Publications — Das Lab

Publications

Search for papers from the Das Lab on PubMed

2026

Townley, J., Kladwang, W., Baker, D., Blair, H. M., Choe, C., El Nesr, G., Favor, A., Fisker, E., Haack, D. B., He, S., Hingey, J., Huang, R., Huang, P.-S., Joshi, C. K., Karagianes, T. G., Kubaney, A., Lio, P., Mancino, A., Romano, J., Rudolfs, B., Spellmon, N., Toor, N., Wu, V., Yu, Z., Eterna players, and Das, R.

"De novo design of RNA pseudoknots with deep learning"

bioRxiv.

Balch, S. Franco-Echevarría, E. Ghanim, G.E. Kretsch, R.C. Das, R. Nguyen, T.H.D.

"Structures of nucleotide-bound human telomerase at several steps of its telomeric DNA repeat addition cycle"

Nature Communications 17, 1847.

2025

Lee, Y.*, He, S.*, Oda, T., Rao, G J., Kim, Y., Kim, R., Kim, H., Keng Heng, C., Kowerko, D., Li, H., Nguyen, H., Sampathkumar, A., Enrique Gomez, R., Chen, M., Yoshizawa, A., Kuraishi, S., Ogawa, K., Zou, S., Paullier, A., Zhao, B., Chen, H.-L., Hsu, T.-A., Hirano, T., Gezelle, J.G., Haack, D., Hong, Y., Jadhav, S., Koirala, D., Kretsch, R.C., Lewicka, A., Li, S., Marcia, M., Piccirilli, J., Rudolfs, B., Srivastava, Y., Steckelberg, A.-L., Su, Z., Toor, N., Wang, L., Yang, Z., Zhang, K., Zou, J., Baker, D., Chen, S.-J., Chiu, W., Demkin, M., Favor, A., M. Hummer, A., K. Joshi, C., Kryshtafovych, A., Kucukbenli, E., Miao, Z., Moult, J., Munley, C., Reade, W., Viel, T., Westhof, E., Zhang, S., and Das, R. (*Co-lead authors)

"Template-based RNA structure prediction advanced through a blind code competition"

bioRxiv.

Topkar, V.V. Wu, V. Ho, L.T. Ambiel, N. Valenzuela, A Yoshimura, K. Zuchero, J.B. Fu, M.-M. Das, R.

"RNA switch model for localization and translation of the myelin basic protein mRNA"

bioRxiv.

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., and Das, R. (*Co-lead authors)

"Compact RNA sensors for increasingly complex functions of multiple inputs"

Nature Chemistry 17, 1839-1852.

Kretsch, R.C., Posani, E., Baulin, E.F., Bujnicki, J.M. Bussi, G. Cheatham III, T.E., Chen, S.-J., Elofsson, A. Farsani, M.A., Fisher, O.N., Gromiha, M.M., Gupta, A., Hamada, M., Harini, K.., Hu, G., Huang, D., Iwakiri, J. Jain, A. Kagaya, Y., Kihara, D., Kmiecik, S. Krishnan, S.R., Kurisaki, I., Languin-Cattoën, O., Li, J., Li, S., Malekzadeh, K., Nakamura, T., Ni, W., Nithin, C., Palo, M.Z., Park, J.H., Pilla, S.P., Poblete, S., Pucci, F., Punuru, P., Saha, A., Sato, K., Srivastava, A., Terashi, G., Tugolukova, E., Verburgt, J., Wuyun, Q., Zerze, G.H., Zhang, K., Zhang, S., Zheng, W., Zhou, Y., Chiu, W., Case, D.A., Das, R.

"Blind prediction of complex water and ion ensembles around RNA in CASP16"

Proteins 94, 381-402.

Kretsch R.C., Hummer, A.M., He, S., Yuan, R., Zhang, J., Karagianes, T., Cong, Q., Kryshtafovych, A., Das, R.

"Assessment of nucleic acid structure prediction in CASP16"

Proteins 94, 192-217.

Zhang J., Yuan R., Kryshtafovych A., Kretsch R.C., Schaeffer R.D., Zhou J., Das R., Grishin N.V., Cong Q.

"Assessment of protein complex predictions in CASP16: Are we making progress?"

Proteins 94, 106-130.

Kretsch, R.C., Albrecht, R., Andersen, E.S., Chen, H., Chiu, W., Das, R., Gezelle, J.G., Hartmann, M.D., Höbartner, C., Hu, Y., Jadhav, S., Johnson, P.E., Jones, P., Koirala, D., Kristoffersen, E.L., Largy, E., Lewicka, A., Mackereth, C.D., Marcia, M., Nigro, M., Ojha, M., Piccirilli, J.A., Rice, P.A., Shin, H., Steckelberg, A., Su, Z., Srivastava, Y., Wang, L., Wu, Y., Xie, J., Zwergius, N.H., Moult, J., Kryshtafovych, A.

"Functional relevance of CASP16 nucleic acid predictions as evaluated by structure providers"

Proteins 94, 51-78.

Balch S., Sekne Z., Franco-Echevarría E., Ludzia P., Kretsch R.C., Sun W., Yu H., Ghanim G.E., Thorkelsson S., Ding Y., Das R., Nguyen T.H.D.

"Cryo-EM structure of human telomerase dimer reveals H/ACA RNP-mediated dimerization"

Science 389, eadr5817.

Rangan, R., Huang, R., Hunter O., Pham P., Ares, Jr., M., Das, R.

"Comprehensive analysis of Saccharomyces cerevisiae intron structures in vivo"

Nature Structural & Molecular Biology 32, 1488-1502.

Tse V., Guiterrez M., Townley J., Romano J., Pearl J., Chacaltana G., Eterna Players, Das R., Sanford J.R., Stone M.D.

"OpenASO: RNA Rescue - designing splice-modulating antisense oligonucleotides through community science"

RNA 31, 1091-1102.

Kretsch, R.C. Wu, Y. Shabalina, S.A. Lee, H. Nye, G. Koonin, E.V. Gao, A. Chiu, W. Das, R.

"Naturally ornate RNA-only complexes revealed by cryo-EM"

Nature 643, 1135-1142.

Kretsch, R.C., Li, S., Pintilie, G., Palo, M.Z., Case, D.A., Das, R., Zhang, K., Chiu, W.

"Complex water networks visualized through 2.2-2.3 Angstrom cryogenic electron microscopy of RNA"

Nature 642, 250-259.

Koodli, R.V., Rudolfs, B., Romano, J., Wayment-Steele, H.K., Dunlap IV, W.A., Eterna Participants, Das, R.

"Redesigning the Eterna100 for the Vienna 2 folding engine"

bioRxiv.

Bu, F., Adam, Y., Adamiak, R.W., Antczak, M., de Aquino, B.R.H., Badepally, N.G., Batey, R.T., Baulin, E.F., Boinski, P., Boniecki, M.J., Bujnicki, J.M., Carpenter, K.A., Chacon, J., Chen, S.J., Chiu, W., Cordero, P., Das, N.K., Das, R., Dawson, W.K., DiMaio, F., Ding, F., Dock-Bregeon, A.C., Dokholyan, N.V., Dror, R.O., Dunin-Horkawicz, S., Eismann, S., Ennifar, E., Esmaeeli, R., Farsani, M.A., Ferré-D’Amaré, A.R., Geniesse, C., et.al.

"RNA-Puzzles Round V: blind predictions of 23 RNA structures"

Nature Methods 22, 399-411.

2024

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., and Das, R. (*Co-lead authors)

"Ribonanza: deep learning of RNA structure through dual crowdsourcing"

bioRxiv.

Kretsch, R.C., Xu, L., Zheludev, I.N., Zhou, X., Huang, R., Nye, G., Li, S., Zhang, K., Chiu, W., Das, R.

"Tertiary folds of the SL5 RNA from the 5’ proximal region of SARS-CoV-2 and related coronaviruses"

PNAS 121, e2320493121.

Tangpradabkul, T., Palo, M., Townley, J., Hsu, K.B., Eterna participants, Smaga, S., Das, R., Schepartz, A.

"Minimization of the E. coli ribosome, aided and optimized by community science"

Nucleic Acids Research 2024, 1-16.

2023

Mulvaney, T., Kretsch, R., Elliott, L., Beton, J., Kryshtafovych, A., Rigden, D.J., Das, R., Topf, M.

"CASP15 cryoEM protein and RNA targets: refinement and analysis using experimental maps"

Proteins: Structure, Function, and Bioinformatics 91, 1935-1951.

Das, R.*, Kretsch, R.*, Simpkin, A., Mulvaney, T., Pham, P., Rangan, R., Bu, F., Keegan, R., Topf, M., Rigden, D., Miao, Z., Westhof, E. (*Co-lead authors)

"Assessment of three-dimensional RNA structure prediction in CASP15"

Proteins: Structure, Function, and Bioinformatics 91, 1747-1770.

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.

"RNA target highlights in CASP15: Evaluation of predicted models by structure providers"

Proteins: Structure, Function, and Bioinformatics 91, 1600-1615.

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.

"New prediction categories in CASP15"

Proteins: Structure, Function, and Bioinformatics 91, 1550-1557.

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.

"Community science designed ribosomes with beneficial phenotypes"

Nature Communications 14, 961.

Watkins, A.M. and Das, R.

"RNA 3D Modeling with FARFAR2, Online"

Methods Mol Biol 2586, 233-249.

Ma, H., Pham, P., Luo, B., Rangan, R., Kappel, K., Su, Z., Das, R.

"Auto-DRRAFTER: automated RNA modeling based on cryo-EM density"

Methods Mol Biol. 2568, 193-211.

2022

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., Öztürk F., Chiu K., Öztürk E., Amer K., Fares M., Eterna Participants, and Das R. (*Co-lead authors)

"Deep learning models for predicting RNA degradation via dual crowdsourcing"

Nature Machine Intelligence 4, 1174–1184.

Kofman, C., Watkins, A., Kim, D., Willi, J., Wooldredge, A., Karim, A., Das, R., Jewett, M.

"Computationally-guided design and selection of high performing ribosomal active site mutants"

Nucleic Acids Research 50(22):13143-13154.

Wayment-Steele, H.K., Kladwang, W., Strom, A.I., Lee, J., Treuille, A., Becka, A., Eterna Participants, Das R.

"RNA secondary structure packages ranked and improved by high-throughput experiments"

Nature Methods 19, 1234-1242.

Paper Link EternaBench repository EternaFold server

Li, S., Palo, M.Z., Pintilie, G., Zhang, X., Su, Z., Kappel, K., Chiu, W., Zhang, K., Das, R.

"Topological crossing in the misfolded Tetrahymena ribozyme resolved by cryo-EM"

Proceedings of the National Academy of Sciences 119, e2209146119.

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.

"Programmable antivirals targeting critical conserved viral RNA secondary structures from influenza A virus and SARS-CoV-2"

Nature Medicine 28, 1944-1955.

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. (*Co-lead authors)

"Three-dimensional structure-guided evolution of a ribosome with tethered subunits"

Nature Chemical Biology 18, 990-998.

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.

"Crowdsourced RNA design discovers diverse, reversible, efficient, self-contained molecular sensors"

PNAS 119, e2112979119.

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., Solórzano, A., Barna, M., Das, R. (*Co-lead authors)

"Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics"

Nature Communications 13, 1536.

2021

Das, R., Russell, R.

"How to Kinetically Dissect an RNA Machine"

Biochemistry 60, 3485-3490.

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.

"Theoretical basis for stabilizing messenger RNA through secondary structure design"

Nucleic Acids Research 49, 10604-10617.

Paper Link Data (OpenVaccine-solves)

Das, R., Watkins, A.W.

"RiboDraw: semiautomated two-dimensional drawing of RNA tertiary structure diagrams"

NAR Genomics and Bioinformatics 3.

Townshend, R. J. L.*, Eismann, S.*, Watkins, A.M.*, Rangan, R., Karelina, M. Das, R., Dror, R.O. (*co-lead authors)

"Geometric deep learning of RNA structure"

Science 373, 1047-1051.

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. (*Co-lead authors)

"Cryo-EM and antisense targeting of the 28-kDa frameshift stimulation element from the SARS-CoV-2 RNA genome"

Nature Structure and Molecular Biology 28, 747-754.

Su, Z.*, Zhang, K.*, Kappel, K.*, Li, S., Palo, M.Z., Pintilie, G.D., Rangan, R., Lou, B., Wei, Yuquan., Das, R., Chiu, W. (*Co-lead authors)

"Cryo-EM structures of full-length Tetrahymena ribozyme at 3.1 Å resolution"

Nature 596, 603-607.

Das R.

"RNA structure: a renaissance begins?"

Nature Methods 18, 439.

Byeon, G.W., Cenik, E.S., Jiang, L., Tang, H., Das, R., Barna, M.

"Functional and structural basis of extreme conservation in vertebrate 5’ untranslated regions"

Nature Genetics 53, 729-741.

Liu, X., Sun, T., Shcberbina, A., Li, Q., Jarmoskaite, I., Kappel, K., Ramaswami, G., Das, R., Kundaje, A., Li, J.B.

"Learning cis-regulatory principles of ADAR-based RNA editing from CRISPR-mediated mutagenesis"

Nature Communications 12.

Ghanim, G. E., Fountain, A. J., van Roon, A. M., Rangan, R., Das, R., Collins, K., Nguyen, T.H.D.

"Structure of human telomerase holoenzyme with bound telomeric DNA"

Nature 593, 449-453.

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.

"PyRosetta jupyter notebooks teach biomolecular structure prediction and design"

The Biophysicist 2, 108-122.

Rangan, R., Watkins, A. M., Chacon, J., Kretsch, R., Kladwang, W., Zheludev, I.N., Townley, J., Rynge, M., Thain, G., Das, R.

"De novo 3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures"

Nucleic Acids Research 49, 3092-3108.

Paper Link Data (Model collection, SARS-CoV-2 structures)Data (Model collection, positive control structures)

2020

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., Schie

"Macromolecular modeling and design in Rosetta: recent methods and frameworks."

Nature Methods 17, 665-680.

Palka, C., Forino, N.M., Henstchel, J., Das, R., Stone, M.D.

"Folding heterogeneity in the essential human telomerase RNA three-way junction"

RNA 26, 1787-1800.

Kappel, 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. (*Co-lead authors)

"Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures"

Nature Methods 17, 699-707.

Watkins, A.M., Rangan, R., Das, R.

"FARFAR2: Improved de novo Rosetta prediction of complex global RNA folds"

Structure 28, 963-976.

Paper Link Server Benchmarking scripts

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.

"RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers"

RNA 26, 982-995.

Jain, N., Blauch, L. R., Szymanski, M. R., Das, R., Tang, S. K. Y., Yin, Y. W., Fire, A. Z.

"Transcription polymerase–catalyzed emergence of novel RNA replicons"

Science 368, eaay0688.

Kladwang, W., Topkar, V.V., Liu, B., Rangan R., Hodges, T.L., Keane, S.C., Al-Hashimi, H., Das, R.

"Anomalous reverse transcription through chemical modifications in polyadenosine stretches"

Biochemistry 59, 2154-2170.

Rangan, R., Zheludev I.N., Hagey, R.J., Pham, E.A., Wayment-Steele, H.K., Glenn, J.S., Das, R.

"RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses: a first look"

RNA 26, 937-959.

Paper Link Code

2019

Zhang, K.*, Li, S.*, Kappel, K.*, Pintilie, G., Su, Z., Mou, T.-C., Schmid, M. F., Das, R., and Chiu, W. (*Co-lead authors)

"Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution"

Nature Communications 10, Article number: 5511.

Magnus, M., Kappel, K., Das, R., Bujnicki, J.M.

"RNA 3D structure prediction guided by independent folding of homologous sequences"

BMC Bioinformatics 20, article 512.

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.

"A unified mechanism for intron and exon definition and back-splicing"

Nature 573, 375-380.

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.

"Computational design of three-dimensional RNA structure and function"

Nature Nanotechnology 14, 866-873.

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.

"A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites"

Nature Communications 10, 3629.

Das, R., Keep, B., Washington, P, Riedel-Kruse, I. H.

"Scientific discovery games for biomedical research"

Annual Review of Biomedical Data Science 2, 253-279.

Yesselman, J.D. Denny, S.K. Bisaria, N. Herschlag, D. Greenleaf, W.J. Das, R.

"Sequence-dependent RNA helix conformational preferences predictably impact tertiary structure formation"

Proceedings of the National Academy of Sciences 116, 16847-16855.

Wu, M.J., Andreasson, J., Kladwang, W., Greenleaf, W.J., and Das, R.

"Automated design of diverse stand-alone riboswitches"

ACS Synthetic Biology 8, 1838-1846.

Koodli, R. V., Keep, B., Coppess, K. R., Portela, F., Eterna Participants, and Das, R.

"EternaBrain: automated RNA design through move sets and strategies from an Internet-scale RNA videogame"

PLOS Computational Biology 15, e1007059.

Paper Link EternaBrain software

Huang, L., Wang, J., Watkins, A. M., Das, R., and Lilley, D. M. J.

"Structure and ligand binding of the glutamine-II riboswitch"

Nucleic Acids Research 47, 7666-7675.

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.

"A quantitative and predictive model for RNA binding by human Pumilio proteins"

Molecular Cell 74, 966-981.

Watkins, A. M., Rangan, R., and Das, R.

"Using Rosetta for RNA homology modeling"

Methods in Enzymology 623, 177-207.

Wayment-Steele, H., Wu, M., Gotrik, M., and Das, R.

"Evaluating riboswitch optimality"

Methods in Enzymology 623, 417-450.

Kappel, K. Jarmoskaite, I. Vaidyanathan, P.P. Greenleaf, W.J. Herschlag, D. and Das R.

"Blind tests of RNA-protein binding affinity prediction"

PNAS 116, 8336-8341.

Paper Link Rosetta RNP-ddG Software ROSIE RNP-ddG Server

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.

"Spontaneous driving forces give rise to protein-RNA condensates with coexisting phases and complex material properties"

PNAS 116, 7889-7898.

Kappel K. and Das R.

"Sampling native-like structures of RNA-protein complexes through Rosetta folding and docking"

Structure 27, 140-151.

Paper Link Rosetta RNP modeling software

2018

Hartwick EW, Costantino DA, MacFadden, A, Nix, JC, Tian S, Das R, and Kieft JS

"Ribosome-induced RNA conformational changes in a viral 3'-UTR sense and regulate translation levels"

Nature Communications 9.

Denny, S.K., Bisaria, N. Yesselman, J.D. Das, R. Herschlag, D. Greenleaf, W.J.

"High-throughput investigation of diverse junction elements in RNA tertiary folding"

Cell 174, 377-390.

Zettl, T., Das, R., Harbury, P.A.B., Herschlag, D., Lipfert, J., Mathew, R.S., and Shi X.

"Recording and analyzing nucleic acid distance distributions with X-ray scattering interferometry (XSI)"

Curr Protoc Nucleic Acid Chem 73, e54.

Kappel, K. Liu, S. Larsen, K.P. Skiniotis, G. Puglisi, E.V., Puglisi, J.D., Zhou, Z.H., Zhao, R., and Das, R.

"De novo computational RNA modeling into cryoEM maps of large ribonucleoprotein complexes"

Nature Methods 15, 947-954.

Paper Link DRRAFTER Rosetta Software

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.

"An activity switch in human telomerase based on RNA conformation and shaped by TCAB1"

Cell 174, 218-230.

Shi, J., Eterna players, Das, R., and Pande, V.S.

"SentRNA: Improving computational RNA design by incorporating a prior of human design strategies"

BioRxiv.

Preprint SentRNA Software

Watkins, A.M., Geniesse, C., Kladwang, W., Zakrevsky, P., Jaeger, L., and Das, R.

"Blind prediction of noncanonical RNA structure at atomic accuracy"

Science Advances 4, eaar5316.

Paper Link Stanford Digital Repository PURL ROSIE server

Wu, M.J., Andreasson, J.O.L, Kladwang, W., Greenleaf, W.J., Eterna players, and Das, R.

"Prospects for recurrent neural network models to learn RNA biophysics from high-throughput data"

BioRxiv.

Das, R.

"LIkelihood-based Fits of Folding Transitions (LIFFT) for Biomolecule Mapping Data"

BioRxiv.

Link LIFFT Software

Gracia, B., Al-Hashimi, H.M., Bisaria N., Das, R., Herschlag, D., and Russell, R.

"Hidden structural modules in a cooperative RNA folding transition"

Cell Reports 22, 3240-3250.

Tian, S., Kladwang, W., and Das, R.

"Allosteric mechanism of the V. vulnificus adenine riboswitch resolved by four-dimensional chemical mapping"

eLife 7, e29602.

Omabegho, T., Gurel, P. S., Cheng, C. Y., Kim, L., Y., Ruijgrok, P. V., Das, R., Alushin, G.M., and Bryant, Z.

"Controllable molecular motors engineered from myosin and RNA"

Nature Nanotechnology 13, 34-40.

Moretti, R., Lyskov, S., Das, R., Meiler, J., and Gray, J.J.

"Web-accessible molecular modeling with Rosetta: The Rosetta Online Server That Includes Everyone (ROSIE)"

Protein Science 27, 259-268.

Paper Link ROSIE Servers

2017

Leppek, K., Das, R., and Barna, M.

"Functional 5' UTR mRNA structures in eukaryotic translation regulation and how to find them"

Nature Reviews Molecular Cell Biology 19, 158-174.

Yesselman, J.D., Tian, S., Liu, X., Shi, L., Li, J.B., and Das, R.

"Updates to the RNA mapping database (RMDB), version 2"

Nucleic Acids Research 46, D375-D379.

Cheng, C.Y., Kladwang, W., Yesselman, J.D., and Das, R.

"RNA structure inference through chemical mapping after accidental or intentional mutations"

Proceedings of the National Academy of Sciences U.S.A. 114, 9876-9881.

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.

"The Rosetta all-atom energy function for macromolecular modeling and design"

Journal of Chemical Theory and Computation 13, 3031-3048.

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., Ferré-D'Amaré, 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.

"RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme"

RNA 23, 655-672.

Parks, J.W., Kappel, K., Das, R., and Stone, M.D.

"Single-molecule FRET-Rosetta reveals RNA structural rearrangements during human telomerase catalysis"

RNA 23, 175-188.

Tian, S., and Das, R.

"Primerize-2D: automated primer design for RNA multidimensional chemical mapping"

Bioinformatics 33, 1405-1406.

2016

Yesselman, J.D., and Das, R.

"Modeling small noncanonical RNA motifs with the Rosetta FARFAR server"

Methods in Molecular Biology 1490, 187-198.

Chou, F-C., Kladwang, W., Kappel, K., and Das, R.

"Blind tests of RNA nearest neighbor energy prediction"

Proceedings of the National Academy of Sciences U.S.A. 113, 8430-8435.

Tian, S., and Das, R.

"RNA structure through multidimensional chemical mapping"

Quarterly Review of Biophysics 49, 1-30.

Anderson-Lee, J., Fisker, E., Kosaraju,V., Wu, M., Kong, J., Lee, J., Lee, M., Zada, M., Treuille, A., Das, R., and Eterna Players

"Principles for predicting RNA secondary structure design difficulty"

Journal of Molecular Biology 428, 748-757.

Chou, F.-C., Echols, N., Terwilliger, T.C., and Das, R.

"RNA structure refinement using the ERRASER-Phenix pipeline"

Methods in Molecular Biology 1320, 269-282.

2015

Cordero, P., and Das, R.

"Rich RNA structure landscapes revealed by mutate-and-map analysis"

PLOS Computational Biology 11, e1004473.

Paper Link Software

Cheng, C.Y., Chou, F.-C., Kladwang, W., Tian, S., Cordero, P., and Das, R.

"Consistent global structures of complex RNA states through multidimensional chemical mapping."

eLife 4, e07600.

Paper Link Software

Tian, S., Yesselman, J.D., Cordero, P., and Das, R.

"Primerize: Automated primer assembly for transcribing non-coding RNA domains."

Nucleic Acid Research 43, W522-W526.

Paper Link Server

Yesselman, J.D., and Das, R.

"RNA-Redesign: A web server for fixed-backbone 3D design of RNA."

Nucleic Acid Research 43, W498-W501.

Paper Link Server

Lee, S., Kim, H., Tian, S., Lee, T., Yoon, S., and Das, R.

"Automated band annotation for RNA structure probing experiments with numerous capillary electrophoresis profiles."

Bioinformatics 31, 2808-2815.

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., Ferré-D'Amaré, 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.

"RNA-Puzzles Round II: Assessment of RNA structure prediction programs applied to three large RNA structures."

RNA 21, 1066-1084.

Cheng, C.Y., Chou, F.-C., and Das, R.

"Modeling complex RNA tertiary folds with Rosetta."

Methods in Enzymology 553, 35-64.

Xue, S., Tian, S., Fujii, K., Kladwang, W., Das, R., and Barna, M.

"RNA regulons in Hox 5' UTRs confer ribosome specificity to gene regulation"

Nature 517, 33-38.

2014

Treuille, A., and Das, R.

"Scientific rigor through videogames."

Trends in Biochemical Sciences 39, 507-509.

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.

"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, 15408-15413.

Chou, F.-C., Lipfert, J., and Das, R.

"Blind predictions of DNA and RNA tweezers experiments with force and torque."

PLOS Computational Biology 10, e1003756.

Paper Link Software

Lipfert, J., Doniach, S., Das, R., and Herschlag, D.

"Understanding nucleic acid-ion interactions"

Annual Review of Biochemistry 83, 813-841.

Cordero, P., Kladwang, W., VanLang, C.C., and Das, R.

"The mutate-and-map protocol for inferring base pairs in structured RNA"

Methods in Molecular Biology 1086, 53-77.

Seetin, M.G., Kladwang, W., Bida, J.P., and Das, R.

"Massively parallel RNA chemical mapping with a reduced bias MAP-Seq protocol"

Methods in Molecular Biology 1086, 95-117.

Tian, S., Cordero, P., Kladwang, W., and Das, R.

"High-throughput mutate-map-rescue evaluates SHAPE-directed RNA structure and uncovers excited states"

RNA 20, 1815-1826.

Kladwang, W., Mann, T.H., Becka, A., Tian, S., Kim, H., Yoon, S., and Das, R.

"Standardization of RNA chemical mapping experiments"

Biochemistry 53, 3063-3065.

Beauchamp, K., Pande, V., and Das, R.

"Bayesian energy landscape tilting: towards concordant models of molecular ensembles"

Biophysics Journal 106, 1381-1390.

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.

"Consistent structure determination of noncanonical RNA motifs from 1H NMR chemical shift data"

Nature Methods 11, 413-416.

Paper Link Server

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.

"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, 26-42.

Lee, J., Kladwang, W., Lee, M., Cantu, D., Azizyan, M., Kim, H., Limpaecher, A., Yoon, S., Treuille, A., Das, R., and EteRNA Participants

"RNA design rules from a massive open laboratory"

Proceedings of the National Academy of Sciences U.S.A. 111, 2122-2127.

Paper Link SHAPE Data Files EternaBot Software

2013

Das, R.

"Atomic-accuracy prediction of protein loop structures enabled by an RNA-inspired ansatz"

PLOS One 8, e74830.

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.

"Adding diverse noncanonical backbones to Rosetta: enabling peptidomimetic and foldamer design"

PLOS One 8, e67051.

Kim, H., Cordero, P., Das, R., and Yoon, S.

"HiTRACE-Web: an online tool for robust analysis of high-throughput capillary electrophoresis"

Nucleic Acid Research 41, 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.

"Serverification of molecular modeling applications: the Rosetta online server that includes everyone (ROSIE)"

PLOS One 8, 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.

"Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems"

Annual Review of Biophysics 42, 265-287.

Molski, M.A., Goodman, J.L, Chou, F-C., Baker, D., Das, R., and Schepartz, A.

"Remodeling a beta-peptide bundle"

Chemical Science 4, 319-324.

Paper Link Design Server

Chou, F.-C., Sripakdeevong, P., Dibrov, S.M, Hermann, T., and Das, R.

"Correcting pervasive errors in RNA crystallography through enumerative structure prediction"

Nature Methods 10, 74-76.

Paper Link ERRASER Server

2012

Cordero, P., Lucks, J., and Das, R.

"An RNA Mapping Database for curating RNA structure mapping experiments"

Bioinformatics 28, 3006-3008.

Paper Link Database

Cordero, P., Kladwang, W., VanLang, C.C., and Das, R.

"Quantitative dimethyl sulfate (DMS) mapping for automated RNA secondary structure inference"

Biochemistry 51, 7037-7039.

Bida, J.P., and Das, R.

"Squaring theory with practice in RNA design"

Current Opinion in Structural Biology 22, 457-466.

Kladwang, W., Hum, J., and Das, R.

"Ultraviolet shadowing of RNA can cause significant chemical damage in seconds"

Scientific Reports 2, 517.

Sripakdeevong, P., Beauchamp, K., and Das, R.

"Why can't we predict RNA structure at atomic resolution?"

in RNA 3D Structure Analysis and Prediction, eds. Leontis, N. and Westhof, E., Nucleic Acids and Molecular Biology 27, 43-65.

Beauchamp, K., Lin, Y-S., Das, R., and Pande. V.S.

"Are protein force fields getting better? A systematic benchmark on 524 diverse NMR measurements"

Journal of Chemical Theory and Computation 8, 1409-1414.

Frederiksen, J.K., Li, N.S., Das, R., Herschlag, D., and Piccirilli, J.A.

"Metal-ion rescue revisited: Biochemical detection of site-bound metal ions important for RNA folding"

RNA 18, 1123-1141.

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.

"RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction"

RNA 18, 610-625.

Kladwang, W., Chou, F.-C., and Das, R.

"Automated RNA structure prediction uncovers a kink-turn linker in double glycine riboswitches"

Journal of the American Chemical Society 134, 1404-1407.

Paper Link Models

Sripakdeevong, P., Kladwang, W., and Das, R.

"An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling"

Proceedings of the National Academy of Sciences U.S.A. 108, 20573-20578.

2011

Kladwang, W., VanLang, C.C., Cordero P., and Das, R.

"A two-dimensional mutate-and-map strategy for non-coding RNA structure"

Nature Chemistry 3, 954-962.

Kladwang, W., VanLang, C.C., Cordero P., and Das, R.

"Understanding the errors of SHAPE-directed RNA structure modeling"

Biochemistry 50, 8049-8056.

Beauchamp, K.A., Ensign, D.L., Das, R., and Pande, V.S.

"Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments"

Proceedings of the National Academy of Sciences U.S.A. 108, 12734-12739.

Das, R.

"Four small puzzles that Rosetta doesn't solve"

PLOS One 6, e20044.

Yoon, S., Kim, J., Hum, J., Kim, H., Park, S., Kladwang, W., and Das, R.

"HiTRACE: High-throughput robust analysis for capillary electrophoresis"

Bioinformatics 27, 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.

"Sharing and archiving nucleic acid structure mapping data"

RNA 17, 1204-1212.

Kladwang, W., Cordero P., and Das, R.

"A mutate-and-map strategy accurately infers the base pairs of a 35-nucleotide model RNA"

RNA 17, 522-534.

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.

"ROSETTA3: An object-oriented software suite for the simulation and design of macromolecules"

Methods in Enzymology 487, 545-574.

2010

Kladwang, W., and Das, R.

"A mutate-and-map strategy for inferring base pairs in structured nucleic acids: proof of concept on a DNA/RNA helix"

Biochemistry 49, 7414-7416.

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.

"Rosetta in CAPRI rounds 13-19"

Proteins 78, 3212-3218.

Das, R., Karanicolas, J., and Baker., D.

"Atomic accuracy in predicting and designing noncanonical RNA structure"

Nature Methods 7, 291-294.

Paper Link Server Models

Previous work by R. Das

2009

Das, R., Andre, I., Shen, Y., Wu, Y., Lemak, A., Bansal, S., Arrowsmith, C.H., Szyperski, T., and Baker, D.

"Simultaneous prediction of protein folding and docking at high resolution"

Proceedings of the National Academy of Sciences U.S.A. 106, 18978-18983.

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.

"Structure prediction for CASP8 with all-atom refinement using Rosetta."

Proteins 77, 88-99.

Kim, J., Yu, S., Shim, B., Kim, H., Min, H., Chung, E-Y., Das, R., and Yoon S.

"A robust peak detection method for RNA structure inference by high-throughput contact mapping"

Bioinformatics 25, 1137-1144.

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.

"Outcome of a workshop on applications of protein models in biomedical research"

Structure 17, 151-159.

Das, R., and Baker, D.

"Prospects for de novo phasing with protein de novo models"

Acta Crystallographica Section D 65, 169-175.

Jonikas, M.A., Radmer, R.J., Laederach, A., Das, R., Pearlman, S., Herschlag D., and Altman, R.B.

"Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters"

RNA 15, 189-199.

2008

Fenn, R.M., Das, R., Silverman, J.A., Fenn, T.D., Walker, P., and Harbury, P.B.

"An X-ray molecular ruler for measuring quantitative distance distributions in solution"

PLOS One 3, e3229.

Fenn, R.M., Das, R., and Harbury, P.B.

"Remeasuring the double helix"

Science 322, 446-449.

Laederach, A., Das, R., Vicens, Q., Pearlman, S., Brenowitz, M., Herschlag, D., and Altman, R.B.

"Semi-automated and rapid quantification of nucleic acid footprinting and structure mapping experiments"

Nature Protocols 3, 1395-1401.

Das, R., and Baker, D.

"Macromolecular modeling with Rosetta"

Annual Review of Biochemistry 77, 363-382.

Das, R., Kudaravalli, M., Jonikas, M., Laederach, A., Fong, R., Schwans, J.P., Baker, D., Piccirilli, J.A., Altman, R.B., and Herschlag, D.

"Structural inference of native and partially folded RNA by high throughput contact mapping"

Proceedings of the National Academy of Sciences U.S.A. 105, 4144-4149.

Paper Link Scripts

2007

Qian, B., Raman, V.S., Das, R., Bradley, P., McCoy, A.J., Read, R.J., and Baker, D.

"High resolution structure prediction and the crystallographic phase problem"

Nature 450, 259-264.

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.

"Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home"

Proteins 69, 118-128.

Das, R., and Baker, D.

"Automated de novo prediction of native-like RNA tertiary structures"

Proceedings of the National Academy of Sciences U.S.A. 104, 14664-14669.

Paper Link Models

Blum, B., Jordan, M.I., Kim, D., Das, R., Bradley, P., and Baker, D.

"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..

Lipfert, J., Das, R., Chu, V.B., Kudaravalli, M., Boyd, N., Herschlag, D. and Doniach, S.

"Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae"

Journal of Molecular Biology 365, 1393-1406.

2006

Russell, R., Das, R., Suh, H., Travers, K., Laederach, A., Engelhardt, M., and Herschlag, D.

"The paradoxical behavior of a highly structured misfolded intermediate in RNA folding"

Journal of Molecular Biology 363, 531-544.

Das, R., and Doniach, S.

"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.

2005

Das, R., Travers, K.J., Bai, Y., and Herschlag, D.

"Determining the Mg2+ stoichiometry for folding an RNA's metal ion core"

Journal of the American Chemical Society 127, 8272-8273.

Bai, Y., Das, R., Millett, I.S., Herschlag, D., and Doniach, S.

"Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution."

Proceedings of the National Academy of Sciences U.S.A. 102, 959-960.

Das, R., Laederach, A., Pearlman, S.M., Herschlag, D., and Altman, R.B.

"SAFA: Semi-Automated Footprinting Analysis software for high-throughput quantification of nucleic acid footprinting experiments."

RNA 11, 344-354.

Paper Link Software

2004

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.

"Spatial distribution of competing ions around DNA in solution."

Physical Review Letters 93, 32767.

Naumov, D. Chukanov, A., Naumova, E., Popv, B., Astier, et al. [NOMAD collaboration]

"A study of strange particles produced in neutrino neutral current interactions in the NOMAD experiment"

Nuclear Physics B 700, 51-68.

Takamoto, K., Das, R., He, Q., Doniach, S., Brenowitz, M., Herschlag, D., and Chance, M.

"Principles of RNA compaction: insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations."

Journal of Molecular Biology 343, 1195-1206.

2003

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.

"The fastest global events in RNA folding: electrostatic relaxation and tertiary collapse of the Tetrahymena ribozyme."

Journal of Molecular Biology 332, 311-319.

Das, R., Mills, T.T., Kwok, L.W., Maskel, G.S., Millett, I.S., Doniach, S., Finkelstein, K.D., Herschlag, D., and Pollack, L.

"The counterion distribution around DNA probed by solution x-ray scattering."

Physical Review Letters 90, 32767.

Bartley, L., Zhuang, X., Das, R., Chu, S., and Herschlag, D.

"Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA."

Journal of Molecular Biology 328, 1011-1026.

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.

"A measurement of H0 from Ryle Telescope, ASCA and ROSAT observations of Abell 773."

Monthly Notices of the Royal Astronomical Society 341, 937-940.

2002

Grainger, W.F., Das, R., Grainge, K., Jones, M. E., Kneissl, R., Pooley, G.G., and Saunders, R.D.E.

"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, 1207-1214.

Cotter, G., Buttery, H.J., Das, R., Jones, M.E., Grainge, K., Pooley, G.G, and Saunders, R.

"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, 323-326.

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.

"Detection of a cosmic microwave background decrement towards a cluster of mJy radio sources."

Monthly Notices of the Royal Astronomical Society 331, 1-6.

2001

Alba, M.M., Das, R., Orengo, C.A., and Kellam, P.

"Genomewide function conservation and phylogeny in the Herpesviridae."

Genomic Research 11, 43-54.

2000

Das, R.

"Theoretical Basis of Likelihood Methods in Molecular Phylogenetic Inference"

M. Res. Thesis, Dept. of Biology, University College London. Supervisors: Z. Yang & J. Mallet..

1999

Das, R.

"Analysis of Sunyaev-Zel'dovich Decrements"

M. Phil. Thesis, Dept. of Physics, Cambridge University. Supervisor: R. Saunders..

1996

Milton, K., and Das, R.

"Finite-element lattice Hamiltonian matrix elements: Anharmonic oscillators"

Letters in Mathematical Physics 36, 177-187.