Daniel M Czajkowsky

Daniel M Czajkowsky

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Daniel M Czajkowsky

Daniel M Czajkowsky

Publications by authors named "Daniel M Czajkowsky"

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51Publications

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Q-Nuc: a bioinformatics pipeline for the quantitative analysis of nucleosomal profiles.

Interdiscip Sci 2020 Mar 16;12(1):69-81. Epub 2019 Dec 16.

State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.

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http://dx.doi.org/10.1007/s12539-019-00354-7DOI Listing
March 2020

Unconventional Atomic Structure of Graphene Sheets on Solid Substrates.

Small 2019 Oct 30;15(42):e1902637. Epub 2019 Aug 30.

Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China.

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http://dx.doi.org/10.1002/smll.201902637DOI Listing
October 2019

Atomic force microscopy-based single-molecule force spectroscopy detects DNA base mismatches.

Nanoscale 2019 Oct 17;11(37):17206-17210. Epub 2019 Sep 17.

Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. and Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.

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http://dx.doi.org/10.1039/c9nr05234hDOI Listing
October 2019

Interplay between the bacterial protein deacetylase CobB and the second messenger c-di-GMP.

EMBO J 2019 09 16;38(18):e100948. Epub 2019 Aug 16.

Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.

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http://dx.doi.org/10.15252/embj.2018100948DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6745502PMC
September 2019

Evidence for heightened genetic instability in precancerous spasmolytic polypeptide expressing gastric glands.

J Med Genet 2019 Mar 15. Epub 2019 Mar 15.

Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.

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http://dx.doi.org/10.1136/jmedgenet-2018-105752DOI Listing
March 2019

Discovery and genetic characterization of intestinal metaplasia in the Helicobacter felis-infected mouse model of gastric cancer.

Acta Biochim Biophys Sin (Shanghai) 2019 Feb;51(2):219-222

Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.

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http://dx.doi.org/10.1093/abbs/gmy160DOI Listing
February 2019

Cell Lysate Microarray for Mapping the Network of Genetic Regulators for Histone Marks.

Mol Cell Proteomics 2018 09 5;17(9):1720-1736. Epub 2018 Jun 5.

From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education); School of Biomedical Engineering; and State Key Laboratory of Oncogenes and Related Genes; Shanghai Jiao Tong University, Shanghai 200240, PR China;

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http://dx.doi.org/10.1074/mcp.RA117.000550DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6126384PMC
September 2018

Helix α-3 inter-molecular salt bridges and conformational changes are essential for toxicity of Bacillus thuringiensis 3D-Cry toxin family.

Sci Rep 2018 07 9;8(1):10331. Epub 2018 Jul 9.

Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, Cuernavaca, 62250, Morelos, Mexico.

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http://dx.doi.org/10.1038/s41598-018-28753-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6037675PMC
July 2018

abLIM1 constructs non-erythroid cortical actin networks to prevent mechanical tension-induced blebbing.

Cell Discov 2018 24;4:42. Epub 2018 Jul 24.

1State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031 China.

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http://www.nature.com/articles/s41421-018-0040-3
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http://dx.doi.org/10.1038/s41421-018-0040-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6056535PMC
July 2018

Identification of Serine 119 as an Effective Inhibitor Binding Site of M. tuberculosis Ubiquitin-like Protein Ligase PafA Using Purified Proteins and M. smegmatis.

EBioMedicine 2018 Apr 27;30:225-236. Epub 2018 Mar 27.

Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China; School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China. Electronic address:

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http://dx.doi.org/10.1016/j.ebiom.2018.03.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5952411PMC
April 2018

Sub-kb Hi-C in D. melanogaster reveals conserved characteristics of TADs between insect and mammalian cells.

Nat Commun 2018 01 15;9(1):188. Epub 2018 Jan 15.

State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, 200240, Shanghai, China.

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http://dx.doi.org/10.1038/s41467-017-02526-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5768742PMC
January 2018

The Ser/Thr Protein Kinase Protein-Protein Interaction Map of .

Mol Cell Proteomics 2017 08 1;16(8):1491-1506. Epub 2017 Jun 1.

From the ‡Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China;

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http://www.mcponline.org/lookup/doi/10.1074/mcp.M116.065771
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http://dx.doi.org/10.1074/mcp.M116.065771DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5546200PMC
August 2017

Improved clearing of lipid droplet-rich tissues for three-dimensional structural elucidation.

Acta Biochim Biophys Sin (Shanghai) 2017 05;49(5):465-467

Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.

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http://dx.doi.org/10.1093/abbs/gmx018DOI Listing
May 2017

Toward the development of magnetic tweezers for high-throughput measurement of protein-protein interactions.

Acta Biochim Biophys Sin (Shanghai) 2017 05;49(5):468-470

School of Biomedical Engineering, Bio-ID Center,Shanghai Jiao Tong University, Shanghai 200240, China.

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http://dx.doi.org/10.1093/abbs/gmx027DOI Listing
May 2017

Glycan-independent binding and internalization of human IgM to FCMR, its cognate cellular receptor.

Sci Rep 2017 02 23;7:42989. Epub 2017 Feb 23.

Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.

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http://www.nature.com/articles/srep42989
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http://dx.doi.org/10.1038/srep42989DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5322398PMC
February 2017

Ultra-deep sequencing of ribosome-associated poly-adenylated RNA in early Drosophila embryos reveals hundreds of conserved translated sORFs.

DNA Res 2016 Dec 24;23(6):571-580. Epub 2016 Aug 24.

Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China

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http://dx.doi.org/10.1093/dnares/dsw040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5144680PMC
December 2016

Complex clonal mosaicism within microdissected intestinal metaplastic glands without concurrent gastric cancer.

J Med Genet 2016 09 9;53(9):643-6. Epub 2016 Jun 9.

Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, P. R. China State Key Laboratory for Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai, P. R. China.

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http://dx.doi.org/10.1136/jmedgenet-2016-103872DOI Listing
September 2016

Development of a low-noise cryogenic atomic force microscope for high resolution imaging of large biological complexes.

Acta Biochim Biophys Sin (Shanghai) 2016 Sep 12;48(9):859-61. Epub 2016 Aug 12.

Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.

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http://dx.doi.org/10.1093/abbs/gmw074DOI Listing
September 2016

Nanoscopic characterization of the water vapor-salt interfacial layer reveals a unique biphasic adsorption process.

Sci Rep 2016 08 16;6:31688. Epub 2016 Aug 16.

Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.

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http://dx.doi.org/10.1038/srep31688DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4985642PMC
August 2016

The non-coding RNA composition of the mitotic chromosome by 5'-tag sequencing.

Nucleic Acids Res 2016 06 25;44(10):4934-46. Epub 2016 Mar 25.

Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China State Key Laboratory of Oncogenes & Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China

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http://dx.doi.org/10.1093/nar/gkw195DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4889943PMC
June 2016

Systematic identification of arsenic-binding proteins reveals that hexokinase-2 is inhibited by arsenic.

Proc Natl Acad Sci U S A 2015 Dec 23;112(49):15084-9. Epub 2015 Nov 23.

Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai 200240, China; School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China; Collaborative Innovation Center of Systems Biomedicine, Shanghai 200240, China

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http://dx.doi.org/10.1073/pnas.1521316112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4679019PMC
December 2015

Single molecule compression reveals intra-protein forces drive cytotoxin pore formation.

Elife 2015 Dec 10;4:e08421. Epub 2015 Dec 10.

State Key Laboratory of Oncogenes and Related Genes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.

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http://dx.doi.org/10.7554/eLife.08421DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4714976PMC
December 2015

YcgC represents a new protein deacetylase family in prokaryotes.

Elife 2015 Dec 30;4. Epub 2015 Dec 30.

Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.

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http://dx.doi.org/10.7554/eLife.05322DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4709262PMC
December 2015

Single-cell codetection of metabolic activity, intracellular functional proteins, and genetic mutations from rare circulating tumor cells.

Anal Chem 2015 Oct;87(19):9761-8

Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California , Los Angeles, California 90095, United States.

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http://dx.doi.org/10.1021/acs.analchem.5b01901DOI Listing
October 2015

Fast immuno-labeling by electrophoretically driven infiltration for intact tissue imaging.

Sci Rep 2015 May 27;5:10640. Epub 2015 May 27.

1] School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China [2] State Key Laboratory for Oncogenes &Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China.

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http://dx.doi.org/10.1038/srep10640DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4603706PMC
May 2015

Identification of the minimal binding region of a Plasmodium falciparum IgM binding PfEMP1 domain.

Mol Biochem Parasitol 2015 May 18;201(1):76-82. Epub 2015 Jun 18.

Institute of Immunology and Infection Research, Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom. Electronic address:

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http://dx.doi.org/10.1016/j.molbiopara.2015.06.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4539346PMC
May 2015

Genome-wide profiling of untranslated regions by paired-end ditag sequencing reveals unexpected transcriptome complexity in yeast.

Mol Genet Genomics 2015 Feb 12;290(1):217-24. Epub 2014 Sep 12.

Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.

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http://dx.doi.org/10.1007/s00438-014-0913-6DOI Listing
February 2015

Illuminated up close: near-field optical microscopy of cell surfaces.

Nanomedicine 2015 Jan 23;11(1):119-25. Epub 2014 Aug 23.

Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S15499634140042
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http://dx.doi.org/10.1016/j.nano.2014.08.002DOI Listing
January 2015

An integrated microfluidic chip system for single-cell secretion profiling of rare circulating tumor cells.

Sci Rep 2014 Dec 16;4:7499. Epub 2014 Dec 16.

1] Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China [2] State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai, China [3] Center for Bio-Detection and Bio-Instrumentation, Shanghai Jiao Tong University, Shanghai, China [4] School of Biomedicial Engineering, Shanghai Jiao Tong University, Shanghai, China.

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http://dx.doi.org/10.1038/srep07499DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4266859PMC
December 2014

Anomalous surface fatigue in a nano-layered material.

Adv Mater 2014 Oct 28;26(37):6478-82. Epub 2014 Aug 28.

Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.

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http://dx.doi.org/10.1002/adma.201401906DOI Listing
October 2014

Molecular threading and tunable molecular recognition on DNA origami nanostructures.

J Am Chem Soc 2013 Aug 7;135(33):12172-5. Epub 2013 Aug 7.

Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.

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http://dx.doi.org/10.1021/ja403863aDOI Listing
August 2013

A novel electromagnetic apparatus for rapid multiplex single molecule force spectroscopy.

J Nanosci Nanotechnol 2013 Feb;13(2):1232-6

Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.

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http://dx.doi.org/10.1166/jnn.2013.6099DOI Listing
February 2013

Fc-fusion proteins: new developments and future perspectives.

EMBO Mol Med 2012 Oct 26;4(10):1015-28. Epub 2012 Jul 26.

Key Laboratory of Systems Biomedicine (Ministry of Education) & State Key Laboratory of Oncogenes & Related Genes, Shanghai Jiao Tong University, Shanghai, P. R. China.

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http://dx.doi.org/10.1002/emmm.201201379DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491832PMC
October 2012

Microdissection of spatially identified single nuclei in a solid tumor for single cell whole genome sequencing.

Biotechniques 2012 Apr 1;52(4). Epub 2012 Apr 1.

Ministry of Education Key Laboratory of Systems Biomedicine.

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http://dx.doi.org/10.2144/000113860DOI Listing
April 2012

Heteroepitaxial streptavidin nanocrystals reveal critical role of proton "fingers" and subsurface atoms in determining adsorbed protein orientation.

ACS Nano 2012 Jan 21;6(1):190-8. Epub 2011 Dec 21.

Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China.

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http://dx.doi.org/10.1021/nn203356pDOI Listing
January 2012

In situ monitoring of single molecule binding reactions with time-lapse atomic force microscopy on functionalized DNA origami.

Nanoscale 2011 Jun 28;3(6):2481-4. Epub 2011 Apr 28.

Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.

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http://dx.doi.org/10.1039/c1nr10181aDOI Listing
June 2011

IgM, Fc mu Rs, and malarial immune evasion.

J Immunol 2010 May;184(9):4597-603

Department of Molecular Physiology and Biological Physics, University of Virginia Health Sciences Center, Charlottesville, VA 22908, USA.

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http://dx.doi.org/10.4049/jimmunol.1000203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2859470PMC
May 2010

The human IgM pentamer is a mushroom-shaped molecule with a flexural bias.

Proc Natl Acad Sci U S A 2009 Sep 17;106(35):14960-5. Epub 2009 Aug 17.

Department of Molecular Physiology and Biological Physics, University of Virginia Health Sciences Center, P.O. Box 800736, Charlottesville, VA 22908, USA.

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http://dx.doi.org/10.1073/pnas.0903805106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2736442PMC
September 2009

Cell cycle-dependent nucleosome occupancy at cohesin binding sites in yeast chromosomes.

Genomics 2008 Mar;91(3):274-80

Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, P.O. Box 800736, Charlottesville, VA 22908, USA.

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http://dx.doi.org/10.1016/j.ygeno.2007.11.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2268989PMC
March 2008

DNA combing reveals intrinsic temporal disorder in the replication of yeast chromosome VI.

J Mol Biol 2008 Jan 23;375(1):12-9. Epub 2007 Oct 23.

Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.

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http://dx.doi.org/10.1016/j.jmb.2007.10.046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2151843PMC
January 2008

Random mutagenesis of Helicobacter pylori vacA to identify amino acids essential for vacuolating cytotoxic activity.

Infect Immun 2006 Nov 5;74(11):6188-95. Epub 2006 Sep 5.

Department of Medicine, Vanderbilt University School of Medicine, and Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN 37232, USA.

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http://dx.doi.org/10.1128/IAI.00915-06DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1695532PMC
November 2006

Localization of linker histone in chromatosomes by cryo-atomic force microscopy.

Biophys J 2006 Aug 16;91(4):L35-7. Epub 2006 Jun 16.

Department of Molecular Physiology and Biological Physics, University of Virginia Health Sciences Center, Charlottesville, Virginia 22908, USA.

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http://dx.doi.org/10.1529/biophysj.106.090423DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1518653PMC
August 2006

Mimicry of a host anion channel by a Helicobacter pylori pore-forming toxin.

Biophys J 2005 Nov 12;89(5):3093-101. Epub 2005 Aug 12.

Department of Molecular Physiology and Biological Physics, University of Virginia Health Sciences Center, Charlottesville, VA 22908, USA.

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http://dx.doi.org/10.1529/biophysj.105.066746DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1366806PMC
November 2005

Vertical collapse of a cytolysin prepore moves its transmembrane beta-hairpins to the membrane.

EMBO J 2004 Aug 5;23(16):3206-15. Epub 2004 Aug 5.

Department of Molecular Physiology and Biological Physics, University of Virginia Health Sciences Center, Charlottesville, VA, USA.

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http://dx.doi.org/10.1038/sj.emboj.7600350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC514522PMC
August 2004

Supported lipid bilayers as effective substrates for atomic force microscopy.

Methods Cell Biol 2002 ;68:231-41

Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA.

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http://dx.doi.org/10.1016/s0091-679x(02)68012-4DOI Listing
January 2003

Monomer-monomer interactions drive the prepore to pore conversion of a beta-barrel-forming cholesterol-dependent cytolysin.

J Biol Chem 2002 Mar 17;277(13):11597-605. Epub 2002 Jan 17.

Department of Microbiology and Immunology, the University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, USA.

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http://www.jbc.org/lookup/doi/10.1074/jbc.M111039200
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http://dx.doi.org/10.1074/jbc.M111039200DOI Listing
March 2002