Benjamin P Berman

Benjamin P Berman

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Benjamin P Berman

Benjamin P Berman

Publications by authors named "Benjamin P Berman"

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GENAVi: a shiny web application for gene expression normalization, analysis and visualization.

BMC Genomics 2019 Oct 16;20(1):745. Epub 2019 Oct 16.

Center for Bioinformatics and Functional Genomics, Department of Biomedical Science, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.

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http://dx.doi.org/10.1186/s12864-019-6073-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6796420PMC
October 2019

Mapping Citrullinated Sites in Multiple Organs of Mice Using Hypercitrullinated Library.

J Proteome Res 2019 May 23;18(5):2270-2278. Epub 2019 Apr 23.

The Smidt Heart Institute, Department of Medicine , Cedars-Sinai Medical Center , Los Angeles , California 90048 , United States.

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http://dx.doi.org/10.1021/acs.jproteome.9b00118DOI Listing
May 2019

Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation.

Sci Adv 2018 12 13;4(12):eaav8550. Epub 2018 Dec 13.

Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.

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http://dx.doi.org/10.1126/sciadv.aav8550DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6292713PMC
December 2018

DNA methylation loss in late-replicating domains is linked to mitotic cell division.

Nat Genet 2018 04 2;50(4):591-602. Epub 2018 Apr 2.

Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA.

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http://dx.doi.org/10.1038/s41588-018-0073-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5893360PMC
April 2018

Granulocyte-Monocyte Progenitors and Monocyte-Dendritic Cell Progenitors Independently Produce Functionally Distinct Monocytes.

Immunity 2017 11;47(5):890-902.e4

Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA. Electronic address:

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http://dx.doi.org/10.1016/j.immuni.2017.10.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5726802PMC
November 2017

Exosomal MicroRNA Transfer Into Macrophages Mediates Cellular Postconditioning.

Circulation 2017 Jul 14;136(2):200-214. Epub 2017 Apr 14.

From Cedars-Sinai Heart Institute, Los Angeles, CA (G.d.C., R.G., L.C., E.J., N.M., J.F.D., B.P.B., E.M.); and Cedars-Sinai Center for Bioinformatics and Functional Genomics, Los Angeles, CA (B.P.B.).

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https://www.ahajournals.org/doi/10.1161/CIRCULATIONAHA.116.0
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http://dx.doi.org/10.1161/CIRCULATIONAHA.116.024590DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5505791PMC
July 2017

Genomic and Epigenomic Heterogeneity of Hepatocellular Carcinoma.

Cancer Res 2017 05 20;77(9):2255-2265. Epub 2017 Feb 20.

Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, California.

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http://dx.doi.org/10.1158/0008-5472.CAN-16-2822DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5413372PMC
May 2017

Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes.

Crit Rev Biochem Mol Biol 2015 8;50(6):550-73. Epub 2015 Oct 8.

a Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California , Los Angeles , CA , USA and.

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http://dx.doi.org/10.3109/10409238.2015.1087961DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4666684PMC
September 2016

Volumetric MRI of the lungs during forced expiration.

Magn Reson Med 2016 06 3;75(6):2295-302. Epub 2015 Jul 3.

Department of Electrical and Computer Engineering, University of Arizona, Tucson, Arizona, USA.

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http://dx.doi.org/10.1002/mrm.25798DOI Listing
June 2016

The PsychENCODE project.

Nat Neurosci 2015 Dec;18(12):1707-12

Yale University, New Haven, Connecticut, USA.

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http://dx.doi.org/10.1038/nn.4156DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4675669PMC
December 2015

Gender-specific postnatal demethylation and establishment of epigenetic memory.

Genes Dev 2015 May;29(9):923-33

Department of Developmental Biology and Cancer Research, Hebrew University Medical School, Jerusalem 91120, Israel;

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http://dx.doi.org/10.1101/gad.259309.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4421981PMC
May 2015

Inferring regulatory element landscapes and transcription factor networks from cancer methylomes.

Genome Biol 2015 May 21;16:105. Epub 2015 May 21.

Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, 1450 Biggy Street, NRT 6503, Los Angeles, CA, 90089-9601, USA.

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http://dx.doi.org/10.1186/s13059-015-0668-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4460959PMC
May 2015

The role of DNA methylation in directing the functional organization of the cancer epigenome.

Genome Res 2015 Apr 6;25(4):467-77. Epub 2015 Mar 6.

USC Epigenome Center, University of Southern California, Los Angeles, California 90033, USA; Department of Preventive Medicine, University of Southern California, Los Angeles, California 90033, USA

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http://dx.doi.org/10.1101/gr.183368.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381519PMC
April 2015

Functional annotation of colon cancer risk SNPs.

Nat Commun 2014 Sep 30;5:5114. Epub 2014 Sep 30.

Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA.

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http://dx.doi.org/10.1038/ncomms6114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4200523PMC
September 2014

Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules.

Genome Res 2012 Dec 7;22(12):2497-506. Epub 2012 Sep 7.

Department of Urology, Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.143008.112
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http://dx.doi.org/10.1101/gr.143008.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514679PMC
December 2012

FunciSNP: an R/bioconductor tool integrating functional non-coding data sets with genetic association studies to identify candidate regulatory SNPs.

Nucleic Acids Res 2012 Oct 8;40(18):e139. Epub 2012 Jun 8.

Norris Cancer Center, University of Southern California, Los Angeles, CA 90033, USA.

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http://dx.doi.org/10.1093/nar/gks542DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3467035PMC
October 2012

Genome-wide Runx2 occupancy in prostate cancer cells suggests a role in regulating secretion.

Nucleic Acids Res 2012 Apr 19;40(8):3538-47. Epub 2011 Dec 19.

Department of Biochemistry and Molecular Biology, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA.

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http://dx.doi.org/10.1093/nar/gkr1219DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3333873PMC
April 2012

Opposing effects of Runx2 and estradiol on breast cancer cell proliferation: in vitro identification of reciprocally regulated gene signature related to clinical letrozole responsiveness.

Clin Cancer Res 2012 Feb 6;18(3):901-11. Epub 2011 Dec 6.

Department of Biochemistry, Institute for Genetic Medicine, USC Epigenome Center, Keck School of Medicine of the University of Southern California, Los Angeles, California 90033, USA.

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http://dx.doi.org/10.1158/1078-0432.CCR-11-1530DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3277803PMC
February 2012

Dynamic nucleosome-depleted regions at androgen receptor enhancers in the absence of ligand in prostate cancer cells.

Mol Cell Biol 2011 Dec 3;31(23):4648-62. Epub 2011 Oct 3.

Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA.

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http://mcb.asm.org/cgi/doi/10.1128/MCB.05934-11
Publisher Site
http://dx.doi.org/10.1128/MCB.05934-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232925PMC
December 2011

Vitamin C promotes widespread yet specific DNA demethylation of the epigenome in human embryonic stem cells.

Stem Cells 2010 Oct;28(10):1848-55

Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia.

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http://dx.doi.org/10.1002/stem.493DOI Listing
October 2010

H2A.Z maintenance during mitosis reveals nucleosome shifting on mitotically silenced genes.

Mol Cell 2010 Sep;39(6):901-11

Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.

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http://dx.doi.org/10.1016/j.molcel.2010.08.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2947862PMC
September 2010

Location, location, (ChIP-)location! Mapping chromatin landscapes one immunoprecipitation at a time.

J Cell Biochem 2009 May;107(1):1-5

USC Epigenome Center, University of Southern California, Los Angeles, California 90033, USA.

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http://doi.wiley.com/10.1002/jcb.22133
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http://dx.doi.org/10.1002/jcb.22133DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2748114PMC
May 2009

Locking in on the human methylome.

Nat Biotechnol 2009 Apr;27(4):341-2

USC Epigenome Center, University of Southern California, Keck School of Medicine, Los Angeles, CA, USA.

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http://dx.doi.org/10.1038/nbt0409-341DOI Listing
April 2009