Affiliation: The Rockefeller University
- A computational investigation of kinetoplastid trans-splicingShuba Gopal
Laboratory of Computational Genomics, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
Genome Biol 6:R95. 2005..We have applied our method to chromosomes 1 and 3 of Leishmania major, with high-confidence predictions for 85% and 88% of annotated genes respectively. We suggest some extensions of our method to other systems...
- Alternative splicing of mouse transcription factors affects their DNA-binding domain architecture and is tissue specificBahar Taneri
The Laboratory of Computational Genomics, The Rockefeller University, New York, NY 10021, USA
Genome Biol 5:R75. 2004..To analyze the impact of alternative splicing on transcription factor (TF) protein structure, we constructed a comprehensive database of splice variants in the mouse transcriptome, called MouSDB3 containing 461 TF loci...
- Archaeal genomicsT Gaasterland
Laboratory of Computational Genomics 1230 York Avenue The Rockefeller University New York, New York, 10021, USA
Curr Opin Microbiol 2:542-7. 1999..These projects cover all branches of the archaeal domain and will lead to new insights into archaeal metabolism, DNA processing, and evolutionary relationships with the Bacteria and Eukarya...
- MAGPIE/EGRET annotation of the 2.9-Mb Drosophila melanogaster Adh regionT Gaasterland
The Rockefeller University, Laboratory of Computational Genomics, New York, New York 10021, USA
Genome Res 10:502-10. 2000..The software modules that add eukaryotic genome annotation capability to MAGPIE are available as EGRET (Eukaryotic Genome Rapid Evaluation Tool)...
- Whole-genome analysis: annotations and updatesT Gaasterland
Laboratory of Computational Genomics, 1230 York Avenue, Rockefeller University, New York, New York 10021, USA
Curr Opin Struct Biol 11:377-81. 2001..These types of information not only improve gene identification, but they also give insights into variation in gene structure and function...
- Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genomeS Gopal
Laboratories of Computational Genomics, The Rockefeller University, New York, New York, USA
Nat Genet 27:337-40. 2001..This annotation strategy is applicable to genomes of all organisms, including human...
- Presence of prokaryotic and eukaryotic species in all subgroups of the PP(i)-dependent group II phosphofructokinase protein familyM Muller
The Rockefeller University, New York, New York 10021, USA
J Bacteriol 183:6714-6. 2001..All four lineages of group II PFKs, as defined by phylogenetic analysis, contained both prokaryotic and eukaryotic species, underlining the complex evolutionary history of this enzyme...
- Characterizing the relationship between protein-fusion and gene co-expressionC S Gunther
Laboratory of Computational Genomics, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
Genome Inform 12:34-43. 2001..Thus, while protein fusion patterns are not predictive of co-expression, they are an important element in explaining co-expression. This justifies the use of curated protein fusion events to help characterize gene co-expression clusters...
- Structural genomics: beyond the human genome projectS K Burley
Howard Hughes Medical Institute, 1230 York Avenue, New York, New York 10021, USA
Nat Genet 23:151-7. 1999..We present the rationale for creation of a structural genomics initiative, recount the efforts of ongoing structural genomics pilot studies, and detail the lofty goals, technical challenges and pitfalls facing structural biologists...
- Microarray-based analysis of early development in Xenopus laevisC R Altmann
Laboratory of Molecular Vertebrate Embryology, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
Dev Biol 236:64-75. 2001..All results obtained by the arrays were independently tested by RT-PCR or by in situ hybridization to provide a direct assessment of the accuracy and reproducibility of these approaches in the context of molecular embryology...