Labs

Jean-Paul Armache's Lab

The Armache Lab uses cryo-EM and other techniques to understand the mechanisms of ATP-dependent chromatin remodeling complexes, their functions and roles in eukaryotic genome regulation.

Cryo-EM structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome. Armache, J.-P., Gamarra, N., Johnson, S.L., Wu, S., Leonard, J., Narlikar, G. and Cheng, Y. (Jun 18, 2019). Elife. 8: e46057


MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Zheng, S.Q., Palovcak, E., Armache, J.-P., Verba, K.A., Cheng, Y. and Agard, D.A. (April 17, 2017). Nature Methods. 14(4): 331–332.

Structure of the TRPA1 ion channel suggests regulatory mechanisms. Paulsen, C. E.*, Armache J.-P.*, Gao Y., Cheng Y., Julius D. (April 8, 2015). Nature. 520(7548): 511–517.

To view a list of all of Jean-Paul Armache's Publications please click here

Lucy Bai's Lab

The Bai Lab uses a variety of strategies to understand the mechanism of gene regulation by chromatin structure at different levels.

Dissociation rate compensation mechanism for budding yeast pioneer transcription factors. Donovan B, Jipa C, Chen HY, Yan C, Bai L & Poirier MG (2019 Mar 19) Elife pii: e43008.

Genome-wide Study of Nucleosome-Depleting Factors in Budding Yeast. Yan C, Chen HY & Bai L (2018 Jul 19) Mol Cell. 71(2): 294–305.

Three distinct mechanisms of long-distance modulation of gene expression in yeast. Du MY, Zhang Q, & Bai L (2017 Apr 20) PLOS Genet. 13(4):e1006736.

To view a list of all of Lucy Bai's Publications please click here

David Gilmour's Lab


We are interested in understanding mechanisms of transcriptional control in eukaryotes and are currently focusing on the function and mechanism of promoter proximal pausing.

The C-Terminal Domain of RNA Polymerase II Is a Multivalent Targeting Sequence that Supports Drosophila Development with Only Consensus Heptads. Lu F, Portz B, Gilmour DS. (2019 Mar 21) Mol Cell. 73(6):1232-1242.e4.

GFZF, a Glutathione S-Transferase Protein Implicated in Cell Cycle Regulation and Hybrid Inviability, Is a Transcriptional Coactivator. Baumann DG, Dai MS, Lu H, Gilmour DS. (2018 Jan 29) Mol Cell Biol. 38(4)

Identification of Regions in the Spt5 Subunit of DRB Sensitivity-inducing Factor (DSIF) That Are Involved in Promoter-proximal Pausing. Qiu Y, Gilmour DS. (2017 Mar 31) J Biol Chem. 292(13):5555-5570

To view a list of all of David Gilmour's Publications please click here

Ross Hardison's Lab

Ross and his co-workers measure transcriptome profiles and use epigenetic marks and comparative genomics to predict gene regulatory modules.

Accurate and reproducible functional maps in 127 human cell types via 2D genome segmentation. Zhang Y, Hardison RC. (2017 Sept 29) Nucleic Acids Res. 45:9823-9836.

Establishment of regulatory elements during erythro-megakaryopoiesis identifies hematopoietic lineage-commitment points. Heuston EF, Keller CA, Lichtenberg J, Giardine B, Anderson SM; NIH Intramural Sequencing Center, Hardison RC, Bodine DM.. (2018 May 28) Epigenetics Chromatin 11(22).

The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries. Hsu SC, Gilgenast TG, Bartman CR, Edwards CR, Stonestrom AJ, Huang P, Emerson DJ, Evans P, Werner MT, Keller CA, Giardine B, Hardison RC, Raj A, Phillips-Cremins JE, Blobel GA. (2017 Apr 6) Mol Cell. 66(1):102-116.e7.

To view a list of all of Ross Hardison's Publications please click here

Manuel Llinás' Lab

Research in our laboratory is focused on understanding the mechanisms of gene regulation in Plasmodium.

Genome-wide real-time in vivo transcriptional dynamics during Plasmodium falciparum blood-stage development. Painter HJ, Chung NC, Sebastian A, Albert I, Storey JD, Llinás M. (2018 Jul 9) Nature Communications. 9(1):2656.

Red blood cell invasion by the malaria parasite is coordinated by the PfAP2-I transcription factor. Santos JM, Josling G, Ross P, Joshi P, Orchard L, Campbell T, Schieler A, Cristea IM, Llinás M. (2017 Jun 14) Cell Host and Microbe. 21(6):731-741.e10

A transcriptional switch underlies commitment to sexual development in malaria parasites. Kafsack BFC, Rovira-Graells N, Clark TG, Bancells C, Crowley VM, Campino SG, Williams AE, Drought LG, Kwiatkowski DP, Baker DA, Cortés A, Llinás M. (2014 Mar 13) Nature. 507(7491):248-52.

To view a list of all of Manuel Llinás' Publications please click here

Shaun Mahony's Lab

We are computational biologists who develop machine-learning methods for understanding gene regulation. In particular, we aim to understand where transcription factors bind in the genome, and what they do once they get there.

Characterizing protein-DNA binding event subtypes in ChIP-exo data. Yamada N, Lai WKM, Farrell N, Pugh BF, Mahony S. (2019 Mar 15) Bioinformatics 35(6):903-913.

Widespread and precise reprogramming of yeast protein-genome interactions in response to heat shock. Vinayachandran V, Reja R, Rossi MJ, Park B, Rieber L, Mittal C, Mahony S, Pugh BF. (2018 Feb 14) Genome Research (3): 357–366

Deconvolving sequence features that discriminate between overlapping regulatory annotations. Kakumanu A, Velasco S, Mazzoni E, Mahony S. (2017 Oct 19) PLoS Computational Biology 13(10):e1005795.

To view a list of all of Shaun Mahony's Publications please click here

B. Franklin Pugh's Lab

Our research is aimed at understanding how genes are regulated. This knowledge is key to understanding and fixing diseases like cancer. We want to know the mechanics by which all gene promoters are turned on and off.

Characterizing protein-DNA binding event subtypes in ChIP-exo data
Yamada N, Lai WKM, Farrell N, Pugh BF, Mahony S. (2019 Mar 15) Bioinformatics 35(6):903-913.

In vivo genome-wide binding interactions of mouse and human constitutive androstane receptors reveal novel gene targets. Niu B, Coslo DM, Bataille AR, Albert I, Pugh BF, Omiecinski CJ. (2018 Sep 19) Nucleic Acids Research 46(16):8385-8403

Simplified ChIP-exo assays. Rossi MJ, Lai WKM, Pugh BF. (2018 Jul 20) Nature Communications 9(1):2842.

To view a list of all of B. Franklin Pugh's Publications please click here

Joseph Reese's Lab

We are interested in understanding chromatin structure, gene expression, and DNA damage resistance pathways.

Ccr4-Not maintains genomic integrity by controlling the ubiquitylation and degradation of arrested RNAPII. Jiang, H., Wolgast, M., Beebe, L.M. and Reese, J.C. (4 Apr 2019) Genes and Development. 33:705-717

Genome-Wide Mapping of Decay Factor-mRNA Interactions in Yeast Identifies Nutrient Responsive Transcripts as Targets of the Deadenylase Ccr4. Miller, J.E., L. Zhang, H. Jiang, Y. Li, B.F. Pugh and J.C. Reese (4 Jan 2018). G3. 8:315-330.

To view a list of all of Joseph Reese's Publications please click here

Scott Showalter's Lab

We apply biophysical chemistry techniques to understand the function of partially disordered proteins that regulate transcription.

Phosphorylation Induces Sequence-Specific Conformational Switches in the RNA Polymerase II C-Terminal Domain. Gibbs, EB, Lu, F, Portz, B, Fisher, MJ, Medellin, BP, Laremore, TN, Zhang, YJ, Gilmour, DS, Showalter, SA. (2017 May 12) Nat Commun. 8: 15233.

Application of NMR to Studies of Intrinsically Disordered Proteins. Gibbs, EB, Cook, EC, Showalter, SA. (2017 Aug 15) Arch Biochem Biophys. 628: 57-70.

The Solution Ensemble of the C-Terminal Domain from the Transcription Factor Pdx1 Resembles an Excluded Volume Polymer. Cook, EC, Sahu, D, Bastidas, M, Showalter, SA. (2019 Jan 10) J. Phys. Chem. B. 123: 106-116.

To view a list of all of Scott Showalter's Publications please click here

Song Tan's Lab

Our goal is to understand how gene expression is regulated. We study the molecular mechanism of gene regulation chromatin enzymes, in particular, the structural basis for how chromatin enzymes recognize and act on their nucleosome substrate.

Structural basis for activation of SAGA histone acetyltransferase Gcn5 by partner subunit Ada2. Sun J, Paduch M, Kim SA, Kramer RM, Barrios AF, Lu V, Luke J, Usatyuk S, Kossiakoff AA, Tan S. (2018 Oct 2) Proc Natl Acad Sci U S A. 115(40):10010-10015.

The pPSU Plasmids for Generating DNA Molecular Weight Markers. Henrici RC, Pecen TJ, Johnston JL1, Tan S. (2017 May 26) Sci Rep. 7(1):2438.

Crystal structure of the PRC1 ubiquitylation module bound to the nucleosome. McGinty RK, Henrici RC, Tan S. (2014 Oct 30) Nature 514(7524):591-6

To view a list of all of Song Tan's Publications please click here