Doctoral Thesis Title: Biochemical and functional characterization of human RNA binding proteins

Publications while at MIT:

1.Expanded encyclopaedias of DNA elements in the human and mouse genomes.

ENCODE Project Consortium, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z.Nature. 2020 Jul;583(7818):699-710. doi: 10.1038/s41586-020-2493-4. Epub 2020 Jul 29.PMID: 32728249 Free PMC article.

2. Perspectives on ENCODE.

ENCODE Project Consortium, Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, Cherry JM, Bernstein BE, Mendenhall EM, Zerbino DR, Frankish A, Flicek P, Myers RM.Nature. 2020 Jul;583(7818):693-698. doi: 10.1038/s41586-020-2449-8. Epub 2020 Jul 29.PMID: 32728248 Free PMC article.

3. A large-scale binding and functional map of human RNA-binding proteins.

Van Nostrand EL, Freese P, Pratt GA, Wang X, Wei X, Xiao R, Blue SM, Chen JY, Cody NAL, Dominguez D, Olson S, Sundararaman B, Zhan L, Bazile C, Bouvrette LPB, Bergalet J, Duff MO, Garcia KE, Gelboin-Burkhart C, Hochman M, Lambert NJ, Li H, McGurk MP, Nguyen TB, Palden T, Rabano I, Sathe S, Stanton R, Su A, Wang R, Yee BA, Zhou B, Louie AL, Aigner S, Fu XD, Lécuyer E, Burge CB, Graveley BR, Yeo GW.Nature. 2020 Jul;583(7818):711-719. doi: 10.1038/s41586-020-2077-3. Epub 2020 Jul 29.PMID: 32728246 Free PMC article.

4. Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA.

Yang EW, Bahn JH, Hsiao EY, Tan BX, Sun Y, Fu T, Zhou B, Van Nostrand EL, Pratt GA, Freese P, Wei X, Quinones-Valdez G, Urban AE, Graveley BR, Burge CB, Yeo GW, Xiao X.Nat Commun. 2019 Mar 22;10(1):1338. doi: 10.1038/s41467-019-09292-w.PMID: 30902979 Free PMC article.

5. 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.

6. Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System.

Martinez FJ, Pratt GA, Van Nostrand EL, Batra R, Huelga SC, Kapeli K, Freese P, Chun SJ, Ling K, Gelboin-Burkhart C, Fijany L, Wang HC, Nussbacher JK, Broski SM, Kim HJ, Lardelli R, Sundararaman B, Donohue JP, Javaherian A, Lykke-Andersen J, Finkbeiner S, Bennett CF, Ares M Jr, Burge CB, Taylor JP, Rigo F, Yeo GW.Neuron. 2016 Nov 23;92(4):780-795. doi: 10.1016/j.neuron.2016.09.050. Epub 2016 Oct 20.PMID: 27773581 Free PMC article.

7. Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses.

Kapeli K, Pratt GA, Vu AQ, Hutt KR, Martinez FJ, Sundararaman B, Batra R, Freese P, Lambert NJ, Huelga SC, Chun SJ, Liang TY, Chang J, Donohue JP, Shiue L, Zhang J, Zhu H, Cambi F, Kasarskis E, Hoon S, Ares M Jr, Burge CB, Ravits J, Rigo F, Yeo GW.Nat Commun. 2016 Jul 5;7:12143. doi: 10.1038/ncomms12143.PMID: 27378374 Free PMC article.

8. Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival.

Conway AE, Van Nostrand EL, Pratt GA, Aigner S, Wilbert ML, Sundararaman B, Freese P, Lambert NJ, Sathe S, Liang TY, Essex A, Landais S, Burge CB, Jones DL, Yeo GW.Cell Rep. 2016 Apr 19;15(3):666-679. doi: 10.1016/j.celrep.2016.03.052. Epub 2016 Apr 7.PMID: 27068461 Free PMC article.

9. Antagonistic regulation of mRNA expression and splicing by CELF and MBNL proteins.

Wang ET, Ward AJ, Cherone JM, Giudice J, Wang TT, Treacy DJ, Lambert NJ, Freese P, Saxena T, Cooper TA, Burge CB.Genome Res. 2015 Jun;25(6):858-71. doi: 10.1101/gr.184390.114. Epub 2015 Apr 16.PMID: 25883322 Free PMC article.