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Items: 1 to 50 of 387

1.

Exploration of the chemical space and its three historical regimes.

Llanos EJ, Leal W, Luu DH, Jost J, Stadler PF, Restrepo G.

Proc Natl Acad Sci U S A. 2019 Jun 11. pii: 201816039. doi: 10.1073/pnas.1816039116. [Epub ahead of print]

PMID:
31186353
2.

The RNA workbench 2.0: next generation RNA data analysis.

Fallmann J, Videm P, Bagnacani A, Batut B, Doyle MA, Klingstrom T, Eggenhofer F, Stadler PF, Backofen R, Grüning B.

Nucleic Acids Res. 2019 May 10. pii: gkz353. doi: 10.1093/nar/gkz353. [Epub ahead of print]

PMID:
31073612
3.

Automatic Curation of Large Comparative Animal MicroRNA Data Sets.

Yazbeck AM, Stadler PF, Tout K, Fallmann J.

Bioinformatics. 2019 Apr 16. pii: btz271. doi: 10.1093/bioinformatics/btz271. [Epub ahead of print]

PMID:
30993337
4.

Ryūtō: network-flow based transcriptome reconstruction.

Gatter T, Stadler PF.

BMC Bioinformatics. 2019 Apr 16;20(1):190. doi: 10.1186/s12859-019-2786-5.

5.

Best match graphs.

Geiß M, Chávez E, González Laffitte M, López Sánchez A, Stadler BMR, Valdivia DI, Hellmuth M, Hernández Rosales M, Stadler PF.

J Math Biol. 2019 Jun;78(7):2015-2057. doi: 10.1007/s00285-019-01332-9. Epub 2019 Apr 9.

6.

Genomic and transcriptomic changes complement each other in the pathogenesis of sporadic Burkitt lymphoma.

López C, Kleinheinz K, Aukema SM, Rohde M, Bernhart SH, Hübschmann D, Wagener R, Toprak UH, Raimondi F, Kreuz M, Waszak SM, Huang Z, Sieverling L, Paramasivam N, Seufert J, Sungalee S, Russell RB, Bausinger J, Kretzmer H, Ammerpohl O, Bergmann AK, Binder H, Borkhardt A, Brors B, Claviez A, Doose G, Feuerbach L, Haake A, Hansmann ML, Hoell J, Hummel M, Korbel JO, Lawerenz C, Lenze D, Radlwimmer B, Richter J, Rosenstiel P, Rosenwald A, Schilhabel MB, Stein H, Stilgenbauer S, Stadler PF, Szczepanowski M, Weniger MA, Zapatka M, Eils R, Lichter P, Loeffler M, Möller P, Trümper L, Klapper W; ICGC MMML-Seq Consortium, Hoffmann S, Küppers R, Burkhardt B, Schlesner M, Siebert R.

Nat Commun. 2019 Mar 29;10(1):1459. doi: 10.1038/s41467-019-08578-3.

7.

SSS-test: a novel test for detecting positive selection on RNA secondary structure.

Walter Costa MB, Höner Zu Siederdissen C, Dunjić M, Stadler PF, Nowick K.

BMC Bioinformatics. 2019 Mar 21;20(1):151. doi: 10.1186/s12859-019-2711-y.

8.

Identification and characterization of novel conserved RNA structures in Drosophila.

Kirsch R, Seemann SE, Ruzzo WL, Cohen SM, Stadler PF, Gorodkin J.

BMC Genomics. 2018 Dec 11;19(1):899. doi: 10.1186/s12864-018-5234-4.

9.

Divergent evolution in the genomes of closely related lacertids, Lacerta viridis and L. bilineata, and implications for speciation.

Kolora SRR, Weigert A, Saffari A, Kehr S, Walter Costa MB, Spröer C, Indrischek H, Chintalapati M, Lohse K, Doose G, Overmann J, Bunk B, Bleidorn C, Grimm-Seyfarth A, Henle K, Nowick K, Faria R, Stadler PF, Schlegel M.

Gigascience. 2019 Feb 1;8(2). pii: giy160. doi: 10.1093/gigascience/giy160.

10.

Superbubbles revisited.

Gärtner F, Müller L, Stadler PF.

Algorithms Mol Biol. 2018 Dec 1;13:16. doi: 10.1186/s13015-018-0134-3. eCollection 2018.

11.

Patterning the insect eye: From stochastic to deterministic mechanisms.

Ebadi H, Perry M, Short K, Klemm K, Desplan C, Stadler PF, Mehta A.

PLoS Comput Biol. 2018 Nov 15;14(11):e1006363. doi: 10.1371/journal.pcbi.1006363. eCollection 2018 Nov.

12.

Combined Experimental and System-Level Analyses Reveal the Complex Regulatory Network of miR-124 during Human Neurogenesis.

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.

Cell Syst. 2018 Oct 24;7(4):438-452.e8. doi: 10.1016/j.cels.2018.08.011. Epub 2018 Oct 3.

13.

Coordinate systems for supergenomes.

Gärtner F, Höner Zu Siederdissen C, Müller L, Stadler PF.

Algorithms Mol Biol. 2018 Sep 24;13:15. doi: 10.1186/s13015-018-0133-4. eCollection 2018.

14.

RNApuzzler: Efficient Outerplanar Drawing of RNA-Secondary Structures.

Wiegreffe D, Alexander D, Stadler PF, Zeckzer D.

Bioinformatics. 2018 Sep 19. doi: 10.1093/bioinformatics/bty817. [Epub ahead of print]

PMID:
30239566
15.

Beyond the 3'UTR binding-microRNA-induced protein truncation via DNA binding.

von Brandenstein M, Bernhart SH, Pansky A, Richter C, Kohl T, Deckert M, Heidenreich A, Stadler PF, Montesinos-Rongen M, Fries JWU.

Oncotarget. 2018 Aug 28;9(67):32855-32867. doi: 10.18632/oncotarget.26023. eCollection 2018 Aug 28.

16.

Noncoding RNA Transcripts during Differentiation of Induced Pluripotent Stem Cells into Hepatocytes.

Skrzypczyk A, Kehr S, Krystel I, Bernhart SH, Giri S, Bader A, Stadler PF.

Stem Cells Int. 2018 Aug 19;2018:5692840. doi: 10.1155/2018/5692840. eCollection 2018.

17.

Nonprotein-Coding RNAs as Regulators of Development in Tunicates.

Velandia-Huerto CA, Brown FD, Gittenberger A, Stadler PF, Bermúdez-Santana CI.

Results Probl Cell Differ. 2018;65:197-225. doi: 10.1007/978-3-319-92486-1_11.

PMID:
30083922
18.

The Sierra Platinum Service for generating peak-calls for replicated ChIP-seq experiments.

Wiegreffe D, Müller L, Steuck J, Zeckzer D, Stadler PF.

BMC Res Notes. 2018 Jul 28;11(1):512. doi: 10.1186/s13104-018-3633-x.

19.

TERribly Difficult: Searching for Telomerase RNAs in Saccharomycetes.

Waldl M, Thiel BC, Ochsenreiter R, Holzenleiter A, de Araujo Oliveira JV, Walter MEMT, Wolfinger MT, Stadler PF.

Genes (Basel). 2018 Jul 26;9(8). pii: E372. doi: 10.3390/genes9080372.

20.

Trichoplax genomes reveal profound admixture and suggest stable wild populations without bisexual reproduction.

Kamm K, Osigus HJ, Stadler PF, DeSalle R, Schierwater B.

Sci Rep. 2018 Jul 24;8(1):11168. doi: 10.1038/s41598-018-29400-y.

21.

Split-inducing indels in phylogenomic analysis.

Donath A, Stadler PF.

Algorithms Mol Biol. 2018 Jul 16;13:12. doi: 10.1186/s13015-018-0130-7. eCollection 2018.

22.

Chemical Transformation Motifs-Modelling Pathways as Integer Hyperflows.

Andersen JL, Flamm C, Merkle D, Stadler PF.

IEEE/ACM Trans Comput Biol Bioinform. 2019 Mar-Apr;16(2):510-523. doi: 10.1109/TCBB.2017.2781724. Epub 2017 Dec 11.

PMID:
29990045
23.

Reconstructing gene trees from Fitch's xenology relation.

Geiß M, Anders J, Stadler PF, Wieseke N, Hellmuth M.

J Math Biol. 2018 Nov;77(5):1459-1491. doi: 10.1007/s00285-018-1260-8. Epub 2018 Jun 27.

PMID:
29951855
24.

Cover-Encodings of Fitness Landscapes.

Klemm K, Mehta A, Stadler PF.

Bull Math Biol. 2018 Aug;80(8):2154-2176. doi: 10.1007/s11538-018-0451-1. Epub 2018 Jun 12.

25.

Phylogenetics beyond biology.

Retzlaff N, Stadler PF.

Theory Biosci. 2018 Nov;137(2):133-143. doi: 10.1007/s12064-018-0264-7. Epub 2018 Jun 21.

26.

Rare Splice Variants in Long Non-Coding RNAs.

Sen R, Doose G, Stadler PF.

Noncoding RNA. 2017 Jul 5;3(3). pii: E23. doi: 10.3390/ncrna3030023.

27.

In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactors.

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.

Genome Res. 2018 May;28(5):699-713. doi: 10.1101/gr.229757.117. Epub 2018 Apr 11.

28.

Tracing the evolution of the heterotrimeric G protein α subunit in Metazoa.

Lokits AD, Indrischek H, Meiler J, Hamm HE, Stadler PF.

BMC Evol Biol. 2018 Apr 11;18(1):51. doi: 10.1186/s12862-018-1147-8.

29.

Finding the K best synthesis plans.

Fagerberg R, Flamm C, Kianian R, Merkle D, Stadler PF.

J Cheminform. 2018 Apr 5;10(1):19. doi: 10.1186/s13321-018-0273-z.

30.

Accurate mapping of tRNA reads.

Hoffmann A, Fallmann J, Vilardo E, Mörl M, Stadler PF, Amman F.

Bioinformatics. 2018 Jul 1;34(13):2339. doi: 10.1093/bioinformatics/bty118. No abstract available.

PMID:
29547898
31.

Time-consistent reconciliation maps and forbidden time travel.

Nøjgaard N, Geiß M, Merkle D, Stadler PF, Wieseke N, Hellmuth M.

Algorithms Mol Biol. 2018 Feb 6;13:2. doi: 10.1186/s13015-018-0121-8. eCollection 2018.

32.

Toward a mechanistic explanation of phenotypic evolution: The need for a theory of theory integration.

Laubichler MD, Prohaska SJ, Stadler PF.

J Exp Zool B Mol Dev Evol. 2018 Jan;330(1):5-14. doi: 10.1002/jez.b.22785. Epub 2018 Jan 22.

PMID:
29356321
33.

Comparative RNA Genomics.

Backofen R, Gorodkin J, Hofacker IL, Stadler PF.

Methods Mol Biol. 2018;1704:363-400. doi: 10.1007/978-1-4939-7463-4_14.

PMID:
29277874
34.

Gene Phylogenies and Orthologous Groups.

Setubal JC, Stadler PF.

Methods Mol Biol. 2018;1704:1-28. doi: 10.1007/978-1-4939-7463-4_1.

PMID:
29277861
35.

Expansion of gene clusters, circular orders, and the shortest Hamiltonian path problem.

Prohaska SJ, Berkemer SJ, Gärtner F, Gatter T, Retzlaff N; Students of the Graphs and Biological Networks Lab 2017, Höner Zu Siederdissen C, Stadler PF.

J Math Biol. 2018 Aug;77(2):313-341. doi: 10.1007/s00285-017-1197-3. Epub 2017 Dec 19.

36.

Accurate mapping of tRNA reads.

Hoffmann A, Fallmann J, Vilardo E, Mörl M, Stadler PF, Amman F.

Bioinformatics. 2018 Apr 1;34(7):1116-1124. doi: 10.1093/bioinformatics/btx756. Erratum in: Bioinformatics. 2018 Jul 1;34(13):2339.

PMID:
29228294
37.

Detailed secondary structure models of invertebrate 7SK RNAs.

Yazbeck AM, Tout KR, Stadler PF.

RNA Biol. 2018 Feb 1;15(2):158-164. doi: 10.1080/15476286.2017.1412913. Epub 2017 Dec 21.

38.

Inferring phylogenetic trees from the knowledge of rare evolutionary events.

Hellmuth M, Hernandez-Rosales M, Long Y, Stadler PF.

J Math Biol. 2018 Jun;76(7):1623-1653. doi: 10.1007/s00285-017-1194-6. Epub 2017 Dec 7.

PMID:
29218395
39.

The fungal snoRNAome.

Canzler S, Stadler PF, Schor J.

RNA. 2018 Mar;24(3):342-360. doi: 10.1261/rna.062778.117. Epub 2017 Dec 1.

40.

Temporal ordering of substitutions in RNA evolution: Uncovering the structural evolution of the Human Accelerated Region 1.

Walter Costa MB, Höner Zu Siederdissen C, Tulpan D, Stadler PF, Nowick K.

J Theor Biol. 2018 Feb 7;438:143-150. doi: 10.1016/j.jtbi.2017.11.015. Epub 2017 Nov 23.

41.

An intermediate level of abstraction for computational systems chemistry.

Andersen JL, Flamm C, Merkle D, Stadler PF.

Philos Trans A Math Phys Eng Sci. 2017 Dec 28;375(2109). pii: 20160354. doi: 10.1098/rsta.2016.0354.

42.

SMORE: Synteny Modulator of Repetitive Elements.

Berkemer SJ, Hoffmann A, Murray CRA, Stadler PF.

Life (Basel). 2017 Oct 31;7(4). pii: E42. doi: 10.3390/life7040042.

43.

Keeping it complicated: Mitochondrial genome plasticity across diplonemids.

Valach M, Moreira S, Hoffmann S, Stadler PF, Burger G.

Sci Rep. 2017 Oct 26;7(1):14166. doi: 10.1038/s41598-017-14286-z.

44.

Tractable RNA-ligand interaction kinetics.

Kühnl F, Stadler PF, Will S.

BMC Bioinformatics. 2017 Oct 16;18(Suppl 12):424. doi: 10.1186/s12859-017-1823-5.

45.

A Support Vector Machine based method to distinguish long non-coding RNAs from protein coding transcripts.

Schneider HW, Raiol T, Brigido MM, Walter MEMT, Stadler PF.

BMC Genomics. 2017 Oct 18;18(1):804. doi: 10.1186/s12864-017-4178-4.

46.

Ecological plant epigenetics: Evidence from model and non-model species, and the way forward.

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, Latzel V, Mirouze M, Opgenoorth L, Paun O, Prohaska SJ, Rensing SA, Stadler PF, Trucchi E, Ullrich K, Verhoeven KJF.

Ecol Lett. 2017 Dec;20(12):1576-1590. doi: 10.1111/ele.12858. Epub 2017 Oct 12. Review.

PMID:
29027325
47.

Similarity-Based Segmentation of Multi-Dimensional Signals.

Machné R, Murray DB, Stadler PF.

Sci Rep. 2017 Sep 27;7(1):12355. doi: 10.1038/s41598-017-12401-8.

48.

Design of Artificial Riboswitches as Biosensors.

Findeiß S, Etzel M, Will S, Mörl M, Stadler PF.

Sensors (Basel). 2017 Aug 30;17(9). pii: E1990. doi: 10.3390/s17091990. Review.

49.

Partially local three-way alignments and the sequence signatures of mitochondrial genome rearrangements.

Al Arab M, Bernt M, Höner Zu Siederdissen C, Tout K, Stadler PF.

Algorithms Mol Biol. 2017 Aug 23;12:22. doi: 10.1186/s13015-017-0113-0. eCollection 2017.

50.

STAT3-induced long noncoding RNAs in multiple myeloma cells display different properties in cancer.

Binder S, Hösler N, Riedel D, Zipfel I, Buschmann T, Kämpf C, Reiche K, Burger R, Gramatzki M, Hackermüller J, Stadler PF, Horn F.

Sci Rep. 2017 Aug 11;7(1):7976. doi: 10.1038/s41598-017-08348-5.

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