Ecosyste.ms: Papers

10.1371/journal.pone.0152123

Who Is Spreading Avian Influenza in the Moving Duck Flock Farming Network of Indonesia?
Cited by: 18
Author(s): Joerg Henning, Dirk U. Pfeiffer, M.A. Stevenson, Didik Yulianto, W. Priyono, J. Meers
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0125725

Using Graph Components Derived from an Associative Concept Dictionary to Predict fMRI Neural Activation Patterns that Represent the Meaning of Nouns
Cited by: 5
Author(s): Hiroyuki Akama, Masakazu Miyake, Jason J. Jung, Brian Murphy
Software Mentions: 2
Published: over 9 years ago

10.1186/s12859-018-2453-2

A nearest-neighbors network model for sequence data reveals new insight into genotype distribution of a pathogen
Cited by: 3
Author(s): Helen N. Catanese, Kelly A. Brayton, Assefaw H. Gebremedhin
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0038039

Transcriptome Profiling of Citrus Fruit Response to Huanglongbing Disease
Cited by: 141
Author(s): Federico Martinelli, Sandra L. Uratsu, Ute Albrecht, Russell L. Reagan, My L. Phu, Monica Britton, Vincent Buffalo, Joseph Fass, Elizabeth Leicht, Wenwei Zhao, Dazhen Lin, Raissa M. D’Souza, Cristina E. Davis, Kim D. Bowman, Abhaya M. Dandekar
Software Mentions: 2
Published: over 12 years ago

10.1002/ece3.7235

Roost sites of chimney swift ( <i>Chaetura pelagica</i> ) form large‐scale spatial networks
Cited by: 5
Author(s): Courtney E. le Roux, Joseph J. Nocera
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0027009

Modeling the Mechanism of Action of a DGAT1 Inhibitor Using a Causal Reasoning Platform
Cited by: 24
Author(s): Ahmed Enayetallah, Daniel Ziemek, Michael T. Leininger, Ranjit Randhawa, Jinlin Yang, Tara B. Manion, Dawn Mather, William J. Zavadoski, Max Kühn, Judith L. Treadway, Shelly Ann G. des Etages, E. Michael Gibbs, Nigel Greene, Claire M. Steppan
Software Mentions: 2
Published: about 13 years ago

10.1186/1471-2105-11-343

A semi-supervised learning approach to predict synthetic genetic interactions by combining functional and topological properties of functional gene network
Cited by: 92
Author(s): Zhu-Hong You, Zhimin Yin, Kyungsook Han, Dongqing Huang, Xiaobo Zhou
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0211227

Dissecting a novel allosteric mechanism of cruzain: A computer-aided approach
Cited by: 13
Author(s): Lilian Hernández Alvarez, Diego E. B. Gomes, Jorge Enrique Hernández González, Pedro Geraldo Pascutti
Software Mentions: 2
Published: almost 6 years ago

10.1111/ele.12898

Contact networks structured by sex underpin sex‐specific epidemiology of infection
Cited by: 29
Author(s): Matthew J. Silk, Nicola Weber, Lucy C. Steward, David J. Hodgson, Mike Boots, Darren P. Croft, Richard J. Delahay, Robbie A. McDonald
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0198222

On an algorithmic definition for the components of the minimal cell
Cited by: 2
Author(s): Octavio Martínez, M. Humberto Reyes-Valdés
Software Mentions: 2
Published: over 6 years ago

10.1186/s12859-019-2746-0

Topological and functional comparison of community detection algorithms in biological networks
Cited by: 37
Author(s): Sara Rahiminejad, Mano Ram Maurya, Shankar Subramaniam
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pntd.0005659

Challenges in developing methods for quantifying the effects of weather and climate on water-associated diseases: A systematic review
Cited by: 35
Author(s): Giovanni Lo Iacono, Ben Armstrong, Lora E. Fleming, Richard Elson, Sari Kovats, Sotiris Vardoulakis, Gordon Nichols
Software Mentions: 2
Published: over 7 years ago

10.1186/s12859-020-03702-3

ImmunoGlobe: enabling systems immunology with a manually curated intercellular immune interaction network
Cited by: 6
Author(s): Michelle Atallah, Varun Tandon, Kamir J Hiam-Galvez, Hunter Boyce, Michelle Hori, Waleed Atallah, Matthew H. Spitzer, Edgar G. Engleman, Parag Mallick
Software Mentions: 2
Published: over 4 years ago

10.3390/e22121383

Research on Community Detection in Complex Networks Based on Internode Attraction
Cited by: 5
Author(s): Jinfang Sheng, Cheng Liu, Long Chen, Bin Wang, Junkai Zhang
Software Mentions: 2
Published: almost 4 years ago

10.3390/e23091204

Granger Causality among Graphs and Application to Functional Brain Connectivity in Autism Spectrum Disorder
Cited by: 4
Author(s): Adele Ribeiro, Maciel Calebe Vidal, João Ricardo Sato, André Fujita
Software Mentions: 2
Published: about 3 years ago

10.7554/eLife.02863

Buffered Qualitative Stability explains the robustness and evolvability of transcriptional networks
Cited by: 34
Author(s): Luca Albergante, J. Julian Blow, T. J. Newman
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pntd.0006070

The introduction of dengue follows transportation infrastructure changes in the state of Acre, Brazil: A network-based analysis
Cited by: 41
Author(s): Raquel Martins Lana, Tiago França Melo de Lima, Nildimar Alves Honório, Cláudia Torres Codeço
Software Mentions: 2
Published: about 7 years ago

10.1016/j.epidem.2015.02.008

Controlling infectious disease through the targeted manipulation of contact network structure
Cited by: 59
Author(s): M. Carolyn Gates, Mark Woolhouse
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pmed.1001810

Geographic and Temporal Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted HIV-1 Drug Resistance: An Individual-Patient- and Sequence-Level Meta-Analysis
Cited by: 187
Author(s): Soo-Yon Rhee, José Luis Santiago Blanco, Michael R. Jordan, Jonathan Taylor, Philippe Lemey, Vici Varghese, Raph L Hamers, Silvia Bertagnolio, Tobias F. Rinke de Wit, Avelin F. Aghokeng, Jan Albert, Radko Avi, Santiago Ávila‐Ríos, Pascal Bessong, James Brooks, Charles A. Boucher, Zabrina L. Brumme, Michael P. Busch, Hermann Bussmann, Marie Laure Chaix, Bum Sik Chin, Toni Thomas d’Aquin, Cillian F. De Gascun, Anne Derache, Diane Descamps, Alaka Deshpande, Cyrille F. Djoko, Susan H. Eshleman, Hervé Fleury, Pierre Frange, Seiichiro Fujisaki, P. Richard Harrigan, Junko Hattori, África Holguín, Gillian Hunt, Hiroshi Ishiguro, Pontiano Kaleebu, David Katzenstein, Sasisopin Kiertiburanakul, Jerome H. Kim, Sung Soon Kim, Yanpeng Li, Irja Lutsar, Lynn Morris, Nicaise Ndembi, Kee Peng Ng, Ramesh Paranjape, Martine Peeters, Mario Poljak, Matt A. Price, Manon Ragonnet‐Cronin, Gustavo Reyes‐Terán, Morgane Rolland, Sunee Sirivichayakul, Davey M. Smith, Marcelo A. Soares, Vincent Soriano, Deogratius Ssemwanga, Maja Stanojević, Mariane A. Stefani, Wataru Sugiura, Somnuek Sungkanuparph, Amílcar Tanuri, Kok Keng Tee, Hong Ha M. Truong, David van de Vijver, Nicole Vidal, Chunfu Yang, Rongge Yang, Gonzalo Yebra, John P. A. Ioannidis, Anne‐Mieke Vandamme, Robert W. Shafer
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pgen.1002612

Metabolic Profiling of a Mapping Population Exposes New Insights in the Regulation of Seed Metabolism and Seed, Fruit, and Plant Relations
Cited by: 109
Author(s): David Toubiana, Yaniv Semel, Takayuki Tohge, Romina Beleggia, Luigi Cattivelli, Leah Rosental, Zoran Nikoloski, Dani Zamir, Alisdair R. Fernie, Aaron Fait
Software Mentions: 2
Published: over 12 years ago

10.1186/s12859-019-2917-z

A dual controllability analysis of influenza virus-host protein-protein interaction networks for antiviral drug target discovery
Cited by: 8
Author(s): Emily E. Ackerman, John F. Alcorn, Takeshi Hase, Jason E. Shoemaker
Software Mentions: 2
Published: over 5 years ago

10.1155/2020/4323989

Korean Traditional Medicine in Treating Patients with Mild Cognitive Impairment: A Multicenter Prospective Observational Case Series
Cited by: 9
Author(s): Yujin Choi, Young Eun Kim, Ui Min Jerng, Hwan Kim, Sung Ik Lee, Ga-Na Kim, Seung-Hun Cho, Hyung Won Kang, In Chul Jung, Kyungsun Han, Jun-Hwan Lee
Software Mentions: 2
Published: over 4 years ago

10.1111/eva.13084

Y‐chromosome haplotypes are associated with variation in size and age at maturity in male Chinook salmon
Cited by: 11
Author(s): Garrett J. McKinney, James E. Seeb, Carita E. Pascal, Daniel E. Schindler, Sara E. Gilk‐Baumer, Lisa W. Seeb
Software Mentions: 2
Published: about 4 years ago

10.1186/s41544-020-00057-y

nSARS-Cov-2, pulmonary edema and thrombosis: possible molecular insights using miRNA-gene circuits in regulatory networks
Cited by: 5
Author(s): Pankaj Khurana, Apoorv Gupta, R. Sugadev, Y. K. Sharma, Rajeev K. Varshney, Lilly Ganju, Bharani Kumar
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pcbi.1004467

Genome-Wide Detection and Analysis of Multifunctional Genes
Cited by: 35
Author(s): Yuri Pritykin, Dario Ghersi, Mona Singh
Software Mentions: 2
Published: about 9 years ago

10.12688/f1000research.12404.1

Exploring Vietnamese co-authorship patterns in social sciences with basic network measures of 2008-2017 Scopus data
Cited by: 19
Author(s): Tung Manh Ho, Ha Viet Nguyen, Thu‐Trang Vuong, Quang-Minh Dam, Hiep‐Hung Pham, Quan‐Hoang Vuong
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pcbi.1007434

Nine quick tips for analyzing network data
Cited by: 21
Author(s): Vincent Miele, Catherine Matias, Stéphane Robin, Stéphane Dray
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pcbi.1003881

Linear Motif-Mediated Interactions Have Contributed to the Evolution of Modularity in Complex Protein Interaction Networks
Cited by: 16
Author(s): Inhae Kim, Heetak Lee, Seong Kyu Han, Sanguk Kim
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pcbi.1008832

Collective predator evasion: Putting the criticality hypothesis to the test
Cited by: 17
Author(s): Pascal P. Klamser, Pawel Romanczuk
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pcbi.1006525

Steered molecular dynamics simulations reveal critical residues for (un)binding of substrates, inhibitors and a product to the malarial M1 aminopeptidase
Cited by: 8
Author(s): Daniel Moore, Conor Brines, Heather Jewhurst, John P. Dalton, Irina G. Tikhonova
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pcbi.1006796

Conformational coupling by trans-phosphorylation in calcium calmodulin dependent kinase II
Cited by: 5
Author(s): Alessandro Pandini, Howard Schulman, Shahid Khan
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pcbi.1004597

Distinctive Behaviors of Druggable Proteins in Cellular Networks
Cited by: 41
Author(s): Costas Mitsopoulos, Amanda C. Schierz, Paul Workman, Bissan Al‐Lazikani
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pcbi.1003302

A Comprehensive Survey of Small-Molecule Binding Pockets in Proteins
Cited by: 102
Author(s): Mu Gao, Jeffrey Skolnick
Software Mentions: 2
Published: about 11 years ago

10.3389/fcimb.2021.641174

Trypanosome KKIP1 Dynamically Links the Inner Kinetochore to a Kinetoplastid Outer Kinetochore Complex
Cited by: 10
Author(s): Lorenzo Brusini, Simon D’Archivio, Jennifer McDonald, Bill Wickstead
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pcbi.1004067

Exploring Bacterial Organelle Interactomes: A Model of the Protein-Protein Interaction Network in the Pdu Microcompartment
Cited by: 24
Author(s): Julien Jorda, Yu Liu, Thomas A. Bobik, Todd O. Yeates
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pcbi.1002187

Heat Shock Partially Dissociates the Overlapping Modules of the Yeast Protein-Protein Interaction Network: A Systems Level Model of Adaptation
Cited by: 56
Author(s): Ágoston Mihalik, Péter Csermely
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pcbi.1006888

Predicting synthetic lethal interactions using conserved patterns in protein interaction networks
Cited by: 29
Author(s): Graeme Benstead-Hume, Xiangrong Chen, Suzanna R. Hopkins, Karen A. Lane, Jessica A. Downs, Frances M. G. Pearl
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2105-13-35

Assessing statistical significance in causal graphs
Cited by: 11
Author(s): Leonid Chindelevitch, Po‐Ru Loh, Ahmed Enayetallah, Bonnie Berger, Daniel Ziemek
Software Mentions: 2
Published: almost 13 years ago

10.3389/fgene.2015.00307

Biological networks: the microscope of the twenty-first century?
Cited by: 0
Author(s): Frank Emmert‐Streib, Matthias Dehmer
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pcbi.1003549

Within-Host Bacterial Diversity Hinders Accurate Reconstruction of Transmission Networks from Genomic Distance Data
Cited by: 146
Author(s): Colin J. Worby, Marc Lipsitch, William P. Hanage
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pcbi.1004372

Do Brain Networks Evolve by Maximizing Their Information Flow Capacity?
Cited by: 33
Author(s): Chris G. Antonopoulos, Suraj Srivastava, Sandro Ely de Souza Pinto, Murilo S. Baptista
Software Mentions: 2
Published: about 9 years ago

10.3389/fgene.2019.00064

Mouse Skull Mean Shape and Shape Robustness Rely on Different Genetic Architectures and Different Loci
Cited by: 11
Author(s): Ceferino Varón‐González, Luisa F. Pallares, Vincent Debat, Nicolas Navarro
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pbio.1001869

Network Analyses Reveal Pervasive Functional Regulation Between Proteases in the Human Protease Web
Cited by: 135
Author(s): Nikolaus Fortelny, Jennifer H. Cox, Reinhild Kappelhoff, Amanda E. Starr, Philipp F. Lange, Paul Pavlidis, Christopher M. Overall
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pbio.1002515

Topological Small-World Organization of the Fibroblastic Reticular Cell Network Determines Lymph Node Functionality
Cited by: 93
Author(s): Mario Novković, Lucas Onder, Jovana Cupovic, Jun Abe, David Bomze, Viviana Cremasco, Elke Scandella, Jens V Stein, Gennady Bocharov, Shannon J. Turley, Burkhard Ludewig
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pbio.2002612

A multiscale cerebral neurochemical connectome of the rat brain
Cited by: 33
Author(s): Hamid Noori, Judith Schöttler, Mária Ercsey-Ravasz, Alejandro Cosa‐Linan, Melinda Varga, Zoltán Toroczkai, Rainer Spanagel
Software Mentions: 2
Published: over 7 years ago

10.1186/s12859-016-1013-x

CompNet: a GUI based tool for comparison of multiple biological interaction networks
Cited by: 29
Author(s): Bhusan K. Kuntal, Anirban Dutta, Sharmila S. Mande
Software Mentions: 2
Published: over 8 years ago

10.1186/s40814-021-00835-x

Feasibility study of peer-led and school-based social network Intervention (STASH) to promote adolescent sexual health
Cited by: 6
Author(s): Kirstin R Mitchell, Carrie Purcell, Sharon Anne Simpson, Chiara Broccatelli, Julia Bailey, Sarah Barry, Lawrie Elliott, Ross Forsyth, Rachael Hunter, Mark McCann, Lisa McDaid, Kirsty Wetherall, Linda Moore
Software Mentions: 2
Published: over 3 years ago

10.3389/fgene.2020.00659

Comprehensive Network Analysis Reveals Alternative Splicing-Related lncRNAs in Hepatocellular Carcinoma
Cited by: 8
Author(s): Junqing Wang, Xiuquan Wang, Akshay Bhat, Yixin Chen, Keli Xu, Yin‐Yuan Mo, S. Stephen Yi, Yunyun Zhou
Software Mentions: 2
Published: over 4 years ago

10.3389/fgene.2021.597983

Identification of the Key Regulators of Spina Bifida Through Graph-Theoretical Approach
Cited by: 2
Author(s): Naaila Tamkeen, Suliman Yousef Alomar, Saeed Awad M Alqahtani, Abdullah Al-jurayyan, Anam Farooqui, Safia Tazyeen, Nadeem Ahmad, Romana Ishrat
Software Mentions: 2
Published: over 3 years ago

10.1094/PHYTO-03-18-0072-R

Modeling Epidemics in Seed Systems and Landscapes To Guide Management Strategies: The Case of Sweet Potato in Northern Uganda
Cited by: 25
Author(s): Kelsey F. Andersen, Christopher E. Buddenhagen, Paul Rachkara, R. W. Gibson, Stephen W. Kalule, David P. Phillips, Karen A. Garrett
Software Mentions: 2
Published: about 5 years ago

10.3390/ijms22031097

In Silico Inference of Synthetic Cytotoxic Interactions from Paclitaxel Responses
Cited by: 0
Author(s): Jeong Hoon Lee, Kye Hwa Lee, Ju Han Kim
Software Mentions: 2
Published: almost 4 years ago

10.1098/rstb.2014.0241

Dynamics of immunoglobulin sequence diversity in HIV-1 infected individuals
Cited by: 30
Author(s): Kenneth B. Hoehn, Astrid Gall, Rachael Bashford-Rogers, Sarah Fidler, Steve Kaye, Jonathan Weber, Myra O. McClure, Spartac Trial Investigators, Paul Kellam, Oliver G. Pybus
Software Mentions: 2
Published: about 9 years ago

10.3389/fimmu.2020.01887

FcRn Overexpression Expands Diversity of the Humoral Immune Response in bFcRn Transgenic Mice
Cited by: 2
Author(s): Bence Szikora, Anita Marx, Péter K. Jani, Orsolya Pipek, Viktor Müller, István Csabai, Imre Kacskovıcs
Software Mentions: 2
Published: over 4 years ago

10.3389/fimmu.2021.644548

Delineating the Association Between Soluble CD26 and Autoantibodies Against G-Protein Coupled Receptors, Immunological and Cardiovascular Parameters Identifies Distinct Patterns in Post-Infectious vs. Non-Infection-Triggered Myalgic Encephalomyelitis/Chronic Fatigue Syndrome
Cited by: 12
Author(s): Marvin Szklarski, Helma Freitag, Siegfried Lorenz, S Becker, Franziska Sotzny, Sandra Bauer, Jelka Hartwig, Harald Heidecke, Kirsten Wittke, Claudia Kedor, Leif G. Hanitsch, Patricia Grabowski, Nuno Sepúlveda, Carmen Scheibenbogen
Software Mentions: 2
Published: over 3 years ago

10.1111/jvim.16058

Peri‐ictal magnetic resonance imaging characteristics in dogs with suspected idiopathic epilepsy
Cited by: 11
Author(s): Aran Nagendran, J. Fraser McConnell, Luisa De Risio, Roberto José‐López, R. Gutierrez Quintana, Kelsey Robinson, Simon Platt, Daniel Sánchez Masián, Thomas W. Maddox, Rita Gonçalves
Software Mentions: 2
Published: almost 4 years ago

10.3389/fimmu.2018.01785

Simulation of the Dynamics of Primary Immunodeficiencies in B Cells
Cited by: 2
Author(s): Gabriel Teku, Mauno Vihinen
Software Mentions: 2
Published: over 6 years ago

10.7717/peerj.9632

The brain-derived neurotrophic factor Val66Met polymorphism increases segregation of structural correlation networks in healthy adult brains
Cited by: 4
Author(s): Issei Ueda, Kazuhiro Takemoto, Keita Watanabe, Katsuhisa Sugimoto, Atsuko Ikenouchi, Shingo Kakeda, Asuka Katsuki, Reiji Yoshimura, Yukunori Korogi
Software Mentions: 2
Published: over 4 years ago

10.7717/peerj.3321

Ranking of critical species to preserve the functionality of mutualistic networks using the <i>k</i>-core decomposition
Cited by: 14
Author(s): Javier García-Algarra, M. Pastor, José María Iriondo, Javier Galeano
Software Mentions: 2
Published: over 7 years ago

10.7717/peerj.8749

Potential of the economic valuation of soil-based ecosystem services to inform sustainable soil management and policy
Cited by: 20
Author(s): Bartosz Bartkowski, Stephan Bartke, Katharina Helming, Carsten Paul, Anja-Kristina Techen, Bernd Hansjürgens
Software Mentions: 2
Published: over 4 years ago

10.3390/ijms22073497

ceRNA Network Regulation of TGF-β, WNT, FOXO, Hedgehog Pathways in the Pharynx of Ciona robusta
Cited by: 4
Author(s): Aiti Vizzini, Angela Bonura, Laura La Paglia, Antonino Fiannaca, Massimo La Rosa, Alfonso Urso, Vincenzo Arizza
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2019.00234

Sperm Microbiota and Its Impact on Semen Parameters
Cited by: 110
Author(s): David Baud, Céline Pattaroni, Nicolas Vulliemoz, Vincent Castella, Benjamin J. Marsland, Miloš Stojanov
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12859-021-04216-2

Exploring the functional composition of the human microbiome using a hand-curated microbial trait database
Cited by: 8
Author(s): Jake L. Weissman, Sonia Dogra, Keyan Javadi, Samantha Bolten, Rachel Flint, Cyrus Davati, Jess Beattie, Keshav Dixit, Tejasvi Peesay, Shehar Awan, Peter Thielen, Florian P. Breitwieser, Philip L. Johnson, David Karig, William F. Fagan, Sharon Bewick
Software Mentions: 2
Published: over 3 years ago

10.3390/pathogens9121077

Analysis of Risk Factors for African Swine Fever in Lombardy to Identify Pig Holdings and Areas Most at Risk of Introduction in Order to Plan Preventive Measures
Cited by: 2
Author(s): Silvia Bellini, Alessandra Scaburri, Marco Tironi, Stefania Calò
Software Mentions: 2
Published: almost 4 years ago

10.3390/pathogens10080922

Transmission Dynamics of Bovine Viral Diarrhea Virus in Hokkaido, Japan by Phylogenetic and Epidemiological Network Approaches
Cited by: 3
Author(s): Shizuka Hirose, Kosuke Notsu, Satoshi Itō, Yoshihiro Sakoda, Norikazu Isoda
Software Mentions: 2
Published: over 3 years ago

10.1186/s40695-020-00060-1

Racial differences in lifestyle, demographic, and health factors associated with quality of life (QoL) in midlife women
Cited by: 4
Author(s): Brandi Patrice Smith, Esmeralda Cardoso-Mendoza, Jodi A. Flaws, Zeynep Madak-Erdoğan
Software Mentions: 2
Published: almost 4 years ago

10.3389/fvets.2016.00048

Impact of Network Activity on the Spread of Infectious Diseases through the German Pig Trade Network
Cited by: 20
Author(s): Karin Lebl, Hartmut H. K. Lentz, Beate Pinior, Thomas Selhorst
Software Mentions: 2
Published: over 8 years ago

10.12688/wellcomeopenres.15268.2

Study design and protocol for investigating social network patterns in rural and urban schools and households in a coastal setting in Kenya using wearable proximity sensors
Cited by: 5
Author(s): Moses Chapa Kiti, Alessia Melegaro, Ciro Cattuto, D. James Nokes
Software Mentions: 2
Published: over 5 years ago

10.3390/v12101087

Network Controllability-Based Prioritization of Candidates for SARS-CoV-2 Drug Repositioning
Cited by: 4
Author(s): Emily E. Ackerman, Jason E. Shoemaker
Software Mentions: 2
Published: about 4 years ago

10.3389/fvets.2019.00071

Equine Rhinitis A Virus Infection at a Standardbred Training Facility: Incidence, Clinical Signs, and Risk Factors for Clinical Disease
Cited by: 3
Author(s): T. M. Rossi, Alison Moore, Terri L. O’Sullivan, Amy L. Greer
Software Mentions: 2
Published: over 5 years ago

10.3390/v4123625

A Systems Biology Starter Kit for Arenaviruses
Cited by: 0
Author(s): Magali E. Droniou-Bonzom, Paula M. Cannon
Software Mentions: 2
Published: almost 12 years ago

10.1534/g3.118.200260

A<i>Cyclin E</i>Centered Genetic Network Contributes to Alcohol-Induced Variation in Drosophila Development
Cited by: 14
Author(s): Tatiana V. Morozova, Yasmeen N. Hussain, Lenovia J. McCoy, Eugenea V Zhirnov, Morgan R. Davis, Victoria A. Pray, Rachel A Lyman, Laura Duncan, Anna McMillen, Aiden Jones, Trudy F. C. Mackay, Robert R. H. Anholt
Software Mentions: 2
Published: over 6 years ago

10.1186/s13567-014-0110-y

Not all cows are epidemiologically equal: quantifying the risks of bovine viral diarrhoea virus (BVDV) transmission through cattle movements
Cited by: 31
Author(s): M. Carolyn Gates, R.W. Humphry, George J. Gunn, Mark Woolhouse
Software Mentions: 2
Published: about 10 years ago

10.1186/1471-2105-8-88

Regulation of metabolic networks by small molecule metabolites
Cited by: 28
Author(s): Alex Gutteridge, Minoru Kanehisa, Susumu Goto
Software Mentions: 2
Published: over 17 years ago

10.1093/g3journal/jkab131

Effects of kinship correction on inflation of genetic interaction statistics in commonly used mouse populations
Cited by: 4
Author(s): Anna L. Tyler, Bahá El Kassaby, Georgi Kolishovski, J. J. Emerson, Ann Wells, James Mahoney, Gregory W. Carter
Software Mentions: 2
Published: over 3 years ago

10.1155/2021/8708023

Tear Film Proteome of Healthy Domestic Cats
Cited by: 2
Author(s): Jéssica Fontes Veloso, Paula Elisa Brandão Guedes, Luciana Carvalho Lacerda, Juliano Oliveira Santana, Irma Yuliana Mora-Ocampo, Carlos Priminho Pirovani, Arianne Pontes Oriá, Alexandre Dias Munhoz, Renata Santiago Alberto Carlos
Software Mentions: 2
Published: over 3 years ago

10.1007/s11252-017-0724-8

The application of graph theory and percolation analysis for assessing change in the spatial configuration of pond networks
Cited by: 10
Author(s): Ian Thornhill, Lesley Batty, Matthew J. Hewitt, Nikolai Friberg, Mark E. Ledger
Software Mentions: 2
Published: almost 7 years ago

10.3390/genes10100776

Patterns and Constraints in the Evolution of Sperm Individualization Genes in Insects, with an Emphasis on Beetles
Cited by: 1
Author(s): Helena I. Vizán‐Rico, Christoph Mayer, Malte Petersen, Duane D. McKenna, Xin Zhou, Jesús Gómez‐Zurita
Software Mentions: 2
Published: about 5 years ago

10.18632/aging.202995

Gene expression signatures differentiating major depressive disorder from subsyndromal symptomatic depression
Cited by: 2
Author(s): Guoqin Hu, Shunying Yu, Chen Yuan, Hong Wu, Zuowei Wang, Ran Zhang, Dongxiang Wang, Zezhi Li, Zhenghui Yi, Yiru Fang
Software Mentions: 2
Published: over 3 years ago

10.3390/genes11030247

Network Properties of Cancer Prognostic Gene Signatures in the Human Protein Interactome
Cited by: 0
Author(s): Jifeng Zhang, Shoubao Yan, Cheng Jiang, Zhicheng Ji, Chenrun Wang, Weidong Tian
Software Mentions: 2
Published: over 4 years ago

10.15252/msb.20156484

An inter‐species protein–protein interaction network across vast evolutionary distance
Cited by: 42
Author(s): Quan Zhong, Samuel Pevzner, Tong Hao, Yang Wang, Roberto Mosca, Jörg Menche, Mikko Taipale, Murat Taşan, Changyu Fan, Xinping Yang, Patrick J. Haley, Ryan R. Murray, Flora Mer, Fana Gebreab, Stanley Tam, Andrew MacWilliams, Amélie Dricot, Patrick Reichert, S. Balaji, Lila Ghamsari, Michael A. Calderwood, Thomas Rolland, Benoît Charloteaux, Susan Lindquist, Albert‐László-L. Barabási, David E. Hill, Patrick Aloy, Michael E. Cusick, Yu Xia, Frederick P. Roth, Marc Vidal
Software Mentions: 2
Published: over 8 years ago

10.15252/msb.20188594

High‐resolution mapping of cancer cell networks using co‐functional interactions
Cited by: 61
Author(s): Evan A. Boyle, Jonathan K. Pritchard, William J. Greenleaf
Software Mentions: 2
Published: almost 6 years ago

10.3390/genes12050740

Evolution of Reproductive Life History in Mammals and the Associated Change of Functional Constraints
Cited by: 6
Author(s): Jiaqi Wu, Takahiro Yonezawa, Hirohisa Kishino
Software Mentions: 2
Published: over 3 years ago

10.1002/mgg3.659

Prioritization and comprehensive analysis of genes related to major depressive disorder
Cited by: 12
Author(s): Yi Liu, Ping Fan, Shiyuan Zhang, Yidan Wang, Dan Liŭ
Software Mentions: 2
Published: over 5 years ago

10.1186/1297-9686-44-17

Genetic diversity and networks of exchange: a combined approach to assess intra-breed diversity
Cited by: 12
Author(s): Jean-François Dumasy, Christel Daniaux, Isabelle Donnay, Philippe Baret
Software Mentions: 2
Published: over 12 years ago

10.3390/molecules26061664

PepFun: Open Source Protocols for Peptide-Related Computational Analysis
Cited by: 11
Author(s): Rodrigo Ochoa, Pilar Cossio
Software Mentions: 2
Published: over 3 years ago

10.1186/gb-2013-14-8-r85

Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits
Cited by: 15
Author(s): Molly Megraw, Sayan Mukherjee, Uwe Ohler
Software Mentions: 2
Published: almost 12 years ago

10.3390/molecules24061081

CuDDI: A CUDA-Based Application for Extracting Drug-Drug Interaction Related Substance Terms from PubMed Literature
Cited by: 2
Author(s): Ling Yin, Aditya Chandra Vothgod Ramachandra, Minh Pham, Yi-Cheng Tu, Feng Cheng
Software Mentions: 2
Published: over 5 years ago

10.1186/s13059-015-0772-4

New genes drive the evolution of gene interaction networks in the human and mouse genomes
Cited by: 85
Author(s): Wenyu Zhang, Patrick Landback, Andrea R. Gschwend, Bairong Shen, Manyuan Long
Software Mentions: 2
Published: about 9 years ago

10.1186/s13059-016-1003-3

Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativity
Cited by: 44
Author(s): Véra Pancaldi, Enrique Carrillo de Santa Pau, Biola M. Javierre, David Juan, Peter Fraser, Mikhail Spivakov, Alfonso Valencia, Daniel Rico
Software Mentions: 2
Published: over 8 years ago

10.2196/12914

Identifying Influence Agents That Promote Physical Activity Through the Simulation of Social Network Interventions: Agent-Based Modeling Study
Cited by: 24
Author(s): Thabo J. van Woudenberg, Bojan Simoski, Eric Fernandes de Mello Araújo, Kirsten E. Bevelander, William J. Burk, Crystal R. Smit, Laura Buijs, Michel Klein, Moniek Buijzen
Software Mentions: 2
Published: over 5 years ago

10.1016/j.molcel.2016.07.008

Molecular Principles of Gene Fusion Mediated Rewiring of Protein Interaction Networks in Cancer
Cited by: 57
Author(s): Natasha S. Latysheva, Matt Oates, Louis Maddox, Tilman Flock, Julian Gough, Marija Buljan, Robert J. Weatheritt, M. Madan Babu
Software Mentions: 2
Published: over 8 years ago

10.1093/molbev/msv058

An<i>Arabidopsis</i>Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors
Cited by: 129
Author(s): Jinpu Jin, Kongwang He, Xing Tang, Zhe Li, Le Lv, Yi Zhao, Jianxun Luo, Ge Gao
Software Mentions: 2
Published: over 9 years ago

10.1093/molbev/msz152

Coevolution of Sites under Immune Selection Shapes Epstein–Barr Virus Population Structure
Cited by: 19
Author(s): Fanny Wegner, Florent Lassalle, Daniel P. Depledge, François Balloux, Judith Breuer
Software Mentions: 2
Published: over 5 years ago

10.3390/microorganisms7120586

Root-Associated Fungal Communities in Two Populations of the Fully Mycoheterotrophic Plant Arachnitis uniflora Phil. (Corsiaceae) in Southern Chile
Cited by: 12
Author(s): Héctor Herrera, Javiera Soto, Luz E. de Bashan, Inmaculada Sampedro, César Arriagada
Software Mentions: 2
Published: about 5 years ago

10.2196/18457

Two Decades of Research Using Taiwan’s National Health Insurance Claims Data: Bibliometric and Text Mining Analysis on PubMed
Cited by: 23
Author(s): Sheng Feng Sung, Cheng‐Yang Hsieh, Yu Hu
Software Mentions: 2
Published: over 4 years ago

10.3390/microorganisms6040101

A Metabolomic-Based Evaluation of the Role of Commensal Microbiota throughout the Gastrointestinal Tract in Mice
Cited by: 20
Author(s): Yurie Yamamoto, Yumiko Nakanishi, S. Murakami, Wanping Aw, Tomoya Tsukimi, Ryoko Nozu, Masaki Ueno, Kyoji Hioki, Kenji Nakahigashi, Akiyoshi Hirayama, Masahiro Sugimoto, Tomoyoshi Soga, Mamoru Ito, Masaru Tomita, Shinji Fukuda
Software Mentions: 2
Published: about 6 years ago

10.1186/s13073-014-0052-z

Molecularly and clinically related drugs and diseases are enriched in phenotypically similar drug-disease pairs
Cited by: 15
Author(s): Ingo Vogt, Jeanette Prinz, Mónica Campillos
Software Mentions: 2
Published: over 10 years ago

10.1186/s13073-017-0507-0

Within-host evolution of Enterococcus faecium during longitudinal carriage and transition to bloodstream infection in immunocompromised patients
Cited by: 23
Author(s): Danesh Moradigaravand, Theodore Gouliouris, Beth Blane, Plamena Naydenova, Catherine Ludden, Charles Crawley, Nicholas M. Brown, M. Estée Török, Julian Parkhill, Sharon J. Peacock
Software Mentions: 2
Published: almost 7 years ago

10.1186/2042-5783-2-8

Analysis of evolutionary patterns of genes in Campylobacter jejuni and C. coli
Cited by: 8
Author(s): Lars Snipen, Trudy M. Wassenaar, Eric Altermann, Jonathan W. Olson, Sophia Kathariou, Karin Lagesen, Mónica Takamiya, Susanne Knøchel, David W. Ussery, Richard J. Meinersmann
Software Mentions: 2
Published: about 12 years ago

10.1099/mgen.0.000203

Extended-spectrum β-lactamase-encoding genes are spreading on a wide range of Escherichia coli plasmids existing prior to the use of third-generation cephalosporins
Cited by: 25
Author(s): Catherine Branger, Alice Ledda, Typhaine Billard-Pomarès, Benoît Doublet, Stéphanie Fouteau, Valérie Barbe, David Roche, Stéphane Cruveiller, Claudine Médigue, Miguel Sautié Castellanos, Dominique Decré, Laurence Drieux-Rouze, Olivier Clermont, Jérémy Glodt, Olivier Tenaillon, Axel Cloeckaert, Guillaume Arlet, Erick Denamur
Software Mentions: 2
Published: about 6 years ago