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Items: 1 to 20 of 55

1.

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
2.

Efficient computation of co-transcriptional RNA-ligand interaction dynamics.

Wolfinger MT, Flamm C, Hofacker IL.

Methods. 2018 Jul 1;143:70-76. doi: 10.1016/j.ymeth.2018.04.036. Epub 2018 May 4.

PMID:
29730250
3.

In silico design of ligand triggered RNA switches.

Findeiß S, Hammer S, Wolfinger MT, Kühnl F, Flamm C, Hofacker IL.

Methods. 2018 Jul 1;143:90-101. doi: 10.1016/j.ymeth.2018.04.003. Epub 2018 Apr 13.

PMID:
29660485
4.

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.

5.

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.

PMID:
29133452
6.

RNAblueprint: flexible multiple target nucleic acid sequence design.

Hammer S, Tschiatschek B, Flamm C, Hofacker IL, Findeiß S.

Bioinformatics. 2017 Sep 15;33(18):2850-2858. doi: 10.1093/bioinformatics/btx263.

7.

Computational Design of a Circular RNA with Prionlike Behavior.

Badelt S, Flamm C, Hofacker IL.

Artif Life. 2016 Spring;22(2):172-84. doi: 10.1162/ARTL_a_00197. Epub 2016 Mar 2.

PMID:
26934089
8.

Practical Guidelines for Incorporating Knowledge-Based and Data-Driven Strategies into the Inference of Gene Regulatory Networks.

Hsiao YT, Lee WP, Yang W, Müller S, Flamm C, Hofacker I, Kügler P.

IEEE/ACM Trans Comput Biol Bioinform. 2016 Jan-Feb;13(1):64-75. doi: 10.1109/TCBB.2015.2465954. Epub 2015 Aug 20.

PMID:
26441429
9.

Sequence-controlled RNA self-processing: computational design, biochemical analysis, and visualization by AFM.

Petkovic S, Badelt S, Block S, Flamm C, Delcea M, Hofacker I, Müller S.

RNA. 2015 Jul;21(7):1249-60. doi: 10.1261/rna.047670.114. Epub 2015 May 21.

10.

Thermodynamic and kinetic folding of riboswitches.

Badelt S, Hammer S, Flamm C, Hofacker IL.

Methods Enzymol. 2015;553:193-213. doi: 10.1016/bs.mie.2014.10.060. Epub 2015 Feb 12.

PMID:
25726466
11.

Atom mapping with constraint programming.

Mann M, Nahar F, Schnorr N, Backofen R, Stadler PF, Flamm C.

Algorithms Mol Biol. 2014 Nov 29;9(1):23. doi: 10.1186/s13015-014-0023-3. eCollection 2014.

12.

Generic strategies for chemical space exploration.

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

Int J Comput Biol Drug Des. 2014;7(2-3):225-58. doi: 10.1504/IJCBDD.2014.061649. Epub 2014 May 28.

PMID:
24878732
13.

Memory-efficient RNA energy landscape exploration.

Mann M, Kucharík M, Flamm C, Wolfinger MT.

Bioinformatics. 2014 Sep 15;30(18):2584-91. doi: 10.1093/bioinformatics/btu337. Epub 2014 May 14.

14.

Automatic ictal HFO detection for determination of initial seizure spread.

Graef A, Flamm C, Pirker S, Baumgartner C, Deistler M, Matz G.

Conf Proc IEEE Eng Med Biol Soc. 2013;2013:2096-9. doi: 10.1109/EMBC.2013.6609946.

PMID:
24110133
15.

Computational design of RNAs with complex energy landscapes.

Höner zu Siederdissen C, Hammer S, Abfalter I, Hofacker IL, Flamm C, Stadler PF.

Biopolymers. 2013 Dec;99(12):1124-36. doi: 10.1002/bip.22337.

PMID:
23818234
16.

A novel method for the identification of synchronization effects in multichannel ECoG with an application to epilepsy.

Graef A, Hartmann M, Flamm C, Baumgartner C, Deistler M, Kluge T.

Biol Cybern. 2013 Jun;107(3):321-35. doi: 10.1007/s00422-013-0552-8. Epub 2013 Feb 22.

17.

A physiologically motivated ECoG segmentation method for epileptic seizure onset zone detection.

Graef A, Flamm C, Pirker S, Deistler M, Baumgartner C.

Conf Proc IEEE Eng Med Biol Soc. 2012;2012:3500-3. doi: 10.1109/EMBC.2012.6346720.

PMID:
23366681
18.

Influence analysis for high-dimensional time series with an application to epileptic seizure onset zone detection.

Flamm C, Graef A, Pirker S, Baumgartner C, Deistler M.

J Neurosci Methods. 2013 Mar 30;214(1):80-90. doi: 10.1016/j.jneumeth.2012.12.025. Epub 2013 Jan 24.

19.

Modelling translation initiation under the influence of sRNA.

Amman F, Flamm C, Hofacker I.

Int J Mol Sci. 2012 Nov 30;13(12):16223-40. doi: 10.3390/ijms131216223.

20.

ViennaRNA Package 2.0.

Lorenz R, Bernhart SH, Höner Zu Siederdissen C, Tafer H, Flamm C, Stadler PF, Hofacker IL.

Algorithms Mol Biol. 2011 Nov 24;6:26. doi: 10.1186/1748-7188-6-26.

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