Courses
4 Required Courses (12 credits)

• BI7534 Bioinformatics I: Sequence Analysis (3 credits)
  Computer representations of nucleic acid and protein sequences, pairwise and multiple alignment methods, available databases of nucleic acid and protein sequences, database search methods, scoring functions for assessment of alignments, nucleic acid to protein sequence translation and codon usage, genomic organization and gene structure in prokaryotes and eukaryotes, introns and exons, prediction of open reading frames, alternative splicing, existing databases of mRNA, DNA, Protein, and genomic information. An overview of available programs and of resources on the web. Prerequisites: CM751 or instructor's permission.
  
  
• BI7544 Bioinformatics II: Protein Structure (3 credits)
  Available online in future semesters
  Protein folding representations, databases of protein folding classes, secondary structure prediction, tertiary structure prediction via computer folding experiments threading, and homology model building, prediction of post translation modification sites, active and binding sites in proteins, representations of contiguous and non-contiguous epitopes on protein surfaces at the sequence level, representations of functional motifs at the three dimensional an at the sequence level. Prerequisites: BI753 (OR BI7534).

• BI7554 Bioinformatics III: Functional Prediction (3 credits)
  Available online in future semesters
  Functional classifications of proteins, prediction of function from sequence and structure, Orthologs and paralogs, representations of biological pathways, available systems for the analysis of whole genomes and for human-assisted and automatic functional prediction. Prerequisites: BI754 (OR BI7544).
  
  
• BI7564 Chemoinformatics
  Available online in future semesters
  Review of Database Theory, Chemical Structure Representation; connection tables, line notations, structure diagrams, Representations of Chemical Reactions, Structure manipulation: Graph Theory, Structure Analysis: ring perception, structural fingerprints, symmetry perception, Molecular Modeling Algorithms, Genetic Algorithms, Simulated Annealing, QSAR historical approaches, Structural Search of Chemical Databases, Commercial Chemical Information Databases, Combinatorial Chemistry and diversity assessment.

2 Basic Core Courses (6 credits):

Students with Computer Science or similar background will take these 2 courses.

• CM7514 Chemical Foundation for Bioinformatics (3-credits)
  An intensive review of those aspects of Organic Chemistry and Biochemistry necessary to begin research in Bioinformatics and to enter graduate courses in Biology. Covalent bonding, quantum mechanical basis of bond formation, three-dimensional structure of molecules, reaction mechanisms, catalysis, polymers, enzymes, thermodynamic and kinetic foundations, metabolic pathways, sequence and structure of macromolecules. This course will make extensive use of computer approaches to convey the essential computational and visual nature of material to be covered. Prerequisites: General chemistry, general physics, organic chemistry, and calculus.
  

• CM7524 Biological Foundation for Bioinformatics (3-credits)
  An intensive review of those aspects of Biochemistry, Molecular Biology and Cell Biology necessary to begin research in Bioinformatics and to enter graduate courses in Biology. The areas covered will include cell structure, intracellular sorting, cellular signaling (i.e. receptors), Cytoskelton, cell cycle, DNA replication, transcription, translation. This course will make extensive use of computer approaches to convey the essential computational and visual nature of the material to be covered. Prerequisites: General chemistry, general physics, organic chemistry, calculus, or permission of instructor.

Students with chemical or biological science background will take these 2 courses.

• CS530 Introduction to Computer Science (3-credits)
  This course provides an introduction to discrete mathematics, computers and programming; running C/C++ programs under UNIX; algorithmic language; pseudocode; problem solving and program structure. Topics covered include constants, variable, data types, assignments, arithmetic expressions, input and output; object-oriented and top down design and procedures, selection and loops; functions; enumerated and sub-range data type; arrays, records and sets; recursion; and searching and sorting.
  
  
• CS540 Data Structures and Algorithms (3-credits)
  This course provides an introduction to data structures. Topics covered include; program specifications and design; abstract data types, stacks, queues; dynamic storage allocation; sequential and linked implementation of stacks and queues; searching methods, sequential and binary; binary trees and general trees; hashing; computational complexity; sorting algorithms - selection sort, insertion sort, heap-sort, merge-sort and quick-sort; comparison of sorting techniques and analysis.

Choose 2 Electives (6 credits):

• CM8064 Liquid Chromatography (3-credits)
  A variety of separation modes using different combinations of stationary phase and mobile phase are being used in liquid chromatography. This course will illuminate the separation mechanism in each of these modes. Starting with fundamentals of liquid chromatography, we will learn about column packing materials, partitioning in different modes of chromatography, preparative separation, and method development including gradient elution.

• CM7064 Chemistry of Colloids (3-credits)
  Colloidal dispersions are heavily being used in today's society from paints and inks to drug delivery systems. This special topics course will cover various topics of colloids ranging from preparation of colloids and characterization methods to thermodynamics. Both aqueous and non-aqueous dispersions will be considered.
  
  
• CM9034 Organic Chemistry I (3-credits)
  Molecular structure and bonding. Stereochemical and conformational principles. Theories of bonding and the physical parameters of stable and reactive molecular states. Applications in biochemistry and polymer chemistry. Prerequisites: undergraduate physical chemistry and organic chemistry.
  
  
• BE6254 Biosensors (3-credits)
  Available online in future semesters.

Guided Studies (8 credits):

• BI7584 Guided Studies/Thesis (3-credits)
  To be arranged with thesis advisor.
  
  
• BI7594 Guided Studies/Thesis (3-credits)
  To be arranged with thesis advisor.

Requirements

Admission to Master of Science in Bioinformatics program requires a bachelor's degree in an appropriate preparatory discipline from an institution acceptable to Polytechnic.

• Completed Application Form
• Transcripts of undergraduate records
• Two (2) letters of recommendation
• TOEFL (for International Applicants)
• Application Fee: $45
• Tuition: $950/credit
• Candidates for the degree Master of Science in Bioinformatics must complete no less than 30 credits of advanced study with an overall GPA of B in all graduate courses as required by the University.

Apply now!

Faculty

Chemistry, Chemical, and Biological Engineering Faculty

• Kalle Levon (Director and Professor)
• Iwao Teraoka (Professor)
• James Gergel (Professor)

Campus Availability:

• Brooklyn
• Online

Applications Accepted for:

• Fall
• Spring

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