Alexander R Pico

Alexander R Pico

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Alexander R Pico

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Identifier Mapping in Cytoscape.

F1000Res 2018 11;7:725. Epub 2018 Jun 11.

Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, 94158, USA.

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http://dx.doi.org/10.12688/f1000research.14807.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6053696.2PMC
September 2019

Cytoscape Automation: empowering workflow-based network analysis.

Genome Biol 2019 09 2;20(1):185. Epub 2019 Sep 2.

Department of Medicine, University of California, La Jolla, San Diego, CA, 92093, USA.

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http://dx.doi.org/10.1186/s13059-019-1758-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6717989PMC
September 2019

Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data.

F1000Res 2019 15;8. Epub 2019 Mar 15.

Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94143, USA.

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http://dx.doi.org/10.12688/f1000research.18490.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6720041PMC
March 2019

Proteins Altered by Surgical Weight Loss Highlight Biomarkers of Insulin Resistance in the Community.

Arterioscler Thromb Vasc Biol 2019 Jan;39(1):107-115

Population Sciences Branch of the National Heart, Lung, and Blood Institute of the National Institutes of Health, Bethesda, MD (S.-J.H., C.Y., D.L.).

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http://dx.doi.org/10.1161/ATVBAHA.118.311928DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6309981PMC
January 2019

MicroRNAs Associated With Reverse Left Ventricular Remodeling in Humans Identify Pathways of Heart Failure Progression.

Circ Heart Fail 2018 02;11(2):e004278

From the Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston (R.S., O.Z., A.Y., X.L., D.R., C.Y.X., A.B., A.R., J.L.J., S.D.); University of Michigan at Ann Arbor (V.M.); Gladstone Institutes, University of California at San Francisco (K.H., A.R.P.); and Abcam Therapeutics, Cambridge, MA (M.T.).

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http://dx.doi.org/10.1161/CIRCHEARTFAILURE.117.004278DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813824PMC
February 2018

Translational Epidemiology: Entering a Brave New World of Team Science.

Circ Res 2016 10;119(10):1060-1062

From the Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston (R.S.); Department of Bioinformatics, Gladstone Institutes, University of California, San Francisco (A.R.P.); and Department of Medicine, University of Massachusetts, Worcester (J.E.F.).

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http://dx.doi.org/10.1161/CIRCRESAHA.116.309881DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5123762PMC
October 2016

Reactome from a WikiPathways Perspective.

PLoS Comput Biol 2016 05 20;12(5):e1004941. Epub 2016 May 20.

Department of Bioinformatics-BiGCaT, Maastricht University, Maastricht, The Netherlands.

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http://dx.doi.org/10.1371/journal.pcbi.1004941DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4874630PMC
May 2016

CyAnimator: Simple Animations of Cytoscape Networks.

F1000Res 2015 5;4:482. Epub 2015 Aug 5.

Resource for Biocomputing, Visualization and Informatics, University of California, San Francisco, CA, USA.

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https://f1000research.com/articles/4-482/v2
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4752027PMC
http://dx.doi.org/10.12688/f1000research.6852.2DOI Listing
March 2016

WikiPathways: capturing the full diversity of pathway knowledge.

Nucleic Acids Res 2016 Jan 19;44(D1):D488-94. Epub 2015 Oct 19.

Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6229 ER Maastricht, The Netherlands

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http://dx.doi.org/10.1093/nar/gkv1024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702772PMC
January 2016

From scientific discovery to cures: bright stars within a galaxy.

Cell 2015 Sep;163(1):21-3

Gladstone Institutes, San Francisco, CA 94158, USA; University of California, San Francisco, San Francisco, CA 94143, USA.

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http://dx.doi.org/10.1016/j.cell.2015.09.007DOI Listing
September 2015

setsApp for Cytoscape: Set operations for Cytoscape Nodes and Edges.

F1000Res 2014 1;3:149. Epub 2014 Jul 1.

Resource for Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA 94143, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4207244PMC
http://dx.doi.org/10.12688/f1000research.4392.2DOI Listing
August 2015

Glioma Groups Based on 1p/19q, IDH, and TERT Promoter Mutations in Tumors.

N Engl J Med 2015 Jun 10;372(26):2499-508. Epub 2015 Jun 10.

From the Departments of Health Sciences Research (J.E.E.-P., P.A.D., H.S., M.L.K.), Laboratory Medicine and Pathology (D.H.L., G.S., A.A.C., T.M.K., C.E.P., A.R.C., C.H., C.G., R.B.J.), Neurology (D.H.L., B.P.O.), and Oncology (J.C.B.), Mayo Clinic, Rochester, MN; the Departments of Neurological Surgery (A.M.M., K.M.W., T.R., I.V.S., H.M.H., L.S.M., S.Z., A.P., M.S.B., S.M.C., M.D.P., J.K.W., M.R.W.), Epidemiology and Biostatistics (A.M.M., P.M.B., J.W., J.K.W., M.R.W.) and Pathology (M.P., R.M., G.F.R., A.P., T.T.) and the Institute of Human Genetics (J.W., J.K.W., M.R.W.), University of California, San Francisco, and the Bioinformatics Core, Gladstone Institutes (A.R.P.) - all in San Francisco; and the Department of Pathology and Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York (J.T.H.).

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http://www.nejm.org/doi/10.1056/NEJMoa1407279
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http://dx.doi.org/10.1056/NEJMoa1407279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489704PMC
June 2015

PathVisio 3: an extendable pathway analysis toolbox.

PLoS Comput Biol 2015 Feb 23;11(2):e1004085. Epub 2015 Feb 23.

Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, The Netherlands.

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http://dx.doi.org/10.1371/journal.pcbi.1004085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4338111PMC
February 2015

NOA: a cytoscape plugin for network ontology analysis.

Bioinformatics 2013 Aug 7;29(16):2066-7. Epub 2013 Jun 7.

Department of Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt334DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3722524PMC
August 2013

Cytoscape app store.

Bioinformatics 2013 May 16;29(10):1350-1. Epub 2013 Apr 16.

Gladstone Institutes, San Francisco, CA 94158, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3654709PMC
May 2013

GO-Elite: a flexible solution for pathway and ontology over-representation.

Bioinformatics 2012 Aug 27;28(16):2209-10. Epub 2012 Jun 27.

Departments of Pharmacology and Medicine, University of California at San Diego, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts366DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413395PMC
August 2012

Mosaic: making biological sense of complex networks.

Bioinformatics 2012 Jul 9;28(14):1943-4. Epub 2012 May 9.

Department of Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts278DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3389769PMC
July 2012

WikiPathways: building research communities on biological pathways.

Nucleic Acids Res 2012 Jan 16;40(Database issue):D1301-7. Epub 2011 Nov 16.

Department of Bioinformatics-BiGCaT, Maastricht University, Maastricht, The Netherlands.

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http://dx.doi.org/10.1093/nar/gkr1074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245032PMC
January 2012

Finding the right questions: exploratory pathway analysis to enhance biological discovery in large datasets.

PLoS Biol 2010 Aug 31;8(8). Epub 2010 Aug 31.

Department of Bioinformatics, BiGCaT, Maastricht University, Maastricht, The Netherlands.

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http://dx.doi.org/10.1371/journal.pbio.1000472DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2930872PMC
August 2010

Structure of the human BK channel Ca2+-activation apparatus at 3.0 A resolution.

Science 2010 Jul 27;329(5988):182-6. Epub 2010 May 27.

Laboratory of Molecular Neurobiology and Biophysics, Rockefeller University, Howard Hughes Medical Institute, 1230 York Avenue, New York, NY 10065, USA.

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http://dx.doi.org/10.1126/science.1190414DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3022345PMC
July 2010

Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursors.

PLoS Comput Biol 2009 Nov 6;5(11):e1000553. Epub 2009 Nov 6.

Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1000553DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2764345PMC
November 2009

Mining biological pathways using WikiPathways web services.

PLoS One 2009 Jul 30;4(7):e6447. Epub 2009 Jul 30.

Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0006447PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2714472PMC
July 2009

SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system.

Nucleic Acids Res 2009 Jan 4;37(Database issue):D803-9. Epub 2008 Nov 4.

Gladstone Institute of Cardiovascular Disease, 1650 Owens Street, San Francisco, CA 94158, USA.

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http://dx.doi.org/10.1093/nar/gkn756DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686434PMC
January 2009

Presenting and exploring biological pathways with PathVisio.

BMC Bioinformatics 2008 Sep 25;9:399. Epub 2008 Sep 25.

Department of Bioinformatics, BiGCaT Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, the Netherlands.

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http://dx.doi.org/10.1186/1471-2105-9-399DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2569944PMC
September 2008

Pathway analysis of single-nucleotide polymorphisms potentially associated with glioblastoma multiforme susceptibility using random forests.

Cancer Epidemiol Biomarkers Prev 2008 Jun;17(6):1368-73

Department of Epidemiology and Biostatistics, University of California, San Francisco, 44 Page Street, Suite 503, San Francisco, CA 94143-1215, USA.

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http://dx.doi.org/10.1158/1055-9965.EPI-07-2830DOI Listing
June 2008