Lachlan Coin

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

Miranda E Pitt, Son H Nguyen, Tânia PS Duarte, Haotian Teng, Mark AT Blaskovich, Matthew A Cooper, Lachlan JM Coin

Journal article  |  2020  |  GigaScience

BACKGROUND: Klebsiella pneumoniae frequently harbours multidrug resistance, and current diagnostics struggle to rapidly identify a..

Quantitative trait loci and differential gene expression analyses reveal the genetic basis for negatively associated β-carotene and starch content in hexaploid sweetpotato [Ipomoea batatas (L.) Lam.].

Dorcus C Gemenet, Guilherme da Silva Pereira, Bert De Boeck, Joshua C Wood, Marcelo Mollinari, Bode A Olukolu, Federico Diaz, Veronica Mosquera, Reuben T Ssali, Maria David, Mercy N Kitavi, Gabriela Burgos, Thomas Zum Felde, Marc Ghislain, Edward Carey, Jolien Swanckaert, Lachlan JM Coin, Zhangjun Fei, John P Hamilton, Benard Yada, et al.

Journal article  |  2020  |  Theoretical and Applied Genetics

KEY MESSAGE: β-Carotene content in sweetpotato is associated with the Orange and phytoene synthase genes; due to physical linkage ..

Retooling phage display with electrohydrodynamic nanomixing and nanopore sequencing.

Lyndon J Raftery, Christopher B Howard, Yadveer S Grewal, Ramanathan Vaidyanathan, Martina L Jones, Will Anderson, Darren Korbie, Tania Duarte, Minh Duc Cao, Son Hoang Nguyen, Lachlan JM Coin, Stephen M Mahler, Matt Trau

Journal article  |  2019  |  Lab on a Chip

Phage display methodologies offer a versatile platform for the isolation of single-chain Fv (scFv) molecules which may be rebuilt ..

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

Jun Xu, Caitlin Falconer, Quan Nguyen, Joanna Crawford, Brett D McKinnon, Sally Mortlock, Anne Senabouth, Stacey Andersen, Han Sheng Chiu, Longda Jiang, Nathan J Palpant, Jian Yang, Michael D Mueller, Alex W Hewitt, Alice Pébay, Grant W Montgomery, Joseph E Powell, Lachlan JM Coin

Journal article  |  2019  |  Genome Biol

A variety of methods have been developed to demultiplex pooled samples in a single cell RNA sequencing (scRNA-seq) experiment whic..

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

Jun Xu, Caitlin Falconer, Quan Nguyen, Joanna Crawford, Brett D McKinnon, Sally Mortlock, Anne Senabouth, Stacey Andersen, Han Sheng Chiu, Longda Jiang, Nathan J Palpant, Jian Yang, Michael D Mueller, Alex W Hewitt, Alice Pébay, Grant W Montgomery, Joseph E Powell, Lachlan JM Coin

Journal article  |  2019  |  Genome Biology

A variety of methods have been developed to demultiplex pooled samples in a single cell RNA sequencing (scRNA-seq) experiment whic..

Plasma lipid profiles discriminate bacterial from viral infection in febrile children.

Xinzhu Wang, Ruud Nijman, Stephane Camuzeaux, Caroline Sands, Heather Jackson, Myrsini Kaforou, Marieke Emonts, Jethro A Herberg, Ian Maconochie, Enitan D Carrol, Stephane C Paulus, Werner Zenz, Michiel Van der Flier, Ronald de Groot, Federico Martinon-Torres, Luregn J Schlapbach, Andrew J Pollard, Colin Fink, Taco T Kuijpers, Suzanne Anderson, et al.

Journal article  |  2019  |  Scientific Reports

Fever is the most common reason that children present to Emergency Departments. Clinical signs and symptoms suggestive of bacteria..

Analysis of polyclonal vector integration sites using Nanopore sequencing as a scalable, cost-effective platform

Ping Zhang, Devika Ganesamoorthy, Son Hoang Nguyen, Raymond Au, Lachlan Coin, Siok-Keen Tey

Journal article  |  2019

Abstract Vector integration site analysis can be important in the follow-up of patients who received gene-modified cells, but curr..

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

Alexessander Couto Alves, N Maneka G De Silva, Ville Karhunen, Ulla Sovio, Shikta Das, H Rob Taal, Nicole M Warrington, Alexandra M Lewin, Marika Kaakinen, Diana L Cousminer, Elisabeth Thiering, Nicholas J Timpson, Tom A Bond, Estelle Lowry, Christopher D Brown, Xavier Estivill, Virpi Lindi, Jonathan P Bradfield, Frank Geller, Doug Speed, et al.

Journal article  |  2019  |  Science Advances

Early childhood growth patterns are associated with adult health, yet the genetic factors and the developmental stages involved ar..

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

Athina Georgiadou, Hyun Jae Lee, Michael Walther, Anna E van Beek, Fadlila Fitriani, Diana Wouters, Taco W Kuijpers, Davis Nwakanma, Umberto D'Alessandro, Eleanor M Riley, Thomas D Otto, Azra Ghani, Michael Levin, Lachlan J Coin, David J Conway, Michael T Bretscher, Aubrey J Cunnington

Journal article  |  2019  |  Nature Microbiology

During infection, increasing pathogen load stimulates both protective and harmful aspects of the host response. The dynamics of th..

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

Seweryn Bialasiewicz, Tania PS Duarte, Son H Nguyen, Vichitra Sukumaran, Alexandra Stewart, Sally Appleton, Miranda E Pitt, Arnold Bainomugisa, Amy V Jennison, Rikki Graham, Lachlan JM Coin, Krispin Hajkowicz

Journal article  |  2019  |  BMC Infectious Diseases

BACKGROUND: Rapid diagnosis and appropriate treatment is imperative in bacterial sepsis due increasing risk of mortality with ever..

High-throughput multiplexed tandem repeat genotyping using targeted long-read sequencing

Devika Ganesamoorthy, Mengjia Yan, Valentine Murigneux, Chenxi Zhou, Minh Duc Cao, Tania PS Duarte, Lachlan JM Coin

Journal article  |  2019

ABSTRACT Tandem repeats (TRs) are highly prone to variation in copy numbers due to their repetitive and unstable nature, which mak..

Identification of regulatory variants associated with genetic susceptibility to meningococcal disease.

Lisa Borghini, Eileen Png, Alexander Binder, Victoria J Wright, Ellie Pinnock, Ronald de Groot, Jan Hazelzet, Marieke Emonts, Michiel Van der Flier, Luregn J Schlapbach, Suzanne Anderson, Fatou Secka, Antonio Salas, Colin Fink, Enitan D Carrol, Andrew J Pollard, Lachlan J Coin, Taco W Kuijpers, Federico Martinon-Torres, Werner Zenz, et al.

Journal article  |  2019  |  Scientific Reports

Non-coding genetic variants play an important role in driving susceptibility to complex diseases but their characterization remain..

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

Ping Zhang, Jyothy Raju, Md Ashik Ullah, Raymond Au, Antiopi Varelias, Kate H Gartlan, Stuart D Olver, Luke D Samson, Elise Sturgeon, Nienke Zomerdijk, Judy Avery, Tessa Gargett, Michael P Brown, Lachlan J Coin, Devika Ganesamoorthy, Cheryl Hutchins, Gary R Pratt, Glen A Kennedy, A James Morton, Cameron I Curley, et al.

Journal article  |  2019  |  Clinical Cancer Research

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

Arnold Bainomugisa, Sushi Pandey, Ellen Donnan, Graham Simpson, J'Belle Foster, Evelyn Lavu, Stenard Hiasihri, Emma S McBryde, Rendi Moke, Steven Vincent, Vitali Sintchenko, Ben J Marais, Lachlan JM Coin, Christopher Coulter

Journal article  |  2019  |  Emerging Infectious Diseases

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

Miranda E Pitt, Duc Cao Minh, Mark S Butler, Soumya Ramu, Devika Ganesamoorthy, Mark AT Blaskovich, Lachlan JM Coin, Matthew A Cooper

Journal article  |  2019  |  Journal of Antimicrobial Chemotherapy

LobSig is a multigene predictor of outcome in invasive lobular carcinoma.

Amy E McCart Reed, Samir Lal, Jamie R Kutasovic, Leesa Wockner, Alan Robertson, Xavier M de Luca, Priyakshi Kalita-de Croft, Andrew J Dalley, Craig P Coorey, Luyu Kuo, Kaltin Ferguson, Colleen Niland, Gregory Miller, Julie Johnson, Lynne E Reid, Renique Males, Jodi M Saunus, Georgia Chenevix-Trench, Lachlan Coin, Sunil R Lakhani, et al.

Journal article  |  2019  |  npj Breast Cancer

Invasive lobular carcinoma (ILC) is the most common special type of breast cancer, and is characterized by functional loss of E-ca..

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

Ji Lu, Yue Wang, Jie Li, Likai Mao, Son Hoang Nguyen, Tania Duarte, Lachlan Coin, Philip Bond, Zhiguo Yuan, Jianhua Guo

Journal article  |  2018  |  Environment International

Evaluating the Genome and Resistome of Extensively Drug-Resistant Klebsiella pneumoniae using Native DNA and RNA Nanopore Sequencing

Miranda Pitt, Son Nguyen, Tânia PS Duarte, Mark AT Blaskovich, Matthew Cooper, Lachlan JM Coin

Journal article  |  2018

ABSTRACT Klebsiella pneumoniae frequently harbour multidrug resistance and current methodologies are struggling to rapidly discern..

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

Haojing Shao, Chenxi Zhou, Duc Cao Minh, Lachlan JM Coin

Journal article  |  2018  |  Scientific Reports

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

Shan Wu, Kin H Lau, Qinghe Cao, John P Hamilton, Honghe Sun, Chenxi Zhou, Lauren Eserman, Dorcus C Gemenet, Bode A Olukolu, Haiyan Wang, Emily Crisovan, Grant T Godden, Chen Jiao, Xin Wang, Mercy Kitavi, Norma Manrique-Carpintero, Brieanne Vaillancourt, Krystle Wiegert-Rininger, Xinsun Yang, Kan Bao, et al.

Journal article  |  2018  |  Nature Communications

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

Victoria J Wright, Jethro A Herberg, Myrsini Kaforou, Chisato Shimizu, Hariklia Eleftherohorinou, Hannah Shailes, Anouk M Barendregt, Stephanie Menikou, Stuart Gormley, Maurice Berk, Long Truong Hoang, Adriana H Tremoulet, John T Kanegaye, Lachlan JM Coin, Mary P Glode, Martin Hibberd, Taco W Kuijpers, Clive J Hoggart, Jane C Burns, Michael Levin

Journal article  |  2018  |  JAMA Pediatrics

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

Chenxi Zhou, Tania Duarte, Rocio Silvestre, Genoveva Rossel, Robert Mwanga, Awais Khan, Andrew George, Zhangjun Fei, Craig Yencho, David Ellis, Lachlan Coin

Journal article  |  2018  |  Gates Open Research

Background: The chloroplast (cp) genome is an important resource for studying plant diversity and phylogeny. Assembly of the cp ge..

Non-antibiotic antimicrobial triclosan induces multiple antibiotic resistance through genetic mutation

Ji Lu, Min Jin, Hoang Nguyen Son, Likai Mao, Jie Li, Lachlan JM Coin, Zhiguo Yuan, Jianhua Guo

Journal article  |  2018  |  Environment International

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

Devika Ganesamoorthy, Duc Cao Minh, Tania Duarte, Wenhan Chen, Lachlan Coin

Journal article  |  2018  |  BMC Bioinformatics

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

Haojing Shao, Devika Ganesamoorthy, Tania Duarte, Duc Cao Minh, Clive J Hoggart, Lachlan JM Coin

Journal article  |  2018  |  BMC Bioinformatics

Integrated pathogen load and dual transcriptome analysis of systemic host-pathogen interactions in severe malaria

Hyun Jae Lee, Athina Georgiadou, Michael Walther, Davis Nwakanma, Lindsay B Stewart, Michael Levin, Thomas D Otto, David J Conway, Lachlan J Coin, Aubrey J Cunnington

Journal article  |  2018  |  Science Translational Medicine

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

Hyun Jae Lee, Athina Georgiadou, Thomas D Otto, Michael Levin, Lachlan J Coin, David J Conway, Aubrey J Cunnington

Journal article  |  2018  |  Microbiology and Molecular Biology Reviews

Life-threatening infections in children in Europe (the EUCLIDS Project): a prospective cohort study.

Federico Martinón-Torres, Antonio Salas, Irene Rivero-Calle, Miriam Cebey-López, Jacobo Pardo-Seco, Jethro A Herberg, Navin P Boeddha, Daniela S Klobassa, Fatou Secka, Stephane Paulus, Ronald de Groot, Luregn J Schlapbach, Gertjan J Driessen, Suzanne T Anderson, Marieke Emonts, Werner Zenz, Enitan D Carrol, Michiel Van der Flier, Michael Levin, undefined EUCLIDS Consortium

Journal article  |  2018  |  The Lancet Child & Adolescent Health

BACKGROUND: Sepsis and severe focal infections represent a substantial disease burden in children admitted to hospital. We aimed t..

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

Michael Bretscher, Athina Georgiadou, Hyun Jae Lee, Michael Walther, Anna van Beek, Fadlila Fitriani, Diana Wouters, Taco Kuijpers, Davis Nwakanma, Umberto D’Alessandro, Eleanor Riley, Michael Levin, Lachlan Coin, Azra Ghani, David Conway, Aubrey Cunnington

Journal article  |  2018

Abstract Improved methods are needed to identify host mechanisms which directly protect against human infectious diseases in order..

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

Miranda Pitt, Minh Duc Cao, Mark Butler, Soumya Ramu, Devika Ganesamoorthy, Mark Blaskovich, Lachlan Coin, Matthew Cooper

Journal article  |  2018

ABSTRACT Polymyxin B and E (colistin) have been pivotal in the treatment of extensively drug-resistant (XDR) Gram-negative bacteri..

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

Haotian Teng, Duc Cao Minh, Michael B Hall, Tania Duarte, Sheng Wang, Lachlan JM Coin

Journal article  |  2018  |  GigaScience

Evolutionary analysis of chromosome end extension

Haojing Shao, Chenxi Zhou, Minh Duc Cao, Lachlan JM Coin

Journal article  |  2018

There are substantial subtelomeric interstitial telomeric sequence (ITS) in the human genome, however the origin of these sequence..

Simulating the dynamics of targeted capture sequencing with CapSim

Duc Cao Minh, Devika Ganesamoorthy, Chenxi Zhou, Lachlan JM Coin

Journal article  |  2018  |  Bioinformatics

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

Miranda E Pitt, Alysha G Elliott, Duc Cao Minh, Devika Ganesamoorthy, Ilias Karaiskos, Helen Giamarellou, Cely S Abboud, Mark AT Blaskovich, Matthew A Cooper, Lachlan JM Coin

Journal article  |  2018  |  Microbial Genomics

Non-antibiotic antimicrobial triclosan induces multiple antibiotic resistance through genetic mutation

Ji Lu, Min Jin, Son Hoang Nguyen, Likai Mao, Jie Li, Lachlan Coin, Zhiguo Yuan, Jianhua Guo

Journal article  |  2018

ABSTRACT Antibiotic resistance poses a major threat to public health. Overuse and misuse of antibiotics are generally recognised a..

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

Arnold Bainomugisa, Evelyn Lavu, Stenard Hiashiri, Suman Majumdar, Alice Honjepari, Rendi Moke, Paison Dakulala, Grant A Hill-Cawthorne, Sushil Pandey, Ben J Marais, Chris Coulter, Lachlan Coin

Journal article  |  2018  |  Microbial Genomics

A complete high quality nanopore-only assembly of an XDR Mycobacterium tuberculosis Beijing lineage strain identifies novel variation in repetitive PE/PPE gene regions

Arnold Bainomugisa, Tania Duarte, Evelyn Lavu, Sushil Pandey, Chris Coulter, Ben Marais, Lachlan Coin

Journal article  |  2018

Abstract A better understanding of the genomic changes that facilitate the emergence and spread of drug resistant M. tuberculosis ..

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

Ulrich von Both, Maurice Berk, Paul-Michael Agapow, Joseph D Wright, Anna Git, Melissa Shea Hamilton, Greg Goldgof, Nazneen Siddiqui, Evangelos Bellos, Victoria J Wright, Lachlan J Coin, Sandra M Newton, Michael Levin

Journal article  |  2018  |  Scientific Reports

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

Devika Ganesamoorthy, Minh Duc Cao, Tania Duarte, Wenhan Chen, Lachlan Coin

Journal article  |  2018

ABSTRACT Background Tandem repeats comprise significant proportion of the human genome including coding and regulatory regions. Th..

Real-time demultiplexing Nanopore barcoded sequencing data with npBarcode

Hoang Nguyen Son, Tania PS Duarte, Lachlan JM Coin, Duc Cao Minh

Journal article  |  2017  |  Bioinformatics

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

Cheryl Hemingway, Maurice Berk, Suzanne T Anderson, Victoria J Wright, Shea Hamilton, Hariklia Eleftherohorinou, Myrsini Kaforou, Greg M Goldgof, Katy Hickman, Beate Kampmann, Johan Schoeman, Brian Eley, David Beatty, Sandra Pienaar, Mark P Nicol, Michael J Griffiths, Simon J Waddell, Sandra M Newton, Lachlan J Coin, David A Relman, et al.

Journal article  |  2017  |  PLOS ONE

Genetic Variants in HLA-C and Class I Pathway Genes Influence Susceptibility to Kawasaki Disease

Chisato Shimizu, Jihoon Kim, Hariklia Eleftherohorinou, Victoria Wright, Long Hoang, Adriana Tremoulet, Alessandra Franco, Martin Hibberd, Atsushi Takahashi, Michiaki Kubo, Kaoru Ito, Toshihiro Tanaka, Yoshihiro Onouchi, Lachlan Coin, Michael Levin, Jane Burns, Hiroko Shike

Conference Proceedings  |  2017  |  ARTHRITIS & RHEUMATOLOGY

Integrated pathogen load and dual transcriptome analysis of systemic host-pathogen interactions in severe malaria

Hyun Jae Lee, Michael Walther, Athina Georgiadou, Davis Nwakanma, Lindsay Stewart, Michael Levin, Thomas Otto, David Conway, Lachlan Coin, Aubrey Cunnington

Journal article  |  2017

Abstract The pathogenesis of severe Plasmodium falciparum malaria is incompletely understood. Since the pathogenic stage of the pa..

Metabolic profiling of polycystic ovary syndrome reveals interactions with abdominal obesity

A Couto Alves, B Valcarcel, V-P Maekinen, L Morin-Papunen, S Sebert, AJ Kangas, P Soininen, S Das, M De Iorio, L Coin, M Ala-Korpela, M-R Jaervelin, S Franks

Journal article  |  2017  |  International Journal of Obesity

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

Haotian Teng, Minh Duc Cao, Michael Hall, Tania Duarte, Sheng Wang, Lachlan JM Coin

Journal article  |  2017

ABSTRACT Sequencing by translocating DNA fragments through an array of nanopores is a rapidly maturing technology which offers fas..

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

Haojing Shao, Devika Ganesamoorthy, Tania Duarte, Minh Duc Cao, Clive Hoggart, Lachlan JM Coin

Journal article  |  2017

ABSTRACT Detection of genomic inversions remains challenging. Many existing methods primarily target inversions with a non repetit..

Multi-clonal evolution of MDR/XDR M. tuberculosis in a high prevalence setting in Papua New Guinea over three decades

Arnold Bainomugisa, Evelyn Lavu, Stenard Hiashiri, Suman Majumdar, Alice Honjepari, Rendi Moke, Paison Dakulala, Grant Hill-Cawthorne, Pandey Sushil, Ben Marais, Christopher Coulter, Lachlan Coin

Journal article  |  2017

Abstract An outbreak of multi-drug resistant tuberculosis has been reported on Daru Island, Papua New Guinea. The Mycobacterium tu..

Genetic architecture of early childhood growth phenotypes gives insights into their link with later obesity

Maneka De Silva, Sylvain Sebert, Alexessander Couto Alves, Ulla Sovio, Shikta Das, Rob Taal, Nicole Warrington, Alexandra Lewin, Marika Kaakinen, Diana Cousminer, Elisabeth Thiering, Nicholas Timpson, Ville Karhunen, Tom Bond, Xavier Estivill, Virpi Lindi, Jonathan Bradfield, Frank Geller, Lachlan JM Coin, Marie Loh, et al.

Journal article  |  2017

Abstract Early childhood growth patterns are associated with adult metabolic health, but the underlying mechanisms are unclear. We..

Multifactorial Chromosomal Variants Regulate Polymyxin Resistance in Extensively Drug-Resistant Klebsiella pneumoniae

Miranda Pitt, Alysha Elliott, Minh Duc Cao, Devika Ganesamoorthy, Ilias Karaiskos, Helen Giamarellou, Cely Abboud, Mark AT Blaskovich, Matthew Cooper, Lachlan Coin

Journal article  |  2017

ABSTRACT Extensively drug-resistant Klebsiella pneumoniae (XDR-KP) infections cause high mortality and are disseminating globally...

Simulating the Dynamics of Targeted Capture Sequencing with CapSim

Minh Duc Cao, Devika Ganesamoorthy, Lachlan JM Coin

Journal article  |  2017

Abstract Motivation Targeted sequencing using capture probes has become increasingly popular in clinical applications due to its s..

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

Myrsini Kaforou, Jethro A Herberg, Victoria J Wright, Lachlan JM Coin, Michael Levin

Journal article  |  2017  |  JAMA

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

Chenxi Zhou, Bode Olukolu, Dorcus Gemenet, Shan Wu, Wolfgang Gruneberg, Minh Duc Cao, Zhangjun Fei, Zhao-Bang Zeng, Andrew George, Awais Khan, Craig Yencho, Lachlan JM Coin

Journal article  |  2017

ABSTRACT The assembly of whole-chromosome pseudomolecules for plant genomes remains challenging due to polyploidy and high repeat ..

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

Wenhan Chen, Alan J Robertson, Devika Ganesamoorthy, Lachlan JM Coin

Journal article  |  2017  |  Nucleic Acids Research

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

Duc Cao Minh, Hoang Nguyen Son, Devika Ganesamoorthy, Alysha G Elliott, Matthew A Cooper, Lachlan JM Coin

Journal article  |  2017  |  Nature Communications

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

Haojing Shao, Chenxi Zhou, Minh Duc Cao, Lachlan JM Coin

Journal article  |  2017

ABSTRACT The majority of human chromosome ends remain incompletely assembled due to their highly repetitive structure. In this stu..

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

Chisato Shimizu, Hariklia Eleftherohorinou, Victoria J Wright, Jihoon Kim, Martin P Alphonse, James C Perry, Rolando Cimaz, David Burgner, Nagib Dahdah, Long T Hoang, Chiea Chuen Khor, Andrea Salgado, Adriana H Tremoulet, Sonia Davila, Taco W Kuijpers, Martin L Hibberd, Todd A Johnson, Atsushi Takahashi, Tatsuhiko Tsunoda, Michiaki Kubo, et al.

Journal article  |  2016  |  Circulation: Cardiovascular Genetics

Natural resistance to Meningococcal Disease related to CFH loci: Meta-analysis of genome-wide association studies

Federico Martinon-Torres, Eileen Png, Chiea Chuen Khor, Sonia Davila, Victoria J Wright, Kar Seng Sim, Ana Vega, Laura Fachal, David Inwald, Simon Nadel, Enitan D Carrol, Nazareth Martinon-Torres, Sonia Marcos Alonso, Angel Carracedo, Elvira Morteruel, Julio Lopez-Bayon, Andres Concha Torre, Cristina Calvo Monge, Pilar Azcon Gonzalez de Aguilar, Elisabeth Esteban Torne, et al.

Journal article  |  2016  |  Scientific Reports

Diagnostic Test Accuracy of a 2-Transcript Host RNA Signature for Discriminating Bacterial vs Viral Infection in Febrile Children

Jethro A Herberg, Myrsini Kaforou, Victoria J Wright, Hannah Shailes, Hariklia Eleftherohorinou, Clive J Hoggart, Miriam Cebey-Lopez, Michael J Carter, Victoria A Janes, Stuart Gormley, Chisato Shimizu, Adriana H Tremoulet, Anouk M Barendregt, Antonio Salas, John Kanegaye, Andrew J Pollard, Saul N Faust, Sanjay Patel, Taco Kuijpers, Federico Martinon-Torres, et al.

Journal article  |  2016  |  JAMA

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

Duc Cao Minh, Devika Ganesamoorthy, Alysha G Elliott, Huihui Zhang, Matthew A Cooper, Lachlan JM Coin

Journal article  |  2016  |  GigaScience

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

G David Poznik, Yali Xue, Fernando L Mendez, Thomas F Willems, Andrea Massaia, Melissa A Wilson Sayres, Qasim Ayub, Shane A McCarthy, Apurva Narechania, Seva Kashin, Yuan Chen, Ruby Banerjee, Juan L Rodriguez-Flores, Maria Cerezo, Haojing Shao, Melissa Gymrek, Ankit Malhotra, Sandra Louzada, Rob Desalle, Graham RS Ritchie, et al.

Journal article  |  2016  |  Nature Genetics

Scaffolding and Completing Genome Assemblies in Real-time with Nanopore Sequencing

Minh Duc Cao, Son Hoang Nguyen, Devika Ganesamoorthy, Alysha Elliott, Matthew Cooper, Lachlan JM Coin

Journal article  |  2016

Abstract Genome assemblies obtained from short read sequencing technologies are often fragmented into many contigs because of the ..

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

Jun Li, Susan L Woods, Sue Healey, Jonathan Beesley, Xiaoqing Chen, Jason S Lee, Haran Sivakumaran, Nicci Wayte, Katia Nones, Joshua J Waterfall, John Pearson, Anne-Marie Patch, Janine Senz, Manuel A Ferreira, Pardeep Kaurah, Robertson Mackenzie, Alireza Heravi-Moussavi, Samantha Hansford, Tamsin RM Lannagan, Amanda B Spurdle, et al.

Journal article  |  2016  |  The American Journal of Human Genetics

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

Alysha G Elliott, Devika Ganesamoorthy, Lachlan Coin, Matthew A Cooper, Duc Cao Minh

Journal article  |  2016  |  Genome Announcements

Realtime analysis and visualization of MinION sequencing data with npReader

Duc Cao Minh, Devika Ganesamoorthy, Matthew A Cooper, Lachlan JM Coin

Journal article  |  2016  |  Bioinformatics

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

Wenhan Chen, Alan Robertson, Devika Ganesamoorthy, Lachlan JM Coin

Journal article  |  2016

Abstract Accurate identification of copy number alterations is an essential step in understanding the events driving tumor progres..

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

Minh Duc Cao, Devika Ganesamoorthy, Alysha Elliott, Huihui Zhang, Matthew Cooper, Lachlan Coin

Journal article  |  2015

Abstract The recently introduced Oxford Nanopore MinION platform generates DNA sequence data in real-time. This opens immense pote..

Metabonomic Signatures of CNVs in TSPAN8 Exonic Regions Associated with Type 2 Diabetes

T De, I Prokopenko, M-R Jarvelin, L Coin

Conference Proceedings  |  2015  |  HUMAN HEREDITY

Detection of Copy Number Variation Associated with Drug-Response Using Whole Genome Sequencing Data

E Loizidou, E Bellos, M Johnson, L Coin, I Prokopenko

Conference Proceedings  |  2015  |  HUMAN HEREDITY

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

Evangelos Bellos, Vikrant Kumar, Clarabelle Lin, Jordi Maggi, Zai Yang Phua, Ching-Yu Cheng, Chui Ming Gemmy Cheung, Martin L Hibberd, Tien Yin Wong, Lachlan JM Coin, Sonia Davila

Journal article  |  2014  |  Nucleic Acids Research

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

Adaikalavan Ramasamy, Daniah Trabzuni, Sebastian Guelfi, Vibin Varghese, Colin Smith, Robert Walker, Tisham De, Lachlan Coin, Rohan de Silva, Mark R Cookson, Andrew B Singleton, John Hardy, Mina Ryten, Michael E Weale

Journal article  |  2014  |  Nature Neuroscience

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

Evangelos Bellos, Lachlan JM Coin

Journal article  |  2014  |  Bioinformatics

Genome-wide association study of sexual maturation in males and females highlights a role for body mass and menarche loci in male puberty.

Diana L Cousminer, Evangelia Stergiakouli, Diane J Berry, Wei Ang, Maria M Groen-Blokhuis, Antje Körner, Niina Siitonen, Ioanna Ntalla, Marcella Marinelli, John RB Perry, Johannes Kettunen, Rick Jansen, Ida Surakka, Nicholas J Timpson, Susan Ring, George Mcmahon, Chris Power, Carol Wang, Mika Kähönen, Jorma Viikari, et al.

Journal article  |  2014  |  Human Molecular Genetics

Little is known about genes regulating male puberty. Further, while many identified pubertal timing variants associate with age at..

Effects of long-term averaging of quantitative blood pressure traits on the detection of genetic associations.

Santhi K Ganesh, Daniel I Chasman, Martin G Larson, Xiuqing Guo, Germain Verwoert, Joshua C Bis, Xiangjun Gu, Albert V Smith, Min-Lee Yang, Yan Zhang, Georg Ehret, Lynda M Rose, Shih-Jen Hwang, George J Papanicolau, Eric J Sijbrands, Kenneth Rice, Gudny Eiriksdottir, Vasyl Pihur, Paul M Ridker, Ramachandran S Vasan, et al.

Journal article  |  2014  |  The American Journal of Human Genetics

Blood pressure (BP) is a heritable, quantitative trait with intraindividual variability and susceptibility to measurement error. G..

Diagnosis of Childhood Tuberculosis and Host RNA Expression in Africa

Suzanne T Anderson, Myrsini Kaforou, Andrew J Brent, Victoria J Wright, Claire M Banwell, George Chagaluka, Amelia C Crampin, Hazel M Dockrell, Neil French, Melissa S Hamilton, Martin L Hibberd, Florian Kern, Paul R Langford, Ling Ling, Rachel Mlotha, Tom HM Ottenhoff, Sandy Pienaar, Vashini Pillay, J Anthony G Scott, Hemed Twahir, et al.

Journal article  |  2014  |  New England Journal of Medicine

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

Fan Zhang, Ruoyan Chen, Dongbing Liu, Xiaotian Yao, Guoqing Li, Yabin Jin, Chang Yu, Yingrui Li, Lachlan JM Coin

Journal article  |  2013  |  BMC Bioinformatics

Dysregulation of Complement System and CD4 T Cell Activation Pathways Implicated in Allergic Response

Alexessander Couto Alves, Soren Bruhn, Adaikalavan Ramasamy, Hui Wang, John W Holloway, Anna-Liisa Hartikainen, Marjo-Riitta Jarvelin, Mikael Benson, David J Balding, Lachlan JM Coin

Journal article  |  2013  |  PLoS ONE

Detection of Tuberculosis in HIV-Infected and -Uninfected African Adults Using Whole Blood RNA Expression Signatures: A Case-Control Study

Myrsini Kaforou, Victoria J Wright, Tolu Oni, Neil French, Suzanne T Anderson, Nonzwakazi Bangani, ClaireM Banwell, Andrew J Brent, Amelia C Crampin, Hazel M Dockrell, Brian Eley, Robert S Heyderman, Martin L Hibberd, Florian Kern, Paul R Langford, Ling Ling, Marc Mendelson, Tom H Ottenhoff, Femia Zgambo, Robert J Wilkinson, et al.

Journal article  |  2013  |  PLoS Medicine

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

Klaus Bonnelykke, Melanie C Matheson, Tune H Pers, Raquel Granell, David P Strachan, Alexessander Couto Alves, Allan Linneberg, John A Curtin, Nicole M Warrington, Marie Standl, Marjan Kerkhof, Ingileif Jonsdottir, Blazenka K Bukvic, Marika Kaakinen, Patrick Sleimann, Gudmar Thorleifsson, Unnur Thorsteinsdottir, Katharina Schramm, Svetlana Baltic, Eskil Kreiner-Moller, et al.

Journal article  |  2013  |  Nature Genetics

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

Renato Puppi Munhoz, Helio A Teive, Hariklia Eleftherohorinou, Lachlan J Coin, Andrew J Lees, Laura Silveira-Moriyama

Journal article  |  2013  |  Journal of Neurology, Neurosurgery & Psychiatry

Rare Genomic Structural Variants in Complex Disease: Lessons from the Replication of Associations with Obesity

Robin G Walters, Lachlan JM Coin, Aimo Ruokonen, Adam J de Smith, Julia S El-Sayed Moustafa, Sebastien Jacquemont, Paul Elliott, Tonu Esko, Anna-Liisa Hartikainen, Jaana Laitinen, Katrin Maennik, Danielle Martinet, David Meyre, Matthias Nauck, Claudia Schurmann, Rob Sladek, Gudmar Thorleifsson, Unnur Thorsteinsdottir, Armand Valsesia, Gerard Waeber, et al.

Journal article  |  2013  |  PLoS ONE

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

Haojing Shao, Evangelos Bellos, Hanjiudai Yin, Xiao Liu, Jing Zou, Yingrui Li, Jun Wang, Lachlan JM Coin

Journal article  |  2013  |  Nucleic Acids Research

The Effect of Genomic Inversions on Estimation of Population Genetic Parameters from SNP Data

Nafisa-Katrin Seich al Basatena, Clive J Hoggart, Lachlan J Coin, Paul F O'Reilly

Journal article  |  2013  |  Genetics

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

Adaikalavan Ramasamy, Mikko Kuokkanen, Sailaja Vedantam, Zofia K Gajdos, Alexessander Couto Alves, Helen N Lyon, Manuel AR Ferreira, David P Strachan, Jing Hua Zhao, Michael J Abramson, Matthew A Brown, Lachlan Coin, Shyamali C Dharmage, David L Duffy, Tari Haahtela, Andrew C Heath, Christer Janson, Mika Kähönen, Kay-Tee Khaw, Jaana Laitinen, et al.

Journal article  |  2013  |  PLoS ONE

[This corrects the article DOI: 10.1371/journal.pone.0044008.].

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

Alexessander Couto-Alves, Victoria J Wright, Karnan Perumal, Alexander Binder, Enitan D Carrol, Marieke Emonts, Ronald de Groot, Jan Hazelzet, Taco Kuijpers, Simon Nadel, Werner Zenz, Padmanabhan Ramnarayan, Michael Levin, Lachlan Coin, David P Inwald

Journal article  |  2013  |  Critical Care

An integrated map of genetic variation from 1,092 human genomes

David M Altshuler, Richard M Durbin, Goncalo R Abecasis, David R Bentley, Aravinda Chakravarti, Andrew G Clark, Peter Donnelly, Evan E Eichler, Paul Flicek, Stacey B Gabriel, Richard A Gibbs, Eric D Green, Matthew E Hurles, Bartha M Knoppers, Jan O Korbel, Eric S Lander, Charles Lee, Hans Lehrach, Elaine R Mardis, Gabor T Marth, et al.

Journal article  |  2012  |  Nature

Gene-Targeted Analysis of Copy Number Variants Identifies 3 Novel Associations With Coronary Heart Disease Traits

Sean J Costelloe, Julia S El-Sayed Moustafa, Fotios Drenos, Jutta Palmen, Li Qiao, Stephen Whiting, Michael Thomas, Mika Kivimaki, Meena Kumari, Aroon D Hingorani, Ioanna Tzoulaki, Jaervelin Marjo-Riitta, Ruokonen Aimo, Anna-Liisa Hartikainen, Anneli Pouta, Robin G Walters, Alexandra IF Blakemore, Steve E Humphries, Lachlan JM Coin, Philippa J Talmud

Journal article  |  2012  |  Circulation: Cardiovascular Genetics

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

Adaikalavan Ramasamy, Mikko Kuokkanen, Sailaja Vedantam, Zofia K Gajdos, Alexessander Couto Alves, Helen N Lyon, Manuel AR Ferreira, David P Strachan, Jing Hua Zhao, Michael J Abramson, Matthew A Brown, Lachlan Coin, Shyamali C Dharmage, David L Duffy, Tari Haahtela, Andrew C Heath, Christer Janson, Mika Kahonen, Kay-Tee Khaw, Jaana Laitinen, et al.

Journal article  |  2012  |  PLoS One

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

Lachlan JM Coin, Dandan Cao, Jingjing Ren, Xianbo Zuo, Liangdan Sun, Sen Yang, Xuejun Zhang, Yong Cui, Yingrui Li, Xin Jin, Jun Wang

Journal article  |  2012  |  Bioinformatics

Novel association approach for variable number tandem repeats (VNTRs) identifies DOCK5 as a susceptibility gene for severe obesity

Julia S El-Sayed Moustafa, Hariklia Eleftherohorinou, Adam J de Smith, Johanna C Andersson-Assarsson, Alexessander Couto Alves, Eleni Hadjigeorgiou, Robin G Walters, Julian E Asher, Leonardo Bottolo, Jessica L Buxton, Rob Sladek, David Meyre, Christian Dina, Sophie Visvikis-Siest, Peter Jacobson, Lars Sjostrom, Lena MS Carlsson, Andrew Walley, Mario Falchi, Philippe Froguel, et al.

Journal article  |  2012  |  Human Molecular Genetics

MultiPhen: Joint Model of Multiple Phenotypes Can Increase Discovery in GWAS

Paul F O'Reilly, Clive J Hoggart, Yotsawat Pomyen, Federico CF Calboli, Paul Elliott, Marjo-Riitta Jarvelin, Lachlan JM Coin

Journal article  |  2012  |  PLoS ONE

Common variants at 12q15 and 12q24 are associated with infant head circumference

H Rob Taal, Beate St Pourcain, Elisabeth Thiering, Shikta Das, Dennis O Mook-Kanamori, Nicole M Warrington, Marika Kaakinen, Eskil Kreiner-Moller, Jonathan P Bradfield, Rachel M Freathy, Frank Geller, Monica Guxens, Diana L Cousminer, Marjan Kerkhof, Nicholas J Timpson, M Arfan Ikram, Lawrence J Beilin, Klaus Bonnelykke, Jessica L Buxton, Pimphen Charoen, et al.

Journal article  |  2012  |  Nature Genetics

Common variants at 6q22 and 17q21 are associated with intracranial volume

M Arfan Ikram, Myriam Fornage, Albert V Smith, Sudha Seshadri, Reinhold Schmidt, Stephanie Debette, Henri A Vrooman, Sigurdur Sigurdsson, Stefan Ropele, H Rob Taal, Dennis O Mook-Kanamori, Laura H Coker, WT Longstreth, Wiro J Niessen, Anita L DeStefano, Alexa Beiser, Alex P Zijdenbos, Maksim Struchalin, Clifford R Jack, Fernando Rivadeneira, et al.

Journal article  |  2012  |  Nature Genetics

Novel Loci for Adiponectin Levels and Their Influence on Type 2 Diabetes and Metabolic Traits: A Multi-Ethnic Meta-Analysis of 45,891 Individuals

Zari Dastani, Marie-France Hivert, Nicholas Timpson, John RB Perry, Xin Yuan, Robert A Scott, Peter Henneman, Iris M Heid, Jorge R Kizer, Leo-Pekka Lyytikainen, Christian Fuchsberger, Toshiko Tanaka, Andrew P Morris, Kerrin Small, Aaron Isaacs, Marian Beekman, Stefan Coassin, Kurt Lohman, Lu Qi, Stavroula Kanoni, et al.

Journal article  |  2012  |  PLoS Genetics

Fine-Scale Estimation of Location of Birth from Genome-Wide Single-Nucleotide Polymorphism Data

Clive J Hoggart, Paul F O'Reilly, Marika Kaakinen, Weihua Zhang, John C Chambers, Jaspal S Kooner, Lachlan JM Coin, Marjo-Riitta Jarvelin

Journal article  |  2012  |  Genetics

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

Fredrik Barrenas, Sreenivas Chavali, Alexessander Couto Alves, Lachlan Coin, Marjo-Riitta Jarvelin, Rebecka Jornsten, Michael A Langston, Adaikalavan Ramasamy, Gary Rogers, Hui Wang, Mikael Benson

Journal article  |  2012  |  Genome Biology

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

Evangelos Bellos, Michael R Johnson, Lachlan JM Coin

Journal article  |  2012  |  Genome Biology

Bioinformatics: living on the edge

Evangelos Bellos, Lachlan JM Coin, Myrsini Kaforou

Journal article  |  2012  |  Genome Biology

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

Iris M Heid, Anne U Jackson, Joshua C Randall, Thomas W Winkler, Lu Qi, Valgerdur Steinthorsdottir, Gudmar Thorleifsson, M Carola Zillikens, Elizabeth K Speliotes, Reedik Maegi, Tsegaselassie Workalemahu, Charles C White, Nabila Bouatia-Naji, Tamara B Harris, Sonja I Berndt, Erik Ingelsson, Cristen J Willer, Michael N Weedon, Jian'an Luan, Sailaja Vedantam, et al.

Journal article  |  2011  |  Nature Genetics

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

John C Chambers, Weihua Zhang, Joban Sehmi, Xinzhong Li, Mark N Wass, Pim Van der Harst, Hilma Holm, Serena Sanna, Maryam Kavousi, Sebastian E Baumeister, Lachlan J Coin, Guohong Deng, Christian Gieger, Nancy L Heard-Costa, Jouke-Jan Hottenga, Brigitte Kuehnel, Vinod Kumar, Vasiliki Lagou, Liming Liang, Jian'an Luan, et al.

Journal article  |  2011  |  Nature Genetics

A genome-wide meta-analysis of genetic variants associated with allergic rhinitis and grass sensitization and their interaction with birth order

Adaikalavan Ramasamy, Ivan Curjuric, Lachlan J Coin, Ashish Kumar, Wendy L McArdle, Medea Imboden, Benedicte Leynaert, Manolis Kogevinas, Peter Schmid-Grendelmeier, Juha Pekkanen, Matthias Wjst, Andreas J Bircher, Ulla Sovio, Thierry Rochat, Anna-Liisa Hartikainen, David J Balding, Marjo-Riitta Jarvelin, Nicole Probst-Hensch, David P Strachan, Deborah L Jarvis

Journal article  |  2011  |  Journal of Allergy and Clinical Immunology

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

Sebastien Jacquemont, Alexandre Reymond, Flore Zufferey, Louise Harewood, Robin G Walters, Zoltan Kutalik, Danielle Martinet, Yiping Shen, Armand Valsesia, Noam D Beckmann, Gudmar Thorleifsson, Marco Belfiore, Sonia Bouquillon, Dominique Campion, Nicole de Leeuw, Bert BA de Vries, Tonu Esko, Bridget A Fernandez, Fernando Fernandez-Aranda, Jose Manuel Fernandez-Real, et al.

Journal article  |  2011  |  Nature

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

Hariklia Eleftherohorinou, Clive J Hoggart, Victoria J Wright, Michael Levin, Lachlan JM Coin

Journal article  |  2011  |  Human Molecular Genetics

Accurate Single-Nucleotide Polymorphism Allele Assignment in Trisomic or Duplicated Regions by Using a Single Base-Extension Assay with MALDI-TOF Mass Spectrometry

Anne L Trewick, Julia S El-Sayed Moustafa, Adam J de Smith, Philippe Froguel, Gottfried Greve, Pal R Njolstad, Lachlan JM Coin, Alexandra IF Blakemore

Journal article  |  2011  |  Clinical Chemistry

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

Yingrui Li, Hancheng Zheng, Ruibang Luo, Honglong Wu, Hongmei Zhu, Ruiqiang Li, Hongzhi Cao, Boxin Wu, Shujia Huang, Haojing Shao, Hanzhou Ma, Fan Zhang, Shuijian Feng, Wei Zhang, Hongli Du, Geng Tian, Jingxiang Li, Xiuqing Zhang, Songgang Li, Lars Bolund, et al.

Journal article  |  2011  |  Nature Biotechnology

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 Coin, Peter Jacobson, Lena MS Carlsson, Alexandra IF Blakemore, Philippe Froguel, Andrew J Walley, Mario Falchi

Journal article  |  2011  |  Bioinformatics

Genome-wide association and genetic functional studies identify autism susceptibility candidate 2 gene (AUTS2) in the regulation of alcohol consumption (vol 108, pg 7119, 2011)

Gunter Schumann, Lachlan J Coin, Anbarasu Lourdusamy, Pimphen Charoen, Karen H Berger, David Stacey, Sylvane Desrivieres, Fazil A Aliev, Anokhi A Khan, Najaf Amin, Yurii S Aulchenko, Georgy Bakalkin, Stephan J Bakker, Beverley Balkau, Joline W Beulens, Ainhoa Bilbao, Rudolf A de Boer, Delphine Beury, Michiel L Bots, Elemi J Breetvelt, et al.

Journal article  |  2011  |  Proceedings of the National Academy of Sciences

Investigation of the HIN200 Locus in UK SLE Families Identifies Novel Copy Number Variants

Michelle MA Fernando, Adam J de Smith, Lachlan Coin, David L Morris, Philippe Froguel, Jonathan Mangion, Alexandra IF Blakemore, Robert R Graham, Timothy W Behrens, Timothy J Vyse

Journal article  |  2011  |  Annals of Human Genetics

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

Gunter Schumann, Lachlan J Coin, Anbarasu Lourdusamy, Pimphen Charoen, Karen H Berger, David Stacey, Sylvane Desrivieres, Fazil A Aliev, Anokhi A Khan, Najaf Amin, Yurii S Aulchenko, Georgy Bakalkin, Stephan J Bakker, Beverley Balkau, Joline W Beulens, Ainhoa Bilbao, Rudolf A de Boer, Delphine Beury, Michiel L Bots, Elemi J Breetvelt, et al.

Journal article  |  2011  |  Proceedings of the National Academy of Sciences

Obesity-susceptibility loci have a limited influence on birth weight: a meta-analysis of up to 28,219 individuals

Tuomas O Kilpelaeinen, Marcel den Hoed, Ken K Ong, Anders Grontved, Soren Brage, Karen Jameson, Cyrus Cooper, Kay-Tee Khaw, Ulf Ekelund, Nicholas J Wareham, Ruth JF Loos

Journal article  |  2011  |  The American Journal of Clinical Nutrition

Transforming Growth Factor-beta Signaling Pathway in Patients With Kawasaki Disease (vol 4, pg 16, 2011)

Chisato Shimizu, Sonia Jain, Sonia Davila, Martin L Hibberd, Kevin O Lin, Delaram Molkara, Jeffrey R Frazer, Shelly Sun, Annette L Baker, Jane W Newburger, Anne H Rowley, Stanford T Shulman, David Burgner, Willemijn B Breunis, Taco W Kuijpers, Victoria J Wright, Michael Levin, Hariklia Eleftherohorinou, Lachlan Coin, Stephen J Popper, et al.

Journal article  |  2011  |  CIRCULATION-CARDIOVASCULAR GENETICS

TTC12-ANKK1-DRD2 and CHRNA5-CHRNA3-CHRNB4 Influence Different Pathways Leading to Smoking Behavior from Adolescence to Mid-Adulthood

Francesca Ducci, Marika Kaakinen, Anneli Pouta, Anna-Liisa Hartikainen, Juha Veijola, Matti Isohanni, Pimphen Charoen, Lachlan Coin, Clive Hoggart, Jesper Ekelund, Leena Peltonen, Nelson Freimer, Paul Elliott, Gunter Schumann, Marjo-Riitta Jaervelin

Journal article  |  2011  |  Biological Psychiatry

Transforming Growth Factor-beta Signaling Pathway in Patients With Kawasaki Disease

Chisato Shimizu, Sonia Jain, Sonia Davila, Martin L Hibberd, Kevin O Lin, Delaram Molkara, Jeffrey R Frazer, Shelly Sun, Annette L Baker, Jane W Newburger, Anne H Rowley, Stanford T Shulman, Sonia Davila, David Burgner, Willemijn B Breunis, Taco W Kuijpers, Victoria J Wright, Michael Levin, Hariklia Eleftherohorinou, Lachlan Coin, et al.

Journal article  |  2011  |  Circulation. Cardiovascular Genetics

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

Ernest Turro, Shu-Yi Su, Angela Goncalves, Lachlan JM Coin, Sylvia Richardson, Alex Lewin

Journal article  |  2011  |  Genome Biology

Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index

Elizabeth K Speliotes, Cristen J Willer, Sonja I Berndt, Keri L Monda, Gudmar Thorleifsson, Anne U Jackson, Hana Lango Allen, Cecilia M Lindgren, Jian'an Luan, Reedik Maegi, Joshua C Randall, Sailaja Vedantam, Thomas W Winkler, Lu Qi, Tsegaselassie Workalemahu, Iris M Heid, Valgerdur Steinthorsdottir, Heather M Stringham, Michael N Weedon, Eleanor Wheeler, et al.

Journal article  |  2010  |  Nature Genetics

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

Iris M Heid, Anne U Jackson, Joshua C Randall, Thomas W Winkler, Lu Qi, Valgerdur Steinthorsdottir, Gudmar Thorleifsson, M Carola Zillikens, Elizabeth K Speliotes, Reedik Maegi, Tsegaselassie Workalemahu, Charles C White, Nabila Bouatia-Naji, Tamara B Harris, Sonja I Berndt, Erik Ingelsson, Cristen J Willer, Michael N Weedon, Jianan Luan, Sailaja Vedantam, et al.

Journal article  |  2010  |  Nature Genetics

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

Hana Lango Allen, Karol Estrada, Guillaume Lettre, Sonja I Berndt, Michael N Weedon, Fernando Rivadeneira, Cristen J Willer, Anne U Jackson, Sailaja Vedantam, Soumya Raychaudhuri, Teresa Ferreira, Andrew R Wood, Robert J Weyant, Ayellet V Segre, Elizabeth K Speliotes, Eleanor Wheeler, Nicole Soranzo, Ju-Hyun Park, Jian Yang, Daniel Gudbjartsson, et al.

Journal article  |  2010  |  Nature

IDENTIFICATION OF GENES ASSOCIATED WITH ALCOHOL CONSUMPTION

G Schumann, L Coin, A Lourdusamy, P Charoen, D Stacey, S Desrivieres, MR Jarvelin, P Elliott

Conference Proceedings  |  2010  |  ALCOHOLISM-CLINICAL AND EXPERIMENTAL RESEARCH

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

Lachlan JM Coin, Julian E Asher, Robin G Walters, Julia S El-Sayed Moustafa, Adam J de Smith, Rob Sladek, David J Balding, Philippe Froguel, Alexandra IF Blakemore

Journal article  |  2010  |  Nature Methods

Inferring combined CNV/SNP haplotypes from genotype data

Shu-Yi Su, Julian E Asher, Marjo-Riita Jarvelin, Phillipe Froguel, Alexandra IF Blakemore, David J Balding, Lachlan JM Coin

Journal article  |  2010  |  Bioinformatics

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

Rachel M Freathy, Dennis O Mook-Kanamori, Ulla Sovio, Inga Prokopenko, Nicholas J Timpson, Diane J Berry, Nicole M Warrington, Elisabeth Widen, Jouke Jan Hottenga, Marika Kaakinen, Leslie A Lange, Jonathan P Bradfield, Marjan Kerkhof, Julie A Marsh, Reedik Maegi, Chih-Mei Chen, Helen N Lyon, Mirna Kirin, Linda S Adair, Yurii S Aulchenko, et al.

Journal article  |  2010  |  Nature Genetics

New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk (vol 42, pg 105, 2010)

Josee Dupuis, Claudia Langenberg, Inga Prokopenko, Richa Saxena, Nicole Soranzo, Anne U Jackson, Eleanor Wheeler, Nicole L Glazer, Nabila Bouatia-Naji, Anna L Gloyn, Cecilia M Lindgren, Reedik Maegi, Andrew P Morris, Joshua Randall, Toby Johnson, Paul Elliott, Denis Rybin, Gudmar Thorleifsson, Valgerdur Steinthorsdottir, Peter Henneman, et al.

Journal article  |  2010  |  Nature Genetics

invertFREGENE: software for simulating inversions in population genetic data

Paul F O'Reilly, Lachlan JM Coin, Clive J Hoggart

Journal article  |  2010  |  Bioinformatics

Can Motor Features of Parkinson's Disease Be Used To Predict Occurrence of Non-Motor Symptoms of the Disease?

Renato P Munhoz, Helio A Teive, Hariklia Eleftherohorinou, Lachlan J Coin, Andrew Lees, Lineu Werneck, Laura Silveira-Moriyama

Conference Proceedings  |  2010  |  NEUROLOGY

Protein Domains: New methods for detection and evolutionary analysis

LJM Coin

Journal article  |  2010

Protein domains are the structural, functional and evolutionary units of proteins. A useful way to predict the function and struct..

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

RG Walters, S Jacquemont, A Valsesia, AJ de Smith, D Martinet, J Andersson, M Falchi, F Chen, J Andrieux, S Lobbens, B Delobel, F Stutzmann, JS El-Sayed Moustafa, J-C Chevre, C Lecoeur, V Vatin, S Bouquillon, JL Buxton, O Boute, M Holder-Espinasse, et al.

Journal article  |  2010  |  Nature

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

Josee Dupuis, Claudia Langenberg, Inga Prokopenko, Richa Saxena, Nicole Soranzo, Anne U Jackson, Eleanor Wheeler, Nicole L Glazer, Nabila Bouatia-Naji, Anna L Gloyn, Cecilia M Lindgren, Reedik Magi, Andrew P Morris, Joshua Randall, Toby Johnson, Paul Elliott, Denis Rybin, Gudmar Thorleifsson, Valgerdur Steinthorsdottir, Peter Henneman, et al.

Journal article  |  2010  |  Nature Genetics

Genome-Wide Association Study Reveals Multiple Loci Associated with Primary Tooth Development during Infancy

Demetris Pillas, Clive J Hoggart, David M Evans, Paul F O'Reilly, Kirsi Sipila, Raija Lahdesmaki, Iona Y Millwood, Marika Kaakinen, Gopalakrishnan Netuveli, David Blane, Pimphen Charoen, Ulla Sovio, Anneli Pouta, Nelson Freimer, Anna-Liisa Hartikainen, Jaana Laitinen, Sarianna Vaara, Beate Glaser, Peter Crawford, Nicholas J Timpson, et al.

Journal article  |  2010  |  PLoS Genetics

Predicting non-motor features of Parkinson's disease

RP Munhoz, H Eleftherohorinou, HHA Teive, LJ Coin, LC Werneck, AJ Lees, L Silveira-Moriyama

Conference Proceedings  |  2010  |  MOVEMENT DISORDERS

Pathway Analysis of GWAS Provides New Insights into Genetic Susceptibility to 3 Inflammatory Diseases

Hariklia Eleftherohorinou, Victoria Wright, Clive Hoggart, Anna-Liisa Hartikainen, Marjo-Riitta Jarvelin, David Balding, Lachlan Coin, Michael Levin

Journal article  |  2009  |  PLoS ONE

CNVs in Obesity: Uncovering a New Level of Genomic Variation

Julia Sarah El-Sayed Moustafa, LJM Coin, AJ de Smith, RG Walters, JL Buxton, JE Asher, D Meyre, C Dina, P Froguel, AIF Blakemore

Conference Proceedings  |  2009  |  JOURNAL OF MEDICAL GENETICS

Identification and validation of novel genomic CNVs associated with Type 2 diabetes

Jessica Buxton, LJM Coin, RG Walters, J Andersson, AJ de Smith, JS El-Sayed Moustafa, R Sladek, P Froguel, AIF Blakemore

Conference Proceedings  |  2009  |  JOURNAL OF MEDICAL GENETICS

Assignment of trisomic genotypes using the Sequenom iPLEX MALDI TOF assay reveals transmission disequilibrium of two SNP loci in the Type VI Collagen gene cluster associated with CHD in Down's Syndrome.

Anne L Trewick, P Froguel, LJM Coin, AIF Blakemore

Conference Proceedings  |  2009  |  JOURNAL OF MEDICAL GENETICS

Genetic Loci Associated With C-Reactive Protein Levels and Risk of Coronary Heart Disease

Paul Elliott, John C Chambers, Weihua Zhang, Robert Clarke, Jemma C Hopewell, John F Peden, Jeanette Erdmann, Peter Braund, James C Engert, Derrick Bennett, Lachlan Coin, Deborah Ashby, Ioanna Tzoulaki, Ian J Brown, Shahrul Mt-Isa, Mark I McCarthy, Leena Peltonen, Nelson B Freimer, Martin Farrall, Aimo Ruokonen, et al.

Journal article  |  2009  |  JAMA

Genome-wide association study identifies eight loci associated with blood pressure

Christopher Newton-Cheh, Toby Johnson, Vesela Gateva, Martin D Tobin, Murielle Bochud, Lachlan Coin, Samer S Najjar, Jing Hua Zhao, Simon C Heath, Susana Eyheramendy, Konstantinos Papadakis, Benjamin F Voight, Laura J Scott, Feng Zhang, Martin Farrall, Toshiko Tanaka, Chris Wallace, John C Chambers, Kay-Tee Khaw, Peter Nilsson, et al.

Journal article  |  2009  |  Nature Genetics

GENETIC LOCI INFLUENCING C-REACTIVE PROTEIN LEVELS AND CORONARY HEART DISEASE RISK: RESULTS OF GENETIC ASSOCIATION AND MENDELIAN RANDOMISATION STUDY WITH META-ANALYSIS IN 80 614 PEOPLE

P Elliott, JC Chambers, W Zhang, R Clarke, JF Peden, J Erdmann, P Braund, J Engert, J Hopewell, Lachlan Coin, D Ashby, MI McCarthy, M Farrall, Marjo-Riitta Jarvelin, J Scott, AS Hall, H Schunkert, SS Anand, R Collins, N Samani, et al.

Conference Proceedings  |  2009  |  HEART

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

Cecilia M Lindgren, Iris M Heid, Joshua C Randall, Claudia Lamina, Valgerdur Steinthorsdottir, Lu Qi, Elizabeth K Speliotes, Gudmar Thorleifsson, Cristen J Willer, Blanca M Herrera, Anne U Jackson, Noha Lim, Paul Scheet, Nicole Soranzo, Najaf Amin, Yurii S Aulchenko, John C Chambers, Alexander Drong, Jian'an Luan, Helen N Lyon, et al.

Journal article  |  2009  |  PLoS Genetics

Genetic Determinants of Height Growth Assessed Longitudinally from Infancy to Adulthood in the Northern Finland Birth Cohort 1966

Ulla Sovio, Amanda J Bennett, Iona Y Millwood, John Molitor, Paul F O'Reilly, Nicholas J Timpson, Marika Kaakinen, Jaana Laitinen, Jari Haukka, Demetris Pillas, Ioanna Tzoulaki, Jassy Molitor, Clive Hoggart, Lachlan JM Coin, John Whittaker, Anneli Pouta, Anna-Liisa Hartikainen, Nelson B Freimer, Elisabeth Widen, Leena Peltonen, et al.

Journal article  |  2009  |  PLoS Genetics

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

David Meyre, Jerome Delplanque, Jean-Claude Chevre, Cecile Lecoeur, Stephane Lobbens, Sophie Gallina, Emmanuelle Durand, Vincent Vatin, Franck Degraeve, Christine Proenca, Stefan Gaget, Antje Koerner, Peter Kovacs, Wieland Kiess, Jean Tichet, Michel Marre, Anna-Liisa Hartikainen, Fritz Horber, Natascha Potoczna, Serge Hercberg, et al.

Journal article  |  2009  |  Nature Genetics

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

Chiara Sabatti, Susan K Service, Anna-Liisa Hartikainen, Anneli Pouta, Samuli Ripatti, Jae Brodsky, Chris G Jones, Noah A Zaitlen, Teppo Varilo, Marika Kaakinen, Ulla Sovio, Aimo Ruokonen, Jaana Laitinen, Eveliina Jakkula, Lachlan Coin, Clive Hoggart, Andrew Collins, Hannu Turunen, Stacey Gabriel, Paul Elliot, et al.

Journal article  |  2009  |  Nature Genetics

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

Cristen J Willer, Elizabeth K Speliotes, Ruth JF Loos, Shengxu Li, Cecilia M Lindgren, Iris M Heid, Sonja I Berndt, Amanda L Elliott, Anne U Jackson, Claudia Lamina, Guillaume Lettre, Noha Lim, Helen N Lyon, Steven A McCarroll, Konstantinos Papadakis, Lu Qi, Joshua C Randall, Rosa Maria Roccasecca, Serena Sanna, Paul Scheet, et al.

Journal article  |  2009  |  Nature Genetics

Variants in MTNR1B influence fasting glucose levels

Inga Prokopenko, Claudia Langenberg, Jose C Florez, Richa Saxena, Nicole Soranzo, Gudmar Thorleifsson, Ruth JF Loos, Alisa K Manning, Anne U Jackson, Yurii Aulchenko, Simon C Potter, Michael R Erdos, Serena Sanna, Jouke-Jan Hottenga, Eleanor Wheeler, Marika Kaakinen, Valeriya Lyssenko, Wei-Min Chen, Kourosh Ahmadi, Jacques S Beckmann, et al.

Journal article  |  2009  |  Nature Genetics

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 JM Coin

Journal article  |  2008  |  BMC Bioinformatics

Alu elements implicated in the generation of 9/20 CNV deletions investigated by breakpoint sequencing

Adam de Smith, RG Walters, LJM Coin, I Steinfeld, Z Yakhini, R Sladek, P Froguel, AIF Blakemore

Conference Proceedings  |  2008  |  JOURNAL OF MEDICAL GENETICS

Small Deletion Variants Have Stable Breakpoints Commonly Associated with Alu Elements

Adam J de Smith, Robin G Walters, Lachlan JM Coin, Israel Steinfeld, Zohar Yakhini, Rob Sladek, Philippe Froguel, Alexandra IF Blakemore

Journal article  |  2008  |  PLoS ONE

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

Shu-Yi Su, David J Balding, Lachlan JM Coin

Journal article  |  2008  |  Bioinformatics

TreeFam: 2008 update

Jue Ruan, Heng Li, Zhongzhong Chen, Avril Coghlan, Lachlan James M Coin, Yiran Guo, Jean-Karim Heriche, Yafeng Hu, Karsten Kristiansen, Ruiqiang Li, Tao Liu, Alan Moses, Junjie Qin, Soren Vang, Albert J Vilella, Abel Ureta-Vidal, Lars Bolund, Jun Wang, Richard Durbin

Journal article  |  2008  |  Nucleic Acids Research

Using haplotype clustering techniques to perform genome-wide disease association studies

S-Y Su, DJ Balding, L Coin

Conference Proceedings  |  2007  |  GENETIC EPIDEMIOLOGY

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

Heng Li, Avril Coghlan, Jue Ruan, Lachlan James Coin, Jean-Karim Heriche, Lara Osmotherly, Ruiqiang Li, Tao Liu, Zhang Zhang, Lars Bolund, Gane Ka-Shu Wong, Weimou Zheng, Paramvir Dehal, Jun Wang, Richard Durbin

Journal article  |  2006  |  Nucleic Acids Research

Neonatal death of a newborn twin

J Goeb, M Leblanc-Deshayes, L Coin, J Malka, C Bouderlique, R Duverger

Journal article  |  2004  |  Archives de Pédiatrie

Improved techniques for the identification of pseudogenes

L Coin, R Durbin

Journal article  |  2004  |  Bioinformatics

Enhanced protein domain discovery using taxonomy

L Coin, A Bateman, R Durbin

Journal article  |  2004  |  BMC Bioinformatics

A census of human cancer genes

PA Futreal, L Coin, M Marshall, T Down, T Hubbard, R Wooster, N Rahman, MR Stratton

Journal article  |  2004  |  Nature Reviews Cancer

The Pfam protein families database

A Bateman, L Coin, R Durbin, RD Finn, V Hollich, S Griffiths-Jones, A Khanna, M Marshall, S Moxon, ELL Sonnhammer, DJ Studholme, C Yeats, SR Eddy

Journal article  |  2004  |  Nucleic Acids Research

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

L Coin, A Bateman, R Durbin

Journal article  |  2003  |  Proceedings of the National Academy of Sciences

Comparative effects of natural and accelerated aging on barley seeds (Hordeum vulgare L)

L Coin, M Vaissiere, A Noirot, A Charrier, S Hamon

Journal article  |  1995  |  SEED SCIENCE AND TECHNOLOGY

MAINS WATER

L COIN

Journal article  |  1977  |  CAHIERS DE NUTRITION ET DE DIETETIQUE

PROBLEM OF CYTOTOXICITY OF WATERS

L COIN, C HANNOUN, JC TRIMOREA

Conference Proceedings  |  1968  |  WATER RESEARCH

MICROBIOLOGICAL AND VIROLOGICAL ASPECTS OF WATER POLLUTION

L COIN, MC HANNOUN, J LABONDE, ML MENETRIER

Conference Proceedings  |  1964  |  AIR AND WATER POLLUTION

MICROBIOLOGICAL AND VIROLOGICAL ASPECTS OF WATER POLLUTION

L COIN, MC HANNOUN, J LABONDE, ML MENETRIER

Conference Proceedings  |  1964  |  JOURNAL WATER POLLUTION CONTROL FEDERATION