Peter F. Stadler - Publications

Affiliations: 
Interdisciplinary Centre for Bioinformatics University Leipzig, Germany 

211 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, 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
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  0.36
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  0.56
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  0.32
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  0.72
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  0.84
2018 Gröbner SN, Worst BC, Weischenfeldt J, Buchhalter I, Kleinheinz K, Rudneva VA, Johann PD, Balasubramanian GP, Segura-Wang M, Brabetz S, Bender S, Hutter B, Sturm D, Pfaff E, Hübschmann D, ... ... Stadler PF, et al. Author Correction: The landscape of genomic alterations across childhood cancers. Nature. PMID 29875405 DOI: 10.1038/s41586-018-0167-2  0.36
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  0.48
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  0.72
2018 Hoffmann A, Fallmann J, Vilardo E, Mörl M, Stadler PF, Amman F. Accurate mapping of tRNA reads. Bioinformatics (Oxford, England). PMID 29547898 DOI: 10.1093/bioinformatics/bty118  0.72
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  0.84
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  0.96
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  0.56
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  0.56
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  0.72
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  0.96
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  0.72
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  0.84
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  0.72
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  0.36
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  0.4
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  0.72
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  0.96
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  0.72
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  0.56
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  0.6
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  0.96
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  0.48
2017 Paschoal AR, Lozada-Chávez I, Domingues DS, Stadler PF. ceRNAs in plants: computational approaches and associated challenges for target mimic research. Briefings in Bioinformatics. PMID 28575144 DOI: 10.1093/bib/bbx058  0.72
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  0.6
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  0.56
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  0.76
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  0.72
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  0.84
2016 Bernhart SH, Kretzmer H, Holdt LM, Jühling F, Ammerpohl O, Bergmann AK, Northoff BH, Doose G, Siebert R, Stadler PF, Hoffmann S. Changes of bivalent chromatin coincide with increased expression of developmental genes in cancer. Scientific Reports. 6: 37393. PMID 27876760 DOI: 10.1038/srep37393  0.56
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  0.96
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  0.76
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  0.56
2016 Hezaveh K, Kloetgen A, Bernhart SH, Mahapatra KD, Lenze D, Richter J, Haake A, Bergmann AK, Brors B, Burkhardt B, Claviez A, Drexler HG, Eils R, Haas S, Hoffmann S, ... ... Stadler PF, et al. Alterations of miRNAs and miRNA-regulated mRNA expression in GC B cell lymphomas determined by integrative sequencing analysis. Haematologica. PMID 27390358 DOI: 10.3324/haematol.2016.143891  0.36
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  0.4
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. Corrigendum: The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nature Genetics. 48: 700. PMID 27230688 DOI: 10.1038/ng0616-700c  0.4
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  0.32
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  0.56
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  0.4
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  1
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  1
2016 Lorenz R, Luntzer D, Hofacker IL, Stadler PF, Wolfinger MT. SHAPE directed RNA folding. Bioinformatics (Oxford, England). 32: 145-7. PMID 26353838 DOI: 10.1093/bioinformatics/btv523  0.72
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  0.32
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  0.56
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  1
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  0.56
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  1
2015 Kretzmer H, Bernhart SH, Wang W, Haake A, Weniger MA, Bergmann AK, Betts MJ, Carrillo-de-Santa-Pau E, Doose G, Gutwein J, Richter J, Hovestadt V, Huang B, Rico D, Jühling F, ... ... Stadler PF, et al. DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control. Nature Genetics. PMID 26437030 DOI: 10.1038/ng.3413  0.56
2015 Kucharík M, Hofacker IL, Stadler PF, Qin J. Pseudoknots in RNA folding landscapes. Bioinformatics (Oxford, England). PMID 26428288 DOI: 10.1093/bioinformatics/btv572  0.56
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  0.56
2015 Engelhardt J, Stadler PF. Evolution of the unspliced transcriptome. Bmc Evolutionary Biology. 15: 166. PMID 26289325 DOI: 10.1186/s12862-015-0437-7  0.6
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  0.56
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  1
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  1
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  1
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  1
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  1
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  1
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  0.36
2015 Hertel J, Stadler PF. The Expansion of Animal MicroRNA Families Revisited. Life (Basel, Switzerland). 5: 905-20. PMID 25780960 DOI: 10.3390/life5010905  1
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  1
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  0.32
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  0.32
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  0.56
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  1
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  0.72
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  1
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  1
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  0.56
2014 Hertel J, Langenberger D, Stadler PF. Computational prediction of microRNA genes. Methods in Molecular Biology (Clifton, N.J.). 1097: 437-56. PMID 24639171 DOI: 10.1007/978-1-62703-709-9_20  1
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  0.36
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  0.44
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  1
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  0.4
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  1
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  1
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  0.4
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  1
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  0.72
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  0.56
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  1
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  1
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  1
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  1
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  1
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  1
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  0.56
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  1
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  0.56
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  1
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  1
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  1
2013 Lorenz R, Bernhart SH, Qin J, Honer 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. PMID 23358314  0.56
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  0.56
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  1
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  0.36
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  0.36
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  0.56
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  1
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  1
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  1
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  0.56
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  1
2012 Richter J, Schlesner M, Hoffmann S, Kreuz M, Leich E, Burkhardt B, Rosolowski M, Ammerpohl O, Wagener R, Bernhart SH, Lenze D, Szczepanowski M, Paulsen M, Lipinski S, Russell RB, ... ... Stadler PF, et al. Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing. Nature Genetics. 44: 1316-20. PMID 23143595 DOI: 10.1038/ng.2469  1
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  0.56
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  1
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  1
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  0.36
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  1
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  0.56
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  0.56
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  0.56
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  1
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  1
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: 10.1093/bioinformatics/btr598  0.36
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2011 Höner zu Siederdissen C, Bernhart SH, Stadler PF, Hofacker IL. A folding algorithm for extended RNA secondary structures. Bioinformatics (Oxford, England). 27: i129-36. PMID 21685061 DOI: 10.1093/bioinformatics/btr220  0.56
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  0.56
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  0.36
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  1
2011 Perseke M, Hetmank J, Bernt M, Stadler PF, Schlegel M, Bernhard D. The enigmatic mitochondrial genome of Rhabdopleura compacta (Pterobranchia) reveals insights into selection of an efficient tRNA system and supports monophyly of Ambulacraria. Bmc Evolutionary Biology. 11: 134. PMID 21599892 DOI: 10.1186/1471-2148-11-134  0.56
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  0.56
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  1
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  0.36
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  1
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  1
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  1
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  1
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  1
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  1
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  0.32
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  1
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  1
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  1
2010 Arnold C, Stadler PF. Polynomial algorithms for the Maximal Pairing Problem: efficient phylogenetic targeting on arbitrary trees. Algorithms For Molecular Biology : Amb. 5: 25. PMID 20525185 DOI: 10.1186/1748-7188-5-25  0.6
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  1
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  0.36
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  1
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  0.56
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  1
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  1
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  1
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  1
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  0.52
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  1
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  0.56
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  0.56
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  1
2009 Marz M, Stadler PF. Comparative analysis of eukaryotic U3 snoRNA. Rna Biology. 6: 503-7. PMID 19875933  1
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  1
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  0.32
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  0.36
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  1
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  0.56
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  0.36
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  1
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  1
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  1
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  1
2009 Jones TA, Otto W, Marz M, Eddy SR, Stadler PF. A survey of nematode SmY RNAs. Rna Biology. 6: 5-8. PMID 19106623  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
1994 Schuster P, Stadler PF. Landscapes: complex optimization problems and biopolymer structures. Computers & Chemistry. 18: 295-324. PMID 7524995  1
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  1
1994 Tacker M, Fontana W, Stadler PF, Schuster P. Statistics of RNA melting kinetics. European Biophysics Journal : Ebj. 23: 29-38. PMID 7515805  1
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  1
1993 Fontana W, Konings DAM, Stadler PF, Schuster P. Statistics of RNA secondary structures Biopolymers. 33: 1389-1404. PMID 7691201  1
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  1
1992 Stadler PF, Schuster P. Mutation in autocatalytic reaction networks Journal of Mathematical Biology. 30: 597-632. PMID 1640182 DOI: 10.1007/BF00175609  1
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: 10.1007/BF02462263  1
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