Abigail L Manson

ResearcherID Loop profile ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 47

Top Topics

Escherichia Coli

Urinary Tract Infection

Top Venues

bioRxiv : the preprint server for biology

Proceedings of the National Academy of Sciences of the United States of America

Briefings in bioinformatics

This page only lists publications with an associated author ORCID identifier.

Publications

Julia A Schwartzman, Francois Lebreton, Rauf Salamzade, Terrance Shea, Melissa J Martin, Katharina Schaufler, Aysun Urhan, Thomas Abeel, Ilana Lopes Baratella da Cunha Camargo, Bruna F Sgardioli, Janira Prichula, Ana Paula Guedes Frazzon, Gonzalo Giribet, Daria Van Tyne, Gregg Treinish, Charles J Innis, Jaap A Wagenaar, Ryan M Whipple, Abigail L Manson, Ashlee M Earl, Michael S Gilmore
Global diversity of enterococci and description of 18 previously unknown species. Proceedings of the National Academy of Sciences of the United States of America 121 (10) (2024)
Julia A Schwartzman, Francois Lebreton, Rauf Salamzade, Terrance Shea, Melissa J Martin, Katharina Schaufler, Aysun Urhan, Thomas Abeel, Ilana Lopes Baratella da Cunha Camargo, Bruna F Sgardioli, Janira Prichula, Ana Paula Guedes Frazzon, Gonzalo Giribet, Daria Van Tyne, Gregg Treinish, Charles J Innis, Jaap A Wagenaar, Ryan M Whipple, Abigail L Manson, Ashlee M Earl, Michael S Gilmore
Global diversity of enterococci and description of 18 previously unknown species. Proceedings of the National Academy of Sciences of the United States of America 121 (10) (2024)
Mark G Young, Timothy J Straub, Colin J Worby, Hayden C Metsky, Andreas Gnirke, Ryan A Bronson, Lucas R van Dijk, Christopher A Desjardins, Christian Matranga, James Qu, Karen L Dodson, Henry Louis Schreiber, Abigail L Manson, Scott J Hultgren, Ashlee M Earl
Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pan-genome hybrid selection. bioRxiv : the preprint server for biology (2024)
Julia A Schwartzman, Francois Lebreton, Rauf Salamzade, Terrance Shea, Melissa J Martin, Katharina Schaufler, Aysun Urhan, Thomas Abeel, Ilana Lopes Baratella da Cunha Camargo, Bruna F Sgardioli, Janira Prichula, Ana Paula Guedes Frazzon, Gonzalo Giribet, Daria Van Tyne, Gregg Treinish, Charles J Innis, Jaap A Wagenaar, Ryan M Whipple, Abigail L Manson, Ashlee M Earl, Michael S Gilmore
Global diversity of enterococci and description of 18 previously unknown species. Proceedings of the National Academy of Sciences of the United States of America 121 (10) (2024)
Mark G Young, Timothy J Straub, Colin J Worby, Hayden C Metsky, Andreas Gnirke, Ryan A Bronson, Lucas R van Dijk, Christopher A Desjardins, Christian Matranga, James Qu, Jesús Bazan Villicana, Philippe Azimzadeh, Andrew L Kau, Karen L Dodson, Henry Louis Schreiber, Abigail L Manson, Scott J Hultgren, Ashlee M Earl
Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection. bioRxiv : the preprint server for biology (2024)
Mark G Young, Timothy J Straub, Colin J Worby, Hayden C Metsky, Andreas Gnirke, Ryan A Bronson, Lucas R van Dijk, Christopher A Desjardins, Christian Matranga, James Qu, Karen L Dodson, Henry Louis Schreiber, Abigail L Manson, Scott J Hultgren, Ashlee M Earl
Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pan-genome hybrid selection. bioRxiv : the preprint server for biology (2024)
Julia A Schwartzman, Francois Lebreton, Rauf Salamzade, Terrance Shea, Melissa J Martin, Katharina Schaufler, Aysun Urhan, Thomas Abeel, Ilana Lopes Baratella da Cunha Camargo, Bruna F Sgardioli, Janira Prichula, Ana Paula Guedes Frazzon, Gonzalo Giribet, Daria Van Tyne, Gregg Treinish, Charles J Innis, Jaap A Wagenaar, Ryan M Whipple, Abigail L Manson, Ashlee M Earl, Michael S Gilmore
Global diversity of enterococci and description of 18 previously unknown species. Proceedings of the National Academy of Sciences of the United States of America 121 (10) (2024)
Julia A Schwartzman, Francois Lebreton, Rauf Salamzade, Terrance Shea, Melissa J Martin, Katharina Schaufler, Aysun Urhan, Thomas Abeel, Ilana Lopes Baratella da Cunha Camargo, Bruna F Sgardioli, Janira Prichula, Ana Paula Guedes Frazzon, Gonzalo Giribet, Daria Van Tyne, Gregg Treinish, Charles J Innis, Jaap A Wagenaar, Ryan M Whipple, Abigail L Manson, Ashlee M Earl, Michael S Gilmore
Global diversity of enterococci and description of 18 previously unknown species. Proceedings of the National Academy of Sciences of the United States of America 121 (10) (2024)
Mark G Young, Timothy J Straub, Colin J Worby, Hayden C Metsky, Andreas Gnirke, Ryan A Bronson, Lucas R van Dijk, Christopher A Desjardins, Christian Matranga, James Qu, Jesús Bazan Villicana, Philippe Azimzadeh, Andrew L Kau, Karen L Dodson, Henry Louis Schreiber, Abigail L Manson, Scott J Hultgren, Ashlee M Earl
Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection. bioRxiv : the preprint server for biology (2024)
Mark G Young, Timothy J Straub, Colin J Worby, Hayden C Metsky, Andreas Gnirke, Ryan A Bronson, Lucas R van Dijk, Christopher A Desjardins, Christian Matranga, James Qu, Karen L Dodson, Henry Louis Schreiber, Abigail L Manson, Scott J Hultgren, Ashlee M Earl
Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pan-genome hybrid selection. bioRxiv : the preprint server for biology (2024)
Mark G Young, Timothy J Straub, Colin J Worby, Hayden C Metsky, Andreas Gnirke, Ryan A Bronson, Lucas R van Dijk, Christopher A Desjardins, Christian Matranga, James Qu, Jesús Bazan Villicana, Philippe Azimzadeh, Andrew L Kau, Karen L Dodson, Henry Louis Schreiber, Abigail L Manson, Scott J Hultgren, Ashlee M Earl
Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection. bioRxiv : the preprint server for biology (2024)
Rauf Salamzade, Patricia Q Tran, Cody Martin, Abigail L Manson, Michael S Gilmore, Ashlee M Earl, Karthik Anantharaman, Lindsay R Kalan
zol & fai: large-scale targeted detection and evolutionary investigation of gene clusters. bioRxiv : the preprint server for biology (2023)
Felix Wong, Erica J Zheng, Jacqueline A Valeri, Nina M Donghia, Melis N Anahtar, Satotaka Omori, Alicia Li, Andres Cubillos-Ruiz, Aarti Krishnan, Wengong Jin, Abigail L Manson, Jens Friedrichs, Ralf Helbig, Behnoush Hajian, Dawid K Fiejtek, Florence F Wagner, Holly H Soutter, Ashlee M Earl, Jonathan M Stokes, Lars David Renner, James J Collins
Discovery of a structural class of antibiotics with explainable deep learning. Nature 626 (7997) (2023)
Felix Wong, Erica J Zheng, Jacqueline A Valeri, Nina M Donghia, Melis N Anahtar, Satotaka Omori, Alicia Li, Andres Cubillos-Ruiz, Aarti Krishnan, Wengong Jin, Abigail L Manson, Jens Friedrichs, Ralf Helbig, Behnoush Hajian, Dawid K Fiejtek, Florence F Wagner, Holly H Soutter, Ashlee M Earl, Jonathan M Stokes, Lars David Renner, James J Collins
Discovery of a structural class of antibiotics with explainable deep learning. Nature (2023)
Alexis Jaramillo Cartagena, Kyra L Taylor, Joshua T Smith, Abigail L Manson, Virginia M Pierce, Ashlee M Earl, Roby P Bhattacharyya
The carbapenem inoculum effect provides insight into the molecular mechanisms underlying carbapenem resistance in Enterobacterales . bioRxiv : the preprint server for biology (2023)
Felix Wong, Erica J Zheng, Jacqueline A Valeri, Nina M Donghia, Melis N Anahtar, Satotaka Omori, Alicia Li, Andres Cubillos-Ruiz, Aarti Krishnan, Wengong Jin, Abigail L Manson, Jens Friedrichs, Ralf Helbig, Behnoush Hajian, Dawid K Fiejtek, Florence F Wagner, Holly H Soutter, Ashlee M Earl, Jonathan M Stokes, Lars David Renner, James J Collins
Discovery of a structural class of antibiotics with explainable deep learning. Nature 626 (7997) (2023)
Felix Wong, Erica J Zheng, Jacqueline A Valeri, Nina M Donghia, Melis N Anahtar, Satotaka Omori, Alicia Li, Andres Cubillos-Ruiz, Aarti Krishnan, Wengong Jin, Abigail L Manson, Jens Friedrichs, Ralf Helbig, Behnoush Hajian, Dawid K Fiejtek, Florence F Wagner, Holly H Soutter, Ashlee M Earl, Jonathan M Stokes, Lars David Renner, James J Collins
Discovery of a structural class of antibiotics with explainable deep learning. Nature 626 (7997) (2023)
Aysun Urhan, Bianca-Maria Cosma, Abigail L Manson, Thomas Abeel
SAP: Synteny-aware gene function prediction for bacteria using protein embeddings. bioRxiv : the preprint server for biology (2023)
Sosie Yorki, Terrance Shea, Christina A Cuomo, Bruce J Walker, Regina C LaRocque, Abigail L Manson, Ashlee M Earl, Colin J Worby
Comparison of long- and short-read metagenomic assembly for low-abundance species and resistance genes. Briefings in bioinformatics (2023)
Aysun Urhan, Bianca-Maria Cosma, Abigail L Manson, Thomas Abeel
SAP: Synteny-aware gene function prediction for bacteria using protein embeddings. bioRxiv : the preprint server for biology (2023)
Sosie Yorki, Terrance Shea, Christina A Cuomo, Bruce J Walker, Regina C LaRocque, Abigail L Manson, Ashlee M Earl, Colin J Worby
Comparison of long- and short-read metagenomic assembly for low-abundance species and resistance genes. Briefings in bioinformatics 24 (2) (2023)
Rauf Salamzade, Christi L McElheny, Abigail L Manson, Ashlee M Earl, Nader Shaikh, Yohei Doi
Genomic epidemiology and antibiotic susceptibility profiling of uropathogenic Escherichia coli among children in the United States. mSphere (2023)
Felix Wong, Erica J Zheng, Jacqueline A Valeri, Nina M Donghia, Melis N Anahtar, Satotaka Omori, Alicia Li, Andres Cubillos-Ruiz, Aarti Krishnan, Wengong Jin, Abigail L Manson, Jens Friedrichs, Ralf Helbig, Behnoush Hajian, Dawid K Fiejtek, Florence F Wagner, Holly H Soutter, Ashlee M Earl, Jonathan M Stokes, Lars David Renner, James J Collins
Discovery of a structural class of antibiotics with explainable deep learning. Nature 626 (7997) (2023)
Sosie Yorki, Terrance Shea, Christina A Cuomo, Bruce J Walker, Regina C LaRocque, Abigail L Manson, Ashlee M Earl, Colin J Worby
Comparison of long- and short-read metagenomic assembly for low-abundance species and resistance genes. Briefings in bioinformatics 24 (2) (2023)
Julia A Schwartzman, Francois Lebreton, Rauf Salamzade, Melissa J Martin, Katharina Schaufler, Aysun Urhan, Thomas Abeel, Ilana L B C Camargo, Bruna F Sgardioli, Janira Prichula, Ana Paula Guedes Frazzon, Daria Van Tyne, Gregg Treinish, Charles J Innis, Jaap A Wagenaar, Ryan M Whipple, Abigail L Manson, Ashlee M Earl, Michael S Gilmore
Global diversity of enterococci and description of 18 novel species. bioRxiv : the preprint server for biology (2023)
Felix Wong, Erica J Zheng, Jacqueline A Valeri, Nina M Donghia, Melis N Anahtar, Satotaka Omori, Alicia Li, Andres Cubillos-Ruiz, Aarti Krishnan, Wengong Jin, Abigail L Manson, Jens Friedrichs, Ralf Helbig, Behnoush Hajian, Dawid K Fiejtek, Florence F Wagner, Holly H Soutter, Ashlee M Earl, Jonathan M Stokes, Lars David Renner, James J Collins
Discovery of a structural class of antibiotics with explainable deep learning. Nature 626 (7997) (2023)
Felix Wong, Erica J Zheng, Jacqueline A Valeri, Nina M Donghia, Melis N Anahtar, Satotaka Omori, Alicia Li, Andres Cubillos-Ruiz, Aarti Krishnan, Wengong Jin, Abigail L Manson, Jens Friedrichs, Ralf Helbig, Behnoush Hajian, Dawid K Fiejtek, Florence F Wagner, Holly H Soutter, Ashlee M Earl, Jonathan M Stokes, Lars David Renner, James J Collins
Discovery of a structural class of antibiotics with explainable deep learning. Nature 626 (7997) (2023)
Felix Wong, Erica J Zheng, Jacqueline A Valeri, Nina M Donghia, Melis N Anahtar, Satotaka Omori, Alicia Li, Andres Cubillos-Ruiz, Aarti Krishnan, Wengong Jin, Abigail L Manson, Jens Friedrichs, Ralf Helbig, Behnoush Hajian, Dawid K Fiejtek, Florence F Wagner, Holly H Soutter, Ashlee M Earl, Jonathan M Stokes, Lars David Renner, James J Collins
Discovery of a structural class of antibiotics with explainable deep learning. Nature (2023)
Sosie Yorki, Terrance Shea, Christina A Cuomo, Bruce J Walker, Regina C LaRocque, Abigail L Manson, Ashlee M Earl, Colin J Worby
Comparison of long- and short-read metagenomic assembly for low-abundance species and resistance genes. Briefings in bioinformatics (2023)
Felix Wong, Erica J Zheng, Jacqueline A Valeri, Nina M Donghia, Melis N Anahtar, Satotaka Omori, Alicia Li, Andres Cubillos-Ruiz, Aarti Krishnan, Wengong Jin, Abigail L Manson, Jens Friedrichs, Ralf Helbig, Behnoush Hajian, Dawid K Fiejtek, Florence F Wagner, Holly H Soutter, Ashlee M Earl, Jonathan M Stokes, Lars David Renner, James J Collins
Discovery of a structural class of antibiotics with explainable deep learning. Nature 626 (7997) (2023)
Felix Wong, Erica J Zheng, Jacqueline A Valeri, Nina M Donghia, Melis N Anahtar, Satotaka Omori, Alicia Li, Andres Cubillos-Ruiz, Aarti Krishnan, Wengong Jin, Abigail L Manson, Jens Friedrichs, Ralf Helbig, Behnoush Hajian, Dawid K Fiejtek, Florence F Wagner, Holly H Soutter, Ashlee M Earl, Jonathan M Stokes, Lars David Renner, James J Collins
Discovery of a structural class of antibiotics with explainable deep learning. Nature 626 (7997) (2023)
Felix Wong, Erica J Zheng, Jacqueline A Valeri, Nina M Donghia, Melis N Anahtar, Satotaka Omori, Alicia Li, Andres Cubillos-Ruiz, Aarti Krishnan, Wengong Jin, Abigail L Manson, Jens Friedrichs, Ralf Helbig, Behnoush Hajian, Dawid K Fiejtek, Florence F Wagner, Holly H Soutter, Ashlee M Earl, Jonathan M Stokes, Lars David Renner, James J Collins
Discovery of a structural class of antibiotics with explainable deep learning. Nature (2023)
Felix Wong, Erica J Zheng, Jacqueline A Valeri, Nina M Donghia, Melis N Anahtar, Satotaka Omori, Alicia Li, Andres Cubillos-Ruiz, Aarti Krishnan, Wengong Jin, Abigail L Manson, Jens Friedrichs, Ralf Helbig, Behnoush Hajian, Dawid K Fiejtek, Florence F Wagner, Holly H Soutter, Ashlee M Earl, Jonathan M Stokes, Lars David Renner, James J Collins
Discovery of a structural class of antibiotics with explainable deep learning. Nature 626 (7997) (2023)
Felix Wong, Aarti Krishnan, Erica J Zheng, Hannes Stärk, Abigail L Manson, Ashlee M Earl, Tommi Jaakkola, James J Collins
Benchmarking AlphaFold-enabled molecular docking predictions for antibiotic discovery. Molecular systems biology 18 (9) (2022)
Erica J Zheng, Ian W Andrews, Alexandra T Grote, Abigail L Manson, Miguel A Alcantar, Ashlee M Earl, James J Collins
Modulating the evolutionary trajectory of tolerance using antibiotics with different metabolic dependencies. Nature communications 13 (1) (2022)
Colin J Worby, Henry L Schreiber, Timothy J Straub, Lucas R van Dijk, Ryan A Bronson, Benjamin S Olson, Jerome S Pinkner, Chloe L P Obernuefemann, Vanessa L Muñoz, Alexandra E Paharik, Philippe N Azimzadeh, Bruce J Walker, Christopher A Desjardins, Wen-Chi Chou, Karla Bergeron, Sinéad B Chapman, Aleksandra Klim, Abigail L Manson, Thomas J Hannan, Thomas M Hooton, Andrew L Kau, H Henry Lai, Karen W Dodson, Scott J Hultgren, Ashlee M Earl
Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women. Nature microbiology 7 (5) (2022)
Allison J Lopatkin, Sarah C Bening, Abigail L Manson, Jonathan M Stokes, Michael A Kohanski, Ahmed H Badran, Ashlee M Earl, Nicole J Cheney, Jason H Yang, James J Collins
Clinically relevant mutations in core metabolic genes confer antibiotic resistance. Science (New York, N.Y.) 371 (6531) (2021)
Ryan A Bronson, Chhavi Gupta, Abigail L Manson, Jan A Nguyen, Asli Bahadirli-Talbott, Nicole M Parrish, Ashlee M Earl, Keira A Cohen
Global phylogenomic analyses of Mycobacterium abscessus provide context for non cystic fibrosis infections and the evolution of antibiotic resistance. Nature communications 12 (1) (2021)
Peijun Ma, Lorrie L He, Alejandro Pironti, Hannah H Laibinis, Christoph M Ernst, Abigail L Manson, Roby P Bhattacharyya, Ashlee M Earl, Jonathan Livny, Deborah T Hung
Genetic determinants facilitating the evolution of resistance to carbapenem antibiotics. eLife 10 (2021)
Keira A Cohen, Katharine E Stott, Vanisha Munsamy, Abigail L Manson, Ashlee M Earl, Alexander S Pym
Evidence for Expanding the Role of Streptomycin in the Management of Drug-Resistant Mycobacterium tuberculosis. Antimicrobial agents and chemotherapy 64 (9) (2020)
Michael S Gilmore, Rauf Salamzade, Elizabeth Selleck, Noelle Bryan, Suelen S Mello, Abigail L Manson, Ashlee M Earl
Genes Contributing to the Unique Biology and Intrinsic Antibiotic Resistance of Enterococcus faecalis. mBio 11 (6) (2020)
Gregory P Donaldson, Wen-Chi Chou, Abigail L Manson, Peter Rogov, Thomas Abeel, James Bochicchio, Dawn Ciulla, Alexandre Melnikov, Peter B Ernst, Hiutung Chu, Georgia Giannoukos, Ashlee M Earl, Sarkis K Mazmanian
Spatially distinct physiology of Bacteroides fragilis within the proximal colon of gnotobiotic mice. Nature microbiology 5 (5) (2020)
Daria Van Tyne, Abigail L Manson, Mark M Huycke, John Karanicolas, Ashlee M Earl, Michael S Gilmore
Impact of antibiotic treatment and host innate immune pressure on enterococcal adaptation in the human bloodstream. Science translational medicine 11 (487) (2020)
João Luis Reis Cunha, Daniella C Bartholomeu, Abigail L Manson, Ashlee M Earl, Gustavo C Cerqueira
ProphET, prophage estimation tool: A stand-alone prophage sequence prediction tool with self-updating reference database. PloS one 14 (10) (2019)
Abigail L Manson, Daria Van Tyne, Timothy J Straub, Sarah Clock, Michael Crupain, Urvashi Rangan, Michael S Gilmore, Ashlee M Earl
Chicken Meat-Associated Enterococci: Influence of Agricultural Antibiotic Use and Connection to the Clinic. Applied and environmental microbiology 85 (22) (2019)
Abigail L Manson, Keira A Cohen, Thomas Abeel, Christopher A Desjardins, Derek T Armstrong, Clifton E Barry, Jeannette Brand, null null, Sinéad B Chapman, Sang-Nae Cho, Andrei Gabrielian, James Gomez, Andreea M Jodals, Moses Joloba, Pontus Jureen, Jong Seok Lee, Lesibana Malinga, Mamoudou Maiga, Dale Nordenberg, Ecaterina Noroc, Elena Romancenco, Alex N Salazar, Willy Ssengooba, A A Velayati, Kathryn Winglee, Aksana Zalutskaya, Laura E Via, Gail H Cassell, Susan E Dorman, Jerrold Ellner, Parissa Farnia, James E Galagan, Alex Rosenthal, Valeriu Crudu, Daniela Homorodean, Po-Ren Hsueh, Sujatha Narayanan, Alexander S Pym, Alena Skrahina, Soumya Swaminathan, Martie Van der Walt, David Alland, William R Bishai, Ted Cohen, Sven Hoffner, Bruce W Birren, Ashlee M Earl
Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance. Nature genetics 49 (3) (2017)
Henry Louis Schreiber, Matt S Conover, Wen-Chi Chou, Michael E Hibbing, Abigail L Manson, Karen W Dodson, Thomas J Hannan, Pacita L Roberts, Ann E Stapleton, Thomas M Hooton, Jonathan Livny, Ashlee M Earl, Scott J Hultgren
Bacterial virulence phenotypes of Escherichia coli and host susceptibility determine risk for urinary tract infections. Science translational medicine 9 (382) (2017)