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The Diploid Genome Sequence of an Individual Human
Presented here is a genome sequence of an individual human. It was produced from ∼32 million random DNA fragments, sequenced by Sanger dideoxy technology and assembled into 4,528 scaffolds,… Expand
Sorting by Transpositions
Sequence comparison in computational molecular biology is a powerful tool for deriving evolutionary and functional relationships between genes. However, classical alignment algorithms handle only… Expand
Genome Rearrangements and Sorting by Reversals
Sequence comparison in molecular biology is in the beginning of a major paradigm shift---a shift from gene comparison based on local mutations (i.e., insertions, deletions, and substitutions of… Expand
The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families
Metagenomics projects based on shotgun sequencing of populations of micro-organisms yield insight into protein families. We used sequence similarity clustering to explore proteins with a… Expand
InsPecT: identification of posttranslationally modified peptides from tandem mass spectra.
Reliable identification of posttranslational modifications is key to understanding various cellular regulatory processes. We describe a tool, InsPecT, to identify posttranslational modifications… Expand
The Dog Genome: Survey Sequencing and Comparative Analysis
A survey of the dog genome sequence (6.22 million sequence reads; 1.5× coverage) demonstrates the power of sample sequencing for comparative analysis of mammalian genomes and the generation of… Expand
A 2-Approximation Algorithm for the Undirected Feedback Vertex Set Problem
- Vineet Bafna, P. Berman, Toshihiro Fujito
- Computer Science, Mathematics
- SIAM J. Discret. Math.
- 1 September 1999
A feedback vertex set of a graph is a subset of vertices that contains at least one vertex from every cycle in the graph. The problem considered is that of finding a minimum feedback vertex set given… Expand
Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer.
While genetic mutation is a hallmark of cancer, many cancers also acquire epigenetic alterations during tumorigenesis including aberrant DNA hypermethylation of tumor suppressors, as well as changes… Expand
A Multidimensional Chromatography Technology for In-depth Phosphoproteome Analysis*S
- Claudio P. Albuquerque, M. Smolka, Samuel H. Payne, Vineet Bafna, J. Eng, H. Zhou
- Medicine, Chemistry
- Molecular & Cellular Proteomics
- 1 July 2008
Protein phosphorylation is a post-translational modification widely used to regulate cellular responses. Recent studies showed that global phosphorylation analysis could be used to study signaling… Expand
HapCUT: an efficient and accurate algorithm for the haplotype assembly problem
MOTIVATION The goal of the haplotype assembly problem is to reconstruct the two haplotypes (chromosomes) for an individual using a mix of sequenced fragments from the two chromosomes. This problem… Expand