping with constraint programming. Algorithms For Molecular Biology : Amb. 9: 23. PMID 25484913 DOI: 10.1186/S13015-014-0023-3  0.57
2014 Qin J, Fricke M, Marz M, Stadler PF, Backofen R. Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures. Algorithms For Molecular Biology : Amb. 9: 19. PMID 25285153 DOI: 10.1186/1748-7188-9-19  0.609
2014 Lechner M, Hernandez-Rosales M, Doerr D, Wieseke N, Thévenin A, Stoye J, Hartmann RK, Prohaska SJ, Stadler PF. Orthology detection combining clustering and synteny for very large datasets. Plos One. 9: e105015. PMID 25137074 DOI: 10.1371/Journal.Pone.0105015  0.677
2014 Müller GA, Wintsche A, Stangner K, Prohaska SJ, Stadler PF, Engeland K. The CHR site: definition and genome-wide identification of a cell cycle transcriptional element. Nucleic Acids Research. 42: 10331-50. PMID 25106871 DOI: 10.1093/Nar/Gku696  0.663
2014 Anthon C, Tafer H, Havgaard JH, Thomsen B, Hedegaard J, Seemann SE, Pundhir S, Kehr S, Bartschat S, Nielsen M, Nielsen RO, Fredholm M, Stadler PF, Gorodkin J. Structured RNAs and synteny regions in the pig genome. Bmc Genomics. 15: 459. PMID 24917120 DOI: 10.1186/1471-2164-15-459  0.395
2014 Sahyoun AH, Bernt M, Stadler PF, Tout K. GC skew and mitochondrial origins of replication. Mitochondrion. 17: 56-66. PMID 24911382 DOI: 10.1016/J.Mito.2014.05.009  0.312
2014 Andersen JL, Flamm C, Merkle D, Stadler PF. Generic strategies for chemical space exploration. International Journal of Computational Biology and Drug Design. 7: 225-58. PMID 24878732 DOI: 10.1504/Ijcbdd.2014.061649  0.599
2014 Backofen R, Amman F, Costa F, Findeiß S, Richter AS, Stadler PF. Bioinformatics of prokaryotic RNAs. Rna Biology. 11: 470-83. PMID 24755880 DOI: 10.4161/Rna.28647  0.749
2014 Rivarola-Duarte L, Otto C, Jühling F, Schreiber S, Bedulina D, Jakob L, Gurkov A, Axenov-Gribanov D, Sahyoun AH, Lucassen M, Hackermüller J, Hoffmann S, Sartoris F, Pörtner HO, Timofeyev M, ... ... Stadler PF, et al. A first glimpse at the genome of the Baikalian amphipod Eulimnogammarus verrucosus. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. 322: 177-89. PMID 24677529 DOI: 10.1002/Jez.B.22560  0.354
2014 Amman F, Wolfinger MT, Lorenz R, Hofacker IL, Stadler PF, Findeiß S. TSSAR: TSS annotation regime for dRNA-seq data. Bmc Bioinformatics. 15: 89. PMID 24674136 DOI: 10.1186/1471-2105-15-89  0.806
2014 Kucharík M, Hofacker IL, Stadler PF, Qin J. Basin Hopping Graph: a computational framework to characterize RNA folding landscapes. Bioinformatics (Oxford, England). 30: 2009-17. PMID 24648041 DOI: 10.1093/Bioinformatics/Btu156  0.372
2014 Stadler PF. Class-specific prediction of ncRNAs. Methods in Molecular Biology (Clifton, N.J.). 1097: 199-213. PMID 24639161 DOI: 10.1007/978-1-62703-709-9_10  0.417
2014 Otto C, Stadler PF, Hoffmann S. Lacking alignments? The next-generation sequencing mapper segemehl revisited. Bioinformatics (Oxford, England). 30: 1837-43. PMID 24626854 DOI: 10.1093/Bioinformatics/Btu146  0.35
2014 Hackermüller J, Reiche K, Otto C, Hösler N, Blumert C, Brocke-Heidrich K, Böhlig L, Nitsche A, Kasack K, Ahnert P, Krupp W, Engeland K, Stadler PF, Horn F. Cell cycle, oncogenic and tumor suppressor pathways regulate numerous long and macro non-protein-coding RNAs. Genome Biology. 15: R48. PMID 24594072 DOI: 10.1186/Gb-2014-15-3-R48  0.351
2014 Marz M, Beerenwinkel N, Drosten C, Fricke M, Frishman D, Hofacker IL, Hoffmann D, Middendorf M, Rattei T, Stadler PF, Töpfer A. Challenges in RNA virus bioinformatics. Bioinformatics (Oxford, England). 30: 1793-9. PMID 24590443 DOI: 10.1093/Bioinformatics/Btu105  0.598
2014 Hoffmann S, Otto C, Doose G, Tanzer A, Langenberger D, Christ S, Kunz M, Holdt LM, Teupser D, Hackermüller J, Stadler PF. A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection. Genome Biology. 15: R34. PMID 24512684 DOI: 10.1186/Gb-2014-15-2-R34  0.39
2014 Dohm JC, Minoche AE, Holtgräwe D, Capella-Gutiérrez S, Zakrzewski F, Tafer H, Rupp O, Sörensen TR, Stracke R, Reinhardt R, Goesmann A, Kraft T, Schulz B, Stadler PF, Schmidt T, et al. The genome of the recently domesticated crop plant sugar beet (Beta vulgaris). Nature. 505: 546-9. PMID 24352233 DOI: 10.1038/Nature12817  0.357
2014 Bartschat S, Kehr S, Tafer H, Stadler PF, Hertel J. snoStrip: a snoRNA annotation pipeline. Bioinformatics (Oxford, England). 30: 115-6. PMID 24174566 DOI: 10.1093/Bioinformatics/Btt604  0.398
2014 Nitsche A, Doose G, Tafer H, Robinson M, Saha NR, Gerdol M, Canapa A, Hoffmann S, Amemiya CT, Stadler PF. Atypical RNAs in the coelacanth transcriptome. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. 322: 342-51. PMID 24174405 DOI: 10.1002/Jez.B.22542  0.383
2014 Kehr S, Bartschat S, Tafer H, Stadler PF, Hertel J. Matching of Soulmates: coevolution of snoRNAs and their targets. Molecular Biology and Evolution. 31: 455-67. PMID 24162733 DOI: 10.1093/Molbev/Mst209  0.412
2014 Wende S, Platzer EG, Jühling F, Pütz J, Florentz C, Stadler PF, Mörl M. Biological evidence for the world's smallest tRNAs. Biochimie. 100: 151-8. PMID 23958440 DOI: 10.1016/J.Biochi.2013.07.034  0.354
2014 Amman F, Wolfinger MT, Hofacker IL, Stadler PF, Findeiß S. TSSAR: transcription start site annotation regime for dRNA-seq data F1000research. 5. DOI: 10.7490/F1000Research.1097124.1  0.777
2014 Kolora R, Weigert A, Gerth M, Sahyoun A, Stadler P, Henle K, Faria R, Bleidorn C, Nowick K, Schlegel M. An NGS-based approach for the comparison of lizard species to detect genome divergence and rearrangements F1000research. 5. DOI: 10.7490/F1000Research.1096546.1  0.696
2014 Hellmuth M, Leydold J, Stadler PF. Convex cycle bases Ars Mathematica Contemporanea. 7: 123-140. DOI: 10.26493/1855-3974.226.0A2  0.618
2014 Misof B, Meusemann K, von Reumont BM, Kück P, Prohaska SJ, Stadler PF. A priori assessment of data quality in molecular phylogenetics Algorithms For Molecular Biology. 9. DOI: 10.1186/S13015-014-0022-4  0.648
2014 Hernandez-Rosales M, Wieseke N, Hellmuth M, Stadler PF. Simulation of gene family histories Bmc Bioinformatics. 15. DOI: 10.1186/1471-2105-15-S3-A8  0.65
2014 Hellmuth M, Ostermeier L, Stadler PF. Unique square property, equitable partitions, and product-like graphs Discrete Mathematics. 320: 92-103. DOI: 10.1016/J.Disc.2013.12.012  0.616
2014 Andersen JL, Flamm C, Merkle D, Stadler PF. 50 shades of rule composition from chemical reactions to higher levels of abstraction Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 8738: 115-135. DOI: 10.1007/978-3-319-10398-3_9  0.557
2014 Marz M, Wehner S, Stadler PF. Homology Search for Small Structured Non-coding RNAs Handbook of Rna Biochemistry: Second, Completely Revised and Enlarged Edition. 2: 619-632. DOI: 10.1002/9783527647064.ch29  0.562
2014 Höner zu Siederdissen C, Prohaska SJ, Stadler PF. Dynamic programming for set data types Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 8826: 57-64.  0.623
2013 Lorenz R, Bernhart SH, Qin J, Höner zu Siederdissen C, Tanzer A, Amman F, Hofacker IL, Stadler PF. 2D meets 4G: G-quadruplexes in RNA secondary structure prediction. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 10: 832-44. PMID 24334379 DOI: 10.1109/Tcbb.2013.7  0.37
2013 Arnold C, Stadler PF, Prohaska SJ. Chromatin computation: epigenetic inheritance as a pattern reconstruction problem. Journal of Theoretical Biology. 336: 61-74. PMID 23880640 DOI: 10.1016/J.Jtbi.2013.07.012  0.635
2013 Holdt LM, Hoffmann S, Sass K, Langenberger D, Scholz M, Krohn K, Finstermeier K, Stahringer A, Wilfert W, Beutner F, Gielen S, Schuler G, Gäbel G, Bergert H, Bechmann I, ... Stadler PF, et al. Alu elements in ANRIL non-coding RNA at chromosome 9p21 modulate atherogenic cell functions through trans-regulation of gene networks. Plos Genetics. 9: e1003588. PMID 23861667 DOI: 10.1371/Journal.Pgen.1003588  0.375
2013 Smith MA, Gesell T, Stadler PF, Mattick JS. Widespread purifying selection on RNA structure in mammals. Nucleic Acids Research. 41: 8220-36. PMID 23847102 DOI: 10.1093/Nar/Gkt596  0.436
2013 Höner Zu Siederdissen C, Hammer S, Abfalter I, Hofacker IL, Flamm C, Stadler PF. Computational design of RNAs with complex energy landscapes. Biopolymers. 99: 1124-36. PMID 23818234 DOI: 10.1002/Bip.22337  0.657
2013 Huang Y, Li Y, Burt DW, Chen H, Zhang Y, Qian W, Kim H, Gan S, Zhao Y, Li J, Yi K, Feng H, Zhu P, Li B, Liu Q, ... ... Stadler PF, et al. The duck genome and transcriptome provide insight into an avian influenza virus reservoir species. Nature Genetics. 45: 776-83. PMID 23749191 DOI: 10.1038/Ng.2657  0.553
2013 Doose G, Alexis M, Kirsch R, Findeiß S, Langenberger D, Machné R, Mörl M, Hoffmann S, Stadler PF. Mapping the RNA-Seq trash bin: unusual transcripts in prokaryotic transcriptome sequencing data. Rna Biology. 10: 1204-10. PMID 23702463 DOI: 10.4161/Rna.24972  0.737
2013 Bernt M, Bleidorn C, Braband A, Dambach J, Donath A, Fritzsch G, Golombek A, Hadrys H, Jühling F, Meusemann K, Middendorf M, Misof B, Perseke M, Podsiadlowski L, von Reumont B, ... ... Stadler PF, et al. A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny. Molecular Phylogenetics and Evolution. 69: 352-64. PMID 23684911 DOI: 10.1016/J.Ympev.2013.05.002  0.33
2013 Müller SA, Findeiß S, Pernitzsch SR, Wissenbach DK, Stadler PF, Hofacker IL, von Bergen M, Kalkhof S. Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics. Journal of Proteomics. 86: 27-42. PMID 23665149 DOI: 10.1016/J.Jprot.2013.04.036  0.71
2013 Sabarinathan R, Tafer H, Seemann SE, Hofacker IL, Stadler PF, Gorodkin J. The RNAsnp web server: predicting SNP effects on local RNA secondary structure. Nucleic Acids Research. 41: W475-9. PMID 23630321 DOI: 10.1093/Nar/Gkt291  0.419
2013 Will S, Siebauer MF, Heyne S, Engelhardt J, Stadler PF, Reiche, Backofen R. LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search. Algorithms For Molecular Biology : Amb. 8: 14. PMID 23601347 DOI: 10.1186/1748-7188-8-14  0.424
2013 Amemiya CT, Alföldi J, Lee AP, Fan S, Philippe H, Maccallum I, Braasch I, Manousaki T, Schneider I, Rohner N, Organ C, Chalopin D, Smith JJ, Robinson M, Dorrington RA, ... ... Stadler PF, et al. The African coelacanth genome provides insights into tetrapod evolution. Nature. 496: 311-6. PMID 23598338 DOI: 10.1038/Nature12027  0.673
2013 Li Y, Podlevsky JD, Marz M, Qi X, Hoffmann S, Stadler PF, Chen JJ. Identification of purple sea urchin telomerase RNA using a next-generation sequencing based approach. Rna (New York, N.Y.). 19: 852-60. PMID 23584428 DOI: 10.1261/Rna.039131.113  0.628
2013 Sabarinathan R, Tafer H, Seemann SE, Hofacker IL, Stadler PF, Gorodkin J. RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs. Human Mutation. 34: 546-56. PMID 23315997 DOI: 10.1002/Humu.22273  0.38
2013 Wachsmuth M, Findeiß S, Weissheimer N, Stadler PF, Mörl M. De novo design of a synthetic riboswitch that regulates transcription termination. Nucleic Acids Research. 41: 2541-51. PMID 23275562 DOI: 10.1093/Nar/Gks1330  0.716
2013 Lehmann J, Stadler PF, Krauss V. Near intron pairs and the metazoan tree. Molecular Phylogenetics and Evolution. 66: 811-23. PMID 23201572 DOI: 10.1016/J.Ympev.2012.11.012  0.389
2013 Langenberger D, Çakir MV, Hoffmann S, Stadler PF. Dicer-processed small RNAs: rules and exceptions. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. 320: 35-46. PMID 23165937 DOI: 10.1002/Jez.B.22481  0.342
2013 Bernt M, Braband A, Schierwater B, Stadler PF. Genetic aspects of mitochondrial genome evolution. Molecular Phylogenetics and Evolution. 69: 328-38. PMID 23142697 DOI: 10.1016/J.Ympev.2012.10.020  0.332
2013 Dieterich C, Stadler PF. Computational biology of RNA interactions. Wiley Interdisciplinary Reviews. Rna. 4: 107-20. PMID 23139167 DOI: 10.1002/Wrna.1147  0.388
2013 Lechner M, Marz M, Ihling C, Sinz A, Stadler PF, Krauss V. The correlation of genome size and DNA methylation rate in metazoans. Theory in Biosciences = Theorie in Den Biowissenschaften. 132: 47-60. PMID 23132463 DOI: 10.1007/S12064-012-0167-Y  0.555
2013 Qi X, Li Y, Honda S, Hoffmann S, Marz M, Mosig A, Podlevsky JD, Stadler PF, Selker EU, Chen JJ. The common ancestral core of vertebrate and fungal telomerase RNAs. Nucleic Acids Research. 41: 450-62. PMID 23093598 DOI: 10.1093/Nar/Gks980  0.644
2013 Bernt M, Braband A, Middendorf M, Misof B, Rota-Stabelli O, Stadler PF. Bioinformatics methods for the comparative analysis of metazoan mitochondrial genome sequences. Molecular Phylogenetics and Evolution. 69: 320-7. PMID 23023207 DOI: 10.1016/J.Ympev.2012.09.019  0.374
2013 Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, Pütz J, Middendorf M, Stadler PF. MITOS: improved de novo metazoan mitochondrial genome annotation. Molecular Phylogenetics and Evolution. 69: 313-9. PMID 22982435 DOI: 10.1016/J.Ympev.2012.08.023  0.409
2013 Hellmuth M, Hernandez-Rosales M, Huber KT, Moulton V, Stadler PF, Wieseke N. Orthology relations, symbolic ultrametrics, and cographs. Journal of Mathematical Biology. 66: 399-420. PMID 22456957 DOI: 10.1007/S00285-012-0525-X  0.659
2013 Langenberger D, Bermudez-Santana CI, Stadler PF, Hoffmann S. Identification and classification of small RNAs in transcriptome sequence data. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 80-7. PMID 19908360 DOI: 10.1142/9789814295291_0010  0.313
2013 Andersen JL, Andersen T, Flamm C, Hanczyc MM, Merkle D, Stadler PF. Navigating the chemical space of hcn polymerization and hydrolysis: Guiding graph grammars by mass spectrometry data Entropy. 15: 4066-4083. DOI: 10.3390/E15104066  0.587
2013 Holdt LM, Hoffmann S, Sass K, Langenberger D, Scholz M, Krohn K, Finstermeier K, Stahringer A, Wilfert W, Beutner F, Gielen S, Schuler G, Gäbel G, Bergert H, Bechmann I, ... Stadler PF, et al. Pivotal role for Alu motif in ANRIL RNA function. Plos Genetics. DOI: 10.1371/Journal.Pgen.1003588.G005  0.351
2013 Andersen JL, Flamm C, Merkle D, Stadler PF. Inferring chemical reaction patterns using rule composition in graph grammars Journal of Systems Chemistry. 4: 4. DOI: 10.1186/1759-2208-4-4  0.588
2013 Flamm C, Ullrich A, Ekker H, Mann M, Högerl D, Rohrschneider M, Sauer S, Scheuermann G, Klemm K, Hofacker IL, Stadler PF. Evolution of metabolic networks: A computational frame-work Journal of Systems Chemistry. 1. DOI: 10.1186/1759-2208-1-4  0.601
2013 Fagerberg R, Flamm C, Merkle D, Peters P, Stadler PF. On the Complexity of Reconstructing Chemical Reaction Networks Mathematics in Computer Science. 7: 275-292. DOI: 10.1007/S11786-013-0160-Y  0.595
2013 Backofen R, Fricke M, Marz M, Qin J, Stadler PF. Distribution of graph-distances in Boltzmann ensembles of RNA secondary structures Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 8126: 112-125. DOI: 10.1007/978-3-642-40453-5_10  0.577
2013 Sabarinathan R, Tafer H, Seemann SE, Hofacker IL, Stadler PF, Gorodkin J. RNAsnp: Efficient Detection of Local RNA Secondary Structure Changes Induced by SNPs: HUMAN MUTATION Human Mutation. 34: 925-925. DOI: 10.1002/Humu.22323  0.314
2012 Lessa FA, Raiol T, Brigido MM, Martins Neto DS, Walter ME, Stadler PF. Clustering rfam 10.1: clans, families, and classes. Genes. 3: 378-90. PMID 24704975 DOI: 10.3390/Genes3030378  0.369
2012 Groenen MA, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, Rogel-Gaillard C, Park C, Milan D, Megens HJ, Li S, Larkin DM, Kim H, Frantz LA, Caccamo M, ... ... Stadler P, et al. Analyses of pig genomes provide insight into porcine demography and evolution. Nature. 491: 393-8. PMID 23151582 DOI: 10.1038/Nature11622  0.38
2012 Jühling F, Pütz J, Florentz C, Stadler PF. Armless mitochondrial tRNAs in Enoplea (Nematoda). Rna Biology. 9: 1161-6. PMID 23018779 DOI: 10.4161/Rna.21630  0.337
2012 Tippmann SC, Ivanek R, Gaidatzis D, Schöler A, Hoerner L, van Nimwegen E, Stadler PF, Stadler MB, Schübeler D. Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels. Molecular Systems Biology. 8: 593. PMID 22806141 DOI: 10.1038/Msb.2012.23  0.347
2012 Niehuis O, Hartig G, Grath S, Pohl H, Lehmann J, Tafer H, Donath A, Krauss V, Eisenhardt C, Hertel J, Petersen M, Mayer C, Meusemann K, Peters RS, Stadler PF, et al. Genomic and morphological evidence converge to resolve the enigma of Strepsiptera. Current Biology : Cb. 22: 1309-13. PMID 22704986 DOI: 10.1016/J.Cub.2012.05.018  0.602
2012 Hertel J, Bartschat S, Wintsche A, Otto C, Stadler PF. Evolution of the let-7 microRNA family. Rna Biology. 9: 231-41. PMID 22617875 DOI: 10.4161/Rna.18974  0.305
2012 Otto C, Stadler PF, Hoffmann S. Fast and sensitive mapping of bisulfite-treated sequencing data. Bioinformatics (Oxford, England). 28: 1698-704. PMID 22581174 DOI: 10.1093/Bioinformatics/Bts254  0.31
2012 Engelhardt J, Stadler PF. Hidden treasures in unspliced EST data. Theory in Biosciences = Theorie in Den Biowissenschaften. 131: 49-57. PMID 22485013 DOI: 10.1007/S12064-012-0151-6  0.423
2012 Will S, Joshi T, Hofacker IL, Stadler PF, Backofen R. LocARNA-P: accurate boundary prediction and improved detection of structural RNAs. Rna (New York, N.Y.). 18: 900-14. PMID 22450757 DOI: 10.1261/Rna.029041.111  0.38
2012 Washietl S, Hofacker IL, Stadler PF, Kellis M. RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction. Nucleic Acids Research. 40: 4261-72. PMID 22287623 DOI: 10.1093/Nar/Gks009  0.329
2012 Jühling F, Pütz J, Bernt M, Donath A, Middendorf M, Florentz C, Stadler PF. Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements. Nucleic Acids Research. 40: 2833-45. PMID 22139921 DOI: 10.1093/Nar/Gkr1131  0.364
2012 Reidys CM, Huang FW, Andersen JE, Penner RC, Stadler PF, Nebel ME. Addendum: topology and prediction of RNA pseudoknots. Bioinformatics (Oxford, England). 28: 300. PMID 22106334 DOI: 10.1093/Bioinformatics/Btr643  0.632
2012 Schmidtke C, Findeiss S, Sharma CM, Kuhfuss J, Hoffmann S, Vogel J, Stadler PF, Bonas U. Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions. Nucleic Acids Research. 40: 2020-31. PMID 22080557 DOI: 10.1093/Nar/Gkr904  0.747
2012 Langenberger D, Pundhir S, Ekstrøm CT, Stadler PF, Hoffmann S, Gorodkin J. deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns. Bioinformatics (Oxford, England). 28: 17-24. PMID 22053076 DOI: 10.7490/F1000Research.2119.1  0.405
2012 Giegé R, Jühling F, Pütz J, Stadler P, Sauter C, Florentz C. Structure of transfer RNAs: similarity and variability. Wiley Interdisciplinary Reviews. Rna. 3: 37-61. PMID 21957054 DOI: 10.1002/Wrna.103  0.407
2012 Hellmuth M, Ostermeier PJ, Stadler PF. Minimum cycle bases of lexicographic products Ars Mathematica Contemporanea. 5: 223-234. DOI: 10.26493/1855-3974.172.8A7  0.602
2012 Andersen JL, Flamm C, Merkle D, Stadler PF. Maximizing output and recognizing autocatalysis in chemical reaction networks is NP-complete Journal of Systems Chemistry. 3. DOI: 10.1186/1759-2208-3-1  0.58
2012 Hernandez-Rosales M, Hellmuth M, Wieseke N, Huber KT, Moulton V, Stadler PF. From event-labeled gene trees to species trees Bmc Bioinformatics. 13. DOI: 10.1186/1471-2105-13-S19-S6  0.633
2012 Hofacker IL, Reidys CM, Stadler PF. Symmetric circular matchings and RNA folding Discrete Mathematics. 312: 100-112. DOI: 10.1016/J.Disc.2011.06.004  0.666
2012 Hellmuth M, Ostermeier L, Stadler PF. Diagonalized Cartesian products of S-prime graphs are S-prime Discrete Mathematics. 312: 74-80. DOI: 10.1016/J.Disc.2011.03.033  0.603
2012 Hellmuth M, Ostermeier L, Stadler PF. A Survey on Hypergraph Products Mathematics in Computer Science. 6: 1-32. DOI: 10.1007/S11786-012-0109-6  0.612
2012 Ostermeier L, Hellmuth M, Stadler PF. The Cartesian product of hypergraphs Journal of Graph Theory. 70: 180-196. DOI: 10.1002/Jgt.20609  0.619
2011 Parikesit AA, Stadler PF, Prohaska SJ. Evolution and quantitative comparison of genome-wide protein domain distributions. Genes. 2: 912-24. PMID 24710298 DOI: 10.3390/Genes2040912  0.653
2011 Lozada-Chávez I, Stadler PF, Prohaska SJ. "Hypothesis for the modern RNA world": a pervasive non-coding RNA-based genetic regulation is a prerequisite for the emergence of multicellular complexity. Origins of Life and Evolution of the Biosphere : the Journal of the International Society For the Study of the Origin of Life. 41: 587-607. PMID 22322874 DOI: 10.1007/S11084-011-9262-1  0.7
2011 Rose D, Stadler PF. Molecular evolution of the non-coding eosinophil granule ontogeny transcript. Frontiers in Genetics. 2: 69. PMID 22303364 DOI: 10.3389/Fgene.2011.00069  0.423
2011 Lorenz R, Bernhart SH, Höner Zu Siederdissen C, Tafer H, Flamm C, Stadler PF, Hofacker IL. ViennaRNA Package 2.0. Algorithms For Molecular Biology : Amb. 6: 26. PMID 22115189 DOI: 10.1186/1748-7188-6-26  0.594
2011 Marz M, Gruber AR, Höner Zu Siederdissen C, Amman F, Badelt S, Bartschat S, Bernhart SH, Beyer W, Kehr S, Lorenz R, Tanzer A, Yusuf D, Tafer H, Hofacker IL, Stadler PF. Animal snoRNAs and scaRNAs with exceptional structures. Rna Biology. 8: 938-46. PMID 21955586 DOI: 10.4161/Rna.8.6.16603  0.629
2011 Bateman A, Agrawal S, Birney E, Bruford EA, Bujnicki JM, Cochrane G, Cole JR, Dinger ME, Enright AJ, Gardner PP, Gautheret D, Griffiths-Jones S, Harrow J, Herrero J, Holmes IH, ... ... Stadler PF, et al. RNAcentral: A vision for an international database of RNA sequences. Rna (New York, N.Y.). 17: 1941-6. PMID 21940779 DOI: 10.1261/Rna.2750811  0.625
2011 Marz M, Stadler PF. RNA interactions. Advances in Experimental Medicine and Biology. 722: 20-38. PMID 21915780 DOI: 10.1007/978-1-4614-0332-6_2  0.59
2011 Findeiss S, Engelhardt J, Prohaska SJ, Stadler PF. Protein-coding structured RNAs: A computational survey of conserved RNA secondary structures overlapping coding regions in drosophilids. Biochimie. 93: 2019-23. PMID 21835221 DOI: 10.1016/J.Biochi.2011.07.023  0.819
2011 Clark MB, Amaral PP, Schlesinger FJ, Dinger ME, Taft RJ, Rinn JL, Ponting CP, Stadler PF, Morris KV, Morillon A, Rozowsky JS, Gerstein MB, Wahlestedt C, Hayashizaki Y, Carninci P, et al. The reality of pervasive transcription. Plos Biology. 9: e1000625; discussion. PMID 21765801 DOI: 10.1371/Journal.Pbio.1000625  0.387
2011 Raincrow JD, Dewar K, Stocsits C, Prohaska SJ, Amemiya CT, Stadler PF, Chiu CH. Hox clusters of the bichir (Actinopterygii, Polypterus senegalus) highlight unique patterns of sequence evolution in gnathostome phylogeny. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. 316: 451-64. PMID 21688387 DOI: 10.1002/Jez.B.21420  0.66
2011 Eggenhofer F, Tafer H, Stadler PF, Hofacker IL. RNApredator: fast accessibility-based prediction of sRNA targets. Nucleic Acids Research. 39: W149-54. PMID 21672960 DOI: 10.1093/Nar/Gkr467  0.372
2011 Fasold M, Langenberger D, Binder H, Stadler PF, Hoffmann S. DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Research. 39: W112-7. PMID 21622957 DOI: 10.1093/Nar/Gkr357  0.406
2011 Rose D, Hiller M, Schutt K, Hackermüller J, Backofen R, Stadler PF. Computational discovery of human coding and non-coding transcripts with conserved splice sites. Bioinformatics (Oxford, England). 27: 1894-900. PMID 21622663 DOI: 10.1093/Bioinformatics/Btr314  0.341
2011 Tafer H, Amman F, Eggenhofer F, Stadler PF, Hofacker IL. Fast accessibility-based prediction of RNA-RNA interactions. Bioinformatics (Oxford, England). 27: 1934-40. PMID 21593134 DOI: 10.1093/Bioinformatics/Btr281  0.386
2011 Lechner M, Findeiss S, Steiner L, Marz M, Stadler PF, Prohaska SJ. Proteinortho: detection of (co-)orthologs in large-scale analysis. Bmc Bioinformatics. 12: 124. PMID 21526987 DOI: 10.1186/1471-2105-12-124  0.794
2011 Otto C, Hoffmann S, Gorodkin J, Stadler PF. Fast local fragment chaining using sum-of-pair gap costs. Algorithms For Molecular Biology : Amb. 6: 4. PMID 21418573 DOI: 10.1186/1748-7188-6-4  0.382
2011 Ullrich A, Rohrschneider M, Scheuermann G, Stadler PF, Flamm C. In silico evolution of early metabolism. Artificial Life. 17: 87-108. PMID 21370961 DOI: 10.1162/Artl_A_00021  0.58
2011 Prohaska SJ, Stadler PF. The use and abuse of -omes. Methods in Molecular Biology (Clifton, N.J.). 719: 173-96. PMID 21370084 DOI: 10.1007/978-1-61779-027-0_8  0.628
2011 Washietl S, Findeiss S, Müller SA, Kalkhof S, von Bergen M, Hofacker IL, Stadler PF, Goldman N. RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data. Rna (New York, N.Y.). 17: 578-94. PMID 21357752 DOI: 10.1261/Rna.2536111  0.737
2011 Findeiss S, Langenberger D, Stadler PF, Hoffmann S. Traces of post-transcriptional RNA modifications in deep sequencing data. Biological Chemistry. 392: 305-13. PMID 21345160 DOI: 10.1515/Bc.2011.043  0.757
2011 Reidys CM, Huang FW, Andersen JE, Penner RC, Stadler PF, Nebel ME. Topology and prediction of RNA pseudoknots. Bioinformatics (Oxford, England). 27: 1076-85. PMID 21335320 DOI: 10.1093/Bioinformatics/Btr090  0.641
2011 Krakauer DC, Collins JP, Erwin D, Flack JC, Fontana W, Laubichler MD, Prohaska SJ, West GB, Stadler PF. The challenges and scope of theoretical biology. Journal of Theoretical Biology. 276: 269-76. PMID 21315730 DOI: 10.1016/J.Jtbi.2011.01.051  0.636
2011 Tramontano A, Donath A, Bernhart SH, Reiche K, Böhmdorfer G, Stadler PF, Bachmair A. Deletion analysis of the 3' long terminal repeat sequence of plant retrotransposon Tto1 identifies 125 base pairs redundancy as sufficient for first strand transfer. Virology. 412: 75-82. PMID 21262516 DOI: 10.1016/J.Virol.2010.12.059  0.31
2011 Menzel P, Stadler PF, Gorodkin J. maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences. Bioinformatics (Oxford, England). 27: 317-25. PMID 21123221 DOI: 10.1093/Bioinformatics/Btq651  0.348
2011 Kehr S, Bartschat S, Stadler PF, Tafer H. PLEXY: efficient target prediction for box C/D snoRNAs. Bioinformatics (Oxford, England). 27: 279-80. PMID 21076148 DOI: 10.1093/Bioinformatics/Btq642  0.334
2011 Otto W, Stadler PF, Prohaska SJ. Phylogenetic footprinting and consistent sets of local aligments Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6661: 118-131. DOI: 10.1007/978-3-642-21458-5_12  0.626
2010 Jänicke S, Heine C, Hellmuth M, Stadler PF, Scheuermann G. Visualization of graph products. Ieee Transactions On Visualization and Computer Graphics. 16: 1082-9. PMID 20975146 DOI: 10.1109/Tvcg.2010.217  0.616
2010 Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Blomberg Le Ann, Bouffard P, Burt DW, Crasta O, Crooijmans RP, Cooper K, Coulombe RA, De S, Delany ME, Dodgson JB, ... ... Stadler PF, et al. Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. Plos Biology. 8. PMID 20838655 DOI: 10.1371/Journal.Pbio.1000475  0.622
2010 Müller SA, Kohajda T, Findeiss S, Stadler PF, Washietl S, Kellis M, von Bergen M, Kalkhof S. Optimization of parameters for coverage of low molecular weight proteins. Analytical and Bioanalytical Chemistry. 398: 2867-81. PMID 20803007 DOI: 10.1007/S00216-010-4093-X  0.679
2010 Yusuf D, Marz M, Stadler PF, Hofacker IL. Bcheck: a wrapper tool for detecting RNase P RNA genes. Bmc Genomics. 11: 432. PMID 20626900 DOI: 10.1186/1471-2164-11-432  0.617
2010 Hofacker IL, Flamm C, Heine C, Wolfinger MT, Scheuermann G, Stadler PF. BarMap: RNA folding on dynamic energy landscapes. Rna (New York, N.Y.). 16: 1308-16. PMID 20504954 DOI: 10.1261/Rna.2093310  0.776
2010 Lehmann J, Eisenhardt C, Stadler PF, Krauss V. Some novel intron positions in conserved Drosophila genes are caused by intron sliding or tandem duplication. Bmc Evolutionary Biology. 10: 156. PMID 20500887 DOI: 10.1186/1471-2148-10-156  0.331
2010 Bermudez-Santana C, Attolini CS, Kirsten T, Engelhardt J, Prohaska SJ, Steigele S, Stadler PF. Genomic organization of eukaryotic tRNAs Bmc Genomics. 11. PMID 20426822 DOI: 10.1186/1471-2164-11-270  0.677
2010 Boria I, Gruber AR, Tanzer A, Bernhart SH, Lorenz R, Mueller MM, Hofacker IL, Stadler PF. Nematode sbRNAs: homologs of vertebrate Y RNAs. Journal of Molecular Evolution. 70: 346-58. PMID 20349053 DOI: 10.1007/S00239-010-9332-4  0.404
2010 Prohaska SJ, Stadler PF, Krakauer DC. Innovation in gene regulation: the case of chromatin computation. Journal of Theoretical Biology. 265: 27-44. PMID 20303358 DOI: 10.1016/J.Jtbi.2010.03.011  0.637
2010 Findeiss S, Schmidtke C, Stadler PF, Bonas U. A novel family of plasmid-transferred anti-sense ncRNAs. Rna Biology. 7: 120-4. PMID 20220307 DOI: 10.4161/Rna.7.2.11184  0.729
2010 Marz M, Vanzo N, Stadler PF. Temperature-dependent structural variability of RNAs: spliced leader RNAs and their evolutionary history. Journal of Bioinformatics and Computational Biology. 8: 1-17. PMID 20183871 DOI: 10.1142/S0219720010004525  0.618
2010 Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, Chabas S, Reiche K, Hackermüller J, Reinhardt R, Stadler PF, Vogel J. The primary transcriptome of the major human pathogen Helicobacter pylori. Nature. 464: 250-5. PMID 20164839 DOI: 10.1038/Nature08756  0.754
2010 Perseke M, Bernhard D, Fritzsch G, Brümmer F, Stadler PF, Schlegel M. Mitochondrial genome evolution in Ophiuroidea, Echinoidea, and Holothuroidea: insights in phylogenetic relationships of Echinodermata. Molecular Phylogenetics and Evolution. 56: 201-11. PMID 20152912 DOI: 10.1016/J.Ympev.2010.01.035  0.357
2010 Amemiya CT, Powers TP, Prohaska SJ, Grimwood J, Schmutz J, Dickson M, Miyake T, Schoenborn MA, Myers RM, Ruddle FH, Stadler PF. Complete HOX cluster characterization of the coelacanth provides further evidence for slow evolution of its genome. Proceedings of the National Academy of Sciences of the United States of America. 107: 3622-7. PMID 20139301 DOI: 10.1073/Pnas.0914312107  0.682
2010 Tafer H, Kehr S, Hertel J, Hofacker IL, Stadler PF. RNAsnoop: efficient target prediction for H/ACA snoRNAs. Bioinformatics (Oxford, England). 26: 610-6. PMID 20015949 DOI: 10.1093/Bioinformatics/Btp680  0.371
2010 Huang FW, Qin J, Reidys CM, Stadler PF. Target prediction and a statistical sampling algorithm for RNA-RNA interaction. Bioinformatics (Oxford, England). 26: 175-81. PMID 19910305 DOI: 10.1093/Bioinformatics/Btp635  0.645
2010 Gruber AR, Findeiß S, Washietl S, Hofacker IL, Stadler PF. RNAz 2.0: improved noncoding RNA detection. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 69-79. PMID 19908359  0.722
2010 Parikesit A, Prohaska S, Stadler P. Protein domain co-occurrences reveal functional changes of regulatory mechanisms during evolution New Biotechnology. 27: S44-S45. DOI: 10.1016/J.Nbt.2010.01.068  0.615
2010 Parikesit AA, Stadler PF, Prohaska SJ. Detection of protein domains in eukaryotic genome sequences Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6268: 71-74. DOI: 10.1007/978-3-642-15060-9_9  0.638
2010 Prohaska SJ, Mosig A, Stadler PF. Regulatory signals in genomic sequences Networks: From Biology to Theory. 189-216. DOI: 10.1007/978-1-84628-780-0_9  0.645
2010 Donath A, Findeiß S, Hertel J, Marz M, Otto W, Schulz C, Stadler PF, Wirth S. Noncoding RNA Evolutionary Genomics and Systems Biology. 251-293. DOI: 10.1002/9780470570418.ch14  0.764
2009 Otto W, Stadler PF, López-Giraldéz F, Townsend JP, Lynch VJ, Wagner GP. Measuring transcription factor-binding site turnover: a maximum likelihood approach using phylogenies. Genome Biology and Evolution. 1: 85-98. PMID 20333180 DOI: 10.1093/Gbe/Evp010  0.512
2009 Marz M, Stadler PF. Comparative analysis of eukaryotic U3 snoRNA. Rna Biology. 6: 503-7. PMID 19875933 DOI: 10.4161/Rna.6.5.9607  0.587
2009 Menzel P, Gorodkin J, Stadler PF. The tedious task of finding homologous noncoding RNA genes. Rna (New York, N.Y.). 15: 2075-82. PMID 19861422 DOI: 10.1261/Rna.1556009  0.379
2009 Copeland CS, Marz M, Rose D, Hertel J, Brindley PJ, Santana CB, Kehr S, Attolini CS, Stadler PF. Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum. Bmc Genomics. 10: 464. PMID 19814823 DOI: 10.1186/1471-2164-10-464  0.624
2009 Mosig A, Zhu L, Stadler PF. Customized strategies for discovering distant ncRNA homologs. Briefings in Functional Genomics & Proteomics. 8: 451-60. PMID 19779009 DOI: 10.1093/Bfgp/Elp035  0.399
2009 Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermüller J. Fast mapping of short sequences with mismatches, insertions and deletions using index structures. Plos Computational Biology. 5: e1000502. PMID 19750212 DOI: 10.1371/Journal.Pcbi.1000502  0.327
2009 Marz M, Donath A, Verstraete N, Nguyen VT, Stadler PF, Bensaude O. Evolution of 7SK RNA and its protein partners in metazoa. Molecular Biology and Evolution. 26: 2821-30. PMID 19734296 DOI: 10.1093/Molbev/Msp198  0.635
2009 Stocsits RR, Letsch H, Hertel J, Misof B, Stadler PF. Accurate and efficient reconstruction of deep phylogenies from structured RNAs. Nucleic Acids Research. 37: 6184-93. PMID 19723687 DOI: 10.1093/Nar/Gkp600  0.416
2009 Huang FW, Qin J, Reidys CM, Stadler PF. Partition function and base pairing probabilities for RNA-RNA interaction prediction. Bioinformatics (Oxford, England). 25: 2646-54. PMID 19671692 DOI: 10.1093/Bioinformatics/Btp481  0.654
2009 Langenberger D, Bermudez-Santana C, Hertel J, Hoffmann S, Khaitovich P, Stadler PF. Evidence for human microRNA-offset RNAs in small RNA sequencing data. Bioinformatics (Oxford, England). 25: 2298-301. PMID 19584066 DOI: 10.1093/Bioinformatics/Btp419  0.376
2009 Stadler PF, Prohaska SJ, Forst CV, Krakauer DC. Defining genes: a computational framework. Theory in Biosciences = Theorie in Den Biowissenschaften. 128: 165-70. PMID 19557452 DOI: 10.1007/S12064-009-0067-Y  0.668
2009 Stadler PF, Chen JJ, Hackermüller J, Hoffmann S, Horn F, Khaitovich P, Kretzschmar AK, Mosig A, Prohaska SJ, Qi X, Schutt K, Ullmann K. Evolution of vault RNAs. Molecular Biology and Evolution. 26: 1975-91. PMID 19491402 DOI: 10.1093/Molbev/Msp112  0.708
2009 Hiller M, Findeiss S, Lein S, Marz M, Nickel C, Rose D, Schulz C, Backofen R, Prohaska SJ, Reuter G, Stadler PF. Conserved introns reveal novel transcripts in Drosophila melanogaster. Genome Research. 19: 1289-300. PMID 19458021 DOI: 10.1101/Gr.090050.108  0.82
2009 Conant GC, Stadler PF. Solvent exposure imparts similar selective pressures across a range of yeast proteins. Molecular Biology and Evolution. 26: 1155-61. PMID 19233963 DOI: 10.1093/Molbev/Msp031  0.604
2009 Chambers KE, McDaniell R, Raincrow JD, Deshmukh M, Stadler PF, Chiu CH. Hox cluster duplication in the basal teleost Hiodon alosoides (Osteoglossomorpha). Theory in Biosciences = Theorie in Den Biowissenschaften. 128: 109-20. PMID 19225820 DOI: 10.1007/S12064-009-0056-1  0.344
2009 Scheibye-Alsing K, Hoffmann S, Frankel A, Jensen P, Stadler PF, Mang Y, Tommerup N, Gilchrist MJ, Nygård AB, Cirera S, Jørgensen CB, Fredholm M, Gorodkin J. Sequence assembly Computational Biology and Chemistry. 33: 121-136. PMID 19152793 DOI: 10.1016/J.Compbiolchem.2008.11.003  0.346
2009 Hertel J, de Jong D, Marz M, Rose D, Tafer H, Tanzer A, Schierwater B, Stadler PF. Non-coding RNA annotation of the genome of Trichoplax adhaerens. Nucleic Acids Research. 37: 1602-15. PMID 19151082 DOI: 10.1093/Nar/Gkn1084  0.65
2009 Jones TA, Otto W, Marz M, Eddy SR, Stadler PF. A survey of nematode SmY RNAs. Rna Biology. 6: 5-8. PMID 19106623 DOI: 10.4161/Rna.6.1.7634  0.64
2009 Benkö G, Centler F, Dittrich P, Flamm C, Stadler BM, Stadler PF. A topological approach to chemical organizations. Artificial Life. 15: 71-88. PMID 18855563 DOI: 10.1162/Artl.2009.15.1.15105  0.602
2009 Ostermeier P, Hellmuth M, Klemm K, Leydold J, Stadler PF. A note on quasi-robust cycle bases Ars Mathematica Contemporanea. 2: 231-240. DOI: 10.26493/1855-3974.104.5B7  0.614
2009 Hellmuth M, Imrich W, Klöckl W, Stadler PF. Approximate graph products European Journal of Combinatorics. 30: 1119-1133. DOI: 10.1016/J.Ejc.2008.09.006  0.616
2009 Mosig A, Biyikoǧlu T, Prohaska SJ, Stadler PF. Discovering cis-regulatory modules by optimizing barbecues Discrete Applied Mathematics. 157: 2458-2468. DOI: 10.1016/J.Dam.2008.06.042  0.652
2009 Hellmuth M, Imrich W, Klöckl W, Stadler PF. Local algorithms for the prime factorization of strong product graphs Mathematics in Computer Science. 2: 653-682. DOI: 10.1007/S11786-009-0073-Y  0.615
2009 Heffel A, Prohaska SJ, Stadler PF, Kauer G, Kuska JP. Automatic classification of embryonic fruit fly gene expression patterns Informatik Aktuell. 415-419.  0.61
2008 Heffel A, Stadler PF, Prohaska SJ, Kauer G, Kuska JP. PROCESS FLOW FOR CLASSIFICATION AND CLUSTERING OF FRUIT FLY GENE EXPRESSION PATTERNS. Proceedings / Icip ... International Conference On Image Processing. 1: 721-724. PMID 20046820 DOI: 10.1109/ICIP.2008.4711856  0.594
2008 Rose D, Jöris J, Hackermüller J, Reiche K, Li Q, Stadler PF. Duplicated RNA genes in teleost fish genomes. Journal of Bioinformatics and Computational Biology. 6: 1157-75. PMID 19090022 DOI: 10.1142/S0219720008003886  0.42
2008 Marz M, Kirsten T, Stadler PF. Evolution of spliceosomal snRNA genes in metazoan animals. Journal of Molecular Evolution. 67: 594-607. PMID 19030770 DOI: 10.1007/S00239-008-9149-6  0.607
2008 Bernhart SH, Hofacker IL, Will S, Gruber AR, Stadler PF. RNAalifold: improved consensus structure prediction for RNA alignments. Bmc Bioinformatics. 9: 474. PMID 19014431 DOI: 10.1186/1471-2105-9-474  0.398
2008 Jühling F, Mörl M, Hartmann RK, Sprinzl M, Stadler PF, Pütz J. tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Research. 37: D159-62. PMID 18957446 DOI: 10.1093/Nar/Gkn772  0.368
2008 Sonnleitner E, Sorger-Domenigg T, Madej MJ, Findeiss S, Hackermüller J, Hüttenhofer A, Stadler PF, Bläsi U, Moll I. Detection of small RNAs in Pseudomonas aeruginosa by RNomics and structure-based bioinformatic tools. Microbiology (Reading, England). 154: 3175-87. PMID 18832323 DOI: 10.1099/Mic.0.2008/019703-0  0.752
2008 Lehmann J, Stadler PF, Prohaska SJ. SynBlast: assisting the analysis of conserved synteny information. Bmc Bioinformatics. 9: 351. PMID 18721485 DOI: 10.1186/1471-2105-9-351  0.672
2008 Dress AW, Flamm C, Fritzsch G, Grünewald S, Kruspe M, Prohaska SJ, Stadler PF. Noisy: identification of problematic columns in multiple sequence alignments. Algorithms For Molecular Biology : Amb. 3: 7. PMID 18577231 DOI: 10.1186/1748-7188-3-7  0.754
2008 Gruber AR, Kilgus C, Mosig A, Hofacker IL, Hennig W, Stadler PF. Arthropod 7SK RNA. Molecular Biology and Evolution. 25: 1923-30. PMID 18566019 DOI: 10.1093/Molbev/Msn140  0.41
2008 Rose D, Hertel J, Reiche K, Stadler PF, Hackermüller J. NcDNAlign: plausible multiple alignments of non-protein-coding genomic sequences. Genomics. 92: 65-74. PMID 18511233 DOI: 10.1016/J.Ygeno.2008.04.003  0.382
2008 Geis M, Flamm C, Wolfinger MT, Tanzer A, Hofacker IL, Middendorf M, Mandl C, Stadler PF, Thurner C. Folding kinetics of large RNAs. Journal of Molecular Biology. 379: 160-73. PMID 18440024 DOI: 10.1016/J.Jmb.2008.02.064  0.791
2008 Amemiya CT, Prohaska SJ, Hill-Force A, Cook A, Wasserscheid J, Ferrier DE, Pascual-Anaya J, Garcia-Fernàndez J, Dewar K, Stadler PF. The amphioxus Hox cluster: characterization, comparative genomics, and evolution. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. 310: 465-77. PMID 18351584 DOI: 10.1002/Jez.B.21213  0.654
2008 Jöchl C, Rederstorff M, Hertel J, Stadler PF, Hofacker IL, Schrettl M, Haas H, Hüttenhofer A. Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis. Nucleic Acids Research. 36: 2677-89. PMID 18346967 DOI: 10.1093/Nar/Gkn123  0.388
2008 Prohaska SJ, Stadler PF. "Genes". Theory in Biosciences = Theorie in Den Biowissenschaften. 127: 215-21. PMID 18320253 DOI: 10.1007/s12064-008-0025-0  0.625
2008 Krauss V, Thümmler C, Georgi F, Lehmann J, Stadler PF, Eisenhardt C. Near intron positions are reliable phylogenetic markers: an application to holometabolous insects. Molecular Biology and Evolution. 25: 821-30. PMID 18296416 DOI: 10.1093/Molbev/Msn013  0.395
2008 Perseke M, Fritzsch G, Ramsch K, Bernt M, Merkle D, Middendorf M, Bernhard D, Stadler PF, Schlegel M. Evolution of mitochondrial gene orders in echinoderms. Molecular Phylogenetics and Evolution. 47: 855-64. PMID 18280182 DOI: 10.1016/J.Ympev.2007.11.034  0.328
2008 Gruber AR, Koper-Emde D, Marz M, Tafer H, Bernhart S, Obernosterer G, Mosig A, Hofacker IL, Stadler PF, Benecke BJ. Invertebrate 7SK snRNAs. Journal of Molecular Evolution. 66: 107-15. PMID 18193315 DOI: 10.1007/S00239-007-9052-6  0.646
2008 Fritzsch G, Böhme MU, Thorndyke M, Nakano H, Israelsson O, Stach T, Schlegel M, Hankeln T, Stadler PF. PCR survey of Xenoturbella bocki Hox genes. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. 310: 278-84. PMID 18161857 DOI: 10.1002/Jez.B.21208  0.309
2008 Xie M, Mosig A, Qi X, Li Y, Stadler PF, Chen JJ. Structure and function of the smallest vertebrate telomerase RNA from teleost fish. The Journal of Biological Chemistry. 283: 2049-59. PMID 18039659 DOI: 10.1074/Jbc.M708032200  0.392
2008 Hertel J, Hofacker IL, Stadler PF. SnoReport: computational identification of snoRNAs with unknown targets. Bioinformatics (Oxford, England). 24: 158-64. PMID 17895272 DOI: 10.1093/Bioinformatics/Btm464  0.427
2008 Bompfünewerer AF, Backofen R, Bernhart SH, Hertel J, Hofacker IL, Stadler PF, Will S. Variations on RNA folding and alignment: lessons from Benasque. Journal of Mathematical Biology. 56: 129-44. PMID 17611759 DOI: 10.1007/S00285-007-0107-5  0.392
2008 Prohaska SJ, Stadler PF. A story of growing confusion: Genes and their regulation Biophysical Reviews and Letters. 3: 285-302. DOI: 10.1142/S1793048008000757  0.676
2008 Klemm K, Flamm C, Stadler PF. Funnels in energy landscapes European Physical Journal B. 63: 387-391. DOI: 10.1140/epjb/e2008-00136-7  0.491
2008 Schuster P, Stadler PF. Early Replicons: Origin and Evolution Origin and Evolution of Viruses. 1-41. DOI: 10.1016/B978-0-12-374153-0.00001-1  0.357
2007 Marz M, Mosig A, Stadler BM, Stadler PF. U7 snRNAs: a computational survey. Genomics, Proteomics & Bioinformatics. 5: 187-95. PMID 18267300 DOI: 10.1016/S1672-0229(08)60006-6  0.619
2007 Perseke M, Hankeln T, Weich B, Fritzsch G, Stadler PF, Israelsson O, Bernhard D, Schlegel M. The mitochondrial DNA of Xenoturbella bocki: genomic architecture and phylogenetic analysis. Theory in Biosciences = Theorie in Den Biowissenschaften. 126: 35-42. PMID 18087755 DOI: 10.1007/S12064-007-0007-7  0.335
2007 Mosig A, Guofeng M, Stadler BM, Stadler PF. Evolution of the vertebrate Y RNA cluster. Theory in Biosciences = Theorie in Den Biowissenschaften. 126: 9-14. PMID 18087752 DOI: 10.1007/S12064-007-0003-Y  0.403
2007 Rose D, Hackermüller J, Washietl S, Reiche K, Hertel J, Findeiss S, Stadler PF, Prohaska SJ. Computational RNomics of drosophilids. Bmc Genomics. 8: 406. PMID 17996037 DOI: 10.1186/1471-2164-8-406  0.831
2007 Bernt M, Merkle D, Ramsch K, Fritzsch G, Perseke M, Bernhard D, Schlegel M, Stadler PF, Middendorf M. CREx: inferring genomic rearrangements based on common intervals. Bioinformatics (Oxford, England). 23: 2957-8. PMID 17895271 DOI: 10.1093/Bioinformatics/Btm468  0.339
2007 Haslinger C, Stadler PF. RNA structures with pseudo-knots: graph-theoretical, combinatorial, and statistical properties. Bulletin of Mathematical Biology. 61: 437-67. PMID 17883226 DOI: 10.1006/Bulm.1998.0085  0.394
2007 Seemann SE, Gilchrist MJ, Hofacker IL, Stadler PF, Gorodkin J. Detection of RNA structures in porcine EST data and related mammals. Bmc Genomics. 8: 316. PMID 17845718 DOI: 10.1186/1471-2164-8-316  0.389
2007 Steigele S, Huber W, Stocsits C, Stadler PF, Nieselt K. Comparative analysis of structured RNAs in S. cerevisiae indicates a multitude of different functions. Bmc Biology. 5: 25. PMID 17577407 DOI: 10.1186/1741-7007-5-25  0.414
2007 Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Stadler PF, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874  0.642
2007 Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermüller J, Hertel J, Lindemeyer M, Reiche K, Tanzer A, Ucla C, Wyss C, Antonarakis SE, Denoeud F, Lagarde J, ... ... Stadler PF, et al. Structured RNAs in the ENCODE selected regions of the human genome. Genome Research. 17: 852-64. PMID 17568003 DOI: 10.1101/Gr.5650707  0.434
2007 Reiche K, Stadler PF. RNAstrand: reading direction of structured RNAs in multiple sequence alignments. Algorithms For Molecular Biology : Amb. 2: 6. PMID 17540014 DOI: 10.1186/1748-7188-2-6  0.431
2007 Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermüller J, Hofacker IL, Bell I, Cheung E, Drenkow J, Dumais E, Patel S, et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science (New York, N.Y.). 316: 1484-8. PMID 17510325 DOI: 10.1126/Science.1138341  0.409
2007 Wagner GP, Otto W, Lynch V, Stadler PF. A stochastic model for the evolution of transcription factor binding site abundance. Journal of Theoretical Biology. 247: 544-53. PMID 17475285 DOI: 10.1016/J.Jtbi.2007.03.001  0.477
2007 Will S, Reiche K, Hofacker IL, Stadler PF, Backofen R. Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering. Plos Computational Biology. 3: e65. PMID 17432929 DOI: 10.1371/Journal.Pcbi.0030065  0.443
2007 Woodhams MD, Stadler PF, Penny D, Collins LJ. RNase MRP and the RNA processing cascade in the eukaryotic ancestor. Bmc Evolutionary Biology. 7: S13. PMID 17288571 DOI: 10.1186/1471-2148-7-S1-S13  0.377
2007 Luo J, Stadler PF, He S, Meyer A. PCR survey of hox genes in the goldfish Carassius auratus auratus. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. 308: 250-8. PMID 17171698 DOI: 10.1002/Jez.B.21144  0.342
2007 Backofen R, Bernhart SH, Flamm C, Fried C, Fritzsch G, Hackermüller J, Hertel J, Hofacker IL, Missal K, Mosig A, Prohaska SJ, Rose D, Stadler PF, Tanzer A, et al. RNAs everywhere: genome-wide annotation of structured RNAs. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. 308: 1-25. PMID 17171697 DOI: 10.1002/Jez.B.21130  0.783
2007 Conant GC, Wagner GP, Stadler PF. Modeling amino acid substitution patterns in orthologous and paralogous genes. Molecular Phylogenetics and Evolution. 42: 298-307. PMID 16942891 DOI: 10.1016/J.Ympev.2006.07.006  0.692
2007 Flamm C, Hofacker IL, Stadler BMR, Stadler PF. Saddles and barrier in landscapes of generalized search operators Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4436: 194-212.  0.539
2006 Heine C, Scheuermann G, Flamm C, Hofacker IL, Stadler PF. Visualization of barrier tree sequences. Ieee Transactions On Visualization and Computer Graphics. 12: 781-8. PMID 17080800 DOI: 10.1109/Tvcg.2006.196  0.643
2006 Hertel J, Stadler PF. Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data. Bioinformatics (Oxford, England). 22: e197-202. PMID 16873472 DOI: 10.1093/Bioinformatics/Btl257  0.425
2006 Reidys C, Stadler PF. Bio-molecular shapes and algebraic structures. Computers & Chemistry. 20: 85-94. PMID 16749182 DOI: 10.1016/S0097-8485(96)80010-6  0.644
2006 Bernhart SH, Tafer H, Mückstein U, Flamm C, Stadler PF, Hofacker IL. Partition function and base pairing probabilities of RNA heterodimers. Algorithms For Molecular Biology : Amb. 1: 3. PMID 16722605 DOI: 10.1186/1748-7188-1-3  0.64
2006 Morgenstern B, Prohaska SJ, Pöhler D, Stadler PF. Multiple sequence alignment with user-defined anchor points. Algorithms For Molecular Biology : Amb. 1: 6. PMID 16722533 DOI: 10.1186/1748-7188-1-6  0.634
2006 Mosig A, Sameith K, Stadler P. Fragrep: an efficient search tool for fragmented patterns in genomic sequences. Genomics, Proteomics & Bioinformatics. 4: 56-60. PMID 16689703 DOI: 10.1016/S1672-0229(06)60017-X  0.423
2006 Prohaska SJ, Stadler PF. Evolution of the vertebrate ParaHox clusters. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. 306: 481-7. PMID 16619246 DOI: 10.1002/Jez.B.21099  0.655
2006 Hertel J, Lindemeyer M, Missal K, Fried C, Tanzer A, Flamm C, Hofacker IL, Stadler PF. The expansion of the metazoan microRNA repertoire. Bmc Genomics. 7: 25. PMID 16480513 DOI: 10.1186/1471-2164-7-25  0.591
2006 Forst CV, Flamm C, Hofacker IL, Stadler PF. Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation. Bmc Bioinformatics. 7: 67. PMID 16478540 DOI: 10.1186/1471-2105-7-67  0.565
2006 Hofacker IL, Stadler PF. Memory efficient folding algorithms for circular RNA secondary structures. Bioinformatics (Oxford, England). 22: 1172-6. PMID 16452114 DOI: 10.1093/Bioinformatics/Btl023  0.382
2006 Mückstein U, Tafer H, Hackermüller J, Bernhart SH, Stadler PF, Hofacker IL. Thermodynamics of RNA-RNA binding. Bioinformatics (Oxford, England). 22: 1177-82. PMID 16446276 DOI: 10.1093/Bioinformatics/Btl024  0.337
2006 Missal K, Zhu X, Rose D, Deng W, Skogerbø G, Chen R, Stadler PF. Prediction of structured non-coding RNAs in the genomes of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. 306: 379-92. PMID 16425273 DOI: 10.1002/Jez.B.21086  0.427
2006 Bernhart SH, Hofacker IL, Stadler PF. Local RNA base pairing probabilities in large sequences. Bioinformatics (Oxford, England). 22: 614-5. PMID 16368769 DOI: 10.1093/Bioinformatics/Btk014  0.421
2006 Fritzsch G, Schlegel M, Stadler PF. Alignments of mitochondrial genome arrangements: applications to metazoan phylogeny. Journal of Theoretical Biology. 240: 511-20. PMID 16325206 DOI: 10.1016/J.Jtbi.2005.10.010  0.353
2006 Crow KD, Stadler PF, Lynch VJ, Amemiya C, Wagner GP. The "fish-specific" Hox cluster duplication is coincident with the origin of teleosts. Molecular Biology and Evolution. 23: 121-36. PMID 16162861 DOI: 10.1093/Molbev/Msj020  0.484
2006 Wolfinger MT, Will S, Hofacker IL, Backofen R, Stadler PF. Exploring the lower part of discrete polymer model energy landscapes Europhysics Letters (Epl). 74: 726-732. DOI: 10.1209/Epl/I2005-10577-0  0.658
2006 Pötzsch S, Scheuermann G, Wolfinger MT, Flamm C, Stadler PF. Visualization of lattice-based protein folding simulations Proceedings of the International Conference On Information Visualisation. 89-94. DOI: 10.1109/IV.2006.127  0.71
2006 Hofacker IL, Stadler PF. RNA Secondary Structures Reviews in Cell Biology and Molecular Medicine. 439-489. DOI: 10.1002/3527600906.Mcb.200500009  0.41
2005 Bompfünewerer AF, Flamm C, Fried C, Fritzsch G, Hofacker IL, Lehmann J, Missal K, Mosig A, Müller B, Prohaska SJ, Stadler BM, Stadler PF, Tanzer A, Washietl S, Witwer C. Evolutionary patterns of non-coding RNAs. Theory in Biosciences = Theorie in Den Biowissenschaften. 123: 301-69. PMID 18202870 DOI: 10.1016/J.Thbio.2005.01.002  0.772
2005 Washietl S, Hofacker IL, Lukasser M, Hüttenhofer A, Stadler PF. Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome. Nature Biotechnology. 23: 1383-90. PMID 16273071 DOI: 10.1038/Nbt1144  0.45
2005 Missal K, Rose D, Stadler PF. Non-coding RNAs in Ciona intestinalis. Bioinformatics (Oxford, England). 21: ii77-8. PMID 16204130 DOI: 10.1093/Bioinformatics/Bti1113  0.419
2005 Böhmdorfer G, Hofacker IL, Garber K, Jelenic S, Nizhynska V, Hirochika H, Stadler PF, Bachmair A. Unorthodox mRNA start site to extend the highly structured leader of retrotransposon Tto1 mRNA increases transposition rate. Rna (New York, N.Y.). 11: 1181-91. PMID 16043504 DOI: 10.1261/Rna.2640105  0.355
2005 Stocsits RR, Hofacker IL, Fried C, Stadler PF. Multiple sequence alignments of partially coding nucleic acid sequences. Bmc Bioinformatics. 6: 160. PMID 15985156 DOI: 10.1186/1471-2105-6-160  0.362
2005 Wagner GP, Takahashi K, Lynch V, Prohaska SJ, Fried C, Stadler PF, Amemiya C. Molecular evolution of duplicated ray finned fish HoxA clusters: increased synonymous substitution rate and asymmetrical co-divergence of coding and non-coding sequences. Journal of Molecular Evolution. 60: 665-76. PMID 15983874 DOI: 10.1007/S00239-004-0252-Z  0.706
2005 Hackermüller J, Meisner NC, Auer M, Jaritz M, Stadler PF. The effect of RNA secondary structures on RNA-ligand binding and the modifier RNA mechanism: a quantitative model. Gene. 345: 3-12. PMID 15716109 DOI: 10.1016/J.Gene.2004.11.043  0.391
2005 Washietl S, Hofacker IL, Stadler PF. Fast and reliable prediction of noncoding RNAs. Proceedings of the National Academy of Sciences of the United States of America. 102: 2454-9. PMID 15665081 DOI: 10.1073/Pnas.0409169102  0.438
2005 Tanzer A, Amemiya CT, Kim CB, Stadler PF. Evolution of microRNAs located within Hox gene clusters. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. 304: 75-85. PMID 15643628 DOI: 10.1002/Jez.B.21021  0.364
2005 Morgenstern B, Werner N, Prohaska SJ, Steinkamp R, Schneider I, Subramanian AR, Stadler PF, Weyer-Menkhoff J. Multiple sequence alignment with user-defined constraints at GOBICS. Bioinformatics (Oxford, England). 21: 1271-3. PMID 15546937 DOI: 10.1093/Bioinformatics/Bti142  0.656
2005 Stephan-Otto Attolini C, Stadler PF. Neutral networks of interacting RNA secondary structures Advances in Complex Systems. 8: 275-283. DOI: 10.1142/S0219525905000427  0.376
2005 SHPAK M, STADLER P, WAGNER G, HERMISSON J. Erratum to “Aggregation of variables and system decomposability: Applications to fitness landscape analysis”[Theory in Biosciences 123 (2004) 33–68] Theory in Biosciences. 124: 87-88. DOI: 10.1016/J.Thbio.2005.05.001  0.413
2005 Attolini CSO, Stadler PF, Flamm C. CelloS: A multi-level approach to evolutionary dynamics Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3630: 500-509. DOI: 10.1007/11553090_51  0.567
2005 Benkö G, Flamm C, Stadler PF. Explicit collision simulation of chemical reactions in a graph based artificial chemistry Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3630: 725-733.  0.525
2004 Shpak M, Stadler P, Wagner GP, Altenberg L. Simon-Ando decomposability and fitness landscapes. Theory in Biosciences = Theorie in Den Biowissenschaften. 123: 139-80. PMID 18236097 DOI: 10.1016/J.Thbio.2004.04.001  0.453
2004 Prohaska SJ, Stadler PF. The duplication of the Hox gene clusters in teleost fishes. Theory in Biosciences = Theorie in Den Biowissenschaften. 123: 89-110. PMID 18202881 DOI: 10.1016/J.Thbio.2004.03.004  0.664
2004 Shpak M, Stadler P, Wagner GP, Hermisson J. Aggregation of variables and system decomposition: Applications to fitness landscape analysis. Theory in Biosciences = Theorie in Den Biowissenschaften. 123: 33-68. PMID 18202879 DOI: 10.1016/J.Thbio.2004.02.001  0.448
2004 Witwer C, Hofacker IL, Stadler PF. Prediction of consensus RNA secondary structures including pseudoknots. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 1: 66-77. PMID 17048382 DOI: 10.1109/Tcbb.2004.22  0.391
2004 Force A, Shashikant CS, Stadler P, Amemiya CT. Comparative genomics, cis-regulatory elements, and gene duplication Methods in Cell Biology. 77: 545-561. PMID 15602931 DOI: 10.1016/S0091-679X(04)77029-6  0.369
2004 Campos PR, de Oliveira VM, Wagner GP, Stadler PF. Gene phylogenies and protein-protein interactions: possible artifacts resulting from shared protein interaction partners. Journal of Theoretical Biology. 231: 197-202. PMID 15380384 DOI: 10.1016/J.Jtbi.2004.06.014  0.497
2004 Stadler PF, Fried C, Prohaska SJ, Bailey WJ, Misof BY, Ruddle FH, Wagner GP. Evidence for independent Hox gene duplications in the hagfish lineage: a PCR-based gene inventory of Eptatretus stoutii. Molecular Phylogenetics and Evolution. 32: 686-94. PMID 15288047 DOI: 10.1016/J.Ympev.2004.03.015  0.711
2004 Wagner GP, Fried C, Prohaska SJ, Stadler PF. Divergence of conserved non-coding sequences: rate estimates and relative rate tests. Molecular Biology and Evolution. 21: 2116-21. PMID 15282332 DOI: 10.1093/Molbev/Msh221  0.722
2004 Hofacker IL, Stadler PF, Stocsits RR. Conserved RNA secondary structures in viral genomes: a survey. Bioinformatics (Oxford, England). 20: 1495-9. PMID 15231541 DOI: 10.1093/Bioinformatics/Bth108  0.388
2004 Thurner C, Witwer C, Hofacker IL, Stadler PF. Conserved RNA secondary structures in Flaviviridae genomes. The Journal of General Virology. 85: 1113-24. PMID 15105528 DOI: 10.1099/Vir.0.19462-0  0.376
2004 Hofacker IL, Bernhart SH, Stadler PF. Alignment of RNA base pairing probability matrices. Bioinformatics (Oxford, England). 20: 2222-7. PMID 15073017 DOI: 10.1093/Bioinformatics/Bth229  0.415
2004 Prohaska SJ, Fried C, Flamm C, Wagner GP, Stadler PF. Surveying phylogenetic footprints in large gene clusters: applications to Hox cluster duplications. Molecular Phylogenetics and Evolution. 31: 581-604. PMID 15062796 DOI: 10.1016/J.Ympev.2003.08.009  0.791
2004 Fried C, Prohaska SJ, Stadler PF. Exclusion of repetitive DNA elements from gnathostome Hox clusters. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. 302: 165-73. PMID 15054859 DOI: 10.1002/Jez.B.20007  0.623
2004 Prohaska SJ, Fried C, Amemiya CT, Ruddle FH, Wagner GP, Stadler PF. The shark HoxN cluster is homologous to the human HoxD cluster. Journal of Molecular Evolution. 58: 212-7. PMID 15042342 DOI: 10.1007/S00239-003-2545-Z  0.666
2004 Copeland CS, Heyers O, Kalinna BH, Bachmair A, Stadler PF, Hofacker IL, Brindley PJ. Structural and evolutionary analysis of the transcribed sequence of Boudicca, a Schistosoma mansoni retrotransposon. Gene. 329: 103-14. PMID 15033533 DOI: 10.1016/J.Gene.2003.12.023  0.388
2004 Fried C, Hordijk W, Prohaska SJ, Stadler CR, Stadler PF. The footprint sorting problem. Journal of Chemical Information and Computer Sciences. 44: 332-8. PMID 15032508 DOI: 10.1021/Ci030411+  0.66
2004 Berger F, Flamm C, Gleiss PM, Leydold J, Stadler PF. Counterexamples in chemical ring perception. Journal of Chemical Information and Computer Sciences. 44: 323-31. PMID 15032507 DOI: 10.1021/Ci030405D  0.585
2004 Hofacker IL, Priwitzer B, Stadler PF. Prediction of locally stable RNA secondary structures for genome-wide surveys. Bioinformatics (Oxford, England). 20: 186-90. PMID 14734309 DOI: 10.1093/Bioinformatics/Btg388  0.435
2004 Chiu CH, Dewar K, Wagner GP, Takahashi K, Ruddle F, Ledje C, Bartsch P, Scemama JL, Stellwag E, Fried C, Prohaska SJ, Stadler PF, Amemiya CT. Bichir HoxA cluster sequence reveals surprising trends in ray-finned fish genomic evolution. Genome Research. 14: 11-7. PMID 14707166 DOI: 10.1101/Gr.1712904  0.695
2004 Wolfinger MT, Svrcek-Seiler WA, Flamm C, Hofacker IL, Stadler PF. Efficient computation of RNA folding dynamics Journal of Physics a: Mathematical and General. 37: 4731-4741. DOI: 10.1088/0305-4470/37/17/005  0.782
2004 Binder H, Kirsten T, Hofacker IL, Stadler PF, Loeffler M. Interactions in Oligonucleotide Hybrid Duplexes on Microarrays The Journal of Physical Chemistry B. 108: 18015-18025. DOI: 10.1021/Jp049592O  0.327
2003 Weberndorfer G, Hofacker IL, Stadler PF. On the evolution of primitive genetic codes. Origins of Life and Evolution of the Biosphere : the Journal of the International Society For the Study of the Origin of Life. 33: 491-514. PMID 14604188 DOI: 10.1023/A:1025753712110  0.304
2003 Fried C, Prohaska SJ, Stadler PF. Independent Hox-cluster duplications in lampreys. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. 299: 18-25. PMID 14508813 DOI: 10.1002/Jez.B.37  0.641
2003 Benkö G, Flamm C, Stadler PF. A graph-based toy model of chemistry. Journal of Chemical Information and Computer Sciences. 43: 1085-93. PMID 12870897 DOI: 10.1021/Ci0200570  0.599
2003 Wagner GP, Stadler PF. Quasi-independence, homology and the unity of type: a topological theory of characters. Journal of Theoretical Biology. 220: 505-27. PMID 12623283 DOI: 10.1006/Jtbi.2003.3150  0.45
2003 Stadler PF, Flamm C. Barrier trees on poset-valued landscapes Genetic Programming and Evolvable Machines. 4: 7-20. DOI: 10.1023/A:1021821009420  0.589
2003 Benkö G, Flamm C, Stadler PF. Generic properties of chemical networks: Artificial chemistry based on graph rewriting Lecture Notes in Artificial Intelligence (Subseries of Lecture Notes in Computer Science). 2801: 10-19.  0.544
2002 Hofacker IL, Fekete M, Stadler PF. Secondary structure prediction for aligned RNA sequences. Journal of Molecular Biology. 319: 1059-66. PMID 12079347 DOI: 10.1016/S0022-2836(02)00308-X  0.409
2002 Stadler BM, Stadler PF, Wagner GP, Fontana W. The topology of the possible: formal spaces underlying patterns of evolutionary change. Journal of Theoretical Biology. 213: 241-74. PMID 11894994 DOI: 10.1006/Jtbi.2001.2423  0.516
2002 Flamm C, Hofacker IL, Stadler PF, Wolfinger MT. Barrier trees of degenerate landscapes Zeitschrift Fur Physikalische Chemie. 216: 155-173. DOI: 10.1524/Zpch.2002.216.2.155  0.744
2002 Reidys CM, Stadler PF. Combinatorial Landscapes Siam Review. 44: 3-54. DOI: 10.1137/S0036144501395952  0.541
2002 Bastert O, Rockmore D, Stadler PF, Tinhofer G. Landscapes on spaces of trees Applied Mathematics and Computation. 131: 439-459. DOI: 10.1016/S0096-3003(01)00164-3  0.314
2002 Schuster P, Stadler PF. Networks in molecular evolution Complexity. 8: 34-42. DOI: 10.1002/Cplx.10052  0.515
2001 Witwer C, Rauscher S, Hofacker IL, Stadler PF. Conserved RNA secondary structures in Picornaviridae genomes. Nucleic Acids Research. 29: 5079-89. PMID 11812840 DOI: 10.1093/Nar/29.24.5079  0.403
2001 Babajide A, Farber R, Hofacker IL, Inman J, Lapedes AS, Stadler PF. Exploring protein sequence space using knowledge-based potentials. Journal of Theoretical Biology. 212: 35-46. PMID 11527443 DOI: 10.1006/Jtbi.2001.2343  0.324
2001 Flamm C, Hofacker IL, Maurer-Stroh S, Stadler PF, Zehl M. Design of multistable RNA molecules Rna. 7: 254-265. PMID 11233982 DOI: 10.1017/S1355838201000863  0.65
2001 GLEISS PM, STADLER PF, WAGNER A, FELL DA. RELEVANT CYCLES IN CHEMICAL REACTION NETWORKS Advances in Complex Systems. 4: 207-226. DOI: 10.1142/S0219525901000140  0.425
2001 Reidys CM, Stadler PF. Neutrality in fitness landscapes Applied Mathematics and Computation. 117: 321-350. DOI: 10.1016/S0096-3003(99)00166-6  0.597
2000 Stadler BMR, Stadler PF, Schuster P. Dynamics of autocatalytic replicator networks based on higher-order ligation reactions Bulletin of Mathematical Biology. 62: 1061-1086. PMID 11127514 DOI: 10.1006/Bulm.2000.0194  0.466
2000 Cupal J, Kopp S, Stadler PF. RNA shape space topology. Artificial Life. 6: 3-23. PMID 10943663 DOI: 10.1162/106454600568294  0.319
2000 Fekete M, Hofacker IL, Stadler PF. Prediction of RNA base pairing probabilities on massively parallel computers. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 7: 171-82. PMID 10890394 DOI: 10.1089/10665270050081441  0.393
2000 Wimmer K, Eckart M, Stadler PF, Rehder H, Fonatsch C. Three different premature stop codons lead to skipping of exon 7 in neurofibromatosis type I patients Human Mutation. 16: 90-91. PMID 10874316 DOI: 10.1002/1098-1004(200007)16:1<90::Aid-Humu20>3.0.Co;2-J  0.3
2000 Stadler PF, Seitz R, Wagner GP. Population dependent Fourier decomposition of fitness landscapes over recombination spaces: evolvability of complex characters. Bulletin of Mathematical Biology. 62: 399-428. PMID 10812714 DOI: 10.1006/Bulm.1999.0167  0.46
1999 Wagner A, Stadler PF. Viral RNA and evolved mutational robustness. The Journal of Experimental Zoology. 285: 119-27. PMID 10440723 DOI: 10.1002/(Sici)1097-010X(19990815)285:2<119::Aid-Jez4>3.0.Co;2-D  0.466
1999 Hofacker IL, Stadler PF. Automatic detection of conserved base pairing patterns in RNA virus genomes. Computers & Chemistry. 23: 401-14. PMID 10404627 DOI: 10.1016/S0097-8485(99)00013-3  0.443
1999 Stadler PF, Wagner GP. Algebraic theory of recombination spaces. Evolutionary Computation. 5: 241-75. PMID 10021760 DOI: 10.1162/Evco.1997.5.3.241  0.461
1999 Flamm C, Hofacker IL, Stadler PF. RNA In Silico The Computational Biology of RNA Secondary Structures Advances in Complex Systems. 2: 65-90. DOI: 10.1142/S0219525999000059  0.674
1999 Stadler P. Fitness landscapes arising from the sequence-structure maps of biopolymers Journal of Molecular Structure: Theochem. 463: 7-19. DOI: 10.1016/S0166-1280(98)00387-X  0.388
1998 Hofacker IL, Fekete M, Flamm C, Huynen MA, Rauscher S, Stolorz PE, Stadler PF. Automatic detection of conserved RNA structure elements in complete RNA virus genomes. Nucleic Acids Research. 26: 3825-36. PMID 9685502 DOI: 10.1093/Nar/26.16.3825  0.658
1998 Hofacker IL, Schuster P, Stadler PF. Combinatorics of RNA secondary structures Discrete Applied Mathematics. 88: 207-237. DOI: 10.1016/S0166-218X(98)00073-0  0.51
1997 Babajide A, Hofacker IL, Sippl MJ, Stadler PF. Neutral networks in protein space: a computational study based on knowledge-based potentials of mean force. Folding & Design. 2: 261-9. PMID 9261065 DOI: 10.1016/S1359-0278(97)00037-0  0.321
1997 Reidys C, Stadler PF, Schuster P. Generic properties of combinatory maps: Neutral networks of RNA secondary structures Bulletin of Mathematical Biology. 59: 339-397. PMID 9116604 DOI: 10.1016/S0092-8240(96)00089-4  0.717
1997 Schuster P, Stadler PF, Renner A. RNA structures and folding: From conventional to new issues in structure predictions Current Opinion in Structural Biology. 7: 229-235. PMID 9094330 DOI: 10.1016/S0959-440X(97)80030-9  0.535
1997 Hecht R, Happel R, Schuster P, Stadler PF. Autocatalytic networks with intermediates I: Irreversible reactions Mathematical Biosciences. 140: 33-74. PMID 9029911 DOI: 10.1016/S0025-5564(96)00152-6  0.472
1996 Baskaran S, Stadler PF, Schuster P. Approximate scaling properties of RNA free energy landscapes. Journal of Theoretical Biology. 181: 299-310. PMID 8949578 DOI: 10.1006/Jtbi.1996.0132  0.492
1996 Huynen MA, Perelson A, Vieira WA, Stadler PF. Base pairing probabilities in a complete HIV-1 RNA. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 3: 253-74. PMID 8811486 DOI: 10.1089/Cmb.1996.3.253  0.333
1996 Stadler PF, Schuster P. Permanence of sparse catalytic networks Mathematical Biosciences. 131: 111-133. PMID 8589540 DOI: 10.1016/0025-5564(95)00033-X  0.467
1996 Huynen MA, Stadler PF, Fontana W. Smoothness within ruggedness: the role of neutrality in adaptation. Proceedings of the National Academy of Sciences of the United States of America. 93: 397-401. PMID 8552647 DOI: 10.1073/Pnas.93.1.397  0.351
1996 Tacker M, Stadler PF, Bornberg-Bauer EG, Hofacker IL, Schuster P. Algorithm independent properties of RNA secondary structure predictions European Biophysics Journal. 25: 115-130. DOI: 10.1007/S002490050023  0.68
1996 Gr�ner W, Giegerich R, Strothmann D, Reidys C, Weber J, Hofacker IL, Stadler PF, Schuster P. Analysis of RNA sequence structure maps by exhaustive enumeration II. Structures of neutral networks and shape space covering Monatshefte F�R Chemie Chemical Monthly. 127: 375-389. DOI: 10.1007/Bf00810882  0.729
1996 Gr�ner W, Giegerich R, Strothmann D, Reidys C, Weber J, Hofacker IL, Stadler PF, Schuster P. Analysis of RNA sequence structure maps by exhaustive enumeration I. Neutral networks Monatshefte F�R Chemie Chemical Monthly. 127: 355-374. DOI: 10.1007/Bf00810881  0.715
1996 Happel R, Stadler PF. Canonical approximation of fitness landscapes Complexity. 2: 53-58. DOI: 10.1002/(Sici)1099-0526(199609/10)2:1<53::Aid-Cplx11>3.0.Co;2-W  0.329
1995 Stadler PF, Schnabl W, Forst CV, Schuster P. Dynamics of small autocatalytic reaction networks-II. Replication, mutation and catalysis Bulletin of Mathematical Biology. 57: 21-61. DOI: 10.1016/0092-8240(94)00022-5  0.447
1994 Stadler PF, Schuster P, Perelson AS. Immune networks modeled by replicator equations Journal of Mathematical Biology. 33: 111-137. PMID 7868989 DOI: 10.1007/Bf00160176  0.438
1994 Schuster P, Stadler PF. Landscapes: complex optimization problems and biopolymer structures. Computers & Chemistry. 18: 295-324. PMID 7524995 DOI: 10.1016/0097-8485(94)85025-9  0.578
1994 Schuster P, Fontana W, Stadler PF, Hofacker IL. From sequences to shapes and back: A case study in RNA secondary structures Proceedings of the Royal Society B: Biological Sciences. 255: 279-284. PMID 7517565 DOI: 10.1098/Rspb.1994.0040  0.56
1994 Tacker M, Fontana W, Stadler PF, Schuster P. Statistics of RNA melting kinetics. European Biophysics Journal : Ebj. 23: 29-38. PMID 7515805 DOI: 10.1007/Bf00192203  0.543
1994 Stadler PF, Grüner W. Anisotropy in fitness landscapes. Journal of Theoretical Biology. 165: 373-88. PMID 7509427 DOI: 10.1006/Jtbi.1993.1195  0.307
1994 Hofacker IL, Fontana W, Stadler PF, Bonhoeffer LS, Tacker M, Schuster P. Fast folding and comparison of RNA secondary structures Monatshefte F�R Chemie Chemical Monthly. 125: 167-188. DOI: 10.1007/Bf00818163  0.558
1994 Bornberg-Bauer EG, Stadler PF. Random structures and evolution of biopolymers Berichte Der Bunsengesellschaft FüR Physikalische Chemie. 98: 1128-1128. DOI: 10.1002/bbpc.19940980910  0.507
1993 Fontana W, Stadler PF, Bornberg-Bauer EG, Griesmacher T, Hofacker IL, Tacker M, Tarazona P, Weinberger ED, Schuster P. RNA folding and combinatory landscapes. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 47: 2083-2099. PMID 9960229 DOI: 10.1103/Physreve.47.2083  0.551
1993 Fontana W, Konings DAM, Stadler PF, Schuster P. Statistics of RNA secondary structures Biopolymers. 33: 1389-1404. PMID 7691201 DOI: 10.1002/Bip.360330909  0.567
1993 Bonhoeffer S, McCaskill JS, Stadler PF, Schuster P. RNA multi-structure landscapes - A study based on temperature dependent partition functions European Biophysics Journal. 22: 13-24. PMID 7685689 DOI: 10.1007/Bf00205808  0.534
1993 Weinberger ED, Stadler PF. Why some fitness landscapes are fractal. Journal of Theoretical Biology. 163: 255-75. PMID 7504147 DOI: 10.1006/Jtbi.1993.1120  0.377
1993 Bonhoeffer S, Stadler PF. Error thresholds on correlated fitness landscapes Journal of Theoretical Biology. 164: 359-372. DOI: 10.1006/Jtbi.1993.1160  0.306
1992 Stadler PF, Schuster P. Mutation in autocatalytic reaction networks Journal of Mathematical Biology. 30: 597-632. PMID 1640182 DOI: 10.1007/Bf00948894  0.459
1991 Schnabl W, Stadler PF, Forst C, Schuster P. Full characterization of a strange attractor. Chaotic dynamics in low-dimensional replicator systems Physica D: Nonlinear Phenomena. 48: 65-90. DOI: 10.1016/0167-2789(91)90052-B  0.471
1991 Fontana W, Griesmacher T, Schnabl W, Stadler PF, Schuster P. Statistics of landscapes based on free energies, replication and degradation rate constants of RNA secondary structures Monatshefte FüR Chemie Chemical Monthly. 122: 795-819. DOI: 10.1007/Bf00815919  0.54
1990 Stadler PF, Schuster P. Dynamics of small autocatalytic reaction networks-I. bifurcations, permanence and exclusion Bulletin of Mathematical Biology. 52: 485-508. PMID 1697772 DOI: 10.1016/S0092-8240(05)80358-1  0.497
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