cran: igraph | Projects | Ecosyste.ms: Papers

10.1101/2020.09.16.20196154

SARS-CoV-2 antibody signatures robustly predict diverse antiviral functions relevant for convalescent plasma therapy
Cited by: 20
Author(s): Harini Natarajan, Andrew R. Crowley, Savannah E. Butler, Shiwei Xu, Joshua A. Weiner, Evan M. Bloch, Kirsten Littlefield, Wendy Wieland-Alter, Ruth I. Connor, Peter F. Wright, Sarah E. Benner, Tania S. Bonny, Oliver Laeyendecker, David J. Sullivan, Shmuel Shoham, Thomas C. Quinn, H. Benjamin Larman, Arturo Casadevall, Andrew Pekosz, Andrew D. Redd, Aaron A.R. Tobian, Margaret E. Ackerman
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41598-020-69494-x

Immune network dysregulation precedes clinical diagnosis of asthma
Cited by: 3
Author(s): Yi-Shin Chang, Benjamin A. Turturice, Cody Schott, Patricia W. Finn, David L. Perkins
Software Mentions: 5
Published: about 6 years ago

10.1186/s12866-020-01938-w

A comprehensive analysis of the microbiota composition and gene expression in colorectal cancer
Cited by: 15
Author(s): Qian Zhang, Huan Zhao, Dedong Wu, D Y Cao, Wei Ma
Software Mentions: 5
Published: almost 6 years ago

10.1007/s00265-015-2050-6

Sex and friendship in a multilevel society: behavioural patterns and associations between female and male Guinea baboons
Cited by: 51
Author(s): Adeelia S. Goffe, Dietmar Zinner, Julia Fischer
Software Mentions: 5
Published: over 10 years ago

10.1128/mSystems.00477-21

Comprehensive Cultivation of the Swine Gut Microbiome Reveals High Bacterial Diversity and Guides Bacterial Isolation in Pigs
Cited by: 11
Author(s): Xiaofan Wang, Samantha Howe, Xiaoyuan Wei, Feilong Deng, Tsung‐Ting Tsai, Jianmin Chai, Yingping Xiao, Hua Yang, C. V. Maxwell, Ying Li, Jiangchao Zhao
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-018-33276-3

Mutation pattern analysis reveals polygenic mini-drivers associated with relapse after surgery in lung adenocarcinoma
Cited by: 5
Author(s): Laura Bennett, Mary Howell, Danish Memon, Chris Smowton, Cong Zhou, Crispin Miller
Software Mentions: 5
Published: almost 8 years ago

10.1038/s41598-018-26484-4

Network-guided genomic and metagenomic analysis of the faecal microbiota of the critically endangered kakapo
Cited by: 11
Author(s): David W. Waite, Melissa Dsouza, Yuji Sekiguchi, Philip Hugenholtz, Michael W. Taylor
Software Mentions: 5
Published: over 8 years ago

10.1093/bioinformatics/btx139

Estimating gene regulatory networks with pandaR
Cited by: 15
Author(s): Daniel Schlauch, Joseph N. Paulson, A. E. Young, Kimberly Glass, John Quackenbush
Software Mentions: 5
Published: over 9 years ago

10.1186/s12866-021-02114-4

Genomic islands mediate environmental adaptation and the spread of antibiotic resistance in multiresistant Enterococci - evidence from genomic sequences
Cited by: 13
Author(s): Weiwei Li, Ailan Wang
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-018-21874-0

Degradation shaped bacterial and archaeal communities with predictable taxa and their association patterns in Zoige wetland at Tibet plateau
Cited by: 40
Author(s): Yunfu Gu, Yan Bai, Quanju Xiang, Xiumei Yu, Ke Zhao, Xiaoping Zhang, Chaonan Li, Songqin Liu, Qiang Chen
Software Mentions: 5
Published: over 8 years ago

10.1038/s41598-018-21988-5

Continental-scale animal tracking reveals functional movement classes across marine taxa
Cited by: 39
Author(s): Stephanie Brodie, Elodie J. I. Lédée, Michelle R. Heupel, Russell C. Babcock, Hamish A. Campbell, Daniel C. Gledhill, Xavier Hoenner, Charlie Huveneers, Fabrice R. A. Jaine, Colin A. Simpfendorfer, Matthew D. Taylor, Vinay Udyawer, Robert Harcourt
Software Mentions: 5
Published: over 8 years ago

10.1038/s41598-020-71309-y

Effects of environmental factors on microbiota of fruits and soil of Coffea arabica in Brazil
Cited by: 25
Author(s): Tomás Gomes Reis Veloso, Marliane de Cássia Soares da Silva, Wilton Soares Cardoso, Rogério Carvalho Guarçoni, Maria Catarina Megumi Kasuya, Lucas Louzada Pereira
Software Mentions: 5
Published: about 6 years ago

10.1038/s41598-018-21118-1

The utility of a network–based clustering method for dimension reduction of imaging and non-imaging biomarkers predictive of Alzheimer’s disease
Cited by: 2
Author(s): Haruhiko Yoshida, Atsushı Kawaguchi, Fumio Yamashita, Kazuhiko Tsuruya
Software Mentions: 5
Published: over 8 years ago

10.1038/s41598-021-81447-6

Acetyl-CoA flux from the cytosol to the ER regulates engagement and quality of the secretory pathway
Cited by: 16
Author(s): Inca A. Dieterich, Yusi Cui, Megan M. Braun, Alexis J. Lawton, Nicklaus H. Robinson, Jennifer L. Peotter, Qing Yu, Jason C. Casler, Benjamin S. Glick, Anjon Audhya, John M. Denu, Lingjun Li, Luigi Puglielli
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-021-85061-4

Gene co-expression network analysis in human spinal cord highlights mechanisms underlying amyotrophic lateral sclerosis susceptibility
Cited by: 12
Author(s): Jerry C. Wang, Gokul Ramaswami, Daniel H. Geschwind
Software Mentions: 5
Published: over 5 years ago

10.3389/fimmu.2019.01463

Contrasting Gene Expression Profiles of Monocytes and Lymphocytes From Peste-Des-Petits-Ruminants Virus Infected Goats
Cited by: 17
Author(s): Sajad A. Wani, Anamika Sahu, Raja Ishaq Nabi Khan, Awadh Bihari Pandey, Shikha Saxena, Neelima Hosamani, Waseem Akram Malla, Dheeraj Chaudhary, Sonam Kanchan, V. K. Sah, Kaushal Kishor Rajak, D. Muthuchelvan, Bina Mishra, Ashok Kumar Tiwari, Aditya Prasad Sahoo, Basavaraj Sajjanar, Yash Pal Singh, Ravi Kumar Gandham, Bishnu Prasad Mishra, Raj Kumar Singh
Software Mentions: 5
Published: about 7 years ago

10.1042/BSR20191547

Transcriptome profiling of digital flexor tendons after injury in a chicken model
Cited by: 1
Author(s): Wenfei Mao, Yancun Yu, Chen Chen, Ya Fang Wu
Software Mentions: 5
Published: over 6 years ago

10.1186/s12859-021-04112-9

NoRCE: non-coding RNA sets cis enrichment tool
Cited by: 4
Author(s): Gülden Olgun, Afshan Nabi, Öznur Taştan
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-021-86544-0

An R package for generic modular response analysis and its application to estrogen and retinoic acid receptor crosstalk
Cited by: 5
Author(s): Gabriel Jiménez-Domínguez, Patrice Ravel, Stéphan Jalaguier, Vincent Cavaillès, Jacques Colinge
Software Mentions: 5
Published: over 5 years ago

10.1038/srep37646

Exploring the molecular basis of age-related disease comorbidities using a multi-omics graphical model
Cited by: 45
Author(s): Jonas Zierer, Tess Pallister, Pei-Chien Tsai, Jan Krumsiek, Jordana T. Bell, Gordan Lauc, Tim D. Spector, Cristina Menni, Gabi Kastenmüller
Software Mentions: 5
Published: almost 10 years ago

10.1038/srep37473

Hydrocarbon degraders establish at the costs of microbial richness, abundance and keystone taxa after crude oil contamination in permafrost environments
Cited by: 55
Author(s): Shuai Yang, Wen Xi, Yulan Shi, Susanne Liebner, Huijun Jin, Amedea Perfumo
Software Mentions: 5
Published: almost 10 years ago

10.1038/srep29647

Tracking Cancer Genetic Evolution using OncoTrack
Cited by: 4
Author(s): Asoke K. Talukder, Mahima Agarwal, Kenneth H. Buetow, Patrice Denèfle
Software Mentions: 5
Published: about 10 years ago

10.1097/MD.0000000000016477

Comparative effectiveness of different forms of traditional Chinese medicine for treatment of post-stroke depression
Cited by: 4
Author(s): Huiling Chen, Meidan Zhao, Xiuming Li, Yanhong Zhang, Hui Yu, Ergang Xiao, Weizhen Gao, Hongwu Wang
Software Mentions: 5
Published: about 7 years ago

10.1038/srep28730

Dispersal similarly shapes both population genetics and community patterns in the marine realm
Cited by: 41
Author(s): Guillem Chust, Ernesto Villarino, Anne Chenuil, Xabier Irigoien, Nihayet Bizsel, Antonio Bode, Cecilie Broms, S. Claus, María Luz Fernández de Puelles, S. Fonda-Umani, Galice Hoarau, Maria Grazia Mazzocchi, Patricija Mozetič, L. Vandepitte, Helena Veríssimo, Soultana Zervoudaki, Ángel Borja
Software Mentions: 5
Published: about 10 years ago

10.1007/s11306-015-0927-z

GC–MS metabolic profiling of Cabernet Sauvignon and Merlot cultivars during grapevine berry development and network analysis reveals a stage- and cultivar-dependent connectivity of primary metabolites
Cited by: 51
Author(s): Álvaro Cuadros-Inostroza, Simón Ruíz-Lara, Enrique González, Änne Eckardt, Lothar Willmitzer, Hugo Peña‐Cortés
Software Mentions: 5
Published: over 10 years ago

10.1038/srep10361

Interactions between tick and transmitted pathogens evolved to minimise competition through nested and coherent networks
Cited by: 57
Author(s): Agustı́n Estrada-Peña, José de la Fuente, Richard S. Ostfeld, Alejandro Cabezas-Cruz
Software Mentions: 5
Published: over 11 years ago

10.1007/s00248-020-01657-9

Identifying Potential Hosts of Short-Branch Microsporidia
Cited by: 3
Author(s): Annemie Doliwa, Micah Dunthorn, Erika Rassoshanska, Frédéric Mahe, David Bass, Camila Duarte Ritter
Software Mentions: 5
Published: over 5 years ago

10.1186/s12864-017-4007-9

Equine skeletal muscle adaptations to exercise and training: evidence of differential regulation of autophagosomal and mitochondrial components
Cited by: 28
Author(s): Kenneth Bryan, Beatrice A. McGivney, Gabriella Farries, Paul A. McGettigan, C. L. McGivney, K. F. Gough, David E. MacHugh, Lisa Katz, Emmeline W. Hill
Software Mentions: 5
Published: about 9 years ago

10.1264/jsme2.ME20153

Inoculation of Mimosa Pudica with Paraburkholderia phymatum Results in Changes to the Rhizoplane Microbial Community Structure
Cited by: 5
Author(s): Shashini U. Welmillage, Qian Zhang, Virinchipuram S. Sreevidya, Michael J. Sadowsky, Prasad Gyaneshwar
Software Mentions: 5
Published: over 5 years ago

10.1186/s12864-020-6517-0

Repetitive DNA content in the maize genome is uncoupled from population stratification at SNP loci
Cited by: 2
Author(s): Simon Renny‐Byfield, Andy Baumgarten
Software Mentions: 5
Published: over 6 years ago

10.1186/s12859-020-03821-x

A method for estimating coherence of molecular mechanisms in major human disease and traits
Cited by: 1
Author(s): Mikhail G. Dozmorov, Kellen Garrison Cresswell, Silviu‐Alin Bacanu, Carl F. Craver, Mark Reimers, Kenneth S. Kendler
Software Mentions: 5
Published: almost 6 years ago

10.1099/mgen.0.000240

Genomic analysis of bacteria in the Acute Oak Decline pathobiome
Cited by: 29
Author(s): James Doonan, Sandra Denman, Justin A. Pachebat, James E. McDonald
Software Mentions: 5
Published: over 7 years ago

10.1186/s12864-016-3254-5

Integrated metagenomic data analysis demonstrates that a loss of diversity in oral microbiota is associated with periodontitis
Cited by: 72
Author(s): Dongmei Ai, Ruocheng Huang, Ji Wen, Chao Li, Jianguo Zhu, Xia Li
Software Mentions: 5
Published: over 9 years ago

10.1038/s41598-021-91399-6

Bacillus amyloliquefaciens FH-1 significantly affects cucumber seedlings and the rhizosphere bacterial community but not soil
Cited by: 15
Author(s): Jingjing Wang, Sheng Xu, Rong Yang, Wei Zhao, Dan Zhu, Xiaoxia Zhang, Zhiyong Huang
Software Mentions: 5
Published: over 5 years ago

10.1038/s41396-018-0321-8

Genomic and transcriptomic insights into the ecology and metabolism of benthic archaeal cosmopolitan, Thermoprofundales (MBG-D archaea)
Cited by: 80
Author(s): Zhichao Zhou, Yang Liu, Karen G. Lloyd, Jie Pan, Yuchun Yang, Ji‐Dong Gu, Meng Li
Software Mentions: 5
Published: almost 8 years ago

10.1038/s41598-021-95486-6

Genetic diversity and population structure of Alternaria species from tomato and potato in North Carolina and Wisconsin
Cited by: 10
Author(s): Tika B. Adhikari, Norman Muzhinji, Dennis Halterman, Frank J. Louws
Software Mentions: 5
Published: about 5 years ago

10.1186/s40168-018-0496-2

Signatures of ecological processes in microbial community time series
Cited by: 64
Author(s): Karoline Faust, Franziska Bauchinger, Béatrice Laroche, Sophie de Buyl, Leo Lahti, Alex D. Washburne, Didier Gonze, Stefanie Widder
Software Mentions: 5
Published: about 8 years ago

10.1186/s40168-021-01001-4

The bacterial communities of Alaskan mosses and their contributions to N2-fixation
Cited by: 26
Author(s): Hannah Holland‐Moritz, Julia Stuart, Lily R. Lewis, Samantha N. Miller, Michelle C. Mack, José Miguel Ponciano, Stuart F. McDaniel, Noah Fierer
Software Mentions: 5
Published: over 5 years ago

10.1186/1471-2105-13-113

Molecular ecological network analyses
Cited by: 1,612
Author(s): Ye Deng, Yi-Huei Jiang, Yunfeng Yang, Zhili He, Feng Luo, Jizhong Zhou
Software Mentions: 5
Published: over 14 years ago

10.1186/s12864-015-1532-2

Pathway reporter genes define molecular phenotypes of human cells
Cited by: 24
Author(s): Jitao David Zhang, Erich Küng, Franziska Boess, Ulrich Certa, Martin Ebeling
Software Mentions: 5
Published: over 11 years ago

10.1186/1471-2148-13-158

Modularity of a leaf moth-wing pattern and a versatile characteristic of the wing-pattern ground plan
Cited by: 25
Author(s): Takao Suzuki
Software Mentions: 5
Published: over 13 years ago

10.1038/s41598-021-98075-9

Distinguishing feature of gut microbiota in Tibetan highland coronary artery disease patients and its link with diet
Cited by: 14
Author(s): Yu-Lan Ma, Lulu Zhu, Zhuo Ma, Zhong-Shan Gao, Yumiao Wei, Youlu Shen, Lin Liu, Xingli Liu, Ming Ren
Software Mentions: 5
Published: about 5 years ago

10.3389/fgene.2018.00670

The Importance of Biologic Knowledge and Gene Expression Context for Genomic Data Interpretation
Cited by: 5
Author(s): Michael T. Zimmermann
Software Mentions: 5
Published: over 7 years ago

10.3390/microorganisms8071032

Structures of the Skin Microbiome and Mycobiome Depending on Skin Sensitivity
Cited by: 10
Author(s): Hye Lim Keum, Hanbyul Kim, Hye-Jin Kim, Taehun Park, Seoyung Kim, Shi An, Woo Jun Sul
Software Mentions: 5
Published: about 6 years ago

10.1098/rspb.2021.0275

Multi-level social organization and nest-drifting behaviour in a eusocial insect
Cited by: 0
Author(s): Thibault Lengronne, David T. Mlynski, Solenn Patalano, Richard James, Laurent Keller, Seirian Sumner
Software Mentions: 5
Published: over 5 years ago

10.1128/mSphere.00982-20

Decreased Ecological Resistance of the Gut Microbiota in Response to Clindamycin Challenge in Mice Colonized with the Fungus Candida albicans
Cited by: 2
Author(s): Laura Markey, Antonia Pugliese, Theresa Tian, Farrah Roy, Kyongbum Lee, Carol A. Kumamoto
Software Mentions: 5
Published: over 5 years ago

10.1007/s11111-019-00329-2

Missing millions: undercounting urbanization in India
Cited by: 17
Author(s): Kyle Onda, Parmanand Sinha, Andrea E. Gaughan, Forrest R. Stevens, Nikhil Kaza
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pone.0244377

A methodology and theoretical taxonomy for centrality measures: What are the best centrality indicators for student networks?
Cited by: 7
Author(s): Kristel Vignery, Wim Laurier
Software Mentions: 5
Published: over 5 years ago

10.3892/mmr.2014.3006

Analysis of the protein-protein interaction networks of differentially expressed genes in pulmonary embolism
Cited by: 5
Author(s): Hao Wang, Chen Wang, Lei Zhang, Yinghua Lu, Qianglin Duan, Zhu Gong, Aibin Liang, Haoming Song, Lemin Wang
Software Mentions: 5
Published: almost 12 years ago

10.1371/journal.pone.0234489

Application of network analysis and cluster analysis for better prevention and control of swine diseases in Argentina
Cited by: 11
Author(s): Jerome N. Baron, María Natalia Aznar, M. Monterubbianesi, Beatriz Martínez‐López
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0228539

Intraspecific perspective of phenotypic coordination of functional traits in Scots pine
Cited by: 13
Author(s): Bárbara Carvalho, Cristina C. Bastías, Adrián Escudero, Fernando Valladares, Raquel Benavides
Software Mentions: 5
Published: over 6 years ago

10.1007/s00572-019-00918-x

Evolution and networks in ancient and widespread symbioses between Mucoromycotina and liverworts
Cited by: 20
Author(s): William R. Rimington, Silvia Pressel, Jeffrey G. Duckett, Katie J. Field, Martin I. Bidartondo
Software Mentions: 5
Published: almost 7 years ago

10.3389/fcell.2020.592348

Limited Mitochondrial Activity Coupled With Strong Expression of CD34, CD90 and EPCR Determines the Functional Fitness of ex vivo Expanded Human Hematopoietic Stem Cells
Cited by: 7
Author(s): Luena Papa, Mansour Djedaini, Tiphaine Martin, Mahtab Zangui, Kristin G. Beaumont, Robert Sebra, Ramon Parsons, Christoph Schaniel, Ronald Hoffman
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12859-017-1673-1

NFPscanner: a webtool for knowledge-based deciphering of biomedical networks
Cited by: 0
Author(s): Wenjian Xu, Yang Cao, Ziwei Xie, Haochen He, Song He, Hong Hao, Xiaochen Bo, Fēi Li
Software Mentions: 5
Published: over 9 years ago

10.3390/insects11070417

Environmental Display Can Buffer the Effect of Pesticides on Solitary Bees
Cited by: 6
Author(s): Samuel Boff, Josué Raizer, D. Lupi
Software Mentions: 5
Published: about 6 years ago

10.1186/1471-2105-14-47

A survey of protein interaction data and multigenic inherited disorders
Cited by: 6
Author(s): Antonio M. Mora, Katerina Michalickova, Ian Donaldson
Software Mentions: 5
Published: over 13 years ago

10.1080/21642850.2018.1521283

Network analysis: a brief overview and tutorial
Cited by: 271
Author(s): David Hevey
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pone.0251458

Statistical privacy-preserving message broadcast for peer-to-peer networks
Cited by: 1
Author(s): David Mödinger, Jan-Hendrik Lorenz, Franz J. Hauck
Software Mentions: 5
Published: over 5 years ago

10.1186/s13099-019-0312-y

Differential genetic and functional background in inflammatory bowel disease phenotypes of a Greek population: a systems bioinformatics approach
Cited by: 11
Author(s): Maria Gazouli, Nikolas Dovrolis, André Franke, George M. Spyrou, Leonardo Antonio Sechi, George Kolios
Software Mentions: 5
Published: over 7 years ago

10.1017/S0031182021000640

Functional traits shape small mammal-helminth network: patterns and processes in species interactions
Cited by: 9
Author(s): Thiago dos Santos Cardoso, Cecilia S. Andreazzi, Arnaldo Maldonado, Rosana Gentile
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0117909

Potential Parasite Transmission in Multi-Host Networks Based on Parasite Sharing
Cited by: 59
Author(s): Shai Pilosof, Sergé Morand, Boris R. Krasnov, Charles L. Nunn
Software Mentions: 5
Published: over 11 years ago

10.1371/journal.pone.0244363

Backbone: An R package for extracting the backbone of bipartite projections
Cited by: 20
Author(s): Rachel Domagalski, Zachary P. Neal, Bruce E. Sagan
Software Mentions: 5
Published: over 5 years ago

10.3390/pathogens3020356

Characterization of Antimicrobial Resistance Dissemination across Plasmid Communities Classified by Network Analysis
Cited by: 22
Author(s): Akifumi Yamashita, Tsuyoshi Sekizuka, Makoto Kuroda
Software Mentions: 5
Published: over 12 years ago

10.7717/peerj.6559

Estimating probabilistic context-free grammars for proteins using contact map constraints
Cited by: 7
Author(s): Witold Dyrka, Mateusz Pyzik, F Coste, Hugo Talibart
Software Mentions: 5
Published: over 7 years ago

10.7717/peerj.4606

Can phosphorus application and cover cropping alter arbuscular mycorrhizal fungal communities and soybean performance after a five-year phosphorus-unfertilized crop rotational system?
Cited by: 21
Author(s): Masao Higo, Ryohei Sato, Ayu Serizawa, Yuichi Takahashi, Kento Gunji, Yuya Tatewaki, Katsunori Isobe
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pone.0242955

Lessons from movement ecology for the return to work: Modeling contacts and the spread of COVID-19
Cited by: 4
Author(s): Allison K. Shaw, Lauren A. White, Matthew Michalska‐Smith, Elizabeth T. Borer, Meggan E. Craft, Eric W. Seabloom, Emilie C. Snell‐Rood, Michael Travisano
Software Mentions: 5
Published: over 5 years ago

10.7717/peerj.229

Pathway-GPS and SIGORA: identifying relevant pathways based on the over-representation of their gene-pair signatures
Cited by: 43
Author(s): Amir Foroushani, Fiona S. L. Brinkman, David J. Lynn
Software Mentions: 5
Published: over 12 years ago

10.1371/journal.pone.0221055

Faecalibacterium diversity in dairy cow milk
Cited by: 8
Author(s): Keith W. Savin, Jody L. Zawadzki, M.J. Auldist, Jianghui Wang, Doris Ram, Simone Rochfort, Benjamin G. Cocks
Software Mentions: 5
Published: about 7 years ago

10.7717/peerj.10539

Composition and distribution of fish environmental DNA in an Adirondack watershed
Cited by: 2
Author(s): Robert S. Cornman, James E. McKenna, Jennifer A. Fike
Software Mentions: 5
Published: over 5 years ago

10.1016/j.gpb.2018.04.008

Agricultural Risk Factors Influence Microbial Ecology in Honghu Lake
Cited by: 25
Author(s): Maozhen Han, Melissa Dsouza, Chunyu Zhou, Hongjun Li, Junqian Zhang, Chaoyun Chen, Qi Yao, Chunrong Zhong, Hao Zhou, Jack A. Gilbert, Zhi Wen, Kang Ning
Software Mentions: 5
Published: over 7 years ago

10.7717/peerj.11950

Rephine.r: a pipeline for correcting gene calls and clusters to improve phage pangenomes and phylogenies
Cited by: 2
Author(s): Jason W. Shapiro, Catherine Putonti
Software Mentions: 5
Published: about 5 years ago

10.3389/fcimb.2021.637018

Identification of Microbiome Etiology Associated With Drug Resistance in Pleural Empyema
Cited by: 12
Author(s): Zhaoyan Chen, Hang Cheng, Zhao Cai, Qingjun Wei, Jinlong Li, Jing Liang, Wenshu Zhang, Zhijian Yu, Dongjing Liu, Lei Liu, Zhenqiang Zhang, Ke Wang, Liang Yang
Software Mentions: 5
Published: over 5 years ago

10.1002/ece3.5691

Metabolically similar cohorts of bacteria exhibit strong cooccurrence patterns with diet items and eukaryotic microbes in lizard guts
Cited by: 7
Author(s): Iris Holmes, Ivan V. Monagan, Daniel L. Rabosky, Alison R. Davis Rabosky
Software Mentions: 5
Published: almost 7 years ago

10.7717/peerj.4571

Pathways of topological rank analysis (PoTRA): a novel method to detect pathways involved in hepatocellular carcinoma
Cited by: 5
Author(s): Chaoxing Li, Li Liu, Valentin Dinu
Software Mentions: 5
Published: over 8 years ago

10.1002/ece3.5060

Urbanization and the temporal patterns of social networks and group foraging behaviors
Cited by: 10
Author(s): Teri B. Jones, Julian C. Evans, Julie Morand‐Ferron
Software Mentions: 5
Published: over 7 years ago

10.1186/s13073-014-0064-8

The `dnet’ approach promotes emerging research on cancer patient survival
Cited by: 41
Author(s): Hai Fang, Julian Gough
Software Mentions: 5
Published: about 12 years ago

10.1002/ece3.5631

Seagrass‐associated fungal communities show distance decay of similarity that has implications for seagrass management and restoration
Cited by: 28
Author(s): Benjamin J. Wainwright, Geoffrey Zahn, Joshua Zushi, Nicole Li Ying Lee, Jillian Lean Sim Ooi, Jen Nie Lee, Danwei Huang
Software Mentions: 5
Published: about 7 years ago

10.1002/ece3.7946

Restored and remnant Banksia woodlands elicit different foraging behavior in avian pollinators
Cited by: 2
Author(s): Alison Ritchie, Catherine Elliott, Elizabeth A. Sinclair, Siegfried L. Krauss
Software Mentions: 5
Published: about 5 years ago

10.1186/s13059-020-02050-y

Dynamic rewiring of the human interactome by interferon signaling
Cited by: 21
Author(s): Craig H. Kerr, Michael A. Skinnider, Daniel D. T. Andrews, Angel M. Madero, Queenie Chan, R. Greg Stacey, Nikolay Stoynov, Eric Jan, Leonard J. Foster
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0184015

Population genetics, community of parasites, and resistance to rodenticides in an urban brown rat (Rattus norvegicus) population
Cited by: 38
Author(s): Amélie Desvars-Larrive, Michel Pascal, Patrick Gasqui, Jean-François Cosson, Etienne Benoît, Virginie Lattard, Laurent Crespin, Olivier Lorvelec, Benoît Pisanu, Alexandre Teynié, Muriel Vayssier‐Taussat, Sarah Bonnet, Philippe Marianneau, Sandra Lacôte, Pascale Bourhy, Philippe Berny, Nicole Pavio, Sophie Le Poder, Emmanuelle Gilot‐Fromont, Elsa Jourdain, Abdessalem Hammed, Isabelle Fourel, Farid Chikh, Gwenaël Vourc’H
Software Mentions: 5
Published: about 9 years ago

10.1111/tpj.14202

Gene networks orchestrated by Me<scp>GI</scp>: a single‐factor mechanism underlying sex determination in persimmon
Cited by: 43
Author(s): Ho Wen Yang, Takashi Akagi, Taiji Kawakatsu, Ryutaro Tao
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pone.0225001

Mammary microbiome of lactating organic dairy cows varies by time, tissue site, and infection status
Cited by: 38
Author(s): Tucker Andrews, Deborah A. Neher, Thomas R. Weicht, John W. Barlow
Software Mentions: 5
Published: almost 7 years ago

10.1186/s40793-021-00377-y

Archaeal and bacterial communities assembly and co-occurrence networks in subtropical mangrove sediments under Spartina alterniflora invasion
Cited by: 45
Author(s): Weidong Chen, Donghui Wen
Software Mentions: 5
Published: over 5 years ago

10.1186/s13059-018-1545-7

Modularity of genes involved in local adaptation to climate despite physical linkage
Cited by: 37
Author(s): Katie E. Lotterhos, Sam Yeaman, Jon C. Degner, Sally N. Aitken, Kathryn A. Hodgins
Software Mentions: 5
Published: almost 8 years ago

10.1371/journal.pcbi.1007481

Bayesian inference of neuronal assemblies
Cited by: 18
Author(s): Giovanni Diana, Thomas T. J. Sainsbury, Martin P. Meyer
Software Mentions: 5
Published: almost 7 years ago

10.1002/sam.11495

A framework for stability‐based module detection in correlation graphs
Cited by: 3
Author(s): Mingmei Tian, Rachael Hageman Blair, Lina Mu, Matthew Bonner, Richard W. Browne, Han Yu
Software Mentions: 5
Published: over 5 years ago

10.1186/s12976-019-0103-7

Gene regulatory networks on transfer entropy (GRNTE): a novel approach to reconstruct gene regulatory interactions applied to a case study for the plant pathogen Phytophthora infestans
Cited by: 19
Author(s): Juan Castro, Iván Valdés, Laura González-García, Giovanna Danies, Silvia Cañas, Flávia Vischi Winck, Carlos Eduardo Ñústez, Silvia Restrepo, Diego Mauricio Riaño‐Pachón
Software Mentions: 5
Published: over 7 years ago

10.3390/genes11070807

Target-Genes Reveal Species and Genotypic Specificity of Anthocyanin Pigmentation in Citrus and Related Genera
Cited by: 7
Author(s): Chiara Catalano, Angelo Ciacciulli, Fabrizio Salonia, Mario Russo, P. Caruso, Marco Caruso, Giuseppe Russo, Gaetano Distefano, Concetta Licciardello
Software Mentions: 5
Published: about 6 years ago

10.3390/genes11070831

Computational Analysis of the Global Effects of Ly6E in the Immune Response to Coronavirus Infection Using Gene Networks
Cited by: 5
Author(s): Fernando M. Delgado-Chaves, Francisco Gómez-Vela, Federico Divina, Miguel García-Torres, Domingo S. Rodríguez–Baena
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0129074

Making Large-Scale Networks from fMRI Data
Cited by: 16
Author(s): Verena D. Schmittmann, Sara Jahfari, Denny Borsboom, Alexander Olof Savi, Lourens J. Waldorp
Software Mentions: 5
Published: about 11 years ago

10.3390/genes11050543

Weighted Gene Correlation Network Meta-Analysis Reveals Functional Candidate Genes Associated with High- and Sub-Fertile Reproductive Performance in Beef Cattle
Cited by: 13
Author(s): Pablo Augusto de Souza Fonseca, Aroa Suárez-Vega, Ángela Cánovas
Software Mentions: 5
Published: over 6 years ago

10.3390/genes10030212

RNA Sequencing Reveals Specific Transcriptomic Signatures Distinguishing Effects of the [SWI+] Prion and SWI1 Deletion in Yeast Saccharomyces cerevisiae
Cited by: 11
Author(s): Yury V. Malovichko, Kirill S. Antonets, Anna R. Maslova, Е. А. Андреева, Sergey G. Inge-Vechtomov, Anton A. Nizhnikov
Software Mentions: 5
Published: over 7 years ago

10.3389/fcimb.2017.00234

Functional Redundancy and Ecological Innovation Shape the Circulation of Tick-Transmitted Pathogens
Cited by: 10
Author(s): Agustı́n Estrada-Peña, José de la Fuente, Alejandro Cabezas-Cruz
Software Mentions: 5
Published: over 9 years ago

10.1534/g3.117.300125

Interchromosomal Transfer of Immune Regulation During Infection of Barley with the Powdery Mildew Pathogen
Cited by: 4
Author(s): Priyanka Surana, Ruo Xu, Greg Fuerst, Antony V. E. Chapman, Dan Nettleton, Roger P. Wise
Software Mentions: 5
Published: almost 9 years ago

10.3389/fvets.2020.00189

Network Analysis of Swine Shipments in China: The First Step to Inform Disease Surveillance and Risk Mitigation Strategies
Cited by: 8
Author(s): Kathleen C. O'Hara, Rui Zhang, Yong Sam Jung, Xiaobing Zhou, Yingjuan Qian, Beatriz Martínez‐López
Software Mentions: 5
Published: over 6 years ago

10.3389/fgene.2021.706854

Crosslink: An R Package for Network Visualization of Grouped Nodes
Cited by: 1
Author(s): Di Liu, Zhijie Bai, Bing Liu, Zongcheng Li
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pcbi.1007564

Regulatory context drives conservation of glycine riboswitch aptamers
Cited by: 6
Author(s): Matt Crum, Nikhil Ram-Mohan, Michelle M. Meyer
Software Mentions: 5
Published: over 6 years ago

10.3389/fendo.2021.679582

Transcriptomic Profiling of Human Placenta in Gestational Diabetes Mellitus at the Single-Cell Level
Cited by: 31
Author(s): Yuqi Yang, Fang Guo, Yue Peng, Rong Chen, Wenbo Zhou, Huihui Wang, Jun Ouyang, Bin Yu, Zhengfeng Xu
Software Mentions: 5
Published: over 5 years ago

10.12688/f1000research.8288.1

MetaNetVar: Pipeline for applying network analysis tools for genomic variants analysis
Cited by: 3
Author(s): Eric Moyer, Megan Hastings Hagenauer, Matthew Lesko, Felix Francis, Oscar J Rodriguez, Vijayaraj Nagarajan, Vojtech Huser, Ben Busby
Software Mentions: 5
Published: over 10 years ago

10.3389/fmicb.2020.00571

Composition, Predicted Functions and Co-occurrence Networks of Rhizobacterial Communities Impacting Flowering Desert Events in the Atacama Desert, Chile
Cited by: 17
Author(s): Marcia Astorga-Eló, Qian Zhang, Giovanni Larama, Alexandra Stoll, Michael J. Sadowsky, Milko A. Jorquera
Software Mentions: 5
Published: over 6 years ago

Projects: cran: igraph

Science Score: 100/100

Bonuses:

Papers Mentioning igraph 1,555