Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 71

1.

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
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.

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.

21.

Physiological environment induces quick response - slow exhaustion reactions.

Hiroi N, Lu J, Iba K, Tabira A, Yamashita S, Okada Y, Flamm C, Oka K, Köhler G, Funahashi A.

Front Physiol. 2011 Sep 21;2:50. doi: 10.3389/fphys.2011.00050. eCollection 2011.

22.

Report on the ASCO 2010 Provider-Payer Initiative Meeting.

Neuss MN, Flamm C, Shulman LN, Tomkins JE, Ward JC.

J Oncol Pract. 2011 May;7(3):136-40. doi: 10.1200/JOP.2011.000279.

23.

In silico evolution of early metabolism.

Ullrich A, Rohrschneider M, Scheuermann G, Stadler PF, Flamm C.

Artif Life. 2011 Spring;17(2):87-108. doi: 10.1162/artl_a_00021. Epub 2011 Mar 3.

PMID:
21370961
24.

BarMap: RNA folding on dynamic energy landscapes.

Hofacker IL, Flamm C, Heine C, Wolfinger MT, Scheuermann G, Stadler PF.

RNA. 2010 Jul;16(7):1308-16. doi: 10.1261/rna.2093310. Epub 2010 May 26.

25.

A topological approach to chemical organizations.

Benkö G, Centler F, Dittrich P, Flamm C, Stadler BM, Stadler PF.

Artif Life. 2009 Winter;15(1):71-88. doi: 10.1162/artl.2009.15.1.15105.

PMID:
18855563
26.

Noisy: identification of problematic columns in multiple sequence alignments.

Dress AW, Flamm C, Fritzsch G, Grünewald S, Kruspe M, Prohaska SJ, Stadler PF.

Algorithms Mol Biol. 2008 Jun 24;3:7. doi: 10.1186/1748-7188-3-7.

27.

Folding kinetics of large RNAs.

Geis M, Flamm C, Wolfinger MT, Tanzer A, Hofacker IL, Middendorf M, Mandl C, Stadler PF, Thurner C.

J Mol Biol. 2008 May 23;379(1):160-73. doi: 10.1016/j.jmb.2008.02.064. Epub 2008 Mar 6.

PMID:
18440024
28.

Evolutionary patterns of non-coding RNAs.

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.

Theory Biosci. 2005 Apr;123(4):301-69. doi: 10.1016/j.thbio.2005.01.002.

PMID:
18202870
29.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ.

Nature. 2007 Jun 14;447(7146):799-816.

30.

A minimal and self-consistent in silico cell model based on macromolecular interactions.

Flamm C, Endler L, Müller S, Widder S, Schuster P.

Philos Trans R Soc Lond B Biol Sci. 2007 Oct 29;362(1486):1831-9.

31.

Wireless capsule endoscopy in patients with obscure small-intestinal bleeding.

Ziegler KM, Flamm CR, Aronson N.

J Am Coll Radiol. 2005 Oct;2(10):818-20. Review.

PMID:
17411940
32.
33.

The Blue Cross Blue Shield Association Technology Evaluation Center: how we evaluate radiology technologies.

Ziegler KM, Flamm CR, Aronson N.

J Am Coll Radiol. 2005 Jan;2(1):33-8. Review.

PMID:
17411757
34.

RNAs everywhere: genome-wide annotation of structured RNAs.

Athanasius F Bompfünewerer Consortium, 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, Washietl S, Will S.

J Exp Zool B Mol Dev Evol. 2007 Jan 15;308(1):1-25. Review.

PMID:
17171697
35.

Visualization of barrier tree sequences.

Heine C, Scheuermann G, Flamm C, Hofacker IL, Stadler PF.

IEEE Trans Vis Comput Graph. 2006 Sep-Oct;12(5):781-8.

PMID:
17080800
36.

A generalized model of the repressilator.

Müller S, Hofbauer J, Endler L, Flamm C, Widder S, Schuster P.

J Math Biol. 2006 Dec;53(6):905-37. Epub 2006 Sep 2.

PMID:
16951971
37.

Structural parameters affecting the kinetics of RNA hairpin formation.

Nagel JH, Flamm C, Hofacker IL, Franke K, de Smit MH, Schuster P, Pleij CW.

Nucleic Acids Res. 2006 Jul 19;34(12):3568-76. Print 2006.

38.

Partition function and base pairing probabilities of RNA heterodimers.

Bernhart SH, Tafer H, Mückstein U, Flamm C, Stadler PF, Hofacker IL.

Algorithms Mol Biol. 2006 Mar 16;1(1):3.

39.

The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks.

Machné R, Finney A, Müller S, Lu J, Widder S, Flamm C.

Bioinformatics. 2006 Jun 1;22(11):1406-7. Epub 2006 Mar 9.

PMID:
16527832
40.

The expansion of the metazoan microRNA repertoire.

Hertel J, Lindemeyer M, Missal K, Fried C, Tanzer A, Flamm C, Hofacker IL, Stadler PF; Students of Bioinformatics Computer Labs 2004 and 2005.

BMC Genomics. 2006 Feb 15;7:25.

41.

Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation.

Forst CV, Flamm C, Hofacker IL, Stadler PF.

BMC Bioinformatics. 2006 Feb 14;7:67.

42.

Challenges in systematic reviews of diagnostic technologies.

Tatsioni A, Zarin DA, Aronson N, Samson DJ, Flamm CR, Schmid C, Lau J.

Ann Intern Med. 2005 Jun 21;142(12 Pt 2):1048-55. Review.

PMID:
15968029
43.

Determination of thermodynamic parameters for HIV DIS type loop-loop kissing complexes.

Weixlbaumer A, Werner A, Flamm C, Westhof E, Schroeder R.

Nucleic Acids Res. 2004 Sep 30;32(17):5126-33. Print 2004.

44.

Surveying phylogenetic footprints in large gene clusters: applications to Hox cluster duplications.

Prohaska SJ, Fried C, Flamm C, Wagner GP, Stadler PF.

Mol Phylogenet Evol. 2004 May;31(2):581-604.

PMID:
15062796
45.

Counterexamples in chemical ring perception.

Berger F, Flamm C, Gleiss PM, Leydold J, Stadler PF.

J Chem Inf Comput Sci. 2004 Mar-Apr;44(2):323-31.

PMID:
15032507
46.

[Intraocular pressure after cyclophotocoagulation with the diode laser].

Flamm C, Wiegand W.

Ophthalmologe. 2004 Mar;101(3):263-7. German.

PMID:
15007607
47.

A graph-based toy model of chemistry.

Benkö G, Flamm C, Stadler PF.

J Chem Inf Comput Sci. 2003 Jul-Aug;43(4):1085-93.

PMID:
12870897
48.

Evidence-based assessment: patient, procedure, or operator factors associated with ERCP complications.

Aronson N, Flamm CR, Bohn RL, Mark DH, Speroff T.

Gastrointest Endosc. 2002 Dec;56(6 Suppl):S294-302. Review. No abstract available.

PMID:
12447284
49.

Evidence-based assessment of ERCP in the treatment of pancreatitis.

Mark DH, Lefevre F, Flamm CR, Aronson N.

Gastrointest Endosc. 2002 Dec;56(6 Suppl):S249-54. Review. No abstract available.

PMID:
12447277
50.

Evidence-based assessment of ERCP approaches to managing pancreaticobiliary malignancies.

Flamm CR, Mark DH, Aronson N.

Gastrointest Endosc. 2002 Dec;56(6 Suppl):S218-25. Review. No abstract available.

PMID:
12447271

Supplemental Content

Support Center