Tatiana T. Marquez-Lago - researchr alias

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Viewing Publication 1 - 29 from 29

2023

The hitchhikers' guide to RNA sequencing and functional analysisJiung-Wen Chen, Lisa Shrestha, George Green, André Leier, Tatiana T. Marquez-Lago. bib, 24(1), January 2023. [doi]

2021

BigFiRSt: A Software Program Using Big Data Technique for Mining Simple Sequence Repeats From Large-Scale Sequencing DataJinxiang Chen, Fuyi Li, Miao Wang, Junlong Li, Tatiana T. Marquez-Lago, André Leier, Jerico Revote, Shuqin Li, Quanzhong Liu, Jiangning Song. fdata, 4, 2021. [doi]

BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteriaJiawei Wang, Jiahui Li, Yi Hou, Wei Dai, Ruopeng Xie, Tatiana T. Marquez-Lago, André Leier, Tieli Zhou, Von Torres, Iain Hay, Christopher Stubenrauch, Yanju Zhang, Jiangning Song, Trevor Lithgow. nar, 49(Database-Issue), 2021. [doi]

DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategyRuopeng Xie, Jiahui Li, Jiawei Wang, Wei Dai, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Trevor Lithgow, Jiangning Song, Yanju Zhang. bib, 22(3), 2021. [doi]

Comprehensive assessment of machine learning-based methods for predicting antimicrobial peptidesJing Xu, Fuyi Li, André Leier, Dongxu Xiang, Hsin-Hui Shen, Tatiana T. Marquez-Lago, Jian Li, Dong-jun Yu, Jiangning Song. bib, 22(5), 2021. [doi]

2020

PROSPECT: A web server for predicting protein histidine phosphorylation sitesZhen Chen 0009, Pei Zhao, Fuyi Li, André Leier, Tatiana T. Marquez-Lago, Geoffrey I. Webb, Abdelkader Baggag, Halima Bensmail, Jiangning Song. jbcb, 18(4), 2020. [doi]

iLearn : an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence dataZhen Chen, Pei Zhao, Fuyi Li, Tatiana T. Marquez-Lago, André Leier, Jerico Nico De Leon Revote, Yan Zhu, David R. Powell, Tatsuya Akutsu, Geoffrey I. Webb, Kuo-Chen Chou, Alexander Ian Smith, Roger J. Daly, Jian Li, Jiangning Song. bib, 21(3):1047-1057, 2020. [doi]

Procleave: Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural InformationFuyi Li, André Leier, Quanzhong Liu, Yanan Wang, Dongxu Xiang, Tatsuya Akutsu, Geoffrey I. Webb, Alexander Ian Smith, Tatiana T. Marquez-Lago, Jian Li 0052, Jiangning Song. gpb, 18(1):52-64, 2020. [doi]

PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impactFuyi Li, Cunshuo Fan, Tatiana T. Marquez-Lago, André Leier, Jerico Nico De Leon Revote, Cangzhi Jia, Yan Zhu, Alexander Ian Smith, Geoffrey I. Webb, Quanzhong Liu, Leyi Wei, Jian Li, Jiangning Song. bib, 21(3):1069-1079, 2020. [doi]

DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sitesFuyi Li, Jinxiang Chen, André Leier, Tatiana T. Marquez-Lago, Quanzhong Liu, Yanze Wang, Jerico Nico De Leon Revote, Alexander Ian Smith, Tatsuya Akutsu, Geoffrey I. Webb, Lukasz A. Kurgan, Jiangning Song. bioinformatics, 36(4):1057-1065, 2020. [doi]

A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding predictionShutao Mei, Fuyi Li, André Leier, Tatiana T. Marquez-Lago, Kailin Giam, Nathan P. Croft, Tatsuya Akutsu, A. Ian Smith, Jian Li, Jamie Rossjohn, Anthony W. Purcell, Jiangning Song. bib, 21(4):1119-1135, 2020. [doi]

Prediction of secondary structure population and intrinsic disorder of proteins using multitask deep learningYing Xu, André Leier, Tatiana T. Marquez-Lago, Jue Xie, Antonio Jimeno-Yepes, James C. Whisstock, Campbell Wilson, Jiangning Song. amia 2020: [doi]

PhosTransfer: A Deep Transfer Learning Framework for Kinase-Specific Phosphorylation Site Prediction in HierarchyYing Xu, Campbell Wilson, André Leier, Tatiana T. Marquez-Lago, James C. Whisstock, Jiangning Song. pakdd 2020: 384-395 [doi]

PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteinsYanju Zhang, Sha Yu, Ruopeng Xie, Jiahui Li, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Alexander Ian Smith, ZongYuan Ge, Jiawei Wang, Trevor Lithgow, Jiangning Song. bioinformatics, 36(3):704-712, 2020. [doi]

2019

Large-scale comparative assessment of computational predictors for lysine post-translational modification sitesZhen Chen, Xuhan Liu, Fuyi Li, Chen Li 0021, Tatiana T. Marquez-Lago, André Leier, Tatsuya Akutsu, Geoffrey I. Webb, Dakang Xu, Alexander Ian Smith, Lei Li 0013, Kuo-Chen Chou, Jiangning Song. bib, 20(6):2267-2290, 2019. [doi]

Bastion3: a two-layer ensemble predictor of type III secreted effectorsJiawei Wang, Jiahui Li, Bingjiao Yang, Ruopeng Xie, Tatiana T. Marquez-Lago, André Leier, Morihiro Hayashida, Tatsuya Akutsu, Yanju Zhang, Kuo-Chen Chou, Joel Selkrig, Tieli Zhou, Jiangning Song, Trevor Lithgow. bioinformatics, 35(12):2017-2028, 2019. [doi]

Systematic analysis and prediction of type IV secreted effector proteins by machine learning approachesJiawei Wang, Bingjiao Yang, Yi An, Tatiana T. Marquez-Lago, André Leier, Jonathan Wilksch, Qingyang Hong, Yang Zhang 0010, Morihiro Hayashida, Tatsuya Akutsu, Geoffrey I. Webb, Richard A. Strugnell, Jiangning Song, Trevor Lithgow. bib, 20(3):931-951, 2019. [doi]

MULTiPly: a novel multi-layer predictor for discovering general and specific types of promotersMeng Zhang, Fuyi Li, Tatiana T. Marquez-Lago, André Leier, Cunshuo Fan, Chee Keong Kwoh, Kuo-Chen Chou, Jiangning Song, Cangzhi Jia. bioinformatics, 35(17):2957-2965, 2019. [doi]

Computational analysis and prediction of lysine malonylation sites by exploiting informative features in an integrative machine-learning frameworkYanju Zhang, Ruopeng Xie, Jiawei Wang, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Geoffrey I. Webb, Kuo-Chen Chou, Jiangning Song. bib, 20(6):2185-2199, 2019. [doi]

2018

Comprehensive assessment and performance improvement of effector protein predictors for bacterial secretion systems III, IV and VIYi An, Jiawei Wang, Chen Li, André Leier, Tatiana T. Marquez-Lago, Jonathan Wilksch, Yang Zhang, Geoffrey I. Webb, Jiangning Song, Trevor Lithgow. bib, 19(1):148-161, 2018. [doi]

iFeature: a Python package and web server for features extraction and selection from protein and peptide sequencesZhen Chen, Pei Zhao, Fuyi Li, André Leier, Tatiana T. Marquez-Lago, Yanan Wang, Geoffrey I. Webb, A. Ian Smith, Roger J. Daly, Kuo-Chen Chou, Jiangning Song. bioinformatics, 34(14):2499-2502, 2018. [doi]

Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteomeFuyi Li, Chen Li 0021, Tatiana T. Marquez-Lago, André Leier, Tatsuya Akutsu, Anthony W. Purcell, A. Ian Smith, Trevor Lithgow, Roger J. Daly, Jiangning Song, Kuo-Chen Chou. bioinformatics, 34(24):4223-4231, 2018. [doi]

PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracyJiangning Song, Fuyi Li, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Gholamreza Haffari, Kuo-Chen Chou, Geoffrey I. Webb, Robert N. Pike. bioinformatics, 34(4):684-687, 2018. [doi]

Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectorsJiawei Wang, Bingjiao Yang, André Leier, Tatiana T. Marquez-Lago, Morihiro Hayashida, Andrea Rocker, Yanju Zhang, Tatsuya Akutsu, Kuo-Chen Chou, Richard A. Strugnell, Jiangning Song, Trevor Lithgow. bioinformatics, 34(15):2546-2555, 2018. [doi]

2017

POSSUM: a bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profilesJiawei Wang, Bingjiao Yang, Jerico Nico De Leon Revote, André Leier, Tatiana T. Marquez-Lago, Geoffrey I. Webb, Jiangning Song, Kuo-Chen Chou, Trevor Lithgow. bioinformatics, 33(17):2756-2758, 2017. [doi]

2014

The Long and Viscous Road: Uncovering Nuclear Diffusion Barriers in Closed MitosisEder Zavala, Tatiana T. Marquez-Lago. ploscb, 10(7), 2014. [doi]

2011

Stochastic adaptation and fold-change detection: from single-cell to population behaviorTatiana T. Marquez-Lago, André Leier. bmcsb, 5:22, 2011. [doi]

2010

Probability distributed time delays: integrating spatial effects into temporal modelsTatiana T. Marquez-Lago, André Leier, Kevin Burrage. bmcsb, 4:19, 2010. [doi]

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