Michael M Hoffman

ResearcherID Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 60

Top Venues

Nature methods

Genome biology

BMJ (Clinical research ed.)

PloS one

University of Toronto

University of Cambridge (PHD)

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

Affiliation History

University of Toronto Sep 01 2014

Canada

Assistant Professor :: Department of Computer Science

University of Toronto Apr 01 2014

Canada

Assistant Professor :: Department of Medical Biophysics

Princess Margaret Cancer Centre Nov 04 2013

Canada

Scientist

Education History

University of Cambridge Oct 01 2003 - Jul 19 2008

United Kingdom

PHD :: EMBL-European Bioinformatics Institute

University of Texas at Austin Aug 26 1998 - May 17 2003

United States

BSC :: Plan II Honors Program

University of Texas at Austin Aug 26 1998 - May 17 2003

United States

BSC :: Department of Chemistry and Biochemistry

Publications

Annika Reinke, Minu D Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A Emre Kavur, Tim Rädsch, Carole H Sudre, Laura Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Florian Buettner, M Jorge Cardoso, Veronika Cheplygina, Jianxu Chen, Evangelia Christodoulou, Beth A Cimini, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Ben Glocker, Patrick Godau, Daniel A Hashimoto, Michael M Hoffman, Merel Huisman, Fabian Isensee, Pierre Jannin, Charles E Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Jens Kleesiek, Florian Kofler, Thijs Kooi, Dominik T Schneider, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M Rafelski, Nasir M Rajpoot, Mauricio Reyes, Michael A Riegler, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Ronald M Summers, Abdel A Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Ziv Rafael Yaniv, Paul F Jaeger, Lena Maier-Hein
Understanding metric-related pitfalls in image analysis validation. Nature methods 21 (2) (2024)
Coby Viner, Charles A Ishak, James Johnson, Nicolas J Walker, Hui Shi, Marcela K Sjöberg-Herrera, Shu Yi Shen, Santana M Lardo, David J Adams, Anne C Ferguson-Smith, Daniel D De Carvalho, Sarah J Hainer, Timothy L Bailey, Michael M Hoffman
Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet. Genome biology 25 (1) (2024)
Gary Stephen Collins, Karel G M Moons, Paula Dhiman, Richard D Riley, Andrew L Beam, Ben Van Calster, Marzyeh Ghassemi, Xiaoxuan Liu, Johannes B Reitsma, Maarten van Smeden, Anne-Laure Boulesteix, Jennifer Catherine Louise Camaradou, Leo Anthony Celi, Spiros Denaxas, Alastair Keith Denniston, Ben Glocker, Robert M Golub, Hugh Harvey, Georg Heinze, Michael M Hoffman, Andre Pascal Kengne, Emily Lam, Naomi Lee, Elizabeth W Loder, Lena Maier-Hein, Bilal Akhter Mateen, Melissa Danielle McCradden, Lauren Oakden-Rayner, Johan Ordish, Richard Parnell, Sherri Rose, Karandeep S Singh, Laure Wynants, Patrícia Logullo
TRIPOD+AI statement: updated guidance for reporting clinical prediction models that use regression or machine learning methods. BMJ (Clinical research ed.) 385 (2024)
Annika Reinke, Minu D Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A Emre Kavur, Tim Rädsch, Carole H Sudre, Laura Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Florian Buettner, M Jorge Cardoso, Veronika Cheplygina, Jianxu Chen, Evangelia Christodoulou, Beth A Cimini, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Ben Glocker, Patrick Godau, Daniel A Hashimoto, Michael M Hoffman, Merel Huisman, Fabian Isensee, Pierre Jannin, Charles E Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Jens Kleesiek, Florian Kofler, Thijs Kooi, Dominik T Schneider, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M Rafelski, Nasir M Rajpoot, Mauricio Reyes, Michael A Riegler, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Ronald M Summers, Abdel A Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Ziv Rafael Yaniv, Paul F Jaeger, Lena Maier-Hein
Understanding metric-related pitfalls in image analysis validation. Nature methods 21 (2) (2024)
Annika Reinke, Minu D Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A Emre Kavur, Tim Rädsch, Carole H Sudre, Laura Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Florian Buettner, M Jorge Cardoso, Veronika Cheplygina, Jianxu Chen, Evangelia Christodoulou, Beth A Cimini, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Ben Glocker, Patrick Godau, Daniel A Hashimoto, Michael M Hoffman, Merel Huisman, Fabian Isensee, Pierre Jannin, Charles E Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Jens Kleesiek, Florian Kofler, Thijs Kooi, Dominik T Schneider, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M Rafelski, Nasir M Rajpoot, Mauricio Reyes, Michael A Riegler, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Ronald M Summers, Abdel A Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Ziv Rafael Yaniv, Paul F Jaeger, Lena Maier-Hein
Understanding metric-related pitfalls in image analysis validation. Nature methods 21 (2) (2024)
Annika Reinke, Minu D Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A Emre Kavur, Tim Rädsch, Carole H Sudre, Laura Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Florian Buettner, M Jorge Cardoso, Veronika Cheplygina, Jianxu Chen, Evangelia Christodoulou, Beth A Cimini, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Ben Glocker, Patrick Godau, Daniel A Hashimoto, Michael M Hoffman, Merel Huisman, Fabian Isensee, Pierre Jannin, Charles E Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Jens Kleesiek, Florian Kofler, Thijs Kooi, Dominik T Schneider, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M Rafelski, Nasir M Rajpoot, Mauricio Reyes, Michael A Riegler, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Ronald M Summers, Abdel A Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Ziv Rafael Yaniv, Paul F Jaeger, Lena Maier-Hein
Understanding metric-related pitfalls in image analysis validation. Nature methods 21 (2) (2024)
Gary Stephen Collins, Karel G M Moons, Paula Dhiman, Richard D Riley, Andrew L Beam, Ben Van Calster, Marzyeh Ghassemi, Xiaoxuan Liu, Johannes B Reitsma, Maarten van Smeden, Anne-Laure Boulesteix, Jennifer Catherine Louise Camaradou, Leo Anthony Celi, Spiros Denaxas, Alastair Keith Denniston, Ben Glocker, Robert M Golub, Hugh Harvey, Georg Heinze, Michael M Hoffman, Andre Pascal Kengne, Emily Lam, Naomi Lee, Elizabeth W Loder, Lena Maier-Hein, Bilal Akhter Mateen, Melissa Danielle McCradden, Lauren Oakden-Rayner, Johan Ordish, Richard Parnell, Sherri Rose, Karandeep S Singh, Laure Wynants, Patrícia Logullo
TRIPOD+AI statement: updated guidance for reporting clinical prediction models that use regression or machine learning methods. BMJ (Clinical research ed.) 385 (2024)
Coby Viner, Charles A Ishak, James Johnson, Nicolas J Walker, Hui Shi, Marcela K Sjöberg-Herrera, Shu Yi Shen, Santana M Lardo, David J Adams, Anne C Ferguson-Smith, Daniel D De Carvalho, Sarah J Hainer, Timothy L Bailey, Michael M Hoffman
Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet. Genome biology 25 (1) (2024)
Annika Reinke, Minu D Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A Emre Kavur, Tim Rädsch, Carole H Sudre, Laura Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Florian Buettner, M Jorge Cardoso, Veronika Cheplygina, Jianxu Chen, Evangelia Christodoulou, Beth A Cimini, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Ben Glocker, Patrick Godau, Daniel A Hashimoto, Michael M Hoffman, Merel Huisman, Fabian Isensee, Pierre Jannin, Charles E Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Jens Kleesiek, Florian Kofler, Thijs Kooi, Dominik T Schneider, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M Rafelski, Nasir M Rajpoot, Mauricio Reyes, Michael A Riegler, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Ronald M Summers, Abdel A Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Ziv Rafael Yaniv, Paul F Jaeger, Lena Maier-Hein
Understanding metric-related pitfalls in image analysis validation. Nature methods 21 (2) (2024)
Gary Stephen Collins, Karel G M Moons, Paula Dhiman, Richard D Riley, Andrew L Beam, Ben Van Calster, Marzyeh Ghassemi, Xiaoxuan Liu, Johannes B Reitsma, Maarten van Smeden, Anne-Laure Boulesteix, Jennifer Catherine Louise Camaradou, Leo Anthony Celi, Spiros Denaxas, Alastair Keith Denniston, Ben Glocker, Robert M Golub, Hugh Harvey, Georg Heinze, Michael M Hoffman, Andre Pascal Kengne, Emily Lam, Naomi Lee, Elizabeth W Loder, Lena Maier-Hein, Bilal Akhter Mateen, Melissa Danielle McCradden, Lauren Oakden-Rayner, Johan Ordish, Richard Parnell, Sherri Rose, Karandeep S Singh, Laure Wynants, Patrícia Logullo
TRIPOD+AI statement: updated guidance for reporting clinical prediction models that use regression or machine learning methods. BMJ (Clinical research ed.) 385 (2024)
Annika Reinke, Minu D Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A Emre Kavur, Tim Rädsch, Carole H Sudre, Laura Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Florian Buettner, M Jorge Cardoso, Veronika Cheplygina, Jianxu Chen, Evangelia Christodoulou, Beth A Cimini, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Ben Glocker, Patrick Godau, Daniel A Hashimoto, Michael M Hoffman, Merel Huisman, Fabian Isensee, Pierre Jannin, Charles E Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Jens Kleesiek, Florian Kofler, Thijs Kooi, Dominik T Schneider, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M Rafelski, Nasir M Rajpoot, Mauricio Reyes, Michael A Riegler, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Ronald M Summers, Abdel A Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Ziv Rafael Yaniv, Paul F Jaeger, Lena Maier-Hein
Understanding metric-related pitfalls in image analysis validation. Nature methods 21 (2) (2024)
Coby Viner, Charles A Ishak, James Johnson, Nicolas J Walker, Hui Shi, Marcela K Sjöberg-Herrera, Shu Yi Shen, Santana M Lardo, David J Adams, Anne C Ferguson-Smith, Daniel D De Carvalho, Sarah J Hainer, Timothy L Bailey, Michael M Hoffman
Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet. Genome biology 25 (1) (2024)
Gary Stephen Collins, Karel G M Moons, Paula Dhiman, Richard D Riley, Andrew L Beam, Ben Van Calster, Marzyeh Ghassemi, Xiaoxuan Liu, Johannes B Reitsma, Maarten van Smeden, Anne-Laure Boulesteix, Jennifer Catherine Louise Camaradou, Leo Anthony Celi, Spiros Denaxas, Alastair Keith Denniston, Ben Glocker, Robert M Golub, Hugh Harvey, Georg Heinze, Michael M Hoffman, Andre Pascal Kengne, Emily Lam, Naomi Lee, Elizabeth W Loder, Lena Maier-Hein, Bilal Akhter Mateen, Melissa Danielle McCradden, Lauren Oakden-Rayner, Johan Ordish, Richard Parnell, Sherri Rose, Karandeep S Singh, Laure Wynants, Patrícia Logullo
TRIPOD+AI statement: updated guidance for reporting clinical prediction models that use regression or machine learning methods. BMJ (Clinical research ed.) 385 (2024)
Coby Viner, Charles A Ishak, James Johnson, Nicolas J Walker, Hui Shi, Marcela K Sjöberg-Herrera, Shu Yi Shen, Santana M Lardo, David J Adams, Anne C Ferguson-Smith, Daniel D De Carvalho, Sarah J Hainer, Timothy L Bailey, Michael M Hoffman
Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet. Genome biology 25 (1) (2024)
Annika Reinke, Minu D Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A Emre Kavur, Tim Rädsch, Carole H Sudre, Laura Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Florian Buettner, M Jorge Cardoso, Veronika Cheplygina, Jianxu Chen, Evangelia Christodoulou, Beth A Cimini, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Ben Glocker, Patrick Godau, Daniel A Hashimoto, Michael M Hoffman, Merel Huisman, Fabian Isensee, Pierre Jannin, Charles E Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Jens Kleesiek, Florian Kofler, Thijs Kooi, Dominik T Schneider, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M Rafelski, Nasir M Rajpoot, Mauricio Reyes, Michael A Riegler, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Ronald M Summers, Abdel A Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Ziv Rafael Yaniv, Paul F Jaeger, Lena Maier-Hein
Understanding metric-related pitfalls in image analysis validation. Nature methods 21 (2) (2024)
Coby Viner, Charles A Ishak, James Johnson, Nicolas J Walker, Hui Shi, Marcela K Sjöberg-Herrera, Shu Yi Shen, Santana M Lardo, David J Adams, Anne C Ferguson-Smith, Daniel D De Carvalho, Sarah J Hainer, Timothy L Bailey, Michael M Hoffman
Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet. Genome biology 25 (1) (2024)
Lena Maier-Hein, Annika Reinke, Patrick Godau, Minu D Tizabi, Florian Buettner, Evangelia Christodoulou, Ben Glocker, Fabian Isensee, Jens Kleesiek, Michal Kozubek, Mauricio Reyes, Michael A Riegler, Manuel Wiesenfarth, A Emre Kavur, Carole H Sudre, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, Tim Rädsch, Laura Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew B Blaschko, M Jorge Cardoso, Veronika Cheplygina, Beth A Cimini, Gary Stephen Collins, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Robert Haase, Daniel A Hashimoto, Michael M Hoffman, Merel Huisman, Pierre Jannin, Charles E Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Alan Karthikesalingam, Florian Kofler, Dominik T Schneider, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Peter Mattson, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Nasir M Rajpoot, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Maarten van Smeden, Ronald M Summers, Abdel Aziz Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Paul F Jaeger
Metrics reloaded: recommendations for image analysis validation. Nature methods 21 (2) (2024)
Coby Viner, Charles A Ishak, James Johnson, Nicolas J Walker, Hui Shi, Marcela K Sjöberg-Herrera, Shu Yi Shen, Santana M Lardo, David J Adams, Anne C Ferguson-Smith, Daniel D De Carvalho, Sarah J Hainer, Timothy L Bailey, Michael M Hoffman
Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet. Genome biology 25 (1) (2024)
Annika Reinke, Minu D Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A Emre Kavur, Tim Rädsch, Carole H Sudre, Laura Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Florian Buettner, M Jorge Cardoso, Veronika Cheplygina, Jianxu Chen, Evangelia Christodoulou, Beth A Cimini, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Ben Glocker, Patrick Godau, Daniel A Hashimoto, Michael M Hoffman, Merel Huisman, Fabian Isensee, Pierre Jannin, Charles E Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Jens Kleesiek, Florian Kofler, Thijs Kooi, Dominik T Schneider, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M Rafelski, Nasir M Rajpoot, Mauricio Reyes, Michael A Riegler, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Ronald M Summers, Abdel A Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Ziv Rafael Yaniv, Paul F Jaeger, Lena Maier-Hein
Understanding metric-related pitfalls in image analysis validation. Nature methods (2024)
Lena Maier-Hein, Annika Reinke, Patrick Godau, Minu D Tizabi, Florian Buettner, Evangelia Christodoulou, Ben Glocker, Fabian Isensee, Jens Kleesiek, Michal Kozubek, Mauricio Reyes, Michael A Riegler, Manuel Wiesenfarth, A Emre Kavur, Carole H Sudre, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, Tim Rädsch, Laura Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew B Blaschko, M Jorge Cardoso, Veronika Cheplygina, Beth A Cimini, Gary Stephen Collins, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Robert Haase, Daniel A Hashimoto, Michael M Hoffman, Merel Huisman, Pierre Jannin, Charles E Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Alan Karthikesalingam, Florian Kofler, Dominik T Schneider, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Peter Mattson, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Nasir M Rajpoot, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Maarten van Smeden, Ronald M Summers, Abdel Aziz Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Paul F Jaeger
Metrics reloaded: recommendations for image analysis validation. Nature methods 21 (2) (2024)
Gary Stephen Collins, Karel G M Moons, Paula Dhiman, Richard D Riley, Andrew L Beam, Ben Van Calster, Marzyeh Ghassemi, Xiaoxuan Liu, Johannes B Reitsma, Maarten van Smeden, Anne-Laure Boulesteix, Jennifer Catherine Louise Camaradou, Leo Anthony Celi, Spiros Denaxas, Alastair Keith Denniston, Ben Glocker, Robert M Golub, Hugh Harvey, Georg Heinze, Michael M Hoffman, Andre Pascal Kengne, Emily Lam, Naomi Lee, Elizabeth W Loder, Lena Maier-Hein, Bilal Akhter Mateen, Melissa Danielle McCradden, Lauren Oakden-Rayner, Johan Ordish, Richard Parnell, Sherri Rose, Karandeep S Singh, Laure Wynants, Patrícia Logullo
TRIPOD+AI statement: updated guidance for reporting clinical prediction models that use regression or machine learning methods. BMJ (Clinical research ed.) 385 (2024)
Lena Maier-Hein, Annika Reinke, Patrick Godau, Minu D Tizabi, Florian Buettner, Evangelia Christodoulou, Ben Glocker, Fabian Isensee, Jens Kleesiek, Michal Kozubek, Mauricio Reyes, Michael A Riegler, Manuel Wiesenfarth, A Emre Kavur, Carole H Sudre, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, Tim Rädsch, Laura Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew B Blaschko, M Jorge Cardoso, Veronika Cheplygina, Beth A Cimini, Gary Stephen Collins, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Robert Haase, Daniel A Hashimoto, Michael M Hoffman, Merel Huisman, Pierre Jannin, Charles E Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Alan Karthikesalingam, Florian Kofler, Dominik T Schneider, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Peter Mattson, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Nasir M Rajpoot, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Maarten van Smeden, Ronald M Summers, Abdel Aziz Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Paul F Jaeger
Metrics reloaded: recommendations for image analysis validation. Nature methods (2024)
Lena Maier-Hein, Annika Reinke, Patrick Godau, Minu D Tizabi, Florian Buettner, Evangelia Christodoulou, Ben Glocker, Fabian Isensee, Jens Kleesiek, Michal Kozubek, Mauricio Reyes, Michael A Riegler, Manuel Wiesenfarth, A Emre Kavur, Carole H Sudre, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, Tim Rädsch, Laura Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew B Blaschko, M Jorge Cardoso, Veronika Cheplygina, Beth A Cimini, Gary Stephen Collins, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Robert Haase, Daniel A Hashimoto, Michael M Hoffman, Merel Huisman, Pierre Jannin, Charles E Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Alan Karthikesalingam, Florian Kofler, Dominik T Schneider, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Peter Mattson, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Nasir M Rajpoot, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Maarten van Smeden, Ronald M Summers, Abdel Aziz Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Paul F Jaeger
Metrics reloaded: recommendations for image analysis validation. Nature methods 21 (2) (2024)
Saumya Agrawal, Andrey Buyan, Jessica Severin, Masaru Koido, Tanvir Alam, Imad Abugessaisa, Howard Y Chang, Josée Dostie, Masayoshi Itoh, Juha Kere, Naoto Kondo, Yunjing Li, Vsevolod J Makeev, Mickaël Mendez, Yasushi Okazaki, Jordan A Ramilowski, Andrey I Sigorskikh, Lisa J Strug, Ken Yagi, Kayoko Yasuzawa, Chi Wai Yip, Chung Chau Hon, Michael M Hoffman, Chikashi C Terao, Ivan V Kulakovskiy, Takeya Kasukawa, Jay W Shin, Piero Carninci, Michiel J L de Hoon
Annotation of nuclear lncRNAs based on chromatin interactions. PloS one 19 (5) (2024)
Lena Maier-Hein, Annika Reinke, Patrick Godau, Minu D Tizabi, Florian Buettner, Evangelia Christodoulou, Ben Glocker, Fabian Isensee, Jens Kleesiek, Michal Kozubek, Mauricio Reyes, Michael A Riegler, Manuel Wiesenfarth, A Emre Kavur, Carole H Sudre, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, Tim Rädsch, Laura Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew B Blaschko, M Jorge Cardoso, Veronika Cheplygina, Beth A Cimini, Gary Stephen Collins, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Robert Haase, Daniel A Hashimoto, Michael M Hoffman, Merel Huisman, Pierre Jannin, Charles E Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Alan Karthikesalingam, Florian Kofler, Dominik T Schneider, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Peter Mattson, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Nasir M Rajpoot, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Maarten van Smeden, Ronald M Summers, Abdel Aziz Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Paul F Jaeger
Metrics reloaded: recommendations for image analysis validation. Nature methods 21 (2) (2024)
Coby Viner, Charles A Ishak, James Johnson, Nicolas J Walker, Hui Shi, Marcela K Sjöberg-Herrera, Shu Yi Shen, Santana M Lardo, David J Adams, Anne C Ferguson-Smith, Daniel D De Carvalho, Sarah J Hainer, Timothy L Bailey, Michael M Hoffman
Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet. Genome biology 25 (1) (2024)
Lena Maier-Hein, Annika Reinke, Patrick Godau, Minu D Tizabi, Florian Buettner, Evangelia Christodoulou, Ben Glocker, Fabian Isensee, Jens Kleesiek, Michal Kozubek, Mauricio Reyes, Michael A Riegler, Manuel Wiesenfarth, A Emre Kavur, Carole H Sudre, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, Tim Rädsch, Laura Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew B Blaschko, M Jorge Cardoso, Veronika Cheplygina, Beth A Cimini, Gary Stephen Collins, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Robert Haase, Daniel A Hashimoto, Michael M Hoffman, Merel Huisman, Pierre Jannin, Charles E Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Alan Karthikesalingam, Florian Kofler, Dominik T Schneider, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Peter Mattson, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Nasir M Rajpoot, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Maarten van Smeden, Ronald M Summers, Abdel Aziz Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Paul F Jaeger
Metrics reloaded: recommendations for image analysis validation. Nature methods 21 (2) (2024)
Annika Reinke, Minu D Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A Emre Kavur, Tim Rädsch, Carole H Sudre, Laura Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Florian Buettner, M Jorge Cardoso, Veronika Cheplygina, Jianxu Chen, Evangelia Christodoulou, Beth A Cimini, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Ben Glocker, Patrick Godau, Daniel A Hashimoto, Michael M Hoffman, Merel Huisman, Fabian Isensee, Pierre Jannin, Charles E Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Jens Kleesiek, Florian Kofler, Thijs Kooi, Dominik T Schneider, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M Rafelski, Nasir M Rajpoot, Mauricio Reyes, Michael A Riegler, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Ronald M Summers, Abdel A Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Ziv Rafael Yaniv, Paul F Jaeger, Lena Maier-Hein
Understanding metric-related pitfalls in image analysis validation. Nature methods 21 (2) (2024)
Coby Viner, Charles A Ishak, James Johnson, Nicolas J Walker, Hui Shi, Marcela K Sjöberg-Herrera, Shu Yi Shen, Santana M Lardo, David J Adams, Anne C Ferguson-Smith, Daniel D De Carvalho, Sarah J Hainer, Timothy L Bailey, Michael M Hoffman
Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet. Genome biology 25 (1) (2024)
Lena Maier-Hein, Annika Reinke, Patrick Godau, Minu D Tizabi, Florian Buettner, Evangelia Christodoulou, Ben Glocker, Fabian Isensee, Jens Kleesiek, Michal Kozubek, Mauricio Reyes, Michael A Riegler, Manuel Wiesenfarth, A Emre Kavur, Carole H Sudre, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, Tim Rädsch, Laura Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew B Blaschko, M Jorge Cardoso, Veronika Cheplygina, Beth A Cimini, Gary Stephen Collins, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Robert Haase, Daniel A Hashimoto, Michael M Hoffman, Merel Huisman, Pierre Jannin, Charles E Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Alan Karthikesalingam, Florian Kofler, Dominik T Schneider, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Peter Mattson, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Nasir M Rajpoot, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Maarten van Smeden, Ronald M Summers, Abdel Aziz Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Paul F Jaeger
Metrics reloaded: recommendations for image analysis validation. Nature methods 21 (2) (2024)
Coby Viner, Charles A Ishak, James Johnson, Nicolas J Walker, Hui Shi, Marcela K Sjöberg-Herrera, Shu Yi Shen, Santana M Lardo, David J Adams, Anne C Ferguson-Smith, Daniel D De Carvalho, Sarah J Hainer, Timothy L Bailey, Michael M Hoffman
Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet. Genome biology 25 (1) (2024)
Coby Viner, Charles A Ishak, James Johnson, Nicolas J Walker, Hui Shi, Marcela K Sjöberg-Herrera, Shu Yi Shen, Santana M Lardo, David J Adams, Anne C Ferguson-Smith, Daniel D De Carvalho, Sarah J Hainer, Timothy L Bailey, Michael M Hoffman
Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet. Genome biology 25 (1) (2024)
Annika Reinke, Minu D Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A Emre Kavur, Tim Rädsch, Carole H Sudre, Laura Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Florian Buettner, M Jorge Cardoso, Veronika Cheplygina, Jianxu Chen, Evangelia Christodoulou, Beth A Cimini, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Ben Glocker, Patrick Godau, Daniel A Hashimoto, Michael M Hoffman, Merel Huisman, Fabian Isensee, Pierre Jannin, Charles E Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Jens Kleesiek, Florian Kofler, Thijs Kooi, Dominik T Schneider, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M Rafelski, Nasir M Rajpoot, Mauricio Reyes, Michael A Riegler, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Ronald M Summers, Abdel A Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Ziv Rafael Yaniv, Paul F Jaeger, Lena Maier-Hein
Understanding metric-related pitfalls in image analysis validation. Nature methods 21 (2) (2024)
Gary Stephen Collins, Karel G M Moons, Paula Dhiman, Richard D Riley, Andrew L Beam, Ben Van Calster, Marzyeh Ghassemi, Xiaoxuan Liu, Johannes B Reitsma, Maarten van Smeden, Anne-Laure Boulesteix, Jennifer Catherine Louise Camaradou, Leo Anthony Celi, Spiros Denaxas, Alastair Keith Denniston, Ben Glocker, Robert M Golub, Hugh Harvey, Georg Heinze, Michael M Hoffman, Andre Pascal Kengne, Emily Lam, Naomi Lee, Elizabeth W Loder, Lena Maier-Hein, Bilal Akhter Mateen, Melissa Danielle McCradden, Lauren Oakden-Rayner, Johan Ordish, Richard Parnell, Sherri Rose, Karandeep S Singh, Laure Wynants, Patrícia Logullo
TRIPOD+AI statement: updated guidance for reporting clinical prediction models that use regression or machine learning methods. BMJ (Clinical research ed.) 385 (2024)
Lena Maier-Hein, Annika Reinke, Patrick Godau, Minu D Tizabi, Florian Buettner, Evangelia Christodoulou, Ben Glocker, Fabian Isensee, Jens Kleesiek, Michal Kozubek, Mauricio Reyes, Michael A Riegler, Manuel Wiesenfarth, A Emre Kavur, Carole H Sudre, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, Tim Rädsch, Laura Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew B Blaschko, M Jorge Cardoso, Veronika Cheplygina, Beth A Cimini, Gary Stephen Collins, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Robert Haase, Daniel A Hashimoto, Michael M Hoffman, Merel Huisman, Pierre Jannin, Charles E Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Alan Karthikesalingam, Florian Kofler, Dominik T Schneider, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Peter Mattson, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Nasir M Rajpoot, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Maarten van Smeden, Ronald M Summers, Abdel Aziz Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Paul F Jaeger
Metrics reloaded: recommendations for image analysis validation. Nature methods 21 (2) (2024)
Annika Reinke, Minu D Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A Emre Kavur, Tim Rädsch, Carole H Sudre, Laura Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Florian Buettner, M Jorge Cardoso, Veronika Cheplygina, Jianxu Chen, Evangelia Christodoulou, Beth A Cimini, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Ben Glocker, Patrick Godau, Daniel A Hashimoto, Michael M Hoffman, Merel Huisman, Fabian Isensee, Pierre Jannin, Charles E Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Jens Kleesiek, Florian Kofler, Thijs Kooi, Dominik T Schneider, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M Rafelski, Nasir M Rajpoot, Mauricio Reyes, Michael A Riegler, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Ronald M Summers, Abdel A Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Ziv Rafael Yaniv, Paul F Jaeger, Lena Maier-Hein
Understanding metric-related pitfalls in image analysis validation. Nature methods 21 (2) (2024)
Lena Maier-Hein, Annika Reinke, Patrick Godau, Minu D Tizabi, Florian Buettner, Evangelia Christodoulou, Ben Glocker, Fabian Isensee, Jens Kleesiek, Michal Kozubek, Mauricio Reyes, Michael A Riegler, Manuel Wiesenfarth, A Emre Kavur, Carole H Sudre, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, Tim Rädsch, Laura Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew B Blaschko, M Jorge Cardoso, Veronika Cheplygina, Beth A Cimini, Gary Stephen Collins, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Robert Haase, Daniel A Hashimoto, Michael M Hoffman, Merel Huisman, Pierre Jannin, Charles E Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Alan Karthikesalingam, Florian Kofler, Dominik T Schneider, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Peter Mattson, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Nasir M Rajpoot, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Maarten van Smeden, Ronald M Summers, Abdel Aziz Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Paul F Jaeger
Metrics reloaded: recommendations for image analysis validation. Nature methods 21 (2) (2024)
Annika Reinke, Minu D Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A Emre Kavur, Tim Rädsch, Carole H Sudre, Laura Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Florian Buettner, M Jorge Cardoso, Veronika Cheplygina, Jianxu Chen, Evangelia Christodoulou, Beth A Cimini, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Ben Glocker, Patrick Godau, Daniel A Hashimoto, Michael M Hoffman, Merel Huisman, Fabian Isensee, Pierre Jannin, Charles E Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Jens Kleesiek, Florian Kofler, Thijs Kooi, Dominik T Schneider, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M Rafelski, Nasir M Rajpoot, Mauricio Reyes, Michael A Riegler, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Ronald M Summers, Abdel A Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Ziv Rafael Yaniv, Paul F Jaeger, Lena Maier-Hein
Understanding metric-related pitfalls in image analysis validation. Nature methods 21 (2) (2024)
Saumya Agrawal, Andrey Buyan, Jessica Severin, Masaru Koido, Tanvir Alam, Imad Abugessaisa, Howard Y Chang, Josée Dostie, Masayoshi Itoh, Juha Kere, Naoto Kondo, Yunjing Li, Vsevolod J Makeev, Mickaël Mendez, Yasushi Okazaki, Jordan A Ramilowski, Andrey I Sigorskikh, Lisa J Strug, Ken Yagi, Kayoko Yasuzawa, Chi Wai Yip, Chung Chau Hon, Michael M Hoffman, Chikashi C Terao, Ivan V Kulakovskiy, Takeya Kasukawa, Jay W Shin, Piero Carninci, Michiel J L de Hoon
Annotation of nuclear lncRNAs based on chromatin interactions. PloS one 19 (5) (2024)
Lena Maier-Hein, Annika Reinke, Patrick Godau, Minu D Tizabi, Florian Buettner, Evangelia Christodoulou, Ben Glocker, Fabian Isensee, Jens Kleesiek, Michal Kozubek, Mauricio Reyes, Michael A Riegler, Manuel Wiesenfarth, A Emre Kavur, Carole H Sudre, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, Tim Rädsch, Laura Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew B Blaschko, M Jorge Cardoso, Veronika Cheplygina, Beth A Cimini, Gary Stephen Collins, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Robert Haase, Daniel A Hashimoto, Michael M Hoffman, Merel Huisman, Pierre Jannin, Charles E Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Alan Karthikesalingam, Florian Kofler, Dominik T Schneider, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Peter Mattson, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Nasir M Rajpoot, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Maarten van Smeden, Ronald M Summers, Abdel Aziz Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Paul F Jaeger
Metrics reloaded: recommendations for image analysis validation. Nature methods 21 (2) (2024)
Gary Stephen Collins, Karel G M Moons, Paula Dhiman, Richard D Riley, Andrew L Beam, Ben Van Calster, Marzyeh Ghassemi, Xiaoxuan Liu, Johannes B Reitsma, Maarten van Smeden, Anne-Laure Boulesteix, Jennifer Catherine Louise Camaradou, Leo Anthony Celi, Spiros Denaxas, Alastair Keith Denniston, Ben Glocker, Robert M Golub, Hugh Harvey, Georg Heinze, Michael M Hoffman, Andre Pascal Kengne, Emily Lam, Naomi Lee, Elizabeth W Loder, Lena Maier-Hein, Bilal Akhter Mateen, Melissa Danielle McCradden, Lauren Oakden-Rayner, Johan Ordish, Richard Parnell, Sherri Rose, Karandeep S Singh, Laure Wynants, Patrícia Logullo
TRIPOD+AI statement: updated guidance for reporting clinical prediction models that use regression or machine learning methods. BMJ (Clinical research ed.) 385 (2024)
Lena Maier-Hein, Annika Reinke, Patrick Godau, Minu D Tizabi, Florian Buettner, Evangelia Christodoulou, Ben Glocker, Fabian Isensee, Jens Kleesiek, Michal Kozubek, Mauricio Reyes, Michael A Riegler, Manuel Wiesenfarth, A Emre Kavur, Carole H Sudre, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, Tim Rädsch, Laura Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew B Blaschko, M Jorge Cardoso, Veronika Cheplygina, Beth A Cimini, Gary Stephen Collins, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Robert Haase, Daniel A Hashimoto, Michael M Hoffman, Merel Huisman, Pierre Jannin, Charles E Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Alan Karthikesalingam, Florian Kofler, Dominik T Schneider, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Peter Mattson, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Nasir M Rajpoot, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Maarten van Smeden, Ronald M Summers, Abdel Aziz Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Paul F Jaeger
Metrics reloaded: recommendations for image analysis validation. Nature methods 21 (2) (2024)
Gary Stephen Collins, Karel G M Moons, Paula Dhiman, Richard D Riley, Andrew L Beam, Ben Van Calster, Marzyeh Ghassemi, Xiaoxuan Liu, Johannes B Reitsma, Maarten van Smeden, Anne-Laure Boulesteix, Jennifer Catherine Louise Camaradou, Leo Anthony Celi, Spiros Denaxas, Alastair Keith Denniston, Ben Glocker, Robert M Golub, Hugh Harvey, Georg Heinze, Michael M Hoffman, Andre Pascal Kengne, Emily Lam, Naomi Lee, Elizabeth W Loder, Lena Maier-Hein, Bilal Akhter Mateen, Melissa Danielle McCradden, Lauren Oakden-Rayner, Johan Ordish, Richard Parnell, Sherri Rose, Karandeep S Singh, Laure Wynants, Patrícia Logullo
TRIPOD+AI statement: updated guidance for reporting clinical prediction models that use regression or machine learning methods. BMJ (Clinical research ed.) 385 (2024)
Mehran Karimzadeh, Christopher Arlidge, Ariana Rostami, Mathieu Lupien, Scott V Bratman, Michael M Hoffman
Human papillomavirus integration transforms chromatin to drive oncogenesis. Genome biology 24 (1) (2023)
Mehran Karimzadeh, Christopher Arlidge, Ariana Rostami, Mathieu Lupien, Scott V Bratman, Michael M Hoffman
Human papillomavirus integration transforms chromatin to drive oncogenesis. Genome biology 24 (1) (2023)
Mehran Karimzadeh, Christopher Arlidge, Ariana Rostami, Mathieu Lupien, Scott V Bratman, Michael M Hoffman
Human papillomavirus integration transforms chromatin to drive oncogenesis. Genome biology 24 (1) (2023)
Danielle Denisko, Coby Viner, Michael M Hoffman
Motif elucidation in ChIP-seq datasets with a knockout control. Bioinformatics advances 3 (1) (2023)
Mehran Karimzadeh, Christopher Arlidge, Ariana Rostami, Mathieu Lupien, Scott V Bratman, Michael M Hoffman
Human papillomavirus integration transforms chromatin to drive oncogenesis. Genome biology 24 (1) (2023)
Luis E Abatti, Patricia Lado-Fernández, Linh Huynh, Manuel Collado, Michael M Hoffman, Jennifer A Mitchell
Epigenetic reprogramming of a distal developmental enhancer cluster drives SOX2 overexpression in breast and lung adenocarcinoma. Nucleic acids research (2023)
Yi Nian Niu, Eric G Roberts, Danielle Denisko, Michael M Hoffman
Assessing and assuring interoperability of a genomics file format. Bioinformatics (Oxford, England) 38 (13) (2022)
Mehran Karimzadeh, Michael M Hoffman
Virtual ChIP-seq: predicting transcription factor binding by learning from the transcriptome. Genome biology 23 (1) (2022)
Benjamin J Heil, Michael M Hoffman, Florian Markowetz, Su-In Lee, Casey S Greene, Stephanie C Hicks
Reproducibility standards for machine learning in the life sciences. Nature methods 18 (10) (2021)
Justin M Burgener, Jinfeng Zou, Zhen Zhao, Yangqiao Zheng, Shu Yi Shen, Shao Hui Huang, Sareh Keshavarzi, Wei Xu, Fei-Fei Liu, Geoffrey Liu, John N Waldron, Ilan Weinreb, Anna Spreafico, Lillian L Siu, John R de Almeida, David P Goldstein, Michael M Hoffman, Daniel D De Carvalho, Scott V Bratman
Tumor-Naïve Multimodal Profiling of Circulating Tumor DNA in Head and Neck Squamous Cell Carcinoma. Clinical cancer research : an official journal of the American Association for Cancer Research 27 (15) (2021)
Samantha L Wilson, Gregory P Way, Wout Bittremieux, Jean Paul Armache, Melissa A Haendel, Michael M Hoffman
Sharing biological data: why, when, and how. FEBS letters 595 (7) (2021)
Maxwell W Libbrecht, Rachel C W Chan, Michael M Hoffman
Segmentation and genome annotation algorithms for identifying chromatin state and other genomic patterns. PLoS computational biology 17 (10) (2021)
Jordan A Ramilowski, Chi Wai Yip, Saumya Agrawal, Jen-Chien Chang, Yari Ciani, Ivan V Kulakovskiy, Mickaël Mendez, Jasmine Li Ching Ooi, John F Ouyang, Nick Parkinson, Andreas Petri, Leonie Roos, Jessica Severin, Kayoko Yasuzawa, Imad Abugessaisa, Altuna Akalin, Ivan V Antonov, Erik Arner, Alessandro Bonetti, Hidemasa Bono, Beatrice Borsari, Frank Brombacher, Christopher JF Cameron, Carlo Vittorio Cannistraci, Ryan Cardenas, Melissa Cardon, Howard Chang, Josée Dostie, Luca Ducoli, Alexander Favorov, Alexandre Fort, Diego Garrido, Noa Gil, Juliette Gimenez, Reto Guler, Lusy Handoko, Jayson Harshbarger, Akira Hasegawa, Yuki Hasegawa, Kosuke Hashimoto, Norihito Hayatsu, Peter Heutink, Tetsuro Hirose, Eddie L Imada, Masayoshi Itoh, Bogumil Kaczkowski, Aditi Kanhere, Emily Kawabata, Hideya Kawaji, Tsugumi Kawashima, S Thomas Kelly, Miki Kojima, Naoto Kondo, Haruhiko Koseki, Tsukasa Kouno, Anton Kratz, Mariola Kurowska-Stolarska, Andrew Tae Jun Kwon, Jeffrey Leek, Andreas Lennartsson, Marina Lizio, Fernando López-Redondo, Joachim Luginbühl, Shiori Maeda, Vsevolod J Makeev, Luigi Marchionni, Yulia A Medvedeva, Aki Minoda, Ferenc Müller, Manuel Muñoz-Aguirre, Mitsuyoshi Murata, Hiromi Nishiyori, Kazuhiro R Nitta, Shuhei Noguchi, Yukihiko Noro, Ramil Nurtdinov, Yasushi Okazaki, Valerio Orlando, Denis Paquette, Callum J C Parr, Owen J L Rackham, Patrizia Rizzu, Diego Fernando Sánchez Martinez, Albin Sandelin, Pillay Sanjana, Colin A M Semple, Youtaro Shibayama, Divya M Sivaraman, Takahiro Suzuki, Suzannah C Szumowski, Michihira Tagami, Martin S Taylor, Chikashi Terao, Malte Thodberg, Supat Thongjuea, Vidisha Tripathi, Igor Ulitsky, Roberto Verardo, Ilya E Vorontsov, Chinatsu Yamamoto, Robert S Young, John Kenneth Baillie, Alistair R R Forrest, Roderic Guigó, Michael M Hoffman, Chung Chau Hon, Takeya Kasukawa, Sakari Kauppinen, Juha Kere, Boris Lenhard, Claudio Schneider, Harukazu Suzuki, Ken Yagi, Michiel J L de Hoon, Jay W Shin, Piero Carnici
Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome research 30 (7) (2020)
Benjamin Haibe-Kains, George Alexandru Adam, Ahmed Hosny, Farnoosh Khodakarami, null null, Levi Waldron, Bo Wang, Chris McIntosh, Anna Goldenberg, Anshul Kundaje, Casey S Greene, Tamara Broderick, Michael M Hoffman, Jeffrey T Leek, Keegan Korthauer, Wolfgang Huber, Alvis Brazma, Joelle Pineau, Robert Tibshirani, Trevor Hastie, John P A Ioannidis, John Quackenbush, Hugo J W L Aerts
Transparency and reproducibility in artificial intelligence. Nature 586 (7829) (2020)
Travers Ching, Daniel Scott Himmelstein, Brett K Beaulieu-Jones, Alexandr A Kalinin, Brian T Do, Gregory P Way, Enrico Ferrero, Paul-Michael Agapow, Michael Zietz, Michael M Hoffman, Wei Xie, Gail L Rosen, Benjamin J Lengerich, Johnny Israeli, Jack Lanchantin, Stephen Woloszynek, Anne E Carpenter, Avanti Shrikumar, Jinbo Xu, Evan M Cofer, Christopher A Lavender, Srinivas C Turaga, Amr M Alexandari, Zhiyong Lu, David J Harris, Dave DeCaprio, Yanjun Qi, Anshul Kundaje, Yifan Peng, Laura K Wiley, Marwin H S Segler, Simina M Boca, S Joshua Swamidass, Austin Huang, Anthony Gitter, Casey S Greene
Opportunities and obstacles for deep learning in biology and medicine. Journal of the Royal Society, Interface 15 (141) (2019)
Danielle Denisko, Michael M Hoffman
Classification and interaction in random forests. Proceedings of the National Academy of Sciences of the United States of America 115 (8) (2018)
Davide Chicco, Michael M Hoffman
Genome Informatics 2016. Genome biology 18 (1) (2017)

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Michael M Hoffman