My functional genomics journal watch - year 2002 [ this week | 2004 Jul-Dec | 2004 Jan-Jun | 2003 Jul-Dec | 2003 Jan-Jun | 2002 | 2001 | 2000 | 1999 | 1998 ]

General
Genome
   Anopheles gambiae
   Arabidopsis thaliana
   Aspergillus fumigatus
   Brucella melitensis
   Brucella suis
   Chlorobium tepidum TLS
   Ciona intestinalis
   Dictyostelium discoideum
   Drosophila Melanogaster/ fruit fly
   Fugu rubripes
   Fusobacterium nucleatum
   Homo Sapiens/ Human
   Methanosarcina acetivorans
   Mus Musculus/ Mouse
   Mycoplasma penetrans
   Oryza sativa L./ Rice
   Plasmodium falciparum
   Ralstonia solanacearum
   Schizosaccharomyces pombe/ fission yeast
   Shewanella oneidensis
   Streptomyces coelicolor
   Thermoanaerobacter tengcongensis
Comparative Genomics
Network/pathway reconstruction and analysis
Metabolomics
Population Genomics/Evolutionary Genomics
Database
Applications
Pharmacogenomics
Single Nucleotide Polymorphisms (SNPs) & haplotyping (typing, validation and mapping)
System Biology
Techniques & Tools
Ethical, Legal and Social issues		 Can't find the functional genomics article published in 2002 in my site? 
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General

  1. Gee H. Genomics: Return of a little squirt. Nature. 2002 Dec 19;420(6917):755-6. [PubMed]
  2. Pennisi E. Genome Institute Wrestles Mightily With Its Future. Science 2002 Dec; 298: 1694-1695. [PubMed]
  3. Sica JM. Genomics and proteomics: the next generation of health care. Empl Benefits J. 2002 Dec;27(4):18-21. [PubMed]
  4. Haulica I. From molecular genetics to functional genomics and physiome. J Cell Mol Med. 2002 Oct-Dec;6(4):648-52. [PubMed]
  5. Wakeland E, Wandstrat A. Analyzing genomes: current realities and future possibilities. Curr Opin Immunol. 2002 Oct;14(5):622. [PubMed]
  6. Gerlai R. Phenomics: fiction or the future? Trends Neurosci. 2002 Oct;25(10):506. [PubMed]
  7. Goffeau A. Greed takes over 'our' yeast genome sequence. Biochem Biophys Res Comm. 2002 Sep 20; 297: 161-162. [PubMed]
  8. Grunenfelder B, Winzeler EA. Treasures and traps in genome-wide data sets: case examples from yeast. Nat Rev Genet. 2002 Sep;3(9):653-61. [PubMed]
  9. Quinn-Senger KE, Ramachandran R, Rininger JA, Kelly KM, Lewin DA. Staking out novelty on the genomic frontier. Curr Opin Chem Biol. 2002 Aug;6(4):418-26. [PubMed]
  10. Lorentz CP, Wieben ED, Tefferi A, Whiteman DA, Dewald GW. Primer on medical genomics part I: History of genetics and sequencing of the human genome. Mayo Clin Proc. 2002 Aug;77(8):773-82. [PubMed]
  11. After the gold-rush. Nature. 2002 Jul 11;418(6894):111. [PubMed]
  12. Rabinowicz PD, Scahidanandam R. Genomics: more than the sum of the parts. Genome Res. 2002 Jul;12(7):1015-6. [PubMed]
  13. Petsko GA. No place like Ome. Genome Biol. 2002 Jul; 3:1010. [PubMed]
  14. Montgomery ND. Functional genomics: A rose by another name. Genesis. 2002 Jul;33(3):140. [PubMed]
  15. Yao T. Bioinformatics for the genomic sciences and towards systems biology. Japanese activities in the post-genome era. Prog Biophys Mol Biol. 2002 Jul;80(1-2):23. [PubMed]
  16. Knight J, Abbott A. Mouse genetics: Full house. Nature. 2002 Jun 20;417(6891):785-6. [PubMed]
  17. Genomics and taxonomy for all. Nature. 2002 Jun 6;417(6889):573. [PubMed]
  18. Joyce EA, Chan K, Salama NR, Falkow S. Redefining bacterial populations: a post-genomic reformation. Nat Rev Genet. 2002 Jun;3(6):462-73. [PubMed]
  19. Baillie DL. Genomes in motion. Genome Res. 2002 Jun;12(6):843. [PubMed]
  20. Schaechter M, Ingraham JL. What limits genomics, proteomics, transcriptomics? Int Microbiol. 2002 Jun;5(2):51-2. [PubMed]
  21. Daniel H, Daniel H. Genomics and proteomics: importance for the future of nutrition research. Br J Nutr. 2002 May;87 Suppl 2:305-11. [PubMed]
  22. Blagosklonny MV, Pardee AB. Conceptual biology: Unearthing the gems. Nature. 2002 Mar 28;416(6879):373. [PubMed]
  23. Aldhous P. Postgenomics: Harvard's melting pot.  Nature. 2002 Mar 21;416(6878):256-7. [PubMed]
  24. Newmark PA, Alvarado AS. Not your father's planarian: a classic model enters the era of functional genomics. Nat Rev Genet. 2002 Mar;3(3):210-9. [PubMed]
  25. Ward DC, White DC. The new 'omics era. Curr Opin Biotechnol. 2002 Feb 1, 13:11-13 [PubMed]
  26. Ooijkaas L. Enzymes enter the field of functional genomics. Trends Biotechnol. 2002 Feb;20(2):88. [PubMed]
  27. Mitchell-Olds T, Clauss MJ. Plant evolutionary genomics. Curr Opin Plant Biol. 2002 Feb;5(1):74-9. [PubMed]
  28. Oliver SG. Functional genomics: lessons from yeast. Philos Trans R Soc Lond B Biol Sci. 2002 Jan 29;357(1417):17-23. [PubMed]
  29. Brussow H, Hendrix RW. Phage Genomics. Small Is Beautiful. Cell. 2002 Jan 11;108(1):13-16. [PubMed]
  30. Turkewitz AP, Orias E, Kapler G. Functional genomics: the coming of age for Tetrahymena thermophila. Trends Genet. 2002 Jan 1;18(1):35-40. [PubMed]
  31. Brett D, Pospisil H, Valcarcel J, Reich J, Bork P. Alternative splicing and genome complexity. Nat Genet. 2002 Jan; 30:29-30. [PubMed]

Genome

  1. Sidow A. Sequence first. Ask questions later. Cell. 2002 Oct 4;111(1):13. [PubMed]
  2. Cyranoski D. Chimpanzee genome: Almost human. Nature. 2002 Aug 29;418(6901):910-2. [PubMed]
  3. Rust AG, Mongin E, Birney E. Genome annotation techniques: new approaches and challenges. Drug Discov Today. 2002 May 6;7(11):S70-S76. [PubMed]
  4. Saha S, Sparks AB, Rago C, Akmaev V, Wang CJ, Vogelstein B, Kinzler KW, Velculescu VE. Using the transcriptome to annotate the genome. Nat Biotechnol. 2002 May;20(5):508-512. [PubMed][web supplement]
  5. Mardis E, McPherson J, Martienssen R, Wilson RK, McCombie WR. What is Finished, and Why Does it Matter. Genome Res. 2002 May;12(5):669-71. [PubMed]
  6. Kemmeren P, van Berkum NL, Vilo J, Bijma T, Donders R, Brazma A, Holstege FC. Protein Interaction Verification and Functional Annotation by Integrated Analysis of Genome-Scale Data. Mol Cell. 2002 May; 9:1133-1143. [PubMed][web supplement]
  7. Myers EW, Sutton GG, Smith HO, Adams MD, Venter JC. On the sequencing and assembly of the human genome. Proc Natl Acad Sci U S A 2002 Apr 2;99(7):4145-6. [PubMed][pdf]
  8. Mullet JE, Klein RR, Klein PE. Sorghum bicolor - an important species for comparative grass genomics and a source of beneficial genes for agriculture. Curr Opin Plant Biol. 2002 Apr;5(2):118-21. [PubMed]
  9. Grivet L, Arruda P. Sugarcane genomics: depicting the complex genome of an important tropical crop. Curr Opin Plant Biol. 2002 Apr;5(2):122-7. [PubMed]
  10. Barnes S. Comparing Arabidopsis to other flowering plants. Curr Opin Plant Biol. 2002 Apr;5(2):128-34. [PubMed]
  11. Osterlund MT, Paterson AH. Applied plant genomics: the secret is integration. Curr Opin Plant Biol. 2002 Apr;5(2):141-5. [PubMed]
  12. Mayer K, Mewes HW. How can we deliver the large plant genomes? Strategies and perspectives. Curr Opin Plant Biol. 2002 Apr;5(2):173-7. [PubMed]
  13. Butler D. Geneticists get steamed up over public access to rice genome. Nature. 2002 Mar 14;416(6877):111-2. [PubMed]
  14. Moran NA. Microbial minimalism. Genome reduction in bacterial pathogens. Cell. 2002 Mar 8;108(5):583-6. [PubMed]
  15. Tammi MT. Separation of nearly identical repeats in shotgun assemblies using defined nucleotide positions, DNPs. Bioinformatics 2002 Mar; 18: 379-388. [PubMed]
  16. Enserink M. Microbial genomics. TIGR begins assault on the anthrax genome. Science. 2002 Feb 22;295(5559):1442-3. [PubMed]
  17. The HGP: end of phase 1. Nat Genet. 2002 Feb;30(2):125. [PubMed]
  18. Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES. ARACHNE: A Whole-Genome Shotgun Assembler. Genome Res. 2002 Jan;12(1):177-89. [PubMed]

Anopheles gambiae

  1. Special issue on Anopheles gambiae Genome (mosquito). Science 2002 Oct 4; 298 (A lot of articles!)

Arabidopsis thaliana

  1. Seki M, Narusaka M, Kamiya A, Ishida J, Satou M, Sakurai T, Nakajima M, Enju A, Akiyama K, Oono Y, Muramatsu M, Hayashizaki Y, Kawai J, Carninci P, Itoh M, Ishii Y, Arakawa T, Shibata K, Shinagawa A, Shinozaki K. Functional Annotation of a Full-Length Arabidopsis cDNA Collection.  Science 2002 Apr 5; 296:141-145. [PubMed][web supplement]

Aspergillus fumigatus

  1. Denning DW, Anderson MJ, Turner G, Latge JP, Bennett JW. Sequencing the Aspergillus fumigatus genome. Lancet Infect Dis. 2002 Apr 1;2(4):251-253. [PubMed]

Brucella melitensis

  1. DelVecchio VG, Kapatral V, Redkar RJ, Patra G, Mujer C, Los T, Ivanova N, Anderson I, Bhattacharyya A, Lykidis A, Reznik G, Jablonski L, Larsen N, D'Souza M, Bernal A,  Mazur M, Goltsman E, Selkov E, Elzer PH, Hagius S, O'Callaghan D, Letesson JJ, Haselkorn R, Kyrpides N, Overbeek R. The genome sequence of the facultative intracellular pathogen Brucella melitensis.  Proc Natl Acad Sci U S A. 2002 Jan 8;99(1):443-448. [PubMed][pdf][web supplement]

Brucella suis

  1. Paulsen IT, Seshadri R, Nelson KE, Eisen JA, Heidelberg JF, Read TD, Dodson RJ, Umayam L, Brinkac LM, Beanan MJ, Daugherty SC, Deboy RT, Durkin AS, Kolonay JF, Madupu R, Nelson WC, Ayodeji B, Kraul M, Shetty J, Malek J, Van Aken SE, Riedmuller S, Tettelin H, Gill SR, White O, Salzberg SL, Hoover DL, Lindler LE, Halling SM, Boyle SM, Fraser CM. The Brucellasuis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc Natl Acad Sci U S A. 2002 Oct 1;99(20):13148-13153. [PubMed]

Chlorobium tepidum TLS

  1. Eisen JA, Nelson KE, Paulsen IT, Heidelberg JF, Wu M, Dodson RJ, Deboy R, Gwinn ML, Nelson WC, Haft DH, Hickey EK, Peterson JD, Durkin AS, Kolonay JL, Yang F, Holt I, Umayam LA, Mason T, Brenner M, Shea TP, Parksey D, Nierman WC, Feldblyum TV, Hansen CL, Craven MB, Radune D, Vamathevan J, Khouri H, White O, Gruber TM, Ketchum KA, Venter JC, Tettelin H, Bryant DA, Fraser CM. The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium. Proc Natl Acad Sci U S A. 2002 Jul 9;99(14):9509-9514. [PubMed][pdf]

Ciona intestinalis

  1. Pennisi E. Comparative genomics. Tunicate genome shows a little backbone. Science. 2002 Dec 13;298(5601):2111-2. [PubMed]
  2. Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, Davidson B, Di Gregorio A, Gelpke M, Goodstein DM, Harafuji N, Hastings KE, Ho I, Hotta K, Huang W, Kawashima T, Lemaire P, Martinez D, Meinertzhagen IA, Necula S, Nonaka M, Putnam N, Rash S, Saiga H, Satake M, Terry A, Yamada L, Wang HG, Awazu S, Azumi K, Boore J, Branno M, Chin-Bow S, DeSantis R, Doyle S, Francino P, Keys DN, Haga S, Hayashi H, Hino K, Imai KS, Inaba K, Kano S, Kobayashi K, Kobayashi M, Lee BI, Makabe KW, Manohar C, Matassi G, Medina M, Mochizuki Y, Mount S, Morishita T, Miura S, Nakayama A, Nishizaka S, Nomoto H, Ohta F, Oishi K, Rigoutsos I, Sano M, Sasaki A, Sasakura Y, Shoguchi E, Shin-i T, Spagnuolo A, Stainier D, Suzuki MM, Tassy O, Takatori N, Tokuoka M, Yagi K, Yoshizaki F, Wada S, Zhang C, Hyatt PD, Larimer F, Detter C, Doggett N, Glavina T, Hawkins T, Richardson P, Lucas S, Kohara Y, Levine M, Satoh N, Rokhsar DS. The Draft Genome of Ciona intestinalis: Insights into Chordate and Vertebrate Origins. Science 2002 Dec 13; 298:2157-2167 [PubMed][web supplement]

Dictyostelium discoideum

  1. Gunter C. Genome sequencing: Stick it in the family album. Nature. 2002 Jul 4;418(6893):30. [PubMed]
  2. Glockner G, Eichinger L, Szafranski K, Pachebat JA, Bankier AT, Dear PH, Lehmann R, Baumgart C, Parra G, Abril JF, Guigo R, Kumpf K, Tunggal B, Cox E, Quail MA, Platzer M, Rosenthal A, Noegel AA, Barrell BG, Rajandream MA, Williams JG, Kay RR, Kuspa A, Gibbs R, Sucgang R, Muzny D, Desany B, Zeng K, Zhu B, De Jong P, Dingermann T, Gerisch G, Philippsen P, Schleicher M, Schuster SC, Winckler T. Sequence and analysis of chromosome 2 of Dictyostelium discoideum. Nature. 2002 Jul 4;418(6893):79-85. [PubMed]

Drosophila Melanogaster/ fluit fly

  1. Misra S., et al. Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biol. 2002 Dec; 12: [PubMed][pdf]
  2. Bergman CM., et al. Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome. Genome Biol. 2002 Dec; 12: [PubMed][pdf]
  3. Celniker SE., et al. Finishing a whole-genome shotgun: Release 3 of the Drosophila melanogaster euchromatic genome sequences. Genome Biol. 2002 Dec; 12: [PubMed][pdf]
  4. Rizzon C, Marais G, Gouy M, Biemont C. Recombination Rate and the Distribution of Transposable Elements in the Drosophila melanogaster Genome. Genome Res. 2002 Mar;12(3):400-7. [PubMed]
  5. Peter A, Schottler P, Werner M, Beinert N, Dowe G, Burkert P, Mourkioti F, Dentzer L, He Y, Deak P, Benos PV, Gatt MK, Murphy L, Harris D, Barrell B, Ferraz C, Vidal S, Brun C, Demaille J, Cadieu E, Dreano S, Gloux S, Lelaure V, Mottier S, Galibert F, Borkova D, Minana B, Kafatos FC, Bolshakov S, Siden-Kiamos I, Papagiannakis G, Spanos L, Louis C, Madueno E, de Pablos B, Modolell J, Bucheton A, Callister D, Campbell L, Henderson NS, McMillan PJ, Salles C, Tait E, Valenti P, Saunders RD, Billaud A, Pachter L, Klapper R, Janning W, Glover DM, Ashburner M, Bellen HJ, Jackle H, Schafer U. Mapping and identification of essential gene functions on the X chromosome of Drosophila. EMBO Reports 2002 Jan;3: 34-38. [PubMed]

Fugu rubripes

  1. Aparicio S, Chapman J, Stupka E, Putnam N, Chia JM, Dehal P, Christoffels A, Rash S, Hoon S, Smit AF, Sollewijn Gelpke MD, Roach J, Oh T, Ho IY, Wong M, Detter C, Verhoef F, Predki P, Tay A, Lucas S, Richardson P, Smith SF, Clark MS, Edwards YJ, Doggett N, Zharkikh A, Tavtigian SV, Pruss D, Barnstead M, Evans C, Baden H, Powell J, Glusman G, Rowen L, Hood L, Tan YH, Elgar G, Hawkins T, Venkatesh B, Rokhsar D, Brenner S. Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes. Science. 2002 Aug 23; 297:1301-1310 [PubMed][web supplement][notes and corrections]

Fusobacterium nucleatum

  1. Kapatral V, Anderson I, Ivanova N, Reznik G, Los T, Lykidis A, Bhattacharyya A, Bartman A, Gardner W, Grechkin G, Zhu L, Vasieva O, Chu L, Kogan Y, Chaga O, Goltsman E, Bernal A,  Larsen N, D'Souza M, Walunas T, Pusch G, Haselkorn R, Fonstein M, Kyrpides N, Overbeek R. Genome Sequence and Analysis of the Oral Bacterium Fusobacterium nucleatum Strain ATCC 25586. J Bacteriol. 2002 Apr;184(7):2005-18. [PubMed]

Homo Sapiens/ Human

A user's guide to human genome - Nature Genetics 2002 Sep; 32 Supp.
  1. Rouchka EC, Gish W, States DJ. Comparison of whole genome assemblies of the human genome. Nucleic Acids Res. 2002 Nov 15;30(22):5004-14. [PubMed]
  2. Fan Y, Linardopoulou E, Friedman C, Williams E, Trask BJ. Genomic structure and evolution of the ancestral chromosome fusion site in 2q13-2q14.1 and paralogous regions on other human chromosomes. Genome Res. 2002 Nov;12(11):1651-62. [PubMed][web supplement]
  3. Fan Y, Newman T, Linardopoulou E, Trask BJ. Gene content and function of the ancestral chromosome fusion site in human chromosome 2q13-2q14.1 and paralogous regions. Genome Res. 2002 Nov;12(11):1663-72. [PubMed]
  4. Wolfsberg TG, Wetterstrand KA, Guyer MS, Collins FS, Baxevanis AD. A user's guide to the human genome. Nat Genet. 2002 Sep;32 Suppl:1-79. [PubMed]
  5. Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero SN, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander ES, Daly MJ, Altshuler D. The structure of haplotype blocks in the human genome.  Science. 2002 Jun 21;296(5576):2225-9. [PubMed][web supplement]
  6. Gardiner K, Slavov D, Bechtel L, Davisson M. Annotation of human chromosome 21 for relevance to down syndrome: gene structure and expression analysis. Genomics. 2002 Jun;79(6):833-43. [PubMed]
  7. Reymond A, Camargo AA, Deutsch S, Stevenson BJ, Parmigiani RB, Ucla C, Bettoni F, Rossier C, Lyle R, Guipponi M, de Souza S, Iseli C, Jongeneel CV, Bucher P, Simpson AJ, Antonarakis SE. Nineteen additional unpredicted transcripts from human chromosome 21.  Genomics. 2002 Jun;79(6):824-32. [PubMed]
  8. Daly MJ. Estimating the Human Gene Count. Cell 2002 May 3; 109:283-284 [PubMed]
  9. Myers EW, Sutton GG, Smith HO, Adams MD, Venter JC. On the sequencing and assembly of the human genome. Proc Natl Acad Sci U S A 2002 Apr 2;99(7):4145-6[PubMed][pdf]
  10. Green P. Whole-genome disassembly. Proc Natl Acad Sci U S A. 2002 Apr 2;99(7):4143-4. [PubMed][pdf]
  11. Waterston RH, Lander ES, Sulston JE. On the sequencing of the human genome. Proc Natl Acad Sci U S A. 2002 Mar 19;99(6):3712-6. [PubMed][pdf]

Methanosarcina acetivorans

  1. Galagan JE, Nusbaum C, Roy A, Endrizzi MG, Macdonald P, FitzHugh W, Calvo S, Engels R, Smirnov S, Atnoor D, Brown A, Allen N, Naylor J, Stange-Thomann N, DeArellano K, Johnson R, Linton L, McEwan P, McKernan K, Talamas J, Tirrell A, Ye W, Zimmer A, Barber RD, Cann I, Graham DE, Grahame DA, Guss AM, Hedderich R, Ingram-Smith C, Kuettner HC, Krzycki JA, Leigh JA, Li W, Liu J, Mukhopadhyay B, Reeve JN, Smith K, Springer TA, Umayam LA, White O, White RH, de Macario EC, Ferry JG, Jarrell KF, Jing H, Macario AJ, Paulsen I, Pritchett M, Sowers KR, Swanson RV, Zinder SH, Lander E, Metcalf WW, Birren B. The Genome of M. acetivorans Reveals Extensive Metabolic and Physiological Diversity. Genome Res. 2002 Apr;12(4):532-42. [PubMed]

Mus Musculus/ Mouse

  1. MOUSE GENOME (Complete issue) - Nature 2002 Dec 5; 420
  2. Gregory SG, Sekhon M, Schein J, Zhao S, Osoegawa K, Scott CE, Evans RS, Burridge PW, Cox TV, Fox CA, Hutton RD, Mullenger IR, Phillips KJ, Smith J, Stalker J, Threadgold GJ, Birney E, Wylie K, Chinwalla A, Wallis J, Hillier L, Carter J, Gaige T, Jaeger S, Kremitzki C, Layman D, Maas J, McGrane R, Mead K, Walker R, Jones S, Smith M, Asano J, Bosdet I, Chan S, Chittaranjan S, Chiu R, Fjell C, Fuhrmann D, Girn N, Gray C, Guin R, Hsiao L, Krzywinski M, Kutsche R, Lee SS, Mathewson C, McLeavy C, Messervier S, Ness S, Pandoh P, Prabhu AL, Saeedi P, Smailus D, Spence L, Stott J, Taylor S, Terpstra W, Tsai M, Vardy J, Wye N, Yang G, Shatsman S, Ayodeji B, Geer K, Tsegaye G, Shvartsbeyn A, Gebregeorgis E, Krol M, Russell D, Overton L, Malek JA, Holmes M, Heaney M, Shetty J, Feldblyum T, Nierman WC, Catanese JJ, Hubbard T, Waterston RH, Rogers J, De Jong PJ, Fraser CM, Marra M, McPherson JD, Bentley DR. A physical map of the mouse genome. Nature 2002 Aug 15; 418:743-754. [PubMed][pdf][web supplement]

Mycoplasma penetrans

Sasaki Y, Ishikawa J, Yamashita A, Oshima K, Kenri T, Furuya K, Yoshino C, Horino A, Shiba T, Sasaki T, Hattori M. The complete genomic sequence of Mycoplasma penetrans, an intracellular bacterial pathogen in humans. Nucleic Acids Res. 2002 Dec 1;30(23):5293-300. [PubMed]

Oryza sativa L./ Rice

  1. Check E. Fresh analyses put rice genomics on the map. Nature. 2002 Nov 21; 48:259. [PubMed]
  2. Sasaki T, Matsumoto T, Yamamoto K, Sakata K, Baba T, Katayose Y, Wu J, Niimura Y, Cheng Z, Nagamura Y, Antonio BA, Kanamori H, Hosokawa S, Masukawa M, Arikawa K, Chiden Y, Hayashi M, Okamoto M, Ando T, Aoki H, Arita K, Hamada M, Harada C, Hijishita S, Honda M, Ichikawa Y, Idonuma A, Iijima M, Ikeda M, Ikeno M, Ito S, Ito T, Ito Y, Ito Y, Iwabuchi A, Kamiya K, Karasawa W, Katagiri S, Kikuta A, Kobayashi N, Kono I, Machita K, Maehara T, Mizuno H, Mizubayashi T, Mukai Y, Nagasaki H, Nakashima M, Nakama Y, Nakamichi Y, Nakamura M, Namiki N, Negishi M, Ohta I, Ono N, Saji S, Sakai K, Shibata M, Shimokawa T, Shomura A, Song J, Takazaki Y, Terasawa K, Tsuji K, Waki K, Yamagata H, Yamane H, Yoshiki S, Yoshihara R, Yukawa K, Zhong H, Iwama H, Endo T, Ito H, Hahn JH, Kim HI, Eun MY, Yano M, Jiang J, Gojobori T. The genome sequence and structure of rice chromosome 1. Nature. 2002 Nov 21; 48:312. [PubMed][pdf][web supplement]
  3. Feng Q, Zhang Y, Hao P, Wang S, Fu G, Huang Y, Li Y, Zhu J, Liu Y, Hu X, Jia P, Zhang Y, Zhao Q, Ying K, Yu S, Tang Y, Weng Q, Zhang L, Lu Y, Mu J, Lu Y, Zhang LS, Yu Z, Fan D, Liu X, Lu T, Li C, Wu Y, Sun T, Lei H, Li T, Hu H, Guan J, Wu M, Zhang R, Zhou B, Chen Z, Chen L, Jin Z, Wang R, Yin H, Cai Z, Ren S, Lv G, Gu W, Zhu G, Tu Y, Jia J, Zhang Y, Chen J, Kang H, Chen X, Shao C, Sun Y, Hu Q, Zhang X, Zhang W, Wang L, Ding C, Sheng H, Gu J, Chen S, Ni L, Zhu F, Chen W, Lan L, Lai Y, Cheng Z, Gu M, Jiang J, Li J, Hong G, Xue Y, Han B. Sequence and analysis of rice chromosome 4. Nature. 2002 Nov 21;420(6913):316-20. [PubMed][pdf][web supplement]
  4. Normile D. Syngenta Agrees to Wider Release. Science. 2002 Jun 7; 296:1785-1787. [PubMed]
  5. Zhao Q, Zhang Y, Cheng Z, Chen M, Wang S, Feng Q, Huang Y, Li Y, Tang Y, Zhou B, Chen Z, Yu S, Zhu J, Hu X, Mu J, Ying K, Hao P, Zhang L, Lu Y, Zhang LS, Liu Y, Yu Z, Fan D, Weng Q, Chen L, Lu T, Liu X, Jia P, Sun T, Wu Y, Zhang Y, Lu Y, Li C, Wang R, Lei H, Li T, Hu H, Wu M, Zhang R, Guan J, Zhu J, Fu G, Gu M, Hong G, Xue Y, Wing R, Jiang J, Han B. A Fine Physical Map of the Rice Chromosome 4. Genome Res. 2002 May; 12: 817-823. [PubMed]
  6. Kennedy D. The importance of rice. Science 2002 Apr 5; 296:13. [PubMed]
  7. Cantrell RP, Reeves TG. THE RICE GENOME: The Cereal of the World's Poor Takes Center Stage. Science 2002 Apr 5; 296:53 [PubMed]
  8. Serageldin I. et al. THE RICE GENOME: World Poverty and Hunger--the Challenge for Science. Science 2002 Apr 5; 296:54-58 [PubMed]
  9. Ronald P, Leung H. THE RICE GENOME: The Most Precious Things Are Not Jade and Pearls... Science 2002 Apr 5; 296:58-59 [PubMed]
  10. Bennetzen J. THE RICE GENOME: Opening the Door to Comparative Plant Biology. Science 2002 Apr 5; 296:60-63 [PubMed]
  11. Marshall E.  THE RICE GENOME: A Deal for the Rice Genome. Science 2002 Apr 5; 296:34 [PubMed]
  12. Normile D. THE RICE GENOME: Beijing Genomics Institute: From Standing Start to Sequencing Superpower. Science 2002 Apr 5; 296:36-39 [PubMed]
  13. Normile D, Pennisi E. The rice genome. Rice: boiled down to bare essentials. Science. 2002 Apr 5;296(5565):32-6. [PubMed]
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Streptomyces coelicolor

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Thermoanaerobacter tengcongensis

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  71. Mostowy S, Behr MA. Comparative Genomics in the Fight Against Tuberculosis: Diagnostics, Epidemiology, and BCG Vaccination. Am J Pharmacogenomics. 2002;2(3):189-96. [PubMed]

Network/pathway reconstruction and analysis

  1. Sambrano GR, Chandy G, Choi S, Decamp D, Hsueh R, Lin KM, Mock D, O'Rourke N, Roach T, Shu H, Sinkovits B, Verghese M, Bourne H. Unravelling the signal-transduction network in B lymphocytes. Nature 2002 Dec 12;420(6916):708-10 [PubMed]
  2. Sambrano GR, Fraser I, Han H, Ni Y, O'Connell T, Yan Z, Stull JT. Navigating the signalling network in mouse cardiac myocytes. Nature. 2002 Dec 12;420(6916):712-4. [PubMed]
  3. Yanai I, DeLisi C. The society of genes: networks of functional links between genes from comparative genomics. Genome Biol. 2002 Oct 25;3(11):RESEARCH0064. [PubMed]
  4. Forst CV. Network genomics--a novel approach for the analysis of biological systems in the post-genomic era. Mol Biol Rep. 2002 Sep;29(3):265-80. [PubMed]
  5. Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabasi AL. Hierarchical organization of modularity in metabolic networks.  Science. 2002 Aug 30;297(5586):1551-5. [PubMed][web supplement]
  6. Fedoroff N, Fontana W. GENETIC NETWORKS: Small Numbers of Big Molecules. Science. 2002 Aug 16;297(5584):1129-31. [PubMed]
  7. Elowitz MB, Levine AJ, Siggia ED, Swain PS. Stochastic gene expression in a single cell. Science. 2002 Aug 16;297(5584):1183-6. [PubMed][web supplement]
  8. Ronen M, Rosenberg R, Shraiman BI, Alon U. Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics. Proc Natl Acad Sci U S A 2002 Aug 6;99(16):10555-60[PubMed][pdf]
  9. Roulet E, Busso S, Camargo AA, Simpson AJ, Mermod N, Bucher P. High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites. Nat Biotechnol. 2002 Aug;20(8):831-5. [PubMed]
  10. Roix J, Misteli T. Genomes, proteomes, and dynamic networks in the cell nucleus. Histochem Cell Biol. 2002 Aug;118(2):105-16. [PubMed]
  11. Banerjee N, Zhang MQ. Functional genomics as applied to mapping transcription regulatory networks. Curr Opin Microbiol. 2002 Jun; 5: 313-317 [PubMed]
  12. Reinke V, White KP. Developmental Genomic Approaches in Model Organisms. Annu Rev Genomics Hum Genet. 2002 Jun 6 [epub ahead of print] [PubMed]
  13. Weckwerth W, Fiehn O. Can we discover novel pathways using metabolomic analysis? Curr Opin Biotechnol. 2002 Apr. 13: 156-160. [PubMed]

Metabolomics

  1. Brindle JT, Antti H, Holmes E, Tranter G, Nicholson JK, Bethell HW, Clarke S, Schofield PM, McKilligin E, Mosedale DE, Grainger DJ. Rapid and noninvasive diagnosis of the presence and severity of coronary heart disease using (1)H-NMR-based metabonomics. Nat Med. 2002 Dec;8(12):1439-1445. [PubMed][web supplement]
  2. Robosky LC, Robertson DG, Baker JD, Rane S, Reily MD. In vivo toxicity screening programs using metabonomics. Comb Chem High Throughput Screen. 2002 Dec;5(8):651-62. [PubMed]
  3. Holmes E, Antti H. Chemometric contributions to the evolution of metabonomics: mathematical solutions to characterising and interpreting complex biological NMR spectra. Analyst. 2002 Dec;127(12):1549-57. [PubMed]
  4. Reo NV. NMR-based metabolomics. Drug Chem Toxicol. 2002 Nov;25(4):375-82. [PubMed]
  5. Keun HC, Ebbels TM, Antti H, Bollard ME, Beckonert O, Schlotterbeck G, Senn H, Niederhauser U, Holmes E, Lindon JC, Nicholson JK. Analytical Reproducibility in (1)H NMR-Based Metabonomic Urinalysis. Chem Res Toxicol. 2002 Nov;15(11):1380-6. [PubMed]
  6. Gavaghan CL, Wilson ID, Nicholson JK. Physiological variation in metabolic phenotyping and functional genomic studies: use of orthogonal signal correction and PLS-DA. FEBS Lett. 2002 Oct 23;530(1-3):191. [PubMed]
  7. Watkins SM. et al. Toward the implementation of metabolomic assessments of human health and nutrition. Curr Opin Biotechnol. 2002 Oct; 13:512-516. [PubMed]
  8. Taylor J, King RD, Altmann T, Fiehn O. Application of metabolomics to plant genotype discrimination using statistics and machine learning. Bioinformatics. 2002 Oct;18 Suppl 2:S241-8. [PubMed]
  9. De La Fuente A, Snoep JL, Westerhoff HV, Mendes P. Metabolic control in integrated biochemical systems. Eur J Biochem. 2002 Sep;269(18):4399-4408. [PubMed]
  10. Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabasi AL. Hierarchical organization of modularity in metabolic networks.  Science. 2002 Aug 30;297(5586):1551-5. [PubMed][web supplement]
  11. Forster J, Gombert AK, Nielsen J. A functional genomics approach using metabolomics and in silico pathway analysis. Biotechnol Bioeng. 2002 Sep 30; 79: 703-712. [PubMed]
  12. Hall R, Beale M, Fiehn O, Hardy N, Sumner L, Bino R. Plant Metabolomics: The Missing Link in Functional Genomics Strategies. Plant Cell. 2002 Jul;14(7):1437-1440. [PubMed]
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  14. Bundy JG, Spurgeon DJ, Svendsen C, Hankard PK, Osborn D, Lindon JC, Nicholson JK. Earthworm species of the genus Eisenia can be phenotypically differentiated by metabolic profiling. FEBS Lett. 2002 Jun 19;521(1-3):115-20. [PubMed]
  15. Mendes P. Emerging bioinformatics for the metabolome. Brief Bioinform. 2002 Jun;3(2):134-45. [PubMed]
  16. Weckwerth W, Fiehn O. Can we discover novel pathways using metabolomic analysis? Curr Opin Biotechnol. 2002 Apr. 13: 156-160. [PubMed]
  17. Phelps TJ, Palumbo AV, Beliaev AS. Metabolomics and microarrays for improved understanding of phenotypic characteristics controlled by both genomics and environmental constraints. Curr Opin Biotechnol. 2002 Feb;13(1):20-4. [PubMed]
  18. Nicholson JK, Connelly J, Lindon JC, Holmes E. Metabonomics: a platform for studying drug toxicity and gene function. Nat Rev Drug Discov. 2002 Feb;1(2):153-61. [PubMed]
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  21. Plumb RS, Stumpf CL, Gorenstein MV, Castro-Perez JM, Dear GJ, Anthony M, Sweatman BC, Connor SC, Haselden JN. Metabonomics: the use of electrospray mass spectrometry coupled to reversed-phase liquid chromatography shows potential for the screening of rat urine in drug development. Rapid Commun Mass Spectrom. 2002;16(20):1991-6. [PubMed]

Population Genomics/Evolutionary Genomics

  1. King MC, Motulsky AG. HUMAN GENETICS: Mapping Human History. Science. 2002 Dec 20;298(5602):2342-3. [PubMed]
  2. Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW. Genetic Structure of Human Populations. Science. 2002 Dec 20;298(5602):2381-2385. [PubMed][web supplement]
  3. Clark AG, Otto SP. Genomes and evolution Population genetics and molecular evolution of whole genomes. Curr Opin Genet Dev. 2002 Dec; 12:631-633. [PubMed]
  4. Schlotterer C. Towards a molecular characterization of adaptation in local populations. Curr Opin Genet Dev. 2002 Dec; 12:683-687. [PubMed]
  5. Akey JM, Zhang G, Zhang K, Jin L, Shriver MD. Interrogating a high-density SNP map for signatures of natural selection. Genome Res. 2002 Dec;12(12):1805-14. [PubMed]
Database
  1. Yazaki J, Kishimoto N, Ishikawa M, Kikuchi S. Rice Expression Database: the gateway to rice functional genomics. Trends Plant Sci. 2002 Dec;7(12):563-4. [PubMed]
  2. Marsh S, Kwok P, McLeod HL. SNP databases and pharmacogenetics: great start, but a long way to go. Hum Mutat. 2002 Sep;20(3):174-9. [PubMed]
  3. Twigger S, Lu J, Shimoyama M, Chen D, Pasko D, Long H, Ginster J, Chen CF, Nigam R, Kwitek A, Eppig J, Maltais L, Maglott D, Schuler G, Jacob H, Tonellato PJ. Rat Genome Database (RGD): mapping disease onto the genome. Nucleic Acids Res. 2002 Jan 1;30(1):125-8. [PubMed]
  4. Blake JA, Richardson JE, Bult CJ, Kadin JA, Eppig JT. The Mouse Genome Database (MGD): the model organism database for the laboratory mouse.  Nucleic Acids Res. 2002 Jan 1;30(1):113-5. [PubMed]
  5. Ware D, Jaiswal P, Ni J, Pan X, Chang K, Clark K, Teytelman L, Schmidt S, Zhao W, Cartinhour S, McCouch S, Stein L. Gramene: a resource for comparative grass genomics. Nucleic Acids Res. 2002 Jan 1;30(1):103-5. [PubMed]
  6. Fumoto M, Miyazaki S, Sugawara H. Genome Information Broker (GIB): data retrieval and comparative analysis system for completed microbial genomes and more.  Nucleic Acids Res. 2002 Jan 1;30(1):66-8. [PubMed]
  7. Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Huminiecki L, Kasprzyk A, Lehvaslaiho H, Lijnzaad P, Melsopp C, Mongin E, Pettett R, Pocock M, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I, Clamp M. The Ensembl genome database project. Nucleic Acids Res. 2002 Jan 1;30(1):38-41. [PubMed]
  8. Hewett M, Oliver DE, Rubin DL, Easton KL, Stuart JM, Altman RB, Klein TE. PharmGKB: the Pharmacogenetics Knowledge Base. Nucleic Acids Res. 2002 Jan 1;30(1):163-5. [PubMed]
  9. Plumb RS, Stumpf CL, Gorenstein MV, Castro-Perez JM, Dear GJ, Anthony M, Sweatman BC, Connor SC, Haselden JN. Metabonomics: the use of electrospray mass spectrometry urine in drug development. Rapid Commun Mass Spectrom. 2002;16(20):1991-6. [PubMed]

Applications

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  27. van Ommen B, Stierum R. Nutrigenomics: exploiting systems biology in the nutrition and health arena. Curr Opin Biotechnol. 2002 Oct; 13:517-521. [PubMed]
  28. Grusak MA. Phytochemicals in plants: genomics-assisted plant improvement for nutritional and health benefits. Curr Opin Biotechnol. 2002 Oct; 13:508-511. [PubMed]
  29. Ye SQ, Usher DC, Zhang LQ. Gene expression profiling of human diseases by serial analysis of gene expression. J Biomed Sci. 2002 Sep-Oct;9(5):384-94. [PubMed]
  30. Zo YG, Rivera IN, Russek-Cohen E, Islam MS, Siddique AK, Yunus M, Sack RB, Huq A, Colwell RR. Genomic profiles of clinical and environmental isolates of Vibrio cholerae O1 in cholera-endemic areas of Bangladesh. Proc Natl Acad Sci U S A. 2002 Sep 17;99(19):12409-12414. [PubMed][pdf][web supplement]
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  32. Thompson LJ, De Reuse H. Genomics of Helicobacter pylori. Helicobacter. 2002 Sep;7 Suppl 1:1-7. [PubMed]
  33. Boon K, Osorio EC, Greenhut SF, Schaefer CF, Shoemaker J, Polyak K, Morin PJ, Buetow KH, Strausberg RL, De Souza SJ, Riggins GJ. An anatomy of normal and malignant gene expression. Proc Natl Acad Sci U S A. 2002 Aug 20;99(17):11287-92. [PubMed]
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  35. Surralles J, Ramirez MJ, Marcos R, Natarajan AT, Mullenders LH. Clusters of transcription-coupled repair in the human genome. Proc Natl Acad Sci U S A. 2002 Aug 6;99(16):10571-10574. [PubMed][pdf]
  36. Plomin R, McGuffin P. Psychopathology in the Postgenomic Era. Annu Rev Psychol. 2002 Aug 6 [epub ahead of print] [PubMed]
  37. Weinstein JN. 'Omic' and hypothesis-driven research in the molecular pharmacology of cancer. Curr Opin Pharmacol. 2002 Aug;2(4):361-5. [PubMed]
  38. Schultz CJ, Rumsewicz MP, Johnson KL, Jones BJ, Gaspar YM, Bacic A. Using genomic resources to guide research directions. The arabinogalactan protein gene family as a test case. Plant Physiol. 2002 Aug;129(4):1448-63. [PubMed]
  39. Stapleton M, Liao G, Brokstein P, Hong L, Carninci P, Shiraki T, Hayashizaki Y, Champe M, Pacleb J, Wan K, Yu C, Carlson J, George R, Celniker S, Rubin GM. The Drosophila Gene Collection: Identification of Putative Full-Length cDNAs for 70% of D. melanogaster Genes. Genome Res. 2002 Aug;12(8):1294-300. [PubMed]
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