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List of co-cited articles
articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


The PARA-suite: PAR-CLIP specific sequence read simulation and processing.
Andreas Kloetgen, Arndt Borkhardt, Jessica I Hoell, Alice C McHardy. PeerJ 2016
8
50

The expanding universe of ribonucleoproteins: of novel RNA-binding proteins and unconventional interactions.
Benedikt M Beckmann, Alfredo Castello, Jan Medenbach. Pflugers Arch 2016
41
50


Computational prediction of associations between long non-coding RNAs and proteins.
Qiongshi Lu, Sijin Ren, Ming Lu, Yong Zhang, Dahai Zhu, Xuegong Zhang, Tingting Li. BMC Genomics 2013
118
50

Principles of protein structural ensemble determination.
Massimiliano Bonomi, Gabriella T Heller, Carlo Camilloni, Michele Vendruscolo. Curr Opin Struct Biol 2017
133
50

catRAPID signature: identification of ribonucleoproteins and RNA-binding regions.
Carmen Maria Livi, Petr Klus, Riccardo Delli Ponti, Gian Gaetano Tartaglia. Bioinformatics 2016
42
50

MEME-ChIP: motif analysis of large DNA datasets.
Philip Machanick, Timothy L Bailey. Bioinformatics 2011
819
50

A deep learning framework to predict binding preference of RNA constituents on protein surface.
Jordy Homing Lam, Yu Li, Lizhe Zhu, Ramzan Umarov, Hanlun Jiang, Amélie Héliou, Fu Kit Sheong, Tianyun Liu, Yongkang Long, Yunfei Li,[...]. Nat Commun 2019
9
50

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.
Daehwan Kim, Geo Pertea, Cole Trapnell, Harold Pimentel, Ryan Kelley, Steven L Salzberg. Genome Biol 2013
50

GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes.
Elizabeth I Boyle, Shuai Weng, Jeremy Gollub, Heng Jin, David Botstein, J Michael Cherry, Gavin Sherlock. Bioinformatics 2004
50


ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq.
Alper Kucukural, Hakan Özadam, Guramrit Singh, Melissa J Moore, Can Cenik. Bioinformatics 2013
28
50

Predicting RNA-protein interactions using only sequence information.
Usha K Muppirala, Vasant G Honavar, Drena Dobbs. BMC Bioinformatics 2011
197
50

Molecular Mechanism of RNA Recognition by Zinc-Finger Antiviral Protein.
Xiu Luo, Xinlu Wang, Yina Gao, Jingpeng Zhu, Songqing Liu, Guangxia Gao, Pu Gao. Cell Rep 2020
29
50

BMix: probabilistic modeling of occurring substitutions in PAR-CLIP data.
Monica Golumbeanu, Pejman Mohammadi, Niko Beerenwinkel. Bioinformatics 2016
8
50

Discovering sequence and structure landscapes in RNA interaction motifs.
Marta Adinolfi, Marco Pietrosanto, Luca Parca, Gabriele Ausiello, Fabrizio Ferrè, Manuela Helmer-Citterich. Nucleic Acids Res 2019
8
50

Quantitative predictions of protein interactions with long noncoding RNAs.
Davide Cirillo, Mario Blanco, Alexandros Armaos, Andreas Buness, Philip Avner, Mitchell Guttman, Andrea Cerase, Gian Gaetano Tartaglia. Nat Methods 2016
67
50

Structural studies of RNA-protein complexes: A hybrid approach involving hydrodynamics, scattering, and computational methods.
Trushar R Patel, Grzegorz Chojnowski, Astha, Amit Koul, Sean A McKenna, Janusz M Bujnicki. Methods 2017
23
50

Small-Angle Neutron Scattering of RNA-Protein Complexes.
Audrone Lapinaite, Teresa Carlomagno, Frank Gabel. Methods Mol Biol 2020
3
50


EuRBPDB: a comprehensive resource for annotation, functional and oncological investigation of eukaryotic RNA binding proteins (RBPs).
Jian-You Liao, Bing Yang, Yu-Chan Zhang, Xiao-Juan Wang, Yushan Ye, Jing-Wen Peng, Zhi-Zhi Yang, Jie-Hua He, Yin Zhang, KaiShun Hu,[...]. Nucleic Acids Res 2020
13
50

Thermodynamic stability of small hairpin RNAs highly influences the loading process of different mammalian Argonautes.
Shuo Gu, Lan Jin, Feijie Zhang, Yong Huang, Dirk Grimm, John J Rossi, Mark A Kay. Proc Natl Acad Sci U S A 2011
61
50

CRAC: an integrated approach to the analysis of RNA-seq reads.
Nicolas Philippe, Mikaël Salson, Thérèse Commes, Eric Rivals. Genome Biol 2013
42
50

The complex transcriptional landscape of the anucleate human platelet.
Paul F Bray, Steven E McKenzie, Leonard C Edelstein, Srikanth Nagalla, Kathleen Delgrosso, Adam Ertel, Joan Kupper, Yi Jing, Eric Londin, Phillipe Loher,[...]. BMC Genomics 2013
399
50

STAR: ultrafast universal RNA-seq aligner.
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
50

Structural Modeling Using Solution Small-Angle X-ray Scattering (SAXS).
Tobias W Gräwert, Dmitri I Svergun. J Mol Biol 2020
8
50

Neurodegenerative diseases: quantitative predictions of protein-RNA interactions.
Davide Cirillo, Federico Agostini, Petr Klus, Domenica Marchese, Silvia Rodriguez, Benedetta Bolognesi, Gian Gaetano Tartaglia. RNA 2013
46
50

A DEAD-box RNA helicase promotes thermodynamic equilibration of kinetically trapped RNA structures in vivo.
Dana J Ruminski, Peter Y Watson, Elisabeth M Mahen, Martha J Fedor. RNA 2016
4
50

omiXcore: a web server for prediction of protein interactions with large RNA.
Alexandros Armaos, Davide Cirillo, Gian Gaetano Tartaglia. Bioinformatics 2017
10
50

Advancing formaldehyde cross-linking towards quantitative proteomic applications.
Cordula Klockenbusch, Jane E O'Hara, Juergen Kast. Anal Bioanal Chem 2012
34
50

RNAcompete methodology and application to determine sequence preferences of unconventional RNA-binding proteins.
Debashish Ray, Kevin C H Ha, Kate Nie, Hong Zheng, Timothy R Hughes, Quaid D Morris. Methods 2017
24
50

A brave new world of RNA-binding proteins.
Matthias W Hentze, Alfredo Castello, Thomas Schwarzl, Thomas Preiss. Nat Rev Mol Cell Biol 2018
431
50

Dynamics of the DEAD-box ATPase Prp5 RecA-like domains provide a conformational switch during spliceosome assembly.
David H Beier, Tucker J Carrocci, Clarisse van der Feltz, U Sandy Tretbar, Joshua C Paulson, Nikolai Grabowski, Aaron A Hoskins. Nucleic Acids Res 2019
4
50

irCLIP platform for efficient characterization of protein-RNA interactions.
Brian J Zarnegar, Ryan A Flynn, Ying Shen, Brian T Do, Howard Y Chang, Paul A Khavari. Nat Methods 2016
114
50

Design and bioinformatics analysis of genome-wide CLIP experiments.
Tao Wang, Guanghua Xiao, Yongjun Chu, Michael Q Zhang, David R Corey, Yang Xie. Nucleic Acids Res 2015
47
50


Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP.
Markus Hafner, Markus Landthaler, Lukas Burger, Mohsen Khorshid, Jean Hausser, Philipp Berninger, Andrea Rothballer, Manuel Ascano, Anna-Carina Jungkamp, Mathias Munschauer,[...]. Cell 2010
50


Site identification in high-throughput RNA-protein interaction data.
Philip J Uren, Emad Bahrami-Samani, Suzanne C Burns, Mei Qiao, Fedor V Karginov, Emily Hodges, Gregory J Hannon, Jeremy R Sanford, Luiz O F Penalva, Andrew D Smith. Bioinformatics 2012
160
50

A census of human RNA-binding proteins.
Stefanie Gerstberger, Markus Hafner, Thomas Tuschl. Nat Rev Genet 2014
807
50

Biological small-angle neutron scattering: recent results and development.
Emilie Mahieu, Frank Gabel. Acta Crystallogr D Struct Biol 2018
19
50


A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins.
Shivendra Kishore, Lukasz Jaskiewicz, Lukas Burger, Jean Hausser, Mohsen Khorshid, Mihaela Zavolan. Nat Methods 2011
316
50

Recent methodology progress of deep learning for RNA-protein interaction prediction.
Xiaoyong Pan, Yang Yang, Chun-Qiu Xia, Aashiq H Mirza, Hong-Bin Shen. Wiley Interdiscip Rev RNA 2019
13
50

DO-RIP-seq to quantify RNA binding sites transcriptome-wide.
Cindo O Nicholson, Matthew B Friedersdorf, Laura S Bisogno, Jack D Keene. Methods 2017
10
50


Deciphering human ribonucleoprotein regulatory networks.
Neelanjan Mukherjee, Hans-Hermann Wessels, Svetlana Lebedeva, Marcin Sajek, Mahsa Ghanbari, Aitor Garzia, Alina Munteanu, Dilmurat Yusuf, Thalia Farazi, Jessica I Hoell,[...]. Nucleic Acids Res 2019
18
50

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution.
Julian König, Kathi Zarnack, Gregor Rot, Tomaz Curk, Melis Kayikci, Blaz Zupan, Daniel J Turner, Nicholas M Luscombe, Jernej Ule. Nat Struct Mol Biol 2010
681
50

Kinetic and Thermodynamic Analyses of Interaction between a High-Affinity RNA Aptamer and Its Target Protein.
Ryo Amano, Kenta Takada, Yoichiro Tanaka, Yoshikazu Nakamura, Gota Kawai, Tomoko Kozu, Taiichi Sakamoto. Biochemistry 2016
25
50

RNA-centric approaches to study RNA-protein interactions in vitro and in silico.
Alessandro Dasti, Fernando Cid-Samper, Elias Bechara, Gian Gaetano Tartaglia. Methods 2020
7
50


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.