cran: igraph | Projects | Ecosyste.ms: Papers

10.1038/s41598-020-60737-5

L-HetNetAligner: A novel algorithm for Local Alignment of Heterogeneous Biological Networks
Cited by: 18
Author(s): Marianna Milano, Tijana Milenković, Mario Cannataro, Pietro Hiram Guzzi
Software Mentions: 3
Published: over 4 years ago

10.1128/mSystems.00450-19

Oral Microbiome Alterations Associated with Early Childhood Caries Highlight the Importance of Carbohydrate Metabolic Activities
Cited by: 53
Author(s): Yuan Wang, Sa Wang, Chunyan Wu, Xi Chen, Zhuhui Duan, Qian Xu, Wen Jiang, Lei Xu, Tingting Wang, Lei Su, Ying Wang, Yadong Chen, Jie Zhang, Yun Huang, Suman Tong, Cheng Zhou, Shengjue Deng, Nan Qin
Software Mentions: 3
Published: almost 5 years ago

10.1016/j.anbehav.2015.12.007

Measuring the robustness of network community structure using assortativity
Cited by: 64
Author(s): Daizaburo Shizuka, Damien R. Farine
Software Mentions: 3
Published: almost 9 years ago

10.3389/fmicb.2020.01261

Can We Use Functional Genetics to Predict the Fate of Nitrogen in Estuaries?
Cited by: 20
Author(s): Eric J. Raes, Kristen Karsh, Adam J. Kessler, Perran L. M. Cook, Bronwyn H. Holmes, Jodie van de Kamp, Levente Bodrossy, Andrew Bissett
Software Mentions: 3
Published: over 4 years ago

10.1186/s12859-019-3041-9

Analyzing the regulation of miRNAs on protein-protein interaction network in Hodgkin lymphoma
Cited by: 2
Author(s): Huimin Lei, Wenxu Liu, Jiarui Si, Ju Wang, Tao Zhang
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2105-11-378

Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data
Cited by: 366
Author(s): Petr Novák, Pavel Neumann, Jiří Macas
Software Mentions: 3
Published: over 14 years ago

10.1186/s12889-018-5709-x

High-resolution epidemic simulation using within-host infection and contact data
Cited by: 21
Author(s): Vān Kính Nguyễn, Rafael Mikolajczyk, Esteban A. Hernandez‐Vargas
Software Mentions: 3
Published: over 6 years ago

10.3389/fpls.2020.575564

Tomato Spotted Wilt Virus Benefits Its Thrips Vector by Modulating Metabolic and Plant Defense Pathways in Tomato
Cited by: 20
Author(s): Punya Nachappa, Jean F. Challacombe, David C. Margolies, James R. Nechols, Anna E. Whitfield, Dorith Rotenberg
Software Mentions: 3
Published: almost 4 years ago

10.3389/fpls.2016.01224

Multiple Assembly Rules Drive the Co-occurrence of Orthopteran and Plant Species in Grasslands: Combining Network, Functional and Phylogenetic Approaches
Cited by: 5
Author(s): Bertrand Fournier, Arnaud Mouly, François Gillet
Software Mentions: 3
Published: over 8 years ago

10.1186/s12870-014-0188-4

Metabolite and transcript profiling of berry skin during fruit development elucidates differential regulation between Cabernet Sauvignon and Shiraz cultivars at branching points in the polyphenol pathway
Cited by: 109
Author(s): Asfaw Degu, Uri Hochberg, Noga Sikron, Luca Venturini, Genny Buson, Ryan Ghan, Inbar Plaschkes, Albert Batushansky, Vered Chalifa‐Caspi, Fulvio Mattivi, Massimo Delledonne, Mario Pezzotti, Shimon Rachmilevitch, Grant R. Cramer, Aaron Fait
Software Mentions: 3
Published: over 10 years ago

10.1038/s41598-020-67718-8

No evidence for a relationship between social closeness and similarity in resting-state functional brain connectivity in schoolchildren
Cited by: 3
Author(s): Carolyn Beth McNabb, Laura Grace Burgess, Amy Fancourt, Nancy Mulligan, Lily FitzGibbon, Patricia M. Riddell, Kou Murayama
Software Mentions: 3
Published: over 4 years ago

10.1186/s12870-020-2254-4

PlaPPISite: a comprehensive resource for plant protein-protein interaction sites
Cited by: 22
Author(s): Xiaodi Yang, Shiping Yang, Huan Qi, Tianpeng Wang, Hong Li, Ziding Zhang
Software Mentions: 3
Published: almost 5 years ago

10.3389/fmicb.2021.704052

Phylogeny of the Varidnaviria Morphogenesis Module: Congruence and Incongruence With the Tree of Life and Viral Taxonomy
Cited by: 13
Author(s): Anthony C. Woo, Morgan Gaïa, Julien Guglielmini, Violette Da Cunha, Patrick Forterre
Software Mentions: 3
Published: over 3 years ago

10.1186/s12860-020-00290-1

Impacts of drug resistance mutations on the structural asymmetry of the HIV-2 protease
Cited by: 4
Author(s): Pierre Laville, Sandrine Fartek, Natacha Cerisier, Delphine Flatters, Michel Petitjean, Leslie Regad
Software Mentions: 3
Published: over 4 years ago

10.3389/fpls.2017.01217

Evolution of Daily Gene Co-expression Patterns from Algae to Plants
Cited by: 26
Author(s): Pedro de los Reyes, Francisco J. Romero–Campero, Marta Ruiz, Javier Romero, Federico Valverde
Software Mentions: 3
Published: over 7 years ago

10.3389/fpls.2017.00893

Network Analysis Reveals a Common Host–Pathogen Interaction Pattern in Arabidopsis Immune Responses
Cited by: 24
Author(s): Hong Li, Yuan Zhou, Ziding Zhang
Software Mentions: 3
Published: over 7 years ago

10.3389/fmicb.2014.00219

Deciphering microbial interactions and detecting keystone species with co-occurrence networks
Cited by: 968
Author(s): David Berry, Stefanie Widder
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pcbi.1005316

Inference of Transmission Network Structure from HIV Phylogenetic Trees
Cited by: 31
Author(s): Federica Giardina, Ethan Romero-Severson, Jan Albert, Tom Britton, Thomas Leitner
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-020-72477-7

Play fighting social networks do not predict injuries from later aggression
Cited by: 12
Author(s): Simon P. Turner, Jennifer E. Weller, Irene Camerlink, Gareth Arnott, Taegyu Choi, Andrea Doeschl‐Wilson, Marianne Farish, Simone Foister
Software Mentions: 3
Published: about 4 years ago

10.1186/s12920-019-0597-1

A network view of microRNA and gene interactions in different pathological stages of colon cancer
Cited by: 5
Author(s): Jia Wen, Benika Hall, Xinghua Shi
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-020-73591-2

The spatial and temporal dynamics of global meat trade networks
Cited by: 15
Author(s): Min Gon Chung, Kelly Kapsar, Kenneth A. Frank, Jianguo Liu
Software Mentions: 3
Published: about 4 years ago

10.1007/s13593-021-00668-1

Social-ecological analysis of timely rice planting in Eastern India
Cited by: 7
Author(s): Anton Urfels, Andrew J. McDonald, Gerardo van Halsema, P.C. Struik, Pankaj Kumar, R. K. Malik, Shishpal Poonia, Balwinder-Singh, Deepak Singh, Mukesh Kumar Singh, Timothy J. Krupnik
Software Mentions: 3
Published: almost 4 years ago

10.3389/fpls.2018.00798

Field-Based Metabolomics of Vitis vinifera L. Stems Provides New Insights for Genotype Discrimination and Polyphenol Metabolism Structuring
Cited by: 35
Author(s): Kévin Billet, Benjamin Houillé, Thomas Dugé de Bernonville, Sébastien Besseau, Audrey Oudin, Vincent Courdavault, Guillaume Delanoue, Laurence Guérin, Marc Clastre, Nathalie Giglioli-Guivarc’h, Arnaud Lanoue
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pcbi.1004068

Prioritizing Therapeutics for Lung Cancer: An Integrative Meta-analysis of Cancer Gene Signatures and Chemogenomic Data
Cited by: 34
Author(s): Kristen Fortney, Joshua Griesman, Max Kotlyar, Chiara Pastrello, Marc Angeli, Ming‐Sound Tsao, Igor Jurišica
Software Mentions: 3
Published: over 9 years ago

10.1186/s12916-016-0664-9

Evaluation in alcohol use disorders – insights from the nalmefene experience
Cited by: 18
Author(s): Florian Naudet, Clément Palpacuer, Rémy Boussageon, Bruno Laviolle
Software Mentions: 3
Published: over 8 years ago

10.1186/1751-0473-7-12

RMol: a toolset for transforming SD/Molfile structure information into R objects
Cited by: 1
Author(s): Martin Grábner, Курт Вармуза, Matthias Dehmer
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pone.0173548

Characterization of the mechanism of drug-drug interactions from PubMed using MeSH terms
Cited by: 28
Author(s): Ling Yin, Bryan Figler, Hong Huang, Yi-Cheng Tu, Wang Ju, Feng Cheng
Software Mentions: 3
Published: over 7 years ago

10.16910/jemr.12.3.4

Improving the pilot selection process by using eye-tracking tools
Cited by: 1
Author(s): Slaviša Vlačić, Aleksandar Knežević, Sanja Rođenkov, Saptarshi Mandal, Panagiotis A. Vitsas
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12879-017-2895-6

Interaction of healthcare worker hands and portable medical equipment: a sequence analysis to show potential transmission opportunities
Cited by: 45
Author(s): Chetan Jinadatha, Frank J. Villamaria, John David Coppin, Charles Dale, Marjory Williams, Ryan Whitworth, Mark Stibich
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12879-021-06475-z

Association between tuberculosis in men and social network structure in Kampala, Uganda
Cited by: 5
Author(s): Paige B. Miller, Sarah Zalwango, Ronald Galiwango, Robert Kakaire, Juliet N. Sekandi, Lauren Steinbaum, John M. Drake, Christopher C. Whalen, Noah Kiwanuka
Software Mentions: 3
Published: about 3 years ago

10.1038/s41598-021-85281-8

Characterization of the microbial communities in wheat tissues and rhizosphere soil caused by dwarf bunt of wheat
Cited by: 13
Author(s): Tongshuo Xu, Wenli Jiang, Dandan Qin, Taiguo Liu, Zhang Jian-min, Wanquan Chen, Li Gao
Software Mentions: 3
Published: over 3 years ago

10.1186/s12865-019-0297-9

Comprehensive analyses of long non-coding RNA expression profiles by RNA sequencing and exploration of their potency as biomarkers in psoriatic arthritis patients
Cited by: 12
Author(s): Tao Yue, Mei Ji, Huanru Qu, Mengru Guo, Fengmin Bai, Zhanming Zhang, Weifeng Wang, Xuming Gong, Zhenghua Zhang
Software Mentions: 3
Published: over 5 years ago

10.1186/s12913-021-06798-2

Empirically identified networks of healthcare providers for adults with mental illness
Cited by: 2
Author(s): Joshua Breslau, Beth Dana, Harold Alan Pincus, Marcela Horvitz-Lennon, Luke J. Matthews
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-021-86124-2

Fine scale infectious disease modeling using satellite-derived data
Cited by: 2
Author(s): Nistara Randhawa, Hugo Mailhot, Duncan Temple Lang, Beatriz Martínez‐López, Kirsten Gilardi, Jonna A. K. Mazet
Software Mentions: 3
Published: over 3 years ago

10.1186/1742-6405-8-26

HIV-1 mutational pathways under multidrug therapy
Cited by: 13
Author(s): Glenn Lawyer, André Altmann, Alexander Thielen, Maurizio Zazzi, Anders Sönnerborg, Thomas Lengauer
Software Mentions: 3
Published: almost 14 years ago

10.1038/s41598-021-86409-6

Variations in Schedule III prescription patterns in a Medicaid population pre- and post-policy
Cited by: 0
Author(s): Radhakrishnan Nagarajan, Jeffery Talbert, Craig S. Miller, Jeffrey L. Ebersole
Software Mentions: 3
Published: over 3 years ago

10.3389/fpsyt.2018.00598

Diffusion of a Peer-Led Suicide Preventive Intervention Through School-Based Student Peer and Adult Networks
Cited by: 30
Author(s): Trevor A. Pickering, Peter A. Wyman, Karen Schmeelk-Cone, Chelsey Hartley, Thomas W. Valente, Anthony R. Pisani, Kelly L. Rulison, Charles H. Brown, Mark LoMurray
Software Mentions: 3
Published: about 6 years ago

10.3389/fpsyt.2018.00602

Genetic and Environmental Influences on the Affective Regulation Network: A Prospective Experience Sampling Analysis
Cited by: 5
Author(s): Laila Hasmi, Marjan Drukker, Sinan Gülöksüz, Wolfgang Viechtbauer, Evert Thiery, Cathérine Derom, Jim van Os
Software Mentions: 3
Published: almost 6 years ago

10.3389/fpsyt.2020.579339

Mapping the Network of Social Cognition Domains in Children With Autism Spectrum Disorder Through Graph Analysis
Cited by: 6
Author(s): Maria Chiara Pino, Roberto Vagnetti, Francesco Masedu, Margherita Attanasio, Sergio Tiberti, Marco Valenti, Monica Mazza
Software Mentions: 3
Published: about 4 years ago

10.1186/s12864-019-5603-7

Genomic comparison of serogroups O159 and O170 with other Vibrio cholerae serogroups
Cited by: 8
Author(s): Zhenpeng Li, Xin Lü, Duochun Wang, Wei Li Liang, Jingyun Zhang, Jie Li, Jialiang Xu, Bo Pang, Biao Kan
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pcbi.1006474

Genomic data integration systematically biases interactome mapping
Cited by: 31
Author(s): Michael A. Skinnider, R. Greg Stacey, Leonard J. Foster
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0153381

Kin-Aggregations Explain Chaotic Genetic Patchiness, a Commonly Observed Genetic Pattern, in a Marine Fish
Cited by: 40
Author(s): Jason D. Selwyn, J. Derek Hogan, Alan M. Downey‐Wall, Lauren Gurski, David S. Portnoy, Daniel D. Heath
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0141191

The Importance of Networking in Autism Gaze Analysis
Cited by: 21
Author(s): Quentin Guillon, Mohammad H. Afzali, Bernadette Rogé, Sophie Baduel, Jeanne Kruck, Nouchine Hadjikhani
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0234095

Validity, reliability and cut-offs of the Patient Health Questionnaire-9 as a screening tool for depression among patients living with epilepsy in Rwanda
Cited by: 12
Author(s): Fidèle Sebera, João Ricardo Nickenig Vissoci, Josiane Umwiringirwa, Dirk E. Teuwen, Paul E. Boon, Peter Dedeken
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pcbi.1005160

Markov Networks of Collateral Resistance: National Antimicrobial Resistance Monitoring System Surveillance Results from Escherichia coli Isolates, 2004-2012
Cited by: 16
Author(s): William J. Love, Kelson Zawack, James G. Booth, Yrjo T. Gröhn, Cristina Lanzas
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0027368

Defining the Role of Essential Genes in Human Disease
Cited by: 85
Author(s): Jonathan E. Dickerson, Ana Zhu, David L. Robertson, Kathryn E. Hentges
Software Mentions: 3
Published: about 13 years ago

10.3389/fpsyg.2016.00018

Social Network Analysis and Nutritional Behavior: An Integrated Modeling Approach
Cited by: 15
Author(s): Alistair M. Senior, Mathieu Lihoreau, Jérôme Buhl, David Raubenheimer, Stephen J. Simpson
Software Mentions: 3
Published: almost 9 years ago

10.1038/tp.2017.37

Modeling anorexia nervosa: transcriptional insights from human iPSC-derived neurons
Cited by: 21
Author(s): Priscilla D. Negraes, Fernanda R. Cugola, Roberto H. Herai, Cleber A. Trujillo, Alexandre S. Cristino, Thanathom Chailangkarn, Alysson R. Muotri, Vikas Duvvuri
Software Mentions: 3
Published: over 7 years ago

10.1186/s12859-019-2915-1

Difficulty in inferring microbial community structure based on co-occurrence network approaches
Cited by: 103
Author(s): Hokuto Hirano, Kazuhiro Takemoto
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2016.00068

Using “Omics” and Integrated Multi-Omics Approaches to Guide Probiotic Selection to Mitigate Chytridiomycosis and Other Emerging Infectious Diseases
Cited by: 105
Author(s): Eria A. Rebollar, Rachael E. Antwis, Matthew H. Becker, Lisa K. Belden, Molly C. Bletz, Robert M. Brucker, Xavier A. Harrison, Myra C. Hughey, Jordan G. Kueneman, Andrew H. Loudon, Valerie J. McKenzie, Daniel Medina, Kevin P. C. Minbiole, Louise A. Rollins‐Smith, Jenifer B. Walke, Sophie Weiss, Douglas C. Woodhams, Reid N. Harris
Software Mentions: 3
Published: almost 9 years ago

10.3389/fmicb.2018.03095

Bacterial and Archaeal Viruses of Himalayan Hot Springs at Manikaran Modulate Host Genomes
Cited by: 23
Author(s): Anukriti Sharma, Matthias Schmidt, Bärbel Kiesel, Nitish Kumar Mahato, Lauren Cralle, Yogendra Singh, Hans H. Richnow, Jack A. Gilbert, Wyatt Arnold, Rup Lal
Software Mentions: 3
Published: almost 6 years ago

10.1186/s40478-018-0524-2

Integrated proteomics and network analysis identifies protein hubs and network alterations in Alzheimer’s disease
Cited by: 111
Author(s): Qi Zhang, Cheng Ma, Marla Gearing, Peng George Wang, Lih‐Shen Chin, Lian Li
Software Mentions: 3
Published: over 6 years ago

10.3390/microorganisms8111677

The Microbial Composition in Circumneutral Thermal Springs from Chignahuapan, Puebla, Mexico Reveals the Presence of Particular Sulfur-Oxidizing Bacterial and Viral Communities
Cited by: 9
Author(s): Hugo G Castelán-Sánchez, Pablo M Meza-Rodríguez, Erika Carrillo, David I Ríos-Vázquez, Arturo Liñan-Torres, Ramón Alberto Batista-García, Ernesto Pérez‐Rueda, Norma Elena Rojas-Ruíz, Sonia Dávila-Ramos
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0142443

Gene Network Rewiring to Study Melanoma Stage Progression and Elements Essential for Driving Melanoma
Cited by: 9
Author(s): Abhinav Kaushik, Yashuma Bhatia, Shakir Ali, Dinesh Gupta
Software Mentions: 3
Published: about 9 years ago

10.1111/eva.12138

Inferring influenza global transmission networks without complete phylogenetic information
Cited by: 4
Author(s): Stéphane Aris‐Brosou
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0224201

MANET 3.0: Hierarchy and modularity in evolving metabolic networks
Cited by: 14
Author(s): Fizza Mughal, Gustavo Caetano‐Anollés
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0202615

Tracking a serial killer: Integrating phylogenetic relationships, epidemiology, and geography for two invasive meningococcal disease outbreaks
Cited by: 8
Author(s): Ifeoma Ezeoke, Madeline R. Galac, Ying Lin, Alvin T. Liem, Pierce A. Roth, Andy Kilianski, Henry S. Gibbons, Danielle Bloch, John Kornblum, Paula Del Rosso, Daniel Janies, Don Weiss
Software Mentions: 3
Published: almost 6 years ago

10.3389/fgene.2020.500064

A Machine Learning Approach to Predicting Autism Risk Genes: Validation of Known Genes and Discovery of New Candidates
Cited by: 22
Author(s): Ying Lin, Shiva Afshar, Anjali M. Rajadhyaksha, James B. Potash, Shizhong Han
Software Mentions: 3
Published: about 4 years ago

10.1155/2019/9736968

The Potential Link between Gut Microbiota and Serum TRAb in Chinese Patients with Severe and Active Graves’ Orbitopathy
Cited by: 13
Author(s): Tingting Shi, Lin Hua, Hua Wang, Xin Zhong
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0248340

Analysis of survey on menstrual disorder among teenagers using Gaussian copula model with graphical lasso prior
Cited by: 3
Author(s): Jiali Wang, Anton H. Westveld, A. H. Welsh, Melissa Parker, Bronwyn Loong
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0111681

Taxonomic and Functional Diversity Provides Insight into Microbial Pathways and Stress Responses in the Saline Qinghai Lake, China
Cited by: 12
Author(s): Qiuyuan Huang, Brandon R. Briggs, Hailiang Dong, Hongchen Jiang, Geng Wu, Christian F. Edwardson, Iwijn De Vlaminck, Stephen R. Quake
Software Mentions: 3
Published: about 10 years ago

10.3389/fpubh.2020.582405

Care Deficiencies and Super-Organization of American Nursing Homes in Hospital Referral Region
Cited by: 3
Author(s): Tyler Pittman
Software Mentions: 3
Published: almost 4 years ago

10.3389/fpubh.2020.587298

Depiction of Vaginal Microbiota in Women With High-Risk Human Papillomavirus Infection
Cited by: 25
Author(s): Zhentong Wei, Hongliang Chen, Chunfeng Wang, Genhua Yang, Song Han, Song‐Ling Zhang
Software Mentions: 3
Published: almost 4 years ago

10.1186/s40168-020-00876-z

Genomic and transcriptomic insights into methanogenesis potential of novel methanogens from mangrove sediments
Cited by: 41
Author(s): Cui-Jing Zhang, Jie Pan, Yang Liu, Changhai Duan, Meng Li
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0088581

High-Throughput Sequence Typing Reveals Genetic Differentiation and Host Specialization among Populations of the Borrelia burgdorferi Species Complex that Infect Rodents
Cited by: 25
Author(s): Maude Jacquot, Maxime Bisseux, David Abrial, Maud Marsot, Elisabeth Ferquel, Jean‐Louis Chapuis, Gwenaël Vourc’H, Xavier Bailly
Software Mentions: 3
Published: almost 11 years ago

10.3389/fgene.2019.00932

Identification and Classification of Differentially Expressed Genes and Network Meta-Analysis Reveals Potential Molecular Signatures Associated With Tuberculosis
Cited by: 25
Author(s): Aftab Alam, Nikhat Imam, Mohd Murshad Ahmed, Safiya Tazyeen, Naaial Tamkeen, Anam Farooqui, Md. Zubbair Malik, Romana Ishrat
Software Mentions: 3
Published: about 5 years ago

10.1186/s12939-019-0911-8

Can social network analysis help to include marginalised young women in structural support programmes in Botswana? A mixed methods study
Cited by: 3
Author(s): David Loutfi, Neil Andersson, Susan Law, Jon Salsberg, Jeannie Haggerty, Leagajang Kgakole, Anne Cockcroft
Software Mentions: 3
Published: almost 6 years ago

10.3389/fbioe.2018.00121

Metabolite-Centric Reporter Pathway and Tripartite Network Analysis of Arabidopsis Under Cold Stress
Cited by: 15
Author(s): İbrahim Koç, İsa Öner Yüksel, Gustavo Caetano‐Anollés
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pcbi.1003243

Simple Topological Features Reflect Dynamics and Modularity in Protein Interaction Networks
Cited by: 38
Author(s): Yuri Pritykin, Mona Singh
Software Mentions: 3
Published: about 11 years ago

10.3389/fvets.2020.583715

Proximity Interactions in a Permanently Housed Dairy Herd: Network Structure, Consistency, and Individual Differences
Cited by: 15
Author(s): Kareemah Chopra, Holly R. Hodges, Z. E. Barker, Jorge A. Vázquez Diosdado, Jonathan Amory, Tom C. Cameron, Darren P. Croft, Nick Bell, Edward A. Codling
Software Mentions: 3
Published: almost 4 years ago

10.1186/1471-2164-16-S10-S7

Reconstruction of composite regulator-target splicing networks from high-throughput transcriptome data
Cited by: 7
Author(s): Panagiotis Papasaikas, Arvind Rao, Peter Huggins, Juan Valcárcel, A. Javier Lopez
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0122477

Mining the Modular Structure of Protein Interaction Networks
Cited by: 6
Author(s): Ariel Berenstein, Janet Piñero, Laura I. Furlong, Ariel Chernomoretz
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0086973

Tracking Socioeconomic Vulnerability Using Network Analysis: Insights from an Avian Influenza Outbreak in an Ostrich Production Network
Cited by: 19
Author(s): Christine Moore, Graeme S. Cumming, Jasper A. Slingsby, John Grewar
Software Mentions: 3
Published: almost 11 years ago

10.1186/s40168-021-01079-w

Low shifts in salinity determined assembly processes and network stability of microeukaryotic plankton communities in a subtropical urban reservoir
Cited by: 158
Author(s): Yuanyuan Mo, Peng Feng, Xiaofei Gao, Peng Xiao, Ramiro Logares, Erik Jeppesen, Kexin Ren, Yuanyuan Xue, Jun Yang
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0218779

Conversion of monoculture cropland and open grassland to agroforestry alters the abundance of soil bacteria, fungi and soil-N-cycling genes
Cited by: 38
Author(s): Lukas Beule, Marife D. Corre, M. Schmidt, Leonie Göbel, Edzo Veldkamp, Petr Karlovský
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0232458

A network analysis of research productivity by country, discipline, and wealth
Cited by: 35
Author(s): Klaus Jaffé, Enrique ter Horst, Laura H Gunn, Juan Diego Zambrano, Germán Molina
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0244299

An avian dominance hierarchy at a supplemental water source in the Patagonian steppe
Cited by: 2
Author(s): Sophie Rabinowicz, Natalia C. García, Tristan Herwood, Amanda Lazar, Benjamin Hein, Eliot T. Miller, Leonardo Campagna
Software Mentions: 3
Published: almost 4 years ago

10.1186/1471-2164-16-S11-S4

A method for developing regulatory gene set networks to characterize complex biological systems
Cited by: 1
Author(s): Chayaporn Suphavilai, Zhu Li, Jake Y. Chen
Software Mentions: 3
Published: about 9 years ago

10.1186/1471-2105-13-75

Quantitatively integrating molecular structure and bioactivity profile evidence into drug-target relationship analysis
Cited by: 5
Author(s): Tianlei Xu, Ruixin Zhu, Qi Liu, Zhiwei Cao
Software Mentions: 3
Published: over 12 years ago

10.1098/rsos.170148

Individual-level movement bias leads to the formation of higher-order social structure in a mobile group of baboons
Cited by: 16
Author(s): Tyler R. Bonnell, Parry M.R. Clarke, S. Peter Henzi, Louise Barrett
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0219771

Descriptive analysis of horse movement networks during the 2015 equestrian season in Ontario, Canada
Cited by: 7
Author(s): Kelsey L. Spence, Terri L. O’Sullivan, Zvonimir Poljak, Amy L. Greer
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0022295

Randomizing Genome-Scale Metabolic Networks
Cited by: 16
Author(s): Areejit Samal, O. C. Martin
Software Mentions: 3
Published: over 13 years ago

10.3389/fcell.2021.703489

Reconstruction of the Cytokine Signaling in Lysosomal Storage Diseases by Literature Mining and Network Analysis
Cited by: 3
Author(s): Silvia Parolo, Danilo Tomasoni, Pranami Bora, Alan Ramponi, Chanchala Kaddi, Karim Azer, Enrico Domenici, Susana Neves-Zaph, Rosario Lombardo
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0246687

Comparison of wild rice (Oryza longistaminata) tissues identifies rhizome-specific bacterial and archaeal endophytic microbiomes communities and network structures
Cited by: 7
Author(s): Xiaojue Peng, Jian Xie, Wenzhuo Li, Haizhu Xie, Yaohui Cai, Xia Ding
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pcbi.1006098

Topological and statistical analyses of gene regulatory networks reveal unifying yet quantitatively different emergent properties
Cited by: 44
Author(s): Wilberforce Zachary Ouma, Katja Pogacar, Erich Grotewold
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0222611

Social and structural factors associated with substance use within the support network of adults living in precarious housing in a socially marginalized neighborhood of Vancouver, Canada
Cited by: 11
Author(s): Verena Knerich, Andrea A. Jones, Sam Seyedin, Christopher Siu, Louie Dinh, Sara Mostafavi, Alasdair M. Barr, William J. Panenka, Allen E. Thornton, William G. Honer, Alexander R. Rutherford
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0148135

Symbiotic Bacteria in Gills and Guts of Chinese Mitten Crab (Eriocheir sinensis) Differ from the Free-Living Bacteria in Water
Cited by: 71
Author(s): Meiling Zhang, Yanfa Sun, Liqiao Chen, Chen Cai, Fang Qiao, Zhen‐Yu Du, Erchao Li
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pcbi.1002002

The Free Energy Landscape of Small Molecule Unbinding
Cited by: 94
Author(s): Danzhi Huang, Amedeo Caflisch
Software Mentions: 3
Published: almost 14 years ago

10.1371/journal.pone.0189223

Systematic integrative analysis of gene expression identifies HNF4A as the central gene in pathogenesis of non-alcoholic steatohepatitis
Cited by: 47
Author(s): Cristina Baciu, Elisa Pasini, Marc Angeli, Katherine J. P. Schwenger, Jenifar Afrin, Atul Humar, Sandra E. Fischer, Keyur Patel, Johane P. Allard, Mamatha Bhat
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0224632

Mitochondrial dysfunction in rheumatoid arthritis: A comprehensive analysis by integrating gene expression, protein-protein interactions and gene ontology data
Cited by: 22
Author(s): Venugopal Panga, Ashwin Adrian Kallor, Arunima Nair, Shilpa Harshan, Srivatsan Raghunathan
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-016-3066-7

Path2enet: generation of human pathway-derived networks in an expression specific context
Cited by: 1
Author(s): Conrad Droste, Javier De Las Rivas
Software Mentions: 3
Published: about 8 years ago

10.1186/s12864-021-07815-8

TAD cliques predict key features of chromatin organization
Cited by: 4
Author(s): Tharvesh Moideen Liyakat Ali, Annaël Brunet, Philippe Collas, Jonas Paulsen
Software Mentions: 3
Published: over 3 years ago

10.1098/rsos.200441

Suppression of the TGF-β pathway by a macrolide antibiotic decreases fibrotic responses by ocular fibroblasts <i>in vitro</i>
Cited by: 5
Author(s): Thomas Stahnke, Beata Gajda-Deryło, Anselm Jünemann, Oliver Stachs, Katharina A Sterenczak, Robert Ręjdak, Julia Beck, Ekkehard Schütz, Steffen Möller, Israel Barrantes, Gregor Warsow, Stephan Struckmann, Georg Fuellen
Software Mentions: 3
Published: about 4 years ago

10.1186/s40168-021-00999-x

Genomic evidence for sulfur intermediates as new biogeochemical hubs in a model aquatic microbial ecosystem
Cited by: 25
Author(s): Adrien Vigneron, Perrine Cruaud, Alexander I. Culley, Raoul-Marie Couture, Connie Lovejoy, Warwick F. Vincent
Software Mentions: 3
Published: almost 4 years ago

10.1186/s13014-016-0672-0

Transcriptomic analyses of the radiation response in head and neck squamous cell carcinoma subclones with different radiation sensitivity: time-course gene expression profiles and gene association networks
Cited by: 37
Author(s): Agata Michna, Ulrike Schötz, Martin Selmansberger, Horst Zitzelsberger, Kirsten Lauber, Kristian Unger, Julia Heß
Software Mentions: 3
Published: over 8 years ago

Projects: cran: igraph

Papers Mentioning igraph 1,555