BMMB

Molecular Biology Scientific Literature

Subject

BMMB

Credits (min)

2

Credits (max)

2

Type

course

Edition

graduate

Source

bulletins.psu.edu

/Maximum of 4 No description.

Subject

BMMB

Credits (min)

2

Credits (max)

2

Credit unit

Credits

Type

course

Edition

graduate

Source

bulletins.psu.edu

Discussion of ethical issues relevant to scientific research in the biomedical sciences.

Subject

BMMB

Credits (min)

1

Credits (max)

1

Credit unit

Credits

Type

course

Edition

graduate

Source

bulletins.psu.edu

The study of molecular and biochemical events that influence immune responses and define current questions in immunology. BMMB 511 / MCIBS 511 / VBSC 511 Molecular Immunology (2) The goals of the course are to integrate the current questions of immunology with other disciplines, in particular cell biology and biochemistry, and to provide training in critical thinking and evaluation of data and experiments. The course will be approximately 2/3 lecture by the instructor and 1/3 student presentations of papers related to the material. In addition, written critical reviews of recently published papers and a short research proposal will be assigned. By focusing on the mechanisms involved in immunity and disease, this course complements several existing courses on

Subject

BMMB

Credits (min)

2

Credits (max)

2

Credit unit

Credits

Type

course

Edition

graduate

Source

bulletins.psu.edu

This course presents graduate students in the life sciences with foundational concepts in the biology of microorganisms in the form of broad graduate-level lectures by research-active faculty and student presentations of related challenge problems/discussion subjects. The course is designed for graduate students studying microbiology, biochemistry, and other life science disciplines. The aim is to increase the students' knowledge and appreciation of diverse aspects of microbial physiology, ecology, pathogenesis, molecular biology, and genomics; to familiarize students with microbial faculty and their research at Penn State; to help students think critically about microbiological research methods, experimental design, and data interpretation; and to help students through participation and feedback to improve their oral and written communication skills in presenting scientific data to others.

Subject

BMMB

Credits (min)

3

Credits (max)

3

Credit unit

Credits

Type

course

Edition

graduate

Source

bulletins.psu.edu

Fundamentals and applications of modern chromatographic separations. Cross-listed with: CHEM 525

Subject

BMMB

Credits (min)

3

Credits (max)

3

Credit unit

Credits

Type

course

Edition

graduate

Source

bulletins.psu.edu

This course presents graduate students in the life sciences with foundational concepts in structural biology in the form of broad graduate- level lectures by research-active faculty. The course is designed for students studying biochemistry and other life-science disciplines. The aim is to increase the students' knowledge and appreciation of (i) macromolecular structure determination at high resolution using two different techniques x-ray crystallography and cryo electron microscopy (Cryo-EM) and (ii) how the structure of the molecules relate to their function as molecular machines in the natural world. The course will help familiarize students with the faculty engaged in this field of research as well as the instrumentation available at Penn State; to think critically about structural biology research methods, design their own experiments, and develop comprehension to critically assess the published works of others.

Subject

BMMB

Credits (min)

3

Credits (max)

3

Credit unit

Credits

Type

course

Edition

graduate

Source

bulletins.psu.edu

Prerequisite

BMB 401

Consequences of evolution of protein-coding sequences: structures and functions. BMMB 533 Protein Evolution (2) Most biological functions are carried out by proteins, and evolutionary logic can be used to infer functions. This course will focus on evolution of protein-coding Graduate - The Pennsylvania State University 2026-2027 949 sequences, conformations and functions of proteins. Different species show varying characteristics of structure, metabolism, and regulatory control networks. Most of these differences are the product of the evolution of protein-coding sequences. DNA mutations can change amino acid sequences, protein structures and protein functions; and favorable mutations are selected, in ways that are integrated to form an organism adapted at both macroscopic and molecular levels. The availability of large databanks of protein amino acid sequences, and protein three-dimensional structures, and the annotation of protein function in the entries in these databanks, has allowed investigation of evolutionary changes that impact proteins. One of the goals of the course will be to describe these databanks and the computational tools available to apply them in research in molecular biology. Many students will find these tools useful in their own research projects. The evolutionary divergence of proteins has shown several types ofeffects. In some cases, related proteins in different species retain similar functions, but show differences in amino acid sequence and structure. The nature of observed changes in sequence and structure will be described and the relationship between sequence changes and structural changes examined in several well-documented examples, including globins, and serine proteases. In some cases, proteins diverge within a single species to form large families of related molecules with specialized functions. For example, the human genome encodes hundreds of odorant receptors. The comparison of related proteins that have adopted novel functions reveals how cells can expand their functional repertoire. In most cases it is easier to adapt an existing structure to a new function than to create a new protein "from scratch". For example, the proteolytic enzymes of the chymotrypsin family are related to haptoglobin, an iron scavenger that has lost its enzymatic activity. Beyond the description of individual proteins and individual protein families, there is the more general question of how changes in functions of individual proteins are integrated to create a smoothly-running cellular "operating system". The evolution of sequences encoding regulatory proteins to achieve this will be discussed. Methods of bioinformatics to address these questions will bepresented, with emphasis on study and comparison of structures with computer graphics.

Subject

BMMB

Credits (min)

2

Credits (max)

2

Credit unit

Credits

Type

course

Edition

graduate

Source

bulletins.psu.edu

The goal of this course is to provide a foundation in development and application of chemical technologies to the understanding and manipulation of biological systems. Chemical biology is a relatively new field that spans the traditional fields of chemistry and biology by applying chemical technologies to the understanding and manipulation of biological systems. As such, this course should be accessible and provide benefit to students working in both chemical and biological areas. Lectures include higher-level biological chemistry (assuming prior knowledge of biological chemistry at an undergraduate level, such as CHEM 476 or BMB 401) and synthetic chemistry and biology principles along with current literature in the field of chemical biology. Cross-listed with: CHEM 536

Subject

BMMB

Credits (min)

3

Credits (max)

3

Credit unit

Credits

Type

course

Edition

graduate

Source

bulletins.psu.edu

Prerequisite

CHEM 476 or B M B401

Foundations in spectroscopic methods employed for the determination of the geometric and electronic structure of transition metal clusters in nature.

Subject

BMMB

Credits (min)

3

Credits (max)

3

Credit unit

Credits

Type

course

Edition

graduate

Source

bulletins.psu.edu

Mechanisms of the most important biochemical reactions, with emphasis on enzyme catalysis. Cross-listed with: CHEM 539

Subject

BMMB

Credits (min)

3

Credits (max)

3

Credit unit

Credits

Type

course

Edition

graduate

Source

bulletins.psu.edu

Prerequisite

CHEM 476 or B M B401

The course emphasizes comparative molecular genetic analyses of developmental gene networks using vertebrate and Drosophila model systems. BMMB 541 BMMB 541 Molecular Biology of Animal Development (3) This is a required course for graduate students in the IBIOS Cell and Developmental Biology Program. Approximately half of the class sessions will consist of lectures and class discussions related to lecture material. The other half will consist of primary literatur presentations by the students and class discussion pursuant to these. The course will provide students with a broad overview of essential signaling pathways and gene regulatory networks that coordinate cellular activities to establish and maintain the complex communities of cells that comprise animal tissues.

Subject

BMMB

Credits (min)

3

Credits (max)

3

Credit unit

Credits

Type

course

Edition

graduate

Source

bulletins.psu.edu

Total Credits 11 Because students in the M.D./Ph.D. program are being trained to combine research and medicine, most likely in medical schools, the MCIBS requirement for exposure to undergraduate teaching is waived. M.D./ Ph.D. candidates are not required to take BIOL 593 (2 credits) or to be teaching assistants. The Emphasis Area requirement and the Quantitative Foundation Course requirement are also waived. In addition to taking the required courses MCIBS 590 (2 cr.), MCIBS 591 (1 cr.), and MCIBS 592 (2 cr.), elective courses are selected in consultation with the student’s dissertation adviser and Ph.D. committee, with guidance from the MCIBS emphasis area course lists and program chair. 6 credits of elective courses will be selected. The M.D./Ph.D. candidate prepares a written comprehensive examination in the format of a grant application and gives an oral presentation of this proposal to their Ph.D. committee. A dissertation must be prepared and defended by each M.D./Ph.D. candidate, as described on the Degree Requirements tab. In addition, M.D./Ph.D. students must have submitted a first-author manuscript before defending their dissertation. Before returning to medical school, the doctoral dissertation must be accepted by the Fox Graduate School. The M.D./Ph.D. program requires that students have one first author peer-reviewed paper published based on their research accepted prior to completing medical school, and preferably accepted for publication prior to returning to the third year of medical school. At the discretion of the College of Medicine Vice Dean for Research and Graduate Studies, in consultation with the MCIBS Program Chair, the requirement for a first author publication prior to completing medical school may be waived. Examples of conditions that might warrant exemptions include: • prolonged illness, • mentor's relocation, • mentor's reluctance to submit the student’s work for publication, • the student’s project is published by another research group, or • delays or challenges in the publication review process beyond the control of the student or dissertation adviser. If a student decides not to return to medical school, or for some other reason is not able to complete the last two years of medical school, but they have successfully completed their Ph.D. dissertation and final oral examination and met all other degree requirements for the Ph.D. in MCIBS, they will eligible to receive the Ph.D. The latter will be conferred after the student notifies the program that she/he wishes to withdraw from the M.D. program and completes all requirements for conferral of the Ph.D. degree.

Subject

BMMB

Credits (min)

3

Credits (max)

3

Type

course

Edition

graduate

Source

bulletins.psu.edu

This course explores structural, biochemical and genetic approaches in gene regulation. BMMB 543 Current Topics in Gene Regulation (3) This course is intended to bring students up to the leading edge of research in gene regulation. It will explore structural, biochemical and genetic approaches in this field of research, covering processes from nuclear structure to RNA decay. It will also illustrate progress from many different model organisms including: prokaryotes, yeast, Drosophila, and humans. This course will include introductory lectures by faculty and student presentations of recent literature.

Subject

BMMB

Credits (min)

3

Credits (max)

3

Credit unit

Credits

Type

course

Edition

graduate

Source

bulletins.psu.edu

Prerequisite

B M B400

This course will deal with the structure and function of genomes including the use of some current web-based tools and resources for studies and research in genomics. The overall objective is to learn current information about the structure and function of genomes, to develop facility in the many web-based tools and resources for further studies and research in genomics, and to appreciate the power and limitations of current resources and knowledge. Cross-listed with: BGEN 551, MCIBS 551

Subject

BMMB

Credits (min)

3

Credits (max)

3

Credit unit

Credits

Type

course

Edition

graduate

Source

bulletins.psu.edu

Expanded overview of current developments and technique in computational biology and genomics. BMMB (MCIBS) 554 Foundations in Data Driven Life Sciences (3) The successful progression of data-driven biomedical research is obscured by a wide-range of logistical problems e related to data handling and processing, a widespread disconnect between developers and consumers of biomedical analysis software, and lack of accessible, well-developed curricula and active learning opportunities necessary for the development of key data analysis skills in the next generation of researchers and clinicians. This course aims a filling these gaps. Topics include fundamental concepts that underpin analysis of sequence data, design of complex experiments, research transparency and reproducibility, as well as result disseminations practices relevant to presentations and publications. Cross-listed with: IBIOS 554, MCIBS 554

Subject

BMMB

Credits (min)

3

Credits (max)

3

Credit unit

Credits

Type

course

Edition

graduate

Source

bulletins.psu.edu

This course covers elegant algorithmic and data structure techniques that underpin modern biological data analysis. Bioinformatics is a growing field with immediate implications for our understanding of biology and treatment of disease. This course covers elegant algorithmic and data structure techniques and their use in bioinformatics. The emphasis is on recurrent ideas that underpin modern biological data analysis, presented in conjunction with their biological applications. The course is suitable both for students interested in doing bioinformatics research and those interested in applications of algorithms to the natural sciences. Some of the algorithms/data-structures that may be covered include exact string matching, suffix trees, suffix arrays, de Bruijn graphs, hidden Markov models, breakpoint graphs, succinct data structures, the Burrows-Wheeler transform, the FM-index, network flow, and bidirected graphs. Some of the biological applications will include sequence alignment and assembly, cancer genomics, phylogeny, gene finding, and variation detection. No prior biological or bioinformatics knowledge is required. A basic understanding of data structures and algorithms (equivalent to CMPSC465) is a prerequisite; however, exceptionally motivated students can contact the instructor to discuss their options. This course is complementary to existing bioinformatics courses offered through other programs on campus. These courses may be taken concurrently but are not prerequisites. Prerequisites: CMPSC465 Cross Listings: BMMB 566 will be added as a cross-listed course. Cross-listed with: CSE 566

Subject

BMMB

Credits (min)

3

Credits (max)

3

Credit unit

Credits

Type

course

Edition

graduate

Source

bulletins.psu.edu

Prerequisite

CMPSC465

Biophysical and biochemical approaches for studying structure- function relationships in nucleic acids. BMMB (CHEM) 572 Nucleic Acids Chemistry (3) The goal of this course is to provide a foundation in biophysical approaches for studying the quantitative and structure- function relationships in nucleic acids systems, including DNA, RNA, and their interactions with proteins, salt, and water. Lectures include basic physical chemistry and statistical mechanics principles along with current literature in the biochemical sciences. At the end of the course, you should be able to meaningfully dissect molecular biological papers at the level of the physical chemistry of these processes. Current topics are introduced through reading and presenting papers from the literature. Cross-listed with: CHEM 572

Subject

BMMB

Credits (min)

3

Credits (max)

3

Credit unit

Credits

Type

course

Edition

graduate

Source

bulletins.psu.edu

Prerequisite

CHEM 212 , CHEM 450

Nuclear magnetic resonance approaches for characterizing the structure and dynamics of synthetic compounds, natural products, and biological macromolecules. Cross-listed with: CHEM 573

Subject

BMMB

Credits (min)

3

Credits (max)

3

Credit unit

Credits

Type

course

Edition

graduate

Source

bulletins.psu.edu

Prerequisite

CHEM 452

The goal of this course is to acquaint students with the many important roles that metal ions play in biological systems (bioinorganic chemistry). We will explore how structural biology, enzymology, spectroscopy, cell biology, and chemical biology methods have been used to understand how metal ions are used in biological molecules. These approaches have enabled discovery of the chemistry of these systems, and an understanding of how that chemistry fits into the broader biological context. We will apply bioinorganic chemistry in solving important challenges in energy, health, and the environment. Course activities include application of basic inorganic chemistry and biochemical principles, discussion of current literature in the biochemical sciences, implementation of biomolecular structure visualization software, and problem solving. At the end of the course, students will be able to critically engage with the bioinorganic literature and propose experimental approaches to unresolved questions in the field. CHEM 412 Cross-listed with: CHEM 574

Subject

BMMB

Credits (min)

3

Credits (max)

3

Credit unit

Credits

Type

course

Edition

graduate

Source

bulletins.psu.edu

Prerequisite

CHEM 476 or BMB 401 Recommended Preparations:

The course will develop a detailed molecular view of the building blocks of biological systems and a brief review of the structural and functional properties of these biomolecules. The course also will cover modern methods of biomolecule synthesis, purification, and modification. Subject matter will be approached using case studies highlighting techniques that allow us to gain a chemical understanding of biological processes. Examples include identification of drug binding sites, probing protein- protein interactions, targeting protein degradation, and modulating Graduate - The Pennsylvania State University 2026-2027 951 transcription. Important advances in our understanding of biological systems brought about by these techniques will also be discussed. Discussion of primary literature readings will include benefits/drawbacks of the various techniques, complementarity of methods, and the applicability of various aspects of chemical biology to dissect new problems.

Subject

BMMB

Credits (min)

3

Credits (max)

3

Credit unit

Credits

Type

course

Edition

graduate

Source

bulletins.psu.edu

This course will develop a detailed view of genetic information, how it is stored and used by cells, and how it can be manipulated and analyzed to answer research questions. Both experimental and computational methods will be covered, with an emphasis on design and analysis of genetic, genomic, imaging, and dry-lab experiments.

Subject

BMMB

Credits (min)

3

Credits (max)

3

Credit unit

Credits

Type

course

Edition

graduate

Source

bulletins.psu.edu

/Maximum of 3 Continuing seminars which consist of a series of individual lectures by faculty, students, or outside speakers.

Subject

BMMB

Credits (min)

1

Credits (max)

3

Credit unit

Credits

Type

course

Edition

graduate

Source

bulletins.psu.edu

/Maximum of 9 Formal courses given on a topical or special interest subject which may be offered infrequently; several different topics may be taught in one year or term.

Subject

BMMB

Credits (min)

1

Credits (max)

9

Credit unit

Credits

Type

course

Edition

graduate

Source

bulletins.psu.edu

/Maximum of 9 Formal courses given on a topical or special interest subject which may be offered infrequently; several different topics may be taught in one year or term.

Subject

BMMB

Credits (min)

1

Credits (max)

9

Credit unit

Credits

Type

course

Edition

graduate

Source

bulletins.psu.edu

Students are required to write a thesis, and at least 6 credits in thesis research (BMMB 600 or BMMB 610) must be taken in conjunction with completing the thesis. The thesis must be accepted by the advisers Graduate - The Pennsylvania State University 2026-2027 143 and/or committee members, the head of the graduate program, and the Graduate School, and the student must pass a thesis defense. Doctor of Philosophy (Ph.D.) Requirements listed here are in addition to Graduate Council policies listed under GCAC-600 Research Degree Policies. (https:// gradschool.psu.edu/graduate-education-policies/) Each student must take a total of 19 credits in 400-,500- and 800-level courses, required and elective, from a list approved by the program faculty. Doctoral students must complete the core courses in BMMB: Code Title Credits

Subject

BMMB

Credits (min)

6

Credits (max)

1

Type

course

Edition

graduate

Source

bulletins.psu.edu

0 Credits/Maximum of 999 No description.

Subject

BMMB

Type

course

Edition

graduate

Source

bulletins.psu.edu

/Maximum of 6 Teaching of biochemistry undergraduate laboratory and recitation classes under faculty supervision.

Subject

BMMB

Credits (min)

1

Credits (max)

3

Credit unit

Credits

Type

course

Edition

graduate

Source

bulletins.psu.edu

/Maximum of 999 No description.

Subject

BMMB

Credits (min)

1

Credits (max)

15

Credit unit

Credits

Type

course

Edition

graduate

Source

bulletins.psu.edu

0 Credits/Maximum of 999 No description.

Subject

BMMB

Type

course

Edition

graduate

Source

bulletins.psu.edu

Microbiology, and Molecular Biology Additional course work and research are individually planned by the student and the research adviser in consultation with the Ph.D. committee. The Ph.D. committee is established in compliance with Graduate Council policy (http://gradschool.psu.edu/graduate-education- policies/gcac/gcac-600/phd-dissertation-committee-formation/) once the student has passed the qualifying examination. Doctoral students must pass a qualifying examination, a comprehensive oral examination, and a final oral examination (the dissertation defense). Continuation in the Ph.D. program is decided on the basis of the student's performance in courses, research and teaching. In addition, an oral qualifying examination is taken during the fall semester of the second year. This examination tests the student's ability to utilize what they have learned in solving problems based on the scientific method. A comprehensive oral examination is taken before the student's Ph.D. committee within approximately three semesters after the student has passed the qualifying examination. The student is expected to present th a written dissertation proposal including data that has been gathered, future research directions, and experimental approaches. Questioning may involve, but is not limited to, that dissertation proposal. ts The faculty requires that each student demonstrate the ability to collect, organize, and present the results of their research in a professional manner before graduation. This is accomplished by preparing a 2 manuscript based on the Ph.D. dissertation research. The manuscript must be written by the student and submitted for publication in a refereed 1 journal prior to the final oral examination (the dissertation defense). The dissertation defense is taken before the student's Ph.D. committee at 1 the end of the program. The student must also present a public seminar 3 on the dissertation research within the two-week period preceding the dissertation defense. To earn the Ph.D. degree, the student’s dissertation must be accepted by the Ph.D. committee, the head of the graduate program, and the Graduate School.

Subject

BMMB

Credits (min)

1

Credits (max)

1

Type

course

Edition

graduate

Source

bulletins.psu.edu

This course provides a foundation for students with biology backgrounds in the computational analysis and interpretation of biological data.

Subject

BMMB

Credits (min)

2

Credits (max)

2

Credit unit

Credits

Type

course

Edition

graduate

Source

bulletins.psu.edu