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BIO 341L   GENETICS LAB

 

 Gene Gateway  NCBI: PubMed Medline Citation Search Google MEDLINEplus Health Information Nat'l Ctr Biotechnology Info

Genetics Journal Online Mendelian Inheritance in Man: OMIM  

Vitrual Fly Lab Online  Drosophila melanogaster (Fruitfly) genomefruit fly

Pedigree Lab (Biology Lab Online)

 Human Genome Project      Essential Genetics BlackBoard: Use Barrynet UserName & Password    50 Greatest Hits of DNA: A Timeline of Achievement BlackboardDOE's next step in genomics Genetic Basics  Genes & Populations (NIGMS) National DNA Day  The Biotechnology Institute: a national nonprofit organization dedicated to education and research about the present and future impact of biotechnology  Link that takes you to the Genetics Education Center Home 

 

  Encyclopedia of Genetics, Four-Volume Set, 1-4   DNA Interactive   Genetics Home Reference: your guide to understanding genetic conditions  Genomes. 2nd ed. Brown, T. A. Oxford, UK: BIOS Scientific Publishers Ltd; 2002Gene & Disease (NCBI)NCBI Handbook

Genes & Disease (NCBI): Collection of articles that discuss genes and the diseases that they cause 

 About this book Coffee Break: Tutorial for NCBI Bioinformatics Tools  TOC

Genomic Biology : Genomics takes a holistic approach to molecular biology and evolution by studying the complete genome and its protein expression patterns 

A Science Primer (NCBI)  Molecular Genetics

Fifty years after the discovery of the double helix structure of DNA, the genome community is celebrating the elucidation of the human DNA reference sequence  Nature: Human Genomes, Everyone's Genome; 15 February 2001  The Human Genome Project, Our genome unveiled, DAVID BALTIMORE, Nature 409, 814 - 816 (2001)  Science: The Human Genome, 16 February 2001  Human BAC Resource  Finished Human Genome: Wellcome To The Genomic Age, The Wellcome Trust Sanger Institute  Ensembl Genome Browser

Family History Tool:  National Society of Genetic CounselorsFamily History Tool   What is in your family history? 
   Learn how to create your own
   family tree and find out

 Genomics:GTL: Genomes to Life

ENCODE: The ENCODE Project: ENCyclopedia Of DNA Elements

Human Genome
Explore human genome resources or browse the human genome sequence using the Map Viewer.

International Consortium Completes Human Genome Project, National Human Genome Research Institute (NHGRI)   National DNA Day   Celebrate DNA! In honor of the 50th anniversary of Watson and Crick's famous discovery, the Biotechnology Institute has developed several activities for families, students and teachers to explore DNA.

The Human Genome Project -- Exploring Our Molecular Selves

All About The Human Genome Project

http://www.genome.gov/10001772

All About The Human Genome Project

Senator Tom Harkin

The Human Genome Project (HGP) was one of the great feats of exploration in history -- an inward voyage of discovery rather than an outward exploration of the planet or the cosmos; an international research effort to sequence and map all of the genes - together known as the genome - of members of our species, Homo sapiens. Completed in April 2003, the HGP gave us the ability to, for the first time, to read nature's complete genetic blueprint for building a human being.

 

 

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Milestones in Genetics: Timeline

An interactive timeline of milestones in genetics, presenting more than 90 key events and discoveries. By clicking on any year in the timeline, the user can read a short, illustrated story and often find archival images and original scientific publications.

DOWNLOAD PC (4.82MB) Macromedia
DOWNLOAD MAC (3.7MB)

 

 

Entrez cross-database search page

 

 

 

 

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Instructor: 

          Dr. Yu-Wai Peter Lin     Office: SNHS 330

              Phone: (305)899-3226

              E-mail: plin@mail.barry.edu  emailed.gif (14893 bytes)

                 

          

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Office Hours:

    Dr Lin:  Mon and Wed   9:00 AM - 11:30 AM

   Posted on office door or by appointment

 

 

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Genetics Lab Class Distribution List (Bucmail):

            Lab 1 : BIO-341L-L1-0501@mail.barry.edu

How do I send email directly without searching the global address book ?

The class list addresses are created using the following format:

Course-ID-Section-YearTerm@mail.barry.edu

For example, Accounting 336 01 held in Fall 2001 would have ACC-336-01-0101@mail.barry.edu as the e-mail address.

Will everyone be able to send messages to my class list ?

No, only members (students registered in the course) of the list will be able to send to the class list.  Instructors are added as members to the class list, allowing them to send messages. 

 

 

Barry's official means of communication with students is BUCMAIL. A student email account is automatically created by the Division of Information Technology for all registered students. The University will communicate with students through this official address, which is recorded in the University's electronic directories and records for each student. All students taking classes that meet on the Barry University campus are required to log in to their official Barry University student email account within one week of the beginning of the semester when they enroll. Faculty or technology coordinators associated with distance education classes or courses that meet off campus should also require students to login to their official Barry University student email accounts

The following are important points to remember about student use of Barry email as well as faculty responsibilities.

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Students should check their email as often as
they check their regular mail. The University recommends checking at least
twice a week;

 

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Students must maintain their mailboxes to
avoid exceeding their mail quotas. That means routinely deleting old mail and
downloading large files, saving them on their own hard drives and deleting the
files from their email mailboxes;

 

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The practice of having Barry email forwarded
to other email addresses (such as Hotmail or Yahoo!) is an option for
students, but instructors might advise students that other email addresses may
have limitations, such as limited space that prevents the student from sending
and receiving messages;

 

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In general, email is not an appropriate medium
for sensitive or confidential information.

 

 

 

 

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Table of Content

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Genetics Lab Objectives

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Format for Lab Reports

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Lab Schedule :

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bulletLinks and Assignments
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Copyright Acknowledgement

 

 

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Objectives:

 

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FORMAT FOR LABORATORY REPORTS*

Major Report (150 total possible points)

Title Page: Include the title of the experiment along with your name, the date and the course title.

Introduction: (New Page) In this section you should give a clear, detailed background of the subject in question. While the hand-out has some background, it is usually no where near being complete. You should utilize other sources. This may include your textbook, review articles, and original research journal articles on the subject. The acceptable format for referencing the cited literature in the body of the text and in the reference section is given below. After your discussion of the background and your clear identification of the subject, clearly state your hypothesis or define the problem with which the laboratory exercise deals. Relate the problem addressed by the laboratory exercise to pertinent observations or information already known from the literature. (50 points possible)

Materials and Methods: Describe the materials and methods in enough detail that the work could be repeated by others. Do not go into unnecessary detail. The style of this section should resemble that in the Proceedings of the National Academy of Sciences (PNAS). Therefore, this section should not include simply a list of the materials used or resemble a recipe book as your lab manual does. Rather the methods should be in concise sentences and paragraphs making special note of how the protocol utilized deviated from that in the laboratory manual. Also, well known methods used without significant modification need not be described but merely cited. For example, "The amount of protein was determined by the method of Bradford (1976) using bovine serum albumin as the standard." (20 points possible)

Results: The data should be presented in a clear manner by the use of properly labelled graphs and tables. Again, consult the Proceedings of the National Academy of Sciences for their style of presentation. The figures should have legends containing sufficient information that they can stand alone. Raw data used to generate the graphs should usually not be included. Although at times the raw material, once properly labelled, is your figure. For example, the picture of the DNA gel that shows the fragment sizes generated by the restriction enzymes, or the copy of the SDS PAGE gel that shows the molecular weight of proteins are both acceptable figures. Make sure to assign numbers to your tables (e.g. Table 1) and figures (e.g. Figure 5) so that you can call attention to important parts of the data in the text portion of the Results or Discussion section. (30 points possible)

Discussion: The purpose of this section is to discuss the meaning or significance of the results especially in light of previous studies. Therefore the literature you used in the introduction is again going to be important here to discuss how your results compare or add new insight to that previously described. It is in this section that you can interpret and speculate on the meaning of your results, especially based on the previous studies. Do your results corroborate or go against previous results? Using your background materials as a basis for argument, what do your results mean? Again be sure to properly cite references utilized using the format shown below. (45 points possible)

References: This section is an alphabetical list of all reference materials that have been cited in the report. Use the style listed below for citation in the text and in the reference section. (5 points possible)

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Examples of References and

Appropriate Methods of Citation

A. Within the text

In the body of the paper, citation to information from other sources are cited in this manner:

"Jones (2004) discovered that..........."

"..........was found by Jones and Edwards (2002) that......."

"High pressure may affect the brain functions responsible for higher student grades (Smith et al., 1999)."

B. Reference section

Jones, J.J. 2004. High temperatures affect student grades. J. Amer. Physiol. 101:122-144.

Jones, J.J. 1999. Temperature has no effect on student grades. Amer. Zool. 6:52-46.

Jones, J.J., and S. Edwards. 2003. High pressure affects student grades. Amer. Zool. 4:43-65.

Smith, R., J.J. Jones, and S. Edwards. 2000. High pressure affects brain function in vertebrates. Brain Research 47:1235-1257.

Zelnich, A.C. 2004. Environmental influences on brain function. Pp. 64-78 in D. Webster ed., Neural Systems. Jones Press, New York.

 

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Links and Assignments

bulletDr. Lin's Biology Links
bulletAssignments

Genetic Basics

National Institutes of Health, National Institute of General Medicine Sciences

http://www.nigms.nih.gov/news/science_ed/genetics/   (Adobe Acrobat Reader Icon PDF Version)

 

  Gene Gateway: Tools for exploring the Human Genome

 

  Course Materials

Population Genetics

 

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SKY (Spectral Karyotype)

http://www.genome.gov/glossary.cfm?key=spectral%20karyotype%20(SKY)

NCBI  GENES AND DISEASE  http://www.ncbi.nlm.nih.gov/disease/

 

 Genes & Populations (NIGMS) 

Genes & Populations: HTML version or print version  (PDF) (requires free Adobe Acrobat Reader to view online)

This educational brochure explains in question-and-answer format why genetics researchers sometimes study identified populations to identify links between genes and diseases. (Also available in Spanish, "Genes y Poblaciones.")

 

 

 

 

 

  LabBench

Molecular Biology
by Theresa Knapp Holtzclaw
© 1998, Peregrine Publishers, Inc. All Rights Reserved.
Development Team

Bacterial Transformation

http://www.biology.com/learning/molecular/concept1.html

   

© 1998, Peregrine Publishers, Inc., All Rights Reserved

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Genetics  Links

 

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The Interactive Fly ©
1995, 1996
Thomas B. Brody, Ph.D.

 

http://flybase.bio.indiana.edu:7081/allied-data/lk/interactive-fly/aimain/1aahome.htm

A cyberspace guide to Drosophila genes and their roles in development

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Mutant Fruit Flies

http://www.exploratorium.edu/exhibits/mutant_flies/mutant_flies.html

Mutant fruit flies
From the Exploratorium in San Francisco

 

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REVIEW

The Genome Sequence of Drosophila melanogaster

http://www.sciencemag.org/feature/data/genomes/landmark.shl

Cover, Vol. 287, Issue 5461      

             Mar 24 2000
             Vol. 287, No. 5461  The Drosophila Genome           

 

Abstract    Full Text   

Coding Content of the Drosophila Genome

 

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Science News Online

The Meaning of Life
Computers are unscrambling genomes to reveal the secrets in
DNA codes


By T. Hesman

mice     

Geneticists predict that computer programs that compare human DNA with mouse DNA will uncover secrets in the human genome. (Human Genome Proj./Oak Ridge Nat. Lab.)

http://www.sciencenews.org/20000429/bob2.asp

 

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NetWatch 
(html version)

http://www.sciencemag.org/content/current/netwatch.shtml

 

DATABASE: Bad Blood

Diseases such as leukemia result from glitches in the control of hematopoiesis, the process that generates mature blood cells from stem cells. The new Hematopoietic Promoter Database, or HemoPDB, from Ohio State University gives cancer researchers information on 246 leukemia- and lymphoma-related genes from mice and humans.

HemoPDB records the proteins that switch each gene on and off and the DNA sequences to which these proteins attach. Users can also find out each gene's function and the types of cells in which it is active. The scientists who assembled HemoPDB from the literature and Web sites hope it will help researchers pinpoint other genes that might be involved in blood cell development and disorders.

bioinformatics.med.ohio-state.edu/HemoPDB

 

AREX: The Arabidopsis Gene Expression Database

DATABASE: Getting to the Root of Gene Expression

Researchers studying genes at work in the mustard plant Arabidopsis should check out AREX, a new gene-expression database sponsored by Philip Benfey's lab at Duke University in Durham, North Carolina. AREX holds activity measurements from the lab's own experiments (Science, 12 December 2003, p. 1956) and from the literature, combining data from microarrays and other techniques. (Here, a glowing protein marks active genes in the root.) Users can glean information on a particular gene's activity in various cell or tissue types and at different developmental stages. The database will eventually include values for the aboveground parts of the plant as well as the root.

www.arexdb.org

 

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Introduction to Virtual FlyLab

Virtual Fly Lab 1

Virtual Fly Lab 2
 
Virtual Fly Lab 3
 
Virtual Fly Lab 4
 
Molecular Genetics Jump Station
The Biology Project: Mendelian Genetics
The Genetic Code (5' -> 3')
 
Morgan: A Genetics Tutorial
The Interactive Fly
A Hypermedia Glossary of Genetic Terms
The Natural History of Genes -Activities
Genetic Odyssey: An Exploration of Genetic Topics
Genetics Education Center

 

MendelWeb To learn more about Mendel and his experiments, follow this link to MendelWeb

 

 

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GENETICS:
Zebrafish Earns Its Stripes in Genetic Screens

Gretchen Vogel

Researchers are using the zebrafish to search for a variety of genes involved in everything from obesity to bone diseases

http://www.sciencemag.org/cgi/content/full/288/5469/1160

Science Volume 288, Number 5469 Issue of 19 May 2000, pp. 1160 - 1161
©2000 by The American Association for the Advancement of Science.

 

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bulletAssignments:

 

Morgan: A Genetics Tutorial http://morgan.rutgers.edu/MorganWebFrames/htmldocs/contents.html

 

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Chapter 3: Animation and Tutorial

You will not be able to access the Animation and Tutorial links listed below unless your browser has either the Macromedia Flash 5 player or the Macromedia Shockwave 8 player. The Flash Animation and Tutorial will open in a secondary window which should be closed after viewing the contents. For more information on this module please reference the "Navigating the Animation and Tutorial" section located within this course.

Monohybrid Cross

Independent Assortment

Probability

Analysis of Human Pedigrees
 

© Prentice-Hall, Inc.
A Division of Pearson Education.
Legal Statement

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The Biology Place: http://www.biology.com

User ID- STU/lin

Password- *********

Interactive Learning Activities (Lab Bench):

 

a) Experimenting with Mendel's Peas http://www.biology.com/learning/peas/intro.html

 

b)  Genetics of Organisms (Drosophila melanogaster)      [http://www.biology.com/learning/genetics/intro.html]
by Theresa Knapp HoltzclawTable of Contents

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c) Solving Mendelian Genetics Problems http://www.biology.com/learning/mendelian/introduction.html

   California State University's Virtual FlyLab site

 

 

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BioCoach

Mendelian Inheritance This BioCoach Activity will help you review the basic concepts of Mendelian genetics.  http://www.biology.com/learning/inheritance/intro.html
by Peter Russell, Reed College

     

Analyzing the Genetic X Files (analyzing genetic crosses)
Genetic X Files Problems

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              tigr_icon.gif (1851 bytes)  The Institute of Genome Research (TIGR)    http://www.tigr.org/tigr_home/index.html

              tdb_li.gif (729 bytes)  TIGR Web site                     http://www.tigr.org/tigr_home/tdb/tdb.html


Designing Experiments to Solve Restriction Mapping
Problems
http://www.biology.com/learning/redlab/introduction.html

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bulletReading Assignments :

Primary Source Article

Genome Sequence

Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. S. T. Cole et.al.  Nature 393:537-544    [M. tuberculosis genome sequence]

Complete genome sequence of Treponema pallidum, the syphilis spirochete. Claire M. Fraser, et. al. Science 281:375-388 (1998) (http://www.sciencemag.org)         [T. pallidium genome sequence]

Lin, Y.-W. P., B. A. Rupnow, D. A. Price, R. M. Greenberg, and R. A. Wallace (1992). Fundulus heteroclitus gonadotropins 3. Molecular cloning and sequencing of beta subunits of two distinct gonadotropins (GTH I and GTH II) from pituitary cDNA library using the Polymerase Chain Reaction. Mol. Cell. Endocrinol. 85: 127-139.                                                                                Medline Accession No.  PMID: 1526312;   UI: 92405806.   /Abstract           

 

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Copyright Acknowledgement

Permission to use the Copyright DNA image granted by:

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             Paul A. | paul@grserv.med.jhmi.edu | Johns Hopkins

        Thiessen | http://cherubino.med.jhmi.edu/~paul | University

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BioMed Central BioMed Central: Genetics (Open Access Journal) BioMed Central: Genomics (Open Access Journal) BioMed Central: Bioinformatics (Open Access Journal) BioMed Central Medical Genetics (Open Access Journal) BioMed Central Biotechnology (Open Access Journal)

Genetics: The Functional Analysis of Genomes , By Philip W Ingham and Tanya T Whitfield

HapMap Project (Haplotype Map)   Protein Structure InitiativeCGAP: Cancer Genome Anatomy Project  VAST search: structure-structure similarity search service  VecScreen  Human–Mouse Homology Maps  hla: Human Major Histocompatibility Complex (MHC) Database  Map Viewer  LocusLink   UniGene   ePCR   Spidey: Spidey aligns one or more mRNA sequences to a single genomic sequence.  ORF: Open Reading Frame Finder  cCAP: Cancer Chromosome Abberation Project; The Cancer Chromosome Aberration Project (CCAP) compiles information on the distinct chromosome aberrations that are associated with different cancers  Retrovirus Resources: Budding HIV-1 particles SNP (Single Nucleotide Polymorphism) Database SKY/M-FISH and CGH database is to provide a public platform for investigators to share and compare their molecular cytogenetic data PASS2: Protein Alignments organised as Structural Superfamilies, National Centre for Biological Sciences, Bangalore, India, 2003

Entrez global query  PMC in Entrez    HomoloGene in Entrez  Entrez Gene  dbMHC (Major Histocompatibility Complex database)  Cancer Chromosomes  HIV-1 database

 Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in 43 complete genomes, representing 30 major phylogenetic lineages Clusters of Orthologous Groups of proteins (COGs)  

Phylogenetic classification of proteins encoded in complete genomes

The Map Viewer supports search and display of genomic information by chromosomal position

    PlasmoDB is the official database of the malaria parasite genome project.

Malaria Triad: Genetics & Genomics

NCBINCBI Bookshelf : The Bookshelf is a growing collection of biomedical books that can be searched directly by typing a concept into the textbox above and selecting "Go".

 Genetic Basics  Genes & Populations (NIGMS)  Cover of Inside the Cell  Human Molecular Genetics 2. 2nd ed. Strachan, Tom and Read, Andrew P. Oxford, UK: BIOS Scientific Publishers Ltd; 1999.Modern Genetic Analysis. Griffiths, Anthony J.F.; Gelbart, William M.; Miller, Jeffrey H.; Lewontin, Richard C. New York: W. H. Freeman & Co.; c1999 Molecular Biology of the Cell. 3rd ed. Alberts, Bruce; Bray, Dennis; Lewis, Julian; Raff, Martin; Roberts, Keith; Watson, James D. New York and London: Garland Publishing; c1994. Molecular Cell Biology. 4th ed.  Lodish, Harvey; Berk, Arnold; Zipursky, S. Lawrence; Matsudaira, Paul; Baltimore, David; Darnell, James E .  New York: W. H. Freeman & Co.; c1999.Coffee Break: Tutorial for NCBI Bioinformatics ToolsIntroduction to Genetic Analysis. 7th ed. Griffiths, Anthony J.F.; Miller, Jeffrey H.; Suzuki, David T.; Lewontin, Richard C.; Gelbart, William M. New York: W. H. Freeman & Co.; c1999.   Annual Reviews Collection [Internet].  Twelve articles reproduced from the Annual Reviews Series. Bethesda (MD): National Library of Medicine (US), NCBI; 2002 Nov.

 OMIM: Online Mendelian Inheritance in Man   Vitrual Fly Lab Online 

IEB: The Information Engineering Branch (IEB) is responsible for designing and building NCBI's production software and databases

U.S. National Library of Medicine Gateway

National Human Genome Research Institute: Genetic Education Modules for Teachers


The Biotechnology Institute

InfoBioGen: French resource centre for Genomics  Atlas of Genetics and Cytogenetics 
in Oncology and Haematology

  Welcome to Access Excellence at the National Health Museum...A Place in Cyberspace for Health and Bioscience Teachers and Learners  Genetics Education Center: University of Kansas Medical Center, For educators interested in human genetics and the human genome project Gene Almanac: Animation Library (PCR, Southern blot, sequencing, polymorphisms), Cold Spring Harbor Lab DNA Learning Center

Gene Almanac: Dolan DNA Learning Center, 1 Bungtown Road, Cold Spring Harbor, NY 11724

   ExPASy (Expert Protein Analysis System) Molecular Biology Server   The NIH's Word on Health

  The Genetic Code: Shaun D. Black, University of Texas Health Center at Tyler

 

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Medline Search:

            (PubMed- http://www.ncbi.nlm.nih.gov/entrez/query.fcgi)