Manuscripts in the process of peer-review
- Junang Li, Andrew M. Leifer, David H. Wolpert, "Measuring amount of computation done by C. elegans using whole brain neural activity" arXiv, arxiv:2504.10300 [q-bio.NC]; 14 April 2025. [PDF].
- Tiannuo Li*, Sandeep Kumar*, Hoikiu Poon, Andrew M Leifer, Chaogu Zheng, "Functional Interrogation of Neuronal Subtypes via Intersectional Expression of Optogenetic Actuator Reveals Non-linear Components in a Linear Circuit" bioRxiv 2025.02.03.636179; 3 Feb (2025). [PDF]
- Sophie Dvali, Caio Seguin, Richard Betzel, Andrew M. Leifer, "Diverging network architecture of the C. elegans connectome and signaling network" arXiv, arXiv:2412.14498 [q-bio.NC]; 19 Dec (2024).
[PDF]
- Matthew S Creamer, Andrew M Leifer, Jonathan W Pillow, "Bridging the gap between the connectome and whole-brain activity in C. elegans" bioRxiv, 2024.09.22.614271(2024).
[PDF]
Peer-reviewed journal articles
- Rizwanul Haque, Hagar Setty, Ramiro Lorenzo, Gil Stelzer, Ron Rotkopf, Yehuda Salzberg, Gal Goldman, Sandeep Kumar, Shiraz Nir Halber, Andrew M. Leifer, Elad Schneidman, Patrick Laurent, Meital Oren-Suissa, "A Blueprint of Sex-Specific Neuronal Regulation in the C. elegans Nervous System at Single-Cell Resolution" bioRxiv 2024.12.27.630541, 27 Dec (2024). In press at Science Advances. [PDF]
- Kevin S. Chen, Anuj K. Sharma, Jonathan W. Pillow, Andrew M. Leifer, "Navigation strategies in Caenorhabditis elegans are differentially altered by learning" PLOS Biology, 23(3): e3003005, (2025).
[PDF]
- Jing Huoa,b,1, Tianqi Xu, Qi Liua, Mahiber Polata, Sandeep Kumar, Xiaoqian Zhang, Andrew M. Leifer, and Quan Wen, "Hierarchical behavior control by a single class of interneurons", Proceedings of the National Academy of Sciences, 121 (47) e2410789121, 12 November (2024).
- Sandeep Kumar, Anuj K Sharma, Andrew M Leifer, "An inhibitory acetylcholine receptor gates context dependent mechanosensory processing in C. elegans," iScience, 21 August (2024). [PDF]
- Anuj K. Sharma, Francesco Randi, Sandeep Kumar, Sophie Dvali, Andrew M. Leifer, "TWISP: A Transgenic Worm for Interrogating Signal Propagation in C. elegans." Genetics, Volume 227, Issue 3, July (2024).
[PDF]
- Wayan Gauthey, Francesco Randi*, Anuj K. Sharma*, Sandeep Kumar, Andrew M. Leifer, "Light evokes stereotyped global brain dynamics in Caenorhabditis elegans." Current Biology Vol 34, Issue 1, Pages R14-R15, 8 January (2024). [PDF, Supplement (PDF)]
- Francesco Randi, Anuj K. Sharma, Sophie Dvali, Andrew M. Leifer, "Neural signal propagation atlas of C. elegans." Nature 623, 406–414 (2023). [PDF, Supplement (PDF), News, Raw data on DANDI (NWB), Jupyter Notebook]
- Sandeep Kumar, Anuj K Sharma, Andrew Tran, Mochi Liu, Andrew Leifer, "Inhibitory feedback from the motor circuit gates mechanosensory processing in Caenorhabditis elegans." PLOS Biology 21(9): e3002280 (2023). [PDF].
- Kevin S. Chen, Rui Wu, Marc H. Gershow, Andrew M. Leifer, "Continuous odor profile monitoring to study olfactory navigation in small animals." eLife, (2023). [PDF]
- Matthew S. Creamer, Kevin S. Chen, Andrew M. Leifer, Jonathan W. Pillow, "Correcting motion induced fluorescence artifacts in two-channel neural imaging." PLOS Computational Biology 28 Sept (2022). [PDF]
- Princeton Open Ventilation Monitor Collaboration, Philippe Bourrianne, Stanley Chidzik, Daniel J Cohen, Peter Elmer, Thomas Hallowell, Todd J Kilbaugh, David Lange, Andrew M Leifer (corresponding author), Daniel R. Marlow, Peter D. Meyers, Edna Normand, Janine Nunes, Myungchul Oh, Lyman Page, Talmo Pereira, Jim Pivarski, Henry Schreiner, Howard A Stone, David W Tank, Stephan Thiberge, Christopher Tully. "Inexpensive multi-patient respiratory monitoring system for helmet ventilation during COVID-19 pandemic." ASME Journal of Medical Devices 16(1): 011003, 3 February (2022). [ PDF, Video, Lecture, PR Video].
- Mochi Liu, Sandeep Kumar, Anuj K Sharma, Andrew M. Leifer. "Closed-loop targeted optogenetic stimulation of C. elegans populations." PloS Biology, 20(1): e3001524 (2022). [PDF]
- Anne E. Urai, Brent Doiron, Andrew M. Leifer, Anne K. Churchland. "Large-scale neural recordings call for new insights to link brain and behavior." Nature Neuroscience, 3 January (2022). [PDF (arXiv)]
- Kelsey M. Hallinen*, Ross Dempsey*, Monika Scholz*, Xinwei Yu, Ashley Linder, Francesco Randi, Anuj Sharma, Joshua W. Shaevitz, Andrew M. Leifer, "Decoding locomotion from population neural activity in moving C. elegans." eLife 10:e66135, 29 July (2021). [PDF]
- Xinwei Yu, Matthew S. Creamer, Francesco Randi, Anuj K. Sharma, Scott W. Linderman, Andrew M. Leifer, "Fast deep neural correspondence for tracking and identifying neurons in C. elegans using semi-synthetic training." eLife, 10:e66410, 14 July (2021). [PDF]
- Francesco Randi and Andrew M Leifer, "Nonequilibrium Green's functions for functional connectivity in the brain." Physical Review Letters 12, 118102, 19 March (2021). [PDF].
- Francesco Randi and Andrew M Leifer. "Measuring and modeling whole-brain neural dynamics in Caenorhabditis elegans," Current Opinion in Neurobiology. Vol 65, Pages 167-157, December (2020). [PDF]
- Robert Datta, David Anderson, Kristin Branson, Peitro Perona, Andrew Leifer. "Computational Neuroethology: A Call to Action" Neuron 104:1, (2019).
- Xiaowen Chen, Francesco Randi, Andrew M. Leifer, William Bialek. "Searching for collective behavior in a small brain" Phys. Rev. E 99, 052418 (2019). [Journal PDF ($)] [ Preprint PDF ]
- Mochi Liu, Anuj K. Sharma, Joshua W. Shaevitz, Andrew M. Leifer. "Temporal processing and context dependency in C. elegans response to mechanosensation" eLife, 7:e36419 (2018). [ PDF ]
- Jeffrey P. Nguyen, Ashley N. Linder, George S. Plummer, Joshua W. Shaevitz, Andrew M. Leifer. "Automatically tracking neurons in a moving and deforming brain" PLOS Computational Biology 13(5): e1005517 (2017). [PDF, Movie, Data and Code]
- Jeffrey P. Nguyen*, Frederick B*. Shipley, Ashley N. Linder, George S. Plummer, Mochi Liu, Sagar U. Setru, Joshua W. Shaevitz, Andrew M. Leifer. "Whole-brain calcium imaging with cellular resolution in freely behaving Caenorhabditis elegans" Proceedings of the National Academy of Sciences of the United States of America, 10.1073/pnas.1507110112, Published online before print December 28, (2015). [PDF and Movies S1, S2, S3 and S4; Code, Processed and Raw Data]. Commentary.
- Frederick B. Shipley, Christopher M. Clark, Mark J. Alkema, Andrew M. Leifer. "Simultaneous optogenetic manipulation and calcium imaging in freely moving C. elegans." Frontiers in Neural Circuits 8:28. (2014). [PDF, Supplement and Video]
- Steven J. Husson, Alexander Gottschalk, Andrew M. Leifer. "Optogenetic manipulation of neural activity in C. elegans: from synapse to circuits and behavior." Biology of the Cell (2013). [PDF via arXiv]
- Jamie L. Donnelly, Christpoher M. Clark, Andrew M. Leifer, Marian Haburacak, Jennifer K. Pirri, Michael M. Francis, Aravinthan D. T. Samuel, and Mark J. Alkema. “Monoaminergic orchestration of motorprograms in a complex behavior in C. elegans.” PLoS Biology 11(4): e1001529 (2013). [PDF] & Synopsis.
- Quan Wen, Michelle D. Po, Elizabeth Hulme, Sway Chen, Xinyu Liu, Sen Wai Kwok, Marc Gershow, Andrew M. Leifer, Victoria Butler, Christopher Fang-Yen, Taizo Kawano, William R. Schafer, George Whitesides, Mattieu Wyart, Dmitri Chklovskii and Aravinthan Samuel, "Proprioceptive coupling within motor neurons drives C. elegans forward locomotion." Neuron, 76, 750-761 (2012). [PDF]
- Chenxiang Lin, Ralf Jungmann, Andrew M. Leifer, Chao Li, Daniel Levner, George M. Church, William M. Shih, Peng Yin. "Sub-micrometer geometrically encoded fluorescent barcodes self-assembled from DNA." Nature Chemistry, 4, 832–839 (2012).
- Andrew M. Leifer*, Christopher Fang-Yen*, Marc Gershow, Mark Alkema, Aravinthan D.T. Samuel, "Optogenetic manipulation of neural activity in freely moving Caenorhabditis elegans," Nature Methods, 8, 147–152 (2011). [PDF]
- Kevin J. Coakley, David S. Simons, Andrew M. Leifer. "Secondary Ion Mass Spectrometry Measurements of Isotopic Ratios: Correction for Time Varying Count Rate." International Journal of Mass Spectrometry, 204 (2005) 107-120.
* denotes equal contribution
Popular press articles featuring our work
- Laurel Oldach, "Brains beyond the wiring diagram," Chemical and Engineering News, Volume 102, Issue 9, 25 March 2024.
- Elissa Welle, "Plugging invisible gaps in the synaptic connectome," The Transmitter 6 December 2023.
- Claudia López Lloreda, "Wi-Fi for neurons: first map of wireless nerve signals unveiled in worms," Nature, 623, 894-895, 21 November 2023.
- "Princeton Open Ventilation Monitor," Princeton University Innovation News, 2 November 2021.
- Toin Feder, "Stuck at home, physicists pivot to combat COVID-19," Physics Today 73, 7, 22 (2020).
- Emily Singer, "Capturing the Whole Brain in Action," Simons Foundation, 22 December 2016.
- Emily Reynolds, "Neural activity of worm captured in mesmerising display," Wired, 5 January 2016.
- Steve Dent, "Watch a worm’s brain light up as it plots its next move," Engadget, 31 December 2015.
- Esther Inglis-Arkell, "We can now watch the inside of a worm brain at work, Gizmodo, 30 December 2015.
- Morgan Kelly, "3-D footage of nematode brains links neurons with motion and behavior," News at Princeton, 30 December 2015.
- "First videos created of whole brain neural activity in an unrestrained Animal," MIT Technology Review, January 25 2015.
- Laura Sanders, "Making a worm do more than squirm," Science News 16 January 2011.
- Davide Castelvecchi, "Single Worm Neurons Remotely Controlled with Lasers", Scientific American 16 January 2011.
Video Recorded Lectures
- Andrew Leifer, "Signal propogation atlas of C. elegans", Department of Physics Hamilton Colloqium, 5 Oct 2023, 58 mins.
- Andrew Leifer, "Measuring neural dynamics, functional connectivity, and behavior in C. elegans", Neurophysics of Locomotion Kavli Institute for Theoretical Physics, University of California Santa Barbara, 20 July 2022, 1hr 29 mins.
- Andrew Leifer, "How does a nervous system transition between behavior states?", Princeton Neuroscience Institute Seminar, Princeton University, 16 February 2016. 29 minutes.
- Andrew Leifer, "Whole-brain neural dynamics and behavior in freely moving C. elegans", Emerging Tools for Acquisition and Interpretation of Whole-Brain Functional Data, HHMI Janelia Research Campus, 3 November 2015. 12 minutes.
- Andrew Leifer, "Whole-brain neural dynamics and behavior in freely moving nematodes", Stanford Neurosciences Institute Seminar Series, Stanford University, 17 February 2015. 1 hour 2 minutes.
Lecture slides
- Francesco Randi, "Whole Brain Imaging Workshop: Microscopy Techniques" International C. elegans Meeting, UCLA, 23 June 2019. [PDF]
- Andrew Leifer, "Optical neurophysiology in freely behaving C. elegans" C. elegans topic meeting: neuronal development, synaptic function and behavior , University of Wisconsin Madison, 9 July 2014. [PDF] [Bibliography]