best papers of 2004

My friend sent me a list of papers, voted best of the year by his lab.
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Jordan IK, Kondrashov FA, Adzhubei IA, Wolf YI, Koonin EV,
Kondrashov AS, Sunyaev S. A universal trend of amino acid gain and
loss in protein evolution. Nature. 2005 Feb 10;433(7026):633-8. Epub
2005 Jan 1 abstract

here

Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen
JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH,
Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R,
Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO. Environmental
genome shotgun sequencing of the Sargasso Sea. Science. 2004 Apr
2;304(5667):66-74. Epub 2004 Mar 4. abstract
here

Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, Zhu X, Rinn JL,
Tongprasit W, Samanta M, Weissman S, Gerstein M, Snyder M. Global
identification of human transcribed sequences with genome tiling
arrays. Science. 2004 Dec 24;306(5705):2242-6. Epub 2004 Nov 11.
abstract
here

Andersen JS, Lam YW, Leung AK, Ong SE, Lyon CE, Lamond AI, Mann M.
Nucleolar proteome dynamics. Nature. 2005 Jan 6;433(7021):77-83.
abstract
here

Sandelin A, Alkema W, Engstrom P, Wasserman WW, Lenhard B. JASPAR:
an open-access database for eukaryotic transcription factor binding
profiles. Nucleic Acids Res. 2004 Jan 1;32(Database issue)D91-4.
abstract
here

Ramachandran N, Hainsworth E, Bhullar B, Eisenstein S, Rosen B, Lau
AY, Walter JC, LaBaer J. Self-assembling protein microarrays.
Science. 2004 Jul 2;305(5680):86-90. abstract
here

Woolfe A, Goodson M, Goode DK, Snell P, McEwen GK, Vavouri T, Smith
SF, North P, Callaway H, Kelly K, Walter K, Abnizova I, Gilks W,
Edwards YJ, Cooke JE, Elgar G. Highly conserved non-coding sequences
are associated with vertebrate development. PLoS Biol. 2005
Jan;3(1):e7. Epub 2004 Nov 1 abstract
here

Gerber AP, Herschlag D, Brown PO. Extensive association of
functionally and cytotopically related mRNAs with Puf family
RNA-binding proteins in yeast. PLoS Biol. 2004 Mar;2(3):E79. Epub
2004 Mar 16. abstract
here

Brown P, Sutikna T, Morwood MJ, Soejono RP, Jatmiko, Saptomo EW, Due
RA. A new small-bodied hominin from the Late Pleistocene of Flores,
Indonesia. Nature. 2004 Oct 28;431(7012):1055-61 abstract
here

Wang C, Lefkowitz EJ. SS-Wrapper: a package of wrapper applications
for similarity searches on Linux clusters. BMC Bioinformatics. 2004
Oct 28;5(1):171. abstract
here

Dwyer MA, Looger LL, Hellinga HW. Computational design of a
biologically active enzyme. Science. 2004 Jun 25;304(5679):1967-71.
abstract
here

Aharoni A, Gaidukov L, Khersonsky O, McQ Gould S, Roodveldt C,
Tawfik DS. The 'evolvability' of promiscuous protein functions. Nat
Genet. 2005 Jan;37(1):73-6. Epub 2004 Nov 28 abstract
here

Segal E, Friedman N, Koller D, Regev A. A module map showing
conditional activity of expression modules in cancer. Nat Genet.
2004 Oct;36(10):1090-8. Epub 2004 Sep 26. abstract
here

Park JW, Parisky K, Celotto AM, Reenan RA, Graveley BR.
Identification of alternative splicing eegulators by RNA
interference in Drosophila. Proc Natl Acad Sci U S A. 2004 Nov
9;101(45):15974-9. Epub 004 Oct 18. abstract
here

Raoult D, Audic S, Robert C, Abergel C, Renesto P, Ogata H, La Scola
B, Suzan M, Claverie JM. The 1.2-megabase genome sequence of
Mimivirus. Science. 2004 Nov 19;306(5700):1344-50. Epub 2004 Oct 14.
abstract
here

King RD, Whelan KE, Jones FM, Reiser PG, Bryant CH, Muggleton SH,
Kell DB, Oliver SG. Functional genomic hypothesis generation and
experimentation by a robot scientist. Nature. 2004 Jan
5;427(6971):247-52. abstract
here