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Journal Articles
- 2024
[j27]Cong Wang, Zhijie He, Runchang Jia, Shirui Pan, Lachlan J. M. Coin, Jiangning Song, Fuyi Li:
PLANNER: A Multi-Scale Deep Language Model for the Origins of Replication Site Prediction. IEEE J. Biomed. Health Informatics 28(4): 2445-2454 (2024)- 2023
- [j26]Ruyi Chen, Fuyi Li
, Xudong Guo, Yue Bi, Chen Li, Shirui Pan, Lachlan J. M. Coin, Jiangning Song:
ATTIC is an integrated approach for predicting A-to-I RNA editing sites in three species. Briefings Bioinform. 24(3) (2023) - [j25]Yan Zhu, Fuyi Li, Xudong Guo, Xiaoyu Wang, Lachlan J. M. Coin, Geoffrey I. Webb, Jiangning Song, Cangzhi Jia:
TIMER is a Siamese neural network-based framework for identifying both general and species-specific bacterial promoters. Briefings Bioinform. 24(4) (2023) - [j24]Fuyi Li, Xudong Guo, Yue Bi, Runchang Jia, Miranda E. Pitt, Shirui Pan, Shuqin Li, Robin B. Gasser, Lachlan J. M. Coin, Jiangning Song:
Digerati - A multipath parallel hybrid deep learning framework for the identification of mycobacterial PE/PPE proteins. Comput. Biol. Medicine 163: 107155 (2023) - 2022
- [j23]Fuyi Li, Shuangyu Dong, André Leier, Meiya Han, Xudong Guo, Jing Xu, Xiaoyu Wang, Shirui Pan, Cangzhi Jia, Yang Zhang, Geoffrey I. Webb, Lachlan J. M. Coin, Chen Li, Jiangning Song:
Positive-unlabeled learning in bioinformatics and computational biology: a brief review. Briefings Bioinform. 23(1) (2022) - [j22]Meng Zhang, Cangzhi Jia, Fuyi Li, Chen Li, Yan Zhu, Tatsuya Akutsu, Geoffrey I. Webb, Quan Zou, Lachlan J. M. Coin, Jiangning Song:
Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction. Briefings Bioinform. 23(2) (2022) - [j21]Quanzhong Liu, Honglin Fang, Xiao Wang, Miao Wang, Shuqin Li, Lachlan J. M. Coin, Fuyi Li, Jiangning Song:
DeepGenGrep: a general deep learning-based predictor for multiple genomic signals and regions. Bioinform. 38(17): 4053-4061 (2022) - [j20]Eike Steinig, Lachlan J. M. Coin:
Nanoq: ultra-fast quality control for nanopore reads. J. Open Source Softw. 7(69): 2991 (2022) - 2021
- [j19]Fuyi Li, Xudong Guo, Peipei Jin, Jinxiang Chen, Dongxu Xiang, Jiangning Song, Lachlan J. M. Coin:
Porpoise: a new approach for accurate prediction of RNA pseudouridine sites. Briefings Bioinform. 22(6) (2021) - [j18]Son Hoang Nguyen, Minh Duc Cao, Lachlan J. M. Coin:
Real-time resolution of short-read assembly graph using ONT long reads. PLoS Comput. Biol. 17(1) (2021) - 2018
- [j17]Minh Duc Cao, Devika Ganesamoorthy, Chenxi Zhou, Lachlan J. M. Coin:
Simulating the dynamics of targeted capture sequencing with CapSim. Bioinform. 34(5): 873-874 (2018) - [j16]Haojing Shao, Devika Ganesamoorthy, Tania P. S. Duarte, Minh Duc Cao, Clive J. Hoggart, Lachlan J. M. Coin:
npInv: accurate detection and genotyping of inversions using long read sub-alignment. BMC Bioinform. 19(1): 261:1-261:13 (2018) - [j15]Devika Ganesamoorthy, Minh Duc Cao, Tania P. S. Duarte, Wenhan Chen, Lachlan James M. Coin:
GtTR: Bayesian estimation of absolute tandem repeat copy number using sequence capture and high throughput sequencing. BMC Bioinform. 19(1): 267:1-267:14 (2018) - 2017
- [j14]Son Hoang Nguyen, Tania P. S. Duarte, Lachlan J. M. Coin, Minh Duc Cao:
Real-time demultiplexing Nanopore barcoded sequencing data with npBarcode. Bioinform. 33(24): 3988-3990 (2017) - 2016
- [j13]Minh Duc Cao, Devika Ganesamoorthy, Matthew A. Cooper, Lachlan J. M. Coin:
Realtime analysis and visualization of MinION sequencing data with npReader. Bioinform. 32(5): 764-766 (2016) - 2014
- [j12]Evangelos Bellos, Lachlan J. M. Coin:
cnvOffSeq: detecting intergenic copy number variation using off-target exome sequencing data. Bioinform. 30(17): 639-645 (2014) - 2013
- [j11]Fan Zhang, Ruoyan Chen, Dongbing Liu, Xiaotian Yao, Guoqing Li, Yabin Jin, Chang Yu, Yingrui Li, Lachlan James M. Coin:
YHap: a population model for probabilistic assignment of Y haplogroups from re-sequencing data. BMC Bioinform. 14: 331 (2013) - 2012
- [j10]Lachlan James M. Coin, Dandan Cao, Jingjing Ren, Xianbo Zuo, Liangdan Sun, Sen Yang, Xuejun Zhang, Yong Cui, Yingrui Li, Xin Jin, Jun Wang:
An exome sequencing pipeline for identifying and genotyping common CNVs associated with disease with application to psoriasis. Bioinform. 28(18): 370-374 (2012) - 2011
- [j9]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:
famCNV: copy number variant association for quantitative traits in families. Bioinform. 27(13): 1873-1875 (2011) - 2010
- [j8]Paul F. O'Reilly, Lachlan J. M. Coin, Clive J. Hoggart:
invertFREGENE: software for simulating inversions in population genetic data. Bioinform. 26(6): 838-840 (2010) - [j7]Shu-Yi Su, Julian E. Asher, Marjo-Riitta Järvelin, Philippe Froguel, Alexandra I. F. Blakemore, David J. Balding, Lachlan J. M. Coin:
Inferring combined CNV/SNP haplotypes from genotype data. Bioinform. 26(11): 1437-1445 (2010) - 2008
- [j6]Shu-Yi Su, David J. Balding, Lachlan J. M. Coin:
Disease association tests by inferring ancestral haplotypes using a hidden markov model. Bioinform. 24(7): 972-978 (2008) - [j5]Shu-Yi Su, Jonathan White, David J. Balding, Lachlan J. M. Coin:
Inference of haplotypic phase and missing genotypes in polyploid organisms and variable copy number genomic regions. BMC Bioinform. 9 (2008) - [j4]Jue Ruan, Heng Li, Zhongzhong Chen, Avril Coghlan, Lachlan James M. Coin, Yiran Guo, Jean-Karim Hériché, Yafeng Hu, Karsten Kristiansen, Ruiqiang Li, Tao Liu, Alan Moses, Junjie Qin, Søren Vang, Albert J. Vilella, Abel Ureta-Vidal, Lars Bolund, Jun Wang, Richard Durbin:
TreeFam: 2008 Update. Nucleic Acids Res. 36(Database-Issue): 735-740 (2008) - 2006
- [j3]Heng Li, Avril Coghlan, Jue Ruan, Lachlan James M. Coin, Jean-Karim Hériché, Lara Osmotherly, Ruiqiang Li, Tao Liu, Zhang Zhang, Lars Bolund, Gane Ka-Shu Wong, Wei-Mou Zheng, Paramvir Dehal, Jun Wang, Richard Durbin:
TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res. 34(Database-Issue): 572-580 (2006) - 2004
- [j2]Lachlan James M. Coin, Alex Bateman, Richard Durbin:
Enhanced protein domain discovery using taxonomy. BMC Bioinform. 5: 56 (2004) - [j1]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, Sean R. Eddy:
The Pfam protein families database. Nucleic Acids Res. 32(Database-Issue): 138-141 (2004)
Conference and Workshop Papers
- 2004
- [c1]Lachlan James M. Coin, Richard Durbin:
Improved techniques for the identification of pseudogenes. ISMB/ECCB (Supplement of Bioinformatics) 2004: 94-100
Coauthor Index
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