cran: igraph | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0014673

Controlling the Response: Predictive Modeling of a Highly Central, Pathogen-Targeted Core Response Module in Macrophage Activation
Cited by: 33
Author(s): Jason McDermott, Michelle Archuleta, Brian D. Thrall, Joshua N. Adkins, Katrina M. Waters
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0141420

A Network Approach to Bipolar Symptomatology in Patients with Different Course Types
Cited by: 29
Author(s): M.A. Koenders, Roy de Kleijn, Erik J. Giltay, Bernet M. Elzinga, Philip Spinhoven, Annet T. Spijker
Software Mentions: 2
Published: almost 11 years ago

10.1186/1471-2148-11-89

Expression level, cellular compartment and metabolic network position all influence the average selective constraint on mammalian enzymes
Cited by: 24
Author(s): Corey Hudson, Gavin C. Conant
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0198525

Exploring novel key regulators in breast cancer network
Cited by: 18
Author(s): Shahnawaz Ali, Md. Zubbair Malik, Keilash Chirom, Romana Ishrat
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0195161

In vitro co-cultures of human gut bacterial species as predicted from co-occurrence network analysis
Cited by: 39
Author(s): Dás P, Boyang Ji, Petia Kovatcheva‐Datchary, Fredrik Bäckhed, Jens Nielsen
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0196211

Social network analysis of stakeholder networks from two community-based obesity prevention interventions
Cited by: 28
Author(s): Jaimie McGlashan, Melanie Nichols, Ariella R. Korn, Lynne Millar, Jennifer B. Marks, Andrew Sanigorski, Mark C. Pachucki, Boyd Swinburn, Steven Allender, Christina D. Economos
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0140085

Seasonal Influenza Vaccination amongst Medical Students: A Social Network Analysis Based on a Cross-Sectional Study
Cited by: 19
Author(s): Rhiannon Edge, Joseph J. Heath, Barry Rowlingson, Thomas Keegan, Rachel Isba
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0205122

Social network properties predict chronic aggression in commercial pig systems
Cited by: 38
Author(s): Simone Foister, Andrea Doeschl‐Wilson, R. Roehe, Gareth Arnott, Laura Boyle, Simon P. Turner
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0172867

Network analysis of wildfire transmission and implications for risk governance
Cited by: 71
Author(s): Alan A. Ager, Cody Evers, Michelle A. Day, Haiganoush K. Preisler, Ana M. G. Barros, Max Nielsen-Pincus
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0213221

A meta-analysis of multiple matched aCGH/expression cancer datasets reveals regulatory relationships and pathway enrichment of potential oncogenes
Cited by: 1
Author(s): Richard Newton, Lorenz Wernisch
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0205295

Combining multi-OMICs information to identify key-regulator genes for pleiotropic effect on fertility and production traits in beef cattle
Cited by: 31
Author(s): Pablo Augusto de Souza Fonseca, Samir Id‐Lahoucine, Antônio Reverter, Juan F. Medrano, M. R. S. Fortes, J. Casellas, F. Miglior, Luiz F. Brito, Maria Raquel Santos Carvalho, F.S. Schenkel, Loan Nguyen, Laércio R. Porto-Neto, M. G. Thomas, Ángela Cánovas
Software Mentions: 2
Published: almost 8 years ago

10.3390/ijerph18083922

Time Granularity Impact on Propagation of Disruptions in a System-of-Systems Simulation of Infrastructure and Business Networks
Cited by: 3
Author(s): Mateusz Iwo Dubaniowski, Hans Rudolf Heinimann
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0190001

Graph complexity analysis identifies an ETV5 tumor-specific network in human and murine low-grade glioma
Cited by: 5
Author(s): Yuan Pan, Christina Durón, Erin C. Bush, Yu Ma, Peter A. Sims, David H. Gutmann, Ami Radunskaya, Johanna Hardin
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0020298

Time-Ordered Networks Reveal Limitations to Information Flow in Ant Colonies
Cited by: 100
Author(s): Benjamin Blonder, Anna Dornhaus
Software Mentions: 2
Published: about 15 years ago

10.1371/journal.pone.0176751

Using null models to infer microbial co-occurrence networks
Cited by: 64
Author(s): Nora Connor, Albert Barberán, Aaron Clauset
Software Mentions: 2
Published: about 9 years ago

10.1093/cercor/bhz244

Ketamine Restores Thalamic-Prefrontal Cortex Functional Connectivity in a Mouse Model of Neurodevelopmental Disorder-Associated 2p16.3 Deletion
Cited by: 11
Author(s): Rebecca Hughes, Jayde Whittingham-Dowd, Rachel E Simmons, Steven J. Clapcote, Susan Broughton, Neil Dawson
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0230693

Urban foraging: Land management policy, perspectives, and potential
Cited by: 27
Author(s): Mallika Sardeshpande, Charlie M. Shackleton
Software Mentions: 2
Published: over 6 years ago

10.1038/s42003-020-01190-y

Network pharmacology suggests biochemical rationale for treating COVID-19 symptoms with a Traditional Chinese Medicine
Cited by: 15
Author(s): Denghai Zhang, Xue Zhang, Bin Peng, Shengqiong Deng, Yufang Wang, Lin Yang, Kai-zheng Zhang, Changquan Ling, Wu Kunlun
Software Mentions: 2
Published: almost 6 years ago

10.1038/s42003-021-02260-5

Serotonin signaling modulates aging-associated metabolic network integrity in response to nutrient choice in Drosophila melanogaster
Cited by: 3
Author(s): Yang Lyu, Daniel Promislow, Scott D. Pletcher
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0238626

Do economic shocks spread randomly?: A topological study of the global contagion network
Cited by: 4
Author(s): Tamás Sebestyén, Zita Iloskics
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0174671

Collaboration patterns in the German political science co-authorship network
Cited by: 14
Author(s): Philip Leifeld, Sandra Andrea Wankmüller, Valentin Tim Zacharias Berger, Karin Ingold, Christiane Steiner
Software Mentions: 2
Published: over 9 years ago

10.1038/s42003-019-0440-4

Combined network analysis and machine learning allows the prediction of metabolic pathways from tomato metabolomics data
Cited by: 52
Author(s): David Toubiana, Rami Puzis, Lingling Wen, Noga Sikron, Assylay Kurmanbayeva, Aigerim Soltabayeva, María del Mar Rubio Wilhelmi, Nir Sade, Aaron Fait, Moshe Sagi, Eduardo Blumwald, Yuval Elovici
Software Mentions: 2
Published: about 7 years ago

10.1186/s40649-016-0029-8

Factorization threshold models for scale-free networks generation
Cited by: 2
Author(s): Akmal Artikov, Aleksandr Dorodnykh, Yana Kashinskaya, Egor Samosvat
Software Mentions: 2
Published: almost 10 years ago

10.3390/ijerph18168388

The Structure of Social Support in Confidant Networks: Implications for Depression
Cited by: 4
Author(s): Liyuan Wang, Lindsay E. Young, Lynn C. Miller
Software Mentions: 2
Published: almost 5 years ago

10.1111/cobi.13580

Assessing the current state of ecological connectivity in a large marine protected area system
Cited by: 18
Author(s): Kimberly A. Roberts, Carly N. Cook, Jutta Beher, Eric A. Treml
Software Mentions: 2
Published: almost 6 years ago

10.1016/j.dib.2020.105629

A dataset of eco-evidence tools to inform early-stage environmental impact assessments of hydropower development
Cited by: 0
Author(s): Ryan A. McManamay, Esther S. Parish, Christopher R. DeRolph
Software Mentions: 2
Published: about 6 years ago

10.1093/database/baaa018

Integrated querying and version control of context-specific biological networks
Cited by: 4
Author(s): Tyler Cowman, Mustafa Coşkun, Ananth Grama, Mehmet Koyutürk
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0222222

Are unpopular children more likely to get sick? Longitudinal links between popularity and infectious diseases in early childhood
Cited by: 4
Author(s): Vidar Ulset, Nikolai Olavi Czajkowski, Brage Kraft, Pål Kraft, Ellen Wikenius, Thomas Haarklau Kleppestø, Mona Bekkhus
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0184532

Emergence of encounter networks due to human mobility
Cited by: 35
Author(s): Alejandro P. Riascos, José L. Mateos
Software Mentions: 2
Published: almost 9 years ago

10.3390/diagnostics10080586

Identifying the Salient Genes in Microarray Data: A Novel Game Theoretic Model for the Co-Expression Network
Cited by: 2
Author(s): Papori Neog Bora, Vishwa Jyoti Baruah, Surajit Borkotokey, Loyimee Gogoi, Priyakshi Mahanta, Ankumon Sarmah, Rajnish Kumar, Stefano Moretti
Software Mentions: 2
Published: almost 6 years ago

10.1242/dmm.042101

Integrated lipidomic and transcriptomic analyses identify altered nerve triglycerides in mouse models of prediabetes and type 2 diabetes
Cited by: 40
Author(s): Phillipe D. O’Brien, Kai Guo, Stéphanie Eid, Amy E. Rumora, Lucy M. Hinder, John M. Hayes, Faye E. Mendelson, Junguk Hur, Eva L. Feldman
Software Mentions: 2
Published: over 7 years ago

10.1016/j.eclinm.2021.100968

HIV-1 Transmission linkages among persons with incident infection to inform public health surveillance
Cited by: 7
Author(s): Ann M. Dennis, Simon D. W. Frost, Kimberly Enders, Andrew Cressman, Erik Volz, Nicole Adams, William C. Miller, Myron S. Cohen, Victoria Mobley, Erika Samoff, Joseph J. Eron
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0016365

Detecting Instability in Animal Social Networks: Genetic Fragmentation Is Associated with Social Instability in Rhesus Macaques
Cited by: 53
Author(s): Brianne A. Beisner, Megan E. Jackson, Ashley Cameron, Brenda McCowan
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0110088

Active Semi-Supervised Community Detection Based on Must-Link and Cannot-Link Constraints
Cited by: 23
Author(s): Jianjun Cheng, Mingwei Leng, Longjie Li, Hanhai Zhou, Xiaoyun Chen
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0225554

Location, location, location: Close ties among older continuing care retirement community residents
Cited by: 4
Author(s): Liat Ayalon, Inbal Yahav
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2407-12-331

A systems biology approach to the global analysis of transcription factors in colorectal cancer
Cited by: 25
Author(s): Meeta Pradhan, Nagendra Prasad, Mathew Palakal
Software Mentions: 2
Published: almost 14 years ago

10.1007/s00442-021-04967-y

The role of habitat configuration in shaping animal population processes: a framework to generate quantitative predictions
Cited by: 8
Author(s): Peng He, Pierre‐Olivier Montiglio, Marius Somveille, Maurício Cantor, Dan Farine
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0255604

Examining the sources of evidence in e-cigarette policy recommendations: A citation network analysis of international public health recommendations
Cited by: 6
Author(s): Marissa J. Smith, Andrew J Baxter, Kathryn Skivington, Mark McCann, Shona Hilton, Srinivasa Vittal Katikireddi
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0179915

Network analysis of pig movements: Loyalty patterns and contact chains of different holding types in Denmark
Cited by: 25
Author(s): Jana Schulz, Anette Boklund, Tariq Hisham Beshara Halasa, Nils Toft, Hartmut H. K. Lentz
Software Mentions: 2
Published: about 9 years ago

10.1038/s41388-018-0651-z

The coordinated action of VCP/p97 and GCN2 regulates cancer cell metabolism and proteostasis during nutrient limitation
Cited by: 32
Author(s): Katarzyna Parzych, Paula Saavedra‐García, Gabriel N. Valbuena, Hibah A Al-Sadah, Mark E. Robinson, Lucy Penfold, Desislava M Kuzeva, Angie Ruiz-Tellez, Sandra Loaiza, Viktoria Holzmann, Valentina S Caputo, David C. Johnson, Martin Kaiser, Anastasios Karadimitris, Eric Lam, Éric Chevet, Niklas Feldhahn, Hector C. Keun, Holger W. Auner
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0241516

Processes and outcomes of diabetes mellitus care by different types of team primary care models
Cited by: 5
Author(s): Fangjian Guo, Yu Li Lin, Mukaila Raji, Bruce Leonard, Lin‐Na Chou, Yong Fang Kuo
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2012.00278

Phylodynamic analysis of a viral infection network
Cited by: 7
Author(s): Teiichiro Shiino
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0102633

Phylodynamic Analysis Reveals CRF01_AE Dissemination between Japan and Neighboring Asian Countries and the Role of Intravenous Drug Use in Transmission
Cited by: 16
Author(s): Teiichiro Shiino, Junko Hattori, Yoshiyuki Yokomaku, Yoshinori Iwatani, Wataru Sugiura
Software Mentions: 2
Published: about 12 years ago

10.3389/fmicb.2020.556002

Effects of Plant and Soil Characteristics on Phyllosphere and Rhizosphere Fungal Communities During Plant Development in a Copper Tailings Dam
Cited by: 15
Author(s): Tong Jia, Yushan Yao, Tingyan Guo, Ruihong Wang, Bo Chai
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0068581

The Community Structure of the European Network of Interlocking Directorates 2005–2010
Cited by: 31
Author(s): Eelke M. Heemskerk, Fabio Daolio, Marco Tomassini
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0036465

Identification and Validation of Ifit1 as an Important Innate Immune Bottleneck
Cited by: 29
Author(s): Jason McDermott, Keri B. Vartanian, Hugh D. Mitchell, Susan L. Stevens, Antonio Sanfilippo, Mary P. Stenzel-Poore
Software Mentions: 2
Published: about 14 years ago

10.1186/1471-2105-12-149

Fast network centrality analysis using GPUs
Cited by: 99
Author(s): Zhiao Shi, Bing Zhang
Software Mentions: 2
Published: about 15 years ago

10.1371/journal.pone.0222357

Bourdieu, networks, and movements: Using the concepts of habitus, field and capital to understand a network analysis of gender differences in undergraduate physics
Cited by: 10
Author(s): Steven Martin Turnbull, Kirsten Locke, Frédérique Vanholsbeeck, Dion R. J. O’Neale
Software Mentions: 2
Published: almost 7 years ago

10.3389/fmicb.2016.00570

Data-based Reconstruction of Gene Regulatory Networks of Fungal Pathogens
Cited by: 5
Author(s): Reinhard Guthke, Silvia Gerber, Theresia Conrad, Sebastian Vlaic, Saliha Durmuş, Tunahan Çakır, Fatih Erdoğan Sevilgen, Ekaterina Shelest, Jörg Linde
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0142407

Coevolved Mutations Reveal Distinct Architectures for Two Core Proteins in the Bacterial Flagellar Motor
Cited by: 8
Author(s): Alessandro Pandini, Jens Kleinjung, Shafqat Rasool, Shahid Khan
Software Mentions: 2
Published: over 10 years ago

10.3389/fmicb.2016.01285

Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System
Cited by: 84
Author(s): Adrian Ho, Roey Angel, Annelies J. Veraart, Anne Daebeler, Zhongjun Jia, Sang Yoon Kim, Frederiek‐Maarten Kerckhof, Nico Boon, Paul L. E. Bodelier
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0194901

Detecting hierarchical levels of connectivity in a population of Acacia tortilis at the northern edge of the species’ global distribution: Combining classical population genetics and network analyses
Cited by: 10
Author(s): Yael S. Rodger, Gili Greenbaum, Micha Silver, Shirli Bar‐David, Gidon Winters
Software Mentions: 2
Published: over 8 years ago

10.1186/s12859-018-2453-2

A nearest-neighbors network model for sequence data reveals new insight into genotype distribution of a pathogen
Cited by: 3
Author(s): Helen N. Catanese, Kelly A. Brayton, Assefaw H. Gebremedhin
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0040337

Information Processing in Social Insect Networks
Cited by: 96
Author(s): James S. Waters, Jennifer H. Fewell
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pone.0140030

Anatomical Network Comparison of Human Upper and Lower, Newborn and Adult, and Normal and Abnormal Limbs, with Notes on Development, Pathology and Limb Serial Homology vs. Homoplasy
Cited by: 28
Author(s): Rui Diogo, Borja Esteve‐Altava, Christopher M. Smith, Julia C. Boughner, Diego Rasskin‐Gutman
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0060982

Autistic Traits in Neurotypical Adults: Correlates of Graph Theoretical Functional Network Topology and White Matter Anisotropy Patterns
Cited by: 30
Author(s): András Jakab, Miklós Emri, Tamás Spisák, Anita Szemán-Nagy, Mónika Béres, Sándor Attila Kis, Péter Molnár, Ervin Berényi
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0208227

The geographic evolution of political cleavages in Switzerland: A network approach to assessing levels and dynamics of polarization between local populations
Cited by: 3
Author(s): Shin Alexandre Koseki
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2105-11-343

A semi-supervised learning approach to predict synthetic genetic interactions by combining functional and topological properties of functional gene network
Cited by: 92
Author(s): Zhu-Hong You, Zhimin Yin, Kyungsook Han, Dongqing Huang, Xiaobo Zhou
Software Mentions: 2
Published: about 16 years ago

10.3389/fmicb.2017.00545

Genetic Characterization of the Exceptionally High Heat Resistance of the Non-toxic Surrogate Clostridium sporogenes PA 3679
Cited by: 16
Author(s): Robert R. Butler, Kristin M. Schill, Yun Wang, Jean‐François Pombert
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0152123

Who Is Spreading Avian Influenza in the Moving Duck Flock Farming Network of Indonesia?
Cited by: 18
Author(s): Joerg Henning, Dirk U. Pfeiffer, M.A. Stevenson, Didik Yulianto, W. Priyono, J. Meers
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0125725

Using Graph Components Derived from an Associative Concept Dictionary to Predict fMRI Neural Activation Patterns that Represent the Meaning of Nouns
Cited by: 5
Author(s): Hiroyuki Akama, Masakazu Miyake, Jason J. Jung, Brian Murphy
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0038039

Transcriptome Profiling of Citrus Fruit Response to Huanglongbing Disease
Cited by: 141
Author(s): Federico Martinelli, Sandra L. Uratsu, Ute Albrecht, Russell L. Reagan, My L. Phu, Monica Britton, Vincent Buffalo, Joseph Fass, Elizabeth Leicht, Wenwei Zhao, Dazhen Lin, Raissa M. D’Souza, Cristina E. Davis, Kim D. Bowman, Abhaya M. Dandekar
Software Mentions: 2
Published: about 14 years ago

10.3389/fmicb.2019.03123

The cyl Genes Reveal the Biosynthetic and Evolutionary Origins of the Group B Streptococcus Hemolytic Lipid, Granadaene
Cited by: 13
Author(s): Blair Armistead, Christopher Whidbey, Lakshminarayan M. Iyer, Pilar Herrero-Foncubierta, Phoenicia Quach, Alí Haïdour, L. Aravind, Juan M. Cuerva, Heather B. Jaspan, Lakshmi Rajagopal
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2020.01361

Scoring Species for Synthetic Community Design: Network Analyses of Functional Core Microbiomes
Cited by: 22
Author(s): Hirokazu Toju, Masato S. Abe, Chiharu Ishii, Haruo Yoshiki, Hiroaki Fujita, Shinji Fukuda
Software Mentions: 2
Published: about 6 years ago

10.1186/s12859-019-2746-0

Topological and functional comparison of community detection algorithms in biological networks
Cited by: 37
Author(s): Sara Rahiminejad, Mano Ram Maurya, Shankar Subramaniam
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0027009

Modeling the Mechanism of Action of a DGAT1 Inhibitor Using a Causal Reasoning Platform
Cited by: 24
Author(s): Ahmed Enayetallah, Daniel Ziemek, Michael T. Leininger, Ranjit Randhawa, Jinlin Yang, Tara B. Manion, Dawn Mather, William J. Zavadoski, Max Kühn, Judith L. Treadway, Shelly Ann G. des Etages, E. Michael Gibbs, Nigel Greene, Claire M. Steppan
Software Mentions: 2
Published: over 14 years ago

10.3389/fmicb.2021.632695

Evaluation of the Inflammatory Cytokines and IL-10 Network in Individuals Co-infected With Human T-Cell Lymphotropic Virus and Hepatitis C Virus (HTLV/HCV)
Cited by: 1
Author(s): Felicidade Mota Pereira, Pablo Ivan Pereira Ramos, Monique Lírio, Ajax Mercês Atta, Ilka Regina Souza de Oliveira, Fabio Carneiro Vosqui Nascimento, Marcelo Costa Silva, Bernardo Galvão–Castro, Maria Fernanda Rios Grassi
Software Mentions: 2
Published: over 5 years ago

10.1186/s12859-020-03702-3

ImmunoGlobe: enabling systems immunology with a manually curated intercellular immune interaction network
Cited by: 6
Author(s): Michelle Atallah, Varun Tandon, Kamir J Hiam-Galvez, Hunter Boyce, Michelle Hori, Waleed Atallah, Matthew H. Spitzer, Edgar G. Engleman, Parag Mallick
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0211227

Dissecting a novel allosteric mechanism of cruzain: A computer-aided approach
Cited by: 13
Author(s): Lilian Hernández Alvarez, Diego E. B. Gomes, Jorge Enrique Hernández González, Pedro Geraldo Pascutti
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2018.02237

Diversity of Yeasts and Molds by Culture-Dependent and Culture-Independent Methods for Mycobiome Surveillance of Traditionally Prepared Dried Starters for the Production of Indian Alcoholic Beverages
Cited by: 34
Author(s): Shankar Prasad Sha, Mangesh V. Suryavanshi, Kunal Jani, Avinash Sharma, Yogesh S. Shouche, Jyoti Prakash Tamang
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0198222

On an algorithmic definition for the components of the minimal cell
Cited by: 2
Author(s): Octavio Martínez, M. Humberto Reyes-Valdés
Software Mentions: 2
Published: about 8 years ago

10.7554/eLife.02863

Buffered Qualitative Stability explains the robustness and evolvability of transcriptional networks
Cited by: 34
Author(s): Luca Albergante, J. Julian Blow, T. J. Newman
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pntd.0005659

Challenges in developing methods for quantifying the effects of weather and climate on water-associated diseases: A systematic review
Cited by: 35
Author(s): Giovanni Lo Iacono, Ben Armstrong, Lora E. Fleming, Richard Elson, Sari Kovats, Sotiris Vardoulakis, Gordon Nichols
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pntd.0006070

The introduction of dengue follows transportation infrastructure changes in the state of Acre, Brazil: A network-based analysis
Cited by: 41
Author(s): Raquel Martins Lana, Tiago França Melo de Lima, Nildimar Alves Honório, Cláudia Torres Codeço
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pmed.1001810

Geographic and Temporal Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted HIV-1 Drug Resistance: An Individual-Patient- and Sequence-Level Meta-Analysis
Cited by: 187
Author(s): Soo-Yon Rhee, José Luis Santiago Blanco, Michael R. Jordan, Jonathan Taylor, Philippe Lemey, Vici Varghese, Raph L Hamers, Silvia Bertagnolio, Tobias F. Rinke de Wit, Avelin F. Aghokeng, Jan Albert, Radko Avi, Santiago Ávila‐Ríos, Pascal Bessong, James Brooks, Charles A. Boucher, Zabrina L. Brumme, Michael P. Busch, Hermann Bussmann, Marie Laure Chaix, Bum Sik Chin, Toni Thomas d’Aquin, Cillian F. De Gascun, Anne Derache, Diane Descamps, Alaka Deshpande, Cyrille F. Djoko, Susan H. Eshleman, Hervé Fleury, Pierre Frange, Seiichiro Fujisaki, P. Richard Harrigan, Junko Hattori, África Holguín, Gillian Hunt, Hiroshi Ishiguro, Pontiano Kaleebu, David Katzenstein, Sasisopin Kiertiburanakul, Jerome H. Kim, Sung Soon Kim, Yanpeng Li, Irja Lutsar, Lynn Morris, Nicaise Ndembi, Kee Peng Ng, Ramesh Paranjape, Martine Peeters, Mario Poljak, Matt A. Price, Manon Ragonnet‐Cronin, Gustavo Reyes‐Terán, Morgane Rolland, Sunee Sirivichayakul, Davey M. Smith, Marcelo A. Soares, Vincent Soriano, Deogratius Ssemwanga, Maja Stanojević, Mariane A. Stefani, Wataru Sugiura, Somnuek Sungkanuparph, Amílcar Tanuri, Kok Keng Tee, Hong Ha M. Truong, David van de Vijver, Nicole Vidal, Chunfu Yang, Rongge Yang, Gonzalo Yebra, John P. A. Ioannidis, Anne‐Mieke Vandamme, Robert W. Shafer
Software Mentions: 2
Published: over 11 years ago

10.1186/s12859-019-2917-z

A dual controllability analysis of influenza virus-host protein-protein interaction networks for antiviral drug target discovery
Cited by: 8
Author(s): Emily E. Ackerman, John F. Alcorn, Takeshi Hase, Jason E. Shoemaker
Software Mentions: 2
Published: about 7 years ago

10.3389/fnins.2015.00472

Identification of Voxels Confounded by Venous Signals Using Resting-State fMRI Functional Connectivity Graph Community Identification
Cited by: 9
Author(s): Klaudius Kalcher, Roland N. Boubela, Wolfgang Huf, Christian Našel, Ewald Moser
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pgen.1002612

Metabolic Profiling of a Mapping Population Exposes New Insights in the Regulation of Seed Metabolism and Seed, Fruit, and Plant Relations
Cited by: 109
Author(s): David Toubiana, Yaniv Semel, Takayuki Tohge, Romina Beleggia, Luigi Cattivelli, Leah Rosental, Zoran Nikoloski, Dani Zamir, Alisdair R. Fernie, Aaron Fait
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pcbi.1004467

Genome-Wide Detection and Analysis of Multifunctional Genes
Cited by: 35
Author(s): Yuri Pritykin, Dario Ghersi, Mona Singh
Software Mentions: 2
Published: almost 11 years ago

10.3389/fonc.2021.720400

Construction and Characterization of Long Non-Coding RNA-Associated Networks to Reveal Potential Prognostic Biomarkers in Human Lung Adenocarcinoma
Cited by: 4
Author(s): Wenting Zhou, Chen Bai, C. B. Long, Li Hu, Yanfei Zheng
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pcbi.1007434

Nine quick tips for analyzing network data
Cited by: 21
Author(s): Vincent Miele, Catherine Matias, Stéphane Robin, Stéphane Dray
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pcbi.1003881

Linear Motif-Mediated Interactions Have Contributed to the Evolution of Modularity in Complex Protein Interaction Networks
Cited by: 16
Author(s): Inhae Kim, Heetak Lee, Seong Kyu Han, Sanguk Kim
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pcbi.1008832

Collective predator evasion: Putting the criticality hypothesis to the test
Cited by: 17
Author(s): Pascal P. Klamser, Pawel Romanczuk
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pcbi.1006525

Steered molecular dynamics simulations reveal critical residues for (un)binding of substrates, inhibitors and a product to the malarial M1 aminopeptidase
Cited by: 8
Author(s): Daniel Moore, Conor Brines, Heather Jewhurst, John P. Dalton, Irina G. Tikhonova
Software Mentions: 2
Published: over 7 years ago

10.3389/fonc.2021.640731

Post-Transformation IGHV-IGHD-IGHJ Mutations in Chronic Lymphocytic Leukemia B Cells: Implications for Mutational Mechanisms and Impact on Clinical Course
Cited by: 9
Author(s): Davide Bagnara, Catherine Tang, Jennifer R. Brown, Siddha Kasar, Stacey M. Fernandes, Monica Colombo, Stefano Vergani, Andrea Nicola Mazzarello, Fabio Ghiotto, Silvia Bruno, Fortunato Morabito, R. Kanti, Jonathan E. Kolitz, Jacqueline C. Barrientos, Steven L. Allen, Franco Fais, Matthew D. Scharff, Thomas MacCarthy, Nicholas Chiorazzi
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pcbi.1006796

Conformational coupling by trans-phosphorylation in calcium calmodulin dependent kinase II
Cited by: 5
Author(s): Alessandro Pandini, Howard Schulman, Shahid Khan
Software Mentions: 2
Published: about 7 years ago

10.3389/fphys.2018.01377

Causality Analysis and Cell Network Modeling of Spatial Calcium Signaling Patterns in Liver Lobules
Cited by: 7
Author(s): Aalap Verma, Anil Noronha Antony, Babatunde A. Ogunnaike, Jan B. Hoek, Rajanikanth Vadigepalli
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pcbi.1004597

Distinctive Behaviors of Druggable Proteins in Cellular Networks
Cited by: 41
Author(s): Costas Mitsopoulos, Amanda C. Schierz, Paul Workman, Bissan Al‐Lazikani
Software Mentions: 2
Published: over 10 years ago

10.3389/fpls.2018.01467

Paving the Way From the Lab to the Field: Using Synthetic Microbial Consortia to Produce High-Quality Crops
Cited by: 55
Author(s): Zhaochen Kong, Miranda M. Hart, Hongguang Liu
Software Mentions: 2
Published: almost 8 years ago

10.1186/1471-2105-13-35

Assessing statistical significance in causal graphs
Cited by: 11
Author(s): Leonid Chindelevitch, Po‐Ru Loh, Ahmed Enayetallah, Bonnie Berger, Daniel Ziemek
Software Mentions: 2
Published: over 14 years ago

10.3389/fpls.2014.00598

Integrated network analysis and effective tools in plant systems biology
Cited by: 40
Author(s): Atsushi Fukushima, Shigehiko Kanaya, Kozo Nishida
Software Mentions: 2
Published: over 11 years ago

10.3389/fpls.2017.01029

Evidence and Consequence of a Highly Adapted Clonal Haplotype within the Australian Ascochyta rabiei Population
Cited by: 23
Author(s): Yasir Mehmood, Prabhakaran Thanjavur Sambasivam, Sukhjiwan Kaur, J. A. Davidson, Audrey E. Leo, Kristy Hobson, Celeste C. Linde, Kevin Moore, Jeremy C. Brownlie, Rebecca Ford
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pcbi.1003302

A Comprehensive Survey of Small-Molecule Binding Pockets in Proteins
Cited by: 102
Author(s): Mu Gao, Jeffrey Skolnick
Software Mentions: 2
Published: almost 13 years ago

10.1186/s12859-016-1013-x

CompNet: a GUI based tool for comparison of multiple biological interaction networks
Cited by: 29
Author(s): Bhusan K. Kuntal, Anirban Dutta, Sharmila S. Mande
Software Mentions: 2
Published: over 10 years ago

10.3389/fpsyg.2015.01111

Second language social networks and communication-related acculturative stress: the role of interconnectedness
Cited by: 58
Author(s): Marina M. Doucerain, Raheleh S. Varnaamkhaasti, Norman Segalowitz, Andrew G. Ryder
Software Mentions: 2
Published: almost 11 years ago

10.3390/ijms22031097

In Silico Inference of Synthetic Cytotoxic Interactions from Paclitaxel Responses
Cited by: 0
Author(s): Jeong Hoon Lee, Kye Hwa Lee, Ju Han Kim
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pcbi.1004067

Exploring Bacterial Organelle Interactomes: A Model of the Protein-Protein Interaction Network in the Pdu Microcompartment
Cited by: 24
Author(s): Julien Jorda, Yu Liu, Thomas A. Bobik, Todd O. Yeates
Software Mentions: 2
Published: over 11 years ago

10.1111/jvim.16058

Peri‐ictal magnetic resonance imaging characteristics in dogs with suspected idiopathic epilepsy
Cited by: 11
Author(s): Aran Nagendran, J. Fraser McConnell, Luisa De Risio, Roberto José‐López, R. Gutierrez Quintana, Kelsey Robinson, Simon Platt, Daniel Sánchez Masián, Thomas W. Maddox, Rita Gonçalves
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pcbi.1002187

Heat Shock Partially Dissociates the Overlapping Modules of the Yeast Protein-Protein Interaction Network: A Systems Level Model of Adaptation
Cited by: 56
Author(s): Ágoston Mihalik, Péter Csermely
Software Mentions: 2
Published: almost 15 years ago

10.3389/fpsyg.2015.00603

Network-based characterization of brain functional connectivity in Zen practitioners
Cited by: 36
Author(s): Phebe Brenne Kemmer, Ying Guo, Yi‐Kai Wang, Giuseppe Pagnoni
Software Mentions: 2
Published: about 11 years ago

Projects: cran: igraph

Science Score: 100/100

Bonuses:

Papers Mentioning igraph 1,555