My Functional Genomics Journal Watch

Here I will provide my collection of recently published functional genomics related articles/papers. The microarray collection is the most complete section. The other collections are much more complete after July 2000. Since the number of publications far exceed what I can keep track on nowadays and I still update this list manually by hand (surprise! :) ), I only include those papers which I find interesting. I hope this limited and biased list is useful for you. Please email your comment to me. I will also appreciate suggestions for automating the update.

Acknowledgement: Many thanks to Mr. Abel C.S Chun for downloading articles that I couldn't access through my university in Hong Kong during year 1998-2002. 

Functional genomics [ this week | 2004 Jul-Dec | 2004 Jan-Jun | 2003 Jul-Dec | 2003 Jan-Jun | 2002 | 2001 | 2000 | 1999 | 1998 ]

Microarrays [ this week | 2004 Oct-Dec | 2004 Jul-Sep | 2004 Apr-Jun | 2004 Jan-Mar | 2003 Oct-Dec | 2003 Jul-Sep | 2003 Apr-Jun | 2003 Jan-Mar | 2002 Jul-Dec | 2002 Jan-Jun | 2001 Jul-Dec | 2001 Jan-Jun | 2000 | 1999 | 1998 | 1997 | 1996 & before ]

Bioinformatics [ this week | 2004 Jul-Dec | 2004 Jan-Jun | 2003 Jul-Dec | 2003 Jan-Jun | 2002 | 2001 | 2000 | 1999 | 1998 | 1997 | 1996 & before ]

Proteomics [ this week | 2004 Jul-Dec | 2004 Jan-Jun | 2003 Jul-Dec | 2003 Jan-Jun | 2002 | 2001 | 2000 | 1999 ]

Complex disease trait mapping, genome mapping & linkage analysis [ this week | 2004 | 2003 | 2002 |  2001 | 2000 | 1999 | 1998 ]

Biotech business [ this week | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | 1998 ]

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Functional genomics

28 Nov 2004 - 6 Dec 2004
  1. Kasukawa T, Katayama S, Kawaji H, Suzuki H, Hume DA, Hayashizaki Y. Construction of representative transcript and protein sets of human, mouse, and rat as a platform for their transcriptome and proteome analysis. Genomics. 2004 Dec;84(6):913-921. [PubMed]  
  2. Goldstein DB, Hirschhorn JN. In genetic control of disease, does 'race' matter? Nat Genet. 2004 Dec;36(12):1243-4. [PubMed] 
  3. Waters MD, Fostel JM. Toxicogenomics and systems toxicology: aims and prospects. Nat Rev Genet. 2004 Dec;5(12):936-48.[PubMed]
  4. Lee JS, Chu IS, Mikaelyan A, Calvisi DF, Heo J, Reddy JK, Thorgeirsson SS. Application of comparative functional genomics to identify best-fit mouse models to study human cancer. Nat Genet. 2004 Dec;36(12):1306-11. [PubMed] 

Microarrays

28 Nov 2004 - 6 Dec 2004
  1. Mukherjee S, Berger MF, Jona G, Wang XS, Muzzey D, Snyder M, Young RA, Bulyk ML. Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat Genet. 2004 Dec;36(12):1331-1339.  [PubMed]
  2. Sarkans U, Parkinson H, Lara GG, Oezcimen A, Sharma A, Abeygunawardena N, Contrino S, Holloway E, Rocca-Serra P, Mukherjee G, Shojatalab M, Kapushesky M, Sansone S, Farne A, Rayner T, Brazma A. The ArrayExpress gene expression database: a software engineering and implementation perspective. Bioinformatics. 2004 Nov 25; [Epub ahead of print][PubMed]
  3. Tsai CA, Wang SJ, Chen DT, Chen JJ. Sample size for gene expression microarray experiments* Bioinformatics. 2004 Nov 25; [Epub ahead of print] [PubMed]
  4. Iwamoto K, Bundo M, Kato T. Altered expression of mitochondria-related genes in postmortem brains of patients with bipolar disorder or schizophrenia, as revealed by large-scale DNA microarray analysis. Hum Mol Genet. 2004 Nov 24; [Epub ahead of print] [PubMed]
  5. Chan SM, Ermann J, Su L, Fathman CG, Utz PJ. Protein microarrays for multiplex analysis of signal transduction pathways. Nat Med. 2004 Nov 21;. [Epub ahead of print] [PubMed]
  6. White P, Brestelli JE, Kaestner KH, Greenbaum LE. Identification of transcriptional networks during liver regeneration. J Biol Chem. 2004 Nov 16;. [Epub ahead of print][PubMed]

Bioinformatics

28 Nov 2004 - 6 Dec 2004
  1. Tu K, Yu H, Guo Z, Li X. Learnability-based further prediction of gene functions in Gene Ontology. Genomics. 2004 Dec;84(6):922-928. [PubMed]
  2. Lee I, Date SV, Adai AT, Marcotte EM. A probabilistic functional network of yeast genes. Science. 2004 Nov 26;306(5701):1555-8.[PubMed]
  3. Finak G, Godin N, Hallett M, Pepin F, Rajabi Z, Srivastava V, Tang Z.  BIAS: bioinformatics integrated application software. Bioinformatics. 2004 Nov 30;. [Epub ahead of print][PubMed]
  4. Urbanczik R, Wagner C. An improved algorithm for stoichiometric network analysis: theory and applications. Bioinformatics. 2004 Nov 11; [Epub ahead of print] [PubMed]
  5. Kemmeren P, Kockelkorn TT, Bijma T, Donders R, Holstege FC. Predicting gene function through systematic analysis and quality assessment of high-throughput data. Bioinformatics. 2004 Nov 5;. [Epub ahead of print][PubMed]
  6. Kimura S, Ide K, Kashihara A, Kano M, Hatakeyama M, Masui R, Nakagawa N, Yokoyama S, Kuramitsu S, Konagaya A. Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm. Bioinformatics. 2004 Oct 28;. [Epub ahead of print][PubMed]
  7. Pinto FR, Cowart LA, Hannun YA, Rohrer B, Almeida JS. Local correlation of expression profiles with gene annotations - proof of concept for a general conciliatory method. Bioinformatics. 2004 Oct 28;. [Epub ahead of print][PubMed]
  8. Kloster M, Tang C, Wingreen NS. Finding regulatory modules through large-scale gene-expression data analysis. Bioinformatics. 2004 Oct 28; [Epub ahead of print][PubMed]
  9. Tsai KY, Wang FS. Evolutionary optimization with data collocation for reverse engineering of biological networks. Bioinformatics. 2004 Oct 28; [Epub ahead of print] [PubMed]
  10. Rajagopalan D, Agarwal P. Inferring pathways from gene lists using a literature-derived network of biological relationships. Bioinformatics. 2004 Oct 27;. [Epub ahead of print][PubMed]
  11. Taguchi YH, Oono Y. Relational patterns of gene expression via nonmetric multidimensional scaling analysis. Bioinformatics. 2004 Oct 27;. [Epub ahead of print][PubMed]
  12. Yang CR, Shapiro BE, Mjolsness ED, Hatfield GW. An enzyme mechanism language for the mathematical modeling of metabolic pathways. Bioinformatics. 2004 Oct 27;. [Epub ahead of print][PubMed]
  13. Ding J, Berleant D. MedKit: A helper toolkit for automatic mining of MEDLINE/PubMed citations. Bioinformatics. 2004 Oct 27;. [Epub ahead of print][PubMed]

Proteomics

28 Nov 2004 - 6 Dec 2004
  1. Huang J, Zhu H, Haggarty SJ, Spring DR, Hwang H, Jin F, Snyder M, Schreiber SL. Finding new components of the target of rapamycin (TOR) signaling network through chemical genetics and proteome chips. Proc Natl Acad Sci U S A. 2004 Nov 23;101(47):16594-9.[PubMed]

Complex disease mapping, genome mapping & linkage analysis

28 Nov 2004 - 6 Dec 2004
  1. Taillon-Miller P, Saccone SF, Saccone NL, Duan S, Kloss EF, Lovins EG, Donaldson R, Phong A, Ha C, Flagstad L, Miller S, Drendel A, Lind D, Miller RD, Rice JP, Kwok PY. Linkage disequilibrium maps constructed with common SNPs are useful for first-pass disease association screens. Genomics. 2004 Dec;84(6):899-912. [PubMed]

Biotech Business

28 Nov 2004 - 6 Dec 2004

no new entry during this period
last updated: 6 Dec 2004
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