{"id":2809,"date":"2024-07-30T21:01:02","date_gmt":"2024-07-30T21:01:02","guid":{"rendered":"https:\/\/daslab-tmp.su.domains\/?page_id=2809"},"modified":"2024-08-22T00:59:38","modified_gmt":"2024-08-22T00:59:38","slug":"publications","status":"publish","type":"page","link":"https:\/\/daslab-tmp.su.domains\/?page_id=2809","title":{"rendered":"Publications"},"content":{"rendered":"

[vc_row][vc_column][vc_column_text]arrow<\/a>Search for papers from the Das Lab on\u00a0PubMed<\/strong><\/span>[\/vc_column_text]

2024<\/h2>

Rangan, R., Huang, R. , Hunter O., Pham P., Ares, Jr., M., Das, R. (2024) “RNA structure landscape of S. cerevisiae introns<\/u>”\u00a0bioRxiv<\/i>\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Preprint<\/a><\/span><\/p>\n<\/div>

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\"\"He, S., Huang, R., Townley, J., C. Kretsch, R., Karagianes, T.G., Cox, D.B.T., Blair, H., Penzar, D., Vyaltsev, V., Aristova, E., Zinkevich, A., Bakulin, A., Sohn, H., Krstevski, D., Fukui, T., Tatematsu, F., Uchida, Y., Jang, D., Seong Lee, J., Shieh, R., Ma, T., Martynov, E., Shugaev, M.V., Bukhari, H.S.T., Fujikawa, K., Onodera, K., Henkel, C., Ron, S., Romano, J., Nicol, J.J. , Nye, G.P., Wu, Y., Choe, C., Reade, W., Eterna participants., Das, R. (2024)
\n“Ribonanza: deep learning of RNA structure through dual crowdsourcing”<\/span><\/strong>
\nbioRxiv<\/i>
\nPreprint\u00a0<\/a>|\u00a0Link<\/a><\/strong><\/span><\/p>\n<\/div>

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Choe, C.A., Andreasson, J.O.L., Melaine, F., Kladwang, W., Wu, M.J., Portela, F., Wellington-Oguri, R., Nicol, J.J., Wayment-Steele, H.K., Gotrik, M., Eterna Participants, Khatri, P., Greenleaf, W.J., Das, R. (2024) “Compact RNA sensors for increasingly complex functions of multiple inputs<\/u>”\u00a0bioRxiv<\/i>\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Preprint<\/a><\/span><\/p>\n<\/div>

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\"SL5_TOC\"Kretsch, R.C., Xu, L., Zheludev, I.N., Zhou, X., Huang, R., Nye, G., Li, S., Zhang, K., Chiu, W., Das, R. (2024)
\n“Tertiary folds of the SL5 RNA from the 5\u2019 proximal region of SARS-CoV-2 and related coronaviruses”<\/span><\/strong>
\nPNAS<\/i>\u00a0121 (10) : e2320493121
\nPaper\u00a0<\/a>|\u00a0Link<\/a><\/strong><\/span><\/p>\n<\/div>

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Tangpradabkul, T., Palo, M., Townley, J., Hsu, K.B., Eterna participants, Smaga, S., Das, R., Schepartz, A. (2024) “Minimization of the E. coli ribosome, aided and optimized by community science<\/u>”\u00a0Nucleic Acids Research<\/i>\u00a02024 : 1 – 16\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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2023<\/h2>

Mulvaney, T., Kretsch, R., Elliott, L., Beton, J., Kryshtafovych, A., Rigden, D.J., Das, R., Topf, M. (2023) “CASP15 cryoEM protein and RNA targets: refinement and analysis using experimental maps<\/u>”\u00a0Proteins: Structure, Function, and Bioinformatics<\/i>\u00a091 (12) : 1935 – 1951\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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\"FP_Cover\"Das, R., Kretsch, R., Simpkin, A., Mulvaney, T., Pham, P., Rangan, R., Bu, F., Keegan, R., Topf, M., Rigden, D., Miao, Z., Westhof, E. (2023)
\n“Assessment of three-dimensional RNA structure prediction in CASP15”<\/span><\/strong>
\nProteins: Structure, Function, and Bioinformatics<\/i>\u00a091 (12) : 1747 – 1770
\nPaper\u00a0<\/a>|\u00a0Link<\/a><\/strong><\/span><\/p>\n<\/div>

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Kretsch, R., Andersen, E., Bujnicki, J., Chiu, W., Das, R., Luo, B., Masquida, B., McRae, E., Schroeder, G., Su, Z., Wedekind, J., Xu, L., Zhang, K., Zheludev, I., Moult, J., Kryshtafovych, A. (2023) “RNA target highlights in CASP15: Evaluation of predicted models by structure providers<\/u>”\u00a0Proteins: Structure, Function, and Bioinformatics<\/i>\u00a091 (12) : 1600 – 1615\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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Kryshtafovych, A., Antczak, M., Szachniuk, M., Zok, T., Kretsch, R., Rangan, R., Pham, P., Das, R., Robin, X., Studer, G., Durairaj, J., Eberhardt, J., Sweeney, A., Topf, M., Schwede, T., Fidelis, K., Moult, J. (2023) “New prediction categories in CASP15<\/u>”\u00a0Proteins: Structure, Function, and Bioinformatics<\/i>\u00a091 (12) : 1550 – 1557\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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Kr\u00fcger, A, Watkins A.M., Wellington-Oguri R., Romano, J., Kofman, C., DeFoe, A., Kim, Y., Anderson-Lee, J., Fisker, E., Townley J., Eterna Participants, d’Aquino, A.E., Das, R., Jewett, M.C. (2023) “Community science designed ribosomes with beneficial phenotypes<\/u>”\u00a0Nature Communications<\/i>\u00a014 : 961\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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Watkins, A.M. and Das, R. (2023) “RNA 3D Modeling with FARFAR2, Online<\/u>”\u00a0Methods Mol Biol<\/i>\u00a02586 : 233 – 249\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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Ma, H., Pham, P., Luo, B., Rangan, R., Kappel, K., Su, Z., Das, R. (2023) “Auto-DRRAFTER: automated RNA modeling based on cryo-EM density<\/u>”\u00a0Methods Mol Biol.<\/i>\u00a02568 : 193 – 211\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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2022<\/h2>

\"dualcrowdsourcing_ryos2_tSNE\"Wayment-Steele H., Kladwang W., Watkins A., Kim D., Tunguz B., Reade W., Demkin M., Romano J., Wellington-Oguri R., Nicol J., Gao J., Onodera K., Fujikawa K., Mao H., Vandewiele G., Tinti M., Steenwinckel B., Ito T., Noumi T., He S., Ishi K., Lee Y., \u00d6zt\u00fcrk F., Chiu K., \u00d6zt\u00fcrk E., Amer K., Fares M., Eterna Participants , Das R. (2022)
\n“Deep learning models for predicting RNA degradation via dual crowdsourcing”<\/span><\/strong>
\nNature Machine Intelligence<\/i>\u00a04, 1174\u20131184
\nPaper\u00a0<\/a>|\u00a0Link<\/a><\/strong><\/span><\/p>\n<\/div>

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Kofman, C., Watkins, A., Kim, D., Willi, J., Wooldredge, A., Karim, A., Das, R., Jewett, M. (2022) “Computationally-guided design and selection of high performing ribosomal active site mutants<\/u>”\u00a0Nucleic Acids Research<\/i>\u00a050(22):13143-13154\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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\"EternaFold\"Wayment-Steele, H.K., Kladwang, W., Strom, A.I., Lee, J., Treuille, A., Becka, A., Eterna Participants, Das R. (2022)
\n“RNA secondary structure packages ranked and improved by high-throughput experiments”<\/span><\/strong>
\nNature Methods<\/i>\u00a019 : 1234 – 1242
\nPaper\u00a0<\/a>|\u00a0Link<\/a>\u00a0|\u00a0EternaBench repository<\/a>\u00a0|\u00a0EternaFold server<\/a><\/strong><\/span><\/p>\n<\/div>

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Li, S., Palo, M.Z., Pintilie, G., Zhang, X., Su, Z., Kappel, K., Chiu, W., Zhang, K., Das, R. (2022) “Topological crossing in the misfolded Tetrahymena ribozyme resolved by cryo-EM<\/u>”\u00a0Proceedings of the National Academy of Sciences<\/i>\u00a0119 (37) : e2209146119\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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Hagey, R.J., Elazar, M., Pham, E.A., Tian, S., Ben-Avi, L., Bernardin-Souibgui, C., Yee, M.F., Moreira, F.R., Rabinovitch, M.V., Meganck, R.M., Fram, B., Beck, A., Gibson, S.A., Lam, G., Devera, J., Kladwang, W., Nguyen, K., Xiong, A., Schaffert, S., Avisar, T., Liu, P., Rustagi, A., Fichtenbaum, C.J., Pang, P.S., Khatri, P., Tseng, C., Taubenberger, J.K., Blish, C.A., Hurst, B.L., Sheahan, T.P., Das, R., Glenn, J.S. (2022) “Programmable antivirals targeting critical conserved viral RNA secondary structures from influenza A virus and SARS-CoV-2<\/u>”\u00a0Nature Medicine<\/i>\u00a028 (9) : 1944 – 1955\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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Kim, D.S., Watkins, A., Bidstrup, E., Lee, J., Topkar, V., Kofman, C., Schwarz, K.J., Liu, Y., Pintilie, G., Roney, E., Das, R., Jewett, M.C. (2022) “Three-dimensional structure-guided evolution of a ribosome with tethered subunits<\/u>”\u00a0Nature Chemical Biology<\/i>\u00a018 (9) : 990 – 998\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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Andreasson, J.O.L., Gotrik, M.R., Wu, M.J., Wayment-Steele, H.K., Kladwang, W., Portela, F., Wellington-Oguri, R., Das, R., Greenleaf, W.J. (2022) “Crowdsourced RNA design discovers diverse, reversible, efficient, self-contained molecular sensors<\/u>”\u00a0PNAS<\/i>\u00a0119 (18) : e2112979119\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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\"\"Leppek, K.*, Byeon, G.W.*, Kladwang, W.*, Wayment-Steele, H.K.*, Kerr, C.H.*, Xu, A.F.*, Kim, D.S.*, Topkar, V.V., Choe, C., Rothschild, D., Tiu, G.C., Wellington-Oguri, R., Fujii, K., Sharma, E., Watkins, A.M., Nicol, J.J., Romano, J., Tunguz, B., Diaz F., Cai, H., Guo, P., Wu, J., Meng, F., Shi, S., Eterna Participants, Dormitzer, P.R., Sol\u00f3rzano, A., Barna, M., Das, R. *These authors contributed equally. (2022)
\n“Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics”<\/span><\/strong>
\nNature Communications<\/i>\u00a013 : 1536
\nPaper\u00a0<\/a>|\u00a0Link<\/a><\/strong><\/span><\/p>\n<\/div>

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2021<\/h2>

Das, R., Russell, R. (2021) “How to Kinetically Dissect an RNA Machine<\/u>”\u00a0Biochemistry<\/i>\u00a060 (46) : 3485 – 3490\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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Das, R., Watkins, A.W. (2021) “RiboDraw: semiautomated two-dimensional drawing of RNA tertiary structure diagrams<\/u>”\u00a0NAR Genomics and Bioinformatics<\/i>\u00a03 (4)\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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\"\"Wayment-Steele, H.K., Kim, D.S., Choe, C.A., Nicol, J.J., Wellington-Oguri, R., Sperberg, R.A.P., Huang, P., Eterna Participants, Das, R. (2021)
\n“Theoretical basis for stabilizing messenger RNA through secondary structure design”<\/span><\/strong>
\nNucleic Acids Research<\/i>\u00a049 (18) : 10604 – 10617
\nPaper\u00a0<\/a>|\u00a0Link<\/a>\u00a0|\u00a0Data (OpenVaccine-solves)<\/a><\/strong><\/span><\/p>\n<\/div>

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Wayment-Steele, H.K., Kladwang, W., Watkins, A.M., Kim, D.S., Tunguz, B., Reade, W., Demkin, M., Romano, J., Wellington-Oguri, R., Nicol, J.J., Jiayang, G., Kazuki, O., Kujikawa, K., Mao, H., Vandewiele, G., Tinti, M., Steenwinckel, B., Ito, T., Noumi, T., He, S., Ishi, K., Lee, Y., Ozturk, F., Chiu, A., Ozturk, E., Amer, K., Fares, M., Eterna Participants, Das, R. (2021) “Predictive models of RNA degradation through dual crowdsourcing<\/span>” arXiv <\/em><\/p>\n<\/div>

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Koodli, R.V., Rudolfs, B., Wayment-Steele, H.K., Eterna Structure Designers, Das, R. (2021) “Redesigning the Eterna100 for the Vienna 2 folding engine<\/u>”\u00a0bioRxiv<\/i>\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Preprint<\/a><\/span><\/p>\n<\/div>

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R. J. L. Townshend, S. Eismann, A.M. Watkins, R. Rangan, M. Karelina, R. Das, R.O. Dror (2021) “Geometric deep learning of RNA structure<\/u>”\u00a0Science<\/i>\u00a0373 (6558) : 1047 – 1051\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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\"\"Zhang, K., Zheludev, I. N., Hagey, R. J., Wu, M. T.-P., Haslecker, R., Hou, Y. J., Kretsch, R., Pintilie, G. D., Rangan, R., Kladwang, W., Li, S., Pham, E. A., Bernardin-Souibgui, C., Baric, R. S., Sheahan, T. P., D Souza, V., Glenn, J. S., Chiu, W., Das, R. (2021)
\n“Cryo-EM and antisense targeting of the 28-kDa frameshift stimulation element from the SARS-CoV-2 RNA genome”<\/span><\/strong>
\nNature Structure and Molecular Biology<\/i>\u00a028 : 747 – 754
\nPaper\u00a0<\/a>|\u00a0Link<\/a><\/strong><\/span><\/p>\n<\/div>

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\"\"Su, Z., Zhang, K., Kappel, K., Li, S., Palo, M.Z., Pintilie, G.D., Rangan, R., Lou, B., Wei, Yuquan., Das, R., Chiu, W. (2021)
\n“Cryo-EM structures of full-length Tetrahymena ribozyme at 3.1 \u00c5 resolution”<\/span><\/strong>
\nNature<\/i>\u00a0596 : 603 – 607
\nPaper\u00a0<\/a>|\u00a0Link<\/a><\/strong><\/span><\/p>\n<\/div>

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Das R. (2021) “RNA structure: a renaissance begins?<\/u>”\u00a0Nature Methods<\/i>\u00a018 : 439\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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Byeon, G.W., Cenik, E.S., Jiang, L., Tang, H., Das, R., Barna, M. (2021) “Functional and structural basis of extreme conservation in vertebrate 5\u2019 untranslated regions<\/u>”\u00a0Nature Genetics<\/i>\u00a053 : 729 – 741\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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Liu, X., Sun, T., Shcberbina, A., Li, Q., Jarmoskaite, I., Kappel, K., Ramaswami, G., Das, R., Kundaje, A., Li, J.B. (2021) “Learning cis-regulatory principles of ADAR-based RNA editing from CRISPR-mediated mutagenesis<\/u>”\u00a0Nature Communications<\/i>\u00a012 (2165)\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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Ghanim, G. E., Fountain, A. J., van Roon, A. M., Rangan, R., Das, R., Collins, K., Nguyen, T.H.D. (2021) “Structure of human telomerase holoenzyme with bound telomeric DNA<\/u>”\u00a0Nature<\/i>\u00a0593 : 449 – 453\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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Le, K., Adolf-Bryfogle, J., Klima, J., Lyskov, S., Labonte, J., Bertolani, S., Roy Burman, S., Leaver-Fay, A., Weitzner, B., Maguire, J., Rangan, R., Adrianowycz, M., Alford, R., Adal, A., Nance, M., Das, R., Dunbrack, R., Schief, W., Kuhlman, B., Siegel, J., Gray, J. (2021) “PyRosetta jupyter notebooks teach biomolecular structure prediction and design<\/u>”\u00a0The Biophysicist<\/i>\u00a02 (1) : 108 – 122\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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Rangan, R., Watkins, A. M., Chacon, J., Kretsch, R., Kladwang, W., Zheludev, I.N., Townley, J., Rynge, M., Thain, G., Das, R. (2021) “De novo 3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures<\/u>”\u00a0Nucleic Acids Research<\/i>\u00a049 (6) : 3092 – 3108\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link\u00a0<\/a>|\u00a0Data (Model collection, SARS-CoV-2 structures)<\/a>\u00a0|\u00a0Data (Model collection, positive control structures<\/a>)<\/span><\/p>\n<\/div>

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2020<\/h2>

Leman, J.K., Weitzner, B.D., Lewis, S.M., Adolf-Bryfogle, J., Alam, N., Alford, R.F., Aprahamian, M., Baker, D., Barlow, K.A., Barth, P., Basanta, B., Bender, B.J., Blacklock, K., Bonet, J., Boyken, S.E., Bradley, P., Bystroff, C., Conway, P., Cooper, S., Correia, B.E., Coventry, B., Das, R., De Jong, R.M., DiMaio, F., Dsilva, L., Dunbrack, R., Ford, A.S., Frenz, B., Fu, D.Y., Geniesse, C., Goldschmidt, L., Gowthaman, R., Gray, J.J., Gront, D., Guffy, S., Horowitz, S., Huang, P.S., Huber, T., Jacobs, T.M., Jeliazkov, J.R., Johnson, D.K., Kappel, K., Karanicolas, J., Khakzad, H., Khar, K.R., Khare, S.D., Khatib, F., Khramushin, A., King, I.C., Kleffner, R., Koepnick, B., Kortemme, T., Kuenze, G., Kuhlman, B., Kuroda, D., Labonte, J.W., Lai, J.K., Lapidoth, G., Leaver-Fay, A., Lindert, S., Linsky, T., London, N., Lubin, J.H., Lyskov, S., Maguire, J., Malmstr\u00f6m, L., Marcos, E., Marcu, O., Marze, N.A., Meiler, J., Moretti, R., Mulligan, V.K., Nerli, S., Norn, C., \u00d3\u2019Conch\u00fair, S., Ollikainen, N., Ovchinnikov, S., Pacella, M.S., Pan, X., Park, H., Pavlovicz, R.E., Pethe, M., Pierce, B.G., Pilla, K.B., Raveh, B., Renfrew, P.D., Burman, S.S.R., Rubenstein, A., Sauer, M.F., Scheck, A., Schief, W., Schueler-Furman, O., Sedan, Y., Sevy, A.M., Sgourakis, N.G., Shi, L., Siegel, J.B., Silva, D.A., Smith, S., Song, Y., Stein, A., Szegedy, M., Teets, F.D., Thyme, S.B., Wang, R.Y., Watkins, A., Zimmerman, L., Bonneau, R. (2020) “Macromolecular modeling and design in Rosetta: recent methods and frameworks.<\/u>”\u00a0Nature Methods<\/i>\u00a017 (7) : 665 – 680<\/p>\n<\/div>

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Palka, C., Forino, N.M., Henstchel, J., Das, R., Stone, M.D. (2020) “Folding heterogeneity in the essential human telomerase RNA three-way junction<\/u>”\u00a0RNA<\/i>\u00a026 : 1787 – 1800\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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\"RibosolveKappel, K., Zhang, K., Su, Z., Watkins, A.M., Kladwang, W., Li, S., Pintilie, G., Topkar, V.V., Rangan, R., Zheludev, I.N., Yesselman, J.D., Chiu, W., and Das, R. (2020)
\n“Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures”<\/span><\/strong>
\nNature Methods<\/i>\u00a017 : 699 – 707
\nPaper\u00a0<\/a>|\u00a0Link<\/a><\/strong><\/span><\/p>\n<\/div>

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Watkins, A.M., Rangan, R., Das, R. (2020) “FARFAR2: Improved de novo Rosetta prediction of complex global RNA folds<\/u>”\u00a0Structure<\/i>\u00a028 (8) : 963 – 976\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link\u00a0<\/a>|\u00a0Server<\/a>\u00a0|\u00a0Benchmarking scripts<\/a><\/span><\/p>\n<\/div>

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ain, N., Blauch, L. R., Szymanski, M. R., Das, R., Tang, S. K. Y., Yin, Y. W., Fire, A. Z. (2020) “Transcription polymerase\u2013catalyzed emergence of novel RNA replicons<\/u>”\u00a0Science<\/i>\u00a0368 : eaay0688\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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Miao, Z., Adamiak, R. W., Antczak, M., Boniecki, M. J., Bujnicki, J., Chen, S.-J., Cheng, C. Y., Cheng, Y., Chou, F.-C., Das, R., Dokholyan, N. V., Ding, F., Geniesse, C., Jiang, Y., Joshi, A., Krokhotin, A., Magnus, M., Mailhot, O., Major, F., Mann, T. H., Piatkowski, P., Pluta, R., Popenda, M., Sarzynska, J., Sun, L., Szachniuk, M., Tian, S., Wang, J., Wang, J., Watkins, A. M., Wiedemann, J., Xiao, Y., Xu, X., Yesselman, J. D., Zhang, D., Zhang, Y., Zhang, Z., Zhao, C., Zhao, P., Zhou, Y., Zok, T., Zyla, A., Ren, A., Batey, R. T., Golden, B. L., Huang, L., Lilley, D. M. J., Liu, Y., Patel, D. J., Westhof, E. (2020) “RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers<\/u>”\u00a0RNA<\/i>\u00a026 : 982 – 995\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Kladwang, W., Topkar, V.V., Liu, B., Rangan R., Hodges, T.L., Keane, S.C., Al-Hashimi, H., Das, R. (2020) “Anomalous reverse transcription through chemical modifications in polyadenosine stretches<\/u>”\u00a0Biochemistry<\/i>\u00a059 (23) : 2154 – 2170\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Rangan, R., Zheludev I.N., Hagey, R.J., Pham, E.A., Wayment-Steele, H.K., Glenn, J.S., Das, R. (2020) “RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses: a first look<\/u>”\u00a0RNA<\/i>\u00a026 : 937 – 959\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link\u00a0<\/a>|\u00a0Code<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

2019<\/h2>

\"sam_iv_map\"Zhang, K., Li, S., Kappel, K., Pintilie, G., Su, Z., Mou, T.-C., Schmid, M. F., Das, R., Chiu, W. (2019)
\n“Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 \u00c5 resolution”<\/span><\/strong>
\nNature Communications<\/i>\u00a010 : Article number: 5511
\nPaper\u00a0<\/a>|\u00a0Link<\/a><\/strong><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Magnus, M., Kappel, K., Das, R., Bujnicki, J.M. (2019) “RNA 3D structure prediction guided by independent folding of homologous sequences<\/u>”\u00a0BMC Bioinformatics<\/i>\u00a020 : article 512\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Li, X., Liu, S., Zhang, L., Issaian, A., Hill, R. C., Espinosa, S., Shi, S., Cui, Y., Kappel, K., Das, R., Hansen, K. C., Zhou, Z. H., Zhao, R. (2019) “A unified mechanism for intron and exon definition and back-splicing<\/u>”\u00a0Nature<\/i>\u00a0573 : 375 – 380\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

\"RNAmake_spinachTTRs\"Yesselman, J.D., Eiler, D., Carlson, E.D., Gotrik, M.R., d’Aquino, A.E., Ooms, A.N., Kladwang, W., Carlson, P.D., Shi, X., Costantino, D., Herschlag, D., Lucks, J.B., Jewett, M.C., Kieft, J.S., and Das, R. (2019)
\n“Computational design of three-dimensional RNA structure and function”<\/span><\/strong>
\nNature Nanotechnology<\/i>\u00a014 : 866 – 873
\nPaper\u00a0<\/a>|\u00a0Link<\/a><\/strong><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Koirala, D., Shao, Y., Koldobskaya, Y., Fuller, J.R., Watkins, A.M., Shelke, S.A., Pilipenko, E.V., Das, R., Rice, P.A., and Piccirilli, J.A. (2019) “A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites<\/u>”\u00a0Nature Communications<\/i>\u00a010 : 3629\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Das, R., Keep, B., Washington, P, Riedel-Kruse, I. H. (2019) “Scientific discovery games for biomedical research<\/u>”\u00a0Annual Review of Biomedical Data Science<\/i>\u00a02 : 253 – 279\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Yesselman, J.D. Denny, S.K. Bisaria, N. Herschlag, D. Greenleaf, W.J. Das, R. (2019) “Sequence-dependent RNA helix conformational preferences predictably impact tertiary structure formation<\/u>”\u00a0Proceedings of the National Academy of Sciences<\/i>\u00a0116 (34) : 16847 – 16855\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Wu, M.J., Andreasson, J., Kladwang, W., Greenleaf, W.J., and Das, R. (2019) “Automated design of diverse stand-alone riboswitches<\/u>”\u00a0ACS Synthetic Biology<\/i>\u00a08 : 1838 – 1846\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Koodli, R. V., Keep, B., Coppess, K. R., Portela, F., Eterna Participants, and Das, R. (2019) “EternaBrain: automated RNA design through move sets and strategies from an Internet-scale RNA videogame<\/u>”\u00a0PLOS Computational Biology<\/i>\u00a015 (6) : e1007059\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link\u00a0<\/a>|\u00a0EternaBrain software<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Wayment-Steele, H., Wu, M., Gotrik, M., and Das, R. (2019) “Evaluating riboswitch optimality<\/u>”\u00a0Methods in Enzymology<\/i>\u00a0623 : 417 – 450\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Watkins, A. M., Rangan, R., and Das, R. (2019) “Using Rosetta for RNA homology modeling<\/u>”\u00a0Methods in Enzymology<\/i>\u00a0623 : 177 – 207\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Jarmoskaite, I., Denny, S. K., Vaidyanathan, P. P., Becker, W. R., Andreasson, J. O. L., Layton, C. J., Kappel, K., Shivashankar, V., Sreenivasan, R., Das, R., Greenleaf, W. J., and Herschlag, D. (2019) “A quantitative and predictive model for RNA binding by human Pumilio proteins<\/u>”\u00a0Molecular Cell<\/i>\u00a074 : 966 – 981\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Huang, L., Wang, J., Watkins, A. M., Das, R., and Lilley, D. M. J. (2019) “Structure and ligand binding of the glutamine-II riboswitch<\/u>”\u00a0Nucleic Acids Research<\/i>\u00a047 (7666) : 7666 – 7675\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

\"MS2_KappelddG2\"Kappel, K. Jarmoskaite, I. Vaidyanathan, P.P. Greenleaf, W.J. Herschlag, D. and Das R. (2019)
\n“Blind tests of RNA-protein binding affinity prediction”<\/span><\/strong>
\nPNAS<\/i>\u00a0116 : 8336 – 8341
\nPaper\u00a0<\/a>|\u00a0Link<\/a>\u00a0|\u00a0Rosetta RNP-ddG Software<\/a>\u00a0|\u00a0ROSIE RNP-ddG Server<\/a><\/strong><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Boeynaems, S., Holehouse, A.S., Weinhardt, V., Kovacs, D., Van Lindt, J., Larabell, C., Van Den Bosch, L., Das, R., Tompa, P.S. Pappu, R.V., and Gitler, A.D. (2019) “Spontaneous driving forces give rise to protein-RNA condensates with coexisting phases and complex material properties<\/u>”\u00a0PNAS<\/i>\u00a0116 : 7889 – 7898\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Kappel K. and Das R. (2019) “Sampling native-like structures of RNA-protein complexes through Rosetta folding and docking<\/u>”\u00a0Structure<\/i>\u00a027 (1) : 140 – 151\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link\u00a0<\/a>|\u00a0Rosetta RNP modeling software<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Koodli, R., Keep, B., Coppess, K.R., Portela, F., Eterna Players, and Das, R. (2019) “RNA design movesets and strategies from an Internet-scale videogame<\/span>” BioRxiv<\/em><\/p>\n<\/div>

<\/div><\/div><\/div>\n

2018<\/h2>

Hartwick EW, Costantino DA, MacFadden, A, Nix, JC, Tian S, Das R, and Kieft JS (2018) “Ribosome-induced RNA conformational changes in a viral 3′-UTR sense and regulate translation levels<\/u>”\u00a0Nature Communications<\/i>\u00a09 (1)\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Denny, S.K., Bisaria, N. Yesselman, J.D. Das, R. Herschlag, D. Greenleaf, W.J. (2018) “High-throughput investigation of diverse junction elements in RNA tertiary folding<\/u>”\u00a0Cell<\/i>\u00a0174 (2) : 377 – 390\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Zettl, T., Das, R., Harbury, P.A.B., Herschlag, D., Lipfert, J., Mathew, R.S., and Shi X. (2018) “Recording and analyzing nucleic acid distance distributions with X-ray scattering interferometry (XSI)<\/u>”\u00a0Curr Protoc Nucleic Acid Chem<\/i>\u00a073 : e54\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

\"Kappel_DRRAFTER_MS2_v2\"Kappel, K. Liu, S. Larsen, K.P. Skiniotis, G. Puglisi, E.V., Puglisi, J.D., Zhou, Z.H., Zhao, R., and Das, R. (2018)
\n“De novo computational RNA modeling into cryoEM maps of large ribonucleoprotein complexes”<\/span><\/strong>
\nNature Methods<\/i>\u00a015 : 947 – 954
\nPaper\u00a0<\/a>|\u00a0Link<\/a>\u00a0|\u00a0DRRAFTER Rosetta Software<\/a><\/strong><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Chen, L., Roake, C.M., Freund, A., Batista, P.J., Tian, S., Yin, Y.A., Gajera, C.R., Lin, S., Lee, B., Pech, M.F., Venteicher, A.S., Das, R., Chang, H.Y., and Artandi, S.E. (2018) “An activity switch in human telomerase based on RNA conformation and shaped by TCAB1<\/u>”\u00a0Cell<\/i>\u00a0174 (1) : 218-230\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Shi, J., Eterna players, Das, R., and Pande, V.S. (2018) “SentRNA: Improving computational RNA design by incorporating a prior of human design strategies<\/u>”\u00a0BioRxiv<\/i>\u00a0|\u00a0Preprint\u00a0<\/a>|\u00a0SentRNA Software<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

\"stepwise_icon\"Watkins, A.M., Geniesse, C., Kladwang, W., Zakrevsky, P., Jaeger, L., and Das, R. (2018)
\n“Blind prediction of noncanonical RNA structure at atomic accuracy”<\/span><\/strong>
\nScience Advances<\/i>\u00a04 (5) : eaar5316
\nPaper\u00a0<\/a>|\u00a0Link<\/a>\u00a0|\u00a0Stanford Digital Repository PURL<\/a>\u00a0|\u00a0ROSIE server<\/a><\/strong><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Wu, M.J., Andreasson, J.O.L, Kladwang, W., Greenleaf, W.J., Eterna players, and Das, R. (2018) “Prospects for recurrent neural network models to learn RNA biophysics from high-throughput data<\/u>”\u00a0BioRxiv<\/i>\u00a0|\u00a0Preprint<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Das, R. (2018) “LIkelihood-based Fits of Folding Transitions (LIFFT) for Biomolecule Mapping Data<\/u>”\u00a0BioRxiv<\/i>\u00a0|\u00a0Preprint\u00a0<\/a>|\u00a0LIFFT Software<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Gracia, B., Al-Hashimi, H.M., Bisaria N., Das, R., Herschlag, D., and Russell, R. (2018) “Hidden structural modules in a cooperative RNA folding transition<\/u>”\u00a0Cell Reports<\/i>\u00a022 : 3240 – 3250\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

\"add_ensemble\"Tian, S., Kladwang, W., and Das, R. (2018)
\n“Allosteric mechanism of the V. vulnificus adenine riboswitch resolved by four-dimensional chemical mapping”<\/span><\/strong>
\neLife<\/i>\u00a07 : e29602
\nPaper\u00a0<\/a>|\u00a0Link<\/a><\/strong><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Omabegho, T., Gurel, P. S., Cheng, C. Y., Kim, L., Y., Ruijgrok, P. V., Das, R., Alushin, G.M., and Bryant, Z. (2018) “Controllable molecular motors engineered from myosin and RNA<\/u>”\u00a0Nature Nanotechnology<\/i>\u00a013 : 34 – 40\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Moretti, R., Lyskov, S., Das, R., Meiler, J., and Gray, J.J. (2018) “Web-accessible molecular modeling with Rosetta: The Rosetta Online Server That Includes Everyone (ROSIE)<\/u>”\u00a0Protein Science<\/i>\u00a027 (1) : 259 – 268\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link\u00a0<\/a>|\u00a0ROSIE Servers<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

2017<\/h2>

Leppek, K., Das, R., and Barna, M. (2017) “Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them<\/u>”\u00a0Nature Reviews Molecular Cell Biology<\/i>\u00a019 : 158 – 174\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Yesselman, J.D., Tian, S., Liu, X., Shi, L., Li, J.B., and Das, R. (2017) “Updates to the RNA mapping database (RMDB), version 2<\/u>”\u00a0Nucleic Acids Research<\/i>\u00a046 (D1) : D375 – D379\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

\"Fig4_FourRNAs_UpdatedForSecondProofs\"Cheng, C.Y., Kladwang, W., Yesselman, J.D., and Das, R. (2017)
\n“RNA structure inference through chemical mapping after accidental or intentional mutations”<\/span><\/strong>
\nProceedings of the National Academy of Sciences U.S.A.<\/i>\u00a0114 (37) : 9876 – 9881
\nPaper\u00a0<\/a>|\u00a0Link<\/a><\/strong><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Alford, R.F., Leaver-Fay, A., Jeliazkov, J.R., O\u2019Meara, M.J., DiMaio, F.D., Park, H., Shapovalov, M.V., Renfrew, P.D., Mulligan, V.K., Kappel, K., Labonte, J.W., Pacella , M.S., Bonneau, R., Bradley, P., Dunbrack, Jr., R.L., Das, R., Baker, D., Kuhlman, B., Kortemme, T., and Gray, J.J. (2017) “The Rosetta all-atom energy function for macromolecular modeling and design<\/u>”\u00a0Journal of Chemical Theory and Computation<\/i>\u00a013 (6) : 3031 – 3048\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

\"Puzzle8MiaoOverlay\"Miao, Z., Adamiak, R. W., Antczak, M., Batey, R. T., Becka, A. J., Biesiada, M., Boniecki, M. J., Bujnicki, J. M., Chen, S.-J., Cheng, C. Y., Chou, F.-C., Ferr\u00e9-D’Amar\u00e9, A. R., Das, R., Dawson, W. K., Ding, F., Dokholyan, N. V., Dunin-Horkawicz, S., Geniesse, C., Kappel, K., Kladwang, W., Krokhotin, A., Lach, G. E., Major, F., Mann, T. H., Magnus, M., Pachulska-Wieczorek, K., Patel, D. J., Piccirilli, J. A., Popenda, M., Purzycka, K. J., Ren, A., Rice, G. M., Santalucia, J. Jr., Sarzynska, J., Szachniuk, M., Tandon, A., Trausch, J. J., Tian, S., Wang, J., Weeks, K. M., Williams, B. II, Xiao, Y., Xu, X., Zhang, D., Zok, T., and Westhof, E. (2017)
\n“RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme”<\/span><\/strong>
\nRNA<\/i>\u00a023 (5) : 655 – 672
\nPaper\u00a0<\/a>|\u00a0Link<\/a><\/strong><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Parks, J.W., Kappel, K., Das, R., and Stone, M.D. (2017) “Single-molecule FRET-Rosetta reveals RNA structural rearrangements during human telomerase catalysis<\/u>”\u00a0RNA<\/i>\u00a023 (2) : 175 – 188\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Tian, S., and Das, R. (2017) “Primerize-2D: automated primer design for RNA multidimensional chemical mapping<\/u>”\u00a0Bioinformatics<\/i>\u00a033 (9) : 1405 – 1406\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

2016<\/h2>

Yesselman, J.D., and Das, R. (2016) “Modeling small noncanonical RNA motifs with the Rosetta FARFAR server<\/u>”\u00a0Methods in Molecular Biology<\/i>\u00a01490 : 187 – 198\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

\"RECCES_preview\"Chou, F-C., Kladwang, W., Kappel, K., and Das, R. (2016)
\n“Blind tests of RNA nearest neighbor energy prediction”<\/span><\/strong>
\nProceedings of the National Academy of Sciences U.S.A.<\/i>\u00a0113 (30) : 8430 – 8435
\nPaper\u00a0<\/a>|\u00a0Link<\/a><\/strong><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Tian, S., and Das, R. (2016) “RNA structure through multidimensional chemical mapping<\/u>”\u00a0Quarterly Review of Biophysics<\/i>\u00a049 (e7) : 1 – 30\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

\"player_JMBdifficulty\"Anderson-Lee, J., Fisker, E., Kosaraju,V., Wu, M., Kong, J., Lee, J., Lee, M., Zada, M., Treuille, A., Das, R., and Eterna Players (2016)
\n“Principles for predicting RNA secondary structure design difficulty”<\/span><\/strong>
\nJournal of Molecular Biology<\/i>\u00a0428 (5) : 748 – 757
\nPaper\u00a0<\/a>|\u00a0Link<\/a><\/strong><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Chou, F.-C., Echols, N., Terwilliger, T.C., and Das, R. (2016) “RNA structure refinement using the ERRASER-Phenix pipeline<\/u>”\u00a0Methods in Molecular Biology<\/i>\u00a01320 : 269 – 282\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

2015<\/h2>

Cordero, P., and Das, R. (2015) “Rich RNA structure landscapes revealed by mutate-and-map analysis<\/u>”\u00a0PLOS Computational Biology<\/i>\u00a011 (11) : e1004473\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link\u00a0<\/a>|\u00a0Software<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

\"2015_Cheng_eLife\"Cheng, C.Y., Chou, F.-C., Kladwang, W., Tian, S., Cordero, P., and Das, R. (2015)
\n“Consistent global structures of complex RNA states through multidimensional chemical mapping.”<\/span><\/strong>
\neLife<\/i>\u00a04 : e07600
\nPaper\u00a0<\/a>|\u00a0Link<\/a>\u00a0|\u00a0Software<\/a><\/strong><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Tian, S., Yesselman, J.D., Cordero, P., and Das, R. (2015) “Primerize: Automated primer assembly for transcribing non-coding RNA domains.<\/u>”\u00a0Nucleic Acid Research<\/i>\u00a043 (W1) : W522 – W526\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link\u00a0<\/a>|\u00a0Server<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Yesselman, J.D., and Das, R. (2015) “RNA-Redesign: A web server for fixed-backbone 3D design of RNA.<\/u>”\u00a0Nucleic Acid Research<\/i>\u00a043 (W1) : W498 – W501\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link\u00a0<\/a>|\u00a0Server<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Lee, S., Kim, H., Tian, S., Lee, T., Yoon, S., and Das, R. (2015) “Automated band annotation for RNA structure probing experiments with numerous capillary electrophoresis profiles.<\/u>”\u00a0Bioinformatics<\/i>\u00a031 (17) : 2808 – 2815\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

\"RNAPuzzle_RoundII\"Miao, Z., Adamiak, R.W., Blanchet, M-F., Boniecki, M., Bujnicki, J.M., Chen, S-J., Cheng, C.Y., Chojnowski, G., Chou, F-C., Cordero, P., Cruz, J.A., Ferr\u00e9-D’Amar\u00e9, A, Das, R., Ding, F., Dokholyan, N.V., Dunin-Horkawicz, S., Kladwang, W., Krokhotin, A., Lach, G., Magnus, M., Major, F., Mann, T.H., Masquida, B., Matelska, D., Meyer, M., Peselis, A., Popenda, M., Purzycka, K.J., Serganov, A., Stasiewicz, J., Szachniuk, M., Tandon, A., Tian, S., Wang, J., Xiao, Y., Xu, X., Zhang, J, Zhao, P., Zok, T., and Westhof, E. (2015)
\n“RNA-Puzzles Round II: Assessment of RNA structure prediction programs applied to three large RNA structures.”<\/span><\/strong>
\nRNA<\/i>\u00a021 (6) : 1066 – 1084
\nPaper\u00a0<\/a>|\u00a0Link<\/a><\/strong><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Cheng, C.Y., Chou, F.-C., and Das, R. (2015) “Modeling complex RNA tertiary folds with Rosetta.<\/u>”\u00a0Methods in Enzymology<\/i>\u00a0553 : 35 – 64\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Xue, S., Tian, S., Fujii, K., Kladwang, W., Das, R., and Barna, M. (2015) “RNA regulons in Hox 5′ UTRs confer ribosome specificity to gene regulation<\/u>”\u00a0Nature<\/i>\u00a0517 (7532) : 33 – 38\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

2014<\/h2>

\"scientificTreuille, A., and Das, R. (2014)
\n“Scientific rigor through videogames.”<\/span><\/strong>
\nTrends in Biochemical Sciences<\/i>\u00a039 (11) : 507 – 509
\nPaper\u00a0<\/a>|\u00a0Link<\/a><\/strong><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Lipfert, J., Skinner, G.M., Keegstra, J.M., Hensgens, T., Jager, T., Dulin, D., K\u00f6ber, M., Yu, Z., Donkers, S.P., Das, R., and Dekker, N.H. (2014) “Double-stranded RNA under force and torque: Similarities to and striking differences from double-stranded DNA.<\/u>”\u00a0Proceedings of the National Academy of Sciences U.S.A.<\/i>\u00a0111 (43) : 15408 – 15413\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Chou, F.-C., Lipfert, J., and Das, R. (2014) “Blind predictions of DNA and RNA tweezers experiments with force and torque.<\/u>”\u00a0PLOS Computational Biology<\/i>\u00a010 (8) : e1003756\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link\u00a0<\/a>|\u00a0Software<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Lipfert, J., Doniach, S., Das, R., and Herschlag, D. (2014) “Understanding nucleic acid-ion interactions<\/u>”\u00a0Annual Review of Biochemistry<\/i>\u00a083 : 813 – 841\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Cordero, P., Kladwang, W., VanLang, C.C., and Das, R. (2014) “The mutate-and-map protocol for inferring base pairs in structured RNA<\/u>”\u00a0Methods in Molecular Biology<\/i>\u00a01086 : 53 – 77\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Seetin, M.G., Kladwang, W., Bida, J.P., and Das, R. (2014) “Massively parallel RNA chemical mapping with a reduced bias MAP-Seq protocol<\/u>”\u00a0Methods in Molecular Biology<\/i>\u00a01086 : 95 – 117\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

\"2014_Tian_RNA\"Tian, S., Cordero, P., Kladwang, W., and Das, R. (2014)
\n“High-throughput mutate-map-rescue evaluates SHAPE-directed RNA structure and uncovers excited states”<\/span><\/strong>
\nRNA<\/i>\u00a020 (11) : 1815 – 1826
\nPaper\u00a0<\/a>|\u00a0Link<\/a><\/strong><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Kladwang, W., Mann, T.H., Becka, A., Tian, S., Kim, H., Yoon, S., and Das, R. (2014) “Standardization of RNA chemical mapping experiments<\/u>”\u00a0Biochemistry<\/i>\u00a053 (19) : 3063 – 3065\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Beauchamp, K., Pande, V., and Das, R. (2014) “Bayesian energy landscape tilting: towards concordant models of molecular ensembles<\/u>”\u00a0Biophysics Journal<\/i>\u00a0106 (6) : 1381 – 1390\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

\"2014_Sripakdeevong_NatMeth\"Sripakdeevong, P., Cevec, M., Chang, A.T., Erat, M.C., Ziegeler, M., Zhao, Q., Fox, G.E., Gao, X., Kennedy, S.D., Kierzek, R., Nikonowicz, E.P., Schwalbe, H., Sigel, R.K.O., Turner, D.H., and Das, R. (2014)
\n“Consistent structure determination of noncanonical RNA motifs from 1H NMR chemical shift data”<\/span><\/strong>
\nNature Methods<\/i>\u00a011 : 413 – 416
\nPaper\u00a0<\/a>|\u00a0Link<\/a>\u00a0|\u00a0Server<\/a><\/strong><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Kryshtafovych, A., Moult, J., Bales, P., Bazan, J.F., Burgin, A., Chen, C., Cochran, F.V., Craig, T.K., Das, R., Fass, D., Garcia-Doval, C., Herzberg, O., Lorimer, D., Luecke, H., Ma, X., Nelson, D., van Raaij, M.J., Rohwer, F., Segall, A., Seguritan, V., Zeth, K., and Schwede, T. (2014) “Challenging the state-of-the-art in protein structure prediction: Highlights of experimental target structures for the 10th critical assessment of techniques for protein structure prediction experiment CASP10<\/u>”\u00a0Proteins<\/i>\u00a082 (S2) : 26 – 42\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

\"2014_Lee_PNAS\"Lee, J., Kladwang, W., Lee, M., Cantu, D., Azizyan, M., Kim, H., Limpaecher, A., Yoon, S., Treuille, A., Das, R., and EteRNA Participants (2014)
\n“RNA design rules from a massive open laboratory”<\/span><\/strong>
\nProceedings of the National Academy of Sciences U.S.A.<\/i>\u00a0111 (6) : 2122 – 2127
\nPaper\u00a0<\/a>|\u00a0Link<\/a>\u00a0|\u00a0SHAPE Data Files<\/a>\u00a0|\u00a0EternaBot Software<\/a><\/strong><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

2013<\/h2>

\"2013_Chou_NatMeth\"Chou, F.-C., Sripakdeevong, P., Dibrov, S.M, Hermann, T., and Das, R. (2013)
\n“Correcting pervasive errors in RNA crystallography through enumerative structure prediction”<\/span><\/strong>
\nNature Methods<\/i>\u00a010 : 74 – 76
\nPaper\u00a0<\/a>|\u00a0Link<\/a>\u00a0|\u00a0ERRASER Server<\/a><\/strong><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

\"2013_Das_PLOSOne\"Das, R. (2013)
\n“Atomic-accuracy prediction of protein loop structures enabled by an RNA-inspired ansatz”<\/span><\/strong>
\nPLOS One<\/i>\u00a08 (10) : e74830
\nPaper\u00a0<\/a>|\u00a0Link<\/a><\/strong><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Drew, K., Renfrew, P.D., Craven, T., Butterfoss, G.L., Chou, F.-C., Lyskov, S., Bullock, B.N., Watkins, A., Leaver-Fay, A., Kuhlman, B., Gray, J.J., Bradley, P., Kirshenbaum, K., Arora, P.S., Das, R., and Bonneau, R. (2013) “Adding diverse noncanonical backbones to Rosetta: enabling peptidomimetic and foldamer design<\/u>”\u00a0PLOS One<\/i>\u00a08 (7) : e67051\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Kim, H., Cordero, P., Das, R., and Yoon, S. (2013) “HiTRACE-Web: an online tool for robust analysis of high-throughput capillary electrophoresis<\/u>”\u00a0Nucleic Acid Research<\/i>\u00a041 (W1) : W492 – W498\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link\u00a0<\/a>|\u00a0Server<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Lyskov, S., Chou, F.-C., \u00d3 Conch\u00fair, S., Der, B.S., Drew, K., Kuroda, D., Xu, J., Weitzner, B.D., Renfrew, P.D., Sripakdeevong, P., Borgo, B., Havranek, J.J., Kuhlman, B., Kortemme, T., Bonneau, R., Gray, J.J., and Das, R. (2013) “Serverification of molecular modeling applications: the Rosetta online server that includes everyone (ROSIE)<\/u>”\u00a0PLOS One<\/i>\u00a08 (5) : e63906\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link\u00a0<\/a>|\u00a0Server<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Adams, P.D., Baker, D., Brunger, A.T., Das, R., DiMaio, F., Read, R.J., Richardson, D.C., Richardson, J.S., and Terwilliger, T.C. (2013) “Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems<\/u>”\u00a0Annual Review of Biophysics<\/i>\u00a042 : 265 – 287\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Molski, M.A., Goodman, J.L, Chou, F-C., Baker, D., Das, R., and Schepartz, A. (2013) “Remodeling a beta-peptide bundle<\/u>”\u00a0Chemical Science<\/i>\u00a04 : 319 – 324\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link\u00a0<\/a>|\u00a0Design Server<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

2012<\/h2>

Cordero, P., Lucks, J., and Das, R. (2012) “An RNA Mapping Database for curating RNA structure mapping experiments<\/u>”\u00a0Bioinformatics<\/i>\u00a028 (22) : 3006 – 3008\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link\u00a0<\/a>|\u00a0Database<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Cordero, P., Kladwang, W., VanLang, C.C., and Das, R. (2012) “Quantitative dimethyl sulfate (DMS) mapping for automated RNA secondary structure inference<\/u>”\u00a0Biochemistry<\/i>\u00a051 (36) : 7037 – 7039\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Kladwang, W., Hum, J., and Das, R. (2012) “Ultraviolet shadowing of RNA can cause significant chemical damage in seconds<\/u>”\u00a0Scientific Reports<\/i>\u00a02 : 517\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

\"2012_Bida_CurrOpinStructBiol\"Bida, J.P., and Das, R. (2012)
\n“Squaring theory with practice in RNA design”<\/span><\/strong>
\nCurrent Opinion in Structural Biology<\/i>\u00a022 (4) : 457 – 466
\nPaper\u00a0<\/a>|\u00a0Link<\/a><\/strong><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Sripakdeevong, P., Beauchamp, K., and Das, R. (2012) “2012_Sripakdeevong_NAMB”\u00a0in RNA 3D Structure Analysis and Prediction, eds. Leontis, N. and Westhof, E., Nucleic Acids and Molecular Biology<\/i>\u00a027 : 43 – 65\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Beauchamp, K., Lin, Y-S., Das, R., and Pande. V.S. (2012) “Are protein force fields getting better? A systematic benchmark on 524 diverse NMR measurements<\/u>”\u00a0Journal of Chemical Theory and Computation<\/i>\u00a08 (4) : 1409 – 1414\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Frederiksen, J.K., Li, N.S., Das, R., Herschlag, D., and Piccirilli, J.A. (2012) “Metal-ion rescue revisited: Biochemical detection of site-bound metal ions important for RNA folding<\/u>”\u00a0RNA<\/i>\u00a018 (6) : 1123 – 1141\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

\"Puzzle1Overlay\"Cruz, J.A., Blanchet, M., Boniecki, M., Bujnicki, J., Chen, S-J., Cao, S., Das, R., Ding, F., Dokholyan, N.V., Flores, S.C., Huang, L., Lavender, C.A., Lisi, V., Major, F., Mikolajczak, K., Patel, D.J., Philips, A., Puton, T., Santalucia, J., Sijenyi, F., Hermann, T., Rother, K., Rother, M., Serganov, A., Skorupski, M., Soltysinski, T., Sripakdeevong, P., Tuszynska, I., Weeks, K.M., Waldsich, C., Wildauer, M., Leontis, N.B., and Westhof, E. (2012)
\n“RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction”<\/span><\/strong>
\nRNA<\/i>\u00a018 (4) : 610 – 625
\nPaper\u00a0<\/a>|\u00a0Link<\/a><\/strong><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Kladwang, W., Chou, F.-C., and Das, R. (2012) “Automated RNA structure prediction uncovers a kink-turn linker in double glycine riboswitches<\/u>”\u00a0Journal of the American Chemical Society<\/i>\u00a0134 (3) : 1404 – 1407\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link\u00a0<\/a>|\u00a0Models<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

\"\"Sripakdeevong, P., Kladwang, W., and Das, R. (2012)
\n“An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling”<\/span><\/strong>
\nProceedings of the National Academy of Sciences U.S.A.<\/i>\u00a0108 (51) : 20573 – 20578
\nPaper\u00a0<\/a>|\u00a0Link<\/a><\/strong><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

2011<\/h2>

Kladwang, W., VanLang, C.C., Cordero P., and Das, R. (2011) “Understanding the errors of SHAPE-directed RNA structure modeling<\/u>”\u00a0Biochemistry<\/i>\u00a050 (37) : 8049 – 8056\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

\"MutateMap_ncRNA_KladwangVanLangCorderoDas_TOC_figure_whitebkgd\"Kladwang, W., VanLang, C.C., Cordero P., and Das, R. (2011)
\n“A two-dimensional mutate-and-map strategy for non-coding RNA structure”<\/span><\/strong>
\nNature Chemistry<\/i>\u00a03 : 954 – 962
\nPaper\u00a0<\/a>|\u00a0Link<\/a><\/strong><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Beauchamp, K.A., Ensign, D.L., Das, R., and Pande, V.S. (2011) “Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments<\/u>”\u00a0Proceedings of the National Academy of Sciences U.S.A.<\/i>\u00a0108 (31) : 12734 – 12739\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Das, R. (2011) “Four small puzzles that Rosetta doesn’t solve<\/u>”\u00a0PLOS One<\/i>\u00a06 (5) : e20044\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Yoon, S., Kim, J., Hum, J., Kim, H., Park, S., Kladwang, W., and Das, R. (2011) “HiTRACE: High-throughput robust analysis for capillary electrophoresis<\/u>”\u00a0Bioinformatics<\/i>\u00a027 (13) : 1798 – 1805\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link\u00a0<\/a>|\u00a0Software<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Rocca-Serra, P., Bellaousov, S., Birmingham, A., Chen, C., Cordero, P., Das, R., Davis-Neulander, L., Duncan, C.D., Halvorsen, M., Knight, R., Leontis, N.B., Mathews, D.H., Ritz, J., Stombaugh, J., Weeks, K.M., Zirbel, C.L., and Laederach, A. (2011) “Sharing and archiving nucleic acid structure mapping data<\/u>”\u00a0RNA<\/i>\u00a017 (7) : 1204 – 1212\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Kladwang, W., Cordero P., and Das, R. (2011) “A mutate-and-map strategy accurately infers the base pairs of a 35-nucleotide model RNA<\/u>”\u00a0RNA<\/i>\u00a017 (3) : 522 – 534\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Leaver-Fay, A., Tyka, M., Lewis, S.M., Lange, O.F., Thompson, J. Jacak, R., Kaufmann, K.W., Renfrew, P.D., Smith, C.A., Sheffler, W., Davis, I.W., Cooper, S., Treuille, A., Mandell, D.J., Richter, F., Ban, YE., Fleishman, S.J., Corn, J.E., Kim, D.E., Lyskov, S., Berrondo, M., Mentzer, S., Popovic, Z., Havranek, J.J., Karanicolas, J., Das, R., Meiler, J., Kortemme, T., Gray, J.J., Kuhlman, B., Baker, D., and Bradley, P. (2011) “ROSETTA3: An object-oriented software suite for the simulation and design of macromolecules<\/u>”\u00a0Methods in Enzymology<\/i>\u00a0487 : 545 – 574\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

2010<\/h2>

\"2010_Kladwang_Biochem\"Kladwang, W., and Das, R. (2010)
\n“A mutate-and-map strategy for inferring base pairs in structured nucleic acids: proof of concept on a DNA\/RNA helix”<\/strong>
\nBiochemistry<\/em> 49 (35) : 7414 – 7416
\nPaper<\/a> | Link<\/a><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Fleishman S.J., Corn J.E., Strauch E.M., Whitehead T.A., Andre I., Thompson J., Havranek J.J., Das, R., Bradley P., and Baker D. (2010) “Rosetta in CAPRI rounds 13-19<\/u>”\u00a0Proteins<\/i>\u00a078 (15) : 3212 – 3218\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Das, R., Karanicolas, J., and Baker., D. (2010) “Atomic accuracy in predicting and designing noncanonical RNA structure<\/u>”\u00a0Nature Methods<\/i>\u00a07 : 291 – 294\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link\u00a0<\/a>|\u00a0Server<\/a>\u00a0|\u00a0Models<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

2009<\/h2>

Das, R., Andre, I., Shen, Y., Wu, Y., Lemak, A., Bansal, S., Arrowsmith, C.H., Szyperski, T., and Baker, D. (2009) “Simultaneous prediction of protein folding and docking at high resolution<\/u>”\u00a0Proceedings of the National Academy of Sciences U.S.A.<\/i>\u00a0106 (45) : 18978 – 18983\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Raman, S., Vernon, R., Thompson, J., Tyka, M., Sadreyev, R., Pei, J., Kim, D., Kellogg, E., DiMaio, F., Lange, O., Kinch, L., Sheffler, W., Kim, B.H., Das, R., Grishin, N.V., and Baker, D. (2009) “Structure prediction for CASP8 with all-atom refinement using Rosetta.<\/u>”\u00a0Proteins<\/i>\u00a077 (S9) : 88 – 99\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Kim, J., Yu, S., Shim, B., Kim, H., Min, H., Chung, E-Y., Das, R., and Yoon S. (2009) “A robust peak detection method for RNA structure inference by high-throughput contact mapping<\/u>”\u00a0Bioinformatics<\/i>\u00a025 (9) : 1137 – 1144\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Schwede T., Sali, A., Honig, B., Levitt, M., Berman, H.M., Jones, D., Brenner, S.E., Burley, S.K., Das, R., Dokholyan, N.V., Dunbrack, R.L., Fidelis, K., Fiser, A., Godzik, A., Huang, Y.J., Humblet, C., Jacobson, M.P., Joachimiak, A., Krystek, S.R., Kortemme, T., Kryshtafovych, A., Montelione, G.T., Moult, J., Murray, D., Sanchez, R., Sosnick, T.R., Standley, D.M., Stouch, T., Vajda, S., Vasquez, M., Westbrook, J.D., and Wilson, I.A. (2009) “Outcome of a workshop on applications of protein models in biomedical research<\/u>”\u00a0Structure<\/i>\u00a017 (2) : 151 – 159\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Das, R., and Baker, D. (2009) “Prospects for de novo phasing with protein de novo models<\/u>”\u00a0Acta Crystallographica Section D<\/i>\u00a065 (5) : 169 – 175\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Jonikas, M.A., Radmer, R.J., Laederach, A., Das, R., Pearlman, S., Herschlag D., and Altman, R.B. (2009) “Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters<\/u>”\u00a0RNA<\/i>\u00a015 (2) : 189 – 199\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

2008<\/h2>

Fenn, R.M., Das, R., and Harbury, P.B. (2008) “Remeasuring the double helix<\/u>”\u00a0Science<\/i>\u00a0322 (5900) : 446 – 449\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Fenn, R.M., Das, R., Silverman, J.A., Fenn, T.D., Walker, P., and Harbury, P.B. (2008) “An X-ray molecular ruler for measuring quantitative distance distributions in solution<\/u>”\u00a0PLOS One<\/i>\u00a03 (10) : e3229\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Laederach, A., Das, R., Vicens, Q., Pearlman, S., Brenowitz, M., Herschlag, D., and Altman, R.B. (2008) “Semi-automated and rapid quantification of nucleic acid footprinting and structure mapping experiments<\/u>”\u00a0Nature Protocols<\/i>\u00a03 : 1395 – 1401\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

<\/div><\/div><\/div>\n

Das, R., and Baker, D. (2008) “Macromolecular modeling with Rosetta<\/u>”\u00a0Annual Review of Biochemistry<\/i>\u00a077 : 363 – 382\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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Das, R., Kudaravalli, M., Jonikas, M., Laederach, A., Fong, R., Schwans, J.P., Baker, D., Piccirilli, J.A., Altman, R.B., and Herschlag, D. (2008) “Structural inference of native and partially folded RNA by high throughput contact mapping<\/u>”\u00a0Proceedings of the National Academy of Sciences U.S.A.<\/i>\u00a0105 (11) : 4144 – 4149\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link\u00a0<\/a>|\u00a0Scripts<\/a><\/span><\/p>\n<\/div>

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2007<\/h2>

Qian, B., Raman, V.S., Das, R., Bradley, P., McCoy, A.J., Read, R.J., and Baker, D. (2007) “High resolution structure prediction and the crystallographic phase problem<\/u>”\u00a0Nature<\/i>\u00a0450 : 259 – 264\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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Das, R., Qian, B., Raman, V.S., Vernon, R., Thompson, J., Bradley, P., Khare, S., Tyka, M., Bhat, D., Chivian, D.C., Kim, D.E., Sheffler, W., Malmstrom, L., Wollacott, A., Wang, C., Andre, I., and Baker, D. (2007) “Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home<\/u>”\u00a0Proteins<\/i>\u00a069 (S8) : 118 – 128\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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Das, R., and Baker, D. (2007) “Automated de novo prediction of native-like RNA tertiary structures<\/u>”\u00a0Proceedings of the National Academy of Sciences U.S.A.<\/i>\u00a0104 (37) : 14664 – 14669\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link\u00a0<\/a>|\u00a0Models<\/a><\/span><\/p>\n<\/div>

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Blum, B., Jordan, M.I., Kim, D., Das, R., Bradley, P., and Baker, D. (2007) “Feature selection methods for improving protein structure prediction with Rosetta<\/u>”\u00a0in Advances in Neural Information Processing Systems (NIPS) 21, eds. Platt, J., Koller, D., Singer, Y., and McCallum, A., MIT Press.<\/i>\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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Lipfert, J., Das, R., Chu, V.B., Kudaravalli, M., Boyd, N., Herschlag, D. and Doniach, S. (2007) “Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae<\/u>”\u00a0Journal of Molecular Biology<\/i>\u00a0365 (2) : 1393 – 1406\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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2006<\/h2>

Russell, R., Das, R., Suh, H., Travers, K., Laederach, A., Engelhardt, M., and Herschlag, D. (2006) “The paradoxical behavior of a highly structured misfolded intermediate in RNA folding<\/u>”\u00a0Journal of Molecular Biology<\/i>\u00a0363 (2) : 531 – 544\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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Das, R., and Doniach, S. (2006) “Structural studies of proteins and nucleic acids in solution using small angle x-ray scattering (SAXS).<\/u>”\u00a0in Soft Matter: Scattering, Imaging and Manipulation, eds. Pecora, R. and Borsali, R., Kluwer Press<\/i>\u00a0: 1083 – 1108\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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2005<\/h2>

Das, R., Travers, K.J., Bai, Y., and Herschlag, D. (2005) “Determining the Mg2+ stoichiometry for folding an RNA’s metal ion core<\/u>”\u00a0Journal of the American Chemical Society<\/i>\u00a0127 (23) : 8272 – 8273\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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Bai, Y., Das, R., Millett, I.S., Herschlag, D., and Doniach, S. (2005) “2005_Bai_PNAS.<\/u>”\u00a0Proceedings of the National Academy of Sciences U.S.A.<\/i>\u00a0102 (4) : 959 – 960\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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Das, R., Laederach, A., Pearlman, S.M., Herschlag, D., and Altman, R.B. (2005) “SAFA: Semi-Automated Footprinting Analysis software for high-throughput quantification of nucleic acid footprinting experiments.<\/u>”\u00a0RNA<\/i>\u00a011 (3) : 344 – 354\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link\u00a0<\/a>|\u00a0Software<\/a><\/span><\/p>\n<\/div>

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2004<\/h2>

Andresen, K., Das, R., Park, H.Y., Smith, H., Kwok, L.W., Lamb, J.S., Kirkland, E.J., Herschlag, D., Finkelstein, K.D., and Pollack, L. (2004) “Spatial distribution of competing ions around DNA in solution.<\/u>”\u00a0Physical Review Letters<\/i>\u00a093 (24) : 32767\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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Naumov, D. Chukanov, A., Naumova, E., Popv, B., Astier, et al. [NOMAD collaboration] (2004) “A study of strange particles produced in neutrino neutral current interactions in the NOMAD experiment<\/u>”\u00a0Nuclear Physics B<\/i>\u00a0700 (1) : 51 – 68\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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Takamoto, K., Das, R., He, Q., Doniach, S., Brenowitz, M., Herschlag, D., and Chance, M. (2004) “Principles of RNA compaction: insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations.<\/u>”\u00a0Journal of Molecular Biology<\/i>\u00a0343 (5) : 1195 – 1206\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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2003<\/h2>

Das, R., Kwok, L.W., Millet, I.S., Bai, Y., Mills, T.T., Jacob, J., Maskel, G.S., Seifert, S., Simon, M.G.J., Thiyagarajan, P., Doniach, S., Pollack, L., and Herschlag, D. (2003) “The fastest global events in RNA folding: electrostatic relaxation and tertiary collapse of the Tetrahymena ribozyme.<\/u>”\u00a0Journal of Molecular Biology<\/i>\u00a0332 (2) : 311 – 319\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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Das, R., Mills, T.T., Kwok, L.W., Maskel, G.S., Millett, I.S., Doniach, S., Finkelstein, K.D., Herschlag, D., and Pollack, L. (2003) “The counterion distribution around DNA probed by solution x-ray scattering.<\/u>”\u00a0Physical Review Letters<\/i>\u00a090 (18) : 32767\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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Bartley, L., Zhuang, X., Das, R., Chu, S., and Herschlag, D. (2003) “Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA.<\/u>”\u00a0Journal of Molecular Biology<\/i>\u00a0328 (5) : 1011 – 1026\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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Saunders, R., Kneissl, R., Grainge, K., Grainger, W.F., Jones, M.E., Maggi, A., Das, R., Edge, A.C., Lasenby, A.N., Pooley, G.G., Shigeru, J.M., Tsuruta, T., Yamashita, K., Tawara, Y., Furuzawa, A., Harada, A., and Hatsukade, I. (2003) “A measurement of H0 from Ryle Telescope, ASCA and ROSAT observations of Abell 773.<\/u>”\u00a0Monthly Notices of the Royal Astronomical Society<\/i>\u00a0341 (3) : 937 – 940\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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2002<\/h2>

Grainger, W.F., Das, R., Grainge, K., Jones, M. E., Kneissl, R., Pooley, G.G., and Saunders, R.D.E. (2002) “A maximum-likelihood approach to removing radio sources from observations of the Sunyaev-Zel’dovich effect, with application to Abell 611.<\/u>”\u00a0Monthly Notices of the Royal Astronomical Society<\/i>\u00a0337 (4) : 1207 – 1214\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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Cotter, G., Buttery, H.J., Das, R., Jones, M.E., Grainge, K., Pooley, G.G, and Saunders, R. (2002) “Observations of the Sunyaev-Zel’dovich effect in the z = 0.78 cluster MS 1137.5+6625.<\/u>”\u00a0Monthly Notices of the Royal Astronomical Society<\/i>\u00a0334 (2) : 323 – 326\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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Cotter G., Buttery, H.J., Rawlings, S., Croft, S., Hill, G.J., Gay, P., Das, R., Drory, N., Grainge, K., Grainger, W.F., Jones, M.E., Pooley, G.G., and Saunders, R. (2002) “Detection of a cosmic microwave background decrement towards a cluster of mJy radio sources.<\/u>”\u00a0Monthly Notices of the Royal Astronomical Society<\/i>\u00a0331 (1) : 1 – 6\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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2001<\/h2>

Alba, M.M., Das, R., Orengo, C.A., and Kellam, P. (2001) “Genomewide function conservation and phylogeny in the Herpesviridae.<\/u>”\u00a0Genomic Research<\/i>\u00a011 : 43 – 54\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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2000<\/h2>

Das, R. (2000) “Theoretical Basis of Likelihood Methods in Molecular Phylogenetic Inference<\/u>”\u00a0M. Res. Thesis, Dept. of Biology, University College London. Supervisors: Z. Yang & J. Mallet.\u00a0<\/i>|\u00a0Paper<\/a><\/span><\/p>\n<\/div>

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1999<\/h2>

Das, R. (1999) “Analysis of Sunyaev-Zel’dovich Decrements<\/u>”\u00a0M. Phil. Thesis, Dept. of Physics, Cambridge University. Supervisor: R. Saunders.<\/i>\u00a0|\u00a0Paper<\/a><\/span><\/p>\n<\/div>

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1996<\/h2>

Milton, K., and Das, R. (1996) “Finite-element lattice Hamiltonian matrix elements: Anharmonic oscillators<\/u>”\u00a0Letters in Mathematical Physics<\/i>\u00a036 (2) : 177 – 187\u00a0|\u00a0Paper<\/a>\u00a0|\u00a0Link<\/a><\/span><\/p>\n<\/div>

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