cran: igraph | Projects | Ecosyste.ms: Papers

10.1186/s12864-017-3777-4

Functional regression method for whole genome eQTL epistasis analysis with sequencing data
Cited by: 3
Author(s): Kelin Xu, Li Jin, Momiao Xiong
Software Mentions: 2
Published: over 9 years ago

Proximity patterns in water buffaloes' activities on pasture
Cited by: 0
Author(s): Eleni T. Tsiobani, M. D. Yiakoulaki, Nikolaos Hasanagas, Ioannis Antoniou
Software Mentions: 2
Published: almost 7 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: about 6 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: over 8 years ago

10.1371/journal.pone.0068927

Spatial Structures of the Environment and of Dispersal Impact Species Distribution in Competitive Metacommunities
Cited by: 21
Author(s): Dexiecuo Ai, Dominique Gravel, Chengjin Chu, Gang Wang
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0138148

Analysing Local Sparseness in the Macaque Brain Network
Cited by: 0
Author(s): R. V. Singh, Seema Nagar, Amit A. Nanavati
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0112821

Community Structure Detection for Overlapping Modules through Mathematical Programming in Protein Interaction Networks
Cited by: 17
Author(s): Laura Bennett, Aristotelis Kittas, Songsong Liu, Lazaros G. Papageorgiou, Sophia Tsoka
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0216784

Sexual network and detection of anogenital human papillomavirus in a community cohort of men who have sex with men in Taiwan
Cited by: 4
Author(s): Carol Strong, Yi Fang Yu, Huachun Zou, Wen Wei Ku, Chia Wen Lee, Nai Ying Ko
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-019-6302-0

A novel algorithm for alignment of multiple PPI networks based on simulated annealing
Cited by: 2
Author(s): Jialu Hu, Junhao He, Jing Li, Yiqun Gao, Yanyan Zheng, Xuequn Shang
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0198166

Novel genetic associations for blood pressure identified via gene-alcohol interaction in up to 570K individuals across multiple ancestries
Cited by: 83
Author(s): Mary F. Feitosa, Aldi T. Kraja, Daniel I. Chasman, Yun Ju Sung, Thomas W. Winkler, Ιωάννα Ντάλλα, Xiuqing Guo, Nora Franceschini, Ching‐Yu Cheng, Xueling Sim, Dina Vojinović, Jonathan Marten, Solomon K. Musani, Changwei Li, Amy R. Bentley, M. R. W. Brown, Karen Schwander, Melissa A. Richard, Raymond Noordam, Hugues Aschard, Traci M. Bartz, Lawrence F. Bielak, Rajkumar Dorajoo, Virginia Fisher, Fernando Pires Hartwig, Andrea R V R Horimoto, Kurt Lohman, Alisa K. Manning, Tuomo Rankinen, Albert V. Smith, Salman M. Tajuddin, Mary K. Wojczynski, Maris Alver, Mathilde Boissel, Qiuyin Cai, Archie Campbell, Jin Chai, Xu Chen, Jasmin Divers, Chuan Gao, Anuj Goel, Yanick Hagemeijer, Sarah E. Harris, Meian He, Fang Chi Hsu, Anne Jackson, Mika Kähönen, Anuradhani Kasturiratne, Pirjo Komulainen, Brigitte Kühnel, Federica Laguzzi, Jian’an Luan, Nana Matoba, Ilja M. Nolte, Sandosh Padmanabhan, Muhammad Riaz, Rico Rueedi, Antonietta Robino, M. Abdullah Said, Robert A. Scott, Tamar Sofer, Alena Stančáková, Fumihiko Takeuchi, Bamidele O. Tayo, Peter J. van der Most, Tibor V. Varga, Véronique Vitart, Yajuan Wang, Erin B. Ware, Helen R. Warren, Stefan Weiß, Wanqing Wen, Lisa R. Yanek, Weihua Zhang, Jing Hua Zhao, Saima Afaq, Najaf Amin, Marzyeh Amini, Dan E. Arking, Tin Aung, Eric Boerwinkle, Ingrid B. Borecki, Ulrich Broeckel, Morris J. Brown, Marco Brumat, Gregory L. Burke, Mickaël Canouil, Aravinda Chakravarti, Charumathi Sabanayagam, Yii Der Ida Chen, John Connell, Adolfo Correa, Lisa de las Fuentes, Renée de Mutsert, H. Janaka De Silva, Xuan Deng, Jingzhong Ding, Qing Duan, Charles B. Eaton, Georg Ehret, Ruben N. Eppinga, Εvangelos Εvangelou, Jessica D. Faul, Stephan B. Felix, Nita G. Forouhi, Terrence Forrester, Oscar H. Franco, Yechiel Friedlander, Ilaria Gandin, He Gao, Mohsen Ghanbari, Bruna Gigante, C. Charles Gu, Dongfeng Gu, Saskia Hagenaars, Göran Hallmans, Tamara B. Harris, Jiang He, Sami Heikkinen, Chew Kiat Heng, Makoto Hirata, Barbara V. Howard, M. Arfan Ikram, Ulrich John, Tomohiro Katsuya, Chiea Chuen Khor, Tuomas O. Kilpeläinen, Woon Puay Koh, José Eduardo Krieger, Stephen B. Kritchevsky, Michiaki Kubo, Johanna Kuusisto, Timo A. Lakka, Carl D. Langefeld, Claudia Langenberg, Lenore J. Launer, Benjamin Lehne, Cora E. Lewis, Yize Li, Shiow J. Lin, Jianjun Li, Jingmin Liu, Marie Loh, Tin Louie, Reedik Mägi, Colin A. McKenzie, Thomas Meitinger, Andres Metspalu, Yuri Milaneschi, Lili Milani, Karen L. Mohlke, Yukihide Momozawa, Mike A. Nalls, Christopher P. Nelson, Nona Sotoodehnia, Jill M. Norris, Jeff O’Connell, Thomas T. Perls, Nancy L. Pedersen, Annette Peters, Patricia A. Peyser, Neil Poulter, Leslie J. Raffel, Olli T. Raitakari, Kathryn Roll, Lynda M. Rose, Frits R. Rosendaal, Jerome I. Rotter, Carsten Oliver Schmidt, Pamela J. Schreiner, Nicole Schupf, William R. Scott, Peter Sever, Yuan Shi, Stephen Sidney, Mario Sims, Colleen M. Sitlani, Jennifer A. Smith, Harold Snieder, John M. Starr, Konstantin Strauch, Heather M. Stringham, Nicholas Tan, Hua Tang, Kent D. Taylor, Yik Ying Teo, Yih Chung Tham, Stephen T. Turner, André G. Uitterlinden, Péter Vollenweider, Mélanie Waldenberger, Lihua Wang, Ya Xing Wang, Wen Bin Wei, Christine A. Williams, Jie Yao, Caizheng Yu, Jian Min Yuan, Wei Zhao, Alan B. Zonderman, Diane M. Becker, Michael Boehnke, Donald W. Bowden, John C. Chambers, Ian J. Deary, Tõnu Esko, Martin Farrall, Paul W. Franks, Barry I. Freedman, Philippe Froguel, Paolo Gasparini, Christian Gieger, Jost B. Jonas, Yoichiro Kamatani, Norihiro Kato, Jaspal S. Kooner, Zoltán Kutalik, Markku Laakso, Cathy C. Laurie, Karin Leander, Terho Lehtimäki, Patrik K. E. Magnusson, Albertine J. Oldehinkel, Brenda W. J. H. Penninx, Ozren Polašek, David J. Porteous, Rainer Rauramaa, Nilesh J. Samani, James G. Scott, Xiao Ou Shu, Pim van der Harst, Lynne E. Wagenknecht, Nicholas J. Wareham, Hugh Watkins, David R. Weir, Ananda R. Wickremasinghe, Tangchun Wu, Wei Zheng, Claude Bouchard, Kaare Christensen, Michele K. Evans, Vilmundur Gudnason, Bernardo Lessa Horta, Sharon L.R. Kardia, Yongmei Liu, Alexandre C. Pereira, Bruce M. Psaty, Paul M. Ridker, Rob M. van Dam, W. James Gauderman, Xiaofeng Zhu, Dennis O. Mook‐Kanamori, Myriam Fornage, Charles N. Rotimi, L. Adrienne Cupples, Tanika N. Kelly, Ervin R. Fox, Caroline Hayward, Cornelia M. van Duijn, E. Shyong Tai, Tien Yin Wong, Charles Kooperberg, Walter Palmas, Kenneth Rice, Alanna C. Morrison, Paul Elliott, Mark J. Caulfield, Patricia B. Munroe, D. C. Rao, Michael A. Province, Daniel Levy
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2164-13-438

Exploration of the core metabolism of symbiotic bacteria
Cited by: 12
Author(s): Cecília C. Klein, Ludovic Cottret, Janice Kielbassa, Hubert Charles, Christian Gautier, Ana Tereza Ribeiro de Vasconcelos, Vincent Lacroix, Marie‐France Sagot
Software Mentions: 2
Published: almost 15 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.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: over 9 years ago

10.7717/peerj.3321

Ranking of critical species to preserve the functionality of mutualistic networks using the <i>k</i>-core decomposition
Cited by: 14
Author(s): Javier García-Algarra, M. Pastor, José María Iriondo, Javier Galeano
Software Mentions: 2
Published: over 9 years ago

10.1186/1752-0509-8-48

Historical contingency and the gradual evolution of metabolic properties in central carbon and genome-scale metabolisms
Cited by: 10
Author(s): Aditya Barve, Sayed-Rzgar Hosseini, Olivier Martin, Andreas Wagner
Software Mentions: 2
Published: over 12 years ago

10.1016/j.heliyon.2020.e05069

Animating inter-organisational resilience communication: A participatory social network analysis of water governance in the UK
Cited by: 6
Author(s): Sarah Ward, Fanlin Meng, Sarah Bunney, Kegong Diao, David Butler
Software Mentions: 2
Published: about 6 years ago

10.1093/gigascience/giaa019

Comparative proteomics analysis of Tibetan hull-less barley under osmotic stress via data-independent acquisition mass spectrometry
Cited by: 17
Author(s): Yulin Wang, Zha Sang, Shaohang Xu, Qijun Xu, Xingquan Zeng, Dunzhu Jabu, Hongjun Yuan
Software Mentions: 2
Published: over 6 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: about 10 years ago

10.1186/s12917-016-0835-0

Emergence of Brucella suis in dogs in New South Wales, Australia: clinical findings and implications for zoonotic transmission
Cited by: 35
Author(s): Siobhan M. Mor, Anke Wiethoelter, Amanda Lee, Barbara Moloney, Daniel James, Richard Malík
Software Mentions: 2
Published: about 10 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: almost 9 years ago

10.1371/journal.pone.0016932

Novel Feature for Catalytic Protein Residues Reflecting Interactions with Other Residues
Cited by: 11
Author(s): Yizhou Li, Gongbing Li, Zhining Wen, Hui Yin, Manman Hu, Jiamin Xiao, Menglong Li
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0160919

Anomaly Detection in Host Signaling Pathways for the Early Prognosis of Acute Infection
Cited by: 12
Author(s): Kun Wang, Stanley Langevin, Corey S. O’Hern, Mark D. Shattuck, Serenity Ogle, Adriana Forero, Juliet Morrison, Richard A. Slayden, Michael G. Katze, Michael Kirby
Software Mentions: 2
Published: about 10 years ago

10.1186/s12933-021-01349-9

A molecular signature for the metabolic syndrome by urine metabolomics
Cited by: 21
Author(s): Chiara Bruzzone, Rubén Gil‐Redondo, Marisa Seco, Rocío Barragán, Laura de la Cruz, Claire Cannet, Hartmut Schäfer, Fang Fang, Tammo Diercks, Maider Bizkarguenaga, Beatriz González-Valle, Ana Laín, Arantza Sanz-Parra, Óscar Coltell, Ander López de Letona, Manfred Spraul, Shelly C. Lu, Elisabetta Buguianesi, Nieves Embade, Quentin M. Anstee, Dolores Corella, José M. Mato, Óscar Millet
Software Mentions: 2
Published: over 5 years ago

10.3390/pathogens10080922

Transmission Dynamics of Bovine Viral Diarrhea Virus in Hokkaido, Japan by Phylogenetic and Epidemiological Network Approaches
Cited by: 3
Author(s): Shizuka Hirose, Kosuke Notsu, Satoshi Itō, Yoshihiro Sakoda, Norikazu Isoda
Software Mentions: 2
Published: over 5 years ago

10.1098/rspb.2015.2359

The social and ecological costs of an ‘over-extended' phenotype
Cited by: 22
Author(s): Lyndon Alexander Jordan, Sean M. Maguire, Hans A. Hofmann, Masanori Kohda
Software Mentions: 2
Published: almost 11 years ago

10.1155/2009/182689

Network Properties for Ranking Predicted miRNA Targets in Breast Cancer
Cited by: 4
Author(s): Jörg Linde, Björn Olsson, Zelmina Lubovac
Software Mentions: 2
Published: over 17 years ago

10.1186/s12917-017-1103-7

Descriptive and network analyses of the equine contact network at an equestrian show in Ontario, Canada and implications for disease spread
Cited by: 8
Author(s): Kelsey L. Spence, Terri L. O’Sullivan, Zvonimir Poljak, Amy L. Greer
Software Mentions: 2
Published: over 9 years ago

10.3390/v4123625

A Systems Biology Starter Kit for Arenaviruses
Cited by: 0
Author(s): Magali E. Droniou-Bonzom, Paula M. Cannon
Software Mentions: 2
Published: almost 14 years ago

10.1186/s12864-016-2364-4

Pangenome-wide and molecular evolution analyses of the Pseudomonas aeruginosa species
Cited by: 72
Author(s): Jeanneth Mosquera-Rendón, Ana Mercedes Rada, Sonia Cárdenas-Brito, Mauricio Corredor, Eliana Restrepo-Pineda, Alfonso Benı́tez-Páez
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0158161

How to Study the City on Instagram
Cited by: 54
Author(s): John D. Boy, Justus Uitermark
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0200079

Urothelial bladder cancer may suppress perforin expression in CD8+ T cells by an ICAM-1/TGFβ2 mediated pathway
Cited by: 14
Author(s): Ciputra Adijaya Hartana, Emma Ahlén Bergman, Ali Zirakzadeh, David H. Krantz, Malin E. Winerdal, Max Winerdal, Markus Johansson, Farhood Alamdari, Tomasz Jakubczyk, Hans Glise, Katrine Riklund, Amir Sherif, Ola Winqvist
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0007441

Stability of Metabolic Correlations under Changing Environmental Conditions in Escherichia coli – A Systems Approach
Cited by: 34
Author(s): Jędrzej Szymański, Szymon Józefczuk, Zoran Nikoloski, Joachim Selbig, Victoria J. Nikiforova, Gareth Catchpole, Lothar Willmitzer
Software Mentions: 2
Published: about 17 years ago

10.1371/journal.pone.0237471

Diffusing science through social networks: The case of breastfeeding communication on Twitter
Cited by: 9
Author(s): Sara Moukarzel, Martin Rehm, Miguel del Fresno, Alan J. Daly
Software Mentions: 2
Published: about 6 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

10.1186/1471-2164-11-380

Response of the mosquito protein interaction network to dengue infection
Cited by: 44
Author(s): Xiang Guo, Yao–Zhong Xu, Guowu Bian, Andrew Pike, Yan Xie, Zhiyong Xi
Software Mentions: 2
Published: over 16 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

10.1371/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.pone.0161474

BRIDES: A New Fast Algorithm and Software for Characterizing Evolving Similarity Networks Using Breakthroughs, Roadblocks, Impasses, Detours, Equals and Shortcuts
Cited by: 4
Author(s): Étienne Lord, Margaux Le Cam, Éric Bapteste, Raphaël Méheust, Vladimir Makarenkov, François‐Joseph Lapointe
Software Mentions: 2
Published: about 10 years ago

10.1186/1471-2164-16-S7-S18

Systems analysis of gene ontology and biological pathways involved in post-myocardial infarction responses
Cited by: 10
Author(s): Nguyen T. Nguyen, Merry L. Lindsey, Yu Jin
Software Mentions: 2
Published: over 11 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: about 11 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: almost 7 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: over 6 years ago

10.1371/journal.pone.0213741

Movements of scalloped hammerhead sharks (Sphyrna lewini) at Cocos Island, Costa Rica and between oceanic islands in the Eastern Tropical Pacific
Cited by: 37
Author(s): Elena Nalesso, Alex Hearn, Óscar Sosa-Nishizaki, Todd Steiner, Alex Antoniou, Andrew Reid, Sandra Bessudo, Germán Soler, A. Peter Klimley, Frida Lara, James T. Ketchum, Rándall Arauz
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-018-4959-4

Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures
Cited by: 85
Author(s): Matej Medvecký, Darina Čejková, Ondřej Polanský, Daniela Karasova, Tereza Kubasová, Alois Čížek, Ivan Rychlı́k
Software Mentions: 2
Published: over 8 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: almost 7 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

10.1371/journal.pone.0121002

Fast Approximate Quadratic Programming for Graph Matching
Cited by: 115
Author(s): Joshua T. Vogelstein, John M. Conroy, Vince Lyzinski, Louis J. Podrazik, Steven G. Kratzer, Eric T. Harley, Donniell E. Fishkind, R. Jacob Vogelstein, Carey E. Priebe
Software Mentions: 2
Published: over 11 years ago

10.3390/pathogens9121077

Analysis of Risk Factors for African Swine Fever in Lombardy to Identify Pig Holdings and Areas Most at Risk of Introduction in Order to Plan Preventive Measures
Cited by: 2
Author(s): Silvia Bellini, Alessandra Scaburri, Marco Tironi, Stefania Calò
Software Mentions: 2
Published: almost 6 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: about 8 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: about 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.pone.0241453

Keystone actors do not act alone: A business ecosystem perspective on sustainability in the global clothing industry
Cited by: 16
Author(s): Jacob Hileman, Ivan Simon Kallstenius, Tiina Häyhä, Celinda Palm, Sarah Cornell
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0170817

Trends of the World Input and Output Network of Global Trade
Cited by: 24
Author(s): R. Maria del Rio-Chanona, Jelena Grujić, Henrik Jeldtoft Jensen
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0223779

Inhibitory interaction networks among coevolved Streptomyces populations from prairie soils
Cited by: 5
Author(s): Daniel Schlatter, Zewei Song, Patricia Vaz-Jauri, Linda L. Kinkel
Software Mentions: 2
Published: about 7 years ago

10.1098/rspb.2019.0681

Hierarchical social modularity in gorillas
Cited by: 28
Author(s): Robin E. Morrison, Milou Groenenberg, Thomas Breuer, Marie L. Manguette, Peter Walsh
Software Mentions: 2
Published: over 7 years ago

10.1186/s12961-021-00774-2

Collaboration on evidence synthesis in Africa: a network study of growing research capacity
Cited by: 2
Author(s): Jiluan Pan, Yongqi Zhong, Sarah Young, Nynke M. D. Niezink
Software Mentions: 2
Published: about 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: about 8 years ago

10.3390/microorganisms6040101

A Metabolomic-Based Evaluation of the Role of Commensal Microbiota throughout the Gastrointestinal Tract in Mice
Cited by: 20
Author(s): Yurie Yamamoto, Yumiko Nakanishi, S. Murakami, Wanping Aw, Tomoya Tsukimi, Ryoko Nozu, Masaki Ueno, Kyoji Hioki, Kenji Nakahigashi, Akiyoshi Hirayama, Masahiro Sugimoto, Tomoyoshi Soga, Mamoru Ito, Masaru Tomita, Shinji Fukuda
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0033799

Hierarchy Measure for Complex Networks
Cited by: 193
Author(s): Enys Mones, Lilla Vicsek, Tamás Vicsek
Software Mentions: 2
Published: over 14 years ago

10.1186/1746-6148-9-198

The performance of approximations of farm contiguity compared to contiguity defined using detailed geographical information in two sample areas in Scotland: implications for foot-and-mouth disease modelling
Cited by: 13
Author(s): Jessica Flood, Thibaud Porphyre, Michael J. Tildesley, Mark E. J. Woolhouse
Software Mentions: 2
Published: almost 14 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: almost 11 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: over 7 years ago

10.1093/biosci/biv122

Ecological Networks in Stored Grain: Key Postharvest Nodes for Emerging Pests, Pathogens, and Mycotoxins
Cited by: 67
Author(s): John Fredy Hernández Nopsa, Gregory J. Daglish, David W. Hagstrum, John F. Leslie, Thomas W. Phillips, Caterina Scoglio, Sara Thomas-Sharma, Gimme H. Walter, Karen A. Garrett
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0112775

Time Development in the Early History of Social Networks: Link Stabilization, Group Dynamics, and Segregation
Cited by: 17
Author(s): Jesper Bruun, I. G. Bearden
Software Mentions: 2
Published: almost 12 years ago

10.1186/2042-5783-2-8

Analysis of evolutionary patterns of genes in Campylobacter jejuni and C. coli
Cited by: 8
Author(s): Lars Snipen, Trudy M. Wassenaar, Eric Altermann, Jonathan W. Olson, Sophia Kathariou, Karin Lagesen, Mónica Takamiya, Susanne Knøchel, David W. Ussery, Richard J. Meinersmann
Software Mentions: 2
Published: about 14 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: almost 11 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

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.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: about 13 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

10.1038/s41416-020-01257-x

Comparative analysis of drug response and gene profiling of HER2-targeted tyrosine kinase inhibitors
Cited by: 27
Author(s): Neil T. Conlon, Jeffrey J. Kooijman, Suzanne J.C. van Gerwen, Winfried R. Mulder, Guido J.R. Zaman, Irmina Diala, Lisa DeFazio-Eli, Alshad S. Lalani, John Crown, Denis M. Collins
Software Mentions: 2
Published: almost 6 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

10.3389/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: about 5 years ago

10.1186/s12862-019-1446-8

Host specialisation and disparate evolution of Pyrenophora teres f. teres on barley and barley grass
Cited by: 7
Author(s): Celeste C. Linde, Leon M. Smith
Software Mentions: 2
Published: over 7 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: about 11 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

10.1371/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

10.3389/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: over 5 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: over 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: about 8 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: about 8 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.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: about 15 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: over 8 years ago

10.1111/hex.13130

A skills network approach to physicians’ competence in shared decision making
Cited by: 4
Author(s): Levente Kriston, Pola Hahlweg, Martin Härter, Isabelle Scholl
Software Mentions: 2
Published: about 6 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: over 15 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: about 8 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: over 9 years ago

10.3390/microorganisms7120586

Root-Associated Fungal Communities in Two Populations of the Fully Mycoheterotrophic Plant Arachnitis uniflora Phil. (Corsiaceae) in Southern Chile
Cited by: 12
Author(s): Héctor Herrera, Javiera Soto, Luz E. de Bashan, Inmaculada Sampedro, César Arriagada
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pcbi.1006888

Predicting synthetic lethal interactions using conserved patterns in protein interaction networks
Cited by: 29
Author(s): Graeme Benstead-Hume, Xiangrong Chen, Suzanna R. Hopkins, Karen A. Lane, Jessica A. Downs, Frances M. G. Pearl
Software Mentions: 2
Published: over 7 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: almost 12 years ago

10.7717/peerj.8749

Potential of the economic valuation of soil-based ecosystem services to inform sustainable soil management and policy
Cited by: 20
Author(s): Bartosz Bartkowski, Stephan Bartke, Katharina Helming, Carsten Paul, Anja-Kristina Techen, Bernd Hansjürgens
Software Mentions: 2
Published: over 6 years ago

10.1099/mgen.0.000203

Extended-spectrum β-lactamase-encoding genes are spreading on a wide range of Escherichia coli plasmids existing prior to the use of third-generation cephalosporins
Cited by: 25
Author(s): Catherine Branger, Alice Ledda, Typhaine Billard-Pomarès, Benoît Doublet, Stéphanie Fouteau, Valérie Barbe, David Roche, Stéphane Cruveiller, Claudine Médigue, Miguel Sautié Castellanos, Dominique Decré, Laurence Drieux-Rouze, Olivier Clermont, Jérémy Glodt, Olivier Tenaillon, Axel Cloeckaert, Guillaume Arlet, Erick Denamur
Software Mentions: 2
Published: about 8 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

10.1371/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: about 6 years ago

10.1186/1475-2875-12-397

The demographics of human and malaria movement and migration patterns in East Africa
Cited by: 56
Author(s): Deepa Pindolia, Andrés J. García, Zhengjing Huang, David L. Smith, Victor A. Alegana, Abdisalan M. Noor, Robert W. Snow, Andrew J. Tatem
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pcbi.1003549

Within-Host Bacterial Diversity Hinders Accurate Reconstruction of Transmission Networks from Genomic Distance Data
Cited by: 146
Author(s): Colin J. Worby, Marc Lipsitch, William P. Hanage
Software Mentions: 2
Published: over 12 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: over 9 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: over 14 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

Projects: cran: igraph

Science Score: 100/100

Bonuses:

Papers Mentioning igraph 1,555