Doctoral Thesis Title: Regulation by RNA-binding proteins: sequence determinants and evolutionary dynamics

Publications while at MIT:

1. Acidification of Tumor at Stromal Boundaries Drives Transcriptome Alterations Associated with Aggressive Phenotypes.

Rohani N, Hao L, Alexis MS, Joughin BA, Krismer K, Moufarrej MN, Soltis AR, Lauffenburger DA, Yaffe MB, Burge CB, Bhatia SN, Gertler FB.

Cancer Res. 2019 Apr 15;79(8):1952-1966. doi: 10.1158/0008-5472.CAN-18-1604. Epub 2019 Feb 12.

PMID:30755444

2. Sequence, Structure, and Context Preferences of Human RNA Binding Proteins.

Dominguez D, Freese P, Alexis MS,Su A, Hochman M, Palden T, Bazile C, Lambert NJ, Van Nostrand EL, Pratt GA, Yeo GW, Graveley BR, Burge CB.

Mol Cell. 2018 Jun 7;70(5):854-867.e9. doi: 10.1016/j.molcel.2018.05.001. Epub 2018 Jun 7.

PMID:29883606 Free PMC Article

3. RNA Sequence Context Effects Measured In Vitro Predict In Vivo Protein Binding and Regulation.

Taliaferro JM, Lambert NJ, Sudmant PH, Dominguez D, Merkin JJ, Alexis MS, Bazile C, Burge CB.

Mol Cell. 2016 Oct 20;64(2):294-306. doi: 10.1016/j.molcel.2016.08.035. Epub 2016 Oct 6.

PMID:27720642 Free PMC Article

4. Meta-analysis of RNA-seq expression data across species, tissues and studies.

Sudmant PH, Alexis MS, Burge CB.

Genome Biol. 2015 Dec 22;16:287. doi: 10.1186/s13059-015-0853-4.

PMID:26694591 Free PMC Article

5. Origins and impacts of new mammalian exons.

Merkin JJ, Chen P, Alexis MS, Hautaniemi SK, Burge CB.

Cell Rep. 2015 Mar 31;10(12):1992-2005. doi: 10.1016/j.celrep.2015.02.058. Epub 2015 Mar 19.

PMID:25801031 Free PMC Article