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. PROGRAM OVERVIEW..................................................................................................................1

A. TIMELINESS ..........................................................................................................................................1 B. VALUE..................................................................................................................................................2

III. ADMISSIONS.....................................................................................................................................2 IV. COURSE OF STUDY ........................................................................................................................5

B. DESCRIPTION........................................................................................................................................5 C. COURSE REQUIREMENTS ......................................................................................................................6

V. FACULTY AND ORGANIZATION ................................................................................................8 A. OVERSIGHT AND ORGANIZATION .........................................................................................................8 B. RESOURCES ..........................................................................................................................................8

VI. COMMITMENT TO DIVERSITY.................................................................................................11 VII. LIBRARY AND TECHNOLOGY ..................................................................................................11 VIII. RESEDENTIAL INFORMATION..................................ERROR! BOOKMARK NOT DEFINED. APPENDIX I ...................................................................................................................................................12

A. BCHB-521 BIOINFORMATICS.............................................................................................................15 B. BCHB-524: BIOINFORMATICS COMPUTING .......................................................................................18 C. BCHB-580 & TBIO-530: SYSTEMS BIOLOGY AND BIOINFORMATICS ...............................................20 D. BCHB-908: 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-throughput 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 coursework, 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

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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

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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 coursework, study-abroad courses, community college courses, and non-degree courses.

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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.

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Tuition Tuition for the Master degrees (30 credits), for full time students, is $35,160 ($17,580 per semester) forthe Fall 2009 and Spring 2010 Semesters. Tuition is subject to change. Currently students taking more than2 semesters to complete the degree will be charged tuition for all semesters following the first two. Weexpect a change in the tuition rate for 2010 where there will be one charge for the degree regardless ofthe 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 at http://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. 5

C. Course Requirements

Degree Credit Requirement: 30 credit hours total Core Courses (20 credit hours)

*BCHB-513 Core Concepts of Biochemistry (4 Fall) BCHB-521 Bioinformatics (3 Fall) BCHB-524 Bioinformatics Computing (3 Fall) BCHB-526 Modern Methods of Biotechnology (3 Fall) BCHB-580 Systems Biology and Bioinformatics (3 Spring) BCHB-908 Bioinformatics Internship (4 Fall/Spring)

*BCHB-501 Biochemical and Cellular Sciences (3 Fall) [Can replace BCHB-513 with permission of the course director]

Recommended Electives (7 credit hours)

BCHB-541 Structural Molecular Biology (2 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 (14) [Core (7), Recommended Electives (7)] BCHB-580 Systems Biology and Bioinformatics (3)

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BCHB-908 Bioinformatics Internship (4) BCHB-541 Structural Molecular Biology (2) BIST-502 Applied Biostatistics (3) PHAR-534 Ethical Issues in Scientific Research (2)

Table 2. Selected Course Descriptions

Course # Title Directors Schedule Description BCHB

501 3 credits

Biochemical & Cellular Sciences

Mark Danielsen Fall

Mon Fri 9 -10:30 am

W 9-10 am

Biochemical processes including protein folding, enzyme kinetics, DNA replication, RNA transcription, and protein synthesis.

BCHB 513

4 credits

Core Concepts in

Biochemistry

Cynthia Rosenthal

Fall

Mon 10 - 11 am Tues Thurs 9 – 10 am

Survey of core topics in biochemistry and molecular biology with emphasis on applications to biotechnology and biomedical sciences.

BCHB 521

3 credits

Bioinformatics Raja Mazumder and

Mark Danielsen

Fall

Tues Thurs 1:30 – 3 pm

Introduction to genomic and protein sequence analysis. Includes both lectures and computer tutorials

BCHB 524

3 credits

Bioinformatics Computing

Nathan Edwards Fall

Wed 1:30 – 4:30 pm

A hands-on, computer lab-based course that introduces basic bioinformatics programming, database design, and web resource development

BCHB 526

3 credits

Core Methods in

Biotechnology

Dean Rosenthal Fall

Tues Thurs 10:30 – 12 pm

Lectures on methods used for analysis, purification, and quantification of nucleic acids and proteins (PCR, hybridization techniques, cloning, and cell culture)

BCHB-541

3 credits

Structural Molecular Biology

Sona Vasudevan

Spring

Thurs 10 – 12 pm

Introduction to three-dimensional structures of biomolecules, structural determination methods, structural databases and visualization tools, molecular modeling methods, protein

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structure-function relationships, and structure-based drug design.

BCHB-580

3 credits

Systems Biology and

Bioinformatics

Nathan Edwards Spring

Wed 1:30 - 3 pm

Fri 11 - 12:30 pm

Discussion of bioinformatics in systems biology, covering microarray data analysis, proteomic & metabolomic informatics, and regulatory network and pathway analysis

BCHB-908

4 credits

Bioinformatics Internship

Mark Danielsen Fall, Spring, Summer

Bioinformatics research or development project. May be performed with faculty on campus or with scientists in other organizations

BIST 502

3 credits

Applied Biostatistics

Rebecca Slack Spring

Mon Wed 11 – 12 pm

Introductory biostatistical theory and application for students pursuing a degree in fields outside of the Department of Biostatistics, Bioinformatics, and Biomathematics.

PHAR 534

2 credits

Ethical Issues in Scientific

Research

Sorell Schwartz Fall, Spring

Mon 3 – 5 pm

Discussions of ethical questions and dilemmas facing scientists today.

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

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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

Raja Mazumder, Ph.D., Assistant Professor and Scientific Coordinator, PIR • Bioinformatics Course Director (BCHB-521) • Course Instructor – Comparative Genomics and Phylogenetics • Trained as a microbiologist, 5 years bioinformatics research experience, specialized in viral

and microbial genome analysis, comparative genomics and phylogenetic analysis 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 Zhang-Zhi Hu, M.D., Associate Professor and Protein Science Associate Team Lead, PIR • Course Instructor – Functional Proteomics, Systems Biology, Biomedical Text Mining • Trained in medicine and molecular biology, 7 years bioinformatics research experience,

specialized in function and pathway analysis of gene expression and proteomic data, and biomedical text mining and protein ontology

Hongzhan Huang, Ph.D., Assistant Professor and Bioinformatics Team Lead, PIR • Course Instructor – Bioinformatics Algorithms and Computing

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• 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

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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 130 foreign 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.

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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 Raja Mazumder and 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

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Instructor Raja Mazumder 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 Director Raja Mazumder 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 Zhangzhi Hu Hongfang Liu 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

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(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 Zhangzhi Hu Hongfang Liu 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 Zhangzhi Hu 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

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Zhangzhi Hu 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 908 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: Raja Mazumder, PhD, rm285@georgetown.edu, (202) 687-9970, 3300 Whitehaven St NW, Suite 1200 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 – December 11, 2008): 3 credits, covering both unit 1 and unit 2

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BCHB-571 (August 28 – September 30, 2008): 1 credit, covering only unit 1 BCHB-572 (October 2 – December 11, 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.

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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

1-4 11-Sep On-line Tutorial Transcript mapping - Genome Browser (HW #4)

1-5 16-Sep DNA sequence/genome databases and genome 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

2 Unit 2: Bioinformatics and Protein Evolution, 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

2-5 16-Oct Protein sequence analysis and database searching - FASTA, BLAST; Multiple sequence alignment

2-6 21-Oct Molecular phylogenetic analysis (HW #7)

2-7 23-Oct Protein and domain based classification: concepts, uses and limitations

2-8 28-Oct Protein family classification and functional annotation

2-9 30-Oct Protein family classification and functional annotation (HW #8)

2-10 4-Nov Term project: functional annotation of protein family 2-11 6-Nov PDB and structure bioinformatics resources

2-12 11-Nov Protein structure, function and homology modeling (HW #9)

2-13 13-Nov Gene Ontology, Protein Ontology and biological 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

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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, 3300 Whitehaven 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)

3-Sep Introduction to Python: Installation, Syntax, Basic Data types, Strings, Control Flow Application: DNA as a string, reverse complement.

10-Sep Advanced Python Datastructures: Lists, Hashes, Sets, Files, Arrays

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Application: DNA translation, reading and writing sequences

17-Sep Advanced Python Idioms: Iterators, Generators, Comprehensions, Functional Programming Application: Sequence database iterator, computing % GC

24-Sep Basic File Parsing: Fasta, CSV, DTA files, Python library, BioPython Application: Amino-acid frequencies, reading and writing SwissProt, Refseq records

1-Oct Advanced File Parsing: Regular Expressions Application: Restriction and digestion enzymes

8-Oct Advanced File Parsing: Introduction to XML, ElementTree Application: Reading pepXML, mzXML

15-Oct Advanced Python Concepts: Modules, Packages, Exceptions, Classes, Inheritance Application: Mass spectrometry I/O module

22-Oct Using Web-Services: NCBI e-Utils, online BLAST Application: Retrieving PubMed references, protein homologs

29-Oct Using Local Tools: Installing & running blast, clustalw, EMBOSS, primer3 Application: Design PCR primers

5-Nov Introduction to Relational Databases: Installing MySQL, Basic SQL concepts Application: Protein and mRNA gene clusters via Unigene

12-Nov Relational Database Design: Normalized Form, Foreign Keys, Indexes, SQLObject Application: Protein and mRNA gene clusters via Unigene

19-Nov Data Warehousing: Large scale databases Application: Peptide sequence confidence assessment

26-Nov Implementing Web-Applications: HTML, TurboGears Application: Enzymatic digest server

3-Dec Graphics and GUIs: pylab, Tkinter Application: Mass spectrum viewer

10-Dec Student Project Presentations (Exam Week)

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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-583 Systems 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.

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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

1-4 16-Jan Expression profiling - differential expression and significance (HW #1)

1-5 21-Jan Clustering analysis - classification of samples (HW #2)

1-6 23-Jan Biological analysis of microarray data - Gene Ontology (HW #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

2-4 20-Feb Proteomic search tools - Mascot, Sequest, X!Tandem (HW #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

3-1 25-Mar Introduction to systems biology 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

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D. BCHB-908: Bioinformatics Internship Course Number: BCHB-908 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.