Skip to main content
Advertisement
Table of Contents

January 2024

Point clouds are commonly used in many scientific fields. Each point of a cloud is typically associated with additional values or features. Thus, having the ability to identify if and how a given feature is structured along the cloud can provide insights for many applications. Here, we present the Structure Index, a graph-based method to quantify the distribution of features over data in arbitrary dimensional spaces. Spaces can be defined by neurons, time stamps, pixels, genes, etc... The image illustrates how the Structure Index eases the interpretation of neural representations from the brain head-direction system. Sebastian, Esparza and de la Prida 2024.

Image Credit: Julio Esparza

Education Articles

Ten simple rules for establishing an experimental lab

Marcus Kaiser

Ten simple rules for using large language models in science, version 1.0

Gabriel Reuben Smith, Carolina Bello, Lalasia Bialic-Murphy, Emily Clark, Camille S. Delavaux, Camille Fournier de Lauriere, Johan van den Hoogen, Thomas Lauber, Haozhi Ma, Daniel S. Maynard, Matthew Mirman, Lidong Mo, Dominic Rebindaine, Josephine Elena Reek, Leland K. Werden, Zhaofei Wu, Gayoung Yang, Qingzhou Zhao, Constantin M. Zohner, Thomas W. Crowther

Research Articles

The spinal cord facilitates cerebellar upper limb motor learning and control; inputs from neuromusculoskeletal simulation

Alice Bruel, Ignacio Abadía, Thibault Collin, Icare Sakr, Henri Lorach, Niceto R. Luque, Eduardo Ros, Auke Ijspeert

Quantifying the distribution of feature values over data represented in arbitrary dimensional spaces

Enrique R. Sebastian, Julio Esparza, Liset M. de la Prida

Wildlife vaccination strategies for eliminating bovine tuberculosis in white-tailed deer populations

Aakash Pandey, Abigail B. Feuka, Melinda Cosgrove, Megan Moriarty, Anthony Duffiney, Kurt C. VerCauteren, Henry Campa III, Kim M. Pepin

Detecting shifts in nonlinear dynamics using Empirical Dynamic Modeling with Nested-Library Analysis

Yong-Jin Huang, Chun-Wei Chang, Chih-hao Hsieh

sc2MeNetDrug: A computational tool to uncover inter-cell signaling targets and identify relevant drugs based on single cell RNA-seq data

Jiarui Feng, S. Peter Goedegebuure, Amanda Zeng, Ye Bi, Ting Wang, Philip Payne, Li Ding, David DeNardo, William Hawkins, Ryan C. Fields, Fuhai Li

Differences in boundary behavior in the 3D vertex and Voronoi models

Elizabeth Lawson-Keister, Tao Zhang, Fatemeh Nazari, François Fagotto, M. Lisa Manning

Explaining the flaws in human random generation as local sampling with momentum

Lucas Castillo, Pablo León-Villagrá, Nick Chater, Adam Sanborn

The role of cryptic ancestral symmetry in histone folding mechanisms across Eukarya and Archaea

Haiqing Zhao, Hao Wu, Alex Guseman, Dulith Abeykoon, Christina M. Camara, Yamini Dalal, David Fushman, Garegin A. Papoian

Genome replication in asynchronously growing microbial populations

Florian G. Pflug, Deepak Bhat, Simone Pigolotti

Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells

Paul F. Lang, David R. Penas, Julio R. Banga, Daniel Weindl, Bela Novak

Are we really Bayesian? Probabilistic inference shows sub-optimal knowledge transfer

Chin-Hsuan Sophie Lin, Trang Thuy Do, Lee Unsworth, Marta I. Garrido

Mapping the dynamics of visual feature coding: Insights into perception and integration

Tijl Grootswagers, Amanda K. Robinson, Sophia M. Shatek, Thomas A. Carlson

Near-term forecasting of Covid-19 cases and hospitalisations in Aotearoa New Zealand

Michael J. Plank, Leighton Watson, Oliver J. Maclaren

Plasticity of growth laws tunes resource allocation strategies in bacteria

Avik Mukherjee, Yu-Fang Chang, Yanqing Huang, Nina Catherine Benites, Leander Ammar, Jade Ealy, Mark Polk, Markus Basan

Adaptive foraging of pollinators fosters gradual tipping under resource competition and rapid environmental change

Sjoerd Terpstra, Flávia M. D. Marquitti, Vítor V. Vasconcelos

Joint representation of molecular networks from multiple species improves gene classification

Christopher A. Mancuso, Kayla A. Johnson, Renming Liu, Arjun Krishnan

Systems approach for congruence and selection of cancer models towards precision medicine

Jian Zou, Osama Shah, Yu-Chiao Chiu, Tianzhou Ma, Jennifer M. Atkinson, Steffi Oesterreich, Adrian V. Lee, George C. Tseng

Transformations of sensory information in the brain suggest changing criteria for optimality

Tyler S. Manning, Emma Alexander, Bruce G. Cumming, Gregory C. DeAngelis, Xin Huang, Emily A. Cooper

Controlling target brain regions by optimal selection of input nodes

Karan Kabbur Hanumanthappa Manjunatha, Giorgia Baron, Danilo Benozzo, Erica Silvestri, Maurizio Corbetta, Alessandro Chiuso, Alessandra Bertoldo, Samir Suweis, Michele Allegra

Transcription factor interactions explain the context-dependent activity of CRX binding sites

Kaiser J. Loell, Ryan Z. Friedman, Connie A. Myers, Joseph C. Corbo, Barak A. Cohen, Michael A. White

Virtual neural network-guided optimization of non-invasive brain stimulation in Alzheimer’s disease

Janne J. Luppi, Cornelis J. Stam, Philip Scheltens, Willem de Haan

A mathematical, classical stratification modeling approach to disentangling the impact of weather on infectious diseases: A case study using spatio-temporally disaggregated Campylobacter surveillance data for England and Wales

Giovanni Lo Iacono, Alasdair J. C. Cook, Gianne Derks, Lora E. Fleming, Nigel French, Emma L. Gillingham, Laura C. Gonzalez Villeta, Clare Heaviside, Roberto M. La Ragione, Giovanni Leonardi, Christophe E. Sarran, Sotiris Vardoulakis, Francis Senyah, Arnoud H. M. van Vliet, Gordon Nichols

Modelling disease mitigation at mass gatherings: A case study of COVID-19 at the 2022 FIFA World Cup

Martin Grunnill, Julien Arino, Zachary McCarthy, Nicola Luigi Bragazzi, Laurent Coudeville, Edward W. Thommes, Amine Amiche, Abbas Ghasemi, Lydia Bourouiba, Mohammadali Tofighi, Ali Asgary, Mortaza Baky-Haskuee, Jianhong Wu

The structure and robustness of ecological networks with two interaction types

Virginia Domínguez-García, Sonia Kéfi

Functional hierarchies in brain dynamics characterized by signal reversibility in ferret cortex

Sebastian Idesis, Sebastián Geli, Joshua Faskowitz, Jakub Vohryzek, Yonatan Sanz Perl, Florian Pieper, Edgar Galindo-Leon, Andreas K. Engel, Gustavo Deco

Postinhibitory excitation in motoneurons can be facilitated by hyperpolarization-activated inward currents: A simulation study

Laura Schmid, Thomas Klotz, Oliver Röhrle, Randall K. Powers, Francesco Negro, Utku Ş. Yavuz

PandoGen: Generating complete instances of future SARS-CoV-2 sequences using Deep Learning

Anand Ramachandran, Steven S. Lumetta, Deming Chen

Inferred regulons are consistent with regulator binding sequences in E. coli

Sizhe Qiu, Xinlong Wan, Yueshan Liang, Cameron R. Lamoureux, Amir Akbari, Bernhard O. Palsson, Daniel C. Zielinski

Predicting primate tongue morphology based on geometrical skull matching. A first step towards an application on fossil hominins

Pablo Alvarez, Marouane El Mouss, Maxime Calka, Anca Belme, Gilles Berillon, Pauline Brige, Yohan Payan, Pascal Perrier, Amélie Vialet

Regulus infers signed regulatory relations from few samples’ information using discretization and likelihood constraints

Marine Louarn, Guillaume Collet, Ève Barré, Thierry Fest, Olivier Dameron, Anne Siegel, Fabrice Chatonnet

Integrated meta-analysis of colorectal cancer public proteomic datasets for biomarker discovery and validation

Javier Robles, Ananth Prakash, Juan Antonio Vizcaíno, J. Ignacio Casal

A genome-wide comprehensive analysis of nucleosome positioning in yeast

Leo Zeitler, Kévin André, Adriana Alberti, Cyril Denby Wilkes, Julie Soutourina, Arach Goldar

Inferring country-specific import risk of diseases from the world air transportation network

Pascal P. Klamser, Adrian Zachariae, Benjamin F. Maier, Olga Baranov, Clara Jongen, Frank Schlosser, Dirk Brockmann

Mutational signature dynamics indicate SARS-CoV-2’s evolutionary capacity is driven by host antiviral molecules

Kieran D. Lamb, Martha M. Luka, Megan Saathoff, Richard J. Orton, My V. T. Phan, Matthew Cotten, Ke Yuan, David L. Robertson

Spatial constraints and stochastic seeding subvert microbial arms race

Raymond Copeland, Christopher Zhang, Brian K. Hammer, Peter J. Yunker

Estimation of introduction and transmission rates of SARS-CoV-2 in a prospective household study

Michiel van Boven, Christiaan H. van Dorp, Ilse Westerhof, Vincent Jaddoe, Valerie Heuvelman, Liesbeth Duijts, Elandri Fourie, Judith Sluiter-Post, Marlies A. van Houten, Paul Badoux, Sjoerd Euser, Bjorn Herpers, Dirk Eggink, Marieke de Hoog, Trisja Boom, Joanne Wildenbeest, Louis Bont, Ganna Rozhnova, Marc J. Bonten, Mirjam E. Kretzschmar, Patricia Bruijning-Verhagen

Vision-based collective motion: A locust-inspired reductionist model

David L. Krongauz, Amir Ayali, Gal A. Kaminka

Radiation necrosis after radiation therapy treatment of brain metastases: A computational approach

Beatriz Ocaña-Tienda, Odelaisy León-Triana, Julián Pérez-Beteta, Juan Jiménez-Sánchez, Víctor M. Pérez-García

A neural network model for the evolution of learning in changing environments

Magdalena Kozielska, Franz J. Weissing

AutoEdge-CCP: A novel approach for predicting cancer-associated circRNAs and drugs based on automated edge embedding

Yaojia Chen, Jiacheng Wang, Chunyu Wang, Quan Zou

Modeling geographic vaccination strategies for COVID-19 in Norway

Louis Yat Hin Chan, Gunnar Rø, Jørgen Eriksson Midtbø, Francesco Di Ruscio, Sara Sofie Viksmoen Watle, Lene Kristine Juvet, Jasper Littmann, Preben Aavitsland, Karin Maria Nygård, Are Stuwitz Berg, Geir Bukholm, Anja Bråthen Kristoffersen, Kenth Engø-Monsen, Solveig Engebretsen, David Swanson, Alfonso Diz-Lois Palomares, Jonas Christoffer Lindstrøm, Arnoldo Frigessi, Birgitte Freiesleben de Blasio

Methods

Somnotate: A probabilistic sleep stage classifier for studying vigilance state transitions

Paul J. N. Brodersen, Hannah Alfonsa, Lukas B. Krone, Cristina Blanco-Duque, Angus S. Fisk, Sarah J. Flaherty, Mathilde C. C. Guillaumin, Yi-Ge Huang, Martin C. Kahn, Laura E. McKillop, Linus Milinski, Lewis Taylor, Christopher W. Thomas, Tomoko Yamagata, Russell G. Foster, Vladyslav V. Vyazovskiy, Colin J. Akerman

Implicit model to capture electrostatic features of membrane environment

Rituparna Samanta, Jeffrey J. Gray

Statistical integration of multi-omics and drug screening data from cell lines

Said el Bouhaddani, Matthias Höllerhage, Hae-Won Uh, Claudia Moebius, Marc Bickle, Günter Höglinger, Jeanine Houwing-Duistermaat

Software

MEDUSA: A cloud-based tool for the analysis of X-ray diffuse scattering to obtain the bending modulus from oriented membrane stacks

Sebastian Himbert, Dorian Gaboo, Emre Brookes, John F. Nagle, Maikel C. Rheinstädter

FindAdapt: A python package for fast and accurate adapter detection in small RNA sequencing

Hua-Chang Chen, Jing Wang, Yu Shyr, Qi Liu