| Year |
Citation |
Score |
| 2022 |
Müller S, Flamm C, Stadler PF. What makes a reaction network "chemical"? Journal of Cheminformatics. 14: 63. PMID 36123755 DOI: 10.1186/s13321-022-00621-8 |
0.419 |
|
| 2020 |
Flamm C, Hellmuth M, Merkle D, Nojgaard N, Stadler PF. Generic Context-Aware Group Contributions. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 32750852 DOI: 10.1109/Tcbb.2020.2998948 |
0.485 |
|
| 2019 |
Silva WMCd, Andersen JL, Holanda MT, Walter MEMT, Brigido MM, Stadler PF, Flamm C. Exploring Plant Sesquiterpene Diversity by Generating Chemical Networks Processes. 7: 240. DOI: 10.3390/PR7040240 |
0.396 |
|
| 2018 |
Wolfinger MT, Flamm C, Hofacker IL. Efficient computation of co-transcriptional RNA-ligand interaction dynamics. Methods (San Diego, Calif.). PMID 29730250 DOI: 10.1016/J.Ymeth.2018.04.036 |
0.371 |
|
| 2018 |
Findeiß S, Hammer S, Wolfinger MT, Kühnl F, Flamm C, Hofacker IL. In silico design of ligand triggered RNA switches. Methods (San Diego, Calif.). PMID 29660485 DOI: 10.1016/J.Ymeth.2018.04.003 |
0.358 |
|
| 2018 |
Fagerberg R, Flamm C, Kianian R, Merkle D, Stadler PF. Finding the K best synthesis plans. Journal of Cheminformatics. 10: 19. PMID 29623440 DOI: 10.1186/S13321-018-0273-Z |
0.448 |
|
| 2017 |
Andersen JL, Flamm C, Merkle D, Stadler PF. Chemical Transformation Motifs --- Modelling Pathways as Integer Hyperflows. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 29990045 DOI: 10.1109/Tcbb.2017.2781724 |
0.523 |
|
| 2017 |
Andersen JL, Flamm C, Merkle D, Stadler PF. An intermediate level of abstraction for computational systems chemistry. Philosophical Transactions. Series a, Mathematical, Physical, and Engineering Sciences. 375. PMID 29133452 DOI: 10.1098/Rsta.2016.0354 |
0.52 |
|
| 2017 |
Hammer S, Tschiatschek B, Flamm C, Hofacker IL, Findeiß S. RNAblueprint: Flexible multiple target nucleic acid sequence design. Bioinformatics (Oxford, England). PMID 28449031 DOI: 10.1093/Bioinformatics/Btx263 |
0.365 |
|
| 2016 |
Badelt S, Flamm C, Hofacker IL. Computational Design of a Circular RNA with Prionlike Behavior. Artificial Life. 1-13. PMID 26934089 DOI: 10.1162/Artl_A_00197 |
0.372 |
|
| 2016 |
Flamm C, Stadler BMR, Stadler PF. Generalized Topologies: Hypergraphs, Chemical Reactions, and Biological Evolution Advances in Mathematical Chemistry and Applications. 2: 300-328. DOI: 10.1016/B978-1-68108-053-6.50013-2 |
0.429 |
|
| 2016 |
Andersen JL, Flamm C, Merkle D, Stadler PF. A software package for chemically inspired graph transformation Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9761: 73-88. DOI: 10.1007/978-3-319-40530-8_5 |
0.416 |
|
| 2016 |
Flamm C, Merkle D, Stadler PF, Thorsen U. Automatic inference of graph transformation rules using the cyclic nature of chemical reactions Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9761: 206-222. DOI: 10.1007/978-3-319-40530-8_13 |
0.444 |
|
| 2015 |
Hsiao YT, Lee WP, Yang W, Muller S, Flamm C, Hofacker I, Kugler P. Practical Guidelines for Incorporating Knowledge-Based and Data-Driven Strategies into the Inference of Gene Regulatory Networks. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. PMID 26441429 DOI: 10.1109/Tcbb.2015.2465954 |
0.32 |
|
| 2015 |
Petkovic S, Badelt S, Block S, Flamm C, Delcea M, Hofacker I, Müller S. Sequence-controlled RNA self-processing: computational design, biochemical analysis, and visualization by AFM. Rna (New York, N.Y.). 21: 1249-60. PMID 25999318 DOI: 10.1261/Rna.047670.114 |
0.39 |
|
| 2015 |
Badelt S, Hammer S, Flamm C, Hofacker IL. Thermodynamic and kinetic folding of riboswitches. Methods in Enzymology. 553: 193-213. PMID 25726466 DOI: 10.1016/Bs.Mie.2014.10.060 |
0.41 |
|
| 2015 |
Andersen JL, Flamm C, Merkle D, Stadler PF. In silico Support for Eschenmoser's Glyoxylate Scenario Israel Journal of Chemistry. 55: 919-933. DOI: 10.1002/Ijch.201400187 |
0.523 |
|
| 2014 |
Mann M, Nahar F, Schnorr N, Backofen R, Stadler PF, Flamm C. Atom mapping with constraint programming. Algorithms For Molecular Biology : Amb. 9: 23. PMID 25484913 DOI: 10.1186/S13015-014-0023-3 |
0.473 |
|
| 2014 |
Andersen JL, Flamm C, Merkle D, Stadler PF. Generic strategies for chemical space exploration. International Journal of Computational Biology and Drug Design. 7: 225-58. PMID 24878732 DOI: 10.1504/Ijcbdd.2014.061649 |
0.537 |
|
| 2014 |
Mann M, KucharÃk M, Flamm C, Wolfinger MT. Memory-efficient RNA energy landscape exploration. Bioinformatics (Oxford, England). 30: 2584-91. PMID 24833804 DOI: 10.1093/Bioinformatics/Btu337 |
0.357 |
|
| 2014 |
Andersen JL, Flamm C, Merkle D, Stadler PF. 50 shades of rule composition from chemical reactions to higher levels of abstraction Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 8738: 115-135. DOI: 10.1007/978-3-319-10398-3_9 |
0.453 |
|
| 2013 |
Höner Zu Siederdissen C, Hammer S, Abfalter I, Hofacker IL, Flamm C, Stadler PF. Computational design of RNAs with complex energy landscapes. Biopolymers. 99: 1124-36. PMID 23818234 DOI: 10.1002/Bip.22337 |
0.536 |
|
| 2013 |
Andersen JL, Andersen T, Flamm C, Hanczyc MM, Merkle D, Stadler PF. Navigating the chemical space of hcn polymerization and hydrolysis: Guiding graph grammars by mass spectrometry data Entropy. 15: 4066-4083. DOI: 10.3390/E15104066 |
0.491 |
|
| 2013 |
Andersen JL, Flamm C, Merkle D, Stadler PF. Inferring chemical reaction patterns using rule composition in graph grammars Journal of Systems Chemistry. 4: 4. DOI: 10.1186/1759-2208-4-4 |
0.515 |
|
| 2013 |
Flamm C, Ullrich A, Ekker H, Mann M, Högerl D, Rohrschneider M, Sauer S, Scheuermann G, Klemm K, Hofacker IL, Stadler PF. Evolution of metabolic networks: A computational frame-work Journal of Systems Chemistry. 1. DOI: 10.1186/1759-2208-1-4 |
0.507 |
|
| 2013 |
Fagerberg R, Flamm C, Merkle D, Peters P, Stadler PF. On the Complexity of Reconstructing Chemical Reaction Networks Mathematics in Computer Science. 7: 275-292. DOI: 10.1007/S11786-013-0160-Y |
0.514 |
|
| 2012 |
Amman F, Flamm C, Hofacker I. Modelling translation initiation under the influence of sRNA. International Journal of Molecular Sciences. 13: 16223-40. PMID 23203192 DOI: 10.3390/Ijms131216223 |
0.31 |
|
| 2012 |
Andersen JL, Flamm C, Merkle D, Stadler PF. Maximizing output and recognizing autocatalysis in chemical reaction networks is NP-complete Journal of Systems Chemistry. 3. DOI: 10.1186/1759-2208-3-1 |
0.503 |
|
| 2011 |
Lorenz R, Bernhart SH, Höner Zu Siederdissen C, Tafer H, Flamm C, Stadler PF, Hofacker IL. ViennaRNA Package 2.0. Algorithms For Molecular Biology : Amb. 6: 26. PMID 22115189 DOI: 10.1186/1748-7188-6-26 |
0.475 |
|
| 2011 |
Hiroi N, Lu J, Iba K, Tabira A, Yamashita S, Okada Y, Flamm C, Oka K, Köhler G, Funahashi A. Physiological environment induces quick response - slow exhaustion reactions. Frontiers in Physiology. 2: 50. PMID 21960972 DOI: 10.3389/Fphys.2011.00050 |
0.334 |
|
| 2011 |
Ullrich A, Rohrschneider M, Scheuermann G, Stadler PF, Flamm C. In silico evolution of early metabolism. Artificial Life. 17: 87-108. PMID 21370961 DOI: 10.1162/Artl_A_00021 |
0.473 |
|
| 2010 |
Hofacker IL, Flamm C, Heine C, Wolfinger MT, Scheuermann G, Stadler PF. BarMap: RNA folding on dynamic energy landscapes. Rna (New York, N.Y.). 16: 1308-16. PMID 20504954 DOI: 10.1261/Rna.2093310 |
0.525 |
|
| 2009 |
Benkö G, Centler F, Dittrich P, Flamm C, Stadler BM, Stadler PF. A topological approach to chemical organizations. Artificial Life. 15: 71-88. PMID 18855563 DOI: 10.1162/Artl.2009.15.1.15105 |
0.518 |
|
| 2009 |
Engl HW, Flamm C, Kügler P, Lu J, Müller S, Schuster P. Inverse problems in systems biology Inverse Problems. 25. DOI: 10.1088/0266-5611/25/12/123014 |
0.498 |
|
| 2008 |
Dress AW, Flamm C, Fritzsch G, Grünewald S, Kruspe M, Prohaska SJ, Stadler PF. Noisy: identification of problematic columns in multiple sequence alignments. Algorithms For Molecular Biology : Amb. 3: 7. PMID 18577231 DOI: 10.1186/1748-7188-3-7 |
0.426 |
|
| 2008 |
Geis M, Flamm C, Wolfinger MT, Tanzer A, Hofacker IL, Middendorf M, Mandl C, Stadler PF, Thurner C. Folding kinetics of large RNAs. Journal of Molecular Biology. 379: 160-73. PMID 18440024 DOI: 10.1016/J.Jmb.2008.02.064 |
0.542 |
|
| 2008 |
Klemm K, Flamm C, Stadler PF. Funnels in energy landscapes European Physical Journal B. 63: 387-391. DOI: 10.1140/epjb/e2008-00136-7 |
0.302 |
|
| 2008 |
Flamm C, Hofacker IL. Beyond energy minimization: Approaches to the kinetic folding of RNA Monatshefte Fur Chemie. 139: 447-457. DOI: 10.1007/S00706-008-0895-3 |
0.386 |
|
| 2007 |
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, ... ... Flamm C, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874 |
0.448 |
|
| 2007 |
Flamm C, Endler L, Müller S, Widder S, Schuster P. A minimal and self-consistent in silico cell model based on macromolecular interactions. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 362: 1831-9. PMID 17510017 DOI: 10.1098/Rstb.2007.2075 |
0.491 |
|
| 2007 |
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, et al. RNAs everywhere: genome-wide annotation of structured RNAs. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. 308: 1-25. PMID 17171697 DOI: 10.1002/Jez.B.21130 |
0.501 |
|
| 2007 |
Flamm C, Hofacker IL, Stadler BMR, Stadler PF. Saddles and barrier in landscapes of generalized search operators Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4436: 194-212. |
0.377 |
|
| 2006 |
Heine C, Scheuermann G, Flamm C, Hofacker IL, Stadler PF. Visualization of barrier tree sequences. Ieee Transactions On Visualization and Computer Graphics. 12: 781-8. PMID 17080800 DOI: 10.1109/Tvcg.2006.196 |
0.527 |
|
| 2006 |
Müller S, Hofbauer J, Endler L, Flamm C, Widder S, Schuster P. A generalized model of the repressilator. Journal of Mathematical Biology. 53: 905-37. PMID 16951971 DOI: 10.1007/S00285-006-0035-9 |
0.482 |
|
| 2006 |
Nagel JH, Flamm C, Hofacker IL, Franke K, de Smit MH, Schuster P, Pleij CW. Structural parameters affecting the kinetics of RNA hairpin formation. Nucleic Acids Research. 34: 3568-76. PMID 16855293 DOI: 10.1093/Nar/Gkl445 |
0.526 |
|
| 2006 |
Bernhart SH, Tafer H, Mückstein U, Flamm C, Stadler PF, Hofacker IL. Partition function and base pairing probabilities of RNA heterodimers. Algorithms For Molecular Biology : Amb. 1: 3. PMID 16722605 DOI: 10.1186/1748-7188-1-3 |
0.492 |
|
| 2006 |
Machné R, Finney A, Müller S, Lu J, Widder S, Flamm C. The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks. Bioinformatics (Oxford, England). 22: 1406-7. PMID 16527832 DOI: 10.1093/Bioinformatics/Btl086 |
0.355 |
|
| 2006 |
Hertel J, Lindemeyer M, Missal K, Fried C, Tanzer A, Flamm C, Hofacker IL, Stadler PF. The expansion of the metazoan microRNA repertoire. Bmc Genomics. 7: 25. PMID 16480513 DOI: 10.1186/1471-2164-7-25 |
0.405 |
|
| 2006 |
Forst CV, Flamm C, Hofacker IL, Stadler PF. Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation. Bmc Bioinformatics. 7: 67. PMID 16478540 DOI: 10.1186/1471-2105-7-67 |
0.453 |
|
| 2006 |
Pötzsch S, Scheuermann G, Wolfinger MT, Flamm C, Stadler PF. Visualization of lattice-based protein folding simulations Proceedings of the International Conference On Information Visualisation. 89-94. DOI: 10.1109/IV.2006.127 |
0.315 |
|
| 2005 |
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. Evolutionary patterns of non-coding RNAs. Theory in Biosciences = Theorie in Den Biowissenschaften. 123: 301-69. PMID 18202870 DOI: 10.1016/J.Thbio.2005.01.002 |
0.488 |
|
| 2005 |
Attolini CSO, Stadler PF, Flamm C. CelloS: A multi-level approach to evolutionary dynamics Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3630: 500-509. DOI: 10.1007/11553090_51 |
0.38 |
|
| 2005 |
Benkö G, Flamm C, Stadler PF. Explicit collision simulation of chemical reactions in a graph based artificial chemistry Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3630: 725-733. |
0.421 |
|
| 2004 |
Weixlbaumer A, Werner A, Flamm C, Westhof E, Schroeder R. Determination of thermodynamic parameters for HIV DIS type loop-loop kissing complexes. Nucleic Acids Research. 32: 5126-33. PMID 15459283 DOI: 10.1093/Nar/Gkh841 |
0.307 |
|
| 2004 |
Prohaska SJ, Fried C, Flamm C, Wagner GP, Stadler PF. Surveying phylogenetic footprints in large gene clusters: applications to Hox cluster duplications. Molecular Phylogenetics and Evolution. 31: 581-604. PMID 15062796 DOI: 10.1016/J.Ympev.2003.08.009 |
0.544 |
|
| 2004 |
Berger F, Flamm C, Gleiss PM, Leydold J, Stadler PF. Counterexamples in chemical ring perception. Journal of Chemical Information and Computer Sciences. 44: 323-31. PMID 15032507 DOI: 10.1021/Ci030405D |
0.456 |
|
| 2004 |
Wolfinger MT, Svrcek-Seiler WA, Flamm C, Hofacker IL, Stadler PF. Efficient computation of RNA folding dynamics Journal of Physics a: Mathematical and General. 37: 4731-4741. DOI: 10.1088/0305-4470/37/17/005 |
0.521 |
|
| 2003 |
Benkö G, Flamm C, Stadler PF. A graph-based toy model of chemistry. Journal of Chemical Information and Computer Sciences. 43: 1085-93. PMID 12870897 DOI: 10.1021/Ci0200570 |
0.543 |
|
| 2003 |
Stadler PF, Flamm C. Barrier trees on poset-valued landscapes Genetic Programming and Evolvable Machines. 4: 7-20. DOI: 10.1023/A:1021821009420 |
0.455 |
|
| 2003 |
Benkö G, Flamm C, Stadler PF. Generic properties of chemical networks: Artificial chemistry based on graph rewriting Lecture Notes in Artificial Intelligence (Subseries of Lecture Notes in Computer Science). 2801: 10-19. |
0.465 |
|
| 2002 |
Flamm C, Hofacker IL, Stadler PF, Wolfinger MT. Barrier trees of degenerate landscapes Zeitschrift Fur Physikalische Chemie. 216: 155-173. DOI: 10.1524/Zpch.2002.216.2.155 |
0.443 |
|
| 2001 |
Flamm C, Hofacker IL, Maurer-Stroh S, Stadler PF, Zehl M. Design of multistable RNA molecules Rna. 7: 254-265. PMID 11233982 DOI: 10.1017/S1355838201000863 |
0.518 |
|
| 2000 |
Flamm C, Fontana W, Hofacker IL, Schuster P. RNA folding at elementary step resolution Rna. 6: 325-338. PMID 10744018 DOI: 10.1017/S1355838200992161 |
0.553 |
|
| 1999 |
Flamm C, Hofacker IL, Stadler PF. RNA In Silico The Computational Biology of RNA Secondary Structures Advances in Complex Systems. 2: 65-90. DOI: 10.1142/S0219525999000059 |
0.497 |
|
| 1998 |
Hofacker IL, Fekete M, Flamm C, Huynen MA, Rauscher S, Stolorz PE, Stadler PF. Automatic detection of conserved RNA structure elements in complete RNA virus genomes. Nucleic Acids Research. 26: 3825-36. PMID 9685502 DOI: 10.1093/Nar/26.16.3825 |
0.497 |
|
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