iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences von Chen, Zhen, Zhao, Pei, Li, Fuyi, Leier, André, Marquez-Lago, Tatiana T, Wang, Yanan, Webb, Geoffrey I, Smith, A Ian, Daly, Roger J, Chou, Kuo-Chen, Song, Jiangning

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Biomass and carbon stocks of four vegetation types in the Llanos Orientales of Colombia (Mapiripán, Meta) von Calderón-Balcázar, Alejandro, Cárdenas, Carlos D., Díaz-Vasco, Oswaldo, Fandiño, Emilio, Márquez, Tatiana, Pizano, Camila

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Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome von Li, Fuyi, Li, Chen, Marquez-Lago, Tatiana T, Leier, André, Akutsu, Tatsuya, Purcell, Anthony W, Ian Smith, A, Lithgow, Trevor, Daly, Roger J, Song, Jiangning, Chou, Kuo-Chen

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Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors von Wang, Jiawei, Yang, Bingjiao, Leier, André, Marquez-Lago, Tatiana T, Hayashida, Morihiro, Rocker, Andrea, Zhang, Yanju, Akutsu, Tatsuya, Chou, Kuo-Chen, Strugnell, Richard A, Song, Jiangning, Lithgow, Trevor

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Comprehensive assessment of machine learning-based methods for predicting antimicrobial peptides von Xu, Jing, Li, Fuyi, Leier, André, Xiang, Dongxu, Shen, Hsin-Hui, Marquez Lago, Tatiana T, Li, Jian, Yu, Dong-Jun, Song, Jiangning

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iLearn: an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data von Chen, Zhen, Zhao, Pei, Li, Fuyi, Marquez-Lago, Tatiana T, Leier, André, Revote, Jerico, Zhu, Yan, Powell, David R, Akutsu, Tatsuya, Webb, Geoffrey I, Chou, Kuo-Chen, Smith, A Ian, Daly, Roger J, Li, Jian, Song, Jiangning

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POSSUM: a bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profiles von Wang, Jiawei, Yang, Bingjiao, Revote, Jerico, Leier, André, Marquez-Lago, Tatiana T, Webb, Geoffrey, Song, Jiangning, Chou, Kuo-Chen, Lithgow, Trevor

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MULTiPly: a novel multi-layer predictor for discovering general and specific types of promoters von Zhang, Meng, Li, Fuyi, Marquez-Lago, Tatiana T, Leier, André, Fan, Cunshuo, Kwoh, Chee Keong, Chou, Kuo-Chen, Song, Jiangning, Jia, Cangzhi

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PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy von Song, Jiangning, Li, Fuyi, Leier, André, Marquez-Lago, Tatiana T, Akutsu, Tatsuya, Haffari, Gholamreza, Chou, Kuo-Chen, Webb, Geoffrey I, Pike, Robert N

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Stochastic model of ERK-mediated progesterone receptor translocation, clustering and transcriptional activity von Marquez-Lago, Tatiana T., Steinberg, Stanly

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A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction von Mei, Shutao, Li, Fuyi, Leier, André, Marquez-Lago, Tatiana T, Giam, Kailin, Croft, Nathan P, Akutsu, Tatsuya, Smith, A Ian, Li, Jian, Rossjohn, Jamie, Purcell, Anthony W, Song, Jiangning

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Bastion3: a two-layer ensemble predictor of type III secreted effectors von Wang, Jiawei, Li, Jiahui, Yang, Bingjiao, Xie, Ruopeng, Marquez-Lago, Tatiana T, Leier, André, Hayashida, Morihiro, Akutsu, Tatsuya, Zhang, Yanju, Chou, Kuo-Chen, Selkrig, Joel, Zhou, Tieli, Song, Jiangning, Lithgow, Trevor

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BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria von Wang, Jiawei, Li, Jiahui, Hou, Yi, Dai, Wei, Xie, Ruopeng, Marquez-Lago, Tatiana T, Leier, André, Zhou, Tieli, Torres, Von, Hay, Iain, Stubenrauch, Christopher, Zhang, Yanju, Song, Jiangning, Lithgow, Trevor

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PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins von Zhang, Yanju, Yu, Sha, Xie, Ruopeng, Li, Jiahui, Leier, André, Marquez-Lago, Tatiana T, Akutsu, Tatsuya, Smith, A Ian, Ge, Zongyuan, Wang, Jiawei, Lithgow, Trevor, Song, Jiangning

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Delays Induce Novel Stochastic Effects in Negative Feedback Gene Circuits von Zavala, Eder, Marquez-Lago, Tatiana T.

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Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods von Li, Fuyi, Wang, Yanan, Li, Chen, Marquez-Lago, Tatiana T, Leier, André, Rawlings, Neil D, Haffari, Gholamreza, Revote, Jerico, Akutsu, Tatsuya, Chou, Kuo-Chen, Purcell, Anthony W, Pike, Robert N, Webb, Geoffrey I, Ian Smith, A, Lithgow, Trevor, Daly, Roger J, Whisstock, James C, Song, Jiangning

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Diet in Southern Chile (36°-42°S). A synthesis from the isotopic data von Campbell, Roberto, Santana-Sagredo, Francisca, Munita, Doina, Mera, Rodrigo, Massone, Mauricio, Andrade, Pedro, Sánchez, Marco, Márquez, Tatiana

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DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites von Li, Fuyi, Chen, Jinxiang, Leier, André, Marquez-Lago, Tatiana, Liu, Quanzhong, Wang, Yanze, Revote, Jerico, Smith, A Ian, Akutsu, Tatsuya, Webb, Geoffrey I, Kurgan, Lukasz, Song, Jiangning

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Simulating Stochastic Reaction-Diffusion Systems on and within Moving Boundaries von Ghosh, Atiyo, Marquez-Lago, Tatiana T

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Asymmetrical Inheritance of Plasmids Depends on Dynamic Cellular Geometry and Volume Exclusion Effects von Denton, Jai A, Ghosh, Atiyo, Marquez-Lago, Tatiana T

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