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Mirny LA, Goloborodko A, Loop Extrusion: A Universal Mechanism of Chromosome Organization. In Modeling the 3D Conformation of Genomes, CRC Press (2019)

Romero Calvo I., Weber C., Ray M, Brown M., Kirby K., Nandi R., Long T., Sparrow S., Ugolkov A., Qiang W., Zhang Y., Brunetti T., Kindler H., Segal J., Rzhetsky A., Mazar A., Buschmann M., Weichselbaum R., Roggin K., and White K. Human organoids share structural and genetic features with primary pancreatic adenocarcinoma tumors. Molecular Cancer Research 17(1):70-83, 2019 PMID: 30171177

Wytock TP, Motter AE, Predicting growth rate from gene expression. Natl. Acad. Sci. USA 116(2), 367-372 (2019). PMCID: PMC6329983. doi:10.1073/pnas.1808080116.

Eshein A, Li Y, Dong B, Almassalha LM, Chandler JE, Nguyen TQ, Hujsak KA, Dravid VP, Sun C, Zhang HF, Backman V. Sub-10-nm imaging of nucleic acids using spectroscopic intrinsic-contrast photon-localization optical nanoscopy (SICLON). Opt Lett. 2018 Dec 1;43(23):5817-5820. doi: 10.1364/OL.43.005817. PubMed PMID:30499949.

Banigan E., Mirny LA, Limits of chromosome compaction by loop-extruding motors. bioRxiv Nov 21, (2018).

Spicer GLC, Almassalha L, Martinez IA, Ellis R, Chandler JE, Gladstein S, Zhang D, Nguyen TQ, Feder S, Subramanian H, de la Rica R, Thompson SA, Backman V. Label free localization of nanoparticles in live cancer cells using spectroscopic microscopy. Nanoscale. 2018 Oct 18;10(40):19125-19130. doi: 10.1039/c8nr07481j. PubMed PMID: 30298892.

Alzrigat M, Jernberg-Wiklund H, Licht JD. Targeting EZH2 in Multiple Myeloma-Multifaceted Anti-Tumor Activity. Epigenomes. 2018 September 3;2(3). PubMed PMID:30761216; PubMed Central PMCID: PMC6370027.

Swaroop A, Oyer JA, Will CM, Huang X, Yu W, Troche C, Bulic M, Durham BH, Wen QJ, Crispino JD, MacKerell AD Jr, Bennett RL, Kelleher NL, Licht JD. An activating mutation of the NSD2 histone methyltransferase drives oncogenic reprogramming in acute lymphocytic leukemia. Oncogene. 2018 Aug 31. doi:10.1038/s41388-018-0474-y. [Epub ahead of print] PubMed PMID: 30171259.

Skoruppa E, Nomidis SK, Marko JF, Carlon E. Bend-Induced Twist Waves and the Structure of Nucleosomal DNA. Phys Rev Lett. 2018 Aug 24;121(8):088101. doi:10.1103/PhysRevLett.121.088101. PubMed PMID: 30192578; PubMed Central PMCID:PMC6132066.

Sun M, Biggs R, Hornick J, Marko JF. Condensin controls mitotic chromosome stiffness and stability without forming a structurally contiguous scaffold. Chromosome Res. 2018 Dec;26(4):277-295. doi: 10.1007/s10577-018-9584-1. Epub 2018 Aug 24. PubMed PMID: 30143891.

Dong H, Zhu M, Meng L, Ding Y, Yang D, Zhang S, Qiang W, Fisher DW, Xu EY. Pumilio2 regulates synaptic plasticity via translational repression of synaptic receptors in mice. 2018 Jan 30;9(63):32134-32148. doi:10.18632/oncotarget.24345. eCollection 2018 Aug 14. PubMed PMID: 30181804; PubMed Central PMCID: PMC6114944.

Melo-Cardenas J, Xu Y, Wei J, Tan C, Kong S, Gao B, Montauti E, Kirsammer G, Licht JD, Yu J, Ji P, Crispino JD, Fang D. USP22 deficiency leads to myeloid leukemia upon oncogenic Kras activation through a PU.1-dependent mechanism. Blood. 2018 Jul 26;132(4):423-434. doi: 10.1182/blood-2017-10-811760. Epub 2018 May 29. PubMed PMID: 29844011; PubMed Central PMCID: PMC6071563.

Haber A, Molnar F, Motter AE. State observation and sensor selection for nonlinear networks. IEEE Trans Control Netw Syst. 2018 Jun;5(2):694-708. doi:10.1109/TCNS.2017.2728201. Epub 2017 Jul 17. PubMed PMID: 30320141; PubMed Central PMCID: PMC6178986. in RPPR

Nuebler J, Fudenberg G, Imakaev M, Abdennur N, Mirny LA. Chromatin organization by an interplay of loop extrusion and compartmental segregation. Proc Natl Acad Sci U S A. 2018 Jul 17;115(29):E6697-E6706. doi:10.1073/pnas.1717730115. Epub 2018 Jul 2. PubMed PMID: 29967174; PubMed Central PMCID: PMC6055145.

Ntai I, Fornelli L, DeHart CJ, Hutton JE, Doubleday PF, LeDuc RD, van Nispen AJ, Fellers RT, Whiteley G, Boja ES, Rodriguez H, Kelleher NL. Precise characterization of KRAS4b proteoforms in human colorectal cells and tumors reveals mutation/modification cross-talk. Proc Natl Acad Sci U S A. 2018 Apr 17;115(16):4140-4145. doi: 10.1073/pnas.1716122115. Epub 2018 Apr 2. PubMed PMID:29610327; PubMed Central PMCID: PMC5910823.

Oomen ME, Dekker J. Epigenetic characteristics of the mitotic chromosome in 1D and 3D. Critical reviews in biochemistry and molecular biology. 2017 April;52(2):185-204. PubMed PMID: 28228067; PubMed Central PMCID: PMC5456460.

Gibcus JH, Samejima K, Goloborodko A, Samejima I, Naumova N, Nuebler J, Kanemaki MT, Xie L, Paulson JR, Earnshaw WC, Mirny LA, Dekker J. A pathway for mitotic chromosome formation. Science (New York, N.Y.). 2018 February 9;359(6376). PubMed PMID: 29348367; PubMed Central PMCID: PMC5924687.

Gong X, Lazaris C, Sakellaropoulos T, Lozano A, Kambadur P, Ntziachristos P, Aifantis I, Tsirigos A. Stratification of TAD boundaries reveals preferential insulation of super-enhancers by strong boundaries. Nature Communications, 2018 February 7;9(1):542. PubMed PMID: 29416042; PubMed Central PMCID: PMC5803259

Brahmachari S, Dittmore A, Takagi Y, Neuman KC, Marko JF. Defect-facilitated buckling in supercoiled double-helix DNA. Physical review. E. 2018 February;97(2-1):022416. PubMed PMID: 29548184; PubMed Central PMCID: PMC5940003.

Stephens AD, Liu PZ, Banigan EJ, Almassalha LM, Backman V, Adam SA, Goldman RD, Marko JF. Chromatin histone modifications and rigidity affect nuclear morphology independent of lamins. Mol Biol Cell. 2018 Jan 15;29(2):220-233. doi: 10.1091/mbc.E17-06-0410. Epub 2017 Nov 15. PubMed PMID: 29142071.

Bennett RL, Licht JD. Targeting Epigenetics in Cancer. Rev. Pharmacology and Toxicology. 2018 January 6;58:187-207. PMCID: PMC5800772.

Kanis MJ, Qiang W, Pineda M, Maniar KP, Kim JJ. A small molecule inhibitor of the perinucleolar compartment, ML246, attenuates growth and spread of ovarian cancer. Gynecologic Oncology Research and Practice. 5:7, 2018 PMID: 30305911 PMCID: PMC6167785

Serna VA, Wu X, Qiang W, Thomas J, Blumenfeld ML, and Kurita T. Cellular kinetics of MED12-mutant uterine leiomyoma growth and regression in vivo. Endocrine-Related Cancer 25(7):747-759, 2018. PMID:29700012; PMCID: PMC6032993

Gladstein S, Stawarz A, Almassalha LM, Cherkezyan L, Chandler JE, Zhou X, Subramanian H, Backman V. Measuring Nanoscale Chromatin Heterogeneity with Partial Wave Spectroscopic Microscopy. Methods in molecular biology (Clifton, N.J.). 2018;1745:337-360. PubMed PMID: 29476478; PubMed Central PMCID: PMC5983358.

Stephens AD, Banigan EJ, Marko JF. Separate roles for chromatin and lamins in nuclear mechanics. 2018 Jan 1;9(1):119-124. doi:10.1080/19491034.2017.1414118. Epub 2017 Dec 28. PubMed PMID: 29227210.

Almassalha LM, Bauer GM, Wu W, Cherkezyan L, Zhang D, Kendra A, Gladstein S, Chandler JE, VanDerWay D, Seagle B-L L, Ugolkov A, Billadeau DD, O’Halloran TV, Mazar AP, Roy HK, Szleifer I, Shahabi S, Backman V. Macrogenomic engineering via modulation of the scaling of chromatin packing densityNature Biomedical Engineering. 2017 Nov 6. 1:902–913 doi:10.1038/s41551-017-0153-2.-a

Brahmachari S, Gunn KH, Giuntoli RD, Mondragón A, Marko JF. Nucleation of Multiple Buckled Structures in Intertwined DNA Double Helices. Phys Rev Lett. 2017 Nov 3;119(18):188103. doi: 10.1103/PhysRevLett.119.188103. Epub 2017 Oct 31.PubMed PMID: 29219598; PubMed Central PMCID: PMC5726782.

Keenholtz RA, Dhanaraman T, Palou R, Yu J, D’Amours D, Marko JF. Oligomerization and ATP stimulate condensin-mediated DNA compaction. Sci Rep. 2017 Oct 27;7(1):14279. doi: 10.1038/ s41598-017-14701-5. PMCID: PMC5660149.

Harada BT, He C. Epigenetics: Making your mark on DNA. Nat Chem. 2017 Oct 24;9(11):1040-1042. doi: 10.1038/nchem.2884. PubMed PMID: 29064503.

Dittmore A, Brahmachari S, Takagi Y, Marko JF, Neuman KC. Supercoiling DNA Locates Mismatches. Phys Rev Lett. 2017 Oct 6;119(14):147801. doi:10.1103/PhysRevLett.119.147801. Epub 2017 Oct 3. PMCID: PMC5661871.

Banigan EJ, Stephens AD, Marko JF. Mechanics and Buckling of Biopolymeric Shells and Cell Nuclei. Biophys J. 2017 Oct 17;113(8):1654-1663. doi:10.1016/j.bpj.2017.08.034. PMCID:PMC5647576.

Zhong ZF, Yu HB, Wang CM, Qiang WA, Wang SP, Zhang JM, Yu H, Cui L, Wu T, Li DQ, Wang YT. Furanodiene Induces Extrinsic and Intrinsic Apoptosis in Doxorubicin-Resistant MCF-7 Breast Cancer Cells via NF-κB-Independent Mechanism. Front Pharmacol. 2017 Sep 14;8:648. doi: 10.3389/ fphar.2017.00648. eCollection 2017. PMCID: PMC5603666.

Dai Q, Moshitch-Moshkovitz S, Han D, Kol N, Amariglio N, Rechavi G,Dominissini D, He C. Nm-seq maps 2′-O-methylation sites in human mRNA with base precision. Nat Methods. 2017 Jul;14(7):695-698. doi: 10.1038/nmeth.4294. Epub 2017 May 15. PubMed PMID: 28504680.

Brahmachari S, Marko JF. Torque and buckling in stretched intertwined double-helix DNAs. Phys Rev E. 2017 May;95(5-1):052401. doi:10.1103/PhysRevE.95.052401. Epub 2017 May 1. PMCID: PMC5505651.

Tocco VJ, Li Y, Christopher KG, Matthews JH, Aggarwal V, Paschall L, Luesch H, Licht JD, Dickinson RB, Lele TP. The nucleus is irreversibly shaped by motion of cell boundaries in cancer and non-cancer cells. J Cell Physiol. 2018 Feb;233(2):1446-1454. doi: 10.1002/jcp.26031. Epub 2017 Jul 31. PMCID: PMC5673577.

McFarland CD, Yaglom JA, Wojtkowiak JW, Scott JG, Morse DL, Sherman MY, Mirny LA. The Damaging Effect of Passenger Mutations on Cancer Progression. Cancer Res. 2017 Sep 15;77(18):4763-4772. doi: 10.1158/0008-5472.CAN-15-3283-T. Epub 2017 May 23. PMCID: PMC5639691.

Nora EP, Goloborodko A, Valton AL, Gibcus JH, Uebersohn A, Abdennur N, Dekker J, Mirny LA, Bruneau BG. Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization. Cell. 2017 May 18;169(5):930-944.e22. doi: 10.1016/j.cell.2017.05.004. PMCID: PMC5538188.

Belaghzal H, Dekker J, Gibcus JH. Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation. Methods. 2017 Jul  1;123:56-65. doi: 10.1016/ j.ymeth.2017.04.004. Epub 2017 Apr 18. PMCID: PMC5522765.

Gunn KH, Marko JF, Mondragón A. An orthogonal single-molecule experiment reveals multiple-attempt dynamics of type IA topoisomerases. Nat Struct Mol Biol. 2017 May;24(5):484-490. doi: 10.1038/ nsmb.3401. Epub 2017 Apr 17. PMCID: PMC5516274.

Dong B, Almassalha LM, Soetikno BT, Chandler JE, Nguyen TQ, Urban BE, Sun C, Zhang HF, Backman V. Stochastic fluorescence switching of nucleic acids under visible light illumination. Opt Express. 2017 Apr 3;25(7):7929-7944. doi:10.1364/OE.25.007929. PMID: 28380910.

Kamar RI, Banigan EJ, Erbas A, Giuntoli RD, Olvera de la Cruz M, Johnson RC, Marko JF. Facilitated dissociation of transcription factors from single DNA binding sites. Proc Natl Acad Sci U S A. 2017 Apr 18;114(16):E3251-E3257. doi:10.1073/pnas.1701884114. Epub 2017 Mar 31. PMCID: PMC5402408.

Cherkezyan L, Zhang D, Subramanian H, Capoglu I, Taflove A, Backman V. Review of interferometric spectroscopy of scattered light for the quantification of subdiffractional structure of biomaterials. J Biomed Opt. 2017 Mar 1;22(3):30901.doi: 10.1117/1.JBO.22.3.030901. PMCID:PMC5348632.

Andrew D. Stephens,*, Edward J. Banigan, Stephen A. Adam, Robert D. Goldman, and John F. Marko. Chromatin and lamin A determine two different mechanical response regimes of the cell nucleus. Mol Biol Cell. 2017 Jul 7;28(14):1984-1996. doi: 10.1091/mbc.E16-09-0653. Epub 2017 Jan 5. PMID: 28057760.

Almassalha LM, Tiwari A, Ruhoff PT, Stypula-Cyrus Y, Cherkezyan L, Matsuda H, Dela Cruz MA, Chandler JE, White C, Maneval C, Subramanian H, Szleifer I, Roy HK, Backman V. The Global Relationship between Chromatin Physical Topology, Fractal Structure, and Gene Expression. Sci Rep. 2017 Jan 24;7:41061. doi:10.1038/srep41061. PMCID: PMC5259786.

Voong LN, Xi L, Sebeson AC, Xiong B, Wang JP, Wang X. Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping. Cell. 2016 Dec 1;167(6):1555-1570.e15. doi: 10.1016/j.cell.2016.10.049. PMCID: PMC5135608.

Almassalha LM, Bauer GM, Chandler JE, Gladstein S, Cherkezyan L, Stypula-Cyrus Y, Weinberg S, Zhang D, Thusgaard Ruhoff P, Roy HK, Subramanian H, Chandel NS, Szleifer I, Backman V. Label-free imaging of the native, living cellular nanoarchitecture using partial-wave spectroscopic microscopy. Proc Natl Acad Sci U S A. 2016 Oct 18;113(42):E6372-E6381. PMCID: PMC5081614.

Almassalha LM, Bauer GM, Chandler JE, Gladstein S, Szleifer I, Roy HK, Backman V. The Greater Genomic Landscape: The Heterogeneous Evolution of Cancer. Cancer Res. 2016 Oct 1;76(19):5605-5609. PMCID: PMC5084919.

Eastland A, Hornick J, Kawamura R, Nanavati D, Marko JF. Dependence of the structure and mechanics of metaphase chromosomes on oxidized cysteines. Chromosome Res. 2016 Sep;24(3):339-53. doi: 10.1007/s10577-016-9528-6. PMCID: PMC4970972.

Bhattacharyya S, Renn JP, Yu H, Marko JF, Matouschek A. An assay for 26S proteasome activity based on fluorescence anisotropy measurements of dye-labeled protein substrates. Anal Biochem. 2016 Sep 15;509:50-9. doi:10.1016/j.ab.2016.05.026. PMCID:PMC4976823.

Han D, Lu X, Shih AH, Nie J, You Q, Xu MM, Melnick AM, Levine RL, He C. A Highly Sensitive and Robust Method for Genome-wide 5hmC Profiling of Rare Cell Populations. Mol Cell. 2016 Aug 18;63(4):711-9. doi:10.1016/j.molcel.2016.06.028. PMCID:PMC4992443.

Hadizadeh N, Johnson RC, Marko JF. Facilitated Dissociation of a Nucleoid Protein from the Bacterial Chromosome. J Bacteriol. 2016 May 27;198(12):1735-42. doi: 10.1128/JB.00225-16. Print 2016 Jun 15. PubMed PMID: 27044624; PubMed Central PMCID: PMC4886758.

Goloborodko A, Marko JF, Mirny LA. Chromosome Compaction by Active Loop Extrusion. Biophys J. 2016 May 24;110(10):2162-8. doi: 10.1016/j.bpj.2016.02.041. PMCID: PMC4880799

Goloborodko A, Imakaev MV, Marko JF, Mirny L. Compaction and segregation of sister chromatids via active loop extrusion. Elife. 2016 May 18;5. pii: e14864. doi: 10.7554/eLife.14864. PMCID:PMC4914367.

Eastland A, Hornick J, Kawamura R, Nanavati D, Marko JFDependence of the structure and mechanics of metaphase chromosomes on oxidized cysteines. Chromosome Res. 2016 May 5. [Epub ahead of print] P PMID: 27145786.

Chandler JE, Stypula-Cyrus Y, Almassalha L, Bauer G, Bowen L, Subramanian H, Szleifer I, Backman VColocalization of cellular nanostructure using confocal fluorescence and partial wave spectroscopy. J Biophotonics. 2016 Apr 25. doi: 10.1002/jbio.201500298. [Epub ahead of print] PMID: 27111884.

Valton AL, Dekker JTAD disruption as oncogenic driver. Curr Opin Genet Dev. 2016 Feb;36:34-40. doi: 10.1016/j.gde.2016.03.008. Epub 2016 Apr 22. Review. PMCID: PMC4880504.

Xiao B, McLean MM, Lei X, Marko JF, Johnson RC. Controlled rotation mechanism of DNA strand exchange by the Hin serine recombinase.Sci Rep. 2016 Apr 1;6:23697. doi: 10.1038/ srep23697. PMCID: PMC4817059.

Dekker J, Mirny L, The 3D genome as moderator of chromosomal communication. Cell. 2016 Mar 10;164(6):1110-21. doi: 10.1016/j.cell.2016.02.007. Review. PMCID: PMC4788811.

Zhao B, Mei Y, Schipma MJ, Roth EW, Bleher R, Rappoport JZ, Wickrema A, Yang J, Ji P. Nuclear Condensation during Mouse Erythropoiesis Requires Caspase-3-Mediated Nuclear Opening. Dev Cell. 2016 Mar 7;36(5):498-510. doi: 10.1016/j.devcel.2016.02.001. PMID: 26954545

Hnisz D, Weintraub AS, Day DS, Valton AL, Bak RO, Li CH, Goldmann J, Lajoie BR, Fan ZP, Sigova AA, Reddy J, Borges-Rivera D, Lee TI, Jaenisch R, Porteus MH, Dekker J, Young RA. Activation of proto-oncogenes by disruption of chromosome neighborhoods. Science. 2016 Mar 25;351(6280):1454-8. doi: 10.1126/science.aad9024. Epub 2016 Mar 3. PMCID: PMC4884612.

Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO, Wong CK, Graim K, Bivol A, Wang H, Zhu F, Afsari B, Danilova LV, Favorov AV, Lee WS, Taylor D, Hu CW, Long BL, Noren DP, Bisberg AJ; HPN-DREAM Consortium, Mills GB, Gray JW, Kellen M, Norman T, Friend S, Qutub AA, Fertig EJ, Guan Y, Song M, Stuart JM, Spellman PT, Koeppl H, Stolovitzky G, Saez-Rodriguez J, Mukherjee S.  Inferring causal molecular networks: empirical assessment through a community-based22. PMID: 26901648. PMCID: PMC4854847

Kharerin H, Bhat PJ, Marko JF, Padinhateeri R. Role of transcription factor- effort. Nat Methods. 2016 Apr;13(4):310-8. doi: 10.1038/nmeth.3773. Epub 2016 Feb mediated nucleosome disassembly in PHO5 gene expression.Sci Rep. 2016 Feb 4;6:20319. doi: 10.1038/srep20319. PMCID: PMC4740855.

Banigan EJ, Marko JF. Self-propulsion and interactions of catalytic particles in a chemically active medium. Phys Rev E. 2016 Jan;93(1):012611. doi: 10.1103/PhysRevE.93.012611. Epub 2016 Jan 25. PMCID: PMC4774268.

Pederson T, King MC, Marko JF. Forces, fluctuations, and self-organization in the nucleus. Mol Biol Cell. 2015 Nov 5;26(22):3915-9. doi: 10.1091/mbc.E15-06-0357. PMCID: PMC4710223.

Giuntoli RD, Linzer NB, Banigan EJ, Sing CE, de la Cruz MO, Graham JS, Johnson RC, Marko JF. DNA-Segment-Facilitated Dissociation of Fis and NHP6A from DNA Detected via Single-Molecule Mechanical Response. J Mol Biol. 2015 Sep 25;427(19):3123-36. doi: 10.1016/j.jmb.2015.07.015. PMCID: PMC4579036.

Wells DK, Kath WL, Motter AE. Control of Stochastic and Induced Switching in Biophysical Networks. Phys Rev X. 2015 Jul-Sep;5  PMCID: PMC4594957.

Philips SJ, Canalizo-Hernandez M, Yildirim I, Schatz GC, Mondragón A, O’Halloran TV. TRANSCRIPTION Allosteric transcriptional regulation via changes in the overall topology of the core promoter. Science. 2015 Aug 21; 349 (6250): 877-81. PMCID: PMC4617686.

Licht JD. DNA Methylation Inhibitors in Cancer Therapy: The Immunity Dimension. Cell. 2015 Aug 27;162(5):938-9. PMID: 26317460.

Pederson T, King MC, Marko JF. Forces, fluctuations, and self-organization in the nucleus. Drubin DG, ed. Molecular Biology of the Cell. 2015;26(22):3915-3919. doi:10.1091/mbc.E15-06-0357.

Barutcu AR, Lajoie BR, McCord RP, Tye CE, Hong D, Messier TL, Browne G, van Wijnen AJ, Lian JB, Stein JL, Dekker J, Imbalzano AN, Stein GS. Chromatin Interaction Analysis Reveals Changes in Small Chromosome and Telomere Clustering Between Epithelial and Breast Cancer Cells. Genome Biology. 2015;16:214. doi:10/1186/s13059-015-0768-0.

Bondarenko G, Ugolkov A, Rohan S, Kulesza P, Dubrovskyi O, Gursel D, Mathews J, O’Halloran TV, Wei JJ, Mazar AP. Patient-Derived Tumor Xenografts Are Susceptible to Formation of Human Lymphocytic Tumors. Neoplasia (New York, NY). 2015;17(9):735-741. doi:10.1016/j.neo.2015.09.004.

Giuntoli RD, Linzer NB, Banigan EJ, Sing CE, de la Cruz MO, Graham JS, Johnson RC, Marko JF. DNA-Segment-Faciliatated Dissociation of Fis and NHP6A from DNA Detected via Single-Molecule Mechanical Response. J Mol Biol. 2015 Sep 25;427(19):3123-36. doi: 10.1016/j.jmb.2015.07.015. Epub 2015 Jul 26.

Ciaccio MF, Chen VC, Jones RB, Bagheri N. The DIONESUS algorithm provides scalable and accurate reconstruction of dynamic phosphoproteomic networks to reveal new drug targets. Integr Biol (Camb). 2015 Jul;7(7):776-91. doi: 10.1039/c5ib00065c. PMID: 26057728. PMCID: PMC4511116

Sebeson A, Xi L, Zhang Q, Sigmund A, Wang JP, Widom J, Wang X. Differential Nucleosome Occupancies across Oct4-Sox2 Binding Sites in Murine Embryonic Stem Cells. PLoS One. 2015 May 18;10(5):e0127214. doi: 10.1371/journal.pone.0127214. eCollection 2015. PMID: 25992972. PMCID: PMC4436218

Hardy KM, Strizzi L, Margaryan NV, Gupta K, Murphy GF, Scolyer RA, Hendrix MJ. Targeting nodal in conjunction with dacarbazine induces synergistic anticancer effects in metastatic melanoma. Mol Cancer Res. 2015 Apr;13(4):670-80. doi: 10.1158/1541-7786.MCR-14-0077. Epub 2015 Mar 12. PMID: 25767211. PMCID: PMC4398626

Hornick JE, Duncan FE, Sun M, Kawamura R, Marko JF, Woodruff TK. Age-associated alterations in the micromechanical properties of chromosomes in the mammalian egg. J Assist Reprod Genet. 2015 May;32(5):765-9. doi: 10.1007/s10815-015-0453-y. Epub 2015 Mar 11. PMID: 25758987. PMCID: PMC4429432

Ji P. New insights into the mechanisms of mammalian erythroid chromatin condensation and enucleation. Int Rev Cell Mol Biol. 2015;316:159-82. doi: 10.1016/bs.ircmb.2015.01.006. Epub 2015 Feb 27. Review. PMID: 25805124.

Fishbain S, Inobe T, Israeli E, Chavali S, Yu H, Kago G, Babu MM, Matouschek A. Sequence composition of disordered regions fine-tunes protein half-life. Nat Struct Mol Biol. 2015 Mar;22(3):214-21. doi: 10.1038/nsmb.2958. Epub 2015 Feb 2. PMID: 25643324. PMCID: PMC4351145

Behnam N, Ó Broin P, Reyes JM, Shieh K, Lin CY, Will CM, Popovic R, Ezponda T, Bradner JE, Golden AA, Licht JD. Deregulation of the Ras-Erk Signaling Axis Modulates the Enhancer Landscape. Cell Reports, 12 (2015), pp. 1300-1313.

Zhang QY, Burdette JE, Wang JP. Integrative network analysis of TCGA data for ovarian cancer. BMC Syst Biol. 2014 Dec 31;8(1):1338. DOI 10.1186/s12918-014-0136-9. PubMed PMID: 25551281; PubMed Central PMCID: PMC4331442.

Mizuguchi T, Fudenberg G, Mehta S, Belton JM, Taneja N, Folco HD, FitzGerald P, Dekker J, Mirny L, Barrowman J, Grewas SI. Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe. Nature. 2014 Dec 18; 516(7531): 432-435. doi:10.1038/nature13833

Forte E, Raja AN, Shamulailatpam P, Manzano M, Schipma MJ, Casey JL, Gottwein E. MicroRNA-mediated transformation by the Kaposi’s sarcoma-associated herpesvirus Kaposin locus. J Virol. 2015 Feb;89(4):2333-41. doi: 10.1128/JVI.03317-14. Epub 2014 Dec 10. PMID: 25505059. PMCID: PMC4338870

Pederson T, Marko JF. Nuclear physics (of the cell, not the atom). Mol Biol Cell. 2014 Nov 5;25(22):3466-9. PMCID:PMC4230604.

Putzel GG, Tagliazucchi M, Szleifer I. Nonmonotonic diffusion of particles among larger attractive crowding spheres. Phys Rev Lett. 2014 Sep 26;113(13):138302. Epub 2014 Sep 25. PMID: 25302920. PMCID: PMC4670031

Popovic R, Martinez-Garcia E, Giannopoulou EG, Zhang Q, Zhang Q, Ezponda T, Shah MY, Zheng Y, Will CM, Small EC, Hua Y, Bulic M, Jiang Y, Carrara M, Calogero RA, Kath WL, Kelleher NL, Wang JP, Elemento O, Licht JD. Histone methyltransferase MMSET/NSD2 alters EZH2 binding and reprograms the myeloma epigenome through global and focal changes in H3K36 and H3K27 methylation. PLoS Genet. 2014 Sep 4;10(9):e1004566. doi: 10.1371/journal.pgen.1004566. eCollection 2014 Sep. PMID: 25188243. PMCID: PMC4154646

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Ezponda T, Licht JD. Molecular pathways: deregulation of histone h3 lysine 27 methylation in cancer-different paths, same destination. Clin Cancer Res. 2014 Oct 1;20(19):5001-8. doi: 10.1158/1078-0432.CCR-13-2499. Epub 2014 Jul 1. Review. PMID: 24987060. PMCID: PMC4184969

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Ciaccio MF, Finkle JD, Xue AY, Bagheri N. A systems approach to integrative biology: an overview of statistical methods to elucidate association and architecture. Integr Comp Biol. 2014 Jul;54(2):296-306. doi: 10.1093/icb/icu037. Epub 2014 May 9. PMID: 24813462. PMCID: PMC4148605

Daugherty RL, Serebryannyy L, Yemelyanov A, Flozak AS, Yu HJ, Kosak ST, deLanerolle P, Gottardi CJ. α-Catenin is an inhibitor of transcription. Proc Natl Acad Sci U S A. 2014 Apr 8;111(14):5260-5. doi: 10.1073/pnas.1308663111. Epub 2014 Mar 25. PMID: 24706864. PMCID: PMC3986139

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Cherkezyan L, Stypula-Cyrus Y, Subramanian H, White C, Dela Cruz M, Wali RK, Goldberg MJ, Bianchi LK, Roy HK, Backman V. Nanoscale changes in chromatin organization represent the initial steps of tumorigenesis: a transmission electron microscopy study. BMC Cancer. 2014 Mar 14;14:189. doi: 10.1186/1471-2407-14-189. PMID: 24629088. PMCID: PMC3995586

Damania D, Subramanian H, Backman V, Anderson EC, Wong MH, McCarty OJ, Phillips KG. Network signatures of nuclear and cytoplasmic density alterations in a model of pre and postmetastatic colorectal cancer. J Biomed Opt. 2014 Jan;19(1):16016. doi: 10.1117/1.JBO.19.1.016016. PMID: 24441943. PMCID: PMC4019418

Kim JS, Szleifer I. Crowding-induced formation and structural alteration of nuclear compartments: insights from computer simulations. Int Rev Cell Mol Biol. 2014;307:73-108. doi: 10.1016/B978-0-12-800046-5.00004-7. Review. PMID: 24380593

Moyle-Heyrman G, Zaichuk T, Xi L, Zhang Q, Uhlenbeck OC, Holmgren R, Widom J, Wang JP. Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning. PNAS. 2013; published ahead of print November 25, 2013, doi:10.1073/pnas.1315809110

Kuo HY, DeLuca TA, Miller WM, Mrksich M. Profiling deacetylase activities in cell lysates with peptide arrays and SAMDI mass spectrometry. Anal Chem. 2013 Nov 19;85(22):10635-42. doi: 10.1021/ac402614x. Epub 2013 Oct 11. PMID: 24088168. PMCID: PMC3912874

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Manzano M, Shamulailatpam P, Raja AN, Gottwein E. Kaposi’s sarcoma-associated herpesvirus encodes a mimic of cellular miR-23. J Virol. 2013 Nov;87(21):11821-30. doi: 10.1128/JVI.01692-13. Epub 2013 Aug 28. PMID: 23986579. PMCID: PMC3807327

Miodragović ĐU, Quentzel JA, Kurutz JW, Stern CL, Ahn RW, Kandela I, Mazar A, O’Halloran TV. Robust structure and reactivity of aqueous arsenous acid-platinum(II) anticancer complexes. Angew Chem Int Ed Engl. 2013 Oct 4;52(41):10749-52. doi: 10.1002/anie.201303251. Epub 2013 Aug 22. PMID: 24038962. PMCID: PMC3932145

Simeon TM, Ratner MA, Schatz GC. Nature of noncovalent interactions in catenane supramolecular complexes: calibrating the MM3 force field with ab initio, DFT, and SAPT methods. J Phys Chem A. 2013 Aug 22;117(33):7918-27. doi: 10.1021/jp400051b. Epub 2013 Aug 13. PubMed PMID: 23941280.

Zheng Y, Thomas PM, Kelleher NL. Measurement of acetylation turnover at distinct lysines in human histones identifies long-lived acetylation sites. Nat Commun. 2013;4:2203. doi: 10.1038/ncomms3203. PubMed PMID: 23892279.

Childs-Disney JL, Stepniak-Konieczna E, Tran T, Yildirim I, Park H, Chen CZ, Hoskins J, Southall N, Marugan JJ, Patnaik S, Zheng W, Austin CP, Schatz GC, Sobczak K, Thornton CA, Disney MD. Induction and reversal of myotonic dystrophy type 1 pre-mRNA splicing defects by small molecules. Nat Commun. 2013;4:2044. doi: 10.1038/ncomms3044. PubMed PMID: 23806903; PubMed Central PMCID: PMC3710115.

Cornelius SP, Kath WL, Motter AE. Realistic control of network dynamics. Nat Commun. 2013;4:1942. doi: 10.1038/ncomms2939. PubMed PMID: 23803966.

Sullivan LB, Martinez-Garcia E, Nguyen H, Mullen AR, Dufour E, Sudarshan S, Licht JD, Deberardinis RJ, Chandel NS. The proto-oncometabolite fumarate binds glutathione to amplify ROS-dependent signaling. Mol Cell. 2013 Jul 25;51(2):236-48. doi: 10.1016/j.molcel.2013.05.003. Epub 2013 Jun 6. Erratum in: Mol Cell. 2013 Jul 25;51(2):273.PubMed PMID: 23747014; PubMed Central PMCID: PMC3775267.

Stypula-Cyrus Y, Damania D, Kunte DP, Cruz MD, Subramanian H, Roy HK, Backman V. HDAC up-regulation in early colon field carcinogenesis is involved in cell tumorigenicity through regulation of chromatin structure. PLoS One. 2013 May 28;8(5):e64600. doi: 10.1371/journal.pone.0064600. Print 2013. PubMed PMID: 23724067; PubMed Central PMCID: PMC3665824.

Béguelin W, Popovic R, Teater M, Jiang Y, Bunting KL, Rosen M, Shen H, Yang SN, Wang L, Ezponda T, Martinez-Garcia E, Zhang H, Zheng Y, Verma SK, McCabe MT, Ott HM, Van Aller GS, Kruger RG, Liu Y, McHugh CF, Scott DW, Chung YR, Kelleher N, Shaknovich R, Creasy CL, Gascoyne RD, Wong KK, Cerchietti L, Levine RL, Abdel-Wahab O, Licht JD, Elemento O, Melnick AM. EZH2 is required for germinal center formation and somatic EZH2 mutations promote lymphoid transformation. Cancer Cell. 2013 May 13;23(5):677-92. doi: 10.1016/j.ccr.2013.04.011. PubMed PMID: 23680150; PubMed Central PMCID: PMC3681809.

Sun M, Nishino T, Marko JF. The SMC1-SMC3 cohesin heterodimer structures DNA through supercoiling-dependent loop formation. Nucleic Acids Res. 2013 Jul;41(12):6149-60. doi: 10.1093/nar/gkt303. Epub 2013 Apr 24. PubMed PMID: 23620281; PubMed Central PMCID: PMC3695518.

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Jin HJ, Zhao JC, Ogden I, Bergan RC, Yu J. Androgen receptor-independent function of FoxA1 in prostate cancer metastasis. Cancer Res. 2013 Jun 15;73(12):3725-36. doi: 10.1158/0008-5472.CAN-12-3468. Epub 2013 Mar 28. PMID: 23539448. PMCID: PMC3686855

Manor O, Segal E. Robust prediction of expression differences among human individuals using only genotype information. PLoS Genet. 2013 Mar;9(3):e1003396. doi: 10.1371/journal.pgen.1003396. Epub 2013 Mar 28. PubMed PMID: 23555302; PubMed Central PMCID: PMC3610805.

Jin HJ, Zhao JC, Ogden I, Bergan RC, Yu J. Androgen receptor-independent function of FoxA1 in prostate cancer metastasis. Cancer Res. 2013 Jun 15;73(12):3725-36. doi: 10.1158/0008-5472.CAN-12-3468. Epub 2013 Mar 28.PubMed PMID: 23539448; PubMed Central PMCID: PMC3686855.

Terekhova K, Marko JF, Mondragón A. Studies of bacterial topoisomerases I and III at the single-molecule level. Biochem Soc Trans. 2013 Apr;41(2):571-5. doi: 10.1042/BST20120297. Review. PubMed PMID: 23514156; PubMed Central PMCID: PMC3767994.

Shalem O, Carey L, Zeevi D, Sharon E, Keren L, Weinberger A, Dahan O, Pilpel Y, Segal E. Measurements of the impact of 3′ end sequences on gene expression reveal wide range and sequence dependent effects. PLoS Comput Biol. 2013;9(3):e1002934. doi: 10.1371/journal.pcbi.1002934. Epub 2013 Mar 7. PubMed PMID: 23505350; PubMed Central PMCID: PMC3591272.

Wu JS, Kim AM, Bleher R, Myers BD, Marvin RG, Inada H, Nakamura K, Zhang XF, Roth E, Li SY, Woodruff TK, O’Halloran TV, Dravid VP. Imaging and elemental mapping of biological specimens with a dual-EDS dedicated scanning transmission electron microscope. Ultramicroscopy. 2013 May;128:24-31. doi: 10.1016/j.ultramic.2013.01.004. Epub 2013 Feb 4. PubMed PMID: 23500508; PubMed Central PMCID: PMC3658130.

Yildirim I, Park H, Disney MD, Schatz GC. A dynamic structural model of expanded RNA CAG repeats: a refined X-ray structure and computational investigations using molecular dynamics and umbrella sampling simulations. J Am Chem Soc. 2013 Mar 6;135(9):3528-38. doi: 10.1021/ja3108627. Epub 2013 Feb 26. PubMed PMID: 23441937; PubMed Central PMCID: PMC3625063.

Yigit E, Zhang Q, Xi L, Grilley D, Widom J, Wang JP, Rao A, Pipkin ME. High-resolution nucleosome mapping of targeted regions using BAC-based enrichment. Nucleic Acids Res. 2013 Apr;41(7):e87. doi: 10.1093/nar/gkt081. Epub 2013 Feb 14. PubMed PMID: 23413004; PubMed Central PMCID: PMC3627574.

Dadiani M, van Dijk D, Segal B, Field Y, Ben-Artzi G, Raveh-Sadka T, Levo M, Kaplow I, Weinberger A, Segal E. Two DNA-encoded strategies for increasing expression with opposing effects on promoter dynamics and transcriptional noise. Genome Res. 2013 Jun;23(6):966-76. doi: 10.1101/gr.149096.112. Epub 2013 Feb 12. PubMed PMID: 23403035; PubMed Central PMCID: PMC3668364.

Yigit E, Bischof JM, Zhang Z, Ott CJ, Kerschner JL, Leir SH, Buitrago-Delgado E, Zhang Q, Wang JP, Widom J, Harris A. Nucleosome mapping across the CFTR locus identifies novel regulatory factors. Nucleic Acids Res. 2013 Mar 1;41(5):2857-68. doi: 10.1093/nar/gks1462. Epub 2013 Jan 15. PubMed PMID: 23325854; PubMed Central PMCID: PMC3597660.

Boedicker JQ, Garcia HG, Phillips R. Theoretical and experimental dissection of DNA loop-mediated repression. Phys Rev Lett. 2013 Jan 4;110(1):018101. Epub 2013 Jan 2. PubMed PMID: 23383841; PubMed Central PMCID: PMC3716456.

Wu L, Runkle C, Jin HJ, Yu J, Li J, Yang X, Kuzel T, Lee C, Yu J. CCN3/NOV gene expression in human prostate cancer is directly suppressed by the androgen receptor. Oncogene. 2013 Jan 14. doi: 10.1038/onc.2012.602. [Epub ahead of print] PubMed PMID: 23318417; PubMed Central PMCID: PMC3796014.

Zhang H, Marko JF. Range of interaction between DNA-bending proteins is controlled by the second-longest correlation length for bending fluctuations. Phys Rev Lett. 2012 Dec 14;109(24):248301. Epub 2012 Dec 10. PubMed PMID: 23368394; PubMed Central PMCID: PMC3759365.

Bruns AM, Pollpeter D, Hadizadeh N, Myong S, Marko JF, Horvath CM. ATP hydrolysis enhances RNA recognition and antiviral signal transduction by the innate immune sensor, laboratory of genetics and physiology 2 (LGP2). J Biol Chem. 2013 Jan 11;288(2):938-46. doi: 10.1074/jbc.M112.424416. Epub 2012 Nov 26. PubMed PMID: 23184951; PubMed Central PMCID: PMC3543043.

Zhu X, Schatz GC. Molecular dynamics study of the role of the spine of hydration in DNA A-tracts in determining nucleosome occupancy. J Phys Chem B. 2012 Nov 26;116(46):13672-81. doi: 10.1021/jp3084887. Epub 2012 Nov 14.PubMed PMID: 23102092; PubMed Central PMCID: PMC3508256.

Xiao B, Freedman BS, Miller KE, Heald R, Marko JF. Histone H1 compacts DNA under force and during chromatin assembly. Mol Biol Cell. 2012 Dec;23(24):4864-71. doi: 10.1091/mbc.E12-07-0518. Epub 2012 Oct 24. PubMed PMID: 23097493; PubMed Central PMCID: PMC3521692.

Hadizadeh Yazdi N, Guet CC, Johnson RC, Marko JF. Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions. Mol Microbiol. 2012 Dec;86(6):1318-33. doi: 10.1111/mmi.12071. PubMed PMID: 23078205; PubMed Central PMCID: PMC3524407.

Alipour E, Marko JF. Self-organization of domain structures by DNA-loop-extruding enzymes. Nucleic Acids Res. 2012 Dec;40(22):11202-12. doi: 10.1093/nar/gks925. Epub 2012 Oct 15. PubMed PMID: 23074191; PubMed Central PMCID: PMC3526278.

Bai H, Kath JE, Zörgiebel FM, Sun M, Ghosh P, Hatfull GF, Grindley ND, Marko JF. Remote control of DNA-acting enzymes by varying the Brownian dynamics of a distant DNA end. Proc Natl Acad Sci U S A. 2012 Oct 9;109(41):16546-51. doi: 10.1073/pnas.1203118109. Epub 2012 Sep 24. PubMed PMID: 23011800; PubMed Central PMCID: PMC3478594.

Min DJ, Ezponda T, Kim MK, Will CM, Martinez-Garcia E, Popovic R, Basrur V, Elenitoba-Johnson KS, Licht JD. MMSET stimulates myeloma cell growth through microRNA-mediated modulation of c-MYC. Leukemia. 2013 Mar;27(3):686-94. doi: 10.1038/leu.2012.269. Epub 2012 Sep 13. PubMed PMID: 22972034.

Odom TW, You EA, Sweeney CM. Multi-scale Plasmonic Nanoparticles and the Inverse Problem. J Phys Chem Lett. 2012 Sep 20;3(18):2611-2616. Epub 2012 Aug 29. PubMed PMID: 23066451; PubMed Central PMCID: PMC3467152.

Seftor RE, Hess AR, Seftor EA, Kirschmann DA, Hardy KM, Margaryan NV, Hendrix MJ. Tumor cell vasculogenic mimicry: from controversy to therapeutic promise. Am J Pathol. 2012 Oct;181(4):1115-25. doi: 10.1016/j.ajpath.2012.07.013. Epub 2012 Aug 31. Review. PubMed PMID: 22944600.

Terekhova K, Gunn KH, Marko JF, Mondragón A. Bacterial topoisomerase I and topoisomerase III relax supercoiled DNA via distinct pathways. Nucleic Acids Res. 2012 Nov 1;40(20):10432-40. doi: 10.1093/nar/gks780. Epub 2012 Aug 25.PubMed PMID: 22923519; PubMed Central PMCID: PMC3488232.

Zheng Y, Sweet SM, Popovic R, Martinez-Garcia E, Tipton JD, Thomas PM, Licht JD, Kelleher NL. Total kinetic analysis reveals how combinatorial methylation patterns are established on lysines 27 and 36 of histone H3. Proc Natl Acad Sci U S A. 2012 Aug 21;109(34):13549-54. doi: 10.1073/pnas.1205707109. Epub 2012 Aug 6. PubMed PMID: 22869745; PubMed Central PMCID: PMC3427122.

Shvartsburg AA, Zheng Y, Smith RD, Kelleher NL. Separation of variant methylated histone tails by differential ion mobility. Anal Chem. 2012 Aug 7;84(15):6317-20. doi: 10.1021/ac301541r. Epub 2012 Jul 18. PubMed PMID: 22812477; PubMed Central PMCID: PMC3418378.

Ezponda T, Popovic R, Shah MY, Martinez-Garcia E, Zheng Y, Min DJ, Will C, Neri A, Kelleher NL, Yu J, Licht JD. The histone methyltransferase MMSET/WHSC1 activates TWIST1 to promote an epithelial-mesenchymal transition and invasive properties of prostate cancer. Oncogene. 2013 Jun 6;32(23):2882-90. doi: 10.1038/onc.2012.297. Epub 2012 Jul 16. PubMed PMID: 22797064; PubMed Central PMCID: PMC3495247.

Brogaard K, Xi L, Wang JP, Widom J. A map of nucleosome positions in yeast at base-pair resolution. Nature. 2012 Jun 28;486(7404):496-501. doi: 10.1038/nature11142. PubMed PMID: 22722846; PubMed Central PMCID: PMC3786739.

Kraut DA, Israeli E, Schrader EK, Patil A, Nakai K, Nanavati D, Inobe T, Matouschek A. Sequence- and species-dependence of proteasomal processivity. ACS Chem Biol. 2012 Aug 17;7(8):1444-53. doi: 10.1021/cb3001155. Epub 2012 Jun 28. PubMed PMID: 22716912; PubMed Central PMCID: PMC3423507.

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Shvartsburg AA, Zheng Y, Smith RD, Kelleher NL. Ion mobility separation of variant histone tails extending to the “middle-down” range. Anal Chem. 2012 May 15;84(10):4271-6. doi: 10.1021/ac300612y. Epub 2012 May 3. PubMed PMID: 22559289; PubMed Central PMCID: PMC3353003.

Popovic R, Licht JD. Emerging epigenetic targets and therapies in cancer medicine. Cancer Discov. 2012 May;2(5):405-13. doi: 10.1158/2159-8290.CD-12-0076. Epub 2012 Apr 23. Review. PubMed PMID: 22588878; PubMed Central PMCID: PMC3381982.

Strizzi L, Hardy KM, Kirschmann DA, Ahrlund-Richter L, Hendrix MJ. Nodal expression and detection in cancer: experience and challenges. Cancer Res. 2012 Apr 15;72(8):1915-20. doi: 10.1158/0008-5472.CAN-11-3419. Review.PubMed PMID: 22508696; PubMed Central PMCID: PMC3334352.

Kirschmann DA, Seftor EA, Hardy KM, Seftor RE, Hendrix MJ. Molecular pathways: vasculogenic mimicry in tumor cells: diagnostic and therapeutic implications. Clin Cancer Res. 2012 May 15;18(10):2726-32. doi: 10.1158/1078-0432.CCR-11-3237. Epub 2012 Apr 2. PubMed PMID: 22474319; PubMed Central PMCID: PMC3354024.

Battistini F, Hunter CA, Moore IK, Widom J. Structure-based identification of new high-affinity nucleosome binding sequences. J Mol Biol. 2012 Jun 29;420(1-2):8-16. doi: 10.1016/j.jmb.2012.03.026. Epub 2012 Apr 1. PubMed PMID: 22472421.

Doré LC, Chlon TM, Brown CD, White KP, Crispino JD. Chromatin occupancy analysis reveals genome-wide GATA factor switching during hematopoiesis. Blood. 2012 Apr 19;119(16):3724-33. doi: 10.1182/blood-2011-09-380634. Epub 2012 Mar 1. PubMed PMID: 22383799; PubMed Central PMCID: PMC3335379.

You EA, Zhou W, Suh JY, Huntington MD, Odom TW. Polarization-dependent multipolar plasmon resonances in anisotropic multiscale au particles. ACS Nano. 2012 Feb 28;6(2):1786-94. doi: 10.1021/nn204845z. Epub 2012 Jan 25.PubMed PMID: 22276641; PubMed Central PMCID: PMC3289737.

Marko JF, Neukirch S. Competition between curls and plectonemes near the buckling transition of stretched supercoiled DNA. Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Jan;85(1 Pt 1):011908. Epub 2012 Jan 11. PubMed PMID: 22400592; PubMed Central PMCID: PMC3763912.

Kim J, Yu J. Interrogating genomic and epigenomic data to understand prostate cancer. Biochim Biophys Acta. 2012 Apr;1825(2):186-96. doi: 10.1016/j.bbcan.2011.12.003. Epub 2012 Jan 3. Review. PubMed PMID: 22240201; PubMed Central PMCID: PMC3307852.

Zhao JC, Yu J, Runkle C, Wu L, Hu M, Wu D, Liu JS, Wang Q, Qin ZS, Yu J. Cooperation between Polycomb and androgen receptor during oncogenic transformation. Genome Res. 2012 Feb;22(2):322-31. doi: 10.1101/gr.131508.111. Epub 2011 Dec 16. PubMed PMID: 22179855; PubMed Central PMCID: PMC3266039.

Graham JS, Johnson RC, Marko JF. Counting proteins bound to a single DNA molecule. Biochem Biophys Res Commun. 2011 Nov 11;415(1):131-4. doi: 10.1016/j.bbrc.2011.10.029. Epub 2011 Oct 12. PubMed PMID: 22020072; PubMed Central PMCID: PMC3215857.

Sheinin MY, Forth S, Marko JF, Wang MD. Underwound DNA under tension: structure, elasticity, and sequence-dependent behaviors. Phys Rev Lett. 2011 Sep 2;107(10):108102. Epub 2011 Sep 1. PubMed PMID: 21981534; PubMed Central PMCID: PMC3201814.

Schrader EK, Harstad KG, Holmgren RA, Matouschek A. A three-part signal governs differential processing of Gli1 and Gli3 proteins by the proteasome. J Biol Chem. 2011 Nov 11;286(45):39051-8. doi: 10.1074/jbc.M111.274993. Epub 2011 Sep 15. PubMed PMID: 21921029; PubMed Central PMCID: PMC3234730.

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Su H, Meng S, Lu Y, Trombly MI, Chen J, Lin C, Turk A, Wang X. Mammalian hyperplastic discs homolog EDD regulates miRNA-mediated gene silencing. Mol Cell. 2011 Jul 8;43(1):97-109. doi: 10.1016/j.molcel.2011.06.013. PubMed PMID: 21726813; PubMed Central PMCID: PMC3147021.

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Padinhateeri R, Marko JF. Nucleosome positioning in a model of active chromatin remodeling enzymes. Proc Natl Acad Sci U S A. 2011 May 10;108(19):7799-803. doi: 10.1073/pnas.1015206108. Epub 2011 Apr 25. PubMed PMID: 21518900; PubMed Central PMCID: PMC3093463.

Marko JF. Scaling of Linking and Writhing Numbers for Spherically Confined and Topologically Equilibrated Flexible Polymers. J Stat Phys. 2011 Apr;142(6):1353-1370. PubMed PMID: 21686050; PubMed Central PMCID: PMC3115200.

Bai H, Sun M, Ghosh P, Hatfull GF, Grindley ND, Marko JF. Single-molecule analysis reveals the molecular bearing mechanism of DNA strand exchange by a serine recombinase. Proc Natl Acad Sci U S A. 2011 May 3;108(18):7419-24. doi: 10.1073/pnas.1018436108. Epub 2011 Apr 18. PubMed PMID: 21502527; PubMed Central PMCID: PMC3088605.

Strizzi L, Hardy KM, Kirsammer GT, Gerami P, Hendrix MJ. Embryonic signaling in melanoma: potential for diagnosis and therapy. Lab Invest. 2011 Jun;91(6):819-24. doi: 10.1038/labinvest.2011.63. Epub 2011 Apr 4. PubMed PMID: 21464823; PubMed Central PMCID: PMC3444148.

Neukirch S, Marko JF. Analytical description of extension, torque, and supercoiling radius of a stretched twisted DNA. Phys Rev Lett. 2011 Apr 1;106(13):138104. Epub 2011 Apr 1. PubMed PMID: 21517425; PubMed Central PMCID: PMC3120040.

Pradhan P, Damania D, Joshi HM, Turzhitsky V, Subramanian H, Roy HK, Taflove A, Dravid VP, Backman V. Quantification of nanoscale density fluctuations by electron microscopy: probing cellular alterations in early carcinogenesis. Phys Biol. 2011 Apr;8(2):026012. doi: 10.1088/1478-3975/8/2/026012. Epub 2011 Mar 25. PubMed PMID: 21441647; PubMed Central PMCID: PMC3332100.

Xiao B, Zhang H, Johnson RC, Marko JF. Force-driven unbinding of proteins HU and Fis from DNA quantified using a thermodynamic Maxwell relation. Nucleic Acids Res. 2011 Jul;39(13):5568-77. doi: 10.1093/nar/gkr141. Epub 2011 Mar 22. PubMed PMID: 21427084; PubMed Central PMCID: PMC3141252.

Fishbain S, Prakash S, Herrig A, Elsasser S, Matouschek A. Rad23 escapes degradation because it lacks a proteasome initiation region. Nat Commun. 2011 Feb 8;2:192. doi: 10.1038/ncomms1194. PubMed PMID: 21304521.

Sun M, Kawamura R, Marko JF. Micromechanics of human mitotic chromosomes. Phys Biol. 2011 Feb;8(1):015003. doi: 10.1088/1478-3975/8/1/015003. Epub 2011 Feb 7. PubMed PMID: 21301072; PubMed Central PMCID: PMC3150456.

Cornelius SP, Lee JS, Motter AE. Dispensability of Escherichia coli’s latent pathways. Proc Natl Acad Sci U S A. 2011 Feb 22;108(8):3124-9. doi: 10.1073/pnas.1009772108. Epub 2011 Feb 7. PubMed PMID: 21300895; PubMed Central PMCID: PMC3044393.

Inobe T, Fishbain S, Prakash S, Matouschek A. Defining the geometry of the two-component proteasome degron. Nat Chem Biol. 2011 Mar;7(3):161-7. doi: 10.1038/nchembio.521. Epub 2011 Jan 30. PubMed PMID: 21278740; PubMed Central PMCID: PMC3129032.

Fu H, Chen H, Zhang X, Qu Y, Marko JF, Yan J. Transition dynamics and selection of the distinct S-DNA and strand unpeeling modes of double helix overstretching. Nucleic Acids Res. 2011 Apr;39(8):3473-81. doi: 10.1093/nar/gkq1278. Epub 2010 Dec 21. PubMed PMID: 21177651; PubMed Central PMCID: PMC3082884.

Hardy KM, Kirschmann DA, Seftor EA, Margaryan NV, Postovit LM, Strizzi L, Hendrix MJ. Regulation of the embryonic morphogen Nodal by Notch4 facilitates manifestation of the aggressive melanoma phenotype. Cancer Res. 2010 Dec 15;70(24):10340-50. doi: 10.1158/0008-5472.CAN-10-0705. PubMed PMID: 21159651; PubMed Central PMCID: PMC3057934.

Graham JS, Johnson RC, Marko JF. Concentration-dependent exchange accelerates turnover of proteins bound to double-stranded DNA. Nucleic Acids Res. 2011 Mar;39(6):2249-59. doi: 10.1093/nar/gkq1140. Epub 2010 Nov 21.PubMed PMID: 21097894; PubMed Central PMCID: PMC3064784.

Park H, Pontius W, Guet CC, Marko JF, Emonet T, Cluzel P. Interdependence of behavioural variability and response to small stimuli in bacteria. Nature. 2010 Dec 9;468(7325):819-23. doi: 10.1038/nature09551. Epub 2010 Nov 14.PubMed PMID: 21076396; PubMed Central PMCID: PMC3230254.

Whichard ZL, Motter AE, Stein PJ, Corey SJ. Slowly produced microRNAs control protein levels. J Biol Chem. 2011 Feb 11;286(6):4742-8. doi: 10.1074/jbc.M110.166348. Epub 2010 Nov 4. PubMed PMID: 21051536; PubMed Central PMCID: PMC3039369.

Malchenko S, Galat V, Seftor EA, Vanin EF, Costa FF, Seftor RE, Soares MB, Hendrix MJ. Cancer hallmarks in induced pluripotent cells: new insights. J Cell Physiol. 2010 Nov;225(2):390-3. doi: 10.1002/jcp.22280. PubMed PMID: 20568225; PubMed Central PMCID: PMC3180883.

Martinez-Garcia E, Popovic R, Min DJ, Sweet SM, Thomas PM, Zamdborg L, Heffner A, Will C, Lamy L, Staudt LM, Levens DL, Kelleher NL, Licht JD. The MMSET histone methyl transferase switches global histone methylation and alters gene expression in t(4;14) multiple myeloma cells. Blood. 2011 Jan 6;117(1):211-20. doi: 10.1182/blood-2010-07-298349. Epub 2010 Oct 25. PubMed PMID: 20974671; PubMed Central PMCID: PMC3037745.

Schrader EK, Wilmington SR, Matouschek A. Making it easier to regulate protein stability. Chem Biol. 2010 Sep 24;17(9):917-8. doi: 10.1016/j.chembiol.2010.09.004. PubMed PMID: 20851337; PubMed Central PMCID: PMC2990474.

Lidor Nili E, Field Y, Lubling Y, Widom J, Oren M, Segal E. p53 binds preferentially to genomic regions with high DNA-encoded nucleosome occupancy. Genome Res. 2010 Oct;20(10):1361-8. doi: 10.1101/gr.103945.109. Epub 2010 Aug 17. PubMed PMID: 20716666; PubMed Central PMCID: PMC2945185.

Damania D, Subramanian H, Tiwari AK, Stypula Y, Kunte D, Pradhan P, Roy HK, Backman V. Role of cytoskeleton in controlling the disorder strength of cellular nanoscale architecture. Biophys J. 2010 Aug 4;99(3):989-96. doi: 10.1016/j.bpj.2010.05.023. PubMed PMID: 20682278; PubMed Central PMCID: PMC2913198.

Marko JF. Linking topology of large DNA molecules. Physica A. 2010 Aug 1;389(15):2997-3001. PubMed PMID: 20606760; PubMed Central PMCID: PMC2896270.

Xi L, Fondufe-Mittendorf Y, Xia L, Flatow J, Widom J, Wang JP. Predicting nucleosome positioning using a duration Hidden Markov Model. BMC Bioinformatics. 2010 Jun 24;11:346. doi: 10.1186/1471-2105-11-346. PubMed PMID: 20576140; PubMed Central PMCID: PMC2900280.

Lee OS, Prytkova TR, Schatz GC. Using DNA to Link Gold Nanoparticles, Polymers and Molecules: a Theoretical Perspective. J Phys Chem Lett. 2010 May 25;1(12):1781-1788. PubMed PMID: 20606716; PubMed Central PMCID: PMC2893743.

Xiao B, Johnson RC, Marko JF. Modulation of HU-DNA interactions by salt concentration and applied force. Nucleic Acids Res. 2010 Oct;38(18):6176-85. doi: 10.1093/nar/gkq435. Epub 2010 May 23. PubMed PMID: 20497998; PubMed Central PMCID: PMC2952867.

Fu H, Chen H, Marko JF, Yan J. Two distinct overstretched DNA states. Nucleic Acids Res. 2010 Sep;38(16):5594-600. doi: 10.1093/nar/gkq309. Epub 2010 Apr 30. PubMed PMID: 20435680; PubMed Central PMCID: PMC2938222.

Kawamura R, Pope LH, Christensen MO, Sun M, Terekhova K, Boege F, Mielke C, Andersen AH, Marko JF. Mitotic chromosomes are constrained by topoisomerase II-sensitive DNA entanglements. J Cell Biol. 2010 Mar 8;188(5):653-63. doi: 10.1083/jcb.200910085. Epub 2010 Mar 1. PubMed PMID: 20194637; PubMed Central PMCID: PMC2835934.

Motter AE. Improved network performance via antagonism: From synthetic rescues to multi-drug combinations. Bioessays. 2010 Mar;32(3):236-45. doi: 10.1002/bies.200900128. PubMed PMID: 20127700; PubMed Central PMCID: PMC2841822.

Joshi HM, Lin YP, Aslam M, Prasad PV, Schultz-Sikma EA, Edelman R, Meade T, Dravid VP. Effects of shape and size of cobalt ferrite nanostructures on their MRI contrast and thermal activation. J Phys Chem C Nanomater Interfaces. 2009;113(41):17761-17767. PubMed PMID: 21850276; PubMed Central PMCID: PMC3156095.