\newcommand{\etalchar}[1]{$^{#1}$}
\begin{thebibliography}{oMUBoR90}

\bibitem[ABB{\etalchar{+}}00]{Ashburner:GO}
M~Ashburner, C~A Ball, J~A Blake, D~Botstein, H~Butler, J~M Cherry, A~P Davis,
  K~Dolinski, S~S Dwight, J~T Eppig, M~A Harris, D~P Hill, L~Issel-Tarver,
  A~Kasarskis, S~Lewis, J~C Matese, J~E Richardson, M~Ringwald, G~M Rubin, and
  G~Sherlock.
\newblock {Gene ontology: tool for the unification of biology. The Gene
  Ontology Consortium}.
\newblock {\em Nat Genet}, 25(1):25--29, May 2000.

\bibitem[AMS{\etalchar{+}}97]{Altschul:BLAST}
S~F Altschul, T~L Madden, A~A Schaffer, J~Zhang, Z~Zhang, W~Miller, and D~J
  Lipman.
\newblock {Gapped BLAST and PSI-BLAST: a new generation of protein database
  search programs}.
\newblock {\em Nucleic Acids Res}, 25(17):3389--3402, Sep 1997.

\bibitem[BD99]{Bortoluzzi:ESTexpression}
S~Bortoluzzi and G~A Danieli.
\newblock {Towards an in silico analysis of transcription patterns}.
\newblock {\em Trends Genet}, 15(3):118--119, Mar 1999.

\bibitem[BH95]{Benjamini:FDR}
Yoav Benjamini and Yosef Hochberg.
\newblock {Controlling the false discovery rate: a practical and powerful
  approach to multiple testing}.
\newblock {\em J. R. Statist. Soc. B}, 57(1):289--300, 1995.

\bibitem[BKML{\etalchar{+}}05]{Benson:GenBank}
Dennis~A Benson, Ilene Karsch-Mizrachi, David~J Lipman, James Ostell, and
  David~L Wheeler.
\newblock {GenBank}.
\newblock {\em Nucleic Acids Res}, 33(Database issue):34--38, Jan 2005.

\bibitem[BWG{\etalchar{+}}04]{Boyle:GoTermFinder}
Elizabeth~I Boyle, Shuai Weng, Jeremy Gollub, Heng Jin, David Botstein,
  J~Michael Cherry, and Gavin Sherlock.
\newblock {GO::TermFinder--open source software for accessing Gene Ontology
  information and finding significantly enriched Gene Ontology terms associated
  with a list of genes}.
\newblock {\em Bioinformatics}, 20(18):3710--3715, Dec 2004.

\bibitem[CDH03]{CCD:genemerge}
Cristian~I Castillo-Davis and Daniel~L Hartl.
\newblock {GeneMerge--post-genomic analysis, data mining, and hypothesis
  testing}.
\newblock {\em Bioinformatics}, 19(7):891--892, May 2003.

\bibitem[CDKHK04]{CCD:twophyla}
Cristian~I Castillo-Davis, Fyodor~A Kondrashov, Daniel~L Hartl, and Rob~J
  Kulathinal.
\newblock {The functional genomic distribution of protein divergence in two
  animal phyla: coevolution, genomic conflict, and constraint}.
\newblock {\em Genome Res}, 14(5):802--811, May 2004.

\bibitem[CDMH{\etalchar{+}}02]{CCD:shortintrons}
Cristian~I Castillo-Davis, Sergei~L Mekhedov, Daniel~L Hartl, Eugene~V Koonin,
  and Fyodor~A Kondrashov.
\newblock {Selection for short introns in highly expressed genes}.
\newblock {\em Nat Genet}, 31(4):415--418, Aug 2002.

\bibitem[CTH00]{Hartl:natyeastexpression}
D~Cavalieri, J~P Townsend, and D~L Hartl.
\newblock {Manifold anomalies in gene expression in a vineyard isolate of
  Saccharomyces cerevisiae revealed by DNA microarray analysis}.
\newblock {\em Proc Natl Acad Sci U S A}, 97(22):12369--12374, Oct 2000.

\bibitem[GBB{\etalchar{+}}03]{Giot:flyPP}
L~Giot, J~S Bader, C~Brouwer, A~Chaudhuri, B~Kuang, Y~Li, Y~L Hao, C~E Ooi,
  B~Godwin, E~Vitols, G~Vijayadamodar, P~Pochart, H~Machineni, M~Welsh, Y~Kong,
  B~Zerhusen, R~Malcolm, Z~Varrone, A~Collis, M~Minto, S~Burgess, L~McDaniel,
  E~Stimpson, F~Spriggs, J~Williams, K~Neurath, N~Ioime, M~Agee, E~Voss,
  K~Furtak, R~Renzulli, N~Aanensen, S~Carrolla, E~Bickelhaupt, Y~Lazovatsky,
  A~DaSilva, J~Zhong, C~A Stanyon, R~L~Jr Finley, K~P White, M~Braverman,
  T~Jarvie, S~Gold, M~Leach, J~Knight, R~A Shimkets, M~P McKenna, J~Chant, and
  J~M Rothberg.
\newblock {A protein interaction map of Drosophila melanogaster}.
\newblock {\em Science}, 302(5651):1727--1736, Dec 2003.

\bibitem[GCN{\etalchar{+}}02]{Giaever:deletion2002}
Guri Giaever, Angela~M Chu, Li~Ni, Carla Connelly, Linda Riles, Steeve
  Veronneau, Sally Dow, Ankuta Lucau-Danila, Keith Anderson, Bruno Andre,
  Adam~P Arkin, Anna Astromoff, Mohamed El-Bakkoury, Rhonda Bangham, Rocio
  Benito, Sophie Brachat, Stefano Campanaro, Matt Curtiss, Karen Davis, Adam
  Deutschbauer, Karl-Dieter Entian, Patrick Flaherty, Francoise Foury, David~J
  Garfinkel, Mark Gerstein, Deanna Gotte, Ulrich Guldener, Johannes~H Hegemann,
  Svenja Hempel, Zelek Herman, Daniel~F Jaramillo, Diane~E Kelly, Steven~L
  Kelly, Peter Kotter, Darlene LaBonte, David~C Lamb, Ning Lan, Hong Liang,
  Hong Liao, Lucy Liu, Chuanyun Luo, Marc Lussier, Rong Mao, Patrice Menard,
  Siew~Loon Ooi, Jose~L Revuelta, Christopher~J Roberts, Matthias Rose, Petra
  Ross-Macdonald, Bart Scherens, Greg Schimmack, Brenda Shafer, Daniel~D
  Shoemaker, Sharon Sookhai-Mahadeo, Reginald~K Storms, Jeffrey~N Strathern,
  Giorgio Valle, Marleen Voet, Guido Volckaert, Ching-yun Wang, Teresa~R Ward,
  Julie Wilhelmy, Elizabeth~A Winzeler, Yonghong Yang, Grace Yen, Elaine
  Youngman, Kexin Yu, Howard Bussey, Jef~D Boeke, Michael Snyder, Peter
  Philippsen, Ronald~W Davis, and Mark Johnston.
\newblock {Functional profiling of the Saccharomyces cerevisiae genome}.
\newblock {\em Nature}, 418(6896):387--391, Jul 2002.

\bibitem[GTHC02]{Grosu:pathwayprocessor}
Paul Grosu, Jeffrey~P Townsend, Daniel~L Hartl, and Duccio Cavalieri.
\newblock {Pathway Processor: a tool for integrating whole-genome expression
  results into metabolic networks}.
\newblock {\em Genome Res}, 12(7):1121--1126, Jul 2002.

\bibitem[GY94]{Goldman:codonmodel}
N~Goldman and Z~Yang.
\newblock {A codon-based model of nucleotide substitution for protein-coding
  DNA sequences}.
\newblock {\em Mol Biol Evol}, 11(5):725--736, Sep 1994.

\bibitem[HF01]{Hirsh:dispense}
A~E Hirsh and H~B Fraser.
\newblock {Protein dispensability and rate of evolution}.
\newblock {\em Nature}, 411(6841):1046--1049, Jun 2001.

\bibitem[HVD01]{Herrero:SOTA}
J~Herrero, A~Valencia, and J~Dopazo.
\newblock {A hierarchical unsupervised growing neural network for clustering
  gene expression patterns}.
\newblock {\em Bioinformatics}, 17(2):126--136, Feb 2001.

\bibitem[ICO{\etalchar{+}}01]{Ito:yeastPP}
T~Ito, T~Chiba, R~Ozawa, M~Yoshida, M~Hattori, and Y~Sakaki.
\newblock {A comprehensive two-hybrid analysis to explore the yeast protein
  interactome}.
\newblock {\em Proc Natl Acad Sci U S A}, 98(8):4569--4574, Apr 2001.

\bibitem[JLKH01]{Jenssen:litnetwork}
T~K Jenssen, A~Laegreid, J~Komorowski, and E~Hovig.
\newblock {A literature network of human genes for high-throughput analysis of
  gene expression}.
\newblock {\em Nat Genet}, 28(1):21--28, May 2001.

\bibitem[KGKN02]{Kanehisa:KEGG}
Minoru Kanehisa, Susumu Goto, Shuichi Kawashima, and Akihiro Nakaya.
\newblock {The KEGG databases at GenomeNet}.
\newblock {\em Nucleic Acids Res}, 30(1):42--46, Jan 2002.

\bibitem[LAB{\etalchar{+}}04]{Li:elegansPP}
Siming Li, Christopher~M Armstrong, Nicolas Bertin, Hui Ge, Stuart Milstein,
  Mike Boxem, Pierre-Olivier Vidalain, Jing-Dong~J Han, Alban Chesneau, Tong
  Hao, Debra~S Goldberg, Ning Li, Monica Martinez, Jean-Francois Rual, Philippe
  Lamesch, Lai Xu, Muneesh Tewari, Sharyl~L Wong, Lan~V Zhang, Gabriel~F
  Berriz, Laurent Jacotot, Philippe Vaglio, Jerome Reboul, Tomoko
  Hirozane-Kishikawa, Qianru Li, Harrison~W Gabel, Ahmed Elewa, Bridget
  Baumgartner, Debra~J Rose, Haiyuan Yu, Stephanie Bosak, Reynaldo Sequerra,
  Andrew Fraser, Susan~E Mango, William~M Saxton, Susan Strome, Sander Van
  Den~Heuvel, Fabio Piano, Jean Vandenhaute, Claude Sardet, Mark Gerstein, Lynn
  Doucette-Stamm, Kristin~C Gunsalus, J~Wade Harper, Michael~E Cusick,
  Frederick~P Roth, David~E Hill, and Marc Vidal.
\newblock {A map of the interactome network of the metazoan C. elegans}.
\newblock {\em Science}, 303(5657):540--543, Jan 2004.

\bibitem[LBL02]{Liu:MDscan}
X~Shirley Liu, Douglas~L Brutlag, and Jun~S Liu.
\newblock {An algorithm for finding protein-DNA binding sites with applications
  to chromatin-immunoprecipitation microarray experiments}.
\newblock {\em Nat Biotechnol}, 20(8):835--839, Aug 2002.

\bibitem[MBR{\etalchar{+}}04]{Martin:GoToolBox}
David Martin, Christine Brun, Elisabeth Remy, Pierre Mouren, Denis Thieffry,
  and Bernard Jacq.
\newblock {GOToolBox: functional analysis of gene datasets based on Gene
  Ontology}.
\newblock {\em Genome Biol}, 5(12):R101, 2004.

\bibitem[MKS04]{Muller:textpresso}
Hans-Michael Muller, Eimear~E Kenny, and Paul~W Sternberg.
\newblock {Textpresso: an ontology-based information retrieval and extraction
  system for biological literature}.
\newblock {\em PLoS Biol}, 2(11):e309, Nov 2004.

\bibitem[NY98]{Nielsen:positiveselection}
R~Nielsen and Z~Yang.
\newblock {Likelihood models for detecting positively selected amino acid sites
  and applications to the HIV-1 envelope gene}.
\newblock {\em Genetics}, 148(3):929--936, Mar 1998.

\bibitem[oMUBoR90]{NLM:visiblehuman}
National~Library of~Medicine (U.S.) Board~of Regents.
\newblock Electronic imaging: Report of the board of regents. {U}.{S}.
  department of health and human services, public health service, national
  institutes of health.
\newblock NIH Publication 90-219, 1990.

\bibitem[PMM{\etalchar{+}}02]{Pletcher:caloric}
Scott~D Pletcher, Stuart~J Macdonald, Richard Marguerie, Ulrich Certa,
  Stephen~C Stearns, David~B Goldstein, and Linda Partridge.
\newblock {Genome-wide transcript profiles in aging and calorically restricted
  Drosophila melanogaster}.
\newblock {\em Curr Biol}, 12(9):712--723, Apr 2002.

\bibitem[RCDMH03]{CCD:sexbias}
Jose~M Ranz, Cristian~I Castillo-Davis, Colin~D Meiklejohn, and Daniel~L Hartl.
\newblock {Sex-dependent gene expression and evolution of the Drosophila
  transcriptome}.
\newblock {\em Science}, 300(5626):1742--1745, Jun 2003.

\bibitem[RSA02]{Raychaudhuri:text2groups}
Soumya Raychaudhuri, Hinrich Schutze, and Russ~B Altman.
\newblock {Using text analysis to identify functionally coherent gene groups}.
\newblock {\em Genome Res}, 12(10):1582--1590, Oct 2002.

\bibitem[Sto02]{Storey:FDR}
John~D Storey.
\newblock {A direct approach to false discovery rates}.
\newblock {\em J. R. Statist. Soc. B}, 64:479--498, 2002.

\bibitem[UGC{\etalchar{+}}00]{Uetz:yeastPP}
P~Uetz, L~Giot, G~Cagney, T~A Mansfield, R~S Judson, J~R Knight, D~Lockshon,
  V~Narayan, M~Srinivasan, P~Pochart, A~Qureshi-Emili, Y~Li, B~Godwin,
  D~Conover, T~Kalbfleisch, G~Vijayadamodar, M~Yang, M~Johnston, S~Fields, and
  J~M Rothberg.
\newblock {A comprehensive analysis of protein-protein interactions in
  Saccharomyces cerevisiae}.
\newblock {\em Nature}, 403(6770):623--627, Feb 2000.

\bibitem[WCDO{\etalchar{+}}03]{CCD:yeast}
Elizabeth~A Winzeler, Cristian~I Castillo-Davis, Guy Oshiro, David Liang,
  Daniel~R Richards, Yingyao Zhou, and Daniel~L Hartl.
\newblock {Genetic diversity in yeast assessed with whole-genome
  oligonucleotide arrays}.
\newblock {\em Genetics}, 163(1):79--89, Jan 2003.

\bibitem[WSA{\etalchar{+}}99]{Winzeler:deletion99}
E~A Winzeler, D~D Shoemaker, A~Astromoff, H~Liang, K~Anderson, B~Andre,
  R~Bangham, R~Benito, J~D Boeke, H~Bussey, A~M Chu, C~Connelly, K~Davis,
  F~Dietrich, S~W Dow, M~El~Bakkoury, F~Foury, S~H Friend, E~Gentalen,
  G~Giaever, J~H Hegemann, T~Jones, M~Laub, H~Liao, N~Liebundguth, D~J
  Lockhart, A~Lucau-Danila, M~Lussier, N~M'Rabet, P~Menard, M~Mittmann, C~Pai,
  C~Rebischung, J~L Revuelta, L~Riles, C~J Roberts, P~Ross-MacDonald,
  B~Scherens, M~Snyder, S~Sookhai-Mahadeo, R~K Storms, S~Veronneau, M~Voet,
  G~Volckaert, T~R Ward, R~Wysocki, G~S Yen, K~Yu, K~Zimmermann, P~Philippsen,
  M~Johnston, and R~W Davis.
\newblock {Functional characterization of the S. cerevisiae genome by gene
  deletion and parallel analysis}.
\newblock {\em Science}, 285(5429):901--906, Aug 1999.

\end{thebibliography}