Publications

JOURNAL PAPERS UNDER REVIEW

L. Ghanbari*M. L. Rynes*J. HuD. Sousa ShulmanG. JohnsonM. LaroqueG. ShullS. B Kodandaramaiah, Principles of Computer Numerical Controlled Machining Applied to Cranial Microsurgery. *Equal contribution

Pre-print of paper posted at Biorxiv: https://www.biorxiv.org/content/early/2018/03/12/280461

L. Ghanbari, R. E. Carter, M. L. Rynes, J. Dominguez, G. Chen, A. Naik, J. Hu, Md. A. K. Sagar, L. Haltom, N. Mossazghi, M. M. Gray, S. L. West, K. W. Eliceiri, T. J. Ebner and S. B. Kodandaramaiah, Cortex-wide neural interfacing via transparent polymer skulls.

Pre-print of paper posted at Biorxiv: https://www.biorxiv.org/content/early/2018/08/07/387142

JOURNAL PUBLICATIONS

1) B. D. Allen,  Caroline Moore-Kochlacs, J. G. Bernstein, J. Kinney, J. Scholvin, L. Seoane, C. Chronopoulos, C. Lamantia, S. B. Kodandaramaiah, M.Tegmark and E. S. Boyden, Automated in vivo patch clamp evaluation of extracellular multielectrode array spike recording capability, J Neurophysiology, 11 July 2018 [Publisher Link]

2) S. B. Kodandaramaiah*, F. J. Flores* , G. L. Holst, A. C. Singer, X. Han , E. N. Brown, Edward S. Boyden^, C. R. Forest^ Multi-neuron intracellular recording in vivo via interacting autopatching robots, Elife, * Equal Contribution, ^ Co-corresponding authors [Publisher Link]

3) I. Kolb, G. Talei Franzesi, M. Wang, S. B. Kodandaramaiah, C. R. Forest, E. S. Boyden, and A. C. Singer, Evidence for long-timescale patterns of synaptic inputs in CA1 of awake behaving mice, J Neuroscience, [Publisher Link]

4) K. D. Piatkevich, H. J. Suk, S. B. Kodandaramaiah, F. Yoshida, E. M. DeGennaro, M. Drobizhev, T. E. Hughes, R. Desimone, E. S Boyden, V. V. Verkhusha, Near-Infrared Fluorescent Proteins Engineered from Bacterial Phytochromes in Neuroimaging, Biophysics Journal, Volume 113, Issue 10, 21 November 2017, 2299-2309,  [Publisher link]

5) H. J. Suk, I. Van Welie, S. B.  Kodandaramaiah, B. D.  Allen, C. R.  Forest, E. S.  Boyden, Closed-Loop Real-Time Imaging Enables Fully Automated Cell-Targeted Patch-Clamp Neural Recording In Vivo, Neuron 2017 [Publisher Link]

6) N. Grossman, D. Bono, N. Dedic, S. B. Kodandaramaiah, A. Rudenko, H. Suk, A. M. Cassara, E. Neufeld, N. Kuster, L. Tsai, A. Pascual-Leone, E. S. Boyden, Noninvasive Deep Brain Stimulation via Temporally Interfering Electric Fields, Cell,  2017, [Publisher Link]

7) A. C. Singer, G. Talei Franzesi, S. B. Kodandaramaiah, F. J. Flores, J. D. Cohen, A. K. Lee, C. Börgers, C. R. Forest, N. J. Kopell, E. S. Boyden, Mesoscale-duration activated states gate spiking in response to fast rises in membrane voltage in the awake brain, J Neurophysiology, 2017, [Publisher Link]

8) Q. Wu, I. Kolb, B. Callahan, Z. Su, W. Stoy, S. B. Kodandaramaiah, R. Neve, H. Zeng, E.S. Boyden, C. R.  Forest, and Alexander Chubykin, Integration of autopatching with automated pipette and cell detection in vitro, Journal of Neurophysiology, 2016, [Publisher Link]

9) S. B. Kodandaramaiah, I. R. Wickersham, G. B. Holst, A. C. Singer, G. Talei-Franzesi, C. R. Forest, E. S. Boyden, Assembly and operation of the autopatcher for automated intracellular neural recording in vivo, Nature Protocols, 2016 [publisher link][Local copy],[Video], Related Coverage:[Nature News][Nature][TIME][Forbes][Scientific American]

10) M.V. Baratta, S.B. Kodandaramaiah, P.E. Monahan, P.-A. Lin, K. Kim, A. Yang C.R. Forest, E.S. Boyden, K.A. Goosens, Stress enables reinforcement-elicited serotonergic consolidation of fear memory. Biological Psychiatry, 2015 [publisher link][Local copy]

11) R. R. Harrison, I. Kolb, S. B. Kodandaramaiah, A. A. Chubykin, A. Yang, M. F. Bear, E. S. Boyden, C. R. Forest, Microchip amplifier for in vitro, in vivo, and automated whole-cell patch-clamp recording, J Neurophysiology, 2014 [publisher link][Local copy]

12) A. S. Chuong, M. L. Miri* , V. Busskamp*, G.A.C. Matthews*, L.C.Acker*, A.T. Soresnsen, A. Young, N. C. Klapoetke, M.A. Henninger, S.B. Kodandaramaiah, M. Ogawa, S. B. Ramanlal, R. C. Bandler, B. D. Allen, C.R. Forest, B.Y.Chow, X. Han, Y. Lin,K.M. Tye, R. Roska , J.A. Cardin, E. S. Boyden, Noninvasive optical inhibition with a red-shifted microbial rhodopsin, Nature Neuroscience, 2014 (*, equal contribution) [publisher link][Local copy]

13) S. B. Kodandaramaiah, E.S. Boyden and C. R. Forest, E. S. Boyden, In Vivo Robotics: Towards the Automation of Neuroscience and Other Intact-System Biological Fields, Annals of New york Academy of Sciences, 2013 [publisher link][Local copy]

14) S.B. Kodandaramaiah, G. Talei Franzesi, B.Y. Chow, E.S. Boyden, C.R. Forest, Automated whole-cell patch clamp electrophysiology of neurons in vivo. Nature Methods2012 [publisher link][pdf], [Video],  Related Coverage: [Nature News][Nature][TIME][Forbes][Scientific American]

PEER REVIEWED CONFERENCE PROCEEDINGS

1) L. Ghanbari, R. Carter, M. Rynes, J. Dominguez, J. Hu, N. Mossazghi, M. Laroque, T. Ebner, S. B. Kodandaramaiah, Brain Windows: Digitally Generated 3D Cranial Windows for Pan Cortical Neural Interfacing, Proceedings of the 2017 Design of Medical Devices Conference, Minneapolis, MN, April 10th-12th, 2018

2) G.Shull, C. Haffner, W. Huttner, S. B. Kodandaramaiah, E. Taverna, A robot for high throughput analysis of neural stem cells in intact tissue, Proceedings of the 2017 Design of Medical Devices Conference, Minneapolis, MN, April 10th-12th, 2018

3) M. Rynes, L. Ghanbari, J. Hu, D. S. Schulman, G. Johnson, M. Laroque, S. B. Kodandaramaiah, Principles of Computer Numerical Control Applied to Small Animal Microsurgical Procedures, Proceedings of the 2017 Design of Medical Devices Conference, Minneapolis, MN, April 10th-12th, 2018

4) G. Johnson, L.Lehto, S. Mangia, O. Gröhn, S. Michaeli, S. B. Kodandaramaiah, Conceptual Design of Flex-DBS, a Mechanically Reconfigurable Deep Brain Stimulation Probe, Proceedings of the 2017 Design of Medical Devices Conference, Minneapolis, MN, April 11th-13th, 2017

5) B. D. Allen, C. Moore-Kochlacs, J. Scholvin, J. B. Kinney, J. Bernstein, S. B. Kodandaramaiah, N. Kopell, E. S. Boyden, Towards ground truth in ultra-dense neural recording, Proceedings of the Computational and Systems Neuroscience (Cosyne) Meeting 2016, Salt Lake City, UT, February 25 – 28, 2016.

6) A. Singer, G.T. Franzesi, S. B. Kodandaramaiah, F. Flores, C. Forest, N. Kopell, E. Boyden, Interaction of Slow Network Integration and Fast Neural Integration Towards Spike Generation, Proceedings of the Computational and Systems Neuroscience (Cosyne) Meeting 2015, Salt Lake City, UT, Mar 5-8, 2015.

7) S.B. Kodandaramaiah, F. Flores, G. Holst, I. Wickersham, E. Brown, C.R. Forest, E.B. Boyden, The Multipatcher: A Robot for High Density Measurement of Intracellular Recordings In Vivo, Proceedings of the Biomedical Engineering Society (BMES) 2014, San Antonio, TX, Oct 22-25, 2014.

8) I. Kolb*, G. Holst*, S.B. Kodandaramaiah, W. Stoy, E.S. Boyden, C.R. Forest. Linear Micro-Actuation System for Patch-Clamp Recording. Proceedings of the 29th Annual Meeting of the American Society for Precision Engineering. Boston, MA.

9) J. Go, A. Fan, C. Lu, S. B. Kodandaramaiah, G. L. Holst, W. Stoy, I. Kolb, E. S. Boyden, C. R. Forest, Fully-automated in vivo single cell electrophysiology, Proceedings of the 28th Annual Meeting of the American Society for Precision Engineering 2013, St. Paul, MN, October 20-October 55, 2013

10) I. Kolb, G. B. Holst, B. Goldstein, S.B. Kodandaramaiah, E.S. Boyden, E. Culurciello, C.R. Forest, Automated, in-vivo, whole-cell electrophysiology using an integrated patch-clamp amplifier, Proceedings of the 22nd Annual Computational Neuroscience Meeting (CNS 2013), Paris, France, July 13-18, 2013.

11) S. B. Kodandaramaiah, A. S. Chuong, M. Ogawa, N. Klapoetke, M. Baratta, L. C. Acker, P. E. Monahan, F. Yoshida, E. S. Boyden, and C. R. Forest, Integration of automated patch clamp electrophysiology system with optogenetics for cell type identification in vivo, Proceedings of the Annual Meeting of the Biomedical Engineering Society (BMES) 2012, Atlanta, GA, October 24-27, 2012

12) D. Chiyo, S. B. Kodandaramaiah, K. Grosh, Z. D. Ma, B. Raju, F. R. Abadi, Reactive Structure and Smart Armor for Army’s Future Ground Vehicles, Proceedings of 25th Annual Army Sciences Conference (ASC 2010), Orlando, Florida, November 29 – December 2, 2010.

13) S. B. Kodandaramaiah, S. Malik, C. R. Forest, Design and performance of telescoping micropipette arrays for high-throughput in vivo patch clamping, Proceedings of the 25th Annual Meeting of the American Society for Precision Engineering, Atlanta, GA, October 31-November 5, 2010, Awarded R.V. Jones Memorial Award for Best Student Paper.

14) N. Pak, C.R. Phaneuf, S. B. Kodandaramaiah, and C.R. Forest, Modulation of electromagnetic radiation using a dot matrix printer, Proceedings of the 25th Annual Meeting of the American Society for Precision Engineering 2010, Atlanta, GA, October 31-November 5, 2010

15) S. B. Kodandaramaiah, N. Chronis, An Opto-fluidic sensor for monitoring Intra-cranial pressure (ICP), Proceedings of the 12th International Conference on micro-Total Analysis Systems, San Diego, CA, October 2008.

16) J. Gregory, Y.S. Ng, E.M. Jung, S. B. Kodandaramaiah, Dielectrophoretic whole blood separation device integrating a spiral pump and cytometry, Proceedings of the 6th IEEE Sensors Conference, Atlanta, GA, October 2007.

INVITED TALKS

1) Technologies for Neural Interfacing at Scale: from Single Cells to the Whole Cortex, Department of Biomedical Engineering Seminar, University of Wisconsin, Madison, WI (November 2017)

2) Technologies for neuronal interfacing at multiple scales – from single cells to whole cortex, Center for Magnetic Resonance Research, University of Minnesota, Twin Citites (September 2017)

3) “Technologies for fully autonomous neuroscience labs”, Transylvania Experimental Neuroscience Summer School, Cluj Napoca, Romania (June 2017)

4) “Robotics for investigating neuronal dynamics in intact brains”, Max Planck Institute of Evolutionary biology, Leipzig, Germany (August 2016)

5) “Robotic Platforms for High throughput neuroscience”, Department Seminar, School of Dentistry, University of Minnesota, Minneapolis, MN (August 2016)

6) “Robotic tools for observing neuronal computations in intact brains.”, Institute for Engineering in Medicine, University of Minnesota, Minneapolis, MN (February 2016)

7) “Robotic technologies for high-throughput in vivo drug discovery”, Novartis Institutes for Biomedical Research, Cambridge, MA (June 2015)

8) “Robotic technologies for high-throughput in vivo neuroscience”, Max Planck Institute for Cellular and Molecular Biology, Dresden, Germany (August 2014)

9) “Robotic technologies for in vivo electrophysiology in awake behaving rodents”, Meeting at the Bio-Computational neuroscience group, Emory University, Atlanta, GA (December 2013)

10) “Robotics for in vivo electrophysiology: current progress and future directions”, Seminar, Cold Spring Harbor Laboratories, Cold Spring Harbor, NY (July 2012)

11) “Automated whole-cell patch clamp electrophysiology of neurons in vivo”, McGovern Institute Special Neurotechnology Seminar, McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge MA (September 2011)

CONFERENCE PRESENTATIONS

1) L. Ghanbari, R. Carter, M. Rynes, J. Dominguez, J. Hu, N. Mossazghi, M. Laroque, T. Ebner, S. B. Kodandaramaiah, Brain Windows: Digitally Generated 3D Cranial Windows for Pan Cortical Neural Interfacing, Neuroscience 2017, Washington D.C, November 11-15, 2017

2) G.Shull, C. Haffner, W. Huttner, S. B. Kodandaramaiah, E. Taverna, A robot for high throughput analysis of neural stem cells in intact tissue, EMBO Conference: Gene regulatory mechanisms in neural fate decisions, Alicante,Spain, Sep. 7-10, 2017

3) M. Rynes, L. Ghanbari, J. Hu, D. S. Schulman, G. Johnson, M. Laroque, S. B. Kodandaramaiah, Principles of Computer Numerical Control Applied to Small Animal Microsurgical Procedures, Society for Neuroscience, Washington, DC, November 11-15, 2017

4) G.Shull, C. Haffner, W. Huttner, E. Taverna, , S. B. Kodandaramiah, Image Guided Robot for Microinjection into Single Cells in Organotypic Slices of Mouse Telencephalon, Institute for Engineering in Medicine Annual Conference and Retreat, Minneapolis,MN,USA, Nov. 6 2017

5) L. Ghanbari, R.  Carter, M. Rynes, J. Dominguez, N. Mossazghi, J. Hu, G. Shull, M. Laroque, T. Ebner, S. B. Kodandaramaiah, Brain Windows: Digitally Generated 3D Cranial Windows for Pan Cortical Neural Interfacing, Institute for Engineering in Medicine Annual Conference and Retreat, Minneapolis, MN, November 6, 2017

6) N. Mossazghi, L. Ghanbari, M. Ryans,  J. Dominguez1, J. Jia Hu, R. Carter, T.J. Ebner, S. B. Kondandaramaiah, Cranial Prostheses for Chronic, Pan-Cortical Two-Photon Imaging in Behaving Mice, McNair Scholars 27th Annual Summer Poster Symposium, Minneapolis, MN, Augst 3, 2017.

7) N. Mossazghi, L. Ghanbari, M. Ryans,  J. Dominguez1, J. Jia Hu, R. Carter, T.J. Ebner, S. B. Kondandaramaiah, Cranial Prostheses for Chronic, Pan-Cortical Two-Photon Imaging in Behaving Mice, 2017 North Star STEM Alliance 10th Annual Kick Off, Minneapolis, MN, September 28, 2017.

8) N. Mossazghi, L. Ghanbari, M. Ryans,  J. Dominguez1, J. Jia Hu, R. Carter, T.J. Ebner, S. B. Kondandaramaiah, Cranial prosthesis for chronic awake imaging in mouse model for episodic ataxia type 2, 2017 Annual Biomedical Reseach Conference for Minority Students, Phoenix, AZ,  November 2017.

9) G. Johnson, L. Lehto, S. Mangia, O. Gröhn, S. Michaeli, S. B.  Kodandaramaiah, Conceptual Design of Flex-DBS, a Mechanically Reconfigurable Deep Brain Stimulation Probe, Design of Medical Devices (DMD) conference, Minneapolis, MN, April 9-12, 2017.

10) A.C. Singer, G. Talei Franzesi, S.B. Kodandaramaiah, M. Tsitsiklis, S. Sharma, D. Bozic, S. Batir, I.R. Wickersham, G.B. Holst, C.R. Forest, C. Borgers, N.J. Kopell, E.S. Boyden, Time course of subthreshold activity preceding spike generation in awake behaving mouse hippocampus, Proceedings of the Annual Meeting of the Society for Neuroscience (Neuroscience 2014), Washington DC, Nov 15-19, 2014.

11) S.B. Kodandaramaiah, F.J. Flores, G. Talei Franzesi, A.C. Singer, G. Holst, I.R. Wickersham, C. Borgers, N.J. Kopell, C.R. Forest, E.N. Brown, E.S. Boyden, Automated multiple-cell patch clamp assessment of multineuron subthreshold dynamics in waking and anesthetized states, Proceedings of the Annual Meeting of the Society for Neuroscience (Neuroscience 2014), Washington DC, Nov 15-19, 2014.

12) G. Holst, S.B. Kodandaramaiah, I. Kolb, W. Stoy, I. Wickersham, A. Singer, L. Li, E.S. Boyden, H. Zeng, C.R. Forest, High­throughput fully automated patch clamp robot for in-vivo electrophysiology and morphology, Proceedings of the Annual Meeting of the Society for Neuroscience (Neuroscience 2014), Washington DC, Nov 15-19, 2014.

13) G.T. Franzesi, A. Singer, I. Kolb, S. Sharma, S. B. Kodandaramaiah, M. Tsitsiklis, I. Wickersham, G. Holst, D. Bozic, S. Batir, C. Forest, C. Borgers, N. Kopell, E.S. Boyden, Automated exploration of intracellular mechanisms of in vivo neural computation, Proceedings of the Annual Meeting of the Society for Neuroscience (Neuroscience 2014), Washington DC, Nov 15-19, 2014.

14) S. B. Kodandaramaiah, F. J. Flores, I. R. Wickersham, G. L. Holst, E. N. Brown, C. R. Forest, E. S. Boyden, The Multipatcher: a robot for high density intracellular recordings in vivo. Proceedings of the 27th Annual Meeting of the Society for Neuroscience, San Diego, CA, November 9-13, 2013

15) A. C. Singer, G. Talei Franzesi, S. B. Kodandaramaiah, I. R. Wickersham, S. Sharma, S. Batir, N. Pak, G. Holst, C. R. Forest, N. J. Kopell, E. S. Boyden, Awake Autopatching: Automatic whole cell patch clamp of hippocampal neurons in awake behaving animals, Proceedings of the 27th Annual Meeting of the Society for Neuroscience, San Diego, CA, November 9-13, 2013

16) G. L. Holst, S. B. Kodandaramaiah, C. R. Phaneuf, W. Stoy, I. Kolb, I. R. Wickersham, N. Killian, B. Buffalo, E. S. Boyden, C. R. Forest, Miniaturized actuation system for automated, in-vivo, patch clamp recording, Proceedings of the 27th Annual Meeting of the Society for Neuroscience, San Diego, CA, November 9-13, 2013

17) J. Go, G. L. Holst, C. Lu, A. Fan, S. B. Kodandaramaiah, C. R. Phaneuf, W. Stoy, I. Kolb, I. R. Wickersham, E. S. Boyden, C. R. Forest, Pipette replacement robot to fully automate sequential patch clamp recordings in-vivo, Proceedings of the 27th Annual Meeting of the Society for Neuroscience, San Diego, CA, November 9-13, 2013

18) W. Stoy, C. Shepard, G. L. Holst, I. Kolb, S. B. Kodandaramaiah, D. Ollerenshaw,  D. Millard, E. S. Boyden, G. B. Stanley, C. R. Forest, Multiple, In vivo patch clamp recordings along the mouse vibrissae pathway. Proceedings of the 27th Annual Meeting of the Society for Neuroscience, San Diego, CA, November 9-13, 2013

19) F. J. Flores, S. B. Kodandaramaiah, I. R. Wickersham, C. R. Forest, E. N. Brown, E. S. Boyden. Multiple whole-cell patch clamp to study state transitions in the awake mouse. IX Annual meeting of the Chilean Society of Neuroscience & VIII IberoAmerican Congress of Biophysics, Valparaiso, Chile, Oct 1-4th, 2013. Voted ‘Best Poster Presentation’

20) S. B. Kodandaramaiah, I. Wickersham, S. R. Bates, A. S. Chuong, M. Ogawa, M. V. Baratta, N. Klapoetke, G. Holst, L. C. Acker, F. Yoshida, P. E. Monahan, B. Tasic, H. Zeng, C. R. Forest, E. S. Boyden, Autopatcher application to single cell RNA analysis and optogenetic cell type identification, Proceedings of the 26th Annual Meeting of the Society for Neuroscience, New Orleans, LA, October 13-17, 2012

21) S. B. Kodandaramaiah, G. Holst, G. Talei Franzesi, A. Singer, I. Wickersham, X. Han, E. S. Boyden, C. R. Forest, The Multipatcher: a robot for automated, simultaneous whole-cell patch clamping of multiple neurons in vivo, Proceedings of the 26th Annual Meeting of the Society for Neuroscience, New Orleans, LA, October 13-17, 2012

22) S.B. Kodandaramaiah, G. Talei Franzesi, N. Klapoetke, B. Chow, E. S. Boyden, C. R. Forest, New tools for the mechanistic dissection of neural networks: a robotic system for automated whole-cell patch clamping in vivo and optimized molecular reagents for multi-pathway optogenetic control. Collaborative Research in Computational Neuroscience (CRCNS) PI Meeting, Princeton University, Princeton, NJ, 2012

23) S.B. Kodandaramaiah, G. Talei Franzesi, B. Chow, E. S. Boyden, C. R. Forest, Automated whole-cell patch clamp electrophysiology of neurons in vivo, Collaborative Research in Computational Neuroscience (CRCNS) PI Meeting, Princeton University, Princeton, NJ, 2011

24) S. B. Kodandaramaiah, E.S. Boyden, C.R. Forest, Automated patch clamping of neurons in the mammalian brain in vivo, Proceedings of the 25th Annual Meeting of the Society for Neuroscience, Washington, DC, November 12-16, 2011

25) S. B. Kodandaramaiah, M. Krijnen, J. Go, S. Malik, J. P. Khatait, E. S. Boyden, R. G.K.M. Aarts, D. M. Brouwer and C. R. Forest, Proceedings of the 25th Annual Meeting of the American Society for Precision Engineering, Denver, CO, October 31-November 5, 2011

26) M.V. Baratta, S. B. Kodandaramaiah, P.E. Monahan, K. Kim, A. Yang, C.R. Forest, K.A. Goosens, E.S. Boyden, Effects of stress on aversive learning require temporally precise serotonergic signaling, Proceedings of the 25th Annual Meeting of the Society for Neuroscience, Washington, DC, November 12-16, 2011.

27) A.S. Chuong, M. Miri, X. Gu, S. B. Kodandaramaiah, M. Ogawa, L.C. Acker, N. Klapoetke, M. A. Henninger, C. R. Forest, B.Y. Chow, X. Han, J. Cardin, E.S. Boyden. Red-shifted optogenetic neural silencers: improvements and in vivo use for inactivation of large brain volumes.  Proceedings of the 25th Annual Meeting of the Society for Neuroscience, Washington, DC, November 12-16, 2011.

28) J. Scholvin, A. N. Zorzos, G. Talei Franzesi, S. B. Kodandaramaiah, B. D. Allen, J. Kinney, C. Moore-Kochlacs, A.C. Singer, S. Wasserman, C. Wentz, M. Yamaguchi, C.R. Forest, N. Kopell, C.G. Fonstad, E.S. Boyden, High channel-count silicon neural recording probes for 3d characterization of optogenetically modulated neural dynamics, Proceedings of the 25th Annual Meeting of the Society for Neurocience, Washington, DC, November 12-16, 2011

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