Degrees Offered

The Bioinformatics and Computational Biology graduate program is designed to provide doctoral (Ph.D.) level training. In certain circumstances, students may be admitted as M.S. candidates. The M.S. degree is not a prerequisite for the Ph.D. program.

Students who are admitted to the Ph.D. program and who later wish to transfer to the M.S. program must make the transfer concomitant with selection of a major professor (before the start of the second year). Students will be financially responsible for their education after the transfer. Transfers after the first year require approval of the BCB Supervisory Committee.

Students who are admitted to the M.S. program and who wish to transfer to the Ph.D. degree program in BCB may request to do so. Applications for transfer are judged on the basis of the same criteria as new applications for direct admission to the Ph.D. program. Students who wish to enter the Ph.D. program in BCB after completion of the M.S. degree in BCB must reapply to the program. Such applications are judged on the basis of the same criteria as new applications to the BCB Ph.D. program. (back to top)

Academic Calendar

The BCB graduate program is a year-round program that includes Fall, Spring and Summer semesters. Students are expected to be registered and to participate in research and courses twelve months per year. A rotating student may take vacation with the approval of his or her temporary advisor and by notifying the Bioinformatics and Computational Biology program assistant. Each student must obtain the required approval and notify the BCB office prior to travel, in order to avoid potential interruption of graduate assistantship support and/or visa problems. See Leave in the Benefits section of the BCB Graduate Student Handbook for information regarding vacation.

Research Expectations

BCB students are trained to develop an independent and creative approach to science through an integrated curriculum and interdisciplinary research projects in the fields of bioinformatics, computational biology, and biological statistics.

Advanced degrees in BCB require that a student's research project be interdisciplinary, including both biological and quantitative/computational components. The POS committee is responsible for determining whether a student's research project meets this condition.

The Ph.D. dissertation must: "demonstrate conclusively the ability of the author to conceive, design, conduct, and interpret independent, original, and creative research. It must attempt to describe significant original contributions to the advancement of knowledge and must demonstrate the ability to organize, analyze, and interpret data. … Dissertation research should be worthy of publication and should appear in appropriate professional journals or in book form. …Since satisfactory completion of the thesis or dissertation can constitute one of the most gratifying experiences in graduate study, the document should reflect the highest standards of scholarship, serving as a measure of quality for the student, major professor, and the program." (from the ISU Graduate College Handbook)

In BCB, the Ph.D. thesis is generally expected to include approximately three published or publishable original manuscripts. For additional details, see Writing the Thesis in the Progressing Through the Degree Program section of the BCB Student Handbook.

The Ph.D. and M.S. degrees are usually completed in five and two years, respectively.

Background Coursework

The foundation disciplines for BCB are genetics, molecular biology, mathematics, computer science, statistics and physics. Students entering the BCB program are expected to have a strong undergraduate background in at least one of these disciplines and additional coursework in another.

The following tables summarize the three areas in which BCB majors must demonstrate basic competence. Students are strongly encouraged to take courses equivalent to the ISU courses listed under Course Prerequisites for Admission to BCB prior to enrollment in the BCB program, but will have the opportunity to make up deficiencies during the first year of BCB graduate training. Courses listed under BCB Background Coursework Requirements are prerequisites for BCB core courses. These background courses should be completed either prior to admission or during the first year of BCB graduate training. The temporary advisor or major professor helps each student determine whether additional courses are needed. The student's POS committee will evaluate competence in the three background areas during the student's second Annual POS Committee meeting.

Required Core Courses

All BCB majors must take at least one core course in molecular genetics and four core courses in computational biology.

Core courses in molecular genetics :

GDCB 511. Molecular Genetics. (Cross-listed with MCDB). (3 cr.) (Spring) Prerequisites: Biol 313 and BBMB 405. The principles of molecular genetics: gene structure and function at the molecular level, including regulation of gene expression, genetic rearrangement, and the organization of genetic information in prokaryotes and eukaryotes. (An equivalent or more advanced course may be substituted with approval of student's POS Committee.)

Core courses in computational biology :

BCB 567. Bioinformatics I (Fundamentals of Genome Informatics). (Cross-listed with COM S, CPR E.) (3-0) Cr. 3. F. Prereq: Com S 208; Com S 330; Stat 341; credit or enrollment in Biol 315, Stat 401, and Stat 432. Potential  Instructors: Srinivas Aluru; David Fernandez-Baca; Oliver Eulenstein.

Catalog description: Biology as an information science. Review of algorithms and information processing. Generative models for sequences. String algorithms. Pairwise sequence alignment. Multiple sequence alignment. Searching sequence databases. Genome sequence assembly.

Expanded description: Biology as an information science. Review of algorithms and information processing: design of algorithms; space and time complexity analysis of algorithms; basic search algorithms; branch and bound search; dynamic programming. Generative models for sequences: multinomial models; Markov models. String algorithms: exact string matching; suffix trees and suffix arrays; approximate string matching (k mismatches, k differences). Pairwise sequence alignment: amino acid substitution scoring matrices; local and global alignment. Multiple sequence alignment: progressive alignment; word-based methods; local multiple alignment (sequence profiles and motifs). Sequence database search: dot matrix methods; heuristic methods; statistics of database searches; Introduction to genome sequence assembly.

BCB 568. Bioinformatics II (Advanced Genome Informatics). (Cross-listed with GDCB, STAT, COM S.) (3-0) Cr. 3. S. Prereq: BCB 567, BBMB 301, Biol 315, Stat 401, Stat 432, credit or enrollment in Gen 411. Potential Instructors: Volker Brendel; Karin Dorman; Xun Gu.

Catalog description: Advanced sequence models. Basic methods in molecular phylogeny. Hidden Markov models. Genome annotation. DNA and protein motifs. Introduction to gene expression analysis.

Expanded description: Applications of sequence models: codon usage; discrete and continuous models of nucleotide substitution; synonymous and nonsynonymous nucleotide substitutions. Basic methods in molecular phylogeny: phylogenetic trees; distance matrix methods; maximum parsimony methods; maximum likelihood methods. Advanced sequence models: Random walks; score-based sequence analysis; Interpolated Markov Models; Markov Random Fields; applications to genome annotation; genome rearrangements. Hidden Markov Models: theory; training; applications to gene structure annotation, sequence alignment, and protein classification. DNA and protein motifs: weight matrices; word-based methods; EM algorithm, Gibbs sampling, and simulated annealing; Bayesian methods. Introduction to gene expression analysis, mRNA and protein expression data analysis, multiple comparisons.

BCB 569. Bioinformatics III (Structural Genome Informatics). (Cross-listed with BBMB, COM S, MATH, CPR E.) (3-0) Cr. 3. F. Prereq: BCB 567, Gen 411, Stat 401, Stat 432. Potential Instructors: Bob Jernigan, Guang Song, Zhijun Wu.

Catalog description: Algorithmic and statistical approaches in structural genomics including protein, DNA and RNA structure. Structure determination, refinement, representation, comparison, visualization, and modeling. Analysis and prediction of protein secondary and tertiary structure, disorder, protein cores and surfaces, protein-protein and protein-nucleic acid interactions, protein localization and function.

Expanded description: Algorithmic and statistical approaches in structural genomics including: Protein, DNA and RNA structure; Protein and Nucleic acid databases; Computational problems in structure determination including structure representation, transformation between coordinate systems, structure comparison (using RMS and distance matrix based methods) and visualization, structure determination with NMR derived distances, Distance-based structure modeling, energy minimization methods for structure refinement, protein structure modeling using threading and homology based methods. Analysis and prediction of protein secondary structure and tertiary structure, ordered and disordered regions, structural domains, 3-dimensional structural motifs, protein cores and surfaces, structural classes, protein function from primary, secondary, or tertiary structure, protein-protein, protein-RNA and protein-DNA interfaces; analysis and prediction of RNA structure.

BCB 570. Bioinformatics IV (Computational Functional Genomics and Systems Biology). (Cross-listed with COM S, GDCB, STAT, CPR E.) (3-0) Cr. 3. S. Prereq: BCB 567, Biol 315, Com S 363, Gen 411, Stat 401, Stat 432. Potential Instructors: Julie Dickerson, Vasant Honavar, Karin Dorman, Steve Proulx.

Catalog description: Algorithmic and statistical approaches in computational functional genomics and systems biology. Biological Information Integration – knowledge (ontology) driven and statistical approaches. Qualitative, probabilistic, and dynamic network models. Modeling, analysis, simulation and inference of transcriptional regulatory modules and networks, protein-protein interaction networks. Metabolic networks; cells and systems.

Recommended (not required) Courses

It is recommended that all BCB graduate students who have not had laboratory experience in biological sciences take at least two 1-credit modules of BCB 542 (Introduction to Molecular Biology Techniques). Similarly, BCB graduate students who come in with a biology undergraduate degree take at least two modules of Introduction to Bioinformatics Tools (including modules on Sequence Analysis, Microarray Data Analysis, Protein Structure Analysis, Phylogenetics etc. to be developed and offered by the Baker Center).

Advanced Electives
In addition to the five core courses, students must complete at least twelve credits of advanced coursework. Suggested electives might include six credits from Category I (Molecular Biology) and at least six credits from either Category II (Computer Science) or Category III (Mathematics/Statistics), i.e., six credits in one of the two areas. The table below provides a list of some of the courses that can be used to fulfill this depth requirement. Not all the listed courses are suited to all programs of study. Students should consult with their POS committees to determine which courses from this list, or not from the list, are most appropriate. Check BCB Courses on the BCB website for new course offerings and updated course lists.

Required Seminars and Activities

Workshops and Symposia

• BCB 593 - Workshop in Bioinformatics and Computational Biology. (1 cr. each time taken) (Fall, Spring, Summer) Current topics in bioinformatics and computational biology research. Lectures by off-campus experts. Students read background literature, attend preparatory seminars, attend all lectures and meet with lecturers.

Seminars

• BCB 690 - Student Seminar. (1 cr.) (Spring) Students present an account of their annual research progress to peers and to two faculty mentors who promote group discussions of experimental procedures and analysis.
• BCB 691 - Faculty Research Seminar. (1 cr.) (Fall) BCB faculty members present summaries of current research in their groups.

In addition, BCB students are expected to participate in a seminar series in their home department and to make an oral presentation (either in a research seminar or journal club) at least once each year.

Scientific Ethics and Good Science and Bioethics Training
All BCB majors are required to attend the Scientific Ethics Workshop, which is part of new student orientation each Fall semester. In this workshop, students are introduced to the concepts of ethical behavior and good practice in science. Discussion includes proper research methods, ways to avoid self-deception in the practice of science, and scientific misconduct.

In addition to attending the Scientific Ethics Workshop, BCB students are required to take BCB-approved bioethics courses or course modules. Students seeking M.S. degrees are required to take at least one BCB-approved bioethics course/module (0.5 credit minimum). Ph.D. students are required to take at least two bioethics modules or another BCB-approved bioethics course (1 credit minimum). The required sessions in general scientific ethics offered during Fall orientation (above) do not count toward this bioethics course requirement. Students supported by special training grants may have additional bioethics training requirements.

BCB-approved bioethics courses include:

Agron/Gen/Pl P/VMPM 565 - Professional Practice in the Life Sciences (usually offered Spring)
1. Professional Practices in Research
2. Intellectual Property and Industrial Interactions
3. Life Science Ethics

Please see BCB Courses on the BCB website for additional information.

Language Requirements
Language requirements are determined by the student's Program of Study Committee.

Graduate English Requirements

• Nonnative Speakers of English
  Graduate students whose native language is not English and who do not have a bachelor's degree from ISU or a U.S. institution must take the English Placement Test at the beginning of their first semester of enrollment. This test is administered by the Department of English. It must be taken in addition to TOEFL (Test of English as a Foreign Language), which is required as part of the admissions process. Students receiving low scores on this test are assigned to appropriate sections of English 99 and 101, which should be completed during the first year of graduate study. (There is a developmental course fee for the 99-level courses.)

  Graduate students whose native language is not English but who have undergraduate degrees from ISU must take the Graduate English Examination for International Students, also administered by the Department of English, at the beginning of their first semester of graduate work. Students who do not pass this test must complete English 101D during their first year of study.

Teaching Requirements
Teaching requirements are determined by the home department. All graduate students are encouraged to participate in teaching seminars and obtain teaching experience as part of their training.

Testing of Nonnative Speaking Students Who Teach
SPEAK/TEACH testing is required of graduate students who fit both of the following categories:

• those who are not native speakers of American English (i.e., learned another language first), and
• those who are to be appointed to or considered for teaching assistantships, or who will have some teaching responsibilities even if they are not teaching assistants (TAs).

The SPEAK/TEACH tests of oral proficiency are given before the beginning of Fall and Spring semesters. Department offices have a schedule of SPEAK/TEACH testing dates. Registration for the test is held the day before the test is administered. Complete information about the SPEAK/TEACH program can be found at http://www.grad-college.iastate.edu/speakteach/. Questions about SPEAK/TEACH testing should be directed to the SPEAK/TEACH office, 1116 Pearson , 515-294-1958, 515-294-7996 or itas@iastate.edu.

A prospective teaching assistant who does not pass these tests is required to successfully complete coursework and be retested. Sections of University Studies 180 are designed to help new teaching assistants. These courses focus on pronunciation, listening, question handling, teaching and lecturing skills, and an introduction to the culture of U.S. university life. Because enrollment in University Studies 180 is restricted, TAs cannot register for the courses through online registration. TAs must appear at the SPEAK/TEACH Office, 201 Lab of Mechanics on the first or second day of classes for Fall or Spring semester to obtain permission to enter the course by completing a course add slip.
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Additional Research Training Opportunities

Participation in International Scientific Conferences and Symposia
Attendance and presentation of research results at professional meetings are an essential part of the BCB graduate training program. Students should attend at least one national or international meeting during their degree program. All BCB students are eligible for financial assistance from the BCB program (as well as from other ISU sources) for conference-related expenses. For additional information, see Grants for Professional Travel in Section VII. Financial Matters.

Internships
BCB students are encouraged to participate in industrial internships as part of their training for careers in industry, government or the public sector. One such internship is available through the Pioneer Hi-Bred International Graduate Research Fellowship. Pioneer Fellows intern at Pioneer Hi-Bred for eight weeks during the summer of their first year of support. Additional internships in subsequent years can be arranged between the student and Pioneer. Formal agreements with other internship partners (e.g., NewLink Genetics) are currently under development. For additional information, please speak with the chair of the BCB program.

International Experiences
BCB students also are encouraged to enrich their educational experience and establish international contacts by participating in international research experiences. The BCB program has had working relationships with four institutions (three in Europe and one in China) with which international training experiences were arranged in the past. Speak with your major professor about arranging these opportunities.

Summary of BCB Requirements for Ph.D. and M.S. Degrees

Graduate Minor

A graduate minor in BCB requires:

• completion of either BCB 567 or BCB 568 (3 credits)
• demonstration of competence in the three categories of required background coursework (Mathematics and Statistics, Molecular Genetics, Computer Science)
• completion of a total of 2 credits chosen from: BCB Workshops, Faculty Seminars or Student Seminars; and
• completion of at least 9 credits in courses listed under BCB Advanced Group Requirements, including at least 6 credits from one subject area and 3 credits from another area. The selected courses must be approved by the Program of Study Committee.

In addition:

• the planned POS must be reviewed by the BCB Chair prior to POS committee approval;
• at least one member of the POS committee must be a BCB faculty member; and
• application for minor must be made prior to PhD preliminary examination.

Co-major or Concurrent Degree Requirements

Students who are admitted to the BCB program as co-major or concurrent degree candidates must fulfill the requirements of the BCB program in addition to those of the co- or concurrent degree program. See the Graduate College Handbook for additional information.

Sample Curricula for BCB Graduate Students

All first year Ph.D. and M.S. degree candidates must:

• take courses to complete required background coursework described above;
• take the required BCB core courses:
  • BCB 567 - Fundamentals of Genomic Informatics and
  • BCB 568 - Advanced Genomic Informatics and
  • GDCB 511 - Molecular Genetics (or equivalent)
• attend BCB 691 - BCB Faculty Research Seminar (Fall)
• participate in BCB 690 - BCB Student Research Seminar (Spring); and
• take courses to fulfill the BCB Bioethics course requirement.

Three examples of first and second year programs for students with prior training in computer science and biological sciences .

Students without Biology prerequisites, but with strong Computer Science background.

Two examples of first, second and third year programs for students without computer science prerequisites, but with strong Biology background.

Example program for students without Statistics prerequisites and computer science, but with strong Biology background.

After the First Year

• Students should register for BCB 699 - Research (rather than BCB 697 - Research Rotation) every semester. Number of credits for BCB 699 will vary depending on other courses taken; students should register for a total of 12 credits every Fall and Spring semester, and a total of 6 credits every Summer semester.
• Students should register for courses to complete Advanced Group Requirements, following the recommendations of their major and co-major professors and POS committee.
• Students should refer to the Summary of BCB Requirements (above) for specific credit hour requirements for seminars, workshops, etc.

Transferability of Credits from Other Institutions

The transferability of credits from other institutions is determined on a case-by-case basis by the student's POS committee and the BCB Chair. To waive a course requirement, the student must attach to the POS form a memo signed by his or her major professor (on behalf of the POS committee) and the instructor of the course the student wishes to waive. The memo must state that the student has already received satisfactory instruction in the subject matter covered by the required course. Credits for seminars, workshops and colloquia are not transferable.
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