1. Systems Biology and Neuroengineering Christine P. Hendon, PhD Columbia University Electrical Engineering Department TRANSCENDING DISCIPLINES, TRANSFORMING LIVES

2. What is Systems Biology and Neuroengineering? Development and application of analytical and theoretical techniques to the study of biological systems Using engineering techniques to understand, repair, or replicate the properties of neural systems Applying systems tools & thinking to biological systems Highly interdisciplinary Biology, Chemistry, Neuroscience, BME, CS, ME, MBBI Key EE areas Biological-artificial systems interfaces NeuroRobotics Neuromorphic systems Synthetic Biology 2 | Systems Biology and Neuroengineering

3. Systems Biology and Neuroengineering Centers at Columbia University The Center for Neural Engineering and Computation The Center for Computational Biology and Bioinformatics The Center for the Multiscale Analysis of Genomic and Cellular Networks Institute for Data Science and Engineering Optical Techniques for Actuation, Sensing and Imaging of Biological Systems 3 | http://www.ee.columbia.edu/systems-biology-and-neuroengineering

4. Systems Biology and Neuroengineering Course Flow

5. 5 | System Biology and Neuroengineering Fall 2016 Courses

6. Previous Courses ECBM E6040 (Spring 2016) - Neural Networks and Deep Learning ELEN E9070 (Spring 2016) - Seminar in Computational Neuroscience and Neuroengineering BMEB W4020 (Fall 2015) - Computational Neuroscience: Circuits in the Brain BMEE E4030 (Fall 2015) - Neural Control Engineering ECBM E4090 (Fall 2015) - Brain Computer Interfaces (BCI) Laboratory EEBM E9070 (Spring 2015) - Computing with Brain Circuits BMEB W4020 (Fall 2014) - Computational Neuroscience: Circuits in the Brain BMEE E4030 (Fall 2014) - Neural Control Engineering ECBM E4090 (Fall 2014) - Brain Computer Interfaces Lab EEBM E6099 (Fall 2014) - Topics in Computational Neuroscience/Neuroengineering EEBM E6092 (Spring 2014) - Big Data in Neuroscience EEBM E9070 (Spring 2014) - Comp-Neuro & Engineering Seminar: Neural Processing of Acoustic Signals BMEB W4020 (Fall 2013) - Computational Neuroscience: Circuits in the Brain BMEE E4030 (Fall 2013) - Neural Control Engineering EEBM E6020 (Spring 2013) - Methods of Computational Neuroscience BMEE E6030 (Spring 2013) - Neural Modeling and Neuroengineering EEBM E9070 (Spring 2012) - Seminar in Neuroengineering and Computation 6 | Systems Biology and Neuroengineering

7. BMEB W4020 Computational Neuroscience: Circuits in the Brain Prof. Aurel Lazar The Biophysics of Computation Modeling Biological Neurons, The Hudgkin-Huxley Neuron, Modeling Channel Conductances and Synapses as Memristive Systems, Bursting Neurons and Central Pattern Generators, I/O Equivalence and Spiking Neuron Models. Encoding with Neural Circuits Stimulus Representation with Time Encoding Machines, Geometry of Time Encoding, Encoding with Neural Circuits with Feedback, Spatio-Temporal Receptive Fields, Population Audio and Video Time Encoding Machines. Functional Identification of Neural Circuits Modeling Dendritic Stimulus Processors, Channel Identification Machines, A Fundamental Duality between Neural Decoding and Functional Identification, Identifying Spatio-Temporal Receptive Fields and Biophysical Spike Generators. Projects in Matlab or Python 7 | Systems Biology and Neuroengineering

8. ECBM E4090 Brain Computer Interface Laboratory Prof. Nima Mesgarani Hands on experience with neural signal recording and analysis Gaining experience with electroencephelography (EEG) Exploring the applications in scientific, engineering and medical fields 8 | Systems Biology and Neuroengineering

9. ECBM E4060 Introduction to Genomic Information Science and Technology Prof. Dimitris Anastassiou Introduction to the information system paradigm of molecular biology. Representation, organization, structure, function and manipulation of the biomolecular sequences of nucleic acids and proteins. The role of enzymes and gene regulatory elements in natural biological functions as well as in biotechnology and genetic engineering. 9 | Systems Biology and Neuroengineering

10. BMEE E4030 Neural Control Engineering Prof. Qi Wang Basic cell biophysics, models of neurons, ion channels, spike generation Large-scale electrophysiological recording methods, sensorimotor integration and optimal state estimation, operant conditioning of neural activity Nonlinear modeling of neural systems, sensory systems Neural encoding model Neuronal response to electrical micro-stimulation, DBS for Parkinson's disease treatment, motor neural prostheses, and sensory neural prostheses. 10 | Systems Biology and Neuroengineering

11. EEBM E6090 Topics in Computatonal Neuroscience/Neuroengineering Prof. Paul Sadja State of the art in Brain Computer Interfaces (BCI) Physiological signals for BCI, decoding of signals, interfaces (invasive and non-invasivve), feedback and brain plasticity Case studies Midterm Exam Final BCI Project 11 | Systems Biology and Neuroengineering

12. ECBM E4040 Neural Networks and Deep Learning Prof. Zoran Kostic Developing features & internal representations of the world, artificial neural networks, classifying handwritten digits with logistics regression, feedforward deep networks, back propagation in multilayer perceptrons, regularization of deep or distributed models, optimization for training deep models, convolutional neural networks, recurrent and recursive neural networks, deep learning in speech and object recognition. Analytical study and software design Team based projects Industry participation 12 | Systems Biology and Neuroengineering

13. Seminars The Forces that Shape Living Tissues: Building the Fruit Fly Embryo Sept 12, 2016| 11AM | 414 CEPSR Dr. Karen Kasza – Columbia Univ Uncovering Latent Representations of Hippocampal Population Codes Sept 19, 2016| 11AM | 414 CEPSR Zhe Chen – NYU School of Medicine Research Exposure Research for Credit Many opportunities to work on neuro/bio related research projects: experimental, medical, computational or theoretical projects. Contact the faculty directly Open Labs 2-4PM 13 | Systems Biology and Neuroengineering

14. Faculty Dimitris Anastassiou – Computational biology and genomics Christine Hendon – optical imaging for cardiovascular and oncology applications Predrag Jelenkovic – Mathematical modeling of biological systems Aurel Lazar – computing with neural circuits Nima Mesgarani – Reverse-engineering the auditory system Ken Shepard – Bioelectronics and neural interfaces Paul Sajda – Neural engineering, neuro-computation Joshua Jacobs - Electrophysiology of navigation and memory, brain stimulation, direct human brain recordings Qi Wang – Neural coding, brain machine interfaces http://www.ee.columbia.edu/systems-biology-and-neuroengineering