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

General
Science Special Issue: Genome: Unlocking Biology's Storehouse 2001 Oct 5; 294
Genome
   Agrobacterium tumefaciens
   Arabidopsis thaliana
   Canis falimiliaris/ Domestic dog
   Caulobacter crescentus
   Danio rerio/ Zebrafish
   Drosophila Melanogaster/ fruit fly
   Encephalitozoon cuniculi
   Escherichia Coli O157:H7
   Helicobacter Pylori
   Homo Sapiens/ Human
   Lactococcus lactis 
   Leprosy bacillus
   Mus Musculus/ Mouse
   Mycobacterium Tuberculosis
   Mycobacterium Leprae
   Ovis aries/ Domestic sheep
   Pasteurella multocida
   Rattus rattus/ Rat
   Salmonella Typhimurium
   Sinorhizobium meliloti
   Streptococcus Pneumoniae
   Yersinia Pestis
Comparative Genomics
Metabolomics
Database
Applications
Pharmacogenomics
Single Nucleotide Polymorphisms (SNPs) (typing, validation and mapping)
System Biology
Techniques & Tools
Ethical, Legal and Social issues		 Can't find the functional genomics article published in 2001 in my site? 
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General

  1. Stillman B. DNA REPLICATION: Enhanced: Genomic Views of Genome Duplication. Science. 2001 Dec 14;294(5550):2301-2304. [PubMed]
  2. Malakoff D. FUNCTIONAL GENOMICS: Pathogen Researchers Get Help From TIGR. Science. 2001 Dec 7;294(5549):2069-2070. [PubMed]
  3. Fell DA. Beyond genomics. Trends Genet. 2001 Dec; 17:680-682 [PubMed]
  4. Birchmeier C, Treier M. Genomics boosts mouse molecular genetics. Trends Genet. 2001 Dec; 17:691-692 [PubMed]
  5. Collins FS, Guttmacher AE. Genetics Moves Into the Medical Mainstream. JAMA. 2001 Nov 14;286(18):2322-2324 [PubMed]
  6. Yaspo ML. Taking a functional genomics approach in molecular medicine. Trends Mol Med. 2001 Nov;7(11):494-501. [PubMed]
  7. Blackwell JM. Genetics and genomics in infectious disease susceptibility. Trends Mol Med. 2001 Nov;7(11):521-6. [PubMed]
  8. Fraser CM, Dando MR. Genomics and future biological weapons:the need for preventive action by the biomedical community. Nat Genet. 2001 Nov;29(3):253-256. [PubMed]
  9. Milburn J. Beyond the genome: turning data into knowledge. Drug Discov Today. 2001 Sep 1;6(17):881-883. [PubMed]
  10. Schultze JL, Vonderheide RH. From cancer genomics to cancer immunotherapy: toward second-generation tumor antigens. Trends Immunol. 2001 Sep;22(9):516-23. [PubMed]
  11. Meltzer SJ. Tumor Genomics vs. Tumor Genetics: A Paradigm Shift? Gastroenterology. 2001 Sep;121(3):726-9. [PubMed]
  12. Asnagli H, Murphy KM. The functional genomics experience (are you experienced?). Nat Immunol. 2001 Sep;2(9):826-8. [PubMed]
  13. Staudt LM, Flavell RA. Genomics, Genetics, and Genes of the Immune System. Immunity. 2001 Sep; 15:335-336. [PubMed]
  14. Honore B. Genome- and proteome-based technologies: status and applications in the postgenomic era. Expert Rev Mol Diagn. 2001 Sep;1(3):265-74. [PubMed]
  15. Cornish-Bowden A, Cardenas ML.. Complex networks of interactions connect genes to phenotypes. Trends Biochem Sci. 2001 Aug;26(8):463-5. [PubMed]
  16. Sweigard JA, Ebbole DJ. Functional analysis of pathogenicity genes in a genomics world. Curr Opin Microbiol. 2001 Aug; 4:387-392. [PubMed]
  17. Tarleton RL, Kissinger J. Parasite genomics: current status and future prospects. Curr Opin Immunol. 2001 Aug; 13:395-402. [PubMed]
  18. Walsh CA.  Neuroscience in the post-genome era: an overview. Trends Neurosci. 2001 Jul;24(7):363-4. [PubMed]
  19. Grant WN, Viney ME.  Post-genomic nematode parasitology. Int J Parasitol. 2001 Jul;31(9):879-88. [PubMed]
  20. Marshall E. DNA sequencing. Genome teams adjust to shotgun marriage. Science. 2001 Jun 15;292(5524):1982-3. [PubMed]
  21. Reichert JM. Medicinal biotechnology products: big problems or big opportunities? Trends Biotechnol 2001. Jun; 19:200-201 [PubMed]
  22. Hope IA.  Broadcast interference - functional genomics. Trends Genet. 2001 Jun;17(6):297-9. [PubMed]
  23. Cyranoski D. Japan speeds up mission to unravel genetic diseases. Nature. 2001 Apr 26;410(6832):1013. [PubMed]
  24. The proteome isn't genome II. Nature. 2001 Apr 12;410(6830):725. [PubMed]
  25. Theologis A. Goodbye to 'one by one' genetics. Genome Biol. 2001 Apr 6;2(4):COMMENT2004. [PubMed]
  26. Kumar A, Snyder M. Emerging technologies in yeast genomics. Nat Rev Genet. 2001 Apr;2(4):302-12. Review. [PubMed]
  27. Williams M.  Genomics, proteomics and gnomics.  Curr Opin Investig Drugs. 2001 Apr;2(4):437-9 [PubMed]
  28. Bottles K.  A revolution in genetics: changing medicine, changing lives. Physician Exec. 2001 Mar-Apr;27(2):58-63. [PubMed]
  29. Abbott A. Trepidation greets plan for cloning humans. Nature 2001. Mar 15; 410: 293 [PubMed]
  30. Abbott A. Free access to cDNA provides impetus for gene function work. Nature 2001. Mar 15; 410:289-290 [PubMed]
  31. Powledge TM. Changing the rules? The agreement between Celera and Science magazine concerning Celera's publication of its human genome sequence is upsetting many researchers in bioinformatics. EMBO reports 2001. Mar 15; 2: 171-172 [PubMed]
  32. Strogatz SH. Exploring complex networks. Nature 2001. Mar 8; 410:268-276. [PubMed]
  33. Harvesting the fruits of the human genome. Nat Genet 2001. Mar; 27:227 [PubMed]
  34. Little P. The end of all human DNA maps? Nat Genet 2001. Mar; 27:229-230 [PubMed][pdf]
  35. Antonarakis SE. BACking up the promises. Nat Genet 2001. Mar; 27:230-232 [PubMed][pdf]
  36. Kruglyak L, Nickerson DA. Variation is the spice of life. Nat Genet 2001. Mar; 27:234-236 [PubMed][pdf]
  37. Komajda M, Charron P. The heart of genomics. Nat Med 2001. Mar; 7:287-288 [PubMed]
  38. Bouchie A. Value of rice genome still in the husk. Nat Biotech 2001. Mar; 19:189 [PubMed]
  39. Strohman RC. Genomics and human life span-what's left to extend. Nat Biotech 2001. Mar; 19:195 [PubMed]
  40. Bailey D, Zanders E, Dean P. The end of the beginning for genomic medicine. Nat Biotech 2001. Mar; 19:207-209 [PubMed]
  41. Tabata S, Caboche M. Genome studies and molecular genetics. We know the sequence, how do we identify the function?  Curr Opin Plant Biol. 2001. Apr 4:103-104 [PubMed]
  42. Davies K. After the genome: DNA and Human Disease. Cell 2001. Feb 23, 104:465-467. [PubMed]
  43. Abbott A. Wheels start to turn for mutant mouse archive. Nature 2001. Feb 22, 409:967-968. [PubMed]
  44. Cyranoski D. Japan's ape sequencing effort set to unravel the brain's secrets. Nature 2001. Feb 8; 409:651-652 [PubMed]
  45. Collins FS, McKusick VA. Implications of the human genome project for medical science. JAMA 2001. Feb 7; 285(5):540-544 [PubMed]
  46. Bumol TF, Watanabe AM. Genetic information, genomic technologies, and the future of drug discovery. JAMA 2001. Feb 7; 285(5):551-555 [PubMed]
  47. Domenech P, Barry CE, Cole ST.  Mycobacterium tuberculosis in the post-genomic age. Curr Opin Microbiol. 2001 Feb 1;4(1):28-34. [PubMed]
  48. Carlson CS, Newman TL, Nickerson DA.  SNPing in the human genome. Curr Opin Chem Biol. 2001 Feb 1;5(1):78-85. [PubMed]
  49. Delneri D, Brancia FL, Oliver SG, Brancia FL. Towards a truly integrative biology through the functional genomics of yeast.  Curr Opin Biotechnol. 2001 Feb 1;12(1):87-91. [PubMed]
  50. Crawford DL. Functional genomics does not have to be limited to a few select organisms.  Genome Biol. 2001 Jan 12; 2(1):INTERACTIONS1001. [PubMed][pdf]
  51. Gross M. European genomics: think big or small? Curr Biol 2001 Jan; 11(1): R1-2 [PubMed]
  52. Lee K. Singapore focuses its life science strategy on humans Curr Biol 2001 Jan; 11(1): R3 [PubMed]
  53. Young DB. A post-genomic perspective. Nat Med. 2001 Jan;7(1):11-13. [PubMed]
  54. Baxevanis AD.The molecular biology database collection: an updated compilation of biological database resources.  Nucleic Acids Res. 2001 Jan 1;29(1):1-10.  [PubMed]
  55. Aljanabi S.  Genomics and plant breeding.  Biotechnol Annu Rev. 2001;7:195-238. [PubMed]

Science Special Issue: Genome: Unlocking Biology's Storehouse 2001 Oct 5; 294

  1. Jasny BR, Roberts L. Unlocking the genome.  Science. 2001 Oct 5;294(5540):81. [PubMed]
  2. Pennisi E. So many choices, so little money.  Science. 2001 Oct 5;294(5540):82-5. [PubMed]
  3. Normile D, Jianxiang Y. Japan and China gear up for 'postgenome' research.  Science. 2001 Oct 5;294(5540):84. [PubMed]
  4. Avise JC. Evolving genomic metaphors: a new look at the language of DNA. Science. 2001 Oct 5;294(5540):86-7. [PubMed]
  5. Singer PA, Daar AS. Harnessing genomics and biotechnology to improve global health equity. Science. 2001 Oct 5;294(5540):87-9. [PubMed]
  6. Stevens RC, Yokoyama S, Wilson IA. Global efforts in structural genomics. Science. 2001 Oct 5;294(5540):89-92. [PubMed]
  7. Baker D, Sali A. Protein structure prediction and structural genomics. Science. 2001 Oct 5;294(5540):93-6. [PubMed]
  8. Gilbert DM. Making sense of eukaryotic DNA replication origins. Science. 2001 Oct 5;294(5540):96-100. [PubMed]

Genome

  1. Brizuela L, Braun P, LaBaer J. FLEXGene repository: from sequenced genomes to gene repositories for high-throughput functional biology and proteomics. Mol Biochem Parasitol. 2001 Dec;118(2):155-165. [PubMed]
  2. Sankoff D. Gene and genome duplication. Curr Opin Genet Dev. 2001 Dec 11:681-684 [PubMed]
  3. Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res. 2001. Nov 15; 29: 4633-4642. [PubMed]
  4. Pennisi E.  Genome sequencing. Insects rank low among genome priorities.  Science. 2001 Nov 9;294(5545):1261-2. [PubMed]
  5. Hacia JG. Genome of the apes. Trends Genet. 2001 Nov; 17:637-645 [PubMed]
  6. Hodgkin J. What does a worm want with 20,000 genes? Genome Biol. 2001 Nov; 11:2008. [PubMed]
  7. Cai WW, Chen R, Gibbs RA, Bradley A. A Clone-Array Pooled Shotgun Strategy for Sequencing Large Genomes. Genome Res. 2001 Oct; 11:1619-1623 [PubMed]
  8. Skovgaard M, Jensen LJ, Brunak S, Ussery D, Krogh A. On the total number of genes and their length distribution in complete microbial genomes. Trends Genet. 2001 Aug; 17:425-428 [PubMed]
  9. Devos D, Valencia A. Intrinsic errors in genome annotation. Trends Genet. 2001 Aug; 17:429-432 [PubMed]
  10. Green ED. Strategies for the systematic sequencing of complex genomes. Nat Rev Genet. 2001 Aug;  2: 573-583 [PubMed]
  11. Gilson PR. Nucleomorph genomes: much ado about practically nothing. Genome Biol. 2001 Jul 30;  2(8): reviews1022.1-1022.5 [PubMed]
  12. Stein L. Genome annotation: from sequence to biology.  Nat Rev Genet. 2001 Jul;2(7):493-503. [PubMed]
  13. Louis A, Ollivier E, Aude JC, Risler JL. Massive sequence comparisons as a help in annotating genomic sequences. Genome Res. 2001 Jul;11(7):1296-303. [PubMed]
  14. Gaasterland T, Oprea M. Whole-genome analysis: annotations and updates. Curr Opin Struct Biol. 2001 Jun;11(3):377-81. [PubMed]
  15. Bernal A, Ear U, Kyrpides N. Genomes OnLine database (GOLD): a monitor of genome projects world-wide. Nucleic Acids Res. 2001 Jan 1;29(1):126-7. [PubMed]

Agrobacterium tumefaciens

  1. Pennisi E. MICROBIAL GENOMES: New Genome a Boost to Plant Studies.  Science. 2001 Dec 14;294(5550):2266. [PubMed]
  2. Wood DW, Setubal JC, Kaul R, Monks DE, Kitajima JP, Okura VK, Zhou Y, Chen L, Wood GE, Almeida Jr NF, Woo L, Chen Y, Paulsen IT, Eisen JA, Karp PD, Bovee Sr D, Chapman P, Clendenning J, Deatherage G, Gillet W, Grant C, Kutyavin T, Levy R, Li MJ, McClelland E, Palmieri A, Raymond C, Rouse G, Saenphimmachak C, Wu Z, Romero P, Gordon D, Zhang S, Yoo H, Tao Y, Biddle P, Jung M, Krespan W, Perry M, Gordon-Kamm B, Liao L, Kim S, Hendrick C, Zhao ZY, Dolan M, Chumley F, Tingey SV, Tomb JF, Gordon MP, Olson MV, Nester EW. The Genome of the Natural Genetic Engineer Agrobacterium tumefaciens C58. Science. 2001 Dec 14; 294:2317-2323 [PubMed][web supplement]
  3. Goodner B, Hinkle G, Gattung S, Miller N, Blanchard M, Qurollo B, Goldman BS, Cao Y, Askenazi M, Halling C, Mullin L, Houmiel K, Gordon J, Vaudin M, Iartchouk O, Epp A, Liu F, Wollam C, Allinger M, Doughty D, Scott C, Lappas C, Markelz B, Flanagan C, Crowell C, Gurson J, Lomo C, Sear C, Strub G, Cielo C, Slater S. Genome Sequence of the Plant Pathogen and Biotechnology Agent Agrobacterium tumefaciens C58. Science. 2001 Dec 14; 294:2323-2328 [PubMed][web supplement]

Arabidopsis thaliana

  1. Martienssen R, McCombie WR. The first plant genome.  Cell. 2001 Jun 1;105(5):571-4. Review. [PubMed]
  2. Bevan M, Mayer K, White O, Eisen JA, Preuss D, Bureau T, Salzberg SL, Mewes H. Sequence and analysis of the Arabidopsis genome. Curr Opin Plant Biol. 2001. Apr 4:105-110 [PubMed]
  3. Poethig RS. Life with 25,000 genes. Genome Res 2001. Mar; 11:313-316. [PubMed]
  4. Rujan T, Martin W. How many genes in Arabidopsis come from cyanobacteria? An estimate from 386 protein phylogenies. Trends Genet 2001. Mar 17:113-120 [PubMed]

Canis falimiliaris/ Domestic dog

  1. Breen M, Jouquand S, Renier C, Mellersh CS, Hitte C, Holmes NG, Cheron A, Suter N, Vignaux F, Bristow AE, Priat C, McCann E, Andre C, Boundy S, Gitsham P, Thomas R, Bridge WL, Spriggs HF, Ryder EJ, Curson A, Sampson J, Ostrander EA, Binns MM, Galibert F. Chromosome-Specific Single-Locus FISH Probes Allow Anchorage of an 1800-Marker Integrated Radiation-Hybrid/Linkage Map of the Domestic Dog Genome to All Chromosomes.  Genome Res. 2001 Oct; 11:1784-1795 [PubMed]

Caulobacter crescentus

  1. Nierman WC, Feldblyum TV, Laub MT, Paulsen IT, Nelson KE, Eisen J, Heidelberg JF, Alley MR, Ohta N, Maddock JR, Potocka I, Nelson WC, Newton A, Stephens C,  Phadke ND, Ely B, DeBoy RT, Dodson RJ, Durkin AS, Gwinn ML, Haft DH, Kolonay JF, Smit J, Craven MB, Khouri H, Shetty J, Berry K, Utterback T, Tran K, Wolf A,  Vamathevan J, Ermolaeva M, White O, Salzberg SL, Venter JC, Shapiro L, Fraser CM. Complete genome sequence of Caulobacter crescentus.  Proc Natl Acad Sci U S A. 2001 Mar 27;98(7):4136-4141. [PubMed][pdf][web supplement]

Danio rerio

  1. Hukriede N et al. The LN54 Radiation Hybrid Map of Zebrafish Expressed Sequences. Genome Res. 2001 Dec; 11: 2127-2132. [PubMed]

Drosophila Melanogaster/ fluit fly

  1. Karlin S, Bergman A, Gentles AJ.  Genomics Annotation of the Drosophila genome.  Nature. 2001 May 17;411(6835):259-60. [PubMed]
  2. 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, Peter A, Schottler P, Werner M, Mourkioti F, Beinert N, Dowe G, Schafer U, Jackle H, Bucheton A, Callister D, Campbell L, Henderson NS, McMillan PJ, Salles C, Tait E, Valenti P, Saunders RD, Billaud A, Pachter L, Glover DM, Ashburner M. From First Base: The Sequence of the Tip of the X Chromosome of Drosophila melanogaster, a Comparison of Two  Sequencing Strategies. Genome Res. 2001 May;11(5):710-30. [PubMed]
  3. Spradling AC. Reflections on the Drosophila genome. Funct Integrative Genomics 2001. 4; 1:221-222. [PubMed]
  4. Biggin MD, Tjian R. Transcriptional regulation in Drosophila: the post-genome challenge. Funct Integrative Genomics 2001. 4; 1:223-224. [PubMed]
  5. Yoshihara M. et. al. Neurobiology and the Drosophila genome. Funct Integrative Genomics 2001. 4; 1:235-240. [PubMed]
  6. Kim J. Descartes' fly: the geometry of genomic annotation. Funct Integrative Genomics 2001. 4; 1:241-249 [PubMed]
  7. Pietrokovski S. et. al. Identification of new signaling components in the Drosophila genome sequence. Funct Integrative Genomics 2001. 4; 1:250-255 [PubMed]

Encephalitozoon Cuniculi

  1. Katinka MD, Duprat S, Cornillot E, Metenier G, Thomarat F, Prensier G, Barbe V, Peyretaillade E, Brottier P, Wincker P, Delbac F, El Alaoui H, Peyret P, Saurin W, Gouy M, Weissenbach J, Vivares CP. Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature. 2001 Nov 22;414(6862):450-3. [PubMed][pdf][web supplement]

Escherichia Coli O157:H7

  1. Lim A, Dimalanta ET, Potamousis KD, Yen G, Apodoca J, Tao C, Lin J, Qi R, Skiadas J, Ramanathan A, Perna NT, Plunkett G 3rd, Burland V, Mau B, Hackett J, Blattner FR,  Anantharaman TS, Mishra B, Schwartz DC.  Shotgun Optical Maps of the Whole Escherichia coli O157:H7 Genome.  Genome Res. 2001 Sep;11(9):1584-1593. [PubMed]
  2. Perna NT, Plunkett G 3rd, Burland V, Mau B, Glasner JD, Rose DJ, Mayhew GF, Evans PS, Gregor J, Kirkpatrick HA, Posfai G, Hackett J,  Klink S, Boutin A, Shao Y, Miller L, Grotbeck EJ, Davis NW, Lim A, Dimalanta ET, Potamousis KD, Apodaca J, Anantharaman TS, Lin J,  Yen G, Schwartz DC, Welch RA, Blattner FR.. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 2001. Jan 25; 409, 529-533 [PubMed][pdf]
  3. Eisen JA. Gastrogenomics. Nature 2001. Jan 25; 409, 463-466 [PubMed][pdf]

Guillardia theta

  1. Pearlman RE.  Lessons from a small genome.  Nat Genet. 2001 May;28(1):6-7. [PubMed]
  2. Douglas S, Zauner S, Fraunholz M, Beaton M, Penny S, Deng LT, Wu X, Reith M, Cavalier-Smith T, Maier UG. The highly reduced genome of an enslaved algal nucleus. Nature 2001. Apr 26; 410:1091-1096. [PubMed][pdf][web supplement]
  3. Gilson PR, McFadden GI. Genome sequencing A grin without a cat. Nature. 2001 Apr 26;410(6832):1040-1041[PubMed][pdf]

Helicobacter Pylori

  1. Bjorkholm BM, Oh JD, Falk PG, Engstrand LG, Gordon JI. Genomics and proteomics converge on Helicobacter pylori. Curr Opin Microbiol. 2001 Jun;4(3):237-45. [PubMed]
  2. Lin LF, Posfai J, Roberts RJ, Kong H.  Comparative genomics of the restriction-modification systems in Helicobacter pylori.  Proc Natl Acad Sci U S A. 2001 Feb 27;98(5):2740-2745. [PubMed][pdf]

Homo Sapiens/ Human

  1. Hattori M, Taylor TD. The human genome: part three in the book of genes. Nature 2001 Dec 20/27; 414:854-855. [PubMed]
  2. Deloukas P, Matthews LH, Ashurst J, Burton J, Gilbert JG, Jones M, Stavrides G, Almeida JP, Babbage AK, Bagguley CL, Bailey J, Barlow KF, Bates KN, Beard LM, Beare DM, Beasley OP, Bird CP, Blakey SE, Bridgeman AM, Brown AJ, Buck D, Burrill W, Butler AP, Carder C, Carter NP, Chapman JC, Clamp M, Clark G, Clark LN, Clark SY, Clee CM, Clegg S, Cobley VE, Collier RE, Connor R, Corby NR, Coulson A, Coville GJ, Deadman R, Dhami P, Dunn M, Ellington AG, Frankland JA, Fraser A, French L, Garner P, Grafham DV, Griffiths C, Griffiths MN, Gwilliam R, Hall RE, Hammond S, Harley JL, Heath PD, Ho S, Holden JL, Howden PJ, Huckle E, Hunt AR, Hunt SE, Jekosch K, Johnson CM, Johnson D, Kay MP, Kimberley AM, King A, Knights A, Laird GK, Lawlor S, Lehvaslaiho MH, Leversha M, Lloyd C, Lloyd DM, Lovell JD, Marsh VL, Martin SL, McConnachie LJ, McLay K, McMurray AA, Milne S, Mistry D, Moore MJ, Mullikin JC, Nickerson T, Oliver K, Parker A, Patel R, Pearce TA, Peck AI, Phillimore BJ, Prathalingam SR, Plumb RW, Ramsay H, Rice CM, Ross MT, Scott CE, Sehra HK, Shownkeen R, Sims S, Skuce CD, Smith ML, Soderlund C, Steward CA, Sulston JE, Swann M, Sycamore N, Taylor R, Tee L, Thomas DW, Thorpe A, Tracey A, Tromans AC, Vaudin M, Wall M, Wallis JM, Whitehead SL, Whittaker P, Willey DL, Williams L, Williams SA, Wilming L, Wray PW, Hubbard T, Durbin RM, Bentley DR, Beck S, Rogers J. The DNA sequence and comparative analysis of human chromosome 20. Nature 2001 Dec 20/27; 414:865-872. [PubMed][web supplement]
  3. Reiss T. Drug discovery of the future: the implications of the human genome project. Trends Biotechnol. 2001 Dec;19(12):496-9. [PubMed]
  4. Wong GK, Passey DA, Yu J. Most of the Human Genome Is Transcribed. Genome Res. 2001 Dec; 11:1975-1977 [PubMed]
  5. McKusick VA. The Anatomy of the Human Genome: A Neo-Vesalian Basis for Medicine in the 21st Century. JAMA. 2001 Nov 14;286(18):2289-2295. [PubMed]
  6. Subramanian G, Adams MD, Venter JC, Broder S. Implications of the Human Genome for Understanding Human Biology and Medicine. JAMA. 2001 Nov 14;286(18):2296-2307. [PubMed]
  7. Watson JD. The Human Genome Revealed. Genome Res. 2001 Nov; 11:1803-1804. [PubMed]
  8. Scherer SW, Cheung J. Discovery of the human genome sequence in the public and private databases. Curr Biol. 2001 Oct 16;11(20):R808-R811. [PubMed]
  9. Horvath JE, Bailey JA, Locke DP, Eichler EE. Lessons from the human genome: transitions between euchromatin and heterochromatin. Hum Mol Genet. 2001 Oct 1;10(20):2215-23. [PubMed]
  10. Goldstein DB. Islands of linkage disequilibrium.  Nat Genet. 2001 Oct;29(2):109-11. [PubMed]
  11. Daly MJ, Rioux JD, Schaffner SF, Hudson TJ, Lander ES. High-resolution haplotype structure in the human genome. Nat Genet. 2001 Oct;29(2):229-32. [PubMed]
  12. Johnson GC, Esposito L, Barratt BJ, Smith AN, Heward J, Di Genova G, Ueda H, Cordell HJ, Eaves IA, Dudbridge F, Twells RC, Payne F, Hughes W, Nutland S, Stevens H,  Carr P, Tuomilehto-Wolf E, Tuomilehto J, Gough SC, Clayton DG, Todd JA.  Haplotype tagging for the identification of common disease genes.  Nat Genet. 2001 Oct;29(2):233-7. [PubMed][web supplement]
  13. Frazer KA, Sheehan JB, Stokowski RP, Chen X, Hosseini R, Cheng JF, Fodor SP, Cox DR, Patil N. Evolutionarily Conserved Sequences on Human Chromosome 21. Genome Res. 2001 Oct; 11:1651-1659 [PubMed]
  14. Katsanis N, Worley KC, Lupski JR. An evaluation of the draft human genome sequence. Nat Genet. 2001 Sep; 29: 88-91 [PubMed]
  15. Kent WJ, Haussler D. Assembly of the Working Draft of the Human Genome with GigAssembler.  Genome Res. 2001 Sep;11(9):1541-1548. [PubMed]
  16. Hogenesch JB, Ching KA, Batalov S, Su AI, Walker JR, Zhou Y, Kay SA, Schultz PG, Cooke MP.  A comparison of the Celera and Ensembl predicted gene sets reveals little overlap in novel genes. Cell. 2001 Aug 24;106(4):413-5. [PubMed]
  17. Tapper WJ, Morton NE, Dunham I, Ke X, Collins A. A sequence-based integrated map of chromosome 22. Genome Res. 2001 Jul;11(7):1290-5. [PubMed]
  18. Zhuo D, Zhao WD, Wright FA, Yang HY, Wang JP, Sears R, Baer T, Kwon DH, Gordon D, Gibbs S, Dai D, Yang Q, Spitzner J, Krahe R, Stredney D, Stutz A, Yuan B. Assembly, Annotation, and Integration of UNIGENE Clusters into the Human Genome Draft. Genome Res. 2001 May;11(5):904-18. [PubMed]
  19. Sanseau P. Impact of human genome sequencing for in silico target discovery. Drug Discov Today. 2001 Mar 1;6(6):316-323. [PubMed]
  20. Mundy C.  The human genome project: a historical perspective. Pharmacogenomics. 2001 Feb;2(1):37-49. [PubMed]
  21. Little P. The end of all human DNA maps? Nat Genet 2001. Mar; 27:229-230 [PubMed][pdf]
  22. Antonarakis SE. BACking up the promises. Nat Genet 2001. Mar; 27:230-232 [PubMed][pdf]
  23. Scherf M, Klingenhoff A, Frech K, Quandt K, Schneider R, Grote K, Frisch M, Gailus-Durner V, Seidel A, Brack-Werner  R, Werner T. First pass annotation of promoters on human chromosome 22. Genome Res 2001. Mar; 11:333-340. [PubMed]
  24. Wiemann S, Weil B, Wellenreuther R, Gassenhuber J, Glassl S, Ansorge W, Bocher M, Blocker H, Bauersachs S, Blum H, Lauber J, Dusterhoft A, Beyer A, Kohrer K, Strack N, Mewes HW, Ottenwalder B, Obermaier B, Tampe J, Heubner D, Wambutt R, Korn B, Klein M, Poustka A. Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. Genome Res 2001. Mar; 11:422-435 [PubMed]
  25. Osoegawa K, Mammoser AG, Wu C, Frengen E, Zeng C, Catanese JJ, de Jong PJ. A bacterial artificial chromosome library for sequencing the complete human genome. Genome Res 2001. Mar; 11:483-496. [PubMed]
  26. Wright FA. A draft annotation and overview of the human genome. Genomebiology 2001. Feb 16: preprint 0001.1 [link to journal]
  27. Human Genome Project Publications:
  28. Deutsch S, Iseli C, Bucher P, Antonarakis SE, Scott HS. A cSNP map and database for human chromosome 21. Genome Res. 2001 Feb 11: 300-307. [PubMed]

Lactococcus lactis

  1. Bolotin A, Wincker P, Mauger S, Jaillon O, Malarme K, Weissenbach J, Ehrlich SD, Sorokin A. The Complete Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis ssp. lactis IL1403. Genome Res. 2001 May;11(5):731-53. [PubMed]

Leprosy bacillus

  1. Cole ST, Eiglmeier K, Parkhill J, James KD, Thomson NR, Wheeler PR, Honore N, Garnier T, Churcher C, Harris D,  Mungall K, Basham D, Brown D, Chillingworth T, Connor R, Davies RM, Devlin K, Duthoy S, Feltwell T, Fraser A,  Hamlin N, Holroyd S, Hornsby T, Jagels K, Lacroix C, Maclean J, Moule S, Murphy L, Oliver K, Quail MA, Rajandream  MA, Rutherford KM, Rutter S, Seeger K, Simon S, Simmonds M, Skelton J, Squares R, Squares S, Stevens K, Taylor K,  Whitehead S, Woodward JR, Barrell BG.. Massive gene decay in the leprosy bacillus. Nature 2001. Feb 22, 409:1007-1011. [PubMed][pdf]

Mus Musculus/ Mouse

  1. Schalkwyk LC, Cusack B, Dunkel I, Hopp M, Kramer M, Palczewski S, Piefke J, Scheel S, Weiher M, Wenske G, Lehrach H, Himmelbauer H. Advanced Integrated Mouse YAC Map Including BAC Framework. Genome Res. 2001 Dec;11(12):2142-50. [PubMed]
  2. Hamilton BA, Frankel WN. Of Mice and Genome Sequence. Cell. 2001 Oct 5; 107:13-16 [PubMed][web supplement]
  3. Butler D. Mouse genome roars ahead with new map. Nature. 2001 Oct 4;413(6855):444. [PubMed]
  4. Hudson TJ, Church DM, Greenaway S, Nguyen H, Cook A, Steen RG, Van Etten WJ, Castle AB, Strivens MA, Trickett P, Heuston C, Davison C, Southwell A, Hardisty R, Varela-Carver A, Haynes AR, Rodriguez-Tome P, Doi H, Ko MS, Pontius J, Schriml L, Wagner L, Maglott D, Brown SD, Lander ES, Schuler G, Denny P. A radiation hybrid map of mouse genes. Nat Genet. 2001 Oct;29(2):201-5. [PubMed]
  5. Avner P, Bruls T, Poras I, Eley L, Gas S, Ruiz P, Wiles MV, Sousa-Nunes R, Kettleborough R, Rana A, Morissette J, Bentley L, Goldsworthy M, Haynes A, Herbert E, Southam  L, Lehrach H, Weissenbach J, Manenti G, Rodriguez-Tome P, Beddington R, Dunwoodie S, Cox RD.  A radiation hybrid transcript map of the mouse genome.  Nat Genet. 2001 Oct;29(2):194-200. [PubMed]
  6. Cai WW, Chow CW, Damani S, Gregory SG, Marra M, Bradley A. An SSLP marker-anchored BAC framework map of the mouse genome. Nat Genet. 2001 Oct;29(2):133-4. [PubMed][web supplement]
  7. Zhao S, Shatsman S, Ayodeji B, Geer K, Tsegaye G, Krol M, Gebregeorgis E, Shvartsbeyn A, Russell D, Overton L, Jiang L, Dimitrov G, Tran K, Shetty J, Malek JA,  Feldblyum T, Nierman WC, Fraser CM. Mouse BAC Ends Quality Assessment and Sequence Analyses.  Genome Res. 2001 Oct; 11:1736-1745 [PubMed]
  8. Rogers J, Bradley A.  The mouse genome sequence: status and prospects.  Genomics. 2001 Oct;77(3):117-8. [PubMed]
  9. Knight J. Mouse genome effort 'on course'. Nature. 2001 May 10;411(6834):121. [PubMed]
  10. The RIKEN Genome Exploration Research Group Phase II Team and the FANTOM Consortium. Functional annotation of a full-length mouse cDNA collection. Nature 2001. Feb 8; 409:685-690.
  11. Nadeau JH, Balling R, Barsh G, Beier D, Brown SD, Bucan M, Camper S, Carlson G, Copeland N, Eppig J, Fletcher C, Frankel WN, Ganten D, Goldowitz D, Goodnow C, Guenet JL, Hicks G, de Angelis MH, Jackson I, Jacob HJ, Jenkins N, Johnson D, Justice M, Kay S, Kingsley D, Lehrach H, Magnuson T, Meisler M, Poustka A, Rinchik EM, Rossant J, Russell LB, Schimenti J, Shiroishi T, Skarnes WC, Soriano P, Stanford W, Takahashi JS, Wurst W, Zimmer A. Sequence interpretation. Functional annotation of mouse genome sequences.  Science. 2001 Feb 16;291(5507):1251-5. [PubMed]

Mycobacterium Tuberculosis

  1. Kato-Maeda M, Rhee JT, Gingeras TR, Salamon H, Drenkow J, Smittipat N, Small PM.  Comparing Genomes within the Species Mycobacterium tuberculosis.  Genome Res. 2001 Apr;11(4):547-554. [PubMed]

Mycobacterium Leprae

  1. Vissa VD, Brennan PJ. The genome of Mycobacterium leprae: a minimal mycobacterial gene set. Genome Biol. 2001 Aug 3;  2(8): reviews1023.1-1023.8 [PubMed]

Ovis aries/ Domestic sheep

  1. Cockett NE, Shay TL, Smit M. Analysis of the sheep genome. Physiol. Genomics. 2001 Dec 21; 7: 69-78 [PubMed]

Pasteurella multocida

  1. May BJ, Zhang Q, Li LL, Paustian ML, Whittam TS, Kapur V.  Complete genomic sequence of Pasteurella multocida,Pm70.  Proc Natl Acad Sci U S A. 2001 Mar 13;98(6):3460-3465. [PubMed][pdf]

Rattus rattus/ Rat

  1. Scheetz TE, Raymond MR, Nishimura DY, McClain A, Roberts C, Birkett C, Gardiner J, Zhang J, Butters N, Sun C,  Kwitek-Black A, Jacob H, Casavant TL, Soares MB, Sheffield VC. Generation of a High-Density rat EST map.  Genome Res 2001. Mar; 11:497-502 [PubMed]

Salmonella Typhimurium

  1. McClelland M, Sanderson KE, Spieth J, Clifton SW, Latreille P, Courtney L, Porwollik S, Ali J, Dante M, Du F, Hou S, Layman D, Leonard S, Nguyen C, Scott K, Holmes A, Grewal N, Mulvaney E, Ryan E, Sun H, Florea L, Miller W, Stoneking T, Nhan M, Waterston R, Wilson RK.  Complete genome sequence of Salmonella enterica serovar Typhimurium LT2.  Nature. 2001 Oct 25;413(6858):852-856. [PubMed][pdf][web supplement]
  2. Parkhill J, Dougan G, James KD, Thomson NR, Pickard D, Wain J, Churcher C, Mungall KL, Bentley SD, Holden MT, Sebaihia M, Baker S, Basham D, Brooks K, Chillingworth T, Connerton P, Cronin A, Davis P, Davies RM, Dowd L, White N, Farrar J, Feltwell T, Hamlin N, Haque A, Hien TT, Holroyd S, Jagels K, Krogh A, Larsen TS, Leather S, Moule S, O'Gaora P, Parry C, Quail M, Rutherford K, Simmonds M, Skelton J, Stevens K, Whitehead S, Barrell BG. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature. 2001 Oct 25;413(6858):848-52 [PubMed][pdf][web supplement]

Sinorhizobium meliloti

  1. Barnett MJ, Fisher RF, Jones T, Komp C, Abola AP, Barloy-Hubler F, Bowser L, Capela D, Galibert F, Gouzy J, Gurjal M, Hong A, Huizar L, Hyman RW, Kahn D, Kahn ML, Kalman S, Keating DH, Palm C, Peck MC, Surzycki R, Wells DH, Yeh KC, Davis RW, Federspiel NA, Long SR.  Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid. Proc Natl Acad Sci U S A. 2001 Aug 14;98(17):9883-9888. [PubMed][pdf][web supplement]
  2. Capela D, Barloy-Hubler F, Gouzy J, Bothe G, Ampe F, Batut J, Boistard P, Becker A, Boutry M, Cadieu E, Dreano S, Gloux S, Godrie T, Goffeau A,  Kahn D, Kiss E, Lelaure V, Masuy D, Pohl T, Portetelle D, Puhler A, Purnelle B, Ramsperger U, Renard C, Thebault P, Vandenbol M, Weidner S,  Galibert F. Analysis of the chromosome sequence of the legume symbiont Sinorhizobium meliloti strain 1021. Proc Natl Acad Sci U S A. 2001 Aug 14;98(17):9877-9882. [PubMed][pdf]
  3. Finan TM, Weidner S, Wong K, Buhrmester J, Chain P, Vorholter FJ, Hernandez-Lucas I, Becker A, Cowie A, Gouzy J, Golding B, Puhler A. The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti.  Proc Natl Acad Sci U S A. 2001 Aug 14;98(17):9889-9894. [PubMed][pdf]
  4. Galibert F, Finan TM, Long SR, Puhler A, Abola P, Ampe F, Barloy-Hubler F, Barnett MJ, Becker A, Boistard P, Bothe G, Boutry M, Bowser L, Buhrmester J, Cadieu E, Capela D, Chain P, Cowie A, Davis RW, Dreano S, Federspiel NA, Fisher RF, Gloux S, Godrie T, Goffeau A, Golding B, Gouzy J, Gurjal M, Hernandez-Lucas I, Hong A,  Huizar L, Hyman RW, Jones T, Kahn D, Kahn ML, Kalman S, Keating DH, Kiss E, Komp C, Lelaure V, Masuy D, Palm C, Peck MC, Pohl TM, Portetelle D, Purnelle B, Ramsperger U, Surzycki R, Thebault P, Vandenbol M, Vorholter FJ, Weidner S, Wells DH, Wong K, Yeh KC, Batut J. The composite genome of the legume symbiont Sinorhizobium meliloti.  Science. 2001 Jul 27;293(5530):668-72. [PubMed]
  5. Downie JA, Young JP.  Genome sequencingThe ABC of symbiosis. Nature. 2001 Aug 9;412(6847):597-8. [PubMed]

Streptococcus Pneumoniae

  1. Tettelin H, Nelson KE, Paulsen IT, Eisen JA, Read TD, Peterson S, Heidelberg J, DeBoy RT, Haft DH, Dodson RJ, Durkin AS, Gwinn M, Kolonay JF, Nelson WC, Peterson JD, Umayam LA, White O, Salzberg SL, Lewis MR, Radune D, Holtzapple E, Khouri H, Wolf AM, Utterback TR, Hansen CL, McDonald LA, Feldblyum TV, Angiuoli S, Dickinson T, Hickey EK, Holt IE, Loftus BJ, Yang F, Smith HO, Venter JC, Dougherty BA, Morrison DA, Hollingshead SK, Fraser CM..  Complete Genome Sequence of a Virulent Isolate of Streptococcus pneumoniae. Science 2001 Jul 20; 293: 498-506 [PubMed][web supplement]
  2. Ferber D. S. pneumoniae Genome Falls to Sequencers. Science 2001 Jul 20; 293: 410. [PubMed]

Yersinia Pestis

  1. Cole ST, Buchrieser C.  Bacterial genomicsA plague o' both your hosts.  Nature. 2001 Oct 4;413(6855):467-470. [PubMed]
  2. Parkhill J, Wren BW, Thomson NR, Titball RW, Holden MT, Prentice MB, Sebaihia M, James KD, Churcher C, Mungall KL, Baker S, Basham D, Bentley SD, Brooks K, Cerdeno-Tarraga AM, Chillingworth T, Cronin A, Davies RM, Davis P, Dougan G, Feltwell T, Hamlin N, Holroyd S, Jagels K, Karlyshev AV, Leather S, Moule S, Oyston PC,  Quail M, Rutherford K, Simmonds M, Skelton J, Stevens K, Whitehead S, Barrell BG. Genome sequence of Yersinia pestis, the causative agent of plague. Nature. 2001 Oct 4;413(6855):523-7. [PubMed][web supplement]

Comparative Genomics

  1. Peichel CL, Nereng KS, Ohgi KA, Cole BL, Colosimo PF, Buerkle CA, Schluter D, Kingsley DM. The genetic architecture of divergence between threespine stickleback species. Nature 2001 Dec 20/27; 414:901-905. [PubMed][web supplement]
  2. Thompson J, Janse CJ, Waters AP. Comparative genomics in Plasmodium: a tool for the identification of genes and functional analysis. Mol Biochem Parasitol. 2001 Dec;118(2):147-154. [PubMed]
  3. Alekshun MN. Beyond comparison - antibiotics from genome data? Nat Biotechnol. 2001 Dec; 19:1124-1125 [PubMed]
  4. Enmark E, Gustafsson J. Comparing nuclear receptors in worms, flies and humans. Trends Pharmacol Sci. 2001 Dec; 22:611-615 [PubMed]
  5. Ragan MA. Detection of lateral gene transfer among microbial genomes. Curr Opin Genet Dev. 2001 Dec 11:620-626 [PubMed]
  6. Aquadro CF, Bauer DuMont V, Reed FA. Genome-wide variation in the human and fruitfly: a comparison. Curr Opin Genet Dev. 2001 Dec 11:627-634 [PubMed]
  7. Liu H, Sachidanandam R, Stein L. Comparative Genomics Between Rice and Arabidopsis Shows Scant Collinearity in Gene Order. Genome Res. 2001 Dec; 11: 2020-2026. [PubMed]
  8. Pennisi E. Microbial genomes: Sequences reveal borrowed genes. Science Nov 23; 294: 1634-1635. [PubMed]
  9. Stoll M, Cowley AW Jr, Tonellato PJ, Greene AS, Kaldunski ML, Roman RJ, Dumas P, Schork NJ, Wang Z, Jacob HJ. A Genomic-Systems Biology Map for Cardiovascular Function. Science Nov 23; 294: 1723-1726. [PubMed]
  10. Dacks JB, Doolittle WF. Reconstructing/Deconstructing the Earliest Eukaryotes: How Comparative Genomics Can Help. Cell. 2001 Nov 16; 107:419-425. [PubMed]
  11. Castresana J. Comparative genomics and bioenergetics. Biochim Biophys Acta. 2001 Nov 1;1506(3):147-62. [PubMed]
  12. Denny P, Bate R, Mallon AM. What use is the human genome for understanding the mouse?  Genome Biol. 2001 Nov; 11:2009 [PubMed]
  13. Chen R, Bouck JB, Weinstock GM, Gibbs RA. Comparing Vertebrate Whole-Genome Shotgun Reads to the Human Genome  Genome Res. 2001 Nov; 11: 1807-1816. [PubMed]
  14. Kwitek AE, Tonellato PJ, Chen D, Gullings-Handley J, Cheng YS, Twigger S, Scheetz TE, Casavant TL, Stoll M, Nobrega MA, Shiozawa M, Soares MB, Sheffield VC, Jacob HJ. Automated Construction of High-Density Comparative Maps Between Rat, Human, and Mouse.  Genome Res. 2001 Nov; 11:1935-1943 [PubMed]
  15. Chen FC, Vallender EJ, Wang H, Tzeng CS, Li WH. Genomic divergence between human and chimpanzee estimated from large-scale alignments of genomic sequences. J Hered. 2001 Nov-Dec;92(6):481-9. [PubMed]
  16. Glaser P, Frangeul L, Buchrieser C, Rusniok C, Amend A, Baquero F, Berche P, Bloecker H, Brandt P, Chakraborty T, Charbit A, Chetouani F, Couve E, de Daruvar A, Dehoux P, Domann E, Dominguez-Bernal G, Duchaud E, Durant L, Dussurget O, Entian KD, Fsihi H, Portillo FG, Garrido P, Gautier L, Goebel W, Gomez-Lopez N, Hain T, Hauf J, Jackson D, Jones LM, Kaerst U, Kreft J, Kuhn M, Kunst F, Kurapkat G, Madueno E, Maitournam A, Vicente JM, Ng E, Nedjari H, Nordsiek G, Novella S, de Pablos B, Perez-Diaz JC, Purcell R, Remmel B, Rose M, Schlueter T, Simoes N, Tierrez A, Vazquez-Boland JA, Voss H, Wehland J, Cossart P.. Comparative Genomics of Listeria Species. Science. 2001 Oct 26; 294:849-852 [PubMed][web supplement]
  17. Popovici C, Leveugle M, Birnbaum D, Coulier F. Coparalogy: physical and functional clusterings in the human genome. Biochem Biophys Res Commun. 2001 Oct 26;288(2):362-70. [PubMed]
  18. Horimoto K, Fukuchi S, Mori K. Comprehensive comparison between locations of orthologous genes on archaeal and bacterial genomes  Bioinformatics 2001 Sep; 17: 791-802. [PubMed]
  19. Yanai I, Derti A, DeLisi C. Genes linked by fusion events are generally of the same functional category: A systematic analysis of 30 microbial genomes. Proc Natl Acad Sci U S A. 2001 Jul 3;98(14):7940-7945. [PubMed][pdf]
  20. Louis A, Ollivier E, Aude JC, Risler JL. Massive sequence comparisons as a help in annotating genomic sequences. Genome Res. 2001 Jul;11(7):1296-303. [PubMed]
  21. Kato-Maeda M, Rhee JT, Gingeras TR, Salamon H, Drenkow J, Smittipat N, Small PM.  Comparing Genomes within the Species Mycobacterium tuberculosis.  Genome Res. 2001 Apr;11(4):547-554. [PubMed]
  22. Friedman R, Hughes AL. Gene duplication and the structure of eukaryotic genomes. Genome Res 2001. Mar; 11:373-381. [PubMed]
  23. Wolf YI, Rogozin IB, Kondrashov AS, Koonin EV. Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context. Genome Res 2001. Mar; 11:356-372. [PubMed]
  24. Rujan T, Martin W. How many genes in Arabidopsis come from cyanobacteria? An estimate from 386 protein phylogenies. Trends Genet 2001. Mar 17:113-120 [PubMed]
  25. Lin LF, Posfai J, Roberts RJ, Kong H.  Comparative genomics of the restriction-modification systems in Helicobacter pylori.  Proc Natl Acad Sci U S A. 2001 Feb 27;98(5):2740-2745. [PubMed][pdf]
  26. Edwards RA, Olsen GJ, Maloy SR. Comparative genomics of closely related salmonellae. Trends Microbiol. 2001 Feb;10(2):94-9. [PubMed]
  27. Suter-Crazzolara C, Kurapkat G. An infrastructure for comparative genomics to functionally characterize genes and proteins. Genome Inform Ser Workshop Genome Inform. 2000;11:24-32. [PubMed]
Metabolomics
  1. Thomas GH. Metabolomics breaks the silence. Trends Microbiol. 2001 Apr;9(4):158. [PubMed]
  2. Raamsdonk LM, Teusink B, Broadhurst D, Zhang N, Hayes A, Walsh MC, Berden JA, Brindle KM, Kell DB, Rowland JJ, Westerhoff HV, van Dam K, Oliver SG. A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations. Nat Biotechnol. 2001 Jan;19(1):45-50. [PubMed]
Database
  1. Brizuela L, Braun P, LaBaer J. FLEXGene repository: from sequenced genomes to gene repositories for high-throughput functional biology and proteomics. Mol Biochem Parasitol. 2001 Dec;118(2):155-165. [PubMed]
  2. Lenhard B, Hayes WS, Wasserman WW. GeneLynx: A Gene-Centric Portal to the Human Genome. Genome Res. 2001 Dec; 11:2151-2157 [PubMed]
  3. Riggins GJ, Strausberg RL . Genome and genetic resources from the Cancer Genome Anatomy Project. Hum Mol Genet. 2001 Apr 1;10(7):663-7. [PubMed]
  4. Deutsch S, Iseli C, Bucher P, Antonarakis SE, Scott HS. A cSNP map and database for human chromosome 21. Genome Res. 2001 Feb 11: 300-307. [PubMed]
  5. Baxevanis AD.The molecular biology database collection: an updated compilation of biological database resources.  Nucleic Acids Res. 2001 Jan 1;29(1):1-10.  [PubMed]
  6. Bernal A, Ear U, Kyrpides N. Genomes OnLine database (GOLD): a monitor of genome projects world-wide. Nucleic Acids Res. 2001 Jan 1;29(1):126-7. [PubMed]
  7. Pruitt KD, Maglott DR. RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res. 2001 Jan 1;29(1):137-40. [PubMed]
  8. Zhao S.A comprehensive BAC resource. Nucleic Acids Res. 2001 Jan 1;29(1):141-3. [PubMed]
  9. Morley M, Arcaro M, Burdick J, Yonescu R, Reid T, Kirsch IR, Cheung VG.GenMapDB: a database of mapped human BAC clones. Nucleic Acids Res. 2001 Jan 1;29(1):144-7. [PubMed]
  10. Sese J, Nikaidou H, Kawamoto S, Minesaki Y, Morishita S, Okubo K. BodyMap incorporated PCR-based expression profiling data and a gene ranking system.Nucleic Acids Res. 2001 Jan 1;29(1):156-8. [PubMed]

Applications

  1. Walke DW et al. In vivo drug target discovery: identifying the best targets from the genome. Curr Opin Biotechnol. 2001 Dec; 12:626-631 [PubMed]
  2. Gabrielson E, Berg K, Anbazhagan R. Functional Genomics, Gene Arrays, and the Future of Pathology. Mod Pathol. 2001 Dec;14(12):1294-1299. [PubMed]
  3. Assaad FF.  Of weeds and men: what genomes teach us about plant cell biology. Curr Opin Plant Biol. 2001 Dec; 4:478-487. [PubMed]
  4. Potuschak T, Doerner P.  Cell cycle controls: genome-wide analysis in Arabidopsis. Curr Opin Plant Biol. 2001 Dec; 4:501-506. [PubMed]
  5. Ko MS. Embryogenomics: developmental biology meets genomics.  Trends Biotechnol. 2001 Dec;19(12):511-8. [PubMed]
  6. Kudoh T, Tsang M, Hukriede NA, Chen X, Dedekian M, Clarke CJ, Kiang A, Schultz S, Epstein JA, Toyama R, Dawid IB. A Gene Expression Screen in Zebrafish Embryogenesis. Genome Res. 2001 Dec; 11:1979-1987 [PubMed]
  7. Matthews LR, Vaglio P, Reboul J, Ge H, Davis BP, Garrels J, Vincent S, Vidal M. Identification of Potential Interaction Networks Using Sequence-Based Searches for Conserved Protein-Protein Interactions or “Interologs". Genome Res. 2001 Dec; 11:2120-2126. [PubMed]
  8. Sakaki Y. Genomics and atherosclerosis. Ann N Y Acad Sci. 2001 Dec;947:254-8. [PubMed]
  9. Eiglmeier K, Simon S, Garnier T, Cole ST. The integrated genome map of Mycobacterium leprae. Lepr Rev. 2001 Dec;72(4):462-9. [PubMed]
  10. Sonstegard TS, Gasbarre LC. Genomic tools to improve parasite resistance. Vet Parasitol. 2001 Nov 22;101(3-4):387-403. [PubMed]
  11. Nestler EJ. Psychogenomics: opportunities for understanding addiction. J Neurosci. 2001 Nov 1;21(21):8324-7. [PubMed]
  12. Willson TM, Jones SA, Moore JT, Kliewer SA. Chemical genomics: Functional analysis of orphan nuclear receptors in the regulation of bile acid metabolism. Med Res Rev. 2001 Nov;21(6):513-22. [PubMed]
  13. Bals R, Jany B. Identification of disease genes by expression profiling. Eur Respir J. 2001 Nov;18(5):882-9. [PubMed]
  14. Maecker B, von Bergwelt-Baildon, Anderson K S, Vonderheide R H, Schultze J L. Linking genomics to immunotherapy by reverse immunology--'immunomics' in the new millennium. Curr Mol Med. 2001 Nov;1(5):609-19. [PubMed]
  15. Strausberg RL, Riggins GJ. Navigating the human transcriptome. Proc Natl Acad Sci U S A. 2001 Oct 9;98(21):11837-8. [PubMed][pdf]
  16. Camargo AA, Samaia HP, Dias-Neto E, Simao DF, Migotto IA, Briones MR, Costa FF, Aparecida Nagai M, Verjovski-Almeida S, Zago MA, Andrade LE, Carrer H, El-Dorry HF,  Espreafico EM, Habr-Gama A, Giannella-Neto D, Goldman GH, Gruber A, Hackel C, Kimura ET, Maciel RM, Marie SK, Martins EA, Nobrega MP, Paco-Larson ML, Pardini MI, Pereira  GG, Pesquero JB, Rodrigues V, Rogatto SR, da Silva ID, Sogayar MC, Sonati Md M, Tajara EH, Valentini SR, Alberto FL, Amaral ME, Aneas I, Arnaldi LA, de Assis AM, Bengtson  MH, Bergamo NA, Bombonato V, de Camargo ME, Canevari RA, Carraro DM, Cerutti JM, Correa ML, Correa RF, Costa MC, Curcio C, Hokama PO, Ferreira AJ, Furuzawa GK,  Gushiken T, Ho PL, Kimura E, Krieger JE, Leite LC, Majumder P, Marins M, Marques ER, Melo AS, Melo M, Mestriner CA, Miracca EC, Miranda DC, Nascimento AL, Nobrega FG, Ojopi EP, Pandolfi JR, Pessoa LG, Prevedel AC, Rahal P, Rainho CA, Reis EM, Ribeiro ML, da Ros N, de Sa RG, Sales MM, Sant'anna SC, dos Santos ML, da Silva AM, da Silva NP,  Silva WA Jr, da Silveira RA, Sousa JF, Stecconi D, Tsukumo F, Valente V, Soares F, Moreira ES, Nunes DN, Correa RG, Zalcberg H, Carvalho AF, Reis LF, Brentani RR, Simpson AJ, de Souza SJ.  The contribution of 700,000 ORF sequence tags to the definition of the human transcriptome. Proc Natl Acad Sci U S A. 2001 Oct 9;98(21):12103-12108. [PubMed][pdf][web supplement]
  17. Singer PA, Daar AS. Harnessing genomics and biotechnology to improve global health equity.  Science. 2001 Oct 5;294(5540):87-9. [PubMed]
  18. Schueler MG, Higgins AW, Rudd MK, Gustashaw K, Willard HF. Genomic and genetic definition of a functional human centromere. Science. 2001 Oct 5;294(5540):109-15. [PubMed][web supplement]
  19. Crasto C, Singer MS, Shepherd GM. The olfactory receptor family album. Genome Biol. 2001 Oct. 2:1027 [PubMed]
  20. Eide DJ. Functional genomics and metal metabolism. Genome Biol. 2001 Oct. 2:1028 [PubMed]
  21. Monni O, Hyman E, Mousses S, Barlund M, Kallioniemi A, Kallioniemi OP. From chromosomal alterations to target genes for therapy: integrating cytogenetic and functional genomic views of the breast cancer genome.  Semin Cancer Biol. 2001 Oct;11(5):395-401. [PubMed]
  22. Roberts MA, Mutch DM, German JB. Genomics: food and nutrition. Curr Opin Biotechnol. 2001 Oct; 12:516-522 [PubMed]
  23. de Vos WM. Advances in genomics for microbial food fermentations and safety. Curr Opin Biotechnol. 2001 Oct; 12:493-498 [PubMed]
  24. Verrips CT, Warmoeskerken MM, Post JA. General introduction to the importance of genomics in food biotechnology and nutrition. Curr Opin Biotechnol. 2001 Oct; 12:483-487 [PubMed]
  25. Margulies EH, Kardia SL, Innis JW. A Comparative Molecular Analysis of Developing Mouse Forelimbs and Hindlimbs Using Serial Analysis of Gene Expression (SAGE).  Genome Res. 2001 Oct; 11:1651-1659 [PubMed]
  26. Dorrell N, Mangan JA, Laing KG, Hinds J, Linton D, Al-Ghusein H, Barrell BG, Parkhill J, Stoker NG, Karlyshev AV, Butcher PD, Wren BW. Whole Genome Comparison of Campylobacter jejuni Human Isolates Using a Low-Cost Microarray Reveals Extensive Genetic Diversity.  Genome Res. 2001 Oct; 11:1706-1715 [PubMed][web supplement]
  27. Tsujimoto G, Katsuma S, Shiojima S, Hirasawa A, Tanoue A. Functional genomic research of alpha1-adrenoceptors. J Cardiovasc Pharmacol. 2001 Oct;38 Suppl 1:S1-5. [PubMed]
  28. Kellam P. Post-genomic virology: the impact of bioinformatics, microarrays and proteomics on investigating host and pathogen interactions.  Rev Med Virol. 2001 Sep-Oct;11(5):313-29. [PubMed]
  29. Flajnik MF, Kasahara M. Comparative Genomics of the MHC: Glimpses into the Evolution of the Adaptive Immune System. Immunity. 2001 Sep; 15:351-362 [PubMed]
  30. Glusman G, Rowen L, Lee I, Boysen C, Roach JC, Smit AF, Wang K, Koop BF, Hood L. Comparative genomics of the human and mouse t cell receptor loci.  Immunity. 2001 Sep;15(3):337-49. [PubMed]
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  32. Fahrer AM, Konigshofer Y, Kerr EM, Ghandour G, Mack DH, Davis MM, Chien Yh. Attributes of gamma delta intraepithelial lymphocytes as suggested by their transcriptional profile. Proc Natl Acad Sci U S A. 2001 Aug 28;98(18):10261-6. [PubMed][pdf][web supplement]
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  70. Burchiel SW, Knall CM, Davis JW, Paules RS, Boggs SE, Afshari CA. Analysis of Genetic and Epigenetic Mechanisms of Toxicity: Potential Roles of Toxicogenomics and Proteomics in Toxicology. Toxicol Sci. 2001 Feb;59(2):193-195. [PubMed]
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Single Nucleotide Polymorphisms (SNPs) (typing, validation and mapping)

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  3. Shapero MH, Leuther KK, Nguyen A, Scott M, Jones KW. SNP Genotyping by Multiplexed Solid-Phase Amplification and Fluorescent Minisequencing. Genome Res. 2001 Nov;11(11):1926-1934. [PubMed]
  4. Miller RD, Kwok PY. The birth and death of human single-nucleotide polymorphisms: new experimental evidence and implications for human history and medicine. Hum Mol Genet. 2001 Oct 1;10(20):2195-8. [PubMed]
  5. Shchepinov MS, Denissenko MF, Smylie KJ, Worl RJ, Leppin AL, Cantor CR, Rodi CP. Matrix-induced fragmentation of P3'-N5' phosphoramidate-containing DNA: high-throughput MALDI-TOF analysis of genomic sequence polymorphisms.  Nucleic Acids Res. 2001 Sep 15; 29: 3864-3872. [PubMed]
  6. Ranade K, Chang MS, Ting CT, Pei D, Hsiao CF, Olivier M, Pesich R, Hebert J, Chen YD, Dzau VJ, Curb D, Olshen R, Risch N, Cox DR, Botstein D. High-throughput genotyping with single nucleotide polymorphisms. Genome Res. 2001 Jul;11(7):1262-8. [PubMed][web supplement]
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Pharmacogenomics

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  36. Danesi R, De Braud F, Fogli S, Di Paolo A, Del Tacca M. Pharmacogenetic determinants of anti-cancer drug activity and toxicity. Trends Pharmacol Sci. 2001 Aug;22(8):420-6 [PubMed]
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  44. Wang W, Marsh S, Cassidy J, McLeod HL.  Pharmacogenomic dissection of resistance to thymidylate synthase inhibitors.  Cancer Res. 2001 Jul 15;61(14):5505-10. [PubMed]
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