Publications by authors named "Arnab Pain"

100Publications

Host-directed editing of the SARS-CoV-2 genome.

Biochem Biophys Res Commun 2020 Nov 5. Epub 2020 Nov 5.

King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia; Research Center for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, N20 W10 Kita-ku, Sapporo, 001-0020, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.bbrc.2020.10.092DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7643664PMC
November 2020

Dynamics and within-host interaction of Theileria lestoquardi and T. ovis among naive sheep in Oman.

Sci Rep 2020 11 13;10(1):19802. Epub 2020 Nov 13.

Department of Biochemistry, College of Medicine and Health Sciences, Sultan Qaboos University, AlKhoud 123, Muscat, Oman.

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http://dx.doi.org/10.1038/s41598-020-76844-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7666211PMC
November 2020

Functional Pangenome Analysis Shows Key Features of E Protein Are Preserved in SARS and SARS-CoV-2.

Front Cell Infect Microbiol 2020 27;10:405. Epub 2020 Jul 27.

Biological and Environmental Science and Engineering (BESE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.

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http://dx.doi.org/10.3389/fcimb.2020.00405DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7396417PMC
September 2020

A genetic barcode of SARS-CoV-2 for monitoring global distribution of different clades during the COVID-19 pandemic.

Int J Infect Dis 2020 Nov 22;100:216-223. Epub 2020 Aug 22.

King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia; Research Center for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, N20 W10 Kita-ku, Sapporo, 001-0020 Japan; Nuffield Division of Clinical Laboratory Sciences (NDCLS), The John Radcliffe Hospital, University of Oxford, Headington, Oxford, OX3 9DU, United Kingdom. Electronic address:

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http://dx.doi.org/10.1016/j.ijid.2020.08.052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7443060PMC
November 2020

Novel tumour suppressor roles for GZMA and RASGRP1 in Theileria annulata-transformed macrophages and human B lymphoma cells.

Cell Microbiol 2020 Dec 29;22(12):e13255. Epub 2020 Sep 29.

Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.

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http://dx.doi.org/10.1111/cmi.13255DOI Listing
December 2020

iSCAN: An RT-LAMP-coupled CRISPR-Cas12 module for rapid, sensitive detection of SARS-CoV-2.

Virus Res 2020 10 18;288:198129. Epub 2020 Aug 18.

Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia. Electronic address:

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http://dx.doi.org/10.1016/j.virusres.2020.198129DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7434412PMC
October 2020

Influx of diverse, drug resistant and transmissible Plasmodium falciparum into a malaria-free setting in Qatar.

BMC Infect Dis 2020 Jun 15;20(1):413. Epub 2020 Jun 15.

Department of Biochemistry, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman.

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http://dx.doi.org/10.1186/s12879-020-05111-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7296620PMC
June 2020

Crohn's Disease Patient Infected With Multiple Co-occurring Nontuberculous Mycobacteria.

Inflamm Bowel Dis 2020 Jun;26(7):e65-e67

Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal-Jeddah, Saudi Arabia.

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http://dx.doi.org/10.1093/ibd/izaa100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7301405PMC
June 2020

Publisher Correction: Genetic tool development in marine protists: emerging model organisms for experimental cell biology.

Authors:
Drahomíra Faktorová R Ellen R Nisbet José A Fernández Robledo Elena Casacuberta Lisa Sudek Andrew E Allen Manuel Ares Cristina Aresté Cecilia Balestreri Adrian C Barbrook Patrick Beardslee Sara Bender David S Booth François-Yves Bouget Chris Bowler Susana A Breglia Colin Brownlee Gertraud Burger Heriberto Cerutti Rachele Cesaroni Miguel A Chiurillo Thomas Clemente Duncan B Coles Jackie L Collier Elizabeth C Cooney Kathryn Coyne Roberto Docampo Christopher L Dupont Virginia Edgcomb Elin Einarsson Pía A Elustondo Fernan Federici Veronica Freire-Beneitez Nastasia J Freyria Kodai Fukuda Paulo A García Peter R Girguis Fatma Gomaa Sebastian G Gornik Jian Guo Vladimír Hampl Yutaka Hanawa Esteban R Haro-Contreras Elisabeth Hehenberger Andrea Highfield Yoshihisa Hirakawa Amanda Hopes Christopher J Howe Ian Hu Jorge Ibañez Nicholas A T Irwin Yuu Ishii Natalia Ewa Janowicz Adam C Jones Ambar Kachale Konomi Fujimura-Kamada Binnypreet Kaur Jonathan Z Kaye Eleanna Kazana Patrick J Keeling Nicole King Lawrence A Klobutcher Noelia Lander Imen Lassadi Zhuhong Li Senjie Lin Jean-Claude Lozano Fulei Luan Shinichiro Maruyama Tamara Matute Cristina Miceli Jun Minagawa Mark Moosburner Sebastián R Najle Deepak Nanjappa Isabel C Nimmo Luke Noble Anna M G Novák Vanclová Mariusz Nowacki Isaac Nuñez Arnab Pain Angela Piersanti Sandra Pucciarelli Jan Pyrih Joshua S Rest Mariana Rius Deborah Robertson Albane Ruaud Iñaki Ruiz-Trillo Monika A Sigg Pamela A Silver Claudio H Slamovits G Jason Smith Brittany N Sprecher Rowena Stern Estienne C Swart Anastasios D Tsaousis Lev Tsypin Aaron Turkewitz Jernej Turnšek Matus Valach Valérie Vergé Peter von Dassow Tobias von der Haar Ross F Waller Lu Wang Xiaoxue Wen Glen Wheeler April Woods Huan Zhang Thomas Mock Alexandra Z Worden Julius Lukeš

Nat Methods 2020 05;17(5):551

Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic.

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http://dx.doi.org/10.1038/s41592-020-0828-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7200595PMC
May 2020

Comparative Genomic and Transcriptomic Analyses of Subtypes Provide New Insights Into Their Pathogenicity and Taxonomy.

Front Cell Infect Microbiol 2020 24;10:122. Epub 2020 Mar 24.

Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.

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http://dx.doi.org/10.3389/fcimb.2020.00122DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7105574PMC
March 2020

Genetic tool development in marine protists: emerging model organisms for experimental cell biology.

Authors:
Drahomíra Faktorová R Ellen R Nisbet José A Fernández Robledo Elena Casacuberta Lisa Sudek Andrew E Allen Manuel Ares Cristina Aresté Cecilia Balestreri Adrian C Barbrook Patrick Beardslee Sara Bender David S Booth François-Yves Bouget Chris Bowler Susana A Breglia Colin Brownlee Gertraud Burger Heriberto Cerutti Rachele Cesaroni Miguel A Chiurillo Thomas Clemente Duncan B Coles Jackie L Collier Elizabeth C Cooney Kathryn Coyne Roberto Docampo Christopher L Dupont Virginia Edgcomb Elin Einarsson Pía A Elustondo Fernan Federici Veronica Freire-Beneitez Nastasia J Freyria Kodai Fukuda Paulo A García Peter R Girguis Fatma Gomaa Sebastian G Gornik Jian Guo Vladimír Hampl Yutaka Hanawa Esteban R Haro-Contreras Elisabeth Hehenberger Andrea Highfield Yoshihisa Hirakawa Amanda Hopes Christopher J Howe Ian Hu Jorge Ibañez Nicholas A T Irwin Yuu Ishii Natalia Ewa Janowicz Adam C Jones Ambar Kachale Konomi Fujimura-Kamada Binnypreet Kaur Jonathan Z Kaye Eleanna Kazana Patrick J Keeling Nicole King Lawrence A Klobutcher Noelia Lander Imen Lassadi Zhuhong Li Senjie Lin Jean-Claude Lozano Fulei Luan Shinichiro Maruyama Tamara Matute Cristina Miceli Jun Minagawa Mark Moosburner Sebastián R Najle Deepak Nanjappa Isabel C Nimmo Luke Noble Anna M G Novák Vanclová Mariusz Nowacki Isaac Nuñez Arnab Pain Angela Piersanti Sandra Pucciarelli Jan Pyrih Joshua S Rest Mariana Rius Deborah Robertson Albane Ruaud Iñaki Ruiz-Trillo Monika A Sigg Pamela A Silver Claudio H Slamovits G Jason Smith Brittany N Sprecher Rowena Stern Estienne C Swart Anastasios D Tsaousis Lev Tsypin Aaron Turkewitz Jernej Turnšek Matus Valach Valérie Vergé Peter von Dassow Tobias von der Haar Ross F Waller Lu Wang Xiaoxue Wen Glen Wheeler April Woods Huan Zhang Thomas Mock Alexandra Z Worden Julius Lukeš

Nat Methods 2020 05 6;17(5):481-494. Epub 2020 Apr 6.

Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic.

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http://dx.doi.org/10.1038/s41592-020-0796-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7200600PMC
May 2020

A landscape of genomic alterations at the root of a near-untreatable tuberculosis epidemic.

BMC Med 2020 02 4;18(1):24. Epub 2020 Feb 4.

South African Medical Research Council Centre for Tuberculosis Research, DST NRF Centre of Excellence for Biomedical Tuberculosis research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.

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http://dx.doi.org/10.1186/s12916-019-1487-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6998097PMC
February 2020

First report of harboring in Saudi Arabia.

Antimicrob Resist Infect Control 2019 19;8:203. Epub 2019 Dec 19.

1Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.

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http://dx.doi.org/10.1186/s13756-019-0653-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6923860PMC
July 2020

Whole genome sequencing provides additional insights into recurrent tuberculosis classified as endogenous reactivation by IS6110 DNA fingerprinting.

Infect Genet Evol 2019 11 2;75:103948. Epub 2019 Jul 2.

NRF/DST Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.

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http://dx.doi.org/10.1016/j.meegid.2019.103948DOI Listing
November 2019

Discovering, Characterizing, and Applying Acyl Homoserine Lactone-Quenching Enzymes to Mitigate Microbe-Associated Problems Under Saline Conditions.

Front Microbiol 2019 17;10:823. Epub 2019 Apr 17.

Water Desalination and Reuse Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.

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https://www.frontiersin.org/article/10.3389/fmicb.2019.00823
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http://dx.doi.org/10.3389/fmicb.2019.00823DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6479171PMC
April 2019

A fast and cost-effective microsampling protocol incorporating reduced animal usage for time-series transcriptomics in rodent malaria parasites.

Malar J 2019 Jan 25;18(1):26. Epub 2019 Jan 25.

Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.

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http://dx.doi.org/10.1186/s12936-019-2659-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6347755PMC
January 2019

Theileria highjacks JNK2 into a complex with the macroschizont GPI (GlycosylPhosphatidylInositol)-anchored surface protein p104.

Cell Microbiol 2019 03 5;21(3):e12973. Epub 2018 Dec 5.

Laboratoire de Biologie Cellulaire Comparative des Apicomplexes, Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris, 75014, France.

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http://doi.wiley.com/10.1111/cmi.12973
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http://dx.doi.org/10.1111/cmi.12973DOI Listing
March 2019

Highly diverged novel subunit composition of apicomplexan F-type ATP synthase identified from Toxoplasma gondii.

PLoS Biol 2018 07 13;16(7):e2006128. Epub 2018 Jul 13.

Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, India.

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http://dx.doi.org/10.1371/journal.pbio.2006128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6059495PMC
July 2018

Genetic Determinants Associated With Survival of in the Model.

Front Microbiol 2018 29;9:1118. Epub 2018 May 29.

School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia.

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http://dx.doi.org/10.3389/fmicb.2018.01118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5987112PMC
May 2018

miR-126-5p by direct targeting of JNK-interacting protein-2 (JIP-2) plays a key role in Theileria-infected macrophage virulence.

PLoS Pathog 2018 03 23;14(3):e1006942. Epub 2018 Mar 23.

Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.

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http://dx.doi.org/10.1371/journal.ppat.1006942DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5892942PMC
March 2018

Timing of host feeding drives rhythms in parasite replication.

PLoS Pathog 2018 02 26;14(2):e1006900. Epub 2018 Feb 26.

Institutes of Evolution, Immunology and Infection Research, University of Edinburgh, Edinburgh, United Kingdom.

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http://dx.doi.org/10.1371/journal.ppat.1006900DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5843352PMC
February 2018

A reference genome and methylome for the Plasmodium knowlesi A1-H.1 line.

Int J Parasitol 2018 03 16;48(3-4):191-196. Epub 2017 Dec 16.

Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom; Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom. Electronic address:

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http://dx.doi.org/10.1016/j.ijpara.2017.09.008DOI Listing
March 2018

Genome-wide mutagenesis and multi-drug resistance in American trypanosomes induced by the front-line drug benznidazole.

Sci Rep 2017 10 31;7(1):14407. Epub 2017 Oct 31.

Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.

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http://dx.doi.org/10.1038/s41598-017-14986-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5663738PMC
October 2017

A multiple genome analysis of Mycobacterium tuberculosis reveals specific novel genes and mutations associated with pyrazinamide resistance.

BMC Genomics 2017 Oct 11;18(1):769. Epub 2017 Oct 11.

Laboratorio de Bioinformática y Biología Molecular. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porras, 31, Lima, Peru.

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http://dx.doi.org/10.1186/s12864-017-4146-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5637355PMC
October 2017

Proteogenomic Investigation of Strain Variation in Clinical Mycobacterium tuberculosis Isolates.

J Proteome Res 2017 10 11;16(10):3841-3851. Epub 2017 Sep 11.

DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University , Cape Town 7505, South Africa.

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http://pubs.acs.org/doi/10.1021/acs.jproteome.7b00483
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http://dx.doi.org/10.1021/acs.jproteome.7b00483DOI Listing
October 2017

Progenitor strain introduction of Mycobacterium bovis at the wildlife-livestock interface can lead to clonal expansion of the disease in a single ecosystem.

Infect Genet Evol 2017 07 13;51:235-238. Epub 2017 Apr 13.

DST/NRF Centre of Excellence in Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Francie van Zijl Drive, Cape Town 8000, South Africa. Electronic address:

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http://dx.doi.org/10.1016/j.meegid.2017.04.012DOI Listing
July 2017

Turkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestor.

Infect Genet Evol 2016 11 14;45:461-473. Epub 2016 Oct 14.

Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.

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http://dx.doi.org/10.1016/j.meegid.2016.10.009DOI Listing
November 2016

The draft genome of Mycobacterium aurum, a potential model organism for investigating drugs against Mycobacterium tuberculosis and Mycobacterium leprae.

Int J Mycobacteriol 2015 09 4;4(3):207-16. Epub 2015 Jun 4.

Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom.

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http://dx.doi.org/10.1016/j.ijmyco.2015.05.001DOI Listing
September 2015

Candidate Essential Genes in Burkholderia cenocepacia J2315 Identified by Genome-Wide TraDIS.

Front Microbiol 2016 22;7:1288. Epub 2016 Aug 22.

Faculty of Science and Technology, School of Biosciences and Biotechnology, Universiti Kebangsaan Malaysia Bangi, Malaysia.

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http://dx.doi.org/10.3389/fmicb.2016.01288DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4993015PMC
September 2016

Genome-scale comparison of expanded gene families in Plasmodium ovale wallikeri and Plasmodium ovale curtisi with Plasmodium malariae and with other Plasmodium species.

Int J Parasitol 2016 10 5;46(11):685-96. Epub 2016 Jul 5.

Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah 23955-6900, Saudi Arabia; Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, N20 W10 Kita-ku, Sapporo 001-0020, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.ijpara.2016.05.009DOI Listing
October 2016

Translational repression of the cpw-wpc gene family in the malaria parasite Plasmodium.

Parasitol Int 2016 Oct 14;65(5 Pt A):463-71. Epub 2016 Jun 14.

Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal; Parasitology, Center for Infectious Diseases, University of Heidelberg Medical School, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.parint.2016.06.007DOI Listing
October 2016

Metabolic pathway redundancy within the apicomplexan-dinoflagellate radiation argues against an ancient chromalveolate plastid.

Commun Integr Biol 2016 Jan-Feb;9(1):e1116653. Epub 2015 Dec 8.

Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology , Thuwal, Saudi Arabia.

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http://dx.doi.org/10.1080/19420889.2015.1116653DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4802802PMC
April 2016

Diversity of extracellular proteins during the transition from the 'proto-apicomplexan' alveolates to the apicomplexan obligate parasites.

Parasitology 2016 Jan 20;143(1):1-17. Epub 2015 Nov 20.

Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division,King Abdullah University of Science and Technology (KAUST),Thuwal,Jeddah 23955-6900,Kingdom of Saudi Arabia.

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http://search.proquest.com/openview/6aa21c9ce24bbbf6c9d4eeac
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http://www.journals.cambridge.org/abstract_S0031182015001213
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http://dx.doi.org/10.1017/S0031182015001213DOI Listing
January 2016

Whole genome sequence analysis of Mycobacterium suricattae.

Tuberculosis (Edinb) 2015 Dec 13;95(6):682-688. Epub 2015 Oct 13.

DST-NRF Centre of Excellence for Biomedical Tuberculosis Research/SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa. Electronic address:

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http://dx.doi.org/10.1016/j.tube.2015.10.001DOI Listing
December 2015

Genome Sequence of a Multidrug-Resistant Strain of Stenotrophomonas maltophilia with Carbapenem Resistance, Isolated from King Abdullah Medical City, Makkah, Saudi Arabia.

Genome Announc 2015 Oct 15;3(5). Epub 2015 Oct 15.

Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia

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http://dx.doi.org/10.1128/genomeA.01166-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4611680PMC
October 2015

Draft genome of the most devastating insect pest of coffee worldwide: the coffee berry borer, Hypothenemus hampei.

Sci Rep 2015 Jul 31;5:12525. Epub 2015 Jul 31.

Pathogen Genomics Laboratory, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal-Jeddah, Saudi Arabia.

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http://dx.doi.org/10.1038/srep12525DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4521149PMC
July 2015

PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis.

BMC Bioinformatics 2015 May 13;16:155. Epub 2015 May 13.

Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel St, London, UK.

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http://dx.doi.org/10.1186/s12859-015-0603-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4429496PMC
May 2015

Endosymbiosis undone by stepwise elimination of the plastid in a parasitic dinoflagellate.

Proc Natl Acad Sci U S A 2015 May 20;112(18):5767-72. Epub 2015 Apr 20.

School of Botany, University of Melbourne, Parkville, Victoria 3010, Australia; Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom

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http://dx.doi.org/10.1073/pnas.1423400112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4426444PMC
May 2015

Comprehensive evaluation of Toxoplasma gondii VEG and Neospora caninum LIV genomes with tachyzoite stage transcriptome and proteome defines novel transcript features.

PLoS One 2015 13;10(4):e0124473. Epub 2015 Apr 13.

Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, Kingdom of Saudi Arabia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0124473PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4395442PMC
April 2016

Divergent mitochondrial respiratory chains in phototrophic relatives of apicomplexan parasites.

Mol Biol Evol 2015 May 6;32(5):1115-31. Epub 2015 Feb 6.

Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic Canadian Institute for Advanced Research, Toronto, ON, Canada

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http://dx.doi.org/10.1093/molbev/msv021DOI Listing
May 2015

A robust SNP barcode for typing Mycobacterium tuberculosis complex strains.

Nat Commun 2014 Sep 1;5:4812. Epub 2014 Sep 1.

1] Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK [2] Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.

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http://dx.doi.org/10.1038/ncomms5812DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4166679PMC
September 2014

The population structure of Vibrio cholerae from the Chandigarh Region of Northern India.

PLoS Negl Trop Dis 2014 Jul 24;8(7):e2981. Epub 2014 Jul 24.

Pathogen Genomics Laboratory, Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.

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http://dx.doi.org/10.1371/journal.pntd.0002981DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4109905PMC
July 2014

SVAMP: sequence variation analysis, maps and phylogeny.

Bioinformatics 2014 Aug 3;30(15):2227-9. Epub 2014 Apr 3.

Pathogen Genomics Laboratory, Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia and Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.

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http://dx.doi.org/10.1093/bioinformatics/btu176DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4103593PMC
August 2014

A promoter-level mammalian expression atlas.

Authors:
Alistair R R Forrest Hideya Kawaji Michael Rehli J Kenneth Baillie Michiel J L de Hoon Vanja Haberle Timo Lassmann Ivan V Kulakovskiy Marina Lizio Masayoshi Itoh Robin Andersson Christopher J Mungall Terrence F Meehan Sebastian Schmeier Nicolas Bertin Mette Jørgensen Emmanuel Dimont Erik Arner Christian Schmidl Ulf Schaefer Yulia A Medvedeva Charles Plessy Morana Vitezic Jessica Severin Colin A Semple Yuri Ishizu Robert S Young Margherita Francescatto Intikhab Alam Davide Albanese Gabriel M Altschuler Takahiro Arakawa John A C Archer Peter Arner Magda Babina Sarah Rennie Piotr J Balwierz Anthony G Beckhouse Swati Pradhan-Bhatt Judith A Blake Antje Blumenthal Beatrice Bodega Alessandro Bonetti James Briggs Frank Brombacher A Maxwell Burroughs Andrea Califano Carlo V Cannistraci Daniel Carbajo Yun Chen Marco Chierici Yari Ciani Hans C Clevers Emiliano Dalla Carrie A Davis Michael Detmar Alexander D Diehl Taeko Dohi Finn Drabløs Albert S B Edge Matthias Edinger Karl Ekwall Mitsuhiro Endoh Hideki Enomoto Michela Fagiolini Lynsey Fairbairn Hai Fang Mary C Farach-Carson Geoffrey J Faulkner Alexander V Favorov Malcolm E Fisher Martin C Frith Rie Fujita Shiro Fukuda Cesare Furlanello Masaaki Furino Jun-ichi Furusawa Teunis B Geijtenbeek Andrew P Gibson Thomas Gingeras Daniel Goldowitz Julian Gough Sven Guhl Reto Guler Stefano Gustincich Thomas J Ha Masahide Hamaguchi Mitsuko Hara Matthias Harbers Jayson Harshbarger Akira Hasegawa Yuki Hasegawa Takehiro Hashimoto Meenhard Herlyn Kelly J Hitchens Shannan J Ho Sui Oliver M Hofmann Ilka Hoof Furni Hori Lukasz Huminiecki Kei Iida Tomokatsu Ikawa Boris R Jankovic Hui Jia Anagha Joshi Giuseppe Jurman Bogumil Kaczkowski Chieko Kai Kaoru Kaida Ai Kaiho Kazuhiro Kajiyama Mutsumi Kanamori-Katayama Artem S Kasianov Takeya Kasukawa Shintaro Katayama Sachi Kato Shuji Kawaguchi Hiroshi Kawamoto Yuki I Kawamura Tsugumi Kawashima Judith S Kempfle Tony J Kenna Juha Kere Levon M Khachigian Toshio Kitamura S Peter Klinken Alan J Knox Miki Kojima Soichi Kojima Naoto Kondo Haruhiko Koseki Shigeo Koyasu Sarah Krampitz Atsutaka Kubosaki Andrew T Kwon Jeroen F J Laros Weonju Lee Andreas Lennartsson Kang Li Berit Lilje Leonard Lipovich Alan Mackay-Sim Ri-ichiroh Manabe Jessica C Mar Benoit Marchand Anthony Mathelier Niklas Mejhert Alison Meynert Yosuke Mizuno David A de Lima Morais Hiromasa Morikawa Mitsuru Morimoto Kazuyo Moro Efthymios Motakis Hozumi Motohashi Christine L Mummery Mitsuyoshi Murata Sayaka Nagao-Sato Yutaka Nakachi Fumio Nakahara Toshiyuki Nakamura Yukio Nakamura Kenichi Nakazato Erik van Nimwegen Noriko Ninomiya Hiromi Nishiyori Shohei Noma Shohei Noma Tadasuke Noazaki Soichi Ogishima Naganari Ohkura Hiroko Ohimiya Hiroshi Ohno Mitsuhiro Ohshima Mariko Okada-Hatakeyama Yasushi Okazaki Valerio Orlando Dmitry A Ovchinnikov Arnab Pain Robert Passier Margaret Patrikakis Helena Persson Silvano Piazza James G D Prendergast Owen J L Rackham Jordan A Ramilowski Mamoon Rashid Timothy Ravasi Patrizia Rizzu Marco Roncador Sugata Roy Morten B Rye Eri Saijyo Antti Sajantila Akiko Saka Shimon Sakaguchi Mizuho Sakai Hiroki Sato Suzana Savvi Alka Saxena Claudio Schneider Erik A Schultes Gundula G Schulze-Tanzil Anita Schwegmann Thierry Sengstag Guojun Sheng Hisashi Shimoji Yishai Shimoni Jay W Shin Christophe Simon Daisuke Sugiyama Takaai Sugiyama Masanori Suzuki Naoko Suzuki Rolf K Swoboda Peter A C 't Hoen Michihira Tagami Naoko Takahashi Jun Takai Hiroshi Tanaka Hideki Tatsukawa Zuotian Tatum Mark Thompson Hiroo Toyodo Tetsuro Toyoda Elvind Valen Marc van de Wetering Linda M van den Berg Roberto Verado Dipti Vijayan Ilya E Vorontsov Wyeth W Wasserman Shoko Watanabe Christine A Wells Louise N Winteringham Ernst Wolvetang Emily J Wood Yoko Yamaguchi Masayuki Yamamoto Misako Yoneda Yohei Yonekura Shigehiro Yoshida Susan E Zabierowski Peter G Zhang Xiaobei Zhao Silvia Zucchelli Kim M Summers Harukazu Suzuki Carsten O Daub Jun Kawai Peter Heutink Winston Hide Tom C Freeman Boris Lenhard Vladimir B Bajic Martin S Taylor Vsevolod J Makeev Albin Sandelin David A Hume Piero Carninci Yoshihide Hayashizaki

Nature 2014 Mar;507(7493):462-70

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http://dx.doi.org/10.1038/nature13182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4529748PMC
March 2014

PolyTB: a genomic variation map for Mycobacterium tuberculosis.

Tuberculosis (Edinb) 2014 May 15;94(3):346-54. Epub 2014 Feb 15.

Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK.

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http://dx.doi.org/10.1016/j.tube.2014.02.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4066953PMC
May 2014