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R

Rhiju Das

Stanford

72H-index
318Paper Count
2.2WCitation Count
Published Papers 113
Publication Date
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Structures of nucleotide-bound human telomerase at several steps of its telomeric DNA repeat addition cycle
errNature Communications
IF15.7
err2026-01-21
err0
errOAAI
errSebastian Balch; Elsa Franco-Echevarría; George E. Ghanim; Rachael C. Kretsch; Rhiju Das; Thi Hoang Duong Nguyen
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errSave
Compact RNA sensors for increasingly complex functions of multiple inputs
errNature Chemistry
IF20.2
err2025-11-12
err0
errOAAI
errChristian A. Choe; Johan O. L. Andreasson; Feriel Melaine; Wipapat Kladwang; Michelle J. Wu; Fernando Portela; Roger Wellington-Oguri; John J. Nicol; Hannah K. Wayment-Steele; Michael Gotrik; Purvesh Khatri; William J. Greenleaf; Rhiju Das
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errSave
Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16
errProteins: Structure, Function, and Bioinformatics
IF0
err2025-11-08
err0
PREAI
errRachael C. Kretsch; Elisa Posani; Eugene F. Baulin; Janusz M. Bujnicki; Giovanni Bussi; Thomas E. Cheatham III; Shi-Jie Chen; Arne Elofsson; Masoud Amiri Farsani; Olivia N. Fisher; M. Michael Gromiha; Ayush Gupta; Michiaki Hamada; K. Harini; Gang Hu; David Huang; Junichi Iwakiri; Anika Jain; Yuki Kagaya; Daisuke Kihara; Sebastian Kmiecik; Sowmya Ramaswamy Krishnan; Ikuo Kurisaki; Olivier Languin-Cattoën; Jun Li; Shanshan Li; Karim Malekzadeh; Tsukasa Nakamura; Wentao Ni; Chandran Nithin; Michael Z. Palo; Joon Hong Park; Smita P. Pilla; Simón Poblete; Fabrizio Pucci; Pranav Punuru; Anouka Saha; Kengo Sato; Ambuj Srivastava; Genki Terashi; Emilia Tugolukova; Jacob Verburgt; Qiqige Wuyun; Gül H. Zerze; Kaiming Zhang; Sicheng Zhang; Wei Zheng; Yuanzhe Zhou; Wah Chiu; David A. Case; Rhiju Das
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errSave
Assessment of Protein Complex Predictions in CASP16: Are We Making Progress?
errProteins: Structure, Function, and Bioinformatics
IF0
err2025-10-31
err0
errOAAI
errJing Zhang; Rongqing Yuan; Andriy Kryshtafovych; Jimin Pei; Rachael C. Kretsch; R. Dustin Schaeffer; Jian Zhou; Rhiju Das; Nick V. Grishin; Qian Cong
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Assessment of Nucleic Acid Structure Prediction in CASP16
errProteins: Structure, Function, and Bioinformatics
IF0
err2025-10-30
err0
PREAI
errRachael C. Kretsch; Alissa M. Hummer; Shujun He; Rongqing Yuan; Jing Zhang; Thomas Karagianes; Qian Cong; Andriy Kryshtafovych; Rhiju Das
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errSave
Functional Relevance of CASP16 Nucleic Acid Predictions as Evaluated by Structure Providers
errProteins: Structure, Function, and Bioinformatics
IF0
err2025-09-04
err0
errOAAI
errRachael C. Kretsch; Reinhard Albrecht; Ebbe S. Andersen; Hsuan-Ai Chen; Wah Chiu; Rhiju Das; Jeanine G. Gezelle; Marcus D. Hartmann; Claudia Höbartner; Yimin Hu; Shekhar Jadhav; Philip E. Johnson; Christopher P. Jones; Deepak Koirala; Emil L. Kristoffersen; Eric Largy; Anna Lewicka; Cameron D. Mackereth; Marco Marcia; Michela Nigro; Manju Ojha; Joseph A. Piccirilli; Phoebe A. Rice; Heewhan Shin; Anna-Lena Steckelberg; Zhaoming Su; Yoshita Srivastava; Liu Wang; Yuan Wu; Jiahao Xie; Nikolaj H. Zwergius; John Moult; Andriy Kryshtafovych
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errSave
Cryo-EM structure of human telomerase dimer reveals H/ACA RNP-mediated dimerization
errScience
IF45.8
err2025-07-10
err0
PREAI
errSebastian Balch; Zala Sekne; Elsa Franco-Echevarría; Patryk Ludzia; Rachael C. Kretsch; Wenqing Sun; Haopeng Yu; George E. Ghanim; Sigurdur Thorkelsson; Yiliang Ding; Rhiju Das; Thi Hoang Duong Nguyen
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errSave
RNA-Puzzles Round V: blind predictions of 23 RNA structures
errNATURE METHODS
IF32.1
err2024-12-02
err0
errOAAI
errBu, Fan; Adam, Yagoub; Adamiak, Ryszard W.; Antczak, Maciej; de Aquino, Belisa Rebeca H.; Badepally, Nagendar Goud; Batey, Robert T.; Baulin, Eugene F.; Boinski, Pawel; Boniecki, Michal J.; Bujnicki, Janusz M.; Carpenter, Kristy A.; Chacon, Jose; Chen, Shi-Jie; Chiu, Wah; Cordero, Pablo; Das, Naba Krishna; Das, Rhiju; Dawson, Wayne K.; Dimaio, Frank; Ding, Feng; Dock-Bregeon, Anne-Catherine; Dokholyan, Nikolay V.; Dror, Ron O.; Dunin-Horkawicz, Stanislaw; Eismann, Stephan; Ennifar, Eric; Esmaeeli, Reza; Farsani, Masoud Amiri; Ferre-D'Amare, Adrian R.; Geniesse, Caleb; Ghanim, George E.; Guzman, Horacio V.; Hood, Iris V.; Huang, Lin; Jain, Dharm Skandh; Jaryani, Farhang; Jin, Lei; Joshi, Astha; Karelina, Masha; Kieft, Jeffrey S.; Kladwang, Wipapat; Kmiecik, Sebastian; Koirala, Deepak; Kollmann, Markus; Kretsch, Rachael C.; Kurcinski, Mateusz; Li, Jun; Li, Shuang; Magnus, Marcin; Masquida, Benoit; Moafinejad, S. Naeim; Mondal, Arup; Mukherjee, Sunandan; Nguyen, Thi Hoang Duong; Nikolaev, Grigory; Nithin, Chandran; Nye, Grace; Pandaranadar Jeyeram, Iswarya P. N.; Perez, Alberto; Pham, Phillip; Piccirilli, Joseph A.; Pilla, Smita Priyadarshini; Pluta, Radoslaw; Poblete, Simon; Ponce-Salvatierra, Almudena; Popenda, Mariusz; Popenda, Lukasz; Pucci, Fabrizio; Rangan, Ramya; Ray, Angana; Ren, Aiming; Sarzynska, Joanna; Sha, Congzhou Mike; Stefaniak, Filip; Su, Zhaoming; Suddala, Krishna C.; Szachniuk, Marta; Townshend, Raphael; Trachman III, Robert J.; Wang, Jian; Wang, Wenkai; Watkins, Andrew; Wirecki, Tomasz K.; Xiao, Yi; Xiong, Peng; Xiong, Yiduo; Yang, Jianyi; Yesselman, Joseph David; Zhang, Jinwei; Zhang, Yi; Zhang, Zhenzhen; Zhou, Yuanzhe; Zok, Tomasz; Zhang, Dong; Zhang, Sicheng; Zyla, Adriana; Westhof, Eric; Miao, Zhichao
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Tertiary folds of the SL5 RNA from the 5′ proximal region of SARS-CoV-2 and related coronaviruses
errPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
IF9.1
err2024-03-01
err5
errOAAI
errKretsch, Rachael C.; Xu, Lily; Zheludev, Ivan N.; Zhou, Xueting; Huang, Rui; Nye, Grace; Li, Shanshan; Zhang, Kaiming; Chiu, Wah; Das, Rhiju
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errSave
Minimization of the E. coli ribosome, aided and optimized by community science
errNUCLEIC ACIDS RESEARCH
IF13.1
err2024-01-12
err1
errOAAI
errTangpradabkul, Tiyaporn; Palo, Michael; Townley, Jill; Hsu, Kenneth B.; Participants, Eterna; Smaga, Sarah; Das, Rhiju; Schepartz, Alanna
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errSave
CASP15 cryo-EM protein and RNA targets: Refinement and analysis using experimental maps
errPROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
IF2.8
err2023-11-23
err3
errOAAI
errMulvaney, Thomas; Kretsch, Rachael C.; Elliott, Luc; Beton, Joseph G.; Kryshtafovych, Andriy; Rigden, Daniel J.; Das, Rhiju; Topf, Maya
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errSave
Assessment of three-dimensional RNA structure prediction in CASP15
errPROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
IF2.8
err2023-10-24
err39
errOAAI
errDas, Rhiju; Kretsch, Rachael C.; Simpkin, Adam J.; Mulvaney, Thomas; Pham, Phillip; Rangan, Ramya; Bu, Fan; Keegan, Ronan M.; Topf, Maya; Rigden, Daniel J.; Miao, Zhichao; Westhof, Eric
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RNA target highlights in CASP15: Evaluation of predicted models by structure providers
errPROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
IF2.8
err2023-07-19
err16
errOAAI
errKretsch, Rachael C. C.; Andersen, Ebbe S. S.; Bujnicki, Janusz M. M.; Chiu, Wah; Das, Rhiju; Luo, Bingnan; Masquida, Benoit; McRae, Ewan K. S.; Schroeder, Griffin M. M.; Su, Zhaoming; Wedekind, Joseph E. E.; Xu, Lily; Zhang, Kaiming; Zheludev, Ivan N. N.; Moult, John; Kryshtafovych, Andriy
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errSave
New prediction categories in CASP15
errPROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
IF2.8
err2023-06-12
err27
errOAAI
errKryshtafovych, Andriy; Antczak, Maciej; Szachniuk, Marta; Zok, Tomasz; Kretsch, Rachael C.; Rangan, Ramya; Pham, Phillip; Das, Rhiju; Robin, Xavier; Studer, Gabriel; Durairaj, Janani; Eberhardt, Jerome; Sweeney, Aaron; Topf, Maya; Schwede, Torsten; Fidelis, Krzysztof; Moult, John
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errSave
Community science designed ribosomes with beneficial phenotypes
errNATURE COMMUNICATIONS
IF15.7
err2023-02-21
err8
errOAAI
errKrueger, Antje M.; Watkins, Andrew; Wellington-Oguri, Roger; Romano, Jonathan; Kofman, Camila; DeFoe, Alysse; Kim, Yejun; Anderson-Lee, Jeff; Fisker, Eli; Townley, Jill E.; d'Aquino, Anne; Das, Rhiju C.; Jewett, Michael
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errSave
Deep learning models for predicting RNA degradation via dual crowdsourcing
errNATURE MACHINE INTELLIGENCE
IF23.9
err2022-12-14
err14
errOAAI
errWayment-Steele, Hannah K.; Kladwang, Wipapat; Watkins, Andrew M.; Kim, Do Soon; Tunguz, Bojan; Reade, Walter; Demkin, Maggie; Romano, Jonathan; Wellington-Oguri, Roger; Nicol, John J.; Gao, Jiayang; Onodera, Kazuki; Fujikawa, Kazuki; Mao, Hanfei; Vandewiele, Gilles; Tinti, Michele; Steenwinckel, Bram; Ito, Takuya; Noumi, Taiga; He, Shujun; Ishi, Keiichiro; Lee, Youhan; Ozturk, Fatih; Chiu, King Yuen; Ozturk, Emin; Amer, Karim; Fares, Mohamed; Participants, Eterna; Das, Rhiju
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Computationally-guided design and selection of high performing ribosomal active site mutants
errNUCLEIC ACIDS RESEARCH
IF13.1
err2022-12-09
err9
errOAAI
errKofman, Camila; Watkins, Andrew M.; Kim, Do Soon; Willi, Jessica A.; Wooldredge, Alexandra C.; Karim, Ashty S.; Das, Rhiju; Jewett, Michael C.
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errSave
Learning RNA structure prediction from crowd-designed RNAs
errNATURE METHODS
IF32.1
err2022-10-03
err0
errOAAI
errWayment-Steele, Hannah K.; Das, Rhiju
errShare
errSave
RNA secondary structure packages evaluated and improved by high-throughput experiments
errNATURE METHODS
IF32.1
err2022-10-03
err32
errOAAI
errWayment-Steele, Hannah K.; Kladwang, Wipapat; Strom, Alexandra I.; Lee, Jeehyung; Treuille, Adrien; Becka, Alex; Das, Rhiju
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errSave
Topological crossing in the misfolded Tetrahymena ribozyme resolved by cryo-EM
errPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
IF9.1
err2022-09-06
err19
errOAAI
errLi, Shanshan; Palo, Michael Z.; Pintilie, Grigore; Zhang, Xiaojing; Su, Zhaoming; Kappel, Kalli; Chiu, Wah; Zhang, Kaiming; Das, Rhiju
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errSave

Research Directions

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Co-authors
Cooperation Journals
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A
Axel T. Brünger
H-index: 115 · Papers: 533
R
Russ B. Altman
H-index: 114 · Papers: 955
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