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List of works by Lachlan Coin

A census of human cancer genes

scientific article

A complete high-quality MinION nanopore assembly of an extensively drug-resistant Mycobacterium tuberculosis Beijing lineage strain identifies novel variation in repetitive PE/PPE gene regions.

scientific article

A genome-wide association search for type 2 diabetes genes in African Americans

scientific article published on 4 January 2012

A new highly penetrant form of obesity due to deletions on chromosome 16p11.2.

scientific article

A new scoring system derived from base excess and platelet count at presentation predicts mortality in paediatric meningococcal sepsis

scientific article published on 11 April 2013

A population model for genotyping indels from next-generation sequence data.

scientific article

An exome sequencing pipeline for identifying and genotyping common CNVs associated with disease with application to psoriasis

scientific article

Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations

scientific article published on 30 October 2020

Bioinformatics: living on the edge ⬇️

scientific article published on October 26, 2012

Childhood tuberculosis is associated with decreased abundance of T cell gene transcripts and impaired T cell function.

scientific article

Chiron: Translating nanopore raw signal directly into nucleotide sequence using deep learning

scientific article published on 10 April 2018

Complete Genome Sequence of Klebsiella quasipneumoniae subsp. similipneumoniae Strain ATCC 700603

scientific article (publication date: 26 May 2016)

Correction: Genome-Wide Association Scan Meta-Analysis Identifies Three Loci Influencing Adiposity and Fat Distribution.

scientific article published on 27 July 2009

Correction: Genome-Wide Association Studies of Asthma in Population-Based Cohorts Confirm Known and Suggested Loci and Identify an Additional Association near HLA

scientific article published in PLoS ONE

Cross-Border Movement of Highly Drug-Resistant Mycobacterium tuberculosis from Papua New Guinea to Australia through Torres Strait Protected Zone, 2010-2015

article

Demographic and motor features associated with the occurrence of neuropsychiatric and sleep complications of Parkinson's disease

scientific article

Detection of tuberculosis in HIV-infected and -uninfected African adults using whole blood RNA expression signatures: a case-control study

scientific article (publication date: October 2013)

Diagnosis of Bacterial Infection Using a 2-Transcript Host RNA Signature in Febrile Infants 60 Days or Younger

scientific article published on April 2017

Diagnosis of Kawasaki Disease Using a Minimal Whole-Blood Gene Expression Signature

article

Diagnosis of childhood tuberculosis and host RNA expression in Africa

scientific article published in May 2014

Disease association tests by inferring ancestral haplotypes using a hidden markov model

scientific article published on 23 February 2008

Enhanced protein domain discovery by using language modeling techniques from speech recognition.

scientific article

Enhanced protein domain discovery using taxonomy

scientific article

Erratum: Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution

scientific article published in November 2011

Erratum: New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk

scientific article published in May 2010

Estimating parasite load dynamics to reveal novel resistance mechanisms to human malaria

article

Evaluating the genome and resistome of extensively drug-resistant Klebsiella pneumoniae using native DNA and RNA Nanopore sequencing

scientific article published on 01 February 2020

GWAS on longitudinal growth traits reveals different genetic factors influencing infant, child, and adult BMI

scientific article published on 04 September 2019

Gene-targeted analysis of copy number variants identifies 3 novel associations with coronary heart disease traits.

scientific article

Genetic Loci associated with C-reactive protein levels and risk of coronary heart disease

scientific article

Genetic Variation in the SLC8A1 Calcium Signaling Pathway Is Associated With Susceptibility to Kawasaki Disease and Coronary Artery Abnormalities

scientific article

Genetic evidence of assortative mating in humans

article

Genetic variability in the regulation of gene expression in ten regions of the human brain

scientific article

Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement

scientific article published in Nature Communications

Genome-wide association analysis of metabolic traits in a birth cohort from a founder population

scientific article

Genome-wide association and genetic functional studies identify autism susceptibility candidate 2 gene (AUTS2) in the regulation of alcohol consumption

scientific journal article

Genome-wide association scan meta-analysis identifies three Loci influencing adiposity and fat distribution

scientific article published in June 2009

Genome-wide association studies of asthma in population-based cohorts confirm known and suggested loci and identify an additional association near HLA.

scientific article

Genome-wide association study for early-onset and morbid adult obesity identifies three new risk loci in European populations

scientific article

Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma

scientific article published on 16 October 2011

Genotype-free demultiplexing of pooled single-cell RNA-seq

scientific article published on 19 December 2019

GtTR: Bayesian estimation of absolute tandem repeat copy number using sequence capture and high throughput sequencing

scholarly article by Devika Ganesamoorthy published in July 2018

Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads.

scientific article

Highly interconnected genes in disease-specific networks are enriched for disease-associated polymorphisms

scientific article published on 15 June 2012

Hundreds of variants clustered in genomic loci and biological pathways affect human height

scientific article

Identification of regulatory variants associated with genetic susceptibility to meningococcal disease

scientific article published on 06 May 2019

Improved techniques for the identification of pseudogenes

scientific article published in 2004

Inference of haplotypic phase and missing genotypes in polyploid organisms and variable copy number genomic regions

scientific article

Inferring combined CNV/SNP haplotypes from genotype data

scientific article

Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes

scientific article published on 05 September 2018

Investigation of the HIN200 locus in UK SLE families identifies novel copy number variants

scientific article published on 14 March 2011

Long-Read RNA Sequencing Identifies Polyadenylation Elongation and Differential Transcript Usage of Host Transcripts During SARS-CoV-2 <i>In Vitro</i> Infection

scientific article published on 06 April 2022

MERITS: a web-based integrated <i>Mycobacterial</i> PE/PPE protein database

scientific article published in 2024

Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution

scientific article

Meta-analysis of genome-wide association studies identifies ten loci influencing allergic sensitization

scientific article

Metabolic profiling of polycystic ovary syndrome reveals interactions with abdominal obesity

scientific article published on 26 May 2017

Mirror extreme BMI phenotypes associated with gene dosage at the chromosome 16p11.2 locus

scientific article

Modelling pathogen load dynamics to elucidate mechanistic determinants of host-Plasmodium falciparum interactions

scientific article published on 17 June 2019

Multi-clonal evolution of multi-drug-resistant/extensively drug-resistant Mycobacterium tuberculosis in a high-prevalence setting of Papua New Guinea for over three decades

scientific article published on 4 January 2018

Multifactorial chromosomal variants regulate polymyxin resistance in extensively drug-resistant Klebsiella pneumoniae

scientific article published on 12 February 2018

Mycobacterium tuberculosis Exploits a Molecular Off Switch of the Immune System for Intracellular Survival

scientific article

Nanopore sequencing as a scalable, cost-effective platform for analyzing polyclonal vector integration sites following clinical T cell therapy

scientific article published on 01 June 2020

Nanoq: ultra-fast quality control for nanopore reads

scientific article published on 08 January 2022

New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk

scientific article

Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals

scientific article

Octapeptin C4 Induces Less Resistance and Novel Mutations in an Epidemic Carbapenemase-producing Klebsiella pneumoniae ST258 Clinical Isolate Compared to Polymyxins

article by Miranda Pitt et al published 28 April 2018 in bioRxiv

Octapeptin C4 and polymyxin resistance occur via distinct pathways in an epidemic XDR Klebsiella pneumoniae ST258 isolate

scientific article published on 01 March 2019

Ongoing human chromosome end extension revealed by analysis of BioNano and nanopore data

scientific article published in Scientific Reports

Pathway analysis of GWAS provides new insights into genetic susceptibility to 3 inflammatory diseases

scientific article

Pathway-driven gene stability selection of two rheumatoid arthritis GWAS identifies and validates new susceptibility genes in receptor mediated signalling pathways

scientific journal article

Phase I Trial of Inducible Caspase 9 T Cells in Adult Stem Cell Transplant Demonstrates Massive Clonotypic Proliferative Potential and Long-term Persistence of Transgenic T Cells

scientific article published on 14 February 2019

Point Mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant

scientific article

Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences

scientific article

Rapid diagnosis of Capnocytophaga canimorsus septic shock in an immunocompetent individual using real-time Nanopore sequencing: a case report

scientific article published on 24 July 2019

Real-time demultiplexing Nanopore barcoded sequencing data with npBarcode

scientific article published on 24 August 2017

Real-time resolution of short-read assembly graph using ONT long reads

scientific article published on 20 January 2021

Realtime analysis and visualization of MinION sequencing data with npReader.

scientific article

Retooling phage display with electrohydrodynamic nanomixing and nanopore sequencing

scientific article published on 12 November 2019

Scaffolding and completing genome assemblies in real-time with nanopore sequencing

scientific article published on 20 February 2017

Simulating the Dynamics of Targeted Capture Sequencing with CapSim

scientific article published on 28 October 2017

Six new loci associated with body mass index highlight a neuronal influence on body weight regulation

scientific article

Small deletion variants have stable breakpoints commonly associated with alu elements.

scientific article

Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinION sequencing

scholarly article published 15 May 2015

Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinION(TM) sequencing

scientific article published on 26 July 2016

Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly

scientific article

TTC12-ANKK1-DRD2 and CHRNA5-CHRNA3-CHRNB4 influence different pathways leading to smoking behavior from adolescence to mid-adulthood

scientific article

The Pfam protein families database

scientific article (publication date: 2004)

The effect of genomic inversions on estimation of population genetic parameters from SNP data

scientific article

Transcriptional and epi-transcriptional dynamics of SARS-CoV-2 during cellular infection

scientific article published on 23 April 2021

Transcriptomic Studies of Malaria: a Paradigm for Investigation of Systemic Host-Pathogen Interactions

scholarly article by Hyun Jae Lee et al published 1 June 2018 in Microbiology and Molecular Biology Reviews

Transforming growth factor-beta signaling pathway in patients with Kawasaki disease

scientific article

TreeFam: a curated database of phylogenetic trees of animal gene families

scientific article

Triclosan at environmentally relevant concentrations promotes horizontal transfer of multidrug resistance genes within and across bacterial genera

article

Variants in ADCY5 and near CCNL1 are associated with fetal growth and birth weight

scientific article

Variants in MTNR1B influence fasting glucose levels

scientific article

Whole genome deep sequencing analysis of cell-free DNA in samples with low tumour content

scientific article published on 20 January 2022

YHap: a population model for probabilistic assignment of Y haplogroups from re-sequencing data.

scientific article

cnvCapSeq: detecting copy number variation in long-range targeted resequencing data.

scientific article

cnvHap: an integrative population and haplotype-based multiplatform model of SNPs and CNVs

scientific article published on 30 May 2010

cnvHiTSeq: integrative models for high-resolution copy number variation detection and genotyping using population sequencing data.

scientific article

cnvOffSeq: detecting intergenic copy number variation using off-target exome sequencing data

scientific article

famCNV: copy number variant association for quantitative traits in families.

scientific article

invertFREGENE: software for simulating inversions in population genetic data.

scientific article

npInv: accurate detection and genotyping of inversions mediated by non-allelic homologous recombination using long read sub-alignment

npInv: accurate detection and genotyping of inversions using long read sub-alignment

scientific article published on 13 July 2018

sCNAphase: using haplotype resolved read depth to genotype somatic copy number alterations from low cellularity aneuploid tumors

scientific article

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