Genomic Engineering
What is Genomic Engineering?
Genomic Engineering is the collection of engineering methods and skills that are useful in reading, organizing, understanding and exploiting for human benefit the contents of the genomes of all living systems. The elucidation of many genomes is widely believed to be the basis for one of the most important expansions of human knowledge and activity in the 21st Century. All such expansions require engineering activity and genomic engineering will be configured to serve this expansion.
Over the last 50 years the arrangement of nucleic acids into genes has become visible. From simple viruses to man, the summation of these genes represents the genome of each living organism.The complexity of these genomes is both satisfying –for all the potentially useful information about life that it seems to allow—and daunting since genomes are microscopic physical databases of a size that challenges all existing techniques of information management and comprehension.Reading these databases (a process which is only beginning with the formal completion of one ‘consensus’ human genome) is an enormous chemical challenge.Fragments must be sequenced and then joined into longer segments, ultimately into the sequences of genes and genomes.Sequencing errors must be found and corrected.Ends and critical intermediate elements of genes must be identified, with massive efforts to re-read parts of genomes in which variations are found among different organisms.Many thousands of human genomes will need to be read, in whole or in part, to unravel the complexities of most important diseases.Many plant and animal genomes are to be read for the directly useful information they may contain and to elucidate better the common basis of all terrestrial life forms.
As with most other databases, organization is important and is driven by at least a vague concept of the possible functions that the database may serve.Functional genomics is a major approach to understanding how genomes influence their organisms.This understanding helps to direct the organization of the genomic database.Between the genome and the corresponding organismic functions lie the proteins that are the exclusive physical expression of the genome.Their identification and structure is the subject of the growing science of proteomics.With the revelation of the genome, much biological research has been reconstituted.Work that previously proceeded from observations of cellular function and morphology to the causative proteins, to the genes encoding these proteins, to the regulatory mechanisms that activated these genes has now largely been reversed.Sequenced genes allow the puzzle of gene networks to be decoded, with difficulty, and the amino acid sequences of proteins coming from these networks are obtainable.Proteomics allows interpretation of the function of these proteins, and this information, in turn, shows how and why the function and morphology of cells comes to be.This reversed approach has both enhanced and complicated biological research and has led to great demand for engineering approaches to experiment design, data analysis, physical measurement, and systems modeling.
At all levels of understanding, great social pressure has been, and will be, applied to achieving immediate benefit from partial understanding of the genome.Nucleic acids and peptides are the basis of many new therapies.These complex and sensitive molecules raise many questions at every stage – from research, to development, to manufacturing, to distribution, and even to how they can be delivered or administered.These questions will be answered with combinationsestablished and startlingly new industrialtechniques.These techniques are likely to be the responsibility of differently trained engineers who are willing to use the thinking methods and techniques of engineering in very new contexts.
Why study Genomic Engineering at Columbia?
Short answer:The tradition is long.The program is solid, both in the core master’s program in chemical engineering and in the genomic engineering course cluster, which was developed with NSF support and is the first of its kind in the country.Forty percent of the ChE faculty is actively involved in biological applications of chemical engineering.The connections with industry and research institutes – in New York, throughout the country, and internationally – are extensive and active.Columbia’s Fu Foundation School of Engineering and Applied Science has multiple complementary activities in biophysics, nanotechnology, and computational biology as well as a new and rapidly growing Department of Biomedical Engineering.There are close connections with Columbia’s Biological Sciences Department where there are further complementary activities in functional genomics, proteomics, and computational biology .Biological Sciences is housed in a contiguous building.There are further connections with genomic activities at Columbia’s Health Sciences campus with excellent electronic and physical ways of communicating.And, Chemical Engineering is the principal connection between the Columbia Genome Center and the main campus.Associate Professor Jingyue Ju directs the Center’s sequencing laboratory and is the principal investigator, along with co-investigator Professor Edward Leonard, of an $11 million Center of Excellence in Genome Science. And, there is the active and accessible research community of metropolitan New York, including the Rockefeller University, Memorial Sloan-Kettering Cancer Center, New York University, the City University of New York, the Mt. Sinai School of Medicine, the Cornell University Medical Center, and many other specialized institutions.Active communications are maintained with most of these institutions.
What is the program like? What can I expect?
Chemical Engineering departments throughout the country are placing increasing emphasis on biological applications, especially bioprocessing.These programs are not all the same and frequently reflect special resources available to, or special relationships already established by, the different departments. Columbia Chemical Engineering has special ties to the Columbia Genome Center especially via Prof. Jingyue Ju, and holds the first NSF CRCD award given to a program in Genomic Engineering (Prof. Leonard, Principal Investigator). The NSF CRCD program has lead to the creation of a cluster of courses in genomic engineering that are offered regularly and that are accepted as fulfilling requirements toward advanced degrees in several engineering departments.The Chemical Engineering Department has gone one step furtherand formally offers the Genomics Engineering Concentration.
It is anticipated that some students enrolled in this program will choose to pursue the PhD degree.Departmental funding is available for all doctoral track students, and research is the focus of the PhD degree.The Department’s graduate student handbook provides a summary ofrequirements.
The curriculum for students having a B.S. degree in Chemical Engineering: This curriculum assumes that the student has taken, in addition to the normal degree requirements for the first degree in chemical engineering,a basic biology course, which emphasizes a molecular viewpoint (equivalent to Columbia’s Biology C2005.Students without this background should take such a course before enrollment in the program.
1.CHEN 4010.Chemical Process Analysis (fall)
2.CHEN 4110.Transport Phenomena III (fall)
3.CHAP 4120. Statistical Mechanics (fall)
4. CHEN 4750. The Genome and the Cell (spring)
5. CHEN 4760. Genomics Sequencing Lab (spring)
6. CHEN 4700. Principles of Genomics Technologies (fall)
7. CBMF 4761. Computational Genomics (spring)8. Technical Elective
9. Technical Elective
10. Technical Elective
Descriptions of these courses are available in the on-line bulletin of FF-SEAS.
The curriculum for students having a B.S. degree in a related science or another branch of engineering:The two-year curriculum for students having a degree in biology, physics, chemistry, or an engineering discipline other than chemical engineering, assumes that the student will have already taken ordinary differential equations (equiv. to E1210), organic chemistry (equiv to C3045), and basic biology (equiv. to C2005).The 3000-level courses are undergraduate Chemical Engineering courses and provide the requisite background to pursue an advanced degree.Students that have already taken an equivalent may not be required to take some of these courses.It is not unusual for a student to finish the program in only three semesters.
Year One:
Fall
1.CHEN 3110.Transport Phenomena I. (4 points)
2. CHEN 3010.Principles of Chemical Engineering Thermodynamics (4 points)
3.CHEN 4700.Principles of Genomic Technologies (3 points)
4.Technical Elective *
Spring
1.CHEN 3120.Transport Phenomena II. (4 points)
2.CHEN 4230.Reactor Design and Control (4 points)
3.CBMF 4761.Computational Genomics (3 points)
4.Technical Elective *
Year Two:
Fall
1.CHEN 4110.Transport Phenomena III (3 points)
2.CHAP 4120. Statistical Mechanics (3 points)
3.CHEN 4140.Chemical and Biochemical Separations (4 points)
4.CHEN 4010.Chemical Process Analysis (3 points)
Spring
1.CHEN 4750.The Genome and the Cell (3 points)
2.CHEN 4760.Genomics Sequencing Lab (3 points)
3.Technical Elective *
4.Technical Elective *
*At least two electives must be in Chemical Engineering.At least one elective must be 4000 level or above.
How can I get further information?
Further information can be obtained from the Departmental Graduate Committee (current chair, ), or from the concentration coordinator, .
How can I apply?
Applications may be made to the office of graduate admissions at FF-SEAS.