Michael Y Tolstorukov

Michael Y Tolstorukov

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Michael Y Tolstorukov

Michael Y Tolstorukov

Publications by authors named "Michael Y Tolstorukov"

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40Publications

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Non-neutral evolution of H3.3-encoding genes occurs without alterations in protein sequence.

Sci Rep 2019 Jun 11;9(1):8472. Epub 2019 Jun 11.

Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA.

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http://dx.doi.org/10.1038/s41598-019-44800-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6560044PMC
June 2019

Low-Input MNase Accessibility of Chromatin (Low-Input MACC).

Curr Protoc Mol Biol 2019 Jun;127(1):e91

Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts.

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http://dx.doi.org/10.1002/cpmb.91DOI Listing
June 2019

Bioinformatic Analysis of Nucleosome and Histone Variant Positioning.

Methods Mol Biol 2018 ;1832:185-203

Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1007/978-1-4939-8663-7_10DOI Listing
April 2019

Single-Assay Profiling of Nucleosome Occupancy and Chromatin Accessibility.

Curr Protoc Mol Biol 2017 10 2;120:21.34.1-21.34.18. Epub 2017 Oct 2.

Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts.

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http://dx.doi.org/10.1002/cpmb.45DOI Listing
October 2017

Histone locus regulation by the dosage compensation adaptor protein CLAMP.

Genes Dev 2017 07 24;31(14):1494-1508. Epub 2017 Aug 24.

Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island 02912, USA.

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http://dx.doi.org/10.1101/gad.300855.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5588930PMC
July 2017

Widespread changes in nucleosome accessibility without changes in nucleosome occupancy during a rapid transcriptional induction.

Genes Dev 2017 03 29;31(5):451-462. Epub 2017 Mar 29.

Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.

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http://dx.doi.org/10.1101/gad.293118.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5393060PMC
March 2017

Resolving Heart Regeneration by Replacement Histone Profiling.

Dev Cell 2017 02;40(4):392-404.e5

Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA; Regeneration Next, Duke University, Durham, NC 27710, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S15345807173004
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http://dx.doi.org/10.1016/j.devcel.2017.01.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5367476PMC
February 2017

Regulated large-scale nucleosome density patterns and precise nucleosome positioning correlate with V(D)J recombination.

Proc Natl Acad Sci U S A 2016 10 3;113(42):E6427-E6436. Epub 2016 Oct 3.

Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114; Department of Genetics, Harvard Medical School, Boston, MA 02115;

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http://dx.doi.org/10.1073/pnas.1605543113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5081657PMC
October 2016

MNase titration reveals differences between nucleosome occupancy and chromatin accessibility.

Nat Commun 2016 05 6;7:11485. Epub 2016 May 6.

Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.

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http://dx.doi.org/10.1038/ncomms11485DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4859066PMC
May 2016

Organization of DNA in a bacterial nucleoid.

BMC Microbiol 2016 Feb 20;16:22. Epub 2016 Feb 20.

Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.

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http://dx.doi.org/10.1186/s12866-016-0637-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4761138PMC
February 2016

The long noncoding RNAs NEAT1 and MALAT1 bind active chromatin sites.

Mol Cell 2014 Sep 21;55(5):791-802. Epub 2014 Aug 21.

Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://www.cell.com/molecular-cell/pdf/S1097-2765(14)00605-4
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http://linkinghub.elsevier.com/retrieve/pii/S109727651400605
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http://dx.doi.org/10.1016/j.molcel.2014.07.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4428586PMC
September 2014

Nucleosomal occupancy changes locally over key regulatory regions during cell differentiation and reprogramming.

Nat Commun 2014 Aug 27;5:4719. Epub 2014 Aug 27.

1] Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/ncomms5719DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4217530PMC
August 2014

Comparative analysis of metazoan chromatin organization.

Nature 2014 Aug;512(7515):449-52

1] Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA [3] Informatics Program, Children's Hospital, Boston, Massachusetts 02215, USA.

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http://dx.doi.org/10.1038/nature13415DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4227084PMC
August 2014

Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells.

Mol Cell 2012 Aug 12;47(4):596-607. Epub 2012 Jul 12.

Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1016/j.molcel.2012.06.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3708478PMC
August 2012

Impact of chromatin structure on sequence variability in the human genome.

Nat Struct Mol Biol 2011 Apr 13;18(4):510-5. Epub 2011 Mar 13.

Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/nsmb.2012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3188321PMC
April 2011

Identification of functional elements and regulatory circuits by Drosophila modENCODE.

Science 2010 Dec 22;330(6012):1787-97. Epub 2010 Dec 22.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.

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http://compbio.mit.edu/publications/46_modENCODE_Science_10.
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http://www.sciencemag.org/cgi/doi/10.1126/science.1198374
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http://dx.doi.org/10.1126/science.1198374DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192495PMC
December 2010

Analysis of primary structure of chromatin with next-generation sequencing.

Epigenomics 2010 Apr;2(2):187-197

Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck St., Boston, MA 02115 USA.

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http://dx.doi.org/10.2217/epi.09.48DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3196531PMC
April 2010

Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes.

Genome Res 2009 Jun 26;19(6):967-77. Epub 2009 Feb 26.

Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1101/gr.084830.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2694475PMC
June 2009

Design and analysis of ChIP-seq experiments for DNA-binding proteins.

Nat Biotechnol 2008 Dec 16;26(12):1351-9. Epub 2008 Nov 16.

Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck St., Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/nbt.1508DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2597701PMC
December 2008

Nucleosome positioning in human HOX gene clusters.

Genome Res 2008 Oct 22;18(10):1554-61. Epub 2008 Aug 22.

Harvard Partners Center for Genetics and Genomics, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1101/gr.075952.107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2556261PMC
October 2008

nuScore: a web-interface for nucleosome positioning predictions.

Bioinformatics 2008 Jun 29;24(12):1456-8. Epub 2008 Apr 29.

Harvard-Partners Center for Genetics and Genomics, Brigham and Women's Hospital, Boston, MA 02115, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn212DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3807124PMC
June 2008

A-tract clusters may facilitate DNA packaging in bacterial nucleoid.

Nucleic Acids Res 2005 15;33(12):3907-18. Epub 2005 Jul 15.

Laboratory of Experimental and Computational Biology, National Cancer Institute Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1093/nar/gki699DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1176013PMC
July 2005

Protein-DNA hydrophobic recognition in the minor groove is facilitated by sugar switching.

J Mol Biol 2004 Mar;337(1):65-76

Laboratory of Experimental and Computational Biology, National Cancer Institute, National Institutes of Health, Bg. 12B, Rm. B116, Bethesda, MD 20892-5677, USA.

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http://dx.doi.org/10.1016/j.jmb.2004.01.011DOI Listing
March 2004

"Antiparallel" DNA loop in gal repressosome visualized by atomic force microscopy.

J Mol Biol 2003 Nov;334(1):53-63

Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1016/j.jmb.2003.09.030DOI Listing
November 2003