John M. Beggs
Indiana University
Department of Physics
Swain West 169
Bloomington, IN 47405-7105
(812) 855-7359
[email protected]
Education and Positions
2010–present
Associate Professor, Department of Physics,
Indiana University
2003-2010
Assistant Professor, Department of Physics,
Indiana University
2009-present
Adjunct professor, School of Informatics,
Indiana University
1999-2003
National Institute of Mental Health
Postdoctoral Fellow, lab of Neural Network Physiology
1998-1999
Yale University
Postdoctoral Fellow in Computational Neuroscience
1990-1998
Yale University
Ph.D. in Behavioral Neuroscience
1986, 1989
Cornell University
M.Eng. in Engineering Physics
1986-1988
Taught calculus and physics, Samoa College, in US Peace Corps
1981-1985
Cornell University
B.S. in Applied Physics
Publications
1. JM Beggs, EW Kairiss (1994). Electrophysiology and morphology of neurons in rat
perirhinal cortex. Brain research 665 (1), 18-32.
2. JM Beggs, TH Brown, JH Byrne, T Crow, JE LeDoux, K LeBar, RF Thompson
(1999). Learning and memory: Basic mechanisms. Fundamental neuroscience,
1411-1454.
3. JM Beggs, JR Moyer, JP McGann, TH Brown (2000). Prolonged synaptic integration
in perirhinal cortical neurons. Journal of neurophysiology 83 (6), 3294.
4. JM Beggs (2001). A statistical theory of long-term potentiation and depression.
Neural computation 13 (1), 87-111.
5. JM Beggs, D Plenz (2003). Neuronal avalanches in neocortical circuits. The Journal
of neuroscience 23 (35), 11167-11177.
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6. JD Johnson, D Plenz, J Beggs, W Li, M Mieier, N Miltner, K Owen (2003). Analysis
of spontaneous activity in cultured brain tissue using the discrete wavelet transform.
Bioinformatics and Bioengineering. Proceedings. Third IEEE Symposium
7. JM Beggs, D Plenz (2004). Neuronal avalanches are diverse and precise activity
patterns that are stable for many hours in cortical slice cultures. The Journal of
neuroscience 24 (22), 5216-5229.
8. C Haldeman, JM Beggs (2005). Critical branching captures activity in living neural
networks and maximizes the number of metastable states. Physical review letters 94
(5), 58101.
9. JM Beggs, C Haldeman (2005). Beggs and Haldeman reply. Physical Review Letters
95 (21), 219802.
10. D Hsu, JM Beggs (2006). Neuronal avalanches and criticality: A dynamical model for
homeostasis. Neurocomputing 69 (10-12), 1134-1136.
11. JM Beggs (2007). Theoretical neuroscience: How to build a critical mind. Nature
Physics 3 (12), 834-835.
12. J Beggs, J Klukas, W Chen (2007). Connectivity and dynamics in local cortical
networks. Handbook of Brain Connectivity, 91-116.
13. JM Beggs (2007). Neuronal avalanche. Scholarpedia 2 (1), 1344
14. D Hsu, A Tang, M Hsu, JM Beggs (2007). Simple spontaneously active Hebbian
learning model: Homeostasis of activity and connectivity, and consequences for
learning and epileptogenesis. Physical Review E 76 (4), 041909.
15. D Hsu, W Chen, M Hsu, JM Beggs (2008). An open hypothesis: Is epilepsy learned,
and can it be unlearned? Epilepsy & Behavior 13 (3), 511-522.
16. JM Beggs (2008). The criticality hypothesis: how local cortical networks might
optimize information processing. Philosophical Transactions of the Royal Society A:
Mathematical, Physical and Engineering Sciences 366 (1864), 329-343.
17. A Tang, D Jackson, J Hobbs, W Chen, JL Smith, H Patel, A Prieto, D Petrusca M
Grivich, A Sher, P Hottowy, W Dabrowski, AM Litke, JM Beggs (2008). A maximum
entropy model applied to spatial and temporal correlations from cortical networks in
vitro. The Journal of Neuroscience 28 (2), 505.
18. P Hottowy, JM Beggs, EJ Chichilnisky, W Dąbrowski, T Fiutowski, DE Gunning, J
Hobbs, L Jepson, S Kachiguine, K Mathieson, P Rydygier, A Sher, A Skoczeń, A M
Litke (2010). 512-electrode MEA system for spatio-temporal distributed stimulation
and recording of neural activity. Proc. 7th Int. Meeting on Substrate-Integrated Micro
Electrode Arrays.
19. FC Yeh, A Tang, JP Hobbs, P Hottowy, W Dabrowski, A Sher, A Litke, JM Beggs
(2010). Maximum entropy approaches to living neural networks. Entropy 12 (1), 89106.
20. JP Hobbs, JL Smith, JM Beggs (2010) Aberrant Neuronal Avalanches in Cortical
Tissue Removed From Juvenile Epilepsy Patients. Journal of Clinical
Neurophysiology 27 (6), 380.
21. W Chen, J Hobbs, A Tang, J Beggs (2010). A few strong connections: optimizing
information retention in neuronal avalanches. BMC neuroscience 11 (1), 3.
22. B Flecker, W Alford, JM Beggs, PL Williams, RD Beer (2011). Partial information
decomposition as a spatiotemporal filter. Chaos: An Interdisciplinary Journal of
Nonlinear Science 21 (3), 037104.
23. S Ito, ME Hansen, R Heiland, A Lumsdaine, AM Litke, JM Beggs (2011). Extending
transfer entropy improves identification of effective connectivity in a spiking cortical
network model. PLOS One 6 (11), e27431.
24. JM Beggs, N Timme (2012). Being critical of criticality in the brain. Frontiers in
Physiology 3, 163.
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25. N Friedman, S Ito, BAW Brinkman, M Shimono, REL DeVille, KA Dahmen, JM
Beggs, TC Butler (2012). Universal critical dynamics in high resolution neuronal
avalanche data. Physical Review Letters 108 (20), 208102.
26. DA Hsu, MA Hsu, JM Beggs (2012). Method For Suppressing And Reversing
Epileptogenesis. US Patent App. 12/426,430.
27. J Peng, JM Beggs (2013). Attaining and maintaining criticality in a neuronal network
model. Physica A: Statistical Mechanics and its Applications 392 (7), 1611-1620.
28. DE Gunning, JM Beggs, W Dabrowski, P Hottowy, CJ Kenney, A Sher, AM Litke, K
Mathieson (2013). Dense arrays of micro-needles for recording and electrical
stimulation of neural activity in acute brain slices. Journal of neural engineering 10
(1), 016007.
29. N Timme, W Alford, B Flecker, JM Beggs (2013). Multivariate information measures:
an experimentalist's perspective. The Journal of Computational Neuroscience, 2013,
Jul 3.
30. JM Beggs (2013) Neuronal networks: focus amidst the noise Nature Physics 9(9)
533-534.
31. A Nakhnikian, GV Rebec, LM Grasse, LL Dwiel, M Shimono, JM Beggs (2014).
Behavior modulates effective connectivity between cortex and striatum PLOS One
DOI: 10.1371/journal.pone.0089443.
32. S Ito, FC Yeh, E Hiolski, P Rydygier, DE Gunning, P Hottowy, N Timme, AM Litke,
JM Beggs (2014). Large-scale, high-resolution multielectrode-array recording
depicts functional network differences of cortical and hippocampal cultures. PLOS
One 9 (8), e105324.
33. Shimono M, Beggs JM (2014). Functional clusters, hubs, and communities in the
cortical microconnectome. Cerebral Cortex, bhu252.
34. Timme N, Ito S, Myroshnychenko M, Yeh F-C, Hiolski E, Litke AM, Beggs JM
(2014). Multiplex Networks of Cortical and Hippocampal Neurons Revealed at
Different Timescales. PLOS One, DOI: 10.1371/journal.pone.011576
35. Rashid V. Williams-García, Mark Moore, John M. Beggs, and Gerardo Ortiz (2014).
Quasicritical brain dynamics on a nonequilibrium Widom line
Phys. Rev. E 90, 062714.
36. JM Beggs (2015). Editorial: Can There Be a Physics of the Brain? Physical Review
Letters 114 (22), 220001.
37. Nigam S, Shimono M, Ito S, Yeh F-C, Timme N, Myroshnychenko M, Lapish C, Tosi
Z, Hottowy P, Smith WC, Masmanidis S, Litke A, Sporns O, Beggs JM (2016). RichClub Organization in Effective Connectivity among Cortical Neurons. The Journal of
Neuroscience 36(3): 670-684.
38. A Nakhnikian, S Ito, LL Dwiel, LM Grasse, GV Rebec, LN Lauridsen, JM Beggs
(2016). A Novel Cross-Frequency Coupling Detection Method Using the Generalized
Morse Wavelets. The Journal of Neuroscience Methods 269:61-73.
doi:10.1016/j.jneumeth.2016.04.019
39. RV Williams-Garcia, JM Beggs, G Ortiz (2016). Unveiling causal activity of complex
networks. arXiv preprint arXiv:1603.05659.
40. Timme N, Ito S, Myroshnychenko M, Nigam S, Shimono M, Yeh F-C, Hottowy P,
Litke A, Beggs JM (2016). High-Degree Neurons Feed Cortical Computations. PLOS
Computational Biology 12 (5), e1004858.
41. N Marshall, NM Timme, N Bennett, M Ripp, E Lautzenhiser, JM Beggs (2016)
Analysis of power laws, shape collapses, and neural complexity: new techniques and
MATLAB support via the NCC toolbox Frontiers in Physiology 7, 250
42. EM Hiolski, S Ito, JM Beggs, KA Lefebvre, AM Litke, DR Smith (2016). Domoic acid
disrupts the activity and connectivity of neuronal networks in organotypic brain slice
cultures Neurotoxicology 56, 215-224
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43. A Nakhnikian, S Ito, LL Dwiel, LM Grasse, GV Rebec, LN Lauridsen, JM Beggs
(2016). A novel cross-frequency coupling detection method using the generalized
Morse wavelets Journal of neuroscience methods 269, 61-73
Google Scholar link to Beggs publications:
https://scholar.google.com/citations?hl=en&user=y9X4_AkAAAAJ&view_op=list_works&
sortby=pubdate
Awards to fund resarch
RI: Medium: An Analysis of the Consequences of Cortical Structure on Computation
NSF Award Number:1513779
Principal Investigator:John Beggs;
Organization:Indiana University;NSF Organization:IIS
Start Date:09/01/2015;
Award Amount:$568,753.00
MRI: Acquisition of a High-Density Microelectrode Array for Recording and Stimulating
Hundreds of Neurons
NSF Award Number:1429500;
Principal Investigator:John Beggs; Co-Principal Investigator:Ken Mackie, Xiaoming Jin;
Organization:Indiana University;
NSF Organization:DBI
Start Date:12/01/2014;
Award Amount:$91,555.00
Testing the Criticality Hypothesis in Local Cortical Circuits
NSF Award Number:1058291;
Principal Investigator:John Beggs;
Organization:Indiana University;NSF Organization:PHY
Start Date:09/15/2011;
Award Amount:$360,000.00
Collaborative Research: Causal Connectivity and Computations in Hundreds of Neurons
in Cortex
NSF Award Number:0904912;
Principal Investigator:John Beggs; Co-Principal Investigator:Alan Litke, Andrew
Lumsdaine;
Organization:Indiana University;NSF Organization:IIS
Start Date:09/15/2009;
Award Amount:$352,120.00
Attractors and Criticality in Cortical Slice Cultures
NSF Award Number:0343636;
Principal Investigator:John Beggs;
Organization:Indiana University;NSF Organization:IOS
Start Date:10/01/2004;
Award Amount:$346,839.00
Imaging network wide neuronal activity in the nematode C. elegans
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FRSP (Indiana University Faculty Research Support Project)
Beggs, Jacobson and Forrester are co-PIs
1/1/2017 – 9/30/2017
Total award amount: $39,000
The identity and role of hub neurons in local cortical networks
IUCRG (Indiana University Collaborative Research Grant)
Beggs and Jin (Co-PIs)
5/1/2014-4/30/2015
Total award amount: $71,000
This research used in vivo calcium imaging to search for hub neurons that have been
seen in vitro.
A new model for neuronal quasi-criticality
FRSP (Indiana University Faculty Research Support Program)
Beggs and Ortiz (Co-PIs)
9/1/2014-8/31/2015
Total award amount: $29,663
This computational project used computer simulations to explore how cortical networks
optimize processing near a critical point.
Neuronal Avalanches and the Microstructure of Consciousness
Mind Science Foundation
Beggs (PI)
2012
Total award amount: $15,000
Here is the website listing the 2011 and previous awardees:
http://www.mindscience.org/research/tom-slick-research-awards-in
consciousness/recipients. I was invited to apply by them.
Power law distributions and fluctuations in neural and behavioral activity
NAKFI (National Academies Keck Futures Initiative) grant
Beggs (PI), written jointly with Chris Kello of UC Merced
2009
Total award amount: $50,000
A 512 electrode array system for recording from cortical networks
NIH R21 grant
Alan Litke (PI), Beggs co-authored but did not receive funds
2006-2009
Total award amount: $399,440
This funded modifications to the 512 array system which had previously been used only
on retina.
State-dependent effects of molecular manipulations
MetaCyt funds through the Indiana University neuroscience node
Beggs (PI)
2006
Total award amount: $60,000
MetaCyt funds are derived from an award by Eli Lilly Foundation to Indiana University.
Information retention in networks of cortical neurons
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Faculty Research Support Program grant,
Beggs (PI), Andrew Lumsdaine, co-PI
2007-2009
Total award amount: $87,746
Purchase of quartz electrode puller
MetaCyt equipment funds
Beggs and de Ruyter, co-PIs
2005
Total award amount: $12,500 (to purchase a quartz electrode puller)
Teaching awards
Indiana University Trustees Teaching Award 2003, 2011, 2016
Student Choice award from the Indiana University Student Alumni Association for
“excellent teaching and general rapport with students,” 2008
Graduate Student award for outstanding contributions to teaching graduate students in
Physics, 2006
Awards to Beggs students and postdocs
Nick Timme: Koss memorial award (highest honor for a graduate student in physics),
2015
Shinya Ito: Outstanding Research for a Graduate Student, Experimental category, 2013
Masanori Shimono won the JSPS postdoctoral fellowship for continued work with our
group, 2012 - 2014
Rashid Williams-Garcia won the Earl Studevant Graduate Fellowship for spring 2014
Alexander Nakhnikian: NSF graduate fellowship, 2009- 2012
Aonan Tang: Dissertation year fellowship, 2009-2010
Jiayi Peng won 2nd prize in the Siemens national science competition for high school
students, 2012. I advised her remotely via Skype for over two years, as she lives in
Chappaqua, New York. She contacted me after reading about neuronal avalanches in
Scientific American. She is now an undergraduate at Harvard.
http://newyork.newsday.com/westchester/horace-greeley-high-s-jiayi-peng-wins-50kscience-prize-1.4290379
Wei Chen: McCormick Science Grant, 2008 from Indiana University awarded for “the
graduate student member of a faculty/graduate student team whose research is judged
to be most creative, visionary and innovative.”
Aonan Tang: McCormick Science Grant, 2006
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Students and postdocs supervised
Past advisees
1. Wei Chen, PhD in physics 2010 (CEO of startup)
2. Joh Hobbs, PhD in neuroscience 2011 (patent lawyer in Japan)
3. Aonan Tang, PhD in physics 2012 (teacher at New Mexico Military Institute)
4. Shinya Ito, PhD in physics 2012 (postdoctoral job at UC Santa Cruz)
5. Alexander Nakhnikian (joint with Prof. George Rebec), PhD in neuroscience 2013
(postdoctoral job at Harvard)
6. Frances Yeh, PhD in physics 2014 (postdoctoral job at Duke U Singapore)
7. Sunny Nigam, PhD in physics 2014 (postdoctoral job at U Houston)
8. Nick Timme, PhD in physics 2015 (postdoctoral job at Indiana University, Purdue
University, Indianapolis)
9. Emily Miller, PhD in physics 2015 (data science for bank)
10. Rashid Williams-Garcia (joint with Prof. Gerardo Ortiz), PhD in physics 2016
(postdoctoral job at U Pittsburgh)
Past postdoctoral advisee
11. Masanori Shimono, postdoc 2012 – 2015 (now professor at Osaka University)
Present advisees
12. Zach Tosi, cognitive science
13. Madhavun Candadai Vasu, cognitive science
14. Hadi Hafizi, neuroscience
15. Josh Barnathan, physics
16. Golam Kashef, physics and neuroscience
17. Samantha Faber, neuroscience (jointly advised with Ehren Newman)
Undergraduates supervised
John Oluwatobi Adebayo (Physics, 2018), Christian Sikoski (Biology, 2017), Makayla
Jordan (Biology, 2016), Najja Marshal (Physics, 2014), Nick Bennett (Biology, 2015),
Leslie Grasse (Neuroscience, 2014), Lucas Dwiel (Neuroscience, 2015), Zachary
Tritsch (Neuroscience, 2014), Kevin Zbikowski (Physics, 2014), Ben Nicholson (Physics,
2013), Sukriti Bansal (Biology, 2013), Robert Koffi (Physics, 2007), Clay Haldeman
(Physics, 2006)
NSF REU summer students supervised
Amy Cohn (Harvard; 2016), Erin Roth (Carelton College, MN; 2015), Natalie DeNigris
(University of Maryland, Baltimore County; 2015),Monica Ripp (U Wisconsin,
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Whitewater; 2013), Nick Bennett and Najja Marshall (Indiana University; 2012), Rachel
Pauplis (Cornell University; 2010), Shannon Harvey (Cornell University; 2009), Matt
Dornfeld (SUNY Binghamton; 2008), Shellie Heuther (U Missouri; 2007), David Jackson
(Brown; 2006), Jeff Klukas (U Wisconsin Madison; 2005)
Courses taught
Physics 582: Biological and Artificial Neural Networks, Fall 2005, 2006, 2010, Spring
2014, Indiana University. Developed this new course and taught a diverse class of
graduate and undergraduate students from physics, chemistry, computer science,
informatics, neuroscience and optometry. Class had 10 – 15 students.
Neuroscience 500: The first year graduate course in neuroscience; team taught by four
faculty. Fall 2014, 2015. I teach the first quarter, covering the action potential, synaptic
transmission, modulation of neuronal firing. 15 – 25 graduate students.
Physics 317: Information processing in living systems, Spring 2009, 2011. Developed
this course to help undergraduate neuroscience majors learn more about quantitative
thinking. Examples are drawn from neuroscience and physical biology that involve
information processing. Class had 10 – 13 students.
Physics 202: Electricity and Magnetism, with Modern Physics, Fall 2003, Spring 2007,
2008, 2010, 2013, 2015, 2016, 2017. Class consists of ~200-300 science majors with a
primary background in biology.
Physics 201: Mechanics, Sound and Heat, Spring 2005 and 2006, Fall 2007, 2009,
2014, 2015, 2016. Indiana University. Class consists of ~200-370 science majors with a
primary background in biology.
Physics 105, The Physics of Sound, Fall 2011, 2012. Taken by ~90 students from the
Music school, Speech and Hearing, and undecided freshmen.
Press coverage (examples)
Paper on rich-club organization of neurons (Nigam et al., 2016):
http://www.kurzweilai.net/information-flows-through-a-subset-of-high-traffic-hubneurons-in-cortical-regions-of-the-brain
http://www.biotechniques.com/news/Not-All-Neurons-Are-Created-Equal/biotechniques363046.html#.V0ZbQ-StgZw
Scientific American (April 7, 2014) article on “Sand Pile model of the Mind grows in
popularity” www.scientificamerican.com/article/sand-pile-model-of-the-mind-grows-inpopularity/ derived from an identical article in Quanta Magazine.
WIRED magazine article on Criticality in biological systems, where I get several quotes:
http://www.wired.com/2014/05/criticality-in-biology/ Title: “Biologists Find New Rules for
Life at the Edge of Chaos”
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Interviewed for New Scientist article on Math in the brain, published as cover story in
Feb 2013. Neuronal avalanches was featured as one of 5 key ideas currently shaping
how math is applied to the brain
http://www.sciencedirect.com/science/article/pii/S0262407913603735
Radio interview for science program “Are we alone?” carried by several NPR stations.
Website: http://radio.seti.org:80/episodes/That_s_So_Random_ Program aired 10
Jan 2011. I was one of five featured scientists interviewed in a 20 minute piece on
randomness in nature. My comments were on the role of randomness in the brain.
New Scientist, June 29, 2009, “Disorderly genius: How chaos drives the brain”:
http://www.newscientist.com/article/mg20227141.200-disorderly-genius-how-chaosdrives-the-brain.html
Research on neuronal avalanches at Indiana University featured in NSF’s FY 2009
Budget request to congress, page 4 of:
http://www.nsf.gov/about/budget/fy2009/pdf/01_fy2009.pdf
Pulse of the Planet Science Diaries: http://pulseplanet.com/sci-diaries/sd_beggs.html
(This audio science diary was first broadcast on National Public Radio in November
2006, and had its final broadcast in March, 2009).
National Geographic, November 6, 2006, “Dominoes, avalanches, give insight to brain
function”: http://news.nationalgeographic.com/news/2006/11/061106-braincascade.html
Physics news update, February 10, 2005, “Memory and critical avalanches in the brain”:
http://www.aip.org/pnu/2005/split/719-1.html
Eureka alert, January, 2005, “Brain avalanches may help store memories”:
http://www.eurekalert.org/pub_releases/2005-01/iu-bm012605.php
PhysOrg, January, 2005, “Brain avalanches may help store memories”:
http://www.physorg.com/news2840.html
Talks (national and international)
Upcoming
Invited speaker, Excellence Workshop "Dynamical Network States, Criticality and
Cortical Function" March 25 - 28, 2017, Bremen Germany: http://www.h-wk.de/index.php?id=2240
Invited workshop participant, “Quantifying collectivity,” at Santa Fe Institute:
https://www.santafe.edu/events/quantifying-collective-behavior-in-living-sys
Past
Invited speaker, workshop on Avalanches in diverse systems, Barcelona, January 2017
Invited speaker, Brandeis University, September 2, 2016
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Invited speaker, workshop on Neural network dynamics, Society for Industrial and
Applied Math, Boston, July 2016
Invited speaker, Banff workshop on Connecting Network Architecture and Computation,
Dec 7-11, 2015 http://www.birs.ca/events/2015/5-day-workshops/15w5158
Physics colloquium, University of Calgary, Nov 2, 2015
Madison, Wisconsin, Conference on Consciousness in neuroscience, Oct 2, 2015
MPI, Dresden, Germany, workshop on Criticality in biological systems, April 7-10, 2015
Paris France conference on power laws in neuronal data (European Human Brain
Project), March 10-13, 2015
Dynamics Days, Rice University, Houston TX, Jan 10, 2015
Condensed matter physics seminar, Penn State, April 1, 2014
Talk to computer science, neuroscience and physics at Texas A&M, April 11, 2014
Physics colloquium, Washington University, St. Louis, April 16, 2014
Invited speaker at causality networks workshop at MPI in Dresden Germany, 16-20
June, 2014
Invited speaker for Festschrift for Jack Cowan, Banff, Canada, July 13-18, 2014
(declined due to conflict)
Invited speaker for neural physics workshop in Natal, Brazil, August 11-17, 2014
UT, San Antonio for workshop on power laws in neural data on Dec 6, 2013
Biophysics seminar at U Pennsylvania on Dec 4, 2013
Physics Colloquium at U Arkansas, Nov 8, 2013
CRCNS PIs meeting, Washington University, St. Louis, June 4, 2:00 PM, 2012.
https://www.confmanager.com/communities/c2626/files/hidden/CRCNS_Agenda_Final.p
df
Invited talk at the Institute for Systems Biology, at their symposium on “Systems Biology
and the Brain”, April 14, 15, 2013. URL:
https://www.systemsbiology.org/symposium/schedule.html
Invited Minisymposium talk at SIAM conference, Snowbird, Utah, May 2013.
Invited speaker for a symposium on “Scale-free dynamics and critical phenomena in
cortical activity” at the Human Brain Mapping Conference in Quebec City, June 26-30,
2011.
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Invited speaker to Computational Neuroscience Seminar, Gatsby Computational
Neuroscience Unit, University College, London, May 25, 2011.
Invited participant for Cortical Circuits Workshop at the National Institute for
Mathematical and Biological Synthesis (NIMBioS), April 19-21, 2011.
http://www.nimbios.org/
Invited speaker to Physics Colloquium seminar at Illinois State University, April 5, 2011.
Invited speaker to “Physics of Living Cells” seminar at University of Illinois, Urbana
Champaign, April 1, 2011.
Invited by Bill Bialek to be a Biophysics workshop speaker/participant, City University of
New York, March 8-18, 2011.
Invited speaker to Biophysics seminar, Princeton University, March 7, 2011.
Invited speaker for 5-day workshop on “Linking neural dynamics and coding:
Correlations, synchrony, and information” held in Banff, Canada, October 2010.
Speaker for minisymposium on Inferring Neural Networks at Society for Industrial and
Applied Math conference on July 12-15, 2010, Pittsburgh, PA.
Speaker at Collaborative Research in Computational Neuroscience (CRCNS) grantee
conference, June 6-8, 2010, Johns Hopkins University, Baltimore, MD.
Invited participant for Cortical Circuits Workshop at the National Institute for
Mathematical and Biological Synthesis (NIMBioS), May 19-22, 2010.
http://www.nimbios.org/
Invited speaker for conference on “Decision making and network science” at University
of North Texas, January, 2010.
Invited speaker for Cognitive seminar at University of California, Merced. November 23,
2009.
Invited speaker for 3-day workshop on “Tools for Epilepsy Research: Tutorials &
Updates” held at the University of Chicago, August 6-8, 2009.
Invited symposium speaker, International Joint Conference on Neural Networks, June
14-19, 2009, Atlanta, Georgia.
Invited minisymposium speaker, Society of Industrial and Applied Mathematics (SIAM)
conference on Dynamical Systems, session on Spatiotemporal Dynamics of Neuronal
Networks, Snowbird Utah, May 17-21, 2009.
Invited session chair on Neural Computation, March Meeting of the American Physical
Society, March 16-20, 2009.
Invited, but declined due to a scheduling conflict with an experiment: Talk in Lisbon at
FLAD Computational Biology Collaboratorium, Instituto Gulbenkian de Ciência, Oeiras,
Portugal http://bc.igc.gulbenkian.pt/collaboratorium (December, 2008).
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Organizer and speaker at Society of Industrial and Applied Mathematics (SIAM)
conference on Mathematical Biology, Montreal, August 7, 2008.
“Information flow in local cortical networks is not democratic.” Invited 20 min talk,
Computational Neuroscience Conference, Portland Oregon, July 19, 2008.
Organizer and one of five invited speakers for a symposium on “Statistical Mechanics in
the Brain” held at the March meeting of the American Physical Society in New Orleans,
March, 2008.
Invited speaker for the University of Florida’s Biomedical Engineering seminar, March 5,
2008.
Invited minisymposium speaker for the Society of Industrial and Applied Mathematics
(SIAM) Conference on Applications of Dynamical Systems in Snowbird, Utah from May
28th-June 1st, 2007.
Invited speaker for the Altenberg Seminar in Theoretical Biology at the Konrad Lorenz
Institute in Vienna, Austria, March 15, 2007.
Invited speaker for the Computational Neuroscience Seminar series, University of
Chicago, February 27, 2007.
Invited speaker for the Northwestern Institute on Complex Systems seminar series,
Northwestern University, February 28, 2007.
Invited minisymposium speaker for the SIAM meeting of Mathematical Biology in
Raleigh, NC. July 31, 2006.
Invited speaker for the Neuro-IT summer school: Genoa, Italy, June 13-17, 2006:
http://www.neuro-it.net/NeuroIT/Activities/Genoa2006/index
Invited speaker for Experimental and Applied Chaos Conference: Sao Paulo, Brazil,
May 31-June 4, 2006: http://complex.gmu.edu/ecc/
Joint Physics and Biology seminar, “Condensed Gray Matter: Emergent Properties in
Networks of Cortical Neurons,” Invited talk at University of California, Santa Cruz,
January 12, 2006.
“Criticality for beginners, with implications for epilepsy.” Invited talk at Neurology Grand
Rounds, University of Wisconsin Medical School, Madison. December 9, 2005.
“A few strong connections: Optimizing information storage in neuronal avalanches.”
Invited talk given at the ALA Scientific symposium on multielectrode recording at the
Society for Neuroscience Conference, Washington, D.C., November 15, 2005.
“Networks with fewer and stronger connections may store more information in neuronal
avalanches” Invited talk, given at the 2005 Computational Neuroscience Conference in
Madison Wisconsin on July 19. Given by my graduate student, Jon Hobbs.
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“Neuronal avalanches may optimize information transmission and storage.” Invited talk,
given at the Center for Theoretical Neuroscience, Columbia University, on June 10,
2005.
“Critical branching captures activity in living neural networks and places constraints on
local network topology.” Invited and sponsored speaker at Brain Connectivity 2005, in
Boca Raton, Florida, April 14-16, 2005. Website: http://www.ccs.fau.edu/~bc2005/
“Living cortical networks at the critical point may optimize information transmission and
storage simultaneously.” Invited talk, Computational Neuroscience 2004 Conference,
Workshop on Nonlinear spatio-temporal neural dynamics - Experiments and Theoretical
Models. Given in Baltimore on July 21, 2004.
“Avalanches and information storage in cultured cortical networks.” Invited talk, Santa
Cruz Institute for Particle Physics, University of California at Santa Cruz, on February
26, 2004.
“Avalanches and information storage in cultured cortical networks.” Invited talk,
Department of Cell and Computational Biology, Montana State University, on February
6, 2004.
“Information Stored in Neuronal Activity Patterns in Cortical Slice Cultures.” Invited talk,
Southern Illinois University Medical School, Springfield Illinois, on August 15, 2003.
“Information stored over many hours by sequences of neural activity in networks of
cortical neurons.” Invited talk, presented at Computational Neuroscience Meeting in
Chicago, July 2002.
Local talks
Physics Colloquium, Ball State, March 16, 2017
Psychological and Brain Sciences seminar at Indiana University, October 14, 2013
Invited Colloquium, Speech and Hearing Sciences, Indiana University, 21 September,
2012
Invited Colloquium, IUPUI Physics Department, January 24, 2013.
Invited speaker to Physics Colloquium seminar at Illinois State University, April 5, 2011.
One of five chosen talks given at IUPUI conference on research and medicine: “A
maximum entropy approach to network correlations,” given by my graduate student, Jon
Hobbs.
“Information flow in networks of cortical neurons,” given at DePauw University,
November 6, 2008.
“Information flow in networks of cortical neurons,” given at Wabash College, October 23,
2008.
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“Brainstorms” talk given to Mentors Science club, consisting of ~25 high school and 5th
grade students, as well as 4 of their teachers, May 10, 2008, at Indiana University.
“Reconfiguration of information flow graphs in local cortical networks” talk given to
undergraduate honors seminar in informatics at Indiana University, April 21, 2008.
“A maximum entropy approach applied to spatial and temporal correlations in neural
networks,” Talk given for Networks and Complex Systems seminar series, School of
Library and Information Sciences, Indiana University, October 1, 2007.
“Brainstorms,” Talk given at Indiana University Physics Open House, September 29,
2007.
Invited speaker for Gill symposium (one of two junior faculty chosen), May 23, 2007,
Indiana University.
Condensed matter/Biophysics seminar, Purdue University Physics department: April 14,
2006.
“Condensed Gray Matter: Emergent Properties in Networks of Cortical Neurons,” Talk
given to the Physics department, University of Evansville, Indiana, April 4, 2006.
“Condensed Gray Matter: Emergent Properties in Networks of Cortical Neurons,” Talk
given to Physics and Biology departments, Valparaiso University, Indiana, January 23,
2006.
“Condensed gray matter: Emergent properties in networks of cortical neurons.” RoseHulman University Physics Department, Terre Haute, Indiana, given on October 20,
2005.
“Condensed gray matter: Emergent properties in networks of cortical neurons.” Ball
State University Physics Department, Muncie, Indiana, given on January 27, 2005.
“Condensed gray matter: Emergent properties in networks of cortical neurons.” Northern
Kentucky University Physics Department, given on November 30, 2004.
“Condensed gray matter: Emergent properties in networks of cortical neurons.” Indiana
University Physics Department Colloquium, given on November 17, 2004.
“Emergent properties in networks of cortical neurons.” Invited talk for the Networks and
Complex Systems Talk Series at Indiana University, on October 4, 2004. Quick time
video of this talk is available at:
http://isdc.stderr.org/content/index.cgi/2004/11/14#nov14.04.beggs
“Avalanches and information storage in cultured cortical networks.” Invited talk,
Cognitive Science Seminar, Indiana University, on March 24, 2004.
“Avalanches and information storage in cultured cortical networks.” Invited talk, Center
for Genomics and Bioinformatics, Indiana University, on February 12, 2004.
“Avalanches and information storage in cultured cortical networks.” Invited talk, Center
for Integrated Study of Animal Behavior, Indiana University, on January 29, 2004.
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“Avalanches and information storage in cultured cortical networks.” Invited talk, School
of Optometry at Indiana University, on January 16, 2004.
“Synapses as probability detectors: A new theory about how the brain could store
information.” Biocomplexity Seminar: Indiana University Department of Physics, on
September 12, 2003.
Service
Reviewer for journals
Reviewer for the following journals: Physical Review Letters, Physical Review E, Nature
Physics, PNAS, Physica D, Scientific Reports, Nature Communications, Journal of
Neuroscience, PLoS One, PLoS Computational Biology, Cerebral Cortex, European
Journal of Neuroscience, Neuroscience, Neurocomputing, BioSystems, Journal of
Neuroinformatics, Biological Cybernetics, Complexity, Journal of Computational
Neuroscience, IEEE Proceedings on Systems Biology, Journal of Neural Engineering,
Scholarpedia web-based encyclopedia, Frontiers in Neuroinformatics, BMC
Neuroscience, Chaos. Typically review 15 manuscripts per year.
On editorial review board for Frontiers in Neuroengineering, Frontiers in Fractal
Physiology
Reviewer for grants
NSF Collaborative Research in Computational Neuroscience (CRCNS) panel, January
18-19, 2016
Marsden foundation grants, New Zealand, 2015-2016
Burroghs-Wellcome Trust postdoctoral fellowship reviewer, 2016
NSF Robust Intelligence panel, May 29-30, 2013
Physics of Living Systems NSF Grant panel, Jan 26, 27, 2012
NIH review panel on the physics of cancer, Rockville, MD, June 29-30, 2009. Here we
reviewed 35 center proposals, each requesting ~$20M.
NIH challenge grant reviewer, 2009.
Panelist for the National Institutes of Health/National Science Foundation joint program
in Multiscale Modeling, Jan 31-Feb1, 2005.
Ad-hoc grant reviewer for: National Science Foundation, Swiss National Science
Foundation, Israel Science Foundation, United States-Israel Binational Science
Foundation, Netherlands Foundation for Fundamental Research on Matter, Marsden
foundation New Zealand
Conference organizing, chairing and reviewing
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Session Chair: “Neural Computation,” March Meeting of the American Physical Society,
Pittsburgh, 2009.
Submissions review committee for Computational Neuroscience Conference, 2009.
Symposium speaker and organizer: “Inferring connectivity from neural network data” for
the Society for Industrial and Applied Mathematics conference in Montreal, August 3-8,
2008.
Symposium speaker and organizer: “Statistical Mechanics in the Brain” for the March
Meeting of the American Physical Society, New Orleans, 2008.
Session Chair: “Nonlinear Dynamics of Neuronal and Cardiac Systems,” March Meeting
of the American Physical Society, New Orleans, 2008.
General committee work
Outreach chair: Oversaw the “Open House”, which was October 27 of 2012. We had an
estimated 900 visitors. New features that year: t-shirt design contest, involvement of
Math Department, new outdoor event called the pumpkin drop.
For outreach, also coordinated a public lecture on the Higgs Boson, given by Harold
Ogren in Whittenberger auditorium on October 22, 2012. For outreach, also gave demo
shows at my daughters’ Montessori school on May 1 and Oct 16 and gave two demo
shows at Center Grove Middle School Central in Greenwood, IN, on November 29.
As the outreach component of my NSF grant, my graduate student Nick Timme
developed an EEG brain wave interactive exhibit to be installed in WonderLab. This
opened in 2016.
Committee for Graduate student recruitment; Committee for Graduate student advising;
Committee for Undergraduate student advising
Committee chair (2009-2011) for Graduate student recruitment
Elected by department vote to be a member of the Executive Committee 2009-2011,
2013Committee for admissions to Program in Neural Science (2013-2016)
Thesis committee work
Committee for candidacy seminars from these students: Theresa Conway (Physics),
Wendy Zhang (Physics), Ben Miller (Neuroscience), Giri Krishnan (Neuroscience), Jon
Hobbs (Neuroscience), Adam Walker (Neuroscience), Chris Honey (Cognitive Science),
Aaron Hanson (Physics)
Committee for thesis seminars from these students: Dragos Amarie (Physics), Samuel
Santana (Physics), Wei Zeng (Physics), Xiaobiao Huang (Physics), Wendy Zhang
(Physics), Marc Benayoun (MD/PhD at University of Chicago), Giri Krishnan
(Neuroscience), Chris Honey (Cognitive Science), Hamed Shoajei (Physics), Ben Miller
(Neuroscience), Di Wu (Physics)
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Committee for undergraduate senior thesis: Alexander Murphy-Nakhnikian
(Neuroscience), Robert Koffie (Physics), Jeffrey Klukas (Physics; Wittenberg College),
Matt Dornfeld (Physics; State University of New York, Binghamton)
Miscellaneous service
Written letters of support for over 100 undergraduate and graduate students,
postdoctoral fellows and faculty members.
Volunteer for Physics Open House: 2003-2016.
Volunteer for Indiana State Science Olympiad, 2008.
Grand Awards judge for the Intel international ISEF science fair, held in Indianapolis, IN,
2006.
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