Computational systems biology

H Kitano - Nature, 2002 - nature.com
To understand complex biological systems requires the integration of experimental and
computational research—in other words a systems biology approach. Computational …

OpenWorm: overview and recent advances in integrative biological simulation of Caenorhabditis elegans

GP Sarma, CW Lee, T Portegys… - … of the Royal …, 2018 - royalsocietypublishing.org
The adoption of powerful software tools and computational methods from the software
industry by the scientific research community has resulted in a renewed interest in …

[HTML][HTML] Neural signal propagation atlas of Caenorhabditis elegans

F Randi, AK Sharma, S Dvali, AM Leifer - Nature, 2023 - nature.com
Establishing how neural function emerges from network properties is a fundamental problem
in neuroscience. Here, to better understand the relationship between the structure and the …

Neural circuit policies enabling auditable autonomy

M Lechner, R Hasani, A Amini, TA Henzinger… - Nature Machine …, 2020 - nature.com
A central goal of artificial intelligence in high-stakes decision-making applications is to
design a single algorithm that simultaneously expresses generalizability by learning …

Liquid time-constant networks

R Hasani, M Lechner, A Amini, D Rus… - Proceedings of the AAAI …, 2021 - ojs.aaai.org
We introduce a new class of time-continuous recurrent neural network models. Instead of
declaring a learning system's dynamics by implicit nonlinearities, we construct networks of …

A circuit for navigation in Caenorhabditis elegans

JM Gray, JJ Hill, CI Bargmann - Proceedings of the …, 2005 - National Acad Sciences
Caenorhabditis elegans explores its environment by interrupting its forward movement with
occasional turns and reversals. Turns and reversals occur at stable frequencies but irregular …

The rich club of the C. elegans neuronal connectome

EK Towlson, PE Vértes, SE Ahnert… - Journal of …, 2013 - Soc Neuroscience
There is increasing interest in topological analysis of brain networks as complex systems,
with researchers often using neuroimaging to represent the large-scale organization of …

Optogenetic manipulation of neural activity in freely moving Caenorhabditis elegans

AM Leifer, C Fang-Yen, M Gershow, MJ Alkema… - Nature …, 2011 - nature.com
We present an optogenetic illumination system capable of real-time light delivery with high
spatial resolution to specified targets in freely moving Caenorhabditis elegans. A tracking …

EAT-4, a homolog of a mammalian sodium-dependent inorganic phosphate cotransporter, is necessary for glutamatergic neurotransmission in Caenorhabditis …

RYN Lee, ER Sawin, M Chalfie… - Journal of …, 1999 - Soc Neuroscience
The Caenorhabditis elegans gene eat-4 affects multiple glutamatergic neurotransmission
pathways. We find that eat-4 encodes a protein similar in sequence to a mammalian brain …

An imbalancing act: gap junctions reduce the backward motor circuit activity to bias C. elegans for forward locomotion

T Kawano, MD Po, S Gao, G Leung, WS Ryu, M Zhen - Neuron, 2011 - cell.com
A neural network can sustain and switch between different activity patterns to execute
multiple behaviors. By monitoring the decision making for directional locomotion through …