Issue Date | Title | Author(s) | Relation | scopus | WOS | Fulltext/Archive link |
2016 | An expanded evaluation of protein function prediction methods shows an improvement in accuracy | Yuxiang Jiang; Tal Ronnen Oron; Wyatt T. Clark; Asma R. Bankapur; Daniel D’Andrea; Rosalba Lepore; Christopher S. Funk; Indika Kahanda; Karin M. Verspoor; Asa Ben-Hur; Da Chen Emily Koo; Duncan Penfold-Brown; Dennis Shasha; Noah Youngs; Richard Bonneau; Alexandra Lin; Sayed M. E. Sahraeian; Pier Luigi Martelli; Giuseppe Profiti; Rita Casadio; Renzhi Cao; Zhaolong Zhong; Jianlin Cheng; Adrian Altenhoff; Nives Skunca; Christophe Dessimoz; Tunca Dogan; Kai Hakala; Suwisa Kaewphan; Farrokh Mehryary; Tapio Salakoski; Filip Ginter; Hai Fang; Ben Smithers; Matt Oates; Julian Gough; Petri Törönen; Patrik Koskinen; Liisa Holm; Ching-Tai Chen; Wen-Lian Hsu; Kevin Bryson; Domenico Cozzetto; Federico Minneci; David T. Jones; Samuel Chapman; Dukka BKC; Ishita K. Khan; Daisuke Kihara; Dan Ofer; Nadav Rappoport; Amos Stern; Elena Cibrian-Uhalte; Paul Denny; Rebecca E. Foulger; Reija Hieta; Duncan Legge; Ruth C. Lovering; Michele Magrane; Anna N. Melidoni; Prudence Mutowo-Meullenet; Klemens Pichler; Aleksandra Shypitsyna; Biao Li; Pooya Zakeri; Sarah ElShal; Léon-Charles Tranchevent; Sayoni Das; Natalie L. Dawson; David Lee; Jonathan G. Lees; Ian Sillitoe; Prajwal Bhat; Tamás Nepusz; Alfonso E. Romero; Rajkumar Sasidharan; Haixuan Yang; Alberto Paccanaro; Jesse Gillis; Adriana E. Sedeño-Cortés; Paul Pavlidis; Shou Feng; Juan M. Cejuela; Tatyana Goldberg; Tobias Hamp; Lothar Richter; Asaf Salamov; Toni Gabaldon; Marina Marcet-Houben; Fran Supek; Qingtian Gong; Wei Ning; Yuanpeng Zhou; Weidong Tian; Marco Falda; Paolo Fontana; Enrico Lavezzo; Stefano Toppo; Carlo Ferrari; Manuel Giollo; Damiano Piovesan; Silvio C.E. Tosatto; Angela del Pozo; José M. Fernández; Paolo Maietta; Alfonso Valencia; Michael L. Tress; Alfredo Benso; Stefano Di Carlo; Gianfranco Politano; Alessandro Savino; Hafeez Ur Rehman; Matteo Re; Marco Mesiti; Giorgio Valentini; Joachim W. Bargsten; Aalt D. J. van Dijk; Branislava Gemovic; Sanja Glisic; Vladmir Perovic; Veljko Veljkovic; Nevena Veljkovic; Danillo C. Almeida-e-Silva; Ricardo Z. N. Vencio; Malvika Sharan; Jörg Vogel; Lakesh Kansakar; Shanshan Zhang; Slobodan Vucetic; Zheng Wang; Michael J. E. Sternberg; Mark N. Wass; Rachael P. Huntley; Maria J. Martin; Claire O’Donovan; Peter N. Robinson; Yves Moreau; Anna Tramontano; Patricia C. Babbitt; Steven E. Brenner; Michal Linial; Christine A. Orengo; Burkhard Rost; Casey S. Greene; Sean D. Mooney; Iddo Friedbergd; Predrag Radivojac | Genome Biology 2016 17:184 | | | |
2006 | HYPLOSP: A Knowledge-based Approach to Protein Local Structure Prediction | Ching-Tai Chen; Hsin-Nan Lin; Ting-Ying Sung; Wen-Lian Hsu | Journal of Bioinformatics and Computational Biology 4(6), 1287-1307 | | | |
2016 | iMet-Q: a user-friendly tool for metabolomics quantitation using dynamic peak-width determination | Hui-Yin Chang; Ching-Tai Chen; T. Mamie Lih; Ke-Shiuan Lynn; Chiun-Gung Juo; Wen-Lian Hsu ; Ting-Yi Sung | PLoS ONE 11(1), e0146112 | | | |
2015 | Informatics View on the Challenges of Identifying Missing Proteins From Shotgun Proteomics | Wai-Kok Choong; Hui-Yin Chang; Ching-Tai Chen; Chia-Feng Tsai; Wen-Lian Hsu ; Ting-Yi Sung ; Yu-Ju Chen | Journal of Proteome Research 14(12), 5396-5407 | | | |
2017 | iTop-Q: an Intelligent Tool for Top-down Proteomics Quantitation Using DYAMOND Algorithm | Hui-Yin Chang; Ching-Tai Chen; Chu-Ling Ko; Yi-Ju Chen; Yu-Ju Chen ; Wen-Lian Hsu ; Chiun-Gung Juo; Ting-Yi Sung | Analytical Chemistry 89(24), 13128-13136 | | | |
2016 | iTop-Q: an intelligent top-down proteomics quantification tool using the DYAMOND algorithm for charge state deconvolution | Hui-Yin Chang; Ching-Tai Chen; Chiun-Gung Juo; Wen-Lian Hsu; Ting-Yi Sung | | | | |
2016 | MAGIC-web: a platform for untargeted and targeted N-linked glycoprotein identification | T. Mamie Lih; Wai-Kok Choong; Chen-Chun Chen; Cheng-Wei Cheng; Hsin-Nan Lin; Ching-Tai Chen; Hui-Yin Chang; Wen-Lian Hsu ; Ting-Yi Sung | Nucleic Acids Research 44(W1), W575-580 | | | |
2021 | Multi-Q 2 software facilitates isobaric labeling quantitation analysis with improved accuracy and coverage | Ching-Tai Chen; Jen-Hung Wang; Cheng-Wei Cheng; Wei-Che Hsu; Chu-Ling Ko; Wai-Kok Choong; Ting-Yi Sung | Scientific Reports 11, 2233 | | | |
2017 | Multi-Q 2: automated and robust isobaric labeling quantitation analysis with enhanced graphical visualization of protein ratio clustering | Ching-Tai Chen; Cheng-Wei Cheng; Wei-Jhe Hsu; Hui-Yin Chang; Chu-Ling Ko; T. Mamie Lih; Yi-Ju Chen; Yu-Ju Chen; Wen-Lian Hsu; Ting-Yi Sung | | | | |
2019 | N-GlyDE: a two-stage N-linked glycosylation site prediction incorporating gapped dipeptides and pattern-based encoding | Thejkiran Pitti; Ching-Tai Chen; Hsin-Nan Lin; Wai-Kok Choong; Wen-Lian Hsu ; Ting-Yi Sung | Scientific Reports 9, 15975 | | | |
2009 | Protein subcellular localization prediction of eukaryotes using a knowledge-based approach | Hsin-Nan Lin; Ching-Tai Chen; Ting-Yi Sung; Shinn-Ying Ho; Wen-Lian Hsu | BMC Bioinformatics 10(Suppl 15), S8 | | | |
2020 | Proteogenomics of Non-smoking Lung Cancer in East Asia Delineates Molecular Signatures of Pathogenesis and Progression | Yi-Ju Chen; Theodoros I Roumeliotis; Ya-Hsuan Chang; Ching-Tai Chen; Chia-Li Han; Miao-Hsia Lin; Huei-Wen Chen; Gee-Chen Chang; Yih-Leong Chang; Chen-Tu Wu; Mong-Wei Lin; Min-Shu Hsieh; Yu-Tai Wang; Yet-Ran Chen ; Inge Jonassen; Fatemeh Zamanzad Ghavidel; Ze-Shiang Lin; Kuen-Tyng Lin; Ching-Wen Chen; Pei-Yuan Sheu; Chen-Ting Hung; Ke-Chieh Huang; Hao-Chin Yang; Pei-Yi Lin; Ta-Chi Yen; Yi-Wei Lin; Jen-Hung Wang; Lovely Raghav; Chien-Yu Lin; Yan-Si Chen; Pei-Shan Wu; Chi-Ting Lai; Shao-Hsing Weng; Kang-Yi Su; Wei-Hung Chang; Pang-Yan Tsai; Ana I Robles; Henry Rodriguez; Yi-Jing Hsiao; Wen-Hsin Chang; Ting-Yi Sung ; Jin-Shing Chen; Sung-Liang Yu; Jyoti S Choudhary; Hsuan-Yu Chen ; Pan-Chyr Yang; Yu-Ju Chen | Cell 182(1), 226-244.e17 | | | |
2018 | WinProphet: a user-friendly pipeline management system based on Trans-Proteomic Pipeline | Ching-Tai Chen; Chu-Ling Ko; Wai-Kok Choong; Jen-Hung Wang; Wen-Lian Hsu; Ting-Yi Sung | | | | |
2019 | WinProphet: A User-Friendly Pipeline Management System for Proteomics Data Analysis Based on Trans-Proteomic Pipeline | Ching-Tai Chen; Chu-Ling Ko; Wai-Kok Choong; Jen-Hung Wang; Wen-Lian Hsu; Ting-Yi Sung | Analytical Chemistry 91(15), 9403-9406 | | | |