Jim Zheng

Jim Zheng

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Jim Zheng

Publications by authors named "Jim Zheng"

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Restructured GEO: restructuring Gene Expression Omnibus metadata for genome dynamics analysis.

Database (Oxford) 2019 01 1;2019. Epub 2019 Jan 1.

Department of Biostatistics & Data Science, School of Public Health, University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, USA.

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http://dx.doi.org/10.1093/database/bay145DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6333964PMC
January 2019

Gene fingerprint model for literature based detection of the associations among complex diseases: a case study of COPD.

BMC Med Inform Decis Mak 2019 01 31;19(Suppl 1):20. Epub 2019 Jan 31.

School of Biomedical Informatics, University of Texas Health Science Center at Houston, 7000 Fannin St Suite 600, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1186/s12911-019-0738-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6354331PMC
January 2019

Predict effective drug combination by deep belief network and ontology fingerprints.

J Biomed Inform 2018 09 3;85:149-154. Epub 2018 Aug 3.

School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jbi.2018.07.024DOI Listing
September 2018

Revealing the Rate-Limiting Li-Ion Diffusion Pathway in Ultrathick Electrodes for Li-Ion Batteries.

J Phys Chem Lett 2018 Sep 24;9(17):5100-5104. Epub 2018 Aug 24.

Chemical Science and Engineering Division , Argonne National Laboratory , Lemont , Illinois 60439 , United States.

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http://pubs.acs.org/doi/10.1021/acs.jpclett.8b02229
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http://dx.doi.org/10.1021/acs.jpclett.8b02229DOI Listing
September 2018

Informatics, Data Science, and Artificial Intelligence.

JAMA 2018 Sep;320(11):1103-1104

School of Biomedical Informatics, University of Texas Health Science Center, Houston.

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http://dx.doi.org/10.1001/jama.2018.8211DOI Listing
September 2018

A study of generalizability of recurrent neural network-based predictive models for heart failure onset risk using a large and heterogeneous EHR data set.

J Biomed Inform 2018 08 15;84:11-16. Epub 2018 Jun 15.

School of Biomedical Informatics, University of Texas Health Science Center at Houston (UTHealth), Houston, TX, United States. Electronic address:

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http://dx.doi.org/10.1016/j.jbi.2018.06.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6076336PMC
August 2018

Electrode Materials, Electrolytes, and Challenges in Nonaqueous Lithium-Ion Capacitors.

Adv Mater 2018 Apr 12;30(17):e1705670. Epub 2018 Mar 12.

Clean Energy Automotive Engineering Center and School of Automotive Studies, Tongji University (Jiading Campus), 4800 Caoan Road, Shanghai, 201804, P. R. China.

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http://doi.wiley.com/10.1002/adma.201705670
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http://dx.doi.org/10.1002/adma.201705670DOI Listing
April 2018

A Multi-Parameter Analysis of Cellular Coordination of Major Transcriptome Regulation Mechanisms.

Sci Rep 2018 04 10;8(1):5742. Epub 2018 Apr 10.

Department of Environmental Toxicology, Texas Tech University, Lubbock, TX, 79409, USA.

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http://dx.doi.org/10.1038/s41598-018-24039-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5893539PMC
April 2018

Self-Healing Phenomenon Observed During Capacity-Control Cycling of Freestanding Si-Based Composite Paper Anodes for Li-Ion Batteries.

ACS Appl Mater Interfaces 2018 Feb 19;10(8):7155-7161. Epub 2018 Feb 19.

Materials Science & Engineering, ‡Aero-propulsion, Mechatronics and Energy Center (AME), §High-Performance Materials Institute (HPMI), and ∥Center for Advanced Power Systems (CAPS), Florida State University , Tallahassee, Florida 32310, United States.

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http://dx.doi.org/10.1021/acsami.7b19246DOI Listing
February 2018

Enhancing Hi-C data resolution with deep convolutional neural network HiCPlus.

Nat Commun 2018 02 21;9(1):750. Epub 2018 Feb 21.

Bioinformatics and Genomics Program, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.

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http://dx.doi.org/10.1038/s41467-018-03113-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5821732PMC
February 2018

The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: from big data to big analytical tools.

BMC Bioinformatics 2017 Oct 3;18(Suppl 11):405. Epub 2017 Oct 3.

Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1186/s12859-017-1797-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5629550PMC
October 2017

The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: putting systems biology to work.

BMC Syst Biol 2017 Oct 3;11(Suppl 5):88. Epub 2017 Oct 3.

The Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1186/s12918-017-0461-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5629615PMC
October 2017

The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: summary and innovation in genomics.

BMC Genomics 2017 Oct 3;18(Suppl 6):703. Epub 2017 Oct 3.

Department of Computer Science, The University of Texas at San Antonio, San Antonio, TX, 78249, USA.

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http://dx.doi.org/10.1186/s12864-017-4018-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5629612PMC
October 2017

A statistical framework for biomedical literature mining.

Stat Med 2017 Sep 4;36(22):3461-3474. Epub 2017 Jul 4.

School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, U.S.A.

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http://dx.doi.org/10.1002/sim.7384DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5657248PMC
September 2017

Modulation of electronic properties of tin oxide nanobelts via thermal control of surface oxygen defects.

Nanotechnology 2017 Feb 23;28(5):055701. Epub 2016 Dec 23.

Department of Physics, Florida State University, Tallahassee, FL 32306, USA.

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http://dx.doi.org/10.1088/1361-6528/28/5/055701DOI Listing
February 2017

A hybrid electrochemical device based on a synergetic inner combination of Li ion battery and Li ion capacitor for energy storage.

Sci Rep 2017 02 7;7:41910. Epub 2017 Feb 7.

School of automotive studies, Tongji University (Jiading Campus), 4800 Caoan Road, Shanghai 201804, China.

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http://dx.doi.org/10.1038/srep41910DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5294406PMC
February 2017

Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature.

Database (Oxford) 2015 8;2015:bav034. Epub 2015 Apr 8.

Center for Computational Biomedicine, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA, Department of Public Health Science, Medical University of South Carolina, 135 Cannon Street, Suite 303, Charleston, SC 29425, USA and Department of Investigational Cancer Therapeutics, Institute for Personalized Cancer Therapy, UT-MD Anderson Cancer Center, 1400 Holcombe Blvd., FC8.3044, Houston, TX 77030, USA

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http://dx.doi.org/10.1093/database/bav034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4390608PMC
December 2015

Colorectal cancer drug target prediction using ontology-based inference and network analysis.

Database (Oxford) 2015 27;2015. Epub 2015 Mar 27.

Center for Computational Biomedicine, School of Biomedical informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA and Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA

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http://dx.doi.org/10.1093/database/bav015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4375358PMC
September 2015

Exploring genomes with a game engine.

Faraday Discuss 2014 31;169:443-53. Epub 2014 Jul 31.

Department of Computer Science and Engineering, University of South Carolina, SC 29205, USA.

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http://dx.doi.org/10.1039/c3fd00152kDOI Listing
June 2015

Finding pathway-modulating genes from a novel Ontology Fingerprint-derived gene network.

Nucleic Acids Res 2014 Oct 24;42(18):e138. Epub 2014 Jul 24.

School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA

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http://dx.doi.org/10.1093/nar/gku678DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4191379PMC
October 2014

Non-destructive monitoring of charge-discharge cycles on lithium ion batteries using ⁷Li stray-field imaging.

Sci Rep 2013 ;3:2596

National High Magnetic Field Laboratory, Florida State University, 1800 E. Paul Dirac Drive, Tallahassee, FL 32310, USA.

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http://dx.doi.org/10.1038/srep02596DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3763251PMC
February 2014

Pharmacokinetic and pharmacodynamic properties of GS-9620, a novel Toll-like receptor 7 agonist, demonstrate interferon-stimulated gene induction without detectable serum interferon at low oral doses.

J Pharmacol Exp Ther 2014 Jan 16;348(1):96-105. Epub 2013 Oct 16.

Departments of Drug Safety Evaluation (A.F., G.W.), Drug Metabolism (J.Z.), Biology (S.P., C.R.F., D.B.T.), Clinical Virology (J.H.), and Medicinal Chemistry (R.L.H.), Gilead Sciences, Inc., Foster City, California.

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http://jpet.aspetjournals.org/cgi/doi/10.1124/jpet.113.20787
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http://dx.doi.org/10.1124/jpet.113.207878DOI Listing
January 2014

Ranking gene-drug relationships in biomedical literature using Latent Dirichlet Allocation.

Pac Symp Biocomput 2012 :422-33

Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37203, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4095990PMC
December 2013

Molecular profiling of multiple human cancers defines an inflammatory cancer-associated molecular pattern and uncovers KPNA2 as a uniform poor prognostic cancer marker.

PLoS One 2013 25;8(3):e57911. Epub 2013 Mar 25.

Department of Microbiology and Immunology, South Carolina Clinical and Translational Research Institute (SCTR), Medical University of South Carolina, Charleston, South Carolina, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0057911PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3607594PMC
December 2013

Identification and optimization of pteridinone Toll-like receptor 7 (TLR7) agonists for the oral treatment of viral hepatitis.

J Med Chem 2013 Sep 9;56(18):7324-33. Epub 2013 Sep 9.

Departments of †Medicinal Chemistry, ‡Clinical Virology, §Drug Metabolism, ∥Biology, and ⊥Structural Chemistry, Gilead Sciences , 333 Lakeside Drive, Foster City, California 94404, United States.

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http://dx.doi.org/10.1021/jm400815mDOI Listing
September 2013

Vanadium oxide-carbon nanotube composite electrodes for energy storage by supercritical fluid deposition: experiment design and device performance.

Nanotechnology 2013 Aug 12;24(31):315401. Epub 2013 Jul 12.

High Performance Materials Institute, Florida State University, Tallahassee, FL 32310, USA.

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http://dx.doi.org/10.1088/0957-4484/24/31/315401DOI Listing
August 2013

Signaling network prediction by the Ontology Fingerprint enhanced Bayesian network.

BMC Syst Biol 2012 17;6 Suppl 3:S3. Epub 2012 Dec 17.

Bioinformatics Graduate Program, Medical University of South Carolina, Charleston, SC 29425, USA.

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http://dx.doi.org/10.1186/1752-0509-6-S3-S3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3524013PMC
June 2013

β-arrestin-selective G protein-coupled receptor agonists engender unique biological efficacy in vivo.

Mol Endocrinol 2013 Feb 11;27(2):296-314. Epub 2013 Jan 11.

Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA.

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http://dx.doi.org/10.1210/me.2012-1091DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3683806PMC
February 2013

Improving transmission efficiency of large sequence alignment/map (SAM) files.

PLoS One 2011 2;6(12):e28251. Epub 2011 Dec 2.

Department of Computer Science & Engineering, University of South Carolina, Columbia, South Carolina, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0028251PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3229529PMC
July 2012

Consistent Differential Expression Pattern (CDEP) on microarray to identify genes related to metastatic behavior.

BMC Bioinformatics 2011 Nov 11;12:438. Epub 2011 Nov 11.

Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 135 Cannon St, Charleston, SC 29425, USA.

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http://dx.doi.org/10.1186/1471-2105-12-438DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3251006PMC
November 2011

Cellular morphogenesis under stress is influenced by the sphingolipid pathway gene ISC1 and DNA integrity checkpoint genes in Saccharomyces cerevisiae.

Genetics 2011 Oct 11;189(2):533-47. Epub 2011 Aug 11.

Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425, USA.

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http://dx.doi.org/10.1534/genetics.111.132092DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3189794PMC
October 2011

Supercritical fluid deposition of vanadium oxide on multi-walled carbon nanotube buckypaper for supercapacitor electrode application.

Nanotechnology 2011 Sep 11;22(36):365402. Epub 2011 Aug 11.

High Performance Materials Institute, Florida State University, Tallahassee, FL 32310, USA.

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http://dx.doi.org/10.1088/0957-4484/22/36/365402DOI Listing
September 2011

Genome3D: a viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome.

BMC Bioinformatics 2010 Sep 2;11:444. Epub 2010 Sep 2.

Department of Biochemistry & Molecular Biology, Medical University of South Carolina, 135 Cannon Street, Suite 303E, Charleston, SC 29425, USA.

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http://dx.doi.org/10.1186/1471-2105-11-444DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2941692PMC
September 2010

Text-mining approach to evaluate terms for ontology development.

J Biomed Inform 2009 Oct 24;42(5):824-30. Epub 2009 Mar 24.

Bioinformatics Graduate Program, Department of Biostatistics, Bioinformatics & Epidemiology, Medical University of South Carolina, 135 Cannon Street, Suite 303, Charleston, SC 29424, USA.

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http://dx.doi.org/10.1016/j.jbi.2009.03.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3153945PMC
October 2009

Evaluation of genome-wide association study results through development of ontology fingerprints.

Bioinformatics 2009 May 5;25(10):1314-20. Epub 2009 Apr 5.

Bioinformatics Graduate Program, Department of Biostatistics, Bioinformatics and Epidemiology, Medical University of South Carolina, Charleston, SC, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp158DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732313PMC
May 2009

A role for Fli-1 in B cell proliferation: implications for SLE pathogenesis.

Clin Immunol 2008 Oct 9;129(1):19-30. Epub 2008 Aug 9.

Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC, USA.

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http://dx.doi.org/10.1016/j.clim.2008.05.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2562591PMC
October 2008

Use artificial neural network to align biological ontologies.

BMC Genomics 2008 Sep 16;9 Suppl 2:S16. Epub 2008 Sep 16.

Dept Biostatistics, Bioinformatics, and Epidemiology, Medical University of South Carolina, Charleston, SC 29425, USA.

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http://dx.doi.org/10.1186/1471-2164-9-S2-S16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2559880PMC
September 2008

A method of microarray data storage using array data type.

Comput Biol Chem 2007 Apr 12;31(2):143-7. Epub 2007 Jan 12.

Bioinformatics Graduate Program, College of Graduate Study, Medical University of South Carolina, Charleston, SC 29425, USA.

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http://dx.doi.org/10.1016/j.compbiolchem.2007.01.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2709412PMC
April 2007

Combining comparative genomics with de novo motif discovery to identify human transcription factor DNA-binding motifs.

BMC Bioinformatics 2006 Dec 12;7 Suppl 4:S21. Epub 2006 Dec 12.

Department of Biostatistics, Bioinformatics and Epidemiology, and Bioinformatics Core Facility, Hollings Cancer Center, Medical University of South Carolina, 135 Cannon Street, Charleston, SC 29425, USA.

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https://bmcbioinformatics.biomedcentral.com/articles/10.1186
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http://dx.doi.org/10.1186/1471-2105-7-S4-S21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1780116PMC
December 2006

Object-oriented biological system integration: a SARS coronavirus example.

Bioinformatics 2005 May 24;21(10):2502-9. Epub 2005 Feb 24.

Department of Biostatistics, Bioinformatics and Epidemiology, Medical University of South Carolina, 135 Cannon Street, PO Box 250835, Charleston, SC 29425, USA.

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http://dx.doi.org/10.1093/bioinformatics/bti344DOI Listing
May 2005

Integration of the Gene Ontology into an object-oriented architecture.

BMC Bioinformatics 2005 May 10;6:113. Epub 2005 May 10.

Department of Biostatistics, Bioinformatics and Epidemiology, Medical University of South Carolina, 135 Cannon Street, Charleston, SC 29425, USA.

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http://dx.doi.org/10.1186/1471-2105-6-113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1156866PMC
May 2005

Capturing biological information with class-responsibility-collaboration cards.

Bioinformatics 2005 Feb 7;21(3):415-7. Epub 2004 Sep 7.

Department of Biostatistics, Bioinformatics and Epidemiology, 135 Cannon Street, P.O. Box 250835, Charleston, SC 29425, USA.

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http://dx.doi.org/10.1093/bioinformatics/bti005DOI Listing
February 2005

A hidden Markov model with molecular mechanics energy-scoring function for transmembrane helix prediction.

Comput Biol Chem 2004 Oct;28(4):265-74

Department of Biostatistics, Bioinformatics and Epidemiology, Medical University of South Carolina, 135 Cannon Street, Suite 303, Charleston, SC 29425, USA.

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http://dx.doi.org/10.1016/j.compbiolchem.2004.07.002DOI Listing
October 2004