cran: igraph | Projects | Ecosyste.ms: Papers

10.1038/srep09512

Uncovering RNA binding proteins associated with age and gender during liver maturation
Cited by: 9
Author(s): Praneeet Chaturvedi, Yaseswini Neelamraju, Waqar Arif, Auinash Kalsotra, Sarath Chandra Janga
Software Mentions: 3
Published: over 11 years ago

10.1038/s41598-019-39796-w

Selecting variants of unknown significance through network-based gene-association significantly improves risk prediction for disease-control cohorts
Cited by: 17
Author(s): Anastasis Oulas, George Minadakis, Margarita Zachariou
Software Mentions: 3
Published: over 7 years ago

10.1038/srep42638

FocusHeuristics – expression-data-driven network optimization and disease gene prediction
Cited by: 16
Author(s): Markus Ernst, Yang Du, Gregor Warsow, Mohamed Hamed, Nicole Endlich, Karlhans Endlich, Hugo Murua Escobar, Lisa-Madeleine Sklarz, Sina Sender, Christian Junghanß, Steffen Möller, Georg Fuellen, Stephan Struckmann
Software Mentions: 3
Published: over 9 years ago

10.1038/srep28429

Exploring pig trade patterns to inform the design of risk-based disease surveillance and control strategies
Cited by: 38
Author(s): Claire Guinat, Anne A. Relun, Ben Wall, Aaron L. Morris, Lucas Dixon, Dirk U. Pfeiffer
Software Mentions: 3
Published: about 10 years ago

10.1038/s41598-018-20721-6

Network analysis of coronary artery disease risk genes elucidates disease mechanisms and druggable targets
Cited by: 42
Author(s): Harri Lempiäinen, Ingrid Brænne, Tom Michoel, Vinicius Tragante, Baiba Vilne, Tom R. Webb, Theodosios Kyriakou, Johannes Eichner, Lingyao Zeng, Christina Willenborg, Oscar Franzén, Arno Ruusalepp, Anuj Goel, Sander W. van der Laan, Claudia Biegert, Stephen E. Hamby, Husain Ahammad Talukdar, Hassan Foroughi Asl, Martin Dichgans, Tobias Dreker, Mira Graettinger, Philip Gribbon, Thorsten Kessler, Rainer Malik, Matthias Prestel, Barbara Stiller, Christine Schofield, Gérard Pasterkamp, Hugh Watkins, Nilesh J. Samani, Timo Wittenberger, Jeanette Erdmann, Heribert Schunkert, Folkert W. Asselbergs, Johan Björkegren
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-018-37706-0

Epidemiological and molecular forensics of cholera recurrence in Haiti
Cited by: 16
Author(s): Stanislas Rebaudet, Sandra Moore, Emmanuel Rossignol, Hervé Bogreau, Jean Gaudart, Anne‐Cécile Normand, Marie-José Laraque, Paul Adrien, Jacques Boncy, Renaud Piarroux
Software Mentions: 3
Published: over 7 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 5 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

10.1007/s13593-021-00668-1

Social-ecological analysis of timely rice planting in Eastern India
Cited by: 7
Author(s): Anton Urfels, Andrew J. McDonald, Gerardo van Halsema, P.C. Struik, Pankaj Kumar, R. K. Malik, Shishpal Poonia, Balwinder-Singh, Deepak Singh, Mukesh Kumar Singh, Timothy J. Krupnik
Software Mentions: 3
Published: over 5 years ago

10.1016/j.anbehav.2015.12.007

Measuring the robustness of network community structure using assortativity
Cited by: 64
Author(s): Daizaburo Shizuka, Damien R. Farine
Software Mentions: 3
Published: over 10 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 5 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

10.1007/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

10.1186/1471-2105-13-75

Quantitatively integrating molecular structure and bioactivity profile evidence into drug-target relationship analysis
Cited by: 5
Author(s): Tianlei Xu, Ruixin Zhu, Qi Liu, Zhiwei Cao
Software Mentions: 3
Published: about 14 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: about 7 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: about 16 years ago

10.1186/s12859-019-2900-8

Identifying lncRNA-mediated regulatory modules via ChIA-PET network analysis
Cited by: 10
Author(s): Denise Thiel, Nataša Djurdjevac Conrad, Evgenia Ntini, Ria X. Peschutter, Heike Siebert, Annalisa Marsico
Software Mentions: 3
Published: about 7 years ago

10.1186/1471-2105-16-S13-S9

Understanding and predicting binding between human leukocyte antigens (HLAs) and peptides by network analysis
Cited by: 18
Author(s): Heng Luo, Yue Hao, Hui Wen Ng, Leming Shi, Weida Tong, William B. Mattes, Donna L. Mendrick, Huasheng Hong
Software Mentions: 3
Published: over 10 years ago

10.1186/s12859-021-04155-y

DeepNetBim: deep learning model for predicting HLA-epitope interactions based on network analysis by harnessing binding and immunogenicity information
Cited by: 13
Author(s): Xiaoyun Yang, Liyuan Zhao, Wei Fang, Jing Li
Software Mentions: 3
Published: about 5 years ago

10.1186/s12859-018-2426-5

SyNDI: synchronous network data integration framework
Cited by: 1
Author(s): Erno Lindfors, Jesse C. J. van Dam, Carolyn M.C. Lam, Niels A. Zondervan, Vítor A. P. Martins dos Santos, María Suárez-Diez
Software Mentions: 3
Published: over 7 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: almost 7 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 10 years ago

10.1186/s12885-019-6180-5

Genome-wide expression profiling in colorectal cancer focusing on lncRNAs in the adenoma-carcinoma transition
Cited by: 35
Author(s): Alexandra Kalmár, Zsófia Brigitta Nagy, Orsolya Galamb, István Csabai, András Bodor, Barnabás Wichmann, Gábor Valcz, Barbara Kinga Barták, Zsolt Tulassay, Péter Igaz, Béla Molnár
Software Mentions: 3
Published: over 6 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: about 5 years ago

10.1186/s12862-015-0534-7

A comparison of human and mouse gene co-expression networks reveals conservation and divergence at the tissue, pathway and disease levels
Cited by: 86
Author(s): Gianni Monaco, Sipko van Dam, João Luis Casal Novo Ribeiro, Anis Larbi, João Pedro de Magalhães
Software Mentions: 3
Published: over 10 years ago

10.1186/s12862-017-1101-1

Musculoskeletal networks reveal topological disparity in mammalian neck evolution
Cited by: 25
Author(s): Patrick Arnold, Borja Esteve‐Altava, Martin S. Fischer
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2164-15-1144

Co-acting gene networks predict TRAIL responsiveness of tumour cells with high accuracy
Cited by: 1
Author(s): Paul G. O’Reilly, Csaba Ortutay, Gráinne Gernon, Enda O’Connell, Cathal Seoighe, Susan Boyce, Luís Serrano, Éva Szegezdi
Software Mentions: 3
Published: over 11 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

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

10.1186/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

10.1186/1471-2164-16-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

10.1186/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/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

10.1186/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/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

10.1186/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

10.1186/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

10.1186/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/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

10.1186/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/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/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

10.1186/1756-0500-4-149

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

10.1186/1756-0500-3-142

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/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

10.1186/1752-0509-6-32

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

10.1186/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

10.1186/1752-0509-8-12

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

10.1186/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

10.1186/1752-0509-5-195

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

10.1186/1752-0509-4-179

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

10.1186/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

10.1093/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

10.1042/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

10.1155/2015/245075

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

10.1186/1745-6150-6-31

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

10.1242/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

10.1155/2017/1016305

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

10.1155/2015/852341

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

10.3390/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

10.1093/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

10.1186/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

10.1002/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

10.1089/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

10.1186/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

10.1155/2021/9960241

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

10.3390/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

10.1007/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: almost 5 years ago

10.1111/2041-210X.12751

Measuring site fidelity and spatial segregation within animal societies
Cited by: 16
Author(s): Thomas O. Richardson, Luca Giuggioli, Nigel R. Franks, Ana B. Sendova‐Franks
Software Mentions: 3
Published: over 9 years ago

10.1186/s40168-021-01033-w

High throughput sequencing provides exact genomic locations of inducible prophages and accurate phage-to-host ratios in gut microbial strains
Cited by: 19
Author(s): Mirjam Zünd, Hans‐Joachim Ruscheweyh, Christopher M. Field, Natalie Meyer, Miguelangel Cuenca, Daniel Hoces, Wolf‐Dietrich Hardt, Shinichi Sunagawa
Software Mentions: 3
Published: over 5 years ago

10.1186/s40168-017-0369-0

Catalogue of antibiotic resistome and host-tracking in drinking water deciphered by a large scale survey
Cited by: 197
Author(s): Liping Ma, Bing Li, Xiaotao Jiang, Yulin Wang, Yu Xia, Andong Li, Tong Zhang
Software Mentions: 3
Published: over 8 years ago

10.1186/s40168-020-00857-2

Earth microbial co-occurrence network reveals interconnection pattern across microbiomes
Cited by: 202
Author(s): Bin Ma, Yiling Wang, Shudi Ye, Shan Liu, Erinne Stirling, Jack A. Gilbert, Karoline Faust, Rob Knight, Janet K. Jansson, César Cardona, Lisa Röttjers, Jia‐Zhuang Xu
Software Mentions: 3
Published: about 6 years ago

10.1186/s40168-021-00999-x

Genomic evidence for sulfur intermediates as new biogeochemical hubs in a model aquatic microbial ecosystem
Cited by: 25
Author(s): Adrien Vigneron, Perrine Cruaud, Alexander I. Culley, Raoul-Marie Couture, Connie Lovejoy, Warwick F. Vincent
Software Mentions: 3
Published: over 5 years ago

10.1186/s40168-021-01079-w

Low shifts in salinity determined assembly processes and network stability of microeukaryotic plankton communities in a subtropical urban reservoir
Cited by: 158
Author(s): Yuanyuan Mo, Peng Feng, Xiaofei Gao, Peng Xiao, Ramiro Logares, Erik Jeppesen, Kexin Ren, Yuanyuan Xue, Jun Yang
Software Mentions: 3
Published: about 5 years ago

10.1186/s40168-020-00876-z

Genomic and transcriptomic insights into methanogenesis potential of novel methanogens from mangrove sediments
Cited by: 41
Author(s): Cui-Jing Zhang, Jie Pan, Yang Liu, Changhai Duan, Meng Li
Software Mentions: 3
Published: about 6 years ago

10.3390/microorganisms8111677

The Microbial Composition in Circumneutral Thermal Springs from Chignahuapan, Puebla, Mexico Reveals the Presence of Particular Sulfur-Oxidizing Bacterial and Viral Communities
Cited by: 9
Author(s): Hugo G Castelán-Sánchez, Pablo M Meza-Rodríguez, Erika Carrillo, David I Ríos-Vázquez, Arturo Liñan-Torres, Ramón Alberto Batista-García, Ernesto Pérez‐Rueda, Norma Elena Rojas-Ruíz, Sonia Dávila-Ramos
Software Mentions: 3
Published: over 5 years ago

10.1038/s41380-018-0200-8

Lipidome alterations in human prefrontal cortex during development, aging, and cognitive disorders
Cited by: 60
Author(s): Qianhui Yu, Zhisong He, Dmitry Zubkov, Shouxiong Huang, Ilia Kurochkin, Xiaode Yang, Tobias B. Halene, Lothar Willmitzer, Patrick Giavalisco, Schahram Akbarian, Philipp Khaitovich
Software Mentions: 3
Published: almost 8 years ago

10.15252/msb.20177532

Quantitative analysis of protein interaction network dynamics in yeast
Cited by: 38
Author(s): Albi Celaj, Ulrich Schlecht, Justin D. Smith, Weihong Xu, Sundari Suresh, Molly Miranda, Ana Aparicio, Michael Proctor, Ronald W. Davis, Frederick P. Roth, Robert P. St.Onge
Software Mentions: 3
Published: about 9 years ago

10.1007/s00572-017-0788-6

Root-associated fungal communities in three Pyroleae species and their mycobiont sharing with surrounding trees in subalpine coniferous forests on Mount Fuji, Japan
Cited by: 4
Author(s): Shuzheng Jia, Takashi Nakano, Masahira Hattori, Kazuhide Nara
Software Mentions: 3
Published: about 9 years ago

10.3390/v11080691

Effects of the Q80K Polymorphism on the Physicochemical Properties of Hepatitis C Virus Subtype 1a NS3 Protease
Cited by: 1
Author(s): Allan Peres-da-Silva, Deborah Antunes, Audálio Rebelo Torres, Ernesto R. Caffarena, Elisabeth Lampe
Software Mentions: 3
Published: almost 7 years ago

10.3390/v12060679

Host–Pathogen Responses to Pandemic Influenza H1N1pdm09 in a Human Respiratory Airway Model
Cited by: 15
Author(s): Elizabeth A. Pharo, Sinéad M. Williams, Victoria Boyd, Vinod Sundaramoorthy, Peter A. Durr, Michelle L. Baker
Software Mentions: 3
Published: about 6 years ago

10.1186/s13071-016-1803-z

Nested coevolutionary networks shape the ecological relationships of ticks, hosts, and the Lyme disease bacteria of the Borrelia burgdorferi (s.l.) complex
Cited by: 34
Author(s): Agustı́n Estrada-Peña, Hein Sprong, Alejandro Cabezas-Cruz, José de la Fuente, Ana Ramo, Elena Claudia Coipan
Software Mentions: 3
Published: almost 10 years ago

10.1186/s13071-019-3583-8

Anaplasma phagocytophilum evolves in geographical and biotic niches of vertebrates and ticks
Cited by: 73
Author(s): Ryanne I. Jaarsma, Hein Sprong, Katsuhisa Takumi, Mária Kazimírová, Cornelia Silaghi, Atle Mysterud, Ivo Rudolf, Relja Beck, Gábor Földvári, Laura Tomassone, Margit Groenevelt, Reinard R. Everts, Jolianne M. Rijks, Frauke Ecke, Birger Hörnfeldt, David Modrý, Karolina Majerová, Jan Votýpka, Agustı́n Estrada-Peña
Software Mentions: 3
Published: about 7 years ago

10.7717/peerj.4042

Uncovering the relationship and mechanisms of Tartary buckwheat (<i>Fagopyrum tataricum</i>) and Type II diabetes, hypertension, and hyperlipidemia using a network pharmacology approach
Cited by: 18
Author(s): Chaolong Lu, Qi Zheng, Qi Shen, Chi Song, Zhiming Zhang
Software Mentions: 3
Published: over 8 years ago

10.7717/peerj.5098

MLSTar: automatic multilocus sequence typing of bacterial genomes in R
Cited by: 18
Author(s): Ignacio Ferrés, Gregorio Iraola
Software Mentions: 3
Published: about 8 years ago

10.7717/peerj.1692

Comparison of three clustering approaches for detecting novel environmental microbial diversity
Cited by: 24
Author(s): Dominik Forster, Micah Dunthorn, Thorsten Stoeck, Frédéric Mahe
Software Mentions: 3
Published: over 10 years ago

10.7717/peerj.4303

Detection of stable community structures within gut microbiota co-occurrence networks from different human populations
Cited by: 41
Author(s): Matthew A. Jackson, Marc Jan Bonder, Zhana Kuncheva, Jonas Zierer, Jingyuan Fu, Alexander Kurilshikov, Cisca Wijmenga, Alexandra Zhernakova, Jordana T. Bell, Tim D. Spector, Claire J. Steves
Software Mentions: 3
Published: over 8 years ago

10.7717/peerj.2568

The use of gene interaction networks to improve the identification of cancer driver genes
Cited by: 11
Author(s): Emilie Ramsahai, Kheston Walkins, Vrijesh Tripathi, McCormick John
Software Mentions: 3
Published: over 9 years ago

10.7717/peerj.8855

Prediction of antiviral drugs against African swine fever viruses based on protein–protein interaction analysis
Cited by: 9
Author(s): Zhaozhong Zhu, Yunshi Fan, Yang Liu, Taijiao Jiang, Yang Cao, Yousong Peng
Software Mentions: 3
Published: over 6 years ago

10.7717/peerj-cs.699

ABCDE: Approximating Betweenness-Centrality ranking with progressive-DropEdge
Cited by: 2
Author(s): Martin Mirakyan
Software Mentions: 3
Published: almost 5 years ago

10.7717/peerj-cs.600

Clustering assessment in weighted networks
Cited by: 2
Author(s): Argimiro Arratia, Martí Renedo Mirambell
Software Mentions: 3
Published: about 5 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: about 7 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: almost 6 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 7 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: over 15 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: about 8 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: almost 13 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: over 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: almost 8 years ago

10.1371/journal.pcbi.1004068

Prioritizing Therapeutics for Lung Cancer: An Integrative Meta-analysis of Cancer Gene Signatures and Chemogenomic Data
Cited by: 34
Author(s): Kristen Fortney, Joshua Griesman, Max Kotlyar, Chiara Pastrello, Marc Angeli, Ming‐Sound Tsao, Igor Jurišica
Software Mentions: 3
Published: over 11 years ago

Projects: cran: igraph

Science Score: 100/100

Bonuses:

Papers Mentioning igraph 1,555