Publications

Increased demand for NAD+ related to ATP drives aerobic glycolysis.

Luengo A, Li Z, Gui DY, Sullivan LB, Zagorulya M, Do BT, Ferreira R, Naamati A, Ali A, Lewis CA, Thomas CJ, Spranger S, Matheson NJ, Vander Heiden MG.
Molecular Cell (2021)

Cell Programmed Nutrient Partitioning in the Tumor Microenvironment.

Reinfeld BI, Madden MZ, Wolf MM, Chytil A, Bader JE, Patterson AR, Cohen AS, Ali A, Do BT, Muir A, Lewis CA, Hongo RA, Young KL, Brown RE, Todd VM, Huffstater T, Abraham A, O’Neil RT, Wilson MH, Xin F, Tantawy MN, Merryman WD, Johnson RW, Williams CS, Mason EF, Mason FM, Beckermann KE, Vander Heiden MG, Manning HC, Rathmell JC, Rathmell WK.
bioRxiv (2020)

Opportunities and obstacles for deep learning in biology and medicine.

Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow P-M, Xie W, Rosen GL, Lengerich BJ, Israeli J, Lanchantin J, Woloszynek S, Carpenter AE, Shrikumar A, Xu J, Cofer EM, Harris DJ, DeCaprio D, Qi Y, Kundaje A, Peng Y, Wiley LK, Segler MHS, Gitter A, Greene CS.
Journal of the Royal Society Interface (2018)
- Most viewed bioRxiv preprint of spring 2017 (link)

The novel lncRNA lnc-NR2F1 is pro-neurogenic and mutated in human neurodevelopmental disorders

Ang CE, Wapinski OL, Ma Q, Fan S, Flynn RA, Coe B, Onoguchi M, Olmos VH, Do BT, Dukes-Rimsky L, Xu J, Lee QY, Tanabe K, Wang L, Elling U, Penninger J, Qu K, Eichler EE, Srivastava A, Chang HY, Wernig M.
eLife (2019)

Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress.

Oh S, Flynn RA, Floor SN, Purzner J, Martin L, Do BT, Schubert S, Vaka D, Adams CM, Leib RD, Doudna JA, Chang HY, Cho YJ.
Oncotarget (2016)

Ultraefficient irCLIP pipeline for characterization for protein-RNA interactions.

Zarnegar B, Flynn RA, Shen Y, Do BT, Chang HY, Khavari PA.
Nature Methods (2016)

Stress from nucleotide depletion activates the transcriptional regulator HEXIM1 to suppress melanoma.

Tan JL, Fogley RD, Flynn RA, Ablain J, Yang S, Saint-Andre V, Fan ZP, Do BT, …, Chang HY, Young RA, Zon LI.
Molecular Cell (2016)

7SK-BAF axis controls pervasive transcription at enhancers.

Flynn RA, Do BT, Rubin A, Calo E, Lee B, Rale M, Kuchelmeister H, Rale M, Chu C, Kool ET, Wysocka J, Khavari PA, Chang HY.
Nature Structural and Molecular Biology (2016)

Dissecting non-coding and pathogen RNA-protein interactomes.

Flynn RA, Martin L, Spitale RC, Do BT, Sagan SM, Zarnegar B, Qu K, Khavari PA, Quake SR, Sarnow P, Chang HY.
RNA (2015)

Dicer-microRNA-Myc circuit promotes transcription of hundreds of long noncoding RNAs.

Zheng GXY, Do BT, Webster DE, Khavari PA, Chang HY.
Nature Structural and Molecular Biology (2014)