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2022
Batut PJ, Bing XYang, Sisco Z, Raimundo J, Levo M, Levine MS. Genome organization controls transcriptional dynamics during development. Science. 2022 ;375(6580):566-570.
Levo M, Raimundo J, Bing XYang, Sisco Z, Batut PJ, Ryabichko S, et al. Transcriptional coupling of distant regulatory genes in living embryos. Nature. 2022 ;605(7911):754-760.
2021
Lim B, Levine MS. Enhancer-promoter communication: hubs or loops?. Curr Opin Genet Dev. 2021 ;67:5-9.
Chetverina D, Erokhin M, Schedl P. GAGA factor: a multifunctional pioneering chromatin protein. Cell Mol Life Sci. 2021 ;78(9):4125-4141.
Arita Y, Kim G, Li Z, Friesen H, Turco G, Wang RY, et al. A genome-scale yeast library with inducible expression of individual genes. Mol Syst Biol. 2021 ;17(6):e10207.
Ing-Simmons E, Vaid R, Bing XYang, Levine M, Mannervik M, Vaquerizas JM. Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning. Nat Genet. 2021 ;53(4):487-499.
Duddy OP, Huang X, Silpe JE, Bassler BL. Mechanism underlying the DNA-binding preferences of the Vibrio cholerae and vibriophage VP882 VqmA quorum-sensing receptors. PLoS Genet. 2021 ;17(7):e1009550.
Lalwani MA, Ip SS, Carrasco-López C, Day C, Zhao EM, Kawabe H, et al.. Optogenetic control of the lac operon for bacterial chemical and protein production. Nat Chem Biol. 2021 ;17(1):71-79.
Ruf-Zamojski F, Zhang Z, Zamojski M, Smith GR, Mendelev N, Liu H, et al. Single nucleus multi-omics regulatory landscape of the murine pituitary. Nat Commun. 2021 ;12(1):2677.
Shidlovskii YV, Bylino OV, Shaposhnikov AV, Kachaev ZM, Lebedeva LA, Kolesnik VV, et al. Subunits of the PBAP Chromatin Remodeler Are Capable of Mediating Enhancer-Driven Transcription in . Int J Mol Sci. 2021 ;22(6).
2020
Zhao EM, Lalwani MA, Lovelett RJ, García-Echauri SA, Hoffman SM, Gonzalez CL, et al.. Design and Characterization of Rapid Optogenetic Circuits for Dynamic Control in Yeast Metabolic Engineering. ACS Synth Biol. 2020 ;9(12):3254-3266.
Hartenian E, Gilbertson S, Federspiel JD, Cristea IM, Glaunsinger BA. RNA decay during gammaherpesvirus infection reduces RNA polymerase II occupancy of host promoters but spares viral promoters. PLoS Pathog. 2020 ;16(2):e1008269.
2019
Kachaev ZM, Lebedeva LA, Shaposhnikov AV, Moresco JJ, Yates JR, Schedl P, et al. Paip2 cooperates with Cbp80 at an active promoter and participates in RNA Polymerase II phosphorylation in Drosophila. FEBS Lett. 2019 ;593(10):1102-1112.
2018
Postika N, Metzler M, Affolter M, Müller M, Schedl P, Georgiev P, et al.. Boundaries mediate long-distance interactions between enhancers and promoters in the Drosophila Bithorax complex. PLoS Genet. 2018 ;14(12):e1007702.
Gilbertson S, Federspiel JD, Hartenian E, Cristea IM, Glaunsinger B. Changes in mRNA abundance drive shuttling of RNA binding proteins, linking cytoplasmic RNA degradation to transcription. Elife. 2018 ;7.
Zhou J, Theesfeld CL, Yao K, Chen KM, Wong AK, Troyanskaya OG. Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk. Nat Genet. 2018 ;50(8):1171-1179.
Zoller B, Little SC, Gregor T. Diverse Spatial Expression Patterns Emerge from Unified Kinetics of Transcriptional Bursting. Cell. 2018 ;175(3):835-847.e25.
Chen H, Levo M, Barinov L, Fujioka M, Jaynes JB, Gregor T. Dynamic interplay between enhancer-promoter topology and gene activity. Nat Genet. 2018 ;50(9):1296-1303.
Ding Q, Nimgaonkar I, Archer NF, Bram Y, Heller B, Schwartz RE, et al. Identification of the Intragenomic Promoter Controlling Hepatitis E Virus Subgenomic RNA Transcription. mBio. 2018 ;9(3).
Kachaev ZM, Lebedeva LA, Kozlov EN, Toropygin IY, Schedl P, Shidlovskii YV. Paip2 is localized to active promoters and loaded onto nascent mRNA in Drosophila. Cell Cycle. 2018 ;17(14):1708-1720.
2017
Santos JMendonca, Josling G, Ross P, Joshi P, Orchard L, Campbell T, et al. Red Blood Cell Invasion by the Malaria Parasite Is Coordinated by the PfAP2-I Transcription Factor. Cell Host Microbe. 2017 ;21(6):731-741.e10.
2016
Mallarino R, Henegar C, Mirasierra M, Manceau M, Schradin C, Vallejo M, et al. Developmental mechanisms of stripe patterns in rodents. Nature. 2016 ;539(7630):518-523.
Fukaya T, Lim B, Levine M. Enhancer Control of Transcriptional Bursting. Cell. 2016 ;166(2):358-368.
Blythe SA, Wieschaus EF. Establishment and maintenance of heritable chromatin structure during early embryogenesis. Elife. 2016 ;5.
Kyrchanova O, Mogila V, Wolle D, Deshpande G, Parshikov A, Cleard F, et al. Functional Dissection of the Blocking and Bypass Activities of the Fab-8 Boundary in the Drosophila Bithorax Complex. PLoS Genet. 2016 ;12(7):e1006188.