A5064637719- Complex Network Analysis Techniques
- Cell Image Analysis Techniques
- Opinion Dynamics and Social Influence
- Mitochondrial Function and Pathology
- Bioinformatics and Genomic Networks
- RNA Research and Splicing
- Cellular Mechanics and Interactions
- Single-cell and spatial transcriptomics
- AI in cancer detection
- Radiomics and Machine Learning in Medical Imaging
- Advanced Fluorescence Microscopy Techniques
- Gene Regulatory Network Analysis
- Urban Design and Spatial Analysis
- RNA and protein synthesis mechanisms
- Topological and Geometric Data Analysis
- Urban Transport and Accessibility
- Sperm and Testicular Function
- Medical Image Segmentation Techniques
- Human Mobility and Location-Based Analysis
- Advanced Image and Video Retrieval Techniques
- COVID-19 epidemiological studies
- Slime Mold and Myxomycetes Research
- Metabolomics and Mass Spectrometry Studies
- Plant and Biological Electrophysiology Studies
- Complex Systems and Time Series Analysis
Allen Institute for Cell Science
2018-2025
Allen Institute
2019-2025
IBM Research - Brazil
2017-2021
Federal University of São João del-Rei
2021
University of California, Irvine
2013-2020
Universidade de São Paulo
2006-2016
Universidad Politécnica de Madrid
2016
Universidade Federal de São Carlos
2008-2015
Instituto de Psicologia Comportamental de São Carlos
2004-2013
Fundação de Amparo à Pesquisa do Estado de São Paulo
2011
The success of new scientific areas can be assessed by their potential in contributing to theoretical approaches and applications real-world problems. Complex networks have fared extremely well both these aspects, with sound basis being developed over the years a variety applications. In this survey, we analyze complex problems data, emphasis representation, analysis modeling. A diversity phenomena are surveyed, which may classified into no less than 11 areas, providing clear indication...
Understanding how a subset of expressed genes dictates cellular phenotype is considerable challenge owing to the large numbers molecules involved, their combinatorics and plethora behaviours that they determine
Bud, This Mitochondrion's for You How is organelle size adjusted to be appropriate cell size? Rafelski et al. (p. 822 ) used a quantitative method measuring mitochondria in living budding yeast cells and found that rather than using the apparently simplest mechanism of dividing organelles equally among mother daughter cells, mitochondrial level bud, independent mother's own content, size, or age.
Bicycle sharing systems exist in hundreds of cities around the world, with aim providing a form public transport associated health and environmental benefits cycling without burden private ownership maintenance. Five have provided research data on journeys (start end time location) taking place their bicycle system. In this paper, we employ visualization, descriptive statistics spatial network analysis tools to explore system usage these cities, using techniques investigate features specific...
We compare the structural properties of street networks ten different European cities using their primal representation. investigate geometry and a set centrality measures highlighting differences similarities between cases. In particular, we found that share due to quasiplanarity but there are also several distinctive geometrical properties. A principal component analysis is performed on distributions centralities respective moments, which used find characteristics by can classify into...
All cellular materials are partitioned between daughters at cell division, but by various mechanisms and with different accuracy. In the yeast Schizosaccharomyces pombe, mitochondria pushed to poles spindle. We found that spatially reequilibrate just before mitochondrial volume DNA-containing nucleoids instead segregate in proportion cytoplasm inherited each daughter. However, nucleoid partitioning errors suppressed control two levels: Mitochondrial is actively distributed throughout a cell,...
Abstract A continuing challenge in quantitative cell biology is the accurate and robust 3D segmentation of structures interest from fluorescence microscopy images an automated, reproducible, widely accessible manner for subsequent interpretable data analysis. We describe Allen Cell Structure Segmenter (Segmenter), a Python-based open source toolkit developed cells intracellular microscope images. This brings together classic image iterative deep learning workflows first to generate initial...
Automatic document layout analysis is a crucial step in cognitive computing and processes that extract information out of images, such as specific-domain knowledge database creation, graphs images understanding, extraction structured data from tables, others. Even with the progress observed this field last years, challenges are still open range accurately detecting content boxes to classifying them into semantically meaningful classes. With popularization mobile devices cloud-based services,...
Mitochondria are dynamic organelles that must precisely control their protein composition according to cellular energy demand. Although nuclear-encoded mRNAs can be localized the mitochondrial surface, importance of this localization is unclear. As yeast switch respiratory metabolism, there an increase in fraction cytoplasm mitochondrial. Our data point change volume increasing certain surface mitochondria. We show mRNA necessary and sufficient production levels required during growth....
Although some cell types may be defined anatomically or by physiological function, a rigorous definition of state remains elusive. Here, we develop quantitative, imaging-based platform for the systematic and automated classification subcellular organization in single cells. We use this to quantify gene expression >30,000 individual human induced pluripotent stem cell-derived cardiomyocytes, producing publicly available dataset that describes population distributions local global sarcomere...
Shortest paths are not always simple. In planar networks, they can be very different from those with the smallest number of turns - simplest paths. The statistical comparison lengths shortest and provides a non trivial local information about spatial organization these graphs. We define simplicity index as average ratio profile characterizes at scales. measure metrics on artificial (roads, highways, railways) natural networks (leaves, slime mould, insect wings) show that there fundamental...
One of the most important prognostic markers to assess proliferation activity breast tumors is estimating number mitotic figures in H&E stained tissue. We propose use a recently published convolutional neural network architecture, Wide Residual Networks, for mitosis detection histology images. The model trained classify each pixel on an image using as context patch centered pixel. apply post-processing output order filter out noise and select true mitosis. Finally, we combine several...
Human mobility is increasing in its volume, speed and reach, leading to the movement introduction of pathogens through infected travelers. An understanding how areas are connected, strength these connections this translates into disease spread valuable for planning surveillance designing control elimination strategies. While analyses have been undertaken identify map connectivity global air, shipping migration networks, such yet be on road networks that carry vast majority travellers low...
This article proposes the concept of neuromorphological space as multidimensional defined by a set measurements morphology representative almost 6000 biological neurons available from Neuromorpho database. For first time, we analyse such large database in order to find general distribution geometrical features. We resort McGhee's shape formalise our analysis, allowing for comparison between geometrically possible tree-like shapes, obtained using simple reference model, and real neuronal...
Knowing which individuals can be more efficient in spreading a pathogen throughout determinate environment is fundamental question disease control. Indeed, over recent years the spread of epidemic diseases and its relationship with topology involved system have been recurrent topic complex network theory, taking into account both models real-world data. In this paper we explore possible correlations between heterogeneous an governed by susceptible–infected–recovered (SIR) model, several...
Higher-functioning mitochondria that are more reduced and have less ROS anchored in the yeast bud tip by Dsl1-family protein Mmr1p. Here we report a role for mitochondrial fusion bud-tip anchorage of mitochondria. Fluorescence loss photobleaching (FLIP) network analysis experiments revealed large buds continuous reticulum is physically distinct from mother cells. FLIP studies also showed enter can fuse with tip. In addition, DNA (mtDNA) deletion outer or inner membrane proteins (Fzo1p Mgm1p)...