cran: igraph | Projects | Ecosyste.ms: Papers

10.1186/s12859-019-2800-y

Integrating data and knowledge to identify functional modules of genes: a multilayer approach
Cited by: 10
Author(s): Lifan Liang, Vicky Chen, Kunju Zhu, Xiao-Nan Fan, Xinghua Lu, Songjian Lu
Software Mentions: 4
Published: over 7 years ago

10.1186/s12859-018-2131-4

On the rank-distance median of 3 permutations
Cited by: 4
Author(s): Leonid Chindelevitch, João Paulo Pereira Zanetti, João Meidânis
Software Mentions: 4
Published: over 8 years ago

10.1186/s12885-020-06774-9

Sepsis-associated pathways segregate cancer groups
Cited by: 5
Author(s): Himanshu Tripathi, Samanwoy Mukhopadhyay, Saroj Kant Mohapatra
Software Mentions: 4
Published: over 6 years ago

10.1186/s12862-020-01690-9

Genotypic similarities among the parthenogenetic Darevskia rock lizards with different hybrid origins
Cited by: 9
Author(s): David Tarkhnishvili, Alexey Yanchukov, Mehmet Kürşat Şahin, Mariam Gabelaia, Marine Murtskhvaladze, Kamίl Candan, Eduard Galoyan, Marine Arakelyan, Giorgi Iankoshvili, Yusuf Kumlutaş, Çetίn Ilgaz, Ferhat Matur, Faruk Çolak, Meriç Erdolu, Sofiko Kurdadze, Natia Barateli, Cort L. Anderson
Software Mentions: 4
Published: about 6 years ago

10.1186/s12862-015-0298-0

A Boolean gene regulatory model of heterosis and speciation
Cited by: 8
Author(s): Peter M. F. Emmrich, Hannah Roberts, Véra Pancaldi
Software Mentions: 4
Published: over 11 years ago

10.1186/s12864-017-4242-0

Unraveling the evolution and coevolution of small regulatory RNAs and coding genes in Listeria
Cited by: 16
Author(s): Franck Cerutti, Ludovic Mallet, Anaïs Painset, Claire Hoede, Annick Moisan, Christophe Bécavin, Manuel Duval, Olivier Dussurget, Pascale Cossart, Christine Gaspin, Hélène Chiapello
Software Mentions: 4
Published: almost 9 years ago

10.1186/s12864-020-07148-y

Analysing the meta-interaction between pathways by gene set topological impact analysis
Cited by: 2
Author(s): Yan Shu, Xu Chi, Xiao Chang, Mengliang Tian
Software Mentions: 4
Published: almost 6 years ago

10.1186/1471-2164-16-S5-S2

Integrative network-based approach identifies key genetic elements in breast invasive carcinoma
Cited by: 27
Author(s): Mohamed Hamed, Christian Spaniol, Alexander Zapp, Volkhard Helms
Software Mentions: 4
Published: over 11 years ago

10.1186/1471-2164-14-728

Quantitative trait loci-dependent analysis of a gene co-expression network associated with Fusarium head blight resistance in bread wheat (Triticum aestivumL.)
Cited by: 80
Author(s): Karl G. Kugler, Gerald Siegwart, Thomas Nußbaumer, Christian Ametz, Manuel Spannagl, Barbara Steiner, Marc Lemmens, Klaus Mayer, Hermann Buerstmayr, Wolfgang Schweiger
Software Mentions: 4
Published: almost 13 years ago

10.1186/s12913-020-05173-x

Care coordination for severe mental health disorders: an analysis of healthcare provider patient-sharing networks and their association with quality of care in a French region
Cited by: 3
Author(s): Coralie Gandré, Laurent Beauguitte, Alexandre Lolivier, Magali Coldefy
Software Mentions: 4
Published: over 6 years ago

10.1186/s12920-017-0250-9

Basal-like breast cancer: molecular profiles, clinical features and survival outcomes
Cited by: 64
Author(s): Heloisa Helena Milioli, Inna Tishchenko, Carlos Riveros, Regina Berretta, Pablo Moscato
Software Mentions: 4
Published: over 9 years ago

10.1186/s12866-020-01827-2

Vital members in the gut microbiotas altered by two probiotic Bifidobacterium strains against liver damage in rats
Cited by: 8
Author(s): Hua Zha, Daiqiong Fang, Aimee L. van der Reis, Kevin Chang, Liya Yang, Jiao-Jiao Xie, Ding Shi, Qiaomai Xu, Yating Li
Software Mentions: 4
Published: over 6 years ago

10.1186/s12870-017-1062-y

Relationships between drought, heat and air humidity responses revealed by transcriptome-metabolome co-analysis
Cited by: 46
Author(s): Elisabeth Georgii, Ming Jin, Jin Zhao, Basem Kanawati, Philippe Schmitt‐Kopplin, Andreas Albert, Jana Barbro Winkler, Anton R. Schäffner
Software Mentions: 4
Published: about 9 years ago

10.1186/s12889-018-5588-1

Development and testing of a novel survey to assess Stakeholder-driven Community Diffusion of childhood obesity prevention efforts
Cited by: 26
Author(s): Ariella R. Korn, Erin Hennessy, Ross A. Hammond, Steven Allender, Matthew W. Gillman, Matt Kasman, Jaimie McGlashan, Lynne Millar, Brynle Owen, Mark C. Pachucki, Boyd Swinburn, Alison Tovar, Christina D. Economos
Software Mentions: 4
Published: over 8 years ago

10.1186/1752-0509-5-1

Metabolomic correlation-network modules in Arabidopsis based on a graph-clustering approach
Cited by: 118
Author(s): Atsushi Fukushima, Miyako Kusano, Henning Redestig, Masanori Arita, Kazuki Saito
Software Mentions: 4
Published: over 15 years ago

10.1186/s12918-017-0412-6

Detection of statistically significant network changes in complex biological networks
Cited by: 27
Author(s): Raghvendra Mall, Luigi Cerulo, Halima Bensmail, Antonio Iavarone, Michele Ceccarelli
Software Mentions: 4
Published: over 9 years ago

10.1186/1752-0509-6-72

Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum
Cited by: 12
Author(s): Daniela Beißer, Markus A. Grohme, Joachim Kopka, Marcus Frohme, Ralph O. Schill, Steffen Hengherr, Thomas Dandekar, Gunnar W. Klau, Marcus Dittrich, Tobias Müller
Software Mentions: 4
Published: about 14 years ago

10.1186/1752-0509-5-127

Exploring pathway interactions in insulin resistant mouse liver
Cited by: 16
Author(s): Thomas Kelder, Lars Eijssen, Robert Kleemann, Marjan van Erk, Teake Kooistra, Chris T. Evelo
Software Mentions: 4
Published: over 15 years ago

10.1186/s12918-016-0313-0

XMRF: an R package to fit Markov Networks to high-throughput genetics data
Cited by: 18
Author(s): Ying-Wooi Wan, Genevera I. Allen, Yulia Baker, Eunho Yang, Pradeep Ravikumar, Matthew L. Anderson, Zhandong Liu
Software Mentions: 4
Published: about 10 years ago

10.1186/s12917-018-1406-3

Dynamic network measures reveal the impact of cattle markets and alpine summering on the risk of epidemic outbreaks in the Swiss cattle population
Cited by: 21
Author(s): Beatriz Vidondo, Bernhard Voelkl
Software Mentions: 4
Published: over 8 years ago

10.3758/s13428-018-1186-5

spreadr: An R package to simulate spreading activation in a network
Cited by: 24
Author(s): Cynthia S. Q. Siew
Software Mentions: 4
Published: over 7 years ago

10.6026/97320630013025

Elucidation of the sequential transcriptional activity in Escherichia coli using time-series RNA-seq data
Cited by: 1
Author(s): Pui Shan Wong, Kosuke Tashiro, Satoru Kuhara, Sachiyo Aburatani
Software Mentions: 4
Published: over 9 years ago

10.1242/bio.049809

Single cell force profiling of human myofibroblasts reveals a biophysical spectrum of cell states
Cited by: 6
Author(s): T. B. Layton, Lynn M. Williams, Huw Colin‐York, Fiona E. McCann, Marisa Cabrita, Marc Feldmann, Cameron Brown, Weilin Xie, Marco Fritzsche, Dominic Furniss, Jagdeep Nanchahal
Software Mentions: 4
Published: over 6 years ago

10.1155/2015/167249

mmnet: An R Package for Metagenomics Systems Biology Analysis
Cited by: 10
Author(s): Yang Cao, Xiaofei Zheng, Fēi Li, Xiaochen Bo
Software Mentions: 4
Published: over 11 years ago

10.3390/biom10060850

Can We Assume the Gene Expression Profile as a Proxy for Signaling Network Activity?
Cited by: 8
Author(s): Mehran Piran, Reza Karbalaei, Mehrdad Piran, Jehad Aldahdooh, Mehdi Mirzaie, Naser Ansari-Pour, Jing Tang, Mohieddin Jafari
Software Mentions: 4
Published: over 6 years ago

10.3390/brainsci11010094

Assessing the Relationship between Verbal and Nonverbal Cognitive Abilities Using Resting-State EEG Functional Connectivity
Cited by: 1
Author(s): Inna Feklicheva, Ilya Zakharov, Nadezda Chipeeva, Ekaterina Maslennikova, Svetlana Korobova, Timofey Adamovich, Victoria Ismatullina, Sergey Malykh
Software Mentions: 4
Published: over 5 years ago

10.1007/s00262-020-02833-z

Early changes in the circulating T cells are associated with clinical outcomes after PD-L1 blockade by durvalumab in advanced NSCLC patients
Cited by: 14
Author(s): Elliot Naidus, Jérôme Bouquet, David Y. Oh, Timothy J. Looney, Hai Yang, Lawrence Fong, Nathan Standifer, Li Zhang
Software Mentions: 4
Published: over 5 years ago

10.3390/metabo9100210

Plasma Metabolic Signature and Abnormalities in HIV-Infected Individuals on Long-Term Successful Antiretroviral Therapy
Cited by: 41
Author(s): Hemalatha Babu, Maike Sperk, Anoop T. Ambikan, Gladys Rachel, Vinod Kumar Viswanathan, Srikanth Tripathy, Piotr Nowak, Luke Elizabeth Hanna, Ujjwal Neogi
Software Mentions: 4
Published: almost 7 years ago

10.3390/metabo10060220

Non-Targeted Metabolite Profiles and Sensory Properties Elucidate Commonalities and Differences of Wines Made with the Same Variety but Different Cultivar Clones
Cited by: 6
Author(s): Álvaro Cuadros-Inostroza, Claudio Verdugo-Alegría, Lothar Willmitzer, Yerko Moreno-Simunovic, José G. Vallarino
Software Mentions: 4
Published: over 6 years ago

10.1007/s00248-021-01719-6

Assessing Biotic and Abiotic Interactions of Microorganisms in Amazonia through Co-Occurrence Networks and DNA Metabarcoding
Cited by: 8
Author(s): Camila Duarte Ritter, Dominik Forster, Josué A. R. Azevedo, Alexandre Antonelli, R. Henrik Nilsson, Martha E. Trujillo, Micah Dunthorn
Software Mentions: 4
Published: over 5 years ago

10.1099/mgen.0.000070

Phylogenetic structure of European Salmonella Enteritidis outbreak correlates with national and international egg distribution network
Cited by: 53
Author(s): Tim Dallman, Thomas Inns, Thibaut Jombart, Philip Ashton, Nicholas J. Loman, Carol Chatt, Ute Messelhaeusser, Wolfgang Rabsch, Sandra Simon, Sergejs Nikisins, Helen Bernard, Simon Le Hello, Nathalie Jourdan da-Silva, Christian Kornschober, Joël Mossong, Peter M. Hawkey, Elizabeth de Pinna, Kathie Grant, Paul Cleary
Software Mentions: 4
Published: about 10 years ago

10.1099/mgen.0.000108

A population genomics approach to exploiting the accessory 'resistome' of Escherichia coli
Cited by: 18
Author(s): Robert Goldstone, David George Emslie Smith
Software Mentions: 4
Published: over 9 years ago

10.1002/mbo3.727

Change in the intestinal bacterial community structure associated with environmental microorganisms during the growth of <i>Eriocheir sinensis</i>
Cited by: 25
Author(s): Chenhe Wang, Yanfeng Zhou, Dawei Lv, You Ge, Huan Li, You Yang
Software Mentions: 4
Published: almost 8 years ago

10.1002/mbo3.1200

Active microbial ecosystem in glacier basal ice fuelled by iron and silicate comminution‐derived hydrogen
Cited by: 2
Author(s): Mario Toubes-Rodrigo, Sanja Potgieter‐Vermaak, Robin Sen, Edda Sigurdís Oddsdóttir, David R. Elliott, Simon J. Cook
Software Mentions: 4
Published: about 5 years ago

10.1186/s40168-019-0721-7

Longitudinal investigation of the swine gut microbiome from birth to market reveals stage and growth performance associated bacteria
Cited by: 231
Author(s): Xiaofan Wang, Tsung Cheng Tsai, Feilong Deng, Xiaoyuan Wei, Jianmin Chai, J. S. Knapp, J. K. Apple, C. V. Maxwell, Jung Ae Lee, Ying Liu, Jiangchao Zhao
Software Mentions: 4
Published: about 7 years ago

10.1186/s40168-020-00827-8

Disentangling the mechanisms shaping the surface ocean microbiota
Cited by: 131
Author(s): Ramiro Logares, Ina Maria Deutschmann, Pedro C. Junger, Caterina R. Giner, Anders K. Krabberød, Thomas Sebastian Benedikt Schmidt, Laura Rubinat-Ripoll, Mireia Mestre, Guillem Salazar, Clara Ruiz‐González, Marta Sebastián, Colomban de Vargas, Silvia G. Acinas, Carlos M. Duarte, Josep M. Gasol, Ramón Massana
Software Mentions: 4
Published: over 6 years ago

10.1186/s40168-015-0089-2

Linear growth faltering in infants is associated with Acidaminococcus sp. and community-level changes in the gut microbiota
Cited by: 101
Author(s): Ethan Gough, David A. Stephens, Erica E. M. Moodie, Andrew J. Prendergast, Rebecca J. Stoltzfus, Jean H. Humphrey, Amee R. Manges
Software Mentions: 4
Published: over 11 years ago

10.1186/s40168-021-01016-x

Revealing taxon-specific heavy metal-resistance mechanisms in denitrifying phosphorus removal sludge using genome-centric metaproteomics
Cited by: 27
Author(s): Yuan Lin, Liye Wang, Ke Xu, Kan Li, Hongqiang Ren
Software Mentions: 4
Published: over 5 years ago

10.1186/s40168-020-00799-9

Rhizosphere protists are key determinants of plant health
Cited by: 123
Author(s): Wu Xiong, Yuqi Song, Kun Yang, Yian Gu, Zhong Wei, George A. Kowalchuk, Yangchun Xu, Alexandre Jousset, Qirong Shen, Stefan Geisen
Software Mentions: 4
Published: over 6 years ago

10.3390/microorganisms7120611

Elevation is Associated with Human Skin Microbiomes
Cited by: 16
Author(s): Huan Li, Yijie Wang, Qiaoling Yu, Tianshu Feng, Rui Zhou, Liye Shao, Jiapeng Qu, Nan Li, Tingbei Bo, Huakun Zhou
Software Mentions: 4
Published: almost 7 years ago

10.3390/microorganisms8111631

Rapid Changes in Microbial Community Structures along a Meandering River
Cited by: 11
Author(s): Perrine Cruaud, Adrien Vigneron, Caetano C. Dorea, Manuel J. Rodriguez, Steve J. Charette
Software Mentions: 4
Published: almost 6 years ago

10.3390/microorganisms8020190

Keystone Species and Modularity in Microbial Hydrocarbon Degradation Uncovered by Network Analysis and Association Rule Mining
Cited by: 5
Author(s): Florian Centler, Sarah Günnigmann, Ingo Fetzer, Annelie Wendeberg
Software Mentions: 4
Published: over 6 years ago

10.3390/microorganisms9030549

Lake Ecosystem Robustness and Resilience Inferred from a Climate-Stressed Protistan Plankton Network
Cited by: 16
Author(s): Dominik Forster, Zhishuai Qu, Gianna Pitsch, Estelle P. Bruni, Barbara Kammerlander, Thomas Pröschold, Bettina Sonntag, Thomas Posch, Thorsten Stoeck
Software Mentions: 4
Published: over 5 years ago

10.1016/j.mcpro.2021.100061

Protein Phosphorylation in Depolarized Synaptosomes: Dissecting Primary Effects of Calcium from Synaptic Vesicle Cycling
Cited by: 8
Author(s): Ivan Silbern, Kuan‐Ting Pan, Maksims Fiošins, Stefan Bonn, Silvio O. Rizzoli, Eugenio F. Fornasiero, Henning Urlaub, Reinhard Jahn
Software Mentions: 4
Published: over 5 years ago

10.3390/molecules24142529

High Impact: The Role of Promiscuous Binding Sites in Polypharmacology
Cited by: 8
Author(s): Natacha Cerisier, Michel Petitjean, Leslie Regad, Quentin Bayard, Manon Réau, Anne Badel, Anne-Claude Camproux
Software Mentions: 4
Published: about 7 years ago

10.3390/molecules15085354

Effects of Time Point Measurement on the Reconstruction of Gene Regulatory Networks
Cited by: 10
Author(s): Wenying Yan, Huangqiong Zhu, Yang Yang, Jiajia Chen, Yuanyuan Zhang, Bairong Shen
Software Mentions: 4
Published: about 16 years ago

10.1002/mgg3.214

Computational assessment of feature combinations for pathogenic variant prediction
Cited by: 12
Author(s): Eva König, Johannes Michael Rainer, Francisco S. Domingues
Software Mentions: 4
Published: over 10 years ago

10.1016/j.jvacx.2019.100019

Mapping the Dutch vaccination debate on Twitter: Identifying communities, narratives, and interactions
Cited by: 18
Author(s): Roel Lutkenhaus, Jeroen Jansz, Martine Bouman
Software Mentions: 4
Published: over 7 years ago

10.14202/vetworld.2018.1203-1209

An innovative approach to predict immune-associated genes mutually targeted by cow and human milk microRNAs expression profiles
Cited by: 6
Author(s): Kaj Chokeshaiusaha, Thanida Sananmuang, Denis Puthier, Catherine Nguyen
Software Mentions: 4
Published: about 8 years ago

10.3390/v12090931

Tracking Community Timing: Pattern and Determinants of Seasonality in Culicoides (Diptera: Ceratopogonidae) in Northern Florida
Cited by: 8
Author(s): Agustín Quaglia, Erik M. Blosser, Bethany L. McGregor, Alfred E. Runkel, Kristin E. Sloyer, Dinesh Erram, Samantha M. Wisely, Nathan D. Burkett‐Cadena
Software Mentions: 4
Published: about 6 years ago

10.3390/v13010063

Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological Conflicts
Cited by: 45
Author(s): Lakshminarayan M. Iyer, Vivek Anantharaman, Arunkumar Krishnan, A. Maxwell Burroughs, L. Aravind
Software Mentions: 4
Published: over 5 years ago

10.3390/pathogens9110903

Quantitative Risk Assessment for the Introduction of Bovine Leukemia Virus-Infected Cattle Using a Cattle Movement Network Analysis
Cited by: 6
Author(s): Kosuke Notsu, Anuwat Wiratsudakul, Shuya Mitoma, Hala El Daous, Chiho Kaneko, Heba M. El-Khaiat, Junzo Norimine, Satoshi Sekiguchi
Software Mentions: 4
Published: almost 6 years ago

10.7717/peerj.6994

RITAN: rapid integration of term annotation and network resources
Cited by: 15
Author(s): Michael T. Zimmermann, Brian Kabat, Diane E. Grill, Richard B. Kennedy, Gregory A. Poland
Software Mentions: 4
Published: about 7 years ago

10.7717/peerj.9691

Delimiting the boundaries of sesamoid identities under the network theory framework
Cited by: 4
Author(s): Gabriela Fontanarrosa, Jéssica Fratani, Miriam Corina Vera
Software Mentions: 4
Published: about 6 years ago

10.7717/peerj.9395

Doing nothing and what it looks like: inactivity in fattening cattle
Cited by: 8
Author(s): Sara Hintze, Freija Maulbetsch, Lucy Asher, Christoph Winckler
Software Mentions: 4
Published: about 6 years ago

10.7717/peerj.10594

Identification of hub genes and biological pathways in hepatocellular carcinoma by integrated bioinformatics analysis
Cited by: 6
Author(s): Qian Zhao, Yan Zhang, Shichun Shao, Yeqing Sun, Zhengkui Lin
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.10057

Brain hothubs and dark functional networks: correlation analysis between amplitude and connectivity for Broca’s aphasia
Cited by: 1
Author(s): Feng Lin, Sheue-yann Cheng, Dongqing Qi, Yu-Er Jiang, Qian-Qian Lyu, Lijuan Zhong, Zhongli Jiang
Software Mentions: 4
Published: almost 6 years ago

10.3390/ph14060553

Equine Mesenchymal Stem/Stromal Cells Freeze-Dried Secretome (Lyosecretome) for the Treatment of Musculoskeletal Diseases: Production Process Validation and Batch Release Test for Clinical Use
Cited by: 8
Author(s): Michela Mocchi, Stefano Grolli, Silvia Dotti, Dario Di Silvestre, Riccardo Villa, Priscilla Berni, Virna Conti, Giulia Passignani, Francesca Brambilla, Maurizio Del Bue, Laura Catenacci, Milena Sorrenti, Lorena Segale, Elia Bari, Pierluigi Mauri, Maria Luisa Torre, Sara Perteghella
Software Mentions: 4
Published: over 5 years ago

10.1098/rstb.2016.0095

Uncertain links in host–parasite networks: lessons for parasite transmission in a multi-host system
Cited by: 28
Author(s): Josephine G. Walker, Michaela Plein, Eric R. Morgan, Peter A. Vesk
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pcbi.1002223

Transcriptomic Coordination in the Human Metabolic Network Reveals Links between n-3 Fat Intake, Adipose Tissue Gene Expression and Metabolic Health
Cited by: 35
Author(s): Melissa J. Morine, Audrey C. Tierney, Ben van Ommen, Hannelore Daniel, Sinéad Toomey, Ingrid M.F. Gjelstad, Isobel Claire Gormley, Pablo Pérez-Martı́nez, Christian A. Drevon, José López‐Miranda, Helen M. Roche
Software Mentions: 4
Published: almost 15 years ago

10.1371/journal.pcbi.1008018

Visual perception of liquids: Insights from deep neural networks
Cited by: 11
Author(s): Jan Jaap R. van Assen, Shin’ya Nishida, Roland W. Fleming
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pcbi.1003808

SANTA: Quantifying the Functional Content of Molecular Networks
Cited by: 56
Author(s): Alex J. Cornish, Florian Markowetz
Software Mentions: 4
Published: about 12 years ago

10.1371/journal.pcbi.1002603

An Integrated Regulatory Network Reveals Pervasive Cross-Regulation among Transcription and Splicing Factors
Cited by: 15
Author(s): Idit Kosti, Predrag Radivojac, Yael Mandel-Gutfreund
Software Mentions: 4
Published: about 14 years ago

10.1371/journal.pone.0070551

The Discrimination Power of Structural SuperIndices
Cited by: 3
Author(s): Matthias Dehmer, Abbe Mowshowitz
Software Mentions: 4
Published: about 13 years ago

10.1371/journal.pone.0057780

Functional and Structural Neural Network Characterization of Serotonin Transporter Knockout Rats
Cited by: 15
Author(s): Kajo van der Marel, Judith R. Homberg, Willem M. Otte, Rick M. Dijkhuizen
Software Mentions: 4
Published: over 13 years ago

10.1371/journal.pone.0202063

Cross-species alcohol dependence-associated gene networks: Co-analysis of mouse brain gene expression and human genome-wide association data
Cited by: 11
Author(s): Kristin M. Mignogna, Silviu‐Alin Bacanu, Brien P. Riley, Aaron R. Wolen, Michael F. Miles
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0165987

Networks Depicting the Fine-Scale Co-Occurrences of Fungi in Soil Horizons
Cited by: 67
Author(s): Hirokazu Toju, Osamu Kishida, Noboru Katayama, Kentaro Takagi
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pone.0123082

Genomic Heterogeneity of Osteosarcoma - Shift from Single Candidates to Functional Modules
Cited by: 27
Author(s): Kathrin Poos, Jan Smida, Doris Maugg, Gertrud Eckstein, Daniel Baumhoer, Michaela Nathrath, Eberhard Korsching
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pone.0252471

Influence of number of individuals and observations per individual on a model of community structure
Cited by: 4
Author(s): Julia Sunga, Quinn M. R. Webber, Hugh G. Broders
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0211546

Factors influencing sedentary behaviour: A system based analysis using Bayesian networks within DEDIPAC
Cited by: 23
Author(s): Christoph Buck, Anne Loyen, Ronja Foraita, Jelle Van Cauwenberg, Marieke De Craemer, Ciarán MacDonncha, Jean‐Michel Oppert, Johannes Brug, Nanna Lien, Greet Cardon, Iris Pigeot, Sébastien Chastin
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0230941

Demarcating geographic regions using community detection in commuting networks with significant self-loops
Cited by: 14
Author(s): Mark He, Joseph Glasser, Nathaniel Pritchard, Shankar Bhamidi, Nikhil Kaza
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0194656

Social network cohesion in school classes promotes prosocial behavior
Cited by: 31
Author(s): Wouter van den Bos, Eveline A. Crone, Rosa Meuwese, Berna Güroğlu
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0028646

RegnANN: Reverse Engineering Gene Networks Using Artificial Neural Networks
Cited by: 10
Author(s): Marco Grimaldi, Roberto Visintainer, Giuseppe Jurman
Software Mentions: 4
Published: over 14 years ago

10.1371/journal.pone.0254852

Ward-level factors associated with methicillin-resistant Staphylococcus aureus acquisition–an electronic medical records study in Singapore
Cited by: 2
Author(s): Zaw Tun, Dale Fisher, Sharon Salmon, Clarence C. Tam
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0231832

Abundance, density, and social structure of African forest elephants (Loxodonta cyclotis) in a human-modified landscape in southwestern Gabon
Cited by: 4
Author(s): Colin M. Brand, Mireille Johnson, Lillian D. Parker, Jesús E. Maldonado, Lisa Körte, Hadrien Vanthomme, Alfonso Alonso, María José Ruiz‐López, Caitlin Wells, Nelson Ting
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0156807

Pyrosequencing Unveils Cystic Fibrosis Lung Microbiome Differences Associated with a Severe Lung Function Decline
Cited by: 23
Author(s): Giovanni Bacci, Patrizia Paganin, Loredana Lopez, Chiara Vanni, Claudia Dalmastri, Cristina Cantale, Loretta Daddiego, Gaetano Perrotta, Daniela Dolce, Patrizia Morelli, Vanessa Tuccio Guarna Assanti, A. De Alessandri, Ersilia Fiscarelli, Giovanni Taccetti, Vincenzina Lucidi, Annamaria Bevivino, Alessio Mengoni
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pone.0249839

A targeted e-learning approach for keeping universities open during the COVID-19 pandemic while reducing student physical interactions
Cited by: 19
Author(s): Sing Chen Yeo, Clin K Y Lai, Jacinda Tan, Joshua J. Gooley
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0122309

Module-Based Association Analysis for Omics Data with Network Structure
Cited by: 5
Author(s): Zhi Wang, Arnab Maity, Chuhsing Kate Hsiao, Deepak Voora, Rima Kaddurah‐Daouk, Jung Ying Tzeng
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pone.0123569

XomAnnotate: Analysis of Heterogeneous and Complex Exome- A Step towards Translational Medicine
Cited by: 5
Author(s): Asoke K. Talukder, Shashidhar Ravishankar, Krittika Sasmal, Santhosh Gandham, Jyothsna Prabhukumar, Prahalad Achutharao, Debmalya Barh, Francesco Blasi
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pone.0041370

Identification of Catalytic Residues Using a Novel Feature that Integrates the Microenvironment and Geometrical Location Properties of Residues
Cited by: 12
Author(s): Lei Han, Yongjun Zhang, Jiangning Song, Ming S. Liu, Ziding Zhang
Software Mentions: 4
Published: about 14 years ago

10.1371/journal.pone.0224197

A new resolution function to evaluate tree shape statistics
Cited by: 7
Author(s): Maryam Hayati, Bita Shadgar, Leonid Chindelevitch
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0246919

Tree rows in temperate agroforestry croplands alter the composition of soil bacterial communities
Cited by: 25
Author(s): Lukas Beule, Petr Karlovský
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0232681

Network analysis of regional livestock trade in West Africa
Cited by: 24
Author(s): Valerie C. Valerio, Olivier Walther, M. Eilittä, Brahima Cissé, Rachata Muneepeerakul, Gregory A. Kiker
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0222016

Impact of care provider network characteristics on patient outcomes: Usage of social network analysis and a multi-scale community detection
Cited by: 13
Author(s): Mina Ostovari, Denny Yu
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0160791

Natural Cubic Spline Regression Modeling Followed by Dynamic Network Reconstruction for the Identification of Radiation-Sensitivity Gene Association Networks from Time-Course Transcriptome Data
Cited by: 31
Author(s): Agata Michna, Herbert Braselmann, Martin Selmansberger, Anne Dietz, Julia Heß, Maria Gomolka, Sabine Hornhardt, Nils Blüthgen, Horst Zitzelsberger, Kristian Unger
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pone.0026605

Leaders Are More Attractive: Birds with Bigger Yellow Breast Patches Are Followed by More Group-Mates in Foraging Groups
Cited by: 20
Author(s): Zoltán Tóth, Matteo Griggio
Software Mentions: 4
Published: almost 15 years ago

10.1371/journal.pone.0107629

Tracking Difference in Gene Expression in a Time-Course Experiment Using Gene Set Enrichment Analysis
Cited by: 4
Author(s): Pui Shan Wong, Michihiro Tanaka, Yoshihiko Sunaga, Masayoshi Tanaka, Tadatsugu Taniguchi, Tomoko Yoshino, Tsuyoshi Tanaka, Wataru Fujibuchi, Sachiyo Aburatani
Software Mentions: 4
Published: almost 12 years ago

10.1371/journal.pone.0115092

Mapping Interdisciplinary Fields: Efficiencies, Gaps and Redundancies in HIV/AIDS Research
Cited by: 23
Author(s): Jeffrey M. Adams, Ryan Light
Software Mentions: 4
Published: almost 12 years ago

10.1371/journal.pone.0255323

Gut microbiota alterations in response to sleep length among African-origin adults
Cited by: 13
Author(s): Na Fei, Candice Choo-Kang, Sirimon Reutrakul, Stephanie J. Crowley, Dale E. Rae, Kweku Bedu-Addo, Jacob Plange‐Rhule, Terrence Forrester, Estelle V. Lambert, Pascal Bovet, Walter Riesen, Wolfgang Korte, Amy Luke, Brian T. Layden, Jack A. Gilbert, Lara R. Dugas
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0084642

Predicting the Vulnerability of Great Apes to Disease: The Role of Superspreaders and Their Potential Vaccination
Cited by: 19
Author(s): Charlotte Carne, Stuart Semple, Helen C. Morrogh‐Bernard, Klaus Zuberbühler, Julia Lehmann
Software Mentions: 4
Published: over 12 years ago

10.1371/journal.pone.0140577

How Many Parasites Species a Frog Might Have? Determinants of Parasite Diversity in South American Anurans
Cited by: 47
Author(s): Karla Magalhães Campião, Augusto Cesar de Aquino Ribas, Drausio Honório Morais, Reinaldo José da Silva, Luiz Eduardo Roland Tavares
Software Mentions: 4
Published: almost 11 years ago

10.1371/journal.pone.0102188

Large-Scale Structure of a Network of Co-Occurring MeSH Terms: Statistical Analysis of Macroscopic Properties
Cited by: 21
Author(s): Andrej Kastrin, Thomas C. Rindflesch, Dimitar Hristovski
Software Mentions: 4
Published: about 12 years ago

10.1371/journal.pone.0208720

Modular structure in fish co-occurrence networks: A comparison across spatial scales and grouping methodologies
Cited by: 9
Author(s): Daniel J. McGarvey, Joseph A. Veech
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pone.0231837

Effects of user behaviors on accumulation of social capital in an online social network
Cited by: 10
Author(s): Yuri Germanovich Rykov, Olessia Koltsova, Yadviga Sinyavskaya
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0214868

Reconstruction and inference of the Lactococcus lactis MG1363 gene co-expression network
Cited by: 5
Author(s): Jimmy Omony, Anne de Jong, Jan Kok, Sacha A. F. T. van Hijum
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0170293

Recent Themes in Social Networking Service Research
Cited by: 20
Author(s): John S. Liu, Mei Hsiu–Ching Ho, Louis Y. Y. Lu
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0197883

The regulatory ancestral network of surgical meshes
Cited by: 21
Author(s): Nasim Zargar, Andrew Carr
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pone.0245409

Social survival: Humpback whales (Megaptera novaeangliae) use social structure to partition ecological niches within proposed critical habitat
Cited by: 3
Author(s): Janie Wray, Eric M. Keen, Éadin O’Mahony
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0235690

Heatmap centrality: A new measure to identify super-spreader nodes in scale-free networks
Cited by: 10
Author(s): Christina Durón
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0019350

Deep Sequencing of Organ- and Stage-Specific microRNAs in the Evolutionarily Basal Insect Blattella germanica (L.) (Dictyoptera, Blattellidae)
Cited by: 82
Author(s): Alexandre S. Cristino, Erica D. Tanaka, Mercedes Rubio, María‐Dolors Piulachs, Xavier Bellés
Software Mentions: 4
Published: over 15 years ago

Projects: cran: igraph

Science Score: 100/100

Bonuses:

Papers Mentioning igraph 1,555