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Items: 1 to 20 of 370

1.

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
2.

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.

3.

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.

4.

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.

5.

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.

6.

Chemical Transformation Motifs --- Modelling Pathways as Integer Hyperflows.

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

IEEE/ACM Trans Comput Biol Bioinform. 2017 Dec 11. doi: 10.1109/TCBB.2017.2781724. [Epub ahead of print]

PMID:
29990045
7.

Reconstructing gene trees from Fitch's xenology relation.

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

J Math Biol. 2018 Jun 27. doi: 10.1007/s00285-018-1260-8. [Epub ahead of print]

PMID:
29951855
8.

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.

9.

Phylogenetics beyond biology.

Retzlaff N, Stadler PF.

Theory Biosci. 2018 Jun 21. doi: 10.1007/s12064-018-0264-7. [Epub ahead of print]

PMID:
29931521
10.

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.

11.

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.

PMID:
29643205
12.

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.

13.

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.

14.

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
15.

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.

16.

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
17.

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
18.

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
19.

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.

20.

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.

PMID:
29228294

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