Selected core work from the lab:

Brain-wide, scale-wide physiology underlying behavioral flexibility in zebrafish
Mu Y, Narayan S, Mensh B, Ahrens MB
Current Opinion in Neurobiology 64, 151-160 (2020)
pdf journal link

Glia accumulate evidence that actions are futile and suppress unsuccessful behavior
Mu Y*, Bennett DV*, Rubinov M*, Narayan S, Yang CT, Tanimoto M, Mensh BD, Looger LL, Ahrens MB
Cell 178, 1-17 (2019)
pdf journal link

Bright and photostable chemigenetic indicators for extended in vivo voltage imaging
Abdelfattah AS*, Kawashima T*, Singh A, Novak O, Liu H, Shuai Y, Huang Y-C, Grimm JB, Patel R, Friedrich J, Mensh BD, Paninski L, Macklin JJ, Podgorski K, Lin B-J, Chen T-W, Turner GC, Liu Z, Koyama M, Svoboda K, Ahrens MB*, Lavis LD*, Schreiter ER*
Science 364, 699–704 (2019)
pdf journal link

Brain-wide optical circuit interrogation at the cellular level guided by online analysis of neuronal function
Vladimirov N*, Wang C*, Hoeckendorf B*, Mu Y, Tanimoto M, Wittenbach JD, Freeman J, Preibisch S, Keller PJ*, Ahrens MB*
Nature Methods 15, 1117-1125 (2018)
pdf journal link

Brain-wide organization of neuronal activity and convergent sensory-motor transformations in larval zebrafish
Chen X*, Mu Y*, Hu Y*, Kuan A*, Nikitchenko M, Randlett O, Chen AB, Gavornik JP, Sompolinsky H*, Engert F*, Ahrens MB*
Neuron 100:876-890 (2018)
pdf journal link

The serotonergic system tracks the outcomes of actions to mediate short-term motor learning
Kawashima T, Zwart MF, Yang C-T, Mensh BD, Ahrens MB
Cell 167(4): 933-946 (2016)
pdf journal link

Brain-wide mapping of neural activity controlling zebrafish exploratory locomotion
Dunn TW*, Mu Y*, Narayan S, Randlett O, Naumann EA, Yang CT, Schier AF, Freeman J*, Engert F*, Ahrens MB*
eLife, e12741 (2016)
pdf journal link

Calcium imaging of neural circuits with extended depth-of-field light-sheet microscopy
Quirin S*, Vladimirov V*, Yang C-T, Peterka DS, Yuste R, Ahrens MB
Optics Letters 41(5), 855-858 (2016)
pdf journal link

Mapping brain activity at scale with cluster computing
Freeman J, Vladimirov N, Kawashima T, Mu Y, Sofroniew NJ, Bennett DV, Rosen J, Yang C-T, Looger LL, Ahrens MB
Nature Methods 11, 941-950 (2014)
pdf journal link

Light-sheet functional imaging in fictively behaving larval zebrafish
Vladimirov N, Mu Y, Kawashima T, Bennett DV, Yang C-T, Looger LL, Keller PJ, Freeman J, Ahrens MB
Nature Methods 11, 883-884 (2014)
pdf journal link

Whole-brain functional imaging at cellular resolution using light-sheet microscopy
Ahrens MB, Orger MB, Robson DN, Li JM, and Keller PJ
Nature Methods 10, 413-420 (2013)
pdf journal link
Other core papers:

Two-photon calcium imaging during fictive navigation in virtual environments
Ahrens MB*, Huang KH*, Narayan S, Mensh BD, Engert F
Frontiers in Neural Circuits, volume 7, article 104 (2013)
pdf journal link

Brain-wide neural dynamics at single-cell resolution during motor adaptation in larval zebrafish
Ahrens MB, Li JM, Orger MB, Robson DN, Schier AF, Engert F, and Portugues R
Nature 485, 471-477 (2012)
pdf journal link
Reviews:

Zebrafish Neuroscience: Using Artificial Neural Networks to Help Understand Brains
Ahrens MB
Current Biology 29(21):R1138-R1140 (2020)
journal link

Integrative whole-brain neuroscience in larval zebrafish
Vanwalleghem GC, Ahrens MB, Scott EK
Curr Opin Neurobiol. 50: 136-145 (2018)
pdf journal link

A practical guide to light sheet microscopy
Bennett DV, Ahrens MB
in Springer Protocols, Zebrafish: Methods and Protocols, Methods in Molecular Biology Vol. 1451 (2016)

Visualizing whole-brain activity and development at the single-cell level using light-sheet microscopy
Keller PJ, Ahrens MB
Neuron 85(3), 462-483 (2015)
pdf journal link

Large-scale imaging in small brains
Ahrens MB and Engert F
Current Opinion in Neurobiology 32, 78-86 (2015)
pdf journal link

Light-sheet imaging for systems neuroscience
Keller PJ, Ahrens MB, Freeman J
Nature Methods 12(1), 27-29 (2015)
pdf journal link
Collaborations and older work:

Precision Calcium Imaging of Dense Neural Populations via a Cell-Body-Targeted Calcium Indicator
Shemesh OA, Linghu C, Piatkevich KD, Goodwin D, Celiker OT, Gritton HJ, Romano MF, Gao R, Yu CJ, Tseng HA, Bensussen S, Narayan S, Yang CT, Freifeld L, Siciliano CA, Gupta I, Wang J, Pak N, Yoon YG, Ullmann JFP, Guner-Ataman B, Noamany H, Sheinkopf ZR, Park WM, Asano S, Keating AE, Trimmer JS, Reimer J, Tolias AS, Bear MF, Tye KM, Han X, Ahrens MB, Boyden ES
Neuron, online ahead of print (2020)
journal link

A bidirectional network for appetite control in larval zebrafish
Wee CL, Song EY, Johnson RE, Ailani D, Randlett O, Kim JY, Nikitchenko M, Bahl A, Yang CT, Ahrens MB, Kawakami K, Engert F, Kunes S
eLife 2019;8:e43775 (2019)
journal link

A genetically encoded fluorescent sensor for in vivo imaging of GABA
Marvin JS, Shimoda Y, Magloire V, Leite M, Kawashima T, Jensen TP, Kolb I, Knott EL, Novak O, Podgorski K, Leidenheimer NJ, Rusakov DA, Ahrens MB, Kullmann DM, Looger LL
Nature Methods 16(8):763-770 (2019)
journal link

A robotic multidimensional directed evolution approach applied to fluorescent voltage reporters
Piatkevich KD, Jung EE, Straub C, Linghu C, Park D, Suk HJ, Hochbaum DR, Goodwin D, Pnevmatikakis E, Pak N, Kawashima T, Yang CT, Rhoades JL, Shemesh O, Asano S, Yoon YG, Freifeld L, Saulnier JL, Riegler C, Engert F, Hughes T, Drobizhev M, Szabo B, Ahrens MB, Flavell SW, Sabatini BL, Boyden ES
Nature Chemical Biology 14(4): 352-360 (2018)

Multi-scale approaches for high-speed imaging and analysis of large neural populations
Friedrich J, Yang W, Soudry D, Mu Y, Ahrens MB, Yuste R, Peterka DS, Paninski L
PLoS Comput Biol. 13(8): e1005685 (2017)

Input-specific gain modulation by local sensory context shapes cortical and thalamic responses to complex sounds
Williamson RS, Ahrens MB, Linden JF, Sahani M
Neuron 91(2): 467-481 (2016)

Neural circuits underlying visuallyl evoked escapes in larval zebrafish
Dunn TW, Gebhardt, Naumann EA, Riegler C, Ahrens MB, Engert F, Del Bene F
Neuron 89(3), 613-628 (2016)

Simultaneous Denoising, Deconvolution, and Demixing of Calcium Imaging Data
Pnevmatikakis EA, Soudry D, Gao Y, Machado TA, Merel J, Pfau D, Reardon T, Mu Y, Lacefield C, Yang W, Ahrens M, Bruno R, Jessell TM, Peterka DS, Yuste R, Paninski L
Neuron 89(2): 285-99 (2016)

Sensitive red protein calcium indicators for imaging neural activity
Dana H, Mohar B, Sun Y, Narayan S, Gordus A, Hasseman JP, Tsegaye G, Holt GT, Hu A, Walpita D, Patel R, Macklin JJ, Bargmann CI, Ahrens MB, Schreiter ER, Jayaraman V, Looger LL, Svoboda K, Kim DS
eLife, e12727 (2016)

Labeling of active neural circuits in vivo with designed calcium integrators
Fosque BF, Sun Y, Dana H, Yang C-T, Ohyama T, Tadross MR, Patel R, Zlatic M, Kim DS, Ahrens MB, Jayaraman V, Looger LL, Schreiter ER
Science 347(6223), 755-760 (2015)

Spinal projection neurons control turning behaviors in zebrafish
Huang KH*, Ahrens MB*, Dunn TW, Engert F
Current Biology 23, 1-8 (2013)

Identification of nonvisual photomotor response cells in the vertebrate hindbrain
Kokel D, Dunn TW, Ahrens MB, Alshut R, Cheung CY, Saint-Amant L, Bruni G, Mateus R, van Ham TJ, Shiraki T, Fukada Y, Kojima D, Yeh JR, Mikut R, von Lintig J, Engert F, Peterson RT
Journal of Neuroscience 33(9): 3834-43 (2013)

Optogenetics in a transparent animal: circuit function in the larval zebrafish
Portugues R, Severi KE, Wyart C, Ahrens MB
Current Opinion in Neurobiology 23(1):119-126 (2013)

Observers exploit stochastic models of sensory change to help judge the passage of time
Ahrens MB, Sahani M
Current Biology 21,1-7 (2011)
pdf journal link

Multilinear models of single cell responses in the medial nucleus of the trapezoid body
Englitz B*, Ahrens M*, Tolnai S, Rubsamen R, Sahani M, Jost J
Network: Computation in Neural Systems 21(1-2), 91-124 (2010)

Nonlinearities and contextual influences in auditory cortical responses modeled with multilinear spectrotemporal methods
Ahrens MB, Linden JF, Sahani M
Journal of Neuroscience 28(8), 1929-1942 (2008)

Inferring input nonlinearities in neural encoding models
Ahrens MB, Paninski L, Sahani M
Network: Computation in Neural Systems 19(1), 35-67 (2008)

Inferring Elapsed Time from Stochastic Neural Processes
Ahrens MB, Sahani M
In Advances in Neural Information Processing Systems, volume 20, MIT Press (2008)

Efficient estimation of detailed single neuron models
Huys QJM*, Ahrens MB*, Paninski L
Journal of Neurophysiology 96, 872-890 (2006)

Large-scale biophysical parameter estimation in single neurons via constrained linear regression
Ahrens MB, Huys QJM, Paninski L
In Advances in Neural Information Processing Systems, vol. 18, MIT Press (2006)