Daniel Falush

Affiliations

The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China.

ORCID: 0000-0002-2956-0795

Publications (14)

The landscape of coadaptation in

eLife

Avec: Yujun Cui , Chao Yang , Hongling Qiu , Hui Wang , Ruifu Yang , Daniel Falush

The Helicobacter pylori Genome Project: insights into H. pylori population structure from analysis of a worldwide collection of complete genomes.

Nature communications

Avec: Kaisa Thorell , Zilia Y Muñoz-Ramírez , Difei Wang , Santiago Sandoval-Motta , Rajiv Boscolo Agostini , Silvia Ghirotto , Roberto C Torres , Auteur inconnu , Daniel Falush , M Constanza Camargo , Charles S Rabkin

Epistasis, core-genome disharmony, and adaptation in recombining bacteria.

mBio

Avec: Aidan J Taylor , Koji Yahara , Ben Pascoe , Seungwon Ko , Leonardos Mageiros , Evangelos Mourkas , Jessica K Calland , Santeri Puranen , Matthew D Hitchings , Keith A Jolley , Carolin M Kobras , Sion Bayliss , Nicola J Williams , Arnoud H M van Vliet , Julian Parkhill , Martin C J Maiden , Jukka Corander , Laurence D Hurst , Daniel Falush , Paul Keim , Xavier Didelot , David J Kelly , Samuel K Sheppard

Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations.

Nature communications

Avec: Harry A Thorpe , Elise Tourrette , Koji Yahara , Filipa F Vale , Siqi Liu , Mónica Oleastro , Teresa Alarcon , Tsachi-Tsadok Perets , Saeid Latifi-Navid , Yoshio Yamaoka , Beatriz Martinez-Gonzalez , Ioannis Karayiannis , Timokratis Karamitros , Dionyssios N Sgouras , Wael Elamin , Ben Pascoe , Samuel K Sheppard , Jukka Ronkainen , Pertti Aro , Lars Engstrand , Lars Agreus , Sebastian Suerbaum , Kaisa Thorell , Daniel Falush

An ancient ecospecies of Helicobacter pylori.

Nature

Avec: Elise Tourrette , Roberto C Torres , Sarah L Svensson , Takashi Matsumoto , Muhammad Miftahussurur , Kartika Afrida Fauzia , Ricky Indra Alfaray , Ratha-Korn Vilaichone , Vo Phuoc Tuan , Auteur inconnu , Difei Wang , Abbas Yadegar , Lisa M Olsson , Zhemin Zhou , Yoshio Yamaoka , Kaisa Thorell , Daniel Falush

The speciation and hybridization history of the genus

Microbial genomics

Avec: Alexis Criscuolo , Sylvie Issenhuth-Jeanjean , Xavier Didelot , Kaisa Thorell , James Hale , Julian Parkhill , Nicholas R Thomson , François-Xavier Weill , Daniel Falush , Sylvain Brisse

Quantifying bacterial evolution in the wild: A birthday problem for Campylobacter lineages.

PLoS genetics

Avec: Jessica K Calland , Ben Pascoe , Sion C Bayliss , Evangelos Mourkas , Elvire Berthenet , Harry A Thorpe , Matthew D Hitchings , Edward J Feil , Jukka Corander , Martin J Blaser , Daniel Falush , Samuel K Sheppard

The Remarkable Genetics of Helicobacter pylori.

mBio

Avec: Daniel Falush

Genealogical inference and more flexible sequence clustering using iterative-PopPUNK.

Genome research

Avec: Bin Zhao , John A Lees , Hongjin Wu , Chao Yang , Daniel Falush

Adapting for life in the extreme.

eLife

Avec: Carolin M Kobras , Daniel Falush

Recent mixing of Vibrio parahaemolyticus populations.

The ISME journal

Avec: Chao Yang , Xiaoyan Pei , Yarong Wu , Lin Yan , Yanfeng Yan , Yuqin Song , Nicola M Coyle , Jaime Martinez-Urtaza , Christopher Quince , Qinghua Hu , Min Jiang , Edward Feil , Dajin Yang , Yajun Song , Dongsheng Zhou , Ruifu Yang , Daniel Falush , Yujun Cui

Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations.

Genome biology

Avec: Nicolai Karcher , Edoardo Pasolli , Francesco Asnicar , Kun D Huang , Adrian Tett , Serena Manara , Federica Armanini , Debbie Bain , Sylvia H Duncan , Petra Louis , Moreno Zolfo , Paolo Manghi , Mireia Valles-Colomer , Roberta Raffaetà , Omar Rota-Stabelli , Maria Carmen Collado , Georg Zeller , Daniel Falush , Frank Maixner , Alan W Walker , Curtis Huttenhower , Nicola Segata

Genomic differentiation within East Asian

Microbial genomics

Avec: Yuanhai You , Kaisa Thorell , Lihua He , Koji Yahara , Yoshio Yamaoka , Jeong-Heon Cha , Kazunari Murakami , Yukako Katsura , TEAMHp , Ichizo Kobayashi , Daniel Falush , Jianzhong Zhang

Centralized industrialization of pork in Europe and America contributes to the global spread of Salmonella enterica.

Nature food

Avec: Heng Li , Yilei Wu , Dan Feng , Quangui Jiang , Shengkai Li , Jie Rong , Ling Zhong , Ulrich Methner , Laura Baxter , Sascha Ott , Daniel Falush , Zhenpeng Li , Xiangyu Deng , Xin Lu , Yi Ren , Biao Kan , Zhemin Zhou

Réseau de co-auteurs

Kaisa Thorell 5 collaborations

Chao Yang 3 collaborations

Koji Yahara 3 collaborations

Ben Pascoe 3 collaborations

Samuel K Sheppard 3 collaborations

Yoshio Yamaoka 3 collaborations

Yujun Cui 2 collaborations

Ruifu Yang 2 collaborations

Difei Wang 2 collaborations

Roberto C Torres 2 collaborations

None None 2 collaborations

Evangelos Mourkas 2 collaborations

Jessica K Calland 2 collaborations

Matthew D Hitchings 2 collaborations

Carolin M Kobras 2 collaborations

Julian Parkhill 2 collaborations

Jukka Corander 2 collaborations

Xavier Didelot 2 collaborations

Harry A Thorpe 2 collaborations

Elise Tourrette 2 collaborations

Zhemin Zhou 2 collaborations

Hongling Qiu 1 collaboration

Hui Wang 1 collaboration

Zilia Y Muñoz-Ramírez 1 collaboration

Santiago Sandoval-Motta 1 collaboration

Rajiv Boscolo Agostini 1 collaboration

Silvia Ghirotto 1 collaboration

M Constanza Camargo 1 collaboration

Charles S Rabkin 1 collaboration

Aidan J Taylor 1 collaboration

Seungwon Ko 1 collaboration

Leonardos Mageiros 1 collaboration

Santeri Puranen 1 collaboration

Keith A Jolley 1 collaboration

Sion Bayliss 1 collaboration

Nicola J Williams 1 collaboration

Arnoud H M van Vliet 1 collaboration

Martin C J Maiden 1 collaboration

Laurence D Hurst 1 collaboration

Paul Keim 1 collaboration

David J Kelly 1 collaboration

Filipa F Vale 1 collaboration

Siqi Liu 1 collaboration

Mónica Oleastro 1 collaboration

Teresa Alarcon 1 collaboration

Tsachi-Tsadok Perets 1 collaboration

Saeid Latifi-Navid 1 collaboration

Beatriz Martinez-Gonzalez 1 collaboration

Ioannis Karayiannis 1 collaboration

Timokratis Karamitros 1 collaboration

Dionyssios N Sgouras 1 collaboration

Wael Elamin 1 collaboration

Jukka Ronkainen 1 collaboration

Pertti Aro 1 collaboration

Lars Engstrand 1 collaboration

Lars Agreus 1 collaboration

Sebastian Suerbaum 1 collaboration

Sarah L Svensson 1 collaboration

Takashi Matsumoto 1 collaboration

Muhammad Miftahussurur 1 collaboration

Kartika Afrida Fauzia 1 collaboration

Ricky Indra Alfaray 1 collaboration

Ratha-Korn Vilaichone 1 collaboration

Vo Phuoc Tuan 1 collaboration

Abbas Yadegar 1 collaboration

Lisa M Olsson 1 collaboration

Alexis Criscuolo 1 collaboration

Sylvie Issenhuth-Jeanjean 1 collaboration

James Hale 1 collaboration

Nicholas R Thomson 1 collaboration

François-Xavier Weill 1 collaboration

Sylvain Brisse 1 collaboration

Sion C Bayliss 1 collaboration

Elvire Berthenet 1 collaboration

Edward J Feil 1 collaboration

Martin J Blaser 1 collaboration

Bin Zhao 1 collaboration

John A Lees 1 collaboration

Hongjin Wu 1 collaboration

Xiaoyan Pei 1 collaboration

Yarong Wu 1 collaboration

Lin Yan 1 collaboration

Yanfeng Yan 1 collaboration

Yuqin Song 1 collaboration

Nicola M Coyle 1 collaboration

Jaime Martinez-Urtaza 1 collaboration

Christopher Quince 1 collaboration

Qinghua Hu 1 collaboration

Min Jiang 1 collaboration

Edward Feil 1 collaboration

Dajin Yang 1 collaboration

Yajun Song 1 collaboration

Dongsheng Zhou 1 collaboration

Nicolai Karcher 1 collaboration

Edoardo Pasolli 1 collaboration

Francesco Asnicar 1 collaboration

Kun D Huang 1 collaboration

Adrian Tett 1 collaboration

Serena Manara 1 collaboration

Federica Armanini 1 collaboration

Debbie Bain 1 collaboration

Sylvia H Duncan 1 collaboration

Petra Louis 1 collaboration

Moreno Zolfo 1 collaboration

Paolo Manghi 1 collaboration

Mireia Valles-Colomer 1 collaboration

Roberta Raffaetà 1 collaboration

Omar Rota-Stabelli 1 collaboration

Maria Carmen Collado 1 collaboration

Georg Zeller 1 collaboration

Frank Maixner 1 collaboration

Alan W Walker 1 collaboration

Curtis Huttenhower 1 collaboration

Nicola Segata 1 collaboration

Yuanhai You 1 collaboration

Lihua He 1 collaboration

Jeong-Heon Cha 1 collaboration

Kazunari Murakami 1 collaboration

Yukako Katsura 1 collaboration

None TEAMHp 1 collaboration

Ichizo Kobayashi 1 collaboration

Jianzhong Zhang 1 collaboration

Heng Li 1 collaboration

Yilei Wu 1 collaboration

Dan Feng 1 collaboration

Quangui Jiang 1 collaboration

Shengkai Li 1 collaboration

Jie Rong 1 collaboration

Ling Zhong 1 collaboration

Ulrich Methner 1 collaboration

Laura Baxter 1 collaboration

Sascha Ott 1 collaboration

Zhenpeng Li 1 collaboration

Xiangyu Deng 1 collaboration

Xin Lu 1 collaboration

Yi Ren 1 collaboration

Biao Kan 1 collaboration