This class analyzes complex biological processes from the molecular, cellular, extracellular, and organ levels of hierarchy. Emphasis is placed on the basic biochemical and biophysical principles that govern these processes. Examples of processes to be studied include chemotaxis, the fixation of nitrogen into organic biological molecules, growth factor and hormone mediated signaling cascades, and signaling cascades leading to cell death in response to DNA damage. In each case, the availability of a resource, or the presence of a stimulus, results in some biochemical pathways being turned on while others are turned off. The course examines the dynamic aspects of these processes and details how biochemical mechanistic themes impinge on molecular/cellular/tissue/organ-level functions. Chemical and quantitative views of the interplay of multiple pathways as biological networks are emphasized. Student work will culminate in the preparation of a unique grant application in an area of biological networks.

This class analyzes complex biological processes from the molecular, cellular, extracellular, and organ levels of hierarchy. Emphasis is placed on the basic biochemical and biophysical principles that govern these processes. Examples of processes to be studied include chemotaxis, the fixation of nitrogen into organic biological molecules, growth factor and hormone mediated signaling cascades, and signaling cascades leading to cell death in response to DNA damage. In each case, the availability of a resource, or the presence of a stimulus, results in some biochemical pathways being turned on while others are turned off. The course examines the dynamic aspects of these processes and details how biochemical mechanistic themes impinge on molecular/cellular/tissue/organ-level functions. Chemical and quantitative views of the interplay of multiple pathways as biological networks are emphasized. Student work will culminate in the preparation of a unique grant application in an area of biological networks.

This is a comprehensive textbook covering life functions that are ultimately interpretable in chemical terms, as chemistry is the logic of biological phenomena.

This educational journal article addresses the implementation of bioinformatics in the classroom. The author explains how bioinformatics could play a key role for science students pursuing higher education, foster inquiry learning of content that has often been taught in a dry manner, provide the thread that ties classes together, improve biology teaching, enhance the learning of biotech issues and ethics, expose students to real-world science, and significantly help to reform biology teaching and improve learning. The article includes links to bioinformatics resources, information about how to get involved in bioinformatics, and a glossary of terms.

This site contains user-friendly tools to launch DNA database searches, statistical analyses, and population modeling from a centralized workspace. Educational databases support investigations of an Alu insertion polymorphism on human chromosome 16 and single nucleotide polymorphisms (SNPs) in the human mitochondrial control region.

Biology of cells of higher organisms: structure, function, and biosynthesis of cellular membranes and organelles; cell growth and oncogenic transformation; transport, receptors and cell signaling; the cytoskeleton, the extracellular matrix, and cell movements; chromatin structure and RNA synthesis.

The goal of this course is to teach both the fundamentals of nuclear cell biology as well as the methodological and experimental approaches upon which they are based. Lectures and class discussions will cover the background and fundamental findings in a particular area of nuclear cell biology. The assigned readings will provide concrete examples of the experimental approaches and logic used to establish these findings. Some examples of topics include genome and systems biology, transcription, and gene expression.

In this interactive activity adapted from the University of Nebraska, learn how and where transcription and translation occur within a cell and observe both processes in detail.

Study and discussion of computational approaches and algorithms for contemporary problems in functional genomics. Topics include DNA chip design, experimental data normalization, expression data representation standards, proteomics, gene clustering, self-organizing maps, Boolean networks, statistical graph models, Bayesian network models, continuous dynamic models, statistical metrics for model validation, model elaboration, experiment planning, and the computational complexity of functional genomics problems.

As a class, students work through an example showing how DNA provides the "recipe" for making our body proteins. They see how the pattern of nucleotide bases (adenine, thymine, guanine, cytosine) forms the double helix ladder shape of DNA, and serves as the code for the steps required to make genes. They also learn some ways that engineers and scientists are applying their understanding of DNA in our world.

This interactive quiz allows you to test your knowledge on all areas of DNA and RNA.

In this visualization adapted from the University of Massachusetts Medical School, discover the role that dengue viral proteins play in a human cell as the virus prepares to replicate.

Dynamic Gene is designed to let students learn about plant genomes by using bioinformatics to analyze newly sequenced genes in rice and maize. Many of these genes have only been predicted by computers and have never been closely examined by human beings! The site's name emphasizes the gene both as a dynamic structure that changes through evolutionary time, but also as a dynamic concept that changes with our increasing knowledge of genome organization. The design for Dynamic Gene recalls the "streamlining movement" that influenced design during the middle of the 20th century with ideas borrowed from aviation and automobile design.

Introduction to computational biology including the fundamentals of protein and nucleic acid sequence analysis, phylogenetic analysis, motif finding, hidden Markov models, and 3D structure prediction and modeling. An overview of emerging fields including expression profiling, quantitative image analysis and the modeling of cellular signal transduction networks are also included. Subject designed for advanced undergraduates and graduate students with strong backgrounds in either molecular biology or computer science but not necessarily both. Two self-study tracks are offered, introducing either basic statistical methods and programming (to biologists) or the fundamentals of molecular biology (to computer scientists). Lectures combine both perspectives to illustrate how computation is having a significant impact on modern biology. Serving as an introduction to computational biology, this course emphasizes the fundamentals of nucleic acid and protein sequence analysis, structural analysis, and the analysis of complex biological systems. The principles and methods used for sequence alignment, motif finding, structural modeling, structure prediction, and network modeling are covered. Students are also exposed to currently emerging research areas in the fields of computational and systems biology.

" During development, the genetic content of each cell remains, with a few exceptions, identical to that of the zygote. Most differentiated cells therefore retain all of the genetic information necessary to generate an entire organism. It was through pioneering technology of somatic cell nuclear transfer (SCNT) that this concept was experimentally proven. Only 10 years ago the sheep Dolly was the first mammal to be cloned from an adult organism, demonstrating that the differentiated state of a mammalian cell can be fully reversible to a pluripotent embryonic state. A key conclusion from these experiments was that the difference between pluripotent cells such as embryonic stem (ES) cells and unipotent differentiated cells is solely a consequence of reversible changes. These changes, which have proved to involve reversible alterations to both DNA and to proteins that bind DNA, are known as epigenetic, to distinguish them from genetic alterations to DNA sequence. In this course we will explore such epigenetic changes and study different approaches that can return a differentiated cell to an embryonic state in a process referred to as epigenetic reprogramming, which will ultimately allow generation of patient-specific stem cells and application to regenerative therapy. This course is one of many Advanced Undergraduate Seminars offered by the Biology Department at MIT. These seminars are tailored for students with an interest in using primary research literature to discuss and learn about current biological research in a highly interactive setting. Many instructors of the Advanced Undergraduate Seminars are postdoctoral scientists with a strong interest in teaching."

Since the discovery of the structure of the DNA double helix in 1953 by Watson and Crick, the information on detailed molecular structures of DNA and RNA, namely, the foundation of genetic material, has expanded rapidly. This discovery is the beginning of the "Big Bang" of molecular biology and biotechnology. In this seminar, students discuss, from a historical perspective and current developments, the importance of pursuing the detailed structural basis of genetic materials.

The course covers basic concepts of biomedical engineering and their connection with the spectrum of human activity. It serves as an introduction to the fundamental science and engineering on which biomedical engineering is based. Case studies of drugs and medical products illustrate the product development-product testing cycle, patent protection, and FDA approval. It is designed for science and non-science majors.

Build a gene network! The lac operon is a set of genes which are responsible for the metabolism of lactose in some bacterial cells. Explore the effects of mutations within the lac operon by adding or removing genes from the DNA.

The goal of the Genetic Origins Program is to allow students to use their own DNA variations (polymorphisms) as a means to explore our shared genetic heritage and its implications for human health and society. Genetic Origins focuses on two types of DNA variations: an Alu insertion polymorphism on chromosome 16 (PV92) and single nucleotide polymorphisms (SNPs) in the control region of the mitochondrial (mt) chromosome. With two alleles and three genotypes, PV92 is a simple genetic system that illustrates Mendelian inheritance on a molecular level. PV92 data is readily analyzed using population statistics. The mt control region is one of the simplest regions of human DNA to sequence. With a high mutation rate, the mt control region is the "classical" system for studying human and primate evolution. The Genetic Origins site and linked Bioservers site have all the information needed for students to perform the Alu and mt DNA experiments and analyze the results - including online protocols, reagents, animations and videos explaining key concepts, and database tools.