cran: igraph | Projects | Ecosyste.ms: Papers

10.18632/oncotarget.14918

A meta-analysis of HLA peptidome composition in different hematological entities: entity-specific dividing lines and “pan-leukemia” antigens
Cited by: 11
Author(s): Linus Backert, Daniel J. Kowalewski, Juliane S. Walz, Heiko Schuster, Claudia Berlin, Marian C. Neidert, Mirle Schemionek, Tim H. Brümmendorf, Vladan Vučinić, Dietger Niederwieser, Lothar Kanz, Helmut R. Salih, Oliver Kohlbacher, Katja Weisel, Hans‐Georg Rammensee, Stefan Stevanović, Juliane S. Walz
Software Mentions: 3
Published: over 9 years ago

10.1186/s12862-017-1101-1

Musculoskeletal networks reveal topological disparity in mammalian neck evolution
Cited by: 25
Author(s): Patrick Arnold, Borja Esteve‐Altava, Martin S. Fischer
Software Mentions: 3
Published: almost 9 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: almost 7 years ago

10.1016/j.gpb.2018.01.001

Comparative Analysis of Human Genes Frequently and Occasionally Regulated by m 6 A Modification
Cited by: 3
Author(s): Yuan Zhou, Qinghua Cui
Software Mentions: 3
Published: over 8 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: over 15 years ago

10.1371/journal.pcbi.1006786

Spatial clustering and common regulatory elements correlate with coordinated gene expression
Cited by: 23
Author(s): Jingyu Zhang, Hengyu Chen, Ruoyan Li, David A. Taft, Guang Yao, Fan Bai, Jianhua Xing
Software Mentions: 3
Published: over 7 years ago

10.3390/ijerph17031009

Geographical Patterns of Algal Communities Associated with Different Urban Lakes in China
Cited by: 15
Author(s): Shengnan Chen, Hao He, Rongrong Zong, Kaiwen Liu, Miaomiao Yan, Lei Xu, Yutian Miao
Software Mentions: 3
Published: over 6 years ago

10.1016/j.gpb.2019.09.004

Machine Learning to Detect Alzheimer’s Disease from Circulating Non-coding RNAs
Cited by: 63
Author(s): Nicole Ludwig, Tobias Fehlmann, Fabian Kern, M. Gogol, Walter Maetzler, Stephanie Deutscher, Simone Gurlit, Claudia Schulte, Anna‐Katharina von Thaler, Christian Deuschle, Florian Metzger, Daniela Berg, Ulrike Suenkel, Verena Keller, Christina Backes, Hans‐Peter Lenhof, Eckart Meese
Software Mentions: 3
Published: about 7 years ago

10.1007/s11357-020-00195-z

Nursing homes and the elderly regarding the COVID-19 pandemic: situation report from Hungary
Cited by: 37
Author(s): Gábor Kemenesi, László Kornya, Gábor Endre Tóth, Kornélia Kurucz, Safia Zeghbib, B Somogyi, Viktor Zöldi, Péter Urbán, Róbert Herczeg, Ferenc Jakab
Software Mentions: 3
Published: over 6 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: over 10 years ago

10.1186/s12862-015-0534-7

A comparison of human and mouse gene co-expression networks reveals conservation and divergence at the tissue, pathway and disease levels
Cited by: 86
Author(s): Gianni Monaco, Sipko van Dam, João Luis Casal Novo Ribeiro, Anis Larbi, João Pedro de Magalhães
Software Mentions: 3
Published: almost 11 years ago

10.1111/2041-210X.12751

Measuring site fidelity and spatial segregation within animal societies
Cited by: 16
Author(s): Thomas O. Richardson, Luca Giuggioli, Nigel R. Franks, Ana B. Sendova‐Franks
Software Mentions: 3
Published: over 9 years ago

10.18632/oncotarget.24795

Molecular signatures associated with tumor-specific immune response in melanoma patients treated with dendritic cell-based immunotherapy
Cited by: 11
Author(s): Tamara García-Salum, Andrea Villablanca, Franziska Matthäus, Andrés Tittarelli, Mauricio Baeza, Carlos Pereda, María Alejandra Gleisner, Fermín E. González, Mercedes López, Jörg D. Hoheisel, Johannes Norgauer, Peter J. Gebicke‐Haerter, Flavio Salazar‐Onfray
Software Mentions: 3
Published: over 8 years ago

10.1007/s11306-021-01841-z

IonFlow: a galaxy tool for the analysis of ionomics data sets
Cited by: 2
Author(s): Jacopo Iacovacci, Wenjian Lin, Julian L. Griffin, Robert C. Glen
Software Mentions: 3
Published: almost 5 years ago

10.3390/metabo11050298

The Impact of Microbiome and Microbiota-Derived Sodium Butyrate on Drosophila Transcriptome and Metabolome Revealed by Multi-Omics Analysis
Cited by: 10
Author(s): Fan Zhou, Biaodi Liu, Xin Liu, Yan Li, Luoluo Wang, Jian Huang, Guan‐Zheng Luo, Xiaoyun Wang
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0083167

Structural Propensities of Human Ubiquitination Sites: Accessibility, Centrality and Local Conformation
Cited by: 9
Author(s): Yuan Zhou, Sixue Liu, Jiangning Song, Ziding Zhang
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pone.0123545

Characterizing Task-Based OpenMP Programs
Cited by: 7
Author(s): Ananya Muddukrishna, Peter Jönsson, Mats Brorsson
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0204186

EMT network-based feature selection improves prognosis prediction in lung adenocarcinoma
Cited by: 6
Author(s): Borong Shao, Maria Moksnes Bjaanæs, Åslaug Helland, Christof Schütte, Tim Conrad
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0106052

Dimensionality of Social Networks Using Motifs and Eigenvalues
Cited by: 30
Author(s): Anthony Bonato, David F. Gleich, Myung‐Hwan Kim, Dieter Mitsche, Paweł Prałat, Yanhua Tian, Stephen J. Young
Software Mentions: 3
Published: about 12 years ago

10.1155/2021/9960241

Exosomes Containing LINC00636 Inhibit MAPK1 through the miR-450a-2-3p Overexpression in Human Pericardial Fluid and Improve Cardiac Fibrosis in Patients with Atrial Fibrillation
Cited by: 13
Author(s): Langsha Liu, Fanyan Luo, Kaibo Lei
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0242621

Victims, offenders and victim-offender overlaps of knife crime: A social network analysis approach using police records
Cited by: 11
Author(s): Louis Bailey, Vincent Harinam, Barak Ariel
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12906-021-03340-z

A systems pharmacology approach based on oncogenic signalling pathways to determine the mechanisms of action of natural products in breast cancer from transcriptome data
Cited by: 2
Author(s): Regan Odongo, Asuman Demiroğlu-Zergeroğlu, Tunahan Çakır
Software Mentions: 3
Published: about 5 years ago

10.1186/s42523-021-00088-2

Effect of milk replacer allowance on calf faecal bacterial community profiles and fermentation
Cited by: 11
Author(s): Shiv Kumar, M. A. Khan, Emma Beijer, Jinxin Liu, Katherine K. Lowe, Wayne Young, David A. Mills, Christina D. Moon
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0078059

Perturbation Centrality and Turbine: A Novel Centrality Measure Obtained Using a Versatile Network Dynamics Tool
Cited by: 25
Author(s): Kristóf Z. Szalay, Péter Csermely
Software Mentions: 3
Published: almost 13 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: over 5 years ago

10.1002/ece3.2749

Ecological consequences of colony structure in dynamic ant nest networks
Cited by: 11
Author(s): Stephen Ellis, Daniel W. Franks, Elva J. H. Robinson
Software Mentions: 3
Published: over 9 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: about 7 years ago

10.18632/oncotarget.25216

Parenclitic networks for predicting ovarian cancer
Cited by: 25
Author(s): Harry J. Whitwell, Oleg Blyuss, Usha Menon, John F. Timms, Alexey Zaikin
Software Mentions: 3
Published: over 8 years ago

10.1186/s12944-019-1032-5

Integrated analysis of gene expression changes associated with coronary artery disease
Cited by: 9
Author(s): Miao Liu, Rui-Xing Yin, Feng Huang, Shuo Yang, Wu-Xian Chen, Jin‐Zhen Wu
Software Mentions: 3
Published: over 7 years ago

10.3390/plants9081008

Semi-Targeted Metabolomics to Validate Biomarkers of Grape Downy Mildew Infection Under Field Conditions
Cited by: 13
Author(s): Kévin Billet, Magdalena Malinowska, Thibaut Munsch, Marianne Unlubayir, Sophie Adler, Guillaume Delanoue, Arnaud Lanoue
Software Mentions: 3
Published: about 6 years ago

10.3390/ijms21093171

DRUGPATH: The Drug Gene Pathway Meta-Database
Cited by: 3
Author(s): Rajeev Jaundoo, Travis J. A. Craddock
Software Mentions: 3
Published: over 6 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: over 15 years ago

10.1371/journal.pone.0111262

Consensus between Pipelines in Structural Brain Networks
Cited by: 20
Author(s): Christopher S. Parker, Fani Deligianni, M. Jorge Cardoso, Pankaj Daga, Marc Modat, Michael Dayan, Chris A. Clark, Sébastien Ourselin, Jonathan D. Clayden
Software Mentions: 3
Published: almost 12 years ago

10.1017/S0950268820002654

Drawing transmission graphs for COVID-19 in the perspective of network science
Cited by: 4
Author(s): Necmi Gürsakal, Bülent Batmaz, Gamze Aktuna
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2021.701331

Modularity in Biological Networks
Cited by: 17
Author(s): Sergio Antonio Alcalá-Corona, Santiago Sandoval-Motta, Jesús Espinal-Enríquez, Enrique Hernández‐Lemus
Software Mentions: 3
Published: about 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 6 years ago

10.1089/brain.2019.0722

Optimizing Connectivity-Driven Brain Parcellation Using Ensemble Clustering
Cited by: 1
Author(s): Anvar Kurmukov, Ayagoz Mussabaeva, Yulia Denisova, Daniel Moyer, Neda Jahanshad, Paul M. Thompson, Boris A. Gutman
Software Mentions: 3
Published: over 6 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: over 10 years ago

10.1371/journal.pgen.1006706

Mapping of 79 loci for 83 plasma protein biomarkers in cardiovascular disease
Cited by: 174
Author(s): Lasse Folkersen, Eric B. Fauman, Maria Sabater‐Lleal, Rona J. Strawbridge, Mattias Frånberg, Bengt Sennblad, Damiano Baldassarre, Fabrizio Veglia, Steve E. Humphries, Rainer Rauramaa, Ulf dé Fairé, Andries J. Smit, Philippe Giral, Sudhir Kurl, Elmo Mannarino, Stefan Enroth, Åsa Johansson, Sofia Bosdotter Enroth, Stefan Gustafsson, Lars Lind, Cecilia M. Lindgren, Andrew P. Morris, Vilmantas Giedraitis, Angela Silveira, Anders Franco‐Cereceda, Elena Tremoli, Ulf Gyllensten, Erik Ingelsson, Søren Brunak, Per Eriksson, Daniel Ziemek, Anders Hamsten, Anders Mälarstig
Software Mentions: 3
Published: over 9 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 8 years ago

10.1371/journal.pgen.1006363

Combined Use of Genome-Wide Association Data and Correlation Networks Unravels Key Regulators of Primary Metabolism in Arabidopsis thaliana
Cited by: 63
Author(s): Si Wu, Saleh Alseekh, Álvaro Cuadros-Inostroza, Corina M. Fusari, Marek Mutwil, Rik Kooke, Joost J. B. Keurentjes, Alisdair R. Fernie, Lothar Willmitzer, Yariv Brotman
Software Mentions: 3
Published: almost 10 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 8 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: almost 11 years ago

10.1371/journal.pgen.1006817

Pervasive antagonistic interactions among hybrid incompatibility loci
Cited by: 45
Author(s): Rafael F. Guerrero, Christopher D. Muir, Sarah Josway, Leonie C. Moyle
Software Mentions: 3
Published: over 9 years ago

10.3389/fgene.2019.00916

An Integrated System Biology Approach Yields Drug Repositioning Candidates for the Treatment of Heart Failure
Cited by: 3
Author(s): Guodong Yang, Aiqun Ma, Zhaohui S. Qin
Software Mentions: 3
Published: almost 7 years ago

10.1002/brb3.834

Graph theory analysis of cortical thickness networks in adolescents with d-transposition of the great arteries
Cited by: 24
Author(s): Christopher G. Watson, Christian Stopp, Jane W. Newburger, Michael J. Rivkin
Software Mentions: 3
Published: over 8 years ago

10.1007/s00251-017-1051-1

Signatures of historical selection on MHC reveal different selection patterns in the moor frog (Rana arvalis)
Cited by: 15
Author(s): Maria Cortázar‐Chinarro, Yvonne Meyer‐Lucht, Anssi Laurila, Jacob Höglund
Software Mentions: 3
Published: over 8 years ago

10.2196/jmir.6045

Characterizing Twitter Discussions About HPV Vaccines Using Topic Modeling and Community Detection
Cited by: 145
Author(s): Didi Surian, Dat Quoc Nguyen, Georgina Kennedy, Mark Johnson, Enrico Coiera, Adam G. Dunn
Software Mentions: 3
Published: about 10 years ago

10.3389/fgene.2017.00043

Pancreatic Islet Protein Complexes and Their Dysregulation in Type 2 Diabetes
Cited by: 18
Author(s): Helle Pedersen, Valborg Guðmundsdóttir, Søren Brunak
Software Mentions: 3
Published: over 9 years ago

10.1186/s12885-019-6180-5

Genome-wide expression profiling in colorectal cancer focusing on lncRNAs in the adenoma-carcinoma transition
Cited by: 35
Author(s): Alexandra Kalmár, Zsófia Brigitta Nagy, Orsolya Galamb, István Csabai, András Bodor, Barnabás Wichmann, Gábor Valcz, Barbara Kinga Barták, Zsolt Tulassay, Péter Igaz, Béla Molnár
Software Mentions: 3
Published: almost 7 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: almost 15 years ago

10.3390/ijms22020953

Steroidal Regulation of Oviductal microRNAs Is Associated with microRNA-Processing in Beef Cows
Cited by: 9
Author(s): Ángela María Gonella-Diaza, E. A. Lopes, Kauê Ribeiro da Silva, Ricardo Perecin Nociti, Gabriella Mamede Andrade, Jorge Eduardo Atuesta-Bustos, Juliano Coelho da Silveira, Flávio Vieira Meirelles, Mário Binelli
Software Mentions: 3
Published: over 5 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 14 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 10 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: almost 11 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 6 years ago

10.1186/s40001-021-00586-8

NR4A3 and CCL20 clusters dominate the genetic networks in CD146+ blood cells during acute myocardial infarction in humans
Cited by: 3
Author(s): Yanhui Wang, Chen-Xin Li, Jessica M. Stephenson, Sean P. Marrelli, Yanming Kou, Dong Meng, Ting Wu
Software Mentions: 3
Published: almost 5 years ago

10.3389/fimmu.2017.01726

Shared IgG Infection Signatures vs. Hemorrhage-Restricted IgA Clusters in Human Dengue: A Phenotype of Differential Class-Switch via TGFβ1
Cited by: 4
Author(s): Chung‐Hao Huang, Ya-Hui Chang, Chun‐Yu Lin, Wen‐Hung Wang, Hui-Chung Kuan, Ya-Ju Hsieh, Yuwei Wang, Chung-Hsiang Yang, Jhen-Yan Chiu, Shih‐Feng Tsai, Yen-Hsu Chen, Hong-Hsing Liu
Software Mentions: 3
Published: almost 9 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: over 5 years ago

10.7554/eLife.62365

A large accessory protein interactome is rewired across environments
Cited by: 23
Author(s): Zhimin Liu, Darach Miller, Fangfei Li, Xianan Liu, Sasha F. Levy
Software Mentions: 3
Published: about 6 years ago

10.1186/s13068-015-0348-2

Phylogeny-structured carbohydrate metabolism across microbiomes collected from different units in wastewater treatment process
Cited by: 16
Author(s): Yu Xia, Francis Y. L. Chin, Yuanqing Chao, Tong Zhang
Software Mentions: 3
Published: almost 11 years ago

10.1172/jci.insight.140028

Identification of antigen-specific TCR sequences based on biological and statistical enrichment in unselected individuals
Cited by: 9
Author(s): Neal Smith, Bert Ruiter, Yamini Virkud, Ang A. Tu, Brinda Monian, James Moon, J. Christopher Love, Wayne Shreffler
Software Mentions: 3
Published: about 5 years ago

10.1200/CCI.17.00079

Overcoming the Straw Man Effect in Oncology: Visualization and Ranking of Chemotherapy Regimens Using an Information Theoretic Approach
Cited by: 1
Author(s): Jeremy L. Warner, Peter Yang, Gil Alterovitz
Software Mentions: 3
Published: almost 9 years ago

10.1093/biosci/biaa067

Global Cropland Connectivity: A Risk Factor for Invasion and Saturation by Emerging Pathogens and Pests
Cited by: 24
Author(s): Yao‐Wu Xing, John Fredy Hernández Nopsa, Kelsey F. Andersen, Jorge Andrade-Piedra, Fenton Beed, Guy Blomme, Mónica Carvajal-Yepes, Danny Coyne, Wilmer J. Cuellar, Gregory A. Forbes, Jan Kreuze, J. Kroschel, P. Lava Kumar, J.P. Legg, Monica Parker, Elmar Schulte-Geldermann, Kalpana Sharma, Karen A. Garrett
Software Mentions: 3
Published: about 6 years ago

10.1098/rstb.2019.0009

Using social network analysis of mixed-species groups in African savannah herbivores to assess how community structure responds to environmental change
Cited by: 18
Author(s): Kristine Meise, Daniel W. Franks, Jakob Bro‐Jørgensen
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0102856

Thermostability of In Vitro Evolved Bacillus subtilis Lipase A: A Network and Dynamics Perspective
Cited by: 23
Author(s): Ashutosh Srivastava, Somdatta Sinha
Software Mentions: 3
Published: about 12 years ago

10.1128/JB.00245-17

Polyvalent Proteins, a Pervasive Theme in the Intergenomic Biological Conflicts of Bacteriophages and Conjugative Elements
Cited by: 28
Author(s): Lakshminarayan M. Iyer, A. Maxwell Burroughs, Swadha Anand, Robson Francisco de Souza, L. Aravind
Software Mentions: 3
Published: about 9 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: almost 7 years ago

10.7717/peerj-cs.600

Clustering assessment in weighted networks
Cited by: 2
Author(s): Argimiro Arratia, Martí Renedo Mirambell
Software Mentions: 3
Published: over 5 years ago

10.7717/peerj-cs.699

ABCDE: Approximating Betweenness-Centrality ranking with progressive-DropEdge
Cited by: 2
Author(s): Martin Mirakyan
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0193425

Consistent individual differences and population plasticity in network-derived sociality: An experimental manipulation of density in a gregarious ungulate
Cited by: 9
Author(s): Paul Philip O'Brien, Quinn M. R. Webber, Eric Vander Wal
Software Mentions: 3
Published: over 8 years ago

10.3390/biom10121595

Identifying Genes Involved in Alkaloid Biosynthesis in Vinca minor through Transcriptomics and Gene Co-Expression Analysis
Cited by: 11
Author(s): Emily Amor Stander, Liuda Johana Sepúlveda, Thomas Dugé de Bernonville, Inês Carqueijeiro, Κωνσταντίνος Κουδούνας, Pamela Lemos Cruz, Sébastien Besseau, Arnaud Lanoue, Nicolas Papon, Nathalie Giglioli-Guivarc’h, Ron P. Dirks, Sarah E. O’Connor, Lucía Atehortúa, Audrey Oudin, Vincent Courdavault
Software Mentions: 3
Published: almost 6 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: almost 12 years ago

10.1155/2015/852341

Clique-Based Clustering of Correlated SNPs in a Gene Can Improve Performance of Gene-Based Multi-Bin Linear Combination Test
Cited by: 8
Author(s): Yung Joon Yoo, Sun Ah Kim, Shelley B. Bull
Software Mentions: 3
Published: over 11 years ago

10.1021/acs.jctc.0c01308

Reconstruction of ARNT PAS-B Unfolding Pathways by Steered Molecular Dynamics and Artificial Neural Networks
Cited by: 12
Author(s): Stefano Motta, Alessandro Pandini, Arianna Fornili, Laura Bonati
Software Mentions: 3
Published: over 5 years ago

10.1155/2017/1016305

Identification of Pharmacologically Tractable Protein Complexes in Cancer Using the R-Based Network Clustering and Visualization Program MCODER
Cited by: 4
Author(s): Gino Kwon, Hyosil Kim
Software Mentions: 3
Published: over 9 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: over 12 years ago

10.1002/ece3.7499

Testing for functional significance of traits: Effect of the light environment in tropical tree saplings
Cited by: 6
Author(s): Guilherme Silva Modolo, Victor Alexandre Hardt Ferreira dos Santos, Marciel José Ferreira
Software Mentions: 3
Published: over 5 years ago

10.1155/2020/2948292

Commonality and Specificity of Acupuncture Point Selections
Cited by: 15
Author(s): Ye-Seul Lee, Yeonhee Ryu, Da-Eun Yoon, Cheol-Han Kim, Geesoo Hong, Ye-Chae Hwang, Younbyoung Chae
Software Mentions: 3
Published: about 6 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: over 12 years ago

10.1371/journal.pone.0244839

A scientometric overview of CORD-19
Cited by: 45
Author(s): Giovanni Colavizza, Rodrigo Costas, Vincent Traag, Nees Jan van Eck, Thed N. van Leeuwen, Ludo Waltman
Software Mentions: 3
Published: over 5 years ago

10.7717/peerj.8855

Prediction of antiviral drugs against African swine fever viruses based on protein–protein interaction analysis
Cited by: 9
Author(s): Zhaozhong Zhu, Yunshi Fan, Yang Liu, Taijiao Jiang, Yang Cao, Yousong Peng
Software Mentions: 3
Published: over 6 years ago

10.1242/bio.056176

A node-based informed modularity strategy to identify organizational modules in anatomical networks
Cited by: 4
Author(s): Borja Esteve‐Altava
Software Mentions: 3
Published: almost 6 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 11 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: over 12 years ago

10.1371/journal.ppat.1001074

Global Genotype-Phenotype Correlations in Pseudomonas aeruginosa
Cited by: 11
Author(s): Claudia Pommerenke, Mathias Müsken, Tanja Becker, Andreas Dötsch, Frank Klawonn, Susanne Häußler
Software Mentions: 3
Published: about 16 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: about 7 years ago

10.1371/journal.ppat.1003403

The Escherichia coli Phosphotyrosine Proteome Relates to Core Pathways and Virulence
Cited by: 65
Author(s): Anne Marie Hansen, Raghothama Chaerkady, Jyoti Sharma, J. Javier Díaz-Mejía, Nidhi Tyagi, Santosh Renuse, Harrys K.C. Jacob, Sneha M. Pinto, Nandini A. Sahasrabuddhe, Min‐Sik Kim, Bernard Delanghe, Narayanaswamy Srinivasan, Andrew Emili, James B. Kaper, Akhilesh Pandey
Software Mentions: 3
Published: over 13 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.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.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.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.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

10.1186/1471-2407-12-331

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: about 14 years ago

10.1371/journal.pone.0095049

The Potential Connectivity of Waterhole Networks and the Effectiveness of a Protected Area under Various Drought Scenarios
Cited by: 22
Author(s): Georgina O’Farrill, Kim Gauthier Schampaert, Bronwyn Rayfield, Örjan Bodin, Sophie Calmé, Raja Sengupta, Andrew Gonzalez
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0237168

Spatiotemporal network structure among “friends of friends” reveals contagious disease process
Cited by: 2
Author(s): Carmel Witte, Laura L. Hungerford, Bruce A. Rideout, Rebecca Papendick, James H. Fowler
Software Mentions: 2
Published: about 6 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: almost 7 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: about 5 years ago

10.1371/journal.pone.0087042

Positive Network Assortativity of Influenza Vaccination at a High School: Implications for Outbreak Risk and Herd Immunity
Cited by: 77
Author(s): Victoria C Barclay, Timo Smieszek, Jianping He, Guohong Cao, Jeanette J. Rainey, Hongjiang Gao, Amra Uzicanin, Marcel Salathé
Software Mentions: 2
Published: over 12 years ago

Projects: cran: igraph

Science Score: 100/100

Bonuses:

Papers Mentioning igraph 1,555