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Sequence analysis

Probabilistic Inference of Transcription Factor Binding from Multiple Data Sources

Harri Lähdesmäki, Alistair G. Rust, Ilya Shmulevich

Improving Phrap-Based Assembly of the Rat Using “Reliable” Overlaps

Michael Roberts, Aleksey V. Zimin, [ ... ], James Yorke

Identification of Direct Target Genes Using Joint Sequence and Expression Likelihood with Application to DAF-16

Ron X. Yu, Jie Liu, Nick True, Wei Wang

Conservation Patterns of HIV-1 RT Connection and RNase H Domains: Identification of New Mutations in NRTI-Treated Patients

André F. A. Santos, Renan B. Lengruber, [ ... ], Marcelo A. Soares

Origin and Evolution of GALA-LRR, a New Member of the CC-LRR Subfamily: From Plants to Bacteria?

Andrey V. Kajava, Maria Anisimova, Nemo Peeters

Recombination and Population Mosaic of a Multifunctional Viral Gene, Adeno-Associated Virus cap

Yasuhiro Takeuchi, Richard Myers, Olivier Danos

Sequence Evidence in the Archaeal Genomes that tRNAs Emerged Through the Combination of Ancestral Genes as 5′ and 3′ tRNA Halves

Kosuke Fujishima, Junichi Sugahara, Masaru Tomita, Akio Kanai

A Three-Stage Colonization Model for the Peopling of the Americas

Andrew Kitchen, Michael M. Miyamoto, Connie J. Mulligan

Accumulating Variation at Conserved Sites in Potyvirus Genomes Is Driven by Species Discovery and Affects Degenerate Primer Design

Linda Zheng, Paul J. Wayper, [ ... ], Mark J. Gibbs

Predicted Functional RNAs within Coding Regions Constrain Evolutionary Rates of Yeast Proteins

Charles D. Warden, Seong-Ho Kim, Soojin V. Yi

An Update on MyoD Evolution in Teleosts and a Proposed Consensus Nomenclature to Accommodate the Tetraploidization of Different Vertebrate Genomes

Daniel J. Macqueen, Ian A. Johnston

The Plasmodium Export Element Revisited

Jan Alexander Hiss, Jude Marek Przyborski, [ ... ], Gisbert Schneider

Natural Selection and Adaptive Evolution of Leptin in the Ochotona Family Driven by the Cold Environmental Stress

Jie Yang, Zhen Long Wang, [ ... ], Hui Fang Tian

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