10.1186/s12859-019-3016-x

NPA: an R package for computing network perturbation amplitudes using gene expression data and two-layer networks
Cited by: 6
Author(s): Florian Martin, Sylvain Gubian, Marja Talikka, Julia Hoeng, Manuel C. Peitsch
Software Mentions: 7
Published: about 7 years ago

10.3389/fpsyg.2021.679016

The Setting Questionnaire for the Ayahuasca Experience: Questionnaire Development and Internal Structure
Cited by: 7
Author(s): Alexandre Augusto de Deus Pontual, Luís Fernando Tófoli, Carlos Fernando Collares, Johannes G. Ramaekers, Clarissa Mendonça Corradi-Webster
Software Mentions: 7
Published: over 5 years ago

10.3389/fpsyg.2019.02783

The Network Structure of Adolescent Well-Being Traits: Results From a Large-Scale Chinese Sample
Cited by: 8
Author(s): Guang Zeng, Kaiping Peng, Hu Chuan-Peng
Software Mentions: 7
Published: almost 7 years ago

10.1016/j.erss.2020.101704

Grounded reality meets machine learning: A deep-narrative analysis framework for energy policy research
Cited by: 20
Author(s): Ramit Debnath, Sarah Darby, Ronita Bardhan, Kamiar Mohaddes, Minna Sunikka-Blank
Software Mentions: 7
Published: almost 6 years ago

10.1007/s00406-019-01078-x

The network structure of schizotypy in the general population
Cited by: 12
Author(s): Bertalan Polner, Eliana Faiola, María Fernanda Urquijo, Inga Meyhöfer, Maria Steffens, Levente Rónai, Nikolaos Koutsouleris, Ulrich Ettinger
Software Mentions: 7
Published: almost 7 years ago

10.1186/s12918-018-0598-2

A systematic survey of centrality measures for protein-protein interaction networks
Cited by: 122
Author(s): Mohieddin Jafari, Ali Salehzadeh‐Yazdi, Zahra Razaghi-Moghadam, Holger Hennig, Olaf Wolkenhauer, Mehdi Mirzaie, Mohieddin Jafari
Software Mentions: 7
Published: about 8 years ago

10.3389/fphys.2020.612598

Physiological Network From Anthropometric and Blood Test Biomarkers
Cited by: 7
Author(s): Antonio Barajas-Martínez, Elizabeth Ibarra-Coronado, Martha Patricia Sierra-Vargas, Ivette Cruz-Bautista, Paloma Almeda‐Valdés, Carlos A. Aguilar-Salinas, Rubén Fossión, Christopher R. Stephens, Claudia Vargas-Domínguez, Octavio Gamaliel Atzatzi-Aguilar, Yazmín Debray-García, Rogelio García-Torrentera, Karen Bobadilla, María Augusta Naranjo Meneses, Dulce Abril Mena Orozco, Cesar Lam, Vania Jocelyn Martínez-Garcés, Octavio A. Lecona, Arlex Marín-García, A. Frank, Ana Leonor Rivera
Software Mentions: 7
Published: over 5 years ago

10.1002/ece3.6479

Generation and application of river network analogues for use in ecology and evolution
Cited by: 38
Author(s): Luca Carraro, Enrico Bertuzzo, Emanuel A. Fronhofer, Reinhard Furrer, Isabelle Gounand, Andrea Rinaldo, Florian Altermatt
Software Mentions: 7
Published: over 6 years ago

10.7717/peerj.5303

Conflict resolution in socially housed Sumatran orangutans (<i>Pongo abelii</i>)
Cited by: 9
Author(s): Kathrin Susanne Kopp, Katja Liebal
Software Mentions: 7
Published: about 8 years ago

10.3389/fnins.2021.600462

Dysregulation of MicroRNAs and PIWI-Interacting RNAs in a Caenorhabditis elegans Parkinson’s Disease Model Overexpressing Human α-Synuclein and Influence of tdp-1
Cited by: 10
Author(s): Linjing Shen, Changliang Wang, Liang Chen, Garry Wong
Software Mentions: 7
Published: over 5 years ago

10.3389/fmicb.2019.02359

Annual Protist Community Dynamics in a Freshwater Ecosystem Undergoing Contrasted Climatic Conditions: The Saint-Charles River (Canada)
Cited by: 21
Author(s): Perrine Cruaud, Adrien Vigneron, Marie‐Stéphanie Fradette, Caetano C. Dorea, Alexander I. Culley, Manuel J. Rodriguez, Steve J. Charette
Software Mentions: 7
Published: almost 7 years ago

10.3390/vetsci7030138

Cattle Manure Trade Network Analysis and the Relevant Spatial Pathways in an Endemic Area of Foot and Mouth Disease in Northern Thailand
Cited by: 0
Author(s): Chalutwan Sansamur, Anuwat Wiratsudakul, Arisara Charoenpanyanet, Veerasak Punyapornwithaya
Software Mentions: 7
Published: about 6 years ago

10.1371/journal.pcbi.1004765

A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers
Cited by: 29
Author(s): Yasin Şenbabaoğlu, S. Onur Sumer, Francisco Sánchez-Vega, Debra L. Bemis, Giovanni Ciriello, Nikolaus Schultz, Chris Sander
Software Mentions: 7
Published: over 10 years ago

10.3389/fmicb.2016.01367

Spatial and Temporal Dynamics of Pacific Oyster Hemolymph Microbiota across Multiple Scales
Cited by: 65
Author(s): Ana Lokmer, M. Anouk Goedknegt, David W. Thieltges, Dario Fiorentino, Sven Kuenzel, John F. Baines, K. Mathias Wegner
Software Mentions: 7
Published: about 10 years ago

10.1371/journal.pcbi.1004575

SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis
Cited by: 292
Author(s): Minzhe Guo, Hui Wang, S. Steven Potter, Jeffrey A. Whitsett, Yan Xu
Software Mentions: 7
Published: almost 11 years ago

10.1186/s40462-020-00233-7

Urban specialization reduces habitat connectivity by a highly mobile wading bird
Cited by: 7
Author(s): Claire S. Teitelbaum, Jeffrey Hepinstall‐Cymerman, Anjelika Kidd-Weaver, Sonia M. Hernández, Sonia Altizer, Richard J. Hall
Software Mentions: 7
Published: almost 6 years ago

10.15252/msb.20188497

netDx: interpretable patient classification using integrated patient similarity networks
Cited by: 59
Author(s): Shraddha Pai, Shirley Hui, Ruth Isserlin, Manjool Shah, Hussam Kaka, Gary D. Bader
Software Mentions: 7
Published: over 7 years ago

10.1186/s40168-019-0736-0

Differential dynamics of microbial community networks help identify microorganisms interacting with residue-borne pathogens: the case of Zymoseptoria tritici in wheat
Cited by: 39
Author(s): Lydie Kerdraon, Matthieu Barret, Valérie Laval, Frédéric Suffert
Software Mentions: 7
Published: about 7 years ago

10.1371/journal.pcbi.1006826

Machine learning analysis of gene expression data reveals novel diagnostic and prognostic biomarkers and identifies therapeutic targets for soft tissue sarcomas
Cited by: 65
Author(s): David G.P. van IJzendoorn, Károly Szuhai, Inge H. Briaire-de Bruijn, Marie Kostine, Marieke L. Kuijjer, Judith V.M.G. Bovée
Software Mentions: 7
Published: over 7 years ago

10.1371/journal.pone.0234669

netboxr: Automated discovery of biological process modules by network analysis in R
Cited by: 2
Author(s): Eric Minwei Liu, Augustin Luna, Guanlan Dong, Chris Sander
Software Mentions: 7
Published: almost 6 years ago

10.3390/ijms19061808

Co-Expression Network Analysis of AMPK and Autophagy Gene Products during Adipocyte Differentiation
Cited by: 8
Author(s): Mahmoud Ahmed, Jin Seok Hwang, Trang Huyen Lai, Sahib Zada, Huynh Quoc Nguyen, Trang Min Pham, Miyong Yun, Deok Ryong Kim
Software Mentions: 7
Published: over 8 years ago

10.3389/fmicb.2021.719486

Compositional Shift of Bacterial, Archaeal, and Fungal Communities Is Dependent on Trophic Lifestyles in Rice Paddy Soil
Cited by: 5
Author(s): Hyun Kim, Jongbum Jeon, Kiseok Keith Lee, Yong-Hwan Lee
Software Mentions: 7
Published: about 5 years ago

10.3390/ijms21176028

Developmental Methylome of the Medicinal Plant Catharanthus roseus Unravels the Tissue-Specific Control of the Monoterpene Indole Alkaloid Pathway by DNA Methylation
Cited by: 12
Author(s): Thomas Dugé de Bernonville, Stéphane Maury, Alain Delaunay, Christian Daviaud, Cristian Chaparro, Jörg Tost, Sarah E. O’Connor, Vincent Courdavault
Software Mentions: 7
Published: about 6 years ago

10.1186/1471-2105-15-132

Investigating perturbed pathway modules from gene expression data via structural equation models
Cited by: 19
Author(s): Daniele Pepe, Mario Grassi
Software Mentions: 7
Published: over 12 years ago

10.3390/microorganisms9020227

Use of Network Analysis and Spread Models to Target Control Actions for Bovine Tuberculosis in a State from Brazil
Cited by: 4
Author(s): Nicolás Céspedes Cárdenas, Pilar Pozo, Francisco Paulo Nunes Lopes, José Henrique Hildebrand Grisi-Filho, Julio Álvarez
Software Mentions: 7
Published: over 5 years ago

10.1186/1471-2105-12-492

Structural Measures for Network Biology Using QuACN
Cited by: 18
Author(s): Laurin A. J. Mueller, Karl G. Kugler, Armin Graber, Frank Emmert‐Streib, Matthias Dehmer
Software Mentions: 7
Published: almost 15 years ago

10.3389/fmicb.2021.658116

Endophytic Fungal Community of Tobacco Leaves and Their Potential Role in the Formation of “Cherry-Red” Tobacco
Cited by: 4
Author(s): Yonglei Jiang, Xing Chen, Gaokun Zhao, Jiahong Liu, Yan Xie, Yong Li, Huaguo Gu, Congming Zou
Software Mentions: 7
Published: about 5 years ago

10.1038/s41598-019-43829-9

Tissue-specific genes as an underutilized resource in drug discovery
Cited by: 29
Author(s): Maria Ryaboshapkina, Mårten Hammar
Software Mentions: 7
Published: over 7 years ago

10.1371/journal.pone.0227804

Exponential random graph model parameter estimation for very large directed networks
Cited by: 26
Author(s): Alex Stivala, Garry Robins, Alessandro Lomi
Software Mentions: 7
Published: over 6 years ago

10.1186/s40168-016-0154-5

Recovering complete and draft population genomes from metagenome datasets
Cited by: 195
Author(s): Naseer Sangwan, Fangfang Xia, Jack A. Gilbert
Software Mentions: 7
Published: over 10 years ago

10.1038/s41598-018-34138-8

A network analysis of female sexual function: comparing symptom networks in women with decreased, increased, and stable sexual desire
Cited by: 8
Author(s): Annika Gunst, Marlene Werner, Lourens J. Waldorp, Ellen Laan, Marianne Källström, Patrick Jern
Software Mentions: 7
Published: almost 8 years ago

10.1038/s41598-019-52865-4

Niche partitioning of microbial communities in riverine floodplains
Cited by: 7
Author(s): Marc Peipoch, Scott R. Miller, Tiago Antão, H. Maurice Valett
Software Mentions: 7
Published: almost 7 years ago

10.1186/s40168-017-0387-y

In-depth resistome analysis by targeted metagenomics
Cited by: 103
Author(s): Val F. Lanza, Fernando Baquero, José Luis Martínez, Ricardo Ramos-Ruíz, Bruno González‐Zorn, Antoine Andremont, Antonio Sánchez-Valenzuela, S. Dusko Ehrlich, Sean Kennedy, Étienne Ruppé, Willem van Schaik, Rob J. L. Willems, Fernando de la Cruz, Teresa M. Coque
Software Mentions: 7
Published: over 8 years ago

10.3389/fimmu.2021.691811

Immune Infiltrating Cells-Derived Risk Signature Based on Large-scale Analysis Defines Immune Landscape and Predicts Immunotherapy Responses in Glioma Tumor Microenvironment
Cited by: 36
Author(s): Nan Zhang, Hao Zhang, Zeyu Wang, Ziyu Dai, Xun Zhang, Quan Cheng, Zhixiong Liu
Software Mentions: 7
Published: about 5 years ago

10.3389/fimmu.2021.687291

Genetic Prioritization, Therapeutic Repositioning and Cross-Disease Comparisons Reveal Inflammatory Targets Tractable for Kidney Stone Disease
Cited by: 5
Author(s): Hai Fang, Lulu Jiang
Software Mentions: 7
Published: about 5 years ago

10.1186/s40168-019-0677-7

Maize synthesized benzoxazinoids affect the host associated microbiome
Cited by: 160
Author(s): Enoch Narh Kudjordjie, Rumakanta Sapkota, Stine K. Steffensen, Inge S. Fomsgaard, Mogens Nicolaisen
Software Mentions: 7
Published: over 7 years ago

10.1186/s12859-016-1088-4

RevEcoR: an R package for the reverse ecology analysis of microbiomes
Cited by: 22
Author(s): Yang Cao, Yuanyuan Wang, Xiaofei Zheng, Fēi Li, Xiaochen Bo
Software Mentions: 7
Published: about 10 years ago

10.1186/s42523-021-00117-0

Gut microbiome is affected by gut region but robust to host physiological changes in captive active-season ground squirrels
Cited by: 3
Author(s): Kirsten Grond, Courtney C. Kurtz, Jasmine J. Hatton, Michelle M. Sonsalla, Khrystyne N. Duddleston
Software Mentions: 7
Published: about 5 years ago

10.7717/peerj.11018

Integrated analysis of immune-related long noncoding RNAs as diagnostic biomarkers in psoriasis
Cited by: 13
Author(s): Feixiang Fan, Zhen Huang, Yongfeng Chen
Software Mentions: 7
Published: over 5 years ago

10.1186/1471-2105-10-S11-S14

NATbox: a network analysis toolbox in R
Cited by: 10
Author(s): Shweta S. Chavan, Michael Bauer, Marco Scutari, Radhakrishnan Nagarajan
Software Mentions: 7
Published: about 17 years ago

10.1038/s41598-017-16050-9

Computational derivation of a molecular framework for hair follicle biology from disease genes
Cited by: 4
Author(s): Rachel K. Severin, Xinwei Li, Kun Qian, Andreas Mueller, Lynn Petukhova
Software Mentions: 7
Published: almost 9 years ago

10.1099/mgen.0.000244

Where the plasmids roam: large-scale sequence analysis reveals plasmids with large host ranges
Cited by: 10
Author(s): Lauren Brooks, Mo Kaze, Mark Sistrom
Software Mentions: 7
Published: almost 8 years ago

10.1007/s00248-019-01426-3

Fusarium Head Blight Modifies Fungal Endophytic Communities During Infection of Wheat Spikes
Cited by: 45
Author(s): Edward C. Rojas, Rumakanta Sapkota, Birgit Jensen, Henning Jørgensen, Tina Henriksson, Lise Nistrup Jørgensen, Mogens Nicolaisen, David B. Collinge
Software Mentions: 7
Published: about 7 years ago

10.1186/s12859-021-04012-y

CeNet Omnibus: an R/Shiny application to the construction and analysis of competing endogenous RNA network
Cited by: 4
Author(s): Wen Xiao, Lin Gao, Tuo Song, Chaoqun Jiang
Software Mentions: 7
Published: over 5 years ago

10.3389/fgene.2021.722981

Landscape of the Dark Transcriptome Revealed Through Re-mining Massive RNA-Seq Data
Cited by: 6
Author(s): Jing Li, Urminder Singh, Zebulun Arendsee, Eve Syrkin Wurtele
Software Mentions: 7
Published: about 5 years ago

10.1111/1751-7915.13640

Synthetic community with six <i>Pseudomonas</i> strains screened from garlic rhizosphere microbiome promotes plant growth
Cited by: 55
Author(s): Lubo Zhuang, Yán Li, Zhenshuo Wang, Yue Yu, Nan Zhang, Chang Yeol Yang, Qingchao Zeng, Qi Wang
Software Mentions: 7
Published: about 6 years ago

10.1371/journal.pone.0178904

Modeling the live-pig trade network in Georgia: Implications for disease prevention and control
Cited by: 28
Author(s): Esther A. Kukielka, Beatriz Martínez‐López, Daniel Beltrán‐Alcrudo
Software Mentions: 7
Published: over 9 years ago

10.3389/fgene.2021.732211

A Ferroptosis-Related Prognostic Signature Based on Antitumor Immunity and Tumor Protein p53 Mutation Exploration for Guiding Treatment in Patients With Head and Neck Squamous Cell Carcinoma
Cited by: 13
Author(s): Xin Fan, YangShaobo Ou, Huijie Liu, Liangzhen Zhan, Xiaohui Zhu, Mingyang Cheng, Qun Li, Dongmei Yin, Lan Liao
Software Mentions: 7
Published: about 5 years ago

10.1590/0074-02760190105

Gene regulatory network inference and analysis of multidrug-resistant Pseudomonas aeruginosa
Cited by: 5
Author(s): Fernando Medeiros Filho, Ana Paula Barbosa do Nascimento, M. Tadeu dos Santos, Ana Paula D’Alincourt Carvalho-Assef, Fabrício Silva
Software Mentions: 7
Published: almost 8 years ago

10.3389/fendo.2021.672319

Adrenocortical Carcinoma Steroid Profiles: In Silico Pan-Cancer Analysis of TCGA Data Uncovers Immunotherapy Targets for Potential Improved Outcomes
Cited by: 6
Author(s): João C. D. Muzzi, Jessica Maria Magno, Milena A. Cardoso, Juliana de Moura, Mauro A. A. Castro, Bonald C. Figueiredo
Software Mentions: 7
Published: over 5 years ago

10.3389/fgene.2019.00516

Microbial Networks in SPRING - Semi-parametric Rank-Based Correlation and Partial Correlation Estimation for Quantitative Microbiome Data
Cited by: 67
Author(s): Grace Yoon, Irina Gaynanova, Christian L. Müller
Software Mentions: 7
Published: over 7 years ago

10.1186/s12864-021-07441-4

A comparative analysis of heart microRNAs in vertebrates brings novel insights into the evolution of genetic regulatory networks
Cited by: 2
Author(s): Pedro Gabriel Nachtigall, Luiz Augusto Bovolenta, James G. Patton, Bastian Fromm, Ney Lemke, Danillo Pinhal
Software Mentions: 7
Published: over 5 years ago

10.7717/peerj.281

<i>Poppr</i>: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction
Cited by: 1,961
Author(s): Zhian N. Kamvar, Javier F. Tabima, Niklaus J. Grünwald
Software Mentions: 7
Published: over 12 years ago

10.7554/eLife.61138

The biphasic and age-dependent impact of klotho on hallmarks of aging and skeletal muscle function
Cited by: 15
Author(s): Zachary Clemens, Sruthi Sivakumar, Abish Pius, Amrita Sahu, Sunita Shinde, Hikaru Mamiya, Nathaniel Luketich, Jian Cui, Purushottam D. Dixit, Joerg D. Hoeck, Sebastian Kreuz, Michael Franti, Aaron Barchowsky, Fabrisia Ambrosio
Software Mentions: 7
Published: over 5 years ago

10.3389/fcell.2020.582320

Microbiome Profiling Reveals Gut Dysbiosis in the Metabotropic Glutamate Receptor 5 Knockout Mouse Model of Schizophrenia
Cited by: 15
Author(s): Carolina Gubert, Geraldine Kong, Volkan Uzungil, Ariel M Zeleznikow-Johnston, Emma L. Burrows, Thibault Renoir, Anthony J Hannan
Software Mentions: 6
Published: almost 6 years ago

10.1038/srep33555

The Tara Oceans voyage reveals global diversity and distribution patterns of marine planktonic ciliates
Cited by: 65
Author(s): Anna Gimmler, Ralf Korn, Colomban de Vargas, Stéphane Audic, Thorsten Stoeck
Software Mentions: 6
Published: about 10 years ago

10.3389/fcell.2021.672248

Immune Infiltrates of m6A RNA Methylation-Related lncRNAs and Identification of PD-L1 in Patients With Primary Head and Neck Squamous Cell Carcinoma
Cited by: 25
Author(s): Ziyi Feng, Haoyu Gao, Tianda Feng
Software Mentions: 6
Published: over 5 years ago

10.1186/s13068-021-01948-4

Differential expression of starch and sucrose metabolic genes linked to varying biomass yield in Miscanthus hybrids
Cited by: 6
Author(s): Jose J De Vega, Ned Peel, Sarah Purdy, Sarah Hawkins, Iain S. Donnison, Sarah Dyer, Kerrie Farrar
Software Mentions: 6
Published: over 5 years ago

10.1093/biosci/biw175

Using Social Network Measures in Wildlife Disease Ecology, Epidemiology, and Management
Cited by: 101
Author(s): Matthew J. Silk, Darren P. Croft, Richard J. Delahay, David J. Hodgson, Mike Boots, Nicola Weber, Robbie A. McDonald
Software Mentions: 6
Published: over 9 years ago

10.12688/f1000research.20887.3

RCy3: Network biology using Cytoscape from within R
Cited by: 72
Author(s): Julia Gustavsen, Shraddha Pai, Ruth Isserlin, Barry Demchak, Alexander R. Pico
Software Mentions: 6
Published: almost 7 years ago

10.1002/2211-5463.12692

Multidimensional profiling of drug‐treated cells by Imaging Mass Cytometry
Cited by: 33
Author(s): Alexandre Bouzekri, Amanda Esch, Olga Ornatsky
Software Mentions: 6
Published: about 7 years ago

10.1186/s42523-020-00032-w

Oyster hemolymph is a complex and dynamic ecosystem hosting bacteria, protists and viruses
Cited by: 18
Author(s): Samuel Dupont, Ana Lokmer, Erwan Corre, Jean‐Christophe Auguet, Bruno Petton, Ève Toulza, Caroline Montagnani, Gwenn Tanguy, David Pecqueur, Christophe Salmeron, Laure Guillou, Christelle Desnues, Bernard La Scola, Jacques Bou Khalil, Julien de Lorgeril, Guillaume Mitta, Yannick Gueguen, Jean-Michel Escoubas
Software Mentions: 6
Published: over 6 years ago

10.3390/biom10060938

CoRNeA: A Pipeline to Decrypt the Inter-Protein Interfaces from Amino Acid Sequence Information
Cited by: 5
Author(s): Kriti Chopra, Bhawna Burdak, Kaushal Sharma, Ajit Kembhavi, Shekhar C. Mande, Radha Chauhan
Software Mentions: 6
Published: over 6 years ago

10.1038/sdata.2017.44

Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.
Cited by: 119
Author(s): Sebastian Beier, Axel Himmelbach, Christian Colmsee, Xiao Qi Zhang, Roberto A. Barrero, Qisen Zhang, Lin Li, Micha Bayer, Dan Bolser, Stefan Taudien, Marco Groth, Marius Felder, Alex Hastie, Hana Šimková, Helena Staňková, Jan Vrána, Saki Chan, María Muñoz‐Amatriaín, Rachid Ounit, Steve Wanamaker, Thomas Schmutzer, Lala Aliyeva-Schnorr, Stefano Grasso, Jaakko Tanskanen, Dharanya Sampath, Darren Heavens, Sujie Cao, Brett Chapman, Fei Dai, Yong Han, Hua Li, Xuan Li, Chongyun Lin, John K. McCooke, Cong Tan, Songbo Wang, Shuya Yin, Gaofeng Zhou, Jesse Poland, M. Bellgard, Andreas Houben, Jaroslav Doležel, Sarah Ayling, Stefano Lonardi, Peter Langridge, Gary J. Muehlbauer, Paul J. Kersey, Matthew D. Clark, Mario Cáccamo, Alan H. Schulman, Matthias Platzer, Timothy J. Close, Mats Hansson, Guoping Zhang, Ilka Braumann, Chengdao Li, Robbie Waugh, Uwe Scholz, Nils Stein, Martin Mascher
Software Mentions: 6
Published: over 9 years ago

10.1126/sciadv.abj1132

Plasma lipids and growth faltering: A longitudinal cohort study in rural Gambian children
Cited by: 2
Author(s): Gerard Bryan Gonzales, Daniëlla Brals, Bakary Sonko, Fatou Sosseh, Andrew M. Prentice, Sophie E. Moore, Albert Koulman
Software Mentions: 6
Published: about 5 years ago

10.1111/eva.12589

Seascape genetics and biophysical connectivity modelling support conservation of the seagrass<i>Zostera marina</i>in the Skagerrak-Kattegat region of the eastern North Sea
Cited by: 38
Author(s): Marlene Jahnke, Per R. Jonsson, Per‐Olav Moksnes, Lars-Ove Loo, Martin Nilsson Jacobi, Jeanine L. Olsen
Software Mentions: 6
Published: over 8 years ago

10.1111/eva.13227

No leading‐edge effect in North Atlantic harbor porpoises: Evolutionary and conservation implications
Cited by: 2
Author(s): Yacine Ben Chehida, Roisin Loughnane, Julie Thumloup, Kristin Kaschner, Cristina Garilao, Patricia E. Rosel, Michaël C. Fontaine
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pmed.1001944

Evidence for Community Transmission of Community-Associated but Not Health-Care-Associated Methicillin-Resistant Staphylococcus Aureus Strains Linked to Social and Material Deprivation: Spatial Analysis of Cross-sectional Data
Cited by: 60
Author(s): Olga Tosas Auguet, Jason R. Betley, Richard A. Stabler, Amita Patel, Avgousta Ioannou, Helene Marbach, Pasco Hearn, Anna Aryee, Simon Goldenberg, Jonathan A. Otter, Nergish Desai, Tacim Karadag, Chris Grundy, Michael W. Gaunt, Ben S. Cooper, Jonathan D Edgeworth, Theodore Kypraios
Software Mentions: 6
Published: over 10 years ago

10.1186/s12859-017-1482-6

GSAR: Bioconductor package for Gene Set analysis in R
Cited by: 34
Author(s): Yasir Rahmatallah, Boris Zybailov, Frank Emmert‐Streib, Galina Glazko
Software Mentions: 6
Published: over 9 years ago

10.1186/s12864-016-2718-y

Ribosome quality control is a central protection mechanism for yeast exposed to deoxynivalenol and trichothecin
Cited by: 11
Author(s): Karl G. Kugler, Zeljkica Jandric, Reinhard Beyer, Eva Klopf, Walter Glaser, Marc Lemmens, Mehrdad Shams, Klaus Mayer, Gerhard Adam, Christoph Schüller
Software Mentions: 6
Published: over 10 years ago

10.1371/journal.pone.0187091

DiffSLC: A graph centrality method to detect essential proteins of a protein-protein interaction network
Cited by: 43
Author(s): Divya Mistry, Roger P. Wise, Julie A. Dickerson
Software Mentions: 6
Published: almost 9 years ago

10.1186/1471-2105-12-455

iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database
Cited by: 62
Author(s): Antonio M. Mora, Ian Donaldson
Software Mentions: 6
Published: almost 15 years ago

10.1371/journal.pntd.0005246

The Biomphalaria glabrata DNA methylation machinery displays spatial tissue expression, is differentially active in distinct snail populations and is modulated by interactions with Schistosoma mansoni
Cited by: 39
Author(s): Kathrin K. Geyer, Umar Niazi, David Timothy Duval, Céline Cosseau, Chad Tomlinson, Iain W. Chalmers, Martin Swain, David Cutress, Utibe Bickham-Wright, Sabrina E. Munshi, Christoph Grunau, Timothy P. Yoshino, Karl F. Hoffmann
Software Mentions: 6
Published: over 9 years ago

10.1371/journal.pone.0193759

Sharing-based social capital associated with harvest production and wealth in the Canadian Arctic
Cited by: 25
Author(s): Elspeth Ready
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pgen.1008198

Bayesian network analysis incorporating genetic anchors complements conventional Mendelian randomization approaches for exploratory analysis of causal relationships in complex data
Cited by: 33
Author(s): Richard Howey, So–Youn Shin, Caroline L Relton, George Davey Smith, Heather J. Cordell
Software Mentions: 6
Published: over 6 years ago

10.1017/S0950268821000510

Epidemiology and transmission characteristics of early COVID-19 cases, 20 January–19 March 2020, in Bavaria, Germany
Cited by: 10
Author(s): Stefanie Böhm, Tom Woudenberg, D. Chen, Durdica Marosevic, Merle M. Böhmer, Lisa Hansen, Jacco Wallinga, Andreas Sing, Katharina Katz
Software Mentions: 6
Published: almost 6 years ago

10.1093/beheco/ary012

Social interactions predict genetic diversification: an experimental manipulation in shorebirds
Cited by: 4
Author(s): Charles Cunningham, Jorge Parra, Lucy Coals, Lucila Marcela Beltrán-Tolosa, Sama Zefania, Tamás Székely
Software Mentions: 6
Published: over 8 years ago

10.1186/s12284-021-00522-8

Strategies and Structure Feature of the Aboveground and Belowground Microbial Community Respond to Drought in Wild Rice (Oryza longistaminata)
Cited by: 11
Author(s): Jian Xie, Xiaoqing Wang, Jiawang Xu, Haizhu Xie, Yaohui Cai, Yizheng Liu, Xia Ding
Software Mentions: 6
Published: about 5 years ago

10.1186/s12917-014-0282-8

Successional changes in the chicken cecal microbiome during 42 days of growth are independent of organic acid feed additives
Cited by: 115
Author(s): Brian B. Oakley, R. J. Buhr, Casey W. Ritz, Brian H. Kiepper, M. E. Berrang, Bruce S. Seal, N. A. Cox
Software Mentions: 6
Published: almost 12 years ago

10.1080/22221751.2020.1799723

Dysregulation in Akt/mTOR/HIF-1 signaling identified by proteo-transcriptomics of SARS-CoV-2 infected cells
Cited by: 203
Author(s): Sofia Appelberg, Soham Gupta, Sara Svensson Akusjärvi, Anoop T. Ambikan, Flora Mikaeloff, Elisa Saccon, Ákos Végvári, Rui Benfeitas, Maike Sperk, Marie Ståhlberg, Shuba Krishnan, Kamal Singh, Josef Penninger, Alì Mirazimi, Ujjwal Neogi
Software Mentions: 6
Published: almost 7 years ago

10.3390/pathogens10030258

Q Fever: Seroprevalence, Risk Factors in Slaughter Livestock and Genotypes of Coxiella burnetii in South Africa
Cited by: 11
Author(s): Maruping L. Mangena, Nomakorinte Gcebe, Rian Pierneef, Peter N. Thompson, Abiodun A. Adesiyun
Software Mentions: 6
Published: over 5 years ago

10.3390/pathogens10040396

Nanopore-Sequencing Characterization of the Gut Microbiota of Melolontha melolontha Larvae: Contribution to Protection against Entomopathogenic Nematodes?
Cited by: 4
Author(s): Ewa Sajnaga, Marcin Skowronek, Agnieszka Kalwasińska, Waldemar Kazimierczak, Karolina Ferenc, Magdalena Lis, Adrian Wiater
Software Mentions: 6
Published: over 5 years ago

10.1186/1752-0509-6-56

Centrality-based pathway enrichment: a systematic approach for finding significant pathways dominated by key genes
Cited by: 62
Author(s): Zuguang Gu, Jialin Liu, Kun-Ming Cao, Junfeng Zhang, Jin Wang
Software Mentions: 6
Published: over 14 years ago

10.7717/peerj.8844

Dynamics of ammonia oxidizers and denitrifiers in response to compost addition in black soil, Northeast China
Cited by: 8
Author(s): Zhihui Yang, Yupeng Guan, Ayodeji Bello, Yanxiang Wu, Jiayi Ding, Leiqi Wang, Yuqing Ren, Guangxin Chen, Wei Yang
Software Mentions: 6
Published: over 6 years ago

10.3389/fonc.2021.597536

Systems Biomedicine of Primary and Metastatic Colorectal Cancer Reveals Potential Therapeutic Targets
Cited by: 7
Author(s): Mehran Piran, Neda Sepahi, Afagh Moattari, A. M. Rahimi, Ali Ghanbariasad
Software Mentions: 6
Published: over 5 years ago

10.1007/s00421-021-04676-7

Individual cardiovascular responsiveness to work-matched exercise within the moderate- and severe-intensity domains
Cited by: 17
Author(s): Felipe Mattioni Maturana, Philipp Schellhorn, Gunnar Erz, Christof Burgstahler, Manuel Widmann, Barbara Munz, Rogério N. Soares, Juan M. Murias, Ansgar Thiel, Andreas M. Nieß
Software Mentions: 6
Published: over 5 years ago

10.1186/1752-0509-8-17

Identification of core T cell network based on immunome interactome
Cited by: 4
Author(s): Gabriel Teku, Csaba Ortutay, Mauno Vihinen
Software Mentions: 6
Published: over 12 years ago

10.1371/journal.pcbi.1007162

Cross-species functional modules link proteostasis to human normal aging
Cited by: 10
Author(s): Andrea Komljenović, Hao Li, Vincenzo Sorrentino, Zoltán Kutalik, Johan Auwerx, Marc Robinson‐Rechavi
Software Mentions: 6
Published: over 7 years ago

10.3389/fnmol.2020.563091

Isolation and Characterization of Multi-Protein Complexes Enriched in the K-Cl Co-transporter 2 From Brain Plasma Membranes
Cited by: 14
Author(s): Joshua L. Smalley, Georgina Kontou, Catherine Choi, Qiang Ren, David Albrecht, Krithika Abiraman, M. Santos, Christopher E. Bope, Tarek Z. Deeb, Paul Davies, Nicholas J. Brandon, Stephen J. Moss
Software Mentions: 6
Published: almost 6 years ago

10.3389/fmicb.2021.617949

Compositional Data Analysis of Periodontal Disease Microbial Communities
Cited by: 9
Author(s): Laura Sisk-Hackworth, Adrian Ortiz-Velez, Micheal Reed, Scott T. Kelley
Software Mentions: 6
Published: over 5 years ago

10.3389/fneur.2017.00223

Efficacy of Drug Interventions for Chemotherapy-Induced Chronic Peripheral Neurotoxicity: A Network Meta-analysis
Cited by: 5
Author(s): Xiaohong Fu, Huihui Wu, Jinyao Li, Can Wang, Ming Li, Qianqian Ma, Wei Yang
Software Mentions: 6
Published: over 9 years ago

10.1371/journal.pone.0230274

Dengue importation into Europe: A network connectivity-based approach
Cited by: 12
Author(s): Donald Salami, César Capinha, Maria do Rosário Oliveira Martins, Carla A. Sousa
Software Mentions: 6
Published: over 6 years ago

10.1016/j.isci.2021.102864

Social bonds provide multiple pathways to reproductive success in wild male chimpanzees
Cited by: 34
Author(s): Joseph T. Feldblum, Christopher Krupenye, Joel Bray, Anne E. Pusey, Ian C. Gilby
Software Mentions: 6
Published: about 5 years ago

10.12688/wellcomeopenres.14073.3

ANIMA: Association network integration for multiscale analysis
Cited by: 4
Author(s): Armin Deffur, Robert J. Wilkinson, Bongani M. Mayosi, Nicola Mulder
Software Mentions: 6
Published: almost 8 years ago

10.3389/fmicb.2014.00358

Demonstrating microbial co-occurrence pattern analyses within and between ecosystems
Cited by: 239
Author(s): Ryan J. Williams, Adina Howe, Kirsten Hofmockel
Software Mentions: 6
Published: about 12 years ago

10.3389/fmicb.2017.01563

Role of Age-Related Shifts in Rumen Bacteria and Methanogens in Methane Production in Cattle
Cited by: 28
Author(s): Chong Liu, Qinghui Meng, Yongxing Chen, Mengsi Xu, Min Shen, Rui Gao, Shangquan Gan
Software Mentions: 6
Published: about 9 years ago

10.3389/fmicb.2019.01637

Characterization of Distinct CyanoHABs-Related Modules in Microbial Recurrent Association Network
Cited by: 30
Author(s): Seong-Jun Chun, Yingshun Cui, Chang‐Soo Lee, A Ra Cho, Kiwoon Baek, Jae‐Suk Choi, So-Ra Ko, Hyung-Gwan Lee, Seungwoo Hwang, Hee‐Mock Oh, Chi‐Yong Ahn
Software Mentions: 6
Published: about 7 years ago

10.1371/journal.pcbi.1005694

PCSF: An R-package for network-based interpretation of high-throughput data
Cited by: 34
Author(s): Murodzhon Akhmedov, Amanda J. Kedaigle, Renan Escalante Chong, Roberto Montemanni, Francesco Bertoni, Ernest Fraenkel, Ivo Kwee
Software Mentions: 6
Published: about 9 years ago

10.1186/s12885-017-3832-1

Comparative gene co-expression network analysis of epithelial to mesenchymal transition reveals lung cancer progression stages
Cited by: 9
Author(s): Daifeng Wang, John D. Haley, Patricia Thompson
Software Mentions: 6
Published: almost 9 years ago

10.1093/ve/vew029

Reconstructing contact network parameters from viral phylogenies
Cited by: 11
Author(s): Rosemary M. McCloskey, Richard Liang, Art F. Y. Poon
Software Mentions: 6
Published: over 10 years ago