Buen Abad Najar CF, Yosef N, Lareau LF. 2019. Coverage-dependent bias creates the appearance of binary splicing in single cells. bioRxiv 2019.12.19.883256; doi: 10.1101/2019.12.19.883256 [pdf]

research publications

Tunney RJ*, McGlincy NJ*, Graham ME, Naddaf N, Pachter L, Lareau LF. 2018. Accurate design of translational output by a neural network model of ribosome distribution. Nature Structural & Molecular Biology 25 (7): 577-582. [pdf] [PubMed]
Lareau LF, Brenner SE. 2015. Regulation of splicing factors by alternative splicing and NMD is conserved between kingdoms yet evolutionarily flexible. Molecular Biology and Evolution doi: 10.1093/molbev/msv002. [pdf] [PubMed]
Lareau LF*, Hite DH*, Hogan GJ, Brown PO. 2014. Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments. eLife 10.7554/eLife.01257. [pdf] [PubMed] (Dwell times of ribosomes on each codon, used to generate figures 5 and 6: codon_occupancy_lareau2014.txt)
Ingolia NT, Lareau LF, Weissman JS. 2011. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147 (4): 789-802. [pdf] [PubMed] (Perspective by Weiss and Atkins in Science: [pdf] [PubMed])
Hansen KD*, Lareau LF*, Blanchette M, Green RE, Meng Q, Rehwinkel J, Gallusser FL, Izaurralde E, Rio DC, Dudoit S, Brenner SE. 2009. Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila. PLoS Genetics 5(6): e1000525. [pdf] [PubMed]
Lareau LF*, Inada M*, Green RE, Wengrod JC, Brenner SE. 2007. Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Nature 446 (7138): 926-9. [pdf] [suppl info pdf] [PubMed]
The FANTOM Consortium. 2005. The transcriptional landscape of the mammalian genome. Science 309 (5740): 1559-63. [pdf] [PubMed]
Green RE, Lewis BP, Hillman RT, Blanchette M, Lareau LF, Garnett A, Rio DC, Brenner SE. 2003. Widespread predicted nonsense-mediated mRNA decay of alternatively-spliced transcripts of human normal and disease genes. Bioinformatics 19 (S1): i118-i121. [PubMed]

review publications

Lareau LF, Brooks AN, Soergel DAW, Meng Q, Brenner SE. 2007. The coupling of alternative splicing and nonsense-mediated mRNA decay. In Blencowe B and Graveley B, ed., Alternative splicing in the post-genomic era, Landes Bioscience. [pdf] [PubMed]
Soergel DAW, Lareau LF, Brenner SE. 2006. Regulation of gene expression by the coupling of alternative splicing and nonsense-mediated mRNA decay. In Maquat L, ed., Nonsense-mediated mRNA decay, Landes Bioscience.
Lareau LF, Green RE, Bhatnagar RS, Brenner SE. 2004. The evolving roles of alternative splicing. Current Opinion in Structural Biology 14 (3): 273-82. [pdf] [PubMed]