25 papers · ranked by Valyu relevance
Micha Sam Brickman Raredon, Junchen Yang, James Garritano, Meng Wang + 9 more
'Dan Kushnir' 'Jonas Christian Schupp' 'Taylor S. Adams' 'Allison M. Greaney' 'Katherine L. Leiby' 'Naftali Kaminski' 'Yuval Kluger' 'Andre Levchenko' 'Laura E. Niklason'] Single-cell RNA-sequencing data has revolutionized our ability to understand of the patterns of cell-cell and ligand-receptor connectivity that…
Micha Sam Brickman Raredon, Junchen Yang, James Garritano, Meng Wang + 9 more
Single-cell RNA-sequencing data can revolutionize our understanding of the patterns of cell-cell and ligand-receptor connectivity that influence the function of tissues and organs. However, the quantification and visualization of these patterns are major computational and epistemological challenges. Here, we present…
Louis K. Scheffer
New reconstruction techniques are generating connectomes of unprecedented size. These must be analyzed to generate human comprehensible results. The analyses being used fall into three general categories. The first is interactive tools used during reconstruction, to help guide the effort, look for possible errors…
Sebastian J. Kopetzky, Markus Butz-Ostendorf
The connectome is regarded as the key to brain function in health and disease. Structural and functional neuroimaging enables us to measure brain connectivity in the living human brain. The field of connectomics describes the connectome as a mathematical graph with its connection strengths being represented by…
Hanspeter Pfister, Verena Kaynig, Charl P. Botha, Stefan Brückner + 3 more
Connectomics is a field of neuroscience that analyzes neuronal connections. A connectome is a complete map of a neuronal system, comprising all neuronal connections between its structures. The term 'connectome' is close to the word 'genome' and implies completeness of all neuronal connections, in the same way as a…
Joshua T Vogelstein
What is the connectome? Although it has been over a century since neuroscientists first conjectured that networks of neurons comprise the brain, technology has limited high-throughput investigations of neural circuitry until very recently. In the last couple of decades, several experimental paradigms have arisen that…
Barry L. Bentley, Robyn Branicky, Christopher L. Barnes, Yee Lian Chew + 4 more
'Yee Lian Chew' 'Eviatar Yemini' 'Edward T. Bullmore' 'Petra E. Vértes' 'William R Schafer'] Connectomics has focused primarily on the mapping of synaptic links in the brain; yet it is well established that extrasynaptic volume transmission, especially via monoamines and neuropeptides, is also critical to brain…
Richard Betzel, Maria Grazia Puxeddu, Caio Seguin
One of the longstanding aims of network neuroscience is to link a connectome’s topological properties–i.e. features defined from connectivity alone–with an organism’s neurobiology. One approach for doing so is to compare connectome properties with maps of metabolic, functional, and neurochemical annotations. This type…
Yijie Yin, Judith Hoeller, Alexander Mathiasen, Joanna Tsang + 2 more
Complete synaptic wiring diagrams, or connectomes, of whole brains open new opportunities for studying the structure-function relationship of neural circuits. However, the large number of nodes and edges in the graphs makes the analysis challenging. Here, we present the Connectome Interpreter, an open-source software…
Caio Seguin, Maria Grazia Puxeddu, Joshua Faskowitz, Richard F. Betzel + 1 more
Connectomes are the structural scaffold for signalling within nervous systems. While many network models have been proposed to describe connectome communication, current approaches assume that every pair of neural elements communicates according to the same principle. Connectomes, however, are heterogeneous networks…
Nardin Samuel, Artur Vetkas, Aditya Pancholi, Can Sarica + 10 more
'Jurgen Germann' 'Irene E. Harmsen' 'Jordy Tasserie' 'Vanessa Milano' 'Kazuaki Yamamoto' 'Suneil K. Kalia' 'Paul N. Kongkham' 'Andres M. Lozano' 'Nils Ole Schmidt'] Simple Summary This manuscript details the literature and discussion around revolutionizing the neurosurgeon’s approach to surgery for brain tumors by…
Dmitrii I. Sukhinin, Andreas K. Engel, Paul Manger, Claus C Hilgetag
Databases of structural connections of the mammalian brain, such as CoCoMac (cocomac.g-node.org) or BAMS (brancusi.usc.edu), are valuable resources for the analysis of brain connectivity and the modeling of brain dynamics in species such as the non-human primate or the rodent, and have also contributed to the…
Vincent Bazinet, Justine Y. Hansen, Reinder Vos de Wael, Boris C. Bernhardt + 2 more
The wiring of the brain connects micro-architecturally diverse neuronal populations. The conventional graph model encodes macroscale brain connectivity as a network of nodes and edges, but abstracts away the rich biological detail of each regional node. Regions are different in terms of their microscale attributes…
Marcus Kaiser
The human connectome at the level of fiber tracts between brain regions has been shown to differ in patients with brain disorders compared to healthy control groups. Nonetheless, there is a potentially large number of different network organizations for individual patients that could lead to cognitive deficits…
Jean Faber, Priscila Correia Antoneli, Guillem Via, Noemi S. Araújo + 2 more
In recent years, new and important perspectives were introduced in the field of neuroimaging with the emergence of the connectionist approach (Williams and Henson 2018). In this new context, it is important to know not only which brain areas are activated by a particular stimulus but, mainly, how these areas are…
Olaf Sporns, Danielle S. Bassett
Connectomics is an integral part of network neuroscience. The field has undergone rapid expansion over recent years and increasingly involves a blend of experimental and computational approaches to brain connectivity. This Focus Feature on “New Trends in Connectomics” aims to track the progress of the field and its…
Joshua T. Vogelstein, Eric W. Bridgeford, Benjamin D. Pedigo, Jaewon Chung + 3 more
Cognitive phenotypes characterize our memories, beliefs, skills, and preferences, and arise from our ancestral, developmental, and experiential histories. These histories are written into our brain structure through the building and modification of various brain circuits. Connectal coding, by way of analogy with neural…
Marcus Kaiser
The human connectome at the level of fiber tracts between brain regions has been shown to differ in patients with brain disorders compared to healthy control groups. Nonetheless, there is a potentially large number of different network organizations for individual patients that could lead to cognitive deficits…
Máté Fellner, Bálint Varga, Vince Grolmusz
While it is still not possible to describe the neural-level connections of the human brain, we can map the human connectome with several hundred vertices, by the application of diffusion-MRI based techniques. In these graphs, the nodes correspond to anatomically identified gray matter areas of the brain, while the…
Richard F. Betzel
Connectomics and network neuroscience offer quantitative scientific frameworks for modeling and analyzing networks of structurally and functionally interacting neurons, neuronal populations, and macroscopic brain areas. This shift in perspective and emphasis on distributed brain function has provided fundamental…
Rahul Biswas, Eli Shlizerman
Representation of brain network interactions is fundamental to the translation of neural structure to brain function. As such, methodologies for mapping neural interactions into structural models, i.e., inference of functional connectome from neural recordings, are key for the study of brain networks. While multiple…
Omar Paredes, Jhonatan B. López, César Covantes-Osuna, Vladimir Ocegueda-Hernández + 3 more
'Vladimir Ocegueda-Hernández' 'Rebeca Romo-Vázquez' 'J. Alejandro Morales' 'Yves De Saá Guerra'] Graph analysis allows exploring transcriptome compartments such as communities and modules for brain mesostructures. In this work, we proposed a bottom-up model of a gene regulatory network to brain-wise connectome…
Andrés López-Cortés, Patricia Guevara-Ramírez, Nikolaos C Kyriakidis, Carlos Barba-Ostria + 21 more
There is pressing urgency to better understand the immunological underpinnings of the coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus clade 2 (SARS-CoV-2) in order to identify potential therapeutic targets and drugs that allow treating patients effectively. To fill in…
Benjamin Ries, Richard J Gowers, James RB Eastwood, Irfan Alibay + 4 more
Alchemical free energy campaigns can be planned using graph theory by building up networks that contain nodes representing molecules that are connected by possible transformations as edges. We introduce Konnektor, an open-source Python package, for systematically planning, modifying, and analyzing free energy…
Kevin Mildau, Christoph Büschl, Jürgen Zanghellini, Justin J.J. van der Hooft
Computational metabolomics workflows have revolutionized the untargeted metabolomics field. However, the organization and prioritization of metabolite features remains a laborious process. Organizing metabolomics data is often done through mass fragmentation-based spectral similarity grouping, resulting in feature sets…