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Resource: Streamlined spatial and environmental expression signatures characterize the minimalist duckweed Wolffia australiana
- Tom Denyer,
- Pin-Jou Wu,
- Kelly Colt,
- Bradley W. Abramson,
- Zhili Pang,
- Pavel Solansky,
- Allen Mamerto,
- Tatsuya Nobori,
- Joseph R. Ecker,
- Eric Lam,
- Todd P. Michael,
- and Marja C.P. Timmermans
Genome Res. July 2024 34: 1106-1120; Published in Advance July 1, 2024, doi:10.1101/gr.279091.124
...phases of the cell cycle show generally broad expression in cells across the atlas, suggesting that a daughter-to-mother state transition is not explained easily by cell cycle activity (Supplemental Data Set S11). Indeed, cell cycle–related genes are not prominent among DEGs for any particular cluster...
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Research: Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling
- Edward S. Rice,
- Satomi Kohno,
- John St. John,
- Son Pham,
- Jonathan Howard,
- Liana F. Lareau,
- Brendan L. O'Connell,
- Glenn Hickey,
- Joel Armstrong,
- Alden Deran,
- Ian Fiddes,
- Roy N. Platt II,
- Cathy Gresham,
- Fiona McCarthy,
- Colin Kern,
- David Haan,
- Tan Phan,
- Carl Schmidt,
- Jeremy R. Sanford,
- David A. Ray,
- Benedict Paten,
- Louis J. Guillette, Jr.,
- and Richard E. Green
Genome Res. May 2017 27: 686-696; Published in Advance January 30, 2017, doi:10.1101/gr.213595.116
...of Biology, St. Cloud State University, St. Cloud, Minnesota 56301, USA; 3Driver Group, LLC, San Francisco, California 94158, USA; 4BioTuring, Incorporated, San Diego, California 92121, USA; 5Department of Biochemistry, Stanford University, Stanford, California 94305, USA; 6California Institute...
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Research: Parallel evolution of transcriptome architecture during genome reorganization
- Sung Ho Yoon,
- David J. Reiss,
- J. Christopher Bare,
- Dan Tenenbaum,
- Min Pan,
- Joseph Slagel,
- Robert L. Moritz,
- Sujung Lim,
- Murray Hackett,
- Angeli Lal Menon,
- Michael W.W. Adams,
- Adam Barnebey,
- Steven M. Yannone,
- John A. Leigh,
- and Nitin S. Baliga
Genome Res. November 2011 21: 1892-1904; Published in Advance July 12, 2011, doi:10.1101/gr.122218.111
...organisms, the six cas genes located directly adjacent to the cmr genes were conditionally regulated during growth (Fig. 3B). We speculate that this growth/physiologic state-associated preparedness against anticipated viral attack is a reflection of a Table 1. Summary of , transcriptome architecture...
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Methods: Inferring genomic flux in bacteria
- Xavier Didelot,
- Aaron Darling,
- and Daniel Falush
Genome Res. February 2009 19: 306-317; Published in Advance November 17, 2008, doi:10.1101/gr.082263.108
...flux. The rate changes identified by our method are associated with microbial lifestyle changes such as transitions from generalist to host-restricted pathogen lifestyles. We have made a software implementation of the algorithm with a graphical interface freely available from http...
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LETTER: Rapid comparative genomic analysis for clinical microbiology: The Francisella tularensis paradigm
- Bernard La Scola,
- Khalid Elkarkouri,
- Wenjun Li,
- Tara Wahab,
- Ghislain Fournous,
- Jean-Marc Rolain,
- Silpak Biswas,
- Michel Drancourt,
- Catherine Robert,
- Stéphane Audic,
- Sven Löfdahl,
- and Didier Raoult
Genome Res. May 2008 18: 742-750; Published in Advance April 11, 2008, doi:10.1101/gr.071266.107
...the assembled contigs obtained in the Rickettsia pyrosequencing run with the 3-kb PCR product that frames the gyrA gene of the URFtCIPR strain, two contigs of 176 bp and 101 bp contained the gyrA sequence and the point mutation associated with quinolone resistance (C to T transition at position 524 of gyr...
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LETTER: How Does Replication-Associated Mutational Pressure Influence Amino Acid Composition of Proteins?
- Pawel Mackiewicz,
- Agnieszka Gierlik,
- Maria Kowalczuk,
- Miroslaw R. Dudek,
- and Stanislaw Cebrat
Genome Res. May 1, 1999 9: 409-416; doi:10.1101/gr.9.5.409
...and Karlin 1998 ). One of the accepted hypotheses states that the potential cause of asymmetry is deamination of methylated cytosines, which leads to thymines. Some investigators believe that this type of substitution differentiates between sense and antisense strands of coding sequences, and transcription...

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