Publications

2024

To reverse engineer an entire nervous system. arXiv. 2024 Sep 18.
Haspel G, Boyden ES, Brown J, Church G, Cohen N, Fang-Yen C, Flavell S, Goodman MB, Hart AC, Hobert O, Kagias K, Lockery S, Lu Y, Marblestone A, Matelsky J, Pfister H, Rotstein HG, Scholz M, Shlizerman E, Simeon Q, Venkatachalam V, Yang GR, Yemini E, Zimmer M, Kording KP.

Unifying community-wide whole-brain imaging datasets enables robust automated neuron identification and reveals determinants of neuron positioning in C. elegans. bioRxiv. 2024 Apr 28.
Sprague DY, Rusch KW, Dunn RL, Borchardt J, Bubnis G, Chiu G, Wen C, Suzuki R, Chaudhary S, Dichter B, Ly R, Onami S, Lu H, Kimura K, Yemini E*, Kato S*.

Alternative splicing across the C. elegans nervous system. bioRxiv. 2024 May 16.
Weinreb A, Varol E, Alec Barrett, McWhirter RM, Taylor SR, Courtney I, Basavaraju M, Poff A, Tipps JA, Collings B, The CeNGEN Consortium, Krishnaswamy S, Miller DM, Hammarlund M

Current Biology Q&A: Eviatar Yemini. Current Biology. 2024 Apr 8.

Learning dynamic representations of the functional connectome in neurobiological networks. ICLR. 2024 Jan 16.
Dyballa L, Lang S, Haslund-Gourley A, Yemini E*, Zucker SW*

2023

Deep learning-based aberration compensation improves contrast and resolution in fluorescence microscopy. bioRxiv. 2023 Oct 15.
Guo M, Wu Y, Su Y, Qian S, Krueger E, Christensen R, Kroeschell G, Bui J, Chaw M, Zhang L, Liu J, Hou X, Han X, Ma X, Zhovmer A, Combs C, Moyle M, Yemini E, Liu H, Liu Z, La Riviere P, Colón-Ramos D, Shroff H.

Systems neuroscience: Foraging through serotonin's tangled web. Current Biology. 2023 Jul 24.
Yemini E

Learning Probabilistic Piecewise Rigid Atlases of Model Organisms via Generative Deep Networks. IPMI. 2023 Jun 8;13939.
Nejatbakhsh A, Dey N, Venkatachalam V, Yemini E, Paninski L, Varol E.

Cell-specific effects of the sole C. elegans Daughterless/E protein homolog, HLH-2, on nervous system development. Development. 2023 Jan 3.
Masoudi N, Schnabel R, Yemini E, Leyva-Díaz E, Hobert O.

2022

Neuropeptide signalling shapes feeding and reproductive behaviours in male Caenorhabditis elegans. Life Science Alliance. 2022 Jun 23.
Gadenne M, Hardege I, Yemini E, Suleski D, Jaggers P, Beets I, Schafer W, and Chew Y.

Toward a more accurate 3D atlas of C. elegans neurons. BMC Bioinformatics. 2022 May 28.
Skuhersky M, Wu T, Yemini E, Nejatbakhsh, Boyden E, Tegmark M.

Integrating bulk and single cell RNA-seq refines transcriptomic profiles of specific C. elegans neurons. bioRxiv. 2022 Apr 8.
Barrett A, Varol E, Weinreb A, Taylor SR, McWhirter R, Cros C, Basavaraju M, Poff A, Tipps JA, Majeed M, Vidal B, Wang C, Yemini E, Bayer EA, Sun HS, Hobert O, Miller DM, Hammarlund M.

2021

Visualizing the organization and differentiation of the male-specific nervous system of C. elegans. Development. 2021 Aug 20.
Tekieli T, Yemini E, Nejatbakhsh A, Wang C, Varol E, Fernandez RW, Masoudi N, Paninski L, Hobert O.

Molecular topography of an entire nervous system. Cell. 2021 Aug 5.
Taylor SR, Santpere G, Weinreb A, Barrett A, Reilly MB, Xu C, Varol E, Oikonomou P, Glenwinkel L, McWhirter R, Poff A, Basavaraju M, Rafi I, Yemini E, Cook SJ, Abrams A, Vidal B, Cros C, Tavazoie S, Sestan N, Hammarlund M, Hobert O, Miller DM.

In silico analysis of the transcriptional regulatory logic of neuronal identity specification throughout the C. elegans nervous system. eLife. 2021 Jun 24.
Glenwinkel L, Taylor SR, Langebeck-Jensen K, Pereira L, Reilly MB, Basavaraju M, Rafi I, Yemini E, Pocock R, Sestan N, Hammarlund M, Miller DM, Hobert O.

Methods for analyzing neuronal structure and activity in Caenorhabditis elegans. Genetics. 2021 Jun 20.
Emmons SW, Yemini E, Zimmer M.

Piecemeal regulation of convergent neuronal lineages by bHLH transcription factors in Caenorhabditis elegans. Development. 2021 Jun 8.
Masoudi N, Yemini E, Schnabel R, Hobert O.

State-dependent network interactions differentially gate sensory input at the motor and command neuron level in Caenorhabditis elegans. bioRxiv. 2021 Apr 9.
Cecere ZT, Quach KT, Yemini E, How JJ, Sharpee TO, Chalasani SH.

NeuroPAL: A Multicolor Atlas for Whole-Brain Neuronal Identification in C. elegans. Cell. 2021 Jan 7;184(1):272-288.e11.
Yemini E, Lin A, Nejatbakhsh A, Varol E, Sun R, Mena GE, Samuel ADT, Paninski L, Venkatachalam V, Hobert O.

2020

Demixing Calcium Imaging Data in C. elegans via Deformable Non-negative Matrix Factorization. MICCAI. 2020 Sep 29;12265:14-24.
Nejatbakhsh A, Varol E, Yemini E, Venkatachalam V, Lin A, Samuel ADT, Hobert O, Paninski L.

Statistical Atlas of C. elegans Neurons. MICCAI. 2020 Sep 29;12265:119-129.
Varol E, Nejatbakhsh A, Sun R, Mena GE, Yemini E, Hobert O, Paninski L.

Probabilistic Joint Segmentation and Labeling of C. elegans Neurons. MICCAI. 2020 Sep 29;12265:130-140.
Nejatbakhsh A, Varol E, Yemini E, Hobert O, Paninski L.

Unique homeobox codes delineate all the neuron classes of C. elegans. Nature. 2020 Aug 19;584(7822):595-601.
Reilly MB, Cros C, Varol E, Yemini E, Hobert O.

The connectome of the Caenorhabditis elegans pharynx. Journal of Comparative Neurology. 2020 Apr 30;10.1002/cne.24932.
Cook SJ, Crouse CM, Yemini E, Hall DH, Emmons SW, Hobert O.

2018

An open-source platform for analyzing and sharing worm-behavior data. Nature Methods. 2018 Sep;15(9):645-646.
Javer A, Currie M, Lee CW, Hokanson J, Li K, Martineau CN, Yemini E, Grundy LJ, Li C, Ch'ng Q, Schafer WR, Nollen EAA, Kerr R, Brown AEX.

2016

The Multilayer Connectome of Caenorhabditis elegans. PLoS Computational Biology. 2016 Dec 16;12(12):e1005283.
Bentley B, Branicky R, Barnes CL, Chew YL, Yemini E, Bullmore ET, Vértes PE, Schafer WR.

2015

Global brain dynamics embed the motor command sequence of Caenorhabditis elegans. Cell. 2015 Oct 22;163(3):656-69.
Kato S, Kaplan HS, Schrödel T, Skora S, Lindsay TH, Yemini E, Lockery S, Zimmer M.

Tracking Single C. elegans Using a USB Microscope on a Motorized Stage. Methods in Molecular Biology. 2015;1327:181-97.
Yemini EI, Brown AE.

A consistent muscle activation strategy underlies crawling and swimming in Caenorhabditis elegans. Journal of the Royal Society Interface. 2015 Jan 6;12(102):20140963.
Butler VJ, Branicky R, Yemini E, Liewald JF, Gottschalk A, Kerr RA, Chklovskii DB, Schafer WR.

2013

A database of Caenorhabditis elegans behavioral phenotypes. Nature Methods. 2013 Sep;10(9):877-9.
Yemini E, Grundy L, Jucikas T, Brown AEX, Schafer WR.

A dictionary of behavioral motifs reveals genes affecting C. elegans locomotion. Proceedings of the National Academy of Sciences of the USA. 2013 Jan 8;110(2):791-6.
Brown AEX, Yemini E, Grundy L, Jucikas T, Schafer WR.

2012

Locomotion analysis identifies roles of mechanosensory neurons in governing locomotion dynamics of C. elegans. Journal of Experimental Biology. 2012 Oct 15;215(Pt 20):3639-48.
Cohen E, Yemini E, Schafer WR, Feitelson DG, Treinin M.

2011

Preparation of samples for single-worm tracking. Cold Spring Harbor Protocols. 2011 Dec 1;2011(12):1475-9.
Yemini E, Kerr RA, Schafer WR.

Illumination for worm tracking and behavioral imaging. Cold Spring Harbor Protocols. 2011 Dec 1;2011(12):1480-2.
Yemini E, Kerr RA, Schafer WR.

Tracking movement behavior of multiple worms on food. Cold Spring Harbor Protocols. 2011 Dec 1;2011(12):1483-7.
Yemini E, Kerr RA, Schafer WR.