Yuri Nikolsky

Yuri Nikolsky

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Yuri Nikolsky

Publications by authors named "Yuri Nikolsky"

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Analysis of cis-Regulatory Elements in Gene Co-expression Networks in Cancer.

Methods Mol Biol 2017 ;1613:291-310

Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA.

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http://dx.doi.org/10.1007/978-1-4939-7027-8_11DOI Listing
May 2018

Drug Repositioning through Systematic Mining of Gene Coexpression Networks in Cancer.

PLoS One 2016 8;11(11):e0165059. Epub 2016 Nov 8.

A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0165059PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5100910PMC
June 2017

Nucleotide diversity analysis highlights functionally important genomic regions.

Sci Rep 2016 10 24;6:35730. Epub 2016 Oct 24.

International Rice Research Institute, Los Baños, Laguna 4031, Philippines.

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http://dx.doi.org/10.1038/srep35730DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5075931PMC
October 2016

Toward high-resolution population genomics using archaeological samples.

DNA Res 2016 Aug 19;23(4):295-310. Epub 2016 Jul 19.

Bioinformatics Center, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA

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http://dx.doi.org/10.1093/dnares/dsw029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4991838PMC
August 2016

The mysterious orphans of Mycoplasmataceae.

Biol Direct 2016 Jan 8;11(1). Epub 2016 Jan 8.

Department of Evolutionary and Environmental Biology and Institute of Evolution, University of Haifa, Haifa, Israel.

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http://dx.doi.org/10.1186/s13062-015-0104-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4706650PMC
January 2016

JARID1B is a luminal lineage-driving oncogene in breast cancer.

Cancer Cell 2014 Jun;25(6):762-77

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02141, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccr.2014.04.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079039PMC
June 2014

Knowledge-based analysis of proteomics data.

BMC Bioinformatics 2012 5;13 Suppl 16:S13. Epub 2012 Nov 5.

Thomson Reuters, IP & Science, 5901 Priestly Dr., #200, Carlsbad, CA 92008, USA.

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http://dx.doi.org/10.1186/1471-2105-13-S16-S13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3489533PMC
May 2013

Putative multifunctional signature of lung metastases in dedifferentiated chondrosarcoma.

Sarcoma 2012 16;2012:820254. Epub 2012 Feb 16.

Cancer Biology and Epigenomics Program, Children's Memorial Research Center, and Department of Pediatrics, Northwestern University Feinberg School of Medicine, 2430 N. Halstead Street, Chicago, IL 60614, USA.

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http://dx.doi.org/10.1155/2012/820254DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3289931PMC
August 2012

A model of early human embryonic stem cell differentiation reveals inter- and intracellular changes on transition to squamous epithelium.

Stem Cells Dev 2012 May 19;21(8):1250-63. Epub 2011 Oct 19.

Developmental Biology Program, iPS and Human Stem Cell Core Facility, Children's Memorial Research Center, Northwestern University, Feinberg School of Medicine, Chicago, Illinois 60614-3394, USA.

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http://dx.doi.org/10.1089/scd.2010.0578DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3353739PMC
May 2012

Altered antisense-to-sense transcript ratios in breast cancer.

Proc Natl Acad Sci U S A 2012 Feb 22;109(8):2820-4. Epub 2010 Nov 22.

Department of Medical Oncology, and Belfer Institute for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA.

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http://www.pnas.org/content/109/8/2820.full.pdf
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http://www.pnas.org/cgi/doi/10.1073/pnas.1010559107
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http://dx.doi.org/10.1073/pnas.1010559107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3286925PMC
February 2012

Functional synergies yet distinct modulators affected by genetic alterations in common human cancers.

Cancer Res 2011 May 11;71(10):3471-81. Epub 2011 Mar 11.

Thomson Reuters, Healthcare & Life Science, St. Joseph, Michigan 49085, USA.

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http://dx.doi.org/10.1158/0008-5472.CAN-10-3038DOI Listing
May 2011

Quantitative knowledge-based analysis in compound safety assessment.

Expert Opin Drug Metab Toxicol 2011 Mar 22;7(3):287-98. Epub 2011 Jan 22.

Thomson Reuters, 169 Saxony Road, Encinitas, CA 92024, USA.

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http://dx.doi.org/10.1517/17425255.2011.553191DOI Listing
March 2011

Systems biology approaches to the study of cardiovascular drugs.

Methods Mol Biol 2010 ;662:221-43

GeneGo, Inc., St.Joseph, MI, USA.

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http://dx.doi.org/10.1007/978-1-60761-800-3_11DOI Listing
December 2010

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models.

Authors:
Leming Shi Gregory Campbell Wendell D Jones Fabien Campagne Zhining Wen Stephen J Walker Zhenqiang Su Tzu-Ming Chu Federico M Goodsaid Lajos Pusztai John D Shaughnessy André Oberthuer Russell S Thomas Richard S Paules Mark Fielden Bart Barlogie Weijie Chen Pan Du Matthias Fischer Cesare Furlanello Brandon D Gallas Xijin Ge Dalila B Megherbi W Fraser Symmans May D Wang John Zhang Hans Bitter Benedikt Brors Pierre R Bushel Max Bylesjo Minjun Chen Jie Cheng Jing Cheng Jeff Chou Timothy S Davison Mauro Delorenzi Youping Deng Viswanath Devanarayan David J Dix Joaquin Dopazo Kevin C Dorff Fathi Elloumi Jianqing Fan Shicai Fan Xiaohui Fan Hong Fang Nina Gonzaludo Kenneth R Hess Huixiao Hong Jun Huan Rafael A Irizarry Richard Judson Dilafruz Juraeva Samir Lababidi Christophe G Lambert Li Li Yanen Li Zhen Li Simon M Lin Guozhen Liu Edward K Lobenhofer Jun Luo Wen Luo Matthew N McCall Yuri Nikolsky Gene A Pennello Roger G Perkins Reena Philip Vlad Popovici Nathan D Price Feng Qian Andreas Scherer Tieliu Shi Weiwei Shi Jaeyun Sung Danielle Thierry-Mieg Jean Thierry-Mieg Venkata Thodima Johan Trygg Lakshmi Vishnuvajjala Sue Jane Wang Jianping Wu Yichao Wu Qian Xie Waleed A Yousef Liang Zhang Xuegong Zhang Sheng Zhong Yiming Zhou Sheng Zhu Dhivya Arasappan Wenjun Bao Anne Bergstrom Lucas Frank Berthold Richard J Brennan Andreas Buness Jennifer G Catalano Chang Chang Rong Chen Yiyu Cheng Jian Cui Wendy Czika Francesca Demichelis Xutao Deng Damir Dosymbekov Roland Eils Yang Feng Jennifer Fostel Stephanie Fulmer-Smentek James C Fuscoe Laurent Gatto Weigong Ge Darlene R Goldstein Li Guo Donald N Halbert Jing Han Stephen C Harris Christos Hatzis Damir Herman Jianping Huang Roderick V Jensen Rui Jiang Charles D Johnson Giuseppe Jurman Yvonne Kahlert Sadik A Khuder Matthias Kohl Jianying Li Li Li Menglong Li Quan-Zhen Li Shao Li Zhiguang Li Jie Liu Ying Liu Zhichao Liu Lu Meng Manuel Madera Francisco Martinez-Murillo Ignacio Medina Joseph Meehan Kelci Miclaus Richard A Moffitt David Montaner Piali Mukherjee George J Mulligan Padraic Neville Tatiana Nikolskaya Baitang Ning Grier P Page Joel Parker R Mitchell Parry Xuejun Peng Ron L Peterson John H Phan Brian Quanz Yi Ren Samantha Riccadonna Alan H Roter Frank W Samuelson Martin M Schumacher Joseph D Shambaugh Qiang Shi Richard Shippy Shengzhu Si Aaron Smalter Christos Sotiriou Mat Soukup Frank Staedtler Guido Steiner Todd H Stokes Qinglan Sun Pei-Yi Tan Rong Tang Zivana Tezak Brett Thorn Marina Tsyganova Yaron Turpaz Silvia C Vega Roberto Visintainer Juergen von Frese Charles Wang Eric Wang Junwei Wang Wei Wang Frank Westermann James C Willey Matthew Woods Shujian Wu Nianqing Xiao Joshua Xu Lei Xu Lun Yang Xiao Zeng Jialu Zhang Li Zhang Min Zhang Chen Zhao Raj K Puri Uwe Scherf Weida Tong Russell D Wolfinger

Nat Biotechnol 2010 Aug 30;28(8):827-38. Epub 2010 Jul 30.

National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, USA.

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http://dx.doi.org/10.1038/nbt.1665DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3315840PMC
August 2010

Integrated network analysis of transcriptomic and proteomic data in psoriasis.

BMC Syst Biol 2010 Apr 8;4:41. Epub 2010 Apr 8.

Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina St, 3 GSP-1, 119991 Moscow, Russia.

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http://dx.doi.org/10.1186/1752-0509-4-41DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2873316PMC
April 2010

Bimodal gene expression patterns in breast cancer.

BMC Genomics 2010 Feb 10;11 Suppl 1:S8. Epub 2010 Feb 10.

Russian Academy of Sciences, Vavilov Institute for General Genetics, ul. Gubkina, 3, Moscow, Russia.

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http://dx.doi.org/10.1186/1471-2164-11-S1-S8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2822536PMC
February 2010

Use of short-term transcriptional profiles to assess the long-term cancer-related safety of environmental and industrial chemicals.

Toxicol Sci 2009 Dec 23;112(2):311-21. Epub 2009 Sep 23.

The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina 27709, USA.

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http://dx.doi.org/10.1093/toxsci/kfp233DOI Listing
December 2009

MetaMiner (CF): a disease-oriented bioinformatics analysis environment.

Methods Mol Biol 2009 ;563:353-67

Johns Hopkins University, Baltimore, MD, USA.

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http://dx.doi.org/10.1007/978-1-60761-175-2_18DOI Listing
October 2009

Protein networks and pathway analysis. Preface.

Methods Mol Biol 2009 ;563:v-vii

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http://dx.doi.org/10.1007/978-1-60761-175-2DOI Listing
October 2009

Nutrigenomics: concepts and applications to pharmacogenomics and clinical medicine.

Pharmacogenomics 2007 Apr;8(4):369-90

Department of Surgery, University of Illinois Chicago, 909 South Wolcott Street MC 958, Chicago, IL 60612, USA.

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http://dx.doi.org/10.2217/14622416.8.4.369DOI Listing
April 2007

Pathway mapping tools for analysis of high content data.

Methods Mol Biol 2007 ;356:319-50

GeneGo, Jerkintown, PA, USA.

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http://dx.doi.org/10.1385/1-59745-217-3:319DOI Listing
November 2006

The case for strategic international alliances to harness nutritional genomics for public and personal health.

Br J Nutr 2005 Nov;94(5):623-32

Center of Excellence in Nutritional Genomics, University of California, Davis, CA 95616, USA.

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http://repositorio.uchile.cl/bitstream/handle/2250/123828/Ka
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http://dx.doi.org/10.1079/bjn20051585DOI Listing
November 2005

A novel method for generation of signature networks as biomarkers from complex high throughput data.

Toxicol Lett 2005 Jul;158(1):20-9

Computational Biology Genego Inc., 500 Renaissance Drive, Suite 106, St. Joseph, MI 49085, USA.

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http://dx.doi.org/10.1016/j.toxlet.2005.02.004DOI Listing
July 2005

Biological networks and analysis of experimental data in drug discovery.

Drug Discov Today 2005 May;10(9):653-62

GeneGo, 500 Renaissance Drive, #106, St. Joseph, MI 49085, USA.

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http://dx.doi.org/10.1016/S1359-6446(05)03420-3DOI Listing
May 2005

Techniques: application of systems biology to absorption, distribution, metabolism, excretion and toxicity.

Trends Pharmacol Sci 2005 Apr;26(4):202-9

GeneGo, 500 Renaissance Drive, Suite 106, St Joseph, MI 49085, USA.

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http://dx.doi.org/10.1016/j.tips.2005.02.006DOI Listing
April 2005

Kohonen maps for prediction of binding to human cytochrome P450 3A4.

Drug Metab Dispos 2004 Oct 1;32(10):1183-9. Epub 2004 Jul 1.

Chemical Diversity Labs, Inc., San Diego, CA, USA.

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http://dx.doi.org/10.1124/dmd.104.000356DOI Listing
October 2004

Early prediction of drug metabolism and toxicity: systems biology approach and modeling.

Drug Discov Today 2004 Feb;9(3):127-35

GeneGo, 500 Renaissance Drive, Suite 106, St Joseph, MI 49085, USA.

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http://dx.doi.org/10.1016/S1359-6446(03)02971-4DOI Listing
February 2004

In silico estimation of DMSO solubility of organic compounds for bioscreening.

J Biomol Screen 2004 Feb;9(1):22-31

Chemical Diversity Labs, Inc., San Diego, CA 92121, USA.

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http://dx.doi.org/10.1177/1087057103260006DOI Listing
February 2004