Yufeng Shen

Yufeng Shen

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Human Intestinal Allografts Contain Functional Hematopoietic Stem and Progenitor Cells that Are Maintained by a Circulating Pool.

Cell Stem Cell 2019 Feb 29;24(2):227-239.e8. Epub 2018 Nov 29.

Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA; Department of Microbiology & Immunology, Columbia University, New York, NY 10032, USA; Department of Surgery, Columbia University, New York, NY 10032, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2018.11.007DOI Listing
February 2019

Synthesis of arctigenin derivatives against infectious hematopoietic necrosis virus.

Eur J Med Chem 2019 Feb 27;163:183-194. Epub 2018 Nov 27.

College of Animal Science and Technology, Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China. Electronic address:

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http://dx.doi.org/10.1016/j.ejmech.2018.11.064DOI Listing
February 2019

Isolation of anti-Saprolegnia lignans from Magnolia officinalis and SAR evaluation of honokiol/magnolol analogs.

Bioorg Med Chem Lett 2019 Feb 17;29(3):389-395. Epub 2018 Dec 17.

College of Animal Science and Technology, Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi 712100, China. Electronic address:

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http://dx.doi.org/10.1016/j.bmcl.2018.12.038DOI Listing
February 2019

Evaluation on the antiviral activity of ribavirin against infectious hematopoietic necrosis virus in epithelioma papulosum cyprini cells.

Virus Res 2019 Jan 14;263:73-79. Epub 2019 Jan 14.

College of Animal Science and Technology, Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China. Electronic address:

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http://dx.doi.org/10.1016/j.virusres.2019.01.008DOI Listing
January 2019

MiR-1301-3p inhibits human breast cancer cell proliferation by regulating cell cycle progression and apoptosis through directly targeting ICT1.

Breast Cancer 2018 Nov 27;25(6):742-752. Epub 2018 Jun 27.

Department of Surgery, Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, Shanghai, 201700, China.

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http://dx.doi.org/10.1007/s12282-018-0881-5DOI Listing
November 2018

Proteomic Analysis of Single Mammalian Cells Enabled by Microfluidic Nanodroplet Sample Preparation and Ultrasensitive NanoLC-MS.

Angew Chem Int Ed Engl 2018 Sep 14;57(38):12370-12374. Epub 2018 Jun 14.

Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA.

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http://dx.doi.org/10.1002/anie.201802843DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6261339PMC
September 2018

Quantifying size and diversity of the human T cell alloresponse.

JCI Insight 2018 Aug 9;3(15). Epub 2018 Aug 9.

Department of Systems Biology and Biomedical Informatics, Columbia University Medical Center, New York, New York, USA.

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http://dx.doi.org/10.1172/jci.insight.121256DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6129121PMC
August 2018

Exome Sequencing in Children With Pulmonary Arterial Hypertension Demonstrates Differences Compared With Adults.

Circ Genom Precis Med 2018 04;11(4):e001887

Department of Pediatrics (N.Z., C.W., L.M., U.K., E.B.R., W.K.C.), Herbert Irving Comprehensive Cancer Center (A.S., W.K.C.), and Department of Medicine (E.B.R., W.K.C.), Columbia University Medical Center, Department of Applied Physics and Applied Mathematics (H.Q.), Department of Systems Biology (N.Z., H.Q., Y.S.), and Department of Biomedical Informatics (Y.S.), Columbia University, New York, NY; Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY (C.G.-J., A.K.K., J.G.R., J.D.O., A.B., F.D.); Department of Pediatric Cardiology, Children's Hospital Colorado, Denver (D.D.I.); Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN (E.D.A., R.H.); and Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, OH (W.C.N., M.W.P., K.A.L.).

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http://dx.doi.org/10.1161/CIRCGEN.117.001887DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5896781PMC
April 2018

Optimized Synthesis of ZSM-11 Catalysts using 1,8-Diaminooctane as a Structure-Directing Agent.

Chemphyschem 2018 02 5;19(4):529-537. Epub 2017 Dec 5.

Department of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Road, Houston, TX, USA.

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http://dx.doi.org/10.1002/cphc.201700968DOI Listing
February 2018

Synthesis and biological evaluation of coumarin derivatives containing imidazole skeleton as potential antibacterial agents.

Eur J Med Chem 2018 Jan 5;143:958-969. Epub 2017 Dec 5.

College of Animal Science and Technology, Northwest A&F University, Xinong Road 22nd, Yangling, Shaanxi, 712100, China. Electronic address:

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http://dx.doi.org/10.1016/j.ejmech.2017.11.100DOI Listing
January 2018

Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra.

Anal Chem 2017 12 21;89(23):12659-12665. Epub 2017 Nov 21.

Earth & Biological Sciences Division, Pacific Northwest National Laboratory (PNNL) , Richland, Washington 99354, United States.

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http://pubs.acs.org/doi/10.1021/acs.analchem.7b03318
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http://dx.doi.org/10.1021/acs.analchem.7b03318DOI Listing
December 2017

Contrasting Determinants of Mutation Rates in Germline and Soma.

Genetics 2017 09 21;207(1):255-267. Epub 2017 Jul 21.

Department of Biological Sciences, Columbia University, New York, New York 10025.

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http://dx.doi.org/10.1534/genetics.117.1114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5586376PMC
September 2017

Human Tissue-Resident Memory T Cells Are Defined by Core Transcriptional and Functional Signatures in Lymphoid and Mucosal Sites.

Cell Rep 2017 Sep;20(12):2921-2934

Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA; Department of Surgery, Columbia University Medical Center, New York, NY 10032, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2017.08.078DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5646692PMC
September 2017

Congenital diaphragmatic hernias: from genes to mechanisms to therapies.

Dis Model Mech 2017 08;10(8):955-970

Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA

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http://dx.doi.org/10.1242/dmm.028365DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5560060PMC
August 2017

High-resolution ultrahigh-pressure long column reversed-phase liquid chromatography for top-down proteomics.

J Chromatogr A 2017 May 5;1498:99-110. Epub 2017 Jan 5.

Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA. Electronic address:

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http://dx.doi.org/10.1016/j.chroma.2017.01.008DOI Listing
May 2017

A Cell Type-Specific Expression Signature Predicts Haploinsufficient Autism-Susceptibility Genes.

Hum Mutat 2017 02 5;38(2):204-215. Epub 2016 Dec 5.

Department of Systems Biology, Columbia University, New York, New York.

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http://dx.doi.org/10.1002/humu.23147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5865588PMC
February 2017

Long-term efficacy of modified retrievable stents for treatment of achalasia cardia.

Surg Endosc 2016 12 8;30(12):5295-5303. Epub 2016 Apr 8.

Department of Gastroenterology, Renji Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai Institute of Digestive Diseases, Shanghai, China.

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http://dx.doi.org/10.1007/s00464-016-4879-9DOI Listing
December 2016

Longterm maintenance of human naive T cells through homeostasis in lymphoid tissue sites.

Sci Immunol 2016 Dec 2;1(6). Epub 2016 Dec 2.

Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA; Department of Surgery, Columbia University Medical Center, New York, NY 10032, USA.

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http://dx.doi.org/10.1126/sciimmunol.aah6506DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5367636PMC
December 2016

Deep Genetic Connection Between Cancer and Developmental Disorders.

Hum Mutat 2016 10 23;37(10):1042-50. Epub 2016 Aug 23.

Department of Systems Biology, Columbia University Medical Center, New York, New York.

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http://dx.doi.org/10.1002/humu.23040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5021574PMC
October 2016

Variants in HNRNPH2 on the X Chromosome Are Associated with a Neurodevelopmental Disorder in Females.

Am J Hum Genet 2016 09 18;99(3):728-734. Epub 2016 Aug 18.

Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA; Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2016.06.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5011042PMC
September 2016

Rare variant phasing and haplotypic expression from RNA sequencing with phASER.

Nat Commun 2016 09 8;7:12817. Epub 2016 Sep 8.

New York Genome Center, New York, NY, 10013, USA.

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http://dx.doi.org/10.1038/ncomms12817DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5025529PMC
September 2016

A New Window into the Human Alloresponse.

Transplantation 2016 Aug;100(8):1639-49

1 Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY.2 Departments of Systems Biology and Biomedical Informatics, Columbia University Medical Center, New York, NY.

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http://dx.doi.org/10.1097/TP.0000000000001064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4940301PMC
August 2016

Diversity and divergence of the glioma-infiltrating T-cell receptor repertoire.

Proc Natl Acad Sci U S A 2016 06 3;113(25):E3529-37. Epub 2016 Jun 3.

Department of Neurological Surgery, Columbia University Medical Center, New York, NY 10032;

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http://dx.doi.org/10.1073/pnas.1601012113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4922177PMC
June 2016

ABC transporters and the proteasome complex are implicated in susceptibility to Stevens-Johnson syndrome and toxic epidermal necrolysis across multiple drugs.

PLoS One 2015 25;10(6):e0131038. Epub 2015 Jun 25.

Department of Systems Biology, Columbia University, New York, New York, United States of America; Department of Biomedical Informatics, Columbia University, New York, New York, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0131038PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4482486PMC
May 2016

HLA-DRB1*16: 01-DQB1*05: 02 is a novel genetic risk factor for flupirtine-induced liver injury.

Pharmacogenet Genomics 2016 May;26(5):218-24

Departments of aSystems Biology bBiomedical Informatics cThe Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York dUNC Eshelman School of Pharmacy, Chapel Hill, North Carolina eTarget Sciences, GSK, King of Prussia, Pennsylvania, USA fInstitute for Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Kiel gDrug Commission of the German Medical Association (DCGMA), Berlin, Germany hInstitute of Cellular Medicine, Newcastle University, Newcastle upon Tyne iNational Institute for Health Research (NIHR), Nottingham Digestive Diseases Biomedical Research Unit, Nottingham University Hospital NHS Trust and University of Nottingham, Nottingham, UK jDivision of Gastroenterology and Hepatology, Department of Internal Medicine, The National University Hospital of Iceland, Faculty of Medicine, University of Iceland, Reykjavik, Iceland.

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http://dx.doi.org/10.1097/FPC.0000000000000209DOI Listing
May 2016

Next-Generation Sequencing of Pulmonary Sarcomatoid Carcinoma Reveals High Frequency of Actionable MET Gene Mutations.

J Clin Oncol 2016 Mar 27;34(8):794-802. Epub 2015 Jul 27.

Xuewen Liu, Mark B. Stoopler, Yufeng Shen, Jinli Chen, Mahesh Mansukhani, Sanjay Koul, Balazs Halmos, and Alain C. Borczuk, Columbia University Medical Center; Haiying Cheng, Montefiore Medical Center/Albert Einstein College of Medicine, New York, NY; Xuewen Liu, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China; and Yuxia Jia, Penn State Milton S. Hershey Medical Center, Penn State College of Medicine, Hershey, PA.

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http://dx.doi.org/10.1200/JCO.2015.62.0674DOI Listing
March 2016

SeqMule: automated pipeline for analysis of human exome/genome sequencing data.

Sci Rep 2015 Sep 18;5:14283. Epub 2015 Sep 18.

Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033, USA.

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http://dx.doi.org/10.1038/srep14283DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4585643PMC
September 2015

RNA sequencing from human neutrophils reveals distinct transcriptional differences associated with chronic inflammatory states.

BMC Med Genomics 2015 Aug 27;8:55. Epub 2015 Aug 27.

Department of Pediatrics, State University of New York at Buffalo School of Medicine, Buffalo, NY, USA.

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http://dx.doi.org/10.1186/s12920-015-0128-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4551565PMC
August 2015

Author response to comment on "Tracking donor-reactive T cells: Evidence for clonal deletion in tolerant kidney transplant patients".

Sci Transl Med 2015 Jul;7(297):297lr1

Columbia University Medical Center, New York, NY 10032, USA.

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http://dx.doi.org/10.1126/scitranslmed.aac9461DOI Listing
July 2015

Coding mutations in SORL1 and Alzheimer disease.

Ann Neurol 2015 Feb;77(2):215-27

Taub Institute for Research on Alzheimer's Disease and the Aging Brain; Gertrude H. Sergievsky Center, Columbia University, New York, NY.

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http://dx.doi.org/10.1002/ana.24305DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4367199PMC
February 2015

Spatial map of human T cell compartmentalization and maintenance over decades of life.

Cell 2014 Nov;159(4):814-28

Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA; Department of Surgery, Columbia University Medical Center, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2014.10.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4243051PMC
November 2014

Comparable frequencies of coding mutations and loss of imprinting in human pluripotent cells derived by nuclear transfer and defined factors.

Cell Stem Cell 2014 Nov 6;15(5):634-42. Epub 2014 Nov 6.

The New York Stem Cell Foundation Research Institute, New York, NY 10032, USA; Naomi Berrie Diabetes Center & Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2014.10.002DOI Listing
November 2014

Characterizing immunoglobulin repertoire from whole blood by a personal genome sequencer.

PLoS One 2013 13;8(9):e75294. Epub 2013 Sep 13.

Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0075294PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3772839PMC
September 2014

The learning effect of a training programme on the diagnosis of oesophageal lesions by narrow band imaging magnification among endoscopists of varying experience.

Dig Liver Dis 2014 Jul 12;46(7):609-15. Epub 2014 Apr 12.

Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai Institute of Digestive Disease, Shanghai, China. Electronic address:

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http://dx.doi.org/10.1016/j.dld.2014.03.004DOI Listing
July 2014

CANOES: detecting rare copy number variants from whole exome sequencing data.

Nucleic Acids Res 2014 Jul 25;42(12):e97. Epub 2014 Apr 25.

Departments of Systems Biology and Biomedical Informatics, Columbia University Medical Center, New York, NY 10032, USA JP Sulzberger Columbia Genome Center, Columbia University Medical Center, New York, NY 10032, USA

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http://dx.doi.org/10.1093/nar/gku345DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4081054PMC
July 2014

Estimating heritability of drug-induced liver injury from common variants and implications for future study designs.

Sci Rep 2014 Jul 21;4:5762. Epub 2014 Jul 21.

1] Department of Biomedical Informatics, Columbia University, New York, NY [2] Department of Systems Biology, Columbia University, New York, NY [3] JP Sulzberger Columbia Genome Center, Columbia University, New York, NY.

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http://dx.doi.org/10.1038/srep05762DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4104390PMC
July 2014

Whole-exome sequencing identifies novel LEPR mutations in individuals with severe early onset obesity.

Obesity (Silver Spring) 2014 Feb 15;22(2):576-84. Epub 2013 Oct 15.

Division of Molecular Genetics Department of Pediatrics, College of Physicians and Surgeons, Columbia University Medical Center, New York, New York, USA; Department of Epidemiology, Mailman School of Public Health, Columbia University Medical Center, New York, New York, USA.

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http://dx.doi.org/10.1002/oby.20492DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791145PMC
February 2014

Defining a comprehensive verotype using electronic health records for personalized medicine.

J Am Med Inform Assoc 2013 Dec 3;20(e2):e232-8. Epub 2013 Sep 3.

Department of Biomedical Informatics, Columbia University, New York, New York, USA.

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http://dx.doi.org/10.1136/amiajnl-2013-001932DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3861934PMC
December 2013

Functionalized ultrasound-propelled magnetically guided nanomotors: toward practical biomedical applications.

ACS Nano 2013 Oct 28;7(10):9232-40. Epub 2013 Aug 28.

Department of Nanoengineering, University of California, San Diego , La Jolla, California 92093, United States.

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http://dx.doi.org/10.1021/nn403851vDOI Listing
October 2013

Molecularly imprinted polymer-based catalytic micromotors for selective protein transport.

J Am Chem Soc 2013 Apr 28;135(14):5336-9. Epub 2013 Mar 28.

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

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http://dx.doi.org/10.1021/ja4018545DOI Listing
April 2013

Variants in GATA4 are a rare cause of familial and sporadic congenital diaphragmatic hernia.

Hum Genet 2013 Mar 9;132(3):285-92. Epub 2012 Nov 9.

Division of Molecular Genetics, Department of Pediatrics, Columbia University Medical Center, 1150 St. Nicholas Avenue, Room 620, New York, NY 10032, USA.

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http://dx.doi.org/10.1007/s00439-012-1249-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3570587PMC
March 2013

Advanced proteomic liquid chromatography.

J Chromatogr A 2012 Oct 9;1261:78-90. Epub 2012 Jul 9.

Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.

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http://dx.doi.org/10.1016/j.chroma.2012.06.098DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463731PMC
October 2012

Protein identification using top-down.

Mol Cell Proteomics 2012 Jun 25;11(6):M111.008524. Epub 2011 Oct 25.

Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, San Diego, California 92093, USA.

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http://dx.doi.org/10.1074/mcp.M111.008524DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3433905PMC
June 2012

Genomewide pharmacogenetics of bisphosphonate-induced osteonecrosis of the jaw: the role of RBMS3.

Oncologist 2012 20;17(2):279-87. Epub 2012 Jan 20.

Center for Computational Biology and Bioinformatics, Columbia University Medical Center, New York, New York 10032, USA.

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http://dx.doi.org/10.1634/theoncologist.2011-0202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3286178PMC
June 2012

High-pH reversed-phase chromatography with fraction concatenation for 2D proteomic analysis.

Expert Rev Proteomics 2012 Apr;9(2):129-34

Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.

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http://dx.doi.org/10.1586/epr.12.15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3337716PMC
April 2012

A hidden Markov model for copy number variant prediction from whole genome resequencing data.

BMC Bioinformatics 2011 28;12 Suppl 6:S4. Epub 2011 Jul 28.

Department of Computer Science, Columbia University, New York, NY 10027, USA.

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http://dx.doi.org/10.1186/1471-2105-12-S6-S4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3194192PMC
December 2011

Effectiveness of CID, HCD, and ETD with FT MS/MS for degradomic-peptidomic analysis: comparison of peptide identification methods.

J Proteome Res 2011 Sep 15;10(9):3929-43. Epub 2011 Aug 15.

Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States.

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http://pubs.acs.org/doi/abs/10.1021/pr200052c
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http://dx.doi.org/10.1021/pr200052cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166380PMC
September 2011

Coverage tradeoffs and power estimation in the design of whole-genome sequencing experiments for detecting association.

Bioinformatics 2011 Jul 2;27(14):1995-7. Epub 2011 Jun 2.

Department of Computer Science, Columbia University, New York, NY 10027, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr305DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129526PMC
July 2011

Blood peptidome-degradome profile of breast cancer.

PLoS One 2010 Oct 18;5(10):e13133. Epub 2010 Oct 18.

Biological Science Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0013133PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2956627PMC
October 2010

Identification of disulfide bonds in protein proteolytic degradation products using de novo-protein unique sequence tags approach.

J Proteome Res 2010 Aug;9(8):4053-60

Biological Sciences Division, and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, USA.

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http://pubs.acs.org/doi/abs/10.1021/pr1002559
Publisher Site
http://dx.doi.org/10.1021/pr1002559DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3217045PMC
August 2010

Strategy for degradomic-peptidomic analysis of human blood plasma.

J Proteome Res 2010 May;9(5):2339-46

Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA.

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http://dx.doi.org/10.1021/pr901083mDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2866148PMC
May 2010

The genome sequence of taurine cattle: a window to ruminant biology and evolution.

Authors:
Christine G Elsik Ross L Tellam Kim C Worley Richard A Gibbs Donna M Muzny George M Weinstock David L Adelson Evan E Eichler Laura Elnitski Roderic Guigó Debora L Hamernik Steve M Kappes Harris A Lewin David J Lynn Frank W Nicholas Alexandre Reymond Monique Rijnkels Loren C Skow Evgeny M Zdobnov Lawrence Schook James Womack Tyler Alioto Stylianos E Antonarakis Alex Astashyn Charles E Chapple Hsiu-Chuan Chen Jacqueline Chrast Francisco Câmara Olga Ermolaeva Charlotte N Henrichsen Wratko Hlavina Yuri Kapustin Boris Kiryutin Paul Kitts Felix Kokocinski Melissa Landrum Donna Maglott Kim Pruitt Victor Sapojnikov Stephen M Searle Victor Solovyev Alexandre Souvorov Catherine Ucla Carine Wyss Juan M Anzola Daniel Gerlach Eran Elhaik Dan Graur Justin T Reese Robert C Edgar John C McEwan Gemma M Payne Joy M Raison Thomas Junier Evgenia V Kriventseva Eduardo Eyras Mireya Plass Ravikiran Donthu Denis M Larkin James Reecy Mary Q Yang Lin Chen Ze Cheng Carol G Chitko-McKown George E Liu Lakshmi K Matukumalli Jiuzhou Song Bin Zhu Daniel G Bradley Fiona S L Brinkman Lilian P L Lau Matthew D Whiteside Angela Walker Thomas T Wheeler Theresa Casey J Bruce German Danielle G Lemay Nauman J Maqbool Adrian J Molenaar Seongwon Seo Paul Stothard Cynthia L Baldwin Rebecca Baxter Candice L Brinkmeyer-Langford Wendy C Brown Christopher P Childers Timothy Connelley Shirley A Ellis Krista Fritz Elizabeth J Glass Carolyn T A Herzig Antti Iivanainen Kevin K Lahmers Anna K Bennett C Michael Dickens James G R Gilbert Darren E Hagen Hanni Salih Jan Aerts Alexandre R Caetano Brian Dalrymple Jose Fernando Garcia Clare A Gill Stefan G Hiendleder Erdogan Memili Diane Spurlock John L Williams Lee Alexander Michael J Brownstein Leluo Guan Robert A Holt Steven J M Jones Marco A Marra Richard Moore Stephen S Moore Andy Roberts Masaaki Taniguchi Richard C Waterman Joseph Chacko Mimi M Chandrabose Andy Cree Marvin Diep Dao Huyen H Dinh Ramatu Ayiesha Gabisi Sandra Hines Jennifer Hume Shalini N Jhangiani Vandita Joshi Christie L Kovar Lora R Lewis Yih-Shin Liu John Lopez Margaret B Morgan Ngoc Bich Nguyen Geoffrey O Okwuonu San Juana Ruiz Jireh Santibanez Rita A Wright Christian Buhay Yan Ding Shannon Dugan-Rocha Judith Herdandez Michael Holder Aniko Sabo Amy Egan Jason Goodell Katarzyna Wilczek-Boney Gerald R Fowler Matthew Edward Hitchens Ryan J Lozado Charles Moen David Steffen James T Warren Jingkun Zhang Readman Chiu Jacqueline E Schein K James Durbin Paul Havlak Huaiyang Jiang Yue Liu Xiang Qin Yanru Ren Yufeng Shen Henry Song Stephanie Nicole Bell Clay Davis Angela Jolivet Johnson Sandra Lee Lynne V Nazareth Bella Mayurkumar Patel Ling-Ling Pu Selina Vattathil Rex Lee Williams Stacey Curry Cerissa Hamilton Erica Sodergren David A Wheeler Wes Barris Gary L Bennett André Eggen Ronnie D Green Gregory P Harhay Matthew Hobbs Oliver Jann John W Keele Matthew P Kent Sigbjørn Lien Stephanie D McKay Sean McWilliam Abhirami Ratnakumar Robert D Schnabel Timothy Smith Warren M Snelling Tad S Sonstegard Roger T Stone Yoshikazu Sugimoto Akiko Takasuga Jeremy F Taylor Curtis P Van Tassell Michael D Macneil Antonio R R Abatepaulo Colette A Abbey Virpi Ahola Iassudara G Almeida Ariel F Amadio Elen Anatriello Suria M Bahadue Fernando H Biase Clayton R Boldt Jeffery A Carroll Wanessa A Carvalho Eliane P Cervelatti Elsa Chacko Jennifer E Chapin Ye Cheng Jungwoo Choi Adam J Colley Tatiana A de Campos Marcos De Donato Isabel K F de Miranda Santos Carlo J F de Oliveira Heather Deobald Eve Devinoy Kaitlin E Donohue Peter Dovc Annett Eberlein Carolyn J Fitzsimmons Alessandra M Franzin Gustavo R Garcia Sem Genini Cody J Gladney Jason R Grant Marion L Greaser Jonathan A Green Darryl L Hadsell Hatam A Hakimov Rob Halgren Jennifer L Harrow Elizabeth A Hart Nicola Hastings Marta Hernandez Zhi-Liang Hu Aaron Ingham Terhi Iso-Touru Catherine Jamis Kirsty Jensen Dimos Kapetis Tovah Kerr Sari S Khalil Hasan Khatib Davood Kolbehdari Charu G Kumar Dinesh Kumar Richard Leach Justin C-M Lee Changxi Li Krystin M Logan Roberto Malinverni Elisa Marques William F Martin Natalia F Martins Sandra R Maruyama Raffaele Mazza Kim L McLean Juan F Medrano Barbara T Moreno Daniela D Moré Carl T Muntean Hari P Nandakumar Marcelo F G Nogueira Ingrid Olsaker Sameer D Pant Francesca Panzitta Rosemeire C P Pastor Mario A Poli Nathan Poslusny Satyanarayana Rachagani Shoba Ranganathan Andrej Razpet Penny K Riggs Gonzalo Rincon Nelida Rodriguez-Osorio Sandra L Rodriguez-Zas Natasha E Romero Anne Rosenwald Lillian Sando Sheila M Schmutz Libing Shen Laura Sherman Bruce R Southey Ylva Strandberg Lutzow Jonathan V Sweedler Imke Tammen Bhanu Prakash V L Telugu Jennifer M Urbanski Yuri T Utsunomiya Chris P Verschoor Ashley J Waardenberg Zhiquan Wang Robert Ward Rosemarie Weikard Thomas H Welsh Stephen N White Laurens G Wilming Kris R Wunderlich Jianqi Yang Feng-Qi Zhao

Science 2009 Apr;324(5926):522-8

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http://dx.doi.org/10.1126/science.1169588DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943200PMC
April 2009

Bos taurus genome assembly.

BMC Genomics 2009 Apr 24;10:180. Epub 2009 Apr 24.

Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.

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http://dx.doi.org/10.1186/1471-2164-10-180DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686734PMC
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Automated metal-free multiple-column nanoLC for improved phosphopeptide analysis sensitivity and throughput.

J Chromatogr B Analyt Technol Biomed Life Sci 2009 Mar 6;877(8-9):663-70. Epub 2009 Jan 6.

Environmental Molecular Sciences Laboratory and Biological Sciences Division, Pacific Northwest National Laboratory, P. O. Box 999, Richland, WA 99352, USA.

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http://dx.doi.org/10.1016/j.jchromb.2008.12.068DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2711447PMC
March 2009

Comparing platforms for C. elegans mutant identification using high-throughput whole-genome sequencing.

PLoS One 2008 24;3(12):e4012. Epub 2008 Dec 24.

Department of Computer Science, Columbia University, New York, New York, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0004012PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2603312PMC
February 2009

[AFLP analysis of genetic diversity of Prunella].

Zhongguo Zhong Yao Za Zhi 2009 Feb;34(3):260-3

College of Agriculture and Biotechnology of Zhengjiang University, Hangzhou 310029, China.

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February 2009

De novo sequencing of unique sequence tags for discovery of post-translational modifications of proteins.

Anal Chem 2008 Oct 11;80(20):7742-54. Epub 2008 Sep 11.

Biological Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA.

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http://dx.doi.org/10.1021/ac801123pDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2752206PMC
October 2008

High Resolution Separations and Improved Ion Production and Transmission in Metabolomics.

Trends Analyt Chem 2008 Mar;27(3):205-214

Biological Sciences Division Pacific Northwest National Laboratory Richland, WA.

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http://dx.doi.org/10.1016/j.trac.2007.11.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2625305PMC
March 2008