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ORCIDEugene W. Myers
Gene Myers
Person information
- affiliation: Max Planck Institute of Molecular Cell Biology and Genetics
- affiliation: Howard Hughes Medical Institute, Janelia Farm Research Campus
- affiliation: University of California, Berkeley, Department of Electrical Engineering and Computer Sciences
- award (2004): Max Planck Research Award
- award (2001): Paris Kanellakis Award
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2020 – today
- 2023
[j59]Marcela Uliano-Silva
, João Gabriel R. N. Ferreira, Ksenia Krasheninnikova, Mark L. Blaxter, Nova Mieszkowska, Neil Hall, Peter Holland, Richard Durbin, Thomas Richards, Paul J. Kersey, Peter Hollingsworth, Willie Wilson, Alex Twyford, Ester Gaya, Mara Lawniczak, Owen Lewis, Gavin Broad, Fergal Martin, Michelle Hart, Ian Barnes, Giulio Formenti, Linelle Abueg, James W. Torrance, Eugene W. Myers, Shane A. McCarthy:
MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads. BMC Bioinform. 24(1): 288 (2023)- [c65]Gene Myers:
Merging Sorted Lists of Similar Strings. CPM 2023: 22:1-22:15 - [c64]Kira Vinogradova, Gene Myers:
Local Interpretable Model-Agnostic Explanations for Multitarget Image Regression. xAI (Late-breaking Work, Demos, Doctoral Consortium) 2023: 47-52 - 2022
- [c63]Kira Vinogradova, Eugene W. Myers:
Estimation of Optical Aberrations in 3D Microscopic Bioimages. ICFSP 2022: 97-103 - [c62]Yoshihiko Suzuki, Gene Myers:
Accurate k-mer Classification Using Read Profiles. WABI 2022: 10:1-10:20 - [i12]Gene Myers:
Merging Sorted Lists of Similar Strings. CoRR abs/2208.09351 (2022) - [i11]Kira Vinogradova, Eugene W. Myers:
Estimation of Optical Aberrations in 3D Microscopic Bioimages. CoRR abs/2209.07911 (2022) - 2021
- [j58]Shinichi Morishita, Kazuki Ichikawa, Eugene W. Myers:
Finding long tandem repeats in long noisy reads. Bioinform. 37(5): 612-621 (2021) - 2020
- [c61]Kira Vinogradova, Alexandr Dibrov, Gene Myers:
Towards Interpretable Semantic Segmentation via Gradient-Weighted Class Activation Mapping (Student Abstract). AAAI 2020: 13943-13944 - [c60]Coleman Broaddus, Alexander Krull, Martin Weigert, Uwe Schmidt, Gene Myers:
Removing Structured Noise with Self-Supervised Blind-Spot Networks. ISBI 2020: 159-163 - [c59]Martin Weigert, Uwe Schmidt, Robert Haase, Ko Sugawara, Gene Myers:
Star-convex Polyhedra for 3D Object Detection and Segmentation in Microscopy. WACV 2020: 3655-3662 - [i10]Kira Vinogradova, Alexandr Dibrov, Gene Myers:
Towards Interpretable Semantic Segmentation via Gradient-weighted Class Activation Mapping. CoRR abs/2002.11434 (2020) - [i9]Debayan Saha, Uwe Schmidt, Qinrong Zhang, Aurelien Barbotin, Qi Hu, Na Ji, Martin J. Booth, Martin Weigert, Eugene W. Myers:
Fast and accurate aberration estimation from 3D bead images using convolutional neural networks. CoRR abs/2006.01804 (2020)
2010 – 2019
- 2019
- [i8]Martin Weigert, Uwe Schmidt, Robert Haase, Ko Sugawara, Gene Myers:
Star-convex Polyhedra for 3D Object Detection and Segmentation in Microscopy. CoRR abs/1908.03636 (2019) - 2018
- [j57]Markus A. Grohme, Siegfried Schloissnig, Andrei Rozanski, Martin Pippel, George R. Young, Sylke Winkler, Holger Brandl, Ian Henry, Andreas Dahl, Sean Powell, Michael Hiller, Eugene W. Myers, Jochen C. Rink:
The genome of Schmidtea mediterranea and the evolution of core cellular mechanisms. Nat. 554(7690): 56-61 (2018) - [j56]Martin Weigert, Kaushikaram Subramanian, Sebastian T. Bundschuh, Eugene W. Myers, Moritz Kreysing:
Biobeam - Multiplexed wave-optical simulations of light-sheet microscopy. PLoS Comput. Biol. 14(4) (2018) - [c58]Uwe Schmidt, Martin Weigert, Coleman Broaddus, Gene Myers:
Cell Detection with Star-Convex Polygons. MICCAI (2) 2018: 265-273 - [i7]Uwe Schmidt, Martin Weigert, Coleman Broaddus, Gene Myers:
Cell Detection with Star-convex Polygons. CoRR abs/1806.03535 (2018) - 2017
- [j55]Corinna Blasse, Stephan Saalfeld, Raphaël Etournay, Andreas Sagner, Suzanne Eaton, Eugene W. Myers:
PreMosa: extracting 2D surfaces from 3D microscopy mosaics. Bioinform. 33(16): 2563-2569 (2017) - [c57]Markus Rempfler, Jan-Hendrik Lange, Florian Jug, Corinna Blasse, Eugene W. Myers, Bjoern H. Menze, Bjoern Andres:
Efficient Algorithms for Moral Lineage Tracing. ICCV 2017: 4705-4714 - [c56]Dmitrij Schlesinger, Florian Jug, Gene Myers, Carsten Rother, Dagmar Kainmueller:
Crowd sourcing image segmentation with iaSTAPLE. ISBI 2017: 401-405 - [c55]Martin Weigert, Loïc Royer, Florian Jug, Gene Myers:
Isotropic Reconstruction of 3D Fluorescence Microscopy Images Using Convolutional Neural Networks. MICCAI (2) 2017: 126-134 - [i6]Markus Rempfler, Jan-Hendrik Lange, Florian Jug, Corinna Blasse, Eugene W. Myers, Bjoern H. Menze, Bjoern Andres:
Efficient Algorithms for Moral Lineage Tracing. CoRR abs/1702.04111 (2017) - [i5]Dmitrij Schlesinger, Florian Jug, Gene Myers, Carsten Rother, Dagmar Kainmüller:
Crowd Sourcing Image Segmentation with iaSTAPLE. CoRR abs/1702.06461 (2017) - [i4]Martin Weigert, Loïc Royer, Florian Jug, Gene Myers:
Isotropic reconstruction of 3D fluorescence microscopy images using convolutional neural networks. CoRR abs/1704.01510 (2017) - 2016
- [j54]Eugene W. Myers:
A history of DNA sequence assembly. it Inf. Technol. 58(3): 126-132 (2016) - [c54]David L. Richmond, Dagmar Kainmueller, Michael Ying Yang, Eugene W. Myers, Carsten Rother:
Mapping Auto-context Decision Forests to Deep ConvNets for Semantic Segmentation. BMVC 2016 - [c53]Florian Jug, Evgeny Levinkov, Corinna Blasse, Eugene W. Myers, Bjoern Andres:
Moral Lineage Tracing. CVPR 2016: 5926-5935 - [c52]Richard Grunzke, Florian Jug, Bernd Schuller, René Jäkel, Gene Myers, Wolfgang E. Nagel:
Seamless HPC Integration of Data-Intensive KNIME Workflows via UNICORE. Euro-Par Workshops 2016: 480-491 - [i3]Gene Myers, Mihai Pop, Knut Reinert, Tandy J. Warnow:
Next Generation Sequencing (Dagstuhl Seminar 16351). Dagstuhl Reports 6(8): 91-130 (2016) - 2015
- [j53]Yinan Wan, Fuhui Long, Lei Qu, Hang Xiao, Michael Hawrylycz, Eugene W. Myers, Hanchuan Peng:
BlastNeuron for Automated Comparison, Retrieval and Clustering of 3D Neuron Morphologies. Neuroinformatics 13(4): 487-499 (2015) - [c51]David L. Richmond, Dagmar Kainmueller, Ben Glocker, Carsten Rother, Gene Myers:
Uncertainty-Driven Forest Predictors for Vertebra Localization and Segmentation. MICCAI (1) 2015: 653-660 - [i2]David L. Richmond, Dagmar Kainmueller, Michael Ying Yang, Eugene W. Myers, Carsten Rother:
Relating Cascaded Random Forests to Deep Convolutional Neural Networks for Semantic Segmentation. CoRR abs/1507.07583 (2015) - [i1]Florian Jug, Evgeny Levinkov, Corinna Blasse, Eugene W. Myers, Bjoern Andres:
Moral Lineage Tracing. CoRR abs/1511.05512 (2015) - 2014
- [c50]Florian Jug, Tobias Pietzsch, Dagmar Kainmüller, Jan Funke, Matthias Kaiser, Erik van Nimwegen, Carsten Rother, Gene Myers:
Optimal Joint Segmentation and Tracking of Escherichia Coli in the Mother Machine. BAMBI 2014: 25-36 - [c49]Dagmar Kainmueller, Florian Jug, Carsten Rother, Gene Myers:
Active Graph Matching for Automatic Joint Segmentation and Annotation of C. elegans. MICCAI (1) 2014: 81-88 - [c48]Gene Myers:
Efficient Local Alignment Discovery amongst Noisy Long Reads. WABI 2014: 52-67 - 2013
- [j52]Fernando Amat, Eugene W. Myers, Philipp J. Keller:
Fast and robust optical flow for time-lapse microscopy using super-voxels. Bioinform. 29(3): 373-380 (2013) - [j51]Saket Navlakha, Parvez Ahammad, Eugene W. Myers:
Unsupervised segmentation of noisy electron microscopy images using salient watersheds and region merging. BMC Bioinform. 14: 294 (2013) - [c47]Gene Myers:
Discrete Methods for Image Analysis Applied to Molecular Biology. CPM 2013: 12 - [p1]Gene Myers:
What's Behind Blast. Models and Algorithms for Genome Evolution 2013: 3-15 - 2012
- [j50]Nathan G. Clack, Daniel H. O'Connor, Daniel Huber, Leopoldo T. Petreanu, Andrew Hires, Simon Peron, Karel Svoboda, Eugene W. Myers:
Automated Tracking of Whiskers in Videos of Head Fixed Rodents. PLoS Comput. Biol. 8(7) (2012) - 2011
- [j49]Hanchuan Peng, Fuhui Long, Gene Myers:
Automatic 3D neuron tracing using all-path pruning. Bioinform. 27(13): 239-247 (2011) - [j48]Lei Qu, Fuhui Long, Xiao Liu, Stuart K. Kim, Eugene W. Myers, Hanchuan Peng:
Simultaneous recognition and segmentation of cells: application in C.elegans. Bioinform. 27(20): 2895-2902 (2011) - [j47]Jun Xie, Ting Zhao, Tzumin Lee, Eugene W. Myers, Hanchuan Peng:
Anisotropic path searching for automatic neuron reconstruction. Medical Image Anal. 15(5): 680-689 (2011) - [j46]Hanchuan Peng, Fuhui Long, Ting Zhao, Eugene W. Myers:
Proof-editing is the Bottleneck Of 3D Neuron Reconstruction: The Problem and Solutions. Neuroinformatics 9(2-3): 103-105 (2011) - [j45]Ting Zhao, Jun Xie, Fernando Amat, Nathan G. Clack, Parvez Ahammad, Hanchuan Peng, Fuhui Long, Eugene W. Myers:
Automated Reconstruction of Neuronal Morphology Based on Local Geometrical and Global Structural Models. Neuroinformatics 9(2-3): 247-261 (2011) - [c46]Min Liu, Hanchuan Peng, Amit K. Roy-Chowdhury, Eugene W. Myers:
3D Neuron Tip Detection in Volumetric Microscopy Images. BIBM 2011: 366-371 - 2010
- [j44]Steffen Jaensch, Markus Decker, Anthony A. Hyman, Eugene W. Myers:
Automated tracking and analysis of centrosomes in early Caenorhabditis elegans embryos. Bioinform. 26(12): 13-20 (2010) - [j43]Laxmi Parida, Gene Myers:
APBC 2010. The Eighth Asia Pacific Bioinformatics Conference Bangalore, India, 18-21 January 2010. BMC Bioinform. 11(S-1): 0 (2010) - [j42]Eldar Giladi, John Healy, Gene Myers, Chris Hart, Philipp Kapranov, Doron Lipson, Steve Roels, Edward C. Thayer, Stan Letovsky:
Error Tolerant Indexing and Alignment of Short Reads with Covering Template Families. J. Comput. Biol. 17(10): 1397-1411 (2010) - [c45]Jun Xie, Ting Zhao, Tzumin Lee, Eugene W. Myers, Hanchuan Peng:
Automatic Neuron Tracing in Volumetric Microscopy Images with Anisotropic Path Searching. MICCAI (2) 2010: 472-479
2000 – 2009
- 2009
- [j41]Hanchuan Peng, Fuhui Long, Eugene W. Myers:
VANO: a volume-object image annotation system. Bioinform. 25(5): 695-697 (2009) - [j40]Marie-France Sagot, B. J. Morrison McKay, Gene Myers:
ISMB/ECCB 2009 Stockholm. Bioinform. 25(12): 1570-1573 (2009) - 2008
- [j39]Hanchuan Peng, Fuhui Long, Xiao Liu, Stuart K. Kim, Eugene W. Myers:
Straightening Caenorhabditis elegans images. Bioinform. 24(2): 234-242 (2008) - [c44]Fuhui Long, Hanchuan Peng, Xiao Liu, Stuart K. Kim, Gene Myers:
Automatic Recognition of Cells (ARC) for 3D Images of C. elegans. RECOMB 2008: 128-139 - 2007
- [j38]Gad M. Landau, Eugene W. Myers, Michal Ziv-Ukelson:
Two algorithms for LCS Consecutive Suffix Alignment. J. Comput. Syst. Sci. 73(7): 1095-1117 (2007) - [c43]Hanchuan Peng, Fuhui Long, Eugene W. Myers:
Straightening Worm Images. ISBI 2007: 292-295 - [c42]Fuhui Long, Hanchuan Peng, Eugene W. Myers:
Automatic Segmentation of Nuclei in 3d Microscopy Images of C.Elegans. ISBI 2007: 536-539 - [c41]Paul Medvedev, Konstantinos Georgiou, Gene Myers, Michael Brudno:
Computability of Models for Sequence Assembly. WABI 2007: 289-301 - 2006
- [j37]Kim R. Rasmussen, Jens Stoye, Eugene W. Myers:
Efficient q-Gram Filters for Finding All epsilon-Matches over a Given Length. J. Comput. Biol. 13(2): 296-308 (2006) - [c40]Gene Myers:
Invited Talk: Imaging-Based Systems Biology. German Conference on Bioinformatics 2006: 92 - [c39]Gene Myers:
Imaging-Based Systems Biology. HiPC 2006: 5 - [c38]Hanchuan Peng, Fuhui Long, Michael B. Eisen, Eugene W. Myers:
Clustering gene expression patterns of fly embryos. ISBI 2006: 1144-1147 - [c37]Tien-ho Lin, Eugene W. Myers, Eric P. Xing:
Interpreting anonymous DNA samples from mass disasters - probabilistic forensic inference using genetic markers. ISMB (Supplement of Bioinformatics) 2006: 298-306 - 2005
- [c36]Eugene W. Myers:
The fragment assembly string graph. ECCB/JBI 2005: 85 - [c35]Robert C. Edgar, Eugene W. Myers:
PILER: identification and classification of genomic repeats. ISMB (Supplement of Bioinformatics) 2005: 152-158 - [c34]Roded Sharan, Eugene W. Myers:
A motif-based framework for recognizing sequence families. ISMB (Supplement of Bioinformatics) 2005: 387-393 - [c33]Kim R. Rasmussen, Jens Stoye, Eugene W. Myers:
Efficient q-Gram Filters for Finding All epsilon-Matches over a Given Length. RECOMB 2005: 189-203 - [e3]Rita Casadio, Gene Myers:
Algorithms in Bioinformatics, 5th International Workshop, WABI 2005, Mallorca, Spain, October 3-6, 2005, Proceedings. Lecture Notes in Computer Science 3692, Springer 2005, ISBN 3-540-29008-7 [contents] - 2004
- [c32]Gad M. Landau, Eugene W. Myers, Michal Ziv-Ukelson:
Two Algorithms for LCS Consecutive Suffix Alignment. CPM 2004: 173-193 - [c31]Eugene W. Myers:
Whole Genome Sequencing, Comparative Genomics, and Systems Biology. CSB 2004: 4 - [c30]Hanchuan Peng, Eugene W. Myers:
Comparing in situ mRNA expression patterns of drosophila embryos. RECOMB 2004: 157-166 - 2003
- [j36]Gene Myers, Richard Durbin:
A Table-Driven, Full-Sensitivity Similarity Search Algorithm. J. Comput. Biol. 10(2): 103-117 (2003) - [c29]Gene Myers:
Advances in DNA Sequencing. PCK50 2003: 9 - [c28]Gene Myers:
ISMB 2003 - Editorial. ISMB (Supplement of Bioinformatics) 2003: 1-2 - 2002
- [j35]Daniel H. Huson, Knut Reinert, Eugene W. Myers:
The greedy path-merging algorithm for contig scaffolding. J. ACM 49(5): 603-615 (2002) - [c27]Gene Myers:
The Assembly of the Human and Mouse Genomes. COCOON 2002: 1 - [c26]Gene Myers, Richard Durbin:
Invited Lecture - Accelerating Smith-Waterman Searches. WABI 2002: 331-342 - [e2]Gene Myers, Sridhar Hannenhalli, David Sankoff, Sorin Istrail, Pavel A. Pevzner, Michael S. Waterman:
Proceedings of the Sixth Annual International Conference on Computational Biology, RECOMB 2002, Washington, DC, USA, April 18-21, 2002. ACM 2002, ISBN 1-58113-498-3 [contents] - 2001
- [c25]Daniel H. Huson, Knut Reinert, Saul A. Kravitz, Karin A. Remington, Arthur L. Delcher, Ian M. Dew, Michael Flanigan, Aaron L. Halpern, Zhongwu Lai, Clark M. Mobarry, Granger G. Sutton, Eugene W. Myers:
Design of a compartmentalized shotgun assembler for the human genome. ISMB (Supplement of Bioinformatics) 2001: 132-139 - [c24]Daniel H. Huson, Knut Reinert, Eugene W. Myers:
The greedy path-merging algorithm for sequence assembly. RECOMB 2001: 157-163 - [c23]Gene Myers:
Comparing sequence scaffolds. RECOMB 2001: 224-230 - [c22]Daniel H. Huson, Aaron L. Halpern, Zhongwu Lai, Eugene W. Myers, Knut Reinert, Granger G. Sutton:
Comparing Assemblies Using Fragments and Mate-Pairs. WABI 2001: 294-306 - 2000
- [c21]Gene Myers:
The whole genome assembly of Drosophila. SODA 2000: 753
1990 – 1999
- 1999
- [j34]Gene Myers:
Whole-genome DNA sequencing. Comput. Sci. Eng. 1(3): 33-43 (1999) - [j33]Gene Myers:
A Fast Bit-Vector Algorithm for Approximate String Matching Based on Dynamic Programming. J. ACM 46(3): 395-415 (1999) - [c20]Gene Myers:
A Whole Genome Assembler for Drosophila. German Conference on Bioinformatics 1999: 44 - [c19]Gene Myers:
A Dataset Generator for Whole Genome Shotgun Sequencing. ISMB 1999: 202-210 - [c18]Eric L. Anson, Eugene W. Myers:
Algorithms for whole genome shotgun sequencing. RECOMB 1999: 1-9 - [c17]Gene Myers:
Progress toward the whole-genome shotgun sequencing of Drosophila. RECOMB 1999: 279 - 1998
- [j32]Samuel Levy, L. Compagnoni, Eugene W. Myers, Gary D. Stormo:
Xlandscape: the graphical display of word frequencies in sequences. Bioinform. 14(1): 74-80 (1998) - [j31]Marie-France Sagot, Eugene W. Myers:
Identifying Satellites and Periodic Repetitions in Biological Sequences. J. Comput. Biol. 5(3): 539-553 (1998) - [j30]Gad M. Landau, Eugene W. Myers, Jeanette P. Schmidt:
Incremental String Comparison. SIAM J. Comput. 27(2): 557-582 (1998) - [c16]Gene Myers:
A Fast Bit-Vector Algorithm for Approximate String Matching Based on Dynamic Programming. CPM 1998: 1-13 - [c15]Eugene W. Myers, Paulo Oliva, Katia S. Guimarães:
Reporting Exact and Approximate Regular Expression Matches. CPM 1998: 91-103 - [c14]Marie-France Sagot, Eugene W. Myers:
Identifying satellites in nucleic acid sequences. RECOMB 1998: 234-242 - 1997
- [j29]Eric L. Anson, Eugene W. Myers:
ReAligner: A Program for Refining DNA Sequence Multi-Alignments. J. Comput. Biol. 4(3): 369-383 (1997) - [j28]Mudita Jain, Eugene W. Myers:
Algorithms for Computing and Integrating Physical Maps Using Unique Probes. J. Comput. Biol. 4(4): 449-466 (1997) - [c13]Stefan Kurtz, Gene Myers:
Estimating the Probability of Approximate Matches. CPM 1997: 52-64 - [c12]Eric L. Anson, Eugene W. Myers:
ReAligner: a program for refining DNA sequence multi-alignments. RECOMB 1997: 9-16 - [c11]Mudita Jain, Eugene W. Myers:
Algorithms for computing and integrating physical maps using unique probes. RECOMB 1997: 151-161 - [c10]Gene Myers, Sanford Selznick, Zheng Zhang, Webb Miller:
Progressive multiple alignment with constraints. RECOMB 1997: 220-225 - 1996
- [j27]Sun Wu, Udi Manber, Eugene W. Myers:
A Subquadratic Algorithm for Approximate Limited Expression Matching. Algorithmica 15(1): 50-67 (1996) - [j26]Gene Myers, Sanford Selznick, Zheng Zhang, Webb Miller:
Progressive Multiple Alignment with Constraints. J. Comput. Biol. 3(4): 563-572 (1996) - [j25]Sampath Kannan, Eugene W. Myers:
An Algorithm for Locating Nonoverlapping Regions of Maximum Alignment Score. SIAM J. Comput. 25(3): 648-662 (1996) - [e1]Daniel S. Hirschberg, Eugene W. Myers:
Combinatorial Pattern Matching, 7th Annual Symposium, CPM 96, Laguna Beach, California, USA, June 10-12, 1996, Proceedings. Lecture Notes in Computer Science 1075, Springer 1996, ISBN 3-540-61258-0 [contents] - 1995
- [j24]Eugene W. Myers:
Guest Editor's Foreword: Special Issue on Computational Molecular Biology. Algorithmica 13(1/2): 1-6 (1995) - [j23]John D. Kececioglu, Eugene W. Myers:
Combinatiorial Algorithms for DNA Sequence Assembly. Algorithmica 13(1/2): 7-51 (1995) - [j22]James R. Knight, Eugene W. Myers:
Super-Pattern Matching. Algorithmica 13(1/2): 211-243 (1995) - [j21]James R. Knight, Eugene W. Myers:
Approximate Regular Expression Pattern Matching with Concave Gap Penalties. Algorithmica 14(1): 85-121 (1995) - [j20]Gene Myers:
Approximately Matching Context-Free Languages. Inf. Process. Lett. 54(2): 85-92 (1995) - [j19]Sun Wu, Udi Manber, Eugene W. Myers:
A Subquadratic Algorithm for Approximate Regular Expression Matching. J. Algorithms 19(3): 346-360 (1995) - [j18]Mudita Jain, Eugene W. Myers:
A Note on Scoring Clones Given a Probe Ordering. J. Comput. Biol. 2(1): 33-37 (1995) - [j17]Eugene W. Myers:
Toward Simplifying and Accurately Formulating Fragment Assembly. J. Comput. Biol. 2(2): 275-290 (1995) - [c9]Gene Myers, Webb Miller:
Chaining Multiple-Alignment Fragments in Sub-Quadratic Time. SODA 1995: 38-47 - 1994
- [j16]