cran: igraph | Projects | Ecosyste.ms: Papers

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

10.1007/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

10.1002/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

10.1186/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

10.1186/1471-2105-14-47

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

10.1186/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

10.1042/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

10.3390/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: over 6 years ago

10.1371/journal.pcbi.1005591

Solving the influence maximization problem reveals regulatory organization of the yeast cell cycle
Cited by: 10
Author(s): David L. Gibbs, Ilya Shmulevich
Software Mentions: 5
Published: over 9 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

10.1371/journal.pcbi.1005711

Polymodal allosteric regulation of Type 1 Serine/Threonine Kinase Receptors via a conserved electrostatic lock
Cited by: 16
Author(s): Wesley M. Botello‐Smith, Abdelaziz Alsamarah, Payal Chatterjee, Chen Xie, Jérôme J. Lacroix, Jijun Hao, Yang Luo
Software Mentions: 5
Published: about 9 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: almost 10 years ago

10.1007/s43926-021-00016-5

Social media analytics of the Internet of Things
Cited by: 4
Author(s): Jim Scheibmeir, Yashwant K. Malaiya
Software Mentions: 5
Published: over 5 years ago

10.1016/j.devcel.2020.11.013

Diverse Routes toward Early Somites in the Mouse Embryo
Cited by: 40
Author(s): Carolina Guibentif, J. B. Griffiths, Iván Imaz-Rosshandler, Shila Ghazanfar, Jennifer Nichols, Valerie Wilson, Berthold Göttgens, John C. Marioni
Software Mentions: 5
Published: almost 6 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: almost 9 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: almost 7 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

10.3390/ani10081321

Social Experience of Captive Livingstone’s Fruit Bats (Pteropus livingstonii)
Cited by: 7
Author(s): Morgan J. Welch, Teresa M. Smith, Charlotte A. Hosie, Dominic Wormell, Eluned C. Price, Christina R. Stanley
Software Mentions: 5
Published: about 6 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

10.1016/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

10.1186/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

10.1371/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

10.1007/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

10.1111/tpj.14202

Gene networks orchestrated by <i>Me<scp>GI</scp></i>: 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

10.1186/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

10.1038/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

10.1186/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: about 8 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

10.7717/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

10.1186/1471-2105-13-113

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

10.1186/1471-2148-13-158

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: almost 14 years ago

10.1186/s12918-016-0298-8

petal: Co-expression network modelling in R
Cited by: 30
Author(s): Juli Petereit, Sebastian Smith, Frederick C. Harris, Karen Schlauch
Software Mentions: 5
Published: about 10 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

10.1128/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

10.7717/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

10.1186/s12918-015-0166-y

Reshaping the epigenetic landscape during early flower development: induction of attractor transitions by relative differences in gene decay rates
Cited by: 29
Author(s): José Dávila-Velderrain, Cuauhtémoc Calderón Villarreal, Elena Álvarez-Buylla
Software Mentions: 5
Published: over 11 years ago

10.1186/1752-0509-7-12

Identification of ovarian cancer associated genes using an integrated approach in a Boolean framework
Cited by: 12
Author(s): Gaurav Kumar, Edmond J. Breen, Shoba Ranganathan
Software Mentions: 5
Published: over 13 years ago

10.1038/s42003-020-0914-4

Birds have peramorphic skulls, too: anatomical network analyses reveal oppositional heterochronies in avian skull evolution
Cited by: 29
Author(s): Olivia Plateau, Christian Foth
Software Mentions: 5
Published: over 6 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

10.7717/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: almost 13 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: over 6 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

10.7717/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

10.3390/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

10.3390/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: over 6 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

10.1101/2020.09.16.20196154

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: about 6 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

10.1371/journal.pone.0044514

Bipartite Graphs as Models of Population Structures in Evolutionary Multiplayer Games
Cited by: 28
Author(s): Jorge Peña, Yannick Rochat
Software Mentions: 5
Published: about 14 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

10.1534/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: about 9 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: almost 6 years ago

10.1371/journal.pone.0057190

The Poultry-Associated Microbiome: Network Analysis and Farm-to-Fork Characterizations
Cited by: 103
Author(s): Brian B. Oakley, Cesar A. Morales, J. Eric Line, M. E. Berrang, Richard J. Meinersmann, Glenn E. Tillman, Mark G. Wise, Gregory R. Siragusa, Kelli L. Hiett, Bruce S. Seal
Software Mentions: 5
Published: over 13 years ago

10.3390/ani11051229

A Preliminary Investigation of Social Network Analysis Applied to Dairy Cow Behavior in Automatic Milking System Environments
Cited by: 2
Author(s): Liliana Fadul-Pacheco, Michael Liou, Douglas J. Reinemann, Víctor E. Cabrera
Software Mentions: 5
Published: over 5 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/fmicb.2021.647861

Nutrient Exposure Alters Microbial Composition, Structure, and Mercury Methylating Activity in Periphyton in a Contaminated Watershed
Cited by: 4
Author(s): Alyssa A. Carrell, Grace E. Schwartz, Melissa Cregger, Caitlin M. Gionfriddo, Dwayne A. Elias, Regina L. Wilpiszeski, Dawn M. Klingeman, Ann M. Wymore, Katherine A. Muller, Scott C. Brooks
Software Mentions: 5
Published: over 5 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

10.1007/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

10.1371/journal.pone.0148459

Assessment of Overlap of Phylogenetic Transmission Clusters and Communities in Simple Sexual Contact Networks: Applications to HIV-1
Cited by: 28
Author(s): Luc Villandré, David A. Stephens, Aurélie Labbe, Huldrych F. Günthard, Roger D. Kouyos, Tanja Stadler
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

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

10.1128/mBio.01870-17

Gene Co-occurrence Networks Reflect Bacteriophage Ecology and Evolution
Cited by: 40
Author(s): Jason W. Shapiro, Catherine Putonti
Software Mentions: 5
Published: over 8 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.0134509

A Social Network Approach Reveals Associations between Mouse Social Dominance and Brain Gene Expression
Cited by: 103
Author(s): Nina L. T. So, Becca Franks, Sean C. Lim, James P. Curley
Software Mentions: 5
Published: about 11 years ago

10.1371/journal.pone.0151342

Mining Social Entrepreneurship Strategies Using Topic Modeling
Cited by: 23
Author(s): Yanto Chandra, Li Jiang, Chengjun Wang
Software Mentions: 5
Published: over 10 years ago

10.1371/journal.pone.0182850

Quantitative approach for the risk assessment of African swine fever and Classical swine fever introduction into the United States through legal imports of pigs and swine products
Cited by: 37
Author(s): Diana María Herrera-Ibatá, Beatriz Martínez‐López, Darla Quijada, Kenneth R. Burton, Lina Mur
Software Mentions: 5
Published: about 9 years ago

10.1186/s12889-016-2893-4

Intimate partner violence norms cluster within households: an observational social network study in rural Honduras
Cited by: 32
Author(s): Holly B. Shakya, Dominic Hughes, Derek Stafford, Nicholas A. Christakis, James H. Fowler, Jay G. Silverman
Software Mentions: 5
Published: over 10 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

10.3389/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: over 7 years ago

10.3389/fimmu.2020.00559

The TCR Repertoire Reconstitution in Multiple Sclerosis: Comparing One-Shot and Continuous Immunosuppressive Therapies
Cited by: 22
Author(s): Roberta Amoriello, Victor Greiff, Alessandra Aldinucci, Elena Bonechi, Alberto Carnasciali, Benedetta Peruzzi, Anna Maria Repice, Alice Mariottini, Riccardo Saccardi, Benedetta Mazzanti, Luca Massacesi, Clara Ballerini
Software Mentions: 5
Published: over 6 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

10.1186/s12889-019-7485-7

The importance of social environment in preventing smoking: an analysis of the Dead Cool intervention
Cited by: 5
Author(s): Jennifer Badham, Helen McAneney, Laura Dunne, Frank Kee, Allen Thurston, Ruth F. Hunter
Software Mentions: 5
Published: about 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: over 6 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

10.3389/fimmu.2015.00644

Dynamic Perturbations of the T-Cell Receptor Repertoire in Chronic HIV Infection and following Antiretroviral Therapy
Cited by: 59
Author(s): James Heather, Katharine Best, Theres Oakes, Eleanor R. Gray, Jennifer Roe, Niclas Thomas, Nir Friedman, Mahdad Noursadeghi, Benjamin M. Chain
Software Mentions: 5
Published: almost 11 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

10.1371/journal.pone.0195070

Bayesian variable selection with graphical structure learning: Applications in integrative genomics
Cited by: 7
Author(s): Suprateek Kundu, Yu‐Shan Cheng, Minsuk Shin, Ganiraju C. Manyam, Bani K. Mallick, Veerabhadran Baladandayuthapani
Software Mentions: 5
Published: about 8 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

10.1038/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

10.3389/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: almost 8 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/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/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: over 8 years ago

10.1371/journal.pone.0223745

Measuring the complexity of directed graphs: A polynomial-based approach
Cited by: 7
Author(s): Matthias Dehmer, Zengqiang Chen, Frank Emmert‐Streib, Shailesh Tripathi, Abbe Mowshowitz, Alexei Leviţchi, Lihua Feng, Yongtang Shi, Tao Jin
Software Mentions: 5
Published: almost 7 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

10.1186/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: about 6 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/s41598-020-71309-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

10.3389/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: over 5 years ago

10.1038/s41598-020-61558-2

Innovation in wild Barbary macaques (Macaca sylvanus)
Cited by: 16
Author(s): Federica Amici, Álvaro López Caicoya, Bonaventura Majolo, Anja Widdig
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-019-52177-7

Dominance relationships and coalitionary aggression against conspecifics in female carrion crows
Cited by: 11
Author(s): Benedikt Holtmann, Julia Buskas, Matthew Steele, Kristaps Solokovskis, Jochen B. W. Wolf
Software Mentions: 5
Published: almost 7 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: almost 6 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.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

10.1371/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

10.1038/s41598-019-47087-7

Systems biology and network pharmacology of frailty reveal novel epigenetic targets and mechanisms
Cited by: 6
Author(s): Juan Carlos Gómez-Verján, Ricardo Ramírez‐Aldana, Mario Ulises Pérez‐Zepeda, Ricardo Quiroz‐Baez, Armando Luna–López, Luis Miguel Gutiérrez Robledo
Software Mentions: 5
Published: about 7 years ago

10.1038/s41598-020-63275-2

Modulation of stress and immune response by Amblyomin-X results in tumor cell death in a horse melanoma model
Cited by: 9
Author(s): Flávio Lichtenstein, Asif Iqbal, Sonia Elisabete Alves de Lima Will, Rosemary Viola Bösch, Carlos DeOcesano-Pereira, Maurício Barbugiani Goldfeder, Roger Chammas, Carlos Eduardo Madureira Trufen, Kátia L.P. Morais, Jean Gabriel de Souza, Renato José Mendonça Natalino, Inácio L.M. Junqueira-de-Azevedo, Milton Yutaka Nishiyama-Jr, Úrsula Castro de Oliveira, F Alves, Jaqueline Mayara Araujo, Aline Ramos Maia Lobba, Ana Marisa Chudzinski‐Tavassi
Software Mentions: 5
Published: over 6 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

10.1099/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: almost 8 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

Projects: cran: igraph

Science Score: 100/100

Bonuses:

Papers Mentioning igraph 1,555