Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data von Doncheva, Nadezhda T, Morris, John H, Gorodkin, Jan, Jensen, Lars J

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CRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters von Alkan, Ferhat, Wenzel, Anne, Anthon, Christian, Havgaard, Jakob Hull, Gorodkin, Jan

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RNAcentral 2021: secondary structure integration, improved sequence search and new member databases von Sweeney, Blake A, Petrov, Anton I, Ribas, Carlos E, Finn, Robert D, Bateman, Alex, Szymanski, Maciej, Karlowski, Wojciech M, Seemann, Stefan E, Gorodkin, Jan, Cannone, Jamie J, Gutell, Robin R, Kay, Simon, Marygold, Steven, dos Santos, Gil, Frankish, Adam, Mudge, Jonathan M, Barshir, Ruth, Fishilevich, Simon, Chan, Patricia P, Lowe, Todd M, Seal, Ruth, Bruford, Elspeth, Panni, Simona, Porras, Pablo, Karagkouni, Dimitra, Hatzigeorgiou, Artemis G, Ma, Lina, Zhang, Zhang, Volders, Pieter-Jan, Mestdagh, Pieter, Griffiths-Jones, Sam, Fromm, Bastian, Peterson, Kevin J, Kalvari, Ioanna, Nawrocki, Eric P, Petrov, Anton S, Weng, Shuai, Bouchard-Bourelle, Philia, Scott, Michelle, Lui, Lauren M, Hoksza, David, Lovering, Ruth C, Kramarz, Barbara, Mani, Prita, Ramachandran, Sridhar, Weinberg, Zasha

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Profiling of Ribose Methylations in RNA by High-Throughput Sequencing von Birkedal, Ulf, Christensen-Dalsgaard, Mikkel, Krogh, Nicolai, Sabarinathan, Radhakrishnan, Gorodkin, Jan, Nielsen, Henrik

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CRISPR/Cas9 gRNA activity depends on free energy changes and on the target PAM context von Corsi, Giulia I., Qu, Kunli, Alkan, Ferhat, Pan, Xiaoguang, Luo, Yonglun, Gorodkin, Jan

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RIsearch: fast RNA-RNA interaction search using a simplified nearest-neighbor energy model von Wenzel, Anne, Akbasli, Erdinç, Gorodkin, Jan

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TISSUES 2.0: an integrative web resource on mammalian tissue expression von Palasca, Oana, Santos, Alberto, Stolte, Christian, Gorodkin, Jan, Jensen, Lars Juhl

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A non-enzymatic, isothermal strand displacement and amplification assay for rapid detection of SARS-CoV-2 RNA von Mohammadniaei, Mohsen, Zhang, Ming, Ashley, Jon, Christensen, Ulf Bech, Friis-Hansen, Lennart Jan, Gregersen, Rasmus, Lisby, Jan Gorm, Benfield, Thomas Lars, Nielsen, Finn Erland, Henning Rasmussen, Jens, Pedersen, Ellen Bøtker, Olinger, Anne Christine Rye, Kolding, Lærke Tørring, Naseri, Maryam, Zheng, Tao, Wang, Wentao, Gorodkin, Jan, Sun, Yi

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Enhancing CRISPR-Cas9 gRNA efficiency prediction by data integration and deep learning von Xiang, Xi, Corsi, Giulia I., Anthon, Christian, Qu, Kunli, Pan, Xiaoguang, Liang, Xue, Han, Peng, Dong, Zhanying, Liu, Lijun, Zhong, Jiayan, Ma, Tao, Wang, Jinbao, Zhang, Xiuqing, Jiang, Hui, Xu, Fengping, Liu, Xin, Xu, Xun, Wang, Jian, Yang, Huanming, Bolund, Lars, Church, George M., Lin, Lin, Gorodkin, Jan, Luo, Yonglun

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RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets von Alkan, Ferhat, Wenzel, Anne, Palasca, Oana, Kerpedjiev, Peter, Rudebeck, Anders Frost, Stadler, Peter F, Hofacker, Ivo L, Gorodkin, Jan

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Differential and coherent processing patterns from small RNAs von Pundhir, Sachin, Gorodkin, Jan

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Genome-wide identification of clusters of predicted microRNA binding sites as microRNA sponge candidates von Pan, Xiaoyong, Wenzel, Anne, Jensen, Lars Juhl, Gorodkin, Jan

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The RNAsnp web server: predicting SNP effects on local RNA secondary structure von Sabarinathan, Radhakrishnan, Tafer, Hakim, Seemann, Stefan E, Hofacker, Ivo L, Stadler, Peter F, Gorodkin, Jan

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Differentially Expressed miRNAs in Ulcerative Colitis and Crohn’s Disease von Yarani, Reza, Shojaeian, Ali, Palasca, Oana, Doncheva, Nadezhda T., Jensen, Lars Juhl, Gorodkin, Jan, Pociot, Flemming

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Simultaneous DNA and RNA Mapping of Somatic Mitochondrial Mutations across Diverse Human Cancers von Stewart, James B, Alaei-Mahabadi, Babak, Sabarinathan, Radhakrishnan, Samuelsson, Tore, Gorodkin, Jan, Gustafsson, Claes M, Larsson, Erik

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Patent data-driven analysis of literature associations with changing innovation trends von Geissler, Adrian Sven, Gorodkin, Jan, Seemann, Stefan Ernst

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The transcriptomic landscape of neurons carrying PSEN1 mutations reveals changes in extracellular matrix components and non-coding gene expression von Corsi, Giulia I., Gadekar, Veerendra P., Haukedal, Henriette, Doncheva, Nadezhda T., Anthon, Christian, Ambardar, Sheetal, Palakodeti, Dasaradhi, Hyttel, Poul, Freude, Kristine, Seemann, Stefan E., Gorodkin, Jan

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The identification and functional annotation of RNA structures conserved in vertebrates von Seemann, Stefan E, Mirza, Aashiq H, Hansen, Claus, Bang-Berthelsen, Claus H, Garde, Christian, Christensen-Dalsgaard, Mikkel, Torarinsson, Elfar, Yao, Zizhen, Workman, Christopher T, Pociot, Flemming, Nielsen, Henrik, Tommerup, Niels, Ruzzo, Walter L, Gorodkin, Jan

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RNAscClust: clustering RNA sequences using structure conservation and graph based motifs von Miladi, Milad, Junge, Alexander, Costa, Fabrizio, Seemann, Stefan E, Havgaard, Jakob Hull, Gorodkin, Jan, Backofen, Rolf

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Massively targeted evaluation of therapeutic CRISPR off-targets in cells von Pan, Xiaoguang, Qu, Kunli, Yuan, Hao, Xiang, Xi, Anthon, Christian, Pashkova, Liubov, Liang, Xue, Han, Peng, Corsi, Giulia I., Xu, Fengping, Liu, Ping, Zhong, Jiayan, Zhou, Yan, Ma, Tao, Jiang, Hui, Liu, Junnian, Wang, Jian, Jessen, Niels, Bolund, Lars, Yang, Huanming, Xu, Xun, Church, George M., Gorodkin, Jan, Lin, Lin, Luo, Yonglun

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