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. 2002 Oct;3(5):398–404. doi: 10.1002/cfg.209

Upstream—News in Genomics

PMCID: PMC2447332  PMID: 18629049

Abstract

This report on the literature spans from May to July, highlighting breakthroughs on several important genomes, including mouse, zebrafish, Fugu and Plasmodium. Recent papers have reported on a mechanism for genome size reduction in Arabidopsis, comparisons and verifications of large-scale protein–protein interaction datasets, developments in RNA interference approaches for mammalian systems and a solidphase peptide tagging method for proteomics.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bentley S. D., Chater K. F., Cerdeño-Tárraga A-M, Challis G. L., Thomson N. R., James K. D., Harris D. E., Quail M. A., Kieser H., Harper D. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature. 2002 May 9;417(6885):141–147. doi: 10.1038/417141a. [DOI] [PubMed] [Google Scholar]
  2. Blumenthal Thomas, Evans Donald, Link Christopher D., Guffanti Alessandro, Lawson Daniel, Thierry-Mieg Jean, Thierry-Mieg Danielle, Chiu Wei Lu, Duke Kyle, Kiraly Moni. A global analysis of Caenorhabditis elegans operons. Nature. 2002 Jun 20;417(6891):851–854. doi: 10.1038/nature00831. [DOI] [PubMed] [Google Scholar]
  3. Brummelkamp Thijn R., Bernards René, Agami Reuven. A system for stable expression of short interfering RNAs in mammalian cells. Science. 2002 Mar 21;296(5567):550–553. doi: 10.1126/science.1068999. [DOI] [PubMed] [Google Scholar]
  4. Devos Katrien M., Brown James K. M., Bennetzen Jeffrey L. Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res. 2002 Jul;12(7):1075–1079. doi: 10.1101/gr.132102. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Gabriel Stacey B., Schaffner Stephen F., Nguyen Huy, Moore Jamie M., Roy Jessica, Blumenstiel Brendan, Higgins John, DeFelice Matthew, Lochner Amy, Faggart Maura. The structure of haplotype blocks in the human genome. Science. 2002 May 23;296(5576):2225–2229. doi: 10.1126/science.1069424. [DOI] [PubMed] [Google Scholar]
  6. Giaever Guri, Chu Angela M., Ni Li, Connelly Carla, Riles Linda, Véronneau Steeve, Dow Sally, Lucau-Danila Ankuta, Anderson Keith, André Bruno. Functional profiling of the Saccharomyces cerevisiae genome. Nature. 2002 Jul 25;418(6896):387–391. doi: 10.1038/nature00935. [DOI] [PubMed] [Google Scholar]
  7. Glöckner Gernot, Eichinger Ludwig, Szafranski Karol, Pachebat Justin A., Bankier Alan T., Dear Paul H., Lehmann Rüdiger, Baumgart Cornelia, Parra Genís, Abril Josep F. Sequence and analysis of chromosome 2 of Dictyostelium discoideum. Nature. 2002 Jul 4;418(6893):79–85. doi: 10.1038/nature00847. [DOI] [PubMed] [Google Scholar]
  8. Kapranov Philipp, Cawley Simon E., Drenkow Jorg, Bekiranov Stefan, Strausberg Robert L., Fodor Stephen P. A., Gingeras Thomas R. Large-scale transcriptional activity in chromosomes 21 and 22. Science. 2002 May 3;296(5569):916–919. doi: 10.1126/science.1068597. [DOI] [PubMed] [Google Scholar]
  9. Kemmeren Patrick, van Berkum Nynke L., Vilo Jaak, Bijma Theo, Donders Rogier, Brazma Alvis, Holstege Frank C. P. Protein interaction verification and functional annotation by integrated analysis of genome-scale data. Mol Cell. 2002 May;9(5):1133–1143. doi: 10.1016/s1097-2765(02)00531-2. [DOI] [PubMed] [Google Scholar]
  10. Lee Nan Sook, Dohjima Taikoh, Bauer Gerhard, Li Haitang, Li Ming-Jie, Ehsani Ali, Salvaterra Paul, Rossi John. Expression of small interfering RNAs targeted against HIV-1 rev transcripts in human cells. Nat Biotechnol. 2002 May;20(5):500–505. doi: 10.1038/nbt0502-500. [DOI] [PubMed] [Google Scholar]
  11. Li Hongwei, Li Wan Xiang, Ding Shou Wei. Induction and suppression of RNA silencing by an animal virus. Science. 2002 May 17;296(5571):1319–1321. doi: 10.1126/science.1070948. [DOI] [PubMed] [Google Scholar]
  12. Maslov Sergei, Sneppen Kim. Specificity and stability in topology of protein networks. Science. 2002 May 3;296(5569):910–913. doi: 10.1126/science.1065103. [DOI] [PubMed] [Google Scholar]
  13. Miyagishi Makoto, Taira Kazunari. U6 promoter-driven siRNAs with four uridine 3' overhangs efficiently suppress targeted gene expression in mammalian cells. Nat Biotechnol. 2002 May;20(5):497–500. doi: 10.1038/nbt0502-497. [DOI] [PubMed] [Google Scholar]
  14. Mural Richard J., Adams Mark D., Myers Eugene W., Smith Hamilton O., Miklos George L. Gabor, Wides Ron, Halpern Aaron, Li Peter W., Sutton Granger G., Nadeau Joe. A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science. 2002 May 31;296(5573):1661–1671. doi: 10.1126/science.1069193. [DOI] [PubMed] [Google Scholar]
  15. Paul Cynthia P., Good Paul D., Winer Ira, Engelke David R. Effective expression of small interfering RNA in human cells. Nat Biotechnol. 2002 May;20(5):505–508. doi: 10.1038/nbt0502-505. [DOI] [PubMed] [Google Scholar]
  16. Rogozin Igor B., Makarova Kira S., Murvai Janos, Czabarka Eva, Wolf Yuri I., Tatusov Roman L., Szekely Laszlo A., Koonin Eugene V. Connected gene neighborhoods in prokaryotic genomes. Nucleic Acids Res. 2002 May 15;30(10):2212–2223. doi: 10.1093/nar/30.10.2212. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Tamas Ivica, Klasson Lisa, Canbäck Björn, Näslund A. Kristina, Eriksson Ann-Sofie, Wernegreen Jennifer J., Sandström Jonas P., Moran Nancy A., Andersson Siv G. E. 50 million years of genomic stasis in endosymbiotic bacteria. Science. 2002 Jun 28;296(5577):2376–2379. doi: 10.1126/science.1071278. [DOI] [PubMed] [Google Scholar]
  18. Thanassi Jane A., Hartman-Neumann Sandra L., Dougherty Thomas J., Dougherty Brian A., Pucci Michael J. Identification of 113 conserved essential genes using a high-throughput gene disruption system in Streptococcus pneumoniae. Nucleic Acids Res. 2002 Jul 15;30(14):3152–3162. doi: 10.1093/nar/gkf418. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Van der Hoeven Rutger, Ronning Catherine, Giovannoni James, Martin Gregory, Tanksley Steven. Deductions about the number, organization, and evolution of genes in the tomato genome based on analysis of a large expressed sequence tag collection and selective genomic sequencing. Plant Cell. 2002 Jul;14(7):1441–1456. doi: 10.1105/tpc.010478. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Watanabe Junichi, Sasaki Masahide, Suzuki Yutaka, Sugano Sumio. Analysis of transcriptomes of human malaria parasite Plasmodium falciparum using full-length enriched library: identification of novel genes and diverse transcription start sites of messenger RNAs. Gene. 2002 May 29;291(1-2):105–113. doi: 10.1016/s0378-1119(02)00552-8. [DOI] [PubMed] [Google Scholar]
  21. Wong Gane Ka-Shu, Wang Jun, Tao Lin, Tan Jun, Zhang JianGuo, Passey Douglas A., Yu Jun. Compositional gradients in Gramineae genes. Genome Res. 2002 Jun;12(6):851–856. doi: 10.1101/gr.189102. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Zhou Huilin, Ranish Jeffrey A., Watts Julian D., Aebersold Ruedi. Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry. Nat Biotechnol. 2002 May;20(5):512–515. doi: 10.1038/nbt0502-512. [DOI] [PubMed] [Google Scholar]
  23. von Mering Christian, Krause Roland, Snel Berend, Cornell Michael, Oliver Stephen G., Fields Stanley, Bork Peer. Comparative assessment of large-scale data sets of protein-protein interactions. Nature. 2002 May 8;417(6887):399–403. doi: 10.1038/nature750. [DOI] [PubMed] [Google Scholar]

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