cran: igraph | Projects | Ecosyste.ms: Papers

10.1007/s11306-021-01841-z

IonFlow: a galaxy tool for the analysis of ionomics data sets
Cited by: 2
Author(s): Jacopo Iacovacci, Wenjian Lin, Julian L. Griffin, Robert C. Glen
Software Mentions: 3
Published: about 3 years ago

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: over 3 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: over 3 years ago

10.3390/ijms22020953

Steroidal Regulation of Oviductal microRNAs Is Associated with microRNA-Processing in Beef Cows
Cited by: 9
Author(s): Ángela María Gonella-Diaza, E. A. Lopes, Kauê Ribeiro da Silva, Ricardo Perecin Nociti, Gabriella Mamede Andrade, Jorge Eduardo Atuesta-Bustos, Juliano Coelho da Silveira, Flávio Vieira Meirelles, Mário Binelli
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0111262

Consensus between Pipelines in Structural Brain Networks
Cited by: 20
Author(s): Christopher S. Parker, Fani Deligianni, M. Jorge Cardoso, Pankaj Daga, Marc Modat, Michael Dayan, Chris A. Clark, Sébastien Ourselin, Jonathan D. Clayden
Software Mentions: 3
Published: about 10 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: almost 9 years ago

10.1371/journal.pcbi.1006474

Genomic data integration systematically biases interactome mapping
Cited by: 31
Author(s): Michael A. Skinnider, R. Greg Stacey, Leonard J. Foster
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 5 years ago

10.1371/journal.pone.0123545

Characterizing Task-Based OpenMP Programs
Cited by: 7
Author(s): Ananya Muddukrishna, Peter Jönsson, Mats Brorsson
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pcbi.1005160

Markov Networks of Collateral Resistance: National Antimicrobial Resistance Monitoring System Surveillance Results from Escherichia coli Isolates, 2004-2012
Cited by: 16
Author(s): William J. Love, Kelson Zawack, James G. Booth, Yrjo T. Gröhn, Cristina Lanzas
Software Mentions: 3
Published: about 8 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: almost 5 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: over 3 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: almost 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: over 4 years ago

10.1038/s41598-019-57142-y

Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain
Cited by: 13
Author(s): Demetrio Raldúa, Marta Casado, Eva Prats, Melissa Faria, Francesc Puig‐Castellví, Yolanda Pérez, Ignacio Alfonso, Chuan-Yu Hsu, Mark A. Arick, Natàlia García-Reyero, Tamar Ziv, Shani Ben-Lulu, Arie Admon, Benjamı́n Piña
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-019-57191-3

Decision-making process during collective movement initiation in golden snub-nosed monkeys (Rhinopithecus roxellana)
Cited by: 8
Author(s): YangQuan Chen, Ruliang Pan, Wang Xiao-wei, Xiao-Guang Qi, Zhao Hong-yan, Songtao Guo, Yi Ren, Weiwei Fu, Zirui Zhu, Baoguo Li
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0246687

Comparison of wild rice (Oryza longistaminata) tissues identifies rhizome-specific bacterial and archaeal endophytic microbiomes communities and network structures
Cited by: 7
Author(s): Xiaojue Peng, Jian Xie, Wenzhuo Li, Haizhu Xie, Yaohui Cai, Xia Ding
Software Mentions: 3
Published: almost 4 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: almost 7 years ago

10.1038/s41598-020-60737-5

L-HetNetAligner: A novel algorithm for Local Alignment of Heterogeneous Biological Networks
Cited by: 18
Author(s): Marianna Milano, Tijana Milenković, Mario Cannataro, Pietro Hiram Guzzi
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0232458

A network analysis of research productivity by country, discipline, and wealth
Cited by: 35
Author(s): Klaus Jaffé, Enrique ter Horst, Laura H Gunn, Juan Diego Zambrano, Germán Molina
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0176500

Simulation of the dynamics of primary immunodeficiencies in CD4+ T-cells
Cited by: 4
Author(s): Gabriel Teku, Mauno Vihinen
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0202615

Tracking a serial killer: Integrating phylogenetic relationships, epidemiology, and geography for two invasive meningococcal disease outbreaks
Cited by: 8
Author(s): Ifeoma Ezeoke, Madeline R. Galac, Ying Lin, Alvin T. Liem, Pierce A. Roth, Andy Kilianski, Henry S. Gibbons, Danielle Bloch, John Kornblum, Paula Del Rosso, Daniel Janies, Don Weiss
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pcbi.1003243

Simple Topological Features Reflect Dynamics and Modularity in Protein Interaction Networks
Cited by: 38
Author(s): Yuri Pritykin, Mona Singh
Software Mentions: 3
Published: about 11 years ago

10.1186/1471-2105-11-378

Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data
Cited by: 366
Author(s): Petr Novák, Pavel Neumann, Jiří Macas
Software Mentions: 3
Published: over 14 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: about 9 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: almost 4 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: over 4 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: almost 4 years ago

10.1038/s41598-020-67718-8

No evidence for a relationship between social closeness and similarity in resting-state functional brain connectivity in schoolchildren
Cited by: 3
Author(s): Carolyn Beth McNabb, Laura Grace Burgess, Amy Fancourt, Nancy Mulligan, Lily FitzGibbon, Patricia M. Riddell, Kou Murayama
Software Mentions: 3
Published: over 4 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: almost 4 years ago

10.1186/s42523-021-00088-2

Effect of milk replacer allowance on calf faecal bacterial community profiles and fermentation
Cited by: 11
Author(s): Shiv Kumar, M. A. Khan, Emma Beijer, Jinxin Liu, Katherine K. Lowe, Wayne Young, David A. Mills, Christina D. Moon
Software Mentions: 3
Published: over 3 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: almost 10 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: almost 8 years ago

10.1371/journal.pone.0248194

Effects of precipitation change and nitrogen addition on the composition, diversity, and molecular ecological network of soil bacterial communities in a desert steppe
Cited by: 24
Author(s): Meiqing Jia, Zhiwei Gao, Huijun Gu, Chenyu Zhao, Meiqi Liu, Fanhui Liu, Lina Xie, Lichun Wang, Guogang Zhang, Yuhua Liu, Guodong Han
Software Mentions: 3
Published: over 3 years ago

10.1186/s12859-016-0989-6

caOmicsV: an R package for visualizing multidimensional cancer genomic data
Cited by: 3
Author(s): Hongen Zhang, Paul S. Meltzer, Sean Davis
Software Mentions: 3
Published: over 8 years ago

10.1186/s12859-019-3041-9

Analyzing the regulation of miRNAs on protein-protein interaction network in Hodgkin lymphoma
Cited by: 2
Author(s): Huimin Lei, Wenxu Liu, Jiarui Si, Ju Wang, Tao Zhang
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-020-72477-7

Play fighting social networks do not predict injuries from later aggression
Cited by: 12
Author(s): Simon P. Turner, Jennifer E. Weller, Irene Camerlink, Gareth Arnott, Taegyu Choi, Andrea Doeschl‐Wilson, Marianne Farish, Simone Foister
Software Mentions: 3
Published: about 4 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: about 4 years ago

10.1038/s41598-020-73591-2

The spatial and temporal dynamics of global meat trade networks
Cited by: 15
Author(s): Min Gon Chung, Kelly Kapsar, Kenneth A. Frank, Jianguo Liu
Software Mentions: 3
Published: about 4 years ago

10.1155/2021/8533464

Identification of a Nomogram from Ferroptosis-Related Long Noncoding RNAs Signature to Analyze Overall Survival in Patients with Bladder Cancer
Cited by: 22
Author(s): Yuanshan Cui, Yumeng Chai, Xuanyan Che, Yong Zhang
Software Mentions: 3
Published: about 3 years ago

10.1002/ece3.7274

Temporal patterns in the social network of core units in Rwenzori Angolan colobus monkeys: Effects of food availability and interunit dispersal
Cited by: 2
Author(s): Frances V. Adams, T. Jean M. Arseneau‐Robar, Tyler R. Bonnell, Samantha M. Stead, Julie A. Teichroeb
Software Mentions: 3
Published: over 3 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: almost 4 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: almost 14 years ago

10.1371/journal.pcbi.1006098

Topological and statistical analyses of gene regulatory networks reveal unifying yet quantitatively different emergent properties
Cited by: 44
Author(s): Wilberforce Zachary Ouma, Katja Pogacar, Erich Grotewold
Software Mentions: 3
Published: over 6 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: almost 10 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 6 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 3 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: almost 11 years ago

10.1038/s41598-021-85281-8

Characterization of the microbial communities in wheat tissues and rhizosphere soil caused by dwarf bunt of wheat
Cited by: 13
Author(s): Tongshuo Xu, Wenli Jiang, Dandan Qin, Taiguo Liu, Zhang Jian-min, Wanquan Chen, Li Gao
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0148135

Symbiotic Bacteria in Gills and Guts of Chinese Mitten Crab (Eriocheir sinensis) Differ from the Free-Living Bacteria in Water
Cited by: 71
Author(s): Meiling Zhang, Yanfa Sun, Liqiao Chen, Chen Cai, Fang Qiao, Zhen‐Yu Du, Erchao Li
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0078059

Perturbation Centrality and Turbine: A Novel Centrality Measure Obtained Using a Versatile Network Dynamics Tool
Cited by: 25
Author(s): Kristóf Z. Szalay, Péter Csermely
Software Mentions: 3
Published: about 11 years ago

10.1038/s41598-021-86124-2

Fine scale infectious disease modeling using satellite-derived data
Cited by: 2
Author(s): Nistara Randhawa, Hugo Mailhot, Duncan Temple Lang, Beatriz Martínez‐López, Kirsten Gilardi, Jonna A. K. Mazet
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pcbi.1002002

The Free Energy Landscape of Small Molecule Unbinding
Cited by: 94
Author(s): Danzhi Huang, Amedeo Caflisch
Software Mentions: 3
Published: almost 14 years ago

10.1038/s41598-021-86409-6

Variations in Schedule III prescription patterns in a Medicaid population pre- and post-policy
Cited by: 0
Author(s): Radhakrishnan Nagarajan, Jeffery Talbert, Craig S. Miller, Jeffrey L. Ebersole
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0129745

'SEEDY' (Simulation of Evolutionary and Epidemiological Dynamics): An R Package to Follow Accumulation of Within-Host Mutation in Pathogens
Cited by: 23
Author(s): Colin J. Worby, Timothy D. Read
Software Mentions: 3
Published: over 9 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: over 4 years ago

10.1371/journal.pcbi.1006786

Spatial clustering and common regulatory elements correlate with coordinated gene expression
Cited by: 23
Author(s): Jingyu Zhang, Hengyu Chen, Ruoyan Li, David A. Taft, Guang Yao, Fan Bai, Jianhua Xing
Software Mentions: 3
Published: over 5 years ago

10.1002/ece3.2983

Geographic characteristics of sable (<i>Martes zibellina</i> ) distribution over time in Northeast China
Cited by: 7
Author(s): Rui Zhang, Li Yang, Li Ai, Yang Qin-ke, Minhao Chen, Jingxi Li, Lei Yang, Xiaofeng Luan
Software Mentions: 3
Published: over 7 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: about 10 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: almost 14 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: almost 13 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 6 years ago

10.7554/eLife.13125

Sequential phenotypic constraints on social information use in wild baboons
Cited by: 35
Author(s): Alecia J. Carter, Miquel Torrents-Ticó, Guy Cowlishaw
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0173548

Characterization of the mechanism of drug-drug interactions from PubMed using MeSH terms
Cited by: 28
Author(s): Ling Yin, Bryan Figler, Hong Huang, Yi-Cheng Tu, Wang Ju, Feng Cheng
Software Mentions: 3
Published: over 7 years ago

10.1038/s42003-019-0333-6

Computational identification of co-evolving multi-gene modules in microbial biosynthetic gene clusters
Cited by: 20
Author(s): Francesco Del Carratore, Konrad Zych, Matthew Cummings, Eriko Takano, Marnix H. Medema, Rainer Breitling
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-90498-8

Evolution of networks of protein domain organization
Cited by: 20
Author(s): M. Fayez Aziz, Gustavo Caetano‐Anollés
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-021-93122-x

Quantum inspired community detection for analysis of biodiversity change driven by land-use conversion and climate change
Cited by: 2
Author(s): Sana Akbar, Sri Khetwat Saritha
Software Mentions: 3
Published: over 3 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: almost 11 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: about 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: over 12 years ago

10.1002/ece3.1632

Modeling directional spatio-temporal processes in island biogeography
Cited by: 11
Author(s): José C. Carvalho, Pedro Cardoso, François Rigal, Kostas A. Triantis, Paulo A. V. Borges
Software Mentions: 3
Published: about 9 years ago

10.3390/plants9081008

Semi-Targeted Metabolomics to Validate Biomarkers of Grape Downy Mildew Infection Under Field Conditions
Cited by: 13
Author(s): Kévin Billet, Magdalena Malinowska, Thibaut Munsch, Marianne Unlubayir, Sophie Adler, Guillaume Delanoue, Arnaud Lanoue
Software Mentions: 3
Published: over 4 years ago

10.18632/oncotarget.25216

Parenclitic networks for predicting ovarian cancer
Cited by: 25
Author(s): Harry J. Whitwell, Oleg Blyuss, Usha Menon, John F. Timms, Alexey Zaikin
Software Mentions: 3
Published: over 6 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: almost 7 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: over 14 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: over 13 years ago

10.1186/s12906-021-03340-z

A systems pharmacology approach based on oncogenic signalling pathways to determine the mechanisms of action of natural products in breast cancer from transcriptome data
Cited by: 2
Author(s): Regan Odongo, Asuman Demiroğlu-Zergeroğlu, Tunahan Çakır
Software Mentions: 3
Published: over 3 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: over 4 years ago

10.3390/ijms22105056

Cross-Predicting Essential Genes between Two Model Eukaryotic Species Using Machine Learning
Cited by: 6
Author(s): Túlio de Lima Campos, Pasi K. Korhonen, Neil D. Young
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0083167

Structural Propensities of Human Ubiquitination Sites: Accessibility, Centrality and Local Conformation
Cited by: 9
Author(s): Yuan Zhou, Sixue Liu, Jiangning Song, Ziding Zhang
Software Mentions: 3
Published: almost 11 years ago

10.1186/1751-0473-7-12

RMol: a toolset for transforming SD/Molfile structure information into R objects
Cited by: 1
Author(s): Martin Grábner, Курт Вармуза, Matthias Dehmer
Software Mentions: 3
Published: about 12 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: over 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: about 6 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: over 4 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: over 10 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: almost 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: over 4 years ago

10.1371/journal.pone.0242621

Victims, offenders and victim-offender overlaps of knife crime: A social network analysis approach using police records
Cited by: 11
Author(s): Louis Bailey, Vincent Harinam, Barak Ariel
Software Mentions: 3
Published: almost 4 years ago

10.3389/fmicb.2016.00068

Using “Omics” and Integrated Multi-Omics Approaches to Guide Probiotic Selection to Mitigate Chytridiomycosis and Other Emerging Infectious Diseases
Cited by: 105
Author(s): Eria A. Rebollar, Rachael E. Antwis, Matthew H. Becker, Lisa K. Belden, Molly C. Bletz, Robert M. Brucker, Xavier A. Harrison, Myra C. Hughey, Jordan G. Kueneman, Andrew H. Loudon, Valerie J. McKenzie, Daniel Medina, Kevin P. C. Minbiole, Louise A. Rollins‐Smith, Jenifer B. Walke, Sophie Weiss, Douglas C. Woodhams, Reid N. Harris
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12859-019-2915-1

Difficulty in inferring microbial community structure based on co-occurrence network approaches
Cited by: 103
Author(s): Hokuto Hirano, Kazuhiro Takemoto
Software Mentions: 3
Published: over 5 years ago

10.1038/tp.2017.37

Modeling anorexia nervosa: transcriptional insights from human iPSC-derived neurons
Cited by: 21
Author(s): Priscilla D. Negraes, Fernanda R. Cugola, Roberto H. Herai, Cleber A. Trujillo, Alexandre S. Cristino, Thanathom Chailangkarn, Alysson R. Muotri, Vikas Duvvuri
Software Mentions: 3
Published: over 7 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: over 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: over 3 years ago

10.3389/fmicb.2018.03095

Bacterial and Archaeal Viruses of Himalayan Hot Springs at Manikaran Modulate Host Genomes
Cited by: 23
Author(s): Anukriti Sharma, Matthias Schmidt, Bärbel Kiesel, Nitish Kumar Mahato, Lauren Cralle, Yogendra Singh, Hans H. Richnow, Jack A. Gilbert, Wyatt Arnold, Rup Lal
Software Mentions: 3
Published: almost 6 years ago

10.1098/rstb.2019.0009

Using social network analysis of mixed-species groups in African savannah herbivores to assess how community structure responds to environmental change
Cited by: 18
Author(s): Kristine Meise, Daniel W. Franks, Jakob Bro‐Jørgensen
Software Mentions: 3
Published: over 5 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: almost 5 years ago

10.18632/oncotarget.8308

Dynamic epigenetic changes to <i>VHL</i> occur with sunitinib in metastatic clear cell renal cancer
Cited by: 14
Author(s): Grant D. Stewart, Thomas Powles, Christophe Van Neste, Alison Meynert, Fiach C. O’Mahony, A. Douglas Laird, Dieter Deforce, Filip Van Nieuwerburgh, Geert Trooskens, Wim Van Criekinge, Tim De Meyer, David J. Harrison
Software Mentions: 3
Published: over 8 years ago

10.1128/mBio.01793-16

Role of the ESCRT Complexes in Telomere Biology
Cited by: 9
Author(s): Anna K. Dieckmann, Vera Babin, Yaniv Harari, Roland Eils, Rainer König, Brian Luke, Martin Kupiec
Software Mentions: 3
Published: almost 8 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: over 8 years ago

10.1128/mBio.02002-18

Network-Guided Discovery of Influenza Virus Replication Host Factors
Cited by: 22
Author(s): Emily E. Ackerman, Eiryo Kawakami, Manami Katoh, Tokiko Watanabe, Shinji Watanabe, Yuriko Tomita, Tiago J. S. Lopes, Yoshikazu Matsuoka, Hiroaki Kitano, Jason E. Shoemaker, Yoshihiro Kawaoka
Software Mentions: 3
Published: almost 6 years ago

Projects: cran: igraph

Papers Mentioning igraph 1,555