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					                               Georgetown University
                          Graduate School of Arts & Sciences




                  Bioinformatics Track Graduate Program
             M.S. Degree In Biochemistry & Molecular Biology
     Department of Biochemistry and Molecular Biology & cellular biology




                            PROGRAM HANDBOOK

                                    2008-2009




TABLE OF CONTENTS

I. INTRODUCTION ……….. 1
II. PROGRAMOVE REVIEW ……….. 1
  A. TIMELINESS ……….. 1
  B. VALUE ……….. 2
III. ADMISSIONS ……….. 2
IV. COURSEOF STUDY ……….. 4
  B. DESCRIPTION ……….. 5
  C. COURSE REQUIREMENTS
V. FACULTY AND ORGANIZATION8
  A. OVERSIGHT AND ORGANIZATION ……….. 8
  B. RESOURCES ……….. 8
VI. COMMITMENT TO DIVERSITY ……….. 11
VII. LIBRARY AND TECHNOLOGY ……….. 11
VIII. RESEDENTIALINFORMATION ……….. 11
APPENDIX I ……….. 12
  A. BCHB-521BIOINFORMATICS ……….. 15
  B. BCHB-524:BIOINFORMATICS COMPUTING ……….. 18
  C. BCHB-580 &TBIO-530: SYSTEMS BIOLOGY AND BIOINFORMATICS
  D. BCHB-907:BIOINFORMATICS INTERNSHIP ……….. 22

TABLE 1. TYPICAL ONE-YEAR COURSE SCHEDULING ……….. 6
TABLE 2. SELECTED COURSE DESCRIPTIONS ……….. 7
TABLE 3. BIOINFORMATICS TRACK FACULTY ……….. 9

I. INTRODUCTION
Bioinformatics is an exciting, emerging field at the intersection of the biological and
computational sciences and is fundamental to the modern day study of biology and
essential to 21st century biomedical research. Bioinformatics encompasses the
development and application of computational tools and techniques for the collection,
analysis, management, and visualization of biological data, as well as modeling and
simulation methods for the study of biological systems. Advances in high-through put
biotechnologies and large-scale-bioscience have resulted in the data explosion of omics
biotechnologies and the promise of systems biology and personal genomics. This in
turn has led to high demand for bioinformatics professionals with computing and
bioscience skills in both academia and industry.

The Bioinformatics Track degree program includes course work, hands-on computer
labs, experience building projects, and a bioinformatics internship. Built upon the
unique research strengths and extensive bioinformatics infrastructure at PIR and
Georgetown University, the curriculum emphasizes bioinformatics of genomics,
proteomics and systems biology.
II. PROGRAM OVERVIEW
The one-year M.S. degree in Biochemistry & Molecular Biology (Bioinformatics
Track) is being offered at the department of Biochemistry and Molecular & Cellular
Biology to provide formal education in the field of bioinformatics. The Department’s
large, vibrant biotechnology program and well-connected PhD program has funding
from industry, National Institutes of Health, National Science foundation and
Department of Defense. The Department is also home to the Protein Information
Resource (PIR), a scientific leader in protein bioinformatics for more than four
decades.


   A. Timeliness and unique strengths of the program

The completion of the human genome sequence marked the beginning of a new era of
biological research, in which scientists began to systematically tackle gene functions
and other complex regulatory processes by studying organisms at the global scale from
genomes, transcriptomes and proteomes to metabolomes and interactomes. With the
enormous quantity and variety of data being produced, biology is becoming an
increasingly quantitative science. Computational approaches, in combination with
empirical methods, have become essential for deriving scientific knowledge and
hypotheses. Advances in high-throughput technologies have also highlighted the
importance of a bioinformatics approach to biotechnology, drug discovery, and disease
diagnosis.

The unique strengths of the program:
•        Flexible – Full-time and part-time options, elective courses, customized
programs
•       Multi-disciplinary –Supported by the Department of Biochemistry & Molecular
and Cellular Biology, Department of Oncology, Department of Biostatistics,
Department of Computer Science, Lombardi Cancer Center, and the Protein
Information Resource
•       Professional experience – A 16-week internship with working bioinformatics
professionals in leading bioinformatics, biomedical and biotechnology institutions,
including National institutes of Health, J. Craig Venter Institute (formerly
TIGR),Protein Information Resource, Children's National Medical Center, Center for
Advanced Research in Biotechnology, National Institutes of Standards and
Technology, and local biotechnology companies.
   B. Value

The M.S. Degree in Biochemistry & Molecular Biology (Bioinformatics Track) has an
interdisciplinary curriculum covering both biomedical and bioinformatics sciences.
With computer-lab based courses and the Bioinformatics Internship, either on or off
campus, students will gain hands-on experience in applying bioinformatics as an
integral approach to biomedical research, from basic molecular sequence analysis to
advanced high-throughput omics data analysis. Graduates of this program can pursue
careers in academia or industry, playing key roles in multidisciplinary teams.

The value of the M.S. degree in Biochemistry & Molecular Biology (Bioinformatics
Track) is multi-fold:

      This Track provides an interdisciplinary program where students can learn from
       and interact with faculty from other departments and institutes at Georgetown
       University.

      This Track trains graduate students to apply bioinformatics as an integral
       approach to biomedical research, and to play a key role in interdisciplinary and
       multidisciplinary research and educational programs. This degree program also
       emphasizes both Biochemistry/Molecular Biology and Bioinformatics.
       Therefore, the Bioinformatics Track is unique to offerings by other related
       computational degree programs in “quantitative” sciences (such as computer
       science, mathematics and biostatistics).

      With a formal education in Bioinformatics individuals can work in the
       pharmaceutical and biotechnology industry, join a private sector consulting
       firm, or a Ph.D. program in many medical or scientific fields or pursue further
       study towards a MD, MBA or law degree.

      The program includes multi-disciplinary topics such as: Bioinformatics and
       Systems Biology; Genomic and Proteomic Informatics; Biomedical Text
       Mining and Ontologies; Data Integration and Data Mining; Function Prediction
       and Protein Structure Analysis; Molecular Evolution and Genetics; Pathway
       and Network Analysis; Algorithm and Data Resource Development


III. ADMISSIONS
Application Deadlines
Rolling Admissions with final dates for submission:
Fall Admission: July 1st
Spring Admission: November 15th
Late applications are considered based on availability of space in the M.S. programs.

Admission Requirements
Applicants to the program must be in the last semester of undergraduate study or hold a
bachelor's degree in biology, chemistry or related science from an accredited college or
university. Applicants with business or law degrees will also be considered. Special
consideration is given to applicants with work experience. Students can be admitted for
full-time or part-time studies. The program admissions committee makes all admission
recommendations on a case-by-case basis. The Dean of the Graduate School makes all
final decisions.

Application Form
Incomplete applications will not be considered and not returned to the applicant.

The online application system allows for the electronic submission of the application form
and supporting application documents, such as the personal statement and résumé, as well
as online recommendations. Apply to this graduate program using our online application
form, located at
http://grad.georgetown.edu/pages/graduate_programs.cfm?dept_id=3&show=admiss

Application checklist:
       application form
       non-refundable application fee
       original undergraduate transcripts
       two letters of recommendation
       statement of purpose
       official transcripts
       official recommendations
       passport style/sized photo(approximately 2" x 2")
       TOEFL (for students from non-English speaking institutions)
       GRE not required

Send all application materials, transcripts, and other credentials to:

Office of Biomedical Graduate Education
Attn: Credentials - (Biochemistry Program)
Box 571411-P
3900 Reservoir Road, N.W.
(NE303 Medical-Dental Building)
Washington, DC 20057-1411

Application Fee
The application form must be submitted with a non-refundable application fee. Check or
money orders should be made payable to Georgetown University. Clearly write the
following information on the check or money order: applicant name, date of birth,
program applying to, and term of application.
     $70 online application fee - pay by check or money order
     $80 paper application fee - pay by check or money order

Academic Statement of Purpose and Resume/CV
The applicant is required to provide a 500-word Academic Statement of Purpose (do not
forget to write your name) describing the reasons for enrolling in the program along with a
resume/CV.

Official Transcript
Applicants must provide hard-copy official transcripts of all work beyond secondary
school - undergraduate coursework, graduate course work, study-abroad courses,
community college courses, and non-degree courses. For foreign applicants official
notarized copies/translations should be submitted in a sealed envelope, signed across the
seal by the notary or appropriate official.

Official Recommendations
Recommendations must be from persons in positions to appraise the applicant's potential
for graduate study.

English
All applicants are required to demonstrate a level of proficiency in the English
language sufficient to meet the admission requirements of the Graduate School of
Arts& Sciences. Proficiency can be demonstrated by the receipt of a bachelor's or
advanced degree from an accredited institution of higher education in the United States
or from a university where English is the primary language of instruction. All other
applicants without this credential must achieve a minimum score on either the Test of
English as a Foreign Language (TOEFL) or the International English Language Testing
System (IELTS) - Academic Module. (Please note that applicants receiving degrees at
universities in U.S. territories, such as Puerto Rico, are required to submit the TOEFL
or IELTS unless the primary language of instruction at the institution is English).

Candidates taking the TOEFL must have a minimum score of 550 (paper-based test),
213 (computer-based test), or 80 (iBT).

TOEFL
The Educational Testing Service (ETS)
P.O. Box 6155
Princeton, NJ 08541-6155
Telephone: 609-771-7100
Internet: http://www.toefl.org/
Georgetown University Graduate School ETS Code: 5244

Candidates taking the IELTS -Academic Module must achieve a minimum academic
band score of 7.0.

IELTS International
100 East Corson St., Suite 200
Pasadena, CA 91103
Telephone: 626-564-2054
Internet: http://www.ielts.org
Email: ielts@ieltsintl.org

The TOEFL or IELTS should be taken in time to allow the official results to be sent to
the Office of Graduate Admissions by the appropriate application deadline.
Photocopied and/or faxed documents may not be used to fulfill this requirement. The
English Language Proficiency requirement will not be waived under any
circumstances.

Transfer of Credits
With pre-approval, up to eight graduate credits may be transferred into the Master of
Science Program. At least a B grade is required for each course that is transferred.

Tuition
Tuition for the Master degrees (30 credits), for full time students, is $35,160 ($17,580
per semester) for the Fall 2009 and Spring 2010 Semesters. Tuition is subject to
change. Currently students taking more than 2 semesters to complete the degree will be
charged tuition for all semesters following the first two. We expect a change in the
tuition rate for 2010 where there will be one charge for the degree regardless of the
number of semesters a student enrolls in the program. However, this has not yet been
approved.

Scholarships and other Financial Aid
M.S. students may apply for merit-based, partial scholarships ($5,000 - $10,000 per
year). To be considered, please simply mark the appropriate box on your application
for admission. Information about student loan programs and other forms of financial
aid    can    be    obtained     from    the    Office    of    Student   Financial
Aid(http://www8.georgetown.edu/admin/provost/osfs/).



IV. COURSE OF STUDY

B. Description

     Name of the Degree Program:
     M.S. Degree in Biochemistry & Molecular Biology (Bioinformatics Track)

     Educational Objectives:
     The Bioinformatics Track in the M.S. Degree in Biochemistry & Molecular
     Biology has an interdisciplinary curriculum covering both biomedical and
     bioinformatics sciences. With computer-lab based courses and the Bioinformatics
     Internship, either on or off campus students will gain hands-on experience in
     applying bioinformatics as an integral approach to biomedical research, from
     basic molecular sequence analysis to advanced high-throughput omics data
     analysis. Graduates of this program can pursue careers in academia or industry,
     playing key roles in multidisciplinary teams.

     Number of Credits Required:
     The one-year (30 credit) program may be completed over a longer time frame for
     part-time students.

     Program Requirements and Admission Requirements for the Degree:
     (Same as the M.S. Degree in Biochemistry &Molecular Biology unless otherwise
     stated in this handbook)

     Please read the complete admissions information found on the Biomedical
     Graduate Education pages athttp://biomedgrad.georgetown.edu/prospective.html

     Applicants to the program must be in the last semester of undergraduate study or
     hold a bachelor's degree in biology, chemistry or related science from an
     accredited college or university with a minimum grade point average of 3.0 or
     higher. Applicants with business or law degrees will also be considered. Special
    consideration is given to applicants with work experience. Students can be
    admitted for full-time or part-time studies. The program admissions committee
    makes all admission recommendations on a case-by-case basis. The Dean of the
    Graduate School makes all final decisions.


C. Course Requirements


    Degree Credit Requirement:
    30 credit hours total

    Core Courses (20 credit hours)
         *
          BCHB-513 Core Concepts of Biochemistry (4Fall)
           BCHB-521 Bioinformatics (3 Fall)
           BCHB-524 Bioinformatics Computing (3Fall)
           BCHB-526 Modern Methods of Biotechnology (3 Fall)
           BCHB-580 Systems Biology and Bioinformatics (3 Spring)
           BCHB-907 Bioinformatics Internship (4 Fall/Spring)
          *
           BCHB-501Biochemical and Cellular Sciences (3 Fall)
           [Can replaceBCHB-513 with permission of the course director]

    Recommended Electives (8 credit hours)
         BCHB-541 Structural Molecular Biology (3 Spring)
         BIST-502 Applied Biostatistics (3 Spring)
         PHAR-534 Ethical Issues in Scientific Research (2 Fall/Spring)

    Other Electives (3 credit hours)
          Any courses offered by the Department of Biochemistry and Molecular &
          Cellular Biology, and most science graduate courses at Georgetown
          University




                 Table 1. Typical One-Year Course Scheduling
            Fall Semester (16) [Core (13), Other (3)]
            BCHB-513 Core Concept of Biochemistry (4)
            BCHB-521 Bioinformatics (3)
            BCHB-524 Bioinformatics Computing (3)
            BCHB-526 Modern Methods of Biotechnology (3)
            Other Electives (3)
            Spring Semester (15) [Core (7), Recommended Electives (8)]
            BCHB-580 Systems Biology and Bioinformatics (3)
            BCHB-907 Bioinformatics Internship (4)
            BCHB-541 Structural Molecular Biology (3)
            BIST-502 Applied Biostatistics (3)
            PHAR-534 Ethical Issues in Scientific Research (2)




                         Table 2. Selected Course Descriptions

Course           Title            Directors        Schedule                  Description
    #
 BCHB        Biochemical      Mark Danielsen          Fall       Biochemical processes including
  501         & Cellular                                         protein folding, enzyme kinetics,
3 credits     Sciences                              Mon Fri      DNA replication, RNA transcription,
                                                  9 -10:30 am    and protein synthesis.
                                                       W
                                                    9-10 am
 BCHB Core Concepts                Cynthia            Fall       Survey of core topics in biochemistry
  513          in                 Rosenthal                      and molecular biology with emphasis
4 credits Biochemistry                               Mon         on applications to biotechnology and
                                                  10 - 11 am     biomedical sciences.
                                                  Tues Thurs
                                                  9 – 10 am
BCHB Bioinformatics           Mark Danielsen          Fall       Introduction to genomic and protein
 521                                                             sequence analysis. Includes both
3 credits                                     Tues Thurs      lectures and computer tutorials
                                              1:30 – 3 pm
 BCHB Bioinformatics        Nathan Edwards        Fall      A hands-on, computer lab-based
  524     Computing                                         course that introduces basic
3 credits                                         Wed       bioinformatics programming,
                                             1:30 – 4:30 pm database design, and web resource
                                                            development
 BCHB Core Methods          Dean Rosenthal        Fall     Lectures on methods used for
  526           in                                         analysis, purification, and
3 credits Biotechnology                       Tues Thurs quantification of nucleic acids and
                                             10:30 – 12 pm proteins (PCR, hybridization
                                                           techniques, cloning, and cell culture)
BCHB-        Structural         Sona             Spring       Introduction to three-dimensional
  541        Molecular        Vasudevan                       structures of biomolecules, structural
3 credits     Biology                           Thurs         determination methods, structural
                                              10 – 12 pm      databases and visualization tools,
                                                              molecular modeling methods, protein
                                                              structure-function relationships, and
                                                              structure-based drug design.
BCHB-        Systems        Nathan Edwards       Spring    Discussion of bioinformatics in
  580      Biology and                                     systems biology, covering microarray
3 credits Bioinformatics                          Wed      data analysis, proteomic &
                                              1:30 - 3 pm metabolomic informatics, and
                                                   Fri     regulatory network and pathway
                                             11 - 12:30 pm analysis
BCHB- Bioinformatics        Mark Danielsen    Fall, Spring,   Bioinformatics research or
  907     Internship                            Summer        development project. May be
4 credits                                                     performed with faculty on campus or
                                                              with scientists in other organizations
  BIST        Applied       Rebecca Slack        Spring       Introductory biostatistical theory and
  502       Biostatistics                                     application for students pursuing a
3 credits                                      Mon Wed        degree in fields outside of the
                                              11 – 12 pm      Department of Biostatistics,
                                                              Bioinformatics, and Biomathematics.
   PHAR Ethical Issues         Sorell Schwartz      Fall, Spring   Discussions of ethical questions and
    534     in Scientific                                          dilemmas facing scientists today.
  2 credits   Research                                  Mon
                                                      3 – 5 pm


Course descriptions, as well as class schedules and other information about
Biochemistry &Molecular Biology course offerings can be found on the
University Registrar's course site located at:
http://explore.georgetown.edu/courses/index.cfm?Action=List&ProgramID=6
For detailed course descriptions please see appendix I. Contact course
directors for final versions.




V. FACULTY AND ORGANIZATION

A. Oversight and Organization

The oversight for this program is provided by the Department Chair, the Chair of the
Department Graduate Advisory Committee, and the Director of the M.S. Degree in
Biochemistry & Molecular Biology. The Bioinformatics Track Graduate Committee
provides academic direction as well as student recruitment and advising for this
program.


B. Resources

This Bioinformatics Track is supported by faculty members in the Department of
Biochemistry and Molecular & Cellular Biology and the Lombardi Cancer Center
(Table 3). Several members of the Bioinformatics Track faculty are also members of
the scientific staff at the Protein Information Research. The Track faculty is involved in
both teaching the bioinformatics courses and mentoring graduate internship projects.
                      Table 3. Bioinformatics Track Faculty

Mark Danielsen, Ph.D., Associate Professor
 Bioinformatics Track Director & Course Director (BCHB-521)
 Course Instructor – Functional Genomics
 A recognized expert on the glucocorticoid receptor and the biochemical detection of pathogens
   and of biological threat agents, developed the Nuclear Receptor Resource and started the first
   graduate bioinformatics course at Georgetown in 2001
Cathy H. Wu, Ph.D., Professor and Director, PIR
 Bioinformatics Track Co-Director
 Course Instructor – Protein Bioinformatics, Systems Biological Data Integration
 Degrees in both biology and computer science, conducted bioinformatics research since 1989
   in areas of protein family classification, functional annotation, biological data integration and
   mining, proteomics, and biomedical text mining and ontology
Nathan Edwards, Ph.D., Assistant Professor
 Bioinformatics Course Director (BCHB-524, BCHB-580)
 Course Instructor – Bioinformatics Computing, Mass Spectrometry Algorithms
 Trained in operations research and scientific computing, 7 years bioinformatics research
   experience, specialized in algorithms for proteomics mass spectrometry data analysis, pathogen
   detection by mass spectrometry, and DNA assay design.
Cecilia Arighi, Ph.D., Assistant Professor and Senior Bioinformatics Scientist, PIR
 Course Instructor – Bioinformatics Databases and Web Resources
 Degree in biological chemistry and experience in protein biochemistry, biophysics, and cell
   biology, specializes in protein functional annotation and bioinformatics resources
Hongzhan Huang, Ph.D., Assistant Professor and Bioinformatics Team Lead, PIR
 Course Instructor – Bioinformatics Algorithms and Computing
 Degrees in mathematics and statistical genetics, 10 years experience in bioinformatics
   algorithm and software system development for protein sequence analysis, family
   classification, biological data integration, and proteomics data mining
Peter McGarvey, Ph.D., Associate Professor and Project Manager, PIR
 Course Instructor – Biodefense Proteomics
 Trained in molecular virology and technology management, 10 years experience in
    bioinformatics, specialized in software quality assurance and biodefense proteomics
Baris Suzek, M.S., Research Associate and Bioinformatics Associate Team Lead, PIR
 Course Instructor – Bioinformatics Computing, caBIG Architecture
 Trained in computer science and computational biology, 6 years experience in developing
    bioinformatics databases, software programs and caBIG architecture
Sona Vasudevan, Ph.D., Assistant Professor and Senior Bioinformatics Scientist, PIR
 Course Instructor – Structural Biology and Structure Bioinformatics
 Trained in medical biophysics, 10 years research experience in crystallography, molecular
       modeling, protein structure-function analysis and ligand-binding proteins
   Lai-Su Yeh, Ph.D., Assistant Professor and Senior Bioinformatics Scientist, PIR
    Bioinformatics Track Coordinator
    Course Instructor – Molecular Databases, Protein Evolution and Functional Annotation
    Degrees in organic chemistry and in biochemistry, over 25 years experience in protein
       sequence database, protein classification and functional annotation




VI. COMMITMENT TO DIVERSITY
This program utilizes the strategies and approaches already exist in the Department of
Biochemistry and Molecular & Cellular Biology and across the Georgetown University
to recruit and retain a diverse student population. In addition, the Bioinformatics Track
faculty who are principal investigators holding NIH research grants will use the
Minority Supplement to NIH Research Grants (http://grants.nih.gov/grants/guide/pa-files/PA-
05-015.html)to request supplemental funds to improve diversity of the bioinformatics
research and educational program. As a bioinformatics component for Georgetown’s
WRICTS Translational Research initiative, we also interact closely with the Howard
University, a historically black university and a member of the WRICTS Consortium
institutions located in the Washington DC area, for student recruitment.


VII. LIBRARY AND TECHNOLOGY
The Georgetown University library's current holdings and subscriptions cover major
bioinformatics journals. In addition, the PIR library has a large collection of
bioinformatics books, many of which are placed on the library reserve each semester as
reference materials for existing bioinformatics courses.

PIR also has extensive computer hardware systems, consisting of three Sun Fire V880
Servers, a 100-CPU Linux cluster, two Dell 8-CPU servers, large disk and tape
storages, and several personal computers and laptops, as well as software and database
systems, including major bioinformatics software programs and the Oracle database
management system. These PIR computing systems is available to this Bioinformatics
Track program.



VIII. Housing
Georgetown University does not provide graduate student housing on-campus. The
area around Georgetown and the surrounding cities have many available housing
opportunities for students. Options include renting a single room in a house, group
houses, and a variety of apartment possibilities. Information on finding affordable and
comfortable housing in the area can be found on pages maintained by the Graduate
School (http://grad.georgetown.edu/pages/grad_housing.cfm)and by the Office of
International programs (http://oip.georgetown.edu/isss/housing.htm).

IX. International Students
Georgetown University takes great pride in its international character. International
students, faculty, and researchers are an extremely important part of the Georgetown
community. Over 2,000 individuals from over 130foreign countries study, research,
and teach at Georgetown.               The Office of International Programs
(http://oip.georgetown.edu) provides a variety of support services to this community,
including immigration advising, cultural and educational programming.

APPENDIX I

                   Brief Descriptions of Bioinformatics Courses

BCHB 521 Bioinformatics
3 Cr
T & R 1:30 to 3 pm
Fall Semester
BACC Computer Lab, DML
Limit of 25 Students
Directors
Mark Danielsen
Instructors
Lai-Su Yeh
Anastasia Nikolskaya
Cholayakanahalli Vinayaka
Cecilia Arighi
Description
A mixture of lectures and hands-on sessions with introduction to bioinformatics
concepts, methods, databases and applications, covering genomic sequence analysis,
molecular evolution, and protein sequence, structural, functional analysis. Non-
bioinformatics major students can take individual units of this course on Genomic
Sequence Analysis (BCHB 571) and Protein Sequence Analysis (BCHB 572).

BCHB 524 Bioinformatics Computing
3 Cr
W 1:30pm to 4:30pm
Fall Semester
BACC Computer Lab, DML
Limit of 25 Students
Director
Nathan Edwards
Description
A hands on introduction to programming for bioinformatics using the scripting
language Python. Students will build a portfolio of scripts that automate common
bioinformatics tasks such as accessing data in relational databases and web-based
repositories, interfacing with external tools such as blast, and building web-based
resources for use by interactive users or as web-services.

BCHB 571 Genomic Sequence Analysis
1 Cr
T & R 1:30 to 3 pm
Fall Semester, Aug 28th to Sept 30th
BACC Computer Lab, DML
Limit of 20 Students
Non bioinformatics students only with permission of course director
Director
Mark Danielsen
Description
A mixture of lectures and hands-on sessions on the analysis of genomic sequences,
covering genome sequence assembly, gene finding, transcript mapping and
comparative genomics. Students should take either BCHB 571 or BCHB 521 but not
both.

BCHB 572 Protein Sequence Analysis
2 Cr
T & R 1:30 to 3 pm
Fall Semester, Oct 2nd to end of semester
BACC Computer Lab, DML
Limit of 20 Students
Non bioinformatics students only with permission of course director
Instructors
Lai-Su Yeh
Anastasia Nikolskaya
Cholayakanahalli Vinayaka
Cecilia Arighi
Description
A mixture of lectures and hands-on sessions on the bioinformatic analysis of protein
sequences, covering phylogenetic analysis, sequence alignment, protein family
classification and structural and functional analysis. Students should take either BCHB
572 or BCHB 521 but not both.


BCHB 580 Systems Biology and Bioinformatics
3 Cr
W 1:30 to 3 pm, F 11:00am to 12:30pm
Spring Semester
BACC Computer Lab, DML
Limit of 25 Students
Director
Nathan Edwards
Instructors
Robert Clarke
Habtom Ressom
Radoslav Goldman
Albert Fornace
Description
An introduction to bioinformatics in systems biology, covering microarray data
analysis, proteomic/metabolomic informatics, and regulatory network and pathway
analysis. Non-bioinformatics major students can take individual units of this course on
Transcriptomics (BCHB 581), Proteomics (BCHB 582) and Systems Biology (BCHB
583).

BCHB 581 Transcritomics: Microarray Data Analysis
1 Cr
W 1:30 to 3 pm, F 11:00am to 12:30pm
Spring Semester, Jan 7th to Feb 6th
BACC Computer Lab, DML
Limit of 20 Students
Non bioinformatics students only with permission of course director
Director
Habtom Ressom
Instructors
Robert Clarke
Description
An introduction to microarray experimental design and data analysis. Students should
take either BCHB 580 or BCHB 581 but not both.

BCHB 582 Proteomics: Mass Spectrometry Data Analysis
1 Cr
W 1:30 to 3 pm, F 11:00am to 12:30pm
Spring Semester, Feb 11th to 20 March
BACC Computer Lab, DML
Limit of 20 Students
Non bioinformatics students only with permission of course director
Directors
Nathan Edwards and Radoslav Goldman
Instructors
Habtom Ressom
Description
An introduction to mass spectrometry data analysis and proteomic biomarker
discovery. Students should take either BCHB 580 or BCHB 582 but not both.

BCHB 583 Systems Biology: Pathway and Network Data Analysis
1 Cr
W 1:30 to 3 pm, F 11:00am to 12:30pm
Spring Semester, 25 March to end of semester
BACC Computer Lab, DML
Limit of 20 Students
Non bioinformatics students only with permission of course director
Director
Nathan Edwards
Instructors
Habtom Ressom
Albert Fornace
Cathy Wu
Description
An introduction to metabolomics, interactomics, regulatory network and pathway
analysis, and omics data integration and mining. Students should take either BCHB
580 or BCHB 583 but not both.

BCHB 907 Bioinformatics Internship
4 Cr
Spring or Fall Semester
Only with permission of course director
Director
Mark Danielsen
Description
Internship for a bioinformatics project with defined objectives in a research laboratory
on campus or off-campus (e.g. NIH, JCVI,CNMC, CARB). Internships can be in
various topics such as genomic and proteomic informatics, protein structural and
functional analysis, comparative genomics, pathway and network analysis, systems
biology, medical informatics, biomedical text mining and ontologies, data integration
and mining, and bioinformatics tool and database development.


                  Detailed Descriptions of Bioinformatics Courses

A. BCHB-521: Bioinformatics
3 Credits, Tuesday and Thursday, 1:30pm-3:00pm
BACC Computer Lab, Dahlgren Medical Library


Course Directors:
Mark Danielsen, PhD, dan@georgetown.edu,(202) 687-4169, Room 355, Basic Science
Building

Course Description:
This course will introduce students to bioinformatics concepts, methods, databases and
applications, covering genomic sequence analysis, comparative genomics, molecular
evolution, and protein sequence, structural, functional analysis. The course will include
lectures, demonstrations, and practice sessions in the computer laboratory of Dahlgren
Medical Library. Most lectures are followed by hands-on tutorials and some also with
take-home assignments to familiarize with the bioinformatics concepts, methods and
web resources.

Course Sections:
This course consists of two units, unit one on “Bioinformatics and Genomics” and unit
two on “Bioinformatics and Protein Evolution, Structure and Function.” Students can
select from one of the three sections below:
BCHB-521 (August 28 – December11, 2008): 3 credits, covering both unit 1 and unit 2
BCHB-571 (August 28 – September30, 2008): 1 credit, covering only unit 1
BCHB-572 (October 2 – December11, 2008): 2 credits, covering only unit 2

Grading:
Grades for the course will be based on take-home assignments and an exam and/or
term project:
BCHB-521: assignments(45%), unit 1 exam (15%), term project presentation and report
(40%)
BCHB-571: assignments (60%),unit 1 exam (40%)
BCHB-572: assignments (40%), term project presentation and report (60%)

Expected background: One computer science-related course would be useful.

Use of computers: Computer workstations are provided; bring your own wireless
laptop if you wish. The GU Blackboard system will be used.
Reading material: Bioinformatics: A practical guide to the analysis of genes and
proteins by Andreas D. Baxevanis and B.F. Francis Ouellette. In addition to this,
several bioinformatics books are on reserve and relevant articles will be provided.
Relevant reading will be indicated each week.


Course Syllabus

         Unit      Date     Topics
          1                 Unit 1: Bioinformatics and Genomics

         1-1       2-Sep    Information storage and retrieval (HW #1)
         1-2       4-Sep    nBLAST (HW #2) Gene finding
         1-3       9-Sep    Genome sequencing - HW #3
                            On-line Tutorial Transcript mapping - Genome
         1-4      11-Sep
                            Browser (HW #4)
                            DNA sequence/genome databases and genome
         1-5      16-Sep
                            annotation HW #5
         1-6      18-Sep    Comparative genomics (HW #6)
         1-7      23-Sep    Gene Prediction
        1-8   25-Sep   Human genetic variation: SNPs and HapMap project
        1-9   30-Sep   Unit exam
                       Unit 2: Bioinformatics and Protein Evolution,
        2
                       Structure and Function
        2-1    2-Oct   UniProt/PIR and protein bioinformatics resources
        2-2    7-Oct   NCBI bioinformatics resource
        2-3    9-Oct   Protein sequence, domain and evolution
        2-4   14-Oct   Current research in protein evolution
                       Protein sequence analysis and database searching -
        2-5   16-Oct
                       FASTA, BLAST; Multiple sequence alignment
        2-6   21-Oct   Molecular phylogenetic analysis (HW #7)
                       Protein and domain based classification: concepts,
        2-7   23-Oct
                       uses and limitations
        2-8   28-Oct   Protein family classification and functional annotation
                       Protein family classification and functional annotation
        2-9   30-Oct
                       (HW #8)
       2-10    4-Nov   Term project: functional annotation of protein family
       2-11    6-Nov   PDB and structure bioinformatics resources
                       Protein structure, function and homology modeling
       2-12   11-Nov
                       (HW #9)
                       Gene Ontology, Protein Ontology and biological
       2-13   13-Nov
                       pathways
       2-14   18-Nov   Genome evolution and comparative genomics
       2-15   20-Nov   Protein annotation jamboree
       2-16   25-Nov   Protein annotation jamboree
       2-17    2-Dec   Protein annotation jamboree
       2-18    4-Dec   Term project: oral presentations
              11-Dec   Term project: written report due




B. BCHB-524: Bioinformatics Computing

FALL 2008
3 Credits, Wednesday, 1:30pm-4:30pm
BACC Computer Lab, Dahlgren Medical Library
   Course Director:
   Nathan Edwards, PhD, nje5@georgetown.edu, (202) 687-7042, 3300Whitehaven St NW,
   Suite 1200

   Course Description
   This course will provide a hands introduction to programming for bioinformatics using
   the scripting language Python. Students will build a portfolio of scripts that automate
   common bioinformatics tasks, from reading and writing common bioinformatics file
   formats and accessing data in relational databases and web-based repositories,
   interfacing with external tools such as blast, and building web-based resources for use
   by interactive users or as web-services. Each class will comprise a lecture and
   computer lab, in which students will practice using newly introduced concepts, and
   begin the weekly programming exercises. Students will also complete a programming
   project implementing a web-application for a specific bioinformatics analysis. Grades
   will be assigned based on weekly programming exercises (60%) and the term project
   (40%).

   Grading:
   Grades will be assigned based on weekly programming exercises (60%) and the term
   project (40%).

   Expected Background:
   One programming or computer science-related course would be useful, but none is
   required.

   Use of Computers:
   Students should have access to a personal computer for use outside of lectures and
   labs; computer workstations will be provided during class.

   Textbook:
   There is no required text, but various web-based and book-based resources will be
   referenced.
   For those with little or no previous programming experience, “Learning Python” by
   Mark Lutz is strongly recommended.

   Course Syllabus

Date    Topics
27-Aug   No class (Monday schedule applies)
         Introduction to Python: Installation, Syntax, Basic Data types, Strings, Control Flow
3-Sep
         Application: DNA as a string, reverse complement.
         Advanced Python Datastructures: Lists, Hashes, Sets, Files, Arrays
10-Sep
         Application: DNA translation, reading and writing sequences
         Advanced Python Idioms: Iterators, Generators, Comprehensions, Functional
17-Sep   Programming
         Application: Sequence database iterator, computing % GC
         Basic File Parsing: Fasta, CSV, DTA files, Python library, BioPython
24-Sep
         Application: Amino-acid frequencies, reading and writing SwissProt, Refseq records
         Advanced File Parsing: Regular Expressions
1-Oct
         Application: Restriction and digestion enzymes
         Advanced File Parsing: Introduction to XML, ElementTree
8-Oct
         Application: Reading pepXML, mzXML
         Advanced Python Concepts: Modules, Packages, Exceptions, Classes, Inheritance
15-Oct
         Application: Mass spectrometry I/O module
         Using Web-Services: NCBI e-Utils, online BLAST
22-Oct
         Application: Retrieving PubMed references, protein homologs
         Using Local Tools: Installing & running blast, clustalw, EMBOSS, primer3
29-Oct
         Application: Design PCR primers
         Introduction to Relational Databases: Installing MySQL, Basic SQL concepts
5-Nov
         Application: Protein and mRNA gene clusters via Unigene
         Relational Database Design: Normalized Form, Foreign Keys, Indexes, SQLObject
12-Nov
         Application: Protein and mRNA gene clusters via Unigene
         Data Warehousing: Large scale databases
19-Nov
         Application: Peptide sequence confidence assessment
         Implementing Web-Applications: HTML, TurboGears
26-Nov
         Application: Enzymatic digest server
         Graphics and GUIs: pylab, Tkinter
3-Dec
         Application: Mass spectrum viewer
10-Dec   Student Project Presentations (Exam Week)
C. BCHB-580& TBIO-530: Systems Biology and Bioinformatics

SPRING 2009
3 Credits, Wednesday,1:30pm-3:00pm & Friday, 11:00am-12:30pm
BACC Computer Lab, Dahlgren Medical Library


Course Directors:
BCHB-580
Nathan Edwards, PhD, nje@georgetown.edu, 7-7042, Harris Building, Room 1215
TBIO-530
Habtom Ressom, PhD,hwr@georgetown.edu,7-2283, Building D, Room 174
Rado Goldman, PhD, rg26@georgetown.edu,7-9868, Lombardi Cancer Center, Room
S-183

Course Description:

This course will introduce students to bioinformatics in systems biology, covering
microarray data analysis, proteomic informatics, and regulatory network and pathway
analysis, and discuss how a global analysis of “omics” data improves understanding of
a biological system.

The course will include lectures and practice sessions in the computer laboratory of
Dahlgren Medical Library.

Course Units:
This course consists of three units on Transcriptomics, Proteomics and Systems
Biology, respectively. Non-bioinformatics major students who wish to take only one or
two of the three units can select from the following courses:
BCHB-581 Transcriptomics: Microarray Data Analysis (1 credit, Jan 7- Feb 6, 2009)
BCHB-582 Proteomics: Mass Spectrometry Data Analysis (1 credit, Feb 11-Mar 20,
2009)
BCHB-583Systems Biology: Pathway & Network Data Analysis (1 credit, Mar 25-May
6,2009)

Grading:
Grades for the course will be based on take-home assignments (55%), unit exams
(30%),and a term project report (15%)

Expected background: One computer science-related course would be useful but not
required.

Use of computers: Computer workstations are provided; bring your own wireless
laptop if you wish. The GU Blackboard system will be used.

Reading material: There is no single required text. However, several bioinformatics
books are on reserve and relevant articles will be provided. Relevant reading will be
indicated each week.
Course Syllabus

   Unit      Date     Topics
     1                Transcriptomics: Microarray Data Analysis
    1-1    7-Jan      Transcriptomics technology - DNA microarray
    1-2    9-Jan      Microarray experimental design and hypothesis testing
    1-3    14-Jan     Microarray data preprocessing and normalization
                      Expression profiling - differential expression and significance
    1-4    16-Jan
                      (HW #1)
    1-5    21-Jan     Clustering analysis - classification of samples (HW #2)
                      Biological analysis of microarray data - Gene Ontology (HW
    1-6    23-Jan
                      #3)
    1-7    28-Jan     Microarray databases and web resources
    1-8    30-Jan     Sequence-based microarray analysis
    1-9    4-Feb      Oncogenomics: Transcriptomics and cancer research
           6-Feb      Unit 1 exam
     2                Proteomics: Mass Spectrometry Data Analysis
    2-1    11-Feb     Proteomics technology - mass spectrometry
    2-2    13-Feb     Protein quantitation (HW #1)
    2-3    18-Feb     Peptide and protein identification
                      Proteomic search tools - Mascot, Sequest, X!Tandem (HW
    2-4    20-Feb
                      #2)
    2-5    25-Feb     Proteomic databases and web resources (HW #3)
    2-6    27-Feb     Mass spectral data analysis
    2-7    4-Mar      Proteomics and glycomics in biomarker discovery
    2-8    6-Mar      Biological analysis of proteomic data - iProXpress
                      Spring break (March 11 &13)
    2-9    18-Mar     Proteomics - past, present and future
           20-Mar     Unit 2 exam
     3                Systems Biology: Pathway & Network Data Analysis
                      Introduction to systems biology
    3-1    25-Mar
                      Term project: Literature review of systems biology
    3-2    27-Mar     Interactomics: protein-protein interactions and networks
    3-3    1-Apr      Reconstruction of metabolic and signaling networks (HW #1)
    3-4    3-Apr      Modeling of gene regulatory networks (HW #2)
    3-5    8-Apr      Metabolomics
                      Easter break (April 10)
    3-6    15-Apr     Systems biology databases and web resources
    3-7    17-Apr     Finding and exploring biological pathways (HW #3)
    3-8    22-Apr     Integrated bioinformatics for systems biology
    3-9    24-Apr     From protein networks to biological systems
           6-May      Literature review term project: written report due
   Unit      Date     Topics



D. BCHB-907: Bioinformatics Internship

Course Number: BCHB-907
Course Title: Bioinformatics Internship
Course Director: Mark Danielsen, PhD, dan@georgetown.edu,(202) 687-4169, Room
355, Basic Science

Course Description: Internship for a bioinformatics research or development project
with defined objectives, with faculty on campus or researchers in DC area research
institutions
Fall Semester: September 1 - December 9
Spring Semester: January 2 - May 7
Summer Semester: June 1 - August 30

Students in the selection of an internship will follow the following guidelines:

    1. Unless special permission is granted, students need to complete 15 semester credit
       hours prior to the start of their internship.
    2. All courses for the semester must be completed with a “B” or better.
    3. Select 3 laboratories/mentors within a list provided by the program. Priority in
       assignments will be made to laboratories where the faculty is a member of the
       Department of Biochemistry and Molecular & Cellular Biology. Co-mentorship by
       faculty on GU campus and a research lab in area institutions can be considered.
    4. There will be some intern positions at local organizations, such as NCI Center for
       Biomedical Informatics and Information Technology, J Craig Venter Institute
       (formerly TIGR), Children's National Medical Center, Center for Advanced
       Research in Biotechnology, National Institutes of Standards and Technology, and
       local biotech companies.
    5. Research internships need to be in the D.C. metropolitan area and must be
       approved by the program.
    6. Each participating mentor will develop with the internship student specific
       objectives to be met during the internship. Fill out the internship forms, submit it to
       the course director, and have it approved by the program prior to the start of the
       internship. Write the objectives as you understand it (not written by your mentor).
       Have your mentor sign the form at the bottom to indicate his/her approval of your
       objectives.
    7. The internship is for a minimum of 320 hours, which for the fall and spring
       translates to 20 hours per week for 16 weeks. For the summer, other arrangements
       are acceptable (i.e. 40 hours per week for 8 weeks).
    8. A final 20-page research paper and a poster presentation are required to complete
       the course. The paper due dates and the poster presentations will be in the last week
       of August (for summer internships), first week of December (for fall internships),
       and first week of May (for spring internships).
    9. The 20-page research paper will follow the following format: Introduction,
       Materials and Methods, Results, Discussion/Conclusion, and References.

				
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