Publications

Deep representation learning improves prediction of LacI-mediated transcriptional repression

Garruss, A., Collins, K., Church, G. (2021). PNAS doi.org/10.1073/pnas.2022838118

A deep learning approach to programmable RNA switches

Angenent-Mari, N., Garruss, A., Soenksen, L., Church, G., Collins, J. (2020) Nature Communications 11, 5057. doi.org/10.1038/s41467-020-18677-1

Engineering an allosteric transcription factor to respond to new ligands

Taylor, N., Garruss, A., Moretti, R., Chan, S., Arbing, M., Cascio, D., Rogers, J., Isaacs, F., Kosuri, S., Baker, D., Fields, S., Church, G., Raman, S. (2016) Nature Methods 13, 177-183. doi.org/10.1038/nmeth.3696

The RNA Pol II Elongation Factor Ell3 Marks Enhancers in ES Cells and Primes Future Gene Activation.

Lin C, Garruss AS, Luo Z, Guo F, Shilatifard A. Cell. 2013;152:144-156.

The Little Elongation Complex Functions at Initiation and Elongation Phases of snRNA Gene Transcription.

Hu D, Smith ER, Garruss AS, Mohaghegh N, Varberg JM, Lin C, Jackson J, Gao X, Saraf A, Florens L, Washburn MP, Eissenberg JC, Shilatifard A. Mol Cell. 2013;51:493-505.

SET for life: biochemical activities and biological functions of SET domain-containing proteins.

Herz HM, Garruss A, Shilatifard A. Trends Biochem Sci. 2013;38:621-639.

Poised RNA Polymerase II Changes over Developmental Time and Prepares Genes for Future Expression.

Gaertner B, Johnston J, Chen K, Wallaschek N, Paulson A, Garruss AS, Gaudenz K, De Kumar B, Krumlauf R, Zeitlinger J. Cell Rep. 2012;2:1670-1683.

Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution.

Smith JJ, Kuraku S, Holt C, Sauka-Spengler T, Jiang N, Campbell MS, Yandell MD, Manousaki T, Meyer A, Bloom OE, Morgan JR, Buxbaum JD, Sachidanandam R, Sims C, Garruss AS, Cook M, Krumlauf R, Wiedemann LM, Sower SA, Decatur WA, Hall JA, Amemiya CT, Saha NR, Buckley KM, Rast JP, Das S, Hirano M, McCurley N, Guo P, Rohner N, Tabin CJ, Piccinelli P, Elgar G, Ruffier M, Aken BL, Searle SM, Muffato M, Pignatelli M, Herrero J, Jones M, Brown CT, Chung-Davidson YW, Nanlohy KG, Libants SV, Yeh CY, McCauley DW, Langeland JA, Pancer Z, Fritzsch B, de Jong PJ, Zhu B, Fulton LL, Theising B, Flicek P, Bronner ME, Warren WC, Clifton SW, Wilson RK, Li W. Nat Genet. 2013;45:415-421.

Enhancer-associated H3K4 monomethylation by Trithorax-related, the Drosophila homolog of mammalian MLL3/MLL4.

Herz HM, Mohan M, Garruss AS, Liang K, Takahashi YH, Mickey K, Voets O, Verrijzer CP, Shilatifard A. Genes Dev. 2012;26:2604-2620.

The Mll2 branch of the COMPASS family regulates bivalent promoters in mouse embryonic stem cells.

Hu D, Garruss AS, Gao X, Morgan MA, Cook M, Smith ER, Shilatifard A. Nat Struct Mol Biol. 2013;20:1092-1097.