Tom Baden
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View article: Zebrafish use spectral information to suppress the visual background
Zebrafish use spectral information to suppress the visual background Open
Vision first evolved in the water, where the spectral content of light informs about viewing distance. However, whether and how aquatic visual systems exploit this "fact of physics" remains unknown. Here, we show that zebrafish use "color"…
View article: A median eye origin of the vertebrate retina explains its unique circuitry
A median eye origin of the vertebrate retina explains its unique circuitry Open
The vertebrate retina is a uniquely complex and evolutionarily conserved structure among bilaterians, combining ciliary (rods and cones) and rhabdomeric (ganglion, amacrine, and horizontal) photoreceptor lineages within a multilayered circ…
View article: A standardized nomenclature for the rods and cones of the vertebrate retina
A standardized nomenclature for the rods and cones of the vertebrate retina Open
Vertebrate photoreceptors have been studied for well over a century, but a fixed nomenclature for referring to orthologous cell types across diverse species has been lacking. Instead, photoreceptors have been variably—and often confusingly…
View article: Comparative transcriptomic insights into the evolution of vertebrate photoreceptor types
Comparative transcriptomic insights into the evolution of vertebrate photoreceptor types Open
To explore the molecular similarities and potential evolutionary origins of vertebrate photoreceptor types, we analyzed single-cell and -nucleus transcriptomic atlases from six vertebrate species: zebrafish, chicken, lizard, opossum, groun…
View article: A Standardized Nomenclature for the Rods and Cones of the Vertebrate Retina
A Standardized Nomenclature for the Rods and Cones of the Vertebrate Retina Open
We propose a standardized naming system for vertebrate visual photoreceptors (i.e., rods and cones) that reflects our current understanding of their evolutionary history. Vertebrate photoreceptors have been studied for well over a century,…
View article: A Standardized Nomenclature for the Rods and Cones of the Vertebrate Retina
A Standardized Nomenclature for the Rods and Cones of the Vertebrate Retina Open
We propose a standardized naming system for vertebrate visual photoreceptors (i.e., rods and cones) that reflects our current understanding of their evolutionary history. Vertebrate photoreceptors have been studied for well over a century,…
View article: Vertebrate vision is ancestrally based on competing cone circuits
Vertebrate vision is ancestrally based on competing cone circuits Open
Vision first evolved in the water, where light becomes increasingly monochromatic with viewing distance. The presence of spectrally broad (′white′) light is therefore the exclusive remit of the visual foreground. However, if and how aquati…
View article: Comparative transcriptomic insights into the evolutionary origin of the tetrapod double cone
Comparative transcriptomic insights into the evolutionary origin of the tetrapod double cone Open
The tetrapod double cone is a pair of tightly associated cones called the “principal” and the “accessory” member. It is found in amphibians, reptiles, and birds, as well as monotreme and marsupial mammals but is absent in fish and eutheria…
View article: Restoration of cone-circuit functionality in the regenerating adult zebrafish retina
Restoration of cone-circuit functionality in the regenerating adult zebrafish retina Open
Unlike humans, teleosts like zebrafish exhibit robust retinal regeneration after injury from endogenous stem cells. However, it is unclear if regenerating cone photoreceptors regain physiological function and integrate correctly into post-…
View article: A microRNA that controls the emergence of embryonic movement
A microRNA that controls the emergence of embryonic movement Open
Movement is a key feature of animal systems, yet its embryonic origins are not fully understood. Here, we investigate the genetic basis underlying the embryonic onset of movement in Drosophila focusing on the role played by small non-codin…
View article: Author response: A microRNA that controls the emergence of embryonic movement
Author response: A microRNA that controls the emergence of embryonic movement Open
View article: Reviewer #2 (Public Review): A microRNA that controls the emergence of embryonic movement
Reviewer #2 (Public Review): A microRNA that controls the emergence of embryonic movement Open
Movement is a key feature of animal systems, yet its embryonic origins are not fully understood. Here we investigate the genetic basis underlying the embryonic onset of movement in Drosophila focusing on the role played by small non-coding…
View article: Reviewer #1 (Public Review): A microRNA that controls the emergence of embryonic movement
Reviewer #1 (Public Review): A microRNA that controls the emergence of embryonic movement Open
Movement is a key feature of animal systems, yet its embryonic origins are not fully understood. Here we investigate the genetic basis underlying the embryonic onset of movement in Drosophila focusing on the role played by small non-coding…
View article: Author response: A microRNA that controls the emergence of embryonic movement
Author response: A microRNA that controls the emergence of embryonic movement Open
Movement is a key feature of animal systems, yet its embryonic origins are not fully understood. Here we investigate the genetic basis underlying the embryonic onset of movement in Drosophila focusing on the role played by small non-coding…
View article: A microRNA that controls the emergence of embryonic movement
A microRNA that controls the emergence of embryonic movement Open
Summary Movement is a key feature of animal systems, yet its embryonic origins are not fully understood. Here we investigate the genetic basis underlying the embryonic onset of movement in Drosophila focusing on the role played by small no…
View article: A heterogeneous population code at the first synapse of vision
A heterogeneous population code at the first synapse of vision Open
SUMMARY Vision begins when photoreceptors convert light fluctuations into temporal patterns of glutamate release that drive the retinal network. The input-output relation at this first stage has not been systematically measured in vivo so …
View article: The vertebrate retina: a window into the evolution of computation in the brain
The vertebrate retina: a window into the evolution of computation in the brain Open
Animal brains are probably the most complex computational machines on our planet, and like everything in biology, they are the product of evolution. Advances in developmental and palaeobiology have been expanding our general understanding …
View article: Ancient origin of the rod bipolar cell pathway in the vertebrate retina
Ancient origin of the rod bipolar cell pathway in the vertebrate retina Open
Vertebrates rely on rod photoreceptors for vision in low-light conditions. The specialized downstream circuit for rod signalling, called the primary rod pathway, is well characterized in mammals, but circuitry for rod signalling in non-mam…
View article: Correction: From water to land: Evolution of photoreceptor circuits for vision in air
Correction: From water to land: Evolution of photoreceptor circuits for vision in air Open
[This corrects the article DOI: 10.1371/journal.pbio.3002422.].
View article: A microRNA that controls the emergence of embryonic movement
A microRNA that controls the emergence of embryonic movement Open
Movement is a key feature of animal systems, yet its embryonic origins are not fully understood. Here, we investigate the genetic basis underlying the embryonic onset of movement in Drosophila focusing on the role played by small non-codin…
View article: New twists in the evolution of retinal direction selectivity
New twists in the evolution of retinal direction selectivity Open
In mammals, starburst amacrine cells are centrally involved in motion vision and a new study in PLOS Biology, by Yan and colleagues finds that zebrafish have them, too. They coexist with a second pair of starburst-like neurons, but neither…
View article: A microRNA that controls the emergence of embryonic movement
A microRNA that controls the emergence of embryonic movement Open
SUMMARY Movement is a key feature of animal systems, yet its embryonic origins are not fully understood. Here we investigate the genetic basis underlying the embryonic onset of movement in Drosophila focusing on the role played by small no…
View article: Ancestral photoreceptor diversity as the basis of visual behaviour
Ancestral photoreceptor diversity as the basis of visual behaviour Open
Animal colour vision is based on comparing signals from different photoreceptors. It is generally assumed that processing different spectral types of photoreceptor mainly serves colour vision. Here I propose instead that photoreceptors are…
View article: From water to land: Evolution of photoreceptor circuits for vision in air
From water to land: Evolution of photoreceptor circuits for vision in air Open
When vertebrates first conquered the land, they encountered a visual world that was radically distinct from that of their aquatic ancestors. Fish exploit the strong wavelength-dependent interactions of light with water by differentially fe…
View article: Spike distance function as a learning objective for spike prediction
Spike distance function as a learning objective for spike prediction Open
Approaches to predicting neuronal spike responses commonly use a Poisson learning objective. This objective quantizes responses into spike counts within a fixed summation interval, typically on the order of 10 to 100 milliseconds in durati…
View article: Restoration of Cone Circuit Functionality in the Regenerating Adult Zebrafish Retina
Restoration of Cone Circuit Functionality in the Regenerating Adult Zebrafish Retina Open
Summary Unlike humans, teleosts like zebrafish exhibit robust retinal regeneration after injury from endogenous stem cells. However, understanding the functional recovery of the regenerated retina remains a challenge. In particular, it is …
View article: Ancient origin of the rod bipolar cell pathway in the vertebrate retina
Ancient origin of the rod bipolar cell pathway in the vertebrate retina Open
Vertebrates rely on rod photoreceptors for vision in low-light conditions. Mammals have a specialized downstream circuit for rod signaling called the primary rod pathway, which comprises specific cell types and wiring patterns that are tho…
View article: Data for Center-surround interactions underlie bipolar cell motion sensitivity in the mouse retina
Data for Center-surround interactions underlie bipolar cell motion sensitivity in the mouse retina Open
Data from the publication "Center-surround interactions underlie bipolar cell motion sensitivity in the mouse retina" published in Nature Communications (2022) https://doi.org/10.1038/s41467-022-32762-7. Code for working with this…
View article: Data for Center-surround interactions underlie bipolar cell motion sensitivity in the mouse retina
Data for Center-surround interactions underlie bipolar cell motion sensitivity in the mouse retina Open
Data from the publication "Center-surround interactions underlie bipolar cell motion sensitivity in the mouse retina" published in Nature Communications (2022) https://doi.org/10.1038/s41467-022-32762-7. Code for working with this…
View article: Ancient origin of the rod bipolar cell pathway in the vertebrate retina
Ancient origin of the rod bipolar cell pathway in the vertebrate retina Open
Vertebrates rely on rod photoreceptors for vision in low-light conditions 1 . Mammals have a specialized downstream circuit for rod signaling called the primary rod pathway, which comprises specific cell types and wiring patterns that are …