Publications by authors named "Raul Rabadan"

100Publications

Mutant SF3B1 promotes AKT and NF-kB driven mammary tumorigenesis.

J Clin Invest 2020 Oct 8. Epub 2020 Oct 8.

Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, United States of America.

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http://dx.doi.org/10.1172/JCI138315DOI Listing
October 2020

CtIP-mediated DNA resection is dispensable for IgH class switch recombination by alternative end-joining.

Proc Natl Acad Sci U S A 2020 Oct 28;117(41):25700-25711. Epub 2020 Sep 28.

Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York, NY 10032;

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http://dx.doi.org/10.1073/pnas.2010972117DOI Listing
October 2020

Identification of relevant genetic alterations in cancer using topological data analysis.

Nat Commun 2020 07 30;11(1):3808. Epub 2020 Jul 30.

Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA, 19104, USA.

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http://dx.doi.org/10.1038/s41467-020-17659-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7393176PMC
July 2020

Recombination and lineage-specific mutations led to the emergence of SARS-CoV-2.

bioRxiv 2020 Mar 23. Epub 2020 Mar 23.

Program for Mathematical Genomics, Columbia University, New York, NY, USA.

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http://dx.doi.org/10.1101/2020.02.10.942748DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217262PMC
March 2020

Active surveillance documents rates of clinical care seeking due to respiratory illness.

Influenza Other Respir Viruses 2020 09 16;14(5):499-506. Epub 2020 May 16.

Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA.

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http://dx.doi.org/10.1111/irv.12753DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7276732PMC
September 2020

Pan-cancer analysis identifies mutations in that recapitulate mutant SF3B1 splicing dysregulation.

Proc Natl Acad Sci U S A 2020 05 24;117(19):10305-10312. Epub 2020 Apr 24.

Program for Mathematical Genomics, Columbia University, New York, NY 10032;

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http://dx.doi.org/10.1073/pnas.1922622117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7229667PMC
May 2020

HLA Typing from RNA Sequencing and Applications to Cancer.

Methods Mol Biol 2020 ;2120:71-92

Department of Systems Biology, Columbia University Irving Cancer Research Center, New York, NY, USA.

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http://dx.doi.org/10.1007/978-1-0716-0327-7_5DOI Listing
January 2020

Tissue-Resident Memory T Cells Mediate Immune Homeostasis in the Human Pancreas through the PD-1/PD-L1 Pathway.

Cell Rep 2019 12;29(12):3916-3932.e5

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.celrep.2019.11.056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6939378PMC
December 2019

Can patient selection and neoadjuvant administration resuscitate PD-1 inhibitors for glioblastoma?

J Neurosurg 2019 Dec 6:1-6. Epub 2019 Dec 6.

2Department of Neurosurgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.

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http://dx.doi.org/10.3171/2019.9.JNS192523DOI Listing
December 2019

Longitudinal molecular trajectories of diffuse glioma in adults.

Nature 2019 12 20;576(7785):112-120. Epub 2019 Nov 20.

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

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http://dx.doi.org/10.1038/s41586-019-1775-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6897368PMC
December 2019

The Long Noncoding RNA Paupar Modulates PAX6 Regulatory Activities to Promote Alpha Cell Development and Function.

Cell Metab 2019 12 10;30(6):1091-1106.e8. Epub 2019 Oct 10.

Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA; Barbara Davis Center, University of Colorado Medical Center, Aurora, CO 80045, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cmet.2019.09.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7205457PMC
December 2019

Disease-Causing Mutations in SF3B1 Alter Splicing by Disrupting Interaction with SUGP1.

Mol Cell 2019 10 29;76(1):82-95.e7. Epub 2019 Aug 29.

Department of Biological Sciences, Columbia University, New York, NY 10027, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2019.07.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7065273PMC
October 2019

A Structure-Informed Atlas of Human-Virus Interactions.

Cell 2019 09 29;178(6):1526-1541.e16. Epub 2019 Aug 29.

Department of Systems Biology, Columbia University Medical Center, New York, NY, USA; Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.08.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6736651PMC
September 2019

Repurposing dasatinib for diffuse large B cell lymphoma.

Proc Natl Acad Sci U S A 2019 08 5;116(34):16981-16986. Epub 2019 Aug 5.

Institute for Cancer Genetics, Columbia University, New York, NY 10032;

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http://dx.doi.org/10.1073/pnas.1905239116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6708382PMC
August 2019

arcasHLA: high-resolution HLA typing from RNAseq.

Bioinformatics 2020 01;36(1):33-40

Department of Systems Biology, Columbia University, New York, NY 10032, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz474DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6956775PMC
January 2020

Longitudinal active sampling for respiratory viral infections across age groups.

Influenza Other Respir Viruses 2019 05 15;13(3):226-232. Epub 2019 Feb 15.

Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York.

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http://doi.wiley.com/10.1111/irv.12629
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http://dx.doi.org/10.1111/irv.12629DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6468062PMC
May 2019

Interrogation of Eukaryotic Stop Codon Readthrough Signals by in Vitro RNA Selection.

Biochemistry 2019 02 13;58(8):1167-1178. Epub 2019 Feb 13.

Department of Chemistry , Columbia University , New York , New York 10027 , United States.

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http://dx.doi.org/10.1021/acs.biochem.8b01280DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6566847PMC
February 2019

Hypermutagenesis in untreated adult gliomas due to inherited mismatch mutations.

Int J Cancer 2019 06 7;144(12):3023-3030. Epub 2019 Jan 7.

Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, Republic of Korea.

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http://dx.doi.org/10.1002/ijc.32054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6590456PMC
June 2019

On statistical modeling of sequencing noise in high depth data to assess tumor evolution.

J Stat Phys 2018 Jul 21;172(1):143-155. Epub 2017 Dec 21.

Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ.

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http://dx.doi.org/10.1007/s10955-017-1945-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6051708PMC
July 2018

The possibility of cancer immune editing in gliomas. A critical review.

Oncoimmunology 2018 9;7(7):e1445458. Epub 2018 Apr 9.

Department of Neurosurgery, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA.

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http://dx.doi.org/10.1080/2162402X.2018.1445458DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5993488PMC
April 2018

A Random Categorization Model for Hierarchical Taxonomies.

Sci Rep 2017 12 6;7(1):17051. Epub 2017 Dec 6.

Center for Cosmology and Particle Physics, Physics Department, New York University, New York, USA.

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http://dx.doi.org/10.1038/s41598-017-17168-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5719047PMC
December 2017

Restoration of Replication Fork Stability in BRCA1- and BRCA2-Deficient Cells by Inactivation of SNF2-Family Fork Remodelers.

Mol Cell 2017 Oct;68(2):414-430.e8

Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2017.09.036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5720682PMC
October 2017

An NF-κB Transcription-Factor-Dependent Lineage-Specific Transcriptional Program Promotes Regulatory T Cell Identity and Function.

Immunity 2017 09 7;47(3):450-465.e5. Epub 2017 Sep 7.

Department of Microbiology & Immunology, Columbia University College of Physicians & Surgeons, New York, NY 10032, USA. Electronic address:

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http://dx.doi.org/10.1016/j.immuni.2017.08.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5679261PMC
September 2017

Single-cell topological RNA-seq analysis reveals insights into cellular differentiation and development.

Nat Biotechnol 2017 06 1;35(6):551-560. Epub 2017 May 1.

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

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http://dx.doi.org/10.1038/nbt.3854DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5569300PMC
June 2017

Germ-Cell-Specific Inflammasome Component NLRP14 Negatively Regulates Cytosolic Nucleic Acid Sensing to Promote Fertilization.

Immunity 2017 04;46(4):621-634

Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University, New York, NY 10032, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10747613173013
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http://dx.doi.org/10.1016/j.immuni.2017.03.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5674777PMC
April 2017

Evolutionary scalpels for dissecting tumor ecosystems.

Biochim Biophys Acta Rev Cancer 2017 Apr 5;1867(2):69-83. Epub 2016 Dec 5.

Department of Systems Biology, Columbia University College of Physicians and Surgeons, 1130 St. Nicholas Avenue, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University College of Physicians and Surgeons, 1130 St. Nicholas Avenue, New York, NY 10032, USA. Electronic address:

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http://dx.doi.org/10.1016/j.bbcan.2016.11.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5704952PMC
April 2017

Genomic Characterization of Dysplastic Nevi Unveils Implications for Diagnosis of Melanoma.

J Invest Dermatol 2017 04 24;137(4):905-909. Epub 2016 Nov 24.

Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jid.2016.11.017DOI Listing
April 2017

Inference of Ancestral Recombination Graphs through Topological Data Analysis.

PLoS Comput Biol 2016 08 17;12(8):e1005071. Epub 2016 Aug 17.

Department of Systems Biology and Department of Biomedical Informatics, Columbia University College of Physicians and Surgeons, New York, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1005071DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4988722PMC
August 2016

Topological Data Analysis Generates High-Resolution, Genome-wide Maps of Human Recombination.

Cell Syst 2016 07 23;3(1):83-94. Epub 2016 Jun 23.

Department of Systems Biology, Columbia University College of Physicians and Surgeons, 1130 St. Nicholas Avenue, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University College of Physicians and Surgeons, 1130 St. Nicholas Avenue, New York, NY 10032, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2016.05.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4965322PMC
July 2016

Reprogramming eukaryotic translation with ligand-responsive synthetic RNA switches.

Nat Methods 2016 05 21;13(5):453-8. Epub 2016 Mar 21.

Department of Chemistry, Columbia University, New York, New York, USA.

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http://dx.doi.org/10.1038/nmeth.3807DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4850110PMC
May 2016

De novo transcriptome reconstruction and annotation of the Egyptian rousette bat.

BMC Genomics 2015 Dec 7;16:1033. Epub 2015 Dec 7.

Department of Biomedical Informatics, Columbia University College of Physicians and Surgeons, 1130 St. Nicholas Ave, New York, USA.

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http://dx.doi.org/10.1186/s12864-015-2124-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4672546PMC
December 2015

Transcriptomics Identify CD9 as a Marker of Murine IL-10-Competent Regulatory B Cells.

Cell Rep 2015 Nov 29;13(6):1110-1117. Epub 2015 Oct 29.

Department of Microbiology and Immunology, 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.celrep.2015.09.070DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4644501PMC
November 2015

JAK-STAT in lymphoproliferative disorders.

Oncoscience 2015 11;2(9):737-8. Epub 2015 Aug 11.

Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4606001PMC
http://dx.doi.org/10.18632/oncoscience.189DOI Listing
October 2015

Distinct Viral and Mutational Spectrum of Endemic Burkitt Lymphoma.

PLoS Pathog 2015 Oct 15;11(10):e1005158. Epub 2015 Oct 15.

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

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http://dx.doi.org/10.1371/journal.ppat.1005158DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4607508PMC
October 2015

Identification of a new subclass of ALK-negative ALCL expressing aberrant levels of ERBB4 transcripts.

Blood 2016 Jan 13;127(2):221-32. Epub 2015 Oct 13.

Department of Molecular Biotechnology and Health Sciences, Center for Experimental Research and Medical Studies, University of Turin, Turin, Italy; Department of Pathology, New York University Cancer Center, New York University School of Medicine, New York, NY.

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http://www.bloodjournal.org/cgi/doi/10.1182/blood-2014-12-61
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http://dx.doi.org/10.1182/blood-2014-12-614503DOI Listing
January 2016

Generation of Live Attenuated Influenza Virus by Using Codon Usage Bias.

J Virol 2015 Nov 12;89(21):10762-73. Epub 2015 Aug 12.

Centre of Influenza Research and School of Public Health, The University of Hong Kong, Hong Kong, SAR, China

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http://dx.doi.org/10.1128/JVI.01443-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4621104PMC
November 2015

Disease-associated mutation in SRSF2 misregulates splicing by altering RNA-binding affinities.

Proc Natl Acad Sci U S A 2015 Aug 10;112(34):E4726-34. Epub 2015 Aug 10.

Department of Biological Sciences, Columbia University, New York, NY 10027;

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http://dx.doi.org/10.1073/pnas.1514105112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4553800PMC
August 2015

An information theoretic method to identify combinations of genomic alterations that promote glioblastoma.

J Mol Cell Biol 2015 Jun 4;7(3):203-13. Epub 2015 May 4.

Department of Systems Biology, Columbia University College of Physicians and Surgeons, New York, NY, USA Department of Biomedical Informatics, Columbia University College of Physicians and Surgeons, New York, NY, USA

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https://academic.oup.com/jmcb/article-lookup/doi/10.1093/jmc
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http://dx.doi.org/10.1093/jmcb/mjv026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4565985PMC
June 2015

Genetic similarity between cancers and comorbid Mendelian diseases identifies candidate driver genes.

Nat Commun 2015 Apr 30;6:7033. Epub 2015 Apr 30.

1] Department of Systems Biology, Columbia University, 1130 St Nicholas Avenue, New York, New York 10032, USA [2] Department of Biomedical Informatics, Columbia University, 1130 St Nicholas Avenue, New York, New York 10032, USA.

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http://dx.doi.org/10.1038/ncomms8033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4416231PMC
April 2015

Convergent mutations and kinase fusions lead to oncogenic STAT3 activation in anaplastic large cell lymphoma.

Cancer Cell 2015 Apr;27(4):516-32

Department of Molecular Biotechnology and Health Science and Center for Experimental Research and Medical Studies, University of Torino, 10126 Torino, Italy; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10021, USA; Department of Pathology and NYU Cancer Center, New York University School of Medicine, New York, NY 10016, USA. Electronic address:

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http://www.cell.com/cancer-cell/pdf/S1535-6108(15)00094-X.pd
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http://linkinghub.elsevier.com/retrieve/pii/S153561081500094
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http://dx.doi.org/10.1016/j.ccell.2015.03.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5898430PMC
April 2015

Transcriptome reconstruction and annotation of cynomolgus and African green monkey.

BMC Genomics 2014 Oct 3;15:846. Epub 2014 Oct 3.

Department of Biomedical Informatics, Columbia University College of Physicians and Surgeons, New York, New York, NY 10032, USA.

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http://dx.doi.org/10.1186/1471-2164-15-846DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4194418PMC
October 2014

Noncoding RNA transcription targets AID to divergently transcribed loci in B cells.

Nature 2014 Oct 6;514(7522):389-93. Epub 2014 Aug 6.

Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA.

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http://dx.doi.org/10.1038/nature13580DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4372240PMC
October 2014

FBXW7 mutations in melanoma and a new therapeutic paradigm.

J Natl Cancer Inst 2014 Jun 16;106(6):dju107. Epub 2014 May 16.

Affiliations of authors: Department of Dermatology (ITY, SJA, AD, DB, JTC) and Department of Pathology (ITA, SJA, MC-M, AD, DB, CC-C, JTC), Icahn School of Medicine at Mount Sinai, New York, NY; Department of Biomedical Informatics (RDM, RR) and Department of Systems Biology (RDM, RR), Columbia University Medical Center, New York, NY; Department of Cancer Research, Skin Cancer Center Hornheide, Munster, Germany (GB); Department of Dermatology, New York University, New York, NY (IO).

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http://jnci.oxfordjournals.org/content/106/6/dju107.full.pdf
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http://jnci.oxfordjournals.org/cgi/doi/10.1093/jnci/dju107
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http://dx.doi.org/10.1093/jnci/dju107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4081626PMC
June 2014