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Vol. 10, Issue 7, 950-958, July 2000
LETTER
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  E. Frittoli, A. Palamidessi, A. Pizzigoni, L. Lanzetti, M. Garre, F. Troglio, A. Troilo, M. Fukuda, P. P. Di Fiore, G. Scita, et al. The Primate-specific Protein TBC1D3 Is Required for Optimal Macropinocytosis in a Novel ARF6-dependent Pathway Mol. Biol. Cell, April 1, 2008; 19(4): 1304 - 1316. [Abstract] [Full Text] [PDF]
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 L. Yang, G. Jin, X. Zhao, Y. Zheng, Z. Xu, and W. Wu PIP: a database of potential intron polymorphism markers Bioinformatics, August 15, 2007; 23(16): 2174 - 2177. [Abstract] [Full Text] [PDF]
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 A. Vishnoi, R. Roy, and A. Bhattacharya Comparative analysis of bacterial genomes: identification of divergent regions in mycobacterial strains using an anchor-based approach Nucleic Acids Res., June 28, 2007; 35(11): 3654 - 3667. [Abstract] [Full Text] [PDF]
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 J. Flannick, A. Novak, B. S. Srinivasan, H. H. McAdams, and S. Batzoglou Graemlin: General and robust alignment of multiple large interaction networks Genome Res., September 1, 2006; 16(9): 1169 - 1181. [Abstract] [Full Text] [PDF]
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M. Stanke, O. Keller, I. Gunduz, A. Hayes, S. Waack, and B. Morgenstern AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W435 - W439. [Abstract] [Full Text] [PDF]
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D. B. Malko, V. J. Makeev, A. A. Mironov, and M. S. Gelfand Evolution of exon-intron structure and alternative splicing in fruit flies and malarial mosquito genomes Genome Res., April 1, 2006; 16(4): 505 - 509. [Abstract] [Full Text] [PDF]
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W. Huang, D. M. Umbach, and L. Li Accurate anchoring alignment of divergent sequences Bioinformatics, January 1, 2006; 22(1): 29 - 34. [Abstract] [Full Text] [PDF]
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M. R. Brent Genome annotation past, present, and future: How to define an ORF at each locus Genome Res., December 1, 2005; 15(12): 1777 - 1786. [Abstract] [Full Text] [PDF]
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A. Lomsadze, V. Ter-Hovhannisyan, Y. O. Chernoff, and M. Borodovsky Gene identification in novel eukaryotic genomes by self-training algorithm Nucleic Acids Res., November 28, 2005; 33(20): 6494 - 6506. [Abstract] [Full Text] [PDF]
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 M. Pritsker, T. T. Doniger, L. C. Kramer, S. E. Westcot, and I. R. Lemischka Diversification of stem cell molecular repertoire by alternative splicing PNAS, October 4, 2005; 102(40): 14290 - 14295. [Abstract] [Full Text] [PDF]
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J. Flannick and S. Batzoglou Using multiple alignments to improve seeded local alignment algorithms Nucleic Acids Res., August 12, 2005; 33(14): 4563 - 4577. [Abstract] [Full Text] [PDF]
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D. Pohler, N. Werner, R. Steinkamp, and B. Morgenstern Multiple alignment of genomic sequences using CHAOS, DIALIGN and ABC Nucleic Acids Res., July 1, 2005; 33(suppl_2): W532 - W534. [Abstract] [Full Text] [PDF]
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W. H. Majoros, M. Pertea, and S. L. Salzberg Efficient implementation of a generalized pair hidden Markov model for comparative gene finding Bioinformatics, May 1, 2005; 21(9): 1782 - 1788. [Abstract] [Full Text] [PDF]
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T. D. Wu and C. K. Watanabe GMAP: a genomic mapping and alignment program for mRNA and EST sequences Bioinformatics, May 1, 2005; 21(9): 1859 - 1875. [Abstract] [Full Text] [PDF]
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 B. J. Wagstaff and D. J. Begun Comparative Genomics of Accessory Gland Protein Genes in Drosophila melanogaster and D. pseudoobscura Mol. Biol. Evol., April 1, 2005; 22(4): 818 - 832. [Abstract] [Full Text] [PDF]
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L. Ye and X. Huang MAP2: multiple alignment of syntenic genomic sequences Nucleic Acids Res., January 7, 2005; 33(1): 162 - 170. [Abstract] [Full Text] [PDF]
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D. GuhaThakurta, L. A. Schriefer, R. H. Waterston, and G. D. Stormo Novel transcription regulatory elements in Caenorhabditis elegans muscle genes Genome Res., December 1, 2004; 14(12): 2457 - 2468. [Abstract] [Full Text] [PDF]
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A. C.E. Darling, B. Mau, F. R. Blattner, and N. T. Perna Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements Genome Res., July 1, 2004; 14(7): 1394 - 1403. [Abstract] [Full Text] [PDF]
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M. Brudno, R. Steinkamp, and B. Morgenstern The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences Nucleic Acids Res., July 1, 2004; 32(suppl_2): W41 - W44. [Abstract] [Full Text] [PDF]
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L. Taher, O. Rinner, S. Garg, A. Sczyrba, and B. Morgenstern AGenDA: gene prediction by cross-species sequence comparison Nucleic Acids Res., July 1, 2004; 32(suppl_2): W305 - W308. [Abstract] [Full Text] [PDF]
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M. Stanke, R. Steinkamp, S. Waack, and B. Morgenstern AUGUSTUS: a web server for gene finding in eukaryotes Nucleic Acids Res., July 1, 2004; 32(suppl_2): W309 - W312. [Abstract] [Full Text] [PDF]
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The Ludwig-FAPESP Transcript Finishing Initiative, M. C. Sogayar, and A. A. Camargo A Transcript Finishing Initiative for Closing Gaps in the Human Transcriptome Genome Res., July 1, 2004; 14(7): 1413 - 1423. [Abstract] [Full Text] [PDF]
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L.-H. Li, J.-C. Li, Y.-F. Lin, C.-Y. Lin, C.-Y. Chen, and S.-F. Tsai Genomic shotgun array: a procedure linking large-scale DNA sequencing with regional transcript mapping Nucleic Acids Res., February 11, 2004; 32(3): e27 - e27. [Abstract] [Full Text] [PDF]
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J. E. Moore and J. A. Lake Gene structure prediction in syntenic DNA segments Nucleic Acids Res., December 15, 2003; 31(24): 7271 - 7279. [Abstract] [Full Text] [PDF]
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E. H. Margulies, M. Blanchette, NISC Comparative Sequencing Program, D. Haussler, and E. D. Green Identification and Characterization of Multi-Species Conserved Sequences Genome Res., December 1, 2003; 13(12): 2507 - 2518. [Abstract] [Full Text] [PDF]
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T. Xie, L. Rowen, B. Aguado, M. E. Ahearn, A. Madan, S. Qin, R. D. Campbell, and L. Hood Analysis of the Gene-Dense Major Histocompatibility Complex Class III Region and Its Comparison to Mouse Genome Res., December 1, 2003; 13(12): 2621 - 2636. [Abstract] [Full Text] [PDF]
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 A. Zhao, J.-L. Lew, L. Huang, J. Yu, T. Zhang, Y. Hrywna, J. R. Thompson, N. de Pedro, R. A. Blevins, F. Pelaez, et al. Human Kininogen Gene Is Transactivated by the Farnesoid X Receptor J. Biol. Chem., August 1, 2003; 278(31): 28765 - 28770. [Abstract] [Full Text] [PDF]
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A. C.-C. Shih and W.-H. Li GS-Aligner: A Novel Tool for Aligning Genomic Sequences Using Bit-Level Operations Mol. Biol. Evol., August 1, 2003; 20(8): 1299 - 1309. [Abstract] [Full Text] [PDF]
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S. Cawley, L. Pachter, and M. Alexandersson SLAM web server for comparative gene finding and alignment Nucleic Acids Res., July 1, 2003; 31(13): 3507 - 3509. [Abstract] [Full Text] [PDF]
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 C. W. Bogue Genetic Models in Applied Physiology: Invited Review: Functional genomics in the mouse: powerful techniques for unraveling the basis of human development and disease J Appl Physiol, June 1, 2003; 94(6): 2502 - 2509. [Abstract] [Full Text] [PDF]
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 R. N. Nurtdinov, I. I. Artamonova, A. A. Mironov, and M. S. Gelfand Low conservation of alternative splicing patterns in the human and mouse genomes Hum. Mol. Genet., June 1, 2003; 12(11): 1313 - 1320. [Abstract] [Full Text] [PDF]
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L. Zhang, V. Pavlovic, C. R Cantor, and S. Kasif Human-Mouse Gene Identification by Comparative Evidence Integration and Evolutionary Analysis Genome Res., June 1, 2003; 13(6): 1190 - 1202. [Abstract] [Full Text] [PDF]
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T. A. Thanaraj, F. Clark, and J. Muilu Conservation of human alternative splice events in mouse Nucleic Acids Res., May 15, 2003; 31(10): 2544 - 2552. [Abstract] [Full Text] [PDF]
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U. Pozzoli, G. Elgar, R. Cagliani, L. Riva, G. P. Comi, N. Bresolin, A. Bardoni, and M. Sironi Comparative Analysis of Vertebrate Dystrophin Loci Indicate Intron Gigantism as a Common Feature Genome Res., May 1, 2003; 13(5): 764 - 772. [Abstract] [Full Text] [PDF]
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M. Brudno, C. B. Do, G. M. Cooper, M. F. Kim, E. Davydov, N. C. S. Program, E. D. Green, A. Sidow, and S. Batzoglou LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA Genome Res., April 1, 2003; 13(4): 721 - 731. [Abstract] [Full Text] [PDF]
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R. Guigo, E. T. Dermitzakis, P. Agarwal, C. P. Ponting, G. Parra, A. Reymond, J. F. Abril, E. Keibler, R. Lyle, C. Ucla, et al. Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes PNAS, February 4, 2003; 100(3): 1140 - 1145. [Abstract] [Full Text] [PDF]
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K. A. Frazer, L. Elnitski, D. M. Church, I. Dubchak, and R. C. Hardison Cross-Species Sequence Comparisons: A Review of Methods and Available Resources Genome Res., January 1, 2003; 13(1): 1 - 12. [Abstract] [Full Text] [PDF]
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P. Flicek, E. Keibler, P. Hu, I. Korf, and M. R. Brent Leveraging the Mouse Genome for Gene Prediction in Human: From Whole-Genome Shotgun Reads to a Global Synteny Map Genome Res., January 1, 2003; 13(1): 46 - 54. [Abstract] [Full Text] [PDF]
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L. Elnitski, R. C. Hardison, J. Li, S. Yang, D. Kolbe, P. Eswara, M. J. O'Connor, S. Schwartz, W. Miller, and F. Chiaromonte Distinguishing Regulatory DNA From Neutral Sites Genome Res., January 1, 2003; 13(1): 64 - 72. [Abstract] [Full Text] [PDF]
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O. Couronne, A. Poliakov, N. Bray, T. Ishkhanov, D. Ryaboy, E. Rubin, L. Pachter, and I. Dubchak Strategies and Tools for Whole-Genome Alignments Genome Res., January 1, 2003; 13(1): 73 - 80. [Abstract] [Full Text] [PDF]
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G. Parra, P. Agarwal, J. F. Abril, T. Wiehe, J. W. Fickett, and R. Guigo Comparative Gene Prediction in Human and Mouse Genome Res., January 1, 2003; 13(1): 108 - 117. [Abstract] [Full Text] [PDF]
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N. Bray, I. Dubchak, and L. Pachter AVID: A Global Alignment Program Genome Res., January 1, 2003; 13(1): 97 - 102. [Abstract] [Full Text] [PDF]
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Z. Kan, D. States, and W. Gish Selecting for Functional Alternative Splices in ESTs Genome Res., December 1, 2002; 12(12): 1837 - 1845. [Abstract] [Full Text] [PDF]
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C. Mathe, M.-F. Sagot, T. Schiex, and P. Rouze Current methods of gene prediction, their strengths and weaknesses Nucleic Acids Res., October 1, 2002; 30(19): 4103 - 4117. [Abstract] [Full Text] [PDF]
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A. Toyoda, H. Noguchi, T. D. Taylor, T. Ito, M. T. Pletcher, Y. Sakaki, R. H. Reeves, and M. Hattori Comparative Genomic Sequence Analysis of the Human Chromosome 21 Down Syndrome Critical Region Genome Res., September 1, 2002; 12(9): 1323 - 1332. [Abstract] [Full Text] [PDF]
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F. R. van der Leij, K. B. Cox, V. N. Jackson, N. C. A. Huijkman, B. Bartelds, J. R. G. Kuipers, T. Dijkhuizen, P. Terpstra, P. A. Wood, V. A. Zammit, et al. Structural and Functional Genomics of the CPT1B Gene for Muscle-type Carnitine Palmitoyltransferase I in Mammals J. Biol. Chem., July 19, 2002; 277(30): 26994 - 27005. [Abstract] [Full Text] [PDF]
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M. Walker, V. Pavlovic, and S. Kasif A comparative genomic method for computational identification of prokaryotic translation initiation sites Nucleic Acids Res., July 15, 2002; 30(14): 3181 - 3191. [Abstract] [Full Text] [PDF]
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C. Chureau, M. Prissette, A. Bourdet, V. Barbe, L. Cattolico, L. Jones, A. Eggen, P. Avner, and L. Duret Comparative Sequence Analysis of the X-Inactivation Center Region in Mouse, Human, and Bovine Genome Res., June 1, 2002; 12(6): 894 - 908. [Abstract] [Full Text] [PDF]
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H. A. Burgess and O. Reiner Alternative Splice Variants of Doublecortin-like Kinase Are Differentially Expressed and Have Different Kinase Activities J. Biol. Chem., May 10, 2002; 277(20): 17696 - 17705. [Abstract] [Full Text] [PDF]
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D. GuhaThakurta, L. Palomar, G. D. Stormo, P. Tedesco, T. E. Johnson, D. W. Walker, G. Lithgow, S. Kim, and C. D. Link Identification of a Novel cis-Regulatory Element Involved in the Heat Shock Response in Caenorhabditis elegans Using Microarray Gene Expression and Computational Methods Genome Res., May 1, 2002; 12(5): 701 - 712. [Abstract] [Full Text] [PDF]
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U. DeSilva, L. Elnitski, J. R. Idol, J. L. Doyle, W. Gan, J. W. Thomas, S. Schwartz, N. L. Dietrich, S. M. Beckstrom-Sternberg, J. C. McDowell, et al. Generation and Comparative Analysis of ~3.3 Mb of Mouse Genomic Sequence Orthologous to the Region of Human Chromosome 7q11.23 Implicated in Williams Syndrome Genome Res., January 1, 2002; 12(1): 3 - 15. [Abstract] [Full Text] [PDF]
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A. A. Camargo, H. P. B. Samaia, E. Dias-Neto, D. F. Simao, I. A. Migotto, M. R. S. Briones, F. F. Costa, M. Aparecida Nagai, S. Verjovski-Almeida, M. A. Zago, et al. From the Cover: The contribution of 700,000 ORF sequence tags to the definition of the human transcriptome PNAS, October 9, 2001; 98(21): 12103 - 12108. [Abstract] [Full Text] [PDF]
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T. Wiehe, S. Gebauer-Jung, T. Mitchell-Olds, and R. Guigo SGP-1: Prediction and Validation of Homologous Genes Based on Sequence Alignments Genome Res., September 1, 2001; 11(9): 1574 - 1583. [Abstract] [Full Text] [PDF]
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C. M. Bergman and M. Kreitman Analysis of Conserved Noncoding DNA in Drosophila Reveals Similar Constraints in Intergenic and Intronic Sequences Genome Res., August 1, 2001; 11(8): 1335 - 1345. [Abstract] [Full Text] [PDF]
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R.-F. Yeh, L. P. Lim, and C. B. Burge Computational Inference of Homologous Gene Structures in the Human Genome Genome Res., May 1, 2001; 11(5): 803 - 816. [Abstract] [Full Text]
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Z. Kan, E. C. Rouchka, W. R. Gish, and D. J. States Gene Structure Prediction and Alternative Splicing Analysis Using Genomically Aligned ESTs Genome Res., May 1, 2001; 11(5): 889 - 900. [Abstract] [Full Text]
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T. Shiraishi, T. Druck, K. Mimori, J. Flomenberg, L. Berk, H. Alder, W. Miller, K. Huebner, and C. M. Croce Sequence conservation at human and mouse orthologous common fragile regions, FRA3B/FHIT and Fra14A2/Fhit PNAS, April 18, 2001; (2001) 91095898. [Abstract] [Full Text]
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