Andrea Califano

Andrea Califano

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Andrea Califano

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SJARACNe: a scalable software tool for gene network reverse engineering from big data.

Bioinformatics 2019 Jun;35(12):2165-2166

Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.

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https://academic.oup.com/bioinformatics/advance-article/doi/
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http://dx.doi.org/10.1093/bioinformatics/bty907DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6581437PMC
June 2019

Cooperation of loss of and inflammation in prostate cancer initiation.

Dis Model Mech 2018 11 16;11(11). Epub 2018 Nov 16.

Departments of Urology, Medicine, Pathology & Cell Biology, and Systems Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA

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http://dx.doi.org/10.1242/dmm.035139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6262819PMC
November 2018

iterClust: a statistical framework for iterative clustering analysis.

Bioinformatics 2018 08;34(16):2865-2866

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

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http://dx.doi.org/10.1093/bioinformatics/bty176DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6084607PMC
August 2018

The number of titrated microRNA species dictates ceRNA regulation.

Nucleic Acids Res 2018 05;46(9):4354-4369

Department of Systems Biology, Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Center for Computational Biology and Bioinformatics, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA.

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http://dx.doi.org/10.1093/nar/gky286DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5961349PMC
May 2018

A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development.

Cell Stem Cell 2018 04;22(4):575-588.e7

Stem Cell Program, Division of Hematology/Oncology, Manton Center for Orphan Disease Research, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2018.03.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5957284PMC
April 2018

Systematic, network-based characterization of therapeutic target inhibitors.

PLoS Comput Biol 2017 Oct 12;13(10):e1005599. Epub 2017 Oct 12.

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

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http://dx.doi.org/10.1371/journal.pcbi.1005599DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5638208PMC
October 2017

Accelerated parallel algorithm for gene network reverse engineering.

BMC Syst Biol 2017 Sep 21;11(Suppl 4):83. Epub 2017 Sep 21.

Department of Systems Biology, 1130 St Nicholas Street, New York, 10032, NY, USA.

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http://dx.doi.org/10.1186/s12918-017-0458-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5615246PMC
September 2017

An Integrated Systems Biology Approach Identifies TRIM25 as a Key Determinant of Breast Cancer Metastasis.

Cell Rep 2017 08;20(7):1623-1640

Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Brain Tumor Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Cellular and Developmental Biology, Weill Cornell Medical College, New York, NY, USA; Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2017.07.052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5985663PMC
August 2017

Transdifferentiation as a Mechanism of Treatment Resistance in a Mouse Model of Castration-Resistant Prostate Cancer.

Cancer Discov 2017 07 14;7(7):736-749. Epub 2017 Apr 14.

Departments of Urology, Medicine, Systems Biology, and Pathology and Cell Biology, Institute of Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York.

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http://dx.doi.org/10.1158/2159-8290.CD-16-1174DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5501744PMC
July 2017

PLATE-Seq for genome-wide regulatory network analysis of high-throughput screens.

Nat Commun 2017 07 24;8(1):105. Epub 2017 Jul 24.

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

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http://dx.doi.org/10.1038/s41467-017-00136-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5524642PMC
July 2017

High-throughput validation of ceRNA regulatory networks.

BMC Genomics 2017 05 30;18(1):418. Epub 2017 May 30.

Columbia Department of Systems Biology, Center for Computational Biology and Bioinformatics, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10032, USA.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864
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http://dx.doi.org/10.1186/s12864-017-3790-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5450082PMC
May 2017

A computational systems approach identifies synergistic specification genes that facilitate lineage conversion to prostate tissue.

Nat Commun 2017 04 21;8:14662. Epub 2017 Apr 21.

Department of Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York 10032, USA.

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http://dx.doi.org/10.1038/ncomms14662DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5413950PMC
April 2017

The recurrent architecture of tumour initiation, progression and drug sensitivity.

Nat Rev Cancer 2017 02 15;17(2):116-130. Epub 2016 Dec 15.

DarwinHealth, Inc., 3960 Broadway, Suite 540, New York, New York 10032, USA.

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http://dx.doi.org/10.1038/nrc.2016.124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5541669PMC
February 2017

HAUSP deubiquitinates and stabilizes N-Myc in neuroblastoma.

Nat Med 2016 10 12;22(10):1180-1186. Epub 2016 Sep 12.

Institute for Cancer Genetics, College of Physicians and Surgeons, Columbia University, New York, New York, USA.

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http://dx.doi.org/10.1038/nm.4180DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5091299PMC
October 2016

Functional characterization of somatic mutations in cancer using network-based inference of protein activity.

Nat Genet 2016 08 20;48(8):838-47. Epub 2016 Jun 20.

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

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http://dx.doi.org/10.1038/ng.3593DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5040167PMC
August 2016

ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information.

Bioinformatics 2016 07 23;32(14):2233-5. Epub 2016 Apr 23.

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

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http://dx.doi.org/10.1093/bioinformatics/btw216DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937200PMC
July 2016

Detection and removal of spatial bias in multiwell assays.

Bioinformatics 2016 07 28;32(13):1959-65. Epub 2016 Feb 28.

Department of Biomedical Informatics (DBMI) Department of Systems Biology Center for Computational Biology and Bioinformatics (C2B2), Columbia University, New York, NY, USA Department of Biochemistry and Molecular Biophysics Institute for Cancer Genetics Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw092DOI Listing
July 2016

Identification of immunotherapeutic targets by genomic profiling of rectal NET metastases.

Oncoimmunology 2016 22;5(11):e1213931. Epub 2016 Jul 22.

Clinical Cooperation Unit "Applied Tumor Immunity", National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Medical Oncology, National Center for Tumor Diseases (NCT) and University Hospital Heidelberg, Heidelberg, Germany.

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http://dx.doi.org/10.1080/2162402X.2016.1213931DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5139646PMC
July 2016

Identification of an NKX3.1-G9a-UTY transcriptional regulatory network that controls prostate differentiation.

Science 2016 Jun;352(6293):1576-80

Departments of Urology, Medicine, Systems Biology, and Pathology and Cell Biology, Institute of Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA.

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http://dx.doi.org/10.1126/science.aad9512DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5507586PMC
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

Mechanism and Role of SOX2 Repression in Seminoma: Relevance to Human Germline Specification.

Stem Cell Reports 2016 05 28;6(5):772-783. Epub 2016 Apr 28.

Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stemcr.2016.04.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4939754PMC
May 2016

Assembly and interrogation of Alzheimer's disease genetic networks reveal novel regulators of progression.

PLoS One 2015 17;10(3):e0120352. Epub 2015 Mar 17.

Taub Institute for Research on Alzheimer's Disease & the Aging Brain and the Department of Pathology & Cell Biology, Columbia University, New York, NY, 10032, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0120352PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4363671PMC
February 2016

Elucidation and Pharmacological Targeting of Novel Molecular Drivers of Follicular Lymphoma Progression.

Cancer Res 2016 Feb 20;76(3):664-74. Epub 2015 Nov 20.

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

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http://dx.doi.org/10.1158/0008-5472.CAN-15-0828DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4738055PMC
February 2016

ScreenBEAM: a novel meta-analysis algorithm for functional genomics screens via Bayesian hierarchical modeling.

Bioinformatics 2016 Jan 28;32(2):260-7. Epub 2015 Sep 28.

Department of Biomedical Informatics, Department of Systems Biology, Center for Computational Biology and Bioinformatics, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA and.

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https://bioinformatics.oxfordjournals.org/content/early/2015
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http://bioinformatics.oxfordjournals.org/content/early/2015/
Web Search
http://bioinformatics.oxfordjournals.org/lookup/doi/10.1093/
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http://dx.doi.org/10.1093/bioinformatics/btv556DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4907394PMC
January 2016

DIGGIT: a Bioconductor package to infer genetic variants driving cellular phenotypes.

Bioinformatics 2015 Dec 2;31(24):4032-4. Epub 2015 Sep 2.

Department of Systems Biology and.

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http://dx.doi.org/10.1093/bioinformatics/btv499DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4692968PMC
December 2015

Identification of neurodegenerative factors using translatome-regulatory network analysis.

Nat Neurosci 2015 Sep 27;18(9):1325-33. Epub 2015 Jul 27.

Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, New York, USA.

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http://dx.doi.org/10.1038/nn.4070DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4763340PMC
September 2015

Predicting Drug Response in Human Prostate Cancer from Preclinical Analysis of In Vivo Mouse Models.

Cell Rep 2015 Sep 17;12(12):2060-71. Epub 2015 Sep 17.

Department of Systems Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA; Institute of Cancer Genetics, 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.celrep.2015.08.051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4591242PMC
September 2015

The Regulatory Machinery of Neurodegeneration in In Vitro Models of Amyotrophic Lateral Sclerosis.

Cell Rep 2015 Jul 2;12(2):335-45. Epub 2015 Jul 2.

Program in Neurobiology and Behavior, Columbia University, New York, NY 10032, USA; Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative and Columbia Translational Neuroscience Initiative, Columbia University, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA; Program in Pathobiology and Molecular Medicine, Columbia University, New York, NY 10032, USA; Department of Neurology, Columbia University, New York, NY 10032, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.06.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4646662PMC
July 2015

Elucidating Compound Mechanism of Action by Network Perturbation Analysis.

Cell 2015 Jul;162(2):441-451

Department of Biomedical Informatics (DBMI), Columbia University, New York, NY 10032, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA; Center for Computational Biology and Bioinformatics (C2B2), Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.05.056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4506491PMC
July 2015

Inferring protein modulation from gene expression data using conditional mutual information.

PLoS One 2014 14;9(10):e109569. Epub 2014 Oct 14.

Department of Systems Biology, Columbia University, New York, New York, United States of America; Center for Computational Biology and Bioinformatics, 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.0109569PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4196905PMC
June 2015

The Cyni framework for network inference in Cytoscape.

Bioinformatics 2015 May 18;31(9):1499-501. Epub 2014 Dec 18.

Systems Biology Lab, Institut Pasteur, 75724 Paris Cedex 15, France and Department of Systems Biology, Columbia University, New York, NY 10032, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu812DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410647PMC
May 2015

Predicting protein networks in cancer.

Authors:
Andrea Califano

Nat Genet 2014 Dec;46(12):1252-3

Department of Systems Biology, the Department of Biochemistry and Molecular Biophysics, and the Department of Biomedical Informatics at Columbia University, New York, New York, USA.

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http://dx.doi.org/10.1038/ng.3156DOI Listing
December 2014

A community computational challenge to predict the activity of pairs of compounds.

Nat Biotechnol 2014 Dec 17;32(12):1213-22. Epub 2014 Nov 17.

1] Department of Systems Biology, Columbia University, New York, New York, USA. [2] Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, USA. [3] Department of Biomedical Informatics, Columbia University, New York, New York, USA. [4] Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA. [5] Institute for Cancer Genetics, Columbia University, New York, New York, USA. [6] Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, USA.

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http://dx.doi.org/10.1038/nbt.3052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4399794PMC
December 2014

Identification of causal genetic drivers of human disease through systems-level analysis of regulatory networks.

Cell 2014 Oct;159(2):402-14

Department of Systems Biology, Columbia University, 1130 Saint Nicholas Avenue, New York, NY 10032, USA; Center for Computational Biology and Bioinformatics, Columbia University, 1130 Saint Nicholas Avenue, New York, NY 10032, USA; Department of Biomedical Informatics, Biochemistry & Molecular Biophysics, and Institute for Cancer Genetics, Columbia University, 1130 Saint Nicholas Avenue, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, 1130 Saint Nicholas Avenue, New York, NY 10032, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2014.09.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4194029PMC
October 2014

Convection-enhanced delivery of etoposide is effective against murine proneural glioblastoma.

Neuro Oncol 2014 Sep 16;16(9):1210-9. Epub 2014 Mar 16.

Gabriele Bartoli Brain Tumor Laboratory, Department of Neurosurgery, Irving Research Cancer Center, Columbia University Medical Center, New York, New York (A.M.S., A.S.C., B.A., R.L., J.Y., C.S., R.R., J.O, P.C., J.N.B.); Department of Systems Biology, Columbia University, New York, New York (M.B., A.C.); Center for Computational Biology and Bioinformatics, Columbia University, New York, New York (M.B., A.C.); Department of Pathology and Cell Biology, Irving Research Cancer Center, Columbia University Medical Center, New York, New York (L.L.); High Throughput Screening Center, Columbia University Medical Center Judith P. Sulzberger Genome Center, New York, New York (R.R., H.L., C.K.); Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, New York (A.C.); Department of Biomedical Informatics, Columbia University, New York, New York (A.C.); Institute for Cancer Genetics, Columbia University, New York, New York (A.C.); Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York (A.C.).

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http://dx.doi.org/10.1093/neuonc/nou026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4136893PMC
September 2014

RECOMB/ISCB systems biology, regulatory genomics, and DREAM 2013 special issue.

J Comput Biol 2014 May;21(5):371-2

1 Departments of Systems Biology, Biochemistry & Molecular Biophysics, Biomedical Informatics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center , New York, New York.

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http://dx.doi.org/10.1089/cmb.2014.009pDOI Listing
May 2014

A promoter-level mammalian expression atlas.

Authors:
Alistair R R Forrest Hideya Kawaji Michael Rehli J Kenneth Baillie Michiel J L de Hoon Vanja Haberle Timo Lassmann Ivan V Kulakovskiy Marina Lizio Masayoshi Itoh Robin Andersson Christopher J Mungall Terrence F Meehan Sebastian Schmeier Nicolas Bertin Mette Jørgensen Emmanuel Dimont Erik Arner Christian Schmidl Ulf Schaefer Yulia A Medvedeva Charles Plessy Morana Vitezic Jessica Severin Colin A Semple Yuri Ishizu Robert S Young Margherita Francescatto Intikhab Alam Davide Albanese Gabriel M Altschuler Takahiro Arakawa John A C Archer Peter Arner Magda Babina Sarah Rennie Piotr J Balwierz Anthony G Beckhouse Swati Pradhan-Bhatt Judith A Blake Antje Blumenthal Beatrice Bodega Alessandro Bonetti James Briggs Frank Brombacher A Maxwell Burroughs Andrea Califano Carlo V Cannistraci Daniel Carbajo Yun Chen Marco Chierici Yari Ciani Hans C Clevers Emiliano Dalla Carrie A Davis Michael Detmar Alexander D Diehl Taeko Dohi Finn Drabløs Albert S B Edge Matthias Edinger Karl Ekwall Mitsuhiro Endoh Hideki Enomoto Michela Fagiolini Lynsey Fairbairn Hai Fang Mary C Farach-Carson Geoffrey J Faulkner Alexander V Favorov Malcolm E Fisher Martin C Frith Rie Fujita Shiro Fukuda Cesare Furlanello Masaaki Furino Jun-ichi Furusawa Teunis B Geijtenbeek Andrew P Gibson Thomas Gingeras Daniel Goldowitz Julian Gough Sven Guhl Reto Guler Stefano Gustincich Thomas J Ha Masahide Hamaguchi Mitsuko Hara Matthias Harbers Jayson Harshbarger Akira Hasegawa Yuki Hasegawa Takehiro Hashimoto Meenhard Herlyn Kelly J Hitchens Shannan J Ho Sui Oliver M Hofmann Ilka Hoof Furni Hori Lukasz Huminiecki Kei Iida Tomokatsu Ikawa Boris R Jankovic Hui Jia Anagha Joshi Giuseppe Jurman Bogumil Kaczkowski Chieko Kai Kaoru Kaida Ai Kaiho Kazuhiro Kajiyama Mutsumi Kanamori-Katayama Artem S Kasianov Takeya Kasukawa Shintaro Katayama Sachi Kato Shuji Kawaguchi Hiroshi Kawamoto Yuki I Kawamura Tsugumi Kawashima Judith S Kempfle Tony J Kenna Juha Kere Levon M Khachigian Toshio Kitamura S Peter Klinken Alan J Knox Miki Kojima Soichi Kojima Naoto Kondo Haruhiko Koseki Shigeo Koyasu Sarah Krampitz Atsutaka Kubosaki Andrew T Kwon Jeroen F J Laros Weonju Lee Andreas Lennartsson Kang Li Berit Lilje Leonard Lipovich Alan Mackay-Sim Ri-ichiroh Manabe Jessica C Mar Benoit Marchand Anthony Mathelier Niklas Mejhert Alison Meynert Yosuke Mizuno David A de Lima Morais Hiromasa Morikawa Mitsuru Morimoto Kazuyo Moro Efthymios Motakis Hozumi Motohashi Christine L Mummery Mitsuyoshi Murata Sayaka Nagao-Sato Yutaka Nakachi Fumio Nakahara Toshiyuki Nakamura Yukio Nakamura Kenichi Nakazato Erik van Nimwegen Noriko Ninomiya Hiromi Nishiyori Shohei Noma Shohei Noma Tadasuke Noazaki Soichi Ogishima Naganari Ohkura Hiroko Ohimiya Hiroshi Ohno Mitsuhiro Ohshima Mariko Okada-Hatakeyama Yasushi Okazaki Valerio Orlando Dmitry A Ovchinnikov Arnab Pain Robert Passier Margaret Patrikakis Helena Persson Silvano Piazza James G D Prendergast Owen J L Rackham Jordan A Ramilowski Mamoon Rashid Timothy Ravasi Patrizia Rizzu Marco Roncador Sugata Roy Morten B Rye Eri Saijyo Antti Sajantila Akiko Saka Shimon Sakaguchi Mizuho Sakai Hiroki Sato Suzana Savvi Alka Saxena Claudio Schneider Erik A Schultes Gundula G Schulze-Tanzil Anita Schwegmann Thierry Sengstag Guojun Sheng Hisashi Shimoji Yishai Shimoni Jay W Shin Christophe Simon Daisuke Sugiyama Takaai Sugiyama Masanori Suzuki Naoko Suzuki Rolf K Swoboda Peter A C 't Hoen Michihira Tagami Naoko Takahashi Jun Takai Hiroshi Tanaka Hideki Tatsukawa Zuotian Tatum Mark Thompson Hiroo Toyodo Tetsuro Toyoda Elvind Valen Marc van de Wetering Linda M van den Berg Roberto Verado Dipti Vijayan Ilya E Vorontsov Wyeth W Wasserman Shoko Watanabe Christine A Wells Louise N Winteringham Ernst Wolvetang Emily J Wood Yoko Yamaguchi Masayuki Yamamoto Misako Yoneda Yohei Yonekura Shigehiro Yoshida Susan E Zabierowski Peter G Zhang Xiaobei Zhao Silvia Zucchelli Kim M Summers Harukazu Suzuki Carsten O Daub Jun Kawai Peter Heutink Winston Hide Tom C Freeman Boris Lenhard Vladimir B Bajic Martin S Taylor Vsevolod J Makeev Albin Sandelin David A Hume Piero Carninci Yoshihide Hayashizaki

Nature 2014 Mar;507(7493):462-70

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http://dx.doi.org/10.1038/nature13182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4529748PMC
March 2014

ZFHX4 interacts with the NuRD core member CHD4 and regulates the glioblastoma tumor-initiating cell state.

Cell Rep 2014 Jan 16;6(2):313-24. Epub 2014 Jan 16.

Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Neurology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.

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http://dx.doi.org/10.1016/j.celrep.2013.12.032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4041390PMC
January 2014

ETV4 promotes metastasis in response to activation of PI3-kinase and Ras signaling in a mouse model of advanced prostate cancer.

Proc Natl Acad Sci U S A 2013 Sep 5;110(37):E3506-15. Epub 2013 Aug 5.

Department of Urology and Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Department of Systems Biology, and Department of Medicine and Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032.

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http://dx.doi.org/10.1073/pnas.1303558110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3773788PMC
September 2013

hARACNe: improving the accuracy of regulatory model reverse engineering via higher-order data processing inequality tests.

Interface Focus 2013 Aug;3(4):20130011

Department of Systems Biology, Biochemistry and Molecular Biophysics, Biomedical Informatics, and Herbert Irving Comprehensive Cancer Center , Columbia University Medical Center , New York, NY 10032 , USA.

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http://dx.doi.org/10.1098/rsfs.2013.0011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3915831PMC
August 2013

Pooled shRNA screenings: computational analysis.

Methods Mol Biol 2013 ;980:371-84

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

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http://dx.doi.org/10.1007/978-1-62703-287-2_22DOI Listing
July 2013

Lineage analysis of basal epithelial cells reveals their unexpected plasticity and supports a cell-of-origin model for prostate cancer heterogeneity.

Nat Cell Biol 2013 Mar 24;15(3):274-83. Epub 2013 Feb 24.

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

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http://dx.doi.org/10.1038/ncb2697DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3743266PMC
March 2013

tRNA-derived microRNA modulates proliferation and the DNA damage response and is down-regulated in B cell lymphoma.

Proc Natl Acad Sci U S A 2013 Jan 7;110(4):1404-9. Epub 2013 Jan 7.

Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center, Department of Genetics and Development, Columbia University, New York, NY 10032, USA.

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http://www.pnas.org/lookup/doi/10.1073/pnas.1206761110
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http://dx.doi.org/10.1073/pnas.1206761110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3557069PMC
January 2013

Leveraging models of cell regulation and GWAS data in integrative network-based association studies.

Nat Genet 2012 Jul 27;44(8):841-7. Epub 2012 Jul 27.

Columbia Initiative in Systems Biology, Columbia University, New York, New York, USA.

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http://dx.doi.org/10.1038/ng.2355DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3593099PMC
July 2012