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Items: 1 to 20 of 93


Molecular Biology and Evolution of Cancer: From Discovery to Action.

Somarelli JA, Gardner H, Cannataro VL, Gunady EF, Boddy AM, Johnson NA, Fisk JN, Gaffney SG, Chuang JH, Li S, Ciccarelli FD, Panchenko AR, Megquier K, Kumar S, Dornburg A, DeGregori J, Townsend JP.

Mol Biol Evol. 2020 Feb 1;37(2):320-326. doi: 10.1093/molbev/msz242.


Editorial overview: Dynamic protein interactions - from complexes to molecular machines.

Fuxreiter M, Panchenko A.

Curr Opin Struct Biol. 2019 Jun;56:vi-viii. doi: 10.1016/ No abstract available.


Histone Octamer Structure Is Altered Early in ISW2 ATP-Dependent Nucleosome Remodeling.

Hada A, Hota SK, Luo J, Lin YC, Kale S, Shaytan AK, Bhardwaj SK, Persinger J, Ranish J, Panchenko AR, Bartholomew B.

Cell Rep. 2019 Jul 2;28(1):282-294.e6. doi: 10.1016/j.celrep.2019.05.106.


Finding driver mutations in cancer: Elucidating the role of background mutational processes.

Brown AL, Li M, Goncearenco A, Panchenko AR.

PLoS Comput Biol. 2019 Apr 29;15(4):e1006981. doi: 10.1371/journal.pcbi.1006981. eCollection 2019 Apr.


Molecular recognition of nucleosomes by binding partners.

Kale S, Goncearenco A, Markov Y, Landsman D, Panchenko AR.

Curr Opin Struct Biol. 2019 Jun;56:164-170. doi: 10.1016/ Epub 2019 Apr 13. Review.


APOBEC Mutagenesis and Copy-Number Alterations Are Drivers of Proteogenomic Tumor Evolution and Heterogeneity in Metastatic Thoracic Tumors.

Roper N, Gao S, Maity TK, Banday AR, Zhang X, Venugopalan A, Cultraro CM, Patidar R, Sindiri S, Brown AL, Goncearenco A, Panchenko AR, Biswas R, Thomas A, Rajan A, Carter CA, Kleiner DE, Hewitt SM, Khan J, Prokunina-Olsson L, Guha U.

Cell Rep. 2019 Mar 5;26(10):2651-2666.e6. doi: 10.1016/j.celrep.2019.02.028.


Structural interpretation of DNA-protein hydroxyl-radical footprinting experiments with high resolution using HYDROID.

Shaytan AK, Xiao H, Armeev GA, Gaykalova DA, Komarova GA, Wu C, Studitsky VM, Landsman D, Panchenko AR.

Nat Protoc. 2018 Nov;13(11):2535-2556. doi: 10.1038/s41596-018-0048-z.


Computational Approaches to Prioritize Cancer Driver Missense Mutations.

Zhao F, Zheng L, Goncearenco A, Panchenko AR, Li M.

Int J Mol Sci. 2018 Jul 20;19(7). pii: E2113. doi: 10.3390/ijms19072113. Review.


Database resources of the National Center for Biotechnology Information.

NCBI Resource Coordinators.

Nucleic Acids Res. 2018 Jan 4;46(D1):D8-D13. doi: 10.1093/nar/gkx1095.


DNA polymerase η mutational signatures are found in a variety of different types of cancer.

Rogozin IB, Goncearenco A, Lada AG, De S, Yurchenko V, Nudelman G, Panchenko AR, Cooper DN, Pavlov YI.

Cell Cycle. 2018;17(3):348-355. doi: 10.1080/15384101.2017.1404208. Epub 2018 Feb 15.


Molecular basis of CENP-C association with the CENP-A nucleosome at yeast centromeres.

Xiao H, Wang F, Wisniewski J, Shaytan AK, Ghirlando R, FitzGerald PC, Huang Y, Wei D, Li S, Landsman D, Panchenko AR, Wu C.

Genes Dev. 2017 Oct 1;31(19):1958-1972. doi: 10.1101/gad.304782.117. Epub 2017 Oct 26.


Hydroxyl-radical footprinting combined with molecular modeling identifies unique features of DNA conformation and nucleosome positioning.

Shaytan AK, Xiao H, Armeev GA, Wu C, Landsman D, Panchenko AR.

Nucleic Acids Res. 2017 Sep 19;45(16):9229-9243. doi: 10.1093/nar/gkx616.


Exploring Protein-Protein Interactions as Drug Targets for Anti-cancer Therapy with In Silico Workflows.

Goncearenco A, Li M, Simonetti FL, Shoemaker BA, Panchenko AR.

Methods Mol Biol. 2017;1647:221-236. doi: 10.1007/978-1-4939-7201-2_15.


Mutational signatures and mutable motifs in cancer genomes.

Rogozin IB, Pavlov YI, Goncearenco A, De S, Lada AG, Poliakov E, Panchenko AR, Cooper DN.

Brief Bioinform. 2018 Nov 27;19(6):1085-1101. doi: 10.1093/bib/bbx049. Review.


Exploring background mutational processes to decipher cancer genetic heterogeneity.

Goncearenco A, Rager SL, Li M, Sang QX, Rogozin IB, Panchenko AR.

Nucleic Acids Res. 2017 Jul 3;45(W1):W514-W522. doi: 10.1093/nar/gkx367.


Annotating Mutational Effects on Proteins and Protein Interactions: Designing Novel and Revisiting Existing Protocols.

Li M, Goncearenco A, Panchenko AR.

Methods Mol Biol. 2017;1550:235-260. doi: 10.1007/978-1-4939-6747-6_17.


MS_HistoneDB, a manually curated resource for proteomic analysis of human and mouse histones.

El Kennani S, Adrait A, Shaytan AK, Khochbin S, Bruley C, Panchenko AR, Landsman D, Pflieger D, Govin J.

Epigenetics Chromatin. 2017 Jan 10;10:2. doi: 10.1186/s13072-016-0109-x. eCollection 2017.


Activation induced deaminase mutational signature overlaps with CpG methylation sites in follicular lymphoma and other cancers.

Rogozin IB, Lada AG, Goncearenco A, Green MR, De S, Nudelman G, Panchenko AR, Koonin EV, Pavlov YI.

Sci Rep. 2016 Dec 7;6:38133. doi: 10.1038/srep38133.


Genomic profiling of multiple sequentially acquired tumor metastatic sites from an "exceptional responder" lung adenocarcinoma patient reveals extensive genomic heterogeneity and novel somatic variants driving treatment response.

Biswas R, Gao S, Cultraro CM, Maity TK, Venugopalan A, Abdullaev Z, Shaytan AK, Carter CA, Thomas A, Rajan A, Song Y, Pitts S, Chen K, Bass S, Boland J, Hanada KI, Chen J, Meltzer PS, Panchenko AR, Yang JC, Pack S, Giaccone G, Schrump DS, Khan J, Guha U.

Cold Spring Harb Mol Case Stud. 2016 Nov;2(6):a001263.


Trajectories of microsecond molecular dynamics simulations of nucleosomes and nucleosome core particles.

Shaytan AK, Armeev GA, Goncearenco A, Zhurkin VB, Landsman D, Panchenko AR.

Data Brief. 2016 May 6;7:1678-81. doi: 10.1016/j.dib.2016.04.073. eCollection 2016 Jun.

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