Publications by authors named "Bing Ren"

100Publications

Direct DNA crosslinking with CAP-C uncovers transcription-dependent chromatin organization at high resolution.

Nat Biotechnol 2020 Aug 24. Epub 2020 Aug 24.

Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.

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http://dx.doi.org/10.1038/s41587-020-0643-8DOI Listing
August 2020

Mischievous malakoplakia: A potential pitfall of mpMRI of the prostate?

Urol Case Rep 2020 Sep 24;32:101222. Epub 2020 Apr 24.

Section of Urology, Department of Surgery, Dartmouth-Hitchcock Medical Center, One Medical Center Drive, Lebanon, NH, 03756, USA.

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http://dx.doi.org/10.1016/j.eucr.2020.101222DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7195523PMC
September 2020

Preparation of Superhydrophobic Surface on Titanium Alloy via Micro-milling, Anodic Oxidation and Fluorination.

Micromachines (Basel) 2020 Mar 17;11(3). Epub 2020 Mar 17.

Key Laboratory of High Efficiency and Clean Manufacturing, School of Mechanical Engineering, Shandong University, Jinan 250061, China.

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http://dx.doi.org/10.3390/mi11030316DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7143463PMC
March 2020

CTCF mediates chromatin looping via N-terminal domain-dependent cohesin retention.

Proc Natl Acad Sci U S A 2020 01 14;117(4):2020-2031. Epub 2020 Jan 14.

Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892;

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http://dx.doi.org/10.1073/pnas.1911708117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6995019PMC
January 2020

Single-cell multimodal omics: the power of many.

Nat Methods 2020 01;17(1):11-14

Ludwig Institute for Cancer Research, La Jolla, CA, USA.

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http://dx.doi.org/10.1038/s41592-019-0691-5DOI Listing
January 2020

Ranking of non-coding pathogenic variants and putative essential regions of the human genome.

Nat Commun 2019 11 20;10(1):5241. Epub 2019 Nov 20.

Scripps Research Translational Institute, La Jolla, CA, 92037, USA.

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http://dx.doi.org/10.1038/s41467-019-13212-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6868241PMC
November 2019

Attention-Based Deep Neural Networks for Detection of Cancerous and Precancerous Esophagus Tissue on Histopathological Slides.

JAMA Netw Open 2019 11 1;2(11):e1914645. Epub 2019 Nov 1.

Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire.

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http://dx.doi.org/10.1001/jamanetworkopen.2019.14645DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6865275PMC
November 2019

Joint profiling of DNA methylation and chromatin architecture in single cells.

Nat Methods 2019 10 5;16(10):991-993. Epub 2019 Aug 5.

Ludwig Institute for Cancer Research, La Jolla, CA, USA.

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http://dx.doi.org/10.1038/s41592-019-0502-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6765429PMC
October 2019

Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF.

Cell Syst 2019 06;8(6):494-505.e14

Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2019.05.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6706282PMC
June 2019

DNA replication acts as an error correction mechanism to maintain centromere identity by restricting CENP-A to centromeres.

Nat Cell Biol 2019 06 3;21(6):743-754. Epub 2019 Jun 3.

Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA.

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http://dx.doi.org/10.1038/s41556-019-0331-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7015266PMC
June 2019

Multi-platform discovery of haplotype-resolved structural variation in human genomes.

Nat Commun 2019 04 16;10(1):1784. Epub 2019 Apr 16.

The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.

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http://www.nature.com/articles/s41467-018-08148-z
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http://dx.doi.org/10.1038/s41467-018-08148-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6467913PMC
April 2019

MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments.

PLoS Comput Biol 2019 04 15;15(4):e1006982. Epub 2019 Apr 15.

Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1006982DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6483256PMC
April 2019

Automated Detection of Celiac Disease on Duodenal Biopsy Slides: A Deep Learning Approach.

J Pathol Inform 2019 8;10. Epub 2019 Mar 8.

Department of Biomedical Data Science, Dartmouth College, Hanover, New Hampshire, USA.

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http://dx.doi.org/10.4103/jpi.jpi_87_18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6437784PMC
March 2019

Dynamic reorganization of the genome shapes the recombination landscape in meiotic prophase.

Nat Struct Mol Biol 2019 03 18;26(3):164-174. Epub 2019 Feb 18.

Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, CA, USA.

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http://dx.doi.org/10.1038/s41594-019-0187-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6403010PMC
March 2019

Significant Polymorphisms of Vitamin D Receptor Gene (rs2189480 and rs3847987) Related to the Risk of Type 2 Diabetes in Henan Rural Area.

Biomed Environ Sci 2019 Jan;32(1):58-62

Department of Nutrition and Food Hygiene, College of Public Health, Zhengzhou University, Zhengzhou 450000, Henan, China.

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http://dx.doi.org/10.3967/bes2019.009DOI Listing
January 2019

Hyper-Editing of Cell-Cycle Regulatory and Tumor Suppressor RNA Promotes Malignant Progenitor Propagation.

Cancer Cell 2019 01 3;35(1):81-94.e7. Epub 2019 Jan 3.

Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2018.11.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6333511PMC
January 2019

Genomic encoding of transcriptional burst kinetics.

Nature 2019 01 2;565(7738):251-254. Epub 2019 Jan 2.

Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.

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http://www.nature.com/articles/s41586-018-0836-1
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http://dx.doi.org/10.1038/s41586-018-0836-1DOI Listing
January 2019

Bioactivity of micropatterned TiO nanotubes fabricated by micro-milling and anodic oxidation.

Mater Sci Eng C Mater Biol Appl 2019 Feb 20;95:114-121. Epub 2018 Oct 20.

Key Laboratory of High Efficiency and Clean Manufacturing, School of Mechanical Engineering, Shandong University, Jinan 250061, China; National Demonstration Center for Experimental Mechanical Engineering Education, Shandong University, Jinan 250061, China.

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https://linkinghub.elsevier.com/retrieve/pii/S09284931183160
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http://dx.doi.org/10.1016/j.msec.2018.10.068DOI Listing
February 2019

Pancreatic Ductal Adenocarcinoma and Its Precursor Lesions: Histopathology, Cytopathology, and Molecular Pathology.

Am J Pathol 2019 01;189(1):9-21

Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire. Electronic address:

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http://dx.doi.org/10.1016/j.ajpath.2018.10.004DOI Listing
January 2019

Using a genetic algorithm to improve oil spill prediction.

Mar Pollut Bull 2018 Oct 20;135:386-396. Epub 2018 Jul 20.

The State Key Laboratory of Coastal and Offshore Engineering, Dalian University of Technology, Dalian 116024, China. Electronic address:

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http://dx.doi.org/10.1016/j.marpolbul.2018.07.026DOI Listing
October 2018

Removal of Cd(II) and Fe(III) from DMSO by silica gel supported PAMAM dendrimers: Equilibrium, thermodynamics, kinetics and mechanism.

Ecotoxicol Environ Saf 2018 Oct 11;162:253-260. Epub 2018 Jul 11.

School of Chemistry and Materials Science, Ludong University, Yantai 264025, China; Collaborative Innovation Center of Shandong Province for High Performance Fibers and Their Composites, Ludong University, Yantai 264025, China.

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http://dx.doi.org/10.1016/j.ecoenv.2018.06.094DOI Listing
October 2018

Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function.

Cell 2018 06 17;173(7):1796-1809.e17. Epub 2018 May 17.

Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, La Jolla, CA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.04.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6003872PMC
June 2018

NDF, a nucleosome-destabilizing factor that facilitates transcription through nucleosomes.

Genes Dev 2018 05 14;32(9-10):682-694. Epub 2018 May 14.

Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1101/gad.313973.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6004073PMC
May 2018

Transcriptional regulatory control of mammalian nephron progenitors revealed by multi-factor cistromic analysis and genetic studies.

PLoS Genet 2018 01 29;14(1):e1007181. Epub 2018 Jan 29.

Department of Stem Cell Biology and Regenerative Medicine, Broad-CIRM Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1007181DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5805373PMC
January 2018

Preventive Inhibition of Liver Tumorigenesis by Systemic Activation of Innate Immune Functions.

Cell Rep 2017 Nov;21(7):1870-1882

Department of Pathology, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2017.10.064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737819PMC
November 2017

The 4D nucleome project.

Nature 2017 09;549(7671):219-226

Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1038/nature23884DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5617335PMC
September 2017

High-Resolution Mapping of Chromatin Conformation in Cardiac Myocytes Reveals Structural Remodeling of the Epigenome in Heart Failure.

Circulation 2017 Oct 11;136(17):1613-1625. Epub 2017 Aug 11.

From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.).

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http://dx.doi.org/10.1161/CIRCULATIONAHA.117.029430DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5648689PMC
October 2017

The Three-Dimensional Organization of Mammalian Genomes.

Authors:
Miao Yu Bing Ren

Annu Rev Cell Dev Biol 2017 10 7;33:265-289. Epub 2017 Aug 7.

Ludwig Institute for Cancer Research, La Jolla, California 92093; email:

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http://dx.doi.org/10.1146/annurev-cellbio-100616-060531DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5837811PMC
October 2017

Comparative analysis of different feeder layers with 3T3 fibroblasts for culturing rabbits limbal stem cells.

Int J Ophthalmol 2017 18;10(7):1021-1027. Epub 2017 Jul 18.

Southwest Hospital, Third Military Medical University, Chongqing 400038, China.

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http://dx.doi.org/10.18240/ijo.2017.07.01DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5514260PMC
July 2017

HUGIn: Hi-C Unifying Genomic Interrogator.

Bioinformatics 2017 Dec;33(23):3793-3795

Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.

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http://dx.doi.org/10.1093/bioinformatics/btx359DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860315PMC
December 2017

Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells.

Cell Stem Cell 2017 04;20(4):533-546.e7

Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0419, USA; Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA 92093-0419, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2017.03.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5444918PMC
April 2017

Human centromeric CENP-A chromatin is a homotypic, octameric nucleosome at all cell cycle points.

J Cell Biol 2017 03 24;216(3):607-621. Epub 2017 Feb 24.

Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093

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http://dx.doi.org/10.1083/jcb.201608083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5350519PMC
March 2017

Neoadjuvant therapy in microsatellite-stable colorectal carcinoma induces concomitant loss of MSH6 and Ki-67 expression.

Hum Pathol 2017 05 21;63:33-39. Epub 2017 Feb 21.

Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA 15213.

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http://dx.doi.org/10.1016/j.humpath.2017.02.003DOI Listing
May 2017

A Scalable Epitope Tagging Approach for High Throughput ChIP-Seq Analysis.

ACS Synth Biol 2017 06 7;6(6):1034-1042. Epub 2017 Mar 7.

Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.

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http://dx.doi.org/10.1021/acssynbio.6b00358DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5536957PMC
June 2017

Improved regulatory element prediction based on tissue-specific local epigenomic signatures.

Proc Natl Acad Sci U S A 2017 02 13;114(9):E1633-E1640. Epub 2017 Feb 13.

Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037;

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http://dx.doi.org/10.1073/pnas.1618353114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5338528PMC
February 2017

Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq.

Cell Res 2016 12 25;26(12):1345-1348. Epub 2016 Nov 25.

Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1038/cr.2016.137DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5143423PMC
December 2016

A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome.

Cell Rep 2016 11;17(8):2042-2059

Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA; Department of Cellular and Molecular Medicine, Moores Cancer Center and Institute of Genome Medicine, UCSD School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.10.061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5478386PMC
November 2016

Genome-wide mapping and analysis of chromosome architecture.

Nat Rev Mol Cell Biol 2016 12 1;17(12):743-755. Epub 2016 Sep 1.

Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Moores Cancer Center and Institute of Genomic Medicine, University of California, San Diego (UCSD) School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1038/nrm.2016.104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5763923PMC
December 2016

Programmed Death-Ligand 1 Expression Is Common in Gastric Cancer Associated With Epstein-Barr Virus or Microsatellite Instability.

Am J Surg Pathol 2016 11;40(11):1496-1506

Departments of *Pathology †Medicine, Division of Hematology Oncology, University of Pittsburgh Medical Center, Pittsburgh, PA.

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http://dx.doi.org/10.1097/PAS.0000000000000698DOI Listing
November 2016

Chromatin Domains: The Unit of Chromosome Organization.

Mol Cell 2016 06;62(5):668-80

Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA 92093-0653, USA; University of California, San Diego School of Medicine, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, 9500 Gilman Drive, La Jolla, CA 92093-0653, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2016.05.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5371509PMC
June 2016

A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening.

Genome Res 2016 Mar 26;26(3):397-405. Epub 2016 Jan 26.

Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, California 92093, USA; Department of Cellular and Molecular Medicine, Institute of Genomic Medicine and Moores Cancer Center, University of California, San Diego, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1101/gr.197152.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4772021PMC
March 2016

Identification of global regulators of T-helper cell lineage specification.

Genome Med 2015 Nov 20;7:122. Epub 2015 Nov 20.

Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.

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http://dx.doi.org/10.1186/s13073-015-0237-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4654807PMC
November 2015

Transcriptional Enhancers: Bridging the Genome and Phenome.

Authors:
Bing Ren Feng Yue

Cold Spring Harb Symp Quant Biol 2015 18;80:17-26. Epub 2015 Nov 18.

Department of Biochemistry and Molecular Biology and Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033.

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http://dx.doi.org/10.1101/sqb.2015.80.027219DOI Listing
January 2018

Complete haplotype phasing of the MHC and KIR loci with targeted HaploSeq.

BMC Genomics 2015 Nov 5;16:900. Epub 2015 Nov 5.

Ludwig Institute for Cancer Research, La Jolla, CA, 92093, USA.

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http://dx.doi.org/10.1186/s12864-015-1949-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636068PMC
November 2015

EGFR Mutation Promotes Glioblastoma through Epigenome and Transcription Factor Network Remodeling.

Mol Cell 2015 Oct 8;60(2):307-18. Epub 2015 Oct 8.

Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA; Department of Pathology, UCSD School of Medicine, La Jolla, CA 92093, USA; Moores Cancer Center, UCSD School of Medicine, La Jolla, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2015.09.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4609298PMC
October 2015

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function.

Cell 2015 Aug;162(4):900-10

Center for Comparative Biomedicine, MOE Key Laboratory of Systems Biomedicine, Institute of Systems Biomedicine, Collaborative Innovation Center of Systems Biomedicine, Shanghai Jiao Tong University (SJTU), Shanghai 200240, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, SJTU, Shanghai 200240, China; Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (MOE), Bio-X Center, School of Life Sciences and Biotechnology, SJTU, Shanghai 200240, China. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.07.038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4642453PMC
August 2015

MPE-seq, a new method for the genome-wide analysis of chromatin structure.

Proc Natl Acad Sci U S A 2015 Jul 15;112(27):E3457-65. Epub 2015 Jun 15.

Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, CA 92093-0653; Department of Cellular and Molecular Medicine, Institute of Genome Medicine, Moores Cancer Center, University of California, San Diego, School of Medicine, La Jolla, CA 92093-0653

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http://dx.doi.org/10.1073/pnas.1424804112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4500276PMC
July 2015

Human body epigenome maps reveal noncanonical DNA methylation variation.

Nature 2015 Jul 1;523(7559):212-6. Epub 2015 Jun 1.

1] Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA [2] Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA.

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http://dx.doi.org/10.1038/nature14465DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4499021PMC
July 2015

A CRISPR Connection between Chromatin Topology and Genetic Disorders.

Cell 2015 May;161(5):955-957

Ludwig Institute for Cancer Research, University of California, San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0653.

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http://dx.doi.org/10.1016/j.cell.2015.04.047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4478077PMC
May 2015

Epigenetic priming of enhancers predicts developmental competence of hESC-derived endodermal lineage intermediates.

Cell Stem Cell 2015 Apr;16(4):386-99

Pediatric Diabetes Research Center, Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093-0983, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA; Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0761, USA; Moores Cancer Center, University of California San Diego, La Jolla, CA 92093-0653, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2015.02.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4478079PMC
April 2015

Chromatin architecture reorganization during stem cell differentiation.

Nature 2015 Feb;518(7539):331-6

1] Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093-0653, USA [2] University of California, San Diego School of Medicine, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, 9500 Gilman Drive, La Jolla, California 92093-0653, USA.

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http://www.nature.com/articles/nature14222
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http://dx.doi.org/10.1038/nature14222DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4515363PMC
February 2015

Integrative analysis of 111 reference human epigenomes.

Nature 2015 Feb;518(7539):317-30

1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/nature14248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4530010PMC
February 2015

[Grain filling dynamics and germination characteristics of Bupleurum chinense seeds].

Zhongguo Zhong Yao Za Zhi 2014 Oct;39(19):3731-5

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October 2014

DNA binding by FOXP3 domain-swapped dimer suggests mechanisms of long-range chromosomal interactions.

Nucleic Acids Res 2015 Jan 7;43(2):1268-82. Epub 2015 Jan 7.

Laboratory of Structural Biology, Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, XiangYa Hospital & State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410008, China Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA

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http://dx.doi.org/10.1093/nar/gku1373DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4333414PMC
January 2015

CRISPR reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells.

PLoS One 2014 8;9(12):e114485. Epub 2014 Dec 8.

Ludwig Institute for Cancer Research, San Diego, California, United States of America; Department of Cellular and Molecular Medicine, Institute of Genome Medicine, Moores Cancer Center, University of California San Diego, School of Medicine, San Diego, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0114485PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4259346PMC
August 2015

A comparative encyclopedia of DNA elements in the mouse genome.

Authors:
Feng Yue Yong Cheng Alessandra Breschi Jeff Vierstra Weisheng Wu Tyrone Ryba Richard Sandstrom Zhihai Ma Carrie Davis Benjamin D Pope Yin Shen Dmitri D Pervouchine Sarah Djebali Robert E Thurman Rajinder Kaul Eric Rynes Anthony Kirilusha Georgi K Marinov Brian A Williams Diane Trout Henry Amrhein Katherine Fisher-Aylor Igor Antoshechkin Gilberto DeSalvo Lei-Hoon See Meagan Fastuca Jorg Drenkow Chris Zaleski Alex Dobin Pablo Prieto Julien Lagarde Giovanni Bussotti Andrea Tanzer Olgert Denas Kanwei Li M A Bender Miaohua Zhang Rachel Byron Mark T Groudine David McCleary Long Pham Zhen Ye Samantha Kuan Lee Edsall Yi-Chieh Wu Matthew D Rasmussen Mukul S Bansal Manolis Kellis Cheryl A Keller Christapher S Morrissey Tejaswini Mishra Deepti Jain Nergiz Dogan Robert S Harris Philip Cayting Trupti Kawli Alan P Boyle Ghia Euskirchen Anshul Kundaje Shin Lin Yiing Lin Camden Jansen Venkat S Malladi Melissa S Cline Drew T Erickson Vanessa M Kirkup Katrina Learned Cricket A Sloan Kate R Rosenbloom Beatriz Lacerda de Sousa Kathryn Beal Miguel Pignatelli Paul Flicek Jin Lian Tamer Kahveci Dongwon Lee W James Kent Miguel Ramalho Santos Javier Herrero Cedric Notredame Audra Johnson Shinny Vong Kristen Lee Daniel Bates Fidencio Neri Morgan Diegel Theresa Canfield Peter J Sabo Matthew S Wilken Thomas A Reh Erika Giste Anthony Shafer Tanya Kutyavin Eric Haugen Douglas Dunn Alex P Reynolds Shane Neph Richard Humbert R Scott Hansen Marella De Bruijn Licia Selleri Alexander Rudensky Steven Josefowicz Robert Samstein Evan E Eichler Stuart H Orkin Dana Levasseur Thalia Papayannopoulou Kai-Hsin Chang Arthur Skoultchi Srikanta Gosh Christine Disteche Piper Treuting Yanli Wang Mitchell J Weiss Gerd A Blobel Xiaoyi Cao Sheng Zhong Ting Wang Peter J Good Rebecca F Lowdon Leslie B Adams Xiao-Qiao Zhou Michael J Pazin Elise A Feingold Barbara Wold James Taylor Ali Mortazavi Sherman M Weissman John A Stamatoyannopoulos Michael P Snyder Roderic Guigo Thomas R Gingeras David M Gilbert Ross C Hardison Michael A Beer Bing Ren

Nature 2014 Nov;515(7527):355-64

Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1038/nature13992DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4266106PMC
November 2014

5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation.

Mol Cell 2014 Oct 25;56(2):286-297. Epub 2014 Sep 25.

Ludwig Institute for Cancer Research, La Jolla, CA 92093-0653, USA; Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA 92093. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2014.08.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4319980PMC
October 2014