Melissa S Cline

Melissa S Cline

UNVERIFIED PROFILE

Are you Melissa S Cline?   Register this Author

Register author
Melissa S Cline

Melissa S Cline

Publications by authors named "Melissa S Cline"

Are you Melissa S Cline?   Register this Author

31Publications

923Reads

14Profile Views

Human genetics special issue on computational molecular medicine.

Hum Genet 2015 May;134(5):455-7

Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, USA,

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00439-015-1545-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405483PMC
May 2015

The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data.

Database (Oxford) 2014 29;2014. Epub 2014 Sep 29.

Biomolecular Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA, USA, Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Annai Systems Inc., 2100 Palomar Airport Road, Suite 210 Carlsbad, California 92011, USA, Cardinal Peak, LLC, 1380 Forest Park Circle, Suite 202 Lafayette, CO 80026, USA and Information Technology Services, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA.

View Article

Download full-text PDF

Source
https://academic.oup.com/database/article-lookup/doi/10.1093
Publisher Site
http://dx.doi.org/10.1093/database/bau093DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4178372PMC
February 2015

A comparative encyclopedia of DNA elements in the mouse genome.

Authors:
Feng Yue Yong Cheng Alessandra Breschi Jeff Vierstra Weisheng Wu Tyrone Ryba Richard Sandstrom Zhihai Ma Carrie Davis Benjamin D Pope Yin Shen Dmitri D Pervouchine Sarah Djebali Robert E Thurman Rajinder Kaul Eric Rynes Anthony Kirilusha Georgi K Marinov Brian A Williams Diane Trout Henry Amrhein Katherine Fisher-Aylor Igor Antoshechkin Gilberto DeSalvo Lei-Hoon See Meagan Fastuca Jorg Drenkow Chris Zaleski Alex Dobin Pablo Prieto Julien Lagarde Giovanni Bussotti Andrea Tanzer Olgert Denas Kanwei Li M A Bender Miaohua Zhang Rachel Byron Mark T Groudine David McCleary Long Pham Zhen Ye Samantha Kuan Lee Edsall Yi-Chieh Wu Matthew D Rasmussen Mukul S Bansal Manolis Kellis Cheryl A Keller Christapher S Morrissey Tejaswini Mishra Deepti Jain Nergiz Dogan Robert S Harris Philip Cayting Trupti Kawli Alan P Boyle Ghia Euskirchen Anshul Kundaje Shin Lin Yiing Lin Camden Jansen Venkat S Malladi Melissa S Cline Drew T Erickson Vanessa M Kirkup Katrina Learned Cricket A Sloan Kate R Rosenbloom Beatriz Lacerda de Sousa Kathryn Beal Miguel Pignatelli Paul Flicek Jin Lian Tamer Kahveci Dongwon Lee W James Kent Miguel Ramalho Santos Javier Herrero Cedric Notredame Audra Johnson Shinny Vong Kristen Lee Daniel Bates Fidencio Neri Morgan Diegel Theresa Canfield Peter J Sabo Matthew S Wilken Thomas A Reh Erika Giste Anthony Shafer Tanya Kutyavin Eric Haugen Douglas Dunn Alex P Reynolds Shane Neph Richard Humbert R Scott Hansen Marella De Bruijn Licia Selleri Alexander Rudensky Steven Josefowicz Robert Samstein Evan E Eichler Stuart H Orkin Dana Levasseur Thalia Papayannopoulou Kai-Hsin Chang Arthur Skoultchi Srikanta Gosh Christine Disteche Piper Treuting Yanli Wang Mitchell J Weiss Gerd A Blobel Xiaoyi Cao Sheng Zhong Ting Wang Peter J Good Rebecca F Lowdon Leslie B Adams Xiao-Qiao Zhou Michael J Pazin Elise A Feingold Barbara Wold James Taylor Ali Mortazavi Sherman M Weissman John A Stamatoyannopoulos Michael P Snyder Roderic Guigo Thomas R Gingeras David M Gilbert Ross C Hardison Michael A Beer Bing Ren

Nature 2014 Nov;515(7527):355-64

Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature13992DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4266106PMC
November 2014

The UCSC Genome Browser database: 2014 update.

Nucleic Acids Res 2014 Jan 21;42(Database issue):D764-70. Epub 2013 Nov 21.

Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkt1168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964947PMC
January 2014

Exploring TCGA Pan-Cancer data at the UCSC Cancer Genomics Browser.

Sci Rep 2013 Oct 2;3:2652. Epub 2013 Oct 2.

Center for Biomolecular Science and Engineering, University of California, Santa Cruz.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/srep02652DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3788369PMC
October 2013

Quaking and PTB control overlapping splicing regulatory networks during muscle cell differentiation.

RNA 2013 May 22;19(5):627-38. Epub 2013 Mar 22.

RNA Center, Department of Molecular, Cell, and Developmental Biology, Sinsheimer Labs, University of California, Santa Cruz, California 95064, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1261/rna.038422.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3677278PMC
May 2013

An encyclopedia of mouse DNA elements (Mouse ENCODE).

August 2012

Using bioinformatics to predict the functional impact of SNVs.

Bioinformatics 2011 Feb 15;27(4):441-8. Epub 2010 Dec 15.

Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA.

View Article

Download full-text PDF

Source
http://bioinformatics.oxfordjournals.org/content/early/2010/
Web Search
http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/btq695DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105482PMC
February 2011

ENCODE whole-genome data in the UCSC genome browser (2011 update).

Nucleic Acids Res 2011 Jan 30;39(Database issue):D871-5. Epub 2010 Oct 30.

Center for Biomolecular Science and Engineering, School of Engineering and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkq1017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013645PMC
January 2011

Aberrant alternative splicing and extracellular matrix gene expression in mouse models of myotonic dystrophy.

Nat Struct Mol Biol 2010 Feb 24;17(2):187-93. Epub 2010 Jan 24.

RNA Center, Department of Molecular, Cell and Developmental Biology, Sinsheimer Labs, University of California, Santa Cruz, California, USA.

View Article

Download full-text PDF

Source
http://www.nature.com/articles/nsmb.1720
Publisher Site
http://dx.doi.org/10.1038/nsmb.1720DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2852634PMC
February 2010

Affy exon tissues: exon levels in normal tissues in human, mouse and rat.

Bioinformatics 2009 Sep 1;25(18):2442-3. Epub 2009 Jul 1.

Center for Biomolecular Science & Engineering, University of California, Santa Cruz, CA 95064, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btp414DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2735668PMC
September 2009

Understanding genome browsing.

Nat Biotechnol 2009 Feb;27(2):153-5

Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nbt0209-153DOI Listing
February 2009

Integrating expression data with domain interaction networks.

Bioinformatics 2008 Nov 18;24(21):2546-8. Epub 2008 Aug 18.

Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1.4, 66123 Saarbrücken, Germany.

View Article

Download full-text PDF

Source
https://academic.oup.com/bioinformatics/article-lookup/doi/1
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/btn437DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2572699PMC
November 2008

Exploring biological networks with Cytoscape software.

Curr Protoc Bioinformatics 2008 Sep;Chapter 8:Unit 8.13

University of Toronto, Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, Canada.

View Article

Download full-text PDF

Source
http://doi.wiley.com/10.1002/0471250953.bi0813s23
Publisher Site
http://dx.doi.org/10.1002/0471250953.bi0813s23DOI Listing
September 2008

Integrative visual analysis of the effects of alternative splicing on protein domain interaction networks.

J Integr Bioinform 2008 Aug 25;5(2). Epub 2008 Aug 25.

Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1.4, 66123 Saarbrücken, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.2390/biecoll-jib-2008-101DOI Listing
August 2008

Unusual intron conservation near tissue-regulated exons found by splicing microarrays.

PLoS Comput Biol 2006 Jan 20;2(1):e4. Epub 2006 Jan 20.

Department of Computer Science, Baskin School of Engineering, University of California Santa Cruz, Santa Cruz, California, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.0020004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1331982PMC
January 2006

ANOSVA: a statistical method for detecting splice variation from expression data.

Bioinformatics 2005 Jun;21 Suppl 1:i107-15

Affymetrix, Inc. 3380 Central Expressway, Santa Clara, CA 95051, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/bti1010DOI Listing
June 2005

Protein-based analysis of alternative splicing in the human genome.

Proc IEEE Comput Soc Bioinform Conf 2002 ;1:118-24

Affymetrix, Inc., Emeryville, CA 94608, USA.

View Article

Download full-text PDF

Source
May 2005

NetAffx Gene Ontology Mining Tool: a visual approach for microarray data analysis.

Bioinformatics 2004 Jun 12;20(9):1462-3. Epub 2004 Feb 12.

Affymetrix Corporation, Bioinformatics, 6550 Vallejo Street, Suite 100, Emeryville, CA 94608, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/bth087DOI Listing
June 2004

Exploring alternative transcript structure in the human genome using blocks and InterPro.

J Bioinform Comput Biol 2003 Jul;1(2):289-306

Bioinformatics Department, Affymetrix, 6550 Vallejo St, Emeryville, CA 94530 USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1142/s0219720003000113DOI Listing
July 2003

Information-theoretic dissection of pairwise contact potentials.

Proteins 2002 Oct;49(1):7-14

Center for Biomolecular Science and Engineering, Baskin School of Engineering, University of California, Santa Cruz, California 95064, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/prot.10198DOI Listing
October 2002