Pre peer-reviewed manuscripts
- Monika Scholz, Ashley N Linder, Francesco Randi, Anuj K Sharma, Xinwei Yu, Joshua W. Shaevitz, Andrew M. Leifer. "Predicting natural behavior from whole-brain neural dynamics" bioRxiv, 17 October (2018). [ PDF, Synopsis, Video 1, 2, Data and Code ]
Peer-reviewed journal articles
- 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 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.
Popular press articles featuring our work
- 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.
- David Castelvecchi, "Single Worm Neurons Remotely Controlled with Lasers", Scientific American 16 January 2011.
Video Recorded Lectures
- 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]