cran: igraph | Projects | Ecosyste.ms: Papers

10.3390/metabo11050298

The Impact of Microbiome and Microbiota-Derived Sodium Butyrate on Drosophila Transcriptome and Metabolome Revealed by Multi-Omics Analysis
Cited by: 10
Author(s): Fan Zhou, Biaodi Liu, Xin Liu, Yan Li, Luoluo Wang, Jian Huang, Guan‐Zheng Luo, Xiaoyun Wang
Software Mentions: 3
Published: about 5 years ago

10.1128/mBio.01470-21

Intra-Ramanome Correlation Analysis Unveils Metabolite Conversion Network from an Isogenic Population of Cells
Cited by: 8
Author(s): Yuehui He, Shi Huang, Peng Zhang, Yicai Ji, Jian Xu
Software Mentions: 3
Published: almost 5 years ago

10.1155/2021/9960241

Exosomes Containing LINC00636 Inhibit MAPK1 through the miR-450a-2-3p Overexpression in Human Pericardial Fluid and Improve Cardiac Fibrosis in Patients with Atrial Fibrillation
Cited by: 13
Author(s): Langsha Liu, Fanyan Luo, Kaibo Lei
Software Mentions: 3
Published: about 5 years ago

10.3389/fmicb.2021.654855

Transcriptome Dynamics Underlying Chlamydospore Formation in Trichoderma virens GV29-8
Cited by: 7
Author(s): Xinhong Peng, Beilei Wu, Shuaihu Zhang, Mei Li, Xiliang Jiang
Software Mentions: 3
Published: about 5 years ago

10.3389/fmicb.2020.01471

Warming, but Not Acidification, Restructures Epibacterial Communities of the Baltic Macroalga Fucus vesiculosus With Seasonal Variability
Cited by: 8
Author(s): Birte Mensch, Sven C. Neulinger, Sven Künzel, Martin Wahl, Ruth A. Schmitz
Software Mentions: 3
Published: about 6 years ago

10.3389/fmicb.2020.01142

Underlying Mechanism of Wild Radix pseudostellariae in Tolerance to Disease Under the Natural Forest Cover
Cited by: 10
Author(s): Hongmiao Wu, Jinshen Xia, Xianjin Qin, Huiming Wu, Shengkai Zhang, Yanlin Zhao, Christopher Rensing, Wenxiong Lin
Software Mentions: 3
Published: about 6 years ago

10.1186/s12944-019-1032-5

Integrated analysis of gene expression changes associated with coronary artery disease
Cited by: 9
Author(s): Miao Liu, Rui-Xing Yin, Feng Huang, Shuo Yang, Wu-Xian Chen, Jin‐Zhen Wu
Software Mentions: 3
Published: over 7 years ago

10.3389/fmicb.2021.665776

Assessing the Response of Ruminal Bacterial and Fungal Microbiota to Whole-Rumen Contents Exchange in Dairy Cows
Cited by: 9
Author(s): Madison S. Cox, Courtney L. Deblois, Garret Suen
Software Mentions: 3
Published: about 5 years ago

10.1089/brain.2019.0722

Optimizing Connectivity-Driven Brain Parcellation Using Ensemble Clustering
Cited by: 1
Author(s): Anvar Kurmukov, Ayagoz Mussabaeva, Yulia Denisova, Daniel Moyer, Neda Jahanshad, Paul M. Thompson, Boris A. Gutman
Software Mentions: 3
Published: about 6 years ago

10.1002/brb3.834

Graph theory analysis of cortical thickness networks in adolescents with d-transposition of the great arteries
Cited by: 24
Author(s): Christopher G. Watson, Christian Stopp, Jane W. Newburger, Michael J. Rivkin
Software Mentions: 3
Published: over 8 years ago

10.1186/s13068-015-0348-2

Phylogeny-structured carbohydrate metabolism across microbiomes collected from different units in wastewater treatment process
Cited by: 16
Author(s): Yu Xia, Francis Y. L. Chin, Yuanqing Chao, Tong Zhang
Software Mentions: 3
Published: almost 11 years ago

10.1093/biosci/biaa067

Global Cropland Connectivity: A Risk Factor for Invasion and Saturation by Emerging Pathogens and Pests
Cited by: 24
Author(s): Yao‐Wu Xing, John Fredy Hernández Nopsa, Kelsey F. Andersen, Jorge Andrade-Piedra, Fenton Beed, Guy Blomme, Mónica Carvajal-Yepes, Danny Coyne, Wilmer J. Cuellar, Gregory A. Forbes, Jan Kreuze, J. Kroschel, P. Lava Kumar, J.P. Legg, Monica Parker, Elmar Schulte-Geldermann, Kalpana Sharma, Karen A. Garrett
Software Mentions: 3
Published: about 6 years ago

10.3390/biom10121595

Identifying Genes Involved in Alkaloid Biosynthesis in Vinca minor through Transcriptomics and Gene Co-Expression Analysis
Cited by: 11
Author(s): Emily Amor Stander, Liuda Johana Sepúlveda, Thomas Dugé de Bernonville, Inês Carqueijeiro, Κωνσταντίνος Κουδούνας, Pamela Lemos Cruz, Sébastien Besseau, Arnaud Lanoue, Nicolas Papon, Nathalie Giglioli-Guivarc’h, Ron P. Dirks, Sarah E. O’Connor, Lucía Atehortúa, Audrey Oudin, Vincent Courdavault
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2020.01296

BALOs Improved Gut Microbiota Health in Postlarval Shrimp (Litopenaeus vannamei) After Being Subjected to Salinity Reduction Treatment
Cited by: 13
Author(s): Qingqing Cao, Farhana Najnine, Hongcao Han, Bing Wu, Jin Cai
Software Mentions: 3
Published: about 6 years ago

10.1155/2015/852341

Clique-Based Clustering of Correlated SNPs in a Gene Can Improve Performance of Gene-Based Multi-Bin Linear Combination Test
Cited by: 8
Author(s): Yung Joon Yoo, Sun Ah Kim, Shelley B. Bull
Software Mentions: 3
Published: over 11 years ago

10.3389/fmicb.2019.00122

A Multi-Kingdom Study Reveals the Plasticity of the Rumen Microbiota in Response to a Shift From Non-grazing to Grazing Diets in Sheep
Cited by: 44
Author(s): Alejandro Belanche, Alison H. Kingston‐Smith, Gareth Griffith, C. J. Newbold
Software Mentions: 3
Published: over 7 years ago

10.1155/2017/1016305

Identification of Pharmacologically Tractable Protein Complexes in Cancer Using the R-Based Network Clustering and Visualization Program MCODER
Cited by: 4
Author(s): Gino Kwon, Hyosil Kim
Software Mentions: 3
Published: over 9 years ago

10.3389/fnmol.2019.00030

An Appraisal of the Influence of the Metabotropic Glutamate 5 (mGlu5) Receptor on Sociability and Anxiety
Cited by: 16
Author(s): Arnau Ramos-Prats, Julia Kölldorfer, Elena Paolo, Maximilian Zeidler, Gabriele Schmid, Francesco Ferraguti
Software Mentions: 3
Published: over 7 years ago

10.1242/bio.056176

A node-based informed modularity strategy to identify organizational modules in anatomical networks
Cited by: 4
Author(s): Borja Esteve‐Altava
Software Mentions: 3
Published: almost 6 years ago

10.3389/fnins.2017.00066

A Statistical Method to Distinguish Functional Brain Networks
Cited by: 14
Author(s): André Fujita, Maciel Calebe Vidal, Daniel Yasumasa Takahashi
Software Mentions: 3
Published: over 9 years ago

10.3389/fnins.2021.642324

Network Analysis of the CSF Proteome Characterizes Convergent Pathways of Cellular Dysfunction in ALS
Cited by: 4
Author(s): Alexander G. Thompson, Gray Eg, P. David Charles, Michele T.M. Hu, Kevin Talbot, Roman Fischer, Benedikt M. Kessler, Martin R Turner
Software Mentions: 3
Published: over 5 years ago

10.3389/fnins.2018.00041

Understanding the Generation of Network Bursts by Adaptive Oscillatory Neurons
Cited by: 22
Author(s): Tanguy Fardet, Mathieu Ballandras, Samuel Bottani, Stéphane Métens, Pascal Monceau
Software Mentions: 3
Published: over 8 years ago

10.1186/1745-6150-6-31

Structural influence of gene networks on their inference: analysis of C3NET
Cited by: 54
Author(s): Gökmen Altay, Frank Emmert‐Streib
Software Mentions: 3
Published: over 15 years ago

10.3389/fonc.2021.656675

Inferring Cell Subtypes and LncRNA Function by a Cell-Specific CeRNA Network in Breast Cancer
Cited by: 2
Author(s): Xin Chen, Jing Xu, Feng Zeng, Chao Yang, Weijun Sun, Yu Tao, Haokun Zhang, Li Yan
Software Mentions: 3
Published: over 5 years ago

10.1155/2015/245075

Characterization of Protein Complexes and Subcomplexes in Protein-Protein Interaction Databases
Cited by: 1
Author(s): Nazar Zaki, Elfadil A. Mohamed, Antonio M. Mora
Software Mentions: 3
Published: over 11 years ago

10.1042/BCJ20200511

Protein tyrosine phosphatases in cell adhesion
Cited by: 19
Author(s): Kung Chia Young, Laura Biggins, Hayley J. Sharpe
Software Mentions: 3
Published: over 5 years ago

10.1093/beheco/aru108

Resource redistribution in polydomous ant nest networks: local or global?
Cited by: 35
Author(s): Stephen Ellis, Daniel W. Franks, Elva J. H. Robinson
Software Mentions: 3
Published: over 12 years ago

10.1128/mSystems.00450-19

Oral Microbiome Alterations Associated with Early Childhood Caries Highlight the Importance of Carbohydrate Metabolic Activities
Cited by: 53
Author(s): Yuan Wang, Sa Wang, Chunyan Wu, Xi Chen, Zhuhui Duan, Qian Xu, Wen Jiang, Lei Xu, Tingting Wang, Lei Su, Ying Wang, Yadong Chen, Jie Zhang, Yun Huang, Suman Tong, Cheng Zhou, Shengjue Deng, Nan Qin
Software Mentions: 3
Published: over 6 years ago

10.3389/fpls.2020.575564

Tomato Spotted Wilt Virus Benefits Its Thrips Vector by Modulating Metabolic and Plant Defense Pathways in Tomato
Cited by: 20
Author(s): Punya Nachappa, Jean F. Challacombe, David C. Margolies, James R. Nechols, Anna E. Whitfield, Dorith Rotenberg
Software Mentions: 3
Published: over 5 years ago

10.3389/fpls.2016.01224

Multiple Assembly Rules Drive the Co-occurrence of Orthopteran and Plant Species in Grasslands: Combining Network, Functional and Phylogenetic Approaches
Cited by: 5
Author(s): Bertrand Fournier, Arnaud Mouly, François Gillet
Software Mentions: 3
Published: almost 10 years ago

10.3389/fpls.2017.01217

Evolution of Daily Gene Co-expression Patterns from Algae to Plants
Cited by: 26
Author(s): Pedro de los Reyes, Francisco J. Romero–Campero, Marta Ruiz, Javier Romero, Federico Valverde
Software Mentions: 3
Published: about 9 years ago

10.3389/fpls.2017.00893

Network Analysis Reveals a Common Host–Pathogen Interaction Pattern in Arabidopsis Immune Responses
Cited by: 24
Author(s): Hong Li, Yuan Zhou, Ziding Zhang
Software Mentions: 3
Published: about 9 years ago

10.3389/fpls.2018.00798

Field-Based Metabolomics of Vitis vinifera L. Stems Provides New Insights for Genotype Discrimination and Polyphenol Metabolism Structuring
Cited by: 35
Author(s): Kévin Billet, Benjamin Houillé, Thomas Dugé de Bernonville, Sébastien Besseau, Audrey Oudin, Vincent Courdavault, Guillaume Delanoue, Laurence Guérin, Marc Clastre, Nathalie Giglioli-Guivarc’h, Arnaud Lanoue
Software Mentions: 3
Published: about 8 years ago

10.3389/fpsyt.2018.00598

Diffusion of a Peer-Led Suicide Preventive Intervention Through School-Based Student Peer and Adult Networks
Cited by: 30
Author(s): Trevor A. Pickering, Peter A. Wyman, Karen Schmeelk-Cone, Chelsey Hartley, Thomas W. Valente, Anthony R. Pisani, Kelly L. Rulison, Charles H. Brown, Mark LoMurray
Software Mentions: 3
Published: over 7 years ago

10.3389/fpsyt.2018.00602

Genetic and Environmental Influences on the Affective Regulation Network: A Prospective Experience Sampling Analysis
Cited by: 5
Author(s): Laila Hasmi, Marjan Drukker, Sinan Gülöksüz, Wolfgang Viechtbauer, Evert Thiery, Cathérine Derom, Jim van Os
Software Mentions: 3
Published: over 7 years ago

10.3389/fpsyt.2020.579339

Mapping the Network of Social Cognition Domains in Children With Autism Spectrum Disorder Through Graph Analysis
Cited by: 6
Author(s): Maria Chiara Pino, Roberto Vagnetti, Francesco Masedu, Margherita Attanasio, Sergio Tiberti, Marco Valenti, Monica Mazza
Software Mentions: 3
Published: over 5 years ago

10.3389/fpsyg.2016.00018

Social Network Analysis and Nutritional Behavior: An Integrated Modeling Approach
Cited by: 15
Author(s): Alistair M. Senior, Mathieu Lihoreau, Jérôme Buhl, David Raubenheimer, Stephen J. Simpson
Software Mentions: 3
Published: over 10 years ago

10.1186/s12918-014-0108-0

Network signatures link hepatic effects of anti-diabetic interventions with systemic disease parameters
Cited by: 4
Author(s): Thomas Kelder, Lars Verschuren, Ben van Ommen, Alain J. van Gool, Marijana Radonjić
Software Mentions: 3
Published: almost 12 years ago

10.3389/fpubh.2020.582405

Care Deficiencies and Super-Organization of American Nursing Homes in Hospital Referral Region
Cited by: 3
Author(s): Tyler Pittman
Software Mentions: 3
Published: over 5 years ago

10.3389/fpubh.2020.587298

Depiction of Vaginal Microbiota in Women With High-Risk Human Papillomavirus Infection
Cited by: 25
Author(s): Zhentong Wei, Hongliang Chen, Chunfeng Wang, Genhua Yang, Song Han, Song‐Ling Zhang
Software Mentions: 3
Published: over 5 years ago

10.1186/1752-0509-4-179

Understanding protein evolutionary rate by integrating gene co-expression with protein interactions
Cited by: 14
Author(s): Kaifang Pang, Chao Cheng, Zhenyu Xuan, Sheng Hu, Xiaotu Ma
Software Mentions: 3
Published: over 15 years ago

10.3389/fvets.2020.583715

Proximity Interactions in a Permanently Housed Dairy Herd: Network Structure, Consistency, and Individual Differences
Cited by: 15
Author(s): Kareemah Chopra, Holly R. Hodges, Z. E. Barker, Jorge A. Vázquez Diosdado, Jonathan Amory, Tom C. Cameron, Darren P. Croft, Nick Bell, Edward A. Codling
Software Mentions: 3
Published: over 5 years ago

10.1186/1752-0509-5-195

Model-based clustering reveals vitamin D dependent multi-centrality hubs in a network of vitamin-related proteins
Cited by: 15
Author(s): Thanh Phương Nguyễn, Marco Scotti, Melissa J. Morine, Corrado Priami
Software Mentions: 3
Published: over 14 years ago

10.1186/s12918-018-0550-5

RETRACTED ARTICLE: Detangling PPI networks to uncover functionally meaningful clusters
Cited by: 5
Author(s): Sarah Hall-Swan, Jake Crawford, Rebecca Newman, Lenore Cowen
Software Mentions: 3
Published: over 8 years ago

10.3389/fvets.2020.00219

Network Analysis of Cattle Movement in Mato Grosso Do Sul (Brazil) and Implications for Foot-and-Mouth Disease
Cited by: 9
Author(s): Taís Cristina de Menezes, Ivette Luna, Sílvia Helena Galvão de Miranda
Software Mentions: 3
Published: about 6 years ago

10.1186/1752-0509-8-12

Influence networks based on coexpression improve drug target discovery for the development of novel cancer therapeutics
Cited by: 10
Author(s): Nadia M. Penrod, Jason H. Moore
Software Mentions: 3
Published: over 12 years ago

10.1534/g3.119.400972

Network Analysis of Linkage Disequilibrium Reveals Genome Architecture in Chum Salmon
Cited by: 21
Author(s): Garrett J. McKinney, Megan V. McPhee, Carita E. Pascal, James E. Seeb, Lisa W. Seeb
Software Mentions: 3
Published: about 6 years ago

10.3390/genes9110519

mully: An R Package to Create, Modify and Visualize Multilayered Graphs
Cited by: 12
Author(s): Zaynab Hammoud, Frank Krämer
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12918-016-0329-5

Identification of key player genes in gene regulatory networks
Cited by: 32
Author(s): Maryam Nazarieh, Andreas Wiese, Thorsten Will, Mohamed Hamed, Volkhard Helms
Software Mentions: 3
Published: almost 10 years ago

10.1007/s41109-018-0087-y

An illustrated approach to Soft Textual Cartography
Cited by: 1
Author(s): Raphaël Ceré, Mattia Egloff
Software Mentions: 3
Published: almost 8 years ago

10.1186/1752-0509-6-32

Gene regulation is governed by a core network in hepatocellular carcinoma
Cited by: 14
Author(s): Zuguang Gu, Chenyu Zhang, Jin Wang
Software Mentions: 3
Published: about 14 years ago

10.3390/genes12030367

Multivariate Analysis Identifies Eight Novel Loci Associated with Meat Productivity Traits in Sheep
Cited by: 5
Author(s): Alexander S. Zlobin, Pavel S. Nikulin, Н. А. Волкова, N. A. Zinovieva, Б. С. Иолчиев, В. А. Багиров, П. М. Бородин, Т. И. Аксенович, Yakov A. Tsepilov
Software Mentions: 3
Published: over 5 years ago

10.1007/s12263-014-0408-4

Genetic associations with micronutrient levels identified in immune and gastrointestinal networks
Cited by: 12
Author(s): Melissa J. Morine, Jacqueline Pontes Monteiro, Carolyn Wise, Candee H. Teitel, Lisa Pence, Anna-leila Williams, Baitang Ning, Beverly McCabe‐Sellers, Catherine M. Champagne, J. Rick Turner, Beatrice Shelby, Margaret L. Bogle, Richard D. Beger, Corrado Priami, Jim Kaput
Software Mentions: 3
Published: about 12 years ago

10.1007/s12263-014-0439-x

White adipose tissue reference network: a knowledge resource for exploring health-relevant relations
Cited by: 10
Author(s): Thomas Kelder, Georg Summer, Martien P. M. Caspers, Evert M. van Schothorst, Jaap Keijer, Loes P. M. Duivenvoorde, К. Schimrigk, Anja Voigt, Laura Bohnert, Catalina Picó, M. Luisa Bonet, A. Dembińska-Kieć, Małgorzata Malczewska-Malec, Beata Kieć‐Wilk, Josep Maria del Bas, Antoni Caimari, Lluı́s Arola, Marjan van Erk, Ben van Ommen, Marijana Radonjić
Software Mentions: 3
Published: over 11 years ago

10.1186/s13104-018-3126-y

Modelling the structure of a ceRNA-theoretical, bipartite microRNA–mRNA interaction network regulating intestinal epithelial cellular pathways using R programming
Cited by: 12
Author(s): Jeffrey M. Robinson, Wendy A. Henderson
Software Mentions: 3
Published: over 8 years ago

10.1186/1756-0500-3-142

Using GeneReg to construct time delay gene regulatory networks
Cited by: 33
Author(s): Tao Huang, Lei Liu, Qian Zhou, Kang Tu, Yixue Li, Lu Xie
Software Mentions: 3
Published: about 16 years ago

10.1186/s13059-015-0592-6

BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies
Cited by: 110
Author(s): Ke Yuan, Thomas Sakoparnig, Florian Markowetz, Niko Beerenwinkel
Software Mentions: 3
Published: over 11 years ago

10.1186/s13059-015-0627-z

Evaluating intra- and inter-individual variation in the human placental transcriptome
Cited by: 45
Author(s): David A. Hughes, Martin Kircher, Zhisong He, Songlin Guo, Genevieve Fairbrother, Carlos S. Moreno, Philipp Khaitovich, Mark Stoneking
Software Mentions: 3
Published: over 11 years ago

10.1186/1756-0500-4-149

Assessment of replicate bias in 454 pyrosequencing and a multi-purpose read-filtering tool
Cited by: 45
Author(s): Jérôme Mariette, Céline Noirot, Christophe Klopp
Software Mentions: 3
Published: about 15 years ago

10.1186/s13059-019-1713-4

Single-cell transcriptomics unveils gene regulatory network plasticity
Cited by: 161
Author(s): Giovanni Iacono, Ramón Massoni-Badosa, Holger Heyn
Software Mentions: 3
Published: about 7 years ago

10.1186/s13059-019-1904-z

CHROMATIX: computing the functional landscape of many-body chromatin interactions in transcriptionally active loci from deconvolved single cells
Cited by: 21
Author(s): Alan Perez-Rathke, Qiu Sun, Boshen Wang, Valentina Boeva, Zongshu Shao, Jie Liang
Software Mentions: 3
Published: over 6 years ago

10.1186/s12889-018-5709-x

High-resolution epidemic simulation using within-host infection and contact data
Cited by: 21
Author(s): Vān Kính Nguyễn, Rafael Mikolajczyk, Esteban A. Hernandez‐Vargas
Software Mentions: 3
Published: about 8 years ago

10.1093/gbe/evw077

“Every Gene Is Everywhere but the Environment Selects”: Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis
Cited by: 80
Author(s): Marco Fondi, Antti Karkman, Manu Tamminen, Emanuele Bosi, Marko Virta, Renato Fani, Eric J. Alm, James O. McInerney
Software Mentions: 3
Published: about 10 years ago

10.1093/gbe/evy042

Conservation of Sex-Linked Markers among Conspecific Populations of a Viviparous Skink, Niveoscincus ocellatus, Exhibiting Genetic and Temperature-Dependent Sex Determination
Cited by: 38
Author(s): Peta Hill, Christopher P. Burridge, Tariq Ezaz, Erik Wapstra
Software Mentions: 3
Published: over 8 years ago

10.1186/1742-6405-8-26

HIV-1 mutational pathways under multidrug therapy
Cited by: 13
Author(s): Glenn Lawyer, André Altmann, Alexander Thielen, Maurizio Zazzi, Anders Sönnerborg, Thomas Lengauer
Software Mentions: 3
Published: over 15 years ago

10.1186/s12870-014-0188-4

Metabolite and transcript profiling of berry skin during fruit development elucidates differential regulation between Cabernet Sauvignon and Shiraz cultivars at branching points in the polyphenol pathway
Cited by: 109
Author(s): Asfaw Degu, Uri Hochberg, Noga Sikron, Luca Venturini, Genny Buson, Ryan Ghan, Inbar Plaschkes, Albert Batushansky, Vered Chalifa‐Caspi, Fulvio Mattivi, Massimo Delledonne, Mario Pezzotti, Shimon Rachmilevitch, Grant R. Cramer, Aaron Fait
Software Mentions: 3
Published: about 12 years ago

10.1186/s12870-020-2254-4

PlaPPISite: a comprehensive resource for plant protein-protein interaction sites
Cited by: 22
Author(s): Xiaodi Yang, Shiping Yang, Huan Qi, Tianpeng Wang, Hong Li, Ziding Zhang
Software Mentions: 3
Published: over 6 years ago

10.1186/s13073-021-00874-2

Human breast microbiome correlates with prognostic features and immunological signatures in breast cancer
Cited by: 85
Author(s): Alice Tzeng, Naseer Sangwan, Margaret Jia, Chin-Chih Liu, Karen Keslar, Erinn Downs‐Kelly, Robert L. Fairchild, Zahraa Al‐Hilli, Stephen R. Grobmyer, Charis Eng
Software Mentions: 3
Published: over 5 years ago

10.1186/s12860-020-00290-1

Impacts of drug resistance mutations on the structural asymmetry of the HIV-2 protease
Cited by: 4
Author(s): Pierre Laville, Sandrine Fartek, Natacha Cerisier, Delphine Flatters, Michel Petitjean, Leslie Regad
Software Mentions: 3
Published: about 6 years ago

10.1016/j.gpb.2018.01.001

Comparative Analysis of Human Genes Frequently and Occasionally Regulated by m 6 A Modification
Cited by: 3
Author(s): Yuan Zhou, Qinghua Cui
Software Mentions: 3
Published: over 8 years ago

10.1186/s40478-018-0524-2

Integrated proteomics and network analysis identifies protein hubs and network alterations in Alzheimer’s disease
Cited by: 111
Author(s): Qi Zhang, Cheng Ma, Marla Gearing, Peng George Wang, Lih‐Shen Chin, Lian Li
Software Mentions: 3
Published: over 8 years ago

10.1016/j.gpb.2019.09.004

Machine Learning to Detect Alzheimer’s Disease from Circulating Non-coding RNAs
Cited by: 63
Author(s): Nicole Ludwig, Tobias Fehlmann, Fabian Kern, M. Gogol, Walter Maetzler, Stephanie Deutscher, Simone Gurlit, Claudia Schulte, Anna‐Katharina von Thaler, Christian Deuschle, Florian Metzger, Daniela Berg, Ulrike Suenkel, Verena Keller, Christina Backes, Hans‐Peter Lenhof, Eckart Meese
Software Mentions: 3
Published: almost 7 years ago

10.1007/s11357-020-00195-z

Nursing homes and the elderly regarding the COVID-19 pandemic: situation report from Hungary
Cited by: 37
Author(s): Gábor Kemenesi, László Kornya, Gábor Endre Tóth, Kornélia Kurucz, Safia Zeghbib, B Somogyi, Viktor Zöldi, Péter Urbán, Róbert Herczeg, Ferenc Jakab
Software Mentions: 3
Published: about 6 years ago

10.1186/s12920-019-0597-1

A network view of microRNA and gene interactions in different pathological stages of colon cancer
Cited by: 5
Author(s): Jia Wen, Benika Hall, Xinghua Shi
Software Mentions: 3
Published: over 6 years ago

10.1186/s12916-016-0664-9

Evaluation in alcohol use disorders – insights from the nalmefene experience
Cited by: 18
Author(s): Florian Naudet, Clément Palpacuer, Rémy Boussageon, Bruno Laviolle
Software Mentions: 3
Published: almost 10 years ago

10.1038/s41396-021-00913-1

Erosion reduces soil microbial diversity, network complexity and multifunctionality
Cited by: 201
Author(s): Liping Qiu, Qian Zhang, Hansong Zhu, Peter B. Reich, Samiran Banerjee, Marcel G. A. van der Heijden, Michael J. Sadowsky, Satoshi Ishii, Xiaoxu Jia, Mingan Shao, Baoyuan Liu, Huan Jiang, Haiqiang Li, Xiaorong Wei
Software Mentions: 3
Published: over 5 years ago

10.1186/s12879-017-2895-6

Interaction of healthcare worker hands and portable medical equipment: a sequence analysis to show potential transmission opportunities
Cited by: 45
Author(s): Chetan Jinadatha, Frank J. Villamaria, John David Coppin, Charles Dale, Marjory Williams, Ryan Whitworth, Mark Stibich
Software Mentions: 3
Published: over 8 years ago

10.1007/s00251-017-1051-1

Signatures of historical selection on MHC reveal different selection patterns in the moor frog (Rana arvalis)
Cited by: 15
Author(s): Maria Cortázar‐Chinarro, Yvonne Meyer‐Lucht, Anssi Laurila, Jacob Höglund
Software Mentions: 3
Published: over 8 years ago

10.1186/s12879-021-06475-z

Association between tuberculosis in men and social network structure in Kampala, Uganda
Cited by: 5
Author(s): Paige B. Miller, Sarah Zalwango, Ronald Galiwango, Robert Kakaire, Juliet N. Sekandi, Lauren Steinbaum, John M. Drake, Christopher C. Whalen, Noah Kiwanuka
Software Mentions: 3
Published: almost 5 years ago

10.1172/jci.insight.140028

Identification of antigen-specific TCR sequences based on biological and statistical enrichment in unselected individuals
Cited by: 9
Author(s): Neal Smith, Bert Ruiter, Yamini Virkud, Ang A. Tu, Brinda Monian, James Moon, J. Christopher Love, Wayne Shreffler
Software Mentions: 3
Published: about 5 years ago

10.1200/CCI.17.00079

Overcoming the Straw Man Effect in Oncology: Visualization and Ranking of Chemotherapy Regimens Using an Information Theoretic Approach
Cited by: 1
Author(s): Jeremy L. Warner, Peter Yang, Gil Alterovitz
Software Mentions: 3
Published: over 8 years ago

10.1186/s12865-019-0297-9

Comprehensive analyses of long non-coding RNA expression profiles by RNA sequencing and exploration of their potency as biomarkers in psoriatic arthritis patients
Cited by: 12
Author(s): Tao Yue, Mei Ji, Huanru Qu, Mengru Guo, Fengmin Bai, Zhanming Zhang, Weifeng Wang, Xuming Gong, Zhenghua Zhang
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12913-021-06798-2

Empirically identified networks of healthcare providers for adults with mental illness
Cited by: 2
Author(s): Joshua Breslau, Beth Dana, Harold Alan Pincus, Marcela Horvitz-Lennon, Luke J. Matthews
Software Mentions: 3
Published: almost 5 years ago

10.1128/JB.00245-17

Polyvalent Proteins, a Pervasive Theme in the Intergenomic Biological Conflicts of Bacteriophages and Conjugative Elements
Cited by: 28
Author(s): Lakshminarayan M. Iyer, A. Maxwell Burroughs, Swadha Anand, Robson Francisco de Souza, L. Aravind
Software Mentions: 3
Published: almost 9 years ago

10.1021/acs.jctc.0c01308

Reconstruction of ARNT PAS-B Unfolding Pathways by Steered Molecular Dynamics and Artificial Neural Networks
Cited by: 12
Author(s): Stefano Motta, Alessandro Pandini, Arianna Fornili, Laura Bonati
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-019-5603-7

Genomic comparison of serogroups O159 and O170 with other Vibrio cholerae serogroups
Cited by: 8
Author(s): Zhenpeng Li, Xin Lü, Duochun Wang, Wei Li Liang, Jingyun Zhang, Jie Li, Jialiang Xu, Bo Pang, Biao Kan
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-16-S10-S7

Reconstruction of composite regulator-target splicing networks from high-throughput transcriptome data
Cited by: 7
Author(s): Panagiotis Papasaikas, Arvind Rao, Peter Huggins, Juan Valcárcel, A. Javier Lopez
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.ppat.1001074

Global Genotype-Phenotype Correlations in Pseudomonas aeruginosa
Cited by: 11
Author(s): Claudia Pommerenke, Mathias Müsken, Tanja Becker, Andreas Dötsch, Frank Klawonn, Susanne Häußler
Software Mentions: 3
Published: almost 16 years ago

10.1371/journal.ppat.1003403

The Escherichia coli Phosphotyrosine Proteome Relates to Core Pathways and Virulence
Cited by: 65
Author(s): Anne Marie Hansen, Raghothama Chaerkady, Jyoti Sharma, J. Javier Díaz-Mejía, Nidhi Tyagi, Santosh Renuse, Harrys K.C. Jacob, Sneha M. Pinto, Nandini A. Sahasrabuddhe, Min‐Sik Kim, Bernard Delanghe, Narayanaswamy Srinivasan, Andrew Emili, James B. Kaper, Akhilesh Pandey
Software Mentions: 3
Published: about 13 years ago

10.1016/j.prevetmed.2021.105443

Spatial and temporal variation in proximity networks of commercial dairy cattle in Great Britain
Cited by: 5
Author(s): Helen R. Fielding, Matthew J. Silk, Trevelyan J. McKinley, Richard J. Delahay, Jared K. Wilson‐Aggarwal, Laetitia Gauvin, Laura Ozella, Ciro Cattuto, Robbie A. McDonald
Software Mentions: 3
Published: almost 5 years ago

10.1098/rspb.2017.2116

Deep pelagic food web structure as revealed by <i>in situ</i> feeding observations
Cited by: 74
Author(s): C. Anela Choy, Steven H. D. Haddock, Bruce H. Robison
Software Mentions: 3
Published: over 8 years ago

10.1098/rspb.2017.1899

Model recommendations meet management reality: implementation and evaluation of a network-informed vaccination effort for endangered Hawaiian monk seals
Cited by: 16
Author(s): Stacie J. Robinson, Michelle Barbieri, Samantha Murphy, Jason D. Baker, Albert L. Harting, Meggan E. Craft, Charles L. Littnan
Software Mentions: 3
Published: over 8 years ago

10.1098/rspb.2018.0023

Collective ritual and social support networks in rural South India
Cited by: 23
Author(s): Eleanor A. Power
Software Mentions: 3
Published: about 8 years ago

10.1098/rspb.2019.2880

A natural catastrophic turnover event: individual sociality matters despite community resilience in wild house mice
Cited by: 17
Author(s): Julian C. Evans, Jonas I. Liechti, Bruce Boatman, Barbara König
Software Mentions: 3
Published: about 6 years ago

10.1186/s42523-021-00116-1

Molecular and culture-based assessment of the microbiome in a zebrafish (Danio rerio) housing system during set-up and equilibration
Cited by: 4
Author(s): Aaron C. Ericsson, Susheel Bhanu Busi, Daniel R. Davis, Henda Nabli, David C. Eckhoff, Rebecca A. Dorfmeyer, Giedre Turner, Payton S. Oswalt, Marcus J Crim, Elizabeth C. Bryda
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12864-016-3066-7

Path2enet: generation of human pathway-derived networks in an expression specific context
Cited by: 1
Author(s): Conrad Droste, Javier De Las Rivas
Software Mentions: 3
Published: almost 10 years ago

10.1186/s12864-021-07815-8

TAD cliques predict key features of chromatin organization
Cited by: 4
Author(s): Tharvesh Moideen Liyakat Ali, Annaël Brunet, Philippe Collas, Jonas Paulsen
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-019-53569-5

Qualitative microbiome profiling along a wastewater system in Kampala, Uganda
Cited by: 4
Author(s): Pierre H. H. Schneeberger, Samuel Fuhrimann, Sören L. Becker, Joël F. Pothier, Brion Duffy, Christian Beuret, Jürg E. Frey, Jürg Utzinger
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-019-54720-y

Statistical characteristics of amino acid covariance as possible descriptors of viral genomic complexity
Cited by: 7
Author(s): C. K. Sruthi, Meher K. Prakash
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-16-S11-S4

A method for developing regulatory gene set networks to characterize complex biological systems
Cited by: 1
Author(s): Chayaporn Suphavilai, Zhu Li, Jake Y. Chen
Software Mentions: 3
Published: over 10 years ago

Projects: cran: igraph

Science Score: 100/100

Bonuses:

Papers Mentioning igraph 1,555