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CSB
2004
IEEE
256views Bioinformatics» more  CSB 2004»
15 years 1 months ago
SUPERCONTIGS: A Contig Scaffolding Tool
SUPERCONTIGS is a genome-finishing tool that orders, orients and groups contigs based on clone pair information and an alignment with a related genome. The program can be used in ...
Daniela Puiu
JBI
2006
14 years 9 months ago
Phylogenetics by likelihood: Evolutionary modeling as a tool for understanding the genome
Molecular evolutionary studies provide a means of investigating how cells function and how organisms adapt to their environment. The products of evolutionary studies provide medic...
Carolin Kosiol, Lee Bofkin, Simon Whelan
BMCBI
2004
154views more  BMCBI 2004»
14 years 9 months ago
Base-By-Base: Single nucleotide-level analysis of whole viral genome alignments
Background: With ever increasing numbers of closely related virus genomes being sequenced, it has become desirable to be able to compare two genomes at a level more detailed than ...
Ryan Brodie, Alex J. Smith, Rachel L. Roper, Vasil...
BMCBI
2004
117views more  BMCBI 2004»
14 years 9 months ago
CisOrtho: A program pipeline for genome-wide identification of transcription factor target genes using phylogenetic footprinting
Background: All known genomes code for a large number of transcription factors. It is important to develop methods that will reveal how these transcription factors act on a genome...
Henry R. Bigelow, Adam S. Wenick, Allan Wong, Oliv...
WABI
2004
Springer
132views Bioinformatics» more  WABI 2004»
15 years 3 months ago
Joint Analysis of DNA Copy Numbers and Gene Expression Levels
Abstract. Genomic instabilities, amplifications, deletions and translocations are often observed in tumor cells. In the process of cancer pathogenesis cells acquire multiple genom...
Doron Lipson, Amir Ben-Dor, Elinor Dehan, Zohar Ya...