Publications by authors named "Guo-Cheng Yuan"

100Publications

Enhancer dependence of cell-type-specific gene expression increases with developmental age.

Proc Natl Acad Sci U S A 2020 09 19;117(35):21450-21458. Epub 2020 Aug 19.

Cancer and Blood Disorders Center, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215;

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http://dx.doi.org/10.1073/pnas.2008672117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7474592PMC
September 2020

Molecular Pathways of Colon Inflammation Induced by Cancer Immunotherapy.

Cell 2020 Aug 29;182(3):655-671.e22. Epub 2020 Jun 29.

Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Immunology, Harvard Medical School, Boston, MA 02115, USA; Department of Neurology, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2020.06.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7415717PMC
August 2020

GiniClust3: a fast and memory-efficient tool for rare cell type identification.

BMC Bioinformatics 2020 Apr 25;21(1):158. Epub 2020 Apr 25.

Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.

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http://dx.doi.org/10.1186/s12859-020-3482-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7183612PMC
April 2020

Distinct Mesenchymal Cell Populations Generate the Essential Intestinal BMP Signaling Gradient.

Cell Stem Cell 2020 03 20;26(3):391-402.e5. Epub 2020 Feb 20.

Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2020.01.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7412576PMC
March 2020

Two faces of bivalent domain regulate VEGFA responsiveness and angiogenesis.

Cell Death Dis 2020 01 30;11(1):75. Epub 2020 Jan 30.

Department of Pediatric Cardiology, Xin Hua Hospital, School of Medicine, Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China.

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http://dx.doi.org/10.1038/s41419-020-2228-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6992747PMC
January 2020

Discovery of specialized NK cell populations infiltrating human melanoma metastases.

JCI Insight 2019 12 5;4(23). Epub 2019 Dec 5.

Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1172/jci.insight.133103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6962021PMC
December 2019

CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis.

Genome Biol 2019 09 9;20(1):192. Epub 2019 Sep 9.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard Chan School of Public Health, Boston, MA, USA.

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http://dx.doi.org/10.1186/s13059-019-1802-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6734249PMC
September 2019

LSD1 suppresses invasion, migration and metastasis of luminal breast cancer cells via activation of GATA3 and repression of TRIM37 expression.

Oncogene 2019 10 13;38(44):7017-7034. Epub 2019 Aug 13.

Division of Genetics, Brigham and Women's Hospital and Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.

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http://www.nature.com/articles/s41388-019-0923-2
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http://dx.doi.org/10.1038/s41388-019-0923-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6823153PMC
October 2019

RESCUE: imputing dropout events in single-cell RNA-sequencing data.

BMC Bioinformatics 2019 Jul 12;20(1):388. Epub 2019 Jul 12.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.

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http://dx.doi.org/10.1186/s12859-019-2977-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6624880PMC
July 2019

Molecular Profiling Establishes Genetic Features Predictive of the Efficacy of the p110β Inhibitor KIN-193.

Cancer Res 2019 09 10;79(17):4524-4531. Epub 2019 Jul 10.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard Chan School of Public Health, Boston, Massachusetts.

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http://dx.doi.org/10.1158/0008-5472.CAN-19-0588DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6726497PMC
September 2019

Accurate estimation of cell-type composition from gene expression data.

Nat Commun 2019 07 5;10(1):2975. Epub 2019 Jul 5.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.

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http://dx.doi.org/10.1038/s41467-019-10802-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6611906PMC
July 2019

Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM.

Nat Commun 2019 04 23;10(1):1903. Epub 2019 Apr 23.

Molecular Pathology Unit & Cancer Center, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, 02114, USA.

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http://dx.doi.org/10.1038/s41467-019-09670-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6478907PMC
April 2019

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH.

Nature 2019 04 25;568(7751):235-239. Epub 2019 Mar 25.

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.

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http://dx.doi.org/10.1038/s41586-019-1049-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6544023PMC
April 2019

Single-Cell Analysis Identifies LY6D as a Marker Linking Castration-Resistant Prostate Luminal Cells to Prostate Progenitors and Cancer.

Cell Rep 2018 12;25(12):3504-3518.e6

Prostate Oncobiology, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park SK10 4TG, UK; Belfast-Manchester Movember Centre of Excellence, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park SK10 4TG, UK. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S22111247183184
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http://dx.doi.org/10.1016/j.celrep.2018.11.069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6315111PMC
December 2018

Revealing the Critical Regulators of Cell Identity in the Mouse Cell Atlas.

Cell Rep 2018 11;25(6):1436-1445.e3

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S22111247183163
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http://dx.doi.org/10.1016/j.celrep.2018.10.045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6281296PMC
November 2018

Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data.

Nat Biotechnol 2018 Oct 29. Epub 2018 Oct 29.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.

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http://www.nature.com/doifinder/10.1038/nbt.4260
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http://dx.doi.org/10.1038/nbt.4260DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6488461PMC
October 2018

Quantitative integration of epigenomic variation and transcription factor binding using MAmotif toolkit identifies an important role of IRF2 as transcription activator at gene promoters.

Cell Discov 2018 10;4:38. Epub 2018 Jul 10.

1CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.

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http://www.nature.com/articles/s41421-018-0045-y
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http://dx.doi.org/10.1038/s41421-018-0045-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6037672PMC
July 2018

GiniClust2: a cluster-aware, weighted ensemble clustering method for cell-type detection.

Genome Biol 2018 05 10;19(1):58. Epub 2018 May 10.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.

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http://dx.doi.org/10.1186/s13059-018-1431-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5946416PMC
May 2018

Integrated design, execution, and analysis of arrayed and pooled CRISPR genome-editing experiments.

Nat Protoc 2018 05 12;13(5):946-986. Epub 2018 Apr 12.

Molecular Pathology Unit and Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.

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http://www.nature.com/doifinder/10.1038/nprot.2018.005
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http://dx.doi.org/10.1038/nprot.2018.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6182299PMC
May 2018

Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing.

Genome Biol 2018 04 5;19(1):47. Epub 2018 Apr 5.

Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China.

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http://dx.doi.org/10.1186/s13059-018-1426-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5887227PMC
April 2018

Direct Promoter Repression by BCL11A Controls the Fetal to Adult Hemoglobin Switch.

Cell 2018 04 29;173(2):430-442.e17. Epub 2018 Mar 29.

Cancer and Blood Disorders Center, Dana Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston, MA, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674183029
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http://dx.doi.org/10.1016/j.cell.2018.03.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5889339PMC
April 2018

Dissecting super-enhancer hierarchy based on chromatin interactions.

Nat Commun 2018 03 5;9(1):943. Epub 2018 Mar 5.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA.

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http://dx.doi.org/10.1038/s41467-018-03279-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5838163PMC
March 2018

Assessing Inequality in Transcriptomic Data.

Cell Syst 2018 Feb;6(2):149-150

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2018.02.007DOI Listing
February 2018

Mapping the Mouse Cell Atlas by Microwell-Seq.

Cell 2018 02;172(5):1091-1107.e17

Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China; Institute of Hematology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674183011
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http://dx.doi.org/10.1016/j.cell.2018.02.001DOI Listing
February 2018

Differential connectivity of gene regulatory networks distinguishes corticosteroid response in asthma.

J Allergy Clin Immunol 2018 04 20;141(4):1250-1258. Epub 2017 Jul 20.

Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass. Electronic address:

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http://dx.doi.org/10.1016/j.jaci.2017.05.052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5775928PMC
April 2018

Dynamic Reorganization of Chromatin Accessibility Signatures during Dedifferentiation of Secretory Precursors into Lgr5+ Intestinal Stem Cells.

Cell Stem Cell 2017 07 22;21(1):65-77.e5. Epub 2017 Jun 22.

Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2017.05.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5505276PMC
July 2017

Gene regulatory pattern analysis reveals essential role of core transcriptional factors' activation in triple-negative breast cancer.

Oncotarget 2017 Mar;8(13):21938-21953

Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Departments of Biochemistry and Molecular Biology, Peking University Cancer Hospital & Institute, Beijing 100036, P. R. China.

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http://dx.doi.org/10.18632/oncotarget.15749DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5400636PMC
March 2017

Multi-scale chromatin state annotation using a hierarchical hidden Markov model.

Nat Commun 2017 04 7;8:15011. Epub 2017 Apr 7.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02215, USA.

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http://dx.doi.org/10.1038/ncomms15011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5385569PMC
April 2017

Analysis of Cardiac Myocyte Maturation Using CASAAV, a Platform for Rapid Dissection of Cardiac Myocyte Gene Function In Vivo.

Circ Res 2017 Jun 29;120(12):1874-1888. Epub 2017 Mar 29.

From the Cardiology, Boston Children's Hospital, MA (Y.G., N.J.V., Q.M., B.D.J., Y.A., D.Z., W.T.P.); Institute of Basic Medicine (L.Z.) and Pharmacology, School of Pharmacy (W.G.), Shanghai University of Traditional Chinese Medicine, China; Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (I.S., G.-C.Y.); Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil (S.G.); Cardiovascular Medicine, Department of Internal Medicine, François M. Abboud Cardiovascular Research Center, University of Iowa Carver College of Medicine, Iowa City (B.C., A.G., L.-S.S.); Veterans Affairs Medical Center, Iowa City (L.-S.S.); and Harvard Stem Cell Institute, Cambridge, MA (W.T.P.).

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http://dx.doi.org/10.1161/CIRCRESAHA.116.310283DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5466492PMC
June 2017

Variant-aware saturating mutagenesis using multiple Cas9 nucleases identifies regulatory elements at trait-associated loci.

Nat Genet 2017 Apr 20;49(4):625-634. Epub 2017 Feb 20.

Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/ng.3793DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5374001PMC
April 2017

The PRC2-binding long non-coding RNAs in human and mouse genomes are associated with predictive sequence features.

Sci Rep 2017 01 31;7:41669. Epub 2017 Jan 31.

Chinese Academy of Sciences Key Laboratory of Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.

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http://dx.doi.org/10.1038/srep41669DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5282597PMC
January 2017

Recent progress in single-cell cancer genomics.

Curr Opin Genet Dev 2017 Feb 23;42:22-32. Epub 2017 Jan 23.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.gde.2017.01.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5446798PMC
February 2017

The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells.

Nat Immunol 2017 02 19;18(2):184-195. Epub 2016 Dec 19.

Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA, and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/ni.3644DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5247321PMC
February 2017

Identification of Transcribed Enhancers by Genome-Wide Chromatin Immunoprecipitation Sequencing.

Methods Mol Biol 2017 ;1468:91-109

Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA.

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http://dx.doi.org/10.1007/978-1-4939-4035-6_8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5111358PMC
January 2018

Single-Cell Transcript Profiles Reveal Multilineage Priming in Early Progenitors Derived from Lgr5(+) Intestinal Stem Cells.

Cell Rep 2016 08 11;16(8):2053-2060. Epub 2016 Aug 11.

Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.07.056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5001892PMC
August 2016

Analyzing CRISPR genome-editing experiments with CRISPResso.

Nat Biotechnol 2016 07;34(7):695-7

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/nbt.3583DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5242601PMC
July 2016

GiniClust: detecting rare cell types from single-cell gene expression data with Gini index.

Genome Biol 2016 07 1;17(1):144. Epub 2016 Jul 1.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.

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http://dx.doi.org/10.1186/s13059-016-1010-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4930624PMC
July 2016

Acquired Tissue-Specific Promoter Bivalency Is a Basis for PRC2 Necessity in Adult Cells.

Cell 2016 Jun 19;165(6):1389-1400. Epub 2016 May 19.

Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.04.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4893000PMC
June 2016

Robust lineage reconstruction from high-dimensional single-cell data.

Nucleic Acids Res 2016 08 20;44(14):e122. Epub 2016 May 20.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA Harvard Stem Cell Institute, Cambridge, MA 02138, USA

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http://dx.doi.org/10.1093/nar/gkw452DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5001598PMC
August 2016

Serum-Based Culture Conditions Provoke Gene Expression Variability in Mouse Embryonic Stem Cells as Revealed by Single-Cell Analysis.

Cell Rep 2016 Feb 21;14(4):956-965. Epub 2016 Jan 21.

Division of Pediatric Hematology/Oncology, Dana Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S22111247150154
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http://dx.doi.org/10.1016/j.celrep.2015.12.089DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4740311PMC
February 2016

Functionally distinct patterns of nucleosome remodeling at enhancers in glucocorticoid-treated acute lymphoblastic leukemia.

Epigenetics Chromatin 2015 2;8:53. Epub 2015 Dec 2.

Department of Oncology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 281, Memphis, TN 38105 USA.

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http://dx.doi.org/10.1186/s13072-015-0046-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4667523PMC
December 2015

Single-Cell Analysis in Cancer Genomics.

Trends Genet 2015 Oct;31(10):576-586

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA. Electronic address:

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http://www.cell.com/trends/genetics/pdf/S0168-9525(15)00140-
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http://linkinghub.elsevier.com/retrieve/pii/S016895251500140
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http://dx.doi.org/10.1016/j.tig.2015.07.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5282606PMC
October 2015

BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis.

Nature 2015 Nov 16;527(7577):192-7. Epub 2015 Sep 16.

Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA.

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https://pdfs.semanticscholar.org/1ddb/3d38167d122b418b8d6968
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http://www.nature.com/doifinder/10.1038/nature15521
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http://dx.doi.org/10.1038/nature15521DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4644101PMC
November 2015

Predicting chromatin organization using histone marks.

Genome Biol 2015 Aug 14;16:162. Epub 2015 Aug 14.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.

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http://dx.doi.org/10.1186/s13059-015-0740-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4549084PMC
August 2015

Impact of the N-Terminal Domain of STAT3 in STAT3-Dependent Transcriptional Activity.

Mol Cell Biol 2015 Oct 13;35(19):3284-300. Epub 2015 Jul 13.

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA Biophysical Collaborative Access Team/Illinois Institute of Technology, Sector 18ID (Advanced Photon Source, Argonne National Laboratory), Lemont, Illinois, USA Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA

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http://dx.doi.org/10.1128/MCB.00060-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4561728PMC
October 2015

A network model for angiogenesis in ovarian cancer.

BMC Bioinformatics 2015 Apr 11;16:115. Epub 2015 Apr 11.

Dana-Farber Cancer Institute, Boston, MA, USA.

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http://dx.doi.org/10.1186/s12859-015-0551-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4408593PMC
April 2015

Haploinsufficiency of Hedgehog interacting protein causes increased emphysema induced by cigarette smoke through network rewiring.

Genome Med 2015 14;7(1):12. Epub 2015 Feb 14.

Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA USA ; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA USA.

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http://dx.doi.org/10.1186/s13073-015-0137-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4355149PMC
March 2015

Developmental control of polycomb subunit composition by GATA factors mediates a switch to non-canonical functions.

Mol Cell 2015 Jan 8;57(2):304-316. Epub 2015 Jan 8.

Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S10972765140095
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http://dx.doi.org/10.1016/j.molcel.2014.12.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4305004PMC
January 2015

Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape.

Proc Natl Acad Sci U S A 2014 Dec 15;111(52):E5643-50. Epub 2014 Dec 15.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02115;

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http://dx.doi.org/10.1073/pnas.1408993111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4284553PMC
December 2014

Sexually-dimorphic targeting of functionally-related genes in COPD.

BMC Syst Biol 2014 Nov 28;8:118. Epub 2014 Nov 28.

Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1186/s12918-014-0118-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4269917PMC
November 2014

CDK7 inhibition suppresses super-enhancer-linked oncogenic transcription in MYCN-driven cancer.

Cell 2014 Nov 6;159(5):1126-1139. Epub 2014 Nov 6.

Department of Pediatric Hematology/Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02215, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2014.10.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4243043PMC
November 2014

Reprogramming committed murine blood cells to induced hematopoietic stem cells with defined factors.

Cell 2014 Apr;157(3):549-64

Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, MA 02116, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2014.04.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4060823PMC
April 2014

Analysis of chromatin-state plasticity identifies cell-type-specific regulators of H3K27me3 patterns.

Proc Natl Acad Sci U S A 2014 Jan 6;111(3):E344-53. Epub 2014 Jan 6.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Heath, Boston, MA 02215.

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http://dx.doi.org/10.1073/pnas.1322570111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3903219PMC
January 2014

Chromatin signature of widespread monoallelic expression.

Elife 2013 Dec 31;2:e01256. Epub 2013 Dec 31.

Department of Cancer Biology and Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, United States.

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http://dx.doi.org/10.7554/eLife.01256DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3873816PMC
December 2013

Modeling the dynamics of bivalent histone modifications.

PLoS One 2013 1;8(11):e77944. Epub 2013 Nov 1.

Department of Physics, University of Maryland, College Park, Maryland, United States of America ; Institute for Research in Electronics and Applied Physics, University of Maryland, College Park, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0077944PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3815350PMC
August 2014

Applications of alignment-free methods in epigenomics.

Brief Bioinform 2014 May 6;15(3):419-30. Epub 2013 Nov 6.

Dipartimento di Matematica e Informatica, Via Archirafi 34, 90123 Palermo-Italy. Guo-Cheng Yuan, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Ave., Boston, MA 02215, USA. E-mail:

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http://dx.doi.org/10.1093/bib/bbt078DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4017331PMC
May 2014

Enhancer transcribed RNAs arise from hypomethylated, Tet-occupied genomic regions.

Epigenetics 2013 Dec 17;8(12):1303-20. Epub 2013 Oct 17.

BloodCenter of Wisconsin; Blood Research Institute; Milwaukee, WI USA; Medical College of Wisconsin; Milwaukee, WI USA; Departments of Cell Biology, Neurobiology, and Anatomy; Medical College of Wisconsin; Milwaukee, WI USA; Department of Pediatrics; Medical College of Wisconsin; Milwaukee, WI USA.

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http://dx.doi.org/10.4161/epi.26597DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3933491PMC
December 2013

Mapping cellular hierarchy by single-cell analysis of the cell surface repertoire.

Cell Stem Cell 2013 Oct 12;13(4):492-505. Epub 2013 Sep 12.

Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1016/j.stem.2013.07.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3845089PMC
October 2013

Passing messages between biological networks to refine predicted interactions.

PLoS One 2013 31;8(5):e64832. Epub 2013 May 31.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0064832PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3669401PMC
January 2014

STAT5 outcompetes STAT3 to regulate the expression of the oncogenic transcriptional modulator BCL6.

Mol Cell Biol 2013 Aug 28;33(15):2879-90. Epub 2013 May 28.

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.

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http://dx.doi.org/10.1128/MCB.01620-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3719667PMC
August 2013

A tiered hidden Markov model characterizes multi-scale chromatin states.

Genomics 2013 Jul 6;102(1):1-7. Epub 2013 Apr 6.

Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA.

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http://dx.doi.org/10.1016/j.ygeno.2013.03.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3676702PMC
July 2013

Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis.

Dev Cell 2012 Oct 4;23(4):796-811. Epub 2012 Oct 4.

Division of Hematology/Oncology, Children's Hospital Boston and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1016/j.devcel.2012.09.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3477283PMC
October 2012

MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets.

Genome Biol 2012 Mar 16;13(3):R16. Epub 2012 Mar 16.

Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.

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http://dx.doi.org/10.1186/gb-2012-13-3-r16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439967PMC
March 2012

Chromatin states accurately classify cell differentiation stages.

PLoS One 2012 20;7(2):e31414. Epub 2012 Feb 20.

Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0031414PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3282719PMC
June 2012

Linking genome to epigenome.

Authors:
Guo-Cheng Yuan

Wiley Interdiscip Rev Syst Biol Med 2012 May-Jun;4(3):297-309. Epub 2012 Feb 17.

Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA.

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http://dx.doi.org/10.1002/wsbm.1165DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3328655PMC
January 2013

A motif-independent metric for DNA sequence specificity.

BMC Bioinformatics 2011 Oct 21;12:408. Epub 2011 Oct 21.

Department of Biostatistics, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA.

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http://dx.doi.org/10.1186/1471-2105-12-408DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3267244PMC
October 2011

The SKP1-Cul1-F-box and leucine-rich repeat protein 4 (SCF-FbxL4) ubiquitin ligase regulates lysine demethylase 4A (KDM4A)/Jumonji domain-containing 2A (JMJD2A) protein.

J Biol Chem 2011 Sep 8;286(35):30462-70. Epub 2011 Jul 8.

Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts 02129, USA.

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http://dx.doi.org/10.1074/jbc.M111.273508DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3162406PMC
September 2011

Epigenetic domains found in mouse embryonic stem cells via a hidden Markov model.

BMC Bioinformatics 2010 Nov 12;11:557. Epub 2010 Nov 12.

Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1186/1471-2105-11-557DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2992069PMC
November 2010

Differential roles of Sall4 isoforms in embryonic stem cell pluripotency.

Mol Cell Biol 2010 Nov 13;30(22):5364-80. Epub 2010 Sep 13.

Dana Farber Cancer Institute, Department of Pediatric Oncology, Boston, MA, USA.

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http://dx.doi.org/10.1128/MCB.00419-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2976381PMC
November 2010

Human LSD2/KDM1b/AOF1 regulates gene transcription by modulating intragenic H3K4me2 methylation.

Mol Cell 2010 Jul;39(2):222-33

Division of Endocrinology, Diabetes, and Hypertension, Department of Medicine, Brigham and Women's Hospital, 221 Longwood Avenue, Boston, MA 02115, USA.

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http://dx.doi.org/10.1016/j.molcel.2010.07.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3518444PMC
July 2010