A hitchhiker's guide to expressed sequence tag (EST) analysis. - Shivashankar H. Nagaraj; Robin B. Gasser; Shoba Ranganathan (Briefings Bioinform., 2007)

ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform. - Shivashankar H. Nagaraj; Nandan Deshpande; Robin B. Gasser; Shoba Ranganathan (Nucleic Acids Res., 2007)

In silico analysis of expressed sequence tags from Trichostrongylus vitrinus (Nematoda): comparison of the automated ESTExplorer workflow platform with conventional database searches. - Shivashankar H. Nagaraj; Robin B. Gasser; Alasdair J. Nisbet; Shoba Ranganathan (BMC Bioinform., 2008)

SBAL: a practical tool to generate and edit structure-based amino acid sequence alignments. - Conan K. Wang; Ursula Broder; Saroja K. Weeratunga; Robin B. Gasser; Alex Loukas; Andreas Hofmann (Bioinform., 2012)

TranSeqAnnotator: large-scale analysis of transcriptomic data. - Ranjeeta Menon; Gagan Garg; Robin B. Gasser; Shoba Ranganathan (BMC Bioinform., 2012)

SchistoDB: an updated genome resource for the three key schistosomes of humans. - Adhemar Zerlotini; Eric R. G. R. Aguiar; Fudong Yu; Huayong Xu; Yixue Li; Neil D. Young; Robin B. Gasser; Anna V. Protasio; Matthew Berriman; David S. Roos; Jessica C. Kissinger; Guilherme C. Oliveira (Nucleic Acids Res., 2013)

A practical Java tool for small-molecule compound appraisal. - Parisa Amani; Todd Sneyd; Sarah Preston; Neil D. Young; Lyndel Mason; Ulla-Maja Bailey; Jonathan B. Baell; David Camp; Robin B. Gasser; Alain-Dominique Gorse; Paul Taylor; Andreas Hofmann (J. Cheminformatics, 2015)

DRfit: a Java tool for the analysis of discrete data from multi-well plate assays. - Andreas Hofmann; Sarah Preston; Megan Cross; H. M. P. Dilrukshi Herath; Anne Simon; Robin B. Gasser (BMC Bioinform., 2019)

OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines. - Sanathoi Gurumayum; Puzi Jiang; Xiaowen Hao; Tulio de Lima Campos; Neil D. Young; Pasi K. Korhonen; Robin B. Gasser; Peer Bork; Xing-Ming Zhao; Lijie He; Wei-Hua Chen (Nucleic Acids Res., 2021)

DEMoS: a deep learning-based ensemble approach for predicting the molecular subtypes of gastric adenocarcinomas from histopathological images. - Yanan Wang 003; Changyuan Hu; Terry Kwok; Christopher A. Bain; Xiangyang Xue 001; Robin B. Gasser; Geoffrey I. Webb; Alex Boussioutas; Xian Shen; Roger J. Daly; Jiangning Song (Bioinform., 2022)

PROST: AlphaFold2-aware Sequence-Based Predictor to Estimate Protein Stability Changes upon Missense Mutations. - Shahid Iqbal; Fang Ge; Fuyi Li; Tatsuya Akutsu; Yuanting Zheng; Robin B. Gasser; Dong-Jun Yu; Geoffrey I. Webb; Jiangning Song (J. Chem. Inf. Model., 2022)

iFeatureOmega: an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets. - Zhen Chen 009; Xuhan Liu; Pei Zhao; Chen Li 021; Yanan Wang 003; Fuyi Li; Tatsuya Akutsu; Chris Bain; Robin B. Gasser; Junzhou Li; Zuoren Yang; Xin Gao 001; et al. (Nucleic Acids Res., 2022)

PFresGO: an attention mechanism-based deep-learning approach for protein annotation by integrating gene ontology inter-relationships. - Tong Pan; Chen Li 021; Yue Bi; Zhikang Wang; Robin B. Gasser; Anthony W. Purcell; Tatsuya Akutsu; Geoffrey I. Webb; Seiya Imoto; Jiangning Song (Bioinform., 2023)

TripletCell: a deep metric learning framework for accurate annotation of cell types at the single-cell level. - Yan Liu 038; Guo Wei; Chen Li 021; Long-Chen Shen; Robin B. Gasser; Jiangning Song; Dijun Chen; Dong-Jun Yu (Briefings Bioinform., 2023)

Digerati - A multipath parallel hybrid deep learning framework for the identification of mycobacterial PE/PPE proteins. - Fuyi Li; Xudong Guo; Yue Bi; Runchang Jia; Miranda E. Pitt; Shirui Pan; Shuqin Li; Robin B. Gasser; Lachlan J. M. Coin; Jiangning Song (Comput. Biol. Medicine, 2023)

Deep domain adversarial neural network for the deconvolution of cell type mixtures in tissue proteome profiling. - Fang Wang 028; Fan Yang 081; Longkai Huang; Wei Li 184; Jiangning Song; Robin B. Gasser; Ruedi Aebersold; Guohua Wang; Jianhua Yao 001 (Nat. Mac. Intell., 2023)

'Bingo' - a large language model- and graph neural network-based workflow for the prediction of essential genes from protein data. - Jiani Ma; Jiangning Song; Neil D. Young; Bill C. H. Chang; Pasi K. Korhonen; Tulio L. Campos; Hui Liu 024; Robin B. Gasser (Briefings Bioinform., 2024)

scRCA: A Siamese network-based pipeline for annotating cell types using noisy single-cell RNA-seq reference data. - Yan Liu 038; Chen Li 021; Long-Chen Shen; He Yan; Guo Wei; Robin B. Gasser; Xiaohua Hu 001; Jiangning Song; Dong-Jun Yu (Comput. Biol. Medicine, 2025)

SCREEN: A Graph-based Contrastive Learning Tool to Infer Catalytic Residues and Assess Enzyme Mutations. - Tong Pan; Yue Bi; Xiaoyu Wang 016; Ying Zhang 053; Geoffrey I. Webb; Robin B. Gasser; Lukasz A. Kurgan; Jiangning Song (Genom. Proteom. Bioinform., 2025)