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Eugene W. Myers

Max Planck Society

DOI: 10.1093/gigascience/giab100
GigaScience ·
2022
DENTIST-using long reads for closing assembly gaps at high accuracy.
Arne Ludwig, Martin Pippel, Eugene W. Myers, Michael Hiller
Computer science
Closing (real estate)
Pipeline (software)
DOI: 10.1073/pnas.2115635118
Proceedings of the National Academy of Sciences of the United States of America ·
2022
The Earth BioGenome Project 2020: Starting the clock
Harris A. Lewin, Stephen Richards, Erez Lieberman Aiden, Miguel L. Allende, John M. Archibald, Miklós Bálint, Katharine Barker, Bridget Baumgartner, Katherine Belov, Giorgio Bertorelle, Mark Blaxter, Jing Cai, Nicolette D. Caperello, Keith Carlson, Juan Carlos Castilla-Rubio, Shu-Miaw Chaw, Lei Chen, Anna K. Childers, Jonathan Coddington, Dalia Amor Conde, Montserrat Corominas, Keith A. Crandall, Andrew J. Crawford, Federica DiPalma, Richard Durbin, ThankGod E. Ebenezer, Scott V. Edwards, Olivier Fedrigo, Paul Flicek, Giulio Formenti, Richard A. Gibbs, M. Thomas P. Gilbert, Melissa M. Goldstein, Jennifer A. Marshall Graves, Henry T. Greely, Igor V. Grigoriev, Kevin J. Hackett, Neil Hall, David Haussler, Kristofer M. Helgen, Carolyn J. Hogg, Sachiko Isobe, Kjetill S. Jakobsen, Axel Janke, Erich D. Jarvis, Warren E. Johnson, Steven J. M. Jones, Elinor K. Karlsson, Paul J. Kersey, J. H. Kim, W. John Kress, Shigehiro Kuraku, Mara K. N. Lawniczak, Jim Leebens-Mack, Xueyan Li, Kerstin Lindblad-Toh, Xin Liu, Jose V. Lopez, Tomas Marques-Bonet, Sophie Mazard, Jonna A. K. Mazet, Camila J. Mazzoni, Eugene W. Myers, Rachel J. O’Neill, Sadye Paez, Hyun Park, Gene E. Robinson, Cristina Roquet, Oliver A. Ryder, Jamal S. M. Sabir, H. B. Shaffer, Timothy M. Shank, Jacob S. Sherkow, Pamela S. Soltis, Boping Tang, Leho Tedersoo
Earth (classical element)
Astrobiology
DOI: 10.1073/pnas.2115639118
Proceedings of the National Academy of Sciences of the United States of America ·
2022
Standards recommendations for the Earth BioGenome Project
Mara K. N. Lawniczak, Richard Durbin, Paul Flicek, Kerstin Lindblad-Toh, Xiaofeng Wei, John M. Archibald, William J. Baker, Katherine Belov, Mark L. Blaxter, Tomas Marques-Bonet, Anna K. Childers, Jonathan Coddington, Keith A. Crandall, Andrew J. Crawford, Robert P. Davey, Federica Di Palma, Qi Fang, Wilfried Haerty, Neil Hall, Katharina J. Hoff, Kerstin Howe, Erich D. Jarvis, Warren E. Johnson, Rebecca N. Johnson, Paul J. Kersey, Xiangjun Liu, Jose V. Lopez, Eugene W. Myers, O. Vinnere Pettersson, Catherine A. Hill, Monica F. Poelchau, Kim D. Pruitt, Arang Rhie, Juan Carlos Castilla-Rubio, Sunil Kumar Sahu, Nicholas A. Salmon, Pamela S. Soltis, David Swarbreck, Françoise Thibaud-Nissen, Sibo Wang, Jill L. Wegrzyn, Guoije Zhang, He Zhang, Harris A. Lewin, Stephen Richards
Flexibility (engineering)
Informatics
Computer science
DOI: 10.1101/2021.07.16.452324
bioRxiv ·
2021
Cited 6 times
Merfin: improved variant filtering and polishing via k-mer validation
Giulio Formenti, Arang Rhie, Brian P. Walenz, Françoise Thibaud-Nissen, Kishwar Shafin, Sergey Koren, Eugene W. Myers, Erich D. Jarvis, Adam M. Phillippy
Materials science
Artificial intelligence
DOI: 10.1111/mec.16027
Molecular Ecology ·
2021
Cited 5 times
Large-scale Genome sampling reveals unique immunity and metabolic adaptations in Bats.
Diana D Moreno Santillán, Tanya M. Lama, Yocelyn T Gutierrez Guerrero, Alexis Brown, Paul Donat, Huabin Zhao, Stephen J. Rossiter, Laurel R Yohe, Joshua H T Potter, Emma C. Teeling, Sonja C. Vernes, Kalina T. J. Davies, Eugene W. Myers, Graham M. Hughes, Zixia Huang, Federico G. Hoffmann, Angelique Corthals, David A. Ray, Liliana M. Dávalos
Evolutionary biology
Ecology
Metagenomics
DOI: 10.1101/2021.05.26.445798
bioRxiv ·
2021
Cited 72 times
The complete sequence of a human genome
Sergey Nurk, Sergey Koren, Arang Rhie, Rautiainen M, Andrey Bzikadze, Alla Mikheenko, Mitchell R. Vollger, Nicolas Altemose, Lev Uralsky, Ariel Gershman, Sergey Aganezov, Hoyt Sj, Mark Diekhans, Glennis A. Logsdon, Michael Alonge, Stylianos E. Antonarakis, Borchers M, Gerry Bouffard, Shelise Brooks, Caldas Gv, Hwei-Ling Cheng, Chen-Shan Chin, William Chow, de Lima Lg, Philip C. Dishuck, Richard Durbin, Tatiana Dvorkina, Ian T. Fiddes, Giulio Formenti, Robert S. Fulton, Arkarachai Fungtammasan, Erik Garrison, P. G. S. Grady, Tina A. Graves-Lindsay, Ira M. Hall, Nancy F. Hansen, Gabrielle A. Hartley, Marina Haukness, Kerstin Howe, Michael W. Hunkapiller, Chirag Jain, Miten Jain, Erich D. Jarvis, Peter Kerpedjiev, Melanie Kirsche, Mikhail Kolmogorov, Jonas Korlach, Milinn Kremitzki, Huiyan Li, Valerie Maduro, Tobias Marschall, Ann McCartney, Jennifer McDaniel, Danny E. Miller, Jim C. Mullikin, Eugene W. Myers, Nathan D. Olson, Benedict Paten, Paul Peluso, Pavel A. Pevzner, David Porubsky, Tamara A. Potapova, Evgeny I. Rogaev, Jill A. Rosenfeld, Steven L. Salzberg, Valerie A. Schneider, Fritz J. Sedlazeck, Kishwar Shafin, Colin J. Shew, Alaina Shumate, Ying Sims, Smit Afa, Daniela C. Soto, Ivan Sović, Jessica M. Storer, Aaron M. Streets, Beth A. Sullivan, Françoise Thibaud-Nissen, James Torrance, Justin Wagner, Brian P. Walenz, Aaron M. Wenger, Wood Jmd, Chunlin Xiao, Stephanie M Yan, Alice Young, Samantha Zarate, Urvashi Surti, Rajiv C. McCoy, Megan Y. Dennis, Ivan Alexandrov, Jennifer L. Gerton, Rachel J. O’Neill, Winston Timp, Justin M. Zook, Michael C. Schatz, Evan E. Eichler, Karen H. Miga, Adam M. Phillippy
Genome
Biology
Human genome
DOI: 10.1093/bioinformatics/btaa865
Bioinformatics ·
2021
Finding long tandem repeats in long noisy reads.
Shinichi Morishita, Kazuki Ichikawa, Eugene W. Myers
Computer science
Genome
Computational biology
DOI: 10.1186/s13059-021-02336-9
Genome Biology ·
2021
Cited 10 times
Complete vertebrate mitogenomes reveal widespread repeats and gene duplications.
Giulio Formenti, Arang Rhie, Jennifer Balacco, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, Samara Brown, Marco Rosario Capodiferro, Farooq O. Al-Ajli, Roberto Ambrosini, Peter Houde, Sergey Koren, Karen Oliver, Michelle Smith, Jason Skelton, Emma Betteridge, Jale Dolucan, Craig Corton, Iliana Bista, James Torrance, Alan Tracey, Jonathan Wood, Marcela Uliano-Silva, Kerstin Howe, Shane A. McCarthy, Sylke Winkler, Woori Kwak, Jonas Korlach, Arkarachai Fungtammasan, Daniel Fordham, Vania Costa, Simon Mayes, Matteo Chiara, David S. Horner, Eugene W. Myers, Richard Durbin, Alessandro Achilli, Edward L. Braun, Adam M. Phillippy, Erich D. Jarvis
Genetics
Gene duplication
Genome evolution
DOI: 10.1101/2021.03.08.434304
Social Science Research Network ·
2021
Expansion-Assisted Iterative-FISH defines lateral hypothalamus spatio-molecular organization
Yuhan Wang, Mark Eddison, Greg M. Fleishman, Martin Weigert, Shengjin Xu, Fredrick E. Henry, Tian Li Wang, Andrew L. Lemire, Uwe Schmidt, Hui Yang, Konrad Rokicki, Cristian Goina, Karel Svoboda, Eugene W. Myers, Stephan Saalfeld, Wyatt Korff, Scott M. Sternson, Paul W. Tillberg
Biology
Fish <Actinopterygii>
Computational biology
DOI: 10.1101/2021.03.08.434304
bioRxiv ·
2021
Expansion-Assisted Iterative-FISH defines lateral hypothalamus spatio-molecular organization
Yuhan Wang, Mark Eddison, Greg M. Fleishman, Martin Weigert, Shengjin Xu, Fredrick E. Henry, Tian Li Wang, Andrew L. Lemire, Uwe Schmidt, Hui Yang, Konrad Rokicki, Cristian Goina, Karel Svoboda, Eugene W. Myers, Stephan Saalfeld, Wyatt Korff, Scott M. Sternson, Paul W. Tillberg
Biology
Fish <Actinopterygii>
Evolutionary biology
DOI: 10.1101/2021.02.08.430189
bioRxiv ·
2021
Bidirectional neuronal migration coordinates retinal morphogenesis by preventing spatial competition
Mauricio Rocha-Martins, Kretzschmar J, Nerli E, Martin Weigert, Jaroslav Icha, Eugene W. Myers, Caren Norden
Biology
Neuroscience
Morphogenesis
DOI: 10.1126/sciadv.abd9230
Science Advances ·
2020
Cited 8 times
Rapid and ongoing evolution of repetitive sequence structures in human centromeres.
Yuta Suzuki, Eugene W. Myers, Shinichi Morishita
Genome
Genetics
Chromosome
DOI: 10.1101/2020.11.19.386565
bioRxiv ·
2020
Cited 3 times
Interactive design of GPU-accelerated Image Data Flow Graphs and cross-platform deployment using multi-lingual code generation
Robert Haase, Akanksha Jain, Stéphane Rigaud, Daniela Vorkel, Pradeep Rajasekhar, Suckert T, Talley J. Lambert, Juan Nunez-Iglesias, Daniel P. Poole, Pavel Tomancak, Eugene W. Myers
Code (set theory)
CUDA
Scene graph
DOI: 10.5281/zenodo.4276076
·
2020
Supplementary Material for Interactive design of GPU-accelerated Image Data Flow Graphs and cross-platform deployment using multi-lingual code generation
Robert Haase, Akanskha Jain, Stéphane Rigaud, Daniela Vorkel, Pradeep Rajasekhar, Theresa Suckert, Talley J. Lambert, Juan Nunez-Iglesias, Daniel P. Poole, Pavel Tomancak, Eugene W. Myers
DOI: 10.1038/s41586-020-2845-0
Nature ·
2020
Cited 41 times
Contrasting signatures of genomic divergence during sympatric speciation
Andreas F. Kautt, Claudius F. Kratochwil, Alexander Nater, Gonzalo Machado-Schiaffino, Melisa Olave, Frederico Henning, Julián Torres-Dowdall, Andreas Härer, C. Darrin Hulsey, Paolo Franchini, Martin Pippel, Eugene W. Myers, Axel Meyer
Divergence (linguistics)
Genetic divergence
Allopatric speciation
DOI: 10.1364/oe.401933
Optics Express ·
2020
Cited 14 times
Practical sensorless aberration estimation for 3D microscopy with deep learning.
Debayan Saha, Uwe Schmidt, Qinrong Zhang, Aurélien Barbotin, Qi Hu, Na Ji, Martin J. Booth, Martin Weigert, Eugene W. Myers
Microscope
Convolutional neural network
Iterative reconstruction
DOI: 10.6084/m9.figshare.12844652.v2
·
2020
Supplementary document for Practical sensorless aberration estimation for 3D microscopy with deep learning - 4780517.pdf
Martin Weigert, Uwe Schmidt, Qinrong Zhang, Aurélien Barbotin, Qi Hu, Na Ji, Martin J. Booth, Eugene W. Myers, Debayan Saha
Computer science
Artificial intelligence
Deep learning
DOI: 10.1038/s41586-020-2486-3
Nature ·
2020
Cited 68 times
Six reference-quality genomes reveal evolution of bat adaptations
David Jebb, Zixia Huang, Martin Pippel, Graham M. Hughes, Ksenia Lavrichenko, Paolo Devanna, Sylke Winkler, Lars S. Jermiin, Emilia C. Skirmuntt, Aris Katzourakis, Lucy Burkitt-Gray, David A. Ray, Kevin A.M. Sullivan, Juliana G. Roscito, Bogdan M. Kirilenko, Liliana M. Dávalos, Angelique Corthals, Megan L. Power, Gareth Jones, Roger D. Ransome, Dina K. N. Dechmann, Andrea G. Locatelli, Sébastien J. Puechmaille, Olivier Fedrigo, Erich D. Jarvis, Michael Hiller, Sonja C. Vernes, Eugene W. Myers, Emma C. Teeling
Genetics
Adaptation (eye)
Computational biology
DOI: 10.1101/2020.06.30.177956
bioRxiv ·
2020
Cited 7 times
Complete vertebrate mitogenomes reveal widespread gene duplications and repeats
Giulio Formenti, Arang Rhie, Jennifer Balacco, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, Samara Brown, Marco Rosario Capodiferro, Farooq O. Al-Ajli, Roberto Ambrosini, Peter Houde, Sergey Koren, Karen Oliver, Michelle Smith, Jason Skelton, Emma Betteridge, Jale Dolucan, Craig Corton, Iliana Bista, James Torrance, Alan Tracey, Jonathan Wood, Marcela Uliano-Silva, Kerstin Howe, Shane A. McCarthy, Sylke Winkler, Woori Kwak, Jonas Korlach, Arkarachai Fungtammasan, Daniel Fordham, Vania Costa, Simon Mayes, Matteo Chiara, David S. Horner, Eugene W. Myers, Richard Durbin, Alessandro Achilli, Edward L. Braun, Adam M. Phillippy, Erich D. Jarvis
Genetics
Evolutionary biology
Gene duplication
DOI: 10.1101/2020.06.11.146704
bioRxiv ·
2020
Bridging scales in scattering tissues via multifocal two-photon microscopy
David Chen, Fabián Segovia-Miranda, Walker N, José Ignacio Valenzuela, Marino Zerial, Eugene W. Myers
Microscopy
Physics
Optics
MAG: 3033829912
arXiv: Image and Video Processing ·
2020
Fast and accurate aberration estimation from 3D bead images using convolutional neural networks
Debayan Saha, Uwe Schmidt, Qinrong Zhang, Aurélien Barbotin, Qi Hu, Na Ji, Martin J. Booth, Martin Weigert, Eugene W. Myers
Computer science
Artificial intelligence
Convolutional neural network
DOI: 10.1364/oe.401933
arXiv: Image and Video Processing ·
2020
Practical sensorless aberration estimation for 3D microscopy with deep learning
Debayan Saha, Uwe Schmidt, Qinrong Zhang, Aurélien Barbotin, Qi Hu, Na Ji, Martin J. Booth, Martin Weigert, Eugene W. Myers
Pattern recognition (psychology)
DOI: 10.1038/s41592-019-0650-1
Nature Methods ·
2020
Cited 36 times
CLIJ: GPU-accelerated image processing for everyone.
Robert Haase, Loic Royer, Peter Steinbach, Deborah Schmidt, Alexandr Dibrov, Uwe Schmidt, Martin Weigert, Nicola Maghelli, Pavel Tomancak, Florian Jug, Eugene W. Myers
CUDA
General-purpose computing on graphics processing units
Artificial intelligence
DOI: 10.7554/elife.49542
eLife ·
2019
Cited 15 times
Rod nuclear architecture determines contrast transmission of the retina and behavioral sensitivity in mice.
Kaushikaram Subramanian, Martin Weigert, Oliver Borsch, Heike Petzold, Alfonso Garcia-Ulloa, Eugene W. Myers, Marius Ader, Irina Solovei, Moritz Kreysing
Biophysics
Chemistry
Biology
DOI: 10.7554/elife.49542.sa2
eLife ·
2019
Author response: Rod nuclear architecture determines contrast transmission of the retina and behavioral sensitivity in mice
Kaushikaram Subramanian, Martin Weigert, Oliver Borsch, Heike Petzold, Alfonso Garcia-Ulloa, Eugene W. Myers, Marius Ader, Irina Solovei, Moritz Kreysing
Sensitivity (control systems)
Retina
Biophysics