Exploring the depth and breadth of the genomics toolbox during the COVID-19 pandemic: insights from Aotearoa New Zealand by Michael Bunce, Jemma L. Geoghegan, David Winter, Joep de Ligt, Siouxsie Wiles

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The Genomic Scrapheap Challenge; Extracting Relevant Data from Unmapped Whole Genome Sequencing Reads, Including Strain Specific Genomic Segments, in Rats. by Robin H van der Weide, Marieke Simonis, Roel Hermsen, Pim Toonen, Edwin Cuppen, Joep de Ligt

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Real-Time Genomics for Tracking Severe Acute Respiratory Syndrome Coronavirus 2 Border Incursions after Virus Elimination, New Zealand by Jordan Douglas, Jemma L. Geoghegan, James Hadfield, Remco Bouckaert, Matthew Storey, Xiaoyun Ren, Joep de Ligt, Nigel French, David Welch

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Lack of N2-gene amplification on the Cepheid Xpert Xpress SARS-CoV-2 assay and potential novel causative mutations: A case series from Auckland, New Zealand by Shivani Fox-Lewis, Andrew Fox-Lewis, Jay Harrower, Richard Chen, Jing Wang, Joep de Ligt, Gary McAuliffe, Susan Taylor, Erasmus Smit

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Tracing the international arrivals of SARS-CoV-2 Omicron variants after Aotearoa New Zealand reopened its border by Jordan Douglas, David Winter, Andrea McNeill, Sam Carr, Michael Bunce, Nigel French, James Hadfield, Joep de Ligt, David Welch, Jemma L. Geoghegan

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Genomic epidemiology of Delta SARS-CoV-2 during transition from elimination to suppression in Aotearoa New Zealand by Lauren Jelley, Jordan Douglas, Xiaoyun Ren, David Winter, Andrea McNeill, Sue Huang, Nigel French, David Welch, James Hadfield, Joep de Ligt, Jemma L. Geoghegan

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A Single Complex Agpat2 Allele in a Patient With Partial Lipodystrophy by Marjoleine F. Broekema, Maarten P. G. Massink, Joep De Ligt, Edwin C. A. Stigter, Houshang Monajemi, Houshang Monajemi, Jeroen De Ridder, Boudewijn M. T. Burgering, Gijs W. van Haaften, Eric Kalkhoven

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Platform comparison of detecting copy number variants with microarrays and whole-exome sequencing by Joep de Ligt, Philip M. Boone, Rolph Pfundt, Lisenka E.L.M. Vissers, Nicole de Leeuw, Christine Shaw, Han G. Brunner, James R. Lupski, Joris A. Veltman, Jayne Y. Hehir-Kwa

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Pangenome graphs in infectious disease: a comprehensive genetic variation analysis of Neisseria meningitidis leveraging Oxford Nanopore long reads by Zuyu Yang, Andrea Guarracino, Andrea Guarracino, Patrick J. Biggs, Patrick J. Biggs, Michael A. Black, Nuzla Ismail, Jana Renee Wold, Tony R. Merriman, Tony R. Merriman, Pjotr Prins, Erik Garrison, Joep de Ligt

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Mapping and phasing of structural variation in patient genomes using nanopore sequencing by Mircea Cretu Stancu, Markus J. van Roosmalen, Ivo Renkens, Marleen M. Nieboer, Sjors Middelkamp, Joep de Ligt, Giulia Pregno, Daniela Giachino, Giorgia Mandrile, Jose Espejo Valle-Inclan, Jerome Korzelius, Ewart de Bruijn, Edwin Cuppen, Michael E. Talkowski, Tobias Marschall, Jeroen de Ridder, Wigard P. Kloosterman

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Natural helix 9 mutants of PPARγ differently affect its transcriptional activity by Marjoleine F. Broekema, Maarten P.G. Massink, Cinzia Donato, Joep de Ligt, Joerg Schaarschmidt, Anouska Borgman, Marieke G. Schooneman, Diana Melchers, Martin N. Gerding, René Houtman, Alexandre M.J.J. Bonvin, Amit R. Majithia, Houshang Monajemi, Gijs W. van Haaften, Maarten R. Soeters, Eric Kalkhoven

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Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand by Jemma L. Geoghegan, Xiaoyun Ren, Matthew Storey, James Hadfield, Lauren Jelley, Sarah Jefferies, Jill Sherwood, Shevaun Paine, Sue Huang, Jordan Douglas, Fábio K. Mendes, Andrew Sporle, Michael G. Baker, David R. Murdoch, Nigel French, Colin R. Simpson, David Welch, Alexei J. Drummond, Edward C. Holmes, Sebastián Duchêne, Joep de Ligt

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COVID-19 vaccine strategies for Aotearoa New Zealand: a mathematical modelling study by Trung Nguyen, PhD, Mehnaz Adnan, PhD, Binh P Nguyen, PhD, Joep de Ligt, PhD, Jemma L Geoghegan, PhD, Richard Dean, MSc, Sarah Jefferies, MD, Michael G Baker, MBChB, Winston KG Seah, DrEng, Andrew A Sporle, MA(Hons), Nigel Peter French, PhD, David R Murdoch, MD, David Welch, PhD, Colin R Simpson, PhD

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Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 [version 1; peer review: 2 approved] by Áine O'Toole, Verity Hill, Oliver G. Pybus, Alexander Watts, Issac I. Bogoch, Kamran Khan, Jane P. Messina, The COVID-19 Genomics UK (COG-UK) consortium, Network for Genomic Surveillance in South Africa (NGS-SA), Brazil-UK CADDE Genomic Network, Houriiyah Tegally, Richard R. Lessells, Jennifer Giandhari, Sureshnee Pillay, Kefentse Arnold Tumedi, Gape Nyepetsi, Malebogo Kebabonye, Maitshwarelo Matsheka, Madisa Mine, Sima Tokajian, Hamad Hassan, Tamara Salloum, Georgi Merhi, Jad Koweyes, Jemma L. Geoghegan, Joep de Ligt, Xiaoyun Ren, Matthew Storey, Nikki E. Freed, Chitra Pattabiraman, Pramada Prasad, Anita S. Desai, Ravi Vasanthapuram, Thomas F. Schulz, Lars Steinbrück, Tanja Stadler, Swiss Viollier Sequencing Consortium, Antonio Parisi, Angelica Bianco, Darío García de Viedma, Sergio Buenestado-Serrano, Vítor Borges, Joana Isidro, Sílvia Duarte, João Paulo Gomes, Neta S. Zuckerman, Michal Mandelboim, Orna Mor, Torsten Seemann, Alicia Arnott, Jenny Draper, Mailie Gall, William Rawlinson, Ira Deveson, Sanmarié Schlebusch, Jamie McMahon, Lex Leong, Chuan Kok Lim, Maria Chironna, Daniela Loconsole, Antonin Bal, Laurence Josset, Edward Holmes, Kirsten St. George, Erica Lasek-Nesselquist, Reina S. Sikkema, Bas Oude Munnink, Marion Koopmans, Mia Brytting, V. Sudha rani, S. Pavani, Teemu Smura, Albert Heim, Satu Kurkela, Massab Umair, Muhammad Salman, Barbara Bartolini, Martina Rueca, Christian Drosten, Thorsten Wolff, Olin Silander, Dirk Eggink, Chantal Reusken, Harry Vennema, Aekyung Park, Christine Carrington, Nikita Sahadeo, Michael Carr, Gabo Gonzalez, SEARCH Alliance San Diego, National Virus Reference Laboratory, SeqCOVID-Spain, Danish Covid-19 Genome Consortium (DCGC), Communicable Diseases Genomic Network (CDGN), Dutch National SARS-CoV-2 surveillance program, Division of Emerging Infectious Diseases (KDCA), Tulio de Oliveira, Nuno Faria, Andrew Rambaut, Moritz U. G. Kraemer

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Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch [version 2; peer review: 3 approved] by Áine O'Toole, Verity Hill, Oliver G. Pybus, Alexander Watts, Issac I. Bogoch, Kamran Khan, Jane P. Messina, The COVID-19 Genomics UK (COG-UK) consortium, Network for Genomic Surveillance in South Africa (NGS-SA), Brazil-UK CADDE Genomic Network, Houriiyah Tegally, Richard R. Lessells, Jennifer Giandhari, Sureshnee Pillay, Kefentse Arnold Tumedi, Gape Nyepetsi, Malebogo Kebabonye, Maitshwarelo Matsheka, Madisa Mine, Sima Tokajian, Hamad Hassan, Tamara Salloum, Georgi Merhi, Jad Koweyes, Jemma L. Geoghegan, Joep de Ligt, Xiaoyun Ren, Matthew Storey, Nikki E. Freed, Chitra Pattabiraman, Pramada Prasad, Anita S. Desai, Ravi Vasanthapuram, Thomas F. Schulz, Lars Steinbrück, Tanja Stadler, Swiss Viollier Sequencing Consortium, Antonio Parisi, Angelica Bianco, Darío García de Viedma, Sergio Buenestado-Serrano, Vítor Borges, Joana Isidro, Sílvia Duarte, João Paulo Gomes, Neta S. Zuckerman, Michal Mandelboim, Orna Mor, Torsten Seemann, Alicia Arnott, Jenny Draper, Mailie Gall, William Rawlinson, Ira Deveson, Sanmarié Schlebusch, Jamie McMahon, Lex Leong, Chuan Kok Lim, Maria Chironna, Daniela Loconsole, Antonin Bal, Laurence Josset, Edward Holmes, Kirsten St. George, Erica Lasek-Nesselquist, Reina S. Sikkema, Bas Oude Munnink, Marion Koopmans, Mia Brytting, V. Sudha rani, S. Pavani, Teemu Smura, Albert Heim, Satu Kurkela, Massab Umair, Muhammad Salman, Barbara Bartolini, Martina Rueca, Christian Drosten, Thorsten Wolff, Olin Silander, Dirk Eggink, Chantal Reusken, Harry Vennema, Aekyung Park, Christine Carrington, Nikita Sahadeo, Michael Carr, Gabo Gonzalez, SEARCH Alliance San Diego, National Virus Reference Laboratory, SeqCOVID-Spain, Danish Covid-19 Genome Consortium (DCGC), Communicable Diseases Genomic Network (CDGN), Dutch National SARS-CoV-2 surveillance program, Division of Emerging Infectious Diseases (KDCA), Tulio de Oliveira, Nuno Faria, Andrew Rambaut, Moritz U. G. Kraemer

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Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes by Megan E Carey, Zoe A Dyson, Danielle J Ingle, Afreenish Amir, Mabel K Aworh, Marie Anne Chattaway, Ka Lip Chew, John A Crump, Nicholas A Feasey, Benjamin P Howden, Karen H Keddy, Mailis Maes, Christopher M Parry, Sandra Van Puyvelde, Hattie E Webb, Ayorinde Oluwatobiloba Afolayan, Anna P Alexander, Shalini Anandan, Jason R Andrews, Philip M Ashton, Buddha Basnyat, Ashish Bavdekar, Isaac I Bogoch, John D Clemens, Kesia Esther da Silva, Anuradha De, Joep de Ligt, Paula Lucia Diaz Guevara, Christiane Dolecek, Shanta Dutta, Marthie M Ehlers, Louise Francois Watkins, Denise O Garrett, Gauri Godbole, Melita A Gordon, Andrew R Greenhill, Chelsey Griffin, Madhu Gupta, Rene S Hendriksen, Robert S Heyderman, Yogesh Hooda, Juan Carlos Hormazabal, Odion O Ikhimiukor, Junaid Iqbal, Jobin John Jacob, Claire Jenkins, Dasaratha Ramaiah Jinka, Jacob John, Gagandeep Kang, Abdoulie Kanteh, Arti Kapil, Abhilasha Karkey, Samuel Kariuki, Robert A Kingsley, Roshine Mary Koshy, AC Lauer, Myron M Levine, Ravikumar Kadahalli Lingegowda, Stephen P Luby, Grant Austin Mackenzie, Tapfumanei Mashe, Chisomo Msefula, Ankur Mutreja, Geetha Nagaraj, Savitha Nagaraj, Satheesh Nair, Take K Naseri, Susana Nimarota-Brown, Elisabeth Njamkepo, Iruka N Okeke, Sulochana Putli Bai Perumal, Andrew J Pollard, Agila Kumari Pragasam, Firdausi Qadri, Farah N Qamar, Sadia Isfat Ara Rahman, Savitra Devi Rambocus, David A Rasko, Pallab Ray, Roy Robins-Browne, Temsunaro Rongsen-Chandola, Jean Pierre Rutanga, Samir K Saha, Senjuti Saha, Karnika Saigal, Mohammad Saiful Islam Sajib, Jessica C Seidman, Jivan Shakya, Varun Shamanna, Jayanthi Shastri, Rajeev Shrestha, Sonia Sia, Michael J Sikorski, Ashita Singh, Anthony M Smith, Kaitlin A Tagg, Dipesh Tamrakar, Arif Mohammed Tanmoy, Maria Thomas, Mathew S Thomas, Robert Thomsen, Nicholas R Thomson, Siaosi Tupua, Krista Vaidya, Mary Valcanis, Balaji Veeraraghavan, François-Xavier Weill, Jackie Wright, Gordon Dougan, Silvia Argimón, Jacqueline A Keane, David M Aanensen, Stephen Baker, Kathryn E Holt, Global Typhoid Genomics Consortium Group Authorship

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