Biology & Life Sciences

Brain Mapping Methods: Connectomics – Methodology

Published October 17, 2016 Curated Collections

Neuroscience is the scientific study of the nervous system and is an interdisciplinary biological science that extends across multiple fields, including, chemistry, computer science, engineering, linguistics, mathematics, medicine, philosophy, physics, and psychology. This collection represents a first step in gathering under easily identifiable rubrics some of the most recent neuroscience research published across the PLOS journals. The collection has been organized into broad categories in response to the commonly articulated request from our users that we provide more structured and efficient access to papers of interest in the PLOS corpus. This section includes papers about connectomics methodologies.

Image Credit: DARPA-SUBNETS / PLOS

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Perspective
Research Articles

Perspective

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10.1371/journal.pcbi.1002311

PLOS Computational Biology Beyond Statistical Significance: Implications of Network Structure on Neuronal Activity
January 26, 2012 Ioannis Vlachos, Ad Aertsen, Arvind Kumar

Research Articles

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10.1371/journal.pcbi.1005203

PLOS Computational Biology Quantifying Differences and Similarities in Whole-Brain White Matter Architecture Using Local Connectome Fingerprints
November 15, 2016 Fang-Cheng Yeh, Jean M. Vettel, Aarti Singh, Barnabas Poczos, Scott T. Grafton, Kirk I. Erickson, Wen-Yih I. Tseng, Timothy D. Verstynen
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10.1371/journal.pcbi.1002311

PLOS Computational Biology Beyond Statistical Significance: Implications of Network Structure on Neuronal Activity
January 26, 2012 Ioannis Vlachos, Ad Aertsen, Arvind Kumar
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10.1371/journal.pcbi.1003491

PLOS Computational Biology Resolving Structural Variability in Network Models and the Brain
March 27, 2014 Florian Klimm, Danielle Bassett, Jean Carlson, Peter Mucha
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10.1371/journal.pone.0084279

PLOS ONE BOLD Granger Causality Reflects Vascular Anatomy
December 13, 2013 J. Webb, Michael Ferguson, Jared Nielsen, Jeffrey Anderson
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10.1371/journal.pone.0073670

PLOS ONE Mapping the Voxel-Wise Effective Connectome in Resting State fMRI
September 12, 2013 Guo-Rong Wu, Wei Liao, Sebastiano Stramaglia, Huafu Chen, Daniele Marinazzo
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10.1371/journal.pone.0071163

PLOS ONE Modulatory Interactions of Resting-State Brain Functional Connectivity
August 30, 2013 Xin Di, Bharat Biswal
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10.1371/journal.pone.0071715

PLOS ONE Machine Learning of Hierarchical Clustering to Segment 2D and 3D Images
August 20, 2013 Juan Nunez-Iglesias, Ryan Kennedy, Toufiq Parag, Jianbo Shi, Dmitri Chklovskii
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10.1371/journal.pone.0072332

PLOS ONE Cluster-Based Statistics for Brain Connectivity in Correlation with Behavioral Measures
August 19, 2013 Cheol Han, Sang Wook Yoo, Sang Won Seo, Duk L. Na, Joon-Kyung Seong
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10.1371/journal.pcbi.1003138

PLOS Computational Biology Successful Reconstruction of a Physiological Circuit with Known Connectivity from Spiking Activity Alone
July 11, 2013 Felipe Gerhard, Tilman Kispersky, Gabrielle Gutierrez, Eve Marder, Mark Kramer, Uri Eden
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10.1371/journal.pone.0068910

PLOS ONE BrainNet Viewer: A Network Visualization Tool for Human Brain Connectomics
July 4, 2013 Mingrui Xia, Jinhui Wang, Yong He
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DARPA-SUBNETS / PLOS

PLOS ONE Spatial vs. Temporal Features in ICA of Resting-State fMRI – A Quantitative and Qualitative Investigation in the Context of Response Inhibition
June 18, 2013 Lixia Tian, Yazhuo Kong, Juejing Ren, Gaël Varoquaux, Yufeng Zang, Stephen Smith
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10.1371/journal.pcbi.1002976

PLOS Computational Biology Automated Analysis of a Diverse Synapse Population
March 28, 2013 Brad Busse, Stephen Smith
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10.1371/journal.pone.0059573

PLOS ONE Automated Transmission-Mode Scanning Electron Microscopy (tSEM) for Large Volume Analysis at Nanoscale Resolution
March 26, 2013 Masaaki Kuwajima, John Mendenhall, Laurence Lindsey, Kristen Harris
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10.1371/journal.pcbi.1002890

PLOS Computational Biology Connecting a Connectome to Behavior: An Ensemble of Neuroanatomical Models of C. elegans Klinotaxis
February 7, 2013 Eduardo Izquierdo, Randall Beer
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10.1371/journal.pone.0053199

PLOS ONE The Problem of Thresholding in Small-World Network Analysis
January 3, 2013 Nicolas Langer, Andreas Pedroni, Lutz Jäncke
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10.1371/journal.pone.0048121

PLOS ONE The Connectome Mapper: An Open-Source Processing Pipeline to Map Connectomes with MRI
December 18, 2012 Alessandro Daducci, Alessandro Daducci, Stephan Gerhard, Alessandra Griffa, Alia Lemkaddem, Leila Cammoun, Xavier Gigandet, Reto Meuli, Patric Hagmann, Jean-Philippe Thiran
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10.1371/journal.pone.0047684

PLOS ONE Reproducibility of Structural, Resting-State BOLD and DTI Data between Identical Scanners
October 25, 2012 Lejian Huang, Xue Wang, Marwan Baliki, Lei Wang, A. Vania Apkarian, Todd Parrish
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10.1371/journal.pone.0040483

PLOS ONE Analyzing Self-Similar and Fractal Properties of the C. elegans Neural Network
October 5, 2012 Daniel Kelleher, Tyler Reese, Dylan Yott, Antoni Brzoska
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10.1371/journal.pone.0045771

PLOS ONE Revealing Topological Organization of Human Brain Functional Networks with Resting-State Functional near Infrared Spectroscopy
September 24, 2012 Haijing Niu, Jinhui Wang, Tengda Zhao, Ni Shu, Yong He
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10.1371/journal.pone.0043415

PLOS ONE Improving DTI Tractography by including Diagonal Tract Propagation
September 6, 2012 Paul Taylor, Kuan-Hung Cho, Ching-Po Lin, Bharat Biswal
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10.1371/journal.pone.0044428

PLOS ONE Consistency of Network Modules in Resting-State fMRI Connectome Data
August 31, 2012 Malaak Moussa, Matthew Steen, Paul Laurienti, Satoru Hayasaka
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DARPA-SUBNETS / PLOS

PLOS Computational Biology Model-Free Reconstruction of Excitatory Neuronal Connectivity from Calcium Imaging Signals
August 23, 2012 Olav Stetter, Demian Battaglia, Jordi Soriano, Theo Geisel
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10.1371/journal.pcbi.1002619

PLOS Computational Biology Combining the Finite Element Method with Structural Connectome-based Analysis for Modeling Neurotrauma: Connectome Neurotrauma Mechanics
August 16, 2012 Reuben Kraft, Phillip McKee, Amy Dagro, Scott Grafton
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10.1371/journal.pone.0040709

PLOS ONE GAT: A Graph-Theoretical Analysis Toolbox for Analyzing Between-Group Differences in Large-Scale Structural and Functional Brain Networks
July 13, 2012 SM Hadi Hosseini, Fumiko Hoeft, Shelli Kesler
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10.1371/journal.pone.0038011

PLOS ONE TrakEM2 Software for Neural Circuit Reconstruction
June 19, 2012 Albert Cardona, Stephan Saalfeld, Johannes Schindelin, Ignacio Arganda-Carreras, Stephan Preibisch, Mark Longair, Pavel Tomancak, Volker Hartenstein, Rodney Douglas
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10.1371/journal.pone.0037911

PLOS ONE Inferring General Relations between Network Characteristics from Specific Network Ensembles
June 6, 2012 Stefano Cardanobile, Volker Pernice, Moritz Deger, Stefan Rotter
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10.1371/journal.pone.0036579

PLOS ONE Knotty-Centrality: Finding the Connective Core of a Complex Network
May 9, 2012 Murray Shanahan, Mark Wildie
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10.1371/journal.pone.0032766

PLOS ONE Effects of Different Correlation Metrics and Preprocessing Factors on Small-World Brain Functional Networks: A Resting-State Functional MRI Study
March 6, 2012 Xia Liang, Jinhui Wang, Chaogan Yan, Ni Shu, Ke Xu, Gaolang Gong, Yong He
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10.1371/journal.pone.0030826

PLOS ONE 3D Multicolor Super-Resolution Imaging Offers Improved Accuracy in Neuron Tracing
January 24, 2012 Melike Lakadamyali, Hazen Babcock, Mark Bates, Xiaowei Zhuang, Jeff Lichtman