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Author Hofacker [71 articles]

Recent papers posted to CiteULike by the author Hofacker.
  • Concurrent neutral evolution of mRNA secondary structures and encoded proteins.
    Journal of molecular evolution, Vol. 50, No. 3. (March 2000), pp. 238-242.
    by J Konecny, M Schöniger, I Hofacker, MD Weitze, GL Hofacker
    posted to cited_by_chamary by bpcusack on 2008-07-15 16:12:51 as **
  • Prediction of locally stable RNA secondary structures for genome-wide surveys.
    Bioinformatics, Vol. 20, No. 2. (22 January 2004), pp. 186-190.
    by IL Hofacker, B Priwitzer, PF Stadler
    posted to no-tag by reyez on 2008-06-26 15:53:51 as ** along with 3 people evaf ilh raylim
  • Alignment of RNA base pairing probability matrices.
    Bioinformatics, Vol. 20, No. 14. (22 September 2004), pp. 2222-2227.
    by IL Hofacker, SH Bernhart, PF Stadler
    posted to no-tag by reyez on 2008-06-26 15:53:46 as ** along with 2 people arcticrasta ilh
  • Vienna RNA secondary structure server.
    Nucleic Acids Research, Vol. 31, No. 13. (1 July 2003), pp. 3429-3431.
    by IL Hofacker
    posted to no-tag by reyez on 2008-06-26 15:53:29 as ** along with 10 people evaf dayjm eckart_bindewald balicea arcticrasta mtagaya dquest ilh onufriev maralena
  • Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation
    BMC Bioinformatics, Vol. 7, No. 1. (2006)
    by Christian Forst, Christoph Flamm, Ivo Hofacker, Peter Stadler
    posted to hypergraphgeneralization hypergraph by uwenagel on 2008-05-28 11:36:26 as ** along with 1 person ilh
  • Folding Kinetics of Large RNAs
    Journal of Molecular Biology, Vol. 379, No. 1. (23 May 2008), pp. 160-173.
    by Michael Geis, Christoph Flamm, Michael T Wolfinger, Andrea Tanzer, Ivo L Hofacker, Martin Middendorf, Christian Mandl, Peter F Stadler, Caroline Thurner
    posted to no-tag by austin on 2008-05-25 17:41:14 as *****
  • The Vienna RNA Websuite.
    Nucleic acids research (19 April 2008)
    by Andreas R R Gruber, Ronny Lorenz, Stephan H H Bernhart, Richard Neuböck, Ivo L L Hofacker
    posted to viennarna by austin on 2008-05-25 17:08:33 as read along with 1 person elfar
  • The impact of target site accessibility on the design of effective siRNAs
    Nature Biotechnology, Vol. 26, No. 5. (27 April 2008), pp. 578-583.
    by Hakim Tafer, Stefan L Ameres, Gregor Obernosterer, Christoph A Gebeshuber, Renée Schroeder, Javier Martinez, Ivo L Hofacker
    posted to rnai design by jyuh on 2008-05-13 09:19:11 as **
  • RNAplex: a fast tool for RNA-RNA interaction search.
    Bioinformatics (Oxford, England) (23 April 2008)
    by Hakim Tafer, Ivo L L Hofacker
    posted to rna-rna interaction by elfar on 2008-05-08 15:08:57 as **
  • RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription
    Science (17 May 2007), 1138341.
    by Philipp Kapranov, Jill Cheng, Sujit Dike, David A Nix, Radharani Duttagupta, Aarron T Willingham, Peter F Stadler, Jana Hertel, Joerg Hackermueller, Ivo L Hofacker, Ian Bell, Evelyn Cheung, Jorg Drenkow, Erica Dumais, Sandeep Patel, Gregg Helt, Madhavan Ganesh, Srinka Ghosh, Antonio Piccolboni, Victor Sementchenko, Hari Tammana, Thomas R Gingeras
    posted to transcriptome methods breakthrough by xingxu on 2008-05-06 14:39:02 as ** along with 11 people and 4 groups marcius alexg dpollard xico mtagaya rdiaz djkt stajich mathijsv asddd elfar EisenLab WetBiology BioinfoCIPF SGU-CIPF
  • RNA folding at elementary step resolution.
    RNA, Vol. 6, No. 3. (March 2000), pp. 325-338.
    by C Flamm, W Fontana, IL Hofacker, P Schuster
    posted to folding kinetics kinfold rna by austin on 2008-04-15 16:44:38 as read along with 4 people arcticrasta ilh mtw Kiarostami
  • Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics.
    J Mol Biol, Vol. 342, No. 1. (3 September 2004), pp. 19-30.
    by S Washietl, IL Hofacker
    posted to no-tag by elfar on 2008-04-09 11:49:51 as ** along with 4 people dayjm arcticrasta Eonwe ilh
  • Strategies for measuring evolutionary conservation of RNA secondary structures
    BMC Bioinformatics, Vol. 9 (26 February 2008), 122.
    by Andreas R Gruber, Stefan H Bernhart, Ivo L Hofacker, Stefan Washietl
    posted to gene_finding noncoding noncoding_rna rna rna_gene by stajich to the group Berkeley Mycology on 2008-04-01 06:25:37 as ** along with 3 people eckart_bindewald ilh gresillaud
  • Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis
    Nucl. Acids Res. (16 March 2008), gkn123.
    by Christoph Jochl, Mathieu Rederstorff, Jana Hertel, Peter F Stadler, Ivo L Hofacker, Markus Schrettl, Hubertus Haas, Alexander Huttenhofer
    posted to aspergillus fungi gene_silencing noncoding_rna transcriptional_regulation by stajich to the group Berkeley Mycology on 2008-04-01 00:55:02 as ** along with 1 person cellison
  • Fast Folding and Comparison of RNA Secondary Structures
    Monatsh.\ Chem., Vol. 125 (1994), pp. 167-188.
    by Ivo L Hofacker, Walter Fontana, Peter F Stadler, Sebastian L Bonhoeffer, Manfred Tacker, Peter Schuster
    posted to folding no-pseudoknot by guxiyou on 2008-03-26 19:20:59 as ** along with 3 people stanley ilh mtw
  • Invertebrate 7SK snRNAs
    Journal of Molecular Evolution, Vol. 66, No. 2. (20 February 2008), pp. 107-115.
    by Andreas Gruber, Dorota Koper-Emde, Manja Marz, Hakim Tafer, Stephan Bernhart, Gregor Obernosterer, Axel Mosig, Ivo Hofacker, Peter Stadler, Bernd-Joachim Benecke
    posted to no-tag by ilh on 2008-03-26 11:05:17 as read
  • Beyond energy minimization: approaches to the kinetic folding of RNA
    Monatshefte für Chemie / Chemical Monthly
    by Christoph Flamm, Ivo L Hofacker
    posted to mypub by ilh on 2008-03-09 17:55:05 as read
  • Fast and reliable prediction of noncoding RNAs.
    Proc Natl Acad Sci U S A, Vol. 102, No. 7. (15 February 2005), pp. 2454-2459.
    by S Washietl, IL Hofacker, PF Stadler
    posted to ncrna prediction by raylim on 2008-03-08 23:11:04 as ** along with 9 people and 3 groups gangli evaf dayjm marcius eckart_bindewald tardigrade dquest Eonwe ilh tulip BioinfoCIPF SGU-CIPF
  • Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome
    Nature Biotechnology, Vol. 23, No. 11. (04 November 2005), pp. 1383-1390.
    by Stefan Washietl, Ivo L Hofacker, Melanie Lukasser, Alexander Hüttenhofer, Peter F Stadler
    posted to ncrna rna_folding by raylim on 2008-03-08 23:07:33 as ** along with 6 people and 3 groups marcius eckart_bindewald tardigrade tabu cdawson ilh BioinfoCIPF SGU-CIPF GIG
  • Local RNA base pairing probabilities in large sequences
    Bioinformatics, Vol. 22, No. 5. (1 March 2006), pp. 614-615.
    by Stephan H Bernhart, Ivo L Hofacker, Peter F Stadler
    posted to genome-wide rna_folding by raylim on 2008-03-08 23:03:02 as ** along with 1 person ilh
  • RNAs everywhere: genome-wide annotation of structured RNAs.
    J Exp Zoolog B Mol Dev Evol (14 December 2006)
    by Rolf Backofen, Stephan H H Bernhart, Christoph Flamm, Claudia Fried, Guido Fritzsch, Jörg Hackermüller, Jana Hertel, Ivo L L Hofacker, Kristin Missal, Axel Mosig, Sonja J J Prohaska, Dominic Rose, Peter F F Stadler, Andrea Tanzer, Stefan Washietl, Sebastian Will
    posted to annotation genome rna by maralena on 2008-02-12 14:26:58 as ** along with 11 people and 5 groups jfr bala marcius eckart_bindewald tardigrade andersbj penka cdawson ilh raylim jayster4 microRNA BioinfoCIPF SGU-CIPF DictyosteliumGroup GIG
  • Secondary structure prediction for aligned RNA sequences.
    J Mol Biol, Vol. 319, No. 5. (21 June 2002), pp. 1059-1066.
    by IL Hofacker, M Fekete, PF Stadler
    posted to no-tag by ppgardne on 2008-02-03 14:20:56 as ** along with 7 people evaf balajis eckart_bindewald arcticrasta ilh xiaobeizhao raylim
  • www.rnaworkbench.com: A new program for analyzing RNA interference.
    Comput Methods Programs Biomed (18 January 2008)
    by Radka Svobodová S Vařeková, Ivan Bradáč, Martin Plchút, Michal Skrdla, Michael Wacenovsky, Helmuth Mahr, Georg Mayer, Herbert Tanner, Hermann Brugger, Josef Withalm, Peter Lederer, Heinrich Huber, Gerhard Gierlinger, Ronald Graf, Hakim Tafer, Ivo Hofacker, Peter Schuster, Martin Polčík
    posted to rnai by jyuh on 2008-01-22 12:49:01 as **
  • The Expansion of the Metazoan MicroRNA Repertoire.
    BMC Genomics, Vol. 7, No. 1. (15 February 2006)
    by Jana Hertel, Manuela Lindemeyer, Kristin Missal, Claudia Fried, Andrea Tanzer, Christoph Flamm, Ivo L Hofacker, Peter F Stadler
    posted to evolution evolutionary-genomics evolvability growth-regulation reviews rna by balicea on 2008-01-20 05:04:00 as *** along with 10 people and 6 groups imouthesmp marcius andersbj dchughes mtagaya ilh brettc mtw akiezun heliopais microRNA G4ID evo-devo BioinfoCIPF SGU-CIPF Genetics-of-Gambling
  • How microRNAs choose their targets
    Nat Genet, Vol. 39, No. 10. (October 2007), pp. 1191-1192.
    by Ivo L Hofacker
    posted to mirna by yavanna on 2007-12-26 07:34:48 as *** along with 6 people and 2 groups dchughes rdiaz ealloza Garamonfok epigenetics heliopais microRNA BioinfoCIPF
  • Variations on RNA folding and alignment: lessons from Benasque
    Journal of Mathematical Biology, Vol. 56, No. 1. (24 January 2008), pp. 129-144.
    by Athanasius Bompfünewerer, Rolf Backofen, Stephan Bernhart, Jana Hertel, Ivo Hofacker, Peter Stadler, Sebastian Will
    posted to rna-rna by Hosna on 2007-12-13 23:27:53 as ****
  • Thermodynamics of RNARNA binding
    Bioinformatics, Vol. 22, No. 10. (15 May 2006), pp. 1177-1182.
    by Ulrike Muckstein, Hakim Tafer, Jorg Hackermuller, Stephan H Bernhart, Peter F Stadler, Ivo L Hofacker
    posted to review rna-rna by Hosna on 2007-11-05 21:19:27 as ** along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
  • Structured RNAs in the ENCODE selected regions of the human genome
    Genome Res., Vol. 17, No. 6. (1 June 2007), pp. 852-864.
    by Stefan Washietl, Jakob S Pedersen, Jan O Korbel, Claudia Stocsits, Andreas R Gruber, Jorg Hackermuller, Jana Hertel, Manja Lindemeyer, Kristin Reiche, Andrea Tanzer, Catherine Ucla, Carine Wyss, Stylianos E Antonarakis, France Denoeud, Julien Lagarde, Jorg Drenkow, Philipp Kapranov, Thomas R Gingeras, Roderic Guigo, Michael Snyder, Mark B Gerstein, Alexandre Reymond, Ivo L Hofacker, Peter F Stadler
    posted to encode by ghattem on 2007-07-13 15:38:48 as ** along with 1 person and 1 group ilh Bioinformatics
  • Visualization of Barrier Tree Sequences
    IEEE Transactions on Visualization and Computer Graphics, Vol. 12, No. 5. (September 2006), pp. 781-788.
    by Christian Heine, Gerik Scheuermann, Christoph Flamm, Ivo L Hofacker, Peter F Stadler
    posted to bioinformatics genetics by dergrosse on 2007-06-26 00:16:51 as ** along with 1 person and 1 group ilh Scientific_Visualization
  • Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering
    PLoS Computational Biology, Vol. 3, No. 4. (1 April 2007), e65.
    by Sebastian Will, Kristin Reiche, Ivo L Hofacker, Peter F Stadler, Rolf Backofen
    posted to no-tag by jayster4 on 2007-06-12 13:21:24 as ***** along with 5 people and 2 groups indigoviolet andersbj mtagaya stajich zwang EisenLab microRNA
  • The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures.
    Nucleic Acids Res (22 April 2007)
    by Andreas R R Gruber, Richard Neuböck, Ivo L L Hofacker, Stefan Washietl
    posted to mypub by ilh on 2007-05-27 17:42:01 as read along with 1 person balajis
  • Thermodynamics of RNA-RNA Binding.
    Bioinformatics (29 January 2006)
    by Ulrike Mückstein, Hakim Tafer, Jörg Hackermüller, Stephan H H Bernhart, Peter F F Stadler, Ivo L L Hofacker
    posted to complexes prediction rna by physics on 2007-05-05 22:30:38 as *** along with 6 people and 3 groups marcius eckart_bindewald andersbj arcticrasta ilh mtw microRNA BioinfoCIPF SGU-CIPF
  • Prediction of Consensus RNA Secondary Structures Including Pseudoknots
    IEEE/ACM Trans. Comput. Biol. Bioinformatics, Vol. 1, No. 2. (April 2004), pp. 66-77.
    by Christina Witwer, Ivo L Hofacker, Peter F Stadler
    posted to wabi by Hosna on 2007-05-02 00:54:22 as **
  • Fast folding and comparison of RNA secondary structures
    Monatshefte für Chemie / Chemical Monthly, Vol. 125, No. 2. (1 February 1994), pp. 167-188.
    by IL Hofacker, W Fontana, PF Stadler, LS Bonhoeffer, M Tacker, P Schuster
    posted to wabi by Hosna on 2007-05-01 23:47:14 as **
  • Conserved RNA secondary structures in viral genomes: a survey
    Bioinformatics, Vol. 20, No. 10. (1 July 2004), pp. 1495-1499.
    by IL Hofacker, PF Stadler, RR Stocsits
    posted to rna secondary_structure virus by raylim on 2007-03-20 00:41:53 as ** along with 1 person ilh
  • Partition function and base pairing probabilities of RNA heterodimers
    Algorithms for Molecular Biology, Vol. 1 (16 March 2006), 3.
    by Stephan H Bernhart, Hakim Tafer, Ulrike Mückstein, Christoph Flamm, Peter F Stadler, Ivo L Hofacker
    posted to vienna rna-structure rna-folding partition-function by cassj on 2007-02-01 02:25:27 as **** along with 1 person ilh
  • Complete suboptimal folding of RNA and the stability of secondary structures.
    Biopolymers, Vol. 49, No. 2. (February 1999), pp. 145-165.
    by S Wuchty, W Fontana, IL Hofacker, P Schuster
    posted to structure stability secondary robustness rna canalization by eckart_bindewald on 2007-01-23 17:14:50 as read along with 3 people and 2 groups marcius arcticrasta ilh BioinfoCIPF SGU-CIPF
  • Stochastic pairwise alignments
    Bioinformatics, Vol. 18, No. Suppl 2. (2002), pp. S152-S160.
    by U Mückstein, IL Hofacker, PF Stadler
    posted to probabilistic_alignment sequence_alignment suboptimal_alignment by rabio on 2006-12-10 21:56:59 as read along with 1 person dgront
  • Complete suboptimal folding of RNA and the stability of secondary structures
    Biopolymers, Vol. 49, No. 2. (1999), pp. 145-165.
    by Stefan Wuchty, Walter Fontana, Ivo L Hofacker, Peter Schuster
    posted to partition_function by Hosna on 2006-11-23 01:40:47 as **
  • Design of multistable RNA molecules.
    RNA, Vol. 7, No. 2. (February 2001), pp. 254-265.
    by C Flamm, IL Hofacker, S Maurer-Stroh, PF Stadler, M Zehl
    posted to multi_stable_rna by Hosna on 2006-11-16 19:58:50 as ***
  • Evolutionary patterns of non-coding RNAs
    Theory in Biosciences, Vol. 123, No. 4. (15 April 2005), pp. 301-369.
    by Athanasius F Bompfunewerer, Christoph Flamm, Claudia Fried, Guido Fritzsch, Ivo L Hofacker, Jorg Lehmann, Kristin Missal, Axel Mosig, Bettina Muller, Sonja J Prohaska
    posted to evolution ncrna by bsmagic on 2006-11-16 13:27:43 as ** along with 3 people and 2 groups evaf Eonwe ilh Bioinformatics bioinplant
  • Combinatorics of RNA secondary structures
    Discrete Appl. Math., Vol. 88, No. 1-3. (1998), pp. 207-237.
    by Ivo L Hofacker, Peter Schuster, Peter F Stadler
    posted to bioinformatics rna secondary_structure by marcius on 2006-07-28 12:38:52 as ** along with 2 people and 2 groups ilh mtw BioinfoCIPF SGU-CIPF
  • From sequences to shapes and back: a case study in RNA secondary structures.
    Proc R Soc Lond B Biol Sci, Vol. 255, No. 1344. (22 March 1994), pp. 279-284.
    by P Schuster, W Fontana, PF Stadler, IL Hofacker
    posted to bioinformatics biophysics rna secondary_structure by marcius on 2006-07-28 12:38:26 as ** along with 3 people and 2 groups evaf ilh mtw BioinfoCIPF SGU-CIPF
  • Efficient computation of RNA folding dynamics
    Journal of Physics A: Mathematical and General, Vol. 37, No. 17. (2004), pp. 4731-4741.
    by Michael T Wolfinger, Andreas, Christoph Flamm, Ivo L Hofacker, Peter F Stadler
    posted to biophysics folding rna by marcius on 2006-07-24 17:47:12 as ** along with 2 people and 2 groups ilh mtw BioinfoCIPF SGU-CIPF
  • Algorithm independent properties of RNA secondary structure predictions
    European Biophysics Journal, Vol. 25, No. 2. (December 1996), pp. 115-130.
    by Manfred Tacker, Peter F Stadler, Erich G Bornberg-Bauer, Ivo L Hofacker, P Schuster
    posted to bioinformatics rna secondary_structure by marcius on 2006-07-18 10:35:20 as ** along with 2 people and 2 groups ilh mtw BioinfoCIPF SGU-CIPF
  • Design of multistable RNA molecules.
    RNA, Vol. 7, No. 2. (February 2001), pp. 254-265.
    by C Flamm, IL Hofacker, S Maurer-Stroh, PF Stadler, M Zehl
    posted to bioengineering biophysics rna by marcius on 2006-07-18 10:33:37 as ** along with 3 people and 2 groups evaf ilh mtw BioinfoCIPF SGU-CIPF
  • Complete suboptimal folding of RNA and the stability of secondary structures.
    Biopolymers, Vol. 49, No. 2. (February 1999), pp. 145-165.
    by S Wuchty, W Fontana, IL Hofacker, P Schuster
    posted to rna by mtw on 2006-07-12 17:49:19 as read along with 1 person evaf
  • RNA folding and combinatory landscapes.
    PHYSICAL REVIEW. E. STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS, Vol. 47, No. 3. (March 1993), pp. 2083-2099.
    by W Fontana, PF Stadler, EG Bornberg-Bauer, T Griesmacher, IL Hofacker, M Tacker, P Tarazona, ED Weinberger, P Schuster
    posted to rna by mtw on 2006-07-12 17:41:27 as *** along with 1 person ilh
  • RNA folding at elementary step resolution.
    RNA, Vol. 6, No. 3. (March 2000), pp. 325-338.
    by C Flamm, W Fontana, IL Hofacker, P Schuster
    posted to kinetics by mtw on 2006-07-12 17:31:15 as read along with 2 people evaf ilh
  • Automatic detection of conserved base pairing patterns in RNA virus genomes
    Computers & Chemistry, Vol. 23, No. 3-4. (15 June 1999), pp. 401-414.
    by Ivo L Hofacker, Peter F Stadler
    posted to mypub by ilh on 2006-07-11 10:52:34 as read
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