Publications by authors named "Thomas Junier"

46Publications

Bacterial spores, from ecology to biotechnology.

Adv Appl Microbiol 2019 27;106:79-111. Epub 2018 Nov 27.

Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00652164183005
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http://dx.doi.org/10.1016/bs.aambs.2018.10.002DOI Listing
February 2020

A historical legacy of antibiotic utilization on bacterial seed banks in sediments.

PeerJ 2018 3;6:e4197. Epub 2018 Jan 3.

Laboratory of Microbiology, Institute of Biology, University of Neuchatel, Neuchâtel, NE, Switzerland.

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http://dx.doi.org/10.7717/peerj.4197DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5756452PMC
January 2018

MAR-Mediated transgene integration into permissive chromatin and increased expression by recombination pathway engineering.

Biotechnol Bioeng 2017 02 3;114(2):384-396. Epub 2016 Oct 3.

Department of Fundamental Microbiology, Institute of Biotechnology, University of Lausanne, and Center for Biotechnology UNIL-EPFL, Lausanne, Switzerland.

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http://dx.doi.org/10.1002/bit.26086DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5215416PMC
February 2017

Physical Isolation of Endospores from Environmental Samples by Targeted Lysis of Vegetative Cells.

J Vis Exp 2016 Jan 21(107):e53411. Epub 2016 Jan 21.

Laboratory of Microbiology, University of Neuchatel;

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http://dx.doi.org/10.3791/53411DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4781691PMC
January 2016

Diversity and ecology of oxalotrophic bacteria.

World J Microbiol Biotechnol 2016 Feb 9;32(2):28. Epub 2016 Jan 9.

Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland.

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http://dx.doi.org/10.1007/s11274-015-1982-3DOI Listing
February 2016

CEGA--a catalog of conserved elements from genomic alignments.

Nucleic Acids Res 2016 Jan 2;44(D1):D96-100. Epub 2015 Nov 2.

Department of Genetic Medicine and Development, University of Geneva Medical School, Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkv1163DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702837PMC
January 2016

MLgsc: A Maximum-Likelihood General Sequence Classifier.

PLoS One 2015 6;10(7):e0129384. Epub 2015 Jul 6.

Laboratory of Microbiology, University of Neuchâtel, Neuchâtel, Neuchâtel, Switzerland.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0129384PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4492669PMC
March 2016

Under-detection of endospore-forming Firmicutes in metagenomic data.

Comput Struct Biotechnol J 2015 25;13:299-306. Epub 2015 Apr 25.

Laboratory of Microbiology, Institute of Biology, University of Neuchatel, CH-2000, Neuchâtel, Switzerland.

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http://dx.doi.org/10.1016/j.csbj.2015.04.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4427659PMC
May 2015

Stage 0 sporulation gene A as a molecular marker to study diversity of endospore-forming Firmicutes.

Environ Microbiol Rep 2013 Dec 8;5(6):911-24. Epub 2013 Sep 8.

Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, CH-2000, Switzerland.

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http://dx.doi.org/10.1111/1758-2229.12094DOI Listing
December 2013

Quantification of endospore-forming firmicutes by quantitative PCR with the functional gene spo0A.

Appl Environ Microbiol 2013 Sep 28;79(17):5302-12. Epub 2013 Jun 28.

Laboratory of Microbiology, Institute of Biology, University of Neuchatel, Neuchatel, Switzerland.

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http://dx.doi.org/10.1128/AEM.01376-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753955PMC
September 2013

Contribution of genetic background, traditional risk factors, and HIV-related factors to coronary artery disease events in HIV-positive persons.

Clin Infect Dis 2013 Jul 26;57(1):112-21. Epub 2013 Mar 26.

Institute of Microbiology, University Hospital Center, University of Lausanne, Lausanne, Switzerland.

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http://dx.doi.org/10.1093/cid/cit196DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3669528PMC
July 2013

Purifying selection in mammalian mitochondrial protein-coding genes is highly effective and congruent with evolution of nuclear genes.

Mol Biol Evol 2013 Feb 14;30(2):347-55. Epub 2012 Sep 14.

Department of Genetic Medicine and Development, University of Geneva Medical School and iGE3 Institute of Genetics and Genomics of Geneva, Switzerland.

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http://dx.doi.org/10.1093/molbev/mss219DOI Listing
February 2013

Rhinovirus genome variation during chronic upper and lower respiratory tract infections.

PLoS One 2011 21;6(6):e21163. Epub 2011 Jun 21.

Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University of Geneva Hospitals, Geneva, Switzerland.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0021163PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3119694PMC
November 2011

Rhinovirus genome evolution during experimental human infection.

PLoS One 2010 May 11;5(5):e10588. Epub 2010 May 11.

Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University of Geneva Hospitals, Geneva, Switzerland.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0010588PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2868056PMC
May 2010

The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell.

Bioinformatics 2010 Jul 13;26(13):1669-70. Epub 2010 May 13.

Department of Genetic Medicine and Development, University of Geneva Medical School, 1 rue Michel-Servet, 1211 Geneva, Switzerland.

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http://dx.doi.org/10.1093/bioinformatics/btq243DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2887050PMC
July 2010

Functional and evolutionary insights from the genomes of three parasitoid Nasonia species.

Authors:
John H Werren Stephen Richards Christopher A Desjardins Oliver Niehuis Jürgen Gadau John K Colbourne John H Werren Stephen Richards Christopher A Desjardins Oliver Niehuis Jürgen Gadau John K Colbourne Leo W Beukeboom Claude Desplan Christine G Elsik Cornelis J P Grimmelikhuijzen Paul Kitts Jeremy A Lynch Terence Murphy Deodoro C S G Oliveira Christopher D Smith Louis van de Zande Kim C Worley Evgeny M Zdobnov Maarten Aerts Stefan Albert Victor H Anaya Juan M Anzola Angel R Barchuk Susanta K Behura Agata N Bera May R Berenbaum Rinaldo C Bertossa Márcia M G Bitondi Seth R Bordenstein Peer Bork Erich Bornberg-Bauer Marleen Brunain Giuseppe Cazzamali Lesley Chaboub Joseph Chacko Dean Chavez Christopher P Childers Jeong-Hyeon Choi Michael E Clark Charles Claudianos Rochelle A Clinton Andrew G Cree Alexandre S Cristino Phat M Dang Alistair C Darby Dirk C de Graaf Bart Devreese Huyen H Dinh Rachel Edwards Navin Elango Eran Elhaik Olga Ermolaeva Jay D Evans Sylvain Foret Gerald R Fowler Daniel Gerlach Joshua D Gibson Donald G Gilbert Dan Graur Stefan Gründer Darren E Hagen Yi Han Frank Hauser Da Hultmark Henry C Hunter Gregory D D Hurst Shalini N Jhangian Huaiyang Jiang Reed M Johnson Andrew K Jones Thomas Junier Tatsuhiko Kadowaki Albert Kamping Yuri Kapustin Bobak Kechavarzi Jaebum Kim Jay Kim Boris Kiryutin Tosca Koevoets Christie L Kovar Evgenia V Kriventseva Robert Kucharski Heewook Lee Sandra L Lee Kristin Lees Lora R Lewis David W Loehlin John M Logsdon Jacqueline A Lopez Ryan J Lozado Donna Maglott Ryszard Maleszka Anoop Mayampurath Danielle J Mazur Marcella A McClure Andrew D Moore Margaret B Morgan Jean Muller Monica C Munoz-Torres Donna M Muzny Lynne V Nazareth Susanne Neupert Ngoc B Nguyen Francis M F Nunes John G Oakeshott Geoffrey O Okwuonu Bart A Pannebakker Vikas R Pejaver Zuogang Peng Stephen C Pratt Reinhard Predel Ling-Ling Pu Hilary Ranson Rhitoban Raychoudhury Andreas Rechtsteiner Justin T Reese Jeffrey G Reid Megan Riddle Hugh M Robertson Jeanne Romero-Severson Miriam Rosenberg Timothy B Sackton David B Sattelle Helge Schlüns Thomas Schmitt Martina Schneider Andreas Schüler Andrew M Schurko David M Shuker Zilá L P Simões Saurabh Sinha Zachary Smith Victor Solovyev Alexandre Souvorov Andreas Springauf Elisabeth Stafflinger Deborah E Stage Mario Stanke Yoshiaki Tanaka Arndt Telschow Carol Trent Selina Vattathil Eveline C Verhulst Lumi Viljakainen Kevin W Wanner Robert M Waterhouse James B Whitfield Timothy E Wilkes Michael Williamson Judith H Willis Florian Wolschin Stefan Wyder Takuji Yamada Soojin V Yi Courtney N Zecher Lan Zhang Richard A Gibbs

The genome sequence of taurine cattle: a window to ruminant biology and evolution.

Authors:
Christine G Elsik Ross L Tellam Kim C Worley Richard A Gibbs Donna M Muzny George M Weinstock David L Adelson Evan E Eichler Laura Elnitski Roderic Guigó Debora L Hamernik Steve M Kappes Harris A Lewin David J Lynn Frank W Nicholas Alexandre Reymond Monique Rijnkels Loren C Skow Evgeny M Zdobnov Lawrence Schook James Womack Tyler Alioto Stylianos E Antonarakis Alex Astashyn Charles E Chapple Hsiu-Chuan Chen Jacqueline Chrast Francisco Câmara Olga Ermolaeva Charlotte N Henrichsen Wratko Hlavina Yuri Kapustin Boris Kiryutin Paul Kitts Felix Kokocinski Melissa Landrum Donna Maglott Kim Pruitt Victor Sapojnikov Stephen M Searle Victor Solovyev Alexandre Souvorov Catherine Ucla Carine Wyss Juan M Anzola Daniel Gerlach Eran Elhaik Dan Graur Justin T Reese Robert C Edgar John C McEwan Gemma M Payne Joy M Raison Thomas Junier Evgenia V Kriventseva Eduardo Eyras Mireya Plass Ravikiran Donthu Denis M Larkin James Reecy Mary Q Yang Lin Chen Ze Cheng Carol G Chitko-McKown George E Liu Lakshmi K Matukumalli Jiuzhou Song Bin Zhu Daniel G Bradley Fiona S L Brinkman Lilian P L Lau Matthew D Whiteside Angela Walker Thomas T Wheeler Theresa Casey J Bruce German Danielle G Lemay Nauman J Maqbool Adrian J Molenaar Seongwon Seo Paul Stothard Cynthia L Baldwin Rebecca Baxter Candice L Brinkmeyer-Langford Wendy C Brown Christopher P Childers Timothy Connelley Shirley A Ellis Krista Fritz Elizabeth J Glass Carolyn T A Herzig Antti Iivanainen Kevin K Lahmers Anna K Bennett C Michael Dickens James G R Gilbert Darren E Hagen Hanni Salih Jan Aerts Alexandre R Caetano Brian Dalrymple Jose Fernando Garcia Clare A Gill Stefan G Hiendleder Erdogan Memili Diane Spurlock John L Williams Lee Alexander Michael J Brownstein Leluo Guan Robert A Holt Steven J M Jones Marco A Marra Richard Moore Stephen S Moore Andy Roberts Masaaki Taniguchi Richard C Waterman Joseph Chacko Mimi M Chandrabose Andy Cree Marvin Diep Dao Huyen H Dinh Ramatu Ayiesha Gabisi Sandra Hines Jennifer Hume Shalini N Jhangiani Vandita Joshi Christie L Kovar Lora R Lewis Yih-Shin Liu John Lopez Margaret B Morgan Ngoc Bich Nguyen Geoffrey O Okwuonu San Juana Ruiz Jireh Santibanez Rita A Wright Christian Buhay Yan Ding Shannon Dugan-Rocha Judith Herdandez Michael Holder Aniko Sabo Amy Egan Jason Goodell Katarzyna Wilczek-Boney Gerald R Fowler Matthew Edward Hitchens Ryan J Lozado Charles Moen David Steffen James T Warren Jingkun Zhang Readman Chiu Jacqueline E Schein K James Durbin Paul Havlak Huaiyang Jiang Yue Liu Xiang Qin Yanru Ren Yufeng Shen Henry Song Stephanie Nicole Bell Clay Davis Angela Jolivet Johnson Sandra Lee Lynne V Nazareth Bella Mayurkumar Patel Ling-Ling Pu Selina Vattathil Rex Lee Williams Stacey Curry Cerissa Hamilton Erica Sodergren David A Wheeler Wes Barris Gary L Bennett André Eggen Ronnie D Green Gregory P Harhay Matthew Hobbs Oliver Jann John W Keele Matthew P Kent Sigbjørn Lien Stephanie D McKay Sean McWilliam Abhirami Ratnakumar Robert D Schnabel Timothy Smith Warren M Snelling Tad S Sonstegard Roger T Stone Yoshikazu Sugimoto Akiko Takasuga Jeremy F Taylor Curtis P Van Tassell Michael D Macneil Antonio R R Abatepaulo Colette A Abbey Virpi Ahola Iassudara G Almeida Ariel F Amadio Elen Anatriello Suria M Bahadue Fernando H Biase Clayton R Boldt Jeffery A Carroll Wanessa A Carvalho Eliane P Cervelatti Elsa Chacko Jennifer E Chapin Ye Cheng Jungwoo Choi Adam J Colley Tatiana A de Campos Marcos De Donato Isabel K F de Miranda Santos Carlo J F de Oliveira Heather Deobald Eve Devinoy Kaitlin E Donohue Peter Dovc Annett Eberlein Carolyn J Fitzsimmons Alessandra M Franzin Gustavo R Garcia Sem Genini Cody J Gladney Jason R Grant Marion L Greaser Jonathan A Green Darryl L Hadsell Hatam A Hakimov Rob Halgren Jennifer L Harrow Elizabeth A Hart Nicola Hastings Marta Hernandez Zhi-Liang Hu Aaron Ingham Terhi Iso-Touru Catherine Jamis Kirsty Jensen Dimos Kapetis Tovah Kerr Sari S Khalil Hasan Khatib Davood Kolbehdari Charu G Kumar Dinesh Kumar Richard Leach Justin C-M Lee Changxi Li Krystin M Logan Roberto Malinverni Elisa Marques William F Martin Natalia F Martins Sandra R Maruyama Raffaele Mazza Kim L McLean Juan F Medrano Barbara T Moreno Daniela D Moré Carl T Muntean Hari P Nandakumar Marcelo F G Nogueira Ingrid Olsaker Sameer D Pant Francesca Panzitta Rosemeire C P Pastor Mario A Poli Nathan Poslusny Satyanarayana Rachagani Shoba Ranganathan Andrej Razpet Penny K Riggs Gonzalo Rincon Nelida Rodriguez-Osorio Sandra L Rodriguez-Zas Natasha E Romero Anne Rosenwald Lillian Sando Sheila M Schmutz Libing Shen Laura Sherman Bruce R Southey Ylva Strandberg Lutzow Jonathan V Sweedler Imke Tammen Bhanu Prakash V L Telugu Jennifer M Urbanski Yuri T Utsunomiya Chris P Verschoor Ashley J Waardenberg Zhiquan Wang Robert Ward Rosemarie Weikard Thomas H Welsh Stephen N White Laurens G Wilming Kris R Wunderlich Jianqi Yang Feng-Qi Zhao

Science 2009 Apr;324(5926):522-8

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http://dx.doi.org/10.1126/science.1169588DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943200PMC
April 2009

Community analysis of betaproteobacterial ammonia-oxidizing bacteria using the amoCAB operon.

Appl Microbiol Biotechnol 2009 May 10;83(1):175-88. Epub 2009 Mar 10.

Ecole Polytechnique Fédérale de Lausanne (EPFL ENAC ISTE EML), CE 1 644 (Centre Est), Station 6, 1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1007/s00253-009-1923-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2845890PMC
May 2009

TRiFLe, a program for in silico terminal restriction fragment length polymorphism analysis with user-defined sequence sets.

Appl Environ Microbiol 2008 Oct 29;74(20):6452-6. Epub 2008 Aug 29.

Environmental Microbiology Laboratory, Ecole Polytechnique Federale de Lausanne, CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1128/AEM.01394-08DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570284PMC
October 2008

The cis-acting replication elements define human enterovirus and rhinovirus species.

RNA 2008 Aug 9;14(8):1568-78. Epub 2008 Jun 9.

Central Laboratory of Virology, Division of Infectious Diseases, University of Geneva Hospitals, 1211 Geneva 14, Switzerland.

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http://dx.doi.org/10.1261/rna.1031408DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2491478PMC
August 2008

Genome-wide search reveals a novel GacA-regulated small RNA in Pseudomonas species.

BMC Genomics 2008 Apr 13;9:167. Epub 2008 Apr 13.

Département de Microbiologie Fondamentale, Biophore, Université de Lausanne, CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1186/1471-2164-9-167DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2375449PMC
April 2008

Biased distributions and decay of long interspersed nuclear elements in the chicken genome.

Genetics 2008 Jan 18;178(1):573-81. Epub 2007 Oct 18.

Department of Ecophysiology, Max Planck Institute of Limnology, Plön, Germany.

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http://dx.doi.org/10.1534/genetics.106.061861DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2206104PMC
January 2008

New complete genome sequences of human rhinoviruses shed light on their phylogeny and genomic features.

BMC Genomics 2007 Jul 10;8:224. Epub 2007 Jul 10.

Central Laboratory of Virology, Division of Infectious Diseases, University of Geneva Hospitals, Geneva, Switzerland.

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http://dx.doi.org/10.1186/1471-2164-8-224DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1949831PMC
July 2007