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Method: Autoencoders for genomic variation analysis
- Margarita Geleta,
- Daniel Mas Montserrat,
- Xavier Giro-i-Nieto,
- and Alexander G. Ioannidis
Genome Res. February 2026 36: 348-360; Published in Advance January 20, 2026, doi:10.1101/gr.280086.124
..., Barcelona 08034, Spain; 3Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, California 94720, USA; 4Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95060, USA; 5Institute for Computational and Mathematical Engineering...
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In memoriam: C. Thomas Caskey (1938–2022)
- Richard A. Gibbs,
- Aravinda Chakravarti,
- Evan E. Eichler,
- Eric D. Green,
- Richard M. Myers,
- Anne C. Ferguson-Smith,
- Kateryna D. Makova,
- and Hillary E. Sussman
Genome Res. March 2022 32: vii-viii; Published in Advance February 17, 2022, doi:10.1101/gr.276658.122
...decades earlier.As an internationalist, Tom both encouraged engagement with scientists of other nations and promoted projects that would build bridges with the USA. He worked closely with Genome Canada and other Canadian agencies to advance genomics. At the same time, in Texas, he spurred the governor...
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Perspective: A vision for ubiquitous sequencing
- Yaniv Erlich
Genome Res. October 2015 25: 1411-1416; doi:10.1101/gr.191692.115
...@cs.columbia.edu Abstract Genomics has recently celebrated reaching the $1000 genome milestone, making affordable DNA sequencing a reality. With this goal successfully completed, the next goal of the sequencing revolution can be sequencing sensors—miniaturized sequencing devices that are manufactured for real...
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Perspective: Half dozen of one, six billion of the other: What can small- and large-scale molecular systems biology learn from one another?
- Ian A. Mellis and
- Arjun Raj
Genome Res. October 2015 25: 1466-1472; doi:10.1101/gr.190579.115
...Half dozen of one, six billion of the other: What can small- and large-scale molecular systems biology learn from one another? Ian A. Mellis 1 and Arjun Raj 2 1Perelman School of Medicine, Genomics and Computational Biology Graduate Group, University...
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Perspective: Functional transcriptomics in the post-ENCODE era
- Jonathan M. Mudge,
- Adam Frankish,
- and Jennifer Harrow
Genome Res. December 2013 23: 1961-1973; Published in Advance October 30, 2013, doi:10.1101/gr.161315.113
...Functional transcriptomics in the post-ENCODE era Jonathan M. Mudge 1 , Adam Frankish and Jennifer Harrow Department of Informatics, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom Abstract The last decade has seen...
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Perspective: Phylogenomics of primates and their ancestral populations
- Adam Siepel
Genome Res. November 2009 19: 1929-1941; Published in Advance October 3, 2009, doi:10.1101/gr.084228.108
...sequence data will put within reach the grand vision of comprehensive genomic resources for primates that was first articulated nearly a decade ago (McConkey andVarki 2000; Boffelli et al. 2003; Enard and Paabo 2004; Goodman et al. 2005). Perhaps the most informative approach available for comparative...
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Commentary: One hundred fifty years without Darwin are enough!
- Francisco J. Ayala
Genome Res. May 2009 19: 693-699; doi:10.1101/gr.084285.108
...Ayala, F.J FJ Ayala F Ayala Ayala, FJ FranciscoJ Ayala Ayala Francisco J. F.J. Ayala Ayala Francisco J Ayala Francisco J, Ayala Ayala, Francisco J Francisco Ayala Francisco Francisco J Ayala, F genome;19/5/693 1088-9051 10.1101/gr.084285.108 One hundred fifty years without Darwin are enough...
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PERSPECTIVE: Comparing the human and chimpanzee genomes: Searching for needles in a haystack
- Ajit Varki and
- Tasha K. Altheide
Genome Res. December 2005 15: 1746-1758; doi:10.1101/gr.3737405
...requires the involvement and cooperation of scientists from a wide variety of fields, far beyond the scope of genomics. Thus, our comments are focused not so much on genomics per se, but are rather addressed to the broader scientific community of “ users.” Sequencing of the chimpanzee Less than a decade...
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COMMENTARY: Contemplating the End of the Beginning
- Francis S. Collins
Genome Res. May 1, 2001 11: 641-643; doi:10.1101/gr.1898
...Genome Sequencing Consortium 2001 ; Venter et al. 2001 ). Although much celebration and press attention had surrounded the earlier announcement in June 2000 of the coverage of the vast majority of the human sequence in working draft form, the publications in February 2001 carried with them the kind...
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COMMENTARY: Race, Ethnicity, and Genomics: Social Classifications as Proxies of Biological Heterogeneity
- Morris W. Foster and
- Richard R. Sharp
Genome Res. June 1, 2002 12: 844-850; doi:10.1101/gr.99202
...Race, Ethnicity, and Genomics: Social Classifications as Proxies of Biological Heterogeneity Morris W. Foster 1 , 3 and Richard R. Sharp 2 1Department of Anthropology, University of Oklahoma, Norman, Oklahoma 73019, USA; Oklahoma Medical Research...

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