Genomes and Genes
Michael F Lin
Affiliation: Massachusetts Institute of Technology
- PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regionsMichael F Lin
Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street 32 D510, Cambridge, MA 02139, USA
Bioinformatics 27:i275-82. 2011....
- Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomesMichael F Lin
Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Genome Res 21:1916-28. 2011..Our results show that overlapping functional elements are common in mammalian genes, despite the vast genomic landscape...
- A high-resolution map of human evolutionary constraint using 29 mammalsKerstin Lindblad-Toh
Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
Nature 478:476-82. 2011..Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease...
- Identification of functional elements and regulatory circuits by Drosophila modENCODESushmita Roy
Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology MIT, Cambridge, MA 02139, USA
Science 330:1787-97. 2010..Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation...
- Discovery of functional elements in 12 Drosophila genomes using evolutionary signaturesAlexander Stark
The Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02140, USA
Nature 450:219-32. 2007..We also study how discovery power scales with the divergence and number of species compared, and we provide general guidelines for comparative studies...
- Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesisAndrea Pauli
Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
Genome Res 22:577-91. 2012..Our study provides the first systematic identification of lncRNAs in a vertebrate embryo and forms the foundation for future genetic, genomic, and evolutionary studies...
- Evidence of abundant stop codon readthrough in Drosophila and other metazoaIrwin Jungreis
MIT Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
Genome Res 21:2096-113. 2011....
- Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammalsMitchell Guttman
Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
Nature 458:223-7. 2009..Together, these results define a unique collection of functional lincRNAs that are highly conserved and implicated in diverse biological processes...
- Distinguishing protein-coding and noncoding genes in the human genomeMichele Clamp
Broad Institute of Massachusetts Institute of Technology and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
Proc Natl Acad Sci U S A 104:19428-33. 2007..It also provides a principled methodology for evaluating future proposed additions to the human gene catalog. Finally, the results indicate that there has been relatively little true innovation in mammalian protein-coding genes...
- Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomesMichael F Lin
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
Genome Res 17:1823-36. 2007..These results affect >10% of annotated fly genes and demonstrate the power of comparative genomics to enhance our understanding of genome organization, even in a model organism as intensively studied as Drosophila melanogaster...