26 Publikationen
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2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941280Zhu, Q., Mai, U., Pfeiffer, W., Janssen, S., Asnicar, F., Sanders, J.G., Belda-Ferre, P., Al-Ghalith, G.A., Kopylova, E., McDonald, D., Kosciolek, T., Yin, J.B., Huang, S., Salam, N., Jiao, J.-Y., Wu, Z., Xu, Z.Z., Cantrell, K., Yang, Y., Sayyari, E., Rabiee, M., Morton, J.T., Podell, S., Knights, D., Li, W.-J., Huttenhower, C., Segata, N., Smarr, L., Mirarab, S., Knight, R.: Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea. Nature Communications. 10, : 5477 (2019).PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
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2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2941281Bouslimani, A., da Silva, R., Kosciolek, T., Janssen, S., Callewaert, C., Amir, A., Dorrestein, K., Melnik, A.V., Zaramela, L.S., Kim, J.-N., Humphrey, G., Schwartz, T., Sanders, K., Brennan, C., Luzzatto-Knaan, T., Ackermann, G., McDonald, D., Zengler, K., Knight, R., Dorrestein, P.C.: The impact of skin care products on skin chemistry and microbiome dynamics. BMC Biology. 17, : 47 (2019).PUB | DOI | WoS | PubMed | Europe PMC
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2019 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2934328Iszatt, N., Janssen, S., Lenters, V., Dahl, C., Stigum, H., Knight, R., Mandal, S., Peddada, S., González, A., Midtvedt, T., Eggesbø, M.: Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month. Microbiome. 7, : 34 (2019).PUB | DOI | WoS | PubMed | Europe PMC
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2921267McDonald, D., Hyde, E., Debelius, J.W., Morton, J.T., Gonzalez, A., Ackermann, G., Aksenov, A.A., Behsaz, B., Brennan, C., Chen, Y., DeRight Goldasich, L., Dorrestein, P.C., Dunn, R.R., Fahimipour, A.K., Gaffney, J., Gilbert, J.A., Gogul, G., Green, J.L., Hugenholtz, P., Humphrey, G., Huttenhower, C., Jackson, M.A., Janssen, S., Jeste, D.V., Jiang, L., Kelley, S.T., Knights, D., Kosciolek, T., Ladau, J., Leach, J., Marotz, C., Meleshko, D., Melnik, A.V., Metcalf, J.L., Mohimani, H., Montassier, E., Navas-Molina, J., Nguyen, T.T., Peddada, S., Pevzner, P., Pollard, K.S., Rahnavard, G., Robbins-Pianka, A., Sangwan, N., Shorenstein, J., Smarr, L., Song, S.J., Spector, T., Swafford, A.D., Thackray, V.G., Thompson, L.R., Tripathi, A., Vázquez-Baeza, Y., Vrbanac, A., Wischmeyer, P., Wolfe, E., Zhu, Q., Knight, R., Mann, A.E., Amir, A., Frazier, A., Martino, C., Lebrilla, C., Lozupone, C., Lewis, C.M., Raison, C., Zhang, C., Lauber, C.L., Warinner, C., Lowry, C.A., Callewaert, C., Bloss, C., Willner, D., Galzerani, D.D., Gonzalez, D.J., Mills, D.A., Chopra, D., Gevers, D., Berg-Lyons, D., Sears, D.D., Wendel, D., Lovelace, E., Pierce, E., TerAvest, E., Bolyen, E., Bushman, F.D., Wu, G.D., Church, G.M., Saxe, G., Holscher, H.D., Ugrina, I., German, J.B., Caporaso, J.G., Wozniak, J.M., Kerr, J., Ravel, J., Lewis, J.D., Suchodolski, J.S., Jansson, J.K., Hampton-Marcell, J.T., Bobe, J., Raes, J., Chase, J.H., Eisen, J.A., Monk, J., Clemente, J.C., Petrosino, J., Goodrich, J., Gauglitz, J., Jacobs, J., Zengler, K., Swanson, K.S., Lewis, K., Mayer, K., Bittinger, K., Dillon, L., Zaramela, L.S., Schriml, L.M., Dominguez-Bello, M.G., Jankowska, M.M., Blaser, M., Pirrung, M., Minson, M., Kurisu, M., Ajami, N., Gottel, N.R., Chia, N., Fierer, N., White, O., Cani, P.D., Gajer, P., Strandwitz, P., Kashyap, P., Dutton, R., Park, R.S., Xavier, R.J., Mills, R.H., Krajmalnik-Brown, R., Ley, R., Owens, S.M., Klemmer, S., Matamoros, S., Mirarab, S., Moorman, S., Holmes, S., Schwartz, T., Eshoo-Anton, T.W., Vigers, T., Pandey, V., Treuren, W.V., Fang, X., Zech Xu, Z., Jarmusch, A., Geier, J., Reeve, N., Silva, R., Kopylova, E., Nguyen, D., Sanders, K., Salido Benitez, R.A., Heale, A.C., Abramson, M., Waldispühl, J., Butyaev, A., Drogaris, C., Nazarova, E., Ball, M., Gunderson, B.: American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 3, e00031-18 (2018).PUB | DOI | WoS | PubMed | Europe PMC
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2921270Minich, J.J., Zhu, Q., Janssen, S., Hendrickson, R., Amir, A., Vetter, R., Hyde, J., Doty, M.M., Stillwell, K., Benardini, J., Kim, J.H., Allen, E.E., Venkateswaran, K., Knight, R.: KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples. mSystems. 3, e00218-17 (2018).PUB | DOI | WoS | PubMed | Europe PMC
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2921268Janssen, S., McDonald, D., Gonzalez, A., Navas-Molina, J.A., Jiang, L., Xu, Z.Z., Winker, K., Kado, D.M., Orwoll, E., Manary, M., Mirarab, S., Knight, R.: Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information. mSystems. 3, e00021-18 (2018).PUB | DOI | WoS | PubMed | Europe PMC
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2921273Kapono, C.A., Morton, J.T., Bouslimani, A., Melnik, A.V., Orlinsky, K., Knaan, T.L., Garg, N., Vázquez-Baeza, Y., Protsyuk, I., Janssen, S., Zhu, Q., Alexandrov, T., Smarr, L., Knight, R., Dorrestein, P.C.: Creating a 3D microbial and chemical snapshot of a human habitat. Scientific Reports. 8, : 3669 (2018).PUB | DOI | WoS | PubMed | Europe PMC
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2018 | Preprint | Veröffentlicht | PUB-ID: 2931839Bolyen, E., Rideout, J.R., Dillon, M.R., Bokulich, N.A., Abnet, C., Al-Ghalith, G.A., Alexander, H., Alm, E.J., Arumugam, M., Asnicar, F., Bai, Y., Bisanz, J.E., Bittinger, K., Brejnrod, A., Brislawn, C.J., Brown, C.T., Callahan, B.J., Caraballo-Rodríguez, A.M., Chase, J., Cope, E., Da Silva, R., Dorrestein, P.C., Douglas, G.M., Durall, D.M., Duvallet, C., Edwardson, C.F., Ernst, M., Estaki, M., Fouquier, J., Gauglitz, J.M., Gibson, D.L., Gonzalez, A., Gorlick, K., Guo, J., Hillmann, B., Holmes, S., Holste, H., Huttenhower, C., Huttley, G., Janssen, S., Jarmusch, A.K., Jiang, L., Kaehler, B., Kang, K.B., Keefe, C.R., Keim, P., Kelley, S.T., Knights, D., Koester, I., Kosciolek, T., Kreps, J., Langille, M.G.I., Lee, J., Ley, R., Liu, Y.-X., Loftfield, E., Lozupone, C., Maher, M., Marotz, C., Martin, B., McDonald, D., McIver, L.J., Melnik, A.V., Metcalf, J.L., Morgan, S.C., Morton, J., Naimey, A.T., Navas-Molina, J.A., Nothias, L.F., Orchanian, S.B., Pearson, T., Peoples, S.L., Petras, D., Preuss, M.L., Pruesse, E., Rasmussen, L.B., Rivers, A., Robeson, II, M.S., Rosenthal, P., Segata, N., Shaffer, M., Shiffer, A., Sinha, R., Song, S.J., Spear, J.R., Swafford, A.D., Thompson, L.R., Torres, P.J., Trinh, P., Tripathi, A., Turnbaugh, P.J., Ul-Hasan, S., van der Hooft, J.J.J., Vargas, F., Vázquez-Baeza, Y., Vogtmann, E., von Hippel, M., Walters, W., Wan, Y., Wang, M., Warren, J., Weber, K.C., Williamson, C.H.D., Willis, A.D., Xu, Z.Z., Zaneveld, J.R., Zhang, Y., Knight, R., Caporaso, J.G.: QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science. PeerJ. (2018).PUB | DOI
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2018 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2931438Gonzalez, A., Navas-Molina, J.A., Kosciolek, T., McDonald, D., Vázquez-Baeza, Y., Ackermann, G., DeReus, J., Janssen, S., Swafford, A.D., Orchanian, S.B., Sanders, J.G., Shorenstein, J., Holste, H., Petrus, S., Robbins-Pianka, A., Brislawn, C.J., Wang, M., Rideout, J.R., Bolyen, E., Dillon, M., Caporaso, J.G., Dorrestein, P.C., Knight, R.: Qiita: rapid, web-enabled microbiome meta-analysis. Nature Methods. 15, 796-798 (2018).PUB | DOI | WoS | PubMed | Europe PMC
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2914868Thompson, L.R., Sanders, J.G., McDonald, D., Amir, A., Ladau, J., Locey, K.J., Prill, R.J., Tripathi, A., Gibbons, S.M., Ackermann, G., Navas-Molina, J.A., Janssen, S., Kopylova, E., Vázquez-Baeza, Y., González, A., Morton, J.T., Mirarab, S., Zech Xu, Z., Jiang, L., Haroon, M.F., Kanbar, J., Zhu, Q., Jin Song, S., Kosciolek, T., Bokulich, N.A., Lefler, J., Brislawn, C.J., Humphrey, G., Owens, S.M., Hampton-Marcell, J., Berg-Lyons, D., McKenzie, V., Fierer, N., Fuhrman, J.A., Clauset, A., Stevens, R.L., Shade, A., Pollard, K.S., Goodwin, K.D., Jansson, J.K., Gilbert, J.A., Knight, R., Rivera, J.L.A., Al-Moosawi, L., Alverdy, J., Amato, K.R., Andras, J., Angenent, L.T., Antonopoulos, D.A., Apprill, A., Armitage, D., Ballantine, K., Bárta, J., Baum, J.K., Berry, A., Bhatnagar, A., Bhatnagar, M., Biddle, J.F., Bittner, L., Boldgiv, B., Bottos, E., Boyer, D.M., Braun, J., Brazelton, W., Brearley, F.Q., Campbell, A.H., Caporaso, J.G., Cardona, C., Carroll, J.L., Cary, S.C., Casper, B.B., Charles, T.C., Chu, H., Claar, D.C., Clark, R.G., Clayton, J.B., Clemente, J.C., Cochran, A., Coleman, M.L., Collins, G., Colwell, R.R., Contreras, M., Crary, B.B., Creer, S., Cristol, D.A., Crump, B.C., Cui, D., Daly, S.E., Davalos, L., Dawson, R.D., Defazio, J., Delsuc, F., Dionisi, H.M., Dominguez-Bello, M.G., Dowell, R., Dubinsky, E.A., Dunn, P.O., Ercolini, D., Espinoza, R.E., Ezenwa, V., Fenner, N., Findlay, H.S., Fleming, I.D., Fogliano, V., Forsman, A., Freeman, C., Friedman, E.S., Galindo, G., Garcia, L., Garcia-Amado, M.A., Garshelis, D., Gasser, R.B., Gerdts, G., Gibson, M.K., Gifford, I., Gill, R.T., Giray, T., Gittel, A., Golyshin, P., Gong, D., Grossart, H.-P., Guyton, K., Haig, S.-J., Hale, V., Hall, R.S., Hallam, S.J., Handley, K.M., Hasan, N.A., Haydon, S.R., Hickman, J.E., Hidalgo, G., Hofmockel, K.S., Hooker, J., Hulth, S., Hultman, J., Hyde, E., Ibáñez-Álamo, J.D., Jastrow, J.D., Jex, A.R., Johnson, L.S., Johnston, E.R., Joseph, S., Jurburg, S.D., Jurelevicius, D., Karlsson, A., Karlsson, R., Kauppinen, S., Kellogg, C.T.E., Kennedy, S.J., Kerkhof, L.J., King, G.M., Kling, G.W., Koehler, A.V., Krezalek, M., Kueneman, J., Lamendella, R., Landon, E.M., Lane-deGraaf, K., LaRoche, J., Larsen, P., Laverock, B., Lax, S., Lentino, M., Levin, I.I., Liancourt, P., Liang, W., Linz, A.M., Lipson, D.A., Liu, Y., Lladser, M.E., Lozada, M., Spirito, C.M., MacCormack, W.P., MacRae-Crerar, A., Magris, M., Martín-Platero, A.M., Martín-Vivaldi, M., Martínez, L.M., Martínez-Bueno, M., Marzinelli, E.M., Mason, O.U., Mayer, G.D., McDevitt-Irwin, J.M., McDonald, J.E., McGuire, K.L., McMahon, K.D., McMinds, R., Medina, M., Mendelson, J.R., Metcalf, J.L., Meyer, F., Michelangeli, F., Miller, K., Mills, D.A., Minich, J., Mocali, S., Moitinho-Silva, L., Moore, A., Morgan-Kiss, R.M., Munroe, P., Myrold, D., Neufeld, J.D., Ni, Y., Nicol, G.W., Nielsen, S., Nissimov, J.I., Niu, K., Nolan, M.J., Noyce, K., O'Brien, S.L., Okamoto, N., Orlando, L., Castellano, Y.O., Osuolale, O., Oswald, W., Parnell, J., Peralta-Sánchez, J.M., Petraitis, P., Pfister, C., Pilon-Smits, E., Piombino, P., Pointing, S.B., Pollock, F.J., Potter, C., Prithiviraj, B., Quince, C., Rani, A., Ranjan, R., Rao, S., Rees, A.P., Richardson, M., Riebesell, U., Robinson, C., Rockne, K.J., Rodriguezl, S.M., Rohwer, F., Roundstone, W., Safran, R.J., Sangwan, N., Sanz, V., Schrenk, M., Schrenzel, M.D., Scott, N.M., Seger, R.L., Seguin-Orlando, A., Seldin, L., Seyler, L.M., Shakhsheer, B., Sheets, G.M., Shen, C., Shi, Y., Shin, H., Shogan, B.D., Shutler, D., Siegel, J., Simmons, S., Sjöling, S., Smith, D.P., Soler, J.J., Sperling, M., Steinberg, P.D., Stephens, B., Stevens, M.A., Taghavi, S., Tai, V., Tait, K., Tan, C.L., Tas, N., Taylor, D.L., Thomas, T., Timling, I., Turner, B.L., Urich, T., Ursell, L.K., van der Lelie, D., Van Treuren, W., van Zwieten, L., Vargas-Robles, D., Thurber, R.V., Vitaglione, P., Walker, D.A., Walters, W.A., Wang, S., Wang, T., Weaver, T., Webster, N.S., Wehrle, B., Weisenhorn, P., Weiss, S., Werner, J.J., West, K., Whitehead, A., Whitehead, S.R., Whittingham, L.A., Willerslev, E., Williams, A.E., Wood, S.A., Woodhams, D.C., Yang, Y., Zaneveld, J., Zarraonaindia, I., Zhang, Q., Zhao, H.: A communal catalogue reveals Earth’s multiscale microbial diversity. Nature. 551, 457-463 (2017).PUB | DOI | WoS | PubMed | Europe PMC
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2017 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2914367Sczyrba, A., Hofmann, P., Belmann, P., Koslicki, D., Janssen, S., Dröge, J., Gregor, I., Majda, S., Fiedler, J., Dahms, E., Bremges, A., Fritz, A., Garrido-Oter, R., Jørgensen, T.S., Shapiro, N., Blood, P.D., Gurevich, A., Bai, Y., Turaev, D., DeMaere, M.Z., Chikhi, R., Nagarajan, N., Quince, C., Meyer, F., Balvočiūtė, M., Hansen, L.H., Sørensen, S.J., Chia, B.K.H., Denis, B., Froula, J.L., Wang, Z., Egan, R., Don Kang, D., Cook, J.J., Deltel, C., Beckstette, M., Lemaitre, C., Peterlongo, P., Rizk, G., Lavenier, D., Wu, Y.-W., Singer, S.W., Jain, C., Strous, M., Klingenberg, H., Meinicke, P., Barton, M.D., Lingner, T., Lin, H.-H., Liao, Y.-C., Silva, G.G.Z., Cuevas, D.A., Edwards, R.A., Saha, S., Piro, V.C., Renard, B.Y., Pop, M., Klenk, H.-P., Göker, M., Kyrpides, N.C., Woyke, T., Vorholt, J.A., Schulze-Lefert, P., Rubin, E.M., Darling, A.E., Rattei, T., McHardy, A.C.: Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software. Nature Methods. 14, 1063-1071 (2017).PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
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2016 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2907305Sampson, T.R., Debelius, J.W., Thron, T., Janssen, S., Shastri, G.G., Ilhan, Z.E., Challis, C., Schretter, C.E., Rocha, S., Gradinaru, V., Chesselet, M.-F., Keshavarzian, A., Shannon, K.M., Krajmalnik-Brown, R., Wittung-Stafshede, P., Knight, R., Mazmanian, S.K.: Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's Disease. Cell. 167, 1469-1480.e12 (2016).PUB | DOI | WoS | PubMed | Europe PMC
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2014 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2700599Janssen, S., Giegerich, R.: The RNA shapes studio. Bioinformatics. 31, 423-425 (2014).PUB | DOI | Download (ext.) | WoS | PubMed | Europe PMC
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2013 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2551798Sauthoff, G., Mohl, M., Janssen, S., Giegerich, R.: Bellman's GAP -- a Language and Compiler for Dynamic Programming in Sequence Analysis. Bioinformatics. 29, 551-560 (2013).PUB | DOI | WoS | PubMed | Europe PMC
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2012 | Sammelwerksbeitrag | PUB-ID: 2439665Janssen, S., Giegerich, R.: Abstract Shape Analysis of RNA. In: Gorodkin, J. and Weinberg, Z. (eds.) RNA Bioinformatics t.b.a. p. 1-35. (2012).PUB
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2011 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 2410526
Janssen, S., Schudoma, C., Steger, G., Giegerich, R.: Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction. BMC Bioinformatics. 12, : 429 (2011).PUB | PDF | DOI | Download (ext.) | WoS | PubMed | Europe PMC -
2011 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 2310489Sauthoff, G., Janssen, S., Giegerich, R.: Bellman's GAP: a declarative language for dynamic programming. Proceedings of the 13th international ACM SIGPLAN symposium on Principles and practices of declarative programming. p. 29-40. ACM, New York, NY, USA (2011).PUB | DOI | Download (ext.)
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2010 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1785497
Schlüter, J.-P., Reinkensmeier, J., Daschkey, S., Evguenieva-Hackenberg, E., Janssen, S., Jaenicke, S., Becker, J.D., Giegerich, R., Becker, A.: A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti. BMC Genomics. 11, : 245 (2010).PUB | PDF | DOI | WoS | PubMed | Europe PMC
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2010 | Datenpublikation | PUB-ID: 2698354
Grond, F., Janssen, S., Schirmer, S., Hermann, T.: Supplementary Material for "Browsing RNA Structures by Interactive Sonification". Bielefeld University (2010).PUB | Dateien verfügbar | DOI
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2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1893988
Grond, F., Janssen, S., Schirmer, S., Hermann, T.: Browsing RNA Structures by Interactive Sonification. In: Bresin, R., Hermann, T., and Hunt, A. (eds.) Proceedings of the 3rd Interactive Sonification Workshop. p. 11-16. KTH School of Computer Science and Communication (CSC), KTH, Stockholm, Sweden (2010).PUB | Datei | Download (ext.)
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2010 | Konferenzbeitrag | Veröffentlicht | PUB-ID: 1894008
Theis, C., Janssen, S., Giegerich, R.: Prediction of RNA Secondary Structure Including Kissing Hairpin Motifs. In: Moulton, V. and Singh, M. (eds.) Algorithms in Bioinformatics. 10th international workshop (WABI 2010), proceedings. Lecture Notes in Bioinformatics. 6293, p. 52-64. Springer, Berlin (2010).PUB | Datei | DOI
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2008 | Zeitschriftenaufsatz | Veröffentlicht | PUB-ID: 1893917
Janssen, S., Reeder, J., Giegerich, R.: Shape based indexing for faster search of RNA family databases. BMC Bioinformatics. 9, 131 (2008).PUB | Dateien verfügbar | DOI | WoS | PubMed | Europe PMC