Tracing the Evolution of Lineage-Specific Transcription Factor Binding Sites in a Birth-Death Framework

Ken Daigoro Yokoyama; Yang Zhang; Jian Ma

doi:10.1371/journal.pcbi.1003771

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Open Access

Peer-reviewed

Research Article

Tracing the Evolution of Lineage-Specific Transcription Factor Binding Sites in a Birth-Death Framework

Ken Daigoro Yokoyama ,

Contributed equally to this work with: Ken Daigoro Yokoyama, Yang Zhang

Affiliation Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
⨯
Yang Zhang ,

Contributed equally to this work with: Ken Daigoro Yokoyama, Yang Zhang

Affiliation Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
⨯
Jian Ma

* E-mail: jianma@illinois.edu

Affiliations Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America, Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
⨯

Tracing the Evolution of Lineage-Specific Transcription Factor Binding Sites in a Birth-Death Framework

Ken Daigoro Yokoyama,
Yang Zhang,
Jian Ma

Published: August 21, 2014
https://doi.org/10.1371/journal.pcbi.1003771

About the Authors

Ken Daigoro Yokoyama

Contributed equally to this work with: Ken Daigoro Yokoyama, Yang Zhang

Affiliation Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America

Yang Zhang

Contributed equally to this work with: Ken Daigoro Yokoyama, Yang Zhang

Affiliation Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America

Jian Ma

* E-mail: jianma@illinois.edu

Affiliations Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America, Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: KDY YZ JM. Performed the experiments: KDY YZ. Analyzed the data: KDY YZ. Contributed reagents/materials/analysis tools: KDY YZ. Contributed to the writing of the manuscript: KDY YZ JM.

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Sequence motif analysis
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Multiple alignment calculation
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Sequence alignment
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Animal phylogenetics
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Death rates
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Mammalian genomics
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Human evolution
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Paleogenetics
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