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Peter Stadler

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.5 Million pre-calculated profiles free of charge to researchers worldwide.

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Publications

TOP 3
Marz Manja; Donath Alexander; Verstraete Nina; Nguyen Van Trung; Stadler Peter F; Bensaude Olivier
Evolution of 7SK RNA and its protein partners in metazoa.
Mosig Axel; Zhu Liang; Stadler Peter F
Customized strategies for discovering distant ncRNA homologs.
Hoffmann Steve; Otto Christian; Kurtz Stefan; Sharma Cynthia M; Khaitovich Philipp; Vogel Jörg; Stadler Peter F; Hackermüller Jörg
Fast mapping of short sequences with mismatches, insertions and deletions using index structures.

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All Publications

2009: Marz Manja; Donath Alexander; Verstraete Nina; Nguyen Van Trung; Stadler Peter F; Bensaude Olivier
Evolution of 7SK RNA and its protein partners in metazoa.
Molecular biology and evolution 2009;26(12):2821-30.
2009: Mosig Axel; Zhu Liang; Stadler Peter F
Customized strategies for discovering distant ncRNA homologs.
Briefings in functional genomics & proteomics 2009;8(6):451-60.
2009: Hoffmann Steve; Otto Christian; Kurtz Stefan; Sharma Cynthia M; Khaitovich Philipp; Vogel Jörg; Stadler Peter F; Hackermüller Jörg
Fast mapping of short sequences with mismatches, insertions and deletions using index structures.
PLoS computational biology 2009;5(9):e1000502.
2009: Langenberger David; Bermudez-Santana Clara; Hertel Jana; Hoffmann Steve; Khaitovich Philipp; Stadler Peter F
Evidence for human microRNA-offset RNAs in small RNA sequencing data.
Bioinformatics (Oxford, England) 2009;25(18):2298-301.
2009: Stadler Peter F; Chen Julian J-L; Hackermüller Jörg; Hoffmann Steve; Horn Friedemann; Khaitovich Phillip; Kretzschmar Antje K; Mosig Axel; Prohaska Sonja J; Qi Xiaodong; Schutt Katharina; Ullmann Kerstin
Evolution of vault RNAs.
Molecular biology and evolution 2009;26(9):1975-91.
2009: Stadler Peter F; Prohaska Sonja J; Forst Christian V; Krakauer David C
Defining genes: a computational framework.
Theory in biosciences = Theorie in den Biowissenschaften 2009;128(3):165-70.
2009: Riester Markus; Stadler Peter F; Klemm Konstantin
FRANz: reconstruction of wild multi-generation pedigrees.
Bioinformatics (Oxford, England) 2009;25(16):2134-9.
2009: Hiller Michael; Findeiss Sven; Lein Sandro; Marz Manja; Nickel Claudia; Rose Dominic; Schulz Christine; Backofen Rolf; Prohaska Sonja J; Reuter Gunter; Stadler Peter F
Conserved introns reveal novel transcripts in Drosophila melanogaster.
Genome research 2009;19(7):1289-300.
2009: Conant Gavin C; Stadler Peter F
Solvent exposure imparts similar selective pressures across a range of yeast proteins.
Molecular biology and evolution 2009;26(5):1155-61.
2009: Chambers Karen E; McDaniell Ryan; Raincrow Jeremy D; Deshmukh Maya; Stadler Peter F; Chiu Chi-hua
Hox cluster duplication in the basal teleost Hiodon alosoides (Osteoglossomorpha).
Theory in biosciences = Theorie in den Biowissenschaften 2009;128(2):109-20.
2009: Scheibye-Alsing K; Hoffmann S; Frankel A; Jensen P; Stadler P F; Mang Y; Tommerup N; Gilchrist M J; Nygård A-B; Cirera S; Jørgensen C B; Fredholm M; Gorodkin J
Sequence assembly.
Computational biology and chemistry 2009;33(2):121-36.
2009: Hertel Jana; de Jong Danielle; Marz Manja; Rose Dominic; Tafer Hakim; Tanzer Andrea; Schierwater Bernd; Stadler Peter F
Non-coding RNA annotation of the genome of Trichoplax adhaerens.
Nucleic acids research 2009;37(5):1602-15.
2009: Kaczkowski Bogumil; Torarinsson Elfar; Reiche Kristin; Havgaard Jakob Hull; Stadler Peter F; Gorodkin Jan
Structural profiles of human miRNA families from pairwise clustering.
Bioinformatics (Oxford, England) 2009;25(3):291-4.
2009: Jones Thomas A; Otto Wolfgang; Marz Manja; Eddy Sean R; Stadler Peter F
A survey of nematode SmY RNAs.
RNA biology 2009;6(1):5-8.
2009: Jühling Frank; Mörl Mario; Hartmann Roland K; Sprinzl Mathias; Stadler Peter F; Pütz Joern
tRNAdb 2009: compilation of tRNA sequences and tRNA genes.
Nucleic acids research 2009;37(Database issue):D159-62.
2009: Copeland Claudia C; Marz Manja; Rose Dominic; Hertel Jana; Brindley Paul J; Santana Clara Bermudez; Kehr Stephanie; Attolini Camille Stephan-Otto; Stadler Peter F
Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum.
BMC genomics 2009;10():464.
2009: Benkö Gil; Centler Florian; Dittrich Peter; Flamm Christoph; Stadler Bärbel M R; Stadler Peter F
A topological approach to chemical organizations.
Artificial life 2009;15(1):71-88.
2008: Rose Dominic; Jöris Julian; Hackermüller Jörg; Reiche Kristin; Li Qiang; Stadler Peter F
Duplicated RNA genes in teleost fish genomes.
Journal of bioinformatics and computational biology 2008;6(6):1157-75.
2008: Marz Manuela; Kirsten Toralf; Stadler Peter F
Evolution of spliceosomal snRNA genes in metazoan animals.
Journal of molecular evolution 2008;67(6):594-607.
2008: Sonnleitner Elisabeth; Sorger-Domenigg Theresa; Madej Monika J; Findeiss Sven; Hackermüller Jörg; Hüttenhofer Alexander; Stadler Peter F; Bläsi Udo; Moll Isabella
Detection of small RNAs in Pseudomonas aeruginosa by RNomics and structure-based bioinformatic tools.
Microbiology (Reading, England) 2008;154(Pt 10):3175-87.
2008: Gruber Andreas R; Kilgus Carsten; Mosig Axel; Hofacker Ivo L; Hennig Wolfgang; Stadler Peter F
Arthropod 7SK RNA.
Molecular biology and evolution 2008;25(9):1923-30.
2008: Hoffmann Steve; Cepok Sabine; Grummel Verena; Lehmann-Horn Klaus; Hackermüller Jörg; Stadler Peter F; Hartung Hans-Peter; Berthele Achim; Deisenhammer Florian; Wassmuth Ralf; Hemmer Bernhard
HLA-DRB1*0401 and HLA-DRB1*0408 are strongly associated with the development of antibodies against interferon-beta therapy in multiple sclerosis.
American journal of human genetics 2008;83(2):219-27.
2008: Prohaska Sonja J; Stadler Peter F
"Genes".
Theory in biosciences = Theorie in den Biowissenschaften 2008;127(3):215-21.
2008: Rose Dominic; Hertel Jana; Reiche Kristin; Stadler Peter F; Hackermüller Jörg
NcDNAlign: plausible multiple alignments of non-protein-coding genomic sequences.
Genomics 2008;92(1):65-74.
2008: Amemiya Chris T; Prohaska Sonja J; Hill-Force Alicia; Cook April; Wasserscheid Jessica; Ferrier David E K; Pascual-Anaya Juan; Garcia-Fernàndez Jordi; Dewar Ken; Stadler Peter F
The amphioxus Hox cluster: characterization, comparative genomics, and evolution.
Journal of experimental zoology. Part B, Molecular and developmental evolution 2008;310(5):465-77.
2008: Geis Michael; Flamm Christoph; Wolfinger Michael T; Tanzer Andrea; Hofacker Ivo L; Middendorf Martin; Mandl Christian; Stadler Peter F; Thurner Caroline
Folding kinetics of large RNAs.
Journal of molecular biology 2008;379(1):160-73.
2008: Jöchl Christoph; Rederstorff Mathieu; Hertel Jana; Stadler Peter F; Hofacker Ivo L; Schrettl Markus; Haas Hubertus; Hüttenhofer Alexander
Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis.
Nucleic acids research 2008;36(8):2677-89.
2008: Krauss Veiko; Thümmler Christian; Georgi Franziska; Lehmann Jörg; Stadler Peter F; Eisenhardt Carina
Near intron positions are reliable phylogenetic markers: an application to holometabolous insects.
Molecular biology and evolution 2008;25(5):821-30.
2008: Perseke Marleen; Fritzsch Guido; Ramsch Kai; Bernt Matthias; Merkle Daniel; Middendorf Martin; Bernhard Detlef; Stadler Peter F; Schlegel Martin
Evolution of mitochondrial gene orders in echinoderms.
Molecular phylogenetics and evolution 2008;47(2):855-64.
2008: Fritzsch Guido; Böhme Manja U; Thorndyke Mike; Nakano Hiroaki; Israelsson Olle; Stach Thomas; Schlegel Martin; Hankeln Thomas; Stadler Peter F
PCR survey of Xenoturbella bocki Hox genes.
Journal of experimental zoology. Part B, Molecular and developmental evolution 2008;310(3):278-84.
2008: Gruber Andreas R; Koper-Emde Dorota; Marz Manja; Tafer Hakim; Bernhart Stephan; Obernosterer Gregor; Mosig Axel; Hofacker Ivo L; Stadler Peter F; Benecke Bernd-Joachim
Invertebrate 7SK snRNAs.
Journal of molecular evolution 2008;66(2):107-15.
2008: Xie Mingyi; Mosig Axel; Qi Xiaodong; Li Yang; Stadler Peter F; Chen Julian J-L
Structure and function of the smallest vertebrate telomerase RNA from teleost fish.
The Journal of biological chemistry 2008;283(4):2049-59.
2008: Hertel Jana; Hofacker Ivo L; Stadler Peter F
SnoReport: computational identification of snoRNAs with unknown targets.
Bioinformatics (Oxford, England) 2008;24(2):158-64.
2008: Bompfünewerer Athanasius F; Backofen Rolf; Bernhart Stephan H; Hertel Jana; Hofacker Ivo L; Stadler Peter F; Will Sebastian
Variations on RNA folding and alignment: lessons from Benasque.
Journal of mathematical biology 2008;56(1-2):129-44.
2008: Bernhart Stephan H; Hofacker Ivo L; Will Sebastian; Gruber Andreas R; Stadler Peter F
RNAalifold: improved consensus structure prediction for RNA alignments.
BMC bioinformatics 2008;9():474.
2008: Lehmann Jörg; Stadler Peter F; Prohaska Sonja J
SynBlast: assisting the analysis of conserved synteny information.
BMC bioinformatics 2008;9():351.
2008: Dress Andreas W M; Flamm Christoph; Fritzsch Guido; Grünewald Stefan; Kruspe Matthias; Prohaska Sonja J; Stadler Peter F
Noisy: identification of problematic columns in multiple sequence alignments.
Algorithms for molecular biology : AMB 2008;3():7.
2007: Marz Manja; Mosig Axel; Stadler Bärbel M R; Stadler Peter F
U7 snRNAs: a computational survey.
Genomics, proteomics & bioinformatics / Beijing Genomics Institute 2007;5(3-4):187-95.
2007: Bernt Matthias; Merkle Daniel; Ramsch Kai; Fritzsch Guido; Perseke Marleen; Bernhard Detlef; Schlegel Martin; Stadler Peter F; Middendorf Martin
CREx: inferring genomic rearrangements based on common intervals.
Bioinformatics (Oxford, England) 2007;23(21):2957-8.
2007: Perseke Marleen; Hankeln Thomas; Weich Bettina; Fritzsch Guido; Stadler Peter F; Israelsson Olle; Bernhard Detlef; Schlegel Martin
The mitochondrial DNA of Xenoturbella bocki: genomic architecture and phylogenetic analysis.
Theory in biosciences = Theorie in den Biowissenschaften 2007;126(1):35-42.
2007: Mosig Axel; Guofeng Meng; Stadler Bärbel M R; Stadler Peter F
Evolution of the vertebrate Y RNA cluster.
Theory in biosciences = Theorie in den Biowissenschaften 2007;126(1):9-14.
2007: Breidbach Olaf; Jost Jürgen; Stadler Peter
Towards theoretical formalisms.
Theory in biosciences = Theorie in den Biowissenschaften 2007;126(1):1-2.
2007: Löffler Dennis; Brocke-Heidrich Katja; Pfeifer Gabriele; Stocsits Claudia; Hackermüller Jörg; Kretzschmar Antje K; Burger Renate; Gramatzki Martin; Blumert Conny; Bauer Kay; Cvijic Helena; Ullmann A Kerstin; Stadler Peter F; Horn Friedemann
Interleukin-6 dependent survival of multiple myeloma cells involves the Stat3-mediated induction of microRNA-21 through a highly conserved enhancer.
Blood 2007;110(4):1330-3.
2007: Wagner Günter P; Otto Wolfgang; Lynch Vincent; Stadler Peter F
A stochastic model for the evolution of transcription factor binding site abundance.
Journal of theoretical biology 2007;247(3):544-53.
2007: Birney Ewan; Stamatoyannopoulos John A; Dutta Anindya; Guigó Roderic; Gingeras Thomas R; Margulies Elliott H; Weng Zhiping; Snyder Michael; Dermitzakis Emmanouil T; Thurman Robert E; Kuehn Michael S; Taylor Christopher M; Neph Shane; Koch Christoph M; Asthana Saurabh; Malhotra Ankit; Adzhubei Ivan; Greenbaum Jason A; Andrews Robert M; Flicek Paul; Boyle Patrick J; Cao Hua; Carter Nigel P; Clelland Gayle K; Davis Sean; Day Nathan; Dhami Pawandeep; Dillon Shane C; Dorschner Michael O; Fiegler Heike; Giresi Paul G; Goldy Jeff; Hawrylycz Michael; Haydock Andrew; Humbert Richard; James Keith D; Johnson Brett E; Johnson Ericka M; Frum Tristan T; Rosenzweig Elizabeth R; Karnani Neerja; Lee Kirsten; Lefebvre Gregory C; Navas Patrick A; Neri Fidencio; Parker Stephen C J; Sabo Peter J; Sandstrom Richard; Shafer Anthony; Vetrie David; Weaver Molly; Wilcox Sarah; Yu Man; Collins Francis S; Dekker Job; Lieb Jason D; Tullius Thomas D; Crawford Gregory E; Sunyaev Shamil; Noble William S; Dunham Ian; Denoeud France; Reymond Alexandre; Kapranov Philipp; Rozowsky Joel; Zheng Deyou; Castelo Robert; Frankish Adam; Harrow Jennifer; Ghosh Srinka; Sandelin Albin; Hofacker Ivo L; Baertsch Robert; Keefe Damian; Dike Sujit; Cheng Jill; Hirsch Heather A; Sekinger Edward A; Lagarde Julien; Abril Josep F; Shahab Atif; Flamm Christoph; Fried Claudia; Hackermüller Jörg; Hertel Jana; Lindemeyer Manja; Missal Kristin; Tanzer Andrea; Washietl Stefan; Korbel Jan; Emanuelsson Olof; Pedersen Jakob S; Holroyd Nancy; Taylor Ruth; Swarbreck David; Matthews Nicholas; Dickson Mark C; Thomas Daryl J; Weirauch Matthew T; Gilbert James; Drenkow Jorg; Bell Ian; Zhao XiaoDong; Srinivasan K G; Sung Wing-Kin; Ooi Hong Sain; Chiu Kuo Ping; Foissac Sylvain; Alioto Tyler; Brent Michael; Pachter Lior; Tress Michael L; Valencia Alfonso; Choo Siew Woh; Choo Chiou Yu; Ucla Catherine; Manzano Caroline; Wyss Carine; Cheung Evelyn; Clark Taane G; Brown James B; Ganesh Madhavan; Patel Sandeep; Tammana Hari; Chrast Jacqueline; Henrichsen Charlotte N; Kai Chikatoshi; Kawai Jun; Nagalakshmi Ugrappa; Wu Jiaqian; Lian Zheng; Lian Jin; Newburger Peter; Zhang Xueqing; Bickel Peter; Mattick John S; Carninci Piero; Hayashizaki Yoshihide; Weissman Sherman; Hubbard Tim; Myers Richard M; Rogers Jane; Stadler Peter F; Lowe Todd M; Wei Chia-Lin; Ruan Yijun; Struhl Kevin; Gerstein Mark; Antonarakis Stylianos E; Fu Yutao; Green Eric D; Karaöz Ulas; Siepel Adam; Taylor James; Liefer Laura A; Wetterstrand Kris A; Good Peter J; Feingold Elise A; Guyer Mark S; Cooper Gregory M; Asimenos George; Dewey Colin N; Hou Minmei; Nikolaev Sergey; Montoya-Burgos Juan I; Löytynoja Ari; Whelan Simon; Pardi Fabio; Massingham Tim; Huang Haiyan; Zhang Nancy R; Holmes Ian; Mullikin James C; Ureta-Vidal Abel; Paten Benedict; Seringhaus Michael; Church Deanna; Rosenbloom Kate; Kent W James; Stone Eric A; Batzoglou Serafim; Goldman Nick; Hardison Ross C; Haussler David; Miller Webb; Sidow Arend; Trinklein Nathan D; Zhang Zhengdong D; Barrera Leah; Stuart Rhona; King David C; Ameur Adam; Enroth Stefan; Bieda Mark C; Kim Jonghwan; Bhinge Akshay A; Jiang Nan; Liu Jun; Yao Fei; Vega Vinsensius B; Lee Charlie W H; Ng Patrick; Shahab Atif; Yang Annie; Moqtaderi Zarmik; Zhu Zhou; Xu Xiaoqin; Squazzo Sharon; Oberley Matthew J; Inman David; Singer Michael A; Richmond Todd A; Munn Kyle J; Rada-Iglesias Alvaro; Wallerman Ola; Komorowski Jan; Fowler Joanna C; Couttet Phillippe; Bruce Alexander W; Dovey Oliver M; Ellis Peter D; Langford Cordelia F; Nix David A; Euskirchen Ghia; Hartman Stephen; Urban Alexander E; Kraus Peter; Van Calcar Sara; Heintzman Nate; Kim Tae Hoon; Wang Kun; Qu Chunxu; Hon Gary; Luna Rosa; Glass Christopher K; Rosenfeld M Geoff; Aldred Shelley Force; Cooper Sara J; Halees Anason; Lin Jane M; Shulha Hennady P; Zhang Xiaoling; Xu Mousheng; Haidar Jaafar N S; Yu Yong; Ruan Yijun; Iyer Vishwanath R; Green Roland D; Wadelius Claes; Farnham Peggy J; Ren Bing; Harte Rachel A; Hinrichs Angie S; Trumbower Heather; Clawson Hiram; Hillman-Jackson Jennifer; Zweig Ann S; Smith Kayla; Thakkapallayil Archana; Barber Galt; Kuhn Robert M; Karolchik Donna; Armengol Lluis; Bird Christine P; de Bakker Paul I W; Kern Andrew D; Lopez-Bigas Nuria; Martin Joel D; Stranger Barbara E; Woodroffe Abigail; Davydov Eugene; Dimas Antigone; Eyras Eduardo; Hallgrímsdóttir Ingileif B; Huppert Julian; Zody Michael C; Abecasis Gonçalo R; Estivill Xavier; Bouffard Gerard G; Guan Xiaobin; Hansen Nancy F; Idol Jacquelyn R; Maduro Valerie V B; Maskeri Baishali; McDowell Jennifer C; Park Morgan; Thomas Pamela J; Young Alice C; Blakesley Robert W; Muzny Donna M; Sodergren Erica; Wheeler David A; Worley Kim C; Jiang Huaiyang; Weinstock George M; Gibbs Richard A; Graves Tina; Fulton Robert; Mardis Elaine R; Wilson Richard K; Clamp Michele; Cuff James; Gnerre Sante; Jaffe David B; Chang Jean L; Lindblad-Toh Kerstin; Lander Eric S; Koriabine Maxim; Nefedov Mikhail; Osoegawa Kazutoyo; Yoshinaga Yuko; Zhu Baoli; de Jong Pieter J
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
Nature 2007;447(7146):799-816.
2007: Washietl Stefan; Pedersen Jakob S; Korbel Jan O; Stocsits Claudia; Gruber Andreas R; Hackermüller Jörg; Hertel Jana; Lindemeyer Manja; Reiche Kristin; Tanzer Andrea; Ucla Catherine; Wyss Carine; Antonarakis Stylianos E; Denoeud France; Lagarde Julien; Drenkow Jorg; Kapranov Philipp; Gingeras Thomas R; Guigó Roderic; Snyder Michael; Gerstein Mark B; Reymond Alexandre; Hofacker Ivo L; Stadler Peter F
Structured RNAs in the ENCODE selected regions of the human genome.
Genome research 2007;17(6):852-64.
2007: Kapranov Philipp; Cheng Jill; Dike Sujit; Nix David A; Duttagupta Radharani; Willingham Aarron T; Stadler Peter F; Hertel Jana; Hackermüller Jörg; Hofacker Ivo L; Bell Ian; Cheung Evelyn; Drenkow Jorg; Dumais Erica; Patel Sandeep; Helt Gregg; Ganesh Madhavan; Ghosh Srinka; Piccolboni Antonio; Sementchenko Victor; Tammana Hari; Gingeras Thomas R
RNA maps reveal new RNA classes and a possible function for pervasive transcription.
Science (New York, N.Y.) 2007;316(5830):1484-8.
2007: Luo Jing; Stadler Peter F; He Shunping; Meyer Axel
PCR survey of hox genes in the goldfish Carassius auratus auratus.
Journal of experimental zoology. Part B, Molecular and developmental evolution 2007;308(3):250-8.
2007: Will Sebastian; Reiche Kristin; Hofacker Ivo L; Stadler Peter F; Backofen Rolf
Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering.
PLoS computational biology 2007;3(4):e65.
2007: Conant Gavin C; Wagner Günter P; Stadler Peter F
Modeling amino acid substitution patterns in orthologous and paralogous genes.
Molecular phylogenetics and evolution 2007;42(2):298-307.
2007: Backofen Rolf; Bernhart Stephan H; Flamm Christoph; Fried Claudia; Fritzsch Guido; Hackermüller Jörg; Hertel Jana; Hofacker Ivo L; Missal Kristin; Mosig Axel; Prohaska Sonja J; Rose Dominic; Stadler Peter F; Tanzer Andrea; Washietl Stefan; Will Sebastian
RNAs everywhere: genome-wide annotation of structured RNAs.
Journal of experimental zoology. Part B, Molecular and developmental evolution 2007;308(1):1-25.
2007: Rose Dominic; Hackermüller Jörg; Washietl Stefan; Reiche Kristin; Hertel Jana; Findeiss Sven; Stadler Peter F; Prohaska Sonja J
Computational RNomics of drosophilids.
BMC genomics 2007;8():406.
2007: Seemann Stefan E; Gilchrist Michael J; Hofacker Ivo L; Stadler Peter F; Gorodkin Jan
Detection of RNA structures in porcine EST data and related mammals.
BMC genomics 2007;8():316.
2007: Kruspe Matthias; Stadler Peter F
Progressive multiple sequence alignments from triplets.
BMC bioinformatics 2007;8():254.
2007: Steigele Stephan; Huber Wolfgang; Stocsits Claudia; Stadler Peter F; Nieselt Kay
Comparative analysis of structured RNAs in S. cerevisiae indicates a multitude of different functions.
BMC biology 2007;5():25.
2007: Reiche Kristin; Stadler Peter F
RNAstrand: reading direction of structured RNAs in multiple sequence alignments.
Algorithms for molecular biology : AMB 2007;2():6.
2007: Woodhams Michael D; Stadler Peter F; Penny David; Collins Lesley J
RNase MRP and the RNA processing cascade in the eukaryotic ancestor.
BMC evolutionary biology 2007;7 Suppl 1():S13.
2006: Heine Christian; Scheuermann Gerik; Flamm Christoph; Hofacker Ivo L; Stadler Peter F
Visualization of barrier tree sequences.
IEEE transactions on visualization and computer graphics 2006;12(5):781-8.
2006: Prohaska Sonja J; Stadler Peter F
Evolution of the vertebrate ParaHox clusters.
Journal of experimental zoology. Part B, Molecular and developmental evolution 2006;306(5):481-7.
2006: Hertel Jana; Stadler Peter F
Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data.
Bioinformatics (Oxford, England) 2006;22(14):e197-202.
2006: Missal Kristin; Zhu Xiaopeng; Rose Dominic; Deng Wei; Skogerbø Geir; Chen Runsheng; Stadler Peter F
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 2006;306(4):379-92.
2006: Fritzsch Guido; Schlegel Martin; Stadler Peter F
Alignments of mitochondrial genome arrangements: applications to metazoan phylogeny.
Journal of theoretical biology 2006;240(4):511-20.
2006: Hofacker Ivo L; Stadler Peter F
Memory efficient folding algorithms for circular RNA secondary structures.
Bioinformatics (Oxford, England) 2006;22(10):1172-6.
2006: Mückstein Ulrike; Tafer Hakim; Hackermüller Jörg; Bernhart Stephan H; Stadler Peter F; Hofacker Ivo L
Thermodynamics of RNA-RNA binding.
Bioinformatics (Oxford, England) 2006;22(10):1177-82.
2006: Bernhart Stephan H; Hofacker Ivo L; Stadler Peter F
Local RNA base pairing probabilities in large sequences.
Bioinformatics (Oxford, England) 2006;22(5):614-5.
2006: Mosig Axel; Sameith Katrin; Stadler Peter
Fragrep: an efficient search tool for fragmented patterns in genomic sequences.
Genomics, proteomics & bioinformatics / Beijing Genomics Institute 2006;4(1):56-60.
2006: Klemm Konstantin; Stadler Peter F
Statistics of cycles in large networks.
Physical review. E, Statistical, nonlinear, and soft matter physics 2006;73(2 Pt 2):025101.
2006: Hsu Paul W C; Huang Hsien-Da; Hsu Sheng-Da; Lin Li-Zen; Tsou Ann-Ping; Tseng Ching-Ping; Stadler Peter F; Washietl Stefan; Hofacker Ivo L
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.
Nucleic acids research 2006;34(Database issue):D135-9.
2006: Crow Karen D; Stadler Peter F; Lynch Vincent J; Amemiya Chris; Wagner Günter P
The "fish-specific" Hox cluster duplication is coincident with the origin of teleosts.
Molecular biology and evolution 2006;23(1):121-36.
2006: Tanzer Andrea; Stadler Peter F
Evolution of microRNAs.
Methods in molecular biology (Clifton, N.J.) 2006;342():335-50.
2006: Bernhart Stephan H; Tafer Hakim; Mückstein Ulrike; Flamm Christoph; Stadler Peter F; Hofacker Ivo L
Partition function and base pairing probabilities of RNA heterodimers.
Algorithms for molecular biology : AMB 2006;1(1):3.
2006: Morgenstern Burkhard; Stadler Peter F
New journal: Algorithms for Molecular Biology.
Algorithms for molecular biology : AMB 2006;1(1):1.
2006: Morgenstern Burkhard; Prohaska Sonja J; Pöhler Dirk; Stadler Peter F
Multiple sequence alignment with user-defined anchor points.
Algorithms for molecular biology : AMB 2006;1(1):6.
2006: Hertel Jana; Lindemeyer Manuela; Missal Kristin; Fried Claudia; Tanzer Andrea; Flamm Christoph; Hofacker Ivo L; Stadler Peter F;
The expansion of the metazoan microRNA repertoire.
BMC genomics 2006;7():25.
2006: Forst Christian V; Flamm Christoph; Hofacker Ivo L; Stadler Peter F
Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation.
BMC bioinformatics 2006;7():67.
2005: Washietl Stefan; Hofacker Ivo L; Lukasser Melanie; Hüttenhofer Alexander; Stadler Peter F
Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome.
Nature biotechnology 2005;23(11):1383-90.
2005: Missal Kristin; Rose Dominic; Stadler Peter F
Non-coding RNAs in Ciona intestinalis.
Bioinformatics (Oxford, England) 2005;21 Suppl 2():ii77-8.
2005: Böhmdorfer Gudrun; Hofacker Ivo L; Garber Karin; Jelenic Srecko; Nizhynska Viktoria; Hirochika Hirohiko; Stadler Peter F; Bachmair Andreas
Unorthodox mRNA start site to extend the highly structured leader of retrotransposon Tto1 mRNA increases transposition rate.
RNA (New York, N.Y.) 2005;11(8):1181-91.
2005: Wagner Günter P; Takahashi Kazuhiko; Lynch Vincent; Prohaska Sonja J; Fried Claudia; Stadler Peter F; Amemiya Chris
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 2005;60(5):665-76.
2005: Morgenstern Burkhard; Werner Nadine; Prohaska Sonja J; Steinkamp Rasmus; Schneider Isabelle; Subramanian Amarendran R; Stadler Peter F; Weyer-Menkhoff Jan
Multiple sequence alignment with user-defined constraints at GOBICS.
Bioinformatics (Oxford, England) 2005;21(7):1271-3.
2005: Washietl Stefan; Hofacker Ivo L; Stadler Peter F
Fast and reliable prediction of noncoding RNAs.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(7):2454-9.
2005: Hackermüller Jörg; Meisner Nicole-Claudia; Auer Manfred; Jaritz Markus; Stadler Peter F
The effect of RNA secondary structures on RNA-ligand binding and the modifier RNA mechanism: a quantitative model.
Gene 2005;345(1):3-12.
2005: Tanzer Andrea; Amemiya Chris T; Kim Chang-Bae; Stadler Peter F
Evolution of microRNAs located within Hox gene clusters.
Journal of experimental zoology. Part B, Molecular and developmental evolution 2005;304(1):75-85.
2005: Stocsits Roman R; Hofacker Ivo L; Fried Claudia; Stadler Peter F
Multiple sequence alignments of partially coding nucleic acid sequences.
BMC bioinformatics 2005;6():160.
2005: Dieterich Christoph; Grossmann Steffen; Tanzer Andrea; Röpcke Stefan; Arndt Peter F; Stadler Peter F; Vingron Martin
Comparative promoter region analysis powered by CORG.
BMC genomics 2005;6(1):24.
2004: Campos Paulo R A; de Oliveira Viviane M; Wagner Günter P; Stadler Peter F
Gene phylogenies and protein-protein interactions: possible artifacts resulting from shared protein interaction partners.
Journal of theoretical biology 2004;231(2):197-202.
2004: Wagner Günter P; Fried Claudia; Prohaska Sonja J; Stadler Peter F
Divergence of conserved non-coding sequences: rate estimates and relative rate tests.
Molecular biology and evolution 2004;21(11):2116-21.
2004: Shpak Max; Stadler Peter; Wagner Gunter P; Altenberg Lee
Simon-Ando decomposability and fitness landscapes.
Theory in biosciences = Theorie in den Biowissenschaften 2004;123(2):139-80.
2004: Stadler Peter F; Fried Claudia; Prohaska Sonja J; Bailey Wendy J; Misof Bernhard Y; Ruddle Frank H; Wagner Günter P
Evidence for independent Hox gene duplications in the hagfish lineage: a PCR-based gene inventory of Eptatretus stoutii.
Molecular phylogenetics and evolution 2004;32(3):686-94.
2004: Hofacker Ivo L; Bernhart Stephan H F; Stadler Peter F
Alignment of RNA base pairing probability matrices.
Bioinformatics (Oxford, England) 2004;20(14):2222-7.
2004: Hofacker I L; Stadler P F; Stocsits R R
Conserved RNA secondary structures in viral genomes: a survey.
Bioinformatics (Oxford, England) 2004;20(10):1495-9.
2004: Shpak Max; Stadler Peter; Wagner Gunter P; Hermisson Joachim
Aggregation of variables and system decomposition: Applications to fitness landscape analysis.
Theory in biosciences = Theorie in den Biowissenschaften 2004;123(1):33-68.
2004: Breidbach Olaf; Jost Jürgen; Stadler Peter; Weingarten Michael
Editorial.
Theory in biosciences = Theorie in den Biowissenschaften 2004;123(1):1-2.
2004: Tanzer Andrea; Stadler Peter F
Molecular evolution of a microRNA cluster.
Journal of molecular biology 2004;339(2):327-35.
2004: Thurner Caroline; Witwer Christina; Hofacker Ivo L; Stadler Peter F
Conserved RNA secondary structures in Flaviviridae genomes.
The Journal of general virology 2004;85(Pt 5):1113-24.
2004: Prohaska Sonja J; Fried Claudia; Flamm Christoph; Wagner Günter P; Stadler Peter F
Surveying phylogenetic footprints in large gene clusters: applications to Hox cluster duplications.
Molecular phylogenetics and evolution 2004;31(2):581-604.
2004: Witwer Christina; Hofacker Ivo L; Stadler Peter F
Prediction of consensus RNA secondary structures including pseudoknots.
IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM 2004;1(2):66-77.
2004: Fried Claudia; Prohaska Sonja J; Stadler Peter F
Exclusion of repetitive DNA elements from gnathostome Hox clusters.
Journal of experimental zoology. Part B, Molecular and developmental evolution 2004;302(2):165-73.
2004: Copeland Claudia S; Heyers Oliver; Kalinna Bernd H; Bachmair Andreas; Stadler Peter F; Hofacker Ivo L; Brindley Paul J
Structural and evolutionary analysis of the transcribed sequence of Boudicca, a Schistosoma mansoni retrotransposon.
Gene 2004;329():103-14.
2004: Fried Claudia; Hordijk Wim; Prohaska Sonja J; Stadler Claus R; Stadler Peter F
The footprint sorting problem.
Journal of chemical information and computer sciences 2004;44(2):332-8.
2004: Berger Franziska; Flamm Christoph; Gleiss Petra M; Leydold Josef; Stadler Peter F
Counterexamples in chemical ring perception.
Journal of chemical information and computer sciences 2004;44(2):323-31.
2004: Prohaska Sonja J; Fried Claudia; Amemiya Chris T; Ruddle Frank H; Wagner Günter P; Stadler Peter F
The shark HoxN cluster is homologous to the human HoxD cluster.
Journal of molecular evolution 2004;58(2):212-7.
2004: Rasmussen Steen J; Chen Liaohai; Stadler Bärbel M R; Stadler Peter F
Proto-organism kinetics: evolutionary dynamics of lipid aggregates with genes and metabolism.
Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life 2004;34(1-2):171-80.
2004: Rasmussen Steen; Chen Liaohai; Deamer David; Krakauer David C; Packard Norman H; Stadler Peter F; Bedau Mark A
Evolution. Transitions from nonliving to living matter.
Science (New York, N.Y.) 2004;303(5660):963-5.
2004: Hofacker I L; Priwitzer B; Stadler P F
Prediction of locally stable RNA secondary structures for genome-wide surveys.
Bioinformatics (Oxford, England) 2004;20(2):186-90.
2004: Chiu Chi-Hua; Dewar Ken; Wagner Günter P; Takahashi Kazuhiko; Ruddle Frank; Ledje Christina; Bartsch Peter; Scemama Jean-Luc; Stellwag Edmund; Fried Claudia; Prohaska Sonja J; Stadler Peter F; Amemiya Chris T
Bichir HoxA cluster sequence reveals surprising trends in ray-finned fish genomic evolution.
Genome research 2004;14(1):11-7.
2004: Force Allan; Shashikant Cooduvalli; Stadler Peter; Amemiya Chris T
Comparative genomics, cis-regulatory elements, and gene duplication.
Methods in cell biology 2004;77():545-61.
2003: Weberndorfer Günter; Hofacker Ivo L; Stadler Peter F
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 2003;33(4-5):491-514.
2003: Fried Claudia; Prohaska Sonja J; Stadler Peter F
Independent Hox-cluster duplications in lampreys.
Journal of experimental zoology. Part B, Molecular and developmental evolution 2003;299(1):18-25.
2003: Benkö Gil; Flamm Christoph; Stadler Peter F
A graph-based toy model of chemistry.
Journal of chemical information and computer sciences 2003;43(4):1085-93.
2003: Wuchty Stefan; Stadler Peter F
Centers of complex networks.
Journal of theoretical biology 2003;223(1):45-53.
2003: Stadler Peter F; Hordijk Wim; Fontanari José F
Phase transition and landscape statistics of the number partitioning problem.
Physical review. E, Statistical, nonlinear, and soft matter physics 2003;67(5 Pt 2):056701.
2003: Wagner Günter P; Stadler Peter F
Quasi-independence, homology and the unity of type: a topological theory of characters.
Journal of theoretical biology 2003;220(4):505-27.
2002: Hofacker Ivo L; Fekete Martin; Stadler Peter F
Secondary structure prediction for aligned RNA sequences.
Journal of molecular biology 2002;319(5):1059-66.
2002: Stadler Bärbel M R; Stadler Peter F
Generalized topological spaces in evolutionary theory and combinatorial chemistry.
Journal of chemical information and computer sciences 2002;42(3):577-85.
2002: Mückstein U; Hofacker I L; Stadler P F
Stochastic pairwise alignments.
Bioinformatics (Oxford, England) 2002;18 Suppl 2():S153-60.
2001: Witwer C; Rauscher S; Hofacker I L; Stadler P F
Conserved RNA secondary structures in Picornaviridae genomes.
Nucleic acids research 2001;29(24):5079-89.
2001: Stadler B M; Stadler P F; Wagner G P; Fontana W
The topology of the possible: formal spaces underlying patterns of evolutionary change.
Journal of theoretical biology 2001;213(2):241-74.
2001: Babajide A; Farber R; Hofacker I L; Inman J; Lapedes A S; Stadler P F
Exploring protein sequence space using knowledge-based potentials.
Journal of theoretical biology 2001;212(1):35-46.
2001: Flamm C; Hofacker I L; Maurer-Stroh S; Stadler P F; Zehl M
Design of multistable RNA molecules.
RNA (New York, N.Y.) 2001;7(2):254-65.
2000: Stadler B M; Stadler P F; Schuster P
Dynamics of autocatalytic replicator networks based on higher-order ligation reactions.
Bulletin of mathematical biology 2000;62(6):1061-86.
2000: Wimmer K; Eckart M; Stadler P F; Rehder H; Fonatsch C
Three different premature stop codons lead to skipping of exon 7 in neurofibromatosis type I patients.
Human mutation 2000;16(1):90-1.
2000: Stadler P F; Seitz R; Wagner G P
Population dependent Fourier decomposition of fitness landscapes over recombination spaces: evolvability of complex characters.
Bulletin of mathematical biology 2000;62(3):399-428.
2000: Campos P R; Fontanari J F; Stadler P F
Error propagation in the hypercycle.
Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics 2000;61(3):2996-3002.
2000: Fekete M; Hofacker I L; Stadler P F
Prediction of RNA base pairing probabilities on massively parallel computers.
Journal of computational biology : a journal of computational molecular cell biology 2000;7(1-2):171-82.
2000: Cupal J; Kopp S; Stadler P F
RNA shape space topology.
Artificial life 2000;6(1):3-23.
1999: Wagner A; Stadler P F
Viral RNA and evolved mutational robustness.
The Journal of experimental zoology 1999;285(2):119-27.
1999: Hofacker I L; Stadler P F
Automatic detection of conserved base pairing patterns in RNA virus genomes.
Computers & chemistry 1999;23(3-4):401-14.
1999: Haslinger C; Stadler P F
RNA structures with pseudo-knots: graph-theoretical, combinatorial, and statistical properties.
Bulletin of mathematical biology 1999;61(3):437-67.
1999: Happel R; Stadler P F
Autocatalytic replication in a CSTR and constant organization.
Journal of mathematical biology 1999;38(5):422-34.
1998: Happel R; Stadler P F
The evolution of diversity in replicator networks.
Journal of theoretical biology 1998;195(3):329-38.
1998: Wills P R; Kauffman S A; Stadler B M; Stadler P F
Selection dynamics in autocatalytic systems: templates replicating through binary ligation.
Bulletin of mathematical biology 1998;60(6):1073-98.
1998: Hofacker I L; Fekete M; Flamm C; Huynen M A; Rauscher S; Stolorz P E; Stadler P F
Automatic detection of conserved RNA structure elements in complete RNA virus genomes.
Nucleic acids research 1998;26(16):3825-36.
1998: Mandl C W; Holzmann H; Meixner T; Rauscher S; Stadler P F; Allison S L; Heinz F X
Spontaneous and engineered deletions in the 3' noncoding region of tick-borne encephalitis virus: construction of highly attenuated mutants of a flavivirus.
Journal of virology 1998;72(3):2132-40.
1997: Rauscher S; Flamm C; Mandl C W; Heinz F X; Stadler P F
Secondary structure of the 3'-noncoding region of flavivirus genomes: comparative analysis of base pairing probabilities.
RNA (New York, N.Y.) 1997;3(7):779-91.
1997: Schuster P; Stadler P F; Renner A
RNA structures and folding: from conventional to new issues in structure predictions.
Current opinion in structural biology 1997;7(2):229-35.
1997: Reidys C; Stadler P F; Schuster P
Generic properties of combinatory maps: neutral networks of RNA secondary structures.
Bulletin of mathematical biology 1997;59(2):339-97.
1997: Hecht R; Happel R; Schuster P; Stadler P F
Autocatalytic networks with intermediates. I: Irreversible reactions.
Mathematical biosciences 1997;140(1):33-74.
1997: Stadler P F; Wagner G P
Algebraic theory of recombination spaces.
Evolutionary computation 1997;5(3):241-75.
1997: Cupal J; Flamm C; Renner A; Stadler P F
Density of states, metastable states, and saddle points exploring the energy landscape of an RNA molecule.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1997;5():88-91.
1997: Babajide A; Hofacker I L; Sippl M J; Stadler P F
Neutral networks in protein space: a computational study based on knowledge-based potentials of mean force.
Folding & design 1997;2(5):261-9.
1996: Baskaran S; Stadler P F; Schuster P
Approximate scaling properties of RNA free energy landscapes.
Journal of theoretical biology 1996;181(4):299-310.
1996: Schwienhorst A; Schober A; Günther R; Stadler P F
Hamming chromatography.
Molecular diversity 1996;1(3):187-92.
1996: Reidys C; Stadler P F
Bio-molecular shapes and algebraic structures.
Computers & chemistry 1996;20(1):85-94.
1996: Stadler P F; Schuster P
Permanence of sparse catalytic networks.
Mathematical biosciences 1996;131(2):111-33.
1996: Huynen M A; Stadler P F; Fontana W
Smoothness within ruggedness: the role of neutrality in adaptation.
Proceedings of the National Academy of Sciences of the United States of America 1996;93(1):397-401.
1996: Huynen M A; Perelson A; Vieira W A; Stadler P F
Base pairing probabilities in a complete HIV-1 RNA.
Journal of computational biology : a journal of computational molecular cell biology 1996;3(2):253-74.
1994: Schuster P; Stadler P F
Landscapes: complex optimization problems and biopolymer structures.
Computers & chemistry 1994;18(3):295-324.
1994: Stadler P F; Nuño J C
The influence of mutation on autocatalytic reaction networks.
Mathematical biosciences 1994;122(2):127-60.
1994: Schuster P; Fontana W; Stadler P F; Hofacker I L
From sequences to shapes and back: a case study in RNA secondary structures.
Proceedings. Biological sciences / The Royal Society 1994;255(1344):279-84.
1994: Stadler P F; Schuster P; Perelson A S
Immune networks modeled by replicator equations.
Journal of mathematical biology 1994;33(2):111-37.
1994: Tacker M; Fontana W; Stadler P F; Schuster P
Statistics of RNA melting kinetics.
European biophysics journal : EBJ 1994;23(1):29-38.
1993: Stadler P F; Grüner W
Anisotropy in fitness landscapes.
Journal of theoretical biology 1993;165(3):373-88.
1993: Fontana W; Konings D A; Stadler P F; Schuster P
Statistics of RNA secondary structures.
Biopolymers 1993;33(9):1389-404.
1993: Weinberger E D; Stadler P F
Why some fitness landscapes are fractal.
Journal of theoretical biology 1993;163(2):255-75.
1993: Stadler P F; Happel R
The probability of permanence.
Mathematical biosciences 1993;113(1):25-50.
1993: Bonhoeffer S; McCaskill J S; Stadler P F; Schuster P
RNA multi-structure landscapes. A study based on temperature dependent partition functions.
European biophysics journal : EBJ 1993;22(1):13-24.
1992: Stadler P F; Schuster P
Mutation in autocatalytic reaction networks. An analysis based on perturbation theory.
Journal of mathematical biology 1992;30(6):597-631.
1991: Stadler P F
Complementary replication.
Mathematical biosciences 1991;107(1):83-109.
1991: Stadler P F
Dynamics of autocatalytic reaction networks. IV: Inhomogeneous replicator networks.
Bio Systems 1991;26(1):1-19.
1990: Stadler P F; Schuster P
Dynamics of small autocatalytic reaction networks--I. Bifurcations, permanence and exclusion.
Bulletin of mathematical biology 1990;52(4):485-508.

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