The Gene Index Publications
|
Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence (1995), Nature, 377(Suppl.): 3-174. Entrez link [96026280] Adams, MD et. al | ||
|
The TIGR Gene Indices: reconstruction and representation of expressed gene sequences. (2000), Nucleic Acids Research", 28, 141-145. Entrez link [10592205] Quackenbush, J., Liang, F., Holt, I., Pertea, G., Upton, J. | ||
|
Gene Index analysis of the human genome estimates approximately 120,000 genes (2000), Nature Genetics, 25, 239-240. Entrez link [10835646] Liang, F.,Holt, I., Pertea, G., Karamycheva, S., Salzberg, S., Quackenbush, J. | ||
|
An optimized protocol for analysis of EST sequences. (2000), Nucleic Acids Research", 28, 3657-3665. Entrez link [10982889] Liang, F., Holt, I., Pertea, G., Karamycheva, S., Salzberg, S., Quackenbush, J. | ||
| ||
|
Sequence evaluation of four pooled-tissue normalized bovine cDNA libraries and construction of a gene index for cattle. (2001), 4, 626-30. Entrez link [11282978] Smith TP, Grosse WM, Freking BA, Roberts AJ, Stone RT, Casas E, Wray JE, White J, Cho J, Fahrenkrug SC, Bennett GL, Heaton MP, Laegreid WW, Rohrer GA,Chitko-McKown CG, Pertea G, Holt I, Karamycheva S, Liang F, Quackenbush J, Keele JW. | ||
|
RESOURCERER: a database for annotating and linking microarray resources within and across species. (2001), Genome Biology, 2(11): software0002.1-0002.4 Tsai J., Sultana R., Lee Y., Pertea G., Karamycheva K., Antonescu V., Cho J., Parvizi P., Cheung F., Quackenbush J. | ||
|
Cross-Referencing Eukaryotic Genomes: TIGR Orthologous Gene Alignments (TOGA) (2002), Genome Research, 12:493-502. Lee Y., Sultana R., Pertea G., Cho J., Karamycheva S., Tsai J., Parvizi B., Cheung F., Antonescu V., White J., Holt I., Liang F., and Quackenbush J. | ||
|
Porcine gene discovery by normalized cDNA-library sequencing and EST cluster assembly. (2002), Mamm Genome 2002 Aug;13(8):475-8. Entrez link [12226715 ] Fahrenkrug SC, Smith TP, Freking BA, Cho J, White J, Vallet J, Wise T, Rohrer G, Pertea G, Sultana R, Quackenbush J, Keele JW. | ||
|
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs (2002), Nature. 2002 Dec 5;420(6915):563-73. Entrez link [12466851] Okazaki Y et. al | ||
|
The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists Nucleic Acids Res. 2003 Jan 1;31(1):229-33. Entrez link [12519988 ] Yuan Q, Ouyang S, Liu J, Suh B, Cheung F, Sultana R, Lee D, Quackenbush J, Buell CR. | ||
|
Comparative analyses of potato expressed sequence tag libraries (2003), Plant Physiol. 2003 Feb;131(2):419-29. Entrez link [12586867] Ronning CM et.al | ||
|
Integrating computationally assembled mouse transcript sequences with the Mouse Genome Informatics (MGI) database (2003), Genome Biol. 2003;4(2):R16. Epub 2003 Feb 03. Entrez link [12620126 ] Zhu Y, King BL, Parvizi B, Brunk BP, Stoeckert CJ Jr, Quackenbush J, Richardson J, Bult CJ. | ||
|
TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. (2003), Bioinformatics. 2003 Mar 22;19(5):651-2. Entrez link [12651724] Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, Tsai J, Quackenbush J. | ||
|
The Schistosoma mansoni gene index: gene discovery and biology by reconstruction and analysis of expressed gene sequences (2003), J Parasitol. 2003 Apr;89(2):261-9. Entrez link [12760639] Merrick JM, Osman A, Tsai J, Quackenbush J, LoVerde PT, Lee NH. |
| Acknowledgements | |
|---|---|
 |
The Gene Index Project is supported in part by funding from the US National Science Foundation through grant #DBI-0552416. |
 
|