Gary B Fogel

Gary B Fogel

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Gary B Fogel

Gary B Fogel

Publications by authors named "Gary B Fogel"

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Emerging Patterns in HIV-1 gp120 Variable Domains in Anatomical Tissues in the Absence of a Plasma Viral Load.

AIDS Res Hum Retroviruses 2019 Jun 10;35(6):588-596. Epub 2019 Apr 10.

6 Departments of Laboratory Medicine, Pathology and Medicine, The University of California at San Francisco, San Francisco, California.

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http://dx.doi.org/10.1089/AID.2018.0267DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6588100PMC
June 2019

Structure-based analysis of Bacilli and plasmid dihydrofolate reductase evolution.

J Mol Graph Model 2017 01 22;71:135-153. Epub 2016 Nov 22.

Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA; Department of Chemistry, Southwestern College, 900 Otay Lakes Rd., Chula Vista, CA 91910, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jmgm.2016.10.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5203806PMC
January 2017

HIV DNA Is Frequently Present within Pathologic Tissues Evaluated at Autopsy from Combined Antiretroviral Therapy-Treated Patients with Undetectable Viral Loads.

J Virol 2016 10 29;90(20):8968-83. Epub 2016 Sep 29.

National Neurological AIDS Bank, Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA David Geffen School of Medicine and Olive View-UCLA Medical Center, Department of Neurology, Los Angeles, California, USA.

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http://jvi.asm.org/content/90/20/8968.full.pdf
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http://dx.doi.org/10.1128/JVI.00674-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5044815PMC
October 2016

HIV-1 Evolutionary Patterns Associated with Metastatic Kaposi's Sarcoma during AIDS.

Sarcoma 2016 29;2016:4510483. Epub 2016 Aug 29.

The AIDS and Cancer Specimen Resource, University of California at San Francisco and the Department of Laboratory Medicine, Pathology, and Medicine, University of California at San Francisco, 1001 Poterero Ave, Bldg 3, Rm 207, UCSF Box 1317, San Francisco, CA 94110, USA.

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http://dx.doi.org/10.1155/2016/4510483DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5019946PMC
September 2016

On the Physicochemical and Structural Modifications Associated with HIV-1 Subtype B Tropism Transition.

AIDS Res Hum Retroviruses 2016 08 1;32(8):829-40. Epub 2016 Jun 1.

4 Department of Laboratory Medicine, Pathology, and Medicine, and the AIDS and Cancer Specimen Resource, University of California , San Francisco, California.

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http://dx.doi.org/10.1089/AID.2015.0373DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4971420PMC
August 2016

2015 Information Processing in Cells and Tissues (IPCAT 2015).

Biosystems 2016 Aug;146:1-2

Intelligent Systems Group, University of York, York YO10 5DD, England, UK.

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http://dx.doi.org/10.1016/j.biosystems.2016.07.001DOI Listing
August 2016

MicroRNA dynamics during human embryonic stem cell differentiation to pancreatic endoderm.

Gene 2015 Dec 20;574(2):359-70. Epub 2015 Aug 20.

Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA 92121 USA. Electronic address:

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http://dx.doi.org/10.1016/j.gene.2015.08.027DOI Listing
December 2015

Identification of dual-tropic HIV-1 using evolved neural networks.

Biosystems 2015 Nov 28;137:12-9. Epub 2015 Sep 28.

University of California at San Francisco, Department of Laboratory Medicine and The AIDS and Cancer Specimen Resource, San Francisco, CA 94143, United States.

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http://dx.doi.org/10.1016/j.biosystems.2015.09.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4921197PMC
November 2015

Tracking the Emergence of Host-Specific Simian Immunodeficiency Virus env and nef Populations Reveals nef Early Adaptation and Convergent Evolution in Brain of Naturally Progressing Rhesus Macaques.

J Virol 2015 Aug 3;89(16):8484-96. Epub 2015 Jun 3.

Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida, USA Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA

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http://dx.doi.org/10.1128/JVI.01010-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4524235PMC
August 2015

sRNA-seq analysis of human embryonic stem cells and definitive endoderm reveals differentially expressed microRNAs and novel IsomiRs with distinct targets.

Stem Cells 2014 Sep;32(9):2360-72

Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, California, USA.

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http://dx.doi.org/10.1002/stem.1739DOI Listing
September 2014

HIV-associated neuropathogenesis: a systems biology perspective for modeling and therapy.

Biosystems 2014 May 13;119:53-61. Epub 2014 Apr 13.

University of Florida, 2055 Mowry Road, Department of Pathology and Laboratory Medicine, Gainesville, FL 32610, USA. Electronic address:

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http://dx.doi.org/10.1016/j.biosystems.2014.04.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4112533PMC
May 2014

Dynamical and topological robustness of the mammalian cell cycle network: a reverse engineering approach.

Biosystems 2014 Jan 6;115:23-32. Epub 2013 Nov 6.

Natural Selection, Inc., 5910 Pacific Center Boulevard, Suite 315, San Diego, CA 92121, USA.

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http://dx.doi.org/10.1016/j.biosystems.2013.10.007DOI Listing
January 2014

From pluripotency to islets: miRNAs as critical regulators of human cellular differentiation.

Adv Genet 2012 ;79:1-34

Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA, USA.

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http://dx.doi.org/10.1016/B978-0-12-394395-8.00001-3DOI Listing
December 2012

Modeling the evolution of drug resistance in malaria.

J Comput Aided Mol Des 2012 Dec 21;26(12):1343-53. Epub 2012 Nov 21.

Southwestern College, Chula Vista, CA 91910, USA.

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http://dx.doi.org/10.1007/s10822-012-9618-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3535480PMC
December 2012

Lynn Margulis (1938-2011).

Biosystems 2012 Feb 20;107(2):65. Epub 2011 Dec 20.

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http://dx.doi.org/10.1016/j.biosystems.2011.12.003DOI Listing
February 2012

Structural-based analysis of dihydrofolate reductase evolution.

Mol Phylogenet Evol 2011 Oct 17;61(1):212-30. Epub 2011 Jun 17.

Southwestern College, 900 Otay Lakes Rd., Chula Vista, CA 91910, USA.

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http://dx.doi.org/10.1016/j.ympev.2011.06.005DOI Listing
October 2011

Features associated with survival in metastatic melanoma patients treated with patient-specific dendritic cell vaccines.

Cancer Biother Radiopharm 2011 Aug 3;26(4):407-15. Epub 2011 Aug 3.

Hoag Cancer Institute; One Hoag Drive, Newport Beach, CA 92658, USA.

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http://dx.doi.org/10.1089/cbr.2011.0973DOI Listing
August 2011

Simulating natural selection as a culling mechanism on finite populations with the hawk-dove game.

Biosystems 2011 Apr 8;104(1):57-62. Epub 2011 Jan 8.

Natural Selection Inc., 9330 Scranton Rd., San Diego, CA 92121, USA.

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http://dx.doi.org/10.1016/j.biosystems.2011.01.002DOI Listing
April 2011

An approach for classification of highly imbalanced data using weighting and undersampling.

Amino Acids 2010 Nov 22;39(5):1385-91. Epub 2010 Apr 22.

School of Electrical and Electronic Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore.

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http://dx.doi.org/10.1007/s00726-010-0595-2DOI Listing
November 2010

HIV-miR-H1 evolvability during HIV pathogenesis.

Biosystems 2010 Aug 31;101(2):88-96. Epub 2010 May 31.

BioInfoExperts, Thibodaux, LA 70302, USA.

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http://dx.doi.org/10.1016/j.biosystems.2010.05.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3478900PMC
August 2010

Di-codon usage for classification of genes.

Biosystems 2009 Oct 3;98(1):1-6. Epub 2009 Jul 3.

BioInfomatics Institute, Singapore.

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http://dx.doi.org/10.1016/j.biosystems.2009.06.005DOI Listing
October 2009

A novel in silico approach to drug discovery via computational intelligence.

J Chem Inf Model 2009 Apr;49(4):1105-21

Southwestern College, 900 Otay Lakes Road, Chula Vista, California 91910, USA.

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http://dx.doi.org/10.1021/ci9000647DOI Listing
April 2009

A transition to a new Editor-in-Chief.

Authors:
Gary B Fogel

Biosystems 2009 Feb;95(2):89

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http://dx.doi.org/10.1016/j.biosystems.2008.12.005DOI Listing
February 2009

Prediction of R5, X4, and R5X4 HIV-1 coreceptor usage with evolved neural networks.

IEEE/ACM Trans Comput Biol Bioinform 2008 Apr-Jun;5(2):291-300

BioInfoExperts, Gainesville, FL 32606, USA.

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http://dx.doi.org/10.1109/TCBB.2007.1074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3523352PMC
July 2008

Computational intelligence approaches for pattern discovery in biological systems.

Authors:
Gary B Fogel

Brief Bioinform 2008 Jul 5;9(4):307-16. Epub 2008 May 5.

Natural Selection, Inc., 9330 Scranton Rd., Suite 150, San Diego, CA 92121, USA.

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http://dx.doi.org/10.1093/bib/bbn021DOI Listing
July 2008

On the relationship between GC content and the number of predicted microRNA binding sites by MicroInspector.

Comput Biol Chem 2008 Jun 10;32(3):222-6. Epub 2008 Mar 10.

Southwestern College, 900 Otay Lakes Road, Chula Vista, CA 91910, USA.

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http://dx.doi.org/10.1016/j.compbiolchem.2008.02.004DOI Listing
June 2008

In silico screening against wild-type and mutant Plasmodium falciparum dihydrofolate reductase.

J Mol Graph Model 2008 Apr 18;26(7):1145-52. Epub 2007 Oct 18.

Natural Selection Inc., 9330 Scranton Road, Suite 150, San Diego, CA 92121, USA.

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http://dx.doi.org/10.1016/j.jmgm.2007.10.006DOI Listing
April 2008

QSAR using evolved neural networks for the inhibition of mutant PfDHFR by pyrimethamine derivatives.

Biosystems 2008 Apr 17;92(1):10-5. Epub 2007 Nov 17.

Southwestern College, 900 Otay Lakes Road, Chula Vista, CA 91910 USA.

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http://dx.doi.org/10.1016/j.biosystems.2007.10.005DOI Listing
April 2008

Modeling the inhibition of quadruple mutant Plasmodium falciparum dihydrofolate reductase by pyrimethamine derivatives.

J Comput Aided Mol Des 2008 Jan 11;22(1):29-38. Epub 2007 Dec 11.

Natural Selection, Inc., 9330 Scranton Road, Suite 150, San Diego, CA 92121, USA.

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http://dx.doi.org/10.1007/s10822-007-9152-9DOI Listing
January 2008

High-throughput ligand screening via preclustering and evolved neural networks.

IEEE/ACM Trans Comput Biol Bioinform 2007 Jul-Sep;4(3):476-84

Southwestern Community College, CA 91910, USA.

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http://dx.doi.org/10.1109/tcbb.2007.1038DOI Listing
October 2007

A statistical analysis of the TRANSFAC database.

Biosystems 2005 Aug;81(2):137-54

Natural Selection, Inc., 3333 N. Torrey Pines Ct., Suite 200, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1016/j.biosystems.2005.03.003DOI Listing
August 2005

Discovery of sequence motifs related to coexpression of genes using evolutionary computation.

Nucleic Acids Res 2004 20;32(13):3826-35. Epub 2004 Jul 20.

Natural Selection, Inc., 3333 N. Torrey Pines Ct., Suite 200, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1093/nar/gkh713DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC506801PMC
July 2004

Evolutionary optimization, backpropagation, and data preparation issues in QSAR modeling of HIV inhibition by HEPT derivatives.

Biosystems 2003 Nov;72(1-2):149-58

Natural Selection, Inc., 3333 N. Torrey Pines Ct., Suite 200, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1016/s0303-2647(03)00140-0DOI Listing
November 2003

Discovery of RNA structural elements using evolutionary computation.

Nucleic Acids Res 2002 Dec;30(23):5310-7

Natural Selection Inc., 3333 North Torrey Pines Court, Suite 200, La Jolla, CA 92037, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC137967PMC
http://dx.doi.org/10.1093/nar/gkf653DOI Listing
December 2002

Quantitative structure-activity relationships by evolved neural networks for the inhibition of dihydrofolate reductase by pyrimidines.

Biosystems 2002 Feb;65(1):37-47

Natural Selection Inc., 3333 N. Torrey Pines Ct., Suite 200, 92037, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1016/s0303-2647(01)00192-7DOI Listing
February 2002