Simon M Lin

Simon M Lin

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The Financial Impact of Genetic Diseases in a Pediatric Accountable Care Organization.

Front Public Health 2020 28;8:58. Epub 2020 Feb 28.

Research Information Solutions and Innovation, The Research Institute at Nationwide Children's Hospital, Columbus, OH, United States.

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http://dx.doi.org/10.3389/fpubh.2020.00058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7059305PMC
February 2020

A deep learning model for pediatric patient risk stratification.

Am J Manag Care 2019 10 1;25(10):e310-e315. Epub 2019 Oct 1.

Nationwide Children's Hospital, 575 Children's Crossroad, Columbus, OH 43215. Email:

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October 2019

Addressing a patient-controlled approach for genomic data sharing.

Genet Med 2017 11 20;19(11):1280-1281. Epub 2017 Apr 20.

Research Information Solutions and Innovation, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.

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http://dx.doi.org/10.1038/gim.2017.36DOI Listing
November 2017

'RE:fine drugs': an interactive dashboard to access drug repurposing opportunities.

Database (Oxford) 2016 17;2016. Epub 2016 May 17.

Research Information Solutions and Innovation, The Research Institute at Nationwide Children's Hospital Columbus, OH 43205, USA

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http://dx.doi.org/10.1093/database/baw083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4869799PMC
January 2017

Patient-centered design criteria for wearable seizure detection devices.

Epilepsy Behav 2016 11 12;64(Pt A):116-121. Epub 2016 Oct 12.

Nationwide Children's Hospital Research Institute, 700 Children's Drive, Columbus, OH 43205, United States.

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http://dx.doi.org/10.1016/j.yebeh.2016.09.012DOI Listing
November 2016

A Review on Genomics APIs.

Comput Struct Biotechnol J 2016 31;14:8-15. Epub 2015 Oct 31.

Research Information Solutions and Innovation, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.

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http://dx.doi.org/10.1016/j.csbj.2015.10.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4669666PMC
December 2015

SeqHBase: a big data toolset for family based sequencing data analysis.

J Med Genet 2015 Apr 13;52(4):282-8. Epub 2015 Jan 13.

Utah Foundation for Biomedical Research, Provo, Utah, USA Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California, USA Department of Psychiatry, University of Southern California, Los Angeles, California, USA.

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http://dx.doi.org/10.1136/jmedgenet-2014-102907DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4382803PMC
April 2015

Opportunities for drug repositioning from phenome-wide association studies.

Nat Biotechnol 2015 Apr;33(4):342-5

1] Biomedical Informatics Research Center, Marshfield Clinic Research Foundation, Marshfield, Wisconsin, USA. [2] Biomedical Statistics and Bioinformatics, Mayo Clinic, Rochester, Minnesota, USA and Nationwide Children's Hospital, Columbus, Ohio, USA.

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http://dx.doi.org/10.1038/nbt.3183DOI Listing
April 2015

Computational evidence of NAGNAG alternative splicing in human large intergenic noncoding RNA.

Biomed Res Int 2014 5;2014:736798. Epub 2014 Jun 5.

Affiliated Hospital of Shandong University of Traditional Chinese Medicine, No. 42 Wenhua West Road, Jinan, Shandong 250011, China.

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http://www.hindawi.com/journals/bmri/2014/736798/
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http://dx.doi.org/10.1155/2014/736798DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4068082PMC
February 2015

A google glass application to support shoppers with dietary management of diabetes.

J Diabetes Sci Technol 2014 Nov 11;8(6):1245-6. Epub 2014 Jul 11.

Biomedical Informatics Research Center, Marshfield Clinic Research Foundation, Marshfield, WI, USA

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http://journals.sagepub.com/doi/10.1177/1932296814543288
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http://dx.doi.org/10.1177/1932296814543288DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4455467PMC
November 2014

Some experiences and opportunities for big data in translational research.

Genet Med 2013 Oct 5;15(10):802-9. Epub 2013 Sep 5.

Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA.

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http://dx.doi.org/10.1038/gim.2013.121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3906918PMC
October 2013

A framework for annotating human genome in disease context.

PLoS One 2012 10;7(12):e49686. Epub 2012 Dec 10.

The Department of Electronics and Information Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0049686PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3519466PMC
June 2013

A statistical framework for accurate taxonomic assignment of metagenomic sequencing reads.

PLoS One 2012 1;7(10):e46450. Epub 2012 Oct 1.

Department of Statistics, Northwestern University, Evanston, Illinois, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0046450PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3462201PMC
February 2013

The Disease and Gene Annotations (DGA): an annotation resource for human disease.

Nucleic Acids Res 2013 Jan 28;41(Database issue):D553-60. Epub 2012 Nov 28.

The Department of Electronics and Information Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.

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http://dx.doi.org/10.1093/nar/gks1244DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531051PMC
January 2013

Opportunities in systems biology to discover mechanisms and repurpose drugs for CNS diseases.

Drug Discov Today 2012 Nov 30;17(21-22):1208-16. Epub 2012 Jun 30.

Informatics and Structure Biology, R&D China, GlaxoSmithKline, Shanghai, China.

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http://dx.doi.org/10.1016/j.drudis.2012.06.015DOI Listing
November 2012

Genome-wide DNA methylation indicates silencing of tumor suppressor genes in uterine leiomyoma.

PLoS One 2012 13;7(3):e33284. Epub 2012 Mar 13.

Division of Reproductive Biology Research, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0033284PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3302826PMC
August 2012

Using the bioconductor GeneAnswers package to interpret gene lists.

Methods Mol Biol 2012 ;802:101-12

Biomedical Informatics Center, Clinical and Translational Sciences Institute, Northwestern University, Chicago, IL, USA.

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http://dx.doi.org/10.1007/978-1-61779-400-1_7DOI Listing
April 2012

Mining the Gene Wiki for functional genomic knowledge.

BMC Genomics 2011 Dec 13;12:603. Epub 2011 Dec 13.

Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1186/1471-2164-12-603DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3271090PMC
December 2011

PLoS Computational Biology Conference Postcards from ISMB/ECCB 2011.

PLoS Comput Biol 2011 Nov 17;7(11):e1002259. Epub 2011 Nov 17.

Institute of Plant Genetics, Polish Academy of Science, Poznań, Poland.

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http://dx.doi.org/10.1371/journal.pcbi.1002259DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3219612PMC
November 2011

Characterising phase variations in MALDI-TOF data and correcting them by peak alignment.

Cancer Inform 2005 ;1:32-40

Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2657651PMC
July 2011

Epithelial regulation of mesenchymal tissue behavior.

J Invest Dermatol 2011 Apr 13;131(4):892-9. Epub 2011 Jan 13.

Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA.

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http://dx.doi.org/10.1038/jid.2010.420DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3137131PMC
April 2011

Visual presentation as a welcome alternative to textual presentation of gene annotation information.

Adv Exp Med Biol 2010 ;680:709-15

The Biomedical Informatics Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.

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http://dx.doi.org/10.1007/978-1-4419-5913-3_79DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3039430PMC
February 2011

Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis.

BMC Bioinformatics 2010 Nov 30;11:587. Epub 2010 Nov 30.

Northwestern University Biomedical Informatics Center (NUBIC), NUCATS, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.

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http://dx.doi.org/10.1186/1471-2105-11-587DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3012676PMC
November 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

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data.

BMC Bioinformatics 2010 May 11;11:237. Epub 2010 May 11.

Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-11-237DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3098059PMC
May 2010

2009 and beyond: the decade of personalised medicine.

Int J Comput Biol Drug Des 2008 ;1(4):329-33

The Biomedical Informatics Center, Northwestern University, Chicago, IL 60611, USA.

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http://dx.doi.org/10.1504/ijcbdd.2008.022205DOI Listing
March 2010

A divide-and-conquer strategy to solve the out-of-memory problem of processing thousands of Affymetrix microarrays.

Int J Comput Biol Drug Des 2008 ;1(4):396-405

Computational Biology and Bioinformatics Program, Northwestemrn University, Evanston, IL 60208, USA.

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http://dx.doi.org/10.1504/ijcbdd.2008.022209DOI Listing
March 2010

A collection of bioconductor methods to visualize gene-list annotations.

BMC Res Notes 2010 Jan 19;3:10. Epub 2010 Jan 19.

Northwestern University Biomedical Informatics Center (NUBIC, part of the Northwestern CTSA) and The Robert H, Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA.

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http://dx.doi.org/10.1186/1756-0500-3-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2829581PMC
January 2010

BALB/c mice genetically susceptible to proteoglycan-induced arthritis and spondylitis show colony-dependent differences in disease penetrance.

Arthritis Res Ther 2009 16;11(1):R21. Epub 2009 Feb 16.

Section of Molecular Medicine, Department of Orthopedic Surgery, Rush University Medical Center, 1735 W, Harrison Street, Cohn Research Building, Chicago, IL 60612, USA.

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http://dx.doi.org/10.1186/ar2613DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688253PMC
September 2009

Annotating the human genome with Disease Ontology.

BMC Genomics 2009 Jul 7;10 Suppl 1:S6. Epub 2009 Jul 7.

Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.

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http://dx.doi.org/10.1186/1471-2164-10-S1-S6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2709267PMC
July 2009

Susceptibility to glaucoma: differential comparison of the astrocyte transcriptome from glaucomatous African American and Caucasian American donors.

Genome Biol 2008 9;9(7):R111. Epub 2008 Jul 9.

Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, E Chicago Ave, Chicago, IL 60611, USA.

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http://dx.doi.org/10.1186/gb-2008-9-7-r111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2530868PMC
October 2008

lumi: a pipeline for processing Illumina microarray.

Bioinformatics 2008 Jul 8;24(13):1547-8. Epub 2008 May 8.

Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn224DOI Listing
July 2008

Model-based variance-stabilizing transformation for Illumina microarray data.

Nucleic Acids Res 2008 Feb 4;36(2):e11. Epub 2008 Jan 4.

Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, 60611, USA.

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http://dx.doi.org/10.1093/nar/gkm1075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2241869PMC
February 2008

Interpreting microarray results with gene ontology and MeSH.

Methods Mol Biol 2007 ;377:223-42

Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.

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http://dx.doi.org/10.1007/978-1-59745-390-5_14DOI Listing
August 2007

nuID: a universal naming scheme of oligonucleotides for illumina, affymetrix, and other microarrays.

Biol Direct 2007 May 31;2:16. Epub 2007 May 31.

Robert H, Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA.

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http://dx.doi.org/10.1186/1745-6150-2-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891274PMC
May 2007

Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching.

Bioinformatics 2006 Sep 4;22(17):2059-65. Epub 2006 Jul 4.

Robert H. Lurie Comprehensive Cancer Center, Northwestern University Chicago, IL 60611, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl355DOI Listing
September 2006

Improved prediction of treatment response using microarrays and existing biological knowledge.

Pharmacogenomics 2006 Apr;7(3):495-501

Northwestern University, Robert H Lurie Cancer Center, Chicago, IL 60611, USA.

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http://dx.doi.org/10.2217/14622416.7.3.495DOI Listing
April 2006

Gene expression profiles of the rat brain both immediately and 3 months following acute sarin exposure.

Biochem Pharmacol 2006 Feb 27;71(4):497-520. Epub 2005 Dec 27.

Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA.

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http://dx.doi.org/10.1016/j.bcp.2005.10.051DOI Listing
February 2006

What is mzXML good for?

Expert Rev Proteomics 2005 Dec;2(6):839-45

Northwestern University, Robert H Lurie Cancer Center, Chicago, IL 60611, USA.

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http://www.tandfonline.com/doi/full/10.1586/14789450.2.6.839
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http://dx.doi.org/10.1586/14789450.2.6.839DOI Listing
December 2005

Irrational exuberance in clinical proteomics.

Clin Cancer Res 2005 Nov;11(22):7963-4

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http://dx.doi.org/10.1158/1078-0432.CCR-05-1744DOI Listing
November 2005

Heterogeneity of Flt3-expressing multipotent progenitors in mouse bone marrow.

J Immunol 2005 Oct;175(8):5016-23

Department of Immunology, Duke University Medical Center, Durham, NC 27710, USA.

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http://dx.doi.org/10.4049/jimmunol.175.8.5016DOI Listing
October 2005

Loss of patched and disruption of granule cell development in a pre-neoplastic stage of medulloblastoma.

Development 2005 May 20;132(10):2425-39. Epub 2005 Apr 20.

Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA.

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http://dev.biologists.org/cgi/doi/10.1242/dev.01793
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http://dx.doi.org/10.1242/dev.01793DOI Listing
May 2005

MedlineR: an open source library in R for Medline literature data mining.

Bioinformatics 2004 Dec 29;20(18):3659-61. Epub 2004 Jul 29.

Duke Comprehensive Cancer Center, Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA.

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http://dx.doi.org/10.1093/bioinformatics/bth404DOI Listing
December 2004

RNA-binding proteins to assess gene expression states of co-cultivated cells in response to tumor cells.

Mol Cancer 2004 Sep 7;3:24. Epub 2004 Sep 7.

Department of Molecular Genetics and Microbiology, Center for RNA biology, 414 Jones Building, Research Drive, Duke University Medical Center, Durham, North Carolina 27710, USA.

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http://dx.doi.org/10.1186/1476-4598-3-24DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC521085PMC
September 2004

Transcriptional profiling of the Sonic hedgehog response: a critical role for N-myc in proliferation of neuronal precursors.

Proc Natl Acad Sci U S A 2003 Jun 30;100(12):7331-6. Epub 2003 May 30.

Department of Pharmacology and Cancer Biology and Bioinformatics Shared Resource, Duke University Medical Center, Durham, NC 27710, USA.

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http://dx.doi.org/10.1073/pnas.0832317100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC165875PMC
June 2003

Microarray analysis: a comparative approach.

Mol Cancer Ther 2002 Jan;1(3):237-8

Duke Bioinformatics Shared Resource, Box 3958, Duke University Medical Center, Durham, NC 27710, USA.

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January 2002