pypi: igraph | Projects | Ecosyste.ms: Papers

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: about 9 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: over 3 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: about 8 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: about 9 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 5 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: over 3 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: over 5 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: about 3 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: almost 7 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

10.1186/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

10.1186/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

10.1186/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/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/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

10.1186/1756-0500-4-149

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

10.1186/1756-0500-3-142

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/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

10.1186/1752-0509-6-32

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

10.1186/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

10.1186/1752-0509-8-12

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/s12918-018-0550-5

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

10.1186/1752-0509-5-195

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

10.1186/1752-0509-4-179

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

10.1186/1742-6405-8-26

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: almost 14 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

10.1042/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

10.1155/2015/245075

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

10.1186/1745-6150-6-31

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

10.1242/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

10.1155/2017/1016305

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

10.1155/2015/852341

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

10.3390/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: about 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

10.1186/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

10.1002/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

10.1089/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

10.1186/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

10.1155/2021/9960241

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/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: over 3 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: about 3 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 7 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 3 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: almost 7 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: over 4 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: almost 4 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: over 3 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: over 4 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: about 4 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: over 6 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: over 7 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: over 7 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: over 5 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: over 4 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: about 8 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: over 5 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: about 7 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: over 6 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: almost 9 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: almost 7 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: almost 8 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 4 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: about 3 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: over 3 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

10.3390/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

10.1371/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

10.1371/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

10.1371/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

10.1371/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

10.1371/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

10.1371/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

10.1371/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 9 years ago

10.1371/journal.pcbi.1005316

Inference of Transmission Network Structure from HIV Phylogenetic Trees
Cited by: 31
Author(s): Federica Giardina, Ethan Romero-Severson, Jan Albert, Tom Britton, Thomas Leitner
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pcbi.1003472

Integrative Computational and Experimental Approaches to Establish a Post-Myocardial Infarction Knowledge Map
Cited by: 9
Author(s): Nguyen T. Nguyen, Xiaolin Zhang, Cathy H. Wu, Richard A. Lange, Robert Chilton, Merry L. Lindsey, Yu Jin
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pcbi.1004088

Mining Host-Pathogen Protein Interactions to Characterize Burkholderia mallei Infectivity Mechanisms
Cited by: 28
Author(s): Vesna Memišević, Nela Zavaljevski, Seesandra V. Rajagopala, Ki-Ryong Kwon, Rembert Pieper, David DeShazer, Jaques Reifman, Anders Wallqvist
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pgen.1005413

A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota
Cited by: 163
Author(s): David J. Roach, Joshua N. Burton, Choli Lee, Bethany Stackhouse, Susan M. Butler-Wu, Brad T. Cookson, Jay Shendure, Stephen J. Salipante
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pgen.1008801

Dynamic genetic architecture of yeast response to environmental perturbation shed light on origin of cryptic genetic variation
Cited by: 14
Author(s): Yanjun Zan, Örjan Carlborg
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1009101

Identity-by-descent with uncertainty characterises connectivity of Plasmodium falciparum populations on the Colombian-Pacific coast
Cited by: 15
Author(s): Aimee R Taylor, Diego F. Echeverry, Timothy J. Anderson, Daniel E. Neafsey, Caroline O. Buckee
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pgen.1006817

Pervasive antagonistic interactions among hybrid incompatibility loci
Cited by: 45
Author(s): Rafael F. Guerrero, Christopher D. Muir, Sarah Josway, Leonie C. Moyle
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pgen.1006363

Combined Use of Genome-Wide Association Data and Correlation Networks Unravels Key Regulators of Primary Metabolism in Arabidopsis thaliana
Cited by: 63
Author(s): Si Wu, Saleh Alseekh, Álvaro Cuadros-Inostroza, Corina M. Fusari, Marek Mutwil, Rik Kooke, Joost J. B. Keurentjes, Alisdair R. Fernie, Lothar Willmitzer, Yariv Brotman
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pgen.1006706

Mapping of 79 loci for 83 plasma protein biomarkers in cardiovascular disease
Cited by: 174
Author(s): Lasse Folkersen, Eric B. Fauman, Maria Sabater‐Lleal, Rona J. Strawbridge, Mattias Frånberg, Bengt Sennblad, Damiano Baldassarre, Fabrizio Veglia, Steve E. Humphries, Rainer Rauramaa, Ulf dé Fairé, Andries J. Smit, Philippe Giral, Sudhir Kurl, Elmo Mannarino, Stefan Enroth, Åsa Johansson, Sofia Bosdotter Enroth, Stefan Gustafsson, Lars Lind, Cecilia M. Lindgren, Andrew P. Morris, Vilmantas Giedraitis, Angela Silveira, Anders Franco‐Cereceda, Elena Tremoli, Ulf Gyllensten, Erik Ingelsson, Søren Brunak, Per Eriksson, Daniel Ziemek, Anders Hamsten, Anders Mälarstig
Software Mentions: 3
Published: over 7 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

10.1371/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

10.1371/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

10.1371/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.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

10.1371/journal.pone.0248340

Analysis of survey on menstrual disorder among teenagers using Gaussian copula model with graphical lasso prior
Cited by: 3
Author(s): Jiali Wang, Anton H. Westveld, A. H. Welsh, Melissa Parker, Bronwyn Loong
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0244839

A scientometric overview of CORD-19
Cited by: 45
Author(s): Giovanni Colavizza, Rodrigo Costas, Vincent Traag, Nees Jan van Eck, Thed N. van Leeuwen, Ludo Waltman
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0193425

Consistent individual differences and population plasticity in network-derived sociality: An experimental manipulation of density in a gregarious ungulate
Cited by: 9
Author(s): Paul Philip O'Brien, Quinn M. R. Webber, Eric Vander Wal
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0102856

Thermostability of In Vitro Evolved Bacillus subtilis Lipase A: A Network and Dynamics Perspective
Cited by: 23
Author(s): Ashutosh Srivastava, Somdatta Sinha
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0244299

An avian dominance hierarchy at a supplemental water source in the Patagonian steppe
Cited by: 2
Author(s): Sophie Rabinowicz, Natalia C. García, Tristan Herwood, Amanda Lazar, Benjamin Hein, Eliot T. Miller, Leonardo Campagna
Software Mentions: 3
Published: almost 4 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.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

Projects: pypi: igraph

Papers Mentioning igraph 1,555