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LETTER: Evolution of Eukaryotic Transcription: Insights From the Genome of Giardia lamblia
- Aaron A. Best,
- Hilary G. Morrison,
- Andrew G. McArthur,
- Mitchell L. Sogin,
- and Gary J. Olsen
Genome Res. August 2004 14: 1537-1547; doi:10.1101/gr.2256604
...al. 2000 ). Thus, it would appear that this mode of recruitment arose early in the evolution of RNAPI transcription, followed by invention of additional RNAPI transcription factors in separate lineages. TFIIH plays roles in both RNAPII transcription initiation and nucleotide excision repair (NER...
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LETTER: The Role of Lineage-Specific Gene Family Expansion in the Evolution of Eukaryotes
- Olivier Lespinet,
- Yuri I. Wolf,
- Eugene V. Koonin,
- and L. Aravind
Genome Res. July 1, 2002 12: 1048-1059; doi:10.1101/gr.174302
...The Role of Lineage-Specific Gene Family Expansion in the Evolution of Eukaryotes Olivier Lespinet , Yuri I. Wolf , Eugene V. Koonin 1 , and L. Aravind National Center for Biotechnology Information, National Library of Medicine, National...
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LETTER: Genome Evolution at the Genus Level: Comparison of Three Complete Genomes of Hyperthermophilic Archaea
- Odile Lecompte,
- Raymond Ripp,
- Valérie Puzos-Barbe,
- Simone Duprat,
- Roland Heilig,
- Jacques Dietrich,
- Jean-Claude Thierry,
- and Olivier Poch
Genome Res. June 1, 2001 11: 981-993; Published in Advance May 8, 2001, doi:10.1101/gr.165301
...; Koonin et al. 2000 ). This underlines the considerable plasticity in biochemical pathways, with several solutions being independently invented in the course of evolution to achieve essential functions. Even at smaller evolutionary intervals, many individual genes show tree topologies in fundamental...
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LETTER: Eukaryote-specific Domains in Translation Initiation Factors: Implications for Translation Regulation and Evolution of the Translation System
- L. Aravind and
- Eugene V. Koonin
Genome Res. August 1, 2000 10: 1172-1184; doi:10.1101/gr.10.8.1172
...are known or predicted to possess an α-helical structure, which suggests that such domains are easier to invent in the course of evolution than are domains of other structural classes. A previously undetected, conserved region predicted to form an α-helical domain is delineated in the initiation factor eIF4...
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Review: Artificial intelligence and machine learning in cell-free-DNA-based diagnostics
- W.H. Adrian Tsui,
- Spencer C. Ding,
- Peiyong Jiang,
- and Y.M. Dennis Lo
Genome Res. January 2025 35: 1-19; doi:10.1101/gr.278413.123
...truly intelligent behavior (Wooldridge 2021). The explosive increase of computational power in the twenty-first century enabled deep learning, which uses “deep” neural networks (DNNs), to be applied widely (Hoffmann 2022). Because of the analogies to neuronal mechanics in the brain, deep learning is now...
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LETTER: Functional Versatility and Molecular Diversity of the Metabolic Map of Escherichia coli
- Sophia Tsoka and
- Christos A. Ouzounis
Genome Res. September 1, 2001 11: 1503-1510; Published in Advance August 16, 2001, doi:10.1101/gr.187501
...are associated with distinct protein families possibly indicates functional properties that have been invented more than once during evolution. The 548 small-molecule metabolic enzymes were clustered into 405 enzyme families, with 316 single-member families and the remaining 232 enzymes classified into 89...
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ARTICLE: Biosynthesis of Isoprenoids via Mevalonate in Archaea: The Lost Pathway
- Arian Smit and
- Arcady Mushegian
Genome Res. October 1, 2000 10: 1468-1484; doi:10.1101/gr.145600
...the alternative pathway. To understand the evolution of isoprenoid biosynthesis, as well as the mechanism of lipid biosynthesis in archaea, sequence motifs in the known enzymes of the two pathways of isoprenoid biosynthesis were analyzed. New sequence relationships were detected, including similarities between...
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Method: Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome
- Jakob Skou Pedersen,
- Eivind Valen,
- Amhed M. Vargas Velazquez,
- Brian J. Parker,
- Morten Rasmussen,
- Stinus Lindgreen,
- Berit Lilje,
- Desmond J. Tobin,
- Theresa K. Kelly,
- Søren Vang,
- Robin Andersson,
- Peter A. Jones,
- Cindi A. Hoover,
- Alexei Tikhonov,
- Egor Prokhortchouk,
- Edward M. Rubin,
- Albin Sandelin,
- M. Thomas P. Gilbert,
- Anders Krogh,
- Eske Willerslev,
- and Ludovic Orlando
Genome Res. March 2014 24: 454-466; Published in Advance December 3, 2013, doi:10.1101/gr.163592.113
...the quagga zebra, a species that became extinct in the early 20th century (Higuchi et al. 1984). Soon after, the invention of PCR unlocked access to this fragmented and degraded DNA material (Pa¨a¨bo 1989), making it possible to amplify short gene markers of interest and compare their sequence to that from...
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Letter: The origins of apicomplexan sequence innovation
- James Wasmuth,
- Jennifer Daub,
- José Manuel Peregrín-Alvarez,
- Constance A.M. Finney,
- and John Parkinson
Genome Res. July 2009 19: 1202-1213; Published in Advance April 10, 2009, doi:10.1101/gr.083386.108
...) are targeted to the apicoplast. Due to their essential role, many enzymes involved in these pathways are the focus of drug target discovery programs. To develop novel antiparasitic compounds and increase our understanding of apicomplexan biology, several largescale-sequencing projects have been initiated...
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Methods: Ortho-proteogenomics: Multiple proteomes investigation through orthology and a new MS-based protocol
- Sébastien Gallien,
- Emmanuel Perrodou,
- Christine Carapito,
- Caroline Deshayes,
- Jean-Marc Reyrat,
- Alain Van Dorsselaer,
- Olivier Poch,
- Christine Schaeffer,
- and Odile Lecompte
Genome Res. January 2009 19: 128-135; Published in Advance October 27, 2008, doi:10.1101/gr.081901.108
...enzymes: Independent inventions in enzyme evolution . Genome Res. 8 : 779 – 790 . ↵ Gevaert, K. , Goethals, M. , Martens, L. , Van Damme, J. , Staes, A. , Thomas, G.R. , Vandekerckhove, J. ( 2003 ) Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N...

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