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Alexander Goncearenco - Publications

Affiliations: 
2013-2019 NIH - NIDDK 
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34 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Peng Y, Markov Y, Goncearenco A, Landsman D, Panchenko AR. Data sets on human histone interaction networks. Data in Brief. 33: 106555. PMID 33299912 DOI: 10.1016/j.dib.2020.106555  0.745
2020 Peng Y, Markov Y, Goncearenco A, Landsman D, Panchenko AR. Human histone interaction networks: an old concept, new trends. Journal of Molecular Biology. PMID 33098859 DOI: 10.1016/j.jmb.2020.10.018  0.751
2020 Goncearenco A, LaBarre BA, Petrykowska HM, Jaratlerdsiri W, Bornman MSR, Turner SD, Hayes VM, Elnitski L. DNA methylation profiles unique to Kalahari KhoeSan individuals. Epigenetics. 1-17. PMID 32892676 DOI: 10.1080/15592294.2020.1809852  0.306
2020 Zhang N, Chen Y, Lu H, Zhao F, Alvarez RV, Goncearenco A, Panchenko AR, Li M. MutaBind2: Predicting the Impacts of Single and Multiple Mutations on Protein-Protein Interactions. Iscience. 23: 100939. PMID 32169820 DOI: 10.1016/J.Isci.2020.100939  0.693
2019 LaBarre BA, Goncearenco A, Petrykowska HM, Jaratlerdsiri W, Bornman MSR, Hayes VM, Elnitski L. MethylToSNP: identifying SNPs in Illumina DNA methylation array data. Epigenetics & Chromatin. 12: 79. PMID 31861999 DOI: 10.1186/S13072-019-0321-6  0.328
2019 Brown AL, Li M, Goncearenco A, Panchenko AR. Finding driver mutations in cancer: Elucidating the role of background mutational processes. Plos Computational Biology. 15: e1006981. PMID 31034466 DOI: 10.1371/Journal.Pcbi.1006981  0.661
2019 Kale S, Goncearenco A, Markov Y, Landsman D, Panchenko AR. Molecular recognition of nucleosomes by binding partners. Current Opinion in Structural Biology. 56: 164-170. PMID 30991239 DOI: 10.1016/J.Sbi.2019.03.010  0.723
2019 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, et al. APOBEC Mutagenesis and Copy-Number Alterations Are Drivers of Proteogenomic Tumor Evolution and Heterogeneity in Metastatic Thoracic Tumors. Cell Reports. 26: 2651-2666.e6. PMID 30840888 DOI: 10.1016/J.Celrep.2019.02.028  0.584
2018 Romero Romero ML, Yang F, Lin YR, Toth-Petroczy A, Berezovsky IN, Goncearenco A, Yang W, Wellner A, Kumar-Deshmukh F, Sharon M, Baker D, Varani G, Tawfik DS. Simple yet functional phosphate-loop proteins. Proceedings of the National Academy of Sciences of the United States of America. PMID 30504143 DOI: 10.1073/Pnas.1812400115  0.342
2018 Zhao F, Zheng L, Goncearenco A, Panchenko AR, Li M. Computational Approaches to Prioritize Cancer Driver Missense Mutations. International Journal of Molecular Sciences. 19. PMID 30037003 DOI: 10.3390/Ijms19072113  0.692
2018 Roper N, Gao J, Banday R, Maity T, Zhang X, Venugopalan A, Patidar R, Sindiri S, Cultraro C, Goncearenco A, Panchenko A, Biswas R, Wang J, Hewitt S, Kleiner D, et al. Abstract A182: Apobec-mutagenesis drives mutational heterogeneity while copy number alterations drive transcriptomic and proteogenomic heterogeneity in metastatic lung adenocarcinoma and thymic carcinoma Molecular Cancer Therapeutics. 17. DOI: 10.1158/1535-7163.Targ-17-A182  0.552
2017 Rogozin IB, Goncearenco A, Lada AG, De S, Nudelman G, Panchenko AR, Cooper DN, Pavlov YI. DNA polymerase η mutational signatures are found in a variety of different types of cancer. Cell Cycle (Georgetown, Tex.). 1-31. PMID 29139326 DOI: 10.1080/15384101.2017.1404208  0.647
2017 Goncearenco A, Li M, Simonetti FL, Shoemaker BA, Panchenko AR. Exploring Protein-Protein Interactions as Drug Targets for Anti-cancer Therapy with In Silico Workflows. Methods in Molecular Biology (Clifton, N.J.). 1647: 221-236. PMID 28809006 DOI: 10.1007/978-1-4939-7201-2_15  0.658
2017 Rogozin IB, Pavlov YI, Goncearenco A, De S, Lada AG, Poliakov E, Panchenko AR, Cooper DN. Mutational signatures and mutable motifs in cancer genomes. Briefings in Bioinformatics. PMID 28498882 DOI: 10.1093/Bib/Bbx049  0.635
2017 Goncearenco A, Rager SL, Li M, Sang QX, Rogozin IB, Panchenko AR. Exploring background mutational processes to decipher cancer genetic heterogeneity. Nucleic Acids Research. PMID 28472504 DOI: 10.1093/Nar/Gkx367  0.683
2017 Li M, Goncearenco A, Panchenko AR. Annotating Mutational Effects on Proteins and Protein Interactions: Designing Novel and Revisiting Existing Protocols. Methods in Molecular Biology (Clifton, N.J.). 1550: 235-260. PMID 28188534 DOI: 10.1007/978-1-4939-6747-6_17  0.693
2016 Rogozin IB, Lada AG, Goncearenco A, Green MR, De S, Nudelman G, Panchenko AR, Koonin EV, Pavlov YI. Activation induced deaminase mutational signature overlaps with CpG methylation sites in follicular lymphoma and other cancers. Scientific Reports. 6: 38133. PMID 27924834 DOI: 10.1038/Srep38133  0.63
2016 Shaytan AK, Armeev GA, Goncearenco A, Zhurkin VB, Landsman D, Panchenko AR. Trajectories of microsecond molecular dynamics simulations of nucleosomes and nucleosome core particles. Data in Brief. 7: 1678-81. PMID 27222871 DOI: 10.1016/J.Dib.2016.04.073  0.726
2016 Li M, Simonetti FL, Goncearenco A, Panchenko AR. MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions. Nucleic Acids Research. 44: W494-501. PMID 27150810 DOI: 10.1093/Nar/Gkw374  0.699
2016 Shaytan AK, Armeev GA, Goncearenco A, Zhurkin VB, Landsman D, Panchenko AR. Trajectories of microsecond molecular dynamics simulations of nucleosomes and nucleosome core particles Data in Brief. 7: 1678-1681. DOI: 10.1016/j.dib.2016.04.073  0.717
2016 Shaytan AK, Armeev GA, Goncearenco A, Zhurkin VB, Landsman D, Panchenko AR. Nucleosome Dynamics at Microsecond Timescale: DNA-Protein Interactions, Water-Mediated Interactions and Nucleosome Formation Biophysical Journal. 110: 405. DOI: 10.1016/J.Bpj.2015.11.2189  0.764
2015 Shaytan AK, Armeev GA, Goncearenco A, Zhurkin VB, Landsman D, Panchenko AR. Coupling between histone conformations and DNA geometry in nucleosomes on a microsecond timescale: atomistic insights into nucleosome functions. Journal of Molecular Biology. PMID 26699921 DOI: 10.1016/J.Jmb.2015.12.004  0.757
2015 Zheng Z, Goncearenco A, Berezovsky IN. Nucleotide binding database NBDB - a collection of sequence motifs with specific protein-ligand interactions. Nucleic Acids Research. PMID 26507856 DOI: 10.1093/Nar/Gkv1124  0.377
2015 Goncearenco A, Shaytan AK, Shoemaker BA, Panchenko AR. Structural Perspectives on the Evolutionary Expansion of Unique Protein-Protein Binding Sites. Biophysical Journal. 109: 1295-306. PMID 26213149 DOI: 10.1016/J.Bpj.2015.06.056  0.72
2015 Shaytan AK, Armeev GA, Goncearenco A, Zhurkin VB, Landsman D, Panchenko AR. 6 Combined influence of linker DNA and histone tails on nucleosome dynamics as revealed by microsecond molecular dynamics simulations. Journal of Biomolecular Structure & Dynamics. 33: 3. PMID 26103217 DOI: 10.1080/07391102.2015.1032630  0.739
2015 Goncearenco A, Berezovsky IN. Protein function from its emergence to diversity in contemporary proteins. Physical Biology. 12: 045002. PMID 26057563 DOI: 10.1088/1478-3975/12/4/045002  0.339
2014 Goncearenco A, Berezovsky IN. The fundamental tradeoff in genomes and proteomes of prokaryotes established by the genetic code, codon entropy, and physics of nucleic acids and proteins. Biology Direct. 9: 29. PMID 25496919 DOI: 10.1186/S13062-014-0029-2  0.35
2014 Goncearenco A, Shoemaker BA, Zhang D, Sarychev A, Panchenko AR. Coverage of protein domain families with structural protein-protein interactions: current progress and future trends. Progress in Biophysics and Molecular Biology. 116: 187-93. PMID 24931138 DOI: 10.1016/J.Pbiomolbio.2014.05.005  0.618
2014 Goncearenco A, Ma BG, Berezovsky IN. Molecular mechanisms of adaptation emerging from the physics and evolution of nucleic acids and proteins. Nucleic Acids Research. 42: 2879-92. PMID 24371267 DOI: 10.1093/Nar/Gkt1336  0.332
2013 Goncearenco A, Mitternacht S, Yong T, Eisenhaber B, Eisenhaber F, Berezovsky IN. SPACER: Server for predicting allosteric communication and effects of regulation. Nucleic Acids Research. 41: W266-72. PMID 23737445 DOI: 10.1093/Nar/Gkt460  0.334
2013 Goncearenco A, Berezovsky IN. Towards Rational Design of Protein Function Biophysical Journal. 104. DOI: 10.1016/J.Bpj.2012.11.3033  0.301
2012 Lasry I, Seo YA, Ityel H, Shalva N, Pode-Shakked B, Glaser F, Berman B, Berezovsky I, Goncearenco A, Klar A, Levy J, Anikster Y, Kelleher SL, Assaraf YG. A dominant negative heterozygous G87R mutation in the zinc transporter, ZnT-2 (SLC30A2), results in transient neonatal zinc deficiency. The Journal of Biological Chemistry. 287: 29348-61. PMID 22733820 DOI: 10.1074/Jbc.M112.368159  0.307
2010 Goncearenco A, Berezovsky IN. Prototypes of elementary functional loops unravel evolutionary connections between protein functions. Bioinformatics (Oxford, England). 26: i497-503. PMID 20823313 DOI: 10.1093/Bioinformatics/Btq374  0.335
2010 Ma BG, Goncearenco A, Berezovsky IN. Thermophilic adaptation of protein complexes inferred from proteomic homology modeling. Structure (London, England : 1993). 18: 819-28. PMID 20637418 DOI: 10.1016/J.Str.2010.04.004  0.311
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