메뉴 건너뛰기




Volumn 6044 LNBI, Issue , 2010, Pages 473-490

Time and space efficient RNA-RNA interaction prediction via sparse folding

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEX JOINTS; ENERGY MODEL; HIGH DEMAND; JOINT STRUCTURE; LINEAR TIME; OPTIMALITY; ORIGINAL ALGORITHMS; RNA-RNA INTERACTION; RUNNING TIME; SPARSIFICATION; TARGET PREDICTION; TIME AND SPACE; TOTAL FREE ENERGY;

EID: 78049479577     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-12683-3_31     Document Type: Conference Paper
Times cited : (39)

References (40)
  • 3
    • 0037123632 scopus 로고    scopus 로고
    • An expanding universe of noncoding RNAs
    • Storz, G.: An expanding universe of noncoding RNAs. Science 296(5571), 1260-1263 (2002).
    • (2002) Science , vol.296 , Issue.5571 , pp. 1260-1263
    • Storz, G.1
  • 4
    • 0347444723 scopus 로고    scopus 로고
    • MicroRNAs: Genomics, biogenesis, mechanism, and function
    • Bartel, D.P.: MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116(2), 281-297 (2004).
    • (2004) Cell , vol.116 , Issue.2 , pp. 281-297
    • Bartel, D.P.1
  • 5
    • 0037062951 scopus 로고    scopus 로고
    • RNA interference
    • Hannon, G.J.: RNA interference. Nature 418(6894), 244-251 (2002).
    • (2002) Nature , vol.418 , Issue.6894 , pp. 244-251
    • Hannon, G.J.1
  • 6
    • 24644446398 scopus 로고    scopus 로고
    • Ribo-gnome: The big world of small RNAs
    • Zamore, P.D., Haley, B.: Ribo-gnome: the big world of small RNAs. Science 309(5740), 1519-1524 (2005).
    • (2005) Science , vol.309 , Issue.5740 , pp. 1519-1524
    • Zamore, P.D.1    Haley, B.2
  • 7
    • 0036575444 scopus 로고    scopus 로고
    • Antisense RNAs everywhere?
    • Wagner, E., Flardh, K.: Antisense RNAs everywhere?. Trends Genet. 18, 223-226 (2002).
    • (2002) Trends Genet. , vol.18 , pp. 223-226
    • Wagner, E.1    Flardh, K.2
  • 8
    • 0037012663 scopus 로고    scopus 로고
    • Antisense-RNA regulation and RNA interference
    • Brantl, S.: Antisense-RNA regulation and RNA interference. Bioch. Biophys. Acta 1575(1-3), 15-25 (2002).
    • (2002) Bioch. Biophys. Acta , vol.1575 , Issue.1-3 , pp. 15-25
    • Brantl, S.1
  • 9
    • 20644462362 scopus 로고    scopus 로고
    • Micros for microbes: Non-coding regulatory RNAs in bacteria
    • Gottesman, S.: Micros for microbes: non-coding regulatory RNAs in bacteria. Trends in Genetics 21(7), 399-404 (2005).
    • (2005) Trends in Genetics , vol.21 , Issue.7 , pp. 399-404
    • Gottesman, S.1
  • 10
    • 14744285972 scopus 로고    scopus 로고
    • From genes to machines: DNA nanomechanical devices
    • Seeman, N.: From genes to machines: DNA nanomechanical devices. Trends Biochem. Sci. 30, 119-125 (2005).
    • (2005) Trends Biochem. Sci. , vol.30 , pp. 119-125
    • Seeman, N.1
  • 11
    • 12544252352 scopus 로고    scopus 로고
    • Nucleic acid nanostructures: Bottom-up control of geometry on the nanoscale
    • Seeman, N.C., Lukeman, P.S.: Nucleic acid nanostructures: bottom-up control of geometry on the nanoscale. Reports on Progress in Physics 68, 237-270 (2005).
    • (2005) Reports on Progress in Physics , vol.68 , pp. 237-270
    • Seeman, N.C.1    Lukeman, P.S.2
  • 12
    • 24644464003 scopus 로고    scopus 로고
    • DNA nanodevices
    • Simmel, F., Dittmer, W.: DNA nanodevices. Small 1, 284-299 (2005).
    • (2005) Small , vol.1 , pp. 284-299
    • Simmel, F.1    Dittmer, W.2
  • 15
    • 33644667975 scopus 로고    scopus 로고
    • IRIS: Intermolecular RNA interaction search
    • Pervouchine, D.D.: IRIS: intermolecular RNA interaction search. Genome Inform. 15(2), 92-101 (2004).
    • (2004) Genome Inform. , vol.15 , Issue.2 , pp. 92-101
    • Pervouchine, D.D.1
  • 16
    • 70349984002 scopus 로고    scopus 로고
    • Partition function and base pairing probabilities for RNA-RNA interaction prediction
    • Huang, F.W., Qin, J., Reidys, C.M., Stadler, P.F.: Partition Function and Base Pairing Probabilities for RNA-RNA Interaction Prediction. Bioinformatics 25(20), 2646-2654 (2009).
    • (2009) Bioinformatics , vol.25 , Issue.20 , pp. 2646-2654
    • Huang, F.W.1    Qin, J.2    Reidys, C.M.3    Stadler, P.F.4
  • 19
    • 70350639137 scopus 로고    scopus 로고
    • Sparse RNA folding: Time and space efficient algorithms
    • Kucherov, G. Ukkonen, E. (eds.), LNCS, Springer, Heidelberg
    • Backofen, R., Tsur, D., Zakov, S., Ziv-Ukelson, M.: Sparse RNA folding: Time and space efficient algorithms. In: Kucherov, G., Ukkonen, E. (eds.) CPM 2009. LNCS, vol. 5577, pp. 249-262. Springer, Heidelberg (2009).
    • (2009) CPM 2009 , vol.5577 , pp. 249-262
    • Backofen, R.1    Tsur, D.2    Zakov, S.3    Ziv-Ukelson, M.4
  • 20
    • 0022146059 scopus 로고
    • Simultaneous solution of the RNA folding, alignment and protosequence problems
    • Sankoff, D.: Simultaneous solution of the RNA folding, alignment and protosequence problems. SIAM J. Appl. Math. 45(5), 810-825 (1985).
    • (1985) SIAM J. Appl. Math. , vol.45 , Issue.5 , pp. 810-825
    • Sankoff, D.1
  • 21
    • 56649106364 scopus 로고    scopus 로고
    • A faster algorithm for RNA co-folding
    • Crandall, K.A. Lagergren, J. (eds.), LNCS (LNBI), Springer, Heidelberg
    • Ziv-Ukelson, M., Gat-Viks, I., Wexler, Y., Shamir, R.: A faster algorithm for RNA co-folding. In: Crandall, K.A., Lagergren, J. (eds.) WABI 2008. LNCS (LNBI), vol. 5251, pp. 174-185. Springer, Heidelberg (2008).
    • (2008) WABI 2008 , vol.5251 , pp. 174-185
    • Ziv-Ukelson, M.1    Gat-Viks, I.2    Wexler, Y.3    Shamir, R.4
  • 22
    • 4644237189 scopus 로고    scopus 로고
    • Fast and effective prediction of microRNA/target duplexes
    • Rehmsmeier, M., Steffen, P., Höchsmann, M., Giegerich, R.: Fast and effective prediction of microRNA/target duplexes. RNA 10(10), 1507-1517 (2004).
    • (2004) RNA , vol.10 , Issue.10 , pp. 1507-1517
    • Rehmsmeier, M.1    Steffen, P.2    Höchsmann, M.3    Giegerich, R.4
  • 24
    • 11844254846 scopus 로고    scopus 로고
    • Secondary structure prediction of interacting RNA molecules
    • Andronescu, M., Zhang, Z.C., Condon, A.: Secondary structure prediction of interacting RNA molecules. Journal of Molecular Biology 345(5), 987-1001 (2005).
    • (2005) Journal of Molecular Biology , vol.345 , Issue.5 , pp. 987-1001
    • Andronescu, M.1    Zhang, Z.C.2    Condon, A.3
  • 27
    • 0028249154 scopus 로고
    • Prediction of RNA secondary structure by energy minimization
    • Zuker, M.: Prediction of RNA secondary structure by energy minimization. Methods in Molecular Biology 25, 267-294 (1994).
    • (1994) Methods in Molecular Biology , vol.25 , pp. 267-294
    • Zuker, M.1
  • 30
    • 57249083988 scopus 로고    scopus 로고
    • IntaRNA: Efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions
    • Busch, A., Richter, A.S., Backofen, R.: IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics 24(24), 2849-2856 (2008).
    • (2008) Bioinformatics , vol.24 , Issue.24 , pp. 2849-2856
    • Busch, A.1    Richter, A.S.2    Backofen, R.3
  • 31
    • 0034725539 scopus 로고    scopus 로고
    • Fhla repression by OxyS RNA: Kissing complex formation at two sites results in a stable antisense-target RNA complex
    • Argaman, L., Altuvia, S.: fhla repression by OxyS RNA: kissing complex formation at two sites results in a stable antisense-target RNA complex. Journal of Molecular Biology 300(5), 1101-1112 (2000).
    • (2000) Journal of Molecular Biology , vol.300 , Issue.5 , pp. 1101-1112
    • Argaman, L.1    Altuvia, S.2
  • 32
    • 70350369558 scopus 로고    scopus 로고
    • Fast prediction of RNA-RNA interaction
    • Salzberg, S.L. Warnow, T. (eds.), LNCS, Springer, Heidelberg
    • Salari, R., Backofen, R., Sahinalp, S.C.: Fast prediction of RNA-RNA interaction. In: Salzberg, S.L., Warnow, T. (eds.) WABI 2009. LNCS, vol. 5724, pp. 261-272. Springer, Heidelberg (2009).
    • (2009) WABI 2009 , vol.5724 , pp. 261-272
    • Salari, R.1    Backofen, R.2    Sahinalp, S.C.3
  • 34
    • 70350361844 scopus 로고    scopus 로고
    • BiRNA: Fast RNA-RNA binding sites prediction
    • Salzberg, S.L. Warnow, T. (eds.), LNCS, Springer, Heidelberg
    • Chitsaz, H., Backofen, R., Sahinalp, S.C.: biRNA: Fast RNA-RNA binding sites prediction. In: Salzberg, S.L., Warnow, T. (eds.) WABI 2009. LNCS, vol. 5724, pp. 25-36. Springer, Heidelberg (2009).
    • (2009) WABI 2009 , vol.5724 , pp. 25-36
    • Chitsaz, H.1    Backofen, R.2    Sahinalp, S.C.3
  • 36
    • 36849111485 scopus 로고
    • Shape of a self-avoiding walk or polymer chain
    • Fisher, M.E.: Shape of a self-avoiding walk or polymer chain. Journal of Chemical Physics 44, 616-622 (1966).
    • (1966) Journal of Chemical Physics , vol.44 , pp. 616-622
    • Fisher, M.E.1
  • 37
    • 0034351060 scopus 로고    scopus 로고
    • Why is the DNA denaturation transition first order?
    • Kafri, Y., Mukamel, D., Peliti, L.: Why is the DNA denaturation transition first order? Phys. Rev. Lett. 85, 4988-4991 (2000).
    • (2000) Phys. Rev. Lett. , vol.85 , pp. 4988-4991
    • Kafri, Y.1    Mukamel, D.2    Peliti, L.3
  • 38
    • 57149104102 scopus 로고    scopus 로고
    • A grammatical approach to rna-rna interaction prediction
    • Kato, Y., Akutsu, T., Seki, H.: A grammatical approach to rna-rna interaction prediction. Pattern Recogn. 42(4), 531-538 (2009).
    • (2009) Pattern Recogn. , vol.42 , Issue.4 , pp. 531-538
    • Kato, Y.1    Akutsu, T.2    Seki, H.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.