Alice Carolyn McHardy (Alice C McHardy)

ResearcherID ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 38

Top Topics

Pseudomonas Aeruginosa

Antimicrobial Resistance

Top Venues

Communications biology

Nature communications

Scientific reports

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

Publications

Hüseyin Anil Gündüz, René Mreches, Julia Moosbauer, Gary Robertson, Xiao-Yin To, Eric A Franzosa, Curtis Huttenhower, Mina Rezaei, Alice Carolyn McHardy, Bernd Bischl, Philipp C Münch, Martin Binder
Optimized model architectures for deep learning on genomic data. Communications biology 7 (1) (2024)
Hüseyin Anil Gündüz, René Mreches, Julia Moosbauer, Gary Robertson, Xiao-Yin To, Eric A Franzosa, Curtis Huttenhower, Mina Rezaei, Alice Carolyn McHardy, Bernd Bischl, Philipp C Münch, Martin Binder
Optimized model architectures for deep learning on genomic data. Communications biology 7 (1) (2024)
Hüseyin Anil Gündüz, René Mreches, Julia Moosbauer, Gary Robertson, Xiao-Yin To, Eric A Franzosa, Curtis Huttenhower, Mina Rezaei, Alice Carolyn McHardy, Bernd Bischl, Philipp C Münch, Martin Binder
Author Correction: Optimized model architectures for deep learning on genomic data. Communications biology 7 (1) (2024)
Hüseyin Anil Gündüz, René Mreches, Julia Moosbauer, Gary Robertson, Xiao-Yin To, Eric A Franzosa, Curtis Huttenhower, Mina Rezaei, Alice Carolyn McHardy, Bernd Bischl, Philipp C Münch, Martin Binder
Optimized model architectures for deep learning on genomic data. Communications biology 7 (1) (2024)
Sama Goliaei, Mohammad-Hadi Foroughmand-Araabi, Aideen Roddy, Ariane Weber, Sanni Översti, Denise Kühnert, Alice Carolyn McHardy
Importations of SARS-CoV-2 lineages decline after nonpharmaceutical interventions in phylogeographic analyses. Nature communications 15 (1) (2024)
Hüseyin Anil Gündüz, René Mreches, Julia Moosbauer, Gary Robertson, Xiao-Yin To, Eric A Franzosa, Curtis Huttenhower, Mina Rezaei, Alice Carolyn McHardy, Bernd Bischl, Philipp C Münch, Martin Binder
Optimized model architectures for deep learning on genomic data. Communications biology 7 (1) (2024)
Sama Goliaei, Mohammad-Hadi Foroughmand-Araabi, Aideen Roddy, Ariane Weber, Sanni Översti, Denise Kühnert, Alice Carolyn McHardy
Importations of SARS-CoV-2 lineages decline after nonpharmaceutical interventions in phylogeographic analyses. Nature communications 15 (1) (2024)
Hüseyin Anil Gündüz, René Mreches, Julia Moosbauer, Gary Robertson, Xiao-Yin To, Eric A Franzosa, Curtis Huttenhower, Mina Rezaei, Alice Carolyn McHardy, Bernd Bischl, Philipp C Münch, Martin Binder
Author Correction: Optimized model architectures for deep learning on genomic data. Communications biology 7 (1) (2024)
Sama Goliaei, Mohammad-Hadi Foroughmand-Araabi, Aideen Roddy, Ariane Weber, Sanni Översti, Denise Kühnert, Alice Carolyn McHardy
Importations of SARS-CoV-2 lineages decline after nonpharmaceutical interventions in phylogeographic analyses. Nature communications 15 (1) (2024)
Sama Goliaei, Mohammad-Hadi Foroughmand-Araabi, Aideen Roddy, Ariane Weber, Sanni Översti, Denise Kühnert, Alice Carolyn McHardy
Importations of SARS-CoV-2 lineages decline after nonpharmaceutical interventions in phylogeographic analyses. Nature communications 15 (1) (2024)
Hüseyin Anil Gündüz, René Mreches, Julia Moosbauer, Gary Robertson, Xiao-Yin To, Eric A Franzosa, Curtis Huttenhower, Mina Rezaei, Alice Carolyn McHardy, Bernd Bischl, Philipp C Münch, Martin Binder
Optimized model architectures for deep learning on genomic data. Communications biology 7 (1) (2024)
Sama Goliaei, Mohammad-Hadi Foroughmand-Araabi, Aideen Roddy, Ariane Weber, Sanni Översti, Denise Kühnert, Alice Carolyn McHardy
Importations of SARS-CoV-2 lineages decline after nonpharmaceutical interventions in phylogeographic analyses. Nature communications 15 (1) (2024)
Sama Goliaei, Mohammad-Hadi Foroughmand-Araabi, Aideen Roddy, Ariane Weber, Sanni Översti, Denise Kühnert, Alice Carolyn McHardy
Importations of SARS-CoV-2 lineages decline after nonpharmaceutical interventions in phylogeographic analyses. Nature communications 15 (1) (2024)
Hüseyin Anil Gündüz, René Mreches, Julia Moosbauer, Gary Robertson, Xiao-Yin To, Eric A Franzosa, Curtis Huttenhower, Mina Rezaei, Alice Carolyn McHardy, Bernd Bischl, Philipp C Münch, Martin Binder
Optimized model architectures for deep learning on genomic data. Communications biology 7 (1) (2024)
Emiley A Eloe-Fadrosh, Christopher John Mungall, Mark Andrew Miller, Montana L Smith, Sujay Sanjeev Patil, Julia M Kelliher, Leah Y D Johnson, Francisca E Rodriguez, Patrick S G Chain, Bin Hu, Michael B Thornton, Lee Ann McCue, Alice Carolyn McHardy, Nomi L Harris, T B K Reddy, Supratim Mukherjee, Christopher I Hunter, Ramona L Walls, Lynn M Schriml
A Practical Approach to Using the Genomic Standards Consortium MIxS Reporting Standard for Comparative Genomics and Metagenomics. Methods in molecular biology (Clifton, N.J.) 2802 (2024)
Katherine M Kennedy, Marcus C de Goffau, Maria Elisa Perez-Munoz, Marie-Claire Arrieta, Fredrik Bäckhed, Peer Bork, Thorsten Braun, Frederic D Bushman, Joel Dore, Willem M de Vos, Ashlee M Earl, Jonathan A Eisen, Michal A Elovitz, Stephanie Christine Ganal-Vonarburg, Michael G Gaenzle, Wendy S Garrett, Lindsay J Hall, Mathias W Hornef, Curtis Huttenhower, Liza Konnikova, Sarah Lebeer, Andrew J Macpherson, Ruth C Massey, Alice Carolyn McHardy, Omry Koren, Trevor D Lawley, Ruth E Ley, Corina M Berset, Paul W O' Toole, Eric G Pamer, Julian Parkhill, Jeroen Raes, Thomas Rattei, Anne Salonen, Eran Segal, Nicola Segata, Fergus Shanahan, Deborah M Sloboda, Gordon C S Smith, Harry Sokol, Timothy D Spector, Michael G Surette, Gerald W Tannock, Alan William Walker, Moran Yassour, Jens Walter
Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 613 (7945) (2023)
Katherine M Kennedy, Marcus C de Goffau, Maria Elisa Perez-Munoz, Marie-Claire Arrieta, Fredrik Bäckhed, Peer Bork, Thorsten Braun, Frederic D Bushman, Joel Dore, Willem M de Vos, Ashlee M Earl, Jonathan A Eisen, Michal A Elovitz, Stephanie Christine Ganal-Vonarburg, Michael G Gaenzle, Wendy S Garrett, Lindsay J Hall, Mathias W Hornef, Curtis Huttenhower, Liza Konnikova, Sarah Lebeer, Andrew J Macpherson, Ruth C Massey, Alice Carolyn McHardy, Omry Koren, Trevor D Lawley, Ruth E Ley, Corina M Berset, Paul W O' Toole, Eric G Pamer, Julian Parkhill, Jeroen Raes, Thomas Rattei, Anne Salonen, Eran Segal, Nicola Segata, Fergus Shanahan, Deborah M Sloboda, Gordon C S Smith, Harry Sokol, Timothy D Spector, Michael G Surette, Gerald W Tannock, Alan William Walker, Moran Yassour, Jens Walter
Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 613 (7945) (2023)
Katherine M Kennedy, Marcus C de Goffau, Maria Elisa Perez-Munoz, Marie-Claire Arrieta, Fredrik Bäckhed, Peer Bork, Thorsten Braun, Frederic D Bushman, Joel Dore, Willem M de Vos, Ashlee M Earl, Jonathan A Eisen, Michal A Elovitz, Stephanie Christine Ganal-Vonarburg, Michael G Gaenzle, Wendy S Garrett, Lindsay J Hall, Mathias W Hornef, Curtis Huttenhower, Liza Konnikova, Sarah Lebeer, Andrew J Macpherson, Ruth C Massey, Alice Carolyn McHardy, Omry Koren, Trevor D Lawley, Ruth E Ley, Corina M Berset, Paul W O' Toole, Eric G Pamer, Julian Parkhill, Jeroen Raes, Thomas Rattei, Anne Salonen, Eran Segal, Nicola Segata, Fergus Shanahan, Deborah M Sloboda, Gordon C S Smith, Harry Sokol, Timothy D Spector, Michael G Surette, Gerald W Tannock, Alan William Walker, Moran Yassour, Jens Walter
Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 613 (7945) (2023)
Katherine M Kennedy, Marcus C de Goffau, Maria Elisa Perez-Munoz, Marie-Claire Arrieta, Fredrik Bäckhed, Peer Bork, Thorsten Braun, Frederic D Bushman, Joel Dore, Willem M de Vos, Ashlee M Earl, Jonathan A Eisen, Michal A Elovitz, Stephanie Christine Ganal-Vonarburg, Michael G Gaenzle, Wendy S Garrett, Lindsay J Hall, Mathias W Hornef, Curtis Huttenhower, Liza Konnikova, Sarah Lebeer, Andrew J Macpherson, Ruth C Massey, Alice Carolyn McHardy, Omry Koren, Trevor D Lawley, Ruth E Ley, Corina M Berset, Paul W O' Toole, Eric G Pamer, Julian Parkhill, Jeroen Raes, Thomas Rattei, Anne Salonen, Eran Segal, Nicola Segata, Fergus Shanahan, Deborah M Sloboda, Gordon C S Smith, Harry Sokol, Timothy D Spector, Michael G Surette, Gerald W Tannock, Alan William Walker, Moran Yassour, Jens Walter
Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 613 (7945) (2023)
Katherine M Kennedy, Marcus C de Goffau, Maria Elisa Perez-Munoz, Marie-Claire Arrieta, Fredrik Bäckhed, Peer Bork, Thorsten Braun, Frederic D Bushman, Joel Dore, Willem M de Vos, Ashlee M Earl, Jonathan A Eisen, Michal A Elovitz, Stephanie Christine Ganal-Vonarburg, Michael G Gaenzle, Wendy S Garrett, Lindsay J Hall, Mathias W Hornef, Curtis Huttenhower, Liza Konnikova, Sarah Lebeer, Andrew J Macpherson, Ruth C Massey, Alice Carolyn McHardy, Omry Koren, Trevor D Lawley, Ruth E Ley, Corina M Berset, Paul W O' Toole, Eric G Pamer, Julian Parkhill, Jeroen Raes, Thomas Rattei, Anne Salonen, Eran Segal, Nicola Segata, Fergus Shanahan, Deborah M Sloboda, Gordon C S Smith, Harry Sokol, Timothy D Spector, Michael G Surette, Gerald W Tannock, Alan William Walker, Moran Yassour, Jens Walter
Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 613 (7945) (2023)
Katherine M Kennedy, Marcus C de Goffau, Maria Elisa Perez-Munoz, Marie-Claire Arrieta, Fredrik Bäckhed, Peer Bork, Thorsten Braun, Frederic D Bushman, Joel Dore, Willem M de Vos, Ashlee M Earl, Jonathan A Eisen, Michal A Elovitz, Stephanie Christine Ganal-Vonarburg, Michael G Gaenzle, Wendy S Garrett, Lindsay J Hall, Mathias W Hornef, Curtis Huttenhower, Liza Konnikova, Sarah Lebeer, Andrew J Macpherson, Ruth C Massey, Alice Carolyn McHardy, Omry Koren, Trevor D Lawley, Ruth E Ley, Corina M Berset, Paul W O' Toole, Eric G Pamer, Julian Parkhill, Jeroen Raes, Thomas Rattei, Anne Salonen, Eran Segal, Nicola Segata, Fergus Shanahan, Deborah M Sloboda, Gordon C S Smith, Harry Sokol, Timothy D Spector, Michael G Surette, Gerald W Tannock, Alan William Walker, Moran Yassour, Jens Walter
Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 613 (7945) (2023)
Curtis Huttenhower, Robert D Finn, Alice Carolyn McHardy
Challenges and opportunities in sharing microbiome data and analyses. Nature microbiology (2023)
Katherine M Kennedy, Marcus C de Goffau, Maria Elisa Perez-Munoz, Marie-Claire Arrieta, Fredrik Bäckhed, Peer Bork, Thorsten Braun, Frederic D Bushman, Joel Dore, Willem M de Vos, Ashlee M Earl, Jonathan A Eisen, Michal A Elovitz, Stephanie Christine Ganal-Vonarburg, Michael G Gaenzle, Wendy S Garrett, Lindsay J Hall, Mathias W Hornef, Curtis Huttenhower, Liza Konnikova, Sarah Lebeer, Andrew J Macpherson, Ruth C Massey, Alice Carolyn McHardy, Omry Koren, Trevor D Lawley, Ruth E Ley, Corina M Berset, Paul W O' Toole, Eric G Pamer, Julian Parkhill, Jeroen Raes, Thomas Rattei, Anne Salonen, Eran Segal, Nicola Segata, Fergus Shanahan, Deborah M Sloboda, Gordon C S Smith, Harry Sokol, Timothy D Spector, Michael G Surette, Gerald W Tannock, Alan William Walker, Moran Yassour, Jens Walter
Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 613 (7945) (2023)
Hüseyin Anil Gündüz, Martin Binder, Xiao-Yin To, René Mreches, Bernd Bischl, Alice Carolyn McHardy, Philipp C Münch, Mina Rezaei
A self-supervised deep learning method for data-efficient training in genomics. Communications biology 6 (1) (2023)
Mohammad-Hadi Foroughmand-Araabi, Sama Goliaei, Alice Carolyn McHardy
Scelestial: Fast and accurate single-cell lineage tree inference based on a Steiner tree approximation algorithm. PLoS computational biology 18 (8) (2022)
Fernando Meyer, Adrian Fritz, Zhi-Luo Deng, David Koslicki, Till Robin Lesker, Alexey Gurevich, Gary Robertson, Mohammed Alser, Dmitry Antipov, Francesco Beghini, Denis Bertrand, Jaqueline J Brito, C Titus Brown, Jan P Buchmann, Aydin Buluç, Bo Chen, Rayan Chikhi, Philip Thomas Lanken Conradsen Clausen, Alexandru Cristian, Piotr Wojciech Dabrowski, Aaron E Darling, Rob Egan, Eleazar Eskin, Evangelos Georganas, Eugene Goltsman, Melissa A Gray, Lars Hestbjerg Hansen, Steven Hofmeyr, Pingqin Huang, Luiz Irber, Huijue Jia, Tue Sparholt Jørgensen, Silas D Kieser, Terje Klemetsen, Axel Kola, Mikhail Kolmogorov, Anton Korobeynikov, Jason Kwan, Nathan LaPierre, Claire Lemaitre, Chenhao Li, Antoine Limasset, Fábio Malcher Miranda, Serghei Mangul, Vanessa R Marcelino, Camille Marchet, Pierre Marijon, Dmitry Meleshko, Daniel R Mende, Alessio Milanese, Niranjan Nagarajan, Jakob Nissen, Sergey Nurk, Leonid Oliker, Lucas Paoli, Pierre Peterlongo, Vitor C Piro, Jacob S Porter, Simon Rasmussen, Evan R Rees, Knut Reinert, Bernhard Y Renard, Espen Mikal Robertsen, Gail L Rosen, Hans-Joachim Ruscheweyh, Varuni Sarwal, Nicola Segata, Enrico Seiler, Lizhen Shi, Fengzhu Sun, Shinichi Sunagawa, Søren Johannes Sørensen, Ashleigh Thomas, Chengxuan Tong, Mirko Trajkovski, Julien Tremblay, Gherman Uritskiy, Riccardo Vicedomini, Zhengyang Wang, Ziye Wang, Zhong Wang, Andrew Warren, Nils Peder Willassen, Katherine Yelick, Ronghui You, Georg Zeller, Zhengqiao Zhao, Shanfeng Zhu, Jie Zhu, Ruben Garrido-Oter, Petra Gastmeier, Stéphane Hacquard, Susanne Häußler, Ariane Khaledi, Friederike Maechler, Fantin Mesny, Simona Radutoiu, Paul Schulze-Lefert, Nathiana Smit, Till Strowig, Andreas Bremges, Alexander Sczyrba, Alice Carolyn McHardy
Critical Assessment of Metagenome Interpretation: the second round of challenges. Nature methods 19 (4) (2022)
David Lähnemann, Johannes Köster, Ute Fischer, Arndt Borkhardt, Alice Carolyn McHardy, Alexander Schönhuth
Accurate and scalable variant calling from single cell DNA sequencing data with ProSolo. Nature communications 12 (1) (2021)
Ariane Khaledi, Aaron Weimann, Monika Schniederjans, Ehsaneddin Asgari, Tzu-Hao Kuo, Antonio Oliver, Gabriel Cabot, Axel Kola, Petra Gastmeier, Michael Hogardt, Daniel Jonas, Mohammad Rk Mofrad, Andreas Bremges, Alice Carolyn McHardy, Susanne Häußler
Predicting antimicrobial resistance in Pseudomonas aeruginosa with machine learning-enabled molecular diagnostics. EMBO molecular medicine 12 (3) (2020)
Susanne Reimering, Sebastian Muñoz, Alice Carolyn McHardy
Phylogeographic reconstruction using air transportation data and its application to the 2009 H1N1 influenza A pandemic. PLoS computational biology 16 (2) (2020)
Ehsaneddin Asgari, Alice Carolyn McHardy, Mohammad R K Mofrad
Probabilistic variable-length segmentation of protein sequences for discriminative motif discovery (DiMotif) and sequence embedding (ProtVecX). Scientific reports 9 (1) (2019)
Thorsten R Klingen, Jens Loers, Stephanie Stanelle-Bertram, Gülsah Gabriel, Alice Carolyn McHardy
Structures and functions linked to genome-wide adaptation of human influenza A viruses. Scientific reports 9 (1) (2019)
Adrian Fritz, Peter Hofmann, Stephan Majda, Eik Dahms, Johannes Dröge, Jessika Fiedler, Till R Lesker, Peter Belmann, Matthew Z DeMaere, Aaron E Darling, Alexander Sczyrba, Andreas Bremges, Alice Carolyn McHardy
CAMISIM: simulating metagenomes and microbial communities. Microbiome 7 (1) (2019)
Andreas Bremges, Alice Carolyn McHardy
Critical Assessment of Metagenome Interpretation Enters the Second Round. mSystems 3 (4) (2018)
Tommi Vatanen, Damian R Plichta, Juhi Somani, Philipp C Münch, Timothy D Arthur, Andrew Brantley Hall, Sabine Rudolf, Edward J Oakeley, Xiaobo Ke, Rachel A Young, Henry J Haiser, Raivo Kolde, Moran Yassour, Kristiina Luopajärvi, Heli Siljander, Suvi M Virtanen, Jorma Ilonen, Raivo Uibo, Vallo Tillmann, Sergei Mokurov, Natalya Dorshakova, Jeffrey A Porter, Alice Carolyn McHardy, Harri Lähdesmäki, Hera Vlamakis, Curtis Huttenhower, Olli H Laitinen, Ramnik J Xavier
Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life. Nature microbiology 4 (3) (2018)
Thorsten R Klingen, Susanne Reimering, Jens Loers, Kyra Mooren, Frank Klawonn, Thomas Krey, Gülsah Gabriel, Alice Carolyn McHardy
Sweep Dynamics (SD) plots: Computational identification of selective sweeps to monitor the adaptation of influenza A viruses. Scientific reports 8 (1) (2018)
Susanne Reimering, Sebastian Muñoz, Alice Carolyn McHardy
A Fréchet tree distance measure to compare phylogeographic spread paths across trees. Scientific reports 8 (1) (2018)
Victoria Grießmeier, Andreas Bremges, Alice Carolyn McHardy, Johannes Gescher
Investigation of different nitrogen reduction routes and their key microbial players in wood chip-driven denitrification beds. Scientific reports 7 (1) (2017)
Alexander Sczyrba, Peter Hofmann, Peter Belmann, David Koslicki, Stefan Janssen, Johannes Dröge, Ivan Gregor, Stephan Majda, Jessika Fiedler, Eik Dahms, Andreas Bremges, Adrian Fritz, Ruben Garrido-Oter, Tue Sparholt Jørgensen, Nicole Shapiro, Philip D Blood, Alexey Gurevich, Yang Bai, Dmitrij Turaev, Matthew Z DeMaere, Rayan Chikhi, Niranjan Nagarajan, Christopher Quince, Fernando Meyer, Monika Balvočiūtė, Lars Hestbjerg Hansen, Søren J Sørensen, Burton K H Chia, Bertrand Denis, Jeff L Froula, Zhong Wang, Robert Egan, Dongwan Don Kang, Jeffrey J Cook, Charles Deltel, Michael Beckstette, Claire Lemaitre, Pierre Peterlongo, Guillaume Rizk, Dominique Lavenier, Yu-Wei Wu, Steven W Singer, Chirag Jain, Marc Strous, Heiner Klingenberg, Peter Meinicke, Michael D Barton, Thomas Lingner, Hsin-Hung Lin, Yu-Chieh Liao, Genivaldo Gueiros Z Silva, Daniel A Cuevas, Robert A Edwards, Surya Saha, Vitor C Piro, Bernhard Y Renard, Mihai Pop, Hans-Peter Klenk, Markus Göker, Nikos C Kyrpides, Tanja Woyke, Julia A Vorholt, Paul Schulze-Lefert, Edward M Rubin, Aaron E Darling, Thomas Rattei, Alice Carolyn McHardy
Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software. Nature methods 14 (11) (2017)