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BMS 537 (02)      HUMAN GENETICS

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Genetics Journal Online Mendelian Inheritance in Man: OMIM Vitrual Fly Lab Online

Human Molecular Genetics 2. 2nd ed. Strachan, Tom and Read, Andrew P. Oxford, UK: BIOS Scientific Publishers Ltd; 1999.

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DNA Interactive   Genetics Home Reference: your guide to understanding genetic conditions

 

 

Human Genetics Course Syllabus

(Three Credit-Hours)

Fall 2002

Section (02) 6:00 PM- 9:00 PM    Thursday   SNHS Bldg. Rm 106

Dr. Yu-Wai Peter Lin MT(ASCP), PhD

Office/Lab: SNHS Bldg. Room 330,   Ph: (305) 899-3226

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

Office Hours:

Posted on office door or by appointment

M  W & F   9:00 - 11:00 AM; 

Evening hour-   Th  5:00 - 6:00 PM or By appointment

 

Human Genetics Class Distribution List (Bucmail): BMS-537-02-0204@mail.barry.edu

 

 

 

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Table of Contents

bulletCourse (Human Genetics) Outline
bulletInstructional Method
bulletClass Schedule
bulletWeek 1-4 (Aug.29 - Sept.19)
bulletWeek 5-9 (Sept.26 - Oct 24)
bulletWeek 10-14  (Oct.31 - Nov.28)
bulletMessage Center
bulletGlossary (NHGRI-NIH)
bulletLinks and Assignments
bulletGenetics in the News
bulletBookmarks
bulletCopyright Acknowledgement

 

 

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Course Outline:

Presentation of reports, discussions, lectures, and papers on selected topics in Human Genetics. An examination of Principles of Heredity, from Genes and Pedigrees to current Molecular and Recombinant DNA techniques for the Identification of Human Diseases.

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Goals and Objectives:

Goals -- The major goal is acquiring an understanding of current theories of mechanisms of inheritance and their implications for both basic knowledge and its application in modern medicine and technology. A secondary aim is to familiarize students with current scientific literature and the use of the vast genetics and biomedical resources on the World Wide Web, for research.

Objectives -- Upon completion of this course the student will be able to:

1. explain the fundamental aspects of chromosome structure and organization as well as eukaryotic gene expression and gene regulation.

2. apply the knowledge of normal gene expression in order to explain what happens under abnormal conditions.

3. discuss the human genome and the study of human genetic diseases on a current, molecular level.

4. increase analytical skills by reading, interpreting and discussing current scientific literature in the field of human genetics.

 

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Text:

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Human Molecular Genetics 2 nd Edition (Required text book)

        http://www.bios.co.uk

Tom Strachan and Andrew P. Read

BIOS Scientific Publishers Limited, A Wiley-Liss & Sons, Inc.

New York, 1999.

ISBN # 0-471-33061-2

 

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The Biology Place (Required subscription)

The Biology Place, a web learning environment that includes learning activities, study and testing aids, and a wide range of content to help you succeed in your course.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               

http://www.biology.com

The Biology Place      Customer Center   Peregrine Publishers

Student Subscription Options: You can purchase a subscription to Biology Place online and pay by credit card to gain immediate access.  If you are ordering by check through the mail, a mail order form will be generated for you at the end of the process.  To order, please click on the link below.

http://www.biology.com/campbell/stureginfo.html

 

 

 

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Clinical Genetics: A Case-Based Approach (Required text book)

D. Bonthron, D. FitzPatrick, M. Porteous & A. Trainer

WB Saunders Company Limited, London, 1998

ISBN # 0 7020 2351 5

 

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Medical Genetics (Reference)

Lynn B. Jorde, John C. Carey and Raymond L. White

Mosby - Year Book, Inc.

St. Louis, Missouri, revised for 1997

ISBN # 0 8016 6414 4

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A Dictionary of Genetics (Reference)

Robert C. King and William D. Stansfield

Oxford University Press

New York, 1997 (Fifth edition)

ISBN # 0 19 509441 7

 

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Instructional Methods:

The lecture portion of the course will consist of oral presentations given by the instructor and supplemented with overhead transparencies and AV slides. Peer review, cooperative learning, and active discussions with the students are encouraged. Critical reading and discussion of recent scientific journal articles will be part of the regular student activities.

Computer assignments (HyperCELL), internet connection to biology web site on the World Wide Web (The Biology Place), online journals (BioMedNet- http://biomednet.com), CD-ROM (Current Content), Medline Search (Internet Grateful Med- http://igm.nlm.nih.gov), web connection to the National Library of Medicine, National Center for Biotechnology Information (PubMed- www.ncbi.nlm.nih.gov/pubmed) and simulations (PCGene) will be used during the course.

We will also utilize a number of On-line Scientific Journals through the Internet (Current Opinion in Genetics- http://biomednet.com, The Journal of the American Medical Association- http://www.ama-assn.org, Medline- http://igm.nlm.nih.gov, NIH AIDS information resources, www.biology.com etc.)

 

 

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BIOLOGY GRADING SCALE

    A = 90-100%

    B = 80-89%

    C = 70-79%

    D = 60-69%

    F = 0-59%

 

Your Final Grade for this course will be determined as follows:

Mid-Term Exam = 300 points

Final Exam = 300 points

Homework/Library assignments = 150 points (50 pt@ x 3)

Surprise Quizzes = 150 points (50 pt@ x 3)

Subjective: Class participation, attendance, etc. = 100 points

Grade = Total points earned / 1000 x 100%

 

Note: All exams, quizzes and written assignments are the property of the School of Natural and Health Sciences.

 

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Quizzes, Homework/Library Assignments:

There will be three (3) surprise quizzes, and three (3) homework/library assignments (worth 50 points each) during the semester. These assignments are important to your grade in the course and are intended to help guide your studying and to familiarize you with the recent and cutting edge scientific literature and research.  Graded assignments will be returned for review within two weeks.

Reading assignments from the text are listed on the course syllabus to correspond with the material to be covered in class on a given week.  The intent of the reading assignments is to reinforce the lecture material and to provide additional information and perspective.  It is essential that you read the material for each section as it is not possible to cover all the appropriate material in class.

To gain the MOST benefit from the reading assignments, you should read the material before class.  You will be responsible for the subject matter presented in class as well as the reading and Internet assignments for the exams.  In studying for exams, use the lecture material as a guide as to the specific areas in the text to focus on.

 

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Mid-Term Exam and Final Exam:

Each exam will consist of multiple choice, problem solving, matching, fill-in-the-blank, and short-essay questions. Material from the lectures AND the assigned readings will be included. The mid-term exam is scheduled for October 11, 2001. The Final Exam is scheduled for Thursday, December 13, 2001, 6:00 - 7:50 PM.

All make-up exams will be oral unless special arrangements are made by the student before hand.

 

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Academic Dishonesty Policy:

Students should be aware that cheating will not be tolerated. Any student caught giving or receiving assistance during an exam, or using cheat sheet, etc. will receive a grade of ZERO for that exam. This zero grade may not be dropped or made up; and WILL be used when determining the student's final grade. Any student caught cheating a second time will receive a grade of "F" for the course and will be referred to his/her Dean for disciplinary action. The same is true with respect for quizzes. A plagiarized written assignment will receive a grade of ZERO.

(For further information concerning the dishonesty policy, please refer to your Barry University 2001-2002 Graduate Catalog.)

 

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Class Attendance:

Attendance is Mandatory.

You are expected to attend and actively participate in all classes. The student who is consistently late or absent will not have the same opportunities to ask questions as punctual students who attend each lecture and seminar. Therefore, consistent tardiness and/or consistent absence will result in a significantly lower evaluation on class participation. Daily sign-in sheets will be provided for the student's protection. A record of students who arrive late for lecture will be kept. You are responsible for all material covered in classes. If you miss classes, you cannot expect to do well in this course.

ABSENCE FROM CLASS IS NO EXCUSE FOR

MISUNDERSTANDINGS ABOUT ASSIGNMENTS OR QUIZZES

 

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Disability Statement:

Students with documented special learning needs may want to inform the instructor so that accommodations may be made, or contact the Barry University Office of Services for Students with Disabilities 305 899 3489

 

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Student Behavior Statement:

All Barry University students are expected to behave according to accepted norms that ensure a climate wherein all can exercise their right to learn. Disruptive behavior is not acceptable in the classroom. Students engaging in such behavior may be asked to leave or may be removed from the class by security personnel. Actions such as violence, shouting, use of cell phones and/or beepers, using profanity, interrupting, and any other behavior that the instructor believes creates an unpleasant environment in the classroom will be grounds for withdrawal from the course, judicial proceedings, or failure of the course.

 

 

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sky.gif (37164 bytes)

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/

 

 

 

BMS 537 (02)      HUMAN GENETICS      Fall 2002

    Tentative Class Schedule:

 

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Week 1-2    Fundamentals of Genes and Chromosomes    pp.1-70

 

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Aug.29    Composition of DNA, Chromosome, RNA,  Proteins

Transcription of eukaryotic genes

RNA splicing

Mutation and DNA repair, DNA Packaging

Chromosome Banding, Centromeres, Telomeres, ORIs

Chromosome Abnormalities

Construction of mammailia artificial chromosomes: prospects for defining an optimal centromere. BioEssays, 21, 76-83; Schindelhauer D (1999). (pdf format)

DOE HGP Genomic Primers

Primer on Molecular Genetics- http://www.ornl.gov/hgmis/publicat/primer/primer.pdf

This primer was prepared by Denise Casey (Human Genome Management Information System - Oak Ridge National Laboratory) for the 1991-92 DOE Human Genome Program Report and modified for Web access by Dan Jacobson

 

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

National Library of Medicine-http://www.nlm.nih.gov

 

Genetics Basis for Bioinformatics: Using Human Genome as an Example. By Ming-yi Chung NYMU,  Dec 24 , 2001;  Genetic basis for bioinformatics [PDF]

 

 

 

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Sep. 5     Genes and Pedigrees

Mendelian Inheritance, Mitochondrial Inheritance

Genetic Imprinting, Mosaicism and Chimerism

 

Internet Tutorial

http://www.biology.com

The Biology Place- Investigative and Learning Activities

 

Ist Assignment (Due Sept 12):

Investigating a Neurological Condition

Keith A. Johnson (keith@bwh.harvard.edu), J. Alex Becker (jabecker@mit.edu)

 

Investigating a Neurological Disorder

http://www.biology.com/learning/neurological/introduction.html

by John Postlethwait, University of Oregon
© 1996, Peregrine Publishers, Inc., All Rights Reserved

 

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Week 3-4    Fundamentals of Gene Cloning and

Molecular Hybridization     pp.71-138

 

Restriction Enzyme Digestion of DNA: An Interactive Study Guide

By Peter Russell, Reed College

http://www.biology.com/learning/red/introduction.html

A Hypothetical (Tutorial) DNA Mapping Example

http://www.biology.com/learning/red/mapping.html

Restriction Enzyme Cleavage of DNA

http://www.people.virginia.edu/~rjh9u/restdna1.html

Edvotek Biotechnology: DNA Mapping / Sequencing / Bioinformatics

206 - Restriction Enzyme Mapping

 

Map construction with probe fingerprints

Map assembly

 

Multiple Complete Digest Mapping

http://www.genome.washington.edu/UWGC/protocols/MapStrategy.cfm

 

 

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Sep. 12     1st assignment due

Principles of DNA Cloning

Vector system, Expression Cloning

Molecular hybridization

 

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Sep. 19     Polymerase Chain Reaction (PCR)

PCR-based DNA Cloning and DNA Analyses

Cloning- http://www.roslin.ac.uk/public/cloning.html

Application of PCR techniuqe:

Cloning and sequencing of Fundulus heteroclitus gonadotropins. 

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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2nd Assignment (Due Oct 3):

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

Cell to Cell and Person to Person:
Investigating AIDS and HIV
Part I: The Discovery and Epidemiology of AIDS
Part II: Investigating HIV so as to Devise AIDS Therapies

http://www.biology.com/learning/hiv2/introduction.html

by John Postlethwait, University of Oregon
© 1997, Peregrine Publishers, Inc., All Rights Reserved

 

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Week 5-6   The Human Genome   pp.139-208

 

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Sept. 26     The Nuclear Genome

Organization of Human Genes

The Immunoglobulin Gene Family

 

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Oct. 03    2nd assignment due

Multi-Gene Families

Human Gene Expression

The Human Gene Map- www.ncbi.nlm.nih.gov/SCIENCE96

Complete Genomes- www.ncbi.nlm.nih.gov/Complete_Genomes

 

 

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Week 7-9   DNA Mutation        pp. 209-240

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Oct. 10     Mid-Term EXAM

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Oct. 17    Mutation, Polymorphism and DNA Repair

Classification of Mutations

 

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3rd Assignment (Due Nov 7):

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

Recent Research on Co-receptor CKR5

http://www.biology.com/learning/hiv2/entry5.html

 

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Oct. 24     Pathogenic Mutations

Pathogenic Potential of Repeated Sequences

 

Cancer Resource- http://cancer.med.upenn.edu

Online Mendelian Inheritance in Man- OMIM online database for genetic diseases- www.ncbi.nlm.nih.gov/Omim

 

 

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Week 10-11   Mapping the Human Genomes    pp. 241-282

 

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Oct.31      Physical Mapping

Low Resolution Physical Mapping

High Resolution Mapping

 

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Nov. 07    3rd assignment due    

Genetic Mapping of Medelian Characters

        Recombinants and Nonrecombinants

        Restriction Fragment Length Polymorphisms (RFLPs)

 

 

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Week 12-14       Human Genome Project     pp.295-314

 

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Nov. 14     Construction of DNA Maps

The Human Genome Project

Gene Identification

 

logoDOE and NIH logos

About the Human Genome Project   Human Genome Project Information

http://www.ornl.gov/TechResources/Human_Genome/home.html

 

To Know Ourselves

http://www.ornl.gov/hgmis/publicat/tko/index.html

 

Exploring the Genomic Landscape

Genomic Geography

http://www.ornl.gov/hgmis/publicat/tko/04a_img.html

 

An emerging gene map

http://www.ornl.gov/hgmis/publicat/tko/04c_img.html

 

The Institute for Genomic Research

U.S. Department of Energy- Human Genome Program-

http://www.er.doe.gov/production/ober/hug_top.html

 

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Nov. 21     Strategies for Gene Therapy        pp.515-543

Ethics of Human Gene Therapy

 

Cancer Genome Anatomy Project-

www.ncbi.nlm.nih.gov/ncicgap

ExPASy-- Molecular Biology Server-

http://expasy.hcuge.ch

 

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Nov. 28     No class,    Thanksgiving Holiday

 

 

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Week 15      Dec. 5      Review

 

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Week 16     Dec. 12    Final EXAM

 

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MESSAGE  CENTER

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Send message to Dr Lin's Mail Box  emailed.gif (14893 bytes)

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Discussion Forum, OPEN  (Public)  MESSAGE BOARD

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Comment ;    Feedback

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bulletLinks and Assignments

 

bulletDr. Lin's Biology Links (framed version)
bulletDr. Lin's Biology Links (unframed version)
bulletDNA Tools
bulletGenetics Links
bulletMolecular Biology Concepts
bulletGenetics Assignments
bulletHuman Genome Project Links
bulletGenetics in the News

Genetics  Links

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Primer on Molecular Genetics- http://ww.gdb.org/Dan/DOE/intro.html

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Medline Search: Internet Grateful Med-http://igm.nlm.nih.gov

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National Library of Medicine-http://www.nlm.nih.gov

bulletOnline Mendelian Inheritance in Man- OMIM online database for genetic diseases- www.ncbi.nlm.nih.gov/Omim
bulletCloning- http://www.roslin.ac.uk/public/cloning.html
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Cloning News: http://www.nap.edu/issues/14.3/cookdg.htm

National Academies on Cloning, NIH search on Cloning

Hello Dolly: A WebQuest   http://powayusd.sdcoe.k12.ca.us/dolly/main.htm

 

 

                                                                             

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globe_6-26.jpg (17130 bytes)    

Copyright (C) 2000 MacNeil-Lehrer Productions. All Rights Reserved.   

GENOME UNRAVELED  

genomebhead.jpg (13411 bytes)
June 26, 2000
http://www.pbs.org/newshour/bb/health/jan-june00/genome_6-26.html

 

 

Copyright © 2000 MacNeil-Lehrer Productions. All Rights Reserved.

http://www.pbs.org/newshour/bb/health/july-dec99/gene_therapy_splash.htm

http://www.pbs.org/newshour/health/genetics/

Cloning

PBS- Cloning

http://www.pbs.org/newshour/health/cloning.html

 

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     The Rough Draft of the Blueprint

The Human Genome is now available! Find out what a "rough" draft means, and what needs to be done to interpret the information encoded in our genes.

 © 2000 Cold Spring Harbor Laboratory

http://vector.cshl.org/resources/abouthumangenome.html

 

 

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[Briefing Room header]

June 25, 2000

PRESIDENT CLINTON ANNOUNCES THE COMPLETION OF THE FIRST SURVEY OF THE ENTIRE HUMAN GENOME 

Hails Public and Private Efforts Leading to This Historic Achievement

THE WHITE HOUSE    Office of the Press Secretary

http://www.ornl.gov/hgmis/project/clinton1.html

 

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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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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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WEBSCAN Genes on the Web 

by Pamela M. Gannon

http://news.bmn.com/hmsbeagle/83/reviews/insitu  

Harvard University's recent conference Internet & Society 2000: Changing Our Lives (IS2K), held May 31 - June 2, 2000, included an exciting breakout session called "Genes on the Web." A panel of experts discussed how the Internet accelerates discoveries related to the human genome and spreads the information to researchers. In the introduction, Josh Lerner of the Harvard Business School called the current state of genomics research the "marriage of information technology with biotechnology and bioinformatics.

BioMedNet

© Elsevier Science Limited 2000

 

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November-December 2000 Issue of
American Scientist

New Technology Unravels the Mystery of Gene Function

Gene Chips and Functional Genomics

A new technology will allow environmental health scientists to track the expressions of thousands of genes in a single, fast and easy test

http://www.amsci.org/amsci/articles/00articles/Hamadeh.html

 

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Genomes to Life is the proposed next step at the Department of Energy to use data and resources from the Human Genome Project to accelerate understanding of dynamic living systems.

DOE's next step in genomics        logo     Genomes to Life

DOE's proposed Genomes to Life program would make important contributions in the quest to venture beyond characterizing such individual life components as genes and other DNA sequences toward a more comprehensive, integrated view of biology at a whole-systems level. The DOE offices of Biological and Environmental Research and Advanced Scientific Computing Research have formed a strategic alliance to meet this grand challenge

http://doegenomestolife.org/

 

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Cloning (Sun-Sentinel Aug 08 2001)

Researchers debate human cloning  

 Cloning  Problems associated with cloning (145K; KRT)  

Problems associated with cloning (145K; KRT) (View Video)