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ARTICLE: AAA⁺: A Class of Chaperone-Like ATPases Associated with the Assembly, Operation, and Disassembly of Protein Complexes
- Andrew F. Neuwald,
- L. Aravind,
- John L. Spouge,
- and Eugene V. Koonin
Genome Res. January 1, 1999 9: 27-43; doi:10.1101/gr.9.1.27
...activase. Alignment of these sequences, in light of the structures of the clamp loader δ′ subunit of Escherichia coli DNA polymerase III and the hexamerization component of N -ethylmaleimide-sensitive fusion protein, provides structural and mechanistic insights into these proteins, collectively...
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LETTER: The Evolution of DNA Regulatory Regions for Proteo-Gamma Bacteria by Interspecies Comparisons
- Nikolaus Rajewsky,
- Nicholas D. Socci,
- Martin Zapotocky,
- and Eric D. Siggia
Genome Res. February 1, 2002 12: 298-308; Published in Advance January 13, 2003, doi:10.1101/gr.207502
...and only as a second step discern individual protein binding sites. We thus impose no preconceptions about what aspects of the module are most important (as measured by conservation) to the regulatory net of the cell. Escherichia coli is the most useful species to examine at the moment since it is the best...
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Resource: ProPhylER: A curated online resource for protein function and structure based on evolutionary constraint analyses
- Jonathan Binkley,
- Kalpana Karra,
- Andrew Kirby,
- Midori Hosobuchi,
- Eric A. Stone,
- and Arend Sidow
Genome Res. January 2010 20: 142-154; Published in Advance October 21, 2009, doi:10.1101/gr.097121.109
...), bacteriophage T4 lysozyme (Rennell et al. 1991), and Escherichia coli lactose repressor (Markiewicz et al. 1994; Suckow et al. 1996). A fourth protein, betaglobin, has many known human germline mutations, and clinical descriptions of each mutation’s effect (http://globin.cse.psu.edu/ globin/hbvar/). The fifth...
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Resource: Assemblathon 1: A competitive assessment of de novo short read assembly methods
- Dent Earl,
- Keith Bradnam,
- John St. John,
- Aaron Darling,
- Dawei Lin,
- Joseph Fass,
- Hung On Ken Yu,
- Vince Buffalo,
- Daniel R. Zerbino,
- Mark Diekhans,
- Ngan Nguyen,
- Pramila Nuwantha Ariyaratne,
- Wing-Kin Sung,
- Zemin Ning,
- Matthias Haimel,
- Jared T. Simpson,
- Nuno A. Fonseca,
- İnanç Birol,
- T. Roderick Docking,
- Isaac Y. Ho,
- Daniel S. Rokhsar,
- Rayan Chikhi,
- Dominique Lavenier,
- Guillaume Chapuis,
- Delphine Naquin,
- Nicolas Maillet,
- Michael C. Schatz,
- David R. Kelley,
- Adam M. Phillippy,
- Sergey Koren,
- Shiaw-Pyng Yang,
- Wei Wu,
- Wen-Chi Chou,
- Anuj Srivastava,
- Timothy I. Shaw,
- J. Graham Ruby,
- Peter Skewes-Cox,
- Miguel Betegon,
- Michelle T. Dimon,
- Victor Solovyev,
- Igor Seledtsov,
- Petr Kosarev,
- Denis Vorobyev,
- Ricardo Ramirez-Gonzalez,
- Richard Leggett,
- Dan MacLean,
- Fangfang Xia,
- Ruibang Luo,
- Zhenyu Li,
- Yinlong Xie,
- Binghang Liu,
- Sante Gnerre,
- Iain MacCallum,
- Dariusz Przybylski,
- Filipe J. Ribeiro,
- Shuangye Yin,
- Ted Sharpe,
- Giles Hall,
- Paul J. Kersey,
- Richard Durbin,
- Shaun D. Jackman,
- Jarrod A. Chapman,
- Xiaoqiu Huang,
- Joseph L. DeRisi,
- Mario Caccamo,
- Yingrui Li,
- David B. Jaffe,
- Richard E. Green,
- David Haussler,
- Ian Korf,
- and Benedict Paten
Genome Res. December 2011 21: 2224-2241; Published in Advance September 16, 2011, doi:10.1101/gr.126599.111
.... In addition to generating reads from the targeta1,2 , three copies of an Escherichia coli sequence (gi 312944605) were added to the two haplotype sequences to yield a ;5% bacterial contamination rate. Bacterial sequence was included as an attempt to model the sort of contamination occasionally present in data...
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LETTER: Very small mobile repeated elements in cyanobacterial genomes
- Jeff Elhai,
- Michiko Kato,
- Sarah Cousins,
- Peter Lindblad,
- and José Luis Costa
Genome Res. September 2008 18: 1484-1499; Published in Advance July 3, 2008, doi:10.1101/gr.074336.107
...related cyanobacterium, Synechocystis PCC 6803, and Escherichia coli ( Table 3 ). View this table: In this window In a new window Table 3. Most numerous 24-nt sequences in N. punctiforme Topping the list of repeated sequences in N. punctiforme are two 24-mers contained within multiple CRISPR families...
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LETTER: Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus
- David A. Ray,
- Cedric Feschotte,
- Heidi J.T. Pagan,
- Jeremy D. Smith,
- Ellen J. Pritham,
- Peter Arensburger,
- Peter W. Atkinson,
- and Nancy L. Craig
Genome Res. May 2008 18: 717-728; Published in Advance March 13, 2008, doi:10.1101/gr.071886.107
...substitution hotspots in Escherichia coli . Nature 274 : 775 – 780 . ↵ Demattei, M.V. , Auge-Gouillou, C. , Pollet, N. , Hamelin, M.H. , Meunier-Rotival, M. , Bigot, Y. ( 2000 ) Features of the mammal mar1 transposons in the human, sheep, cow, and mouse s and implications for their evolution . Mamm. Genome 11...
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ARTICLE: Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world
- Minglei Wang,
- Liudmila S. Yafremava,
- Derek Caetano-Anollés,
- Jay E. Mittenthal,
- and Gustavo Caetano-Anollés
Genome Res. November 2007 17: 1572-1585; Published in Advance October 1, 2007, doi:10.1101/gr.6454307
...indicative of a probable common evolutionary origin (they group one or more sequence-related FF). F group FSF with secondary structures that are similarly arranged in 3D space but that may not necessarily be evolutionarily related. The vast majority of F and FSF represent highly successful architectural...
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METHODS: Predicting Deleterious Amino Acid Substitutions
- Pauline C. Ng and
- Steven Henikoff
Genome Res. May 1, 2001 11: 863-874; doi:10.1101/gr.176601
...inducer, LacI no longer binds to DNA, thus allowing the organism to use lactose as an energy source. Positions in the Escherichia coli lac repressor gene were mutated individually to amber nonsense codons ( Markiewicz et al. 1994 ; Suckow et al. 1996 ). In each mutant, nonsense suppressor tRNAs that would...
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PERSPECTIVE: Genomics in C. elegans: So many genes, such a little worm
- LaDeana W. Hillier,
- Alan Coulson,
- John I. Murray,
- Zhirong Bao,
- John E. Sulston,
- and Robert H. Waterston
Genome Res. December 2005 15: 1651-1660; doi:10.1101/gr.3729105
...al. 2000 ; Maeda et al. 2001 ; Kamath and Ahringer 2003 ; Sonnichsen et al. 2005 ), and currently &gt;18,000 Escherichia coli strains have been constructed and have been widely distributed. Initial screens were for easily scored phenotypes such as viability, slow growth, or altered movement and body...
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LETTER: Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin
- Steven M. Johnson,
- Frederick J. Tan,
- Heather L. McCullough,
- Daniel P. Riordan,
- and Andrew Z. Fire
Genome Res. December 2006 16: 1505-1516; Published in Advance October 12, 2006, doi:10.1101/gr.5560806
.... elegans (WS154) was carried out with a local installation of BLAT (ver. 32x1) using default parameters ( Kent 2002 ). Of the 312,492 sequence reads, 283,745 (90.8%) showed significant matches to C. elegans assembly WS154. Additionally, there were 1919 sequences (0.6%) matching the Escherichia coli K12...

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