One fly–one genome: chromosome-scale genome assembly of a single outbred Drosophila melanogaster
Adams, Matthew, McBroome, Jakob, Maurer, Nicholas, Pepper-Tunick, Evan, Saremi, Nedda F, Green, Richard E, Vollmers, Christopher, Corbett-Detig, Russell B
Published in Nucleic acids research (27.07.2020)
Published in Nucleic acids research (27.07.2020)
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Journal Article
Standardized Phylogenetic Classification of Human Respiratory Syncytial Virus below the Subgroup Level
Goya, Stephanie, Ruis, Christopher, Neher, Richard A, Meijer, Adam, Aziz, Ammar, Hinrichs, Angie S, von Gottberg, Anne, Roemer, Cornelius, Amoako, Daniel G, Acuña, Dolores, McBroome, Jakob, Otieno, James R, Bhiman, Jinal N, Everatt, Josie, Muñoz-Escalante, Juan C, Ramaekers, Kaat, Duggan, Kate, Presser, Lance D, Urbanska, Laura, Venter, Marietjie, Wolter, Nicole, Peret, Teresa C T, Salimi, Vahid, Potdar, Varsha, Borges, Vítor, Viegas, Mariana
Published in Emerging infectious diseases (01.08.2024)
Published in Emerging infectious diseases (01.08.2024)
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Journal Article
Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape
Turakhia, Yatish, Thornlow, Bryan, Hinrichs, Angie, McBroome, Jakob, Ayala, Nicolas, Ye, Cheng, Smith, Kyle, De Maio, Nicola, Haussler, David, Lanfear, Robert, Corbett-Detig, Russell
Published in Nature (London) (29.09.2022)
Published in Nature (London) (29.09.2022)
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Journal Article
A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees
McBroome, Jakob, Thornlow, Bryan, Hinrichs, Angie S, Kramer, Alexander, De Maio, Nicola, Goldman, Nick, Haussler, David, Corbett-Detig, Russell, Turakhia, Yatish
Published in Molecular biology and evolution (09.12.2021)
Published in Molecular biology and evolution (09.12.2021)
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Journal Article
Fine-Scale Position Effects Shape the Distribution of Inversion Breakpoints in Drosophila melanogaster
McBroome, Jakob, Liang, David, Corbett-Detig, Russell
Published in Genome biology and evolution (01.08.2020)
Published in Genome biology and evolution (01.08.2020)
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Journal Article
Online Phylogenetics with matOptimize Produces Equivalent Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Implementations
Kramer, Alexander M, Thornlow, Bryan, Ye, Cheng, De Maio, Nicola, McBroome, Jakob, Hinrichs, Angie S, Lanfear, Robert, Turakhia, Yatish, Corbett-Detig, Russell
Published in Systematic biology (01.11.2023)
Published in Systematic biology (01.11.2023)
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Journal Article
BTE: a Python module for pandemic-scale mutation-annotated phylogenetic trees
McBroome, Jakob, Turakhia, Yatish, Corbett-Detig, Russell
Published in Journal of open source software (05.09.2022)
Published in Journal of open source software (05.09.2022)
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Journal Article
Fine-Mapping Complex Inversion Breakpoints and Investigating Somatic Pairing in the Anopheles gambiae Species Complex Using Proximity-Ligation Sequencing
Corbett-Detig, Russell B, Said, Iskander, Calzetta, Maria, Genetti, Max, McBroome, Jakob, Maurer, Nicholas W, Petrarca, Vincenzo, Della Torre, Alessandra, Besansky, Nora J
Published in Genetics (Austin) (01.12.2019)
Published in Genetics (Austin) (01.12.2019)
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Journal Article
A framework for automated scalable designation of viral pathogen lineages from genomic data
McBroome, Jakob, de Bernardi Schneider, Adriano, Roemer, Cornelius, Wolfinger, Michael T., Hinrichs, Angie S., O’Toole, Aine Niamh, Ruis, Christopher, Turakhia, Yatish, Rambaut, Andrew, Corbett-Detig, Russell
Published in Nature microbiology (01.02.2024)
Published in Nature microbiology (01.02.2024)
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Journal Article
A lung-specific mutational signature enables inference of viral and bacterial respiratory niche
Ruis, Christopher, Peacock, Thomas P, Polo, Luis M, Masone, Diego, Alvarez, Maria Soledad, Hinrichs, Angie S, Turakhia, Yatish, Cheng, Ye, McBroome, Jakob, Corbett-Detig, Russell, Parkhill, Julian, Floto, R Andres
Published in Microbial genomics (01.05.2023)
Published in Microbial genomics (01.05.2023)
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Journal Article
Fine-Mapping Complex Inversion Breakpoints and Investigating Somatic Pairing in the Anopheles gambiae Species Complex Using Proximity-Ligation Sequencing
Corbett-Detig, Russell B, Said, Iskander, Calzetta, Maria, Genetti, Max, McBroome, Jakob, Maurer, Nicholas W, Petrarca, Vincenzo, Della Torre, Alessandra, Besansky, Nora J
Published in Genetics (Austin) (01.12.2019)
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Published in Genetics (Austin) (01.12.2019)
Journal Article
Fine-Mapping Complex Inversion Breakpoints and Investigating Somatic Pairing in the Anopheles gambiae Species Complex Using Proximity-Ligation Sequencing
Corbett-Detig, Russell B, Said, Iskander, Calzetta, Maria, Genetti, Max, McBroome, Jakob, Maurer, Nicholas W, Petrarca, Vincenzo, Della Torre, Alessandra, Besansky, Nora J
Published in Genetics (Austin) (01.12.2019)
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Published in Genetics (Austin) (01.12.2019)
Journal Article
Pandemic-scale phylogenetics
Ye, Cheng, Thornlow, Bryan, Kramer, Alexander, McBroome, Jakob, Hinrichs, Angie, Corbett-Detig, Russell, Turakhia, Yatish
Published in bioRxiv : the preprint server for biology (06.12.2021)
Published in bioRxiv : the preprint server for biology (06.12.2021)
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Journal Article
A daily-updated database and tools for comprehensive SARS-CoV-2 mutation-annotated trees
McBroome, Jakob, Thornlow, Bryan, Hinrichs, Angie S, De Maio, Nicola, Goldman, Nick, Haussler, David, Corbett-Detig, Russell, Turakhia, Yatish
Published in bioRxiv : the preprint server for biology (13.07.2021)
Published in bioRxiv : the preprint server for biology (13.07.2021)
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Journal Article
Online Phylogenetics using Parsimony Produces Slightly Better Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Approaches
Thornlow, Bryan, Kramer, Alexander, Ye, Cheng, De Maio, Nicola, McBroome, Jakob, Hinrichs, Angie S, Lanfear, Robert, Turakhia, Yatish, Corbett-Detig, Russell
Published in bioRxiv (18.05.2022)
Published in bioRxiv (18.05.2022)
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Journal Article
Paper
A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control
Thornlow, Bryan, Hinrichs, Angie S, Jain, Miten, Dhillon, Namrita, La, Scott, Kapp, Joshua D, Anigbogu, Ikenna, Cassatt-Johnstone, Molly, McBroome, Jakob, Haeussler, Maximilian, Turakhia, Yatish, Chang, Terren, Olsen, Hugh E, Sanford, Jeremy, Stone, Michael, Vaske, Olena, Bjork, Isabel, Akeson, Mark, Shapiro, Beth, Haussler, David, Kilpatrick, A Marm, Corbett-Detig, Russell
Published in bioRxiv : the preprint server for biology (06.04.2021)
Published in bioRxiv : the preprint server for biology (06.04.2021)
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