Publications

Lu Bai

Lucy Bai's Publications

- 3D clustering of co-regulated genes and its effect on gene expression.
Du MY & Bai L (2017)
Current Genetics, doi: 10.1007/s00294-017-0712-9. Review. [PDF]

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

- Inter-allelic interaction and gene regulation in budding yeast.
Zhang DY & Bai L (2016)
PNAS, 113:4428-33. [PDF]
David Gilmour

David Gilmour's Publications

- RNAi screen in Drosophila larvae identifies histone deacetylase 3 as a positive regulator of the hsp70 heat shock gene expression during heat shock.
Achary, B.G., K.M. Campbell, I.S. Co, D.S. Gilmour (2014)
BBA – Gene Regulatory Mechanisms 1839:355-363.

- Negative elongation factor (NELF) coordinates RNA polymerase II pausing, premature termination, and chromatin remodeling to regulate HIV transcription.
Natarajan, M., G.M. Schiralli Lester, C. Lee, A. Missra, G.A. Wasserman, M. Steffen, D.S. Gilmour, A.J. Henderson (2013)
Journal of Biological Chemistry 288:25995-26003.

- Kinetic Competition between Elongation Rate and Binding of NELF Controls Promoter-Proximal Pausing.
Li, J, Y. Liu, H.S. Rhee, S.K. Ghosh, L. Bai, B.F. Pugh, D.S. Gilmour (2013)
Molecular Cell 6:711-722.
Ross Hardison

Ross Hardison's Publications

- Cognitive decline and brain amyloid-β accumulation across 3 years in adults with Down syndrome.
Hartley SL, Handen BL, Devenny D, Mihaila I, Hardison R, Lao PJ, Klunk WE, Bulova P, Johnson SC, Christian BT.
Neurobiol Aging.2017 Jun 2;58:68-76. doi: 10.1016/j.neurobiolaging.2017.05.019. [Epub ahead of print] PubMed PMID:28715661.


- An Aggregate Biomarker Risk Score Predicts High Risk of Near-Term Myocardial Infarction and Death: Findings From BARI 2D (Bypass Angioplasty Revascularization Investigation 2 Diabetes).
Ghasemzadeh N, Brooks MM, Vlachos H, Hardison R, Sikora S, Sperling L, Quyyumi AA, Epstein SE.
J Am Heart Assoc. 2017 Jul 3;6(7). pii: e003587. doi: 10.1161/JAHA.116.003587. PubMed PMID: 28673897.


- 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.
Mol Cell. 2017 Apr 6;66(1):102-116.e7. doi: 10.1016/j.molcel.2017.02.027. PubMed PMID: 28388437
Manuel Llinas

Manuel Llinás' Publications

- Transcriptional profiling defines histone acetylation as a regulator of gene expression during human-to-mosquito transmission of the malaria parasite Plasmodium falciparum.
Ngwa CJ, Kiesow MJ, Papst O, Orchard LM, Filarsky M, Rosinski AN, Voss TS, Llinás M, Pradel G.
Frontiers in Cellular and Infection Microbiology. (2017 July 24); doi:10.3389/fcimb.2017.00320. (Supplement)

- Nutrient sensing modulates malaria parasite virulence.
Mancio-Silva L, Slavic K, Ruivo MTG, Grosso AR, Modrzynska KK, Vera IM, Sales-Dias J, Gomes AR, McPherson CR, Crozet P, Adamo M, Baena-Gonzalez E, Tewari R, Llinás M, Billker O, Mota MM.
Nature. (2017 July 05);doi:10.1038/nature23009. (Supplement)(Read PSU Press Release Summary)

- 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.
Cell Host and Microbe. (2017 Jun 14);21(6):731-741.e10. doi: 10.1016/j.chom.2017.05.006. (Supplement)(Read PSU Press Release Summary)(Read Summary from Voice of America)
Shaun Mahony

Shaun Mahony's Publications

- miniMDS: 3D structural inference from high-resolution Hi-C data
L Rieber, S Mahony
Bioinformatics (2017) 33 (14):i261-i266 [Open Access Article]

- A multi-step transcriptional and chromatin state cascade underlies motor neuron programming
S Velasco*, MM Ibrahim*, A Kakumanu*, G Garipler, B Aydin, MA Al-Sayegh, A Hirsekorn, F Abdul-Rahman, R Satija, U Ohler†, S Mahony†, EO Mazzoni†
Cell Stem Cell (2017) 20(2):205-217.e8 [Article]

- The pioneer transcription factor FoxA maintains an accessible nucleosome configuration at enhancers for tissue-specific gene activation
M Iwafuchi-Doi, G Donahue, A Kakumanu, JA Watts, S Mahony, BF Pugh, D Lee, KH Kaestner, KS Zaret
Molecular Cell (2016) 62(1): 72-91 [Article]
Frank Pugh

B. Franklin Pugh's Publications

- Correspondence: DNA shape is insufficient to explain binding.
Rossi MJ, Lai WKM, Pugh BF. (2017)
Nat Commun. PMID: 28580956

- Understanding nucleosome dynamics and their links to gene expression and DNA replication.
Lai WKM, Pugh BF. (2017)
Nat Rev Mol Cell Biol. PMID: 28537572

- Genome-wide uniformity of human open pre-initiation complexes.
Lai, W.K., and Pugh, B.F. (2016).
Genome Res, in press.
Joe Reese

Joseph Reese's Publications

- The elongation factor Spt4/5 regulates RNA polymerase II transcription through the nucleosome.
Crickard, J.B. , Lee, J, Lee, T-H and Reese, J.C. (2017).
Nucleic Acids Research, 45:6362-6374.

- Biochemical Analysis of Yeast Suppressor of Ty 4/5 (Spt4/5) Reveals the Importance of Nucleic Acid Interactions in the Prevention of RNA Polymerase II Arrest
Crickard, J.B., J. Fu and J.C. Reese. (2016).
J. Biol. Chemistry 291, 9853-9870.

- Ccr4-Not and TFIIS function cooperatively to rescue arrested RNA polymerase II.
Dutta, A, V Babbarwal, J Fu, D Brunke-Reese, DM Libert, J Willis and JC Reese (2015)
Mol. Cell Biol, 35:1915-1925.
Scott Showalter

Scott Showalter's Publications

- Application of NMR to Studies of Intrinsically Disordered Proteins.
Gibbs, E.B., Cook, E.C., & Showalter, S.A. (2017)
Arch. Biochem. Biophys., accepted.

- Phosphorylation Induces Sequence-Specific Conformational Switches in the RNA Polymerase II C-Terminal Domain.
Gibbs, E.B., Lu, F., Portz, B., Fisher, M.J., Medellin, B.P., Laremore, T.N., Zhang, Y.J., Gilmour, D.S., & Showalter, S.A. (2017)
Nat. Commun., 8, 15233.

- Structural Heterogeneity in the Intrinsically Disordered RNA Polymerase II C-terminal Domain.
Portz, B., Lu, F., Gibbs, E.B., Mayfield, J.E., Mehaffey, M.R., Zhang, Y.J., Brodbelt, J.S., Showalter, S.A., & Gilmour, D.S. (2017)
Nat. Commun., 8, 15231.
Song Tan

Song Tan's Publications

- The pPSU plasmids for generating DNA molecular weight markers
Henrici, R.C., Pecen, T.J., Johnston, J.L and Tan, S. (2017)
Scientific Reports, 7:2438.

- Preparation, crystallization, and structure determination of chromatin enzyme/nucleosome complexes
McGinty, R.K., R.D. Makde and S. Tan (2016).
Method Enzymol, 573:43-65.

- Multivalent interactions by the Set8 histone methyltransferase with its nucleosome substrate
Girish, T.S., R.K. McGinty and S. Tan (2016).
J. Mol Biol., 428:1531-1543.
Yanming Wang

Yanming Wang's Publications

- Priming of neutrophils toward netosis promotes tumor growth.
Demers M, Wong SL, Martinod K, Gallant M, Cabral JE, Wang Y, Wagner DD (2016)
OncoImmunology. 5(5):e1134073. DOI:10.1080/2162402X.2015.1134073

- Iron chelating agents desferrioxamine and L-mimosine stimulate neutrophil extracellular traps (NETs) 36(3).
Vollger L, Akong-Moore K, Cox L, Goldmann O, Wang Y, Schafer S, Naim H, Nizet V, von Kockritz-Blickwede M (2016)
pii: e00333. DOI: 10.1042/BSR20160031.

- Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition).
Klionsky DJ et al. …Wang Y… (2016)
Autophagy. 12(1):1-222.