18 papers · ranked by Valyu relevance
Ana Zúñiga, Sarah Guiziou, Pauline Mayonove, Zachary Ben Meriem + 5 more
Genetic programs operating in an history-dependent fashion are ubiquitous in nature and govern sophisticated processes such as development and differentiation. The ability to systematically and predictably encode such programs would advance the engineering of synthetic organisms and ecosystems with rich signal…
Livnat Jerby-Arnon, Aviv Regev
Tissue homeostasis relies on orchestrated multicellular circuits, where interactions between different cell types dynamically balance tissue function. While single-cell genomics identifies tissues’ cellular components, deciphering their coordinated action remains a major challenge. Here, we tackle this problem through…
Dylan Kotliar, Adrian Veres, M. Aurel Nagy, Shervin Tabrizi + 3 more
Identifying gene expression programs underlying cell-type identity as well as cellular activities (e.g. life-cycle processes, responses to environmental cues) is crucial for understanding the organization of cells and tissues. Although single-cell RNA-Seq (scRNA-Seq) can quantify transcripts in individual cells, each…
Patrik Christen
—This study explores running times of different ways to program cellular automata in C and C++, i.e. looping through arrays by different means, the effect of structures and objects, and the choice of data structure (array versus vector in C++) and compiler (GNU gcc versus Apple clang). Using arrays instead of vectors…
Soroor Hediyeh-zadeh, Holly J. Whitfield, Malvika Kharbanda, Fabiola Curion + 3 more
As single cell molecular data expand, there is an increasing need for algorithms that efficiently query and prioritize gene programs, cell types and states in single-cell sequencing data, particularly in cell atlases. Here we present scDECAF, a statistical learning algorithm to identify cell types, states and programs…
Han Zhang, Binfeng Lu, Aodong Qiu, Gregory F. Cooper + 4 more
Cells within a tissue microenvironment communicate through intricate cell-cell communication (CCC) networks. In this meta-analysis of eight single-cell cohorts encompassing 153 patients and 279 samples, we advance the understanding of CCC networks in colorectal cancers through a novel analytical framework. Employing…
Ben T. Larson, Jack Garbus, Jordan B. Pollack, Wallace F. Marshall
Cells are complex biochemical systems whose behavior emerges from interactions among myriad molecular components. The idea that cells execute computational processes is often invoked as a general framework for understanding cellular complexity. However, the manner in which cells might embody computational processes in…
Robert W Gregg, Panayiotis V Benos, Lenore Cowen
Cellular Potts Models (CPMs) are a popular method to simulate multiscale cellular behaviors because they retain some spatial information like cellular geometry but avoid the computational complexity of a full physics simulation. Their applications are general, but many researchers have focused on using these models to…
Leonardo Bonati, Salvatore D’Oro, Lorenzo Bertizzolo, Emrecan Demirors + 3 more
'Emrecan Demirors' 'Zhangyu Guan' 'Stefano Basagni' 'Tommaso Melodia'] 1 This article has been published on Computer Networks. Please cite it as L. Bonati, S. D'Oro, L. Bertizzolo, E. Demirors, Z. Guan, S. Basagni, and T. Melodia, "CellOS: Zero-touch Softwarized Open Cellular Networks," Computer Networks, vol. 180…
Thouis R Jones, In Han Kang, Douglas B Wheeler, Robert A Lindquist + 4 more
'Adam Papallo' 'David M Sabatini' 'Polina Golland' 'Anne E Carpenter'] Background Image-based screens can produce hundreds of measured features for each of hundreds of millions of individual cells in a single experiment. Results Here, we describe CellProfiler Analyst, open-source software for the interactive…
Lei Shi, Evanny Obregon, Ki Won Sung, Jens Zander + 1 more
—As mobile IP-access is becoming the dominant technology for providing wireless services, the demand for more spectrum for this type of access is increasing rapidly. Since IP-access can be used for all types of services, instead of a plethora of dedicated, single-service systems, there is a significant potential to…
Alan Godoy, Pedro Tabacof, Fernando J. Von Zuben, Dante R. Chialvo
How can systems in which individuals’ inner workings are very similar to each other, as neural networks or ant colonies, produce so many qualitatively different behaviors, giving rise to roles and specialization? In this work, we bring new perspectives to this question by focusing on the underlying network that defines…
Federico Frascoli, Barry D. Hughes, Muhammad H. Zaman, Kerry A. Landman + 1 more
'Kerry A. Landman' 'Roeland MH. Merks'] Cell migration in healthy and diseased systems is a combination of single and collective cell motion. While single cell motion has received considerable attention, our understanding of collective cell motion remains elusive. A new computational framework for the migration of…
Asaf Liberman, Danny Kario, Matan Mussel, Jacob Brill + 3 more
'Kenneth Buetow' 'Sol Efroni' 'Uri Nevo'] The field of computer modeling and simulation of biological systems is rapidly advancing, backed by significant progress in the fields of experimentation techniques, computer hardware, and programming software. The result of a simulation may be delivered in several ways, from…
Tayeb Lemlouma, Yoann Lefebvre, Frederic Cespedes
—In this paper, we present PCNM, a new mobile platform for cellular networks measurements. PCNM is based on a set of techniques that tailors theoretical calculations and simulations to the real cellular network environment. It includes: (a) modules that measure different parameters of a base station (BS) such as…
Scott Christley, Briana Lee, Xing Dai, Qing Nie
Background Simulation of sophisticated biological models requires considerable computational power. These models typically integrate together numerous biological phenomena such as spatially-explicit heterogeneous cells, cell-cell interactions, cell-environment interactions and intracellular gene networks. The recent…
Authors not listed
Self-organizing tissues, such as organoids, offer transformative potential beyond healthcare by enabling the sustainable production of advanced materials. Resource scarcity and global warming drive the need for innovative fabrication solutions. This prospective review explores developmental biology as a manufacturing…
Nathalie E. Williams, Timothy A. Thomas, Matthew D. Dunbar, Nathan Eagle + 1 more
'Nathan Eagle' 'Adrian Dobra'] Abstract. In the past decade, large scale mobile phone data have become available for the study of human movement patterns. These data hold an immense promise for understanding human behavior on a vast scale, and with a precision and accuracy never before possible with censuses, surveys…