My bioinformatics journal watch - year 2004 Jan-Jun [ this week | 2004 Jul-Dec | 2004 Jan-Jun | 2003 Jul-Dec | 2003 Jan-Jun | 2002 | 2001 | 2000 | 1999 | 1998 | 1997 | 1996 & before ]

General Applications Data mining    Literature mining    Database mining in silico biology/computational modelling Network/pathway reconstruction and analysis*    Promter/regulatory sequence analysis* Protein-protein interaction analysis Gene prediction Gene function prediction Structure prediction Comparative Genomics (theoretical) Languages and Algorithms Software Databases Conference proceedings *Network/pathway studies using microarray technology are put under the microarray section of My functional genomics journal watch; the articles in this page are primarily theoretical.

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General

1. Greenbaum D, Douglas SM, Smith A, Lim J, Fischer M, Schultz M, Gerstein M. Computer security in academia-a potential roadblock to distributed annotation of the human genome. Nat Biotechnol. 2004 Jun;22(6):771-2. [PubMed]
2. Bottomley S. Bioinformatics: smartest software is still just a tool. Nature. 2004 May 20;429(6989):241. [PubMed]
3. Vaidyanathan G. InfoEvolve: moving from data to knowledge using information theory and genetic algorithms. Ann N Y Acad Sci. 2004 May;1020:227-38. [PubMed]
4. Buckingham S. Bioinformatics: Data's future shock. Nature. 2004 Apr 15;428(6984):774-7. [PubMed]
5. Pevzner PA. Educating biologists in the 21st century: bioinformatics scientists vs. bioinformatics technicians. Bioinformatics. 2004 Apr 8 [Epub ahead of print] [PubMed]
6. Rat Genome Special Issue. Genome Research 2004 Apr.
7. Beaumont MA. et al., THE BAYESIAN REVOLUTION IN GENETICS. Nat Rev Genet. 2004 Apr [PubMed]
8. Bialek W, Botstein D. Introductory science and mathematics education for 21st-Century biologists. Science. 2004 Feb 6;303(5659):788-90. [PubMed]
9. May RM. Uses and abuses of mathematics in biology. Science. 2004 Feb 6;303(5659):790-3. [PubMed]
10. Yu U, Lee SH, Kim YJ, Kim S. Bioinformatics in the Post-genome Era. J Biochem Mol Biol. 2004 Jan 31;37(1):75-82. [PubMed]

Applications

1. Kalir S, Alon U. Using a quantitative blueprint to reprogram the dynamics of the flagella gene network. Cell. 2004 Jun 11;117(6):713-20. [PubMed]
2. Lopez-Bigas N, Ouzounis CA. Genome-wide identification of genes likely to be involved in human genetic disease. Nucleic Acids Res. 2004 Jun 04;32(10):3108-14. [PubMed]
3. Berardini TZ, Mundodi S, Reiser L, Huala E, Garcia-Hernandez M, Zhang P, Mueller LA, Yoon J, Doyle A, Lander G, Moseyko N, Yoo D, Xu I, Zoeckler B, Montoya M, Miller N, Weems D, Rhee SY. Functional Annotation of the Arabidopsis Genome Using Controlled Vocabularies. Plant Physiol. 2004 Jun 1;. [Epub ahead of print] [PubMed]
4. Martone ME, Gupta A, Ellisman MH. e-Neuroscience: challenges and triumphs in integrating distributed data from molecules to brains. Nat Neurosci. 2004 May;7(5):467-472. [PubMed]
5. Yeh I, Hanekamp T, Tsoka S, Karp PD, Altman RB. Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery. Genome Res. 2004 May;14(5):917-24. [PubMed]
6. Edwards D, Batley J. Plant bioinformatics: from genome to phenome. Trends Biotechnol. 2004 May;22(5):232-7. [PubMed]
7. McCarthy JF, Marx KA, Hoffman PE, Gee AG, O'Neil P, Ujwal ML, Hotchkiss J. Applications of machine learning and high-dimensional visualization in cancer detection, diagnosis, and management. Ann N Y Acad Sci. 2004 May;1020:239-62. [PubMed]
8. Pekurovsky D, Shindyalov IN, Bourne PE. A case study of high-throughput biological data processing on parallel platforms. Bioinformatics. 2004 Mar 25 [Epub ahead of print] [PubMed]
9. Nowak MA, Sigmund K. Evolutionary dynamics of biological games. Science. 2004 Feb 6;303(5659):793-9. [PubMed]
10. Papin J. et al., Bioinformatics and cellular signaling. Curr Opin Biotechnol. 2004 Feb; [PubMed]
11. Martin-Sanchez F, Iakovidis I, Norager S, Maojo V, De Groen P, Van Der Lei J, Jones T, Abraham-Fuchs K, Apweiler R, Babic A, Baud R, Breton V, Cinquin P, Doupi P, Dugas M, Eils R, Engelbrecht R, Ghazal P, Jehenson P, Kulikowski C, Lampe K, De Moor G, Orphanoudakis S, Rossing N, Sarachan B, Sousa A, Spekowius G, Thireos G, Zahlmann G, Zvarova J, Hermosilla I, Vicente FJ. Synergy between medical informatics and bioinformatics: facilitating genomic medicine for future health care. J Biomed Inform. 2004 Feb;37(1):30-42. [PubMed]

Data mining

1. King RD, Wise PH, Clare A. Confirmation of data mining based predictions of protein function. Bioinformatics. 2004 May 1;20(7):1110-8.[PubMed]
   
2. Mapping Knowledge Domains Supplemental Issues. Proc Natl Acad Sci U S A. 2004 Apr 6

Literature mining

1. Daraselia N, Yuryev A, Egorov S, Novichkova S, Nikitin A, Mazo I. Extracting human protein interactions from MEDLINE using a full-sentence parser. Bioinformatics 2004 Mar 22; 20: 604-611. [PubMed]
2. Wren JD, Bekeredjian R, Stewart JA, Shohet RV, Garner HR. Knowledge discovery by automated identification and ranking of implicit relationships. Bioinformatics. 2004 Feb 12;20(3):389-98. [PubMed]
   

Database mining

1. Daraselia N, Yuryev A, Egorov S, Novichkova S, Nikitin A, Mazo I. Extracting human protein interactions from MEDLINE using a full-sentence parser. Bioinformatics 2004 Mar 22; 20: 604-611. [PubMed]
   

in silico biology/computational modelling

1. Rangel C, Angus J, Ghahramani Z, Lioumi M, Sotheran E, Gaiba A, Wild DL, Falciani F. Modeling T-cell activation using gene expression profiling and state-space models. Bioinformatics. 2004 Jun 12;20(9):1361-72. [PubMed]
2. Herrgard MJ, Palsson BO. Flagellar biosynthesis in silico; building quantitative models of regulatory networks. Cell. 2004 Jun 11;117(6):689-90. [PubMed]
3. Goldstein B, Faeder JR, Hlavacek WS. Mathematical and computational models of immune-receptor signalling. Nat Rev Immunol. 2004 Jun;4(6):445-56. [PubMed]
4. Carlson R, Srienc F. Fundamental Escherichia coli biochemical pathways for biomass and energy production: creation of overall flux states. Biotechnol Bioeng. 2004 Apr 20;86(2):149-62. [PubMed]
5. Meng TC, Somani S, Dhar P. Modeling and simulation of biological systems with stochasticity. In Silico Biol. 2004 Apr 16 [Epub ahead of print] [PubMed]
6. Takahashi K, Kaizu K, Hu B, Tomita M. A multi-algorithm, multi-timescale method for cell simulation. Bioinformatics. 2004 Mar 1;20(4):538-46.[PubMed]
7. Hammer GL, Sinclair TR, Chapman SC, Van Oosterom E. On systems thinking, systems biology, and the in silico plant. Plant Physiol. 2004 Mar;134(3):909-11. [PubMed]
8. Puchalka J, Kierzek AM. Bridging the Gap between Stochastic and Deterministic Regimes in the Kinetic Simulations of the Biochemical Reaction Networks. Biophys J. 2004 Mar;86(3):1357-72. [PubMed]
9. Kiehl TR, Mattheyses RM, Simmons MK. Hybrid simulation of cellular behavior. Bioinformatics. 2004 Feb 12;20(3):316-22. [PubMed]
10. Rangel C, Angus J, Ghahramani Z, Lioumi M, Sotheran E, Gaiba A, Wild DL, Falciani F. Modeling T-cell activation using gene expression profiling and state space models. Bioinformatics. 2004 Feb 12 [Epub ahead of print][PubMed]
11. Bulter T, Lee SG, Wong WW, Fung E, Connor MR, Liao JC. Design of artificial cell-cell communication using gene and metabolic networks. Proc Natl Acad Sci U S A. 2004 Feb 6 [Epub ahead of print] [PubMed]
12. Patil KR. et al., Use of genome-scale microbial models for metabolic engineering. Curr Opin Biotechnol. 2004 Feb; [PubMed]
13. Palsson BO. In silico biotechnology: Era of reconstruction and interrogation. Curr Opin Biotechnol. 2004 Feb; [PubMed]
14. Keane JF, Bradley C, Ebeling C. A Compiled Accelerator for Biological Cell Signaling Simulations.  FPGA2004. 2004 Feb; [Link to article]
    
15. Maly IV, Wiley HS, Lauffenburger DA. Self-Organization of Polarized Cell Signaling via Autocrine Circuits: Computational Model Analysis. Biophys J. 2004 Jan; 86(1): 10-22. [PubMed]
16. Zhu H, Huang S, Dhar P. The next step in systems biology: simulating the temporospatial dynamics of molecular network. Bioessays. 2004 Jan;26(1):68-72. [PubMed]
17. Wall ME, Hlavacek WS, Savageau MA. Design of gene circuits: lessons from bacteria. Nat Rev Genet. 2004 Jan;5(1):34-42. [PubMed]
18. Raghunathan A, Price ND, Galperin MY, Makarova KS, Purvine S, Picone AF, Cherny T, Xie T, Reilly TJ, Munson R Jr, Tyler RE, Akerley BJ, Smith AL, Palsson BO, Kolker E. In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium. OMICS. 2004 Spring;8(1):25-41. [PubMed]

Network/pathway reconstruction and analysis*

1. Batada NN. CNplot: visualizing pre-clustered networks. Bioinformatics. 2004 Jun 12;20(9):1455-6. [PubMed]
2. Yu H, Greenbaum D, Xin Lu H, Zhu X, Gerstein M. Genomic analysis of essentiality within protein networks. Trends Genet. 2004 Jun;20(6):227-31. [PubMed]
3. Iossifov I, Krauthammer M, Friedman C, Hatzivassiloglou V, Bader JS, White KP, Rzhetsky A. Probabilistic inference of molecular networks from noisy data sources. Bioinformatics. 2004 May 22;20(8):1205-13. [PubMed]
4. Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO. Integrating high-throughput and computational data elucidates bacterial networks. Nature. 2004 May 6;429(6987):92-6. [PubMed]
5. Teichmann SA, Babu MM. Gene regulatory network growth by duplication. Nat Genet. 2004 May;36(5):492-6. [PubMed]
6. Simonis N, Van Helden J, Cohen GN, Wodak SJ. Transcriptional regulation of protein complexes in yeast. Genome Biol. 2004;5(5):R33.  [PubMed]
7. Basu S, Mehreja R, Thiberge S, Chen MT, Weiss R. Spatiotemporal control of gene expression with pulse-generating networks. Proc Natl Acad Sci U S A. 2004 Apr 27;101(17):6355-60. [PubMed]
8. Wei GH, Liu DP, Liang CC. Charting gene regulatory networks: strategies, challenges and perspectives. Biochem J. 2004 Apr 13 [Epub ahead of print] [PubMed]
9. Datta A, Choudhary A, Bittner ML, Dougherty ER. External control in Markovian genetic regulatory networks: the imperfect information case. Bioinformatics 2004 Apr 12; 20:924-930 [PubMed]
10. Doi A, Fujita S, Matsuno H, Nagasaki M, Miyano S. Constructing biological pathway models with hybrid functional Petri nets. In Silico Biol. 2004 Apr 7 [Epub ahead of print] [PubMed]
11. Yook SH, Oltvai ZN, Barabasi AL. Functional and topological characterization of protein interaction networks. Proteomics. 2004 Apr;4(4):928-42. [PubMed]
12. Li Z. et al., Inferring pathways and networks with a Bayesian framework. FASEB J 2004 Apr; 2004 [PubMed]
13. Daraselia N, Yuryev A, Egorov S, Novichkova S, Nikitin A, Mazo I. Extracting human protein interactions from MEDLINE using a full-sentence parser. Bioinformatics 2004 Mar 22; 20: 604-611. [PubMed]
14. Gao F, Foat BC, Bussemaker HJ. Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data. BMC Bioinformatics. 2004 Mar 18;5(1):31. [PubMed]
15. Milo R, Itzkovitz S, Kashtan N, Levitt R, Shen-Orr S, Ayzenshtat I, Sheffer M, Alon U. Superfamilies of evolved and designed networks. Science. 2004 Mar 5;303(5663):1538-42. [PubMed]
16. Van Noort V, Snel B, Huynen MA. The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model. EMBO Rep. 2004 Mar;5(3):280-284.[PubMed]
17. Amoutzias GD, Robertson DL, Oliver SG, Bornberg-Bauer E. Convergent evolution of gene networks by single-gene duplications in higher eukaryotes. EMBO Rep. 2004 Feb 13;5(3):274-279. [PubMed]
18. Demir E, Babur O, Dogrusoz U, Gursoy A, Ayaz A, Gulesir G, Nisanci G, Cetin-Atalay R. An ontology for collaborative construction and analysis of cellular pathways. Bioinformatics. 2004 Feb 12;20(3):349-56. [PubMed]
19. Friedman N. Inferring cellular networks using probabilistic graphical models. Science. 2004 Feb 6;303(5659):799-805. [PubMed][Supporting Online Material]  
20. Plavec I, Sirenko O, Privat S, Wang Y, Dajee M, Melrose J, Nakao B, Hytopoulos E, Berg EL, Butcher EC. Method for analyzing signaling networks in complex cellular systems. Proc Natl Acad Sci U S A. 2004 Feb 3;101(5):1223-8. [PubMed]
21. Barabasi AL, Oltvai ZN. Network biology: understanding the cell's functional organization. Nat Rev Genet. 2004 Feb;5(2):101-113. [PubMed]
22. McDermott J, Samudrala R. Enhanced functional information from predicted protein networks. Trends Biotechnol. 2004 Feb;22(2):60-2. [PubMed]
23. Date SV, Marcotte EM. Response to McDermott and Samudrala: Enhanced functional information from predicted protein networks. Trends Biotechnol. 2004 Feb;22(2):62-3. [PubMed]
24. Herrgård MJ et al., Reconstruction of microbial transcriptional regulatory networks. Curr Opin Biotechnol. 2004 Feb; [PubMed]
25. Burgard AP, Nikolaev EV, Schilling CH, Maranas CD. Flux coupling analysis of genome-scale metabolic network reconstructions. Genome Res. 2004 Feb;14(2):301-12. [PubMed][Supplemental Research Data] 
26. Klamt S, Gilles ED. Minimal cut sets in biochemical reaction networks. Bioinformatics. 2004 Jan 22; 20(2): 226-34. [PubMed]  
27. Wren JD, Garner HR. Shared relationship analysis: ranking set cohesion and commonalities within a literature-derived relationship network. Bioinformatics. 2004 Jan 22; 20(2): 191-198. [PubMed]
28. Wong MS, Raab RM, Rigoutsos I, Stephanopoulos GN, Kelleher JK. Metabolic and transcriptional patterns accompanying glutamine depletion and repletion in mouse hepatoma cells: a model for physiological regulatory networks. Physiol Genomics. 2004 Jan 15; 16(2): 247-55. [PubMed]
29. Yu H, Zhu X, Greenbaum D, Karro J, Gerstein M. TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics. Nucleic Acids Res. 2004 Jan 14;32(1):328-37. [PubMed]
30. Francois P, Hakim V. Design of genetic networks with specified functions by evolution in silico. Proc Natl Acad Sci U S A. 2004 Jan 13; 101(2): 580-5. [PubMed] [PDF] [Supporting Information]
31. Kao KC, Yang YL, Boscolo R, Sabatti C, Roychowdhury V, Liao JC. Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis. Proc Natl Acad Sci U S A. 2004 Jan 13; 101(2): 641-6. [PubMed][PDF]
32. Lemke N, Heredia F, Barcellos CK, Dos Reis AN, Mombach JC. Essentiality and damage in metabolic networks. Bioinformatics. 2004 Jan 1;20(1):115-9. [PubMed]
33. Pereira-Leal JB, Enright AJ, Ouzounis CA. Detection of functional modules from protein interaction networks. Proteins. 2004 Jan 1;54(1):49-57. [PubMed]
34. Lappe M, Holm L. Unraveling protein interaction networks with near-optimal efficiency. Nat Biotechnol. 2004 Jan;22(1):98-103. [PubMed][web supplement]
35. Bader JS, Chaudhuri A, Rothberg JM, Chant J. Gaining confidence in high-throughput protein interaction networks. Nat Biotechnol. 2004 Jan;22(1):78-85. [PubMed][web supplement]
36. Ihmels J, Levy R, Barkai N. Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae. Nat Biotechnol. 2004 Jan;22(1):86-92. [PubMed]
37. Parsons AB, Brost RL, Ding H, Li Z, Zhang C, Sheikh B, Brown GW, Kane PM, Hughes TR, Boone C. Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways. Nat Biotechnol. 2004 Jan;22(1):62-9. [PubMed]
38. Wall ME, Hlavacek WS, Savageau MA. Design of gene circuits: lessons from bacteria. Nat Rev Genet. 2004 Jan;5(1):34-42. [PubMed]
39. Brun C, Chevenet F, Martin D, Wojcik J, Guenoche A, Jacq B. Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network. Genome Biol. 2003;5(1):R6. [PubMed]
40. Haverty PM, Hansen U, Weng Z. Computational inference of transcriptional regulatory networks from expression profiling and transcription factor binding site identification. Nucleic Acids Res. 2004;32(1):179-88. [PubMed]
41. Di Bernardo D, Gardner TS, Collins JJ. Robust identification of large genetic networks. Pac Symp Biocomput. 2004;:486-97. [PubMed]
42. Gat-Viks I, Shamir R, Karp RM, Sharan R. Reconstructing chain functions in genetic networks. Pac Symp Biocomput. 2004;:498-509. [PubMed]
43. Kightley DA, Chandra N, Elliston K. Inferring gene regulatory networks from raw data--a molecular epistemics approach. Pac Symp Biocomput. 2004;:510-20. [PubMed]
44. Lu X, Hauskrecht M, Day RS. Modeling cellular processes with variational Bayesian cooperative vector quantizer. Pac Symp Biocomput. 2004;:533-44. [PubMed]
45. Talcott C, Eker S, Knapp M, Lincoln P, Laderoute K. Pathway logic modeling of protein functional domains in signal transduction. Pac Symp Biocomput. 2004;:568-80. [PubMed]

Promter/regulatory sequence analysis*

1. Long F, Liu H, Hahn C, Sumazin P, Zhang MQ, Zilberstein A. Genome-wide prediction and analysis of function-specific transcription factor binding sites. In Silico Biol. 2004 Jun 26;4(3):0033. [Epub ahead of print][PubMed]
2. Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: A Sequence Logo Generator. Genome Res. 2004 Jun;14(6):1188-90. [PubMed]
3. Keles S, Van Der Laan MJ, Vulpe C. Regulatory motif finding by logic regression. Bioinformatics. 2004 May 27 [Epub ahead of print] [PubMed]
4. Zhou M, Cui Y. GeneInfoViz: Constructing and visualizing gene relation networks. In Silico Biol. 2004 Apr 23 [Epub ahead of print] [PubMed]
5. Zhou Q, Liu JS. Modeling within-motif dependence for transcription factor binding site predictions. Bioinformatics 2004 Apr 12; 20:909-916 [PubMed]
6. Wasserman WW. et al., APPLIED BIOINFORMATICS FOR THE IDENTIFICATION OF REGULATORY ELEMENTS. Nat Rev Genet. 2004 Apr [PubMed]
   
7. Phuong TM, Lee D, Lee KH. Regression trees for regulatory element identification. Bioinformatics. 2004 Mar 22;20(5):750-7. [PubMed]
8. Romero PR, Karp PD. Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databases. Bioinformatics. 2004 Mar 22;20(5):709-17. [PubMed]
9. Mullan L. Tutorial section: domains and motifs - proteins in bite-sized chunks. Brief Bioinform. 2004 Mar;5(1):71-4. [PubMed]
10. Van Helden J. Metrics for comparing regulatory sequences on the basis of pattern counts. Bioinformatics. 2004 Feb 12;20(3):399-406. [PubMed]
11. Marino-Ramirez L, Spouge JL, Kanga GC, Landsman D. Statistical analysis of over-represented words in human promoter sequences. Nucleic Acids Res. 2004 Feb 12;32(3):949-958. [PubMed]
12. Bulyk ML, McGuire AM, Masuda N, Church GM. A motif co-occurrence approach for genome-wide prediction of transcription-factor-binding sites in Escherichia coli. Genome Res. 2004 Feb;14(2):201-8. [PubMed]
    
13. Sun H, Davuluri RV. Java-based application framework for visualization of gene regulatory region annotations. Bioinformatics. 2004 Jan 29 [Epub ahead of print] [PubMed]
14. Pritsker M, Liu YC, Beer MA, Tavazoie S. Whole-genome discovery of transcription factor binding sites by network-level conservation. Genome Res. 2004 Jan; 14(1): 99-108.[PubMed]
15. Berezikov E, Guryev V, Plasterk RH, Cuppen E. CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting. Genome Res. 2004 Jan; 14(1): 170-8. [PubMed][Supplemental Research Data] 
16. Bulyk ML. Computational prediction of transcription-factor binding site locations. Genome Biol. 2003;5(1):201. [PubMed]
17. Haverty PM, Hansen U, Weng Z. Computational inference of transcriptional regulatory networks from expression profiling and transcription factor binding site identification. Nucleic Acids Res. 2004;32(1):179-88. [PubMed]
    

Protein-protein interaction analysis

1. Fernandez-Recio J, Totrov M, Abagyan R. Identification of protein-protein interaction sites from docking energy landscapes. J Mol Biol. 2004 Jan 16;335(3):843-65. [PubMed]
   

Gene prediction

1. Chen X, Su Z, Dam P, Palenik B, Xu Y, Jiang T. Operon prediction by comparative genomics: an application to the Synechococcus sp. WH8102 genome. Nucleic Acids Res. 2004 Apr 19;32(7):2147-57. [PubMed]
2. Beer MA, Tavazoie S. Predicting gene expression from sequence. Cell. 2004 Apr 16;117(2):185-98. [PubMed]
3. Nadershahi A, Fahrenkrug SC, Ellis LB. Comparison of computational methods for identifying translation initiation sites in EST data. BMC Bioinformatics. 2004 Feb 16 [Epub ahead of print] [PubMed]
4. Brendel V, Xing L, Zhu W. Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus. Bioinformatics. 2004 Feb 5 [Epub ahead of print] [PubMed]
5. Allen JE, Pertea M, Salzberg SL. Computational gene prediction using multiple sources of evidence. Genome Res. 2004 Jan; 14(1): 142-8. [PubMed]
   

Gene function prediction

1. Cai YD, Doig AJ. Prediction of Saccharomyces cerevisiae protein functional class from functional domain composition. Bioinformatics. 2004 May 22;20(8):1292-300. [PubMed]
2. King RD, Wise PH, Clare A. Confirmation of data mining based predictions of protein function. Bioinformatics. 2004 May 1;20(7):1110-8.[PubMed]
3. Karaoz U, Murali TM, Letovsky S, Zheng Y, Ding C, Cantor CR, Kasif S. Whole-genome annotation by using evidence integration in functional-linkage networks. Proc Natl Acad Sci U S A. 2004 Mar 2;101(9):2888-93. [PubMed]
4. Deng M, Tu Z, Sun F, Chen T. Mapping gene ontology to proteins based on protein–protein interaction data. Bioinformatics 2004 Apr 12; 20:895-902 [PubMed]
5. McAuliffe JD, Pachter L, Jordan MI. Multiple-sequence functional annotation and the generalized hidden Markov phylogeny. Bioinformatics. 2004 Feb 26 [Epub ahead of print] [PubMed]
6. Cai Y, Doig AJ. Prediction of Saccharomyces cerevisiae protein functional class from functional domain composition. Bioinformatics. 2004 Feb 19 [Epub ahead of print] [PubMed]
7. Arakaki AK, Zhang Y, Skolnick J. Large scale assessment of the utility of low resolution protein structures for biochemical function assignment. Bioinformatics. 2004 Feb 5 [Epub ahead of print] [PubMed]
8. Krebs WG, Bourne PE. Statistically rigorous automated protein annotation. Bioinformatics. 2004 Feb 5 [Epub ahead of print] [PubMed]
9. King RD, Wise PH, Clare A. Confirmation of data mining based predictions of protein function. Bioinformatics. 2004 Feb 5 [Epub ahead of print] [PubMed]
10. Sjolander K. Phylogenomic inference of protein molecular function: advances and challenges. Bioinformatics. 2004 Jan 22; 20(2): 170-9. [PubMed]
11. Frith MC, Hansen U, Spouge JL, Weng Z. Finding functional sequence elements by multiple local alignment. Nucleic Acids Res. 2004 Jan 02;32(1):189-200. [PubMed]
12. Hild M, Beckmann B, Haas S, Koch B, Solovyev V, Busold C, Fellenberg K, Boutros M, Vingron M, Sauer F, Hoheisel J, Paro R. An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome. Genome Biol. 2003;5(1):R3. [PubMed]
    

Structure prediction

1. Nagarajan N, Yona G. Automatic prediction of protein domains from sequence information using a hybrid learning system. Bioinformatics. 2004 Jun 12;20(9):1335-60. [PubMed]
2. Zhang Y, Skolnick J. Automated structure prediction of weakly homologous proteins on a genomic scale. Proc Natl Acad Sci U S A. 2004 May 18;101(20):7594-9. [PubMed]
3. Wood MJ, Hirst JD. Predicting protein secondary structure by cascade-correlation neural networks. Bioinformatics. 2004 Feb 12;20(3):419-20. [PubMed]
4. Comeau SR, Gatchell DW, Vajda S, Camacho CJ. ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics. 2004 Jan 1;20(1):45-50. [PubMed]
   

Comparative Genomics (theoretical)

1. Yu H, Luscombe NM, Lu HX, Zhu X, Xia Y, Han JD, Bertin N, Chung S, Vidal M, Gerstein M.  Annotation Transfer Between Genomes: Protein-Protein Interologs and Protein-DNA Regulogs. Genome Res. 2004 Jun;14(6):1107-18. [PubMed]
2. Simillion C, Vandepoele K, Saeys Y, Van De Peer Y. Building genomic profiles for uncovering segmental homology in the twilight zone. Genome Res. 2004 Jun;14(6):1095-106. [PubMed]
3. Bellgard M, Ye J, Gojobori T, Appels R. The bioinformatics challenges in comparative analysis of cereal genomes-an overview. Funct Integr Genomics. 2004 Feb 10 [Epub ahead of print] [PubMed]
4. Chapman BA, Bowers JE, Schulze SR, Paterson AH. A comparative phylogenetic approach for dating whole genome duplication events. Bioinformatics. 2004 Jan 22; 20(2): 180-5. [PubMed]
   

Languages and Algorithms

1. Aladjem MI, Pasa S, Parodi S, Weinstein JN, Pommier Y, Kohn KW. Molecular interaction maps--a diagrammatic graphical language for bioregulatory networks. Sci STKE. 2004 Feb 24;2004(222):pe8. [PubMed]
2. Yang ZR, Chou KC. Bio-support vector machines for computational proteomics. Bioinformatics. 2004 Jan 29 [Epub ahead of print] [PubMed]
3. Liu L, Gong G, Liu Y, Natarajan S, Larkin DM, Everts-Van Der Wind A, Rebeiz M, Beever JE. Multi-species comparative mapping in silico using the COMPASS strategy. Bioinformatics. 2004 Jan 22; 20(2): 148-54. [PubMed]
   

Software

1. Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: A Sequence Logo Generator. Genome Res. 2004 Jun;14(6):1188-90. [PubMed]
2. Dhar P, Meng TC, Somani S, Ye L, Sairam A, Chitre M, Hao Z, Sakharkar K. Cellware--a multi-algorithmic software for computational systems biology. Bioinformatics. 2004 May 22;20(8):1319-21.[PubMed]
3. Zhou M, Cui Y. GeneInfoViz: Constructing and visualizing gene relation networks. In Silico Biol. 2004 Apr 23 [Epub ahead of print] [PubMed]
4. Diemand AV, Scheib H. MolTalk - a programming library for protein structures and structure analysis. BMC Bioinformatics. 2004 Apr 19 [Epub ahead of print] [PubMed]
5. Shapiro BE, Hucka M, Finney A, Doyle J. MathSBML: a package for manipulating SBML-based biological models. Bioinformatics. 2004 Apr 15 [Epub ahead of print] [PubMed]
6. Zhang B, Schmoyer D, Kirov S, Snoddy J. GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies. BMC Bioinformatics. 2004 Feb 18 [Epub ahead of print] [PubMed]
7. Dhar P, Meng TC, Somani S, Ye L, Sairam A, Chitre M, Hao Z, Sakharkar K. Cellware--a multi-algorithmic software for computational systems biology. Bioinformatics. 2004 Feb 10 [Epub ahead of print] [PubMed]
8. Sun H, Davuluri RV. Java-based application framework for visualization of gene regulatory region annotations. Bioinformatics. 2004 Jan 29 [Epub ahead of print] [PubMed]
9. Stocker G, Rieder D, Trajanoski Z. ClusterControl: a web interface for distributing and monitoring bioinformatics applications on a Linux cluster. Bioinformatics. 2004 Jan 29 [Epub ahead of print] [PubMed]
10. Yu H, Zhu X, Greenbaum D, Karro J, Gerstein M. TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics. Nucleic Acids Res. 2004 Jan 14;32(1):328-37. [PubMed]
11. Kasprzyk A, Keefe D, Smedley D, London D, Spooner W, Melsopp C, Hammond M, Rocca-Serra P, Cox T, Birney E. EnsMart: a generic system for fast and flexible access to biological data. Genome Res. 2004 Jan; 14(1): 160-9. [PubMed]
12. Berezikov E, Guryev V, Plasterk RH, Cuppen E. CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting. Genome Res. 2004 Jan; 14(1): 170-8. [PubMed][Supplemental Research Data] 

Databases

1. Hammond MP, Birney E.  Genome information resources - developments at Ensembl. Trends Genet. 2004 Jun;20(6):268-72. [PubMed]
2. Blake J. Bio-ontologies-fast and furious. Nat Biotechnol. 2004 Jun;22(6):773-4. [PubMed]
3. Cuticchia AJ, Silk GW. Bioinformatics needs a software archive. Nature. 2004 May 20;429(6989):241. [PubMed]
4. Quackenbush J. Data standards for 'omic' science. Nat Biotechnol. 2004 May;22(5):613-4. [PubMed]
5. Genome Research 2004 May; 14 ENSEMBL Special
• Birney E, Andrews TD, Bevan P, Caccamo M, Chen Y, Clarke L, Coates G, Cuff J, Curwen V, Cutts T, Down T, Eyras E, Fernandez-Suarez XM, Gane P, Gibbins B, Gilbert J, Hammond M, Hotz HR, Iyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Keenan S, Lehvaslaiho H, McVicker G, Melsopp C, Meidl P, Mongin E, Pettett R, Potter S, Proctor G, Rae M, Searle S, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Ureta-Vidal A, Woodwark KC, Cameron G, Durbin R, Cox A, Hubbard T, Clamp M. An Overview of Ensembl. Genome Res. 2004 May;14(5):925-8. [PubMed]
6. Schaefer CF. Pathway databases. Ann N Y Acad Sci. 2004 May;1020:77-91. Review. [PubMed]
   
7. Normile D. Genomics. New global database lends a hand to gene hunters. Science. 2004 Apr 16;304(5669):368. [PubMed]
8. Chagoyen M, Kurul ME, De-Alarcon PA, Carazo JM, Gupta A. 'Designing and executing scientific workflows with a programmable integrator' Bioinformatics. 2004 Apr 1 [Epub ahead of print] [PubMed]
9. Gilbert D, Ugawa Y, Buchhorn M, Wee TT, Mizushima A, Kim H, Chon K, Weon S, Ma J, Ichiyanagi Y, Liou DM, Keretho S, Napis S. Bio-Mirror project for public bio-data distribution. Bioinformatics. 2004 Apr 1 [Epub ahead of print][PubMed]
10. Riva AA, Kohane IS. A SNP-centric database for the investigation of the human genome. BMC Bioinformatics. 2004 Mar 26 [Epub ahead of print] [PubMed]
11. Xirasagar S, Gustafson S, Merrick BA, Tomer KB, Stasiewicz S, Chan DD, Yost KJ 3rd, Yates JR 3rd, Sumner S, Xiao N, Waters MD. CEBS object model for systems biology data, SysBio-OM. Bioinformatics. 2004 Mar 25 [Epub ahead of print] [PubMed]
12. De Knikker R, Guo Y, Li JL, Kwan AK, Yip KY, Cheung DW, Cheung KH. A web services choreography scenario for interoperating bioinformatics applications. BMC Bioinformatics. 2004 Mar 10 [Epub ahead of print] [PubMed]
13. Mattes WB, Pettit SD, Sansone SA, Bushel PR, Waters MD. Database development in toxicogenomics: issues and efforts. Environ Health Perspect. 2004 Mar;112(4):495-505. [PubMed]
14. Bard JB, Rhee SY. Ontologies in biology: design, applications and future challenges. Nat Rev Genet. 2004 Mar;5(3):213-222. [PubMed]
15. Hayashizaki Y, Kawai J. Innovation: A new approach to the distribution and storage of genetic resources. Nat Rev Genet. 2004 Mar;5(3):223-228. [PubMed]
16. Clark T, Martin S, Liefeld T. Globally distributed object identification for biological knowledgebases. Brief Bioinform. 2004 Mar;5(1):59-70. [PubMed]
17. Apweiler R. et al., Protein sequence databases. Curr Opin Chem Biol.  2004 Feb [PubMed]
18. Crass T, Antes I, Basekow R, Bork P, Buning C, Christensen M, Claussen H, Ebeling C, Ernst P, Gailus-Durner V, Glatting KH, Gohla R, Gossling F, Grote K, Heidtke K, Herrmann A, O'Keeffe S, Kiesslich O, Kolibal S, Korbel JO, Lengauer T, Liebich I, Van Der Linden M, Luz H, Meissner K, Von Mering C, Mevissen HT, Mewes HW, Michael H, Mokrejs M, Muller T, Pospisil H, Rarey M, Reich JG, Schneider R, Schomburg D, Schulze-Kremer S, Schwarzer K, Sommer I, Springstubbe S, Suhai S, Thoppae G, Vingron M, Warfsmann J, Werner T, Wetzler D, Wingender E, Zimmer R. The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources. Bioinformatics. 2004 Jan 22; 20(2): 268-270. [PubMed]
19. Burger A, Davidson D, Baldock R. Formalization of mouse embryo anatomy. Bioinformatics. 2004 Jan 22; 20(2): 259-67. [PubMed]
20. Nucleic Acid Research January 1, 2004 issue - The Molecular Biology Database Collection - The link to the complete issue
• Camon E, Magrane M, Barrell D, Lee V, Dimmer E, Maslen J, Binns D, Harte N, Lopez R, Apweiler R.  The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res. 2004 Jan 1;32(1):D262-6. [PubMed]
• Babnigg G, Giometti CS. GELBANK: a database of annotated two-dimensional gel electrophoresis patterns of biological systems with completed genomes. Nucleic Acids Res. 2004 Jan 1;32(1):D582-5. [PubMed]
• Peri S, Navarro JD, Kristiansen TZ, Amanchy R, Surendranath V, Muthusamy B, Gandhi TK, Chandrika KN, Deshpande N, Suresh S, Rashmi BP, Shanker K, Padma N, Niranjan V, Harsha HC, Talreja N, Vrushabendra BM, Ramya MA, Yatish AJ, Joy M, Shivashankar HN, Kavitha MP, Menezes M, Choudhury DR, Ghosh N, Saravana R, Chandran S, Mohan S, Jonnalagadda CK, Prasad CK, Kumar-Sinha C, Deshpande KS, Pandey A. Human protein reference database as a discovery resource for proteomics. Nucleic Acids Res. 2004 Jan 1;32(1):D497-501. [PubMed]
• Komatsu S, Kojima K, Suzuki K, Ozaki K, Higo K. Rice Proteome Database based on two-dimensional polyacrylamide gel electrophoresis: its status in 2003. Nucleic Acids Res. 2004 Jan 1;32(1):D388-92. [PubMed]
• Bult CJ, Blake JA, Richardson JE, Kadin JA, Eppig JT. The Mouse Genome Database (MGD): integrating biology with the genome. Nucleic Acids Res. 2004 Jan 1;32(1):D476-81. [PubMed]
• Birney E, Andrews D, Bevan P, Caccamo M, Cameron G, Chen Y, Clarke L, Coates G, Cox T, Cuff J, Curwen V, Cutts T, Down T, Durbin R, Eyras E, Fernandez-Suarez XM, Gane P, Gibbins B, Gilbert J, Hammond M, Hotz H, Iyer V, Kahari A, Jekosch K, Kasprzyk A, Keefe D, Keenan S, Lehvaslaiho H, McVicker G, Melsopp C, Meidl P, Mongin E, Pettett R, Potter S, Proctor G, Rae M, Searle S, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Ureta-Vidal A, Woodwark C, Clamp M, Hubbard T. Ensembl 2004. Nucleic Acids Res. 2004 Jan 1;32(1):D468-70. [PubMed]
• Dong Q, Schlueter SD, Brendel V. PlantGDB, plant genome database and analysis tools. Nucleic Acids Res. 2004 Jan 1;32(1):D354-9. [PubMed]
• Schoof H, Ernst R, Nazarov V, Pfeifer L, Mewes HW, Mayer KF. MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics. Nucleic Acids Res. 2004 Jan 1;32(1):D373-6. [PubMed]
• Kulkarni-Kale U, Bhosle S, Manjari GS, Kolaskar AS. VirGen: a comprehensive viral genome resource. Nucleic Acids Res. 2004 Jan 1;32(1):D289-92. [PubMed]
• Golovin A, Oldfield TJ, Tate JG, Velankar S, Barton GJ, Boutselakis H, Dimitropoulos D, Fillon J, Hussain A, Ionides JM, John M, Keller PA, Krissinel E, McNeil P, Naim A, Newman R, Pajon A, Pineda J, Rachedi A, Copeland J, Sitnov A, Sobhany S, Suarez-Uruena A, Swaminathan GJ, Tagari M, Tromm S, Vranken W, Henrick K. E-MSD: an integrated data resource for bioinformatics. Nucleic Acids Res. 2004 Jan 1;32(1):D211-6. [PubMed]
• Kulikova T, Aldebert P, Althorpe N, Baker W, Bates K, Browne P, Van Den Broek A, Cochrane G, Duggan K, Eberhardt R, Faruque N, Garcia-Pastor M, Harte N, Kanz C, Leinonen R, Lin Q, Lombard V, Lopez R, Mancuso R, McHale M, Nardone F, Silventoinen V, Stoehr P, Stoesser G, Tuli MA, Tzouvara K, Vaughan R, Wu D, Zhu W, Apweiler R. The EMBL Nucleotide Sequence Database. Nucleic Acids Res. 2004 Jan 1;32(1):D27-30. [PubMed]
• Krieger CJ, Zhang P, Mueller LA, Wang A, Paley S, Arnaud M, Pick J, Rhee SY, Karp PD. MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. 2004 Jan 1;32(1):D438-42. [PubMed]
• Harris TW, Chen N, Cunningham F, Tello-Ruiz M, Antoshechkin I, Bastiani C, Bieri T, Blasiar D, Bradnam K, Chan J, Chen CK, Chen WJ, Davis P, Kenny E, Kishore R, Lawson D, Lee R, Muller HM, Nakamura C, Ozersky P, Petcherski A, Rogers A, Sabo A, Schwarz EM, Van Auken K, Wang Q, Durbin R, Spieth J, Sternberg PW, Stein LD. WormBase: a multi-species resource for nematode biology and genomics. Nucleic Acids Res. 2004 Jan 1;32(1):D411-7. [PubMed]
• Yazaki J, Kojima K, Suzuki K, Kishimoto N, Kikuchi S. The Rice PIPELINE: a unification tool for plant functional genomics. Nucleic Acids Res. 2004 Jan 1;32(1):D383-7. [PubMed]
• Zhao W, Wang J, He X, Huang X, Jiao Y, Dai M, Wei S, Fu J, Chen Y, Ren X, Zhang Y, Ni P, Zhang J, Li S, Wang J, Wong GK, Zhao H, Yu J, Yang H, Wang J. BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics. Nucleic Acids Res. 2004 Jan 1;32(1):D377-82. [PubMed]
• Fleming K, Muller A, MacCallum RM, Sternberg MJ. 3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes. Nucleic Acids Res. 2004 Jan 1;32(1):D245-50. [PubMed]
• Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A, Webb B, Greenblatt D, Huang CC, Ferrin TE, Sali A. MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 2004 Jan 1;32 DATABASE ISSUE:D217-D222. [PubMed]
• Espadaler J, Fernandez-Fuentes N, Hermoso A, Querol E, Aviles FX, Sternberg MJ, Oliva B. ArchDB: automated protein loop classification as a tool for structural genomics. Nucleic Acids Res. 2004 Jan 1;32(1):D185-8. [PubMed]
21. Klein TE, Altman RB. PharmGKB: the pharmacogenetics and pharmacogenomics knowledge base. Pharmacogenomics J. 2004; 4(1): 1. [PubMed]
22. Mattingly CJ, Colby GT, Rosenstein MC, Forrest JN, Boyer JL. Promoting comparative molecular studies in environmental health research: an overview of the comparative toxicogenomics database (CTD). Pharmacogenomics J. 2004; 4(1): 5-8. [PubMed]

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