Improved techniques for the identification of pseudogenes. - Lachlan James M. Coin; Richard Durbin (ISMB/ECCB (Supplement of Bioinformatics), 2004)

Enhanced protein domain discovery using taxonomy. - Lachlan James M. Coin; Alex Bateman; Richard Durbin (BMC Bioinform., 2004)

The Pfam protein families database. - Alex Bateman; Lachlan James M. Coin; Richard Durbin; Robert D. Finn; Volker Hollich; Sam Griffiths-Jones; Ajay Khanna; Mhairi Marshall; Simon Moxon; Erik L. L. Sonnhammer; David J. Studholme; Corin Yeats; et al. (Nucleic Acids Res., 2004)

TreeFam: a curated database of phylogenetic trees of animal gene families. - Heng Li 002; Avril Coghlan; Jue Ruan; Lachlan James M. Coin; Jean-Karim Hériché; Lara Osmotherly; Ruiqiang Li; Tao Liu; Zhang Zhang 002; Lars Bolund; Gane Ka-Shu Wong; Wei-Mou Zheng; et al. (Nucleic Acids Res., 2006)

Disease association tests by inferring ancestral haplotypes using a hidden markov model. - Shu-Yi Su; David J. Balding; Lachlan J. M. Coin (Bioinform., 2008)

Inference of haplotypic phase and missing genotypes in polyploid organisms and variable copy number genomic regions. - Shu-Yi Su; Jonathan White; David J. Balding; Lachlan J. M. Coin (BMC Bioinform., 2008)

TreeFam: 2008 Update. - Jue Ruan; Heng Li 002; Zhongzhong Chen; Avril Coghlan; Lachlan James M. Coin; Yiran Guo; Jean-Karim Hériché; Yafeng Hu; Karsten Kristiansen; Ruiqiang Li; Tao Liu; Alan Moses; et al. (Nucleic Acids Res., 2008)

invertFREGENE: software for simulating inversions in population genetic data. - Paul F. O'Reilly; Lachlan J. M. Coin; Clive J. Hoggart (Bioinform., 2010)

Inferring combined CNV/SNP haplotypes from genotype data. - Shu-Yi Su; Julian E. Asher; Marjo-Riitta Järvelin; Philippe Froguel; Alexandra I. F. Blakemore; David J. Balding; Lachlan J. M. Coin (Bioinform., 2010)

famCNV: copy number variant association for quantitative traits in families. - Hariklia Eleftherohorinou; Johanna C. Andersson-Assarsson; Robin G. Walters; Julia S. El-Sayed Moustafa; Lachlan J. M. Coin; Peter Jacobson; Lena M. S. Carlsson; Alexandra I. F. Blakemore; Philippe Froguel; Andrew J. Walley; Mario Falchi (Bioinform., 2011)

An exome sequencing pipeline for identifying and genotyping common CNVs associated with disease with application to psoriasis. - Lachlan James M. Coin; Dandan Cao; Jingjing Ren; Xianbo Zuo; Liangdan Sun; Sen Yang; Xuejun Zhang; Yong Cui; Yingrui Li; Xin Jin; Jun Wang 004 (Bioinform., 2012)

YHap: a population model for probabilistic assignment of Y haplogroups from re-sequencing data. - Fan Zhang 090; Ruoyan Chen; Dongbing Liu; Xiaotian Yao; Guoqing Li; Yabin Jin; Chang Yu; Yingrui Li; Lachlan James M. Coin (BMC Bioinform., 2013)

cnvOffSeq: detecting intergenic copy number variation using off-target exome sequencing data. - Evangelos Bellos 002; Lachlan J. M. Coin (Bioinform., 2014)

Realtime analysis and visualization of MinION sequencing data with npReader. - Minh Duc Cao; Devika Ganesamoorthy; Matthew A. Cooper; Lachlan J. M. Coin (Bioinform., 2016)

Real-time demultiplexing Nanopore barcoded sequencing data with npBarcode. - Son Hoang Nguyen; Tania P. S. Duarte; Lachlan J. M. Coin; Minh Duc Cao (Bioinform., 2017)

Simulating the dynamics of targeted capture sequencing with CapSim. - Minh Duc Cao; Devika Ganesamoorthy; Chenxi Zhou; Lachlan J. M. Coin (Bioinform., 2018)

GtTR: Bayesian estimation of absolute tandem repeat copy number using sequence capture and high throughput sequencing. - Devika Ganesamoorthy; Minh Duc Cao; Tania P. S. Duarte; Wenhan Chen; Lachlan James M. Coin (BMC Bioinform., 2018)

npInv: accurate detection and genotyping of inversions using long read sub-alignment. - Haojing Shao; Devika Ganesamoorthy; Tania P. S. Duarte; Minh Duc Cao; Clive J. Hoggart; Lachlan J. M. Coin (BMC Bioinform., 2018)

Porpoise: a new approach for accurate prediction of RNA pseudouridine sites. - Fuyi Li; Xudong Guo; Peipei Jin; Jinxiang Chen; Dongxu Xiang; Jiangning Song; Lachlan J. M. Coin (Briefings Bioinform., 2021)

Real-time resolution of short-read assembly graph using ONT long reads. - Son Hoang Nguyen; Minh Duc Cao; Lachlan J. M. Coin (PLoS Comput. Biol., 2021)

Positive-unlabeled learning in bioinformatics and computational biology: a brief review. - Fuyi Li; Shuangyu Dong; André Leier; Meiya Han; Xudong Guo; Jing Xu 008; Xiaoyu Wang 016; Shirui Pan; Cangzhi Jia; Yang Zhang 010; Geoffrey I. Webb; Lachlan J. M. Coin; et al. (Briefings Bioinform., 2022)

Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction. - Meng Zhang 046; Cangzhi Jia; Fuyi Li; Chen Li 021; Yan Zhu 006; Tatsuya Akutsu; Geoffrey I. Webb; Quan Zou 001; Lachlan J. M. Coin; Jiangning Song (Briefings Bioinform., 2022)

DeepGenGrep: a general deep learning-based predictor for multiple genomic signals and regions. - Quanzhong Liu; Honglin Fang; Xiao Wang; Miao Wang; Shuqin Li; Lachlan J. M. Coin; Fuyi Li; Jiangning Song (Bioinform., 2022)

Nanoq: ultra-fast quality control for nanopore reads. - Eike Steinig; Lachlan J. M. Coin (J. Open Source Softw., 2022)

ATTIC is an integrated approach for predicting A-to-I RNA editing sites in three species. - Ruyi Chen; Fuyi Li; Xudong Guo; Yue Bi; Chen Li 021; Shirui Pan; Lachlan J. M. Coin; Jiangning Song (Briefings Bioinform., 2023)

TIMER is a Siamese neural network-based framework for identifying both general and species-specific bacterial promoters. - Yan Zhu 006; Fuyi Li; Xudong Guo; Xiaoyu Wang 016; Lachlan J. M. Coin; Geoffrey I. Webb; Jiangning Song; Cangzhi Jia (Briefings Bioinform., 2023)

ProsperousPlus: a one-stop and comprehensive platform for accurate protease-specific substrate cleavage prediction and machine-learning model construction. - Fuyi Li; Cong Wang 044; Xudong Guo; Tatsuya Akutsu; Geoffrey I. Webb; Lachlan J. M. Coin; Lukasz A. Kurgan; Jiangning Song (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)

PLANNER: A Multi-Scale Deep Language Model for the Origins of Replication Site Prediction. - Cong Wang 044; Zhijie He; Runchang Jia; Shirui Pan; Lachlan J. M. Coin; Jiangning Song; Fuyi Li (IEEE J. Biomed. Health Informatics, 2024)