Rangan, R., Huang, R. , Hunter O., Pham P., Ares, Jr., M., Das, R. (2024) “RNA structure landscape of S. cerevisiae introns” bioRxiv | Paper | Preprint

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” bioRxiv | Paper | Preprint

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” Nucleic Acids Research 2024 : 1 – 16 | Paper | Link

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” Proteins: Structure, Function, and Bioinformatics 91 (12) : 1935 – 1951 | Paper | Link

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” Proteins: Structure, Function, and Bioinformatics 91 (12) : 1600 – 1615 | Paper | Link

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” Proteins: Structure, Function, and Bioinformatics 91 (12) : 1550 – 1557 | Paper | Link

Krüger, 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” Nature Communications 14 : 961 | Paper | Link

Watkins, A.M. and Das, R. (2023) “RNA 3D Modeling with FARFAR2, Online” Methods Mol Biol 2586 : 233 – 249 | Paper | Link

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” Methods Mol Biol. 2568 : 193 – 211 | Paper | Link

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” Nucleic Acids Research 50(22):13143-13154 | Paper | Link

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” Proceedings of the National Academy of Sciences 119 (37) : e2209146119 | Paper | Link

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” Nature Medicine 28 (9) : 1944 – 1955 | Paper | Link

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” Nature Chemical Biology 18 (9) : 990 – 998 | Paper | Link

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” PNAS 119 (18) : e2112979119 | Paper | Link

Das, R., Russell, R. (2021) “How to Kinetically Dissect an RNA Machine” Biochemistry 60 (46) : 3485 – 3490 | Paper | Link

Das, R., Watkins, A.W. (2021) “RiboDraw: semiautomated two-dimensional drawing of RNA tertiary structure diagrams” NAR Genomics and Bioinformatics 3 (4) | Paper | Link

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” arXiv

Koodli, R.V., Rudolfs, B., Wayment-Steele, H.K., Eterna Structure Designers, Das, R. (2021) “Redesigning the Eterna100 for the Vienna 2 folding engine” bioRxiv | Paper | Preprint

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” Science 373 (6558) : 1047 – 1051 | Paper | Link

Das R. (2021) “RNA structure: a renaissance begins?” Nature Methods 18 : 439 | Paper | Link

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’ untranslated regions” Nature Genetics 53 : 729 – 741 | Paper | Link

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” Nature Communications 12 (2165) | Paper | Link

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” Nature 593 : 449 – 453 | Paper | Link

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” The Biophysicist 2 (1) : 108 – 122 | Paper | Link

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” Nucleic Acids Research 49 (6) : 3092 – 3108 | Paper | Link | Data (Model collection, SARS-CoV-2 structures) | Data (Model collection, positive control structures)

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., Malmström, L., Marcos, E., Marcu, O., Marze, N.A., Meiler, J., Moretti, R., Mulligan, V.K., Nerli, S., Norn, C., Ó’Conchúir, 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.” Nature Methods 17 (7) : 665 – 680

Palka, C., Forino, N.M., Henstchel, J., Das, R., Stone, M.D. (2020) “Folding heterogeneity in the essential human telomerase RNA three-way junction” RNA 26 : 1787 – 1800 | Paper | Link

Watkins, A.M., Rangan, R., Das, R. (2020) “FARFAR2: Improved de novo Rosetta prediction of complex global RNA folds” Structure 28 (8) : 963 – 976 | Paper | Link | Server | Benchmarking scripts

ain, N., Blauch, L. R., Szymanski, M. R., Das, R., Tang, S. K. Y., Yin, Y. W., Fire, A. Z. (2020) “Transcription polymerase–catalyzed emergence of novel RNA replicons” Science 368 : eaay0688 | Paper | Link

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” RNA 26 : 982 – 995 | Paper | Link

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” Biochemistry 59 (23) : 2154 – 2170 | Paper | Link

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” RNA 26 : 937 – 959 | Paper | Link | Code

Magnus, M., Kappel, K., Das, R., Bujnicki, J.M. (2019) “RNA 3D structure prediction guided by independent folding of homologous sequences” BMC Bioinformatics 20 : article 512 | Paper | Link

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” Nature 573 : 375 – 380 | Paper | Link

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” Nature Communications 10 : 3629 | Paper | Link

Das, R., Keep, B., Washington, P, Riedel-Kruse, I. H. (2019) “Scientific discovery games for biomedical research” Annual Review of Biomedical Data Science 2 : 253 – 279 | Paper | Link

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” Proceedings of the National Academy of Sciences 116 (34) : 16847 – 16855 | Paper | Link

Wu, M.J., Andreasson, J., Kladwang, W., Greenleaf, W.J., and Das, R. (2019) “Automated design of diverse stand-alone riboswitches” ACS Synthetic Biology 8 : 1838 – 1846 | Paper | Link

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” PLOS Computational Biology 15 (6) : e1007059 | Paper | Link | EternaBrain software

Wayment-Steele, H., Wu, M., Gotrik, M., and Das, R. (2019) “Evaluating riboswitch optimality” Methods in Enzymology 623 : 417 – 450 | Paper | Link

Watkins, A. M., Rangan, R., and Das, R. (2019) “Using Rosetta for RNA homology modeling” Methods in Enzymology 623 : 177 – 207 | Paper | Link

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” Molecular Cell 74 : 966 – 981 | Paper | Link

Huang, L., Wang, J., Watkins, A. M., Das, R., and Lilley, D. M. J. (2019) “Structure and ligand binding of the glutamine-II riboswitch” Nucleic Acids Research 47 (7666) : 7666 – 7675 | Paper | Link

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” PNAS 116 : 7889 – 7898 | Paper | Link

Kappel K. and Das R. (2019) “Sampling native-like structures of RNA-protein complexes through Rosetta folding and docking” Structure 27 (1) : 140 – 151 | Paper | Link | Rosetta RNP modeling software

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” BioRxiv

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” Nature Communications 9 (1) | Paper | Link

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” Cell 174 (2) : 377 – 390 | Paper | Link

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)” Curr Protoc Nucleic Acid Chem 73 : e54 | Paper | Link

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” Cell 174 (1) : 218-230 | Paper | Link

Shi, J., Eterna players, Das, R., and Pande, V.S. (2018) “SentRNA: Improving computational RNA design by incorporating a prior of human design strategies” BioRxiv | Preprint | SentRNA Software

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” BioRxiv | Preprint

Das, R. (2018) “LIkelihood-based Fits of Folding Transitions (LIFFT) for Biomolecule Mapping Data” BioRxiv | Preprint | LIFFT Software

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” Cell Reports 22 : 3240 – 3250 | Link

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” Nature Nanotechnology 13 : 34 – 40 | Paper | Link

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)” Protein Science 27 (1) : 259 – 268 | Paper | Link | ROSIE Servers

Leppek, K., Das, R., and Barna, M. (2017) “Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them” Nature Reviews Molecular Cell Biology 19 : 158 – 174 | Paper | Link

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” Nucleic Acids Research 46 (D1) : D375 – D379 | Paper | Link

Alford, R.F., Leaver-Fay, A., Jeliazkov, J.R., O’Meara, 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” Journal of Chemical Theory and Computation 13 (6) : 3031 – 3048 | Paper | Link

Parks, J.W., Kappel, K., Das, R., and Stone, M.D. (2017) “Single-molecule FRET-Rosetta reveals RNA structural rearrangements during human telomerase catalysis” RNA 23 (2) : 175 – 188 | Paper | Link

Tian, S., and Das, R. (2017) “Primerize-2D: automated primer design for RNA multidimensional chemical mapping” Bioinformatics 33 (9) : 1405 – 1406 | Paper | Link

Yesselman, J.D., and Das, R. (2016) “Modeling small noncanonical RNA motifs with the Rosetta FARFAR server” Methods in Molecular Biology 1490 : 187 – 198 | Paper | Link

Tian, S., and Das, R. (2016) “RNA structure through multidimensional chemical mapping” Quarterly Review of Biophysics 49 (e7) : 1 – 30 | Paper | Link

Chou, F.-C., Echols, N., Terwilliger, T.C., and Das, R. (2016) “RNA structure refinement using the ERRASER-Phenix pipeline” Methods in Molecular Biology 1320 : 269 – 282 | Paper | Link

Cordero, P., and Das, R. (2015) “Rich RNA structure landscapes revealed by mutate-and-map analysis” PLOS Computational Biology 11 (11) : e1004473 | Paper | Link | Software

Tian, S., Yesselman, J.D., Cordero, P., and Das, R. (2015) “Primerize: Automated primer assembly for transcribing non-coding RNA domains.” Nucleic Acid Research 43 (W1) : W522 – W526 | Paper | Link | Server

Yesselman, J.D., and Das, R. (2015) “RNA-Redesign: A web server for fixed-backbone 3D design of RNA.” Nucleic Acid Research 43 (W1) : W498 – W501 | Paper | Link | Server

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.” Bioinformatics 31 (17) : 2808 – 2815 | Paper | Link

Cheng, C.Y., Chou, F.-C., and Das, R. (2015) “Modeling complex RNA tertiary folds with Rosetta.” Methods in Enzymology 553 : 35 – 64 | Paper | Link

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” Nature 517 (7532) : 33 – 38 | Paper | Link

Lipfert, J., Skinner, G.M., Keegstra, J.M., Hensgens, T., Jager, T., Dulin, D., Köber, 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.” Proceedings of the National Academy of Sciences U.S.A. 111 (43) : 15408 – 15413 | Paper | Link

Chou, F.-C., Lipfert, J., and Das, R. (2014) “Blind predictions of DNA and RNA tweezers experiments with force and torque.” PLOS Computational Biology 10 (8) : e1003756 | Paper | Link | Software

Lipfert, J., Doniach, S., Das, R., and Herschlag, D. (2014) “Understanding nucleic acid-ion interactions” Annual Review of Biochemistry 83 : 813 – 841 | Paper | Link

Cordero, P., Kladwang, W., VanLang, C.C., and Das, R. (2014) “The mutate-and-map protocol for inferring base pairs in structured RNA” Methods in Molecular Biology 1086 : 53 – 77 | Paper | Link

Seetin, M.G., Kladwang, W., Bida, J.P., and Das, R. (2014) “Massively parallel RNA chemical mapping with a reduced bias MAP-Seq protocol” Methods in Molecular Biology 1086 : 95 – 117 | Paper | Link

Kladwang, W., Mann, T.H., Becka, A., Tian, S., Kim, H., Yoon, S., and Das, R. (2014) “Standardization of RNA chemical mapping experiments” Biochemistry 53 (19) : 3063 – 3065 | Paper | Link

Beauchamp, K., Pande, V., and Das, R. (2014) “Bayesian energy landscape tilting: towards concordant models of molecular ensembles” Biophysics Journal 106 (6) : 1381 – 1390 | Paper | Link

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” Proteins 82 (S2) : 26 – 42 | Paper | Link

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” PLOS One 8 (7) : e67051 | Paper | Link

Kim, H., Cordero, P., Das, R., and Yoon, S. (2013) “HiTRACE-Web: an online tool for robust analysis of high-throughput capillary electrophoresis” Nucleic Acid Research 41 (W1) : W492 – W498 | Paper | Link | Server

Lyskov, S., Chou, F.-C., Ó Conchúir, 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)” PLOS One 8 (5) : e63906 | Paper | Link | Server

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” Annual Review of Biophysics 42 : 265 – 287 | Paper | Link

Molski, M.A., Goodman, J.L, Chou, F-C., Baker, D., Das, R., and Schepartz, A. (2013) “Remodeling a beta-peptide bundle” Chemical Science 4 : 319 – 324 | Paper | Link | Design Server

Cordero, P., Lucks, J., and Das, R. (2012) “An RNA Mapping Database for curating RNA structure mapping experiments” Bioinformatics 28 (22) : 3006 – 3008 | Paper | Link | Database

Cordero, P., Kladwang, W., VanLang, C.C., and Das, R. (2012) “Quantitative dimethyl sulfate (DMS) mapping for automated RNA secondary structure inference” Biochemistry 51 (36) : 7037 – 7039 | Paper | Link

Kladwang, W., Hum, J., and Das, R. (2012) “Ultraviolet shadowing of RNA can cause significant chemical damage in seconds” Scientific Reports 2 : 517 | Paper | Link

Sripakdeevong, P., Beauchamp, K., and Das, R. (2012) “2012_Sripakdeevong_NAMB” in RNA 3D Structure Analysis and Prediction, eds. Leontis, N. and Westhof, E., Nucleic Acids and Molecular Biology 27 : 43 – 65 | Paper | Link

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” Journal of Chemical Theory and Computation 8 (4) : 1409 – 1414 | Paper | Link

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” RNA 18 (6) : 1123 – 1141 | Paper | Link

Kladwang, W., Chou, F.-C., and Das, R. (2012) “Automated RNA structure prediction uncovers a kink-turn linker in double glycine riboswitches” Journal of the American Chemical Society 134 (3) : 1404 – 1407 | Paper | Link | Models

Kladwang, W., VanLang, C.C., Cordero P., and Das, R. (2011) “Understanding the errors of SHAPE-directed RNA structure modeling” Biochemistry 50 (37) : 8049 – 8056 | Paper | Link

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” Proceedings of the National Academy of Sciences U.S.A. 108 (31) : 12734 – 12739 | Paper | Link

Das, R. (2011) “Four small puzzles that Rosetta doesn’t solve” PLOS One 6 (5) : e20044 | Paper | Link

Yoon, S., Kim, J., Hum, J., Kim, H., Park, S., Kladwang, W., and Das, R. (2011) “HiTRACE: High-throughput robust analysis for capillary electrophoresis” Bioinformatics 27 (13) : 1798 – 1805 | Paper | Link | Software

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” RNA 17 (7) : 1204 – 1212 | Paper | Link

Kladwang, W., Cordero P., and Das, R. (2011) “A mutate-and-map strategy accurately infers the base pairs of a 35-nucleotide model RNA” RNA 17 (3) : 522 – 534 | Paper | Link

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” Methods in Enzymology 487 : 545 – 574 | Paper | Link

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” Proteins 78 (15) : 3212 – 3218 | Paper | Link

Das, R., Karanicolas, J., and Baker., D. (2010) “Atomic accuracy in predicting and designing noncanonical RNA structure” Nature Methods 7 : 291 – 294 | Paper | Link | Server | Models

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” Proceedings of the National Academy of Sciences U.S.A. 106 (45) : 18978 – 18983 | Paper | Link

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.” Proteins 77 (S9) : 88 – 99 | Paper | Link

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” Bioinformatics 25 (9) : 1137 – 1144 | Paper | Link

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” Structure 17 (2) : 151 – 159 | Paper | Link

Das, R., and Baker, D. (2009) “Prospects for de novo phasing with protein de novo models” Acta Crystallographica Section D 65 (5) : 169 – 175 | Paper | Link

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” RNA 15 (2) : 189 – 199 | Paper | Link

Fenn, R.M., Das, R., and Harbury, P.B. (2008) “Remeasuring the double helix” Science 322 (5900) : 446 – 449 | Paper | Link

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” PLOS One 3 (10) : e3229 | Paper | Link

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” Nature Protocols 3 : 1395 – 1401 | Paper | Link

Das, R., and Baker, D. (2008) “Macromolecular modeling with Rosetta” Annual Review of Biochemistry 77 : 363 – 382 | Paper | Link

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” Proceedings of the National Academy of Sciences U.S.A. 105 (11) : 4144 – 4149 | Paper | Link | Scripts

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” Nature 450 : 259 – 264 | Paper | Link

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” Proteins 69 (S8) : 118 – 128 | Paper | Link

Das, R., and Baker, D. (2007) “Automated de novo prediction of native-like RNA tertiary structures” Proceedings of the National Academy of Sciences U.S.A. 104 (37) : 14664 – 14669 | Paper | Link | Models

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” in Advances in Neural Information Processing Systems (NIPS) 21, eds. Platt, J., Koller, D., Singer, Y., and McCallum, A., MIT Press. | Paper | Link

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” Journal of Molecular Biology 365 (2) : 1393 – 1406 | Paper | Link

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” Journal of Molecular Biology 363 (2) : 531 – 544 | Paper | Link

Das, R., and Doniach, S. (2006) “Structural studies of proteins and nucleic acids in solution using small angle x-ray scattering (SAXS).” in Soft Matter: Scattering, Imaging and Manipulation, eds. Pecora, R. and Borsali, R., Kluwer Press : 1083 – 1108 | Paper | Link

Das, R., Travers, K.J., Bai, Y., and Herschlag, D. (2005) “Determining the Mg2+ stoichiometry for folding an RNA’s metal ion core” Journal of the American Chemical Society 127 (23) : 8272 – 8273 | Paper | Link

Bai, Y., Das, R., Millett, I.S., Herschlag, D., and Doniach, S. (2005) “2005_Bai_PNAS.” Proceedings of the National Academy of Sciences U.S.A. 102 (4) : 959 – 960 | Paper | Link

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.” RNA 11 (3) : 344 – 354 | Paper | Link | Software

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.” Physical Review Letters 93 (24) : 32767 | Paper | Link

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” Nuclear Physics B 700 (1) : 51 – 68 | Paper | Link

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.” Journal of Molecular Biology 343 (5) : 1195 – 1206 | Paper | Link

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.” Journal of Molecular Biology 332 (2) : 311 – 319 | Paper | Link

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.” Physical Review Letters 90 (18) : 32767 | Paper | Link

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.” Journal of Molecular Biology 328 (5) : 1011 – 1026 | Paper | Link

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.” Monthly Notices of the Royal Astronomical Society 341 (3) : 937 – 940 | Paper | Link

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.” Monthly Notices of the Royal Astronomical Society 337 (4) : 1207 – 1214 | Paper | Link

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.” Monthly Notices of the Royal Astronomical Society 334 (2) : 323 – 326 | Paper | Link

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.” Monthly Notices of the Royal Astronomical Society 331 (1) : 1 – 6 | Paper | Link

Alba, M.M., Das, R., Orengo, C.A., and Kellam, P. (2001) “Genomewide function conservation and phylogeny in the Herpesviridae.” Genomic Research 11 : 43 – 54 | Paper | Link

Das, R. (2000) “Theoretical Basis of Likelihood Methods in Molecular Phylogenetic Inference” M. Res. Thesis, Dept. of Biology, University College London. Supervisors: Z. Yang & J. Mallet. | Paper

Das, R. (1999) “Analysis of Sunyaev-Zel’dovich Decrements” M. Phil. Thesis, Dept. of Physics, Cambridge University. Supervisor: R. Saunders. | Paper

Milton, K., and Das, R. (1996) “Finite-element lattice Hamiltonian matrix elements: Anharmonic oscillators” Letters in Mathematical Physics 36 (2) : 177 – 187 | Paper | Link